# Patent

## Title
Kallikrein-inhibitor therapies

## Abstract

Methods are described for preventing or reducing ischemia, e.g., cerebral ischemia, and/or reperfusion injury, e.g., reperfusion injury associated with cerebral ischemia, in a patient.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of Ser. No. 10/953,902, filed on Sep. 27, 2004, which is a continuation-in-part of U.S. patent application Ser. No. 10/456,986, filed Jun. 6, 2003, which claims priority to U.S. provisional application No. 60/387,239, filed on Jun. 7, 2002, and 60/407,003, filed on Aug. 28, 2002, the contents of all of which are incorporated herein by reference.


SUMMARY
Serine proteases such as, kallikrein (e.g., plasma kallikrein), are involved in pathways leading to excessive perioperative blood loss, the onset of systemic inflammatory response and nervous system pathophysiology. Inhibitors of kallikrein include proteinaceous and non-proteinaceous molecules. Exemplary plasma kallikrein inhibitors include those described in U.S. Pat. Nos. 6,333,402 and 6,057,287, the contents of which are incorporated herein by reference in their entirety.
Polypeptide and other inhibitors of plasma kallikrein can be used in therapeutic methods and compositions suitable for use in eliminating or reducing various ischemias, including but not limited to perioperative blood loss, cerebral ischemia, the onset of systemic inflammatory response, and/or reperfusion injury, e.g., reperfusion injury associated with cerebral ischemia or a focal brain ischemia. Perioperative blood loss results from invasive surgical procedures that lead to contact activation of complement components and the coagulation/fibrinolysis systems. The kallikrein inhibitors can be used to reduce or prevent perioperative blood loss and a systemic inflammatory response in patients subjected to invasive surgical procedures, especially cardiothoracic surgeries. The kallikrein inhibitors can also be used to reduce or prevent cerebral ischemia such as stroke, and/or reperfusion injury associated with cerebral ischemia. They can also prevent neurological and cognitive deficits associated with stroke, blood lose, and cerebral ischemia, e.g., events that are not associated with surgical intervention. The inhibitors can be administered prior to, during, or after an event, e.g., a cardiovascular event that can damage the central nervous system.
A variety of inhibitors of a kallikrein, e.g., a plasma kallikrein are described herein. Any one of these, or a combination of more than one of these, can be used in the following methods.
In one aspect, the disclosure features a method for preventing or reducing ischemia in a patient including administering to the patient a composition that includes an inhibitor of kallikrein, e.g., a plasma kallikrein. Typically the patient is a human patient. The composition can be administered in an amount effective to prevent or reduce ischemia in the patient. In a particular embodiment, the ischemia is at least partially due to blood loss, e.g., perioperative blood loss due to a surgical procedure performed on the patient. The surgical procedure can be, e.g., a cardiothoracic surgery, such as, for example, cardiopulmonary bypass or coronary artery bypass grafting. The inhibitor can be administered before, during, or after the procedure.
In another aspect, the disclosure features a method for preventing or reducing a systemic inflammatory response, e.g., a response associated with a surgical procedure in a patient or its onset. The method includes: administering to the patient a composition including an inhibitor of kallikrein, e.g., a plasma kallikrein. The composition can be administered before, during, or after surgery. In one embodiment, the surgical procedure is a cardiothoracic surgery, such as, for example, cardiopulmonary bypass or coronary artery bypass grafting. In another aspect, the disclosure features a method for treating a brain or central nervous system (CNS) injury. The method can be used to prevent or reduce adverse effects of cerebral ischemia, e.g., stroke, and/or reperfusion injury, e.g., reperfusion injury associated with cerebral ischemia, in a patient including administering to the patient a composition including an inhibitor of kallikrein, e.g., a plasma kallikrein. In one embodiment, the cerebral ischemia is stroke, e.g., embolism-, thrombus- or hemorrhage-associated stroke. The method can include administering the inhibitor, before, during, or after the ischemia, e.g., at the time of reperfusion or at a time between 1-12 hours after an ischemic event, e.g., between 1-5 hours after such an event.
The inhibitor used in any disclosed method can have a Ki for kallikrein, e.g., plasma kallikrein of less than 50 nM, 5 nM, 1 nM, 500 pM, 100 pM, 50 pM, e.g., about 44 pM. The inhibitor can preferentially inhibit plasma kallikrein at least 100, 200, 500, or 1000 more than another kallikrein, e.g., human urine kallikrein, or another protease, e.g., plasmin or thrombin. For example, the inhibitor is other than aprotinin.
In one embodiment, the inhibitor is an agent that can cross the blood-brain barrier.
In one embodiment, the inhibitor includes a polypeptide that includes a Kunitz domain such as the amino acid sequence: Xaa1 Xaa2 Xaa3 Xaa4 Cys Xaa6 Xaa7 Xaa8 Xaa9 Xaa10 Xaa11 Gly Xaa13 Cys Xaa15 Xaa16 Xaa17 Xaa18 Xaa19 Xaa20 Xaa21 Xaa22 Xaa23 Xaa24 Xaa25 Xaa26 Xaa27 Xaa28 Xaa29 Cys Xaa31 Xaa32 Phe Xaa34 Xaa35 Gly Gly Cys Xaa39 Xaa40 Xaa41 Xaa42 Xaa43 Xaa44 Xaa45 Xaa46 Xaa47 Xaa48 Xaa49 Xaa50 Cys Xaa52 Xaa53 Xaa54 Cys Xaa56 Xaa57 Xaa58 (SEQ ID NO:1).
The framework of the Kunitz domain can be human or can differ from a human Kunitz domain framework by fewer than six, five, four, three, or two amino acids. For example, the framework of the Kunitz domain can be the framework of one of the Kunitz domains of human lipoprotein-associated coagulation inhibitor (LACI) protein, e.g., the first second or third Kunitz domain. Typically the polypeptide differs from BPTI and/or one or more of the LACI Kunitz domains by at least one, two, three, or four amino acids, e.g., at least one, two or tree amino acids in the binding loops and/or at least two, three, four, or six amino acids in the framework region. For example, the polypeptide can include a non-naturally occurring Kunitz domain that is derived from a naturally occurring Kunitz domain, e.g., a human Kunitz domain. In one embodiment, an inhibitor that includes a Kunitz domain binds to plasma kallikrein with an affinity that is at least 10, 100, or 500 fold better than BPTI and/or LACI.
In one embodiment the polypeptide that inhibits kallikrein is not immunogenic on second use.
In one embodiment, the polypeptide can have one or more of the following features: Xaa1, Xaa2, Xaa3, Xaa4, Xaa56, Xaa57 or Xaa58 are each individually an amino acid or absent; Xaa10 is an amino acid selected from the group consisting of: Asp and Glu; Xaa11 is an amino acid selected from the group consisting of: Asp, Gly, Ser, Val, Asn, Ile, Ala and Thr; Xaa13 is an amino acid selected from the group consisting of: Arg, His, Pro, Asn, Ser, Thr, Ala, Gly, Lys and Gln; Xaa15 is an amino acid selected from the group consisting of: Arg, Lys, Ala, Ser, Gly, Met, Asn and Gln; Xaa16 is an amino acid selected from the group consisting of: Ala, Gly, Ser, Asp and Asn; Xaa17 is an amino acid selected from the group consisting of: Ala, Asn, Ser, Ile, Gly, Val, Gln and Thr; Xaa18 is an amino acid selected from the group consisting of: His, Leu, Gln and Ala; Xaa19 is an amino acid selected from the group consisting of: Pro, Gln, Lou, Asn and Ile; Xaa21 is an amino acid selected from the group consisting of: Trp, Phe, Tyr, His and Ile; Xaa22 is an amino acid selected from the group consisting of: Tyr and Phe; Xaa23 is an amino acid selected from the group consisting of: Tyr and Phe; Xaa31 is an amino acid selected from the group consisting of: Glu, Asp, Gln, Asn, Ser, Ala, Val, Leu, Ile and Thr; Xaa32 is an amino acid selected from the group consisting of: Glu, Gln, Asp Asn, Pro, Thr, Leu, Ser, Ala, Gly and Val; Xaa34 is an amino acid selected from the group consisting of: Thr, He, Ser, Val, Ala, Asn, Gly and Leu; Xaa35 is an amino acid selected from the group consisting of: Tyr, Trp and Phe; Xaa39 is an amino acid selected from the group consisting of: Glu, Gly, Ala, Ser and Asp; Xaa40 is an amino acid selected from the group consisting of: Gly and Ala; Xaa43 is an amino acid selected from the group consisting of: Asn and Gly; Xaa45 is an amino acid selected from the group consisting of: Phe and Tyr; and wherein the polypeptide inhibits kallikrein.
In a particular embodiment, individual amino acid positions of SEQ ID NO:1 can be one or more of the following: Xaa10 is Asp, Xaa11 is Asp, Xaa13 is Pro, Xaa15 is Arg, Xaa16 is Ala, Xaa17 is Ala, Xaa18 is His, Xaa19 is Pro, Xaa21 is Trp, Xaa31 is Glu, Xaa32 is Glu, Xaa34 is Ile, Xaa35 is Tyr, Xaa39 is Glu.
The polypeptide can include (or consist of) the following amino acid sequence: Glu Ala Met His Ser Phe Cys Ma Phe Lys Ala Asp Asp Gly Pro Cys Arg Ala Ala His Pro Arg Trp Phe Phe Asn Ile Phe Thr Arg Gin Cys Glu Glu Phe Ile Tyr Gly Gly Cys Glu Gly Asn Gln Asn Arg Phe Glu Ser Leu Glu Glu Cys Lys Lys Met Cys Thr Arg Asp (SEQ ID NO:2), or a fragment thereof, e.g., amino acids 3-60 of SEQ ID NO:2 or other fragment that binds and inhibits kallikrein. For example, the polypeptide can have fewer than 80, 70, 65, or 60 amino acids.
In one embodiment, the polypeptide is modified, e.g., to include one or more polymer moieties, e.g., a plurality of polymer moieties, e.g., as described in U.S. Ser. No. 10/931,153, filed Aug. 30, 2004, bearing attorney docket number 10280-119001. For example, the polypeptide can include a plurality of polyethylene glycol moieties, e.g., one on an N-terminal amine and one attached to each lysine of the polypeptide. The polyethylene glycol moieties can be less than 10, 8, 7, or 6 kDa in average molecular weight. Other exemplary modifications include a label, e.g., a radioactive or MRI-detectable label.
In one embodiment, the inhibitor does not include a peptide or polypeptide. For example, the inhibitor can be small molecule, e.g., a compound described in WO 04/062657, e.g., an acylated 4-amidino- or 4-guanidinobenzylamines. The compound can have the general formula (I) P4-P3-P2-P1 (I), where P4 is a mono- or poly-substituted or unsubstituted benzylsulphonyl group, P3 is a mono- or poly-substituted or unsubstituted, natural or unnatural alpha-amino or alpha-imino acid with the D-configuration, P2 is a mono- or poly-substituted or unsubstituted natural or unnatural alpha-amino or alpha-imino acid with the L-configuration and P1 is a mono- or poly-substituted or unsubstituted 4-amidino- or 4-guanidinobenzylamine group.
The methods described herein can include administering an effective amount of the inhibitor of kallikrein. Such an amount can be an amount sufficient to produce an improvement detectable to one skilled in the art, to ameliorate at least one symptom, or to modulate (e.g., improve) at least one physiological parameter, e.g., to a statistically significant degree.
All patents, patent applications, and publications cited herein are incorporated herein by reference. In the case of conflict, the present application controls.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a simplified diagram of major multiple pathways and related events involved in the contact activation system and systemic inflammatory response (SIR) that may arise in a patient subjected to soft and bone tissue trauma such as that associated with a coronary artery bypass grafting (CABG) procedure, especially when the CABG procedure involves extra-corporeal blood circulation, such as cardiopulmonary bypass (Bypass Apparatus). Arrows indicate activation from one component or event to another component or event in the cascade. Arrows in both directions indicate activating effects of components or events in both directions. Broken arrows indicate likely participation of one component or event in the activation of another component or event. Abbreviations: “tPA”, tissue plasminogen activator; “C5a”, a protein component of the complement system; “fXIIa”, activator protein of prekallikrein to form active kallikrein; “Extrinsic”, extrinsic coagulation system; “Intrinsic”, intrinsic coagulation system.
FIG. 2 shows a portion of a DNA and corresponding deduced amino acid for an exemplary kallikrein inhibitor polypeptide in plasmid pPIC-K503. The inserted DNA encodes the matα Prepro signal peptide of Saccharomyces cerevisiae (underlined) fused in frame to the amino terminus of the PEP-1 polypeptide having the amino acid sequence enclosed by the boxed area. The amino acid sequence of the PEP-1 polypeptide shown in the boxed region is SEQ ID NO:2, and the corresponding nucleotide coding sequence is SEQ ID NO:3. The dashed arrows indicate the location and direction of two PCR primer sequences in AOX regions that were used to produce sequencing templates. DNA sequence for the entire nucleotide sequence of the figure includes the structural coding sequence for the fusion protein and is designated SEQ ID NO:27. The double underlined portion of the sequence indicates a diagnostic probe sequence. BstB I and EcoR I indicate locations of their respective palindromic, hexameric, restriction endonuclease sites in the sequence. Asterisks denote translational stop codons. See text for details.
FIGS. 3A and 3B show an alignment of exemplary amino acid sequences, the native LACI sequence from which these variants were derived (SEQ ID NO:32), and other known Kunitz domains (SEQ ID NOS:29-31 and 33-53). Cysteine residues are highlighted.
FIG. 4 is a graph depicting ischemic volume in C57B1/6 mice subjected to transient focal cerebral ischemia by middle cerebral artery occlusion (MCAO) using 5-0 microfilament and administered saline (control) or a kallikrein inhibitor polypeptide (DX-88) at various doses (10 μg, 30 μg, 90 μg). The saline or kallikrein inhibitor polypeptide was administered at the beginning of the ischemic period.
FIG. 5 is a graph depicting ischemic volume in C57B1/6 mice subjected to transient focal cerebral ischemia by middle cerebral artery occlusion (MCAO) using 6-0 microfilament and administered saline (control) or a kallikrein inhibitor polypeptide (DX-88) at various periods before and after ischemic damage. The kallikrein inhibitor polypeptide was administered at the beginning of the ischemic period (DX-88 pre), at the end of the ischemic period (DX-88 post), or at one hour after the beginning of the ischemic period (DX-88 1 h post). The kallikrein inhibitor polypeptide was administered at 30 μg.
FIG. 6 is a graph depicting general neurological deficits in C57B1/6 mice subjected to transient focal cerebral ischemia by middle cerebral artery occlusion (MCAO) using 6-0 microfilament and administered saline (control) or a kallikrein inhibitor polypeptide (DX-88) at various periods before and after ischemic damage. The kallikrein inhibitor polypeptide was administered at the beginning of the ischemic period DX-88 pre), at the end of the ischemic period DX-88 post), or at one hour after the beginning of the ischemic period (DX-88 1 h post). The kallikrein inhibitor polypeptide was administered at 30 μg. General neurological deficits were measured based upon evaluation of the hair, ears, eyes, posture, spontaneous activity and epileptic behavior in the mice.
FIG. 7 is a graph depicting focal neurological deficits in C57B1/6 mice subjected to transient focal cerebral ischemia by middle cerebral artery occlusion (MCAO) using 6-0 microfilament and administered saline (control) or a kallikrein inhibitor polypeptide (DX-88) at various periods before and after ischemic damage. The kallikrein inhibitor polypeptide was administered at the beginning of the ischemic period (DX-88 pre), at the end of the ischemic period (DX-88 post), or at one hour after the beginning of the ischemic period DX-88 1 h post). The kallikrein inhibitor polypeptide was administered at 30 μg. Focal neurological deficits were measured based upon evaluation of the body symmetry, gait, climbing ability, circling behavior, front limb symmetry, compulsory circling and whisker response in the mice.
FIG. 8 is a graph depicting the levels of a kallikrein activity found in the cerebral spinal fluid (CSF) of either untreated mice (normal CSF) or mice treated with a kallikrein inhibitor polypeptide (DX-88) at various doses (10 μg or 30 μg) measured at 30 or 60 minutes after administration.



