# Patent

## Title
Antibodies to plasminogen activator inhibitor-1 (PAI-1) and uses thereof

## Abstract

The invention provides antibodies that specifically bind to Plasminogen Activator Inhibitor type-1 (PAI-1), The invention also provides pharmaceutical compositions, as well as nucleic acids encoding anti-PAI-1 antibodies, recombinant expression vectors and host cells for making such antibodies, or fragments thereof. Methods of using antibodies to modulate PAI-1 activity or detect PAI-1, either in vitro or in vivo, are also provided. The disclosure further provides methods of making antibodies that specifically bind to PAI-1 in the active conformational state.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims priority to U.S. Provisional Application No. 61/865,451, filed Aug. 13, 2013, and European Patent Application No. 14305757.8, filed May 22, 2014, which are incorporated herein by reference in their entireties.


BACKGROUND
Plasminogen Activator Inhibitor type-1 (PAI-1) is the main inhibitor of tissue-type plasminogen activator (tPA) and urokinase-type plasminogen activator (uPA), the key serine proteases responsible for plasmin generation. PAI-1 regulates fibrinolysis by inhibiting plasminogen activation in the vascular compartment. Fibrinolysis is a tightly coordinated process for degrading fibrin clots formed by activation of the coagulation cascade. Dysregulation of the coagulation/fibrinolysis balance leads to abnormal haemostasis events like bleeding or thrombotic diseases. PAI-1 is also a key regulator of plasminogen activation in the pericellular compartment (intravascular and tissular) where receptor bound plasminogen is activated mainly by urokinase bound to the urokinase receptor (uPAR). By inhibiting pericellular proteolysis, PAI-1 regulates numerous cellular functions like extracellular matrix (ECM) degradation, growth factors activation and release from ECM, matrix metalloproteinases (MMP) activation and cellular apoptosis. Recently, protease-independent effects of PAI-1 have been identified through its interaction with cofactors (like vitronectin, heparin, glycosaminoglycan), uPAR-urokinase complexes or cellular receptors (LRP: low-density Lipoprotein Receptor-related Protein) or integrins affecting cell functions like adhesion/de-adhesion, migration, proliferation and intracellular bioactivity. By these cellular mechanisms and anti-fibrinolytic effects, a pathogenic role of PAI-1 has been established in tumor growth and metastasis, fibrosis, acute myocardial infarction and metabolic disorders like atherosclerosis, obesity and diabetes.
The Human SERPINE1 (PAI-1) gene is localized to chromosome 7, consists of eight introns and nine exons, and has a size of 12,169 b (Klinger, K. W. et al. Proc. Natl. Acad. Sci. USA 84:8548, 1987). PAI-1 is a single chain glycoprotein of approximately 50 kDa (379 amino acids) from the SERPIN (serine protease inhibitor) superfamily that is synthesized in the active conformation but spontaneously becomes latent in the absence of vitronectin (Vn). Vitronectin, the main cofactor of PAI-1, stabilizes the active conformation with the Reactive Center Loop (RCL) which is approximately 20 amino acids that are exposed on the surface. The mechanism of inhibition of PAI-1's two main targets (tPA and uPA) is a suicide inhibition. The RCL region of PAI-1 bears the bait peptide bond (R346-M347, also called P1-P′1), which bears the cleavage site for this serine protease. A Michaelis complex with tPA or uPA forms first, then the catalytic triad reacts with the bait peptide bond to form an acyl-enzyme complex that, after cleavage of the P1-P′1 peptide bond, induces strong conformation changes. The conformational changes cause insertion of the cleaved RCL into a β-strand with the protease staying covalently bound as an acyl enzyme with PAI-1. Under non-physiological circumstances, hydrolysis of this acyl-enzyme complex may induce release of the cleaved PAI-1 and free active protease (Blouse et al., Biochemistry, 48:1723, 2009).
PAI-1 circulates in blood at highly variable levels (nM range) and in excess over t-PA or uPA concentrations. PAI-1 exhibits structural flexibility and can be found in one of three conformations: (1) a latent conformation, (2) an active conformation, or (3) a substrate conformation (see FIG. 1). PAI-1 is mainly found as a noncovalent complex with vitronectin (Kd ̃1 nM) that decreases latency transition by 1.5 to 3 fold. Latent, cleaved or complexed PAI-1 affinity for vitronectin is significantly reduced. Matrix bound vitronectin also localizes with PAI-1 in the pericellular space. Endothelial cells, monocytes, macrophages and vascular smooth muscle cells synthesize this PAI-1 which then can be stored in large amounts under latent form by platelets (in the α granule). PAI-1 is a fast and specific inhibitor (with the second order rate constant of 106 to 107 M−1s−1) of tPA and uPA in solution, but inactive against protease bound either to fibrin or their cellular receptors. Other proteases like thrombin, plasmin, activated Protein C cart be also inhibited by PAI-1 but less efficiently.
Several 3D structures of human PAI-1 have been solved since the first one described in 1992 (Mottonen et al., Nature 355:270, 1992) in the latent conformation. These 3D structures include mutant forms of PAI-1 in the substrate (Aertgeerts et al., Proteins 23:118, 1995), stabilized active conformation (Sharp et al., Structure 7:111, 1999), PAI complexed to Vitronectin-somatomedin B domain (Zhou et al., Nat. Struct. Biol. 10:541, 2003) or with inhibiting pentapeptide from the RCL loop (Xue et al., Structure 6:627, 1998). More recently, mouse PAI-1 structure in latent conformation was elucidated by Dewilde et al. (J. Struct. Biol. 171:95, 2010) and revealed differences with human PAI-1 in the RCL position, gate region and position of α-helix A. Structure/function relationships in PAI-1 have been studied by using more than 600 mutant proteins (reviewed by De Taeye et al., Thromb. Haemost. 92:898, 2004) to localize domains involved in the various activities of this multifunctional serpin.
Since PAI-1 can be synthesized by almost every cell type including hepatocyte, adipocyte, mesangial cell, fibroblast, myofibroblast, and epithelial cell, its expression greatly varies under physiological (e.g., circadian variation of plasma PAI-1 level) and pathological conditions (e.g., obesity, metabolic syndrome, insulin resistance, infection, inflammatory diseases, cancer). PAI-1 is considered to be an acute phase protein. Transcriptional regulation of PAI-1 mRNA expression is induced by several cytokines and growth factors (e.g., TGFβ, TNFα, EGF, FGF, Insulin, angiotensin II & IV), hormones (e.g., aldosterone, glucocorticoids, PMA, high glucose) and stress factors (e.g., hypoxia, reactive oxygen species, lipopolysaccharides).
Moreover, a polymorphism in the promoter (position-675) of the PAI-1 gene affects expression level. The 4G allele increases PAI-1 level and the 4G/4G variant (occurring in around 25% of the population) induces an increase of approximately 25% of plasma PAI-1 level in comparison to 5G/5G (25% occurrence and 4G/5G 50% occurrence). The 4G/4G polymorphism has been linked to myocardial infarction (Dawson et al., Arterioscler Thromb. 11:183, 1991), a specific type of pulmonary fibrosis (idiopathic interstitial pneumonia) (Kim et al., Mol Med. 9:52, 2003) and the 4G/4G genotype donor group is an independent risk factor for kidney graft loss due to Interstitial Fibrosis & Tubular Atrophy (Rerolle et al., Nephrol. Dial. Transplant 23:3325, 2008).
Several pathogenic roles have been attributed to PAI-1 in thrombotic diseases such as arterial and venous thrombosis, acute myocardial infarction, and atherosclerosis. Its involvement in metabolic disorders like insulin resistance syndrome and obesity is well recognized. PAI-1 is also known as a profibrotic factor for several organs and has been shown to be over-expressed in fibrotic tissues (i.e., liver, lung, kidney, heart, abdominal adhesions, skin: scar or scleroderma) (reviewed by Ghosh and Vaughan, J. Cell Physiol. 227:493, 2012). PAI-1 knock-out (KO) mice are protected from fibrosis in different models, such as liver (bile duct ligation or xenobiotic), kidney (unilateral ureteral obstruction model (UUO)), lung (bleomycin inhalation) (Bauman et al., J. Clin. Invest. 120:1950, 2010; Hattori et al., Am. J. Pathol. 164:1091, 2004; Chuang-Tsai et al., Am. J. Pathol.163:445, 2003) whereas in heart this deletion is protected from induced fibrosis (Takeshita et al., AM. J. Pathol. 164:449, 2004) but prone to age-dependent cardiac selective fibrosis (Moriwaki et al., Cric. Res. 95:637, 2004). Down-regulation of PAI-1 expression by siRNA (Senoo et al., Thorax 65:334, 2010) or inhibition by chemical compounds (Izuhara et al., Arterioscler. Thromb. Vasc. Biol. 28:672, 2008; Huang et al., Am. J. Respir. Cell Mol. Biol. 46:87, 2012) have been reported to decrease lung fibrosis whereas PAI-1 overexpression of wild type (Eitzman et al., J. Clin. Invest. 97:232, 1996) or a PAI-1 mutant retaining only vitronectin binding but not tPA inhibitor function exacerbates lung fibrosis (Courey et al., Blood 118:2313, 2011).
Bile duct ligation (BDL) liver fibrosis is attenuated by antibody neutralizing PAI-1 (U.S. Pat. No. 7,771,720) whereas down-regulation by siRNA attenuates BDL and xenobiotic induced liver fibrosis (Hu et al., J. Hepatol. 51:102, 2009). PAI-1 KO mice were protected from cholestatic-induced liver damage and fibrosis in BDL (Bergheim et al., J. Pharmacol. Exp. Ther. 316:592, 2006; Wang et al., FEBS Lett. 581:3098, 2007; Wang et al., Hepatology 42:1099, 2005) and from angiotensin II induced liver fibrosis (Beier et al., Arch. Bioch. Biophys. 510:19, 2011).
PAI-1 KO mice are protected from renal fibrosis in the UUO model (Oda et al., Kidney Int. 60, 587, 2001), in diabetic nephropathy (Nicholas et al., Kidney Int. 67:1297, 2005) and in angiotensin II induced nephropathy (Knier et al., J. Hypertens. 29:1602, 2011; for reviews see Ma et al. Frontiers Biosci. 14:2028, 2009 and Eddy A. A. Thromb. Haemost. 101:656, 2009). In contrast, PAI-1 over expressing mice display more severe fibrosis and increased macrophage recruitment following UUO (Matsuo et al., Kidney Int. 67:2221, 2005; Bergheim et al., J. Pharmacol. Exp. Ther. 316:592, 2006). Non-inhibitory PAI-1 mutant (PAI-1 R) has been shown to protect mice from the development of fibrosis in experimental glomerulonephritis (thy1) in rat by decreasing urinary protein expression and glomerular matrix accumulation (Huang et al., Kidney Int. 70:515, 2006). Peptides blocking PAI-1 inhibit collagen 3, 4 and fibronectin accumulation in UUO mice (Gonzalez et al., Exp. Biol. Med. 234:1511, 2009).
PAI-1, as a target for numerous pathologies, has been the focus of intensive research to inhibit its activity or to regulate its expression for the last 20 years. Chemical compounds (Suzuki et al., Expert Opin. Investig. Drugs 20:255, 2011), monoclonal antibodies (Gils and Declerk, Thromb Haemost; 91:425, 2004), peptides, mutants (Cale and Lawrence, Curr. Drug Targets 8:971, 2007), siRNA or anti-sense RNA have been designed to inhibit its various function or to regulate its expression. However, despite the intensive research, the problem of developing a therapeutically effective modulator of PAI-1 still remains to be solved. Accordingly, there is a need in the art for novel agents that inhibit the PAI-1 activity for use in the treatment of PAI-1-mediated human pathologies.
SUMMARY OF THE DISCLOSURE
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to human Plasminogen Activator Inhibitor type-1 (PAI-1), wherein the antibody comprises a heavy chain variable region, said heavy chain variable region comprising CDR1 (SEQ ID NO: 34), CDR2 (SEQ ID NO: 33), and CDR3 (SEQ ID NO: 32) of SEQ ID NO: 6, and a light chain variable region, said light chain variable region comprising CDR1 (SEQ ID NO: 37), CDR2 (SEQ ID NO: 36), and CDR3 (SEQ ID NO: 35) of SEQ ID NO: 7. In an additional aspect the heavy chain comprises a heavy chain variable region comprising SEQ ID NO: 6, and the light chain comprises a light chain variable region comprising SEQ ID NO: 7. In a further aspect, heavy chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 6, and the light chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 7. All % identity approximations indicate the minimum % identity; higher % identity than the recited values are also encompassed by the disclosure.
In another aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 34, a heavy chain CDR2 region comprising SEQ ID NO: 33, and a heavy chain CDR3 region comprising SEQ ID NO: 32; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 37, a light chain CDR2 region comprising SEQ ID NO: 36, and a light chain CDR3 region comprising SEQ ID NO: 35. In certain aspects, the antibody heavy chain comprises heavy chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the heavy chain framework regions of SEQ ID NO: 6, and the antibody light chain comprises light chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the framework regions of SEQ ID NO: 7.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to human Plasminogen Activator Inhibitor type-1 (PAI-1), wherein the antibody comprises a heavy chain variable region, said heavy chain variable region comprising CDR1 (SEQ ID NO: 22), CDR2 (SEQ ID NO: 21), and CDR3 (SEQ ID NO: 20) of SEQ ID NO: 2, and a light chain variable region, said light chain variable region comprising CDR1 (SEQ ID NO: 25), CDR2 (SEQ ID NO: 24), and CDR3 (SEQ ID NO: 23) of SEQ ID NO: 3. In an additional aspect the heavy chain comprises a heavy chain variable region comprising SEQ ID NO: 2, and the light chain comprises a light chain variable region comprising SEQ ID NO: 3. In a further aspect, heavy chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 2, and the light chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 3.
In an additional aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 22, a heavy chain CDR2 region comprising SEQ ID NO: 21, and a heavy chain CDR3 region comprising SEQ ID NO: 20; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 25, a light chain CDR2 region comprising SEQ ID NO: 24, and a light chain CDR3 region comprising SEQ ID NO: 23. In certain aspects, the antibody heavy chain comprises heavy chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the heavy chain framework regions of SEQ ID NO: 26, and the antibody light chain comprises light chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the framework regions of SEQ ID NO: 3.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to human Plasminogen Activator Inhibitor type-1 (PAI-1), wherein the antibody comprises a heavy chain variable region, said heavy chain variable region comprising CDR1 (SEQ ID NO: 28), CDR2 (SEQ ID NO: 27), and CDR3 (SEQ ID NO: 26) of SEQ ID NO: 4, and a light chain variable region, said light chain variable region comprising CDR1 (SEQ ID NO: 31), CDR2 (SEQ ID NO: 30), and CDR3 (SEQ ID NO: 29) of SEQ ID NO: 5. In an additional aspect the heavy chain comprises a heavy chain variable region comprising SEQ ID NO: 4, and the light chain comprises a light chain variable region comprising SEQ ID NO: 5. In a further aspect, heavy chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 4, and the light chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 5.
In an addition aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 28, a heavy chain CDR2 region comprising SEQ ID NO: 27, and a heavy chain CDR3 region comprising SEQ ID NO: 26; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 31, a light chain CDR2 region comprising SEQ ID NO: 30, and a light chain CDR3 region comprising SEQ ID NO: 29. In certain aspects, the antibody heavy chain comprises heavy chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the heavy chain framework regions of SEQ ID NO: 4, and the antibody light chain comprises light chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the framework regions of SEQ ID NO: 5.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to human Plasminogen Activator Inhibitor type-1 (PAI-1), wherein the antibody comprises a heavy chain variable region, said heavy chain variable region comprising CDR1 (SEQ ID NO: 40), CDR2 (SEQ ID NO: 39), and CDR3 (SEQ ID NO: 38) of SEQ ID NO: 8, and a light chain variable region, said light chain variable region comprising CDR1 (SEQ ID NO: 43), CDR2 (SEQ ID NO: 42), and CDR3 (SEQ ID NO: 41) of SEQ ID NO: 9. In an additional aspect the heavy chain comprises a heavy chain variable region comprising SEQ ID NO: 8, and the light chain comprises a light chain variable region comprising SEQ ID NO: 9. In a further aspect, heavy chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 8, and the light chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 9.
In another aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 40, a heavy chain CDR2 region comprising SEQ ID NO: 39, and a heavy chain CDR3 region comprising SEQ ID NO: 38; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 43, a light chain CDR2 region comprising SEQ ID NO: 42, and a light chain CDR3 region comprising SEQ ID NO: 41. In certain aspects, the antibody heavy chain comprises heavy chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the heavy chain framework regions of SEQ ID NO: 8, and the antibody light chain comprises light chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the framework regions of SEQ ID NO: 9.
In one aspect, disclosed herein is An isolated monoclonal antibody that binds specifically to human Plasminogen Activator Inhibitor type-1 (PAI-1), wherein the antibody comprises a heavy chain variable region, said heavy chain variable region comprising CDR1 (SEQ ID NO: 52), CDR2 (SEQ ID NO: 51), and CDR3 (SEQ ID NO: 50) of SEQ ID NO: 10, and a light chain variable region, said light chain variable region comprising CDR1 (SEQ ID NO: 55), CDR2 (SEQ ID NO: 54), and CDR3 (SEQ ID NO: 53) of SEQ ID NO: 11. In an additional aspect the heavy chain comprises a heavy chain variable region comprising SEQ ID NO: 10, and the light chain comprises a light chain variable region comprising SEQ ID NO: 11. In a further aspect, heavy chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 10, and the light chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 11.
In an additional aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 52, a heavy chain CDR2 region comprising SEQ ID NO: 51, and a heavy chain CDR3 region comprising SEQ ID NO: 50; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 55, a light chain CDR2 region comprising SEQ ID NO: 54, and a light chain CDR3 region comprising SEQ ID NO: 53. In certain aspects, the antibody heavy chain comprises heavy chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the heavy chain framework regions of SEQ ID NO: 10, and the antibody light chain comprises light chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the framework regions of SEQ ID NO: 11.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to human Plasminogen Activator Inhibitor type-1 (PAI-1), wherein the antibody comprises a heavy chain variable region, said heavy chain variable region comprising CDR1 (SEQ ID NO: 58), CDR2 (SEQ ID NO: 57), and CDR3 (SEQ ID NO: 56) of SEQ ID NO: 12, and a light chain variable region, said light chain variable region comprising CDR1 (SEQ ID NO: 61), CDR2 (SEQ ID NO: 60), and CDR3 (SEQ ID NO: 59) of SEQ ID NO: 13. In an additional aspect the heavy chain comprises a heavy chain variable region comprising SEQ ID NO: 12, and the light chain comprises a light chain variable region comprising SEQ ID NO: 13. In a further aspect, heavy chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 12, and the light chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 13.
In another aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 58, a heavy chain CDR2 region comprising SEQ ID NO: 57, and heavy chain CDR3 region comprising SEQ ID NO: 56; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 61, a light chain CDR2 region comprising SEQ ID NO: 60, and a light chain CDR3 region comprising SEQ ID NO: 59. In certain aspects, the antibody heavy chain comprises heavy chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the heavy chain framework regions of SEQ ID NO: 12, and the antibody light chain comprises light chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the framework regions of SEQ ID NO: 13.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to human Plasminogen Activator Inhibitor type-1 (PAI-1), wherein the antibody comprises a heavy chain variable region, said heavy chain variable region comprising CDR1 (SEQ ID NO: 64), CDR2 (SEQ ID NO: 63), and CDR3 (SEQ ID NO: 62) of SEQ ID NO: 14, and a light chain variable region, said light chain variable region comprising CDR1 (SEQ ID NO: 67), CDR2 (SEQ ID NO: 66), and CDR3 (SEQ ID NO: 65) of SEQ ID NO: 15. In an additional aspect the heavy chain comprises a heavy chain variable region comprising SEQ ID NO: 14, and the light chain comprises a light chain variable region comprising SEQ ID NO: 15. In a further aspect, heavy chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 14, and the light chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 15.
In an additional aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 64, a heavy chain CDR2 region comprising SEQ ID NO: 63, and a heavy chain CDR3 region comprising SEQ ID NO: 62; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 67, a light chain CDR2 region comprising SEQ ID NO: 66, and a light chain CDR3 region comprising SEQ ID NO: 65. In certain aspects, the antibody heavy chain comprises heavy chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the heavy chain framework regions of SEQ ID NO: 14, and the antibody light chain comprises light chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the framework regions of SEQ ID NO: 15.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to human Plasminogen Activator Inhibitor type-1 (PAI-1), wherein the antibody comprises a heavy chain variable region, said heavy chain variable region comprising CDR1 (SEQ ID NO: 70), CDR2 (SEQ ID NO: 69), and CDR3 (SEQ ID NO: 68) of SEQ ID NO: 16, and a light chain variable region, said light chain variable region comprising CDR1 (SEQ ID NO: 73), CDR2 (SEQ ID NO: 72), and CDR3 (SEQ ID NO: 71) of SEQ ID NO: 17.
In an additional aspect the heavy chain comprises a heavy chain variable region comprising SEQ ID NO: 16, and the light chain comprises a light chain variable region comprising SEQ ID NO: 17. In a further aspect, heavy chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 16, and the light chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 17.
In an additional aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 70, a heavy chain CDR2 region comprising SEQ ID NO: 69, and a heavy chain CDR3 region comprising SEQ ID NO: 68; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 73, a light chain CDR2 region comprising SEQ ID NO: 72, and a light chain CDR3 region comprising SEQ ID NO: 71. In certain aspects, the antibody heavy chain comprises heavy chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the heavy chain framework regions of SEQ ID NO: 16, and the antibody light chain comprises light chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the framework regions of SEQ ID NO: 17.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to human Plasminogen Activator Inhibitor type-1 (PAI-1), wherein the antibody comprises a heavy chain variable region, said heavy chain variable region comprising CDR1 (SEQ ID NO: 46), CDR2 (SEQ ID NO: 45), and CDR3 (SEQ ID NO: 44) of SEQ ID NO: 80, and a light chain variable region, said light chain variable region comprising CDR1 (SEQ ID NO: 49), CDR2 (SEQ ID NO: 48), and CDR3 (SEQ ID NO: 47) of SEQ ID NO: 81.
In an additional aspect the heavy chain comprises a heavy chain variable region comprising SEQ ID NO: 80, and the light chain comprises a light chain variable region comprising SEQ ID NO: 81. In a further aspect, heavy chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 80, and the light chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 81.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 46, a heavy chain CDR2 region comprising SEQ ID NO: 45, and a heavy chain CDR3 region comprising SEQ ID NO: 44; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 49, a light chain CDR2 region comprising SEQ ID NO: 48, and a light chain CDR3 region comprising SEQ ID NO: 47. In certain aspects, the antibody heavy chain comprises heavy chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the heavy chain framework regions of SEQ ID NO: 80, and the antibody light chain comprises light chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the framework regions of SEQ ID NO: 81.
In another aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to Plasminogen Activator Inhibitor type-1 (PAI-1), wherein the antibody comprises a heavy chain variable region, said heavy chain variable region comprising CDR1 (SEQ ID NO: 76), CDR2 (SEQ ID NO: 75), and CDR3 (SEQ ID NO: 74) of SEQ ID NO: 18, and a light chain variable region, said light chain variable region comprising CDR1 (SEQ ID NO: 79), CDR2 (SEQ ID NO: 78), and CDR3 (SEQ ID NO: 77) of SEQ ID 19. In an additional aspect the heavy chain comprises a heavy chain variable region comprising SEQ ID NO: 18, and the light chain comprises a light chain variable region comprising SEQ ID NO: 19. In a further aspect, heavy chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 18, and the light chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to SEQ ID NO: 19.
An isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 76, heavy chain CDR2 region comprising SEQ ID NO: 75, and a heavy chain CDR3 region comprising SEQ ID NO: 74; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 79, a light chain CDR2 region comprising SEQ ID NO: 78, and a light chain CDR3 region comprising SEQ ID NO: 77. In certain aspects, the antibody heavy chain comprises heavy chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the heavy chain framework regions of SEQ ID NO: 18, and the antibody light chain comprises light chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the framework regions of SEQ ID NO: 19.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 33, heavy chain CDR2 region comprising SEQ ID NO: 146, and a heavy chain CDR3 region comprising SEQ ID NO: 32; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 37, a light chain CDR2 region comprising SEQ ID NO: 145, and a light chain CDR3 region comprising SEQ ID NO: 35.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 147, heavy chain CDR2 region comprising SEQ ID NO: 33, and a heavy chain CDR3 region comprising SEQ ID NO: 32; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 37, a light chain CDR2 region comprising SEQ ID NO: 36, and a light chain CDR3 region comprising SEQ ID NO: 35.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 147, heavy chain CDR2 region comprising SEQ ID NO: 33, and a heavy chain CDR3 region comprising SEQ ID NO: 32; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 37, a light chain CDR2 region comprising SEQ ID NO: 145, and a light chain CDR3 region comprising SEQ ID NO: 35.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 146, heavy chain CDR2 region comprising SEQ ID NO: 33, and a heavy chain CDR3 region comprising SEQ ID NO: 32; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 37, a light chain CDR2 region comprising SEQ ID NO: 145, and a light chain CDR3 region comprising SEQ ID NO: 35.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 34, heavy chain CDR2 region comprising SEQ ID NO: 33, and a heavy chain CDR3 region comprising SEQ ID NO: 32; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 37, a light chain CDR2 region comprising SEQ ID NO: 145, and a light chain CDR3 region comprising SEQ ID NO: 35.
In an additional aspect, disclosed herein is an isolated monoclonal antibody that binds to essentially the same epitope on PAI-1 as an isolated monoclonal antibody, comprising a heavy chain variable region, wherein the heavy chain variable region comprises CDR1 (SEQ ID NO: 34), CDR2 (SEQ ID NO: 33), and CDR3 (SEQ ID NO: 32) of SEQ ID NO: 6, and a light chain variable region, wherein the light chain variable region comprises CDR1 (SEQ ID NO: 37), CDR2 (SEQ ID NO: 36), and CDR3 (SEQ ID NO: 35) of SEQ ID NO: 7.
In a certain aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, comprising: (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 76, heavy chain CDR2 region comprising SEQ ID NO: 75, and a heavy chain CDR3 region comprising SEQ ID NO: 74; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 79, a light chain CDR2 region comprising SEQ ID NO: 78, and a light chain CDR3 region comprising SEQ ID NO: 77.
In one aspect, disclosed herein is a humanized monoclonal antibody that binds specifically to human PAI-1, wherein the antibody comprises: (a) a heavy chain having, a heavy chain variable region comprising SEQ ID NO: 82, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 91, or an antigen-binding fragment thereof; (b)
a heavy chain having a heavy chain variable region comprising SEQ ID NO: 83, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 92, or an antigen-binding fragment thereof; (c) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 84, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 93, or an antigen-binding fragment thereof; (d) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 85, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 91, or an antigen-binding fragment thereof; (e) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 85, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 93, or an antigen-binding fragment thereof; (f) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 86, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 94, or an antigen-binding fragment thereof; (g) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 87, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 95, or an antigen-binding fragment thereof; (h) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 88, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 96, or an antigen-binding fragment thereof; (i) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 89, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 97, or an antigen-binding fragment thereof; (j) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 90, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 98, or an antigen-binding fragment thereof; (k) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 86, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 93, or an antigen-binding fragment thereof; (l) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 86, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 95, or an antigen-binding fragment thereof; (m) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 89, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 93, or an antigen-binding fragment thereof; or (n) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 89, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 95, or an antigen-binding fragment thereof. In a further aspect, the humanized heavy chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to any of the previously disclosed human heavy chain variable regions, and the humanized light chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to any of the previously disclosed human light chain variable regions.
In one aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1 comprising: (a) a heavy chain framework region and a heavy chain variable region comprising SEQ ID NO: 86, and (b) a light chain framework region and a light chain variable region comprising SEQ ID NO: 93. In certain aspects, the isolated monoclonal heavy chain comprises heavy chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the heavy chain framework regions of SEQ ID NO: 86, and the isolated monoclonal antibody light chain comprises light chain framework regions that are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to the framework regions of SEQ ID NO: 93. In certain other aspects, the isolated monoclonal antibody heavy chain comprises heavy chain framework regions that are 95% identical to the heavy chain framework regions of SEQ ID NO: 86, and the isolated monoclonal antibody light chain comprises light chain framework regions that are 95% identical to the framework regions of SEQ ID NO: 93.
In another aspect, disclosed herein is a humanized monoclonal antibody that binds specifically to human PAI-1, wherein the antibody comprises a heavy chain having a heavy chain variable region comprising SEQ ID NO: 154, or an antigen-binding fragment thereof; and a light chain having a light chain variable region comprising SEQ ID NO: 153, or an antigen-binding fragment thereof. In another aspect, disclosed herein is a humanized monoclonal antibody that binds specifically to human PAI-1, wherein the antibody comprises a heavy chain having a heavy chain variable region comprising SEQ ID NO: 155, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 153, or an antigen-binding fragment thereof. In a further aspect, the humanized heavy chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to any of the previously disclosed human heavy chain variable regions, and the humanized light chain variable region is 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to any of the previously disclosed human light chain variable regions.
In another aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, wherein the antibody binds a polypeptide comprising SEQ ID NO: 158. In another embodiment, the isolate monoclonal antibody binds a fragment of a polypeptide comprising SEQ ID NO: 158. In yet another embodiment, the isolated monoclonal antibody that binds specifically to PAI-1 binds a polypeptide comprising SEQ ID NO: 156 and/or SEQ ID NO: 158. In another embodiment, the isolated monoclonal antibody that binds specifically to PAI-1 binds a polypeptide comprising SEQ ID NO: 156, SEQ ID NO: 158, and/or SEQ ID NO: 157. In still another embodiment, the isolated monoclonal antibody that binds specifically to PAI-1 comprises specific binding affinity for residues 160, 262, 296-297, 300-307, and/or 310-316 of SEQ ID NO: 1. In certain embodiments, the isolated monoclonal antibody disclosed herein interacts with at least residues 311, 312, and 313 (D-Q-E) of SEQ ID NO: 1. In certain embodiments, the PAI-1 bound by the antibody is human PAI-1. In other embodiments, the PAI-1 bound by the antibody is the active form of human PAI-1.
In other embodiments, the isolated monoclonal antibody that binds specifically to PAI-1 disclosed herein binds a polypeptide comprising SEQ ID NO: 161. In still other embodiments, the isolated monoclonal antibody binds a polypeptide comprising SEQ ID NO: 159 and/or SEQ ID NO: 161. In still other embodiments, the isolated monoclonal antibody binds a polypeptide comprising SEQ ID NO: 159, SEQ ID NO: 160, and/or SEQ ID NO: 161. In still another embodiment, the isolated monoclonal antibody that binds specifically to PAI-1 comprises specific binding affinity for residues 44-64 and/or residues 307-321 of cyno-PAI-1 (SEQ ID NO: 162). In certain embodiments, the PAI-1 bound by the antibody is cyno-PAI-1. In other embodiments, the PAI-1 bound by the antibody is the latent form of cyno-PAI-1.
In a further aspect, disclosed herein is an isolated monoclonal antibody that competitively inhibits binding of any of the disclosed antibodies to PAI-1. In an embodiment, disclosed herein is an isolated monoclonal antibody that competes for binding and/or competitively inhibits binding with any of the isolated monoclonal antibodies disclosed herein. In certain embodiments, the isolated monoclonal antibody competes or competitively inhibits binding, to human PAI-1. In certain embodiments, the isolated monoclonal antibody competes or competitively inhibits binding to a polypeptide comprising SEQ ID NO: 156, SEQ ID NO: 157, and/or SEQ ID NO: 158. In another embodiment, the isolated monoclonal antibody competes or competitively inhibits binding to a polypeptide comprising SEQ ID NO: 159, SEQ ID NO: 160, and/or SEQ ID NO: 161. In an embodiment, the isolated antibody competes for binding to a polypeptide comprising SEQ ID NO: 156, 157, and/or 158 with an isolated monoclonal antibody comprising (a) heavy chain framework regions, a heavy chain CDR1 region comprising SEQ ID NO: 34, heavy chain CDR2 region comprising SEQ ID NO: 33, and a heavy chain CDR3 region comprising SEQ ID NO: 32; and (b) light chain framework regions, a light chain CDR1 region comprising SEQ ID NO: 37, a light chain CDR2 region comprising SEQ ID NO: 145, and a light chain CDR3 region comprising SEQ ID NO: 35.
In another aspect, disclosed herein are nucleotides encoding any of the isolated monoclonal antibodies disclosed herein.
In one aspect, disclosed herein is a method of treating a condition caused by increased expression of PAI-1 or increased sensitivity to PAI-1 comprising administering to a patient or other subject orally, parenterally by a solution for injection, by inhalation, or topically a pharmaceutically effective amount of a PAI-1 antibody.
In one aspect, disclosed herein is a method restoring plasmin generation comprising administering to a patient or other subject in need thereof orally, parenterally by a solution for injection, by inhalation, or topically a pharmaceutically effective amount of a PAI-1 antibody. Parenteral administration disclosed herein includes intravenous, drip, intraarterial, intraperitoneal, intramuscular, subcutaneous, rectal or vaginal, intravenous, intraarterial, subcutaneous, and intramuscular forms of parenteral administration. In some embodiments, the administration to a patient or other subject comprises multiple administrations. In another aspect, the method of restoring plasmin generation facilitates therapeutic treatment of a condition comprising increased levels of fibrotic tissue. In some aspects, the condition is characterized by fibrosis. In some aspects, the condition is fibrosis, skin fibrosis, systemic sclerosis, lung fibrosis, idiopathic pulmonary fibrosis, interstitial lung disease, and chronic lung disease. In other aspects, the plasmin generation facilitates therapeutic treatment of liver fibrosis, kidney fibrosis, including chronic kidney disease, thrombosis, venous and arterial thrombosis, deep vein thrombosis, peripheral limb ischemia, disseminated intravascular coagulation thrombosis, acute ischemic stroke with and without thrombolysis, or stent restenosis.
In another aspect, disclosed herein is the use of a pharmaceutically effective amount of a PAI-1 antibody for the manufacture of a medicament for treating a condition caused by increased expression of PAI-1 or increased sensitivity to PAI-1 comprising administering to a patient or other subject orally, parenterally by a solution for injection, by inhalation, or topically.
In one aspect, the medicament is for treating a condition comprising increased levels of fibrotic tissue. In some aspects, the condition is characterized by fibrosis. In some aspects, the condition is fibrosis, skin fibrosis, systemic sclerosis, lung fibrosis, idiopathic pulmonary fibrosis, interstitial lung disease, and chronic lung disease. In other aspects, the medicament is for treating a condition comprising liver fibrosis, kidney fibrosis, including chronic kidney disease, thrombosis, venous and arterial thrombosis, deep vein thrombosis, peripheral limb ischemia, disseminated intravascular coagulation thrombosis, acute ischemic stroke with and without thrombolysis, or stent restenosis.
In another aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, wherein the antibody inhibits lung fibrosis. In certain embodiments, the antibody inhibits fibrosis in the lung of a subject. In certain embodiments, the antibody inhibits fibrosis in the lung of a subject with idiopathic pulmonary fibrosis (IPF). In some embodiments, the isolated monoclonal antibody disclosed herein induces an increase in fibrin degradation in a subject. In certain embodiments, the antibody increases fibrin degradation in the plasma of the subject. In some other embodiments, the isolated monoclonal antibody disclosed herein inhibits collagen accumulation in the lung of a subject. In some embodiments, the subject has IPF. In some other embodiments, the isolated monoclonal antibody disclosed herein increases D-dimer levels in the bronchoalveolar lavage fluid (BALF) of a subject. In some embodiments, the subject has IPF. In some other embodiments, the isolated monoclonal antibody disclosed herein binds specifically to PAI-1, wherein the antibody inhibits the increase in lung weight due to fibrosis in a subject. In one embodiment, the subject has IPF.
In another aspect, disclosed herein is the use of a pharmaceutically effective amount of a PAI-1 antibody for the manufacture of a medicament for treating a condition caused by increased expression of PAI-1 or increased sensitivity to PAI-1 comprising administering to a patient orally, parenterally by a solution for injection, by inhalation, or topically, wherein the condition is idiopathic pulmonary fibrosis.
In another aspect, disclosed herein is a method restoring plasmin generation comprising administering to a to a patient or other subject thereof orally, parenterally by a solution for injection, by inhalation, or topically a pharmaceutically effective amount of a PAI-1 antibody, wherein the plasmin generation facilitates therapeutic treatment of idiopathic pulmonary fibrosis.
In another aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, wherein the antibody restores fibrinolytic activity in a subject. In certain embodiments, the antibody restores fibrinolytic activity in a subject with acute ischemic stroke. The acute ischemic stroke can be either with or without thrombolysis. In some embodiments, the isolated monoclonal antibody restores clot lysis. In certain embodiments, the antibody restores in vitro clot lysis. In still other embodiments, the antibody restores in vitro clot lysis with an IC50 of about 2 nM.
In other aspects, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, wherein the antibody restores fibrin breakdown in a subject. In some embodiments, the subject has acute ischemic stroke.
In another aspect, disclosed herein is the use of a pharmaceutically effective amount of a PAI-1 antibody for the manufacture of a medicament for treating a condition caused by increased expression of PAI-1 or increased sensitivity to PAI-1 comprising administering to a patient orally, parenterally by a solution for injection, by inhalation, or topically, wherein the condition is acute ischemic stroke with and without thrombolysis.
In another aspect, disclosed herein is a method restoring plasmin generation comprising administering to a patient or other subject in need thereof orally, parenterally by a solution for injection, by inhalation, or topically a pharmaceutically effective amount of a PAI-1 antibody, wherein the plasmin generation facilitates therapeutic treatment of acute ischemic stroke with and without thrombolysis.
In another aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, wherein the antibody inhibits formation of adhesions in a subject. In some embodiments, the adhesion formation is following surgery or injury to the subject. In some embodiments, the adhesion formation in the subject is abdominal. In other embodiments, the adhesion formation occurs in the shoulder, pelvis, heart, spine, hand, and other body regions of the subject.
In another aspect, disclosed herein is the use of a pharmaceutically effective amount of a PAI-1 antibody for the manufacture of a medicament for treating or preventing a condition caused by increased expression of PAI-1 or increased sensitivity to PAI-1 comprising administering to a patient orally, parenterally by a solution for injection, by inhalation, or topically, wherein the condition is abdominal adhesion formation.
In another aspect, disclosed herein is a method of restoring plasmin generation comprising administering to a to a patient or other subject in need thereof orally, parenterally by a solution for injection, by inhalation, or topically a pharmaceutically effective amount of a PAI-1 antibody, wherein the plasmin generation facilitates therapeutic treatment or prevention of adhesion formation. In some embodiments, the adhesion formation in the subject is abdominal.
In another aspect, disclosed herein is an isolated monoclonal antibody that binds to a PAI-1/vitronectin complex. In another aspect, disclosed herein is an isolated monoclonal antibody that neutralizes PAI-1 activity by inducing PAI-1 substrate conformation. In an embodiment, the antibody restores or is capable of restoring plasmin generation. In another embodiment, the isolated monoclonal antibody induces or is capable of inducing fibronectin degradation. In yet another embodiment, the isolated monoclonal antibody induces or is capable of inducing matrix metalloproteinases (MMP) activation.
In another aspect, the isolated monoclonal antibody disclosed herein is an antibody fragment. In some embodiments, the antibody is a single-chain Fv antibody. In other embodiments, the heavy chain and light chain are connected by a flexible linker to form a single-chain antibody. In other embodiments, the antibody is a Fab, Fab′, or (Fab′)2 antibody.
In another aspect, disclosed herein is an isolated monoclonal antibody that binds specifically to PAI-1, wherein the antibody is a crystallized antibody. In an embodiment, disclosed herein is an isolated crystal comprising the Fab′ fragment of monoclonal antibody A44, wherein the Fab′ fragment consists of light chain sequence SEQ ID NO:7 and heavy chain sequence SEQ ID NO:6. In another embodiment, disclosed herein is an isolated crystal comprising a Fab′ fragment comprising light chain sequence SEQ ID NO:93 and heavy chain sequence SEQ ID NO:86. In an embodiment, the isolated crystal comprises asymmetric unit cell dimensions a=105 Å, b=152 Å and c−298 Å. In an embodiment, the isolated crystal belongs to P212121 space group. In another embodiment, the isolated crystal comprises a 3.3 Å resolution of x-ray diffraction. In an embodiment, the isolated crystal retains the biological activity of the crystallized antibody. In some embodiments, the isolated crystal has a greater half life in vivo than the soluble counterpart of the crystallized antibody.
In one aspect, disclosed herein is a pharmaceutical composition comprising: (a) the crystallized antibody that binds specifically to PAI-1 and (b) at least one pharmaceutical excipient which embeds or encapsulates the crystal.
In another aspect, disclosed herein is a pharmaceutical composition comprising a pharmaceutically acceptable carrier and a therapeutically effective amount of any of the antibodies disclosed herein.
In one aspect, disclosed herein is a method of generating an antibody against PAI-1 comprising immunizing a mammal with a complex composed of PAI-1, or a fragment thereof, and vitronectin.
In another aspect, disclosed herein is a method of screening a PAI-1 antibody in an ELISA for its ability to block PAI-1's function as a tPA activity inhibitor, comprising the steps of: (a) binding PAI-1 to an ELISA plate; (b) incubating the ELISA plate with the PAI-1 antibody; (c) incubating the ELISA plate with tPA; (d) incubating the ELISA plate with labeled anti-tPA antibody; and (e) measuring the OD405 emitted by the labeled anti-tPA antibody; wherein a positive readout indicates that the PAI-1 antibody binds to PAI-1 but does not block formation of the covalent bond between PAI-1 and tPA, and a negative readout indicates that the PAI-1 antibody blocks tPA interaction with PAI-1.
In another aspect, disclosed herein is a method of screening hybridomas. In certain embodiments, the method of screening comprises a reverse screening method using anti-mouse immobilized anti-PAI-1 antibodies. In other embodiments, the method of screening comprises or a forward screening assay using free PAI-1 as a ligand or against immobilized vitronectin. In certain embodiments, the method is applied to determine the affinity of an antibody for a PAI-1/vitronectin complex. In some embodiments, the method comprises: immobilizing vitronectin to a surface; contacting PAI-1 with the vitronectin immobilized to the surface, thereby forming a complex; contacting the surface comprising the complex with the antibody; separating the antibody bound to the complex from unbound antibody; detecting the antibody bound to the complex, and analyzing the levels of antibody bound to the complex to determine the affinity of the antibody for the complex.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 depicts a schematic representation of the mechanisms between PAI-1 and the serine proteases tissue-type plasminogen activator (tPA) and urokinase-type plasminogen activator (uPA). PAI-1 exhibits structural flexibility and can occur in a latent conformation or an active conformation when it is bound to vitronectin (Vn). The RCL region of PAI-1 bears the bait peptide bond (also called P1-P1′) that is the cleavage site by the serine protease. A Michaelis complex with tPA or uPA forms first, then the catalytic triad reacts with the bait peptide bond to form an acyl-enzyme complex that, after cleavage of the P1-P′1 peptide bond, induces strong conformation changes. Acyl enzyme is a labile complex formed by covalent bond between the serine residue (black triangle) from catalytic triad from serine protease (tPA) and amino-acid from the substrate (black circle) that undergoes further hydrolysis. The conformational changes causes insertion of the cleaved RCL into a β-strand with the protease staying covalently bound as an acyl enzyme with PAI-1. Under non physiological circumstance, hydrolysis of this acyl-enzyme complex may induce release of the cleaved PAI-1 and free active protease.
FIG. 2 depicts a typical standard curve for antibody titration in the binding ELISA as described in Example 2. The antibodies 31C9, 33B8 and 33H1 were positive controls and IgG1 was as a negative control.
FIG. 3 depicts a representation curve for a functional ELISA to select antibodies that block the interaction of PAI-1 with tPA as described in Example 4. The antibody 33H1 is a positive control, IgG1 is a negative control and A44 was identified as a positive antibody clone.
FIG. 4A depicts neutralization of human PAI-1 blocking activity of tPA by A44 and commercially available antibodies (33B8 and 33H1) in the chromogenic assay described in Example 4. FIG. 4B shows sigmoidal dose-response (variable slope) best-fit values of the results depicted in FIG. 4A.
FIG. 5A depicts neutralization of human PAI-1 blocking activity of tPA by a selection of antibodies produced from different fusions (see Example 4). FIG. 5B shows hillslope and EC50 values of the results depicted in FIG. 5A.
FIG. 6A depicts human PAI-1 and its orthologs block human tPA activity in chromogenic assay with the similar potency. FIG. 6B shows hillslope and EC50 values of the results depicted in FIG. 6A.
FIG. 7A depicts neutralization of cynomolgus (cyno) and mouse PAI-1 blocking activity of human tPA by A44 and 33B8 (commercially available) antibodies in the chromogenic assay described in Example 4. FIG. 7B shows hillslope and EC50 values of the results depicted in FIG. 7A.
FIG. 8 depicts SDS-Page analysis of the mechanism of action for antibodies 33H8 (converts PAI-1 from active to latent confirmation), 33H1 (converts PAI-1 from active to substrate conformation) and A44 to block the interaction of PAI-1 with tPA. Lane 1: molecular weight standards; Lane 2: PAI-1 only; Lane 3: tPA only; Lane 4: PAI-1 in the presence of tPA; Lane 5: 33B8+PAI-1+tPA; Lane 6: 33H1+PAI-1+tPA; Lane 7: A44+PAI-1+tPA; Lane 8: mAb is an isotype control antibody.
FIG. 9 depicts SDS-Page analysis of the mechanism of action for antibodies 33H8 (converts PAI-1 from active to latent confirmation), 33H1 (converts PAI-1 from active to substrate conformation) and antibodies developed from fusions C26, E16 and E21 to block the interaction of PAI-1 with tPA. Lane 1: molecular weight standards; Lane 2: PAI-1 only; Lane 3: tPA only; Lane 4: PAI-1 in the presence of tPA: Lane 5: 33B8+PAI-1+tPA; Lane 6: 33H1+PAI-1+tPA: Lane 7: C26+PAI-1+tPA; Lane 8: E16+PAI-1+tPA: Lane 9: E21+PAI-1+tPA; Lane 10: mAb is an isotype control antibody.
FIG. 10 depicts SDS-Page analysis of the mechanism of action for antibodies 33H8 (converts PAI-1 from active to latent confirmation), 33H1 (converts PAI-1 from active to substrate conformation) and antibodies developed from fusions A39, B109 and C45 to block the interaction of PAI-1 with tPA. Lane 1: molecular weight standards; Lane 2: PAI-1 only; Lane 3: tPA only; Lane 4: PAI-1 in the presence of tPA; Lane 5: 33B8 ±tPA; Lane 6: 33H1+PAI-1-tPA; Lane 7: A39+PAI-1+tPA; Lane 8: B109+PAI-1+tPA; Lane 9: C45+PAI-1+tPA; Lane 10: mAb is an isotype control antibody.
FIG. 11 depicts the alignment of the light chain of the following murine antibodies: A105 (SEQ ID NO: 3), A39 (SEQ ID NO: 5), A44 (SEQ ID NO: 7), A71 (SEQ ID NO: 9), A75 (SEQ ID NO: 81), B109 (SEQ ID NO: 11), B28 (SEQ ID NO: 13), C45 (SEQ ID NO: 15), E16 (SEQ ID NO: 17), and E21 (SEQ ID NO: 19). CDRs are highlighted in hold.
FIG. 12 depicts the alignment of the heavy chain of the following murine antibodies: A105 (SEQ ID NO: 2), A39 (SEQ ID NO: 4), A44 (SEQ ID NO: 6), A71 (SEQ ID NO: 8), A75 (SEQ ID NO: 80), B109 (SEQ ID NO: 10), B28 (SEQ ID NO: 12), C45 (SEQ ID NO: 14), E16 (SEQ ID NO: 16), and E21 (SEQ ID NO: 18), CDRs, as defined by IMGT, are highlighted in bold.
FIG. 13 depicts the alignment of marine A44 light chain (SEQ ID NO: 7) with vk1 (SEQ ID NO: 101) and vlambda3 (SEQ ID NO: 102).
FIG. 14 depicts the alignment of murine A44 heavy chain (SEQ ID NO: 6) with vh2 (SEQ ID NO: 103) and vh4 (SEQ ID NO: 104).
FIG. 15 depicts clone A44 humanization VL with all constructs aligned: LC1a (SEQ ID NO: 91), LC1b (SEQ ID NO: 92), LC2 (SEQ ID NO: 93), LC3 (SEQ ID NO: 94), LC4 (SEQ ID NO: 95), LC5a (SEQ ID NO: 96), LC5b (SEQ ID NO: 97), and LC5c (SEQ ID NO: 98). All aligned sequences are further described below in Table 25. Black boxes represent CDR domains. Highlighted residues vary in sequence from the residue directly above in the alignment. Residue numbering is as described by IMGT.
FIG. 16 depicts clone A44 humanization VH with all constructs aligned: HC1a (SEQ ID NO: 82), HC1b (SEQ ID NO: 83), HC2a (SEQ ID NO: 84), HC2b (SEQ ID NO: 85), HC3 (SEQ ID NO: 86), HC4 (SEQ ID NO: 87), HC5a (SEQ ID NO: 88), HC5b (SEQ ID NO: 89), and HC5c (SEQ ID NO: 90), All aligned sequences are further described below in Table 25. Black boxes represent CDR domains. Highlighted residues vary in sequence from the residue directly above in the alignment. Residue numbering is as described by IMGT.
FIG. 17 depicts percent inhibition of PAI-1 activity was plotted as a function of mAb concentration and IC50 was determined Imax using Biostat speed software.
FIG. 18 depicts purification of homogeneity recombinant 6-His tagged Fab A44.
FIG. 19 depicts SPR analysis with Biacore 2000 using single kinetic analysis of human PAI-1 glycosylated binding to immobilized APG antibody. A sensogram from single-cycle kinetic is shown in grey. Fit model is shown in black.
FIG. 20 depicts human plasma PAI-1 neutralization by APG, APGv2, and APGv4 antibodies as determined by UK-PAI-1 complex formation detection by ELISA. Percent inhibition of PAI-1 activity was plotted as a function of concentration of APG, APGv2, or APGv4 antibodies.
FIG. 21 depicts restoration of human plasma clot lysis by A44V11 (1, 3 or 10 nM) in the presence of tPA 1 nM and PAI-1 3 nM as detected by turbidimetry kinetic measurement by absorbance reading at 340 nm as a function of time (min).
FIG. 22 depicts absence of restoration of human plasma clot lysis by human IgG1 negative controle (1, 3 or 10 nM) in the presence of tPA 1 nM and PAI-1 3 nM as detected by absorbance at 340 nm as a function of time (min).
FIG. 23 depicts restoration of human plasma clot lysis by A44V11 or human IgG1 isotype negative control at various concentrations.
FIG. 24 depicts restoration of human plasma clot lysis by APG, APGV2 or APGV4 at 3 nM in the presence of tPA 1 nM and PAI-1 3 nM as detected by absorbance at 340 nm as a function of time (min).
FIG. 25 depicts restoration of human plasma clot lysis by APG variant 2 and 4 at various concentrations.
FIG. 26 depicts in anti-PAI-1 on human LL29 myofibroblast supernatants at 48 H after treatment by A44V11 or IgG isotype control mAb at 50 nM and TGFβ 5 ng/ml.
FIG. 27 depicts generic MMP activity in human primary lung fibroblasts after cell treatment for 48 hr with PBS (control), plasminogen (Pg), A44V11 and plasminogen (A+Pg) or negative human IgG and plasminogen (Neg+Pg).
FIG. 28 depicts human active PAI-1 level in broncho-alveolar lavage fluid (BALF) (A) and in lung lysate (B) from bleomycin treated mice at day 7 and day 9 following treatment at day 4 with A44 or IgG1 at 10 mg/kg or PBS by i.p. administration. Active PAI-1 determined by ELISA (#HPAIKT Molecular Innovation). Percentage of inhibition were calculated by dividing the difference between A44 bleo and IgG bleo by the difference between IgG bleo and untreated (PBS) mice group.
FIG. 29 depicts mouse D-Dimer level in BALF from bleomycin treated mice at day 7 and day 9 following treatment at day 4 with A44 or IgG1 at 10 mg/kg or PBS by i.p. administration as determined by ELISA (Asserachrom D-Di, Diagnostica Stago). Fold increase in D-dimer induced by A44 in comparison to IgG are indicated.
FIG. 30 depicts right lung weight from transgenic humanized mice 21 days after either saline or bleomycin treatment followed by PBS (vehicle), IgG1 or A44 10 mg/kg i.p. administration from day 4 to day 20 every 3 days.
FIG. 31 depicts hydroxyproline lung content in transgenic humanized mice 21 days after either saline or bleomycin treatment followed by PBS (vehicle), IgG1 or A44 10 mg/kg i.p. administration from day 4 to day 20 every 3 days.
FIG. 32 depicts active PAI-1 level in plasma from monkeys treated by A44V 11 (A) mAb (n=5) or with IgG1 isotype control (B) (n=4) (5 mg/kg ip) 24 hours before LPS challenge (100 ug/kg iv). Blood samples were harvested at the indicated time point and active PAI-1 levels were determined in plasma using the ELISA (#HPAIKT from Molecular Innovation).
FIG. 33 depicts active PAI-1 level in liver biopsy from monkeys treated by A44V11 (A) mAb (n=5) or with IgG1 isotype control (B) (n=4) (5 mg/kg ip) 24 hours before LPS challenge (100 ug/kg iv). Liver biopsies were harvested in anesthetized monkeys at the indicated time point and active PAI-1 levels were determined in lysates using the ELISA (#HPAIKT from Molecular innovation).
FIG. 34 depicts D-dimer level in plasma from monkeys treated by A44V11 (A) mAb (n=5) or with IgG1 isotype control (B) (n=4) (5 mg/kg ip) 24 hours before LPS challenge (100 ug/kg iv). Blood samples were harvested at the indicated time point and D-dimer levels were determined in plasma using the ELISA.
FIG. 35 depicts Plasmin-α2 Antiplasmin (PAP) complexes level in plasma from monkeys treated by A44V11 (A) mAb (n=5) or with IgG1 isotype control (B) (n=4) (5 mg/kg ip) 24 hours before LPS challenge (100 ug/kg iv). Blood samples were harvested at the indicated time point and PAP levels were determined in plasma using the ELISA (# Asserachrom PAP from Diagnostica Stago).
FIG. 36 depicts level of active PAI-1 in intraperitoneal fluid (IPF) and uterine horn lysates. Active PAI-1 levels in the intraperitoneal fluid (A) and uterine horn lysates (B). At the 6 hour and Day 7 time points active PAI-1 levels were lower in both intraperitoneal fluid (IPF) and Uterine Horn (UH) Lysates in the animals treated with A44V11 antibody in comparison to the isotype control antibody treated animals, no difference was observed at 72 hour time point. (*p<0.001 calculated by the Student T-test)
FIG. 37 depicts another example of purification of homogeneity recombinant 6-His tagged Fab A44.
FIG. 38 depicts purification of homogeneity recombinant 6-His tagged Fab A44 complexed with the human wt PAI-1 protein.
FIG. 39(a) depicts the complex crystallization of the Fab A44/PAI-1 complex, and FIG. 39(b) depicts the best optimized crystals.
FIG. 40 depicts the rod-like single crystals of the Fab A44/PAI-1 complex.
FIG. 41 depicts Fab A44 recognition the active form of human PAI-1 and the latent form of cyno PAI-1.
FIG. 42 depicts the PAI-1 epitope recognized by Fab A44 in (A) active human PAI-1 and (B) latent cyno PAI-1.
FIG. 43 depicts the heavy chain paratope of the Fab A44/PAI-1 complex.
FIG. 44 depicts the light chain paratope of the Fab A44/PAI-1 complex.
FIG. 45 depicts a sequence alignment of the proposed A44 binding epitopes of cyno, human, rat, and mouse PAI-1. Sequences are excerpted from SEQ ID NO:1 (PAI-1 human), SEQ ID NO:162 (PAI-1 cyno), SEQ ID NO:163 (PAI-1 mouse), and SEQ ID NO:164 (PAI-1 rat).
FIG. 46 depicts the comparison of the mouse PAI-1 structure with the structure of the human PAI-1/A44V11 complex.
FIG. 47 shows the structure of human PAI-1/A44V11 complex and the model of vitronectin binding to PAI-1.
FIG. 48 depicts peptic peptide coverage of cyno-PAI-1 (SEQ ID NO:162); 95.3% sequence coverage is obtained from 150 overlapping peptic peptides.
FIG. 49 depicts representative deuterium uptake plots for cyno-PAI-1 peptides in the unbound (circle lines), APGv2-bound (x-lines) and A44v11-bound (diamond lines) states. Residue ranges/positions are from SEQ ID NO:162. (A) most of the peptic peptides showed no difference between cyno-PAI-1 alone or bound to either mAb. (B), peptides covering residues 44-64 showed similar protection from exchange in both mAb-bound states. (C), peptides incorporating residues 295-322 incorporate less deuterium in both mAb-bound states, however the magnitude of protection is greater for A44v11.
FIG. 50 depicts hydrogen/deuterium exchange (HDX) comparison of cyno-PAI-1 alone and bound to A44v11. (A), butterfly plot of the average relative fractional exchange with the unbound state above and the bound state below. The lines correspond to data acquired for the 10 sec, 1 min, 5 min, and 240 min time points. In (B), plot of the difference data (in daltons) from the above plot in (A) for cyno-PAI-1 alone or bound to A44v11.
FIG. 51 depicts HDX comparison of cyno-PAI-1 alone and bound to APGv2. In (A), butterfly plot of the average relative fractional exchange with the unbound state above and the bound state below. The lines correspond to data acquired for the 10 sec, 1 min, 5 min and 240 min time points. In (B), plot of the difference data from panel (A) above for cyno-PAI-1 alone or bound to APGv2.
FIG. 52 depicts HDX comparison of cyno-PAI-1 bound to A44v11 and bound to APGv2. In (A), butterfly plot of the average relative fractional exchange with the APGv2 bound state above and the A44v11 bound state below. The lines correspond to data acquired for the 10 sec, 1 min, 5 min and 240 min time points. In (B), plot of the difference data from panel (A) above for cyno-PAI-1 bound to APGv2 or A44v11.
FIG. 53 depicts the cyno-PAI-1:A44v11 epitope determined by HDX MS. The residues of cynoPAI-1 (SEQ ID NO: 162) which show protection from exchange in the A44v11 antibody-bound state are shown in bold. The residues of cyno-PAI-1:A44v11 epitope determined from the crystallization studies is shown in boxes.



