Patent Application
20120135931
The present invention relates to methods of modifying serine protease inhibitors in order to acquire or enhance any one of a variety of desired properties. The present invention also relates to the products of such modifications and the uses of such products, in particular, their use in therapy.
Serine proteases, also known as serine endopeptidases, are protein digesting enzymes containing a serine residue at the active site. These enzymes are widespread in nature, and play a part in a wide range of biological functions including digestion, blood clotting, the immune system and inflammation.
Due to the widespread distribution and function of serine proteases, inhibitors for these enzymes are common. Many proteinaceous serine protease inhibitors can be found in nature, and many synthetic, chemical serine protease inhibitors have been developed for use in research and therapy.
Thrombin is a member of the serine protease family which plays a central role in blood coagulation; the process by which circulating zymogens of serine proteases are sequentially activated by limited proteolysis to produce fibrin clots in response to vascular injury. Thrombin interacts with most of the zymogens and their cofactors, playing multiple procoagulant and anticoagulant roles in blood coagulation (Huntington (2005), and Di Cera (2003)). As a procoagulant protease, the first traces of thrombin generated in the initiation phase activate factor V (FV) and factor VIII (FVIII) to provide positive feedback leading to thrombin burst. Thrombin can also activate factor XI, triggering the intrinsic pathway. Thrombin cleaves fibrinogen to fibrin, forming insoluble clots. Fibrin polymers are further strengthened and stabilized through covalent cross-linking driven by thrombin activated factor XIII. Thrombin also contributes to the generation of a platelet plug, possibly through two mechanisms: (a) it activates platelets by interacting with protease-activated receptors (PARs) and glycoprotein V; and (b) it prevents destabilization of the platelet plug, by inactivating ADAMTS13, a disintegrin and metalloprotease with a thrombospondin type 1 motif, that cleaves von Willebrand factor (VWF). As an anticoagulant protease, thrombin activates protein C (APC) in the presence of the cofactor thrombomodulin. APC inactivates factor Va (FVa) and factor VIIIa (FVIIIa), down-regulating the generation of thrombin (Huntington (2005), Di Cera (2003), Davie et al. (1991), Davie (2003), and Lane et al. (2005)).
Due to its central role, thrombin is a prime target for inhibition in order to control the coagulation cascade, and many thrombin inhibitors have been used in therapy and research for many years. Heparin is the archetypal thrombin inhibitor, and functions as an indirect inhibitor of thrombin, meaning that it acts via an anti-thrombin complex and does not interact directly with the active site of thrombin. Indirect thrombin inhibitors can only interact with soluble thrombin and are therefore unable to inhibit thrombin once a clot has formed.
More recently, a number of direct thrombin inhibitors including hirudin, bivalirudin, argatroban and dabigatran etexilate have been isolated and/or developed. These have the therapeutic advantage of being able to inhibit thrombin in both its soluble and fibrin-bound form. However, such direct inhibitors have certain properties which are far from optimal. For example, hirudin causes risk of bleeding, pharmacokinetics that depends on renal function, lack of antidote, immunogenicity and rebound hypercoagulability. Bivalirudin, which is eliminated by a combination of proteolysis and renal routes, has negligible immunogenic potential, but still has sub-optimal therapeutic properties.
In view of the therapeutic importance of serine protease inhibitors, there is a need to identify additional serine protease inhibitors which display improved properties. In particular, there is a need to identify direct thrombin inhibitors with the ability to inhibit thrombin in both its soluble and fibrin-bound form but without the disadvantages associated with currently available direct thrombin inhibitors.
The present invention provides modified serine protease inhibitors, methods of producing modified serine protease inhibitors, and methods of using modified serine protease inhibitors, e.g., for inhibiting a target serine protease in a subject.
Accordingly, in a first aspect, the invention provides a method of producing a modified serine protease inhibitor (SPI) displaying enhanced inhibition of a target serine protease (SP), comprising modifying the SPI such that binding of the SPI to its target SP displaces one or more of the amino acid residues in the catalytic triad of the target SP, or one or more atoms of said amino acid residues.
In one embodiment of this aspect, the method comprises the introduction of one or more amino acid residues into the SPI which are capable of displacing one or more of the amino acid residues of the catalytic triad of the target SP, or one or more atoms of said amino acid residues. In another embodiment, method produces a modified SPI which displays a prolonged duration of inhibition. In one embodiment, said one or more introduced amino acid residues are introduced by substitution or insertion.
