# Patent

## Title
Human TIMP-1 antibodies

## Abstract

Human antibodies that bind to TIMP-1 can be used as reagents to diagnose and treat disorders in which TIMP-1 is elevated, such as liver fibrosis, alcoholic liver disease, cardiac fibrosis, acute coronary syndrome, lupus nephritis, glomerulosclerotic renal disease, benign prostate hypertrophy, colon cancer, lung cancer, and idiopathic pulmonary fibrosis.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
Under 35 USC § 120, this application is a continuation application of U.S. application Ser. No. 10/128,520 filed Apr. 24, 2002, now issued as U.S. Pat. No. 7,091,323; which claims the benefit under 35 USC § 119(e) to U.S. Application Ser. No. 60/285,683 filed Apr. 24, 2001, now abandoned. The disclosure of each of the prior applications is considered part of and is incorporated by reference in the disclosure of this application.


This application incorporates by reference the sequence listing contained on a compact disc, which is part of the application. The sequence listing is a 1.17 MB ASCII file named “Human TIMP-1 Antibodies sequence listing.txt,” created on Apr. 23, 2002.
FIELD OF THE INVENTION
The invention relates to TIMP-1-binding human antibodies.
BACKGROUND OF THE INVENTION
Tissue inhibitors of metalloproteases (TIMPs) inhibit metalloproteases, a family of endopeptide hydrolases. Metalloproteases are secreted by connective tissue and hematopoietic cells, use Zn2+ or Ca2+ for catalysis, and may be inactivated by metal chelators as well as TIMP molecules. Matrix metalloproteases (MMPs) participate in a variety of biologically important processes, including the degradation of many structural components of tissues, particularly the extracellular matrix (ECM).
Degradation of extracellular matrix tissue is desirable in processes where destruction of existing tissues is necessary, e.g., in embryo implantation (Reponen et al., Dev. Dyn. 202, 388-96, 1995), embryogenesis, and tissue remodeling. Imbalance between synthesis and degradation of matrix proteins, however, can result in diseases such as liver fibrosis (Iredale et al., Hepatology 24, 176-84, 1996). This imbalance can occur, for example, if levels of TIMPs are increased. Disorders in which TIMP-1 levels of increased include, for example, liver fibrosis, alcoholic liver disease, cardiac fibrosis, acute coronary syndrome, lupus nephritis, glomerulosclerotic renal disease, idiopathic pulmonary fibrosis, benign prostate hypertrophy, lung cancer, and colon cancer. See, e.g., Inokubo et al., Am. Heart J 141, 211-17, 2001; Ylisirnio et al., Anticancer Res. 20, 1311-16, 2000; Holten-Andersen et al., Clin. Cancer Res. 6, 4292-99, 2000; Holten-Andersen et al., Br. J. Cancer 80, 495-503, 1999; Peterson et al., Cardiovascular Res. 46, 307-15, 2000; Arthur et al., Alcoholism: Clinical and Experimental Res. 23, 840-43, 1999; Iredale et al., Hepatol. 24, 176-84, 1996.
There is a need in the art for reagents and methods of inhibiting TIMP-1 activity, which can be used to provide therapeutic effects.
BRIEF SUMMARY OF THE INVENTION
It is an object of the present invention to provide reagents and methods of inhibiting TIMP-1 activity. This and other objects of the invention are provided by one or more of the embodiments described below.
One embodiment of the invention is a purified preparation of a human antibody, wherein the antibody binds to a tissue inhibitor of metalloprotease-1 (TIMP-1) and neutralizes a matrix metalloprotease (MMP)-inhibiting activity of the TIMP-1.
Another embodiment of the invention is a purified preparation of a first human antibody which comprises a VHCDR3 region comprising an amino acid sequence selected from the group consisting of SEQ ID NOS:1-43 and 360.
Still another embodiment of the invention is a purified preparation of a first human antibody which comprises a VLCDR3 region comprising an amino acid sequence selected from the group consisting of SEQ ID NOS:44-86 and 365-379.
Yet another embodiment of the invention is a purified preparation of a first human antibody which has TIMP-1 binding and MMP-inhibiting activity characteristics of a second human antibody. The second antibody comprises a VHCDR3 and VLCDR3 amino acid sequence pair selected from the group consisting of SEQ ID NOS:1 and 44, SEQ ID NOS:2 and 45, SEQ ID NO:3 and 46, SEQ ID NOS:4 and 47, SEQ ID NOS:5 and 48, SEQ ID NOS:6 and 49, SEQ ID NOS:7 and 50, SEQ ID NOS:3 and 44, SEQ ID NOS:3 and 45, SEQ ID NOS:3 and 47, SEQ ID NOS:3 and 48, SEQ ID NOS:3 and 49, SEQ ID NOS:3 and 50, SEQ ID NOS:7 and 44, SEQ ID NOS:7 and 45, SEQ ID NOS:7 and 47, SEQ ID NOS:7 and 48, SEQ ID NOS:8 and 51, SEQ ID NOS:9 and 52, SEQ ID NOS:10 and 53, SEQ ID NOS:11 and 54, SEQ ID NOS:12 and 55, SEQ ID NOS:13 and 56, SEQ ID NOS:14 and 57, SEQ ID NOS:15 and 58, SEQ ID NOS:16 and 59, SEQ ID NOS:17 and 60, SEQ ID NOS:18 and 61, SEQ ID NOS:19 and 62, SEQ ID NOS:20 and 63, SEQ ID NOS:21 and 64, SEQ ID NOS:22 and 65, SEQ ID NOS:23 and 66, SEQ ID NOS:24 and 67, SEQ ID NOS:25 and 68, SEQ ID NOS:26 and 69, SEQ ID NOS:27 and 70, SEQ ID NOS:28 and 71, SEQ ID NOS:29 and 72, SEQ ID NOS:30 and 73, SEQ ID NOS:31 and 74, SEQ ID NOS:32 and 75, SEQ ID NOS:33 and 76, SEQ ID NOS:34 and 77, SEQ ID NOS:35 and 78, SEQ ID NOS:36 and 79, SEQ ID NOS:37 and 80, SEQ ID NOS:38 and 81, SEQ ID NOS:39 and 82, SEQ ID NOS:40 and 83, SEQ ID NOS:41 and 84, SEQ ID NOS:42 and 85, SEQ ID NOS:43 and 86, SEQ ID NOS:3 and 48, SEQ ID NOS:360 and 48, SEQ ID NOS:3 and 365, SEQ ID NOS:16 and 59, SEQ ID NOS:18 and 61, SEQ ID NOS:34 and 77, SEQ ID NOS:34 and 379, SEQ ID NOS:18 and 376, SEQ ID NOS:18 and 377, and SEQ ID NOS:18 and 378.
Even another embodiment of the invention is a purified preparation of a human antibody comprising a VHCDR3 and VLCDR3 amino acid sequence pair selected from the group consisting of SEQ ID NOS:1 and 44, SEQ ID NOS:2 and 45, SEQ ID NO:3 and 46, SEQ ID NOS:4 and 47, SEQ ID NOS:5 and 48, SEQ ID NOS:6 and 49, SEQ ID NOS:7 and 50, SEQ ID NOS:3 and 44, SEQ ID NOS:3 and 45, SEQ ID NOS:3 and 47, SEQ ID NOS:3 and 48, SEQ ID NOS:3 and 49, SEQ ID NOS:3 and 50, SEQ ID NOS:7 and 44, SEQ ID NOS:7 and 45, SEQ ID NOS:7 and 47, SEQ ID NOS:7 and 48, SEQ ID NOS:8 and 51, SEQ ID NOS:9 and 52, SEQ ID NOS:10 and 53, SEQ ID NOS:11 and 54, SEQ ID NOS:12 and 55, SEQ ID NOS:13 and 56, SEQ ID NOS:14 and 57, SEQ ID NOS:15 and 58, SEQ ID NOS:16 and 59, SEQ ID NOS:17 and 60, SEQ ID NOS:18 and 61, SEQ ID NOS:19 and 62, SEQ ID NOS:20 and 63, SEQ ID NOS:21 and 64, SEQ ID NOS:22 and 65, SEQ ID NOS:23 and 66, SEQ ID NOS:24 and 67, SEQ ID NOS:25 and 68, SEQ ID NOS:26 and 69, SEQ ID NOS:27 and 70, SEQ ID NOS:28 and 71, SEQ ID NOS:29 and 72, SEQ ID NOS:30 and 73, SEQ ID NOS:31 and 74, SEQ ID NOS:32 and 75, SEQ ID NOS:33 and 76, SEQ ID NOS:34 and 77, SEQ ID NOS:35 and 78, SEQ ID NOS:36 and 79, SEQ ID NOS:37 and 80, SEQ ID NOS:38 and 81, SEQ ID NOS:39 and 82, SEQ ID NOS:40 and 83, SEQ ID NOS:41 and 84, SEQ ID NOS:42 and 85, SEQ ID NOS:43 and 86, SEQ ID NOS:3 and 48, SEQ ID NOS:360 and 48, SEQ ID NOS:3 and 365, SEQ ID NOS: 16 and 59, SEQ ID NOS:18 and 61, SEQ ID NOS:34 and 77, SEQ ID NOS:34 and 379, SEQ ID NOS:18 and 376, SEQ ID NOS:18 and 377, and SEQ ID NOS:18 and 378.
A further embodiment of the invention is a purified preparation of a human antibody which comprises a heavy chain and a light chain amino acid pair selected from the group consisting of SEQ ID NOS:140 and 97, SEQ ID NOS:141 and 98, SEQ ID NOS:142 and 99, SEQ ID NOS:143 and 100, SEQ ID NOS:144 and 101, SEQ ID NOS:145 and 102, SEQ ID NOS:146 and 103, SEQ ID NOS:142 and 97, SEQ ID NOS:142 and 98, SEQ ID NOS:142 and 100, SEQ ID NOS:142 and 101, SEQ ID NOS:142 and 102, SEQ ID NOS:142 and 103, SEQ ID NOS:146 and 97, SEQ ID NOS:146 and 98, SEQ ID NO:146 and 100, SEQ ID NOS:146 and 101, SEQ ID NOS:148 and 104, SEQ ID NOS:148 and 105, SEQ ID NOS:149 and 106, SEQ ID NOS:150 and 107, SEQ ID NOS:151 and 108, SEQ ID NOS:152 and 109, SEQ ID NOS:153 and 110, SEQ ID NOS:154 and 111, SEQ ID NOS:155 and 112, SEQ ID NOS:156 and 113, SEQ ID NOS:157 and 114, SEQ ID NOS:158 and 115, SEQ ID NOS:159 and 116, SEQ ID NOS:160 and 117, SEQ ID NOS:161 and 118, SEQ ID NOS:162 and 119, SEQ ID NOS:163 and 120, SEQ ID NOS:164 and 121, SEQ ID NOS:165 and 122, SEQ ID NOS:166 and 123, SEQ ID NOS:167 and 124, SEQ ID NOS:168 and 125, SEQ ID NOS:169 and 126, SEQ ID NOS:170 and 127, SEQ ID NOS:171 and 128, SEQ ID NOS:172 and 129, SEQ ID NOS:173 and 130, SEQ ID NOS:174 and 131, SEQ.ID NOS:175 and 132, SEQ ID NOS:176 and 133, SEQ ID NOS:177 and 134, SEQ ID NOS:178 and 135, SEQ ID NOS:179 and 136, SEQ ID NOS:180 and 137, SEQ ID NOS:181 and 138, and SEQ ID NOS:182 and 139.
Another embodiment of the invention is a pharmaceutical composition comprising a human antibody and a pharmaceutically acceptable carrier. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1.
Yet another embodiment of the invention is a purified polynucleotide which encodes a human antibody comprising a VHCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-43 and 360. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1.
Even another embodiment of the invention is a purified polynucleotide which encodes a human antibody comprising a VLCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:44-86 and 365-379. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1.
Still another embodiment of the invention is an expression vector comprising a polynucleotide which encodes a human antibody comprising a VHCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-43 and 360. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1.
A further embodiment of the invention is an expression vector comprising a polynucleotide which encodes a human antibody comprising a VHCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-43 and 360. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1. The VHCDR3 region is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NOS:227-269.
Another embodiment of the invention is an expression vector comprising a polynucleotide which encodes a human antibody comprising a VLCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:44-86 and 365-379. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1.
Yet another embodiment of the invention is an expression vector comprising a polynucleotide which encodes a human antibody comprising a VLCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:44-86 and 365-379. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1. The VLCDR3 region is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NOS:184-226.
Still another embodiment of the invention is an expression vector comprising a polynucleotide which encodes a human antibody comprising a VHCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-43 and 360. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1. The human antibody comprises a heavy chain having an amino acid sequence selected from the group consisting of SEQ ID NOS:140-182.
Even another embodiment of the invention is an expression vector comprising a polynucleotide which encodes a human antibody comprising a VHCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-43 and 360. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1. The human antibody comprises a heavy chain having an amino acid sequence selected from the group consisting of SEQ ID NOS:140-182. The heavy chain is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NOS:269-311.
A further embodiment of the invention is an expression vector comprising a polynucleotide which encodes a human antibody comprising a VLCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:44-86 and 365-379. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1. The human antibody comprises a light chain having an amino acid sequence selected from the group consisting of SEQ ID NOS:97-139.
Another embodiment of the invention is an expression vector comprising a polynucleotide which encodes a human antibody comprising a VLCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:44-86 and 365-379. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1. The human antibody comprises a light chain having an amino acid sequence selected from the group consisting of SEQ ID NOS:97-139. The light chain is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NOS:312-354.
Yet another embodiment of the invention is a host cell comprising an expression vector. The expression vector comprises a polynucleotide which encodes a human antibody comprising a VHCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-43 and 360, wherein the human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1.
Yet another embodiment of the invention is a host cell comprising an expression vector. The expression vector comprises a polynucleotide which encodes a human antibody comprising a VHCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-43 and 360, wherein the human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1. The VHCDR3 region is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NOS:227-269.
Still another embodiment of the invention is a host cell comprising an expression vector. The expression vector comprises a polynucleotide which encodes a human antibody comprising a VLCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:44-86 and 365-379. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1.
A further embodiment of the invention is a host cell comprising an expression vector. The expression vector comprises a polynucleotide which encodes a human antibody comprising a VLCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:44-86 and 365-379. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1. The VLCDR3 region is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NOS:184-226.
Another embodiment of the invention is a host cell comprising an expression vector. The expression vector comprises a polynucleotide which encodes a human antibody comprising a VHCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-43 and 360, wherein the human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1. The human antibody comprises a heavy chain having an amino acid sequence selected from the group consisting of SEQ ID NOS:140-182.
Still another embodiment of the invention is a host cell comprising an expression vector. The expression vector comprises a polynucleotide which encodes a human antibody comprising a VHCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ D NOS:1-43 and 360, wherein the human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1. The human antibody comprises a heavy chain having an amino acid sequence selected from the group consisting of SEQ ID NOS:140-182. The heavy chain is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NOS:269-311.
Yet another embodiment of the invention is a host cell comprising an expression vector. The expression vector comprises a polynucleotide which encodes a human antibody comprising a VLCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:44-86 and 365-379. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1. The human antibody comprises a light chain having an amino acid sequence selected from the group consisting of SEQ ID NOS:97-139.
Even another embodiment of the invention is a host cell comprising an expression vector. The expression vector comprises a polynucleotide which encodes a human antibody comprising a VLCDR3 region which comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:44-86 and 365-379. The human antibody (1) binds to a TIMP-1 and (2) neutralizes an MMP-inhibiting activity of the TIMP-1. The human antibody comprises a light chain having an amino acid sequence selected from the group consisting of SEQ ID NOS:97-139. The light chain is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NOS:312-354.
A further embodiment of the invention is a method of making a human antibody. The host cell of claim 43 is cultured under conditions whereby the antibody is expressed. The human antibody is purified from the host cell culture.
Another embodiment of the invention is a method of decreasing an MMP-inhibiting activity of a TIMP-1. The TIMP-1 is contacted with a human antibody that binds to the TIMP-1. The MMP-inhibiting activity of the TIMP-1 is decreased relative to MMP-inhibiting activity of the TIMP-1 in the absence of the antibody.
Still another embodiment of the invention is a method of ameliorating symptoms of a disorder in which TIMP-1 is elevated. An effective amount of a human antibody which neutralizes an MMP-inhibiting activity of the TIMP-1 is administered to a patient having the disorder. Symptoms of the disorder are thereby ameliorated.
A further embodiment of the invention is a method of detecting a TIMP-1 in a test preparation. The test preparation is contacted with a human antibody that specifically binds to the TIMP-1. The test preparation is assayed for the presence of an antibody-TIMP-1 complex.
Even another embodiment of the invention is a method to aid in diagnosing a disorder in which a TIMP-1 level is elevated. A sample from a patient suspected of having the disorder is contacted with a human antibody that binds to TIMP-1. The sample is assayed for the presence of an antibody-TIMP-1 complex. Detection of an amount of the complex which is greater than an amount of the complex in a normal sample identifies the patient as likely to have the disorder.
The invention thus provides human antibodies which bind to TIMP-1 and neutralize MMP-inhibiting activity of TIMP-1. These antibodies can be used, inter alia, in diagnostic and therapeutic methods.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. Protein sequences encoded by the HuCAL® VH and VL Fab master genes. Seven VH and VL sequences are aligned, and the approximate location of restriction endonuclease sites introduced into the corresponding DNA sequences are indicated. The numbering is according to VBASE except for the gap in V1 position 9. In VBASE the gap is set at position 10. See also Chothia et al. (1992) J. Mol. Biol. 227, 776-798, Tomlinson et al. (1995) EMBO J. 14, 4628-4638 and Williams et al. (1996) J. Mol. Biol. 264, 220-232).
FIG. 2. Nucleotide sequences of the HuCAL® VH and VL Fab master genes.
FIG. 3. Fab display vector pMORPH® 18 Fab 1.
FIG. 4. Vector map of pMORPH® x9Fab1_FS.
FIG. 5. Sequence comparison between human and rat TIMP-1. Sequence regions in bold were used for peptide synthesis. Residues that make stronger direct contacts with MMP-3 are italicized, and residues that make weaker direct contacts with MMP-3 are underlined (Gomis-Ruth et al., 1997).
FIG. 6. Activity of MS-BW-3 in human TIMP-1/MMP-1 assay. Antibody Fab fragments were diluted in triplicate to the indicated concentrations in assay buffer containing 0.05% BSA. After addition of TIMP (final conc. 1.2 nM), MMP (final conc. 1.2 nM), and peptide substrate (final conc. 50 μM) and incubation for 1-3 h at 37° C. fluorescence at Ex320 nm/Em 430 nm was measured. IC50 was calculated as outlined in material and methods section, using 100% MMP-1 activity (in absence of TIMP-1) and 27% MMP-1 activity (in absence of antibody) as reference values.
FIG. 7. Activity of MS-BW-44 in human TIMP-1/MMP-1 assay. Antibody Fab fragments were diluted in triplicate to the indicated concentrations in assay buffer containing 0.05% BSA. After addition of TIMP (final conc. 1.2 nM), MMP (final conc. 1.2 nM), and peptide substrate (final conc. 50 μM) and incubation for 1-3 h at 37° C. fluorescence at Ex320 nm/Em 430 nm was measured. IC50 was calculated as outlined in material and methods section, using 100% MMP-1 activity (in absence of TIMP-1) and 25% MMP-1 activity (in absence of antibody) as reference values.
FIG. 8. Activity of MS-BW-44, -44-2, 44-6 in human TIMP-1/MMP-1 assay. Fab antibody fragments were diluted in triplicate to the indicated concentrations in assay buffer containing 0.05% BSA. After addition of TIMP (final conc. 0.4 nM), MMP (final conc. 0.4 nM) and peptide substrate (final conc. 50 μM) and incubation for 7 h at 37° C. fluorescence at Ex320 nm/Em 430 nm was measured. IC50 was calculated as outlined in material and methods section, using 100% MMP-1 activity (in absence of TIMP-1) and 55% MMP-1 activity (in absence of antibody) as reference values.
FIG. 9. Activity of MS-BW-44, -44-2-4, 44-6-1 in human TIMP-1/MMP-1 assay. Antibody Fab fragments were diluted in triplicate to the indicated concentrations in assay buffer containing 0.05% BSA. After addition of TIMP (final conc. 0.4 nM), MMP (final conc. 0.4 nM), and peptide substrate (final conc. 50 μM) and incubation for 7 h at 37° C. fluorescence at Ex320 nm/Em 430 nm was measured. IC50 was calculated as outlined in material and methods section, using 100% MMP-1 activity (in absence of TIMP-1) and 50% MMP-1 activity (in absence of antibody) as reference values.
FIG. 10. Binding of Fab fragments to human TIMP-1, -2, -3 and -4. TIMP-1, -2, -3, -4 proteins were immobilized on an ELISA plate, and binding of purified Fab fragments was measured by incubation with alkaline phosphatase conjugated anti-Fab antibody (Dianova) followed by development with Attophos substrate (Roche) and measurement at Ex405 nm/Em535 nm.
FIG. 11. Activity of MS-BW-14, -17, -54 in rat TIMP-1/MMP-13 assay. Antibody Fab fragments were diluted in triplicate to the indicated concentrations in assay buffer containing 0.05% BSA. After addition of TIMP (final conc. 1.2 nM), MMP (final conc. 1.2 nM), and peptide substrate (to final conc. 50 μM) and incubation for 1-3 h at 37° C. fluorescence at Ex320 nm/Em 430 nm was measured. IC50 was calculated as outlined in material and methods section, using 100% MMP-13 (in absence of TIMP-1) activity and 20% MMP-13 activity (in absence of antibody) as reference values.
FIG. 12. Activity of MS-BW-14 Fab and IgG1 and MS-BW-3 IgG1 in rat TIMP-1/MMP-13 assay. Antibodies were diluted in triplicate to the indicated concentrations in assay buffer containing 0.05% BSA. After addition of TIMP (final conc. 1.2 nM), MMP (final conc. 1.2 nM) and peptide substrate (to final conc.50 μM) and incubation for 1-3 h at 37° C., fluorescence at Ex320 nm/Em 430 nm was measured. IC50 was calculated as outlined in material and methods section, using 100% MMP-13 activity (in absence of TIMP-1) and 30% MMP-13 activity (in absence of antibody) as reference values.
FIG. 13. Activity of MS-BW-17-1 Fab and IgG1 in rat TIMP-1/MMP-13 assay. Fab antibody fragments were diluted in triplicate to the indicated concentrations in assay buffer containing 0.05% BSA. After addition of TIMP (final conc. 1.2 nM), MMP (final conc. 1.2 nM) and peptide substrate (to final conc.50 μM) and incubation for 1-3 h at 37° C. fluorescence at Ex320 nm/Em 430 nm was measured. IC50 was calculated as outlined in material and methods section, using 100% MMP-13 activity (in absence of TIMP-1) and 15% MMP-13 activity (in absence of antibody) as reference values.
FIG. 14. Effect of the inhibitory effect of MS-BW-17-1 TIMP-1 antibody on bleomycin-induced lung fibrotic collagen.
FIG. 15. Effect of anti-TIMP-1 antibody on fibrotic collagen as stained by Sirus Red in carbon tetrachloride-induced rat liver fibrosis model. Sirius Red-stained area as percent of total field in carbon tetrachloride-treated rats treated with PBS, control antibody, and MS-BW-14 anti-TIMP-1 antibody.