DETAILED DESCRIPTION
Kallikrein inhibitors, particularly inhibitors of plasma kallikrein, can be used to prevent or treat disorders associated with blood loss or blood fluidity. For example, such inhibitors can be used to treat or prevent perioperative blood loss, a systemic inflammatory response (SIR) induced by kallikrein (especially, for example, in patients undergoing surgical procedures and particularly surgical procedures involving cardiothoracic surgery, e.g., cardiopulmonary bypass (CPB), such as a coronary artery bypass graft (CABG) procedures as well as in patients with other disorders), cerebral ischemia and/or reperfusion injury associated with ischemia, e.g., cerebral ischemia.
Further examples of applications for kallikrein inhibitors include pediatric cardiac surgery, lung transplantation, total hip replacement and orthotopic liver transplantation, and to reduce or prevent perioperative stroke during CABG, extracorporeal membrane oxygenation (ECMO) and cerebrovascular accidents (CVA) during these procedures. Kallikrein inhibitors can also be used for stroke, e.g., embolism, thrombus and/or hemorrhage associated stroke and for reperfusion injury associated with stroke.
Cardiothoracic surgery is surgery of the chest area, most commonly the heart and lungs. Typical diseases treated by cardiothoracic surgery include coronary artery disease, tumors and cancers of the lung, esophagus and chest wall, heart vessel and valve abnormalities, and birth defects involving the chest or heart. Where cardiothoracic surgery is utilized for treatment, the risk of blood loss (e.g., surgery-induced ischemia) and the onset of a systemic inflammatory response (SIR) is incurred. Surgery-induced SIR can result in severe organ dysfunction (systemic inflammatory response syndrome; SIRS).
Kunitz Domains
A number of useful inhibitors of kallikrein include a Kunitz domain.
As used herein, a “Kunitz domain” is a polypeptide domain having at least 51 amino acids and containing at least two, and preferably three, disulfides. The domain is folded such that the first and sixth cysteines, the second and fourth, and the third and fifth cysteines form disulfide bonds (e.g., in a Kunitz domain having 58 amino acids, cysteines can be present at positions corresponding to amino acids 5, 14, 30, 38, 51, and 55, according to the number of the BPTI sequence provided below, and disulfides can form between the cysteines at position 5 and 55, 14 and 38, and 30 and 51), or, if two disulfides are present, they can form between a corresponding subset of cysteines thereof. The spacing between respective cysteines can be within 7, 5, 4, 3 or 2 amino acids of the following spacing between positions corresponding to: 5 to 55, 14 to 38, and 30 to 51, according to the numbering of the BPTI sequence provided below. The BPTI sequence can be used a reference to refer to specific positions in any generic Kunitz domain. Companion of a Kunitz domain of interest to BPTI can be performed by identifying the best fit alignment in which the number of aligned cysteines in maximized.
The 3D structure (at high resolution) of the Kunitz domain of BPTI is known. One of the X-ray structures is deposited in the Brookhaven Protein Data Bank as “6PTI”. The 3D structure of some BPTI homologues (Eigenbrot et al., (1990) Protein Engineering, 3(7):591-598; Hynes et al., (1990) Biochemistry, 29:10018-10022) are known. At least seventy Kunitz domain sequences are known. Known human homologues include three Kunitz domains of LACI (Wun et al., (1988) J. Biol. Chem. 263(13):6001-6004; Girard et al., (1989) Nature, 338:518-20; Novotny et al, (1989) J. Biol. Chem., 264(31):18832-18837) two Kunitz domains of Inter-α-Trypsin Inhibitor, APP-I (Kido et al., (1988) J. Biol. Chem., 263(34):18104-18107), a Kunitz domain from collagen, and three Kunitz domains of TFPI-2 (Sprecher et al., (1994) PNAS USA, 91:3353-3357). LACI is a human serum phosphoglycoprotein with a molecular weight of 39 kDa (amino acid sequence in Table 1) containing three Kunitz domains.







TABLE 1





Exemplary Natural Kunitz Domains


















LACI;
  1
MIYTMKXVHA LWASVCLLLN LAPAPLNAds eedeehtiit dtelpplklM



(SEQ ID NO.54)



 51
HSFCAFKADD GPCKAIMKRF FFNIFTRQCE EFIYGGCEGN QNRFESLEEC


 



101
KKMCTRDnan riikttlqqe kpdfCfleed pgiCrgyitr yfynnqtkqC


 



151
erfkyggClg nmnnfetlee CkniCedgpn gfqvdnygtq lnavnnsltp


 



201
qstkvpslfe fhgpswCltp adrglCrane nrfyynsvig kCrpfkysgC


 



251
ggnennftsk qeClraCkkg fiqriskggl iktkrkrkkq rvkiayeeif


 



301
vknm


 










The signal sequence (1-28) is uppercase and underscored




LACI-K1 is uppercase



LACI-K2 is underscored



LACI-K3 is bold



 









BPTI
    1    2    3    4    5



(SEQ ID NO:55)
1234567890123456789012345678901234567890123456789012345678



RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA









The Kunitz domains above are referred to as LACI-K1 (residues 50 to 107), LACI-K2 (residues 121 to 178), and LACI-K3 (213 to 270). The cDNA sequence of LACI is reported in Wun et al. (J. Biol. Chem., 1988, 263(13):6001-6004). Girard et al. (Nature, 1989, 338:518-20) reports mutational studies in which the P1 residues of each of the three Kunitz domains were altered. LACI-K1 inhibits Factor VIIa (F.VIIa) when F.VIIa is complexed to tissue factor and LACI-K2 inhibits Factor Xa.
Proteins containing exemplary Kunitz domains include the following, with SWISS-PROT Accession Numbers in parentheses:

















A4_HUMAN
(P05067),
A4_MACFA
(P53601),
A4_MACMU
(P29216),


A4_MOUSE
(P12023),
A4_RAT
(P08592),
A4_SAISC
(Q95241),


AMBP_PLEPL
(P36992),
APP2_HUMAN
(Q06481),
APP2_RAT
(P15943),


AXP1_ANTAF
(P81547),
AXP2_ANTAF
(P81548),
BPT1_BOVIN
(P00974),


BPT2_BOVIN
(P04815),
CA17_HUMAN
(Q02388),
CA36_CHICK
(P15989),


CA36_HUMAN
(P12111),
CRPT_BOOMI
(P81162),
ELAC_MACEU
(O62845),


ELAC_TRIVU
(Q29143),
EPPI_HUMAN
(O95925),
EPPI_MOUSE
(Q9DA01),


HTIB_MANSE
(P26227),
IBP_CARCR
(P00993),
IBPC_BOVIN
(P00976),


IBPI_TACTR
(P16044),
IBPS_BOVIN
(P00975),
ICS3_BOMMO
(P07481),


IMAP_DROFU
(P11424),
IP52_ANESU
(P10280),
ISC1_BOMMO
(P10831),


ISC2_BOMMO
(P10832),
ISH1_STOHE
(P31713),
ISH2_STOHE
(P81129),


ISIK_HELPO
(P00994),
ISP2_GALME
(P81906),
IVB1_BUNFA
(P25660),


IVB1_BUNMU
(P00987),
IVB1_VIPAA
(P00991),
IVB2_BUNMU
(P00989),


IVB2_DABRU
(P00990),
IVB2_HEMHA
(P00985),
IVB2_NAJNI
(P00986),


IVB3_VIPAA
(P00992),
IVBB_DENPO
(P00983),
IVBC_NAJNA
(P19859),


IVBC_OPHHA
(P82966),
IVBE_DENPO
(P00984),
IVBI_DENAN
(P00980),


IVBI_DENPO
(P00979),
IVBK_DENAN
(P00982),
IVBK_DENPO
(P00981),


IVBT_ERIMA
(P24541),
IVBT_NAJNA
(P20229),
MCPI_MELCP
(P82968),


SBPI_SARBU
(P26228),
SPT3_HUMAN
(P49223),
TKDl_BOVIN
(Q28201),


TKD1_SHEEP
(Q29428),
TXCA_DENAN
(P81658),
UPTI_PIG
(Q29100),


AMBP_BOVIN
(P00978),
AMBP_HUMAN
(P02760),
AMBP_MERUN
(Q62577),


AMBP_MESAU
(Q60559),
AMBP_MOUSE
(Q07456),
AMBP_PIG
(P04366),


AMBP_RAT
(Q64240),
IATR_HORSE
(P04365),
IATR_SHEEP
(P13371),


SPT1_HUMAN
(O43278),
SPT1_MOUSE
(Q9R097),
SPT2_HUMAN
(O43291),


SPT2_MOUSE
(Q9WU03),
TFP2_HUMAN
(P48307),
TFP2_MOUSE
(O35536),


TFPI_HUMAN
(P10646),
TFPI_MACMU
(Q28864),
TFPI_MOUSE
(O54819),


TFPI_RABIT
(P19761),
TFPI_RAT
(Q02445),
YN81_CAEEL
(Q03610)