In another embodiment of this aspect, said one or more amino acid residues capable of displacing one or more of the residues of the catalytic triad of the target SP, or one or more atoms thereof comprises a histidine residue. In one embodiment, said one or more introduced amino acids comprises a methionine-histidine sequence. In a further embodiment, said one or more introduced amino acids comprises a methionine-histidine-lysine sequence. In another embodiment, said one or more introduced amino acids comprises a methionine-histidine-lysine-threonine sequence. In one embodiment, the one or more residues in the catalytic triad of the target serine protease which is displaced comprises the catalytic serine residue.
In another embodiment of this aspect, the method further contains a step of modifying the SPI so that it is capable of being neutralised, comprising the introduction of an area of ionic charge into the SPI, wherein the area of ionic charge is capable of interacting with an area of opposite ionic charge on a neutralising agent. In one embodiment, said introduced area of ionic charge is introduced towards the carboxy-terminus of the SPI. In another embodiment, said introduced area of ionic charge is an area of anionic charge. In one embodiment, said introduced area of ionic charge comprises one or more acidic residues. In another embodiment, said one or more acidic residues comprises one or more glutamine residues. In a further embodiment, said neutralising agent is protamine sulphate.
In an exemplary embodiment of the foregoing methods, the SPI is a thrombin inhibitor. In another exemplary embodiment, the SPI is selected from the group consisting of any one of SEQ ID NOs: 14 and 17-153.
In another aspect, the invention provides a modified SPI obtainable or obtained by any of the foregoing methods, or a fragment or functional equivalent thereof. In one embodiment, said modified SPI is a thrombin inhibitor. In an exemplary embodiment, the modified SPI contains the following consensus sequence: N-terminal peptide) —X1—H—X2-(G)n- (exosite I binding peptide) (SEQ ID NO: 771).
In another aspect, the invention provides a modified SPI which displays enhanced inhibition of a target SP, wherein the binding of the SPI to its target SP displaces one or more of the amino acid residues in the catalytic triad of the target SP, or one or more atoms of said amino acid residues. In one embodiment of this aspect, the modified SPI comprises one or more amino acid residues which are capable of displacing one or more of the amino acid residues of the catalytic triad of the target SP, or one or more atoms of said amino acid residues. In another embodiment, the modified SPI displays a prolonged duration of inhibition.
In another embodiment of this aspect, the one or more amino acid residues capable of displacing one or more of the residues of the catalytic triad of the target SP, or one or more atoms thereof comprises a histidine residue. In another embodiment, the one or more amino acid residues capable of displacing one or more of the residues of the catalytic triad of the target SP comprises a methionine-histidine sequence. In another embodiment, the one or more amino acid residues capable of displacing one or more of the residues of the catalytic triad of the target SP comprises a methionine-histidine-lysine sequence. In a further embodiment, the one or more amino acid residues capable of displacing one or more of the residues of the catalytic triad of the target SP comprises a methionine-histidine-lysine-threonine sequence. In another embodiment, the one or more amino acid residues in the catalytic triad of the target serine protease which is displaced comprises the catalytic serine residue.
In another embodiment of this aspect, the modified SPI further comprises an area of ionic charge, wherein the area of ionic charge is capable of interacting with an area of opposite ionic charge on a neutralising agent. In one embodiment, the area of ionic charge is positioned towards the carboxy-terminus of the SPI. In another embodiment, the area of ionic charge is an area of anionic charge. In one embodiment, the area of ionic charge comprises one or more acidic residues. In another embodiment, the one or more acidic residues comprise one or more glutamine residues. In an exemplary embodiment, the neutralising agent is protamine sulphate. In another exemplary embodiment, the foregoing modified SPIs are thrombin inhibitors. In one embodiment, the modified SPIs contain the following consensus sequence: N-terminal peptide) —X1—H—X2-(G)n- (exosite I binding peptide) (SEQ ID NO: 771).
In another aspect, the invention provides a modified SPI comprising a sequence selected from any one of SEQ ID NOs: 158-770, or a fragment or functional equivalent thereof. In a further aspect, the invention provides a modified SPI consisting of a sequence selected from any one of SEQ ID NOs: 158-770, or a fragment or functional equivalent thereof.
In another aspect, the invention provides a nucleic acid molecule encoding a modified SPI described herein. In another aspect, the invention provides an anti-sense nucleic acid molecule which hybridises under high stringency hybridisation conditions to nucleic acid molecule encoding a modified SPI described herein.
In one embodiment, the invention comprises a vector containing a nucleic acid sequence encoding a modified SPI described herein, or an anti-sense nucleic acid molecule which hybridizes under high stringency hybridisation conditions to nucleic acid molecule encoding a modified SPI described herein. In another embodiment, the invention provides a host cell containing the foregoing vector, and/or the foregoing nucleic acid molecule.