DETAILED DESCRIPTION OF THE INVENTION
The invention provides human antibodies that bind to TIMP-1. These antibodies are useful for a variety of therapeutic and diagnostic purposes.
Characteristics of Human TIMP-1 Antibodies
“Antibody” as used herein includes intact immunoglobulin molecules (e.g., IgG1, IgG2a, IgG2b, IgG3, IgM, IgD, IgE, IgA), as well as fragments thereof, such as Fab, F(ab′)2, scFv, and Fv, which are capable of specific binding to an epitope of a human and/or rat TIMP-1 protein. Antibodies that specifically bind to TIMP-1 provide a detection signal at least 5-, 10-, or 20-fold higher than a detection signal provided with other proteins when used in an immunochemical assay. Preferably, antibodies that specifically bind to human and/or rat TIMP-1 do not detect other proteins in immunochemical assays and can immunoprecipitate the TIMP-1 from solution.
The Kd of human antibody binding to TIMP-1 can be assayed using any method known in the art, including technologies such as real-time Bimolecular Interaction Analysis (BIA) (Sjolander & Urbaniczky, Anal. Chem. 63, 2338-45, 1991, and Szabo et al., Curr. Opin. Struct. Biol. 5, 699-705, 1995). BIA is a technology for studying biospecific interactions in real time, without labeling any of the interactants (e.g., BlAcoreTM). Changes in the optical phenomenon surface plasmon resonance (SPR) can be used as an indication of real-time reactions between biological molecules.
In a BlAcoreTM assay, some human antibodies of the invention specifically bind to human TIMP-1 with a Kd of about 0.1 nM to about 10 μM, about 2 nM to about 1 μM, about 2 nM to about 200 nM, about 2 nM to about 150 nM, about 50 nM to about 100 nM, about 0.2 nM to about 13 nM, about 0.2 nM to about 0.5 nM, about 2 nM to about 13 nM, and about 0.5 nM to about 2 nM. More preferred human antibodies specifically bind to human TIMP-1 with a Kd selected from the group consisting of about 0.2 nM, about 0.3 nM, about 0.5 M, about 0.6 nM, about 2 nM, about 7 nM, about 10 nM, about 11 nM, and about 13 nM.
Other human antibodies of the invention specifically bind to rat TIMP-1 with a Kd of about 0.1 nM to about 10 μM, about 2 nM to about 1 μM, about 2 nM to about 200 nM, about 2 nM to about 150 nM, about 50 nM to about 100 nM, about 1.3 nM to about 13 nM, about 1.8 nM to about 10 nM, about 2 nM to about 9 nM, about 1.3 nM to about 9 nM, and about 2 nM to about 10 nM. Preferred Kd s range from about 0.8 nM, about 1 nM, about 1.3 nM, about 1.9 nM, about 2 nM, about 3 nM, about 9 nM, about 10 nM, about 13 nM, about 14 nM, and about 15 nM.
Preferably, antibodies of the invention neutralize an MMP-inhibiting activity of the TIMP-1. The MMP can be, for example, MMP-1, MMP-2, MMP-3, MMP-7, MMP-8, MMP-9, MMP-10, MMP-11, MMP-12, MMP-13, MMP-19, MMP-20 or MMP-23.
IC50 for neutralizing MMP-inhibiting activity of TIMP-1 can be measured by any means known in the art. Preferably, IC50 is determined using the high throughput fluorogenic assay described in Bickett et al., Anal. Biochem. 212, 58-64, 1993. In a typical fluorogenic assay, the IC50 of a human antibody for neutralizing human TIMP-1 MMP-inhibiting activity ranges from about 0.1 nM to about 200 nM, about 1 nM to about 100 nM, about 2 nM to about 50 nM, about 5 nM to about 25 nM, about 10 nM to about 15 nM, about 0.2 nM to about 11 nM, about 0.2 nM to about 4 nM, and about 4 nM to about 11 nM. The IC50 for neutralizing human TIMP-1 MMP-inhibiting activity of some human antibodies is about 0.2 nM, about 0.3 nM, about 0.4 nM, about 4 nM, about 7 nM, about 9 nM, and about 11 nM.
A typical IC50 for neutralizing rat TIMP-1 MMP-inhibiting activity ranges from about 0.1 nM to about 300 nM, about 1 nM to about 100 nM, about 2 nM to about 50 nM, about 5 nM to about 25 nM, about 10 nM to about 15 nM, about 1.1 nM to about 14 nM, about 1.6 nM to about 11 nM, about 3 nM to about 7 nM, about 1.1 nM to about 7 nM, about 1.1 nM to about 11 nM, about 3 nM to about 11 nM, and about 3 nM to about 14 nM. The IC50 for neutralizing rat TIMP-1 MMP-inhibiting activity of some human antibodies is about 1.1 nM, about 1.6 nM, about 3 nM, about 7 nM, about 11 nM, about 14 nM, about 19 nM, about 20 nM, about 30 nM, and about 100 nM.
Preferred human antibodies of the invention are those for which the Kd for binding to TIMP-1 and the IC50 for neutralizing the MMP-inhibiting activity of the TIMP-1 are approximately equal.
A number of human antibodies having the TIMP-1 binding and MMP-inhibiting activity neutralizing characteristics described above have been identified by screening the MorphoSys HuCAL® Fab 1 library. The CDR cassettes assembled for the HuCAL® library were designed to achieve a length distribution ranging from 5 to 28 amino acid residues, covering the stretch from position 95 to 102. Knappik et al., J. Mol. Biol. 296, 57-86, 2000. Some clones, however, had shorter VHCDR3 regions. In fact, it is a striking feature of anti-human TIMP-1 human antibodies identified from this library that they all exhibit the combination VH312 and a relatively short VHCDR3 region, typically four amino acids.
In some embodiments of the invention, the VHCDR3 region of a human antibody has an amino acid sequence shown in SEQ ID NOS:1-43. In other embodiments of the invention, the VLCDR3 region of a human antibody has an amino acid sequence shown in SEQ ID NOS:44-86. See Tables 2, 3, and 7. Human antibodies which have TIMP-binding and MMP-inhibiting activity neutralizing characteristics of antibodies such as those described above and in Tables 2, 3, and 7 also are human antibodies of the invention.
Obtaining Human Antibodies
Human antibodies with the TIMP-1 binding and MMP-activity neutralizing characteristics described above can be identified from the MorphoSys HuCAL® library as follows. Human or rat TIMP-1, for example, is coated on a microtiter plate and incubated with the MorphoSys HuCAL® Fab phage library (see Example 1, below). Those phage-linked Fabs not binding to TIMP-1 can be washed away from the plate, leaving only phage which tightly bind to TIMP-1. The bound phage can be eluted, for example, by a change in pH or by elution with E. coli and amplified by infection of E. coli hosts. This panning process can be repeated once or twice to enrich for a population of antibodies that tightly bind to TIMP-1. The Fabs from the enriched pool are then expressed, purified, and screened in an ELISA assay. The identified hits are then screened in the enzymatic assay described in Bickett et al., 1993, and Bodden et al., 1994. Those Fabs that lead to the degradation of the peptide are likely the ones which bind to TIMP-1, thereby blocking its interaction to MMP-1.
The initial panning of the HuCAL® Fab 1 library also can be performed with TIMP-1 as the antigen in round one, followed in round 2 by TIMP-1 peptides fused to carrier proteins, such as BSA or transferrin, and in round 3 by TIMP-1 again. Human TIMP-1 peptides which can be used for panning include human TIMP-1 residues 2-12 (TCVPPHPQTAF, SEQ ID NO:87; CTSVPPHPQTAF, SEQ ID NO:88; STCVPPHPQTAF, SEQ ID NO:89; STSVPPHPQTAFC, SEQ ID NO:90), 28-36 (CEVNQTTLYQ, SEQ ID NO:91), 64-75 (PAMESVCGYFHR, SEQ ID NO:92), 64-79 (PAMESVCGYFHRSHNR, SEQ ID NO:93; CPAMESVSGYFHRSHNR, SEQ ID NO:94; PAMESVSGYFHRSHNRC, SEQ ID NO:95), and 145-157 (CLWTDQLLQGSE, SEQ ID NO:96). These peptide sequences are selected from regions of human TIMP-1 that are predicted to interact with MMPs. See Gomis-Ruth et al., Nature 389, 77-81, 1997. Directing Fabs toward the MMP-interacting region of human TIMP-1 in round 2 should increase the chance of identifying Fabs that can block the ability of human TIMP-1 to inhibit human MMP-1 activity.
Another method that can be used to improve the likelihood of isolating neutralizing Fabs is the panning on human TIMP-1 and eluting the binding Fabs with human MMP-1. This strategy should yield higher affinity antibodies than would otherwise be obtained.
Details of the screening process are described in the specific examples, below. Other selection methods for highly active specific antibodies or antibody fragments can be envisioned by those skilled in the art and used to identify human TIMP-1 antibodies.
Human antibodies with the characteristics described above also can be purified from any cell that expresses the antibodies, including host cells that have been transfected with antibody-encoding expression constructs. The host cells are cultured under conditions whereby the human antibodies are expressed. A purified human antibody is separated from other compounds that normally associate with the antibody in the cell, such as certain proteins, carbohydrates, or lipids, using methods well known in the art. Such methods include, but are not limited to, size exclusion chromatography, ammonium sulfate fractionation, ion exchange chromatography, affinity chromatography, and preparative gel electrophoresis. A preparation of purified human antibodies is at least 80% pure; preferably, the preparations are 90%, 95%, or 99% pure. Purity of the preparations can be assessed by any means known in the art, such as SDS-polyacrylamide gel electrophoresis. A preparation of purified human antibodies of the invention can contain more than one type of human antibody with the TIMP-1 binding and neutralizing characteristics described above.
Alternatively, human antibodies can be produced using chemical methods to synthesize its amino acid sequence, such as by direct peptide synthesis using solid-phase techniques (Merrifield, J. Am. Chem. Soc. 85, 2149-54, 1963; Roberge et al., Science 269, 202-04, 1995). Protein synthesis can be performed using manual techniques or by automation. Automated synthesis can be achieved, for example, using Applied Biosystems 431 A Peptide Synthesizer (Perkin Elmer). Optionally, fragments of human antibodies can be separately synthesized and combined using chemical methods to produce a full-length molecule.
The newly synthesized molecules can be substantially purified by preparative high performance liquid chromatography (e.g., Creighton, PROTEINS: STRUCTURES AND MOLECULAR PRINCIPLES, WH Freeman and Co., New York, N.Y., 1983). The composition of a synthetic polypeptide can be confirmed by amino acid analysis or sequencing (e.g., using Edman degradation).
Assessment of Therapeutic Utility of Human Antibodies
To assess the ability of a particular antibody to be therapeutically useful to treat, liver fibrosis, for example, the antibody can be tested in vivo in a rat liver fibrosis model. Thus, preferred human antibodies of the invention are able to block both human and rat TIMP-1 activity. If desired, human Fab TIMP-1 antibodies can be converted into full immunoglobulins, for example IgG1 antibodies, before therapeutic assessment. This conversion is described in Example 5, below.
To identify antibodies that cross-react with human and rat TIMP-1, an ELISA can be carried out using rat TIMP-1. Functional cross-reactivity can be confirmed in an enzymatic assay, as described in Bickett et al., Anal. Biochem. 212, 58-64, 1993. The assay uses human or rat TIMP-1, human MMP-1 or rat MMP-13 (the rat counterpart of human MMP-1), and a synthetic fluorogenic peptide substrate. Enzyme activity of uncomplexed MMP-1 (or MMP-13) is assessed by observing an increase in a fluorescence signal.
Antibodies that block human and/or rat TIMP-1 activity can be screened in an ELISA assay that detects the decrease of TIMP-1/MMP-1 complex formation in cultures of HepG2 cells. Antibodies that meet this criteria can then be tested in a rat liver fibrosis model to assess therapeutic efficacy and correlate this efficacy with the ability of the antibodies to block TIMP-1 inhibition of MMP-1 in vitro.
Antibodies that demonstrate therapeutic efficacy in the rat liver fibrosis model can then be tested for binding to and blockade of TIMP-2, -3, and -4 in an in vitro enzymatic assay. Blocking the minimum number of TIMPs necessary for efficacy in liver fibrosis or other TIMP-associated pathology is preferable to minimize potential side effects.
Polynucleotides Encoding Human TIMP-1 Antibodies
The invention also provides polynucleotides encoding human TIMP-1 antibodies. These polynucleotides can be used, for example, to produce quantities of the antibodies for therapeutic or diagnostic use.
Polynucleotides that can be used to encode the VHCDR3 regions shown in SEQ ID NOS:1-43 are shown in SEQ ID NOS:226-268, respectively. Polynucleotides that can be used to encode the VLCDR3 region shown in SEQ ID NOS:44-86 are shown in SEQ ID NOS:183-225, respectively. Polynucleotides that encode heavy chains (SEQ ID NOS:140-182) and light chains (SEQ ID NOS:97-139) of human antibodies of the invention that have been isolated from the MorphoSys HuCAL® library are shown in SEQ ID NOS:269-311 and SEQ ID NOS:312-354, respectively.
Polynucleotides of the invention present in a host cell can be isolated free of other cellular components such as membrane components, proteins, and lipids. Polynucleotides can be made by a cell and isolated using standard nucleic acid purification techniques, or synthesized using an amplification technique, such as the polymerase chain reaction (PCR), or by using an automatic synthesizer. Methods for isolating polynucleotides are routine and are known in the art. Any such technique for obtaining a polynucleotide can be used to obtain isolated polynucleotides encoding antibodies of the invention. For example, restriction enzymes and probes can be used to isolate polynucleotides which encode the antibodies. Isolated polynucleotides are in preparations that are free or at least 70, 80, or 90% free of other molecules.
Human antibody-encoding DNA molecules of the invention can be made with standard molecular biology techniques, using mRNA as a template. Thereafter, DNA molecules can be replicated using molecular biology techniques known in the art and disclosed in manuals such as Sambrook et al. (1989). An amplification technique, such as PCR, can be used to obtain additional copies of the polynucleotides.
Alternatively, synthetic chemistry techniques can be used to synthesize polynucleotides encoding antibodies of the invention. The degeneracy of the genetic code allows alternate nucleotide sequences to be synthesized that will encode an antibody having, for example, one of the VHCDR3, VLCDR3, light chain, or heavy chain amino acid sequences shown in SEQ ID NOS:1-43, 44-86, 97-139, or 140-182, respectively.
Expression of Polynucleotides