DETAILED DESCRIPTION
The present invention provides antibodies and fragments thereof that specifically bind to human PAI-1 and modulate the biological functions of PAI-1. Such antibodies are particularly useful for treating PAI-1-associated disease or disorders (e.g., fibrosis). The invention also provides pharmaceutical compositions, as well as nucleic acids encoding PAI-1 antibodies, recombinant expression vectors and host cells for making such antibodies, or fragments thereof. Methods of using antibodies as disclosed herein to detect PAI-1 or to modulate PAI-1 activity, either in vitro or in vivo, are also encompassed by the invention.
I. Definitions
In order that the present invention may be more readily understood, certain terms are first defined.
As used herein, the term “human PAI-1” refers to a peptide comprising or consisting of the amino acid sequence listed below:







(SEQ ID NO. 1)


VHHPPSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTT


 


GGETQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQ


 


RDLKLVQGFMPHFFRLFRSTVKQVDFSEVERARFIINDWVKTHTKGMISN


 


LLGKGAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVP


 


MMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMHAAPYEKEVPLSALT


 


NILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRQ


 


FQADFTSLSDQEPLHVAQALQKVKIEVNESGTVASSSTAVIVSARMAPEE


 


IIMDRPFLFVVRHNPTGTVLFMGQVMEP,






or a fragment thereof.

As used herein, the term “antibody” refers to immunoglobulin molecules comprising four polypeptide chains, two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, as well as multimers thereof (e.g., IgM). Each heavy chain comprises a heavy chain variable region (abbreviated VH or VH) and a heavy chain constant region (CH or CH). The heavy chain constant region comprises three domains, CH1, CH2 and CH3. Each light chain comprises a light chain variable region (abbreviated VL or VL) and a light chain constant region (CL or CL). The light chain constant region comprises one domain (CL1). The VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDRs), interspersed with regions that are more conserved, termed framework regions (FR). Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
As used herein, the term “antigen-binding fragment” of an antibody includes any naturally occurring, enzymatically obtainable, synthetic, or genetically engineered polypeptide or glycoprotein that specifically binds an antigen to form a complex. Antigen-binding fragments of an antibody may be derived, e.g., from full antibody molecules using any suitable standard techniques such as proteolytic digestion or recombinant genetic engineering techniques involving the manipulation and expression of DNA encoding antibody variable and optionally constant domains. Non-limiting examples of antigen-binding portions include: (i) Fab fragments; (ii) F(ab′)2 fragments; (iii) Fd fragments; (iv) Fv fragments; (v) single-chain Fv (scFv) molecules; (vi) dAb fragments; and (vii) minimal recognition units consisting of the amino acid residues that mimic the hypervariable region of an antibody (e.g., an isolated complementarily determining region (CDR)). Other engineered molecules, such as diabodies, triabodies, tetrabodies and minibodies, are also encompassed within the expression “antigen-binding fragment.”
As used herein, the term “CDR” or “complementarity determining region” means the noncontiguous antigen combining sites found within the variable region of both heavy and light chain polypeptides. These particular regions have been described by Kabat et al., J. Biol. Chem. 252, 6609-6616 (1977) and Kabat et al., Sequences of protein of immunological interest. (1991), and by Chothia et al., J. Mol. Biol. 196:901-917 (1987) and by MacCallum et al., J. Mol. Biol. 262:732-745 (1996) where the definitions include overlapping or subsets of amino acid residues when compared against each other. The Kabat definition is based on sequence variability. The IMGT unique numbering for all IG and TR V-regions of all species relies on the high conservation of the structure of the variable region (Lefranc, Mp et al., Dev comp. Immunol. 27:55-77, 2003), IMGT numbering, set up after aligning more than 5,000 sequences takes into account and combines the definition of the framework and CDRs. The Clothia definition is based on the location of the structural loop regions. The Contact definition (MacCallum et al.) is based on an analysis of the complex crystal structures and antibody-antigen interactions. The amino acid residues which encompass the CDRs as defined by each of the above cited references are set forth for comparison. In one embodiment disclosed herein, the term “CDR” is a CDR as defined by the Kabat definition. In another embodiment disclosed herein, the CDR is a CDR as defined by IMGT.
As used herein the term “framework (FR) amino acid residues” refers to those amino acids in the framework region of an Ig chain. The term “framework region” or “FR region” as used herein, includes the amino acid residues that are part of the variable region, but are not part of the CDRs (e.g., using the Contact definition of CDRs). Therefore, a variable region framework is between about 100-120 amino acids in length but includes only those amino acids outside of the CDRs.
The present invention also encompasses “conservative amino acid substitutions” in the CDR amino acid sequences of the antibodies disclosed herein, i.e., amino acid sequence modifications which do not abrogate the binding of the antibody to the antigen, i.e., PAI-1. A conservative substitution is a substitution of a native amino acid residue with a nonnative residue such that there is little or no effect on the polarity or charge of the amino acid residue at that position. For example, a conservative substitution results from the replacement of a non-polar residue in a polypeptide with any other non-polar residue. Furthermore, any native residue in the polypeptide may also be substituted with alanine, as has been previously described for “alanine scanning mutagenesis” (Cunningham et al., Science 244:1081-85 (1989)). Conservative amino acid substitutions include the substitution of an amino acid in one class by an amino acid of the same class, where a class is defined by common physicochemical amino acid side chain properties and high substitution frequencies in homologous proteins found in nature, as determined, for example, by a standard Dayhoff frequency exchange matrix or BLOSUM matrix. Six general classes of amino acid side chains have been categorized and include: Class I (Cys); Class II (Ser, Thr, Pro, Ala, Gly); Class III (Asn, Asp, Gln, Glu); Class IV (His, Arg, Lys); Class V (Ile, Leu, Val, Met); and Class VI (Phe, Tyr, Trp). For example, substitution of an Asp for another class III residue such as Asn, Gln, or Glu, is a conservative substitution. Thus, a predicted nonessential amino acid residue in a PAI-1 antibody is replaced with another amino acid residue from the same class. Methods of identifying amino acid conservative substitutions which do not eliminate antigen binding are well-known in the art (see, e.g., Brummell et al., Biochem. 32:1180, 1993; Kobayashi et al. Protein Eng. 12:879, 1999; and Burks et al. Proc. Natl. Acad. Sci. USA 94:412, 1997). General rules for conservative amino acid substitutions are set forth in Table 1 below.







TABLE 1







Conservative Amino Acid Substitutions









Original
Exemplary
Select


Residues
Substitutions
Substitutions





Ala
Val, Leu, Ile
Val


Arg
Lys, Gln, Asn
Lys


Asn
Gln, His, Lys, Arg
Gln


Asp
Glu
Glu


Cys
Ser
Ser


Gln
Asn
Asn


Glu
Asp
Asp


Gly
Pro, Ala
Ala


His
Asn, Gln, Lys, Arg
Arg


Ile
Leu, Val, Met, Ala,
Leu



Phe, Norleucine



Leu
Norleucine, Ile,
Ile



Val, Met, Ala, Phe



Lys
Arg, Gln, Asn
Arg


Met
Leu, Phe, Ile
Leu


Phe
Leu, Val, Ile, Ala,
Leu



Tyr



Pro
Ala
Ala


Ser
Thr
Thr


Thr
Ser
Ser


Trp
Tyr, Phe
Tyr


Tyr
Trp, Phe, Thr, Ser
Phe


Val
Ile, Met, Leu, Phe, 
Leu



Ala, Norleucine









Conservative amino acid substitutions also encompass non-naturally occurring amino acid residues that are typically incorporated by chemical peptide synthesis rather than by synthesis in biological systems. These include peptidomimetics, and other reversed or inverted forms of amino acid moieties.
Conservative modifications to the amino acid sequence (and the corresponding modifications to the encoding nucleotides) are expected to produce PAI-1 antibodies having functional and chemical characteristics similar to those of naturally occurring PAI-1 antibodies. In contrast, substantial modifications in the functional or chemical characteristics of PAI-1 antibodies may be accomplished by selecting substitutions that differ significantly in their effect on maintaining (a) the structure of the molecular backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain. Naturally occurring residues may be divided into groups based on common side chain properties:
1) hydrophobic: norleucine, Met, Ala, Val, Leu, Ile;
2) neutral hydrophilic: Cys, Ser, Thr;
3) acidic: Asp, Glu;
4) basic: Asn, Gln, His, Lys, Arg;
5) residues that influence chain orientation: Gly, Pro; and
6) aromatic: Trp, Tyr, Phe.
Non-conservative substitutions may involve the exchange of a member of one of these classes for a member from another class. Such substituted residues may be introduced into regions of the human PAI-1 antibody that are homologous with non-human PAI-1 antibody, or into the non-homologous regions of the molecule.
In certain aspects, the heavy or light chain variable regions may be 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% identical to any of the variable region sequences disclosed herein.
As used herein, the term “specifically binds to” refers to the ability of an antibody or an antigen-binding fragment thereof to bind to an antigen with an Kd that is lower than 1×10−6 M, 1×10−7 M, 1×10−8M, 1×10−9 M, 1×10−10 M, 1×10−11M, 1×10−12 M, or less. The term also encompasses refers to the ability of an antibody or an antigen-binding fragment thereof to bind to an antigen with an affinity that is at least two-fold greater than its affinity for a nonspecific antigen.
The disclosure also provides antibodies that competitively inhibit binding of an antibody to an epitope disclosed herein as determined by any method known in the art for determining competitive binding, for example, the immunoassays described herein. In certain embodiments, the antibody competitively inhibits binding to the epitope by at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 60%, or at least 50%.
As used herein, the term “antigen” refers to the binding site or epitope recognized by an antibody or antigen binding fragment thereof.
As used herein, the term “vector” is intended to refer to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a “plasmid,” which refers to a circular double stranded DNA loop into which additional DNA segments may be ligated. Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) can be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as “recombinant expression vectors” (or simply, “expression vectors”). In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. The terms, “plasmid” and “vector” may be used interchangeably. However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.
Numerous expression vector systems may be employed for the purposes of this invention. For example, one class of vector utilizes DNA elements which are derived from animal viruses such as bovine papilloma virus, polyoma virus, adenovirus, vaccinia virus, baculovirus, retroviruses (RSV, MMTV or MOMLV) or SV40 virus. Others involve the use of polycistronic systems with internal ribosome binding sites. Additionally, cells which have integrated the DNA into their chromosomes may be selected by introducing one or more markers which allow selection of transfected host cells. The marker may provide for prototrophy to an auxotrophic host, biocide resistance (e.g., antibiotics) or resistance to heavy metals such as copper. The selectable marker gene can either be directly linked to the DNA sequences to be expressed, or introduced into the same cell by cotransformation. Additional elements may also be needed for optimal synthesis of mRNA. These elements may include signal sequences, splice signals, as well as transcriptional promoters, enhancers, and termination signals. In particular embodiments the cloned variable region genes are inserted into an expression vector along with the heavy and light chain constant region genes (e.g. human) synthetic as discussed above.
More generally, once a vector or DNA sequence encoding an antibody, or fragment thereof, has been prepared, the expression vector may be introduced into an appropriate host cell. That is, the host cells may be transformed. Introduction of the plasmid into the host cell can be accomplished by various techniques well known to those of skill in the art. These include, but are not limited to, transfection (including electrophoresis and electroporation), protoplast fusion, calcium phosphate precipitation, cell fusion with enveloped DNA, microinjection, and infection with intact virus. See, Ridgway, A. A. G. “Mammalian Expression Vectors” Chapter 24.2, pp. 470-472 Vectors, Rodriguez and Denhardt, Eds. (Butterworths, Boston, Mass. 1988). An embodiment disclosed herein is plasmid introduction into the host via electroporation. The transformed cells are grown under conditions appropriate to the production of the light chains and heavy chains, and assayed for heavy or light chain protein synthesis. Exemplary assay techniques include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), or fluorescence-activated cell sorter analysis (FACS), immunohistochemistry and the like.
As used herein, the term “transformation” shall be used in a broad sense to refer to the introduction of DNA into a recipient host cell that changes the genotype and consequently results in a change in the recipient cell.
“Host cells” refers to cells that have been transformed with vectors constructed using recombinant DNA techniques and encoding at least one heterologous gene. In descriptions of processes for isolation of polypeptides from recombinant hosts, the terms “cell” and “cell culture” are used interchangeably to denote the source of antibody unless it is clearly specified otherwise. In other words, recovery of polypeptide from the “cells” may mean either from spun down whole cells, or from the cell culture containing both the medium and the suspended cells.
It should be understood that this term is intended to refer not only to the particular subject cell but to the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein.
As used herein, the term “treat,” “treating,” and “treatment” refer to therapeutic or preventative measures described herein. The methods of “treatment” employ administration to a subject, an antibody or antigen binding fragment disclosed herein, for example, a subject having a PAI-1-associated disease or disorder (e.g., a fibrotic disease) or predisposed to having such a disease or disorder, in order to prevent, cure, delay, reduce the severity of, or ameliorate one or more symptoms of the disease or disorder or recurring disease or disorder, or in order to prolong the survival of a subject beyond that expected in the absence of such treatment.
As used herein, the term “PAI-1-associated disease or disorder” includes disease states with or without symptoms associated with a disease state, where altered levels or activity of PAI-1 are found. Exemplary PAI-1-associated diseases or disorders include various types of fibrosis.
As used herein, the term “effective amount” refers to that amount of an antibody or an antigen binding fragment thereof that binds PAI-1, which is sufficient to effect treatment, prognosis or diagnosis of a PAI-1-associated disease or disorder, as described herein, when administered to a subject. A therapeutically effective amount will vary depending upon the subject and disease condition being treated, the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art. The dosages for administration can range from, for example, about 1 ng to about 10,000 mg, about 1 ug to about 5,000 mg, about 1 mg to about 1,000 mg, about 10 mg to about 100 mg, of an antibody or antigen binding fragment thereof, disclosed herein. Dosage regiments may be adjusted to provide the optimum therapeutic response. An effective amount is also one in which any toxic or detrimental effects (i.e., side effects) of an antibody or antigen binding fragment thereof are minimized or outweighed by the beneficial effects.
As used herein, the term “subject” or “mammal” includes any human or non-human animal.
As used herein, the term “epitope” refers to an antigenic determinant that interacts with a specific antigen binding site in the variable region of an antibody molecule known as a paratope. A single antigen may have more than one epitope. Thus, different antibodies may bind to different areas on an antigen and may have different biological effects. Epitopes may be either conformational or linear. A conformational epitope is produced by spatially juxtaposed amino acids from different segments of the linear polypeptide chain. A linear epitope is one produced by adjacent amino acid residues in a polypeptide chain.
It is noted here that, as used in this specification and the appended claims, the singular forms “a” “an” and “the” include plural reference unless the context clearly dictates otherwise.
II. Anti-PAI-1 Antibodies
In one aspect the invention provides antibodies, or antigen binding fragments thereof, that specifically bind to human PAI-1. Exemplary VH, VL and CDR amino acid sequences and nucleotide sequences of the antibodies disclosed herein are set forth in Table 2. CDR regions shown in Table 2 are defined by IMGT.