In another aspect, the invention provides a method of inhibiting a target SP comprising administering a modified SPI described herein. In another aspect, the invention provides a method of treating a subject suffering from a coagulopathy or preventing a subject from developing a coagulopathy comprising administering a modified SPI, e.g., a thrombin inhibitor, described herein. In another embodiment, the invention provides a method of neutralising thrombin inhibition in a subject comprising administering a modified thrombin inhibitor described herein, and subsequently administering to the subject an amount of protamine sulphate sufficient to result in neutralisation of the thrombin inhibition.
Other features and advantages of the invention will be apparent from the following detailed description, and from the claims.
The present invention provides a method of producing a modified serine protease inhibitor (SPI) displaying enhanced inhibition of a target serine protease (SP) comprising modifying the SPI such that binding of the SPI to its target SP displaces one or more of the amino acid residues in the catalytic triad of the target SP, or one or more atoms of said amino acid residues.
As discussed above, serine proteases are peptide cleaving enzymes. It is accepted in the art that these enzymes act via a catalytic triad, present in the active site of the enzyme, and comprising a serine residue, a histidine residue and an aspartate residue. The function of the histidine and aspartate residues is to activate the serine residue through a charge relay system, making it nucleophilic and capable of cleaving the scissile bond of the substrate. The interaction between the residues of the catalytic triad in a typical serine protease is shown in
The inventors have surprisingly established that in addition to sterically blocking the active site in the manner of a conventional competitive inhibitor, variegin, a direct inhibitor of the serine protease thrombin, also acts by disrupting the interaction between the residues of the catalytic triad of thrombin, thereby inhibiting its catalytic activity. Variegin is a protein having the amino acid sequence shown in SEQ ID NO: 1. It is a tick-derived protein first described in WO03/091284. The ability of variegin to bind thrombin is described in WO08/155,658. However, neither document suggests that variegin acts to disrupt interactions between amino acids in the catalytic triad of thrombin. The contents of WO03/091284 and WO08/155,658 are incorporated herein by reference in their entirety.
The realisation by the inventors that the potent anti-thrombin activity of variegin is at least partly due to the disruption of the catalytic triad in the active site of thrombin and the mechanism by which this is achieved can be applied to other serine protease inhibitors including thrombin inhibitors. In particular, the properties of known serine protease inhibitors can be improved by modification so that they disrupt interactions between residues of the catalytic triad of the target serine protease. Such modifications function to improve the properties of the serine protease inhibitor, and overcome many of the disadvantages of existing serine protease inhibitors, in particular known direct thrombin inhibitors.
The term “target serine protease”, or “target SP” relates to the serine protease which is normally inhibited by a given serine protease inhibitor. One example of a target SP is thrombin. Further examples of target SPs according to the invention include the coagulation factors FXa, FVIIa, FXIIa, FXIa, and FIXa.
The serine protease inhibitor or SPI which is modified by the method of the invention may be a direct SPI or an indirect SPI. The term “direct SPI” means that the SPI interacts with its target SP at the active site of the SP without being present as part of an anti-SP complex or acting through an intermediate. The term “indirect SPI” means that the SPI does not interact directly with the active site of the target SP. An indirect SPI may interact with a site on the target SP which is distinct from the active site, or the indirect SPI may interact with the active site or another site on the target SP through an anti-SP complex comprising the indirect SPI.
Examples of SPIs that may be modified by the method of the invention include hirulog (SEQ ID NO: 14), Kunitz/BPTI-type inhibitors (e.g. bovine pancreatic trypsin inhibitor, shown in SEQ ID NO: 776), hirudin-related thrombin inhibitors, serpins, heparin cofactors, α1-antitrypsin-like serpins, kazal type direct inhibitors, and kunitz type/STI (sybean trypsin inhibitor) inhibitors. Further examples of SPIs which may be modified by the method of the invention are given in SEQ ID NOs: 17-153. By “displaced” is meant that the amino acid residue in the target SP or one or more atoms within the amino acid residue occupy a conformation in space which is different from that which it would naturally adopt in the absence of any outside influences. It should be appreciated that such displacement may be in any direction.
In one aspect, the displacement may be such that the interaction between the amino acid residues of the catalytic triad of the target SP is disrupted. Such disruption may be complete, i.e. the residues of the catalytic triad no longer interact, or it may be partial, i.e. the interaction between the residues is only 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, or less as strong as it would have been if one or more of the residues of the catalytic triad was not displaced. The presence of an interaction between the amino acid residues of the catalytic triad may be measured by any method known in the art, e.g crystallography or NMR, computational methods including but not limited to molecular mechanics, molecular dynamics and docking, hydrogen/deuterium exchange and mass spectroscopy.