To express a polynucleotide encoding a human antibody of the invention, the polynucleotide can be inserted into an expression vector that contains the necessary elements for the transcription and translation of the inserted coding sequence. Methods that are well known to those skilled in the art can be used to construct expression vectors containing sequences encoding human antibodies and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described, for example, in Sambrook et al. (1989) and in Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, N.Y., 1995. See also Examples 1-3, below.
A variety of expression vector/host systems can be utilized to contain and express sequences encoding a human antibody of the invention. These include, but are not limited to, microorganisms, such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors, insect cell systems infected with virus expression vectors (e.g., baculovirus), plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids), or animal cell systems.
The control elements or regulatory sequences are those non-translated regions of the vector—enhancers, promoters, 5′ and 3′ untranslated regions—which interact with host cellular proteins to carry out transcription and translation. Such elements can vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, can be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the BLUESCRIPT phagemid (Stratagene, LaJolla, Calif.) or pSPORT1 plasmid (Life Technologies) and the like can be used. The baculovirus polyhedrin promoter can be used in insect cells. Promoters or enhancers derived from the genomes of plant cells (e.g., heat shock, RUBISCO, and storage protein genes) or from plant viruses (e.g., viral promoters or leader sequences) can be cloned into the vector. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are preferable. If it is necessary to generate a cell line that contains multiple copies of a nucleotide sequence encoding a human antibody, vectors based on SV40 or EBV can be used with an appropriate selectable marker.
Large scale production of human TIMP-1 antibodies can be carried out using methods such as those described in Wurm et al., Ann. N. Y. Acad. Sci. 782, 70-78, 1996, and Kim et al., Biotechnol. Bioengineer. 58, 73-84, 1998.
Pharmaceutical Compositions
Any of the human TIMP-1 antibodies described above can be provided in a pharmaceutical composition comprising a pharmaceutically acceptable carrier. The pharmaceutically acceptable carrier preferably is non-pyrogenic. The compositions can be administered alone or in combination with at least one other agent, such as stabilizing compound, which can be administered in any sterile, biocompatible pharmaceutical carrier, including, but not limited to, saline, buffered saline, dextrose, and water. A variety of aqueous carriers may be employed, e.g., 0.4% saline, 0.3% glycine, and the like. These solutions are sterile and generally free of particulate matter. These solutions may be sterilized by conventional, well known sterilization techniques (e.g., filtration). The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, etc. The concentration of the antibody of the invention in such pharmaceutical formulation can vary widely, i.e., from less than about 0.5%, usually at or at least about 1% to as much as 15 or 20% by weight and will be selected primarily based on fluid volumes, viscosities, etc., according to the particular mode of administration selected. See U.S. Pat. No. 5,851,525. If desired, more than one type of human antibody, for example with different Kd for TIMP-1 binding or with different IC50s for MMP-inhibiting activity neutralization, can be included in a pharmaceutical composition.
The compositions can be administered to a patient alone, or in combination with other agents, drugs or hormones. In addition to the active ingredients, these pharmaceutical compositions can contain suitable pharmaceutically-acceptable carriers comprising excipients and auxiliaries that facilitate processing of the active compounds into preparations which can be used pharmaceutically. Pharmaceutical compositions of the invention can be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, transdermal, subcutaneous, intraperitoneal, intranasal, parenteral, topical, sublingual, or rectal means.
After pharmaceutical compositions have been prepared, they can be placed in an appropriate container and labeled for treatment of an indicated condition. Such labeling would include amount, frequency, and method of administration.
Methods of Decreasing MMP-Inhibiting Activity of Human TIMP-1
The invention provides methods of decreasing an MMP-inhibiting activity of human or rat TIMP-1. Such methods can be used therapeutically, as described below, or in a research setting. Thus, the methods can be carried out in a cell-free system, in a cell culture system, or in vivo. In vivo methods of decreasing MMP-inhibiting activity of human or rat TIMP-1 are described below.
Human TIMP-1 is contacted with a human antibody that binds to the human TIMP-1, thereby decreasing the MMP-inhibiting activity of the human TIMP-1 relative to human TIMP-1 activity in the absence of the antibody. The antibody can be added directly to the cell-free system, cell culture system, or to an animal subject or patient, or can be provided by means of an expression vector encoding the antibody.
Diagnostic Methods
The invention also provides diagnostic methods, with which human or rat TIMP-1 can be detected in a test preparation, including without limitation a sample of serum, lung, liver, heart, kidney, colon, a cell culture system, or a cell-free system (e.g., a tissue homogenate). Such diagnostic methods can be used, for example, to diagnose disorders in which TIMP-1 is elevated. Such disorders include, but are not limited to, liver fibrosis, alcoholic liver disease, cardiac fibrosis, acute cardiac syndrome, lupus nephritis, glomerulosclerotic renal disease, benign prostate hypertrophy, lung cancer, colon cancer, and idiopathic pulmonary fibrosis. When used for diagnosis, detection of an amount of the antibody-TIMP-1 complex in a test sample from a patient which is greater than an amount of the complex in a normal sample identifies the patient as likely to have the disorder.
The test preparation is contacted with a human antibody of the invention, and the test preparation is then assayed for the presence of an antibody-TIMP-1 complex. If desired, the human antibody can comprise a detectable label, such as a fluorescent, radioisotopic, chemiluminescent, or enzymatic label, such as horseradish peroxidase, alkaline phosphatase, or luciferase.
Optionally, the antibody can be bound to a solid support, which can accommodate automation of the assay. Suitable solid supports include, but are not limited to, glass or plastic slides, tissue culture plates, microtiter wells, tubes, silicon chips, or particles such as beads (including, but not limited to, latex, polystyrene, or glass beads). Any method known in the art can be used to attach the antibody to the solid support, including use of covalent and non-covalent linkages, passive absorption, or pairs of binding moieties attached to the antibody and the solid support. Binding of TIMP-1 and the antibody can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtiter plates, test tubes, and microcentrifuge tubes.
Therapeutic Methods
The invention also provides methods of ameliorating symptoms of a disorder in which TIMP-1 is elevated. These disorders include, without limitation, liver fibrosis alcoholic liver disease, cardiac fibrosis, acute coronary syndrome, lupus nephritis, glomerulosclerotic renal disease, idiopathic pulmonary fibrosis, benign prostate hypertrophy, lung cancer, colon cancer, and scarring. See, e.g., Inokubo et al., Am. Heart J. 141, 211-17, 2001; Ylisirnio et al., Anticancer Res. 20, 1311-16, 2000; Holten-Andersen et al., Clin. Cancer Res. 6, 4292-99, 2000; Holten-Andersen et al., Br. J. Cancer 80, 495-503, 1999; Peterson et al., Cardiovascular Res. 46, 307-15, 2000; Arthur et al., Alcoholism: Clinical and Experimental Res. 23, 840-43, 1999; Iredale et al., Hepatol. 24, 176-84, 1996.
Human antibodies of the invention are particularly useful for treating liver fibrosis. All chronic liver diseases cause the development of fibrosis in the liver. Fibrosis is a programmed uniform wound healing response. Toxic damage or injury caused by foreign proteins cause the deposition of extracellular matrix such as collagen, fibronectin, and laminin. Liver fibrosis and cirrhosis can be caused by chronic degenerative diseases of the liver such as viral hepatitis, alcohol hepatitis, autoimmune hepatitis, primary biliary cirrhosis, cystic fibrosis, hemochromatosis, Wilson's disease, and non-alcoholic steato-hepatitis, as well as chemical damage.
Altered degradation and synthesis of extracellular matrix (particularly collagens) play central roles in pathogenesis of liver fibrosis. In the early phases, hepatic stellate cells (HSC) are initially activated and release matrix metalloproteases with the ability to degrade the normal liver matrix. When HSC are fully activated, there is a net down-regulation of matrix degradation mediated by increased synthesis and extracellular release of tissue inhibitors of metalloprotease (TIMP)-1 and -2. The dynamic regulation of activity of metalloproteases during liver fibrosis makes them and their inhibitors targets for therapeutic intervention.
Human antibodies of the invention are also particularly useful for treating lung fibrosis. Lung airway fibrosis is a hallmark of airway remodeling in patients with chronic asthma, so human antibodies of the invention are also particularly useful for chronic asthma. Airway remodeling is a well-recognized feature in patients with chronic asthma. TIMP-1 but not TIMP-2 levels were significantly higher in untreated asthmatic subjects than in glucocorticoid-treated subjects or controls (p<0.0001), and were far greater than those of MMP-1, MMP-2, MMP-3, and MMP-9 combined (Mautino et al., Am J Respir Crit Care Med 1999 160:324-330). TIMP-1 mRNA and protein expression are selectively and markedly increased in a murine model of bleomycin-induced pulmonary fibrosis (Am. J. Respir. Cell Mol. Biol. 24:599-607, 2001). This specific elevation of TIMP-1 without increase in MMPs in asthma patients suggests that inhibition of TIMP-1 by an antibody can restore normal collagen degradation in the lung.
Human antibodies of the invention are also particularly useful for treating cancer. TIMP-1 protein has been found to be elevated in plasma of colon (Holten-Andersen et al., Br J Cancer 1999, 80:495-503) and prostate (Jung et al., Int J Cancer, 1997, 74:220-223) cancer patients, and high TIMP-1 plasma level correlates with poor clinical outcome of colon cancer (Holten-Andersen et al., Clin Cancer Res 2000 6:4292-4299). TIMP-1 induces dose-dependent proliferation of breast tumorigenic clonal cell line and tyrosine phosphorylation (Luparello et al, Breast Cancer Res Treat, 1999, 54:235-244). Therefore, the use of antibody against TIMP-1 may block its ability to induce cancer.
Human TIMP-1 antibodies can be used to prevent or diminish scar formation, such as scar formation after surgery (particularly ophthalmic surgery) or injury (such as a bum, scrape, crush, cut or tear injury).
In one embodiment of the invention, a therapeutically effective dose of a human antibody of the invention is administered to a patient having a disorder in which TIMP-1 is elevated, such as those disorders described above. Symptoms of the disorder, including deposition of extracellular matrix, as well as loss of tissue or organ function, are thereby ameliorated.
Determination of a Therapeutically Effective Dose
The determination of a therapeutically effective dose is well within the capability of those skilled in the art. A therapeutically effective dose refers to that amount of human antibody that reduces MMP-inhibiting activity of the TIMP-1 relative to the activity which occurs in the absence of the therapeutically effective dose.
The therapeutically effective dose can be estimated initially either in cell culture assays or in animal models, usually rats, mice, rabbits, dogs, or pigs. The animal model also can be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans. A rat liver fibrosis model is described in Example 6.
Therapeutic efficacy and toxicity, e.g., ED50 (the dose therapeutically effective in 50% of the population) and LD50 (the dose lethal to 50% of the population) of a human antibody, can be determined by standard pharmaceutical procedures in cell cultures or experimental animals. The dose ratio of toxic to therapeutic effects is the therapeutic index, and it can be expressed as the ratio, LD50/ED50.
Pharmaceutical compositions that exhibit large therapeutic indices are preferred. The data obtained from cell culture assays and animal studies is used in formulating a range of dosage for human use. The dosage contained in such compositions is preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage varies within this range depending upon the dosage form employed, sensitivity of the patient, and the route of administration.
The exact dosage will be determined by the practitioner, in light of factors related to the patient who requires treatment. Dosage and administration are adjusted to provide sufficient levels of the human antibody or to maintain the desired effect. Factors that can be taken into account include the severity of the disease state, general health of the subject, age, weight, and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy. Long-acting pharmaceutical compositions can be administered every 3 to 4 days, every week, or once every two weeks depending on the half-life and clearance rate of the particular formulation.
Polynucleotides encoding human antibodies of the invention can be constructed and introduced into a cell either ex vivo or in vivo using well-established techniques including, but not limited to, transferrin-polycation-mediated DNA transfer, transfection with naked or encapsulated nucleic acids, liposome-mediated cellular fusion, intracellular transportation of DNA-coated latex beads, protoplast fusion, viral infection, electroporation, “gene gun,” and DEAE- or calcium phosphate-mediated transfection.