TABLE 2 







VH, VL and CDR amino acid sequences of exemplary anti-PAI-1 


antibodies or fragments thereof









ANTIBODY
SEQUENCE
SEQ ID NO












mA105 VH
QVQLQQSGAELMKPGASVKISCKATGFTSIYWIEWVKQRPG
2



LGLEWIGEILPGSGSTNYNEKFKGKATFTADTSSNTAFMQLSS




LTSEDSAVYYCARGGLYYDLDYWGQGTILTVSSAKTTPP



 


mA105 VL
DVVMTQTPLTLSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQ
3



RPGQSPQRLISLVSKLDSGVPDRFTGSGSGTDFTLKLSRVEGA




DLGVYYCWQDRHFPRTFGGGTKLEIKRAD



 


mA39 VH
QVQLQQSGAELMKPGASVKISCKATGYTFNIYWIQWVKQRP
4



GHGLEWIGEILPGSNTNYNEKFKDKATFTADSSSNTAYMQLSS




LTSEDSAVYYCARLGIGLRGALDYWGQGTSVTVSSAKTTPP



 


mA39 VL
DIQMTHSPASLSASVGETVTITCRASENIYSYLAWYHQKQGKS
5



PQLLVYNAKTLAEGVPSRFSGSGSGTQFSLNIKSLQPEDFGTFY




CQHRYGSPWTFGGGTKLEIKRAD



 


mA44 VH
EMQLQESGPSLVKPSQTLSLTCSVTGDSMTNGYWNWIRKFPG
6



NKLEYMGYITYSGSTYYNPSLKGRISITRNTSKNQYYLQLSSV




TTEDTATYYCARWHYGSPYYFDYWGQGTTLTVSSAKTTPP



 


mA44 VL
DIKMTQSPSSMYASLGERVTITCKASQDINSYLSWLQQKPGKS
7



PKTLIYRANRSVDGVPSRFSGSGSGQDYSLTISSLEYEDMGIYY




CLQYDEFPPTFGGGTKLEIKRAD



 


mA71 VH
QVQLQQSGAELMKPGASVKISCKATGFTFSTYWIEWIKQRPG
8



HGLDWIGEILPGSGNTNYNEKFKGKATFTADTSSNTVYMQLS




SLTSEDSAVYYCARGGLYYNLDSWGQGTTLTVSSAKTTPP



 


mA71 VL
DVVMTQTPLTLSVTIGQPASISCKSSQSLLDSDGKTYLYWLLQ
9



RPGQSPKRLIYLVSKLDSGVPDRFTGSGSGTDFTLKISRVEAED




LGVYYCWQDTHFPRTFGGGTKLEIKRAD



 


mA75 VH
QGQLQQSGAELMKPGASVKISCKASGFTFSTYWIAWLKQRPG
80



HGLEWIAEILPGSGLTNYNEIFRGKATFTADTSSNTAYMQLSS




LTSEDSAVYYCARGGLYYAMDYWGQGTSVTVSSAKTTAP



 


mA75 VL
DVVMTQTPLTLSVTIGQPASICKSSQSLLDSEGKTYLNWLFQR
81



PGQSPKRLIYLVCKLDCGVPDRFTGSGSGTDFTLKISRVEGED




LGVYYCWQGSHFPQTFGGGTKLEIKRAD



 


mB109 VH
EVQLQQSGSVLARPGTSVKMSCKASGYSFTSYWMHWVKQRP
10



GQGLEWMGAIYPGNSGQGLDWIGAIYPGNSDTTYNQKFEDK




AKLTAVASASTAYMEVSSLTNEDSAVYYCTRGLRRWGAMD




YWGQGTSVTVSSAKTTPP



 


mB109 VL
DIVMTQSHKFMSTSAGDRVSIPCKASQDVSSAVAWYQQKLG
11



QSPKLLIYSASFRYTGVPDRFTGSGSGTDFTFTISSVQAEDLAV




YYCQQHYSSPYTFGGGTNLEIKRAD



 


mB28 VH
QVQLQQSGAELMKPGASVKISCKATGYTFSISWIEWIKQRPGG
12



LEWIGKILPGSGGANYNEKFKGKATVTADTSSNTVYMQLSSL




TSEDSAVYYCARLSTGTRGAFDYWGQGTTLTVSSAKTTPP



 


mB28 VL
DIQLTQSPASLSASVGATVTITCRASENVYSYLAWYQQKQGK
13



SPQLLVYNAKTLAEGVPSRFSGSGSGTQFSLKINYLQPEDFGS




YYCQHHYGTPPTFGGGTKVEIKRAD



 


mC45 VH
QVQLQQSGVELVRPGTSVKVSCKASGYAFTNYLIEWIKQRPG
14



QGLEWIGVIHPGSGVTNYNEKFKGKAILTADKSSSTAYMQLSS




LTSDDSAVYFCARDYYGSSHGLMDYWGQGTSVTVSS



 


mC45 VL
DIKMTQSPSSMYASLGERVTITCKASQDINSYLSWFQQKPGKS
15



PKTLIYRANRLVDGVPSRFSGSGSGQDYSLTISSLEYEDMGIYY




CLQYDEFPRTFGGGTKLEIK



 


mE16 VH
EVKLVESGGGLVKPGGSLKLSCAASGFTFSNYGMSWVRQTPE
16



KGLGWVASLRTGGNTYYSDSVKGRFTISRDNDRNILYLQMSS




LTSEDTAVYYCARGLRHWGYFDVWGAGTTVTVSS



 


mE16 VL
DIVMTQSHKFMSTSVGDRVNITCKASQDVSTAVGWYQQEPG
17



QSPKLLIYSASNRHTGVPDRFTGSGSGTDFTFTISSVQAEDLAV




YYCQQHYSSPWTFGGGTKLEIK



 


mE21 VH
EVQLQQSGAELVRSGASVKLSCTASGFNIKDYYMHWVKQRP
18



EQGLEWIGWIDPENGDTEYDPKFQAKATMTADTSSNTAYLQL




SSLTSEDTAVYYCMYGNYPYYFDYWGQGTTLTVSS



 


mE21 VL
DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGT
19



VKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYF




CQQGNTLPWTFGGGTKLEIK



 


mA105 
ARGGLYYDLDY
20


HCDR3




 


mA105
ILPGSGST
21


HCDR2




 


mA105
GFTFSIYW
22


HCDR1




 


mA105
WQDRHFPRT
23


LCD3 




 


mA105
LVS
24


mA71




LCDR2




 


mA105
QSLLDSDGKTY
25


mA71




LCDR1




 


mA39
ARLGIGLRGALDY
26


HCDR3




 


mA39
ILPGSNT
27


HCDR2




 


mA39
GYTFNIYW
28


HCDR1




 


mA39 LCDR3
QHRYGSPWT
29


 


mA39 LCDR2
NAK
30


 


mA39 LCDR1 
ENIYSY
31


 


mA44
ARWHYGSPYYFDY
32


HCDR3




 


mA44
ITYSGST
33


HCDR2




 


mA44
GDSMTNGY
34


HCDR1




 


mA44
LQYDEFPPT
35


LCDR3




 


mA44
RAN
36


LCDR2




 


mA44
QDINSY
37


LCDR1




 


mA71
ARGGLYYNLDS
38


HCDR3




 


mA71
ILPGSGNT
39


HCDR2




 


mA71
GFTFSTYW
40


HCDR1




 


mA71 LCDR3
WQDTHFPRT
41


 


mA71 LCDR2
LVS
42


 


mA71 LCDR1
QSLLDSDGKTY
43


 


mA75
ARGGLYYAMDY
44


HCDR3




 


mA75
ILPGSGLT
45


HCDR2




 


mA75
GFTFSTYW
46


HCDR1




 


mA75
WQGSHFPQT
47


LCDR3




 


mA75
LVC
48


LCDR2




 


mA75
QSLLDSEGKTY
49


LCDR1




 


mB109
TRGLRRWGAMDY
50


HCDR3




 


mB109 
ILPGSGLT
51


HCDR2




 


mB109
GFTFSTYW
52


HCDR1




 


mB109
QQHYSSPYT
53


LCDR3




 


mB109
SAS
54


LCDR2




 


mB109
QDVSSA
55


LCDR1




 


mB28
ARLSTGTRGAFDY
56


HCDR3




 


mB28
ILPGSGGA
57


HCDR2




 


mB28
GYTESISW
58


HCDR1




 


mB28 LCDR3
QHHYGTPPT
59


 


mB28 LCDR2
NAK
60


 


mB28 LCDR1
ENVYSY
61


 


mC45
ARDYYGSSHGLMDY
62


HCDR3




 


mC45
IHPGSGVT
63


HCDR2




 


mC45
GYAFTNYL
64


HCDR1




 


mC45
LQYDEFPRT
65


LCDR3




 


mC45
RAN
66


LCDR2




 


mC45
QDINSY
67


LCDR1




 


mE16
ARGLRHWGYFDV
68


HCDR3




 


mE16
LRTGGNT
69


HCDR2




 


mE16
GFTFSNYG
70


HCDR1




 


mE16 
QQHYSSPWT
71


LCDR3




 


mE16
SAS
72


LCDR2




 


mE16
QDISNY
73


LCDR1




 


mE21
MYGNYPYYFDY
74


HCDR3




 


mE21
IDPENGDT
75


HCDR2




 


mE21
GFNIKDYY
76


HCDR1




 


mE21
QQGNTLPWT
77


LCDR3




 


mE21
YTS
78


LCDR2




 


mE21
QDISNY
79


LCDR1





m = murine;


VH = variable heavy chain;


VL = variable light chain;






In another embodiment, the present invention provides anti-PAI-1 antibodies that bind to the same epitope or competitively inhibit an antibody, or antigen binding fragment thereof comprising the VH and VL region amino acid sequences set forth in SEQ ID NO: 6 and 7 respectively. Such antibodies can be identified using routine competition binding assays including, for example, surface plasmon resonance (SPR)-based competition assays.
III. Modified Anti-PAI-1 Antibodies
In certain embodiments, anti-PAI-1 antibodies disclosed herein may comprise one or more modifications. Modified forms of anti-PAI-1 antibodies disclosed herein can be made using any techniques known in the art.
i) Reducing Immunogenicity
In certain embodiments, anti-PAI-1 antibodies, or antigen binding fragments thereof, disclosed herein are modified to reduce their immunogenicity using art-recognized techniques. For example, antibodies, or fragments thereof, can be chimerized, humanized, or deimmunized.
In one embodiment, an antibody, or antigen binding fragments thereof, disclosed herein may be chimeric. A chimeric antibody is an antibody in which different portions of the antibody are derived from different animal species, such as antibodies having a variable region derived from a murine monoclonal antibody and a human immunoglobulin constant region. Methods for producing chimeric antibodies, or fragments thereof, are known in the art. See e.g., Morrison, Science 229:1202, 1985; Oi et al., BioTechniques 4:214, 1986; Gillies et al., J. Immunol. Methods 125:191, 1989; U.S. Pat. Nos. 5,807,715; 4,816,567; and 4,816,397, which are incorporated herein by reference in their entireties. Techniques developed for the production of “chimeric antibodies” (Morrison et al., Proc. Natl. Acad. Sci. 81:851, 1984; Neuberger et al., Nature 312:604, 1984; Takeda et al., Nature 314:452, 1985) may be employed for the synthesis of said molecules. For example, a genetic sequence encoding a binding specificity of a mouse anti-PAI-1 antibody molecule may be fused together with a sequence from a human antibody molecule of appropriate biological activity. As used herein, a chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a marine monoclonal antibody and a human immunoglobulin constant region, e.g., humanized antibodies.
In another embodiment, an antibody, or antigen binding fragment thereof, as disclosed herein is humanized. Humanized antibodies have a binding specificity comprising one or more complementarity determining regions (CDRs) from a non-human antibody and framework regions from a human antibody molecule. Often, framework residues in the human framework regions will be substituted with the corresponding residue from the CDR donor antibody to alter, or improve, antigen binding. These framework substitutions are identified by methods well known in the art, e.g., by modeling of the interactions of the CDR and framework residues to identify framework residues important for antigen binding and sequence comparison to identify unusual framework residues at particular positions. See e.g. Queen et al., U.S. Pat. No. 5,585,089; Riechmann et al., Nature 332:323, 1988, which are incorporated herein by reference in their entireties. Antibodies can be humanized using a variety of techniques known in the art including, for example, CDR-grafting (EP 239,400; International Publication No. WO 91/09967; U.S. Pat. Nos. 5,225,539; 5,530,101; and 5,585,089), veneering or resurfacing (EP 592,106; EP 519,596; Padlan, Molecular Immunology 28:489, 1991; Studnicka et al., Protein Engineering 7:805, 1994; Roguska. et al., PNAS 91:969, 1994), and chain shuffling (U.S. Pat. No. 5,565,332).
In a particular embodiment, a humanization method is employed that is based on the impact of the molecular flexibility of the antibody during and at immune recognition (see International Publication No. WO2009/032661, which is incorporated herein by reference in its entirety). Protein flexibility is related to the molecular motion of the protein molecule. Protein flexibility is the ability of a whole protein, a part of a protein or a single amino acid residue to adopt an ensemble of conformations which differ significantly from each other. Information about protein flexibility can be obtained by performing protein X-ray crystallography experiments (see, for example, Kundu et al., Biophys. J. 83:723, 2002), nuclear magnetic resonance experiments (see, example, Freedberg et al., J. Am. Chem. Soc. 120:7916, 1998) or by running molecular dynamics (MD) simulations. An MD simulation of a protein is done on a computer and allows one to determine the motion of all protein atoms over a period of time by calculating the physical interactions of the atoms with each other. The output of a MD simulation is the trajectory of the studied protein over the period of time of the simulation. The trajectory is an ensemble of protein conformations, also called snapshots, which are periodically sampled over the period of the simulation, e.g. every 1 picosecond (ps). It is by analyzing the ensemble of snapshots that one can quantify the flexibility of the protein amino acid residues. Thus, a flexible residue is one which adopts an ensemble of different conformations in the context of the polypeptide within which that residue resides. MD methods are known in the art, see, e.g., Brooks et al. “Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics” (Wiley, New York, 1988). Several software enable MD simulations, such as Amber (see Case et al. Comp. Chem. 26:1668, 2005; Brooks et al. J. Comp. Chem. 4:187, 1983; and MacKerell et al. (1998) in “The Encyclopedia of Computational Chemistry” vol. 1:271-177, Schleyer et al., eds. Chichester: John Wiley & Sons) or impact (see Rizzo et al. J. Am. Chem. Soc.; 122:12898, 2000).
Most protein complexes share a relatively large and planar buried surface and it has been shown that flexibility of binding partners provides the origin for their plasticity, enabling them to conformationally adapt to each other (Sundberg and Mariuzza, Structure 8, R137-R142, 2000). As such, examples of “induced fit” have been shown to play a dominant role in protein-protein interfaces. In addition, there is a steadily increasing body of data showing that proteins actually bind ligands of diverse shapes, sizes and composition (Protein Science 11:184-187, 2002) and that the conformational diversity appears to be an essential component of the ability to recognize different partners (James et al., Science 299:1362, 2003). Flexible residues are involved in the binding of protein-protein partners (Grunberg et al., Structure 14, 683, 2006).
The flexible residues can adopt a variety of conformations that provide an ensemble of interaction areas that are likely to be recognized by memory B cells and to trigger an immunogenic response. Thus, an antibody can be humanized by modifying a number of residues from the framework so that the ensemble of conformations and of recognition areas displayed by the modified antibody resemble as much as possible those adopted by a human antibody. That can be achieved by modifying a limited number of residues by: (1) building a homology model of the parent mAb and running an MD simulation; (2) analyzing the flexible residues and identification of the most flexible residues of a non-human antibody molecule, as well as identifying residues or motifs likely to be a source of heterogeneity or of degradation reaction; (3) identifying a human antibody which displays the most similar ensemble of recognition areas as the parent antibody; (4) determining the flexible residues to be mutated, residues or motifs likely to be a source of heterogeneity and degradation are also mutated; and (5) checking for the presence of known T cell or B cell epitopes. The flexible residues can be found using an MD calculation as taught herein using an implicit solvent model, which accounts for the interaction of the water solvent with the protein atoms over the period of time of the simulation.
Once the set of flexible residues has been identified within the variable light and heavy chains, a set of human heavy and light chain variable region frameworks that closely resemble that of the antibody of interest is identified. That can be done, for example, using a BLAST search on the set of flexible residues against a database of antibody human germ line sequence. It can also be done by comparing the dynamics of the parent mAb with the dynamics of a library of germ line canonical structures. The CDR residues and neighboring residues are excluded from the search to ensure high affinity for the antigen is preserved. Flexible residues then are replaced.
When several human residues show similar homologies, the selection is driven also by the nature of the residues that are likely to affect the solution behavior of the humanized antibody. For instance, polar residues will often occur in exposed flexible loops over hydrophobic residues. Residues which are a potential source of instability and heterogeneity are also mutated even if there are found in the CDRs. That will include exposed methionines sulfoxide formation can result from oxygen radicals, proteolytic cleavage of acid labile bonds such as those of the Asp-Pro dipeptide (Drug Dev. Res. 61:137, 2004), deamidation sites found with an exposed asparagine residue followed by a small amino acid, such as Gly, Ser, Ala, His, Asn or Cys (J. Chromatog. 837:35, 2006) and N-glycosylation sites, such as the Asn-X-Ser/Thr site. Typically, exposed methionines will be substituted by a Leu, exposed asparagines will be replaced by a glutamine or by an aspartate, or the subsequent residue will be changed. For the glycosylation site (Asn-X-Ser/Thr), either the Asn or the Ser/Thr residue will be changed.
The resulting composite antibody sequence is checked for the presence of known B cell or linear T-cell epitopes. A search is performed, for example, with the publicly available Immune Epitope Data Base (IEDB) (PLOS Biol. (2005) 3(3)e91). If a known epitope is found within the composite sequence, another set of human sequences is retrieved and substituted. Thus, unlike the resurfacing method of U.S. Pat. No. 5,639,641, both B-cell-mediated and T-cell-mediated immunogenic responses are addressed by the method. The method also avoids the issue of loss of activity that is sometimes observed with CDR grafting (U.S. Pat. No. 5,530,101). In addition, stability and solubility issues also are considered in the engineering and selection process, resulting in an antibody that is optimized for low immunogenicity, high antigen affinity and improved biophysical properties.
In some embodiments, de-immunization can be used to decrease the immunogenicity of and antibody, or antigen binding fragment thereof. As used herein, the term “de-immunization” includes alteration of an antibody, or antigen binding fragment thereof, to modify T cell epitopes (see, e.g., International Publication Nos. WO9852976A1, WO0034317A2). For example, VH and VL sequences from the starting antibody may be analyzed and a human T cell epitope “map” may be generated from each V region showing the location of epitopes in relation to complementarily-determining regions (CDRs) and other key residues within the sequence. Individual T cell epitopes from the T cell epitope map are analyzed in order to identify alternative amino acid substitutions with a low risk of altering activity of the final antibody. A range of alternative VH and VL sequences are designed comprising combinations of amino acid substitutions and these sequences are subsequently incorporated into a range of PAI-1-specific antibodies or fragments thereof for use in the diagnostic and treatment methods disclosed herein, which are then tested for function. Typically, between 12 and 24 variant antibodies are generated and tested. Complete heavy and light chain genes comprising modified V and human C regions are then cloned into expression vectors and the subsequent plasmids introduced into cell lines for the production of whole antibody. The antibodies are then compared in appropriate biochemical and biological assays, and the optimal variant is identified.
ii) Effector Functions and Fc Modifications
Anti-PAI-1 antibodies disclosed herein may comprise an antibody constant region (e.g. an IgG constant region, a human IgG constant region, a human IgG1 or IgG4 constant region) which mediates one or more effector functions. For example, binding of the C1 component of complement to an antibody constant region may activate the complement system. Activation of complement is important in the opsonization and lysis of cell pathogens. The activation of complement also stimulates the inflammatory response and may also be involved in autoimmune hypersensitivity. Further, antibodies bind to receptors on various cells via the Fc region, with a Fc receptor binding site on the antibody Fc region binding to a Fc receptor (FcR) on a cell. There are a number of Fc receptors which are specific for different classes of antibody, including IgG (gamma receptors), IgE (epsilon receptors), IgA (alpha receptors) and IgM (mu receptors). Binding of antibody to Fc receptors on cell surfaces triggers a number of important and diverse biological responses including engulfment and destruction of antibody-coated particles, clearance of immune complexes, lysis of antibody-coated target cells by killer cells (called antibody-dependent cell-mediated cytotoxicity, or ADCC), release of inflammatory mediators, placental transfer and control of immunoglobulin production. In certain embodiments, the antibodies, or fragments thereof, disclosed herein bind to an Fc-gamma receptor. In alternative embodiments, anti-PAI-1 antibodies disclosed herein may comprise a constant region which is devoid of one or more effector functions (e.g., ADCC activity) or is unable to bind Fc receptor.
Certain embodiments disclosed herein include anti-PAI-1 antibodies in which at least one amino acid in one or more of the constant region domains has been deleted or otherwise altered so as to provide desired biochemical characteristics such as reduced or enhanced effector functions, the ability to non-covalently dimerize, increased ability to localize at a particular site in the body (e.g., the site of a tumor or to a particular organ), reduced serum half-life, or increased serum half-life when compared with a whole, unaltered antibody of approximately the same immunogenicity. For example, certain antibodies, or fragments thereof, for use in the diagnostic and treatment methods described herein are domain deleted antibodies which comprise a polypeptide chain similar to an immunoglobulin heavy chain, but which lack at least a portion of one or more heavy chain domains. For instance, in certain antibodies, one entire domain of the constant region of the modified antibody will be deleted, for example, all or part of the CH2 domain will be deleted.
In certain other embodiments, anti-PAI-1 antibodies comprise constant regions derived from different antibody isotypes (e.g., constant regions from two or more of a human IgG1, IgG2, IgG3, or IgG4). In other embodiments, anti-PAI-1 antibodies comprises a chimeric hinge (i.e., a hinge comprising hinge portions derived from hinge domains of different antibody isotypes, e.g., an upper hinge domain from an IgG4 molecule and an IgG1 middle hinge domain). In one embodiment, an anti-PAI-1 antibody comprises an Fc region or portion thereof from a human IgG4 molecule and a Ser228Pro mutation (Kabat numbering) in the core hinge region of the molecule.
In certain anti-PAI-1 antibodies, the Fc portion may be mutated to increase or decrease effector function using techniques known in the art. For example, the deletion or inactivation (through point mutations or other means) of a constant region domain may reduce Fc receptor binding of the circulating modified antibody thereby increasing tumor localization. In other cases it may be that constant region modifications consistent with the instant invention moderate complement binding and thus reduce the serum half-life and nonspecific association of a conjugated cytotoxin. Yet other modifications of the constant region may be used to modify disulfide linkages or oligosaccharide moieties that allow for enhanced localization due to increased antigen specificity or flexibility. The resulting physiological profile, bioavailability and other biochemical effects of the modifications, such as tumor localization, biodistribution and serum half-life, may easily be measured and quantified using well know immunological techniques without undue experimentation.
In certain embodiments, an Fc domain employed in an antibody disclosed herein is an Fc variant. As used herein, the term “Fc variant” refers to an Fc domain having at least one amino acid substitution relative to the wild-type Fc domain from which said Fc domain is derived. For example, wherein the Fc domain is derived from a human IgG1 antibody, the Fc variant of said human IgG1 Fc domain comprises at least one amino acid substitution relative to said Fc domain.
The amino acid substitution(s) of an Fc variant may be located at any position (i.e., any EU convention amino acid position) within the Fc domain. In one embodiment, the Fc variant comprises a substitution at an amino acid position located in a hinge domain or portion thereof. In another embodiment, the Fc variant comprises a substitution at an amino acid position located in a CH2 domain or portion thereof. In another embodiment, the Fc variant comprises a substitution at an amino acid position located in a CH3 domain or portion thereof. In another embodiment, the Fc variant comprises a substitution at an amino acid position located in a CH4 domain or portion thereof.
The antibodies disclosed herein may employ any art-recognized Fc variant which is known to impart an improvement (e.g., reduction or enhancement) in effector function or FcR binding. Said Fc variants may include, for example, any one of the amino acid substitutions disclosed in International PCT Publications WO88/07089A1, WO96/14339A1, WO98105787A1, WO98/23289A1, WO99/51642A1, WO99/58572A1, WO00/09560A2, WO00/32767A1, WO00/42072A2, WO02/44215A2, WO02/060919A2, WO03/074569A2, WO04/016750A2, WO04/029207A2, WO04/035752A2, WO04/063351A2, WO04/074455A2, WO04/099249A2, WO05/040217A2, WO05/070963A1, WO05/077981A2, WO05/092925A2, WO05/123780A2, WO06/019447A1, WO06/047350 A2, and WO06/085967A2 or U.S. Pat. Nos. 5,648,260; 5,739,277; 5,834,250; 5,869,046; 6,096,871; 6,121,022; 6,194,551; 6,242,195; 6,277,375; 6,528,624; 6,538,124; 6,737,056; 6,821,505; 6,998,253; and 7,083,784, each of which is incorporated by reference herein. In one exemplary embodiment, an antibody disclosed herein may comprise an Fc variant comprising an amino acid substitution at EU position 268 (e.g., H268D or H268E). In another exemplary embodiment, an antibody disclosed herein may comprise an amino acid substitution at EU position 239 (e.g., S239D or S239E) or EU position 332 (e.g., I332D or I332Q).
In certain embodiments, an antibody disclosed herein may comprise an Fc variant comprising an amino acid substitution which alters the antigen-independent effector functions of the antibody, in particular the circulating half-life of the antibody. Such antibodies exhibit either increased or decreased binding to FcRn when compared to antibodies lacking these substitutions, therefore, have an increased or decreased half-life in serum, respectively, Fc variants with improved affinity for FcRn are anticipated to have longer serum half-lives, and such molecules have useful applications in methods of treating mammals where long half-life of the administered antibody is desired, e.g., to treat a chronic disease or disorder. In contrast, Fc variants with decreased FcRn binding affinity are expected to have shorter half-lives, and such molecules are also useful, for example, for administration to a mammal where a shortened circulation time may be advantageous, e.g. for in vivo diagnostic imaging or in situations where the starting antibody has toxic side effects when present in the circulation for prolonged periods. Fc variants with decreased FcRn binding affinity are also less likely to cross the placenta and, thus, are also useful in the treatment of diseases or disorders in pregnant women. In addition, other applications in which reduced FcRn binding affinity may be desired include those applications in which localization the brain, kidney, or liver is desired. In one exemplary embodiment, the altered antibodies disclosed herein exhibit reduced transport across the epithelium of kidney glomeruli from the vasculature. In another embodiment, the altered antibodies disclosed herein exhibit reduced transport across the blood brain barrier (BBB) from the brain, into the vascular space. In one embodiment, an antibody with altered FcRn binding comprises an Fc domain having one or more amino acid substitutions within the “FcRn binding loop” of an Fc domain. The FcRn binding loop is comprised of amino acid residues 280-299 (according to Kabat numbering). Exemplary amino acid substitutions which altered FcRn binding activity are disclosed in International PCT Publication No. WO05/047327 which is incorporated by reference herein. In certain exemplary embodiments, the antibodies, or fragments thereof, disclosed herein comprise an Fc domain having one or more of the following substitutions: V284E, H285E, N286D, K290E and S304D (Kabat numbering).
In other embodiments, antibodies, for use in the diagnostic and treatment methods described herein have a constant region, e.g., an IgG1 or IgG4 heavy chain constant region, which is altered to reduce or eliminate glycosylation. For example, an antibody disclosed herein may also comprise an Fc variant comprising an amino acid substitution which alters the glycosylation of the antibody. For example, said Fc variant may have reduced glycosylation N- or O-linked glycosylation). In exemplary embodiments, the Fc variant comprises reduced glycosylation of the N-linked glycan normally found at amino acid position 297 (EU numbering). In another embodiment, the antibody has an amino acid substitution near or within a glycosylation motif, for example, an N-linked glycosylation motif that contains the amino acid sequence NXT or NXS. In a particular embodiment, the antibody comprises an Fc variant with an amino acid substitution at amino acid position 228 or 299 (EU numbering). In more particular embodiments, the antibody comprises an IgG1 or IgG4 constant region comprising an S228P and a T299A mutation (EU numbering).
Exemplary amino acid substitutions which confer reduce or altered glycosylation are disclosed in International PCT Publication No. WO05/018572, which is incorporated by reference herein. In certain embodiments, the antibodies, or fragments thereof, disclosed herein are modified to eliminate glycosylation. Such antibodies, or fragments thereof, may be referred to as “agly” antibodies, or fragments thereof, (e.g. “agly” antibodies). While not being bound by theory, it is believed that “agly” antibodies, or fragments thereof, may have an improved safety and stability profile in vivo. Exemplary agly antibodies, or fragments thereof, comprise an aglycosylated Fc region of an IgG4 antibody which is devoid of Fc-effector function thereby eliminating the potential for Fc mediated toxicity to the normal vital organs that express PAI-1. In yet other embodiments, antibodies, or fragments thereof, disclosed herein comprise an altered glycan. For example, the antibody may have a reduced number of fucose residues on an N-glycan at Asn297 of the Fc region, i.e., is afucosylated. In another embodiment, the antibody may have an altered number of sialic acid residues on the N-glycan at Asn297 of the Fc region.
iii) Covalent Attachment
Anti-PAI-1 antibodies disclosed herein may be modified, e.g., by the covalent attachment of a molecule to the antibody such that covalent attachment does not prevent the antibody from specifically binding to its cognate epitope. For example, but not by way of limitation, the antibodies, or fragments thereof, disclosed herein may be modified by glycosylation, acetylation, pegylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to a cellular ligand or other protein, etc. Any of numerous chemical modifications may be carried out by known techniques, including, but not limited to specific chemical cleavage, acetylation, formylation, etc. Additionally, the derivative may contain one or more non-classical amino acids.
Antibodies, or fragments thereof, disclosed herein may further be recombinantly fused to a heterologous polypeptide at the N- or C-terminus or chemically conjugated (including covalent and non-covalent conjugations) to polypeptides or other compositions. For example, anti-PAI-1 antibodies may be recombinantly fused or conjugated to molecules useful as labels in detection assays and effector molecules such as heterologous polypeptides, drugs, radionuclides, or toxins. See, e.g., International PCT publication Nos. WO 92/08495; WO 91/14438; WO 89/12624; U.S. Pat. No. 5,314,995; and EP 396,387.
Anti-PAI-1 antibodies may be fused to heterologous polypeptides to increase the in vivo half-life or for use in immunoassays using methods known in the art. For example, in one embodiment, PEG can be conjugated to the anti-PAI-1 antibodies disclosed herein to increase their half-life in vivo. (Leong, S. R., et al., Cytokine 16:106, 2001; Adv. in Drug Deliv. Rev. 54:531, 2002; or Weir et al., Biochem. Soc. Transactions 30:512, 2002).
Moreover, anti-PAI-1 antibodies disclosed herein can be fused to marker sequences, such as a peptide to facilitate their purification or detection. In certain embodiments, the marker amino acid sequence is a hexa-histidine peptide, such as the tag provided in a pQE vector (QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, Calif., 91311), among others, many of which are commercially available. As described in Gentz et al., Proc. Natl. Acad. Sci. USA 86:821-824, 1989, for instance, hexa-histidine provides for convenient purification of the fusion protein. Other peptide tags useful for purification include, but are not limited to, the “HA” tag, which corresponds to an epitope derived from the influenza hemagglutinin protein (Wilson et al., Cell 37:767, 1984) and the “flag” tag.
Anti-PAI-1 antibodies disclosed herein may be used in non-conjugated form or may be conjugated to at least one of a variety of molecules, e.g., to improve the therapeutic properties of the molecule, to facilitate target detection, or for imaging or therapy of the patient. Anti-PAI-1 antibodies disclosed herein can be labeled or conjugated either before or after purification, when purification is performed. In particular, anti-PAI-1 antibodies disclosed herein may be conjugated to therapeutic agents, prodrugs, peptides, proteins, enzymes, viruses, lipids, biological response modifiers, pharmaceutical agents, or PEG.
The present invention further encompasses anti-PAI-1 antibodies conjugated to a diagnostic or therapeutic agent. The anti-PAI-1 antibodies can be used diagnostically to, for example, monitor the development or progression of a immune cell disorder (e.g., CLL) as part of a clinical testing procedure to, e.g., determine the efficacy of a given treatment or prevention regimen. Detection can be facilitated by coupling the anti-PAI-1 antibodies to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, radioactive materials, positron emitting metals using various positron emission tomographies, and nonradioactive paramagnetic metal ions. See, for example, U.S. Pat. No. 4,741,900 for metal ions which can be conjugated to antibodies for use as diagnostics according to the present invention. Non-limiting examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase; non-limiting examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; non-limiting examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; a non-limiting example of a luminescent material includes luminol; non-limiting examples of bioluminescent materials include luciferase, luciferin, and aequorin; and non-limiting examples of suitable radioactive material include 125I, 131I, 111In or 99Tc.
Anti-PAI-1 antibodies for use in the diagnostic and treatment methods disclosed herein may be conjugated to cytotoxins (such as radioisotopes, cytotoxic drugs, or toxins) therapeutic agents, cytostatic agents, biological toxins, prodrugs, peptides, proteins, enzymes, viruses, lipids, biological response modifiers, pharmaceutical agents, immunologically active ligands (e.g., lymphokines or other antibodies wherein the resulting molecule binds to both the neoplastic cell and an effector cell such as a T cell), or PEG.
In another embodiment, an anti-PAI-1 antibody for use in the diagnostic and treatment methods disclosed herein can be conjugated to a molecule that decreases tumor cell growth. In other embodiments, the disclosed compositions may comprise antibodies, or fragments thereof, coupled to drugs or prodrugs. Still other embodiments disclosed herein comprise the use of antibodies, or fragments thereof, conjugated to specific biotoxins or their cytotoxic fragments such as ricin, gelonin, Pseudomonas exotoxin or diphtheria toxin. The selection of which conjugated or unconjugated antibody to use will depend on the type and stage of cancer, use of adjunct treatment (e.g., chemotherapy or external radiation) and patient condition. It will be appreciated that one skilled in the art could readily make such a selection in view of the teachings herein.
It will be appreciated that, in previous studies, anti-tumor antibodies labeled with isotopes have been used successfully to destroy tumor cells in animal models, and in some cases in humans. Exemplary radioisotopes include: 90Y, 125I, 131I, 123I, 111In, 105Rh, 153Sm, 67Cu, 67Ga, 166Ho, 177Lu, 186Re and 188Re. The radionuclides act by producing ionizing radiation which causes multiple strand breaks in nuclear DNA, leading to cell death. The isotopes used to produce therapeutic conjugates typically produce high energy alpha- or beta-particles which have a short path length. Such radionuclides kill cells to which they are in close proximity, for example neoplastic cells to which the conjugate has attached or has entered. They have little or no effect on non-localized cells. Radionuclides are essentially non-immunogenic.
IV. Expression of Anti-PAI-1 Antibodies, or Antigen Binding Fragments Thereof
Following manipulation of the isolated genetic material to provide anti-PAI-1 antibodies disclosed herein as set forth above, the genes are typically inserted in an expression vector for introduction into host cells that may be used to produce the desired quantity of the claimed antibodies, or fragments thereof.
In other embodiments the anti-PAI-1 antibodies, or fragments thereof, disclosed herein may be expressed using polycistronic constructs. In such expression systems, multiple gene products of interest such as heavy and light chains of antibodies may be produced from a single polycistronic construct. These systems advantageously use an internal ribosome entry site (IRES) to provide relatively high levels of polypeptides disclosed herein in eukaryotic host cells. Compatible IRES sequences are disclosed in U.S. Pat. No. 6,193,980, that is incorporated by reference herein. Those skilled in the art will appreciate that such expression systems may be used to effectively produce the full range of polypeptides disclosed in the instant application.
In one embodiment, the host cell line used for antibody expression is of mammalian origin; those skilled in the art can determine particular host cell lines which are best suited for the desired gene product to be expressed therein. Exemplary host cell lines include, but are not limited to, DG44 and DUXB11 (Chinese Hamster Ovary lines, DHFR minus), HELA (human cervical carcinoma), CVI (monkey kidney line), COS (a derivative of CVI with SV40 T antigen), R1610 (Chinese hamster fibroblast) BALBC/3T3 (mouse fibroblast), HAK (hamster kidney line), SP2/O (mouse myeloma), BFA-1c1BPT (bovine endothelial cells), RAJI (human lymphocyte), 293 (human kidney). In one embodiment, the cell line provides for altered glycosylation, e.g., afucosylation, of the antibodyexpressed therefrom (e.g., PER.C6® (Crucell) or FUT8-knock-out CHO cell lines (Potelligent® Cells) (Biowa, Princeton, N.J.)). In one embodiment NS0 cells may be used. CHO cells can be used in certain specific embodiments. Host cell lines are typically available from commercial services, the American Tissue Culture Collection or from published literature.
In vitro production allows scale-up to give large amounts of the desired polypeptides. Techniques for mammalian cell cultivation under tissue culture conditions are known in the art and include homogeneous suspension culture, e.g. in an airlift reactor or in a continuous stirrer reactor, or immobilized or entrapped cell culture, e.g. in hollow fibers, microcapsules, on agarose microbeads or ceramic cartridges. If necessary or desired, the solutions of polypeptides can be purified by the customary chromatography methods, for example gel filtration, ion-exchange chromatography, chromatography over DEAE-cellulose or (immuno-)affinity chromatography.
Genes encoding the anti-PAI-1 antibodies, or fragments thereof, disclosed herein can also be expressed non-mammalian cells such as bacteria or yeast or plant cells. In this regard it will be appreciated that various unicellular non-mammalian microorganisms such as bacteria can also be transformed; i.e. those capable of being grown in cultures or fermentation. Bacteria, which are susceptible to transformation, include members of the enterobacteriaceae, such as strains of Escherichia coli or Salmonella; Bacillaceae, such as Bacillus subtilis; Pneumococcus; Streptococcus, and Haemophilus influenzae. It will further be appreciated that, when expressed in bacteria, the polypeptides can become part of inclusion bodies. The polypeptides must be isolated, purified and then assembled into functional molecules.
In addition to prokaryotes, eukaryotic microbes may also be used. Saccharomyces cerevisiae, or common baker's yeast, is the most commonly used among eukaryotic microorganisms although a number of other strains are commonly available. For expression in Saccharomyces, the plasmid YRp7, for example, (Stinchcomb et al., Nature, 282:39 (1979); Kingsman et al., Gene, 7:141 (1979); Tschemper et al., Gene, 10:157 (1980)) is commonly used. This plasmid already contains the TRP1 gene which provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example ATCC No. 44076 or PEP4-1 (Jones, Genetics, 85:12 (1977)). The presence of the trp1 lesion as a characteristic of the yeast host cell genome then provides an effective environment for detecting transformation by growth in the absence of tryptophan.
V. Pharmaceutical Formulations and Methods of Administration of Anti-PAI-1 Antibodies.
In another aspect, the invention provides pharmaceutical compositions comprising an anti-PAI-1 antibody, or fragment thereof.
Methods of preparing and administering antibodies, or fragments thereof, disclosed herein to a subject are well known to or are readily determined by those skilled in the art. The route of administration of the antibodies, or fragments thereof, disclosed herein may be oral, parenteral, by inhalation or topical. The term parenteral as used herein includes intravenous, intraarterial, intraperitoneal, intramuscular, subcutaneous, rectal or vaginal administration. The intravenous, intraarterial, subcutaneous and intramuscular forms of parenteral administration can be used in certain embodiments. While all these forms of administration are clearly contemplated as being within the scope disclosed herein, a form for administration would be a solution for injection, in particular for intravenous or intraarterial injection or drip. Usually, a suitable pharmaceutical composition for injection may comprise a buffer (e.g. acetate, phosphate or citrate buffer), a surfactant (e.g. polysorbate), optionally a stabilizer agent (e.g. human albumin), etc. However, in other methods compatible with the teachings herein, the polypeptides can be delivered directly to the site of the adverse cellular population thereby increasing the exposure of the diseased tissue to the therapeutic agent.
Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. In the subject invention, pharmaceutically acceptable carriers include, but are not limited to, 0.01-0.1M (e.g. 0.05M) phosphate buffer or 0.8% saline. Other common parenteral vehicles include sodium phosphate solutions, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers, such as those based on Ringer's dextrose, and the like. Preservatives and other additives may also be present such as for example, antimicrobials, antioxidants, chelating agents, and inert gases and the like. More particularly, pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In such cases, the composition must be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and will in an embodiment be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal and the like. In certain embodiments, isotonic agents are included, for example, sugars, polyalcohols, such as mannitol, sorbitol, or sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
In any case, sterile injectable solutions can be prepared by incorporating an active compound (e.g., an antibody by itself or in combination with other active agents) in the required amount in an appropriate solvent with one or a combination of ingredients enumerated herein, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle, which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the methods of preparation can be vacuum drying and freeze-drying, which yields a powder of an active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. The preparations for injections are processed, filled into containers such as ampoules, bags, bottles, syringes or vials, and sealed under aseptic conditions according to methods known in the art. Further, the preparations may be packaged and sold in the form of a kit such as those described in co-pending U.S. Ser. No. 09/259,337 and U.S. Ser. No. 09/259,338 each of which is incorporated herein by reference. Such articles of manufacture will in an embodiment have labels or package inserts indicating that the associated compositions are useful for treating a subject suffering from, or predisposed to autoimmune or neoplastic disorders.
Effective doses of the stabilized antibodies, or fragments thereof, disclosed herein, for the treatment of the above described conditions vary depending upon many different factors, including means of administration, target site, physiological state of the patient, whether the patient is human or an animal, other medications administered, and whether treatment is prophylactic or therapeutic. Usually, the patient is a human, but non-human mammals including transgenic mammals can also be treated. Treatment dosages may be titrated using routine methods known to those of skill in the art to optimize safety and efficacy.
For passive immunization with an antibody disclosed herein, the dosage may range, e.g., from about 0.0001 to 100 mg/kg, and more usually 0.01 to 5 mg/kg (e.g., 0.02 mg/kg, 0.25 mg/kg, 0.5 mg/kg, 0.75 mg/kg, 1 mg/kg, 2 mg/kg, etc.), of the host body weight. For example dosages can be 1 mg/kg body weight or 10 mg/kg body weight or within the range of 1-10 mg/kg, or in particular embodiments at least 1 mg/kg. Doses intermediate in the above ranges are also intended to be within the scope disclosed herein.
Subjects can be administered such doses daily, on alternative days, weekly or according to any other schedule determined by empirical analysis. An exemplary treatment entails administration in multiple dosages over a prolonged period, for example, of at least six months. Additional exemplary treatment regimens entail administration once per every two weeks or once a month or once every 3 to 6 months. Exemplary dosage schedules include 1-10 mg/kg or 15 mg/kg on consecutive days, 30 mg/kg on alternate days or 60 mg/kg weekly. In some methods, two or more monoclonal antibodies with different binding specificities are administered simultaneously, in which case the dosage of each antibody administered may fall within the ranges indicated.
Antibodies or fragments thereof, disclosed herein can be administered on multiple occasions. Intervals between single dosages can be, e.g., daily, weekly, monthly or yearly. Intervals can also be irregular as indicated by measuring blood levels of polypeptide or target molecule in the patient. In some methods, dosage is adjusted to achieve a certain plasma antibody or toxin concentration, e.g., 1-1000 ug/ml or 25-300 ug/ml. Alternatively, antibodies, or fragments thereof, can be administered as a sustained release formulation, in which case less frequent administration is required. Dosage and frequency vary depending on the half-life of the antibody in the patient. In general, humanized antibodies show the longest half-life, followed by chimeric antibodies and nonhuman antibodies. In one embodiment, the antibodies, or fragments thereof, disclosed herein can be administered in unconjugated form. In another embodiment, the antibodies disclosed herein can be administered multiple times in conjugated form. In still another embodiment, the antibodies, or fragments thereof, disclosed herein can be administered in unconjugated form, then in conjugated form, or vice versa.
The dosage and frequency of administration can vary depending on whether the treatment is prophylactic or therapeutic. In prophylactic applications, compositions containing the present antibodies or a cocktail thereof are administered to a patient not already in the disease state to enhance the patient's resistance. Such an amount is defined to be a “prophylactic effective dose.” In this use, the precise amounts again depend upon the patient's state of health and general immunity, but generally range from 0.1 to 25 mg per dose, especially 0.5 to 2.5 mg per dose. A relatively low dosage is administered at relatively infrequent intervals over a long period of time. Some patients continue to receive treatment for the rest of their lives.
In therapeutic applications, a relatively high dosage (e.g., from about 1 to 400 mg/kg of antibody per dose, with dosages of from 5 to 25 mg being more commonly used for radioimmunoconjugates and higher doses for cytotoxin-drug conjugated molecules) at relatively short intervals is sometimes required until progression of the disease is reduced or terminated, and, in particular embodiments, until the patient shows partial or complete amelioration of symptoms of disease. Thereafter, the patient can be administered a prophylactic regime.
In one embodiment, a subject can be treated with a nucleic acid molecule encoding a polypeptide disclosed herein (e.g., in a vector). Doses for nucleic acids encoding polypeptides range from about 10 ng to 1 g, 100 ng to 100 mg, 1 ug to 10 mg, or 30-300 ug DNA per patient. Doses for infectious viral vectors vary from 10-100, or more, virions per dose.
Therapeutic agents can be administered by parenteral, topical, intravenous, oral, subcutaneous, intraarterial, intracranial, intraperitoneal, intranasal or intramuscular means for prophylactic or therapeutic treatment. Intramuscular injection or intravenous infusion can be used for administration of an antibody disclosed herein. In some methods, therapeutic antibodies, or fragments thereof, are injected directly into the cranium. In sonic methods, antibodies, or fragments thereof, are administered as a sustained release composition or device, such as a MedipadTM device.
Agents disclosed herein can optionally be administered in combination with other agents that are effective in treating the disorder or condition in need of treatment (e.g., prophylactic or therapeutic). Additional agents are those which are art recognized and are routinely administered for a particular disorder.
Effective single treatment dosages (i.e., therapeutically effective amounts) of 90Y-labeled antibodies disclosed herein range from between about 5 and about 75 mCi, and in an embodiment between about 10 and about 40 mCi. Effective single treatment non-marrow ablative dosages of 131I-labeled antibodies range from between about 5 and about 70 mCi, and in an embodiment between about 5 and about 40 mCi. Effective single treatment ablative dosages (i.e., may require autologous bone marrow transplantation) of 131I-labeled antibodies range from between about 30 and about 600 mCi, and in an embodiment between about 50 and less than about 500 mCi. In conjunction with a chimeric modified antibody, owing to the longer circulating half-life vis-a-vis murine antibodies, an effective single treatment non-marrow ablative dosages of iodine-131 labeled chimeric antibodies range from between about 5 and about 40 mCi, and in an embodiment, less than about 30 mCi. Imaging criteria for, e.g., the 111In label, are typically less than about 5 mCi.
While a great deal of clinical experience has been gained with 131I and 90Y, other radiolabels are known in the art and have been used for similar purposes. Still other radioisotopes are used for imaging. For example, additional radioisotopes which are compatible with the scope of the instant invention include, but are not limited to 123I, 125I, 32P, 57Co, 64Cu, 67Cu, 77Br, 81Rb, 81Kr, 87Sr, 113In, 127Cs, 129Cs, 132I, 197Hg, 203Pb, 206Bi, 177Lu, 186Re, 212Pb, 212Bi, 47Sc, 105Rh, 109Pd, 153Sm,188Re, 199Au, 225Ac, 211A 213Bi. In this respect alpha, gamma and beta emitters are all compatible with in the instant invention. Further, in view of the instant disclosure it is submitted that one skilled in the art could readily determine which radionuclides are compatible with a selected course of treatment without undue experimentation. To this end, additional radionuclides which have already been used in clinical diagnosis include 125I, 123I, 99Tc, 43K, 52Fe, 67Ga, 68Ga, as well as 111In. Antibodies have also been labeled with a variety of radionuclides for potential use in targeted immunotherapy (Peirersz et al., Immunol. Cell Biol. 65: 111, 1987). These radionuclides include 188Re and 186Re as well as 199Au and 67Cu to a lesser extent. U.S. Pat. No. 5,460,785 provides additional data regarding such radioisotopes and is incorporated herein by reference.
As previously discussed, the antibodies, or fragments thereof, disclosed herein, can be administered in a pharmaceutically effective amount for the in vivo treatment of mammalian disorders. In this regard, it will be appreciated that the disclosed antibodies, or fragments thereof, will be formulated so as to facilitate administration and promote stability of the active agent. and In certain embodiments, pharmaceutical compositions in accordance with the present invention comprise a pharmaceutically acceptable, non-toxic, sterile carrier such as physiological saline, non-toxic buffers, preservatives and the like. For the purposes of the instant application, a pharmaceutically effective amount of an antibody disclosed herein, conjugated or unconjugated to a therapeutic agent, shall be held to mean an amount sufficient to achieve effective binding to a target and to achieve a benefit, e.g., to ameliorate symptoms of a disease or disorder or to detect a substance or a cell. In the case of tumor cells, the polypeptide will in certain embodiments be capable of interacting with selected immunoreactive antigens on neoplastic or immunoreactive cells and provide for an increase in the death of those cells. Of course, the pharmaceutical compositions disclosed herein may be administered in single or multiple doses to provide for a pharmaceutically effective amount of the polypeptide.
In keeping with the scope of the present disclosure, the antibodies disclosed herein may be administered to a human or other animal in accordance with the aforementioned methods of treatment in an amount sufficient to produce a therapeutic or prophylactic effect. The polypeptides disclosed herein can be administered to such human or other animal in a conventional dosage form prepared by combining the antibody disclosed herein with a conventional pharmaceutically acceptable carrier or diluent according to known techniques. It will be recognized by one of skill in the art that the form and character of the pharmaceutically acceptable carrier or diluent is dictated by the amount of active ingredient with which it is to be combined, the route of administration and other well-known variables. Those skilled in the art will further appreciate that a cocktail comprising one or more species of polypeptides according to the present invention may prove to be particularly effective.
VI. Methods of Treating PAI-1-Associated Disease or Disorders
The anti-PAI-1 antibodies, or fragments thereof, disclosed herein are useful for antagonizing PAI-1 activity. Accordingly, in another aspect, the invention provides methods for treating PAI-1-associated diseases or disorders by administering to a subject in need of thereof a pharmaceutical composition comprising one or more anti-PAI-1 antibodies, or antigen binding fragments thereof disclosed herein.
PAI-1-associated diseases or disorders amenable to treatment include, without limitation, pathophysiologic conditions such as kidney, liver or lung fibrosis or prevention of abdominal adhesion formation.
The occurrence of intra-abdominal adhesions is a major cause of human illness. Complications of adhesions may be as serious as a life-threatening bowel obstruction, but chronic pelvic pain and infertility in women are also common sequelae to peritoneal adhesions. The majority of adhesions is induced by surgery but in some cases also has been shown to be caused by inflammation, endometriosis, chemical peritonitis, radiotherapy, foreign body reaction, and continuous ambulatory peritoneal dialysis. Peritoneal damage causes a local inflammatory response that leads to fibrin deposition. It is assumed that a posttraumatic insufficiency in peritoneal fibrinolytic activity, caused by a decrease in tissue plasminogen activator (tPA) and an increase in the plasminogen activator inhibitors PAI-1 and PAI-2, permits the deposited fibrin to become organized into permanent adhesions.
Currently available and effective treatment option like Seprafilm® has limitations for use only in the open access (laparotomy) and cannot be used in the laparoscopy. The search for potential treatment is ongoing.
In certain exemplary embodiments, antibodies disclosed herein may be issued to treat renal fibrosis and associated acute kidney injury as well as chronic kidney diseases which are the main causes of end-stage renal failure.
One skilled in the art would be able, by routine experimentation, to determine what an effective, non-toxic amount of antibody (or additional therapeutic agent) would be for the purpose of treating a PAI-1-associated disease or disorder. For example, a therapeutically active amount of a polypeptide may vary according to factors such as the disease stage (e.g., stage I versus stage IV), age, sex, medical complications (e.g., immunosuppressed conditions or diseases) and weight of the subject, and the ability of the antibody to elicit a desired response in the subject. The dosage regimen may be adjusted to provide the optimum therapeutic response. For example, several divided doses may be administered daily, or the dose may be proportionally reduced as indicated by the exigencies of the therapeutic situation. Generally, however, an effective dosage is expected to be in the range of about 0.05 to 100 milligrams per kilogram body weight per day and in an embodiment from about 0.5 to 10, milligrams per kilogram body weight per day.
The different aspects disclosed herein and their embodiments can be combined with each other. In addition, any of the aspects and their embodiments described above can be combined with any of the particular aspects and embodiments described herein below.
Some particular aspects and embodiments that further serve to illustrate the present invention are given in the following:
DESCRIPTION OF PARTICULAR ASPECTS AND EMBODIMENTS