A variety of methods can be used to identify a Kunitz domain from a sequence database. For example, a known amino acid sequence of a Kunitz domain, a consensus sequence, or a motif (e.g., the ProSite Motif) can be searched against the GenBank sequence databases (National Center for Biotechnology Information, National Institutes of Health, Bethesda Md.), e.g., using BLAST; against Pfam database of HMMs (Hidden Markov Models) (e.g., using default parameters for Pfam searching; against the SMART database; or against the ProDom database. For example, the Pfam Accession Number PF00014 of Pfam Release 9 provides numerous Kunitz domains and an HMM for identify Kunitz domains. A description of the Pfam database can be found in Sonhammer et al. (1997) Proteins 28(3):405-420 and a detailed description of HMMs can be found, for example, in Gribskov et al. (1990) Meth. Enzymol. 183:146-159; Gribskov et al. (1987) Proc. Natl. Acad. Sci. USA 84:4355-4358; Krogh et al. (1994) J. Mol. Biol. 235:1501-1531; and Stultz et al. (1993) Protein Sci. 2:305-314. The SMART database (Simple Modular Architecture Research Tool, EMBL, Heidelberg, Del.) of HMMs as described in Schultz et al. (1998), Proc. Natl. Acad. Sci. USA 95:5857 and Schultz et al. (2000) Nucl. Acids Res 28:231. The SMART database contains domains identified by profiling with the hidden Markov models of the HMMer2 search program (R. Durbin et al. (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press). The database also is annotated and monitored. The ProDom protein domain database consists of an automatic compilation of homologous domains (Corpet et al. (1999), Nucl. Acids Res. 27:263-267). Current versions of ProDom are built using recursive PSI-BLAST searches (Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402; Gouzy et al. (1999) Computers and Chemistry 23:333-340.) of the SWISS-PROT 38 and TREMBL protein databases. The database automatically generates a consensus sequence for each domain. Prosite lists the Kunitz domain as a motif and identifies proteins that include a Kunitz domain. See, e.g., Falquet et al. Nucleic Acids Res. 30:235-238 (2002).
Kunitz domains interact with target protease using, primarily, amino acids in two loop regions (“binding loops”). The first loop region is between about residues corresponding to amino acids 15-20 of BPTI. The second loop region is between about residues corresponding to amino acids 31-37 of BPTI. An exemplary library of Kunitz domains varies one or more amino acid positions in the first and/or second loop regions. Particularly useful positions to vary, when screening for Kunitz domains that interact with kallikrein or when selecting for improved affinity variants, include: positions 13, 16, 17, 18, 19, 31, 32, 34, and 39 with respect to the sequence of BPTI. At least some of these positions are expected to be in close contact with the target protease. It is also useful to vary other positions, e.g., positions that are adjacent to the aforementioned positions in the three-dimensional structure.
The “framework region” of a Kunitz domain is defined as those residues that are a part of the Kunitz domain, but specifically excluding residues in the first and second binding loops regions, i.e., about residues corresponding to amino acids 15-20 of BPTI and 31-37 of BPTI. Conversely, residues that are not in the binding loop may tolerate a wider range of amino acid substitution (e.g., conservative and/or non-conservative substitutions).
In one embodiment these Kunitz domains are variant forms of the looped structure including Kunitz domain 1 of human lipoprotein-associated coagulation inhibitor (LACI) protein. LACI contains three internal, well-defined, peptide loop structures that are paradigm Kunitz domains (Girard, T. et al., 1989. Nature, 338:518-520). Variants of Kunitz domain 1 of LACI described herein have been screened, isolated and bind kallikrein with enhanced affinity and specificity (see, for example, U.S. Pat. Nos. 5,795,865 and 6,057,287, incorporated herein by reference). These methods can also be applied to other Kunitz domain frameworks to obtain other Kunitz domains that interact with kallikrein, e.g., plasma kallikrein. Useful modulators of kallikrein function typically bind and/or inhibit kallikrein, as determined using kallikrein binding and inhibition assays.
An exemplary polypeptide that includes a Kunitz domain that inhibits kallikrein has the amino acid sequence defined by amino acids 3-60 of SEQ ID NO:2.
An exemplary polypeptide includes the amino acid sequence:
Xaa1 Xaa2 Xaa3 Xaa4 Cys Xaa6 Xaa7 Xaa8 Xaa9 Xaa10 Xaa11 Gly Xaa13 Cys Xaa15 Xaa16 Xaa17 Xaa18 Xaa19 Xaa20 Xaa21 Xaa22 Xaa23 Xaa24 Xaa25 Xaa26 Xaa27 Xaa28 Xaa29 Cys Xaa31 Xaa32 Phe Xaa34 Xaa35 Gly Gly Cys Xaa39 Xaa40 Xaa41 Xaa42 Xaa43 Xaa44 Xaa45 Xaa46 Xaa47 Xaa48 Xaa49 Xaa50 Cys Xaa52 Xaa53 Xaa54 Cys Xaa56 Xaa57 Xaa58 (SEQ ID NO:1)
“Xaa” refers to a position in a peptide chain that can be any of a number of different amino acids. In a first example, Xaa can by any amino acid except cysteine. In another example, one or more of the following apply: Xaa10 can be Asp or Glu, Xaa11 can be Asp, Gly, Ser, Val, Asn, Ile, Ala or Thr; Xaa13 can be Pro, Arg, His, Asn, Ser, Thr, Ala, Gly, Lys or Gln; Xaa15 can be Arg, Lys, Ala, Ser, Gly, Met, Asn or Gln; Xaa16 can be Ala, Gly, Ser, Asp or Asn; Xaa17 can be Ala, Asn, Ser, Ile, Gly, Val, Gln or Thr; Xaa18 can be His, Leu, Gln or Ala; Xaa19 can be Pro, Gln, Leu, Asn or Ile; Xaa21 can be Trp, Phe, Tyr, His or Ile; Xaa31 can be Glu, Asp, Gln, Asn, Ser, Ala, Val, Leu, Ile or Thr; Xaa32 can be Glu, Gin, Asp Asn, Pro, Thr, Leu, Ser, Ala, Gly or Val; Xaa34 can be Ile, Thr, Ser, Val, Ala, Asn, Gly or Leu; Xaa35 can be Tyr, Trp or Phe; Xaa39 can be Glu, Gly, Ala, Ser or Asp. Amino acids Xaa6, Xaa7, Xaa8, Xaa9, Xaa20, Xaa24, Xaa25, Xaa26, Xaa27, Xaa28, Xaa29, Xaa41, Xaa42, Xaa44, Xaa46, Xaa47, Xaa48, Xaa49, Xaa50, Xaa52, Xaa53 and Xaa54 can be any amino acid.
Additionally, each of the first four and at last three amino acids of SEQ ID NO:1 can optionally be present or absent and can be any amino acid, if present, e.g., any non-cysteine amino acid.
In one embodiment, the polypeptide has a sequence with one or more of the following properties: Xaa11 can be Asp, Gly, Ser or Val; Xaa13 can be Pro, Arg, His or Asn; Xaa15 can be Arg or Lys; Xaa16 can be Ala or Gly; Xaa17 can be Ala, Asn, Ser or Ile; Xaa18 can be His, Leu or Gln; Xaa19 can be Pro, Gln or Leu; Xaa21 can be Trp or Phe; Xaa31 is Glu; Xaa32 can be Glu or Gln; Xaa34 can be Ile, Thr or Ser; Xaa35 is Tyr; and Xaa39 can be Glu, Gly or Ala.
An exemplary polypeptide can include the following amino acids: Xaa10 is Asp; Xaa11 is Asp; Xaa13 can be Pro or Arg; Xaa15 is Arg; Xaa16 can be Ala or Gly; Xaa17 is Ala; Xaa18 is His; Xaa19 is Pro; Xaa21 is Trp; Xaa31 is Glu; Xaa32 is Glu; Xaa34 can be Ile or Ser; Xaa35 is Tyr; and Xaa39 is Gly.
It is also possible to use portions of the polypeptides described herein. For example, polypeptides could include binding domains for specific kallikrein epitopes. For example, the binding loops of Kunitz domains can by cyclized and used in isolation or can be grafted onto another domain, e.g., a framework of another Kunitz domain. It is also possible to remove one, two, three, or four amino acids from the N-terminus of an amino acid sequence described herein, and/or one, two, three, four, or five amino acids from the C-terminus of an amino acid sequence described herein.
Examples of sequences encompassed by SEQ ID NO:1 are described by the following (where not indicated, “Xaa” refers to any amino acid, any non-cysteine amino acid or any amino acid from the same set of amino acids that are allowed for SEQ ID NO:1):








(SEQ ID NO:56)









Met His Ser Phe Cys Ala Phe Lys Ala Xaa10 Xaa11



 


Gly Xaa13 Cys Xaa15 Xaa16 Xaa17 Xaa18 Xaa19 Arg


 


Xaa21 Phe Phe Asn Ile Phe Thr Arg Gln Cys Xaa31


 


Xaa32 Phe Xaa34 Xaa35 Gly Gly Cys Xaa39 Gly Asn


 


Gln Asn Arg Phe Glu Ser Leu Gln Gln Cys Lys Lys


 


Met Cys Thr Arg Asp.


 








(SEQ ID NO:57)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Asp Gly



 


Pro Cys Arg Ala Ala His Pro Arg Trp Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Gln Glu Phe Ile Tyr Gly


 


Gly Cys Gln Gly Asn Gln Asn Arg Phe Gln Ser Leu


 


Gln Glu Cys Lys Lys Met Cys Thr Arg Asp (amino


 


acids 3-60 of SEQ ID NO:2),


 








(SEQ ID NO:4)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Asp Gly



 


Pro Cys Lys Ala Asn His Leu Arg Phe Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:5)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Asp Gly



 


His Cys Lys Ala Asn His Gln Arg Phe Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Thr Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:6)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Asp Gly



 


His Cys Lys Ala Asn His Gln Arg Phe Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Gln Phe Thr Tyr Gly


 


Gly Cys Ala Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:7)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Asp Gly



 


His Cys Lys Ala Ser Leu Pro Arg Phe Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ile Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:8)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Asp Gly



 


His Cys Lys Ala Asn His Gln Arg Phe Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:9)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Asp Gly



 


His Cys Lys Gly Ala His Leu Arg Phe Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ile Tyr Gly


 


Gly Cys Glu Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:10)









Met His Ser The Cys Ala Phe Lys Ala Asp Asp Gly



 


Arg Cys Lys Gly Ala His Leu Arg Phe Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ile Tyr Gly


 


Gly Cys Gln Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:11)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Gly Gly



 


Arg Cys Arg Gly Ala His Pro Arg Trp Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:12)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Asp Gly



 


Pro Cys Arg Ala Ala His Pro Arg Trp Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:13)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Val Gly



 


Arg Cys Arg Gly Ala His Pro Arg Trp Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:14)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Val Gly



 


Arg Cys Arg Gly Ala Gln Pro Arg Phe Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:15)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Asp Gly



 


Ser Cys Arg Ala Ala His Leu Arg Trp Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:16)









Met His Ser Phe Cys Ala Phe Lys Ala Glu Gly Gly



 


Ser Cys Arg Ala Ala His Gln Arg Trp Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:17)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Asp Gly



 


Pro Cys Arg Gly Ala His Leu Arg Phe Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:18)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Asp Gly



 


His Cys Arg Gly Ala Leu Pro Arg Trp Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:19)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Ser Gly



 


Asn Cys Arg Gly Asn Leu Pro Arg Phe Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:20)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Ser Gly



 


Arg Cys Arg Gly Asn His Gln Arg Phe Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Glu Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Glu Ser Leu


 


Glu Glu Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:21)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Gly Gly



 


Arg Cys Arg Ala Ile Gln Pro Arg Trp Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Gln Gln Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Gln Ser Leu


 


Gln Gln Cys Lys Lys Met Cys Thr Arg Asp,


 








(SEQ ID NO:22)









Met His Ser Phe Cys Ala Phe Lys Ala Asp Asp Gly



 


Arg Cys Arg Gly Ala His Pro Arg Trp Phe Phe Asn


 


Ile Phe Thr Arg Gln Cys Glu Gln Phe Ser Tyr Gly


 


Gly Cys Gly Gly Asn Gln Asn Arg Phe Gln Ser Leu


 


Gln Gln Cys Lys Lys Met Cys Thr Arg Asp.