Effective in vivo dosages of an antibody are in the range of about 5 mg to about 50 mg/kg, about 50 mg to about 5 mg/kg, about 100 mg to about 500 mg/kg of patient body weight, and about 200 to about 250 mg/kg of patient body weight. For administration of polynucleotides encoding the antibodies, effective in vivo dosages are in the range of about 100 ng to about 200 ng, 500 ng to about 50 mg, about 1 mg to about 2 mg, about 5 mg to about 500 mg, and about 20 mg to about 100 mg of DNA.
The mode of administration of human antibody-containing pharmaceutical compositions of the invention can be any suitable route which delivers the antibody to the host. Pharmaceutical compositions of the invention are particularly useful for parenteral administration, i.e., subcutaneous, intramuscular, intravenous, or intranasal administration.
All patents, patent applications, and references cited in this disclosure are expressly incorporated herein by reference. The above disclosure generally describes the present invention. A more complete understanding can be obtained by reference to the following specific examples, which are provided for purposes of illustration only and are not intended to limit the scope of the invention.
EXAMPLE 1
Construction of a Human Combinatorial Antibody Library (HuCAL® Fab 1)
Cloning ofHuCAL® Fab 1. HuCAL® Fab 1 is a fully synthetic, modular human antibody library in the Fab antibody fragment format. HuCAL® Fab 1 was assembled starting from an antibody library in the single-chain format (HuCAL®-scFv; Knappik et al., J. Mol. Biol. 296, 55, 2000). HuCAL® Fab 1 was cloned into a phagemid expression vector pMORPH® 18 Fab1 (FIG. 3). This vector comprises the Fd fragment with a phoA signal sequence fused at the C-terminus to a truncated gene III protein of filamentous phage, and further comprises the light chain VL-CL with an ompA signal sequence. Both chains are under the control of the lac operon. The constant domains Cλ, Cκ, and CH are synthetic genes fully compatible with the modular system of HuCAL® (Knappik et al., 2000).
First, the Vλ and Vκ libraries were isolated from HuCAL®-scFv. Vλl fragments were amplified by 15 PCR cycles (Pwo polymerase) with primers 5′-GTGGTGGTTCCGATATC-3′ (SEQ ID NO:380) and 5′- AGCGTCACA-CTCGGTGCGGCTTTCGGCTGGCCAAGAACGGTTA-3′ (SEQ ID NO:381). PCR-products were digested with EcoRV/DraIII and gel-purified. VLκ-chains were obtained by restriction digest with EcoRV/BsiWI and gel-purified. These Vλ and Vκ libraries were cloned into pMORPH® 18 Fab1 cut with EcoRV/DraIII and EcoRV/BsiWI, respectively. After ligation and transformation in E. coli TG-1, library sizes of 4.14×108 and 1.6×108, respectively, were obtained, in both cases exceeding the Vλ, diversity of HuCAL®-scFv.
Similarly, the VH library was isolated from HuCAL®-scFv by restriction digest using StyI/MunI. This VH library was cloned into the pMORPH® 18-Vλ and Vκ libraries cut with StyI/MunI. After ligation and transformation in E. coli TG-1, a total library size of 2.09×1010 was obtained, with 67% correct clones (as identified by sequencing of 207 clones).
Phagemid rescue, phage amplification andpurification. HuCAL® Fab was amplified in 2×TY medium containing 34 μg/ml chloramphenicol and 1% glucose (2×TY-CG). After helper phage infection (VCSM13) at 37° C. at an OD600 of about 0.5, centrifugation and resuspension in 2×TY/34 μg/ml chloramphenicol/50 μg/ml kanamycin, cells were grown overnight at 30° C. Phage were PEG-precipitated from the supernatant (Ausubel et al., 1998), resuspended in PBS/20% glycerol, and stored at −80° C. Phage amplification between two panning rounds was conducted as follows: mid-log phase TG1-cells were infected with eluted phage and plated onto LB-agar supplemented with 1% of glucose and 34 μg/ml of chloramphenicol. After overnight incubation at 30° C., colonies were scraped off and adjusted to an OD600 of 0.5. Helper phage were added as described above.
EXAMPLE 2
Solid Phase Panning
Wells of MaxiSorpTM microtiter plates (Nunc) were coated with rat- or human TIMP protein diluted to 50 μg/ml dissolved in PBS (2 μg/well). After blocking with 5% non-fat dried milk in PBS, 1-5×1012 HuCAL® Fab phage purified as above were added for 1 h at 20° C. After several washing steps, bound phage were eluted by pH-elution with 100 mM triethylamine and subsequent neutralization with 1M TRIS-C1 pH 7.0. See Krebs et al., J. Immunol. Meth. 254, 67, 2001. Two to three rounds of panning were performed with phage amplification conducted between each round as described above.
EXAMPLE 3
Solution Panning
Biotinylated antigen was diluted to 40 nM in PBS, 1013 HuCAL®-Fab 1 phage were added and incubated for 1 h at 20° C. Phage-antigen complexes were captured on Neutravidin plates (Pierce). After several washing steps, bound phages were eluted by different methods (Krebs et al., 2001). Two rounds of panning were routinely performed.
EXAMPLE 4
Subcloning of Selected Fab Fragments for Expression
The Fab-encoding inserts of the selected HuCAL® Fab 1 fragments were subcloned into the expression vector pMORPH® x7_FS (Knappik et al., J. Mol. Biol. 296, 55, 2000) to facilitate rapid expression of soluble Fab. The DNA preparation of the selected HuCAL® Fab 1 clones was digested with XbaI/EcoRI, thus cutting out the Fab encoding insert (ompA-VL and phoA-Fd). Subcloning of the purified inserts into the XbaI/EcoRI cut vector pMORPH® x7, previously carrying a scFv insert, produces a Fab expression vector designated pMORPH® x9_Fab1_FS (FIG. 4). Fabs expressed in this vector carry two C-terminal tags (FLAGTM and Strep-tagII) for detection and purification.
EXAMPLE 5
Identification of TIMP-binding Fab Fragments by ELISA
The wells of 384-well Maxisorp ELISA plates were coated with 20 μl/well solutions of rat TIMP or human TIMP at a concentration of 5 μg/ml diluted in coating buffer. Expression of individual Fab in E. coli TG-1 from expression vector pMORPH®x9_FS was induced with 0.5 mM IPTG for 12 h at 30° C. Soluble Fab was extracted from the periplasm by osmotic shock (Ausubel et al., 1998) and used in an ELISA. The Fab fragment was detected after incubation with alkaline phosphatase-conjugated anti-Fab antibody (Dianova), followed by development with Attophos substrate (Roche) and measurement at Ex450 nm/Em535 nm. Values at 370 nm were read out after addition of horseradish peroxidase-conjugated anti-mouse IgG antibody and POD soluble substrate (Roche Diagnostics).
EXAMPLE 6
Expression and Purification of HuCAL®-Fab 1 Antibodies in E. coli 
Expression of Fab fragments encoded by pMORPH® x9_FS in TG-1 cells was carried out in shaker flask cultures with 1 liter of 2×TY medium supplemented with 34 μg/ml chloramphenicol. After induction with 0.5 mM IPTG, cells were grown at 22° C. for 16 h. Periplasmic extracts of cell pellets were prepared, and Fab fragments were isolated by Strep-tactin® chromatography (IBA, Goettingen, Germany). The apparent molecular weights were determined by size exclusion chromatography (SEC) with calibration standards. Concentrations were determined by UV-spectrophotometry.
EXAMPLE 7
Construction of HuCAL® Immunoglobulin Expression Vectors
Heavy chain cloning. The multiple cloning site of pcDNA3.1+ (Invitrogen) was removed (NheI/ApaI), and a stuffer compatible with the restriction sites used for HuCAL® design was inserted for the ligation of the leader sequences (NheI/EcoRI), VH-domains (EcoRI/BlpI), and the immunoglobulin constant regions (BlpI/ApaI). The leader sequence (EMBL M83133) was equipped with a Kozak sequence (Kozak, 1987). The constant regions of human IgG1 (PIR J00228), IgG4 (EMBL K01316), and serum IgA1 (EMBL J00220) were dissected into overlapping oligonucleotides with lengths of about 70 bases. Silent mutations were introduced to remove restriction sites non-compatible with the HuCAL® design. The oligonucleotides were spliced by overlap extension-PCR.
Light chain cloning. The multiple cloning site of pcDNA3.1/Zeo+ (Invitrogen) was replaced by two different stuffers. The κ-stuffer provided restriction sites for insertion of a κ-leader (NheI/EcoRV), HuCAL®-scFv Vκ-domains (EcoRV/BsiWI,) and the κ-chain constant region (BsiWI/ApaI). The corresponding restriction sites in the λ-stuffer were NheI/EcoRV (λ-leader), EcoRV/HpaI (Vλ-domains), and HpaI/ApaI (λ-chain constant region). The κ-leader (EMBL Z00022) as well as the λ-leader (EMBL L27692) were both equipped with Kozak sequences. The constant regions of the human κ-(EMBL J00241) and λ-chain (EMBL M18645) were assembled by overlap extension-PCR as described above.
Generation of IgG-expressing CHO-cells. CHO-K1 cells were co-transfected with an equimolar mixture of IgG heavy and light chain expression vectors. Double-resistant transfectants were selected with 600 μg/ml G418 and 300 μg/ml Zeocin (Invitrogen) followed by limiting dilution. The supernatant of single clones was assessed for IgG expression by capture-ELISA (see below). Positive clones were expanded in RPMI-1640 medium supplemented with 10% ultra-low IgG-FCS (Life Technologies). After adjusting the pH of the supernatant to 8.0 and sterile filtration, the solution was subjected to standard protein A column chromatography (Poros 20 A, PE Biosystems).
EXAMPLE 8
Design of the CDR3 Libraries
Vλ positions 1 and 2. The original HuCAL® master genes were constructed with their authentic N-termini: Vλ11: QS (CAGAGC), Vλ12: QS (CAGAGC), and Vλ13: SY (AGCTAT). Sequences containing these amino acids are shown in WO 97/08320. During HuCAL® library construction, the first two amino acids were changed to DI to facilitate library cloning (EcoRI site). All HuCAL® libraries contain VλI genes with the EcoRV site GATATC (DI) at the 5′-end. All HuCAL® kappa genes (master genes and all genes in the library) contain DI at the 5′-end.
VH position 1. The original HuCAL® master genes were constructed with their authentic N-termini: VH1A, VH1B, VH2, VH4, and VH6 with Q (=CAG) as the first amino acid and VH3 and VH5 with E (=GAA) as the first amino acid. Sequences containing these amino acids are shown in WO 97/08320. In the HuCAL® Fab 1 library, all VH chains contain Q (=CAG) at the first position.
Vκ1/Vκ3 position 85. Because of the cassette mutagenesis procedure used to introduce the CDR3 library (Knappik et al., J. Mol. Biol. 296, 57-86, 2000), position 85 of Vκ1 and Vκ3 can be either T or V. Thus, during HuCAL® scFv 1 library construction, position 85 of Vκ1 and Vκ3 was varied as follows: Vκ1 original, 85T (codon ACC); WI library, 85T or 85V (TRIM codons ACT or GTT); Vκ3 original, 85V (codon GTG); Vκ3 library, 85T or 85V (TRIM codons ACT or GTT); the same applies to HuCAL® Fab1.
CDR3 design. All CDR3 residues which were kept constant are indicated in FIG. 1.
CDR3 length. The designed CDR3 length distribution is as follows. Residues which were varied are shown in brackets (x) in FIG. 1. V kappa CDR3, 8 amino acid residues (position 89 to 96) (occasionally 7 residues), with Q90 fixed; V lambda CDR3, 8 to 10 amino acid residues (position 89 to 96) (occasionally 7-10 residues), with Q89, S90, and D92 fixed; and VH CDR3, 5 to 28 amino acid residues (position 95 to 102) (occasionally 4-28), with D101 fixed.
EXAMPLE 9
Chronic Carbon Tetrachloride-induced Liver Fibrosis
Sprague Dawley rats (200-220 g) are used in an in vivo model of liver fibrosis. To maximally induce microsomal metabolism of carbon tetrachloride metabolism, animals receive 1 g/1 isoniazid with their drinking water starting one week before the administration of carbon tetrachloride. Carbon tetrachloride (1:1 in mineral oil) is administered orally every fifth day at a dose of 0.2 ml/100 g body weight. A human TIMP-1 antibody is administered intravenously, either once or repeatedly, during the period of carbon tetrachloride treatment. Necropsy is performed after 5-7 weeks of treatment. McLean et al., Br. J. Exp. Pathol. 50, 502-06, 1969.
Transverse cylinders of liver tissue are cut from the right liver lobe, fixed in formaldehyde, and embedded in paraffin. The amount of fibrosis in the liver is indicated by the picrosirius red-stained fibrotic areas. Picrosirius-positive areas are determined in several centrilobular fields in each section. Parameters of color detection are standardized and kept constant throughout the experiment. The field are selected using a standardized grid which covers an area of 31 mm2. A Leica Quantimed 500 MC system is used for morphometry.
EXAMPLE 10
Hydroxyproline Determination
The method of Prockop & Udenfried, Anal. Biochem. 1, 228-39,1960, can be used to determine hydroxyproline is liver tissues, with the following modifications. Liver specimens of 60-90 mg wet weight are dried and hydrolyzed in 6 N HCl at 100° C. for 17 h. The hydrolyzed material is dried and reconstituted in 5 ml of deionized water. Two hundred microliters of this hydrolysate are mixed with 200 ml of ethanol and 200 ml chloramin T solution (0.7% in citrate buffer [5.7 g sodium acetate, 3.75 g trisodium citrate, 0.55 g citric acid, 38.5 ml ethanol, made up to 100 ml with water]) and allowed to oxidize for 20 min at room temperature. Four hundred microliters of Ehrlich's reagent (12 g p-dimethylaminobenzldehyde in 40 ml ethanol and 2.7 ml H2SO4) are added. After incubation for 3 h at 35° C., absorbance at 573 nm is measured.
EXAMPLE 11
Affinity Determination by Surface Plasmon Resonance Measurements (BlAcoreTM)
For affinity determination, monomeric fractions of affinity and SEC purified Fab fragments or purified IgG1 molecules were used. All experiments were conducted in HBS buffer at a flow rate of 20 μl/min at 25° C. on a BlAcoreTM instrument. Antigens in 100 mM sodium acetate pH 5.0 were coupled to a CM 5 sensor chip using standard EDC-NHS coupling chemistry. Applying 3-4 μl of 5 μg/ml TIMP-1 typically resulted in 500 resonance units for kinetic measurements. All sensograms were fitted globally using BIA evaluation software. For monovalent Fab fragments a monovalent fit (Langmuir binding) and for IgGs a bivalent fit was applied.
EXAMPLE 12
IC50 Determination in Human TIMP-1/human MMP-1 and Rat TIMP-1/rat MMP-13 Assay
Purified Fab fragments or IgGs were used for IC50 determination. Antibodies were diluted in triplicate to the indicated concentrations in assay buffer containing 0.05% BSA. After addition of TIMP (final conc. 1.2 nM or 0.4 nM for modified in human TIMP-1/human MMP-1 assay), MMP (final conc. 1.2 nM or 0.4 nM for modified in human TIMP-1/human MMP-1 assay), and peptide substrate (final conc. 50 μM) and incubation for 1-3 h at 37° C., fluorescence at Ex320 nm/Em430 nm was measured.
The following controls were included in the assay and used as reference values for IC50 determination:

    
    
        A: MMP+substrate: this value was defined as 100% MMP activity in absence of antibody and TIMP.
        B: MMP+TIMP+substrate: this value was defined as maximum inhibition achieved in the assay and calculated as a % of total MMP activity.
    
    


To define the concentration of antibody that resulted in 50% reversal of inhibition (IC50), the following procedure was used:

    
    
        The value for 50% reversal of inhibition (expressed as % activity MMP) was calculated as: Y=[(A−B)/2]+B.
        MMP activity was plotted against concentration of antibody in the assay.
        The concentration of antibody that results in 50% reversal of inhibition (Y) was read on the x-axis and defined as IC50.
        Error bars in the graphs were derived from triplicate wells in one assay.
        Standard deviations for IC50 values were calculated from 3 independent assays.
    
    


EXAMPLE 13
Affinity Maturation of Selected Fab by Stepwise Exchange of CDR Cassettes
To increase affinity and biological activity of selected antibody fragments, CDR regions were optimized by cassette mutagenesis using trinucleotide directed mutagenesis (Virnekäs et al., 1994). Fab fragments in expression vector PMORPH® x9 were cloned into phagemid vector pMORPH®—18 using EcoRI/XbaI restriction sites. CDR cassettes containing several diversified positions were synthesized and cloned into Fab fragments in pMORPH®—18 using unique restriction sites (Knappik et al., 2000). Affinity maturation libraries were generated by transformation into E. coli TOP10F, and phage were prepared as described above. Phage displaying Fab fragments with improved affinity were selected by 2-3 rounds solution panning using stringent washing conditions (e.g., competition with 1 μM non-biotinylated antigen or washing for up to 48 h with frequent buffer exchange) and limited amounts of antigen (0.04-4 nM). Seventeen human TIMP-1 antibodies were tested for affinity to human TIMP-1 (with some tested for affinity to rat TIMP-1) using a BIAcoreTM assay. The Kd of these antibodies for human TIMP-1 and rat TIMP-1 are shown in Table 1.