    Embodiment I. An isolated monoclonal antibody that binds specifically to PAI-1, comprising:
    
        (a) a heavy chain framework region and a heavy chain variable region, the heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 34, a heavy chain CDR2 region comprising SEQ ID NO: 33, and a heavy chain CDR3 region comprising SEQ ID NO: 32; and
        (b) a light chain framework region and a light chain variable region, the light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 37, a light chain CDR2 region comprising SEQ ID NO: 145, and a light chain CDR3 region comprising SEQ ID NO: 35.
    
    
    Embodiment II. An isolated monoclonal antibody that binds specifically to PAI-1 comprising:
    
        (a) a heavy, chain framework region and a heavy chain variable region comprising SEQ ID NO: 86, and
        (b) a light chain framework region and a light chain variable region comprising SEQ ID NO: 93.
    
    
    Embodiment III. An isolated monoclonal antibody that binds specifically to PAI-1 comprising:
    
        (a) a heavy chain variable region that is at least 95% identical to the heavy chain variable region of the antibody of Embodiment II, and/or
        (b) a light chain variable region that is at least 95% identical to the light chain variable region of the antibody of Embodiment II.
    
    
    Embodiment IV. An isolated monoclonal antibody that binds to essentially the same epitope as the antibody of Embodiment I.
    Embodiment V. An isolated monoclonal antibody that binds specifically to PAI-1, comprising:
    
        (a) a heavy chain framework region and a heavy chain variable region, the heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 34, a heavy chain CDR2 region comprising SEQ ID NO: 33, and a heavy chain CDR3 region comprising SEQ ID NO: 32; and
        (b) a light chain framework region and a light chain variable region, the light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 37, a light chain CDR2 region comprising SEQ ID NO: 36, and a light chain CDR3 region comprising SEQ ID NO: 35.
    
    
    Embodiment VI. The antibody of Embodiment V, wherein the heavy chain variable region comprises SEQ ID NO: 6, and the light chain variable region comprises SEQ ID NO: 7.
    Embodiment VII. An isolated monoclonal antibody that binds to essentially the same epitope as the antibody of Embodiment V.
    Embodiment VIII. A humanized monoclonal antibody that binds specifically to human PAI-1 wherein the antibody comprises:
    
        (a) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 82, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 91, or an antigen-binding fragment thereof;
        (b) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 83, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 92, or an antigen-binding fragment thereof;
        (c) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 84, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 93, or an antigen-binding fragment thereof;
        (d) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 85, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 91, or an antigen-binding fragment thereof;
        (e) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 85, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 93, or an antigen-binding fragment thereof;
        (f) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 86, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 94, or an antigen-binding fragment thereof;
        (g) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 87, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 95, or an antigen-binding fragment thereof;
        (h) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 88, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 96, or an antigen-binding fragment thereof;
        (i) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 89, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 97, or an antigen-binding fragment thereof;
        (j) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 90, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 98, or an antigen-binding fragment thereof;
        (l) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 86, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 95, or an antigen-binding fragment thereof;
        (m) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 89, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 93, or an antigen-binding fragment thereof; or
        (n) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 89, or an antigen-binding fragment thereof, and a light chain having a light chain variable region comprising SEQ ID NO: 95, or an antigen-binding fragment thereof.
    
    
    Embodiment IX. An isolated monoclonal antibody that binds specifically to PAI-1, comprising
    
        (a) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 22, a heavy chain CDR2 region comprising SEQ ID NO: 21, and a heavy chain CDR3 region comprising SEQ ID NO: 20; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 25, a light chain CDR2 region comprising SEQ ID NO: 24, and a light chain CDR3 region comprising SEQ ID NO: 23,
        (b) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 28, a heavy chain CDR2 region comprising SEQ ID NO: 27, and a heavy chain CDR3 region comprising SEQ ID NO: 26; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 31, a light chain CDR2 region comprising SEQ ID NO: 30, and a light chain CDR3 region comprising SEQ ID NO: 29,
        (c) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 40, a heavy chain CDR2 region comprising SEQ ID NO: 39, and a heavy chain CDR3 region comprising SEQ ID NO: 38; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 43, a light chain CDR2 region comprising SEQ ID NO: 42, and a light chain CDR3 region comprising SEQ ID NO: 41,
        (d) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 46, a heavy chain CDR2 region comprising SEQ ID NO: 45, and a heavy chain CDR3 region comprising SEQ ID NO: 44; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 49, a light chain CDR2 region comprising SEQ ID NO: 48, and a light chain CDR3 region comprising SEQ ID NO: 47,
        (e) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 52, a heavy chain CDR2 region comprising SEQ ID NO: 51, and a heavy chain CDR3 region comprising SEQ ID NO: 50; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 55, a light chain CDR2 region comprising SEQ ID NO: 54, and a light chain CDR3 region comprising SEQ ID NO: 53,
        (f) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 58, a heavy chain CDR2 region comprising SEQ ID NO: 57, and heavy chain CDR3 region comprising SEQ ID NO: 56; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 61, a light chain CDR2 region comprising SEQ ID NO: 60, and a light chain CDR3 region comprising SEQ ID NO: 59,
        (g) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 64, a heavy chain CDR2 region comprising SEQ ID NO: 63, and a heavy chain CDR3 region comprising SEQ ID NO: 62; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 67, a light chain CDR2 region comprising SEQ ID NO: 66, and a light chain CDR3 region comprising SEQ ID NO: 65,
        (h) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 70, a heavy chain CDR2 region comprising SEQ ID NO: 69, and a heavy chain CDR3 region comprising SEQ ID NO: 68; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 73, a light chain CDR2 region comprising SEQ ID NO: 72, and a light chain CDR3 region comprising SEQ ID NO: 71; or
        (i) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 76, heavy chain CDR2 region comprising SEQ ID NO: 75, and a heavy chain CDR3 region comprising SEQ ID NO: 74; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 79, a light chain CDR2 region comprising SEQ ID NO: 78, and a light chain CDR3 region comprising SEQ ID NO: 77.
    
    
    Embodiment X. An isolated monoclonal antibody that binds specifically to PAI-1, that binds to essentially the same epitope PAI-1 as the humanized monoclonal antibody of Embodiment VIII or Embodiment IX.
    Embodiment XI. A method of restoring plasmin generation comprising administering to a subject in need thereof orally, parenterally by a solution for injection, by inhalation, or topically a pharmaceutically effective amount of a PAI-1 antibody.
    Embodiment XII. The method of Embodiment XI, wherein the method treats a condition comprising increased levels of fibrotic tissue.
    Embodiment XIII. The method of Embodiment XII, wherein the condition is fibrosis, skin fibrosis, systemic sclerosis, lung fibrosis, idiopathic pulmonary fibrosis, interstitial lung disease, chronic lung disease, liver fibrosis, kidney fibrosis, chronic kidney disease, thrombosis, venous and arterial thrombosis, deep vein thrombosis, peripheral limb ischemia, disseminated intravascular coagulation thrombosis, acute ischemic stroke with and without thrombolysis, or stent restenosis.
    Embodiment XIV. The method of Embodiment XI, XII, or XIII wherein the PAI-1 antibody comprises the antibody of any of the preceding Embodiments.
    Embodiment XV. Use of a pharmaceutically effective amount of a PAI-1 antibody for the manufacture of a medicament for treating a condition caused by increased levels of PAI-1 or increased sensitivity to PAI-1, comprising administering to a patient orally, parenterally by a solution for injection, by inhalation, or topically.


EXAMPLES
The present invention is further illustrated by the following examples which should not be construed as further limiting. The contents of Sequence Listing, Figures and all references, patents and published patent applications cited throughout this application are expressly incorporated herein by reference.
Furthermore, in accordance with the present invention there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook, Fritsch & Maniatis, Molecular Cloning: A Laboratory Manual, Second Edition (1989) Cold Spring. Harbor Laboratory Press, Cold Spring Harbor, N.Y. (herein “Sambrook et al., 1989”); DNA Cloning: A Practical Approach, Volumes I and II (D. N. Glover ed. 1985); Oligonucleotide Synthesis (M. J. Gait ed. 1984); Nucleic Acid Hybridization [B. D. Hames & S. J. Higgins eds. (1985)]; Transcription And Translation [B. D. Hames & S. J. Higgins, eds. (1984)]; Animal Cell Culture [R. I. Freshney, ed. (1986)]; Immobilized Cells And Enzymes [IRL Press, (1986)]; B. Perbal, A Practical Guide To Molecular Cloning (1984); F. M. Ausubel et al. (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, Inc. (1994).
Example 1
Hybridoma Generation: Immunization of Mice with PAI-1 Protein and Antibody Generation
Antibodies were developed that would be cross-reactive to human (h) and cynomolgus (cyno) monkey active PAI-1 (glycosylated or non-glycosylated form) and that would neutralize the inhibitory activity of PAI-1 and restore downstream production of plasmin thereby being an effective therapeutic for treatment of kidney, liver or lung fibrosis or prevention of abdominal adhesion formation and keloid scar formation. Neutralization of PAI-1 inhibitory function by monoclonal antibodies has been described to fall under three mechanisms: (1) blocking PAI-1 to tPA or uPA by steric hindrance, (2) converting PAI-1 into a latent conformation, or (3) converting PAI-1 into a substrate conformation.
a) Antigens
PAI-1 is secreted from the cells in an active conformation stabilized by its binding with subnanomolar affinity to vitronectin. PAI-1 undergoes spontaneous conformational change from active conformation into a latent conformation within minutes at 37° C. and within hours at room temperature. Once bound to vitronectin, PAI-1 becomes more resistant to the conformational change which prolongs the half-life of PAI-1 in active conformation from minutes to hours. To extend active conformation PAI-1 half-life in the immunized animals and to allow the mouse immune system to recognize the active PAI-1 conformation, a complex of vitronectin and PAI-1 was used for immunizations.
Human glycosylated PAI-1 produced in insect cells was purchased from Innovative Research (Cat #IGLYHPAI-A). Vitronectin (Cat #IHVN) and tPA (Cat #HTPA-TC) were also purchased from Innovative Research. To produce immunogens PAI-1 was incubated with vitronectin at a 1:1 molar ratio for 1 hour at room temperature, or with tPA at a 1:1 molar ratio for 15 minutes at 37° C. All immunogens were prepared using sterile saline as diluent.
b) Immunizations
Standard hybridoma production protocols known in the art were implemented to produce antibodies. Standard approaches previously described in the literature used PAI-1 only or PAI-1/tPA complex. The inventors instead generated antibodies against the active conformation of PAI-1. PAI-1/vitronectin complex was used as a novel approach to generating antibodies to PAI-1. A three-prong strategy, outlined below, was taken to generate antibodies:

    
    
        (1) Classical immunization of mice with PAI-1/vitronectin complex to obtain mouse splenocytes for fusion with mouse myeloma cell line as a fusion partner to produce hybridoma;
        (2) Classical immunization of mice with PAI-1/tPA complex to obtain mouse splenocytes for fusion with mouse myeloma cell line as a fusion partner to produce hybridoma; and
        (3) Classical immunization of mice with PAI-1 only to obtain mouse splenocytes for fusion with mouse myeloma cell line as a fusion partner to produce hybridoma.
    
    


Three mice per antigen (PAI-1 only, Vn/PAI-1 complex, tPA/PAI-1 complex) were used in the study. The mice were 9-20 week-old naïve female BALB/c Mice (Charles River, strain code 028). On day 0, nine mice were immunized intraperitoneally with PAI-1 alone, Vn/PAI-1 or tPA/PAI-1 complexes in phosphate-buffered saline (PBS). A total of 10 ug of antigen per mouse was mixed at 1:1 volume to volume ratio of Sigma Adjuvant System (Sigma cat #6322) in a total volume of 200 μl per mouse. On day 14, mice were boosted with the same amount of antigen and prepared the same way as on day 0. On day 21, blood samples were collected for PAI-1 specific antibody titer evaluation. Mice immunized with PAI-1/tPA complexes showed very low specific reactivity against PAI-1 and high anti-tPA titers and were not used for downstream fusions.
On day 51, the mouse with the highest anti-PAI-1 specific antibody titer and the lowest titer against the protein that PAI-1 was complexed to (i.e., either Vn or tPA) while those having the highest titer against mouse and rat PAI-1 orthologs were selected for fusion. The mice selected for fusion were boosted with PAI-1 only or PAI-1/Vn complex in PBS as an antigen total of 10 ug per mouse mixed at 1:1 ratio of Sigma Adjuvant System (Sigma cat #6322) in a total volume of 200 μl per mouse as described above. At day 55 mice were sacrificed by CO2 chamber, blood was collected through the cardiac puncture and spleen was harvested for hybridoma production. The other four mice underwent the same procedure at later times (2-4 months after the first mouse was used for fusion).
Serum titrations were performed on three mice for PAI-1 only and PAI-1/tPA and two mice for PAI-1/Vn using the ELISA protocol described in Example 2 (Binding ELISA).







TABLE 3







Serum Titers for Mouse immunized with PAI-1, PAI-1/Vn or PAI-1/tPA









Serum Titer Against PAI-1 (OD405)











Immunogen
Mouse #
OD 1:100
OD 1:1000
OD 1:10000














PAI-1
1
2.1
1.9
1


PAI-1
2
2.1
1.4
1


PAI-1
3
2.0
1.4
1


PAI-1/Vn
2
2.15
1.5
1


PAI-1/Vn
3
1.7
1.25
1


PAI-1/tPA
1
1.2
0.8
0.3


PAI-1/tPA
2
1.3
0.9
0.7


PAI-1/tPA
3
1.3
0.9
0.5


NMS
n/a
0.4
0.12
0.07





NMS = normal mouse serum;


n/a = not applicable


OD405 using BioTek Synergy HT instrument






The mice immunized with PAI-1/tPA complex did not reach high specific titer criteria and were not used for fusions (Table 3). Based on the serum titers presented in Table 3, a total of 5 mice with high specific titer against PAI-1 were selected for fusions.
b) Fusions
The five mice having the highest specific titer against PAI-1 were selected for fusions. On the day of the fusion, the mice were sacrificed in a CO2 chamber, blood was collected through cardiac puncture and the spleens removed and placed into a Petri dish containing 10 ml of serum free Hybridoma Fusion Medium (IMDM; Iscove's Modified Dulbecco's Medium 500 ml (HyClone SH30259.01). Splenocytes were squeezed out of the fibroelastic coat by forceps and washed twice in 10 ml of serum free IMDM (including initial spin).
Cells were counted in a Countess Automated Cell Counter. Fusion partner cells (myeloma: FO (ATCC ref CRL-1646)) and splenocytes were then combined in one 50 ml tube at ratio of 1:2 to 1:10 (by cell number) and spun down at 970 rpm for 10 min (slow spin) to form a loose pellet. Preheated (at 37° C.) 1 ml PEG (PEG 1500 in 75 mM Hepes 50% w/v, Roche cat #783641 (10783641001) was added drop by drop to the cell pellet over 1 minute period of time and cells were mixed after every drop of PEG was added. The pellet was incubated with PEG for another 1 minute followed by addition of 10 ml of serum-free IMDM medium over 1 minute, such that the first 1 ml out of 10 is added over 30 sec. Cells underwent slow spin at 970 rpm for 10 min to preserve viability. Fused cells were plated in 96-well plates at 200 ul in selection medium (200 ml Gibco Hybridoma (SFM #12045), 20 ml 10% HyClone SuperLow IgG Defined TBS (#S1130898.03), 2 ml penicillin/streptomycin, 4 ml (Hybridoma Fusion and Cloning Supplement (Roche Diagnostics 11 363 735 001 (50×)) and 4 ml of HAT (hypoxanthine-aminopterin-thymidine) (Sigma-Aldrich #HO262 (50×)). Fusions were ready for screening about 10 to 14 days later, or when medium in the wells turned yellow. Supernatants from the developed hybridomas were then tested by ELISA (Example 2) for the presence of antibodies binding to PAI-1 and PAI-1/Vn complexes.
Example 2
Binding ELISA for Hybridoma Supernatant Screening for Specificity to PAI-1-Vitronectin Complex
Each fusion from the spleens of the five mice selected resulted in about 5000 clones that needed to be screened for binding to PAI-1/Vn complex as a first-step primary screen. Primary screening of the hybridoma supernatants was performed in parallel using ELISA against either PAI-1 or PAI-1-Vitronectin complexes to select hybridomas binding specifically to PAI-1 complexed to Vitronectin. The materials used for the ELISA were the following: Immulon 4 HBX ELISA plates (Dynax cat #N054121.6); human monomeric Vitronectin at 5 ug/ml (Innovative Research cat #IHVN); glycosylated human PAI-1 (active form) (Molecular Innovations cat #GLYHPAI-A); non-glycosylated mouse PAi-1 in some fusions (Molecular Innovations cat #MPAI-A); a secondary antibody that was HRP-goat anti-mouse IgG (H+L) (Jackson ImmunoResearch Labs #115-035-166); and, ABTS substrate: Roche Diagnostics (#11 204 521 001).
Control antibodies used were:


    
    
        a) 33B8, a mouse monoclonal inhibitory antibody against PAI-1 (IgG1; Innovative Research cat #IMA-33B8);
        b) 33H1, a mouse monoclonal inhibitory antibody against PAI-1(IgG1; Innovative Research cat #IMA-33H1);
        c) 31C9, a mouse monoclonal non-inhibitory antibody against PAI-1 (IgG1; Innovative Research cat #IMA-31C9); and
        d) 1B7.11, a IgG1 isotype control antibody (anti-TNP mAb—produced in-house from hybridoma cell line purchased from ATCC (Cat #TIB-191)
    
    


The ELISA method was as follows: plates coated with 5 ug/ml Vn in PBS overnight at 4° C. at 50 ul/well; the next day plates were blocked 1 hour with 200 ul 1% bovine serum alburnin in PBS (BSA/PBS); plates were washed four times with 200 ul/well PBS; active PAI-1 at 2 ug/ml in 1% BSA/PBS was added to the plates at 50 ul/well and incubated 1 hour; plates were washed four times with 200 ul/well PBS; antibody dilutions in 1% BSA/PBS or hybridoma supernatants from the original 96-well plates were added to ELISA plates at 50 ul/well; plates were incubated 1 hour at room temperature (RT); plates were washed four times with 200 ul/well PBS; HRP-anti-mouse IgG 50 ul 1:2000 in 1% BSA/PBS was added and incubated 1 hour at room temperature; plates were washed four times with 200 ul/well PBS; ABTS substrate (one pill dissolved in 5 ml) at 50 ul/well was added to the plates) and then plates were read on BioTek Synergy HT instrument using OD405. A typical standard curve for antibody titration in the binding ELISA is shown in FIG. 2. The antibodies 31C9, 33B8 and 33H1 served as positive controls and IgG1 served as a negative control. Table 4 shows that of the about 5000 clones generated, 675 clones were positive for binding to both PAI-1 and PAI-1/Vn. These clones were then screened for PAI-1 affinity.







TABLE 4







Number of Clones Positive for Binding to Both PAI-1 and PAI-1/Vn













# of Clones Positive for Binding to


Fusion
Immunogen
Mouse #
Both PAI-1 and PAI-1/Vn





A
PAI-1/Vn
2
131


B
PAI-1
2
146


C
PAI-1/Vn
3
145


D
PAI-1
3
104


E
PAI-1
1
149









Example 3
Biacore Screening of Hybridoma Supernatants by Affinity Ranking
Further selection of a high affinity antibody with low off-rate was performed by Biacore. Biacore hybridoma supernatant screening was performed either by: (1) reverse screening using anti-mouse immobilized anti-PAI-1 antibodies or (2) forward screening assay using free PAI-1 as a ligand or against immobilized Vn.
The instruments used were the BIACORE 2000 or BIACORE 3000 (GE Healthcare), designed for biomolecular interaction analysis (BIA) in real time. The sensor chip used was the CM5 chip (GE Healthcare) with carboxymethylated dextran matrix on the surface. Each sensor chip has four parallel flow cells (Fc). Every flow cell was coupled with anti-mouse IgG Fc mAb via standard amine coupling according to the manufacture's protocol for chip preparation.
In the Biacore reverse screening assay, ELISA positive hybridoma supernatants were selected and filtered through 0.2 μm filters before being injected onto Biacore chip surface. Each hybridoma supernatant was injected onto one flow cell of flow cells Fc2-Fc4 and the IgG in the hybridoma supernatant would be captured to the chip surface by anti-mouse IgG Fc mAb, while Fc1 was left alone as reference cells. Human PAI-1 protein in PBS was then injected to Fc1 to Fc4. PBS buffer was also injected over the chip surface as a blank. After subtracting signals of Fc1 and blank buffer runs, the binding affinity (KD)/disassociation rate (kd) of the antibody from the supernatants to PAI-1 protein was analyzed and ranked using Scrubber 2 software.
In the Biacore forward screening assay, purified human vitronectin protein was immobilized to CM5 chip flow cells Fc1 to Fc4. Human or cyno PAI-1 were captured onto all flow cells. Filtered selected hybridoma supernatants then were injected over captured PAI-1 one per flow cell, except Fc1 which was reserved as the reference flow cell. PBS buffer was also injected over the chip surface as a blank. After subtracting signals of Fc1 and blank buffer runs, binding affinity of antibody in hybridoma supernatant to the vitronectin captured PAI-1 was analyzed and ranked using Scrubber 2 software (version 2.0a, 2005; BioLogic Software, BioLogic Software Rty Ltd., 116 Blarney Court, Campbell, ACT 2612 Australia).
Table 5 shows a selection of positive and negative antibody clones from the fusions A, B, C, D and E. Not all data was shown because of the large number of antibody clones that were screened. Only the antibody clones that demonstrated superior (kd<10−4 l/s) binding dissociation rate against human and cyno PAI-1 proteins were selected for the functional chromogenic assay.







TABLE 5







Hybridoma Supernatant Binding to Human PAI-1


Affinity/Off Rate Screening in Biacore Assay










Binding to hPAI-1















Off-rate <=
cyno



CLONE
Binding
10−4
PAI-1







A9
ND
ND
ND



A20
+
−
−



A37
+
−
−



A39
+
+
−



A41
ND
ND
ND



A44
+
+
+



A47
+
+
+



A52
ND
ND
ND



A71
+
+
+



A75
+
+/−
+/−



A83
+
+/−
−



A89
+
+/−
−



A93
+
+/−
−



A98
+
−
−



A99
+
+
+/−



A105
+
+
+



A107
+
−
−



A113
+
+
+



A119
+
+/−
+/−



B16
ND
ND
ND



B18
+
−
−



B28
+
+
−



B29
+
−
−



B32
+
+
+



B58
+
+
−



B85
ND
ND
ND



B89
+
+
+/−



B99
+
−
+/−



B105
+
+
+/−



B109
+
+
+



B118
ND
ND
ND



C26
+
−
−



C45
+
+
+/−



C46
+
+
+



C49
+
+/−
ND



C61
+
+/−
+/−



C66
+
−
−



C69
+
+
+/−



C76
ND
ND
ND



C79
+
−
−



C85
ND
ND
ND



C109
+
−
−



C118
+
+/−
ND



C134
ND
ND
ND



C145
+
−
+/−



D4
−
−
−



D12
+
−
−



D13
−
−
ND



D15
−
−
ND



D31
+
−
−



D33
+
+/−
−



D37
+
−
−



D48
+
+
+/−



D52
+
+
+



E4
+
+
−



E5
+
+
−



E11
+
+
−



E16
+
+
+/−



E20
+
ND
ND



E21
+
+
−







“+” = represents positive binding to h/cPAI-1 or an off-rate of less than or equal to 10−4



“”+/−“ = represents partial binding to h/cPAI-1 or an off-rate slightly higher than to 10−4



“−” = represents low or no binding to h/cPAI-1 or an off-rate higher than to 10−4



ND = not determined






Example 4
Functional ELISA for Hybridoma Supernatant Screening to Select for Antibodies that Block the Interaction of PAI-1 with tPA
To allow for selection of functional antibodies, a novel ELISA was developed to allow distinguishing between antibodies that only bind to PAI-1 versus those antibodies that blocked PAI-1's function as tPA inhibitor (functional ELISA).
Hybridoma supernatants were screened in a novel functional ELISA to identify hybridoma supernatant from different clones having the ability to block tPA-PAI-1 interaction. The design of the functional ELISA is as follows: (1) if the antibody binds to PAI-1 but the antibody binding does not block formation of the covalent bond between PAI-1 and tPA, the anti-tPA antibody will bind to the tPA that is bound to the plate through PAI-1 and gives a positive readout; (2) if the antibody blocks PAI-1 and thereby blocks the tPA interaction by either changing PAI-1 confirmation or by steric hindrance, the anti-tPA antibody will not be able to bind to the plate and readout will be negative (lower OD405). In parallel, hybridoma supernatants were tested for binding, to PAI-1 in the ELISA described in Example 2. Since the amount of antibody in the hybridoma supernatant is unknown, a lower than control reading (i.e., below the isotype control reading) was considered to be identifying an antibody of interest. Due to the variable antibody concentration in the supernatant, blocking in some cases was only partial.
Streptavidin coated plates (NUNC #436014) were incubated for 2 hours at RT with 2 ug/ml biotin-PAI-1 (human PAI-1 having N-terminal biotin labelled, active fraction; Molecular innovations cat #NTBIOPAI-A) in 1% BSA/PBS at 50 ul/ml. Plates were blocked 1 hour with 200 ul 1% BSA/PBS at RT and washed four times with 200 ul/well PBS. Purified antibody dilutions and hybridoma supernatants were added to wells at 50 ul/well and incubated for 15 minutes. Plates were washed four times with 200 ul/well PBS. Two-chain tPA (Innovative Research cat #HTPA-TC) at 1 ug/ml was added to the plates at 50 ul/well and incubated for 30 minutes at RT. Plates were washed four times with 200 ul/well PBS. Anti-tPA HRP conjugated antibody (Life Span Technologies, cat #LS-C39721) at 1:3000 dilution were added to the plates and incubated for 45 minutes. Plates were washed four times with 200 ul/well PBS. ABTS substrate (one Tablet dissolved in 5 ml; Roche Diagnostics #11 204 521 001) at 50 ul/well was added to the plates and time allowed for color to develop. Plates were read on BioTek Synergy HT instrument using OD405. ODs with the values that are lower than IgG isotype control indicate blocking of tPA binding to PAI-1.
In some cases functional ELISA was performed prior to Biacore supernatant screening and served as a selection step that was more important for hybridoma development. A representation curve with 33H1 as positive control, IgG1 as negative control and A44 as an identified positive antibody clone is shown in FIG. 3.