Additional examples of sequence include those that differ by at least one amino acid, but fewer than seven, six, five, four, three, or two amino acids differences relative to an amino acid sequence described herein, e.g., an amino acid sequence provided above. In one embodiment, fewer than three, two, or one differences are in one of the binding loops. For example, the first binding loop may have no differences relative to an amino acid sequence described herein, e.g., an amino acid sequence provided above. In another example, neither the first nor the second binding loop differs from an amino acid sequence described herein, e.g., an amino acid sequence provided above.
FIGS. 3A and 3B provides an amino acid sequence alignment of these sequences, the native LACI sequence from which these variants were derived (SEQ ID NO:32), and other known Kunitz domains (SEQ ID NOS: 29-31 and 33-53). Still others polypeptides that inhibit kallikrein include an about 58-amino acid sequence of amino acids 3-60 of SEQ ID NO:2 or the PEP-1 polypeptide having the 60-amino acid sequence of SEQ ID NO:2. The term “PEP-1” and “DX-88” as used herein refer to the 60-amino acid sequence of SEQ ID NO:2. A nucleotide sequence encoding the amino acid sequence of SEQ ID NO:2 is provided in SEQ ID NO:3 (see, e.g., nucleotides 309-488 in FIG. 2). It is understood that based on the known genetic code, degenerate forms of the nucleotide sequence of SEQ ID NO:3 can be obtained by simply substituting one or more of the known degenerate codons for each amino acid encoded by the nucleotide sequence. Nucleotides 7-180 of SEQ ID NO:3, and degenerate forms thereof encode the non-naturally occurring Kunitz domain polypeptide tat includes the 58-amino acid sequence of amino acids 3-60 of SEQ ID NO:2, a related sequence, or a functional fragment thereof.
In one embodiment, the polypeptide that inhibits kallikrein is aprotinin. In another embodiment, the polypeptide is other than aprotinin, e.g., differs from aprotinin, by at least one, two, three, five, ten, or fifteen amino acids.
Polypeptides described herein can be made synthetically using any standard polypeptide synthesis protocol and equipment. For example, the stepwise synthesis of a polypeptide can be carried out by the removal of an amino (N) terminal-protecting group from an initial (i.e., carboxy-terminal) amino acid, and coupling thereto of the carboxyl end of the next amino acid in the sequence of the polypeptide. This amino acid is also suitably protected. The carboxyl group of the incoming amino acid can be activated to react with the N-terminus of the bound amino acid by formation into a reactive group such as formation into a carbodiimide, a symmetric acid anhydride, or an “active ester” group such as hydroxybenzotriazole or pentafluorophenyl esters. Preferred solid-phase peptide synthesis methods include the BOC method, which utilizes tert-butyloxycarbonyl as the α-amino protecting group, and the FMOC method, which utilizes 9-fluorenylmethloxycarbonyl to protect the α-amino of the amino acid residues. Both methods are well known to those of skill in the art (Stewart, J. and Young, J., Solid-Phase Peptide Synthesis (W. H. Freeman Co., San Francisco 1989); Merrifield, J., 1963. Am. Chem. Soc., 85:2149-2154; Bodanszky, M. and Bodanszky, A., The Practice of Peptide Synthesis (Springer-Verlag, New York 1984)). If desired, additional amino- and/or carboxy-terminal amino acids can be designed into the amino acid sequence and added during polypeptide synthesis.
Polypeptides can also be produced using recombinant technology. Recombinant methods can employ any of a number of cells and corresponding expression vectors, including but not limited to bacterial expression vectors, yeast expression vectors, baculovirus expression vectors, mammalian viral expression vectors, and the like, A polypeptide described herein can be produced by a transgenic animal, e.g., in the mammary gland of a transgenic animal. In some cases, it could be necessary or advantageous to fuse the coding sequence for a polypeptide that inhibits kallikrein (e.g., a polypeptide that includes a Kunitz domain) to another coding sequence in an expression vector to form a fusion polypeptide that is readily expressed in a host cell. Part or all of the additional sequence can be removed, e.g., by protease digestion.
An exemplary recombinant expression system for producing a polypeptide that inhibits kallikrein (e.g., a polypeptide that includes a Kunitz domain) is a yeast expression vector, which permits a nucleic acid sequence encoding the amino acid sequence for the inhibitor polypeptide to be linked in the same reading frame with a nucleotide sequence encoding the MATα prepro leader peptide sequence of Saccharomyces cerevisiae, which in turn is under the control of an operable yeast promoter. The resulting recombinant yeast expression plasmid can be transformed by standard methods into the cells of an appropriate, compatible yeast host, which cells are able to express the recombinant protein from the recombinant yeast expression vector. Preferably, a host yeast cell transformed with such a recombinant expression vector is also able to process the fusion protein to provide an active inhibitor polypeptide. An other exemplary yeast host for producing recombinant polypeptides is Pichia pastoris. 
As noted above, polypeptides that inhibit kallikrein can include a Kunitz domain polypeptide described herein. Some polypeptides can include an additional flanking sequence, preferably of one to six amino acids in length, at the amino and/or carboxy-terminal end, provided such additional amino acids do not significantly diminish kallikrein binding affinity or kallikrein inhibition activity so as to preclude use in the methods and compositions described herein. Such additional amino acids can be deliberately added to express a polypeptide in a particular recombinant host cell or can be added to provide an additional function, e.g., to provide a linker to another molecule or to provide an affinity moiety that facilitates purification of the polypeptide. Preferably, the additional amino acid(s) do not include cysteine, which could interfere with the disulfide bonds of the Kunitz domain.
An exemplary Kunitz domain polypeptide includes the amino acid sequence of residues 3-60 of SEQ ID NO:2. When expressed and processed in a yeast fusion protein expression system (e.g., based on the integrating expression plasmid pHIL-D2), such a Kunitz domain polypeptide retains an additional amino terminal Glu-Ala dipeptide from the fusion with the MATalpha-prepro leader peptide sequence of S. cerevisiae. When secreted from the yeast host cell, most of the leader peptide is processed from the fusion protein to yield a functional polypeptide (referred to herein as “PEP-1”) having the amino acid sequence of SEQ ID NO:2 (see boxed region in FIG. 2).
In one embodiment an inhibitor of kallikrein, e.g., a polypeptide inhibitor, has a binding affinity for kallikrein that is on the order of 1000 times higher than that of aprotinin, which is currently approved for use in CABG procedures to reduce blood loss. The surprisingly high binding affinities of such kallikrein inhibitors combined with their high degree of specificity for kallikrein to the exclusion of other molecular targets (see Table 1, below) provide for particularly useful inhibitors. However, inhibitors with lesser affinity or specificity also have their applications.
A typical Kunitz domain, e.g., that includes, SEQ ID NO:1, contains a number of invariant positions, e.g., positions corresponding to position 5, 14, 30, 51 and 55 in the BPTI numbering scheme are cysteine. The spacing between these positions may vary to the extent allowable within the Kunitz domain fold, e.g., such that three disulfide bonds are formed. Other positions such as, for example, positions 6, 7, 8, 9, 20, 24, 25, 26, 27, 28, 29, 41, 42, 44, 46, 47, 48, 49, 50, 52, 53 and 54, or positions corresponding to those positions, can be any amino acid (including non-naturally occurring amino acids). In a particularly preferred embodiment, one or more amino acids correspond to that of a native sequence (e.g., SEQ ID NO:32, see FIG. 3). In another embodiment, at least one variable position is different from that of the native sequence. In yet another preferred embodiment, the amino acids can each be individually or collectively substituted by a conservative or non-conservative amino acid substitution.
Conservative amino acid substitutions replace an amino acid with another amino acid of similar chemical structure and may have no affect on protein function. Non-conservative amino acid substitutions replace an amino acid with another amino acid of dissimilar chemical structure. Examples of conserved amino acid substitutions include, for example, Asn->Asp, Arg->Lys and Ser->Thr. In a preferred embodiment, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 and/or 21 of these amino acids can be independently or collectively, in any combination, selected to correspond to the corresponding position of SEQ ID NO:2.
Other positions, for example, positions 10, 11, 13, 15, 16, 17, 18, 19, 21, 22, 23, 31, 32, 34, 35, 39, 40, 43 and 45, or positions corresponding to those positions can be any of a selected set of amino acids. For example, SEQ ID NO:1 defines a set of possible sequences. Each member of this set contains, for example, a cysteine at positions 5, 14, 30, 51 and 55, and any one of a specific set of amino acids at positions 10, 11, 13, 15, 16, 17, 18, 19, 21, 22, 23, 31, 32, 34, 35, 39, 40, 43 and 45, or positions corresponding to those positions. In a preferred embodiment, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 and/or 19 of these amino acids can be independently or collectively, in any combination, selected to correspond to the corresponding position of SEQ ID NO:2. The polypeptide preferably has at least 80%, 85%, 90%, 95, 97, 98, or 99% identity to SEQ ID NO:2.
As used herein, the term “substantially identical” (or “substantially homologous”) is used herein to refer to a first amino acid or nucleotide sequence that contains a sufficient number of identical or equivalent (e.g., with a similar side chain, e.g., conserved amino acid substitutions) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences have similar activities. In the case of antibodies, the second antibody has the same specificity and has at least 50% of the affinity of the same.
Calculations of “homology” between two sequences can be performed as follows. The sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). In a preferred embodiment, the length of a reference sequence aligned for comparison purposes is at least 30%, preferably at least 40%, more preferably at least 50%, even more preferably at least 60%, and even more preferably at least 70%, 80%, 90%, 100% of the length of the reference sequence. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid “homology”). The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
The comparison of sequences and determination of percent homology between two sequences can be accomplished using a mathematical algorithm. In a preferred embodiment, the percent homology between two amino acid sequences is determined using the Needleman and Wunsch (1970), J. Mol. Biol. 48:444-453, algorithm which has been incorporated into the GAP program in the GCG software package, using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6. In yet another preferred embodiment, the percent homology between two nucleotide sequences is determined using the GAP program in the GCG software package, using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6. A particularly preferred set of parameters (and the one that should be used if the practitioner is uncertain about what parameters should be applied to determine if a molecule is within a homology limitation) are a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.
Useful polypeptides can also be encoded by a nucleic acid that hybridizes to a nucleic acid that encodes a polypeptide described herein. The nucleic acids can hybridize under medium, high, or very high stringency conditions. As used herein, the term “hybridizes under low stringency, medium stringency, high stringency, or very high stringency conditions” describes conditions for hybridization and washing. Guidance for performing hybridization reactions can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6, which is incorporated by reference. Aqueous and nonaqueous methods are described in that reference and either can be used. Specific hybridization conditions referred to herein are as follows: (1) low stringency hybridization conditions in 6× sodium chloride/sodium citrate (SSC) at about 45° C., followed by two washes in 0.2×SSC, 0.1% SDS at least at 50° C. (the temperature of the washes can be increased to 55° C. for low stringency conditions); (2) medium stringency hybridization conditions in 6×SSC at about 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 60° C.; (3) high stringency hybridization conditions in 6×SSC at about 45° C., followed by one or more washes in 0.2×SSC 0.1% SDS at 65° C.; and (4) very high stringency hybridization conditions are 0.5M sodium phosphate, 7% SDS at 65° C., followed by one or more washes at 0.2×SSC, 1% SS at 65° C.
Kallikrein Inhibitors—Antibodies
One class of kallikrein inhibitors includes antibodies. Exemplary antibodies bind, e.g., specifically to kallikrein, e.g., plasma kallikrein. An antibody can inhibit kallikrein in a number of ways. For example, it can contact one or more residues of the active site, sterically hinder or obstruct access to the active site, prevent maturation of kallikrein, or destabilize a conformation required for catalytic activity.
As used herein, the term “antibody” refers to a protein that includes at least one immunoglobulin variable domain or immunoglobulin variable domain sequence. For example, an antibody can include a heavy (H) chain variable region (abbreviated herein as VH), and a light (L) chain variable region (abbreviated herein as VL). In another example, an antibody includes two heavy (R) chain variable regions and two light (L) chain variable regions. The term “antibody” encompasses antigen-binding fragments of antibodies (e.g., single chain antibodies, Fab fragments, F(ab′)2, a Fd fragment, a Fv fragments, and dAb fragments) as well as complete antibodies.
The VH and VL regions can be further subdivided into regions of hypervariability, termed “complementarity determining regions” (“CDR”), interspersed with regions that are more conserved, termed “framework regions” (FR). The extent of the framework region and CDR's has been precisely defined (see, Kabat, E. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242, and Chothia, C. et al. (1987) J. Mol. Biol. 196:901-917). Kabat definitions are used herein. Each VH and VL is typically composed of three CDR's and four FR's, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
An “immunoglobulin domain” refers to a domain from the variable or constant domain of immunoglobulin molecules. Immunoglobulin domains typically contain two β-sheets formed of about seven β-strands, and a conserved disulphide bond (see, e.g., A. F. Williams and A. N. Barclay 1988 Ann. Rev Immunol. 6:381-405).
As used herein, an “immunoglobulin variable domain sequence” refers to an amino acid sequence which can form the structure of an immunoglobulin variable domain. For example, the sequence may include all or part of the amino acid sequence of a naturally-occurring variable domain. For example, the sequence may omit one, two or more N- or C-terminal amino acids, internal amino acids, may include one or more insertions or additional terminal amino acids, or may include other alterations. In one embodiment, a polypeptide that includes immunoglobulin variable domain sequence can associate with another immunoglobulin variable domain sequence to form a target binding structure (or “antigen binding site”), e.g., a structure that preferentially interacts with an activated integrin structure or a mimic of an activated integrin structure, e.g., relative to an non-activated structure.