TABLE 1







Overview of species cross-reactive Fab












Monovalent






KD



Human
Monovalent KD
IC50 in human
IC50 in rat


Fab
TIMP-1
rat TIMP-1
protease assay
protease assay


















MS-BW-25
25 +/− 16
nM*
4517 +/− 2400
nM
115 +/− 15
nM
>300
nM












MS-BW-27
~74
nM
~3200
nM
Non blocking















MS-BW-21
520 +/− 20
nM
36 +/− 2
nM
>300
nM
67 +/− 5
nM


MS-BW-38
~3
nM
~353
nM
~11
nM
>300
nM


MS-BW-39
~7500
nM
~108
nM
>100
nM
>100
nM





*In cases where standard deviations are given, three independent measurements were done with Fab from three different protein expressions/purifications.


~Indicates preliminary data, in cases where measurement was done only once.






EXAMPLE 14
Screening for Fab with Improved Off-rates by Koff Ranking Using Surface Plasmon Resonance
Phage eluted after solution panning were used to infect E. coil TG-1 and plated on agar plates containing 34 μg/ml chloramphenicol. Clones were picked into 96 well plates and used to produce Fab fragments. On the same plate, parental clones were inoculated as controls. Soluble Fab was extracted from the periplasm by osmotic shock (Ausubel et al., 1998) and used for koff ranking in BIAcoreTM.
All measurements were conducted in HBS buffer at a flow rate of 20 μl/min at 25° C. on a BIAcoreTM instrument. Antigens in 100 mM sodium acetate pH 4.5 were coupled to a CM 5 sensor chip using standard EDC-NHS coupling chemistry. Applying 10 μl of 25 μg/ml TIMP-1 typically resulted in 5000 resonance units for koff ranking. All sensograms were fitted using BIA evaluation software. Clones with improved off rate were selected by comparison to parental clones.
EXAMPLE 15
Generation of Species Cross-reactive Antibodies
To maximize the likelihood of obtaining blocking antibodies that are cross-reactive between human and rat TIMP-1, alternating pannings were carried out on rat and human protein. Additionally, all antibodies selected by pannings on solely the human or rat TIMP-1 protein were analyzed for cross-reactivity in order to check for cross-reactive antibodies that might be selected by chance. Antibodies selected from these pannings were analyzed for cross-reactivity in ELISA using crude E. coli extracts. Cross-reactive antibodies in this assay were subjected to expression in 1-liter scale followed by purification. Purified antibodies were tested for cross-reactivity in BIAcoreTM and protease assays (Table 1).
As shown in Table 1, a total of five different Fab cross-reactive with human and rat TIMP-1 were generated. BIAcoreTM measurements revealed that although these antibodies clearly bind to human and rat TIMP-1, affinities for both species differ by at least a factor of 50. An antibody used for human therapy or in an animal model should have an affinity to the target protein in the low nanomolar, preferably in the sub-nanomolar range. As none of the above-described antibodies had affinities in this range for both species, these antibodies were not considered useful for further experiments or development.
EXAMPLE 16
Generation of Blocking Antibodies against Human TIMP-1
To generate blocking antibodies against human TIMP-1, the HuCAL®-Fab 1 library was used for antibody selection (AutoPan®) on purified TIMP-1 protein followed by subdloning and expression of the selected Fab fragments in E. coli. Crude antibody-containing E. coli extracts were used for primary antibody characterization in ELISA (AutoScreen®). Purified Fab proteins were subjected to further characterization in ELISA, TIMP-1/MMP-1 assay and BIAcoreTM. A total of 6100 clones were analyzed in AutoScreen®, 670 of them showed binding to human TIMP-1. Sequence analysis revealed that in total seven unique antibody clones had been selected (Table 2). For these seven Fab clones, the affinities measured in BIAcoreTM were in the range of 10-180 nM (Table 4). When tested in the human protease assay, five of them were able to block the interaction between human TIMP-1 and MMP-1. The concentration of monovalent Fab needed to reverse the inhibitory effect of human TIMP-1 on human MMP-1 activity by 50% (IC50) was in the range of 11-100 nM (Table 2). The most active Fab clones are MS-BW-3 (Kd 13 nM; IC50 11 nM) and MS-BW-28 (Kd 10 nM; IC50 22 nM).
A striking feature of antibodies selected against human TIMP-1 is that they all exhibit the combination VH312 and a relatively short VH-CDR3 region, predominantly four amino acids (see Table 2). The HCDR3 cassettes assembled for the HuCAL®-Fab 1 library were designed to achieve a length distribution ranging from 5 to 28 amino acid residues. A four amino acid HCDR3 can occur in the library due to TRIM deletion, but is considered a very rare event. Another remarkable feature was the high degree of sequence homology among the selected LCDR3 sequences.







TABLE 2







Overview of anti-human TIMP-1 Fab












Framework + CDR 3 sequence
Monovalent KD
IC50 in human














Fab
VH
HCDR3
VL
LCDR3
to human TIMP-1
protease assay

















MS-BW-1
H3
FMDI,
λ2
QSYDYQQFT,
 65 +/− 13 nM*
>100 nM





SEQ ID NO:1

SEQ ID NO:44


 


MS-BW-2
H3
GFDY,
λ2
QSYDFKTYL,
180 +/− 28 nM 
>100 nM




SEQ ID NO:2

SEQ ID NO:45


 


MS-BW-3
H3
FLDI,
λ2
QSYDFLRFS,
13 +/− 2 nM 
11 +/− 2 nM




SEQ ID NO:3

SEQ ID NO:46


 


MS-BW-25
H3
TFPIDADS,
λ2
QSYDFINVI,
25 +/− 16 nM
115 +/− 15 nM




SEQ ID NO:4

SEQ ID NO:47


 


MS-BW-26
H3
GHVDY,
λ2
QSYDFVRFM,
~100 nM
non blocking




SEQ ID NO:5

SEQ ID NO:48


 


MS-BW-27
H3
YWRGLSFDI,
λ2
QSYDFYKFN,
~74
non blocking




SEQ ID NO:6

SEQ ID NO:49


 


MS-BW-28
H3
FFDY,
λ2
QSYDFRRFS,
10 +/− 1 nM 
22 +/− 2 nM




SEQ ID NO:7

SEQ ID NO:50





*In cases where standard deviations are given, three independent measurements were done with Fab from three different protein expressions/purifications.


~Indicates preliminary data, in cases where measurement was done only once.






EXAMPLE 17
Increasing the Affinity of Selected Anti-human TIMP-1 Antibodies
In order to increase the affinity of monovalent anti-human TIMP-1 Fab fragments to the sub-nanomolar range, a step-wise affinity maturation approach was applied, by optimizing CDR sequences and keeping framework regions constant.
Affinity Maturation by Light Chain Cloning
The CDR3 sequences of the two antibody fragments with highest affinity (MS-BW-3 and MS-BW-28) had the remarkable feature of an unusually short four amino acid HCDR3 sequence. Furthermore, each Fab had a very similar LCDR3 sequence. This indicates that MS-BW-3 and MS-BW-28 bind to the same epitope and that this epitope might tolerate only a very small subset of CDR3 sequences. As a four amino acid HCDR3 is a very rare event in the library, it can be anticipated that in the initial library not all possible combinations of the short HCDR3 and the preferred LCDR3 are present. Therefore, it was considered that another combination of the selected HCDR3 and LCDR3 sequences might increase the affinity. For this approach, the heavy chain of MS-BW-3 and MS-BW-28 were paired with the light chains of MS-BW-1, -2, -3, -25, -26, -27, and -28 by cloning.
The resulting constructs were transformed into E. coli and expressions/purifications in 1-liter scale were performed. Of the 12 new constructs, 10 resulted in functional Fab molecules. These were analyzed in BIAcoreTM and human protease assay as summarized in Table 3. The best antibody named MS-BW-44 had a monovalent affinity of 2 nM and an IC50 of 4 nM (FIG. 7) and was thus improved by a factor of 6.5 (Kd) or 2.75 (IC50).







TABLE 3







Overview of Fab derived from light chain cloning












Framework + CDR 3 sequence
Monovalent KD
IC50* in human














Fab
VH
HCDR3
VL
LCDR3
to human TIMP-1
protease assay

















MS-BW-40
H3
FLDI,
λ2
QSYDYQQFT,
~49 nM
>100 nM





SEQ ID NO:3

SEQ ID NO:44


 


MS-BW-41
H3
FLDI,
λ2
QSYDFKTYL,
 ~6 nM
29 +/− 6 nM 




SEQ ID NO:3

SEQ ID NO:45


 


MS-BW-43
H3
FLDI,
λ2
QSYDFINVI,
~65 nM
>100 nM




SEQ ID NO:3

SEQ ID NO:47


 


MS-BW-44
H3
FLDI,
λ2
QSYDFVRFM,
   2 +/− 0.4 nM*
4 +/− 1 nM




SEQ ID NO:3

SEQ ID NO:48


 


MS-BW-45
H3
FLDI,
λ2
QSYDFYKFN,
8 +/− 5 nM
9 +/− 3 nM




SEQ ID NO:3

SEQ ID NO:49


 


MS-BW-46
H3
FLDI,
λ2
QSYDFRRFS,
6 +/− 3 nM
  4 +/− 0.5 nM




SEQ ID NO:3

SEQ ID NO:50


 


MS-BW-47
H3
FFDY,
λ2
QSYDYQQFT,
~152 nM 
>100 nM




SEQ ID NO:7

SEQ ID NO:44


 


MS-BW-49
H3
FFDY,
λ2
QSYDFKTYL,
~21 nM
>100 nM




SEQ ID NO:7

SEQ ID NO:45


 


MS-BW-51
H3
FFDY,
λ2
QSYDFINVI,
 ~7 nM
7 +/− 1 nM




SEQ ID NO:7

SEQ ID NO:47


 


MS-BW-52
H3
FFDY,
λ2
QSYDFVRFM,
~11 nM
9 +/− 1 nM




SEQ ID NO:7

SEQ ID NO:48





*In cases were standard deviations are given, three independent measurements were done with Fab from three different protein expressions/purifications.


~Indicates preliminary data, in cases where measurement was done only once.






Affinity Maturation by Optimizing HCDR1 and HCDR2
In the HuCAL®-Fab 1 library, only the CDRs HCDR3 and LCDR3 are diversified to a high extent. Although it is known from crystallographic studies that amino acids from these two CDRs make most of the antibody antigen contacts, the residual four CDRs are also important for antigen binding. However, their contribution to the binding energy can vary from antibody to antibody. In the HuCAL®-Fab 1 library those CDRs exhibit only a limited variability due to the presence of the different master frameworks (Knappik et al., 2000). In order to improve the affinity of the selected antibodies, an affinity maturation approach by randomizing HCDR1 and HCDR2 was applied. For this approach two affinity maturation libraries based on MS-BW-44 cloned into phage display vector pMORPH® 18 were created. In library 1, only HCDR2 of MS-BW-44 was diversified using “TRIM technology” as described in Virnekäs et al., Nucl. Acids. Res. 22, 5600-07, 1994; Knappik et al., J. Mol. Biol. 296, 57-86, 2000. In library 2, both HCDR1 and HCDR2 were diversified using the TRIM technology. In both cases, phage antibody libraries comprising 1×108 different clones were obtained. Both libraries were mixed and used as input for a modified AutoPan® procedure. In order to select antibodies having an increased affinity to human TIMP-1, solution panning using limiting amounts of biotinylated antigen and stringent washing conditions were applied. Antibody off rates were ranked by BIAcoreTM using crude E. coli extracts of selected antibodies. Clones with slower off rate than parental clone MS-BW-44 were subjected to 1-liter scale expression and purification. Purified Fab were analyzed in BIAcoreTM and human protease assay (Table 4).







TABLE 4







Comparison of Fab derived from HCDR1 and HCDR2 optimization with


parental clone MS-BW-44












Monovalent KD
IC50 in human



Fab
to human TIMP-1
protease assay*







MS-BW-44
  2 +/− 0.4 nM
  2 +/− 0.5 nM



MS-BW-44-2
0.5 +/− 0.2 nM
0.4 +/− 0.3 nM



MS-BW-44-6
0.6 +/− 0.2 nM
0.2 +/− 0.1 nM







*IC50 values derived from modified protease assay using decreased amounts of TIMP-1 and MMP-1 (0.4 nM each).






Clone MS-BW-44-2 was derived from library 1 thus having a modified HCDR2 cassette. Its affinity measured by BIAcoreTM was 0.5 nM. Clone MS-BW-44-6 was derived from library 2 having a modified HCDR 1 and HCDR 2 cassette and the affinity measured by BIAcoreTM was 0.6 nM. A sequence comparison between the affinity matured antibodies and their parental clones is shown in Table 8.