TABLE 6







Functional ELISA for Hybridoma Supernatant Screening to Select


for Antibodies that Block the Interaction of PAI-1 with tPA














tPA/PAI-1





PAI-1
Binding



CLONE
ELISA
Inhibition
Selected







A9
+
−
no



A20
+
−
no



A37
+
+
yes



A39
+
+/−
yes



A41
+
+
yes



A44
+
+
yes



A47
+
+
yes



A52
+
−
no



A71
+
+
yes



A73
+
−
no



A75
+
+
yes



A83
+
+
yes



A89
+
+
yes



A93
+
−
no



A98
+
+
yes



A99
+
−
no



A105
+
+
yes



A107
+
+
yes



A113
+
+
yes



A119
+
+
yes



B16
+
−
no



B18
+
+
yes



B28
+
+/−
yes



B29
+
+
yes



B32
+
+
yes



B58
+
+
yes



B85
+
−
no



B89
+
+
yes



B99
+
+
yes



B105
+
+
yes



B109
+
+
yes



B118
+
+
yes



C26
+
+
yes



C45
+
+
yes



C46
+
−
no



C49
+
−
no



C61
+
+
yes



C66
+
+
yes



C69
+
+
yes



C76
+
−
no



C79
+
+
yes



C85
+
−
no



C109
+
+
yes



C118
+
+
yes



C134
+
−
no



C145
+
+
yes



D4
+
−
no



D12
+
+
yes



D13
+
+
yes



D15
+
+
yes



D31
+
+
yes



D33
+
+
yes



D37
+
+
yes



D44
+
+
yes



D47
+
+
yes



D48
+
+
yes



D52
+
+
yes



D55
+
+
yes



E4
+
−
no



E5
+
−
no



E11
+
+
yes



E16
+
+
yes



E20
+
−
no



E21
+
+
yes







PAI-1 ELISA = a “+” represents binding to PAI-1 (see Example 2)



tPA/PAI-1 Binding Inhibition = a “+” score represents the interaction of tPA with PAI-1 is inhibited;



+/− = partial inhibition of the interaction of tPA with PAI-1






Over 200 supernatants were screened. Table 6 shows a selection of positive and negative hybridoma supernatants. About 10 hybridomas per fusion showed ability to block PAI-1 from binding to tPA in functional ELISA. Based on the data from the hybridoma supernatants, hybridomas were selected for sequencing and medium scale antibody production. Even though D4 did not bind well to non-glycosylated PAI-1, it was selected for purification and sequencing based on its Biacore binding to glycosylated PAI-1. The purified antibodies were further characterized in Biacore for affinity kinetics, and in chromogenic and cellular assays for potency in comparison to the commercially available antibodies.
Example 5
Sequencing by 5′-RACE (Rapid Amplification of cDNA Ends) and Mouse Antibody Purification
Antibodies for a specific target generated from a series of fusions could have the same sequences. By performing antibody gene sequencing at an early stage of antibody generation, any possibly redundant antibodies were eliminated and the correct antibody gene sequences guided antibody selection and humanization as well as chimeric antibody construction.
5′-RACE is a procedure for amplification of nucleic acid sequences from a messenger RNA template between a defined internal site and unknown sequences at the 3′ or the 5′ end of the mRNA. This methodology of amplification with single-sided specificity has been described as “one-sided” PCR or “anchored” PCR. The original variable murine anti-human PAI-1 antibody sequence of the lead antibody was determined by 5′-RACE cDNA sequencing and confirmed by N-terminal protein sequencing.
To determine variable heavy (VH) and light chain (VL) IgG sequences, total RNA from hybridoma cells was isolated using RNeasy Mini Kit (QIAGEN, Cat No. 74104) according to the manufacturer's instructions. Briefly, cells (5×106 cells) were lysed in 350 ul of the kit's RLT buffer followed by capturing total RNAs on spin column. RNA was eluted in the kit's TE buffer and stored on ice.
First-strand cDNA was prepared using SMARTerTM RACE cDNA Amplification Kit (ClonTech, Cat No. 634923). The 5′-RACE protocol was performed according to the manufacturer's instructions. VH and VL chain cDNAs were separately amplified by polymerase chain reaction (PCR) using the 5′-primers supplied with the SMARTerTM kit and the 3′ VH and VL gene specific primers listed below:









Heavy Chain 3′-Primer:



(SEQ ID NO: 105)



5′-TATGCAAGGCTTACAACCACA-3′ 



 



Light Chain 3′-Primer:



(SEQ ID NO: 106)



5′-CTCATTCCTGTTGAAGCTCTTGAG-3′






The amplified VH and VL genes were separately cloned into TOPO vector using TOPO TA cloning Kit (Invitrogen, Cat No. K4520-01). The procedures were performed according to the manufacturer's instructions. To transform bacteria, reaction mixtures were added into competent E. coli cells and incubated on ice for 20 minutes. The tubes, which contained the E. coli cells and the reaction mixture, were heated at 42° C. for 40 seconds and added 250 microliters of lit's SOC medium. After incubating the E. coli at 37° C. for 60 minutes with shaking at 300 rpm, the bacteria were spread on LB agar plate containing 100 micrograms per ml of ampicillin followed by incubating at 37° C., overnight.
Upon confirmation of the inserted VH and VL gene by PCR, five bacteria clones were selected and propagated in LB broth containing 100 micrograms per ml of ampicillin for plasmid DNA preparation. The plasmid DNAs were isolated using QIAprep Spin Miniprep Kit (QIAGEN, Cat No. 27104) according to manufacturer's instructions. The VH and VL IgG genes of hybridomas were sequenced by the Sanger method and the CDRs were determined using the Contact definition (MacCallum et al.).
Monoclonal antibodies were produced in CELLine bioreactor flasks (Wilson Wolf Manufacturing Corp.; Cat. #CL350 or Cat #CL1000) according to the manufacturer's instructions in serum-free medium (Gibco Cat. #12045) and purified by Protein A/G chromatography (GE Healthcare Life Sciences, Cat. #28-4083-47 and #28-4082-53). Purified antibodies were further characterized in Biacore for affinity kinetics, and in chromogenic and cellular assays for potency in comparison to the commercially available antibodies.
Example 6
Functional Chromogenic Assay Using Purified Antibody
Purified antibodies were tested in a chromogenic assay for the ability to block PAI-1. PAI-1 inhibits tPA function, therefore, antibodies that block PAI-1 will result in restoring tPA function. Chromogenic assays utilize proteolytic enzymes that act on their natural substrates (proteins and peptides) by hydrolyzing one or more peptide bond(s). This process is usually highly specific in the sense that only peptide bonds adjacent to certain amino acids are cleaved. Chromogenic substrates are peptides that react with proteolytic enzymes resulting in the formation of color which is quantifiable. Chromogenic substrates are made synthetically and are designed to possess selectivity similar to that of the natural substrate for the enzyme. Attached to the peptide part of the chromogenic substrate is a chemical group which when released after the enzyme cleavage gives rise to color. The color change can be followed spectrophotometrically and is proportional to the proteolytic activity.
A chromogenic assay was used to confirm the ability of the antibody to neutralize PAI-1 function as a tPA inhibitor. tPA is able to release pNA from the chromogenic substrate S2288. S228 in solution has no color, but after being exposed to tPA and subsequent release of pNA, the solution develops a yellow color that can be read at OD405. Color formation can be observed over 2-3 hours to determine kinetics of the enzymatic reaction. PAI-1 is able to block the enzymatic activity of tPA in a concentration dependent manner.
A two-step chromogenic assay was performed. All reagents are at 10× concentration until the step when they were added to substrate solution. In the first step, PAI-1 potency in tPA inhibition was measured using the chromogenic assay (PAI-1 titration with fixed tPA concentration). The PAI-1 titration curve was analyzed to determine IC50 for PAI-1 blocking tPA activity. Afterward, the IC80 calculated from the curve was selected for further antibody interrogation for ability to neutralize PAI-1 blocking function and restore tPA enzymatic activity. Equal volumes (25 ul) of tPA (at 14 nM) (Innovative Research, Cat. No. IHTPA-TC) and glycosylated (active form) human PAI-1 (Molecular Innovations, Cat. No. GLYHPAI-A) or non-glycosylated (active form) mouse PAI-1 (Molecular Innovations Cat. #IMPAI) were combined and incubated using 3-fold serial dilutions of PAI-1 starting at 108 nM and fixed concentration of tPA. All protein dilutions were made with 1% BSA/PBS. The mixture was incubated in the wells of a 96-well microtiter plate for 15 minutes at room temperature. Then 200 ul chromogenic substrate S2288 (1.25 mM) (Chromogenix, Cat. No. S-820852) diluted according to manufacturer's instructions is added to the wells and OD405 absorbance change at 405 nm it over 2 hours every 10 minutes is recorded to measure the residual tPA activity. For controls, background was measured in the absence of tPA (no enzymatic reaction), a positive control was no PAI-1 (100% tPA activity) and a negative control was PAI-1 at 10-fold excess of tPA (complete blocking or tPA activity). See FIG. 4 for representative curves for 33B8, A44, 33H1 and IgG1.
For the second step, the functional properties of the antibodies were determined by assessing their ability to inhibit active PAI-1 and restore tPA function utilizing the PAI-1 neutralization assay. For this step, active PAI-1 12.5 ul (at 56 nM) was incubated with an equal volume of either PBS (Invitrogen, Cat. No. 14190-144) containing 1% BSA (Sigma, Cat. No. A3059) or with serial 3-fold dilutions of antibody starting at 2 uM. Control and unknown antibodies were incubated at concentrations (5 fold dilutions) ranging from 0.1 to 300 nM with 3 nM PAI-1 and tPA was added to the mixture. All the ingredients were incubated at 10× concentration at room temperature and further diluted 10 fold with tPA substrate S2288 which upon cleavage by tPA changes color from clear to yellow. Samples were read at OD405 for 2 hours every 10 minutes at 37° C. The mixture was allowed to react in the wells of a 96-well microtiter plate for 30 minutes at room temperature to achieve antibody-antigen complex formation. Then 25 ul of tPA (at 14 nM which corresponds to IC80 inhibition of tPA activity) was added to the wells and incubated for 15 minutes at room temperature. Finally, 200 ul 1.25 mM substrate S2288 diluted according to manufacturer's instructions was added to the mix. The absorbance change at 405 nm is recorded to measure the residual tPA activity for 2 hours every 10min. One hundred percent PAI-1 activity is defined as the PAI-1 activity observed in the absence of antibody. Neutralization of PAI-1 activity by the antibody is calculated from the residual PAI-1 activity measured in the presence of the antibody. Controls were IgG1 as an isotype control (negative) and 33H1 mAb and 33B8 mAb as positive controls. See FIG. 5 for representative curves for B28, E16, E21, A75 and IgG1.
Orthologs of human PAI-1 inhibiting human tPA were tested in the two step chromogenic assay system. Titration of orthologs was performed as described above for human PAI-1 (see FIG. 6 for representative curves of titrations) and tPA activity was determined by chromogenic method (see FIG. 7 for representation curves for 33B8 and A44 against cyno and mouse PAI-1). Final concentration of human tPA used in the assay was 1.4 nM. 12.5 ul active PAI-1 (56 nM) was incubated with an equal volume of either PBS containing 1% BSA or with serial 3-fold dilutions of antibody starting at 2 uM. The mixture was allowed to react in the wells of a 96-well microtiter plate for 30 minutes at room temperature. Then 25 ul of tPA (14 nM) was added to the wells and incubated for 15 minutes at room temperature. To finalize reaction 200 ul tPA substrate S2288 (Chromogenix) (1.25 mM) was added to the mixture. Ortholog PAI-1 was obtained from Molecular Innovations: mouse PAI-1 (wild type active fraction; cat #MPAI); rat PAI-1 (wild type active fraction; cat #RPAI); and rabbit PAI-1 (stable mutant; cat #RbPAI-I91L) cyno PAI-1 (active cyno PAI-1) was produced in-house in E. coli. Because of the poor off-rates of the rabbit and rat orthologs in the Biacore screening (data not shown), screening of the antibodies against these orthologs was not performed.







TABLE 7







Activity of Antibodies against Orthologs and Glycosylation 


States of PAI-1 in Functional Chromogenic Assay











PAI-1 Ortholog and Glycosylation Status














non-gly
gly
non-gly
non-gly


Clone ID
Isotype
hPAI-1
hPAI-1
cPAI-1
mPAI-1





A37
IgG1
+/−
−
−
−


A39
IgG1
−
+++
−
−


A41
IgG1
+/−
−
−
−


A44
IgG1
+++
+++
+++
−


A47
IgG1
nd
−
−
−


A71
IgG1
+++
+++
+++
−


A75
IgG2a
+++
+++
+++
−


A83
IgG1
nd
+/−
+/−
−


A89
IgG2b
−
−
−
−


A98
IgG1
nd
nd
nd
nd


A105
IgG1
+++
+++
+++
−


A107
IgG1
+/−
−
−
−


A113
IgG1
−
−
−
−


A119
IgG2a
−
−
−
−


B18
IgG1
+
+
+
−


B28
IgG2b
−
+++
−
−


B29
IgG1
−
−
−
−


B32
IgG1
nd
−
−
−


B58
IgG1
nd
+
+
−


B89
IgG1
nd
−
−
−


B99
IgG2a
nd
+
+
−


B105
IgG1
−
−
−
−


B109
IgG1
+++
+++
+++
−


B118
IgG1
+
+
+
−


C26
IgG1
++
++
++
+


C45
IgG2b
+++
+++
+++
−


C61
IgG1
+
+
+
−


C66
IgG1
+
+
+
−


C69
IgG1
++
++
++
−


C79
IgG2b
+/−
+/−
+/−
−


C109
IgG2b
+/−
+/−
+/−
−


C118
IgG1
++
++
++
−


C145
IgG2b
++
++
++
−


D4
IgG2a
+
++
+
−


D12
IgG1
+
+
+
−


D13
IgG1
−
−
−
−


D15
IgG1
+
+
+
−


D31
IgG1
++
++
++
−


D33
IgG1
−
−
−
−


D37
IgG2a
−
−
−
−


D48
IgG2a
−
+/−
−
−


D52
IgG1
+
+
+
−


E11
IgG1
++
++
++
−


E16
IgG1
+++
+++
+++
−


E21
IgG2b
+++
+++
+++
−





h = human,


c = cynomolgus monkey,


m = mouse,


nd = not determined


“−” = no activity,


“+/−” = partial activity' 


“+” = slight activity,


“++” = moderate activity,


“+++” = strong activity






One or more antibodies from each fusion demonstrated ability to block both cyno and human PAI-1 inhibitory function in this assay, with about 14 antibodies having moderate to strong blocking activity. A39 and B28 had a unique profile in that these two antibodies blocked glycosylated hPAI-1 but had no activity against human or cyno non-glycosylated PAI-1. None of the antibodies were able to block mouse PAI-1 activity efficiently (within 10 fold of the human PAI-1) except for C26.
Example 7
Mechanism of Action for Monoclonal Antibodies
Monoclonal antibodies can inhibit PAI-1 by three different mechanisms: a) by steric hindrance, b) by converting PAI-1 into a latent conformation upon binding, and c) by converting PAI-1 into a substrate for tPA conformation instead of the inhibitor (“substrate conformation”). PAI-1 makes a covalent bond with tPA upon interaction with serine protease.
The chromogenic assay and SDS-PAGE techniques were used to identify antibody mechanism of action. A reaction between monoclonal antibody (or control antibodies), PAI-1 and tPA was carried out as described above for the functional chromogenic assay. Samples were mixed with Laemmli sample buffer and loaded on SDS-PAGE gel under non-reducing conditions and ran for 30 minutes. Afterwards, the gels were stained with Coomassie blue to visualize proteins, complexes and the cleaved form of PAI-1. Control monoclonal antibodies with known mechanism of action were used as comparators. 33B8 is known to convert PAI-1 into a latent conformation and 33H1 is known to convert PAI-1 into a substrate conformation. This assay could positively identify the substrate conformation but was unable to distinguish between latent conformation or steric hindrance. Representative SDS-gels are shown in FIGS. 8, 9 and 10.







Table 8







Mechanism of Action of Monoclonal Antibodies








Antibody
Mechanism of Action





A44
Converts PAI-1 from Active → Substrate Conformation


C26
Converts PAI-1 from Active → Substrate Conformation


C45
Converts PAI-1 from Active → Substrate Conformation


E21
Converts PAI-1 from Active → Substrate Conformation


A39
Converts PAI-1 from Active → Latent Conformation or 



Steric Hindrance


B109
Converts PAI-1 from Active → Latent Conformation or 



Steric Hindrance


E16
Converts PAI-1 from Active → Latent Conformation or 



Steric Hindrance









A44, C26, C45 and E21 block PAI-1 activity by converting PAI-1 form the active conformation to the substrate conformation. A39 and B109 have a different mechanism of action, but the assay was unable to distinguish whether these antibodies block PAI-1 activity by changing PAI-1 from the active conformation to the latent conformation or by steric hindrance.

Example 8
Purified Antibody Binding Kinetics
In kinetics measurement, the antibodies were evaluated in reverse at 25° C. In the reverse assay, PAI-1 antibodies were captured to the anti-mouse IgG Fc antibody surface prepared on CM5 chip followed by injecting the serial 2× dilutions of PAI-1 proteins (human or cyno) starting at 40 nM. A high flow rate was chosen at 50 ul/min to avoid mass transportation limitation. Two thousand seconds was allowed for dissociation time to accommodate for the slow off rate of the selected antibodies. The chip was regenerated by glycine-HCl, pH 1.7 buffer after each round of antibody-PAI-1 binding. Kinetics data analysis was performed using Biacore BIAevaluation software. The sensorgrams were double-referenced by subtracting the reference flow cell values and the blank buffer values. The sensorgrams were fitted by using the simulated kinetics 1:1 (Langmuir) model with local Rmax. The data for the antibodies tested are shown below in Table 9.







TABLE 9







Binding Kinetics by Biacore Reverse Assay










human PAI-1
cyno PAI-1












Dissociation
Affinity 
Dissociation 
Affinity 


Antibody
Rate kd (l/s)
KD (M)
Rate kd (l/s)
KD (M)





A39
7.09E−05
1.16E−11
ND
ND


A44
1.49E−05
3.76E−12
<=1.0E−6
<=1.0E−13


A75
4.76E−04
1.20E−10
ND
ND


A105
1.64E−04
4.23E−11
ND
ND


B28
4.61E−04
 6.5E−10
ND
ND





ND = not determined






Binding kinetics of representative antibodies were further analyzed and compared in Biacore forward assay with vitronectin and PAI-1 complex. In the forward assay, human vitronectin protein was immobilized onto the CM5 chip in flow cells Fc1-Fc4 by amine coupling. Human PAI-1 was then captured to the vitronectin surface in flow cells Fc2-Fe4 as ligand. Fc1 was reserved as reference cell. The antibodies were diluted 2× starting from 40 nM and injected to Fc1-4. Kinetics data analysis was performed using Biacore BIAevaluation software. The sensorgrams were first double-referenced by subtracting the reference cell values and the blank buffer values, and then fitted by 1:1 (Langmuir) model was used with global Rmax.







TABLE 10







Kinetics of A44 binding to human vitronectin captured 


human PAI-1 in Biacore forward assay










kd (l/s)
KD (M)





A44 binding to Vn
<=1.0E−6
<=1.0E−12


captured hPAI-1









Data in Table 10 indicated that A44 binds free human PAI-1as well as PAI-1 in vitronectin complex.

Example 9
Functional Assay in Primary Human Cells
To further investigate each antibody's ability to restore downstream plasmin production by primary human cells, a plasmin generation assay was used. Only antibodies that showed high potency in the chromogenic assay and good affinity in Biacore were used tested in this assay.
On day 1, human primary hepatic stellate cells (Sciencell CA, cat no SC5300) were plated at 20000 cells/well in starvation medium (DMEM Gibco+glutamax-1 4.5 g/L D-Glucose, Pyruvate (31966-021), 0.2% Fetal Bovine Serum gold PAA (A11-152)) at 37° C. under 5% CO2. On day 2, to neutralize PAI-1 activity, antibodies were pre-incubated with recombinant PAI-1 (Molecular Innovation, cat #IGLYHPAI-A, recombinant Glycosylated human PAI-1, final concentration 5 nM) for 15 minutes at room temperature. At the same time, tPA (Molecular Innovations (cat #HTPA-TC), 5 nM in DMEM without red phenol) was incubated with cells for 15 minutes at 37° C. After washing unbound tPA, PAI-1/mAb mixtures were added on the cells and then residual tPA activity was measured by adding and glu-Plasminogen/Substrate mixture (Glu-Pg: Sigma cat #9001-91-6; 0.5 μM final concentration) and plasmin chromogenic substrate: (CBS00.65 Stago cat #00128, 0.5 mM final concentration).
Plasminogen activation to plasmin is detected by kinetic reading every 45 seconds of A405/492 nm using spectrophotometer (IEMS, Thermofisher) thermostated at 37° C. Biolise software (Thermofischer) calculates the maximal rate of chromogenic substrate cleavage: plasmin generation expressed as Vmax: maximal rate of A405/492 nm per min (mDO/min) calculated. PAI-1 inhibition is then calculated with tPA alone as reference (100% inhibition) and PAI-1 (without mAb, as no inhibition) and plotted using Biostat speed software to calculate IC50 and Imax.







TABLE 11







Plasminogen Generation in Human Primary Hepatic Stellate Cells










Antibody
IC50abs mean ± sem (nM)
Imax mean (%)
n





A44
3.32 ± 0.34
97
7


A39
5.4 ± 0.8
99
3


A71
8.61 ± 3.6 
90
3


A75
22.6 ± 8.2 
66
4


A105
 27 ± 7.8
88
3


B28
7.28 ± 2.7 
90
3


B109
6.11 ± 0.88
94
3


C26
Inactive
n/a
2


C45
 6.5 ± 1.11
97
4


E16
4.74 ± 2.27
95
3


E21
Inactive
n/a
3


33H1
22.92 ± 12  
56
3


33B8
Inactive
n/a
3





n/a = not applicable






Example 10
Antibody Binding Epitope Exploration by Biacore Competition Assay
A selected group of anti-PAI-1 antibodies with superior binding and blocking activities were explored for their potential binding epitopes in Biacore competition assays. In the assays, the newly identified antibodies as well as several commercially available anti-PAI-1 antibodies with known binding site on human PAI-1 were set up to compete for binding to human PAI-1 protein. Each antibody was immobilized onto a flow cell in Biacore CM5 chip using standard amine coupling reaction. All tested antibodies except for clone B28 retained binding site activity after amine coupling. Human PAI-1 protein was captured to the immobilized antibody on the chip followed by injection of each antibody as analyte. Only the analyte antibodies that have different binding sites on human PAI-1 from the immobilized antibody will show additional binding signals in Biacore. The competition experiments were repeated twice for each immobilized antibody and the results are show in the following Table.












Analyte Antibody

























33H1
33B8
A44
31C9
A71
A75
B109





Immobilized 
33H1
c/c
b/c
b/b
b/b
b/b
b/b
b/b


Antibody
33B8
b/b
c/c
b/b
b/c
b/b
b/b
b/b



A44
b/b
b/b
c/c
b/b
b/b
b/b
b/b



31C9
nt
nt
nt
nt
nt
nt
nt



A71
b/b
b/c
b/b
b/b
c/c
c/c
b/b



A75
b/b
p/p
b/b
p/p
c/c
c/c
b/b



B109
b/b
c/c
b/b
b/b
b/b
b/b
c/c



B28
—
—
—
—
—
—
—



C45
b/b
p/b
c/c
b/b
b/b
b/b
b/b



C26
b/c
p/c
b/b
b/b
b/b
b/b
b/b



E16
b/b
p/b
b/c
b/b
b/b
p/b
b/b



E21
b/c
b/c
b/b
b/c
b/c
b/b
b/b




















B28
C45
C26
E16
E21






Immobilized 
33H1
b/b
b/b
c/c
b/b
b/c



Antibody
33B8
p/b
b/b
b/b
b/b
b/b




A44
b/b
c/c
b/b
c/c
b/b




31C9
nt
nt
nt
nt
nt




A71
b/b
b/b
b/b
b/b
b/b




A75
b/b
b/b
b/b
b/b
b/b




B109
c/c
b/b
b/b
b/c
b/b




B28
—
—
—
—
—




C45
b/b
c/c
b/b
b/b
b/b




C26
b/c
b/b
c/c
b/b
c/c




E16
b/c
b/b
b/b
c/c
b/b




E21
b/c
b/b
b/c
b/b
c/c





p = partial binding by the analyte antibody,


c = competition by the analyte antibody,


b = binding by the analyte antibody;


“ — ” = no PAI-1 binding to the immobilized antibody;


nt = not tested






When A44 is immobilized and binds PAI-1, C45 (analyte antibody) is unable to bind to PAI-1 that is bound by A44. Therefore, C45 competes for the same binding site that A44 binds on PAI-1 (denoted in Table 12 as “c/c”) or A44 binding to PAI-1 interferes with C45 binding to PAI-1. This analysis is confirmed when the experiment is repeated in the reverse order. Specifically, when C45 is the immobilized antibody and is bound to PAI-1, A44 as the analyte antibody is unable to bind the PAI-1 that is bound to C45 (denoted in Table 12 as “c/c”). In a similar analysis, A71 and A75 compete for the same site on PAI-1. The Biacore analysis confirmed that A44 and C45, as well as A71 and A75, compete with or to interfere with each other when binding to PAI-1.
Conversely, the commercially available antibodies, 33H1 and 33B8, do not compete with A44. When A44 is the immobilized antibody and is bound to PAI-1, both 33H1 and 33B8 are able to still bind to the PAI-1 that is bound to A44 (denoted as “b/b” in Table 12). This is confirmed in the reverse experiment. When PAI-1 is bound to immobilized 33H1 or immobilized 33H8, A44 is still able to bind to PAI-1. Thus, the commercial antibodies 33H1 and 33B8 do not compete with or interfere with A44 binding to PAI-1.
Interestingly, some immobilized antibodies (i.e., B109) blocked analyte antibody (i.e., 33B8) from binding to the captured PAI-1 protein; but, when switching the positions of the immobilized antibody to the analyte antibody (e.g., flipping the pair on the chip), the antibody pair no longer competed for binding with each other to PAI-1. For example, when B109 was the immobilized antibody bound to PAI-1, 33B8 was unable to bind PAI-1. However, when 33B8 was the immobilized antibody binding PAI-1, B109 was able to bind PAI-1. One possible explanation for this result is that when the immobilized antibody is bound to PAI-1, PAI-1 may shift to an unfavorable conformation for the second or analyte antibody and prevents the analyte antibody from binding (for instance, when B109 is the immobilized antibody and 33B8 is the analyte antibody). However, when the antibody pair is reversed, the immobilizing antibody may bind in such a manner that PAI-1 conformation is relatively unchanged, thus allowing the analyte antibody to bind to the bound PAI-1 (i.e., the analyte antibody B109 is able to bind PAI-1 that is bound by the immobilized antibody 33B8). Therefore, the competition observed between 33B8 and B109 was not due to overlapping binding sites on PAI-1 but likely due to a conformational change in PAI-1 when bound to B109.
Another interesting observation was that B28 lost binding to human PAI-1 when immobilized via amine coupling, suggesting B28's CDR regions involve amino acids with primary amine group(s).
Example 11
Selection of Mouse Monoclonal Antibody for Humanization
Table 13 shows a summary of the in vitro data characterizing the most active monoclonal antibodies from the five fusions performed. Based on these data, A44 was selected for humanization because A44 was the most potent antibody in the chromogenic assay and in plasmin generation while having the highest affinity in Biacore.







TABLE 13







Summary of Monoclonal Antibody Affinity and Potency 


against Human Glycosylated PAI-1













Plasmin





Chromogenic
Generation
Affinity 
Mechanism 


Antibody
Assays (nM)
(nM)
Kd (M)
of Action














A39 (IgG1/k)
1.70, 1.00
5.4
1.16E−11
SH or latent


A44 (IgG1/k)
1.66, 1.50, 1.70
3.32
4.20E−14
substrate


A71 (IgG1/k)
Approx. 4.00
8.61
ND
SH or latent


A75 (IgG2a/k)
3.00
22.6
1.20E−10
SH or latent


A105 (IgG1/k)
7.00
27.0
4.20E−11
SH or latent


B28 (IgG2b/k)
1.80
7.28
 6.5E−10
SH or latent


B109 (IgG1/k)
0.23
6.11
ND
SH or latent


C26 (IgG1/k)
5.00
Inactive
ND
substrate


C45 (IgG2b)
0.5
10.6
ND
substrate


E16 (IgG1)
1.1
4.74
ND
SH or latent


E21 (IgG2b)
1.3
216.0
ND
substrate





SH = steric hindrance;


ND = not determined






The heavy and light chain sequences shown in Table 1 are aligned in FIG. 12 and CDRs, as defined by IMGT, are highlighted in bold. Based on the in vitro data presented in the Table 13, A44 was selected for humanization.
Example 12
Engineering of the Anti-PAI-1 A44 Fab: Humanization, Stabilization and Mutation of Unwanted Sequence Motifs
Several approaches discussed below were taken to humanize, stabilize and optimize the sequence motifs of the A44 murine antibody against PAI-1.
1) Humanization
The humanization protocol used has been described in PCT/US08/74381 (US20110027266), herein incorporated by reference in its entirety. The variable light (VL) and variable heavy (VH) sequences of marine A44 were used to build a homology model of anti-PAI-1 A44 light chain (LC) and heavy chain (HC) in Molecular Operating Environment (MOE; v.2010.10; Chemical Computing Group). The following templates were used: light chain framework—ID51 (94% identity in the framework regions), heavy chain framework—3KSO (96% identity in the framework regions), L1—1D5I (94% identity), L2—1D5I (94% identity), L3—1AXS (72% identity), H1—1IC7 (82% identity), H2—1MBU (68% identity) and H3—2WDB (62% identity). The H3 loop was particularly difficult to model since Trp is the first residue. 2WDB, although a shorter loop, also has a Trp at the beginning of the loop and the same Phe-Asp-Tyr sequence at the end of the H3 loop. The side-chains of Glu-105 (LC) and His-99 were rebuilt and the subsequent model was energy minimized using the standard procedures implemented in MOE. A molecular dynamics (MD) simulation of the minimized 3D homology model of the murine A44 was subsequently performed, with constraints on the protein backbone at 500 K temperature for 1.1 nanoseconds (ns) in Generalized Born implicit solvent. Ten diverse conformations were extracted from this first MD run every 100 picoseconds (ps) for the last 1 ns. These diverse conformations were the each submitted to a MD simulation, with no constraints on the protein backbone and at 300 K temperature, for 2.3 ns. For each of the 10 MD runs, the last 2,000 snapshots, one every ps, from the MD trajectory were then used to calculate, for each murine A44 amino acid, its root mean square deviations (rmsd) compared to a reference medoid position. By comparing the average rmsd on the 10 separate MD runs of a given amino-acid to the overall average rmsd of all A44 marine amino-acids, one decides if the amino-acid is flexible enough, as seen during the MD to be considered as likely to interact with T-cell receptors and responsible for activation of the immune response. 37 amino-acids were identified as flexible in the murine A44 antibody, excluding the CDR and its immediate 5 Å vicinity.
The motion of the 62 most flexible murine A44 amino acids, during the 20 ns (10×2 ns), were then compared to the motion of the corresponding flexible amino-acids of 49 human germline homology models, for each of which were run the 10×2 ns MD simulations. The 49 human germline models were built by systematically combining the 7 most common human germline light chains (vk1, vk2, vk3, vk4, vlambda1, vlambda2, vlambda3) and 7 most common human germline heavy chains (vh1a, vh1b, vh2, vh3, vh4, vh5, vh6). The vk1-vh2 human germline antibody showed 0.58 4D similarity of its flexible amino-acids compared to the flexible amino-acids of the murine A44 antibody; the vk1-vh2 germline antibody was therefore used to humanize A44 antibody focusing on the flexible amino-acids. The vlambda3-vh4 human germline showed the second highest 4D similarity, 0.57, and was also used as the basis for humanization of the A44 antibody. For the pair wise amino-acid association between murine A44 and vk1-vh2 amino-acids, the 2 sequences were aligned based on the optimal 3D superposition of the alpha carbons of the 2 corresponding homology models. The pair wise amino-acid association between murine A44 and vlambda3-vh4 was performed in a similar manner. FIG. 13 shows the alignment of murine A44 light chain with vk1 and vlambda3. FIG. 14 shows the alignment of marine A44 heavy chain with vh2 and vh4.
2) Stabilization
a) Knowledge-based Approach
The amino-acids of the light and heavy chains with low frequency of occurrence vs. their respective canonical sequences, excluding the CDRs, were proposed to be mutated into the most frequently found amino-acids (ΔΔGth>0.5 kcal/mol; (E. Monsellier, H. Bedouelle. J. Mol. Biol. 362, 2006, p. 580-593)). This first list of consensus mutations for the LC and HC has been restricted to the amino-acids found in the closest human germline (vk1-vh2). Suggested changes in the immediate vicinity of the CDRs (5 Angstroms “Vernier” zone (J. Mol. Biol. 224, 1992, p. 487-499)) were removed from consideration. This resulted in two stabilizing mutations in the LC (see Table 15) and live stabilizing mutations in the HC (see Table 16). Other criteria were taken into account to consider these mutations for potentially stabilizing the anti-PAI-1 A44 antibody. These criteria were a favorable change of hydropathy at the surface or a molecular mechanics based predicted stabilization of the mutant. Also, additional stabilizing mutations reported to be successful in the literature (E. Monsellier & H. Bedouelle, J. Mol. Biol., 362, 2006, p. 580-59:3; B. J. Steipe et al. J. Mol. Biol, 1994, 240, 188-192) and were considered (see Tables 17 & 18), however, no additional mutations were suggested.







TABLE 15







Stabilizing Changes Proposed in Light Chain










Residue
Proposed Change
Calculated ΔΔGth
Accept Change





Lys-3
Val
2.23998
No—not in germline


Met-11
Leu
0.766432
Already changed in





humanization


Tyr-12
Ser
2.04389
Already changed in





humanization


Leu-36
Val
2.17091
No—Vernier


Lys-42
Gln
0.939652
No—not in germline


Thr-46
Leu
2.01966
No—Vernier


Gln-69
Thr
2.16357
No—Vernier


Tyr-80
Ala
2.92454
Already changed in





humanization


Met-83
Leu
2.57007
Already changed in





humanization


Gly-84
Ala
0.597822
Yes


Ile-85
Thr
1.27255
Yes
















TABLE 16







Stabilizing Changes Proposed in Heavy Chain










Residue
Proposed Change
Calculated ΔΔGth
Accept Change





Glu-1
Gln
0.562423
Yes


Met-2
Val
3.41361
No—Vernier


Glu-6
Gln
0.655069
No—Not in germline


Pro-9
Ala
0.505324
No—Not in germline


Ser-10
Glu
2.40018
Already changed in





humanization


Gln-16
Ala
1.11244
No—Not in germline


Thr-17
Ser
1.79135
No—Not in germline


Leu-18
Val
0.760243
No—Not in germline


Ser-19
Lys
1.20539
No—Not in germline


Thr-21
Ser
1.3289
No—Not in germline


Ser-23
Lys
1.82798
No—Not in germline


Val-24
Ala
1.35286
No—Not in germline


Thr-25
Ser
1.72008
Yes


Ile-37
Val
1.66985
No—Not in germline


Arg-38
Lys
0.568427
No—Not in germline


Lys-39
Gln
2.27769
Yes


Phe-40
Arg
1.81199
No—Not in germline


Asn-43
Lys
1.42568
Already changed in





humanization


Lys-44
Gly
2.01606
Already changed in





humanization


Tyr-47
Trp
2.62805
No—Vernier


Met-48
Ile
1.67766
No—Vernier


Pro-61
Glu
1.08569
No—Not in germline


Ser-62
Lys
0.840485
No—Not in germline


Leu-63
Phe
1.25428
No—Not in germline


Arg-66
Lys
0.528008
No—Not in germline


Ile-67
Ala
1.93707
No—Vernier


Ser-68
Thr
1.36475
Yes


Ile-69
Leu
0.550185
No—Vernier


Arg-71
Val
0.61536
No—Vernier


Asn-72
Asp
3.40632
Yes


Thr-73
Lys
0.5597
No—Vernier


Lys-75
Ser
0.81321
No—Not in germline


Asn-76
Ser
0.744463
No—Not in germline


Gln-77
Thr
1.30652
No—Not in germline


Tyr-78
Ala
2.54699
No—Vernier


Val-85
Leu
1.71111
No—Not in germline


Thr-87
Ser
1.30394
No—Not in germline


Thr-90
Ser
0.557686
No—Not in germline


Thr-92
Val
1.13795
No—Not in germline
















TABLE 17







Combinations of stabilizing mutations evaluated










Additional changes 
Accept 


Combination*
suggested
Change





L1 (40 −> P & 42 −> Q)
None—neither changed
No changes


L2 (45 −> K)
None—already K45
None


L3 (74 −> T)
None—already T74
None


L4 (76 −> S)
None—already S76
None


L5 (84 −> A, 85 −> T)
None—already changed in
None



stabilization



H1 (15 −> G)
None—not in germline
None


H2 (61 −> E, 62 −> Lys, 63 −> Phe)
None in germline
None


H3 (86 −> T, 87 −> S, 88 −> E)
87 and 88 not in germline 
None


S1 (L1 & L5)
None
No


S2 (H1 & H3)
None
No





*Note:


Sequential numbering used to refer to residues













TABLE 18*







Stabilization mutations evaluated











Light Chain 
Additional changes 




Residue*
suggested
Accept Change







 15 −> L
V15 −> L
No—V15 in Vk1 germline



 90 −> Q
None—already Q90
None



 32 −> Y
None—already Y32
None



106 −> I
None—already I106
None



 63 −> S
None—already S63
None



 21 −> I
None—already M21
None







*Note:



Sequential numbering used to refer to residues






b) 3D and MD-based Approaches
3D and MD-based approaches have been previously reported (Seco J., Luque F. J., Barril X., J. Med. Chem. 2009 Apr. 23:52(8):2363-71; Malin Jonsson et al., J. Phys. Chem. B 2003, 107:5511-5518). Hydrophobic regions of the antibody were explicitly identified by analyzing the molecular dynamics simulation of the Fab in a binary solvent (20% isopropanol in water, 20 ns production simulation). Additional analysis using a hydrophobic surface map within Schrodinger's maestro software (v. 8.5.207) was completed. The protein surface analyzed by these two methods is quite hydrophilic. Even with both these techniques, no residues contributing to any hydrophobic patches on the surfaces were present therefore, no anti-aggregation mutations were suggested.
3) Humanization by Grafting
Humanization using grafting techniques has previously been reported (P. T. Jones, P. H. Dear, J. Foote, M. S. Neuberger, G. Winter, Nature 1986, 321:522-525). The humanization started by identifying the two closest human germlines to anti-PAT1 A44 variable domain light and heavy chains. This was done by performing a BLAST search vs. all the human germlines which were systematically enumerated (all possible combinations of the V & J domains for the kappa and lambda chains; V, D and J domains for the heavy chains). The BLAST searches were performed using an intranet application linked to the Sequence Information Retrieval and Analysis (SIRA) service provide by the National Center for Biotechnology Information (NCBI).
The closest human germline were identified with 70% and 67% sequence identity to anti-PAI1 A44 variable domain light and heavy chains, respectively. Using the internal VBASE germline sequences, the light chain was found to be close to V I-O18 (approximately 64% identity) locus and the heavy chain was close to 4-30 (approximately 69% identity) locus of the VH4 sub-family. CDR regions (based on Kabat) and Vernier residues are indicated in italics for mA44 light chain (A44LC) and for IGVK1-33-01_IGKJ4-01 (IGVK1). Vernier residues as defined in J. Mol. Biol, 1992, 224, 487 are underlined. The humanizing mutations (in boldface) were obtained by performing a pairwise comparison of the two aligned sequences, excluding the CDR & Vernier zone residues (also underlined in marine) as defined above. T46L and Q69T from the murine light chain and M2V in the murine heavy chain (Vernier zone residue) were mutated to the predominantly conserved human germline sequence as one part of the humanization by grafting approach (LC5a, HC5a). In another variant, these three Vernier zone residues were retained as seen in the original marine sequence (LC5b, HC5b).