The VH or VL chain of the antibody can further include all or part of a heavy or light chain constant region, to thereby form a heavy or light immunoglobulin chain, respectively. In one embodiment, the antibody is a tetramer of two heavy immunoglobulin chains and two light immunoglobulin chains, wherein the heavy and light immunoglobulin chains are inter-connected by, e.g., disulfide bonds. The heavy chain constant region includes three domains, CH1, CH2 and CH3. The light chain constant region includes a CL domain. The variable region of the heavy and light chains contains a binding domain that interacts with an antigen. The constant regions of the antibodies typically mediate the binding of the antibody to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (Clq) of the classical complement system. The term “antibody” includes intact immunoglobulins of types IgA, IgG, IgE, IgD, IgM (as well as subtypes thereof). The light chains of the immunoglobulin may be of types kappa or lambda. In one embodiment, the antibody is glycosylated. An antibody can be functional or non-functional for antibody-dependent cytotoxicity and/or complement-mediated cytotoxicity.
One or more regions of an antibody can be human or effectively human. For example, one or more of the variable regions can be human or effectively human. For example, one or more of the CDRs can be human, e.g., HC CDR1, HC CDR2, HC CDR3, LC CDR1, LC CDR2, and LC CDR3. Each of the light chain CDRs can be human. HC CDR3 can be human. One or more of the framework regions can be human, e.g., FR1, FR2, FR3, and FR4 of the HC or LC. In one embodiment, all the framework regions are human, e.g., derived from a human somatic cell, e.g., a hematopoietic cell that produces immunoglobulins or a non-hematopoietic cell. In one embodiment, the human sequences are germline sequences, e.g., encoded by a germline nucleic acid. One or more of the constant regions can be human or effectively human. In another embodiment, at least 70, 75, 80, 85, 90, 92, 95, or 98% of, or the entire antibody can be human or effectively human. An “effectively human” immunoglobulin variable region is an immunoglobulin variable region that includes a sufficient number of human framework amino acid positions such that the immunoglobulin variable region does not elicit an immunogenic response in a normal human. An “effectively human” antibody is an antibody that includes a sufficient number of human amino acid positions such that the antibody does not elicit an immunogenic response in a normal human.
All or part of an antibody can be encoded by an immunoglobulin gene or a segment thereof. Exemplary human immunoglobulin genes include the kappa, lambda, alpha (IgA1 and IgA2), gamma (IgG1, IgG2, IgG3, IgG4), delta, epsilon and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Full-length immunoglobulin “light chains” (about 25 Kd or 214 amino acids) are encoded by a variable region gene at the NH2-terminus (about 110 amino acids) and a kappa or lambda constant region gene at the COOH-terminus. Full-length immunoglobulin “heavy chains” (about 50 Kd or 446 amino acids), are similarly encoded by a variable region gene (about 116 amino acids) and one of the other aforementioned constant region genes, e.g., gamma (encoding about 330 amino acids).
One exemplary method for identifying antibodies that bind to and inhibit kallikrein includes immunizing a non-human animal with kallikrein or a fragment thereof. Even small peptides can be used as immunogens. In one embodiment, a mutated kallikrein which has reduced or no catalytic activity is used as immunogen. Spleen cells can be isolated from the immunized animal and used to produce hybridoma cells using standard methods. In one embodiment, the non-human animal includes one or more human immunoglobulin genes.
Another exemplary method for identifying proteins that bind to and inhibit kallikrein includes: providing a library of proteins and selecting from the library one or more proteins that bind to a kallikrein or a fragment thereof. The selection can be performed in a number of ways. For example, the library can be provided in the format of a display library or a protein array. Prior to selecting, the library can be pre-screened (e.g., depleted) to remove members that interact with a non-target molecule, e.g., protease other than a kallikrein or a kallikrein in which the active site is inaccessible, e.g., bound by an inhibitor, e.g., aprotinin.
Antibody libraries, e.g., antibody display libraries, can be constructed by a number of processes (see, e.g., de Haard et al. (1999) J. Biol. Chem 274:18218-30; Hoogenboom et al. (1998) Immunotechnology 4:1-20. and Hoogenboom et al. (2000) Immunol Today 21:371-8). Further, elements of each process can be combined with those of other processes. The processes can be used such that variation is introduced into a single immunoglobulin domain (e.g., VH or VL) or into multiple immunoglobulin domains (e.g., VH and VL). The variation can be introduced into an immunoglobulin variable domain, e.g., in the region of one or more of CDR1, CDR2, CDR3, FR1, FR2, FR3, and FR4, referring to such regions of either and both of heavy and light chain variable domains. In one embodiment, variation is introduced into all three CDRs of a given variable domain. In another preferred embodiment, the variation is introduced into CDR1 and CDR2, e.g., of a heavy chain variable domain. Any combination is feasible.
In an exemplary system for recombinant expression of an antibody (e.g., a full length antibody or an antigen-binding portion thereof), a recombinant expression vector encoding both the antibody heavy chain and the antibody light chain is introduced into dhfr- CHO cells by calcium phosphate-mediated transfection. Within the recombinant expression vector, the antibody heavy and light chain genes are each operatively linked to enhancer/promoter regulatory elements (e.g., derived from SV40, CMV, adenovirus and the like, such as a CMV enhancer/AdMLP promoter regulatory element or an SV40 enhancer/AdMLP promoter regulatory element) to drive high levels of transcription of the genes. The recombinant expression vector also carries a DHFR gene, which allows for selection of CHO cells that have been transfected with the vector using methotrexate selection/amplification. The selected transformant host cells are cultured to allow for expression of the antibody heavy and light chains and intact antibody is recovered from the culture medium. Standard molecular biology techniques are used to prepare the recombinant expression vector, transfect the host cells, select for transformants, culture the host cells, and recover the antibody from the culture medium. For example, some antibodies can be isolated by affinity chromatography with a Protein A or Protein G. Antibodies can also be produced by a transgenic animal.
Kallikrein Inhibitors—Peptides
The binding ligand can include a peptide of 32 amino acids or less that independently binds to a target molecule. Some such peptides can include one or more disulfide bonds. Other peptides, so-called “linear peptides,” are devoid of cysteines. In one embodiment, the peptides are artificial, i.e., not present in a Nature or not present in a protein encoded by one or more genomes of interest, e.g., the human genome. Synthetic peptides may have little or no structure in solution (e.g., unstructured), heterogeneous structures (e.g., alternative conformations or “loosely structured), or a singular native structure (e.g., cooperatively folded). Some synthetic peptides adopt a particular structure when bound to a target molecule. Some exemplary synthetic peptides are so-called “cyclic peptides” that have at least a disulfide bond and, for example, a loop of about 4 to 12 non-cysteine residues. Exemplary peptides are less than 28, 24, 20, or 18 amino acids in length.
Peptide sequences that independently bind kallikrein can be identified by any of a variety of methods. For example, they can be selected from a display library or an array of peptides. After identification, such peptides can be produced synthetically or by recombinant means. The sequences can be incorporated (e.g., inserted, appended, or attached) into longer sequences.
The following are some exemplary phage libraries that can be screened to find at least some of the peptide ligands described herein. Each library displays a short, variegated exogenous peptide on the surface of M13 phage. The peptide display of five of the libraries was based on a parental domain having a segment of 4, 5, 6, 7, 8, 10, 11, or 12 amino acids, respectively, flanked by cysteine residues. The pairs of cysteines are believed to form stable disulfide bonds, yielding a cyclic display peptide. The cyclic peptides are displayed at the amino terminus of protein III on the surface of the phage. The libraries were designated TN6/7, TN7/4, TN8/9, TN9/4, TN10/10. TN11/1, and TN12/1. A phage library with a 20-amino acid linear display was also screened; this library was designated Lin20.
The TN6/7 library was constructed to display a single cyclic peptide contained in a 12-amino acid variegated template. The TN6/6 library utilized a template sequence of Xaa1-Xaa2-Xaa3-Cys4-Xaa5-Xaa6-Xaa7-Xaa8-Cys9-Xaa10-Xaa11-Xaa12, where each variable amino acid position in the amino acid sequence of the template is indicated by a subscript integer. Each variable amino acid position (Xaa) in the template was varied to contain any of the common α-amino acids, except cysteine (Cys).
The TN7/4 library was constructed to display a single cyclic peptide contained in a 12-amino acid variegated template. The TN7/4 library utilized a template sequence of Xaa1-Xaa2-Xaa3-Cys4-Xaa5-Xaa6-Xaa7-Xaa8-Xaa9-Cys10-Xaa11-Xaa12-Xaa13, where each variable amino acid position in the amino acid sequence of the template is indicated by a subscript integer. Each variable amino acid position (Xaa) in the template was varied to contain any of the common α-amino acids, except cysteine (Cys).
The TN8/9 library was constructed to display a single binding loop contained in a 14-amino acid template. The TN8/9 library utilized a template sequence of Xaa1-Xaa2-Xaa3-Cys-Xaa5-Xaa6-Xaa7-Xaa8-Xaa9-Xaa10-Cys-Xaa12-Xaa13-Xaa14. Each variable amino acid position (Xaa) in the template were varied to permit any amino acid except cysteine (Cys).
The TN9/4 library was constructed to display a single binding loop contained in a 15-amino acid template. The TN9/4 library utilized a template sequence Xaa1-Xaa2-Xaa3-Cys4-Xaa5-Xaa6-Xaa7-Xaa8-Xaa9-Xaa10-Xaa11-Cys12-Xaa13-Xaa14-Xaa15. Each variable amino acid position (Xaa) in the template were varied to permit any amino acid except cysteine (Cys).
The TN10/10 library was constructed to display a single cyclic peptide contained in a 16-amino acid variegated template. The TN10/9 library utilized a template sequence Xaa1-Xaa2-Xaa3-Cys4-Xaa5-Xaa6-Xaa7-Xaa8-Xaa9-Xaa10-Xaa11-Xaa12-Cys13-Xaa14-Xaa15-Xaa16, where each variable amino acid position in the amino acid sequence of the template is indicated by a subscript integer. Each variable amino acid position (Xaa) was to permit any amino acid except cysteine (Cys).
The TN11/1 library was constructed to display a single cyclic peptide contained in a 17-amino acid variegated template. The TN11/1 library utilized a template sequence Xaa1-Xaa2-Xaa3-Cys4-Xaa5-Xaa6-Xaa7-Xaa8-Xaa9-Xaa10-Xaa11-Xaa12-Xaa13-Cys14-Xaa15-Xaa16-Xaa17, where each variable amino acid position in the amino acid sequence of the template is indicated by a subscript integer. Each variable amino acid position (Xaa) was to permit any amino acid except cysteine (Cys).
The TN12/1 library was constructed to display a single cyclic peptide contained in an 18-amino acid template. The TN12/1 library utilized a template sequence Xaa1-Xaa2-Xaa3-Cys4-Xaa5-Xaa6-Xaa7-Xaa8-Xaa9-Xaa10-Xaa11-Xaa12-Xaa13-Xaa14-Cys15-Xaa16-Xaa17-Xaa18, where each variable amino acid position in the amino acid sequence of the template is indicated by a subscript integer. The amino acid positions Xaa1, Xaa2, Xaa17 and Xaa18 of the template were varied, independently, to permit each amino acid selected from the group of 12 amino acids consisting of Ala, Asp, Phe, Gly, His, Leu, Asn, Pro, Arg, Ser, Trp, and Tyr. The amino acid positions Xaa3, Xaa5, Xaa6, Xaa7, Xaa8, Xaa9, Xaa10, Xaa11, Xaa12, Xaa13, Xaa14, Xaa16, of the template were varied, independently, to permit any amino acid except cysteine (Cys).
The Lin20 library was constructed to display a single linear peptide in a 20-amino acid template. The amino acids at each position in the template were varied to permit any amino acid except cysteine (Cys).
The techniques discussed in Kay et al., Phage Display of Peptides and Proteins: A Laboratory Manual (Academic Press, Inc., San Diego 1996) and U.S. Pat. No. 5,223,409 are useful for preparing a library of potential binders corresponding to the selected parental template. The libraries described above can be prepared according to such techniques, and screened, e.g., as described above, for peptides that bind to and inhibit kallikrein.
In addition phage libraries or selected populations from phage libraries can be counter-selected, e.g., using kallikrein that is inactivated, e.g., by binding of aprotinin or another kallikrein inhibitor. Such procedures can be used to discard peptides that do not contact the active site.
Peptides can also be synthesized using alternative backbones, e.g., a peptoid backbone, e.g., to produce a compound which has increased protease resistance. In particular this method can be used to make a compound that binds to and inhibits kallikrein and which is not itself effectively cleaved by kallikrein.
Modifications
It is possible to modify polypeptides that inhibit a Kunitz domain in a variety of ways, For example, the polypeptides can be attached to one or more polyethylene glycol moieties to stabilize the compound or prolong retention times, e.g., by at least two, four, five, or eight fold.
A polypeptide that inhibits kallikrein can be associated with (e.g., conjugated to) a polymer, e.g., a substantially non-antigenic polymers, such as polyalkylene oxides or polyethylene oxides. Suitable polymers will vary substantially by weight. Polymers having molecular number average weights ranging from about 200 to about 35,000 (or about 1,000 to about 15,000, and 2,000 to about 12,500) can be used. A plurality of polymer moieties can be attached to one polypeptide, e.g., at least two, three, or four such moieties, e.g., having an average molecular weight of about 2,000 to 7,000 Daltons.
For example, the polypeptide can be conjugated to a water soluble polymer, e.g., hydrophilic polyvinyl polymers, e.g. polyvinylalcohol and polyvinylpyrrolidone. A non-limiting list of such polymers include polyalkylene oxide homopolymers such as polyethylene glycol (PEG) or polypropylene glycols, polyoxyethylenated polyols, copolymers thereof and block copolymers thereof, provided that the water solubility of the block copolymers is maintained. Additional useful polymers include polyoxyalkylenes such as polyoxyethylene, polyoxypropylene, and block copolymers of polyoxyethylene and polyoxypropylene (Pluronics); polymethacrylates; carbomers; branched or unbranched polysaccharides which comprise the saccharide monomers D-mannose, D- and L-galactose, fucose, fructose, D-xylose, L-arabinose, D-glucuronic acid, sialic acid, D-galacturonic acid, D-mannuronic acid (e.g. polymannuronic acid, or alginic acid), D-glucosamine, D-galactosamine, D-glucose and neuraminic acid including homopolysaccharides and heteropolysaccharides such as lactose, amylopectin, starch, hydroxyethyl starch, amylose, dextrane sulfate, dextran, dextrins, glycogen, or the polysaccharide subunit of acid mucopolysaccharides, e.g. hyaluronic acid; polymers of sugar alcohols such as polysorbitol and polymannitol; heparin or heparon.
Other compounds can also be attached to the same polymer, e.g., a cytotoxin, a label, or another targeting agent or an unrelated agent. Mono-activated, alkoxy-terminated polyalkylene oxides (PAO's), e.g., monomethoxy-terminated polyethylene glycols (mPEG's); C1-4 alkyl-terminated polymers; and bis-activated polyethylene oxides (glycols) can be used for crosslinking. See, e.g., U.S. Pat. No. 5,951,974
Kallikrein Inhibitors—Small Molecules
An inhibitor of a kallikrein, e.g., plasma kallikrein, can also be a compound that is smaller than 3000, 2000 or 1000 Daltons. For example, the compound is a non-proteinaceous compound or a compound that includes fewer than five peptide bonds.
For example, the inhibitor can be a compound described in WO 04/062657, e.g., an acylated 4-amidino- or 4-guanidinobenzylamine. The compound can have the general formula (I) P4-P3-P2-P1 (I), where P4 is a mono- or poly-substituted or unsubstituted benzylsulphonyl group, P3 is a mono- or poly-substituted or unsubstituted, natural or unnatural alpha-amino or alpha-imino acid with the D-configuration, P2 is a mono- or poly-substituted or unsubstituted natural or unnatural alpha-amino or alpha-imino acid with the L-configuration and P1 is a mono- or poly-substituted or unsubstituted 4-amidino- or 4-guanidinobenzylamine group.
Another example is a compound represented by Structural Formula (I):