The displacement of one or more residues of the catalytic triad of the target SP, or one or more atoms of said amino acid residues may disrupt the charge replay system of the catalytic triad of the target SP.
In one aspect of the invention, the displacement of one or more of the residues of the catalytic triad of the target SP may comprise the displacement of the serine residue of the catalytic triad. In one aspect, the γO atom of the serine residue of the catalytic triad may be displaced. In another aspect the βC of the serine residue of the catalytic triad may be displaced. In another aspect the γC of the serine residue of the catalytic triad may be displaced.
In one aspect, the atom of the serine residue of the catalytic triad may be displaced by 0.1 Å. In further aspects, the atom of the serine residue of the catalytic triad may be displaced by 0.2 Å, 0.3 Å, 0.4 Å, 0.5 Å, 0.6 Å, 0.7 Å, 0.8 Å, 0.9 Å, 1.0 Å, 1.1 Å, 1.2 Å, 1.3 Å, 1.4 Å, 1.5 Å, 1.6 Å, 1.7 Å, 1.8 Å, 1.9 Å, 2.0 Å, 2.5 Å, 3.0 Å, or more.
In one aspect of the invention, the displacement of one or more of the residues of the catalytic triad may comprise the displacement of the histidine residue of the catalytic triad. In one aspect, the γC atom of the histidine residue of the catalytic triad may be displaced. In another aspect the δC atom of the histidine residue of the catalytic triad may be displaced. In another aspect the εN2 atom of the histidine residue of the catalytic triad may be displaced. In another aspect the atom of the histidine residue of the catalytic triad may be displaced. In another aspect the δN1 atom of the histidine residue of the catalytic triad may be displaced. In another aspect the βC atom of the histidine residue of the catalytic triad may be displaced. In another aspect the αC atom of the histidine residue of the catalytic triad may be displaced.
In one aspect, the atom of the histidine residue of the catalytic triad may be displaced by 0.1 Å. In further aspects, the atom of the histidine residue of the catalytic triad may be displaced by 0.2 Å, 0.3 Å, 0.4 Å, 0.5 Å, 0.6 Å, 0.7 Å, 0.8 Å, 0.9 Å, 1.0 Å, 1.1 Å, 1.2 Å, 1.3 Å, 1.4 Å, 1.5 Å, 1.6 Å, 1.7 Å, 1.8 Å, 1.9 Å, 2.0 Å, 2.5 Å, 3.0 Å, or more.
In one aspect of the invention, the displacement of one or more of the residues of the catalytic triad may comprise the displacement of the aspartate residue of the catalytic triad. In one aspect the γO atom of the aspartate residue of the catalytic triad may be displaced. In another aspect the βC atom of the aspartate residue of the catalytic triad may be displaced. In another aspect the αC atom of the aspartate residue of the catalytic triad may be displaced. In another aspect the γC atom of the aspartate residue of the catalytic triad may be displaced. In another aspect the δO1 atom of the aspartate residue of the catalytic triad may be displaced. In another aspect the δO2 atom of the serine residue of the catalytic triad may be displaced.
In one aspect, the atom of the aspartate residue of the catalytic triad may be displaced by 0.1 Å. In further aspects, the atom of the aspartate residue of the catalytic triad may be displaced by 0.2 Å, 0.3 Å, 0.4 Å, 0.5 Å, 0.6 Å, 0.7 Å, 0.8 Å, 0.9 Å, 1.0 Å, 1.1 Å, 1.2 Å, 1.3 Å, 1.4 Å, 1.5 Å, 1.6 Å, 1.7 Å, 1.8 Å, 1.9 Å, 2.0 Å, 2.5 Å, 3.0 Å, or more.
The displacement of one or more amino acid residues of the target SP, or one or more atom of said amino acid residues may be measured by any method known in the art, e.g crystallography or NMR, computational methods including but not limited to molecular mechanics, molecular dynamics and docking, hydrogen/deuterium exchange and mass spectroscopy.
In one aspect of the invention, the SPI is a protein and the modification comprises the introduction of one or more amino acid residues into the SPI which are capable of displacing one or more of the amino acid residues in the catalytic triad of the target SP, or one or more atoms of said amino acid residues. These amino acid residues may displace the amino acid residues in the catalytic triad by interacting with them. The introduced amino acid residues may comprise a histidine residue. Such a histidine residue may be present as part of any other sequence which may be introduced into the SPI in addition to the histidine residue. In one embodiment, the introduced amino acids may comprise a methionine-histidine (MH) sequence. In another embodiment the introduced amino acids may comprise a methionine-histidine-lysine (MHK) sequence. In another embodiment the introduced amino acid may comprise a methionine-histidine-arginine (MHR) sequence. In a further embodiment, the introduced amino acids may comprise a methionine-histidine-lysine-threonine (MHKT) sequence. In another embodiment the introduced amino acids may comprise a methionine-histidine-arginine-threonine (MHRT) sequence. In another embodiment the introduced amino acids may comprise a methionine-histidine-lysine-threonine-alanine (MHKTA) sequence. In another embodiment the introduced amino acids may comprise a methionine-histidine-arginine-threonine-alanine (MHRTA) sequence.