mA44-Light chain 



(SEQ ID NO: 141)



DIKMTQSPSS MYASLGERVT ITCKASQDIN SYLSWLQQKP 



 



GKSPKTLIYR ANRSVDCVPS RFSGSGSGQD YSLTISSLEY 



 



EDMGIYYCLQ YDEFPPTFGG GTKLEIK



 



IGKV1-33-01_IGKJ4-01 



(SEQ ID NO: 107)



DIQMTQSRSS LSASVGDRVT ITCQASQDIS NYLNWYQQKP 



 



GKAPKLLIYDA SNLETGVPS RFSGSGSGTD FTFTISSLQP 



 



EDIATYYCQQ YDNLPLTFGG GTKVEIK



 



mA44 Heavy chain 



(SEQ ID NO: 140)



EMQLQESGPS LVKPSQTLSL TCSVTGDSMT NGYWNWIRKF



 



PGNKLEYMGY ITYSGSTYYN PSLKGRISIT RNTSKNQYYL



 



QLSSVTTEDT ATYYCARWHY GSPYYFDYWG QGTTLTVSS



 



IGHV4-59-02_IGHD6-13-01_IGJ4-02 



(SEQ ID NO: .t 08)



QVQLQESGPG LVKPSETLSL TCTVSGGSVS SYYWSWIRQP



 



PGKGLEWIGY IYYSGSTNYN PSLKSPVTIS VDTSKNOFSL



 



KLSSVTAADT AVYYCARGYS SSWYYFDYWG QGTLVTVSS






The next closest human germline was identified with 59% and 58% sequence identity to anti-PAI1 A44 variable domain light and heavy chains, respectively. Using the internal VBASE germline, this light chain is found to be close to VκIII-L6 ( ̃56% identity) locus and the heavy chain close to 6-01 locus of the VH6 sub-family. CDR regions (based on Kabat) and Vernier regions and are indicated in italics. Vernier regions (as defined in J. Mol. Biol., 1992, 224, 487) and underlined. The humanizing mutations were obtained by performing a pairwise comparison of the 2 aligned sequences, excluding the CDR & Vernier zone residues (also underlined in murine) as defined above and are shown in boldface.







mA44-Light Chain 


(SEQ ID NO: 141)


DIKMTQSPSS MYASLGERVT ITCKASQDIN SYLSWLQQKP 


 


GKSPKTLIYR ANRSVDGVPS RFSGSGSGQD YSLTISSLEY 


 


EDMGIYYCLQ YDEEPPTFGG GTKLEIK


 


IGKV3-11-02_IGKJ4-01 


(SEQ ID NO: 143)


EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP 


 


GQAPRLLTYD ASNRATGIPA RFSGSGSGRD FTLTISSLEP 


 


EDFAVYYCQQ RSNWPLTFGG GTKVEIK


 


mA44-Heavy Chain 


(SEQ ID NO: 140)


EMQLQESGPS LVKTSQTLSL TCSVTGDSMT N..GYWNWTR


 


KFPGNKLEYM GYIT..YSGS TYYNPSLKGR ISITRNTSKN


 


QYYLQLSSVT TEDTATYYCA RWHYGSPYYF DYWGQGTTLT VSS


 


IGHV6-1-02_IGHD6-13-01_IGHJ4-02 


(SEQ ID NO: 144)


QVQLQQSGPG INKPSQTLSL TCAISGDSVS SNSAAWNWIR


 


QSPSRGLEWL GRTYYRSKWY NDYAVSVKSR ITINPDTSKN


 


QFSLQLNSVT PEDTAVYYCA RGYSSSWYYF DYWGQGTLVT VSS






4) Mutation of Unwanted Sequence Motifs

The following motifs of sequences were considered: Asp-Pro (acid labile bond), Asn-X-Ser/Thr (glycosylation, X=any amino-acid but Pro), Asp-Gly/Ser/Thr (succinimide/iso-asp formation in flexible regions), Asn-Gly/His/Ser/Ala/Cys (exposed deamidation sites), and Met (oxidation in exposed areas). The VL & VH domains of murine anti-PAI1 A44 possess two potential glycosylation sites: N52RS (in CDR2) in the LC and N72TS in the HC. One exposed deamidation site is present in CDR1 of the HC (N31G). Three potential sites of succinimide formation were identified in the original murine sequence: D56G (end of CDR2) in the LC, and D27S (in CDR1) and D89T in the HC. The LC problematic motifs, N52RS and D56G, are both in CDR2. Since these mutations occur in a CDR, they were addressed by mutation in two proposed engineered sequences below (LC2 and LC4). N52 was conservatively mutated to Gln and D56 was mutated to Glu. There are four existing problematic residues in the HC. The first two occur in CDR1: the potential succinimide formation site, D27S, and the deamidation site N31G. Two additional problematic motifs also occur in the third framework region. In CDR1, D27 was mutated to an E to avoid the formation of succinimide, while N31 was altered to a Q. N72 and D89 were altered to Q and E, respectively. These problematic motifs were addressed in engineered sequences HC2a and HC4 described below. The HC2b variant contains only the mutation of the N31G deamidation site.
The resulting humanized sequences were blasted for sequence similarity against the IEDB database (found on the world wide web at immuneepitope.com, version June 2009; Vita R., Zarebeski L., Greenbaum J. A., Emami H., Hoof I., Salimi N., Damle R., Sette A., Peters B. The immune epitope database 2.0 Nucleic Acids Res. 2010, January, 38 (Database issue):D854-62. Epub 2009, Nov. 11) to ensure that none of the sequences contain any known human B- or T-cell epitopes (sequence identity of 70% used as cut-off for the results obtained through BLAST search and considering only the results from human species). DeClerck, et al., (International Publication No. WO 2002034776) have disclosed antibody binding epitopes of PAI-1, none of which are problematic for the epitopes disclosed herein.
For the murine A44 LC, there is one human epitope from Kirschmann et al. (The Journal of Immunology, 1995, 155, 5655-5662). It possesses 71% identity over a 14 amino acid stretch as seen below. The subject sequence was a partial sequence that had not been verified by mass spectrometry. No binding data is reported for this peptide. This epitope was seen in all the LC variants proposed. No potentially problematic epitopes were identified when a similar search was performed for the HC.
5) Original Sequences of Anti-PAI1 Variable Domains
CDRs are highlighted in bold and Vernier regions are (as defined by Foote & Winter, J. Mol. Biol., 1992, 224:487-499) are underlined.








Light Chain 



(SEQ. ID NO: 142)



  1 DIKMTQSPSS MYASLGERVT ITCKASQDIN SYLSWLQQKP GKSPKTLIYR 



 


 51 ANRSVDCVPS RFSGSGSGQD YSLTISSLEY EDMGIYYCLQ YDEFPPTFGG


 


101 GTKLEIKRAD AAPTVSIF






Germinality index=70% with IGKV1-33-01_IGKJ4-01 [V I-O18]









Heavy Chain 



(SD) ID NC): 140)



  1 EMQLQESGPS LVKPSQTLSL TCSVTGDSMT NGYWNWIRKF PGNKLEYMGY



 


 51 ITYSGSTYYN PSLKGRISIT RNTSKNQYYL QLSSVTTEDT ATYYCARWHY


 


101 GSPYYFDYWG QGTTLTVSS






Germinality index=67% with IGHV4-59-02_IGHD6-137-01_IGHJ4-02 [VH4 4-30]

6) Engineered Sequences

4D humanization and grafting approaches were applied to the closest two human germline sequences
a) Engineered Light Chain Sequences
LC1a contains seven mutations derived from the 4D humanization method using the closest germline sequence, vk1. LC1b has 12 mutations derived from the 4D humanization to the second closest human germline sequence, vl3. LC2 contains 2 additional mutations in CDR2 as compared to LC1a. These mutations address a potential glycosylation site (N52RS) and a potential site of succinimide formation (D56G). LC3 contains the mutations from the 4D humanization to the closest germline sequence with an additional 2 stabilizing mutations. LC4 combines the humanizing, stabilizing and unwanted motif mutations. CDRs and vernier zones are in italics, vernier residues are underlined, humanizing mutations are in boldface, problematic motifs are in double strikethrough and stabilizing mutations are shown in lower case. FIGS. 16 and 17 show summaries of the mutations.








LC1a (SEQ ID NO: 91):



 


  1 DIKMTQSPSS LSASVGDRVT ITCKASQDIN SYLSWLQQKP GKSPKTLIVR


 


 51 ANRSVDGVPS RFSGSGSGQD YSLTISSLQP EDLGIYYCLQ YDEFPPTFGG


 


101 GTKLEIK






No additional human epitopes for sequence LC1a found in IEDB database. LC1a germinality index=76% with IGKV1-33-01_IGKJ4-01 [VκI-O18].









LC1b (SEQ ID NO: 92):



  1 DIKMTQSPSS VSVSPGQTVT ITCKASQPIN SYLSWLQQKP GQSPKTLIYR


 


 51 ANRSVDGVPS RFSGSGSGQD YSLTISSLQA MDEGIYYCLQ YDEFPPTFGG


 


101 GTKLTIK






In addition to the epitope described in section 4 above, K39PGQSPKTLI has 70% sequence identity to KPGQPPRLLI (Kirschmann et al. J. Immun., 1995, 155, 5655-5662). This peptide is reported to have an IC50>100,000 nM against all the HLA-DR alleles for which it was tested. LC1b germinality index=67% with IGKV1-33-01_IGKJ4-01 [VκI-O18].









LC2 (SEQ ID NO: 93):



  1 DIKMTQSPSS LSASVGDRVT ITCKASODIN SYLSWLQQKP GKSPKTLIYR


 


 51 A  RSV  GVPS RFSGSGSGQD YSLTISSLQP EDLGIYYCLQ YDEFPPTFGG


 


101 GTKLE1K






No additional human epitopes for sequence LC2 were found in IEDB database. LC2 germinality index=76% with IGKV1-33-01_IGKJ4-01 [VκI-O18].









LC3 (SEQ ID NO: 94):



  1 DIKMTQSPSS LSASVGDRVT ITCKASQDIN SYLSWLQQKP GKSPKTLIYR


 


 51 ANRSVDGVPS RFSGSGSGQD YSLTISSLQP EDLatYYCLQ YDEFPPTFGG


 


101 GTKLEIK






No additional human epitopes for sequence LC3 were found in IEDB database. LC3 germinality index=78% with IGKV1-33-01_IGKJ4-01 [VκI-O18],









LC4 (SEQ ID NO: 95):



  1 DIKMTQSPSS LSASVGDRVT ITCKASQDIN SYLSWLQQKP GKSPKTLIYR


 


 51 A  RSV  GVPS RFSGSGSGQD YSLTISSLQP EDLatYYCLQ YDEFPPTFGG


 


101 GTKLEIK






No additional human epitopes for sequence LC4 were found in IEDB database. LC4 germinality index=78% with IGKV1-33-01_IGKJ4-01 [VκI-O18].









LC5a (SEQ ID NO: 96):



  1 DIQMTQSPSS LSASVGDRVT ITCKASQDIN SYLSWLQQKP GKAPKLLIYR


 


 51 ANRSVDGVPS RFSGSGSGTD YTFTISSLQP EDIATYYCLQ YDEFPPTFGG


 


101 GTKVEIK






In addition to the epitope described in section 4 above, A43PKLLIYRAN has 80% sequence identity to APKLLIYAASSL (Kirschmann et al. J. Immun., 1995, 155, 5655-5662). The molecular weight was not determined on this peptide and no binding data was reported. LC5a germinality index=85% with IGKV1-33-01_IGKJ4-01 [VκI-O18].









LC5b (SEQ ID NO: 97):



  1 DIQMTQSPSS LSASVGDRVT ITCKASQDIN SYLSWLQQKP GKAPKTLIYR


 


 51 ANRSVDGVPS RFSGSGSGQD YTFTISSLQP EDIATYYCLQ YDEFPPTFGG


 


101 GTKVEIK






No additional human epitopes for sequence LC5b were identified in IEDB database. LC5b germinality index =83% with IGKV1-33-01_IGKJ4-01 [VκI-O18].









LC5c (SEQ ID NO: 98):










  1
DIQMTQSPSS LSASVGDRVT ITCKASQDIN SYLSWLQQKP GKAPKTLIYR



 


 51
ANRSVDGVPS RFSGSGSGQD YTFTISSLQP EDIATYYCLQ YDEFPPTFGG


 


101
GTKVEIK






In addition to the epitope described in section 4 above, K39PGQAPRTLI has 80% sequence identity to KPGQPPRLLI (Kirschmann et al., J. Immun., 1995, 155, 5655-5662). This peptide is reported to have an IC50>100,000 nM against all the HLA-DR alleles for which it was tested. LC5c germinality index=79% with IGKV3-11-02_IGKJ4-01 [VκIII-L6]. A schematic of all light chain mutations is shown in FIG. 15.

b) Engineered Heavy Chain Sequences
HC1a contains eight mutations derived from the 4D humanization method to the closest human germline sequence. HC1b contains six mutations derived from the 4D humanization method to the 2nd closest germline sequence. HC2a contains four additional mutations when compared to HC1a to address unwanted sequence motifs. HC2b only addresses the deamidation site in CDR1 (N31G). HC3 contains the humanizing mutations from HC1a with an additional five stabilizing mutations. HC4 contains humanizing mutations from HC1a, stabilizing mutations from HC3 and the mutations addressing problematic motifs from HC2a. CDRs and vernier zones are in italics, vernier residues are underlined, humanizing mutations are in boldface, problematic motifs are in double strikethrough and stabilizing mutations are shown in lower case.








HC1a (SEQ ID NO: 82):










  1
EMTLKESGPT LVKPTQTLSL TCSVTGDSMT NGYWNWIRKF PGKALEYMGY



 


 51
ITYSGSTYYN PSLKGRISIT RNTSKNQYYL TLSSVTTVDT ATYYCARWHY


 


101
GSPYYFDYWG QGTTLTVSS






No human epitopes were identified for sequence HC1a in IEDB database. HC1a germinality index=68% with IGHV4-31-03_IGHD6-25-01_IGHJ4-02.









HC1b (SEQ ID NO: 83):










  1
EMQLQESGPG LVKPSETLSL TCSVTGDSMT NGYWNWIRKF PGKGLEYMGY



 


 51
ITYSGSTYYN PSLKGRISIT RNTSKNQYYL KLSSVTTADT ATYYCARWHY


 


101
GSPYYFDYWG QGTTLTVSS






No human epitopes were identified for sequence HC1b in IEDB database. HC1b germinality index=73% with IGHV4-31-03_IGHD6-25-01_IGHJ4-02.









HC2a (SEQ ID NO: 84):










  1
EMTLKESGPT LVKPTQTLSL TCSVTG GYWNWIRKF PGKALEYMGY



 


 51
ITYSGSTYYN PSLKGRISIT  SKNQYYL TLSSVTTV T ATYYCARWHY


 


101
GSPYYFDYWG QGTILTVSS






No human epitopes were identified for sequence HC2a in IEDB database. HC2a germinality index=67% with IGHV4-31-03_IGHD6-25-01_IGHJ4-02.









HC2b (SEQ ID NO: 85):










  1
EMTLKESGPT LVKPTQTLSL TCSVTGDSMT  GYWNWIRKF PGKALEYMGY



 


 51
ITYSGSTYYN PSLKGRISIT RNTSKNQYYL TLSSVTTVDT ATYYCARWHY


 


101
GSPYYFDYWG QGTTLTVSS






No human epitopes were identified for sequence HC2b in IEDB database. HC2b germinality index=67% with IGHV4-31-03_IGHD6-25-01_IGHJ4-02.









HC3 (SEQ ID NO: 86):










  1
qMTLKESGPT LVKPTQTLSL TCSVsGDSMT NGYWNWIRqF PGKALEYMGY



 


 51
ITYSGSTYYN PSLKGRItIT RdTSKNQYYL TLSSVTTVDT ATYYCARWHY


 


101
GSPYYFDYWG QGTTLTVSS






No human epitopes were identified for sequence HC3 in IEDB database. HC3 germinality index=72% with IGHV4-31-03_IGHD6-25-01_IGHJ4-02.









HC4 (SEQ ID NO: 87):










  1
qMTLKESGPT LVKPTQTLSL TCSVsG GYWNWIRqF PGKALEYMGY



 


 51
ITYSGSTYYN PSLKGRItIT  SKNQYYL TLSSVTTV T ATYYCARWHY


 


101
GSPYYFDYWG QGTTLTVSS






No human epitopes were identified for sequence HC4 in IEDB database. HC4 germinality index=70% with IGHV4-31-03_IGHD6-25-01_IGHJ4-02.









HC5a (SEQ ID NO: 88):










  1
QVQLQESGPG LVKPSETLSL TCTVSGDSMT NGYWNWIRQP PGKGLEYMGY



 


 51
ITYSGSTYYN PSLKSRITIS RNTSKNQYSL KLSSVTAADT AVYYCARWHY


 


101
GSPYYFDYWG QGTLVTVSS






No human epitopes were identified for sequence HC5a in IEDB database HC5a germinality index=84% with IGHV4-59-02_IGHD6-13-01_IGHJ4-02 [VH4 4-59].









HC5b (SEQ ID NO: 89):










  1
QMQLQESGPG LVKPSETLSL TCTVSGDSMT NGYWNWIRQP PGKGLEYMGY



 


 51
ITYSGSTYYN PSLKSRITIS RDTSKNQYSL KLSSVTAADT AVYYCARWHY


 


101
GSPYYFDYWG QGTLVTVSS






No human epitopes were identified for sequence HC5b in IEDB database. HC5b germinality index=84% with IGHV4-59-02_IGHD6-13-01_IGHJ4-02 [VH4 4-59].









HC5c (SEQ ID NO: 90):










  1
QMQLQQSGPG LVKPSQTLSL TCAISGDSMT NGYWNWIRQS PSRGLEYMGY



 


 51
ITYSGSTYYA VSVKSRITIN RDTSKNQYSL QLSSVTPEDT AVYYCARWHY


 


101
GSPYYFDYWG QGTLVTVSS






No human epitopes were identified for sequence HC5c in IEDB database. HC5c germinality index=78% with IGHV6-1-02_IGHD6-13-01_IGHJ4-02 [VH6 6-01]. A schematic of all heavy chain mutations is shown in FIG. 16.

c) Combinations of Heavy and Light Chain Variant Sequences
For grafting, three versions for the light chain (LC5a, LC5b, LC5c) and three versions of the heavy chain (HC5a, HC5b, HC5c) were created. LC5a contains 16 mutations derived from grafting to the closest human germline sequence and retaining the murine CDR and most of the murine Vernier zone residues. Two murine Vernier residues, T46 and N69 are not present in any human germline sequence and were conservatively mutated. LC5b contains 14 mutations derived from grafting to the closest human germline sequence and retained the murine CDR and all the murine Vernier zone residues. LC5c contains 22 mutations derived from grafting to the second closest human germline sequence and retained the murine CDR and all the murine Vernier zone residues.
HC5a contains 20 mutations derived from grafting to the closest human germline sequence and retained the murine CDR and most of the murine Vernier zone residues with the exception of M2V. Met occurs with a very low propensity at this position in human germline sequences. HC5b contains 20 mutations derived from grafting to the closest human germline sequence and retained the murine CDR and all the murine Vernier zone residues. HC5c contains 23 mutations derived from grafting to the second closest human germline sequence and retained the murine CDR and all the murine Vernier zone residues.
Ten combinations were prepared in total (summarized in Table 19):


    
    
        LC1a×HC1a (mutations addressing 4D humanization based on the closest germline sequence)
        LC1b×HC1b (mutations addressing 4D humanization based on the 2nd closest germline sequence)
        LC2×HC2a (mutations addressing 4D humanization and unwanted sequences)
        LC2×HC2b (mutations addressing 4D humanization and unwanted sequences)
        LC1a×HC2b (mutations addressing 4D humanization and unwanted sequences)
        LC3×HC3 (mutations addressing 4D humanization and stabilization)
        LC4×HC4 (mutations addressing 4D humanizing, unwanted sequences and stabilization)
        LC5a×HC5a (mutations addressing humanization by grafting retaining CDRs and incorporating 3 conservative Vernier modifications)
        LC5b×HC5b (mutations addressing humanization by Grafting retaining CDRs and Vernier regions)
        LC5c×HC5c (mutations addressing humanization by grafting retaining CDRs and Vernier regions)
    
    









TABLE 19







Summary of the Ten LC × HC Combinations


















LC2
LC3
LC4






LC1a
LC1b
(H +
(H +
(H +
LC5a
LC5b
LC5c



(H)
(H)
UM)
S)
UM + S)
(G)
(G)
(G)



















HC1a
X(1)









(H)


HC1b

X(2)


(H)


HC2a


X(3)


(H + UM)


Low


HC2b
X(4)

X(5) 


(H + UM)


HC3


X(11)
X(6)
X (12)


(H + S)


HC4




X(7)


(H +




Low


UM + S)


HC5a





X(8)


(G)


HC5b


X(13)

 X(14)

X(9)


(G)


HC5c







X(10)


(G)







Low





H = humanizing;


UM = unwanted motifs;


S = stabilizing;


G = grafting


Low = low expression levels


Number within the ( ) indicates the variant number;


note:


variants 11-14 were added following characterization of the original ten variants (variants 1-10)













TABLE 21







Mutations of the eight LC variants of the anti-PAI1 A44 antibody















LC Sequential
LC1a
LC1b
LC2
LC3
LC4
LC5a
LC5b
LC5c


Numbering
(H)
(H)
(H − UM)
(H + S)
(H − UM + S)
(G)
(G)
(G)





Asp1







Glu


Lys3





Gln
Gln
Val


Ser9







Ala


Ser10







Thr


Met11
Leu
Val
Leu
Leu
Leu
Leu
Leu
Leu


Tyr12
Ser
Ser
Ser
Ser
Ser
Ser
Ser
Ser


Ala13

Val





Leu


Leu15
Val
Pro
Val
Val
Val
Val
Val
Pro


Glu17
Asp
Gln
Asp
Asp
Asp
Asp
Asp


Arg18

Thr


Val19







Ala


Ile21







Leu


Thr22







Ser


Lys42

Gln





Gln


Ser43





Ala
Ala
Ala


Lys45







Arg


Thr46





Leu


Asn52


Gln

Gln


Asp56


Glu

Glu


Val58







Ile


Ser60







Ala


Gln69





Thr


Ser72





Thr
Thr
Thr


Leu73





Phe
Phe


Glu79
Gln
Gln
Gln
Gln
Gln
Gln
Gln


Tyr80
Pro
Ala
Pro
Pro
Pro
Pro
Pro
Pro


Glu81

Met


Met83
Leu
Glu
Leu
Leu
Leu
Ile
Ile
Phe


Gly84



Ala
Ala
Ala
Ala
Ala


Ile85



Thr
Thr
Thr
Thr
Val


Leu104





Val
Val
Val


Glu105

Thr


Number of
7
12
9
9
11
16
14
22


mutations





H = humanizing;


UM = unwanted motifs;


S = stabilizing;


G = grafting













TABLE 22







Mutations of the nine HC variants of the anti-PAI1 A44 antibody
















HC Sequential
HC1a
HC1b
HC2a
HC2b
HC3
HC4
HC5a
HC5b
HC5c


Numbering
(H)
(H)
(H − UM)
(H − UM)
(H + S)
(H − UM + S)
(G)
(G)
(G)





Glu1




Gln
Gln
Gln
Gln
Gln


Met2






Val


Gln3
Thr

Thr
Thr
Thr
Thr


Glu5
Lys

Lys
Lys
Lys
Lys


Gln


Ser10
Thr
Gly
Thr
Thr
Thr
Thr
Gly
Gly
Gly


Ser15
Thr

Thr
Thr
Thr
Thr


Gln16

Glu




Glu
Glu


Ser23






Thr
Thr
Ala


Val24








Ile


Thr25




Ser
Ser
Ser
Ser
Ser


Asp27


Glu


Glu


Asn31


Gln
Gln

Gln


Lys39




Gln
Gln
Gln
Gln
Gln


Phe40






Pro
Pro
Ser


Gly42








Ser


Asn43
Lys
Lys
Lys
Lys
Lys
Lys
Lys
Lys
Arg


Lys44
Ala
Gly
Ala
Ala
Ala
Ala
Gly
Gly
Gly


Asn60








Ala


Pro61








Val


Leu63








Val


Gly65






Ser
Ser
Ser


Ser68




Thr
Thr
Thr
Thr
Thr


Thr70






Ser
Ser
Asn


Asn72


Gln

Asp
Gln

Asp
Asp


Tyr79






Ser
Ser
Ser


Gln81
Thr
Lys
Thr
Thr
Thr
Thr
Lys
Lys


Thr87






Ala
Ala
Pro


Glu88
Val
Ala
Val
Val
Val
Val
Ala
Ala


Asp89


Glu


Glu


Thr92






Val
Val
Val


Thr114






Leu
Leu
Leu


Leu115






Val
Val
Val


Number of
8
6
12
9
13
16
20
20
23


mutations





H = humanizing;


UM = unwanted motifs;


S = stabilizing;


G = grafting






In summary, ten variants were generated during the humanization process. These variants were expressed and characterized in several in vitro assays as described below.

7) Characterization of Humanization Variants
Based on the in silico modeling presented in the above example, ten variants were generated (variants 1-8 by 4D humanization and variants 9-10 by CDR grafting; variants 3 and 10 were created on the second closest germline). The variable region of the light chain and heavy chain DNA of humanized A44 were prepared for HEK293 expression. Proteins were generated after cloning the corresponding DNA into pXL plasmids (New England Biolabs; NheI/Eco47III for the HC, NheI/BsiWI for the LC). Humanized sequences were codon optimized for HEK expression and gene synthesized by GeneArt (subsidiary of Life Technologies). The resulting plasmids were co-transfected and transiently expressed in FreeStyleTM 293 Expression System (Invitrogen, Cat #K9000-01). Variants 3 and 10 were very poorly expressed and were not further pursued. All other variants were expressed and purified using Protein A columns. Analytical gels showed partial glycosylation (about 5-10%) of the light chains in variants 6 and 9 and heavy chains in variants 5 and 7 (data not shown). The remaining eight variants were tested in the chromogenic assay using hPAI and plasmin generation assay in human stellate cells using human glycosylated PAI. Results are shown in Table 23.







TABLE 23







Characterization of humanization variants in plasmin 


generation and chromogenic assay










Plasminogen Activation
Chromogenic Assay










mAb
IC50 (nM)
Y50%
IC50 (nM)





A44
3.17
45.99
0.44


A44-hv1
3.12
44.99
0.49


A44-hv2
Not determined
Not determined
0.60


A44-hv4
Inactive
26.00
0.52


A44-hv5
Not determined
Not determined
1.11


A44-hv6
1.78
56.94
0.82


A44-hv7
Not determined
Not determined
0.59


A44-hv8
Inactive
11.00
0.76


A44-hv9
1.9
46.53
0.86









Variants 6 and 9 showed the best potency in the plasmin generation assay but had partial (5-10%) glycosylation in the light chain. Based on these results, new variants 11-14 were produced using combinations of heavy chains from variants 6 and 9 and light chains from variants 5 and 7. Table 24 summarizes all the variants created.







TABLE 24







Humanization variants











Variant #
Description
SEQ ID NOs







A44-hv1
LC1a × HC1a
109



A44-hv2
LC1b × HC1b
110



A44-hv3
 LC2 × HC2a
111



A44-hv4
LC1a × HC2b
112



A44-hv5
 LC2 × HC2b
113



A44-hv6
 LC3 × HC3
114



A44-hv7
 LC4 × HC4
115



A44-hv8
LC5a × HC5a
116



A44-hv9
LC5b × HC5b
117



A44-hv10
LC5c × HC5c
118



A44-hv11
 LC2 × HC3
119



A44-hv12
 LC4 × HC3
120



A44-hv13
 LC2 × HC5b 
121



A44-hv14
 LC4 × HC5b
122

















TABLE 25







DNA Sequence Humanization variants










Gene
Protein





HC1a
GAGATGACCCTGAAAGAGTCCGGCCCCACCCTGG
EMTLKESGPTLVKPTQ



TCAAACCCACCCAGACCCTGAGCCTGACCTGCAG
TLSLTCSVTGDSMTNG



CGTGACCGGCGACAGCATGACCAACGGCTACTGG
YWNWIRKFPGKALEYM



AACTGGATCCGGAAGTTCCCCGGCAAGGCCCTCG
GYITYSGSTYYNPSLK



AGTACATGGGCTACATCACCTACAGCGGCAGCAC
GRISITRNTSKNQYYL



CTACTACAACCCCAGCCTGAAGGGCCGGATCAGC
TLSSVTTVDTATYYCA



ATCACCCGGAACACCAGCAAGAACCAGTACTACC
RWHYGSPYYFDYWGQG



TGACCCTGTCCAGCGTG
TTLTVSS



(SEQ ID NO: 123)
(SEQ ID NO: 82)


 


HC1b
GAGATGCAGCTGCAGGAAAGCGGCCCTGGCCTGG
EMQLQESGPGLVKPSE



TCAAACCCAGCGAGACACTGAGCCTGACCTGCAG
TLSLTCSVTGDSMTNG



CGTGACCGGCGACAGCATGACCAACGGCTACTGG
YWNWIRKFPGKGLEYM



AACTGGATCCGGAAGTTCCCCGGCAAGGGCCTCG
GYITYSGSTYYNPSLK



AGTACATGGGCTACATCACCTACAGCGGCAGCAC
GRISITRNTSKNQYYL



CTACTACAACCCCAGCCTGAAGGGCCGGATCAGC
KLSSVTTADTATYYCA



ATCACCCGGAACACCAGCAAGAACCAGTACTACC
RWHYGSPYYFDYWGQG



TGAAGCTGTCCAGCGTG
TTLTVSS



(SEQ ID NO: 124)
(SEQ ID NO: 83)


 


HC2a
GAGATGACCCTGAAAGAGTCCGGCCCCACCCTGG
EMTLKESGPTLVKPTQ



TCAAACCCACCCAGACCCTGAGCCTGACCTGCAG
TLSLTCSVTGESMTQG



CGTGACCGGCGAGAGCATGACCCAGGGCTACTGG
YWNWIRKFPGKALEYM



AACTGGATCCGGAAGTTCCCCGGCAAGGCCCTCG
GYITYSGSTYYNPSLK



AGTACATGGGCTACATCACCTACAGCGGCAGCAC
GRISITRQTSKNQYYL



CTACTACAACCCCAGCCTGAAGGGCCGGATCAGC
TLSSVTTVETATYYCA



ATCACCCGGCAGACCAGCAAGAACCAGTACTACC
RWHYGSPYYFDYWGQG



TGACCCTGTCCAGCGTG
TTLTVSS



(SEQ ID NO: 125)
(SEQ ID NO: 84)


 


HC2b
GAGATGACCCTGAAAGAGTCCGGCCCCACCCTGG
EMTLKESGPTLVKPTQ



TCAAACCCACCCAGACCCTGAGCCTGACCTGCAG
TLSLTCSVTGDSMTQG



CGTGACCGGCGACAGCATGACCCAGGGCTACTGG
YWNWIRKFPGKALEYM



AACTGGATCCGGAAGTTCCCCGGCAAGGCCCTCG
GYITYSGSTYYNPSLK



AGTACATGGGCTACATCACCTACAGCGGCAGCAC
GRISITRNTSKNQYYL



CTACTACAACCCCAGCCTGAAGGGCCGGATCAGC
TLSSVTTVDTATYYCA



ATCACCCGGAACACCAGCAAGAACCAGTACTACC
RWHYGSPYYFDYWGQG



TGACCCTGTCCAGCGTG
TTLTVSS



(SEQ ID NO: 126)
(SEQ ID NO: 85)


 


HC3
CAGATGACCCTGAAAGAGTCCGGCCCCACCCTGG
QMTEKESGPTEVKPTQ



TCAAACCCACCCAGACCCTGAGCCTGACCTGCAG
TESETCSVSGDSMTNG



CGTGTCCGGCGACAGCATGACCAACGGCTACTGG
YWNWIRQFPGKALEYM



AACTGGATCCGGCAGTTCCCCGGCAAGGCCCTCG
GYITYSGSTYYNPSLK



AGTACATGGGCTACATCACCTACAGCGGCAGCAC
GRITITRDTSKNQYYL



CTACTACAACCCCAOCCTGAAGGGCCGGATCACC
TLSSVTTVDTATYYCA



ATCACCCGGGACACCAGCAAGAACCAGTACTACC
RWHYGSPYYFDYWGQG



TGACCCTGAGCAGCGTG
TTLTVSS



(SEQ ID NO: 127)
(SEQ ID NO: 86)


 


HC4
CAGATGACCCTGAAAGAGTCCGGCCCCACCCTGG
QMTLKESGPTLVKPTQ



TCAAACCCACCCAGACCCTGAGCCTGACCTGCAG
TLSLTCSVSGESMTQG



CGTGTCCGGCGAGAGCATGACCCAGGGCTACTGG
YWNWIRQFPGKALEYM



AACTGGATCCGGCAGITCCCCGGCAAGGCCCTCG
GYITYSGSTYYNPSLK



AGTACATGGGCTACATCACCTACAGCGGCAGCAC
GRITITRQTSKNQYYL



CTACTACAACCCCAGCCTGAAGGGCCGGATCACC
TLSSVTTVETATYYCA



ATCACCCGGCAGACCAGCAAGAACCAGTACTACC
RWHYGSPYYFDYWGQG



TGACCCTGAGCAGCGTG
TTLTVSS



(SEQ ID NO: 128)
(SEQ ID NO: 87)


 


HC5a
CAGGTGCAGCTGCAGGAAAGCGGCCCTGGCCTGG
QVQLQESGPGLVKPSE



TCAAACCCAGCGAGACACTGAGCCTGACCTGCAC
TLSLTCTVSGDSMTNG



CGTGTCCGGCGACAGCATGACCAACGGCTACTGG
YWNWIRQPPGKGLEYM



AACTGGATCCGGCAGCCCCCTGGCAAGGGCCTCG
GYITYSGSTYYNPSLK



AGTACATGGGCTACATCACCTACAGCGGCAGCAC
SRITISRNTSKNQYSL



CTACTACAACCCCAGCCTGAAGTCCCGGATCACC
KLSSVTAADTAVYYCA



ATCAGCCGGAACACCAGCAAGAACCAGTACAGCC
RWHYGSPYYFDYWGQG



TGAAGCTGAGCAGCGTG
TLVTVSS



(SEQ ID NO: 129)
(SEQ ID NO: 88)


 


HC5b
CAGATGCAGCTGCAGGAAAGCGGCCCTGGCCTGG
QMQLQESGPGINKPSE



TCAAACCCAGCGAGACACTGAGCCTGACCTGCAC
TLSLTCTVSGDSMTNG



CGTGTCCGGCGACAGCATGACCAACGGCTACTGG
YWNWIRQPPGKGLEYM



AACTGGATCCGGCAGCCCCCTGGCAAGGGCCTCG
GYITYSGSTYYNPSLK



AGTACATGGGCTACATCACCTACAGCGGCAGCAC
SRITISPDTSKNQYSL



CTACTACAACCCCAGCCTGAAGTCCCGGATCACC
KLSSVTAADTAVYYCA



ATCAGCCGGGACACCAGCAAGAACCAGTACAGCC
RWHYGSPYYFDYWGQG



TGAAGCTGAGCAGCGTG
TLVTVSS



(SEQ ID NO: 130)
(SEQ ID NO: 89)


 


HC5c
CAGATOCAGCTGCAGCAGAGCGGCCCTGGCCTGG
QMQLQQSGPGLVKPSQ



TCAAACCCAGCCAGACCCTGAGCCTGACCTGCGC
TLSLTCAISGDSMTNG



CATCAGCGGCGACAGCATGACCAACGGCTACTGG
YWNWIRQSPSRGLEYM



AACTGGATCCGGCACAGCCCCAGCAGAGGCCTCG
GYITYSGSTYYAVSVK



AGTACATGGGCTACATCACCTACAGCGGCAGCAC
SRITINRDTSKNQYSL



CTACTACGCCGTGTCCGTGAAGTCCCGGATCACC
QLSSVTPEDTAVYYCA



ATCAACCGGGACACCAGCAAGAACCAGTACAGCC
RWHYGSPYYFDYWGQG



TGCAGCTGAGCAGCGTG
TLVTVSS



(SEQ ID NO: 131)
(SEQ ID NO: 90)


 


LC1a
GACATCAAGATGACCCAGAGCCCCAGCAGCCTGA
DIKMTQSPSSLSASVG



GCGCCAGCGTGGGCGACAGAGTGACCATCACATG
DRVTITCKASQDINSY



CAAGGCCAGCCAGGACATCAACAGCTACCTGAGC
LSWLQQKPGKSPKTLI



TGGCTGCAGCAGAAGCCCGGCAAGAGCCCCAAGA
YRANRSVDGVPSRFSG



CCCTGATCTACCGGGCCAACCGCAGCGTGGACGG
SGSGQDYSLTISSLQP



CGTGCCAAGCAGATTTTCCGGCAGCGGCAGCGGC
EDLGIYYCLQYDEFPP



CAGGACTACAGCCTGACCATCAGCAGCCTGCAGC
TFGGGTKLEIK



CCGAGGACCTGGGCATC
(SEQ ID NO: 91)



(SEQ ID NO: 132)



 


LC1b
GACATCAAGATGACCCAGAGCCCCAGCAGCGTGT
DIKMTQSPSSVSVSPG



CCGTGTCTCCTGGCCAGACCGTGACCATCACATG
QTVTITCKASQDINSY



CAAGGCCAGCCAGGACATCAACAGCTACCTGAGC
LSWLQQKPGQSPKTLI



TGGCTGCAGCAGAAGCCCGGCCAGTCCCCCAAGA
YRANRSVDGVPSRFSG



CCCTGATCTACCGGGCCAACCGCAGCGTGGACGG
SGSGQDYSLTISSLQA



CGTGCCAAGCAGATTTTCCGGCAGCGGCAGCGGC
MDEGIYYCLQYDEFPP



CAGGACTACAGCCTGACCATCAGCAGCCTGCAGG
TFGGGTKLTIK



CCATGGACGAGGGCATC
(SEQ ID NO: 92)



(SEQ ID NO: 133)



 


LC2
GACATCAAGATGACCCAGAGCCCCAGCAGCCTGA
DIKMTQSPSSLSASVG



GCGCCAGCGTGGGCGACAGAGTGACCATCACATG
DRVTITCKASQDINSY



CAAGGCCAGCCAGGACATCAACAGCTACCTGAGC
LSWLQQKPGKSPKTLI



TGGCTGCAGCAGAAGCCCGGCAAGAGCCCCAAGA
YRAQRSVEGVPSRFSG



CCCTGATCTACCGGGCCCAGCGGAGCGTGGAAGG
SGSGQDYSLTISSLQP



CGTGCCAAGCAGATTCAGCGGCAGCGGCTCCGGC
EDLGIYYCLQYDEFPP



CAGGACTACAGCCTGACCATCAGCAGCGGCAGCC
TFGGGTKLEIK



CGAGGACCTGGGCATC
(SEQ ID NO: 93)



(SEQ ID NO: 134)



 


LC3
GACATCAAGATGACCCAGAGCCCCAGCAGCCTGA
DIKMTQSPSSLSASVG



GCGCCAGCGTGGGCGACAGAGTGACCATCACATG
DRVTITCKASQDINSY



CAAGGCCAGCCAGGACATCAACAGCTACCTGAGC
LSWLQQKPGKSPKTLI



TGGCTGCAGCAGAAGCCCGGCAAGAGCCCCAAGA
YRANRSVDGVPSRFSG



CCCTGATCTACCGGGCCAACCGCAGCGTGGACGG
SGSGQDYSLTISSLQP



CGTGCCAAGCAGATTTTCEGGCAGCGGCAGCGGC
EDLATYYCLQYDEFPP



CAGGACTACAGCCTGACCATCAGCAGCGGCAGCC
TFGGGTKLEIK



CGAGGACCTGGCCACC
(SEQ ID NO: 94)



(SEQ ID NO: 135)



 


LC4
GACATCAAGATGACCCAGAGCCCCAGCAGCCTGA
DIKMTQSPSSLSASVG



GCGCCAGCGTGGGCGACAGAGTGACCATCACATG
DRVTITCKASQDINSY



CAAGGCCAGCCAGGACATCAACAGCTACCTGAGC
LSWLQQKPGKSPKTLI



TGGCTGCAGCAGAAGCCCGGCAAGAGCCCCAAGA
YRAQRSVEGVPSRFSG



CCCTGATCTACCGGGCCCAGCGGAGCGTGGAAGG
SGSGQDYSLTISSLQP



CGTGCCAAGCAGATTCAGCGGCAGCGGCTCCGGC
EDLATYYCLQYDEFPP



CAGGACTACAGCCTGACCATCAGCAGCGGCAGCC
TFGGGTKLEIK



CGAGGACCTGGCCACC
(SEQ ID NO: 95)



(SEQ ID NO: 136)



 


LC5a
GACATCCAGATGACCCAGAGCCCCAGCAGCCTGA
DIQMTQSPSSLSASVG



GCGCCAGCGTGGGCGACAGAGTGACCATCACATG
DRVTITCKASQDINSY



CAAGGCCAGCCAGGACATCAACAGCTACCTGAGC
LSWLQQKPGKAPKLLI



TGGCTGCAGCAGAAGCCCGGCAAGGCCCCCAAGC
YRANRSVDGVPSRFSG



TGCTGATCTACCGGGCCAACCGCAGCGTGGACGG
SGSGTDYTFTISSLQP



CGTGCCAAGCAGATTTTCCGGCAGCGGCTCCGGC
EDIATYYCLQYDEFPP



ACCGACTACACCTTCACCATCAGCAGCCTGCAGC
TFGGGTKVEIK



CCGAGGATATCGCCACC
(SEQ ID NO: 96)



(SEQ ID NO: 137)



 


LC5b
GACATCCAGATGACCCAGAGCCCCAGCAGCCTGA
DIQMTQSPSSLSASVG



GCGCCAGCGTGGGCGACAGAGTGACCATCACATG
DRVTITCKASQDINSY



CAAGGCCAGCCAGGACATCAACAGCTACCTGAGC
LSWLQQKPCGKAPKTL



TGGCTGCAGCAGAAGCCCGGCAAGGCCCCCAAGA
IYRANRSVDGVPSRFS



CCCTGATCTACCGGGCCAACCGCAGCGTGGACGG
GSGSGQDYTFTISSLQ



CGTGCCAAGCAGATTTTCCGGCAGCGGCAGCGGC
PEDIATYYCLQYDEFP



CAGGACTACACCTTCACCATCAGCAGCCTGCAGC
PTFGGGTKVEIK



CCGAGGATATCGCCACC
(SEQ ID NO: 97)



(SEQ ID NO: 138)



 


LC5c
GAGATCGTGATGACCCAGAGCCCCGCCACCCTGT
EIVMTQSPATLSPGER



CTCTGAGCCCTGGCGAGAGAGCCACCCTGAGCTG
ATLSCKASQDINSYLS



CAAGGCCAGCCAGGACATCAACAGCTACCTGAGC
WLQQKPGQAPRTLIYR



TGGCTGCAGCAGNAGCCCGGCCAGGCCCCCAGAA
ANRSVDGIPARFSGSG



CCCTGATCTACCGGGCCAACAGAAGCGTGGACGG
SGQDYTLTISSLEPED



CATCCCCGCCAGATTCAGCGGCAGCGGCTCCGGC
FAVYYCLQYDEFPPTE



CAGGACTACACCCTGACCATCAGCAGCCTGGAAC
GGGTKVEIK



CCGAGGACTTCGCCGTG
(SEQ ID NO: 98)



(SEQ ID NO: 139)



 







Protein








CH
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA



VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCP



PCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGV



EVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTIS



KAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGF (SEQ ID NO: 99)


 


CL
RTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQES



VTEQDSKDSTYSLSSTLTLSKADYEKHKVYACETHQGLSSPVTKSFNRGEC



(SEQ ID NO: 100)









All variants, except poorly expressed variants 3 and 10, were tested in Biacore against human and cyno PAI-1 and Vitronectin-PAI-1 complex. The data is presented in Table 26.