R1 is a substituted or unsubstituted aryl group or alkyl group; R2 is a substituted or unsubstituted aryl group or cycloalkyl group; Ar is a substituted or unsubstituted aryl group; X is a —CH2-, —O—, —S— or —CO—; m is an integer from zero to two; n is an integer from 0-2 when X is —O—, —S— and 1-2 when X is —CH2- or —CO—. Exemplary compounds are described in US 2004-044075.
Methods and Compositions
The inhibitors described herein can be used in methods for preventing or reducing ischemia and/or reperfusion injury associated with ischemia; methods for preventing or reducing perioperative blood loss and/or a systemic inflammatory response (SIR) in a patient, especially associated with cardiothoracic surgery. The method includes administering a inhibitor of kallikrein, e.g., plasma kallikrein.
In one embodiment, a method for treatment involves the administration of a polypeptide comprising a Kunitz domain. One embodiment of the method involves using a polypeptide containing an amino acid sequence of SEQ ID NO:1 that has an affinity for kallikrein that is approximately 1000-fold or more higher than that of a broad range serine protease, e.g., aprotinin, which is isolated from bovine lung and currently approved for use in CABG procedures (TRASYLOLTM, Bayer Corporation Pharmaceutical Division, West Haven, Conn.).
Patients subjected to any of a number of surgical procedures, especially those involving extra-corporeal circulation, e.g., cardiothoracic surgery, such as, for example, CPB, and/or bone trauma, such as sty split or hip replacement, are at risk for perioperative blood loss and inflammation. Contact of a patient's blood with the cut surfaces of bone or of CPB equipment is sufficient to activate one or several undesirable cascade responses, including a contact activation system (CAS), which can lead to extensive perioperative blood loss requiring immediate blood transfusion, as well as a systemic inflammatory response (SIR), which, in turn, can result in permanent damage to tissues and organs. While not desiring to be limited to any particular mechanism or theory, it appears that the blood loss that occurs associated with cardiothoracic surgery, e.g., CPB, as in a CABG procedure, probably results from extensive capillary leakage, which can result in significant loss of blood that must be replaced by immediate blood transfusion.
The inhibitors described herein can be used to prevent or reduce various ischemias including, for example, perioperative blood loss and SIR in a patient subjected to a surgical procedure, and especially wherein the surgical procedure requires extra-corporeal circulation, e.g., cardiothoracic surgery, such as, for example, CPB. The inhibitors can be particularly useful for preventing or reducing perioperative blood loss and/or SIR in a patient subjected to a CABG procedure requiring CPB or other cardiac surgery. Further, the inhibitors described herein can be used to prevent or reduce cerebral ischemia (such as stroke) and/or reperfusion injury associated with cerebral ischemia (e.g., stroke).
Exemplary compositions for medical use comprise a kallikrein inhibitor described herein. Such compositions can further include one or more pharmaceutically acceptable buffers, carriers, and excipients, which can provide a desirable feature to the composition including, but not limited to, enhanced administration of the composition to a patient, enhanced circulating half-life of the inhibitor, enhanced compatibility of the inhibitor with patient blood chemistry, enhanced storage of the composition, and/or enhanced delivery and/or efficacy of the inhibitor upon administration to a patient. In addition to an inhibitor described herein, compositions can further include one or more other pharmaceutically active compounds that provide an additional prophylactic or therapeutic benefit to a patient, e.g., a patient of an invasive surgical procedure or a patent otherwise at risk for, having or previously had cerebral ischemia and/or reperfusion injury associated with cerebral ischemia. For example, the compositions can include another compound described herein.
Perioperative Blood Loss and Reduced Heart Bloodflow
Due to the many advances in medicine, a number of highly invasive surgical procedures are carried out each day that result in blood loss, or place patients at a high risk for blood loss. Such patients are generally carefully monitored to restore and maintain normal blood supply and hemostasis, and they may need blood transfusions. Surgical procedures that involve blood loss include those involving extra-corporeal circulation methods such as cardiothoracic surgery, e.g., CPB. In such methods, a patient's heart is stopped and the circulation, oxygenation, and maintenance of blood volume are carried out artificially using an extra-corporeal circuit and a synthetic membrane oxygenator. These techniques are commonly used during cardiac surgery. Additionally, it is apparent that surgery involving extensive trauma to bone, such as the sternal split necessary in CABG or hip replacement procedures, is also associated with activation of the CAS, which can result in a variety of disruptions in the blood and vasculature.
Atherosclerotic coronary artery disease (CAD) causes a narrowing of the lumen of one or several of the coronary arteries; this limits the flow of blood to the myocardium (i.e., the heart muscle) and can cause angina, heart failure, and myocardial infarcts. In the end stage of coronary artery atherosclerosis, the coronary circulation can be almost completely occluded, causing life threatening angina or heart failure, with a very high mortality. CABG procedures may be required to bridge the occluded blood vessel and restore blood to the heart; these are potentially life saving. CABG procedures are among the most invasive of surgeries in which one or more healthy veins or arteries are implanted to provide a “bypass” around the occluded area of the diseased vessel. CABG procedures carry with them a small but important perioperative risk, but they are very successful in providing patients with immediate relief from the mortality and morbidity of atherosclerotic cardiovascular disease. Despite these very encouraging results, repeat CABG procedures are frequently necessary, as indicated by an increase in the number of patients who eventually undergo second and even third procedures; the perioperative mortality and morbidity seen in primary CABG procedures is increased in these re-do procedures.
There have been improvements in minimally invasive surgical techniques for uncomplicated CAD. However, nearly all CABG procedures performed for valvular and/or congenital heart disease, heart transplantation, and major aortic procedures, are still carried out on patients supported by CPB. In CPB, large cannulae are inserted into the great vessels of a patient to permit mechanical pumping and oxygenation of the blood using a membrane oxygenator. The blood is returned to the patient without flowing through the lungs, which are hypoperfused during this procedure. The heart is stopped using a cardioplegic solution, the patient cooled to help prevent brain damage, and the peripheral circulating volume increased by an extracorporeal circuit, i.e., the CPB circuit which requires “priming” with donor blood and saline mixtures are used to fill the extracorporeal circuit. CPB has been extensively used in a variety of procedures performed for nearly half a century with successful outcomes. The interaction between artificial surfaces, blood cells, blood proteins, damaged vascular endothelium, and extravascular tissues, such as bone, disturbs hemostasis and frequently activates the CAS, which, as noted above, can result in a variety of disruptions in the blood and vasculature. Such disruption leads to excess perioperative bleeding, which then requires immediate blood transfusion. A consequence of circulating whole blood through an extracorporeal circuit in CPB can also include the systemic inflammatory response (SIR), which is initiated by contact activation of the coagulation and complement systems. Indeed, much of the morbidity and mortality associated with seemingly mechanically successful CPB surgical procedures is the result of the effects of activating coagulation, fibrinolysis, or complement systems. Such activation can damage the pulmonary system, leading to adult respiratory distress syndrome (ARDS), impairment of kidney and splanchnic circulation, and induction of a general coagulopathy leading to blood loss and the need for transfusions. In addition to the dangers of perioperative blood loss, additional pathologies associated with SIR include neurocognitive deficits, stroke, renal failure, acute myocardial infarct, and cardiac tissue damage.
Blood transfusions also present a significant risk of infection and elevate the cost of CABG or other similar procedures that require CPB. In the absence of any pharmacological intervention, three to seven units of blood must typically be expended on a patient, even with excellent surgical techniques. Accordingly, there is considerable incentive for the development of new and improved pharmacologically effective compounds to reduce or prevent perioperative bleeding and SIR in patients subjected to CPB and CABG procedures. Use of the inhibitors described herein can improve these various treatments and lead to amelioration of the undesirable symptoms that can occur.
Cerebral Ischemia and Reperfusion Injury
The methods described herein are useful for reducing or preventing cerebral ischemia as well as reperfusion injury associated with cerebral ischemia. A “cerebral ischemic attack” or “cerebral ischemia” is an ischemic condition in which blood supply to the brain is blocked. This interruption in the blood supply to the brain may result from a variety of causes including, but not limited to, an intrinsic blockage or occlusion of the blood vessel itself, a remotely originated source of occlusion, decreased perfusion pressure or increased blood viscosity resulting in decreased cerebral blood flow, or ruptured or leaky blood vessels in the subarachnoid space or intracerebral tissue. Cerebral ischemia may result in either transient or permanent deficits and the seriousness of the neurological damage in a patient who has experienced cerebral ischemia depends on the intensity and duration of the ischemia event. A transient ischemia attack (TIA) is one in which the blood flow to the brain is briefly interrupted and causes temporary neurological deficits. Symptoms of TIA include numbness of weakness of face or limbs, loss of ability to speak clearly and/or understand the speech of others, a loss of vision or is dimness of vision and dizziness. Permanent cerebral ischemia attacks, also called strokes, are caused by a longer interruption in blood flow to the brain resulting from an embolism, a thrombus or bleeding in the brain (e.g., a hemorrhage). The term “thromboembolic stroke” or “thromboembolism” is used herein to refer to a stroke caused by either a thrombosis or an embolism. A stroke causes a loss of neurons typically resulting in a neurological deficit that may improve but does not entirely resolve. The inhibitors described herein are useful in preventing or reducing stroke including embolic-, thrombolic-, thromboembolic- and hemorrhage-associated strokes. Strokes can be caused by a variety of causes. One category includes perioperative strokes that can be associated with thrombus or embolism formation.
In stroke patients, there is a core of the neurological deficit marked by total ischemia and/or tissue necrosis. This area is normally surrounded by ischemic tissue, referred to as the ischemic penumbra, that receives collateral circulation. Ischemia in the penumbra does not always result in irreversible damage. In some cases, restoration of blood flow (reperfusion) into the penumbra may prevent total ischemia and necrosis in this area. However, reperfusion has also been associated with injury to the tissue surrounding the core. Once blood flow is returned, blood cells such as neutrophils, attack the damaged tissue which can cause additional inflammation and/or damage. Reperfusion injury is associated with an influx of neutrophils into the affected tissue and subsequent activation of the neutrophils. Neutrophils can release lytic enzymes that directly induce tissue damage and proinflammatory mediators such as cytokines that amplify local inflammatory reaction. The influx of neutrophils to a site of ischemic damage can also plug capillaries and cause vasoconstriction. It has been found that kallikrein plays a role in neutrophil chemotaxis, neutrophil activation and reperfusion injury. Thus, the kallikrein inhibitors described herein can be used to prevent or reduce reperfusion injury, e.g., by reducing or preventing one or more of: 1) neutrophil infiltration, 2) neutrophil activation; 3) cytokine release; 4) elastase release; and 5) vasodilation. For example, a kallikrein inhibitor can be used to inhibit bradykinin and Factor XII.
Administration
A kallikrein inhibitor can be administered to a patient before, during, and/or after an ischemia event e.g., a surgical procedure or cerebral ischemic attack, in a pharmaceutically acceptable composition or in connection with another disorder or event described herein. The patient is generally a human, but may also be a non-human mammal. Human patients include adults, e.g., patients between ages 19-25, 26-40, 41-55, 56-75, and 76 and older, and pediatric patients, e.g., patients between ages 0-2, 3-6, 7-12, and 13-18.
The term “pharmaceutically acceptable” composition refers to a non-toxic carrier or excipient that may be administered to a patient, together with a kallikrein inhibitor described herein. The carrier or excipient is chosen to be compatible with the biological or pharmacological activity of the composition. The inhibitors described herein can be administered locally or systemically by any suitable means for delivery of a kallikrein inhibitory amount of the inhibitor to a patient including but not limited to systemic administrations such as, for example, intravenous and inhalation. Parenteral administration is particularly preferred.
For parenteral administration, the polypeptides can be injected intravenously, intramuscularly, intraperitoneally, or subcutaneously. Intravenous administration is preferred. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Other pharmaceutically acceptable carriers include, but are not limited to, sterile water, saline solution, and buffered saline (including buffers like phosphate or acetate), alcohol, vegetable oils, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, paraffin, etc. Where necessary, the composition can also include a solubilizing agent and a local anaesthetic such as lidocaine to ease pain at the site of the injection, preservatives, stabilizers, wetting agents, emulsifiers, salts, lubricants, etc. as long as they do not react deleteriously with the active compounds. Similarly, the composition can comprise conventional excipients, e.g., pharmaceutically acceptable organic or inorganic carrier substances suitable for parenteral, enteral or intranasal application which do not deleteriously react with the active compounds. Generally, the ingredients will be supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent in activity units. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade “water for injection” or saline. Where the composition is to be administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients can be mixed prior to administration.
In one embodiment, the inhibitor is administered to a patient as an intravenous infusion according to any approved procedure. For example, an inhibitor described herein can be administered to a patient subjected to a CABG procedure at the times similar to those currently used in approved protocols for administering aprotinin and in an amount necessary to provide a patient with a required number or concentration of kallikrein inhibitory units (KIU).
An inhibitor described herein can also be administered to a patient in the immediate postoperative period, when bleeding abnormalities can occur as a consequence of downstream effects of SIR. For example, in a procedure involving CPB, an inhibitor described herein can be administered to a patient as an initial loading dose, e.g., an effective amount over the course of a convenient time, such as 10 minutes, prior to induction of anesthesia. Then, at induction of anesthesia, a second dose of the inhibitor can be injected into the CPB priming fluid (“pump prime volume”). The patient can then be placed on a continuous and controlled intravenous infusion dose for the duration of the surgical procedure, and after the procedure if indicated.
In other embodiments, an inhibitor can be administered after an ischemic event, e.g., after a stroke, e.g., 5, 10, 15, 30, 45 minutes, 1, 2, 3, 5, 10, 15, 20 hours or more after a stroke. Preferably, the inhibitor is administered within 12 to 60 hours, e.g., within 24 to 48 hours, after a stroke. In some embodiments, an inhibitor is administered after an ischemic event, e.g., after a stroke, but prior to reperfusion of the damaged tissue. In other embodiments, an inhibitor is administered during reperfusion or after reperfusion has begun. In yet another embodiment, an inhibitor is administered after reperfusion has occurred.
An effective amount of an inhibitor (e.g., a Kunitz domain polypeptide or other compound described herein) can be administered alone or in combination with another therapeutic for the treatment of cerebral ischemia and/or reperfusion injury associated with cerebral ischemia. An effective amount is an amount sufficient to reduce one or more symptoms associated with cerebral ischemia and/or reperfusion injury associated with cerebral ischemia which otherwise would have occurred in a subject experiencing a cerebral ischemia and/or reperfusion injury associated with cerebral ischemia absent the treatment. Several physiological parameters may be used to assess stroke and reperfusion injury associated with stroke including infarct size, regional cerebral blood flow, intracranial pressure, anterograde amnesia, retrograde amnesia, dementia, cognitive function and/or emotion, and cerebral edema, for example, as compared to pretreatment patient parameters, untreated stroke patients or stroke patients treated with the other therapeutic agent but not the combination with the inhibitor (e.g., the Kunitz domain polypeptide or other compound described herein).
With respect to an implementation in which DX-88 or a DX-88-related inhibitor is used, the affinity constant (Ki) of DX-88 is at least about 1000 times greater than aprotinin for kallikrein inhibition. Accordingly, the dose of DX-88 or an inhibitor of similar affinity could be at least about 10, 50, 100, 500, or 1000 times lower than aprotinin on a mole per mole basis. The dose could also be modulated as a function of the amount of kallikrein activated during an event (e.g., CPB), the specificity of the DX-88-kallikrein interaction in vivo, the concentration of kallikrein eliciting SIRS, and pharmacological distribution.
The total amount of circulating prekallikrein in plasma is reported to be approximately 50 g/mL or 500 nM. If all prekallikrein is activated, at least 500 nmoles/L of DX-88 can be used to inhibit kallikrein in a stoichiometric manner. An individual having 5 L of plasma would require a dose of 2500 nmoles DX-88, or approximately 18 mg based on the molecular weight of DX-88 of 7,054 Daltons. The dose can be reduced proportionally if not all of the prekallikrein is activated.
As the concentration of active kallikrein may have to rise above a certain level to contribute to increased fluid and blood loss post-operatively, in many cases, it is not necessary to inactivate all active kallikrein. DX-88 would be expected to be effective at a significantly lower dose compared to aprotinin on the basis of its higher affinity for kallikrein. A plasma level of 10 nM DX-88 would inhibit 99.6% of the kallikrein present at a plasma concentration of 1 nM (i.e., only 0.4 pM free kallikrein remaining), while only 24.5% of the activated kallikrein would be inhibited by 10 nM aprotinin. These values were calculated using the standard equilibrium equation that relates the Ki of the binding interaction to the relative concentration of enzyme (plasma kallikrein) and inhibitor (DX-88). Plasma levels of at least 3 μM aprotinin would be required to inhibit kallikrein to the same extent as 10 nM DX-88. In other words, the high affinity of DX-88 for kallikrein can allow for a rapid therapeutic effect without maintaining high plasma inhibitor levels.
DX-88 also has greater specificity for kallikrein inhibition compared to aprotinin in vitro. Therefore, proteases other than kallikrein that are inhibited by aprotinin may lower the effective concentration of the inhibitor, thereby increasing the amount of aprotinin needed for a therapeutic effect.
An initial clinical dose of DX-88 for patients undergoing CPB has been estimated from the recommended high dose regimen of aprotinin (2×106 KIU). Aprotinin is administered in three stages of 2×106 KIU each, consisting of a loading dose, a pump priming dose and a continuous intravenous infusion during CPB. Aprotinin is reported to have a specific inhibitory activity of 7,143 KIU/mgv, determined using a dog blood pressure assay. Therefore, 2×106 KIU of aprotinin is equivalent to 280 mg of the protein. In a patient having a plasma volume of 5 liters, 280 mg corresponds to approximately 8.6 μM aprotinin. The specific activity of aprotinin in the inhibitory assay used for DX-88 is approximately 0.5 KIU/mg determined using an enzymatic assay. A dose of 280 mg would correspond to a loading dose for aprotinin of approximately 140 KIU. The specific activity of DX-88 using the same assay is approximately 10 KIU/mg. A dose of only 14 mg of DX-88 would be required to provide a number of inhibitory units equivalent to 280 mg aprotinin. Thus, in certain embodiments, about 5-20, or 10-20 mg of DX-88 can be administered to a subject.
Administered “in combination,” as used herein, means that two (or more) different treatments are delivered to the subject once the subject has been determined to be at risk for the disorder or during the course of the subject's affliction with the disorder, e.g., the two or more treatments are delivered after the subject has been diagnosed as at risk for the disorder or the two or more agents are delivered after the subject has been diagnosed with the disorder and before the disorder has been cured or eliminated. In some embodiments, the delivery of one treatment is still occurring when the delivery of the second begins, so that there is overlap. This is sometimes referred to herein as “simultaneous” or “concurrent delivery.” In other embodiments, the delivery of one treatment ends before the delivery of the other treatment begins. In some embodiments of either case, the treatment is more effective because of combined administration. For example, the second treatment is more effective, e.g., an equivalent effect is seen with less of the second treatment, or the second treatment reduces symptoms to a greater extent, than would be seen if the second treatment were administered in the absence of the first treatment, or the analogous situation is seen with the first treatment. In some embodiments, delivery is such that the reduction in a symptom, or other parameter related to the disorder is greater than what would be observed with one treatment delivered in the absence of the other. The effect of the two treatments can be partially additive, wholly additive, or greater than additive. The delivery can be such that an effect of the first treatment delivered is still detectable when the second is delivered. The Kunitz domain polypeptide or other inhibitor can be administered before, concurrently with, or after the administration of another therapeutic, e.g., an anticoagulant agent, an antiplatelet agent or a thrombolytic agent.
Anticoagulation agents prevent the coagulation of blood components and thus prevent clot formation. Anticoagulants include, but are not limited to, heparin, warfarin, coumadin, dicumarol, phenprocoumon, acenocoumarol, ethyl biscoumacetate, hirudin, bivalarutin, and other direct thrombin inhibitors, and indandione derivatives.
Anti-platelet agents inhibit platelet aggregation and are often used to prevent thromboembolic stroke in patients who have experienced a transient ischemic attack or stoke. Anti-platelet agents include, but are not limited to, aspirin, thienopyridine derivatives such as ticlopodine and clopidogrel, dipyridamole and sulfinpyrazone, as well as RGD mimetics.
Thrombolytic agents lyse clots that cause the thromboembolic stroke. Thrombolytic agents have been used in the treatment of acute venous thromboembolism and pulmonary emboli and are well known in the art (e.g. see Hennekens et al, J Am Coll Cardiol; v. 25 (7 supp), p. 18S-22S (1995); Holmes, et al, J Am Coll Cardiol; v. 25 (7 suppl), p. 10S-17S (1995)). Thrombolytic agents include, but are not limited to, plasminogen, a2-antiplasmin, streptokinase, antistreplase, TNK, tissue plasminogen activator (tPA), and urokinase. “tPA” as used herein includes native tPA and recombinant tPA, as well as modified forms of tPA that retain the enzymatic or fibrinolytic activities of native tPA. The enzymatic activity of tPA can be measured by assessing the ability of the molecule to convert plasminogen to plasmin. The fibrinolytic activity of tPA may be determined by any in vitro clot lysis activity known in the art, such as the purified clot lysis assay described by Carlson, et al., Anal. Biochem. 168, 428-435 (1988) and its modified form described by Bennett, W. F. et al., 1991, supra.
Currently there are two regimens approved in the United States for administering aprotinin to a patient undergoing a CABG procedure (see, product label and insert for TRASYLOLTM, Bayer Corporation Pharmaceutical Division, West Haven, Conn.). One such approved regimen uses a 2 million KIU intravenous loading dose, 2 million KIU into the pump prime volume, and 500,000 KIU per hour of surgery. Another approved regimen uses 1 million KIU intravenous loading dose, 1 million KIU into the pump prime volume, and 250,000 KIU per hour of surgery. As these regimens are based on KIU, the regimens are readily adapted to other kallikrein inhibitors described herein once the specific activity and KIU of a particular inhibitor has been determined by standard assays. Owing to the enhanced binding affinity and inhibitory activity in representative polypeptide inhibitors of kallikrein described herein relative to aprotinin, it is expected that the compositions and methods described herein are likely to require fewer milligrams (mg) per patient to provide a patient with the required number or concentration of KIU.
Several considerations regarding dosing with a polypeptide inhibitor of kallikrein can be illustrated by way of example with the representative PEP-1 KI polypeptide having the amino sequence of SEQ ID NO:2 (molecular weight of 7,054 Daltons).
Table 1, below, provides a comparison of the affinity (Ki,app) of the PEP-1 KI polypeptide for kallikrein and eleven other known plasma proteases.