Alternative amino acid residues may also be introduced provided they are capable of displacing one or more residues of the catalytic triad of the target SP, or one or more atoms thereof. When considering the MHKT sequence, for example, leucine, isoleucine, valine or alanine may be used in place of methionine and/or lysine, arginine or tyrosine may be used in place of histidine, and/or serine or alanine may be used in place of threonine.
In another aspect the introduced one or more amino acid residues may comprise a linker region. In another aspect the linker region may comprise one or more amino acids e.g. glycine or alanine. In a further aspect the linker region may comprise one, two, three, four, or five glycine residues. In another aspect, the linker region may consist of one, two, three, four, or five glycine residues.
In aspects of the invention where the target SP is thrombin, the method of producing a modified SPI may involve the introduction or maintenance of a peptide sequence which is capable of interacting with exosite I of thrombin. By maintenance of such a peptide sequence is meant that the peptide sequence is already present in the SPI sequence prior to modification, and that this sequence is not disrupted or removed by the modification.
In one aspect, the peptide sequence which is capable of interacting with exosite I of thrombin may comprise one of the following sequences:
The modified SPI produced by any of the methods of the invention displays enhanced inhibition of its target SP compared to the unmodified SPI.
It will be apparent to a person skilled in the art that any one of a variety of assays may be used to determine the extent of SP inhibition, and to confirm that the modification enhances inhibition of a target SP. By way of example, where the SP is thrombin such an assay may be an amidolytic assay, wherein the formation of p-nitroaniline following incubation of thrombin with the modified thrombin inhibitor in the presence of S2238 is detected.
The modified SPIs of the invention may have an IC50 of less than 30 nM, less than 25 nM, less than 20 nM, less than 15 nM, less than 14 nM, less than 13 nM, less than 12 nM, less than 11 nM, less than 10 nM, less than 9 nM, less than 8 nM, less than 7 nM, less than 6 nM, less than 5 nM, less than 4 nM, less than 3 nM, less than 2 nM or less than 1 nM. SPIs produced according to the method of the invention may have a Ki of less than less than 15 nM, less than 10 nM, less than 5 nM, less than 1 nM, less than 750 pM, less than 500 pM, less than 400 pM, less than 300 pM, less than 250 pM, less than 200 pM, less than 150 pM, less than 100 pM, less than 50 pM, less than 30 pM, less than 25 pM, less than 20 pM, less than 15 pM, less than 10 pM, less than 5 pM, less than 1 pM, or less than 100 pM.
It has been established that conventional direct SPIs act by binding to at least the active site of the target SP, where they may be cleaved by the target SP, therefore competing with the substrate of the target SP for binding, and competitively inhibiting the target SP. An example of a SPI which acts in this manner is hirulog-1. Although such competitive inhibition can be an effective inhibitory mechanism, it has certain drawbacks, in particular in relation to the transient nature of the inhibition, and the rapid depletion of the SPI.
As described in J. Biol. Chem., 2007, 282(40) 29101-29113 (Cho Yeow Koh, Maria Kazimirova, Adama Trimnell, Peter Takac, Milan Labuda, Patricia A. Nuttall, and R. Manjunatha Kini), variegin functions as a competitive inhibitor in the same manner as other direct SPIs. However, upon cleavage of variegin by thrombin a fragment of variegin known as MH22, shown as SEQ ID NO: 3, remains bound to thrombin, and functions as a non-competitive inhibitor of thrombin. This increases the inhibitory potential of variegin, and overcomes some of the disadvantages of other direct SPIs. Upon analysing the crystal structure of variegin bound to thrombin, the inventors have surprisingly discovered that MH22 binds to the active site of thrombin. This is unusual since non-competitive inhibitors generally bind at a site distinct from the enzyme active site. Furthermore, the crystal structure revealed that the histidine residue of variegin which is responsible for displacing one or more of the residues of the catalytic triad of thrombin is part of the MH22 sequence, and that this variegin fragment therefore disrupts the catalytic triad of thrombin, following cleavage of variegin, resulting in an increased duration of inhibition.