Vitronectin Chip/Human PAI-1










mAb/hPAI-1/Vn
ka1 (1/Ms)
kd 1 (1/s)
KD (M)





A44 parental*
5.68E+06
2.29E−04
4.04E−11


A44-hv1*
1.10E+07
5.55E−04
5.26E−11


A44-hv2**
2.99E+06
4.03E−04
1.35E−10


A44-hv4*
4.59E+06
8.80E−05
1.92E−11


A44-hv5*
2.72E+06
2.76E−05
1.02E−11


A44-hv6*
4.38E+06
5.68E−05
1.33E−11


A44-hv7**
4.14E+06
3.94E−04
9.64E−11


A44-hv8*
n/a
n/a
n/a


A44-hv9*
6.36E+06
1.03E−04
1.70E−11


A44-hv11*
7.66E+06
1.22E−04
1.56E−11


A44-hv12*
5.15E+06
8.14E−05
1.61E−11


A44-hv13**
2.40E+06
4.36E−04
1.79E−10


A44-hv14*
4.06E+06
3.95E−05
9.57E−12










Vitronectin Chip/Cyno PAI-1










mAb/cPAI-1/Vn
ka1 (1/Ms)
kd 1 (1/s)
KD (M)





A44 parental*
3.98E+06
2.75E−04
6.96E−11


A44-hv1**
3.37E+06
8.27E−03
2.45E−09


A44-hv2**
2.30E+06
3.14E−04
1.37E−10


A44-hv4**
2.26E+05
1.70E−04
7.52E−10


A44-hv5*
3.40E+06
1.11E−04
3.26E−11


A44-hy6*
5.26E+06
2.51E−05
5.01E−12


A44-hv7**
2.50E+06
2.39E−04
9.56E−11


A44-hv8*
n/a
n/a
n/a


A44-hv9*
6.51E+06
1.34E−04
2.15E−11


A44-hv11**
1.56E+06
6.00E−04
3.87E−10


A44-hv12*
4.26E+06
2.35E−04
5.69E−11


A44-hv13**
2.12E+06
2.43E−04
1.15E−10


A44-hv14*
5.86E+06
2.13E−04
3.86E−11










Anti-human IgG Fc chip/human PAI-1










mAb/hPAI-1*
ka1 (1/Ms)
kd 1 (1/s)
KD (M)





A44-hv11/hPAI-1
1.57E+06
6.68E−05
4.25E−11


A44-hv12/hPAI-1
1.62E+06
6.70E−05
4.14E−11


A44-hv13/hPAI-1
1.54E+06
2.52E−05
1.64E−11


A44-hv14/hPAI-1
1.25E+06
3.42E−05
2.70E−11










Anti-human IgG Fc chip/cyno PAI-1










mAb/cPAI-1*
ka1 (1/Ms)
kd 1 (1/s)
KD (M)





A44-hv11/hPAI-1
1.87E+06
5.60E−05
3.00E−11


A44-hv12/hPAI-1
2.24E+06
5.45E−05
2.44E−11


A44-hv13/hPAI-1
1.89E+06
5.08E−05
2.70E−11


A44-hv14/hPAI-1
2.32E+06
2.69E−05
1.15E−11





n/a means the variant did not bind effectively to vitronectin/PAI-1 complex


*1:1 molecular interaction model


**Two state reaction (conformation change) model






Biacore data did not reveal significant differences between humanized variants. All humanized variants, except variant 8, showed affinity to both cyno PAI-1 and human PAI-1 and PAI-1 complexed to vitronectin within an acceptable range. In comparison to parental A44, humanization did not appear to change antibody affinity.
Although affinity and potency of the humanized variants didn't differ significantly in the chromogenic and Biacore assays, the ability of the variants to restore plasmin generation in the cellular assays was significantly lower than parental mouse antibody for some variants (see Table 27 summarizing comparison of chromogenic assay and cellular assay below). Humanized variants 11-14 were tested for the ability to block PAI-1 in the cellular assay.







TABLE 27







Characterization of humanization variants 11-14 in plasmin generation









Plasminogen Activation










mAb
IC50 (nM)
Y50%
n





A44
3.13
79.79
6


A44-hv11
2.01
85.82
6


A44-hv12
1.99
76.70
6


A44-hv13
1.82
71.10
6


A44-hv14
1.82
61.22
6


A44-hv9
1.51
50.92 
4


A44-hv1
2.08
58.50
2









Variants 11 through 14 showed good potency in the plasmin generation assay and were further characterized in additional in vitro assays.
8) Characterization of Humanization Variants in Human Liver
Additional screening of the humanized variants 11-14 was performed using endogenously produced human PAI-1 from human plasma and human fibrotic liver samples.
PAI-1 activity was evaluated by measuring the ability of this serpin to form a stable complex with urokinase immobilized on 96 well plates. After washing unbound PAI-1, uPA-PAI-1 complexes were detected by the use of polyclonal antiPAI-1 antibodies. The bound polyclonal anti-PAI-1 antibodies (which is proportional to active PAI-1 in the sample) was then detected by using a horseradish peroxidase conjugated secondary antibody (Molecular Innovation Cat. No. HPAIKT). Various concentrations of A44 humanized variants were incubated for 15 minutes at room temperature with either human or cynomolgus recombinant PAI-1 (0.31 nM final concentration) and then tested for functional active PAI-1 by uPA-PAI-1 complex using the ELISA described above. Samples were compared to a human PAI-1 standard. Human plasma from high BMI patients with high active PAI-1 levels were diluted 4-fold and were incubated with increasing amounts of A44 humanized variants. Remaining active PAI-1 levels were determined using uPA-PAI-1 complex detection by ELISA. Cyno recombinant PAI-1 neutralization was also tested by plasmin generation to confirm cross-reactivity.







TABLE 28







Humanized variant ability to block endogenous PAI-1 activity









hPAI-1 Standard
hPlasma TH1782
Cyno PAI-1
















IC50(nM)
Y50%
n
mAb
IC50(nM)
Y50%
N
IC50(nM)
Y50%
n





1.31E−01
50.80
2
A44-hv11
1.57E−02
37.50
2
4.24E−02
50.80
2


1.14E−01
53.45
2
A44-hv12
3.35E−03
37.68
2
2.66E−02
53.45
2


1.66E−01
52.82
2
A44-hv13
3.11E−02
61.35
2
2.81E−02
52.82
2


5.63E−02
52.47
2
A44- hv14
5.86E−02
73.90
2
2.87E−02
52.47
2









Human fibrotic liver samples (provided by Biopredic International, Rennes, France from surgical resection of hepatic colon metastasis) were homogenized as follows: weighed frozen liver samples were homogenized in dry tubes containing ceramic beads (Cat No 03961-1-003, Bertin Technology, France) using Precellys homogeniser (Bertin Technology, France; 4° C., 2×30seconds at 6800 rpm) and then dissolved using 1 ml/g of lysis buffer (NaCl 1.5M in TBS—Tris Buffer Solution 0.1M Tris+0.15M NaCl pH17.4). After centrifugation at 4° C. at 5000 g for 10 min, the liver lysate in the supernatant was harvested and stored frozen at −80° C. Total protein concentration using standard BCA assay and active & total PAI-1 levels (determined by UK-PAI complex ELISA provided by Mol Innov Cat No HPAIKT & Cat No MPAIKT-TOT) were performed following manufacturer instructions by plotting standard human PAI-1 concentration vs A450 nm using Biostat Calibration software. Increasing, concentrations of A44 humanized variants incubated with liver lysate diluted to 2.5 nM of active PAI-1 were evaluated as described previously and data analyzed. Inhibition of PAI-1 activity (PAI-1 activity without mAb being 0% inhibition, no significant and dose-dependent inhibition of PAI-1 occurred with IgG1) was calculated for each mAb concentration. Percent inhibition of PAI-1 activity was plotted as a function of mAb concentration and IC50 was determined Imax using Biostat speed software. Data is shown in FIG. 17 and in Table 29.







TABLE 29







PAI-1 activity neutralization by A44-hv11 in human liver










IC50 (nM)
Imax (%)












A44-hv11 (1 nM)
0.0365
99.997


A44-hv11 (2 nM)
0.0503
99.99


A44-hv11 (3 nM)
0.0465
99.99


Mean +/− sem
0.0444 +/− 0.004
99.99









Based on the above data, A44-hv11 was selected for further characterization in additional structural studies and additional in vitro and in vivo studies.

Example 13
Humanization of APG Antibody by Grafting
Humanization using grafting techniques has previously been reported (P. T. Jones, et al., Nature 1986, 321:522-525). The humanization of the anti-PAI1 murine antibody APG began with the murine light chain (SEQ ID NO: 148) and murine heavy chain (SEQ ID NO: 149) from German Patent App. No. DE2000153251; this murine antibody is also described in Debrock et al., Biochimica et Biophysica Acta, 1337(2):257-266 (1997). Identifying the germline and canonical classes of the HC and LC chain of the murine antibody yielded muIGHV1-39 and muIGKV1.4-111, respectively. Next the list of close human germlines to anti-PAI1 APG variable domain light and heavy chains were identified and ranked by percent identity. Both steps were done by performing a BLAST search vs. all the human germlines which were systematically enumerated (all possible combinations of the V & J domains for the kappa and lambda chains; V, D and J domains for the heavy chains). The BLAST searches were performed using the IMGT/DomainGapAlign tool provided at http://www.imgt.org. (See Ehrenmann, et al. Cold Spring Harbor Protocols 2011.6 (2011)). The closest human germlines were identified with 67.4% and 63.3% sequence identity to anti-PAI1 APG variable domain light and heavy chains, respectively. Using the IMGT database, the light chain was found to be close to HuIGKV1-33 and the heavy chain was close to HuIGHV1-46. The closest human germline to the anti-PAI1 APG variable domain heavy chain with a matching canonical class was found to be HuIGHV7-4-1 with a sequence identity of 62.2%.
CDR regions (based on a combination of Kabat and IMGT for APG) and Vernier residues are indicated in italics for the parent murine APG (mAPG) light chain (SEQ ID NO: 148), IGKV1-33-01_IGKJ4-01 (IGKV1a) (SEQ ID NO: 107) and for IGKV1-33-01_IGKJ2-02 (IGKV1b) (SEQ ID NO: 150) (see Table 30, below). Vernier residues as defined in Foote, et al. J. Mol. Biol. 224(2):487-99 (1992) are underlined. The humanizing mutations (in boldface) were obtained by performing a pairwise comparison of the two aligned sequences, excluding the CDR & Vernier zone residues (also underlined in mAPG sequences, Table 30) as defined above. No further engineering was performed on the murine APG antibody. These humanized antibodies were named APGv2 and APGv4.







TABLE 30





APG humanization sequences
















APG
DIKLTQSPSS MYASLGERVT ITCKASQDIY


Light Chain
SYLSWFQQKP GKSPKTLIYR ANRLIDGVPS



RFSGSGSGQD YSLTISSLEY EHMGIYYCLQ



YDEFPFTFGS GTKLEIK



(SEQ ID NO: 148)


 


APG
QVKLQESGPE LVKPGASVKI SCKASGYSFT


Heavy Chain
DYNMNWVKQS KGKSLEWIGI IHPNSGTTTY



NQKFKGKATL TVDQSSSTAY LQLNSLTSED



SAVYYCARSK LRFFDYWGQG TTVTVSS



(SEQ ID NO: 149)


 


IGKV1-33-
DIQMTQSPSS LSASVGDRVT ITCQASQDIS


01_IGKJ4-01
NYLNWYQQKP GKAPKLLIYD ASNLETGVPS


(IGKV1a)
RFSGSGSGTD FTFTISSLQP EDIATYYCQQ



YDNLPLTFGG GTKVEIK



(SEQ ID NO: 107)


 


IGKV1-33-
DIQMTQSPSS LSASVGDRVT ITCQASQDIS


01_IGKJ2-02
NYLNWYQQKP GKAPKLLIYD ASNLETGVPS


(IGKV1b)
RFSGSGSGTD FTFTISSLQP EDIATYYCQQ 



YDNLPCSFGQ GTKLEIK



(SEQ ID NO: 150)


 


IGHV7-4-
QVQLVQSGSELKKPGASVKVSCKASGYTFTSY


1-02_
AMNWVRQAPGQGLEWMQWINTNTGNPTYAQGF


IGHJ4-03
TGRFVFSLDTSVSTAYLQISSLKAEDTAVYYC



ARxxxxxYFDYWGQGTLVTVSS



(SEQ ID NO: 151)


 


IGHV1-46-
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSY


01_IGHJ4-
YMHWVRQAPGQGLEWMGIINPSGGSTSYAQKF


03
QGRVTMTRDTSTSTVYMELSSLRSEDTAVYYC



ARxxxxxYFDYWGQGTLVTVSS



(SEQ ID NO: 152)


 


APGv2_VL2
DIQLTQSPSS LSASVGDRVT ITCKASQDIY



SYLSWFQQKP GKAPKTLIYR ANRLIDGVPS



RFSGSGSGQD YTFTISSLQP EDIATYYCLQ



YDEFPFTFGQ GTKLEIK



(SEQ ID NO: 153)


 


APGv2_VH2
QVQLVQSGSE LKKPGASVKV SCKASGYSFT



DYNMNWVRQA PGQGLEWIGI IHPNSGTTTY



NQKFKGRAVL SVDQSVSTAY LQISSLKAED



TAVYYCARSK LRFFDYWGQG TLVTVSS



(SEQ ID NO: 154)


 


APGv4_VH4
QVQLVQSGAE VKKPGASVKV SCKASGYSFT



DYNMNWVRQA PGQGLEWIGI IHPNSGTTTY



NQKFKGRATL TVDQSTSTAY MELSSLRSED



TAVYYCARSK LRFFDYWGQG TLVTVSS



(SEQ ID NO: 155)









Engineered Sequences

4D humanization and grafting approaches were applied to the human germline sequence matches described above. For the engineered light chain sequences, APGv2 contains the murine light chain CDRs grafted into the human IGKV1-33 germline (APGv2 germinality index=94% with IGKV1-33-01_IGKJ2-01). For the engineered heavy chain sequences, APGv2 and APGv4 contain the murine heavy chain CDRs grafted into the human IGHV7-4-1 and IGHV1-46 germlines respectively (APG_VH2 germinality index=91% with IGHV7-4-1-02_IGHD6-25-01_IGHJ4-02; APG_VH4 germinality index=91% with IGHV1-46-01_IGHD6-25-01_IGHJ4-02). See Table 30 above.
Combinations of Heavy and Light Chain Variant Sequences
For grafting, one version of the light chain (APGv2_VL2; SEQ ID NO: 153) and two versions of the heavy chain (APGv2_VH2; SEQ ID NO: 154 and APGv4_VH4: SEQ ID NO: 155) were created. APG_VL2 contains 15 mutations derived from grafting to the closest human germline sequence and retaining the murine CDR and Vernier zone residues. APG_VH2 contains 21 mutations derived from grafting to the closest human germline sequence with a matching canonical class and retaining the murine CDR and Vernier zone residues. APG_VH4 contains 20 mutations derived from grafting to the closest human germline sequence and retaining the murine CDR and Vernier zone residues. The delimitations of the CDRs for this grafting protocol are loosely based on the various different definitions available in the literature.

    
    
        APG_VL2×APG_VH2 (mutations addressing humanization by grafting retaining CDRs and Vernier regions)
        APG_VL2×APG_VH4 (mutations addressing humanization by grafting retaining CDRs and Vernier regions)

Two mAPG variants were generated during this humanization campaign, which were named APGv2 and APGv4. These variants were expressed and characterized in several in vitro assays as described below.

    
    


Example 14
Affinity Kinetics for APG Antibodies by Surface Plasmon Resonance
Affinity to human glycosylated PAI-1 (GLYHPAI-A, Molecular Innovation) was investigated by Surface Plasmon Resonance (SPR) for mouse APG and the two humanized variants (APGv2 & APGv4) using a Biacore 2000 instrument (GE Healthcare, Uppsala, Sweden).
First, the surface of a Sensor Chip CM5 (GE Healthcare, Uppsala, Sweden) was prepared using routine amine coupling for the capture of the mouse and human anti-Fc (Anti-human IgG (Fc) antibody & Anti-mouse IgG antibody kits, GE Healthcare). All monoclonal antibodies (mAbs) were diluted to 5 nM using HBS-EP running buffer. Each purified mAb was captured for three minutes on a different flow cell surface. Human PAI-1 was injected at various concentrations (2.5, 5, 10, 20 and 40 nM) with short dissociation times in between and a long dissociation time at the end (contact time: 120 seconds, short dissociation: 90 seconds; long dissociation: 1800 seconds, flow rate: 50 μl/min). The chip was regenerated by glycine-HCl, pH 1.7 buffer after each round of antibody-PAI-1 binding. Kinetics data analysis was performed using Biacore BIAevaluation software. The sensorgrams were double-referenced by subtracting the reference flow cell values and the blank buffer values. The sensorgrams were fitted by using the simulated kinetics 1:1 (Langmuir) model with local Rmax. (see FIG. 19). The data for the three APG antibodies are shown in Table 31.







TABLE 31







Binding Kinetics by Biacore Reverse Assay











human PAI-1












Dissociation Rate



Antibody
ka (Ms−1s−1)
kd (1/s)
Affinity KD (M)





APG
3.82E+06
4.32E−04
1.131E−10


APGv2
6.58E+06
2.69E−04
4.080E−11


APGv4
9.48E+06
3.59E−04
3.800E−11









Example 15
Characterization of APG Antibodies in Human Plasma
The mouse APG and the humanized variants APGv2 and APGv4 were screened for their ability to block PAI-1 according to the functional assays disclosed herein (see, e.g., Examples 6 and 9, above). Briefly, PAI-1 activity was evaluated by the ability of this serpin to form stable complex with urokinase immobilized on 96 well plates. After washing unbound PAI-1, uPA-PAI-1 complexes were detected by the use of polyclonal antiPAI-1 antibodies. The bound polyclonal anti-PAI-1 antibodies (which is proportional to active PAI-1 in the sample) was then detected using a horseradish peroxidase conjugated secondary antibody according to manufacturer instructions (Molecular Innovation, Cat #HPAIKT).
Various concentrations of APG humanized variants (APGv2, APGv4) or parental mouse APG antibodies were incubated for 15 min at room temperature with undiluted human plasma having a high active PAI-1 level. Remaining active PAI-1 level was determined using uPA-PAI-1 complex detection by ELISA as described above (see, e.g., Example 6) and according to the manufacturer instruction.
Inhibition of PAI-1 activity was calculated for each mAb concentration. Percent inhibition of PAI-1 activity was plotted as a function of concentration of APG humanized variants (APGv2, APGv4) or parental mouse APG antibody. Biostat speed software was used to determine IC50 and Imax after three independent experiments (in duplicate) (see FIG. 20). Data is presented below in Table 32.







TABLE 32







Plasminogen Generation in Human Plasma









Antibody
IC50abs mean ± sem (nM)
Imax mean (%)





mAPG
1.81
89.7


APGv2
9.62E−1
94.5


APGv4
1.28
94.4









Example 16
Clot Lysis Assay in Plasma: A44V11, mAPG, and APG Variant Activity
The fibrinolytic system is often altered in patients with stroke. A clot lysis assay can be used to determine fibrinolytic activity by measuring the degree of fibrin breakdown. See generally Lindgren, A. et al. Stroke 27:1066-1071 (1996). Clot lysis assays have been described in detail elsewhere. See, e.g., Beebe, et al. Thromb. Res. 47:123-8 (1987): Tilley et al., J. Vis. Exp. 67:e3822.
The functional activity of A44V11 and other PAI-1 neutralizing antibodies was determined using a human plasma clot lysis assay. Briefly, the assay applied here induces clot formation using a mixture of Tissue Factor/Ca2+ in the presence of tPA and a concentration of PAI-1 known to inhibit clot lysis. Fibrin polymerization induces an increase of turbidimetry that was detected by absorbance measurement at 340 nm. The ability of the antibody to restore clot lysis was determined by incubating increasing doses of antibody with normal human platelet poor plasma.
Briefly, clot lysis experiments were performed in microliter plates. Citrated human plasma (Biopredic International, Rennes, France) was incubated with anti-PAI-1 antibody or isotype controle IgG diluted in assay buffer (NaCl, Tris-HCl pH 7.4). After 15 min incubation at room temperature, human glycosylated PAI-1 (GLYHPAI-A, Molecular Innovation) was added to a final concentration of 3 nM and incubated for an additional 10 min. t-PA (sctPA, Molecular innovation) was then added to a final concentration of 1 nM. Clot formation was induced by an activation mix comprising Tissue Factor (Innovin®, Siemens Healthcare Diagnostics, Marburg, Germany) diluted to a final concentration of 7.5 mM in calcium assay buffer (CaCl2).
Kinetic reading of absorbance at 340 nm was performed every 30 sec for 5 hours with an iEMS microplate reader (ThermoFischer) or a SpectrostarNano (BMG Labtech). To quantify the effect on clot lysis, the area under curve (AUC) which reflects the balance between clot formation and clot lysis was calculated using GraphPad Prism Software. The restoration of clot lysis after antibody treatment was determined according to the following calculation:




  Restoration
  =
  
    100
    ×
    
      
        
          AU
          
            max
            ⁢
            
              
            
            ⁢
            lysis
          
        
        -
        
          AUC
          treated
        
      
      
        
          AUC
          
            no
            ⁢
            
              
            
            ⁢
            lysis
          
        
        -
        
          AUC
          
            max
            ⁢
            
              
            
            ⁢
            lysis
          
        
      
    
  




IC50 and Imax were calculated using Biostat speed software.

The 1 nM concentration of t-PA yielded complete lysis of normal plasma within 2 hours. The 3 nM-concentration of PAI-1 inhibited t-PA-induced clot lysis. Addition of either t-PA or PAI-1 alone did not affect clot formation. Addition of neither t-PA or PAI-1 did not affect clot formation.
The A44V11 anti-PAI-1 antibody restored human platelet poor plasma clot lysis (see FIG. 21), while the isotype IgG1 did not (see FIG. 22). A44V11 exhibited an IC50 or 2 nM with an Imax of 103% at 100 nM (see FIG. 23).
The humanized variants of APG anti-PAI-1 antibody also restored human platelet poor plasma clot lysis (see FIG. 24). APGv2 exhibited an IC50 of 2.1 nM and an Imax of 114% at 100 nM. APG v4 exhibited an IC50 of 2.8 nM and an Imax of 116% at 100 nM (see FIG. 25). The clot lysis data is summarized below in Table 33.







TABLE 33







Inhibition of clot lysis by anti-PAI-1 antibodies









Antibody
IC50 (nM)
Imax @ 100 nM





A44V11
1.38
113%


APG V2
2.08
114%


APG V4
2.82
116%


mAPG
2.34
123%









Example 17
Assessment of A44V11 Neutralization of PAI-1 in Primary Human Lung Cells
The effect of antibody A44V11 on neutralization of PAI-1 was investigated in a lung cell-based system. TGFβ is considered to be the most potent and ubiquitous profibrogenic cytokine. TGFβ has been shown to induce PAI-1 expression and inhibit the activities of t-PA and plasmin as well as collagen degradation in cultured murine embryo fibroblasts (NIH3T3 cells). See Liu, R-M. Antioxid Redox Signal. 10(2): 303-319 (2008). Primary lung fibroblasts strains LL29 (CCL-134) and LL97A (CCL-191) from ATCC (Manassas, Va.) were plated overnight in a 12-well plate at a concentration of 200,000 cells per well. Cells were incubated for 48 hours with A44V11 antibody or isotype control (IgG) and TGFβ (R&D Systems, Minneapolis, Minn., cat. #100-B-001) at a concentration of 5 ng/ml. After 48 hours, cell supernatants were harvested and analyzed by Western Blot for detection of PAI-1 forms with a rabbit pAb anti PAI-1 (abeam, ab66705).
Cells treated with A44V11 antibody after TGFβ stimulation display PAI-1 band as a doublet, which corresponds to the cleaved form of PAI-1 (see FIG. 26, lane 5). Cells treated with control IgG do not show this doublet formation (see FIG. 26, lane 6). This study demonstrates that treatment of primary human lung cells with A44V11 induces endogenous PAI-1 substrate conformation, which allows PAI-1 to be cleaved by protease.
Example 18
A44V11 Increases Activation of MMPs
Plasmin can activate MMPs, enzymes that can degrade most ECM proteins, including collagen, the major proteinaceous component of fibrotic tissue. In this regard, plasmin is often cited as a general activator of MMPs. (See Loskutoff, et al. J. Clin. Invest. 106(12):1441-43 (2000)). PAI-1 decreases MMP activation and matrix degradation by blocking plasmin generation, followed by inhibition of fibroblast apoptosis. The ability of A44V11 to stimulate activation of MMPs was investigated in a lung cell-based system. Primary lung fibroblasts LL29 (CCL-134) and LL97A (CCL-191) from ATCC (Manassas, Va.) were plated overnight in a 12-well plate at a concentration of 250,000 cells per well. Cells were incubated for 48 hours with A44V11 or isotype control (IgG) and Lays-Plasminogen (Molecular Innovation, cat. #HGPG-712) at a concentration of 0.1 μM. After 48 hours, cell supernatants were harvested and the activities of a variety of MMPs (including, for example, MMP-1, 2, 3, 7, 8, 9, 12, 13, and 14) were detected using a Sensolyte 520 Generic MMP Assay kit (AnaSpec, Fremont, Calif., cat. #71158) according to the manufacturer's instructions.
As shown in FIG. 27, A44V11 stimulates the activation of plasmin-dependent MMPs in human lung fibroblasts. The chart shows two representative separate experiments. Cells treated with A44V11 and plasminogen showed substantially increased activation when compared to cells treated with an negative IgG1 antibody. This study demonstrates that A44V11 stimulates MMPs activation in a plasmin-mediated phenomenon.
Example 19
Analysis of A44V11 Potency in Lung Fibrosis Mouse Model (Bleomycin Challenge)
Experimental lung fibrosis induced by bleomycin is a well-studied model of fibrogenesis supported by ample literature. This model of pulmonary fibrosis resembles that seen in humans and has been used to assess the effects of potential therapeutic agents as well as basic research. (see, e.g., Molina-Molina et al. Thorax 61:604-610 (2006)).
Pharmacodynamics Study in Bleomycin Treated Mice (Fibrosis Model)
Transgenic mice that express human PAI-1 (humanized PAI-1 transgenic mice) were generated by replacing the mouse PAI-1 (SERPINE1) gene CDS (exons and introns) (NCBI Ref. No. NM_008871) with the corresponding human wild type PAI-1 gene CDS (NCBI Ref. No. NM_000602.3; NC_000007.13) (see Klinger, K. W. et al. Proc. Natl. Acad. Set. USA 84:8548 (1987)) under the control of the endogenous mouse PAI-1 gene regulatory sequences in C57BL/6×129 mice (The Jackson Laboratory, Bar Harbor, Me.). Molecular cloning and generation of transgenic mice are performed according to conventional techniques and according to manufacturer and breeder instructions. Expression of human PAI-1 and non-expression of mouse PAI-1 was confirmed in homozygous mice. Both mRNA and protein levels were confirmed by standard qPCP and by ELISA, respectively. Female homozygous humanized PAI-1 transgenic mice aged 8-9 weeks and weighing 22-25 g were used for these procedures. Rodent food and water were provided ad libitum.
Mice received 50 μl of Bleomycin® (Sanofi, France) dissolved in 0.9% NaCl by intra-tracheal injection via microspayer at a dose of 2 mg/kg. Control mice received 50 μl of 0.9% NaCl. For these procedures, mice were anesthetized with isoflurane (TEM, Lormont, France) by inhalation and then intubated with a 18 G cannula. The cannula was connected to a ventilator fed with an oxygen/isoflurane mixture to maintain the anaesthesia. Following anesthetization, the microsprayer was introduced in the cannula for bleomycin injection directly into the lungs. Mice were then extubated and allowed to recover from anaesthesia. At day 4, after randomization in 3 groups, mice were treated once by intra-peritoneal administration of either A44v11 or negative control mouse IgG1 at 10 mg/kg in PBS (1 mg/ml).
At designated time points (day 7 or day 9) after bleomycin challenge, mice were anesthetized with a xylazine/ketamine mix and euthanized by chest opening. A blood collection was performed by intra-cardiac harvest on a citrate coated tube. Left bronchia was clamped and the left lung was removed and fixed with a fixator (FineFix®, Leica Biosystems, Buffalo Grove, Ill.) under controlled pressure for histological analysis A cannula was then placed into the trachea for the broncho-alveolar lavage (BAL) procedure (1.5 ml of 0.9% NaCl injected and harvest in three injections of 0.5 ml). The four lobes of the right lung were then harvested, cut in two pieces and lysed for protein analysis. All experiments were performed in accordance with European ethical lows and approved by internal ethical comity (CEPAL, sanofi).
A44V11 levels were determined using ELISA (Molecular Innovation, cat. #HPAIKT) with coated biotinylated human PAI-1 plates and detected using secondary anti mouse IgG sulfo-tag labeled (MesoScale Discovery, Gaithersburg, Md.). For Day 7 mice treated with A44V11, the result was 200 nM in plasma, 11 nM in BALF and 12 nM in lung lysate.
As shown in FIG. 28, administration of a single intra-peritoneal dose (10 mg/kg) of A44V11 at day 4 achieves nearly full inhibition of human active PAI-1 both in BAL fluid and in lung lysate in animals sacrificed at day 7 after bleomycin challenge. For day 9 animals, A44V11 (10 mg/kg) achieves nearly full inhibition of human active PAI-1 in lung lysates, but achieves only partial inhibition in BALF.
D-dimers, a fibrin degradation product, can be measured to assess the degree of fibrin breakdown. To measure fibrin degradation, the levels of D-dimer in BALF were detected by ELISA (Asserachrom D-Di, Diagnostica Stago, Asnieres, France) according to manufacturer instructions. D-dimer levels in the BALF of the A44V11-treated group were increased approximately 2.8-fold at day 7 and 1.6-fold at day 9 when compared to the IgG1 negative control group, suggesting A44V11 treatment increases fibrin degradation (see FIG. 29).
Additional studies were performed to further assess A44V11 activity in reducing fibrosis in mouse lung challenged with bleomycin. For these studies, mice were subjected to a similar protocol to the pharmacodynamy study described above, except that the study duration length was 21 days from bleomycin challenge, and treatment with antibody (either A44V 11 or IgG1 control antibody at 10 mg/kg) was repeated every 3 days starting at day 4 until day 20. At day 21 after bleomycin challenge, the animals were sacrificed as described above.
Increase in lung weight is known to be an indicator of increased fibrosis. The right lung weight, as a measure of fibrosis, was determined for mice in all experimental groups. As shown in FIG. 30, bleomycin instillation induces an increase in right lung weight that was partially inhibited by repeated dosing of A44V11 antibody at 10 mg/kg. Repeated dosing using the IgG1 negative control antibody did not inhibit the increase in right lung weight due to bleomycin challenge. The reduction in bleomycin-induced right lung weight increase in A44V11-treated mice was statistically significant when compared to similar bleomycin-induced mice that were treated with IgG1 negative control antibody (p<0.001). Statistical analysis was performed by one-way ANOVA followed by Newman-Keuls test. This result indicates that A44V11 inhibits bleomycin-induced fibrosis in the humanized PAI-1 mouse lung, whereas a control IgG1 antibody does not.
Collagen accumulation in the lung is another known indicator of fibrosis. To assay collagen accumulation, lung tissues from mice sacrificed at day 21 were prepared and separated by HPLC, followed by the measurement of hydroxyproline. This technique is detailed elsewhere, for example in Hattori, et al. J. Clin Invest. 106(11):1341-1350 (2000). In brief, lung tissue was prepared by hydrolysis under acidic condition (6M HCl) for 22 hours at 105° C., followed by evaporation. Primary amines were blocked in the lung tissue by OPA (phthalaldehyde), and proline/hydroxyprolines were specifically labeled using NBD (4-chloro-7-nitrobenzofurazan) (Santa Cruz Biotech., Santa Cruz, Calif.). Hydrolysates were then separated on SynergiTM 4 μm Hydro-RP 80 Å, LC Column 150×3 mm columns (Phenomenex, Torrance, Calif., cat. #00F-4375-Y0) using HPLC (Shimazu Corp., Kyoto, Japan) under acetonitrile gradient. Standard curves of known amounts of hydroxyproline were used as reference to quantify peak(s). A representation of the quantified data are shown in FIG. 31.
Lung collagen accumulation as detected by hydroxyproline content was increased in bleomycin challenged animals. This increase in lung collagen accumulation was statistically reduced (p<0.08) by repeated dosing of A44V11 antibody at 10 mg/kg. (see FIG. 31). Repeated dosing using the IgG1 negative control antibody did not inhibit the increase in lung collagen accumulation due to bleomycin challenge. The reduction in bleomycin-induced collagen accumulation increase in A44V11-treated mice was statistically significant when compared to similar bleomycin-induced mice that were treated with IgG1 negative control antibody (p<0.05). A44V11-treated mice showed approximately 44% less of an increase in collagen accumulation than IgG1 control-treated mice.
Example 20
Assessment of A44V11 Activity in LPS Challenge Model in Monkeys
An acute lipopolysaccharide (LPS) challenge model in monkeys was applied to determine the PAI-1 neutralization efficacy of A44V11 in vivo. The LPS challenge model is described in Hattori, et al. J Clin Invest. 106(11):1341-1350 (2000). The activity of A44V11 mAb on PAI-1 in monkey plasma and liver samples was evaluated. Specifically, the experiment was designed to assess the impact of a high dose of LPS (100 μg/kg—IV) on plasma and tissue levels of PAI-1 in the anesthetized monkey pre-treated (24 hours before) either with A44V 11 (5 mg/kg, IP) or IgG1 (negative control, 5 mg/kg, intra peritoneal administration). Experiments were performed in accordance with European ethical lows and approved by internal ethical comity (CEPAL, sanofi).
Cynomolgus Macaca fascicularis (male and female) weighing 4 to 9 kg were food-deprived overnight before long-term anesthesia (at least 8 hours), including IM induction with Zoletil 50 (Virbac, Taguig City, Philippines) at 0.12 to 0.16 mL/kg followed by inhalation of a gaseous mix of air/oxygen and isoflurane (1 to 3%). Monkey body temperature was maintained within physiological ranges using a heating pad. After catheterization, LPS (Serotype 0127-B8) was administered as a 1 min bolus in the cephalic accessory vein at a dose of 100 μg/kg (0.4 mL/kg). At various time points, blood samples and liver samples were taken. Blood samples (on citrate/EDTA) were harvested and centrifuged to isolate platelet poor plasma. Liver biopsies and terminal necropsy were stored at −80° C.
Active PAI-1, D-dimer and plasmin-α2 antiplasmin levels were determined using commercially available ELISA assays (Mol. Innovation, cat. #HPAIKT; Asserachrom D-Dimer; Plasmin-A2 antiplasmin, Diagnostica Stago) according to manufacturer instructions.
In plasma, active PAI-1 level decreases from about 30 ng/ml to below 10 ng/ml in all monkeys administered with A44v11. (See FIG. 32(A)). There was no increase in active PAI-1 levels after LPS administration (100 ug/kg). (See FIG. 32(A). In contrast, monkeys treated with negative IgG1 control show a strong increase in active PAI-1 levels following LPS administration, with a maximum occurring at about 4 hr (approximately 50 to about 250 ng/ml). (See FIG. 32(B)). Thus, treatment with negative IgG1 control does not reduce the active PAI-1 levels in plasma that were strongly increased after LPS administration. (See FIG. 32(B)).
In liver biopsy lysates, a similar phenomenon was observed. Monkeys that were treated with A44V11 mAb did not show an increase in active PAI-1 levels following LPS treatment. (See FIG. 33(A)). In contrast, LPS administration induced a strong increase of active PAI-1 (up to 3 ng/mg) in liver biopsy lysates from negative IgG1 control-treated monkeys (see FIG. 33(B)).
Simultaneously to PAI-1 neutralization, the D-dimer levels in A44V11-treated monkeys (see FIG. 34(A)) was found to generally he higher than negative IgG control-treated monkeys (see FIG. 34(B)) thus suggesting that A44V11 treatment in monkeys also induces an increase of fibrin degradation in plasma.
Finally, plasma samples of A44V11-treated monkeys showed an increased level of plasmin-α2 antiplasmin (PAP) complexes when compared to the PAP levels in negative IgG control-treated monkeys. (see FIGS. 35(A) and (B)). The increase in PAP complex and D-dimer in the presence of A44V11 indicates increases in plasmin generation.
Example 21
Assessment of A44V11 Activity in Abdominal Adhesion Mouse Model
The effect of treatment with anti-PAI-1 antibody A44V11 on the formation of adhesions was evaluated in a mouse uterine horn model of surgical injury. The mouse uterine horn approximation and electrocautery procedure disrupts the serosal surface, causes thermal damage to the uterine tissue, and approximates damaged tissue surfaces during the healing process that ultimately results in post-surgical adhesions in 100% of untreated animals. The model and surgical procedure has been previously described in Haney A. F. et al., (1993). Fertility and Sterility, 60(3): 550-558.
For these adhesion studies, the transgenic female mice generated above that express humanized PAI-1 transgene, approximately 9 weeks old, weighing approximately 20 g, were used. Forty-two mature transgenic female mice were divided into two groups and subjected to the surgical procedure designed to create adhesions between the uterine horns (UH), as described in detail in Haney A. F. et al., (1993). Briefly, each animal was anesthetized with isoflurane for the surgery according to IACUC guidelines, and a routine midline laparotomy was performed approximately 1.0 cm caudal to the xyphoid process. The UH were identified, approximated medially with a single 7-0 Prolene suture (Ethicon Inc., Somerville, N.J.) carefully placed through the muscle wall of each horn, and the horns tied together immediately below the junction of the oviducts at the uterotubal junction. Care was taken not to damage the ovarian vascular supply. To induce electrocautery injury, a bipolar electro cautery unit was used (Valley Lab Surgistat, Solid state Electrosurgery Unit, Model No. B-20) on the medial surfaces of each uterine horn, covering an area of approximately 2×6 mm. The cautery unit was set as follows: Volts 100, 130 Hz, 50-60 Amps. A 3 mm wide cautery tip was used with pure coagulating current at a setting of 3, power was initiated, and the tissue touched for 1 second at two burn spots per horn. The muscle incision was closed with 5-0 Vicryl, BV-1 taper needle (Ethicon Inc.) in a continuous suture pattern. Skin was closed with 5-0 Prolene, BV-1 Taper needle (Ethicon Inc.), in a horizontal mattress suture pattern.
Following the creation of the UH injury, Group 1 animals were treated with a volume of 0.16 mL of an Isotype Control antibody (30 mg/kg), which was applied to the cautery burns. Group 2 animals were treated with a volume of 0.16 mL of A44V11 antibody (30 mg/kg) in the same manner. For each group, animals were euthanized at 6 hours (n=5), 72 hours (n=4), or at Day 7 (n=12). (See Table 34 below). Animals that were scheduled for euthanasia at 72 hours and Day 7 had second dose of antibody (30 mg/kg) injected intraperitoneally (IP) 48 hours after surgery.
