TABLE 8





Overview and sequence comparison of affinity matured Fab



fragments against human TIMP-1. Sequence changes compared


to parental Fab fragments (bold) are italicized



















VH
VL

















HDCR1
HCDR2
HCDR3

LCDR1



Clone
Frame-
sequence
sequence
sequence
Frame-
sequence


MS-BW-
work
(SEQ ID NO: )
(SEQ ID NO: )
(SEQ ID NO: )
work
(SEQ ID NO: )

















3
VH3
GFTFSSYAMS
AISGSGGSTYYADSVKG
FLDI
VL2
TGTSSDVGGYNYVS





(355)
(357)
(3)

(363)


 


44
VH3
GFTFSSYAMS
AISGSGGSTYYADSVKG
FLDI
VL2
TGTSSDVGGYNYVS




(355)
(357)
(3)

(363)


 


44-6
VH3
GFTFNSYAMS
VISGNGSNTYYADSVKG
FLDI
VL2
TGTSSDVGGYNYVS




(356)
(358)
(3)

(363)


 


44-2
VH3
GFTFSSYAMS
GISGNGVLIFYADSVKG
FLDI
VL2
TGTSSDVGGYNYVS




(355)
(359)
(3)

(363)


 


44-2-4
VH3
GFTFSSYAMS
GISGNGVLIFYADSVKG
GLMDY
VL2
TGTSSDVGGYNYVS




(355)
(359)
(360)

(363)


 


44-2-15
VH3
GFTFSSYAMS
GISGNGVLIFYADSVKG
WFDH
VL2
TGTSSDVGGYNYVS




(355)
(359)
(361)

(363)


 


44-2-16
VH3
GFTFSSYAMS
GISGNGVLIFYADSVKG
WFDV
VL2
TGTSSDVGGYNYVS




(355)
(359)
(362)

(363)


 


44-6-1
VH3
GFTFNSYAMS
VISGNGSNTYYADSVKG
FLDI
VL2
TGTSSDVGGYNYVS




(356)
(358)
(3)

(363)

















VL
Monov. KD
IC50 in
















LCDR2
LCDR3
to human
human




Clone
sequence
sequence
TIMP-1
protease



MS-BW-
(SEQ ID NO: )
(SEQ ID NO: )
(nM)
assay (nM)







3
DVSNRPS
QSYDFLRFS
 13 +/− 2  
 11 +/− 2   





(364)
(47)



 



44
DVSNRPS
QSYDFVRPM
  2 +/− 0.4
  4 +/− 1   




(364)
(48)



 



44-6
DVSNRPS
QSYDFVRFM
0.6 +/− 0.2
0.2 +/− 0.1*




(364)
(48)



 



44-2
DVSNRPS
QSYDFVRFM
0.5 +/− 0.2
0.4 +/− 0.3*




(364)
(48)



 



44-2-4
DVSNRPS
QSYDFVRFM
 0.2 +/− 0.02
0.2 +/− 0.1*




(364)
(48)



 



44-2-15
DVSNRPS
QSYDFVRFM
0.3 +/− 0.1
0.2 +/− 0.1*




(364)
(48)



 



44-2-16
DVSNRPS
QSYDFVRFM
0.5 +/− 0.2
0.3 +/− 0.1*




(364)
(48)



 



44-6-1
DVSNRPS
QSYDFVRFM
0.2 +/− 0.04
0.2 +/− 0.1*




(364)
(365)







*IC50 values derived from modified protease assay using decreased amounts of TIMP-1 and MMP-1; IC50 of MS-BW-44 is 2 nM under these conditions






When initially analyzed in the human TIMP-1/MMP-1 assay, it was not possible to distinguish a Fab with a sub-nanomolar affinity from a Fab with 1 nM affinity, most likely because the concentration of Fab required to reverse the inhibitory effect of human TIMP-1 on human MMP-1 activity by 50% was below the concentration of total TIMP-1 in the assay. When a modified assay was used with concentrations of TIMP-1 and MMP-1 decreased from 1.2 nM to 0.4 nM, it was possible to distinguish a 2 nM Fab from a sub-nanomolar Fab (Table 4, FIG. 8). Using this modified protease assay, MS-BW-44-2 and MS-BW-44-6 had IC50 values of 0.4 nM and 0.2 nM respectively. Parental clone MS-BW-44 had an IC50 of 2 nM under these conditions. Thus, by this affinity maturation approach, an affinity gain of a factor of 5 (Kd) or 5-10 (IC50) was achieved.
Affinity Maturation by Optimizing HCDR3
As mentioned above, amino acid residues in HCDR3 and LCDR3 are considered the most important for antigen binding. Taking into account that a four amino acid HCDR3 was not planned in the design of HuCAL®-Fab 1 and thus only occurs as a rare case due to a TRIM deletion, probably not all possible combinations of the four amino acids in HCDR3 were represented in the original HuCAL®-Fab 1 library. Therefore, an affinity maturation library was constructed with four and five amino acid HCDR3 maturation cassettes inserted into Fab derived from the previous maturation cycle (among them MS-BW-44-2 and MS-BW-44-6). The obtained affinity maturation library had a diversity of 1×108 clones, therefore theoretically covering all possible four and five amino acid HCDR3 variations. Applying very stringent panning conditions, the best antibody identified, MS-BW-44-2-4, had an affinity measured by BIAcoreTM of 0.2 nM and an IC50 in human TIMP-1/MMP-1 assay of 0.2 nM. A sequence comparison between the affinity matured antibodies and their parental clones is shown in Table 8. The improvement factor gained by this affinity maturation approach is 2.5 with respect to the affinity and 2 with respect to the IC50.
Affinity Maturation by Optimizing LCDR3
As an alternative approach, a maturation strategy was used to further optimize the light chain CDR3 sequence. This was due to the fact that in the first maturation cycle where light chain exchange cloning between selected antibodies was applied, only a very limited subset of sequence variation had been exploited. Therefore, a maturation library was constructed in which, using TRIM technology, a diversified LCDR3 cassette was inserted into Fab derived from HCDR1 and HCDR2 optimization (among them MS-BW-44-2 and MS-BW-44-6). The best Fab identified with this maturation strategy was MS-BW-44-6-1 with an affinity measured by BIAcoreTM of 0.15 nM and an IC50 in a human TIMP-1/MMP-1 assay of 0.2 nM. A sequence comparison between the affinity matured antibody and its parental clones is shown in Table 8. The improvement factor gained by this maturation approach is 4 with respect to affinity. A further improvement of the IC50 in the protease assay could not be measured due to limitations in the assay.
As a result of a step-wise affinity maturation approach using four different maturation strategies, the monovalent affinity of an anti-human TIMP-1 specific Fab fragment was improved by a factor of 87 and its activity in human TIMP-1/MMP-1 assay by a factor of 55. The decision for defining the best Fab fragment has been made on the basis of Kd measurements using BIAcoreTM, as this method proved to be reliable for ranking antibodies with sub-nanomolar affinities, whereas the sensitivity of the human TIMP-1/MMP-1 assay was considered not suitable to rank activity of the best Fabs in the sub-nanomolar range with respect to each other.
The best Fab MS-BW-44-6-1 has an affinity measured by BIAcoreTM of 0.15 nM and an IC50 in human TIMP-1/MMP-1 assay of 0.2 nM. Compared to its parental clone, MS-BW-3, it has optimized LCDR3, HCDR1 and HCDR2 sequences.
EXAMPLE 18
Cross Reactivity of Selected Anti-human TIMP-1 Fab with TIMP-2, TIMP-3, and TIMP-4
TIMP-1 belongs to a family of closely related protease inhibitors all binding to various members of the MMP family of proteases. To date there are four human TIMP proteins described. To investigate potential cross-reactivity of antibody fragments selected against human TIMP-1 with other members of the human TIMP family, an ELISA was performed in which binding of antibody fragments to immobilized purified human TIMP-1, -2, -3 or -4 was analyzed (FIG. 10). Antibody fragments binding to immobilized human TIMP-1 showed no binding to human TIMP-2, -3, -4 above background level when compared to unrelated control protein BSA.
EXAMPLE 19
Generation of Blocking Antibodies against Rat TIMP-1
To generate blocking antibodies against rat TIMP-1, the HuCAL®-Fab 1 library was used for antibody selection (AutoPan®) on immobilized rat TIMP-1 followed by subcloning and expression of the selected Fab fragments in E. coli. Crude antibody-containing E. coli extracts were used for primary antibody characterization in ELISA (AutoScreen®). Purified Fab proteins were subjected to further characterization in ELISA, protease assays, and BIAcoreTM. Of the 8,450 selected clones were analyzed in AutoScreen®, 750 of them showed binding to rat TIMP-1. Sequence analysis revealed that in total 36 unique Fab clones specific for rat TIMP-1 were enriched during selection (Table 7). Their affinities were measured by BIAcoreTM and were found to be in the range of 9-1000 nM (Table 7). When tested in the rat protease assay, all but one of them were able to block the interaction between rat TIMP-1 and rat MMP-13 (Table 7). The concentration of monovalent Fab needed to reverse the inhibitory effect of rat TIMP-1 on rat MMP-13 activity by 50% (IC50) was in the range of 7-300 nM. The most active Fab clones are MS-BW-14 (Kd 10 nM; IC50 14 nM), MS-BW-17 (Kd 13 nM; IC50 11 nM), and MS-BW-54 (Kd 9 nM; IC50 7 nM).







TABLE 7







Overview of anti-rat TIMP-1 Fab












Framework + CDR 3 sequence
Monovalent KD
IC50* in rat














Fab
VH
HCDR3
VL
LCDR3
to rat TIMP-1
protease assay

















MS-BW-5
H1A
GLYWAVYPYFDF,
λ1
QSRDFNRGP,
~210 nM
non blocking





SEQ ID NO:8

SEQ ID NO:51


 


MS-BW-6
H3
LDTYYPDLFDY,
λ1
QSYDQRKW,
 ~68 nM
~100 nM




SEQ ID NO:9

SEQ ID NO:52


 


MS-BW-7
H1A
TYYYFDS,
κ3
QQLYGTVS,
~168 nM
>300 nM




SEQ ID NO:10

SEQ ID NO:53


 


MS-BW-9
H3
YMAYMAEAIDV,
λ1
QSYDGFKTH,
~256 nM
>300 nM




SEQ ID NO:11

SEQ ID NO:54


 


MS-BW-10
H1B
LVGIVGYKPDELLYFDV,
λ3
QSYDYSLL,
~200 nM
 ~30 nM




SEQ ID NO:12

SEQ ID NO:55


 


MS-BW-11
H3
YGAYFGLDY,
λ3
QSYDFNFH,
~200 nM
>300 nM




SEQ ID NO:13

SEQ ID NO:56


 


MS-BW-12
H6
GYADISFDY,
λ3
QSYDMIARYP,
~419 nM
>300 nM




SEQ ID NO:14

SEQ ID NO:57


 


MS-BW-13
H3
YYLLLDY,
λ3
QSWDIHPFDV,
~939 nM
not tested




SEQ ID NO:15

SEQ ID NO:58


 


MS-BW-14
H1A
WSDQSYHYYWHPYFDV,
λ1
QSWDLEPY,
10 +/− 5 nM
14 +/− 3 nM




SEQ ID NO:16

SEQ ID NO:59


 


MS-BW-15
H3
LIGYFDL,
λ2
QSYDVLDSE,
 ~80 nM
~200 nM




SEQ ID NO:17

SEQ ID NO:60


 


MS-BW-17
H5
LTNYFDSIYYDH,
λ2
QSYDPSHPSK,
13 +/− 3 nM
11 +/− 3 nM




SEQ ID NO:18

SEQ ID NO:61


 


MS-BW-18
H5
LVGGGYDLMFDS,
λ2
QSYDDMQF,
~153 nM
>300 nM




SEQ ID NO:19

SEQ ID NO:62


 


MS-BW-19
H5
YVTYGYDDYHFDY,
λ2
QSWDINHAI,
~187 nM
>300 nM




SEQ ID NO:20

SEQ ID NO:63


 


MS-BW-57
H5
LYPEDLIYFDY,
λ2
QSWDVQTDK,
 ~39 nM
 ~60 nM




SEQ ID NO:37

SEQ ID NO:80


 


MS-BW-58
H6
WMTPPGHYYGYTFDV,
λ3
QSWDPSHYY,
~138 nM
not tested




SEQ ID NO:38

SEQ ID NO:81


 


MS-BW-59
H5
LRVHDYAMYFDL,
λ2
QSYDIMPER,
 ~15 nM
30 +/− 5 nM




SEQ ID NO:39

SEQ ID NO:82


 


MS-BW-60
H5
FVSYNGSVPYFDY,
λ2
QSMDFRLMH,
 ~30 nM
>100 nM




SEQ ID NO:40

SEQ ID NO:83


 


MS-BW-61
H5
IIGDYVIFFDV,
λ2
QSFDMIHPY,
 ~51 nM
>100 nM




SEQ ID NO:41

SEQ ID NO:84


 


MS-BW-62
H5
LFTYPFLYFDV,
λ2
QSDFPVM,
 ~36 nM
19 +/− 2   




SEQ ID NO:42

SEQ ID NO:85


 


MS-BW-63
H5
ILTGHVLLFDY,
λ2
QSDNPYL,
 ~14 nM
20 +/− 1 nM




SEQ ID NO:43

SEQ ID NO:86





*In cases were standard deviations are given, three independent measurements were done with Fab from three different protein expressions/purifications.


~Indicates preliminary data, in cases where measurement was done only once.