The method of the invention may thus result in a modified SPI that remains bound to the target SP following cleavage of the modified SPI by the target SP. Such modified SPIs display an increased duration of inhibition.
By the term “prolonged duration of action” is meant that the duration of inhibition of the target SP is increased relative to the duration of inhibition using a non-modified SPI. In one aspect the duration of action may be increased at least two-fold. In another aspect the duration of action may be increased at least three-fold, at least four-fold, at least five-fold, at least six-fold, at least seven-fold, at least eight-fold, at least nine-fold, or more relative to the duration of inhibition using a non-modified SPI. The duration of inhibition by the modified SPI may be greater than 5 minutes, great than 10 minutes, greater than 15 minutes, greater than 20 minutes, greater than 25 minutes, greater than 30 minutes, greater than 1 hour, greater than 2 hours, greater than 3 hours, greater than 4 hours, greater than 5 hours, greater than 6 hours, greater than 12 hours, greater than 1 day, greater than 2 days, greater than 3 days or more. Methods for determination of the extent of inhibition of the target SP have been described above. In certain aspects of the invention, the one or more introduced amino acid residues described above may be positioned towards the amino-terminus of the portion of the modified SPI retained in the active site following cleavage by the target SP.
By “towards the amino-terminus” is intended to mean that the one or more introduced residues are within five amino acids of the amino-terminus of the retained portion of the SPI following cleavage by the target SP. In certain aspects, the one or more introduced residues may be within one residue, within two residues, within three residues, within four residues or within five residues of the amino-terminus of the portion of the modified direct SPI retained in the active site following cleavage by the target SP.
It will be apparent to the skilled person that in order for the one or more introduced residues to be “towards the amino-terminus” of the portion of the modified direct SPI retained in the active site following cleavage by the target SP, the one or more introduced residues must be within five residues of the cleavage site of the modified direct SPI.
In one aspect, the method of the invention may comprise the additional or alternative step of modifying an SPI to make it capable of being neutralised, comprising introducing an area of ionic charge into the SPI, wherein the area of ionic charge is capable of interacting with an area of opposite ionic charge on a neutralising agent such that the resulting ionic interaction between the modified SPI and the neutralising agent neutralises the inhibitory activity of the modified SPI, such that the modified SPI no longer displaces one or more of the amino acid residues in the catalytic triad of the target SP, or one or more atoms of said amino acid residues.
Based on the sequence of variegin and data obtained from the crystal structure of variegin bound to thrombin, the inventors have surprisingly discovered that the inhibitory activity of variegin can be neutralised. This neutralisation mechanism is based on the finding of an ionic interaction between an area of ionic charge on the carboxy-terminus of variegin, and an area of opposite ionic charge on a neutralisation agent. The ionic interaction between variegin and the neutralising agent appears to neutralise the inhibitory activity of variegin by disrupting an ionic interaction between an area of ionic charge on variegin and an area of opposite ionic charge on thrombin. From analysis of the structure of variegin bound to thrombin, it is thought that the area of ionic charge on thrombin is within exosite-I.
This information allows other SPIs to be modified so they are capable of being neutralised. Given the therapeutic uses of SPIs, which are discussed above, modified SPIs that are capable of being neutralised will have considerable therapeutic benefits. By “capable of being neutralised” is meant that the activity of the SPI is able to be wholly or partially undone by the addition of a neutralising agent, i.e. the activity of the SP is able to be restored upon addition of a neutralising agent. Within this definition, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, or 100% of the SP activity may be restored. Taken another way, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, 5%, 1% of the inhibitory activity of the SPI may remain following disruption of the ionic interaction between the modified SPI and the target SP.
It will be apparent to a person skilled in the art that the action of most inhibitors which act by binding to their target, including but not limited to competitive inhibitors, will be neutralisable to some extent due to the inherent equilibrium which is set up between bound and unbound inhibitor. This equilibrium position is altered upon the addition of a certain substance; described herein as a “neutralising agent”, which acts to bias the equilibrium in favour of unbound inhibitor, and therefore undo the inhibitory effects of the inhibitor. However, in the case of a “non-neutralisable” inhibitor, this equilibrium is heavily biased towards bound inhibitor, and the addition of the neutralising agent does not upset the equilibrium balance.
In the context of the invention, the term “neutralisation” is intended to relate only to neutralisation brought about by the addition of a neutralising agent, which disrupts the equilibrium balance, and not to inherent neutralisation which is a by-product of such an inherent equilibrium.