Time point
# of
Dosing (30


Group
Treatment
Euthanized
Animals
mg/kg)



















Group 1
Isotype Control mAb
 6 hours
5
Time 0



(0.16 mL)
72 hours
4
Time 0 + 48






hours




Day 7
12
Time 0 + 48






hours


Group 2
Anti-PAI-1 A44
 6 hours
5
Time 0



humanized mAb
72 hours
4
Time 0 + 48



(0.16 mL)


hours




Day 7
12
Time 0 + 48






hours









Efficacy Evaluation of Analysis:

Animals were euthanized at the indicated time points and the formation of adhesions was evaluated. Briefly, the length of the horns was measured from the uterine bifurcation to the approximation suture placed just below the oviducts. The two external sutures surrounding the uterine horns were removed and the length of adhesion between uterine horns was measured with the aid of a microscope, documented, and noted as present or absent (Yes/No). Also, any tissues involved in the adhesion formation will be recorded but may not be included in the length of adhesed area. The distribution of the average percent of adhesed length between uterine horns was checked for normality using the Shapiro-Wilk Test. The groups were compared with each other using Tukey Kramer analysis if normally distributed and Wilcoxon Rank-Sum analysis if not normally distributed. In all cases, a p-value≦0.05 was considered statistically significant. Animals treated with A44 V11 showed significantly lower percent of length of adhesion formation between approximated uterine horns (see Table 35)







TABLE 35







Uterine Horn length measurement results.













% of Length with Adhesions





between the Uterine Horns



Group
N
(Mean ± SEM)







Isotype Control mAb
12
84 ± 3



(0.16 mL)





A44V11 mAb
11
61 ± 7*



(0.16 mL)

(p = 0.02)







*p = statistically significant relative to the Isotype Control by Wilcoxon Rank Sum Analysis, Chi Square Approximation






Detection of Active PAI-1 and tPA Levels

Following euthanasia, animals had blood (plasma), intraperitoneal fluid (IPF), and uterine horn samples collected for evaluation. Collection of samples were performed using conventional techniques. Plasma, IPF, and uterine horn samples were evaluated for active PAI-1 and tPA levels using ELISA. (Human PAI-1 Activity ELISA kits, Cat. #HPAIKT, Molecular Innovations, Novi, Mich.). Data was processed using Excel, JMP, and Prism Graph pad software. In all cases, a p-value≦0.05 was considered statistically significant. At 6 hour and Day 7 time point, decreased levels of active PAI-1 were found in the IP Fluid and Uterine Horn Lysates in the animals treated with A44V11 versus Isotype Control. (See FIG. 36). The decreased levels of active PAI-1 in the IPF at 6 hours was statistically significant result shown in IP Fluid at 6 hour time point in animals treated with A44 versus to Isotype Control (p<0.001 by Student T-test).
Example 22
Crystal Structure of Humanized Antibody A44V11
Expression and Purification of Fab A44V11
Recombinant Fab (rFab) was obtained from transiently transfected HEK293 cells, using two plasmids encoding the light chain or the C-terminal His-tagged heavy chain. After centrifugation and filtering, rFab from the cell supernatant was applied to an immobilized-metal affinity resin. After elution from the resin, the rFab was extensively dialyzed against PBS & stored at 4° C.
Source of Macaca fascicularis PAI-1, Referred as Cynomolgous or Cyno PAI-1:
Recombinant mature cynomolgous PAI-1 (24-402) was expressed as inclusion bodies in E. coli and the recombinant protein was purified using conventional methods.
Source of Human PAI-1:
Recombinant mature human PAI-1 (24-402) was purchased from Molecular Innovations Inc. (catalogue number CPAI). It was a stabilized in active conformation by introducing mutations (N150H, K154T, Q319L, M354I), as described by Berkenpas et al. (1995, EMBO J., 14, 2969-2977).
Preparation & Purification of the Complexes:
Recombinant Fab & antigen were mixed at a 1.5:1 molar ratio, incubated 30 min at room temperature, and the complexes were further purified by preparative size exclusion on a Superdex 200 PG column (GE Healthcare), equilibrated with 25 mM MES pH 6.5, 150 mM NaCl.
Crystallization of the Fab A44V11+Cyno PAI-1 Complex
The complex was concentrated to 10 mg/ml in 25 mM MES pH 6.5, 150 mM NaCl. It crystallizes in 16-24% ethanol, 100 nM Tris pH 8.5. Ethylene glycol (30%) was used as cryoprotectant. Crystals diffracted to about 3.3 Å in space group P321 (a=b=193 Å, c=144 Å) on ID29 beamline of ESRF. Data was processed with a combination of XDS and Scala (GlobalPhasing Ltd., Cambridge, UK)
Structure Determination of the Complex Fab A44V11/Cyno-PAI-1:
A model of the Fab variable domain was constructed using Prime in Maestro (Schrodinger, New York, N.Y.). The constant domain was obtained from published structure 3FO2. Two different models of human PAI-1 were used: the latent conformation was obtained from 1LJ5, the active conformation from 1OC0. Calculation of Matthews Coefficient (VM, crystal volume per unit of protein molecular weight) suggests that there are up to four complexes in the asymmetric unit (VM 2. 2 assuming a complex size of 90 kilodaltons (KD). Molecular Replacement was done using Phaser (CCP4 suite) (McCoy, et al. J. Appl. Cryst. 40: 658-674 (2007), which identified two monomers of latent PAI-1 and two variable domains of Fab. Additional density was clearly visible for the constant domains, which had to be placed manually. This solution, which corresponds to a VM of 4.3 (71% solvent), was also carefully examined for packing consistency. The structure was refined with Buster (GlobalPhasing) using non crystallographic symmetry, to an Rfree of 29.2% (Rfactor 25.8%). The constant domains are not stabilized by crystal packing and are poorly resolved in the electron density map.
Crystallization of the Fab A44V11+Human PAI-1 Complex
Protein crystallization is a bottleneck of biomolecular structure determination by x-ray crystallography methods. Success in protein crystallization is directly proportional to the quality of the protein molecules used in the crystallization experiments, where the most important quality criteria are purity and homogeneity (both molecular and conformational) of the proteins in solution.
Initially, to determine the PAI-1/Fab mAb complex structure a native mAb A44 was used to prepare its Fab fragment by papain digestion. This Fab scaled up preparation resulted heterogeneous Fab fragments which were complexed and purified in complex with human wild type (wt) PAI-1 protein. The obtained protein complex was concentrated to 7 mg/ml concentration and screened for crystallization under 800 individual crystallization conditions at two different temperatures, 4° C. and 19° C. No crystallization hits were detected. In order to improve the protein complex homogeneity recombinant 6-His tagged Fab A44 was produced, purified and complexed with the human wild type PAI-1 protein (see FIG. 36).
The complex crystallization screening resulted first crystallization hits under 20% PEG10K+0.1M Sodium Acetate pH4.6 conditions. Crystallization optimization by conventional crystallization methods, Microseed Matrix Seeding, and in situ Trypsinolysis crystallization did not significantly improve the quality of crystals. The best obtained crystals were needle-like and were diffracting x-rays with insufficient resolution for structure determination (10 Å).
The failure with the complex crystals crystallization could potentially be explained by the complex conformational heterogeneity. The wild type PAI-1 molecule is known to adopt three distinct conformations (active, latent, and substrate) which may interfere with crystallization. To improve the quality of the crystals, 6-His tagged A44 Fab in complex with latent PAI-1 was produced. (see FIG. 37).
The corresponding complex was produced and screened for crystallization de novo and under conditions previously used for 6-His tagged Fab A44/wt PAI-1 protein complex. The only crystallization hit out of the more than 1000 conditions tested was identified for the complex under 20% PEG3350+0.2M nH4 Acetate+4% MPD+50 mM Mes pH6 conditions (see FIG. 39(a)). After extensive optimization 3D crystals were obtained. X-Ray diffraction tests using synchrotron high intensity X-Ray beam showed no diffraction sign (see FIG. 39(b), depicting representative optimized crystals).
To reduce the flexibility of portions of the protein it was decided to produce A44 Fab fragment recombinantly but without an artificial tag such as the 6-His tag used previously. To further increase the chances for successful crystallization, an active form mutant of PAI-1 (N150H, K154T, Q319L, M354I) was purchased from Molecular Innovations (Cat. #CPAI, Novi, Mich.) and used for complex preparation with Fab A44 protein lacking artificial tag. The complex was concentrated to 12 mg/ml in 25 mM MES pH 6.5, 150 mM NaCl. Acceptable rod-like single crystals were obtained in 10% PEG3350, 100 mM ammonium sulfate and cryoprotected by the addition of 30% ethylene glycol (see FIG. 40). These crystals diffracted to 3.7 Å resolution, and after extensive cryoprotection optimization, resulted in an x-ray diffraction data set suitable for the structure determination (3.3 Å). A dataset was collected to 3.3 Å at beamline Proxima 1 of synchrotron SOLEIL (Saint-Aubin, France). Spacegroup is P212121 (a=105, b=152 c=298). Data was processed using XDSme scripts (XDS ref, Xdsme ref).
Structure Determination of the Complex Fab A44V11/Human-PAI-1:
Pointless (CCP4) indicated only a 40% confidence in spacegroup identification. In consequence, initial Molecular Replacement was carried out with Amore (CCP4) to test all possible space group variants of the P222 point group: P212121 was unambiguously confirmed. Final Molecular Replacement with Phaser (Phaser, CCP4) identified four dimers of active PAI-1/variable domain of Fab in the asymmetric unit. The constant domains were added manually in the electron density map. The structure was refined with Buster (GlobalPhasing) using non crystallographic symmetry, to a Rfree of 28% (Rfactor 24.1%).
Epitope and Paratope Structural Analysis
Epitope and paratope regions were identified as formed in the cyno and human complexes, and the complexes were compared. The crystal structures were determined to 3.3 Å for A44V11 in complex with human and cyno PAI-1. The superimposition of both structures (see FIG. 40) shows that the paratope of A44V11 is similar for both latent and active forms of PAI-1. Fab A44 recognized the active form of human PAI-1 and the latent form of cyno PAI-1. FIG. 42 depicts the PAI-1 epitope recognized by Fab A44 in both active human PAI-1 (FIG. 42(A)), and latent cyno PAI-1 (FIG. 42(B)). The paratope-recognizing the latent conformation is part of the paratope recognizing the active conformation.
PAI-1 interacts mostly with the heavy chain of A44V11, as can be seen from the analysis of the surface areas of interaction. Surface area of the interaction between active human PAI-1 and the heavy chain (average of 4 complexes) is 674 Å2. Surface area of the interaction between active human PAI-1 and the light chain (average of 4 complexes) is 372 Å2. Surface area of the interaction between latent cyno PAI-1 and the heavy chain (average of 2 complexes) is 703 Å2. Surface area of the interaction between latent cyno PAI-1 and the light chain (average of 2 complexes) is 360 Å2. See FIGS. 43 and 44 for depictions of the paratopes of the heavy chain and light chain, respectively.
The residues of the A44V11 part of the paratope are shown below in Table 36. Residues in italic are involved in the interactions with active PAI-1 but not the latent form, while residues underlined are interacting only with the latent form. All other residues are involved in both interfaces.







TABLE 36







A44V11 residues involved in paratope with PAI-1








Location
Residues










Heavy Chain (FIG. 43)








Loop H1
Thr30, Asn31, Gly32, Tyr33 and Asn35


Loop H2 and neighboring 
Tyr47, Tyr50, Thr52, Tyr53, Ser54, Gly55, 


β-strands
Ser56, Thr57 and Tyr58


Loop H3
Trp98, Tyr100 and Tyr104







Light Chain (FIG. 44)








Loop L1:
Asn30 and Tyr32


Loop L2:
Arg50 and Arg53


Loop L3:
Tyr91, Asp92, Glu93, Phe94 and Pro96









Despite the different conformations of the human and cyno PAI-1 molecules, the same residues are involved in interactions with the Fab A44 (bolded residues shown below in the sequence of human PAI-1) (SEQ ID NO:1):









VHHPPSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAML



 



QLTTGGETQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEIS



 



TTDAIFVQRDLKLVQGFMPHFFRLFRSTVKQVDFSEVERARFIIND



 



WVKTHTKGMISHLLGTGAVDQLTRLVLVNALYFNGQWKTPFPDSST



 



HRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHG



 



DTLSMFIAAPYEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLP



 



KFSLETEVDLRKPLENLGMTDMFRQFQADFTSLSDQEPLHVALALQ



 



KVKIEVNESGTVASSSTAVIVSARMAPEEIIIDRPFLFVVRHNPTG



 



TVLFMGQVMEP






Short-hand for the A44V11 binding epitope for human PAI-1 is as follows:










(SEQ ID NO: 156)



E-X-X-Q;



 



(SEQ ID NO: 157)



L-X-R;



 



(SEQ ID NO: 158)



T-D-X-X-R-Q-F-Q-A-D-F-T-X-X-S-D-Q-E-P-L






In summary, the cyno and human epitopes of PAI-1 recognizing FabA44 are identical in both conformations, Fab A44 recognizes both human and cyno PAI-1 but likely not mouse or rat PAI-1.
Example 23
Determination of A44V11 Specificity and Cross-reactivity
To determine the specificity and reactivity of A44V11, the sequence of the A44V11 epitope (see above) was used to search for similar epitopes in other proteins using a motif search with ScanProsite (SIB Swiss Institute of Bioinformatics) database. For additional details see Artimo, P. et al. Nucleic Acids Res. 40(W1): W597-603 (2012). All of the epitope sequence matches located in the search were related to PAI-1, suggesting that the A44V11 antibody is specific for PAI-1.
The A44V11 epitope was also compared to other known x-ray structures (3D search) using in silico profiling and molecular modeling according to Med-SuMo, which detects and compares the biochemical functions on proteins surfaces, including for example hydrogen bonds, charges, hydrophobic and aromatic groups. Med-SuMo molecular modeling is further described in Jambon, et al. Bioinformatics 21(20):3929-30 (2005). The 3D search of the A44V11 epitope located a similar motif in human alpha-1-antitrypsin (AAT1). However, upon further investigation, the AAT1 motif was found to have significant differences between the A44V11 epitope, such that A44V11 is unlikely to bind. Therefore, sequence pattern and 3D pattern analysis of the A44V11 epitope suggests that there should be minimal cross-reactivity with other human proteins.
The human and cyno PAI-1 epitopes for A44V11 were compared to proposed epitopes from mouse and rat PAI-1. Sequences are excerpted from SEQ ID NO:1 (PAI-1 human), SEQ ID NO:162 (PAI-1 cyno), SEQ ID NO:163 (PAI-1 mouse), and SEQ ID NO:164 (PAI-1 rat). Rat and mouse PAI-1 have respectively 75% and 79% sequence identity with human PAI-1. Alignment of the different PAI-1 sequences show significant differences between rat/mouse and human/cyno sequence in their respective epitopes, suggesting that A44V11 is unlikely to recognize rat or mouse PAI-1 (See FIG. 45). For example, mouse PAI-1 amino acids Ser300, Thr302, Gln314 are different from the human/cyno PAI-1 counterparts. The differences in these residues represent a change in proposed epitopes, such that mouse PAI-1 cannot he recognized by A44V11. The structural comparison of the mouse PAI-1 with the structure of the complex human PAI-1/A44V11 (FIG. 46) further indicates that it should not he possible to obtain both human and mouse activity from the A44V11 antibody.
To further validate the identified epitope for A44V11, the human and cyno A44V11 epitopes were compared to binding regions of vibronectin. The structure of human PAI1 in complex with the somatomedin B domain of vibronectin has been published (1OC0). The structures of these two complexes were compared (see FIG. 47). The structural comparison suggests that the binding of A44V11 will not impact PAI-1 interaction with vibronectin.
The A44V11 epitope was compared to the epitopes of other published anti-PAI1 antibodies. No overlap of the A44V11 epitopes was found with other published anti-PAI-1 antibodies MA-55F4C2 and MA-33H1, which bind residues in the 128-156 region (see Debrock et al. Thromb Haemost, 79:597-601 (1998)).
Finally, the specificity and lack of cross-reactivity of the A44V11 antibody was confirmed by Biacore. Based on the predicted unique sequence and 3D structure of the A44V11 epitope, molecular modeling studies indicate strongly that the A44V11 is specific for human and cyno PAI-1.
Example 24
Epitope Mapping by Hydrogen/Deuterium Exchange Mass Spectrometry (HDX MS)
Hydrogen/deuterium exchange (HDX) monitored by mass spectrometry (MS) was applied to the PAI-1-binding antibodies disclosed herein to further characterize the epitopes of each antibody. HDX MS is a particularly useful technique for comparing multiple states of the same protein. Detailed methodology and applications of HDX MS to protein therapeutics are disclosed in Wei, et al., Drug Discovery Today, 19(1): 95-102 (2014). Briefly, if an aqueous, all-H2O solvent is replaced with an isotope of hydrogen that has distinctive spectroscopic properties, then one can follow this exchange process. For most modern HDX experiments, deuterated or “heavy” water (D2O) is used. In particular, the hydrogen bonded to the backbone nitrogen (also referred to as the backbone amide hydrogen) is useful for probing protein conformation. See, e.g., Marcsisin, et al. Anal Bioanal Chem. 397(3): 967-972 (2010). The exposed and dynamic regions of proteins will exchange quickly, while protected and rigid regions of proteins will exchange slower. All of the relevant conditions (pH, temperature, ionic strength, etc.) are kept constant, so only the difference in structure (solvent accessibility, hydrogen bonding) impacts this exchange. The interaction of the antibody with PAI-1 will block the labeling of certain portions of the antigen, thus producing a different readout based on the site of binding (epitope).
Experimental Method:
Stock solutions of cyno-PAI-1 (10 uM), cyno-PAI-1 bound to A44V11 (10 μm each) and cyno-PAI-1 bound to APGv2 (10 μm each) were prepared in PBS, pH 7.2. The protein solutions were allowed to reach binding equilibrium by incubating for 1 hour at room temperature. Based on a Kd value of <50 pM, each of the antibody:antigen complexes were >99% bound under the labeling conditions described below.
Deuterium exchange, quenching, and sample injection were handled by an automated robotics system (LEAP Tech., Carrboro, N.C.). An aliquot of the protein solution was diluted 10-fold with labeling buffer (PBS in 99.9% D2O, pD 7.2) and allowed to incubate at 20° C. for 10 sec, 1 min, 5 min, or 4 hours. At the end of the deuterium exchange time point, the labeling reaction was quenched by adding 50 μL of the labeling solution to an equal volume of pre-chilled (0° C.) 100 mM sodium phosphate, 4 M guanidine hydrochloride, 0.5 M TCEP, pH 2.5. Undeuterated controls were prepared in an identical fashion by diluting, 10-fold with PBS in H2O.
Each quenched sample (50 μL, 50 pmol of each protein) was immediately injected into a Waters nanoAcquity with HDX Technology (Waters Corp., Milford, Mass.). The proteins were digested online with a 2.1 mm×30 mm Enzymate BEH pepsin column (Waters Corp.) which was held at 20° C. All of the chromatographic elements were held at 0.0±0.1° C. inside the cooling chamber of the ultra-performance liquid chromatography (UPLC) system. The resulting peptides were trapped and desalted for 3 min at 100 μL/min and then separated on a 1.0×100.0 mm ACQUITY UPLC HSS T3 column (Waters Corp.) with a 12 min, 2-40% acetonitrile:water gradient at 40 μL/min. Deuterium levels were not corrected for back exchange and were reported as relative. All comparison experiments were done under identical conditions, negating the need for back exchange correction. All experiments were performed in triplicate. Peptide carryover between injections was eliminated by injecting 50 μL of 1.5 M guanidine hydrochloride, 0.8% formic acid, and 4% acetonitrile over all columns after each run.
Mass spectra were acquired with a Waters Synapt G2-Si instrument equipped with a standard electrospray source (Waters Corp.) run in HDMSe mode. Instrument settings were as follows: capillary was 3.5 kV, sampling cone was 30 V, source offset was 30 V, source temperature, was 80° C., desolvation temperature was 175° C., cone gas was 50 L/hr, desolvation gas was 600 L/h, and nebulizer gas was 6.5 bar. Mass spectra were acquired over an m/z range of 50-1700. Mass accuracy was maintained through each run by simultaneous infusion of 100 fmol/uL human [Glu1]-Fibrinopeptide B through the lockmass probe.
MSE identification of the undeuterated peptic peptides was preformed using ProteinLynx Global Server software (Waters Corp.). Deuterium uptake for each peptide was determined using DynamX 2.0 software (Waters Corp.). Relative deuterium levels were calculated by subtracting the centroid of the isotopic distribution for undeuterated peptides from the corresponding centroid of the deuterium-labeled peptide. Deuterium uptake plots were generated automatically by the software.
Monitoring Deuterium Uptake for PAI-1 States
After online pepsin digestion, 150 overlapping cyno-PAI-1 peptic peptides were identified, resulting in 95.3% sequence coverage (see FIG. 48). Deuterium uptake was monitored (from 10 sec to 4 hours) in all 150 peptides for three different protein states: (1) cyno-PAI-1 alone; (2) A44v11 bound to cyno-PAI-1; and (3) APGv2 bound to cyno-PAI-1.
The majority of the cyno-PAI-1 peptides showed nearly identical deuterium uptake between the three states, which indicates that there is no interaction between cyno-PAI-1 and either mAb in these regions. See FIG. 49(A), which depicts one representative peptide region with this result (residues 139-152). In contrast, peptides incorporating residues 44-64 showed significant protection from exchange (reduced deuterium uptake) when bound to either A44v11 or APGv2 (FIG. 49(B)). In addition, peptides incorporating residues 295-322 also showed significant protection from exchange when bound to either A44v11 or APGv2 (FIG. 49(C)). For this region, the magnitude of protection was greater when cyno-PAI-1 was bound to A44v11 rather than APGv2 (See FIG. 49(C)). This indicates that A44v11 may provide greater overall protection from exchange than APGv2 when bound to cyno-PAI-1.
Comparison Studies:
For comparison studies, deuterium uptake was monitored for all of the 150 peptides generated from each of the three cyno-PAI-1 states. (See, generally, Wei, et al., Drug Discovery Today, 19(1): 95-102 (2014)). Data plots from each of the three states were compared to one another and a butterfly plot was generated to facilitate data interpretation (see, e.g., FIGS. 50(A), 51(A), and 52(A)). For each butterfly plot, the x-axis is the calculated peptide midpoint position, i, of each of the 150 peptides compared; the y-axis is the average relative fractional exchange (ratio).
Difference plots were also generated for each comparison between the cyno-PAI-1 states (see, e.g., FIGS. 50(B), 51(B), and 52(B)). In these plots, the deuterium uptake from one state is subtracted from the other and plotted similarly to the butterfly plots. The sum of the differences for each peptide is represented by a vertical bar. The horizontal dashed lines represent the values at which either individual measurements (±0.5 Da) or the sum of the differences (±1.1 Da) exceed the error of the measurement and can be considered as real differences between the two states. Additional details regarding this technique are disclosed in Houde D. et al., J. Pharm. Sci. 100(6):2071-86 (2011).
First, cyno-PAI-1 alone was compared to the A44v11:cyno-PAI-1 bound state (FIG. 50). The butterfly plot for this comparison is shown in FIG. 50(A). The difference plot for this comparison is shown in FIG. 50(B). The observed differences between cyno-PAI-1 bound to A44v11 and free form cyno-PAI-1 are located primarily in two regions of cyno-PAI-1. One region is near the N-terminus (residues 44-64) and the other region is near the C-terminus (residues 307-321) (see FIG. 50(B)).
Next, cyno-PAI-1 alone was compared to the APGv2:cyno-PAI-1 bound state (FIG. 51). The butterfly plot for this comparison is shown in FIG. 51(A). The difference plot for this comparison is shown in FIG. 51(B). The observed differences between cyno-PAI-1 bound to APGv2 and free form cyno-PAI-1 are located primarily in two regions of cyno-PAI-1. One region is near the N-terminus and the other near the C-terminus, which is similar to the A44v11:cyno-PAI-1 result. The A44v11 and APGv2 complexes with cyno-PAI-1 share peptides showing reduced deuterium uptake when in the bound state, which may indicate that the epitopes for the two antibodies are similar.
Finally, the two antibody bound cyno-PAI-1 states were compared to each other (FIG. 52). The butterfly plot for this comparison is shown in FIG. 52(A). The difference plot for this comparison is shown in FIG. 52(B). The observed difference between A44v11:cyno-PAI-1 and APGv2:cyno-PAI-1 is located in the C-terminal region of cyno-PAI-1. (See FIG. 52(B)).
Example 25
Epitope Comparison of Antibodies A44v11 and APGv2
HDX MS was used to further define the epitopes of the A44v11 and APGv2 antibodies. By using the overlapping peptides generated in HDX MS, an antibody epitope can be refined to slightly better than peptide-level resolution (for example, see FIG. 48). The HDX MS data for the peptides which showed significant protection from exchange with A44V11 binding was further analyzed to determine the epitope for the cyno-PAI-1:A44v11 interaction. The HDX data for the A44V11 epitope of cyno-PAI-1 was found to be consistent with the epitope determined using the crystallography approach. The A44V11 epitope of cyno-PAI-1 identified using HDX MS appears in FIG. 53 (bold), and below in shorthand format:









(SEQ ID NO: 159)



T-T-G-G-E-T-R-Q-Q-I-Q:



 



(SEQ ID NO: 160)



R-H-L;



 



(SEQ ID NO: 161)



T-D-M-X-X-X-F-Q-A-D-F-T-S-L-S-N-Q-E-P-L-H-V






The HDX MS data for the cyno-PAI-1 peptides which showed significant protection from exchange with APGv2 binding was analyzed to further determine the epitope for the cyno-PAI-1:APGv2 interaction. The HDX MS epitope mapping data for A44V11 and APG-v2 show that the epitopes are in the same region, as seen generally in FIG. 52. In the region of residues 307-321 the same peptides show protection in the antibody-bound state for both A44v11 and APGv2. However, the magnitude of protection is greater when cyno-PAI-1 is bound to A44v11 rather than APGv2 (see FIG. 49(C)). This finding is more apparent in FIG. 52(B), which depicts the difference peaks in the residue 307-321 region of cyno-PAI-1. This indicates that there are differences in the specific contacts made between cyno-PAI-1 and each of the A44V11 and APGv2 antibodies. Therefore, it appears that while the epitopes of both A44V11 and APGv2 are located in a similar region of PAI-1, the epitopes for each antibody are not the same.

## Claims

1. An isolated monoclonal antibody that binds specifically to PAI-1, comprising:
(a) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 34, a heavy chain CDR2 region comprising SEQ ID NO: 33, and a heavy chain CDR3 region comprising SEQ ID NO: 32; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 37, a light chain CDR2 region comprising SEQ ID NO: 145 or SEQ ID NO: 36, and a light chain CDR3 region comprising SEQ ID NO: 35; or
(b) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 22, a heavy chain CDR2 region comprising SEQ ID NO: 21, and a heavy chain CDR3 region comprising SEQ ID NO: 20; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 25, a light chain CDR2 region comprising SEQ ID NO: 24, and a light chain CDR3 region comprising SEQ ID NO: 23; or
(c) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 28, a heavy chain CDR2 region comprising SEQ ID NO: 27, and a heavy chain CDR3 region comprising SEQ ID NO: 26; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 31, a light chain CDR2 region comprising SEQ ID NO: 30, and a light chain CDR3 region comprising SEQ ID NO: 29; or
(d) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 40, a heavy chain CDR2 region comprising SEQ ID NO: 39, and a heavy chain CDR3 region comprising SEQ ID NO: 38; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 43, a light chain CDR2 region comprising SEQ ID NO: 42, and a light chain CDR3 region comprising SEQ ID NO: 41; or
(e) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 46, a heavy chain CDR2 region comprising SEQ ID NO: 45, and a heavy chain CDR3 region comprising SEQ ID NO: 44; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 49, a light chain CDR2 region comprising SEQ ID NO: 48, and a light chain CDR3 region comprising SEQ ID NO: 47; or
(f) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 52, a heavy chain CDR2 region comprising SEQ ID NO: 51, and a heavy chain CDR3 region comprising SEQ ID NO: 50; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 55, a light chain CDR2 region comprising SEQ ID NO: 54, and a light chain CDR3 region comprising SEQ ID NO: 53; or
(g) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 58, a heavy chain CDR2 region comprising SEQ ID NO: 57, and heavy chain CDR3 region comprising SEQ ID NO: 56; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 61, a light chain CDR2 region comprising SEQ ID NO: 60, and a light chain CDR3 region comprising SEQ ID NO: 59; or
(h) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 64, a heavy chain CDR2 region comprising SEQ ID NO: 63, and a heavy chain CDR3 region comprising SEQ ID NO: 62; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 67, a light chain CDR2 region comprising SEQ ID NO: 66, and a light chain CDR3 region comprising SEQ ID NO: 65; or
(i) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 70, a heavy chain CDR2 region comprising SEQ ID NO: 69, and a heavy chain CDR3 region comprising SEQ ID NO: 68; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 73, a light chain CDR2 region comprising SEQ ID NO: 72, and a light chain CDR3 region comprising SEQ ID NO: 71; or
(j) a heavy chain variable region comprising a heavy chain CDR1 region comprising SEQ ID NO: 76, heavy chain CDR2 region comprising SEQ ID NO: 75, and a heavy chain CDR3 region comprising SEQ ID NO: 74; and a light chain variable region comprising a light chain CDR1 region comprising SEQ ID NO: 79, a light chain CDR2 region comprising SEQ ID NO: 78, and a light chain CDR3 region comprising SEQ ID NO: 77.

2. The antibody of claim 1, wherein the heavy chain variable region comprises SEQ ID NO: 6, and the light chain variable region comprises SEQ ID NO: 7.

3. An isolated monoclonal antibody that binds specifically to PAI-1 comprising:
(a) a heavy chain framework region and a heavy chain variable region comprising SEQ ID NO: 86, and
(b) a light chain framework region and a light chain variable region comprising SEQ ID NO: 93.

4. A humanized monoclonal antibody, or an antigen-binding fragment thereof, that binds specifically to human PAI-1, wherein the antibody or an antigen-binding fragment thereof comprises:
(a) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 82, and a light chain having a light chain variable region comprising SEQ ID NO: 91; or
(b) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 83, and a light chain having a light chain variable region comprising SEQ ID NO: 92; or
(c) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 84, and a light chain having a light chain variable region comprising SEQ ID NO: 93; or
(d) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 85, and a light chain having a light chain variable region comprising SEQ ID NO: 91; or
(e) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 85, and a light chain having a light chain variable region comprising SEQ ID NO: 93; or
(f)a heavy chain having a heavy chain variable region comprising SEQ ID NO: 86, and a light chain having a light chain variable region comprising SEQ ID NO: 94; or
(g) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 87, and a light chain having a light chain variable region comprising SEQ ID NO: 95; or
(h) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 88, and a light chain having a light chain variable region comprising SEQ ID NO: 96; or
(i) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 89, and a light chain having a light chain variable region comprising SEQ ID NO: 97; or
(j) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 90, and a light chain having a light chain variable region comprising SEQ ID NO: 98; or
(k) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 86, and a light chain having a light chain variable region comprising SEQ ID NO: 95; or
(l) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 89, and a light chain having a light chain variable region comprising SEQ ID NO: 93; or
(m) a heavy chain having a heavy chain variable region comprising SEQ ID NO: 89, and a light chain having a light chain variable region comprising SEQ ID NO: 95.

5. An isolated monoclonal antibody that binds specifically to PAI-1, that binds to the same epitope on PAI-1 as the humanized monoclonal antibody of claim 4.

6. A method of restoring plasmin generation comprising administering to a subject in need thereof orally, parenterally by a solution for injection, by inhalation, or topically, a pharmaceutically effective amount of the isolated monoclonal antibody of claim 1.

7. The method of claim 6, wherein the method treats a condition comprising increased levels of fibrotic tissue.

8. The method of claim 7, wherein the condition is fibrosis, systemic sclerosis, interstitial lung disease, chronic lung disease, chronic kidney disease, peripheral limb ischemia, acute ischemic stroke with and without thrombolysis, or stent restenosis.

9. The method of claim 6, wherein the method treats a condition comprising skin fibrosis, lung fibrosis, idiopathic pulmonary fibrosis, liver fibrosis, or kidney fibrosis.

10. The method of claim 6, wherein the method treats a condition comprising venous and arterial thrombosis, deep vein thrombosis, or disseminated intravascular coagulation thrombosis.