TABLE 1






PEP-1 Ki, app
Aprotinin Ki, app


Protease Substrate
(pM)
(pM)







human plasma kallikrein
44
 3.0 × 104


human urine kallikrein
  >1 × 108
 4.0 × 103


porcine pancreatic
 2.7 × 107
550


kallikrein


human C1r, activated
>2.0 × 108
>1.0 × 107


human C1s, activated
>2.0 × 107
>1.0 × 108


human plasma factor XIa
 1.0 × 104
ND


human plasma factor Xlla
>2.0 × 107
>1.0 × 108


human plasmin
 1.4 × 105
894


human pancreatic trypsin
  >2 × 107
ND


human pancreatic
>2.0 × 107
 7.3 × 105


chymotrypsin


human neutrophil elastase
>2.0 × 107
 1.7 × 106


human plasma thrombin
>2.0 × 107
>1.0 × 108





ND = not determined






Clearly, the PEP-1 KI polypeptide is highly specific for human plasma kallikrein. Furthermore, the affinity (Ki,app) of PEP-1 for kallikrein is 1000 times higher than the affinity of aprotinin for kallikrein: the Ki,app of PEP-1 for kallikrein is about 44 pM (Table 1), whereas the Ki,app of aprotinin for kallikrein is 30,000 pM. Thus, a dose of PEP-1 could be approximately 1000 times lower than that used for aprotinin on a per mole basis. However, consideration of several other factors may provide a more accurate estimation of the dose of PEP-1 required in practice. Such factors include the amount of kallikrein activated during CPB in a particular patient, the concentration of kallikrein required to elicit an SIR, and the bioavailability and pharmacological distribution of PEP-1 in a patient. Nevertheless, use of a polypeptide that includes a Kunitz domain that inhibits kallikrein in doses currently approved for the use of aprotinin is still expected to provide significant improvements over the current use of the less specific, lower affinity, bovine aprotinin. Accordingly, lower doses, e.g., at least half, or a tenth of the approved aprotinin dose may be used for a kallikrein inhibitor which inhibits kallikrein at least 2, 10, 50, or 100 fold better than aprotinin.
For example, the total amount of circulating prekallikrein in plasma is estimated at approximately 500 nM (Silverberg, M. et al., “The Contact System and Its Disorders,” in Blood: Principles and Practice of Hematology, Handin, R. et al., eds., J B Lippincott Co., Philadelphia, 1995). If all of the prekallikrein were activated, then at least 500 nM of PEP-1 would be required for a stoichiometric inhibition of kallikrein. An individual having 5 liters of plasma would therefore require about 18 mg of PEP-1 to achieve a plasma concentration of 500 nM.
Another factor to consider is the threshold concentration of kallikrein required to induce a SIR in a patient. If the concentration of active kallikrein must be maintained below, e.g., 1 nM, then owing to its high affinity for kallikrein, PEP-1 offers a significant advantage over aprotinin in the amount of protein that would be required to inhibit SIR. In particular, a concentration of PEP-1 of 1 nM would inhibit 99.6% of kallikrein present at 1 nM (i.e., only 0.4 pM free kallikrein remaining in the blood), whereas, an aprotinin concentration of 1 nM would only inhibit 24.5% of the kallikrein present at 1 nM. For aprotinin to inhibit 99% of the kallikrein at 1 nM, an aprotinin concentration in the plasma of at least 3 uM is required (i.e., 3000 times higher concentration than for PEP-1).
For a patient undergoing CPB, an initial clinical dose of PEP-1 can be estimated from a recommended dose regimen of aprotinin (1×106 KIU) mentioned above. Aprotinin is reported in a package insert to have as specific inhibitory activity of 7143 KIU/mg determined using a dog blood pressure assay. Therefore, 1×106 KIU of aprotinin is equivalent to 140 mg of aprotinin (i.e., 1×106 KIU/7143 KIU/mg=140 mg of aprotinin). In a patient having a blood plasma volume of 5 liters, 140 mg corresponds to approximately 4.3 μM aprotinin (molecular weight of aprotinin is 6512 Daltons). The specific activity of aprotinin in the standard inhibitory assay used for PEP-1 is 0.4 KIU/mg of polypeptide. A dose of 140 mg would correspond to a loading dose for aprotinin of 56 KIU (140 mg×0.4 KIU/mg=56 KIU). In contrast, since the specific activity of the PEP-1 KI polypeptide is 10 KIU/mg in the standard inhibition assay, a dose of only 5.6 mg of PEP-1 would be required to provide the number of KIUs equivalent to 140 mg of aprotinin. In a patient with a plasma volume of 5 liters, this corresponds to about 160 nM PEP-1 (molecular weight of PEP-1 is 7054 Daltons), although a higher dose of the PEP-1 KI polypeptide can be required if all of the plasma kallikrein (500 nM) is activated and/or if this KI polypeptide is poorly distributed in a patient.
In some embodiment, the Kunitz domain polypeptide or KI polypeptide is administered in a dose of about 1-500 mg/m2, preferably about 1-250 mg/m2, 1-100 mg/m2. For example, a KI polypeptide, e.g., a KI polypeptide described herein, can be administered to a subject at risk for cerebral ischemia, suffering from cerebrial ischemia, or who has suffered a cerebral ischemic attack at a dose of 1-100 mg/m2.
Furthermore, the KI polypeptides can be non-naturally occurring, and they can be produced synthetically or recombinantly, as noted above, thereby avoiding potential contamination of transmissible diseases that can arise during isolation of a protein from a natural animal source, such as in the case of aprotinin, which is isolated from bovine lung. Increasingly important to administrative and public acceptance of a treatment or pharmaceutical composition comprising a polypeptide is the avoidance of possible contamination with and transmission to human patients of various pathological agents. Of particular interest for the safety of proteins isolated from a bovine tissue is the elimination of the possible risk of exposure to viral mediated diseases, bacterial mediated diseases, and, especially, transmissible bovine spongiform encephalopathies.
As variants of the Kunitz domain 1 of the human LACI protein, fewer side effects are expected from administering the KI polypeptides to patients than for aprotinin, which is a bovine protein that is documented to cause anaphylactic and anaphylactoid responses in patients, especially in repeat administrations, such as second time CABG procedures. Additionally, the highly specific binding of the KI polypeptides described herein to kallikrein will effectively limit or eliminate the thrombotic tendencies observed with aprotinin, and reduce the problems observed with graft patency following CABG procedures.
The invention will be further described with reference to the following non-limiting examples. The teachings of all the patents, patent applications and all other publications and websites cited herein are incorporated by reference in their entirety.
EXAMPLES
Example 1
An Exemplary Kallikrein Inhibitor Polypeptide
An exemplary non-naturally occurring, KI polypeptide (PEP-1) was identified as a kallikrein binding polypeptide displayed on a recombinant phage from a phage display library. PEP-1 has the amino acid sequence:








(SEQ ID NO:2)









Glu Ala Met His Ser Phe Cys Ala Phe Lys Ala Asp



 


Asp Gly Pro Cys Arg Ala Ala His Pro Arg Trp Phe


 


Phe Asn Ile Phe Thr Arg Gln Cys Glu Gln Phe Ile


 


Tyr Gly Gly Cys Glu Gly Asn Gln Asn Arg Phe Glu


 


Ser Leu Glu Glu Cys Lys Lys Met Cys Thr Arg Asp.






The molecular weight of PEP-1 is 7,054 Daltons.