The neutralising agent may function to neutralise the inhibitory activity of the modified SPI by possessing an area of ionic charge opposite to the area of ionic charge introduced onto the modified SPI. The formation of an ionic interaction between the modified SPI and the neutralising agent may result in the disruption of an ionic interaction between the area of ionic charge on the modified SPI and an area of opposite ionic charge on the target SP. The area of ionic charge on the target SP may be within one of the exosites. In another aspect, the area of ionic charge may be within exosite-L In one aspect of the invention, the area of ionic charge on the neutralising agent may be an area of cationic charge. In this aspect of the invention, the area of ionic charge introduced into the SPI by the method of the invention may therefore be an area of anionic charge. In another aspect of the invention, the area of ionic charge on the target SP may be an area of cationic charge.
The area of ionic charge introduced into the SPI may be introduced towards the carboxy-terminus of the SPI. By “towards the carboxy-terminus” is intended to mean that the introduced area of ionic charge is located within ten amino acids of the carboxy-terminus of the modified SPI. The introduced area of ionic charge may be within one residue, within two residues, within three residues, within four residues, within five residues, within six residues, within seven residues, within eight residues, within nine residues or within ten residues of the carboxy-terminus of the modified SPI. The neutralising agent may be a cationic substance. Such a cationic substance may compete with the SP for binding to the area of anionic charge on the target SPI, resulting in a displacement of the modified SPI, and a loss of inhibition of the target SP. The neutralising agent may be a cationic peptide, such as protamine sulphate.
The area of ionic charge which is introduced into the SPI may comprise one or more acidic residues. The one or more acidic residues may comprise one, two, three, four, five or more acidic residues. The term “acidic residue” may comprise aspartate and glutamate. The one or more acidic residues may comprise a glutamine residue and/or an aspartate residue.
A specific example of an area of ionic charge that may be introduced comprises two glutamate amino acid residues and two aspartate amino acid residues. In a further specific example an area of ionic charge that may be introduced comprises the sequence glu-glu-X-X-asp-asp, where X is any amino acid residue. In a still further example, a region of ionic charge that may be introduced comprises the sequence glu-glu-tyr-lys-asp-asp.
Certain general aspects of the invention will now be described. The features and methods included in this section are applicable to any of the methods of the invention described above.
As described in the preceding sections, the methods of the invention may comprise the introduction of one or more residues into the SPI. In one aspect, such introduced residues may be introduced by insertion. In another aspect, residues may be introduced by substitution.
Methods of substitution or insertion will be apparent to a person skilled in the art. By way of example, but not limitation, these may include site-directed mutagenesis, PCR mutagenesis, transposon mutagenesis, directed mutagenesis, insertional mutagenesis, targeted mutagenesis, and chemical protein synthesis (Sambrook et al. (2000)).
In certain aspects of the invention the method of modifying the SPI may comprise one or more additional steps. In certain embodiments, one or more of the additional steps may be initial additional steps, meaning that these steps take place before other steps of the method of modification.
In one aspect, the method of the invention may comprise the additional step of analysing the structure of the SPI to determine the modification to be made to the SPI. The analysis may involve analysis of the amino acid sequence of the SPI and/or computational modelling of the structure of the SPI. Additionally or alternatively, the method may involve analysis of the structure of the SP or of the SPI bound to the SP. Such a structure may be in the form of a crystal structure, an infra-red spectrum, circular dichroism data, an ultra-violet spectrum, NMR spectroscopy, computational methods including but not limited to molecular mechanics, molecular dynamics and docking or hydrogen/deuterium exchange and mass spectroscopy.
The analysis may involve determination of the region of the SPI which is responsible for the interaction between the SP and the SPI which will be altered according to the method of modification of the SPI. For example, the method of modifying a SPI to enhance inhibition of a target SP described above may comprise the initial step of identifying residues in the SPI that interact with the catalytic triad of the target SP. The amino acid residues that interact with the catalytic triad may then be modified to displace one or more residues of the catalytic triad, or one or more atoms thereof, e.g. by the introduction of an MHKT sequence at this location.
The invention may comprise the additional step of analysing the structure of the target SP to determine the modification to be made to the SPI. The analysis may involve determination of the region and/or the residues of the target SP which is responsible for the interaction between the target SP and the SPI which will be altered according to the method of modification of the SPI. The analysis may involve structural analysis of the SP in the form of a crystal structure, an infra-red spectrum, circular dichroism data, an ultra-violet spectrum, an NMR spectrum or data from a computational method.
The analysis described above may involve comparing the structure of the SPI with the structure of another SPI, whose structure and/or function has previously been analysed. Such analysis may be performed on any data produced in relation to the SPI to be modified and another SP. In particular, such data may be derived from a crystal structure, an infra-red spectrum, circular dichroism data, or an ultra-violet spectrum, and NMR spectrum or data from a computational method.