EXAMPLE 20
Increasing the Affinity of Selected Anti-rat TIMP-1 Antibodies
Affinity maturation was applied to increase the affinity of monovalent anti-rat TIMP-1 Fab fragments to the sub-nanomolar range. No clear sequence homology could be identified among the light chain CDR3 sequences of the selected antibody fragments, indicating that an optimal light chain CDR3 sequence was probably not present or had not been selected from the original HuCAL®-Fab 1 library. We therefore started with modification of LCDR3 to increase the affinity of Fabs.
Two affinity maturation libraries based on MS-BW-14, -17, and -54 cloned into phage display vector pMORPH® 18 were created. In library 1, only LCDR3 was diversified using TRIM technology, as described in Virnekäs et al., Nucl. Acids. Res. 22, 5600-07, 1994; Knappik et al., J. Mol. Biol. 296, 57-86, 2000. In library 2, LCDR1, LCDR2, and LCDR3 were diversified simultaneously using the TRIM technology, while the connecting framework regions were kept constant. In both cases, phage antibody libraries comprising 3×108 different clones were obtained. Both libraries were mixed and used as input for a modified AutoPan® procedure. To select antibodies having an increased affinity to rat TIMP-1, solution panning using limiting amounts of biotinylated antigen and stringent washing conditions were applied.
Antibody-off-rates were ranked by BIAcoreTM using crude E. coli extracts. Clones with slower off rate than parental clones MS-BW-14, -17, or -54 were subjected to expression and purification in 1-liter scale. Purified Fab were analyzed in BIAcoreTM and rat protease assays (Table 6). MS-BW-17-1 (Kd 0.8 nM, IC50 1.6 nM), MS-BW-17-2 (Kd 1.3 nM, IC50 1.1 nM), and MS-BW-17-3 (Kd 1.9 nM, IC50 3 nM) were derived from affinity maturation library 1 having an optimized LCDR3 sequence, whereas MS-BW-54-1 (Kd 2 nM, IC50 3 nM) was derived from affinity maturation library 2 having an optimized LCDRI, -2, and -3 sequence (Table 9).








TABLE 9





Overview and sequence comparison of affinity matured Fab



fragments against rat TIMP-1. Sequence changes compared


to parental Fab fragments (bold) are italicized.



















VH
VL

















HDCR1
HCDR2
HCDR3

LCDR1



Clone
Frame-
sequence
sequence
sequence
Frame-
sequence


MS-BW-
work
(SEQ ID NO: )
(SEQ ID NO: )
(SEQ ID NO: )
work
(SEQ ID NO: )





14
VH1A
GGTFSSYAIS
GIIPIFGTANYAQKFQG
WSDQSYHYYWHPYFDV
VL1
SGSSSNIGSNYVS




(366)
(368)
(370)

(371)


 


17
VH5
GYSFTSYWIG
IIYPGDSDTRYSPSFQG
LTNYFDSIYYDH
VL2
TGTSSDVGGYNYVS




(367)
(369)
(18)

(363)


 


54
VH5
GYSFTSYWIG
IIYPGDSDTRYSPSFQG
YYGFEYDLLFDN
VL2
TGTSSDVGGYNYVS




(367)
(369)
(34)

(363)


 


17-1
VH5
GYSFTSYWIG
IIYPGDSDTRYSPSFQG
LTNYFDSIYYDH
VL2
TGTSSDVGGYNYVS




(367)
(369)
(18)

(363)


 


17-2
VH5
GYSFTSYWIG
IIYPGDSDTRYSPSFQG
LTNYFDSIYYDH
VL2
TGTSSDVGGYNYVS




(367)
(369)
(18)

(363)


 


17-3
VH5
GYSFTSYWIG
IIYPGDSDTRYSPSFQG
LTNYFDSIYYDH
VL2
TGTSSDVGGYNYVS




(367)
(369)
(18)

(363)


 


54-1
VH5
GYSFTSYWIG
IIYPGDSDTRYSPSFQG
YYGFEYDLLFDN
VL2
TGTSSDLGGYNYVS




(367)
(369)
(34)

(372)

















VL
Monov. KD
IC50 in
















LCDR2
LCDR3
to rat
rat




Clone
sequence
sequence
TIMP-1
protease



MS-BW-
(SEQ ID NO: )
(SEQ ID NO: )
(nM)
assay (nM)







14
LMIYDNNQRPS
QSWDLEPY
10 +/− 5
14 +/− 3





(373)
(59)



 



17
LMIYDVSNRPS
QSYDPSHPSk
13 +/− 3
11 +/− 3




(374)
(61)



 



54
LMIYDVSNRPS
QSYDISGYP
 9 +/− 1
7




(374)
(77)



 



17-1
LMIYDVSNRPS
QAFDVAPNGk
0.8
1.6




(374)
(376)



 



17-2
LMIYDVSNRPS
QAFAVMPNVE
1.3
1.1




(374)
(377)



 



17-3
LMIYDVSNRPS
QSFTVSPGAD
1.9
3




(374)
(378)



 



54-1
LMIYAGNNRPS
QAYDSSGYP
2
3




(375)
(379)










The improvement gained by these different one-step maturation strategies was up to a factor of 16.3 with regard to affinity and 10 with regard to functional activity in the protease assay.
EXAMPLE 21
Conversion of Anti-TIMP-1 Fab Fragments into Human IgG1 Molecules for Use in the Rat Model of Chronic Carbon Tetrachloride-Induced Liver Fibrosis
Anti-TIMP-1 Fab fragments were converted into human IgG1 molecules to create antibody molecules with prolonged in vivo half-lives for the use in the rat model of chronic carbon tetrachloride-induced liver fibrosis. This was done by cloning the heavy and light chain variable regions of the Fab into two separate vectors for mammalian IgG1 expression (Krebs et al., 2001)
Anti-rat TIMP-1 clone MS-BW-14 was chosen for the first in vivo study, and IgG1 protein was produced by transient expression. Anti-human TIMP-1 clone MS-BW-3 was selected as a negative control IgG1 and was also produced by transient expression. Purified IgG1 proteins MS-BW-14 and MS-BW-3 were subjected to quality control in BIAcoreTM and rat TIMP-1/rat MMP-13 assays. Bivalent affinity for rat TIMP-1 measured in BIAcoreTM (chip density 500 RU, fitting model for bivalent analyte) is 0.2 nM for MS-BW-14, compared to 13 nM for the corresponding monovalent Fab fragment. This increase in affinity for the IgG1 is due to the avidity effects caused by binding of bivalent IgG1 to immobilized rat TIMP-1 protein on the BIAcoreTM chip. As expected, the negative control IgG1 MS-BW-3 showed no binding to rat TIMP-1 but bound to human TIMP-1 with a bivalent affinity of approximately 0.4 nM.
FIG. 12 shows the activity of MS-BW-14 Fab and IgG1 and MS-BW-3 IgG1 in a rat TIMP-1/rat MMP-13 assay. The IC50 of MS-BW-14 Fab and IgG1 are nearly identical. The avidity effect seen in BIAcoreTM does not occur in this assay because, in contrast to the BIAcoreTM experiment, this assay is based on a monovalent interaction in solution between TIMP-1 and the IgG1. As expected, MS-BW-3 has no effect on rat TIMP-1 binding to rat MMP-13 and thus is a suitable negative control for a rat in vivo study.
Affinity matured clone MS-BW-17-1 was then converted from a monovalent Fab fragment to a bivalent IgG1. Protein was produced by stable transfection. Purified protein was subjected to quality control in BIAcoreTM and rat TIMP-1/rat MMP-13 assays (FIG. 13). In BIAcoreTM an increased bivalent affinity (avidity) of 0.04 nM for IgG1 compared to 0.8 nM for monovalent Fab fragment was seen, whereas the activity in the rat TIMP-1/rat MMP-13 assay was comparable for IgG1 and Fab as expected.
EXAMPLE 22
Cross-reactivity of Anti-rat TIMP-1 IgG1 MS-BW-17-1 with Mouse TIMP-1
Species cross-reactivity of MS-BW-17-1 IgG1 and Fab with mouse TIMP-1 was determined by BIAcoreTM to investigate the feasibility of alternative in vivo models that use mice instead of rats. Although MS-BW-17-1 clearly bound to mouse TIMP-1 immobilized to the chip surface, the affinity of both Fab (180 nM) and IgG1 (9 nM) was 225-fold weaker than the affinity to rat TIMP-1. As the interaction between mouse TIMP-1 and BW-17-1 IgG1 in serum is most likely monovalent, the affinity of BW-17-1 Fab probably reflects the “real” affinity of this interaction. Therefore, the Fab affinity value should be considered when calculating the feasibility of using BW-17-1 IgG1 in a mouse in vivo study.
EXAMPLE 23
Effect of Timp-1 Antibody on the Development of Bleomycin-induced Pulmonary Fibrosis
The following example demonstrates the ability of a human anti-rat Timp-1 antibody (BW 17.1) to prevent fibrotic collagen deposition in a bleomycin-induced rat lung fibrosis model.
Male Lewis rats (6 weeks of age) received a single intratracheal challenge with bleomycin (0.3 mg/rat, in saline) or vehicle (saline) on day 0. Fourteen days later, animals were euthanized, the lung excised, fixed, and processed for evaluation of lung fibrosis. Lung tissue sections were cut, and quantitative assessment by image analysis of lung collagen in lung tissue sections stained with Mason Trichrome stain performed.
Antibody administration: A 20 mg/kg dose of human ant-rat TIMP-1 antibody or control human antibody (IgG) was administered subcutaneously on day -1. Subsequently, a 10 mg/kg dose of human ant-rat TIMP-1 antibody or control human antibody (IgG) was administered s.c. on days 2, 5, 8, and 11. The following five groups of animals were studied: Saline i.t. challenge+antibody vehicle (PBS); Saline i.t. challenge+TIMP-1 antibody; Bleomycin i.t. challenge+TIMP-1 antibody; Bleomycin i.t. challenge+antibody vehicle (PBS); Bleomycin i.t. challenge+control antibody.
FIG. 14 shows the effect of the inhibitory effect of TIMP-1 antibody on bleomycin-induced lung fibrotic collagen.
EXAMPLE 24
Effect of BW-14 Anti-TIMP-1 Antibody in a Rat Model with CC14-induced Liver Fibrosis
Carbon tetrachloride (CC14) was used to induce liver fibrosis as described in Example 9. A single intravenous dose of 3 mg/kg BW-14 or control antibody BW-3, respectively, was administered on day 19. At this time, total liver collagen (hydroxyproline determined according to Prockop and Udenfried) is already significantly increased by CC14, and fibrotic collagen rapidly accumulates during the following weeks. The rats were sacrificed on day 28. The treatment groups were: no CC14+control antibody BW 3 (n=10 rats), CC14+control antibody BW 3 (n=20 rats), and CC14+BW 14 (n=20 rats).
The effect of control vs. TIMP-1 antibody as reflected in morphometric measurements of fibrous collagen (Sirius Red stained area as percentage of the total field) is shown in FIG. 15. Comparison of both control antibody treated groups shows that CC14 caused an approximately three-fold increase in collagen area. BW-14 antibody treatment reduced the pathological collagen increment by 26%. The lower fibrous collagen value of the CC14+BW-14 group compared to the CC14+BW-3 group was statistically significant (p<0.05, Kolmogorow-Smirnow test).
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## Claims

1. A purified polynucleotide which encodes a human antibody, wherein the antibody comprises:
a VHCDR1 region comprising an amino acid sequence as set forth in SEQ ID NO:355;
a VHCDR2 region comprising an amino acid sequence as set forth in SEQ ID NO:359;
a VHCDR3 region comprising an amino acid sequence as set forth in SEQ ID NO:360;
a VLCDR1 region comprising an amino acid sequence as set forth in SEQ ID NO:363;
a VLCDR2 region comprising an amino acid sequence as set forth in SEQ ID NO:364; and
a VLCDR3 region comprising an amino acid sequence as set forth in SEQ ID NO:48.

2. An expression vector comprising the polynucleotide of claim 1.

3. A host cell comprising the expression vector of claim 2.

4. A method of making a human antibody, comprising the steps of:
culturing the host cell of claim 3 under conditions whereby the antibody is expressed; and
purifying the human antibody from the host cell culture.

5. The method of claim 4 wherein the expression vector comprises a polynucleotide sequence selected from the group consisting of SEQ ID NOS:183-357.

6. The purified polynucleotide of claim 1 wherein the VLCDR3 region is SEQ ID NOS:187.

7. An expression vector comprising the polynucleotide of claim 6.

8. A host cell comprising the expression vector of claim 7.

9. The purified polynucleotide of claim 1 wherein the human antibody comprises a heavy chain having an amino acid sequence selected from the group consisting of SEQ ID NOS:140-182.

10. An expression vector comprising the polynucleotide of claim 9.

11. A host cell comprising the expression vector of claim 10.

12. The purified polynucleotide of claim 9 wherein the heavy chain is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NOS:269-311.

13. An expression vector comprising the polynucleotide of claim 12.

14. A host cell comprising the expression vector of claim 13.

15. The purified polynucleotide of claim 9 wherein the human antibody comprises a light chain having an amino acid sequence selected from the group consisting of SEQ ID NOS:97-139.

16. An expression vector comprising the polynucleotide of claim 15.

17. A host cell comprising the expression vector of claim 16.

18. The purified polynucleotide of claim 15 wherein the light chain is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NOS:312-354.

19. An expression vector comprising the polynucleotide of claim 18.

20. A host cell comprising the expression vector of claim 19.