The nucleotide sequence (SEQ ID NO:3) of the recombinant phage DNA encoding the PEP-1 amino acid sequence (amino acids 1-60 of SEQ ID NO:2) was isolated and sequenced by standard methods determined from the recombinant phage DNA.
PEP-1 was produced in amounts useful for further characterization as a recombinant protein in His4− phenotype host cells of yeast strain Pichia pastoris. 
Example 2
Construction of a Recombinant Plasmid to Express KI Polypeptides
The initial plasmid, pHIL-D2, was ampicillin resistant and contained a wild type His4 of P. pastoris. The final DNA sequence comprising the coding sequence for the matα Prepro-PEP-1 fusion protein in the recombinant expression plasmid pPIC-K503 is shown in FIG. 2. The DNA sequence of pHIL-D2 was modified to produce pPIC-K503, as follows:
1. The BstBI site in the 3′ AOXI region of pHIL-D2, located downstream of the His4 gene, was removed by partial restriction digestion, fill-in, and ligation, altering the sequence from TTCGAA (SEQ ID NO:23) to TTCGCGAA (SEQ ID NO:24). This modification was made in order to facilitate and direct the cloning of the expression cassette into the plasmid.
2. The AatII site bear the b/a gene located downstream of His4 was removed by restriction digestion, fill-in, and ligation modifying the sequence from GACGTC (SEQ ID NO:25) to GACGTACGTC (SEQ ID NO:26). This modification was made to facilitate the cloning of expression cassettes having AatII sites into the plasmid.
The DNA encoding PEP-1 was synthesized based on the nucleotide sequence from the original, kallikrein binding, display phage and consisted of 450 base pairs (bp). The final DNA sequence of the insert in the pHIL-D2 plasmid would be flanked by a 5′ AOX1 sequence and a 3′ AOX1 sequence (portions of which are shown in FIG. 2) and encode a fusion protein comprising the mat Prepro signal peptide of S. cerevisiae fused to the structural coding sequence for the PEP-1 KI polypeptide. The signal peptide was added to facilitate the secretion of PEP-1 from the yeast host cells. The oligonucleotides to form the insert were synthesized and obtained commercially (Genesis Labs, The Woodlands, Tex.) and linked by polymerase chain reaction (PCR). The linked synthetic DNA encoding the matα Prepro-PEP-1 fusion protein was then incorporated by ligation into the modified pHIL-D2 plasmid between the BstBI and EcoRI sites.
The ligation products were used to transform Escherichia coli strain XL1 Blue. A PCR assay was used to screen E. coli transformants for the desired plasmid construct. DNA from cell extracts was amplified by PCR using primers containing the 5′AOX1 and 3′AOX1 sequences (see above and FIG. 2). PCR products of the correct number of base pairs were sequenced. Approximately 20-50 bp on either side of the cloning sites, in addition to the insert, were sequenced, and the expected sequence was obtained. The final DNA sequence of the insert in the pHIL-D2 plasmid (to yield plasmid pPIC-K503) is shown in FIG. 2 along with portions of flanking 5′ and 3′ AOX1 sequences (SEQ ID NO:27) and corresponding amino acid sequence of the fusion protein comprising the matα Prepro signal peptide of S. cerevisiae fused to the structural coding sequence for the PEP-1 KI polypeptide (SEQ ID NO:28). A transformant with the desired expression plasmid construct, plasmid pPIC-K503, was selected for preparing yeast cell lines for routine production of PEP-1.
Example 3
Manufacture of PEP-1 from Recombinant Yeast Cell Line
Spheroplasts of P. pastoris GS115 having the His4− phenotype were transformed with the expression plasmid pPIC-K503 (above) following linearization of the plasmid at the SacI site and homologous recombination of the plasmid DNA into the host 5′AOX1 locus. The phenotype of the production strain is His4+. The entire plasmid was inserted into the 5′AOX1 genomic sequence of the yeast.
Isolates from the transformation were screened for growth in the absence of exogenous histidine with methanol as the sole carbon source. Greater than 95% of the transformants retained the wild type ability to grow with methanol as the sole carbon source, demonstrating that the plasmid had been inserted into the host genome by homologous recombination rather than transplacement, and did not require exogenous histidine for growth, demonstrating that the plasmid was integrated into the host genome. Selected colonies were cloned. Small culture expression studies were performed to identify clones secreting the highest levels of active PEP-1 into the culture medium. PEP-1 secretion levels in clarified culture supernatant solutions were quantified for PEP-1 levels by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and evaluated for kallikrein inhibition. A yeast clone was selected for PEP-1 production based on its high level of PEP-1 expression among cultures sampled.
Master and working cell banks of PEP-1 producing P. pastoris were prepared commercially, MDS Pharma Services, Bothell, Wash.). A standard production of PEP-1 in yeast comprised three steps: (1) preparation of the seed culture, (2) fermentation, and (3) recovery of the culture.
The seed culture step consisted of the inoculation of six flasks (300 ml) containing sterile inoculum broth (yeast nitrogen base, potassium phosphate, and glycerol, pH 5) with the contents of a single vial of a working cell bank of PEP-1 producing P. pastoris. Flasks were inoculated in an orbital shaker (300 rpm) for approximately 13 hours at 30° C.±2° C.
Fermentations were performed in a closed 100 liter Braun fermenter filled with sterile broth. Each fermentation was initiated with the transfer of the contents of the six seed culture flasks to the fermenter. After approximately 24 hours, the glycerol in the fermenter became exhausted and additional glycerol was added for approximately 8 additional hours.
A mixed feed phase, which lasted approximately 83 hours, was then initiated by the addition of a glycerol and methanol feed. At the end of his time, the fermentation was terminated, and the fermenter contents were diluted with purified water.
The purification and processing of PEP-1 consisted of five steps: (1) expanded bed chromatography, (2) cation exchange chromatography, (3) hydrophobic interaction chromatography (HIC), (4) ultrafiltration and diafiltration, and (5) final filtration and packaging.
The initial purification step consisted of expanded bed chromatography. The diluted fermenter culture was applied to the equilibrated column packed with Streamline SP resin (Amersham Pharmacia Streamline 200 chromatography column, Amersham Pharmacia, Piscataway, N.J.). The diluted fermenter culture was applied to the equilibrated column. The column was then washed (50 mM acetic acid, pH 3.0-3.5) in an up-flow mode to flush the yeast cells from the expanded bed. The top adaptor was raised above the expanded bed enhance washing. The flow was stopped and the bed was allowed to settle. The adaptor was moved down so that it was slightly above the settled bed. The direction of the flow was reversed. The effluent was collected. Washing was continued in a downward mode using 50 mM sodium acetate, pH 4.0. The effluent was collected. PEP-1 was eluted from the column using 50 mM sodium acetate, pH 6.0. The eluate was collected in a 50 liter container. The eluate was then filtered through a 0.22μ filter into a clean container located in the purification site. Additional samples were collected for the determination of PEP-1 concentration.
A cation exchange chromatography step was then performed using the filtered eluate from the expanded bed column. PEP-1 eluted from the column using 15 mM trisodium citrate, pH 6.2.
Additional proteins were removed from the PEP-1 preparation by hydrophobic interaction chromatography (HIC). Prior to HIC, the eluate from the cation exchange column was diluted with ammonium sulfate. The eluate was applied to the column, and the PEP-1 was eluted using ammonium sulfate (0.572 M) in potassium phosphate (100 mM), pH 7.0. The eluate was collected in fractions based on A280 values. All fractions were collected into sterile, pre-weighed PETG bottles.
Selected fractions were pooled into a clean container. The pool was concentrated by ultrafiltration. The concentrated PEP-1 preparation was immediately diafiltered against ten volumes of PBS, pH 7.0.
A final filtration step was performed prior to packaging in order to minimize the bioburden in the bulk PEP-1. The bulk solution was filtered through a 22μ filter and collected into a sterile, pre-weighed PETG bottle. A sample was removed for lot release testing. The remainder of the bulk was dispensed aseptically into sterile PETG bottles and stored at −20° C.
Example 4
Kallikrein Inhibition Assay
The potency assay of KI polypeptides, such as PEP-1, described herein was a kinetic test, which measured fluorescence generation following the kallikrein-mediated cleavage of a substrate, prolylphenylalanylarginyl amino methyl coumarin. A known amount of kallikrein was incubated with buffer, with a serially diluted KI polypeptide reference standard, or serially diluted KI polypeptide test samples. Each sample was run in triplicate. The substrate solution was added, and the plate read immediately using an excitation wavelength of 360 nm and an emission wavelength of 460 nm. At least two each of the reference standard and sample curves were required to have an R-squared value of ≧0.95 to be considered valid.
Example 5
Neuroprotective Effect of Kallikrein Inhibitor Polypeptide at Various Doses on Brain Ischemia/reperfusion Injury
The presence of tissue kallikrein in the brain and the identification of bradykinin B2 receptors on brain cells suggest that kinin system could play a role in the nervous system pathophysiology. Recent data showing the effectiveness of bradykinin B2 receptor antagonists in reducing ischemic brain damage further supports such a hypothesis.
In this example, a kallikrein inhibitor polypeptide (DX-88) is effective in reducing neurological deficits and brain injury after transient focal brain ischemia.
In vitro analysis was performed to determine whether DX-88 was able to cross the blood-brain barrier. Non-ischemic mice were treated iv with saline or DX-88 (10 μg/mouse or 30 μg/mouse) and plasma was drawn 30 or 60 min after administration. Thirty minutes after DX-88 treatment, plasma kallikrein inhibitory activity was 2 and 4 times higher in mice treated with 30 and 10 μg, respectively. Such a difference was not seen in plasma drawn 60 min after the infusion. In cerebral spinal fluid (CSF) from mice treated with 30 μg of DX-88, there was marked inhibitory activity with no difference between CSF drawn 30 or 60 min after DX-88 administration.
Ischemia was induced by occlusion of the middle cerebral artery (MCAO). At the end of the ischemic period (30 min), the filament was removed and reperfusion allowed. Mice received different doses of DX-88 iv at the beginning of the ischemic period. Twenty four hours after ischemia, neurological deficits and infarct size were evaluated. While saline treated mice showed stable scores, those who received 30 mg of DX-88 had significantly reduced general (13 and 10.5, median of saline and DX-88 treated mice, respectively) and focal (26 and 15.5, median of saline and DX-88 treated mice, respectively) deficits scores. In these mice the ischemic volume was also significantly reduced (22.86±5.82 mm3, 23.04±4.34 mm3 respectively) compared to saline treated mice (63.12±7.69 mm3). This study shows that: i) DX-88, in its active form, can cross rapidly the intact blood-brain barrier and thus reach brain tissue; ii) DX-88 has a significant neuroprotective effect against adverse consequences of brain ischemia and reperfusion injury.
Example 6
Neuroprotective Effect of Kallikrein Inhibitor Polypeptide Administered at Different Times During Brain Ischemia and Reperfusion Injury
Ischemia was induced by occlusion of the middle cerebral artery by MCAO using a 6-0 monofilament. At the end of the 30 min ischemic period, the filament was removed and reperfusion allowed. Mice received DX-88 iv at the beginning of the ischemic period or at the end of it, during reperfusion.
It was first analyzed whether DX-88 was able to cross the blood-brain barrier and found that thirty minutes after treatment with 30 μg/mouse iv, a marked inhibitory activity was present in CSF. The same dose of DX-88 was given at the beginning of ischemic period. Twenty four hours after ischemia, neurological deficits and infarct size were evaluated. While saline treated mice showed stable scores, those who received of DX-88 had significantly reduced general (by 37.5%) and focal (by 50.0%) deficits scores. In these mice the ischemic volume was also significantly reduced by 50.9%. When given at reperfusion, DX-88 was similarly effective in improving general (by 38%) and focal (by 50.1%) deficits scores as well as the ischemic volume that was reduced by 58%.
This study shows that: i) this specific kallikrein inhibitor can cross rapidly the intact blood-brain barrier and thus possibly reach brain tissue in its active form; ii) it has a significant neuroprotective effect against adverse consequences of brain ischemia and reperfusion injury.
Other variations and embodiments of the invention described herein will now be apparent to those of ordinary skill in the art without departing from the scope of the invention or the spirit of the claims below.

## Claims

1. A method for reducing reperfusion injury in a patient, the method comprising:
administering to the patient a composition comprising an inhibitor of plasma kallikrein, in an amount effective to reduce neurocognitive defects due to reperfusion injury, wherein the inhibitor of plasma kallikrein comprises a polypeptide that comprises the amino acid sequence of SEQ ID NO: 57.

2. The method of claim 1, wherein the reperfusion injury is reperfusion injury associated with cerebral ischemia.

3. The method of claim 2, wherein the cerebral ischemia is a stroke.

4. The method of claim 3, wherein the stroke is selected from the group consisting of an embolism associated stroke, a thrombus-associated stroke, a thromboembolitic stroke and a hemorrhage-associated stroke.

5. The method of claim 3, wherein the stroke is an embolism-associated stroke.

6. The method of claim 3, wherein the stroke is a thrombus-associated stroke.

7. The method of claim 6, wherein the thrombus-associated stroke is a perioperative stroke.

8. The method of claim 1, wherein the polypeptide comprises the amino acid sequence of SEQ ID NO:2.

9. The method of claim 1, wherein the inhibitor of plasma kallikrein is administered parenterally.

10. The method of claim 9, wherein the inhibitor of plasma kallikrein is administered intravenously.

11. The method of claim 9, wherein the inhibitor of plasma kallikrein is administered intraperitoneally.

12. The method of claim 1, wherein the inhibitor of plasma kallikrein is conjugated to a water soluble polymer.

13. The method of claim 12, wherein the water soluble polymer is a hydrophilic polyvinyl polymer or polymers.

14. The method of claim 13, wherein the hydrophilic polyvinyl polymer is selected from the group consisting of polyvinylalcohol and polyvinylpyrrolidone.

15. The method of claim 13, wherein the hydrophilic polyvinyl polymer is selected from the group consisting of polyalkylene oxide homopolymers, polypropylene glycols, polyoxyethylenated polyols, and copolymers thereof.

16. The method of claim 13, wherein the water soluble polymer is polyethylene glycol (PEG).