In a further aspect of the invention, the SPI whose structure and/or function has previously been analysed may be a thrombin inhibitor. In yet a further aspect of the invention, the SPI whose structure and/or function has previously been analysed may be variegin.
In one aspect of the invention, the SPI which is to be modified by the method of the invention may be a thrombin inhibitor. According to another aspect of the invention, the SPI which is to be modified by the method of the invention may be selected from the group consisting of hirulog (SEQ ID NO: 14), Kunitz/BPTI-type inhibitors (e.g. bovine pancreatic trypsin inhibitor, shown in SEQ ID NO: 776), hirudin-related thrombin inhibitors, serpins, heparin cofactors, α1-antitrypsin-like serpins, kazal type direct inhibitors, and kunitz type/STI (soybean trypsin inhibitor) inhibitors. In another aspect, the SPI which is to be modified by the method of the invention may be any one of SEQ ID NOs: 17-153. Modified SPIs
The invention also includes modified SPIs obtainable or obtained by the methods of the invention.
In another aspect, the invention relates to modified SPIs which are obtained by any means. For example, the modified SPIs obtainable by the methods of the invention may also be produced by any methodology known in the art. Exemplary techniques useful for producing the modified SPIs described herein include chemical peptide synthesis, solid-phase or solution-phase peptide synthesis, in vitro translation from a nucleic acid molecule encoding a modified SPI, or cell-based production methods employing prokaryotic or eukaryotic recombinant expression systems. In an exemplary embodiment, a modified SPI is a polypeptide comprising a sequence set forth in any of SEQ ID NOs: 158-770. Such modified SPI compositions may be used in the methods of the invention, including methods of inhibiting a SP, as described below. In one aspect of the invention, the modified SPI obtainable or obtained by the methods of the invention may be a modified thrombin inhibitor.
In one aspect of the invention, the modified SPI obtainable or obtained by the methods of the invention may be a modified version of hirulog (SEQ ID NO: 14), Kunitz/BPTI-type inhibitors (e.g. bovine pancreatic trypsin inhibitor, shown in SEQ ID NO: 776), hirudin-related thrombin inhibitors, serpins, heparin cofactors, α1-antitrypsin-like serpins, kazal type direct inhibitors, and kunitz type/STI (sybean trypsin inhibitor) inhibitors. In another aspect, the SPI which is modified by the method of the invention may be any one of SEQ ID NOs: 17-153.
Modified versions of hirulog obtainable or obtained by methods of the invention may have the following consensus sequence:
(N-terminal peptide) —X1—H—X2-(G)n- (exosite I binding peptide) (SEQ ID NO: 771)
In one aspect, the N-terminal peptide may comprise the sequence phenylalanine, phenylalanine-proline, phenylalanine-proline-arginine, or phenylalanine-proline, lysine.
In another aspect, the amino-terminal phenylalanine residue may be a modified phenylalanine residue. In one example this modified residue may be a D-phenylalanine residue.
In one aspect, X1 may be any amino acid. In another aspect, X1 may be a methionine residue.
In one aspect, X2 may be any amino acids. In another aspect, X2 may be lysine or arginine residue.
In one aspect n may be one or more glycine amino acid residues. In another aspect n may be two, three, four, five or more glycine amino acid residues.
In one aspect the modified SPI may include one or more sulphated amino acid residues. In another aspect, the SPI may include one or more sulphated tyrosine residues.
In one aspect, the exosite I binding peptide may comprise one of the following sequences:
The exosite I binding peptide may further comprise an area of ionic charge comprising one or more acidic residues. The one or more acidic residues may comprise one, two, three, four, five or more acidic residues. The term “acidic residue” may comprise aspartate and glutamate. The one or more acidic residues may comprise a glutamine residue and/or an aspartate residue. The area of ionic charge may comprise two glutatmate amino acids residues and two aspartate amino acid residues. The area of ionic charge that may comprise the sequence glu-glu-X-X-asp-asp, where X is any amino acid residue. In a still further example, a region of ionic charge may comprise the sequence glu-glu-tyr-lys-asp-asp.
In one aspect, the modified SPI may comprise a sequence selected from SEQ ID NOs: 158 to 770. In another aspect the modified SPI consists of one or more of SEQ ID NOs: 158 to 770.
Modified SPIs of the invention may be produced by chemical peptide synthesis, by recombinant peptide synthesis or using a host cell system.
The invention also includes functional equivalents of modified SPIs according to the invention, which retain the enhanced ability to inhibit SPs, as described previously. In one aspect, the term “functional equivalent” is intended to encompass peptide molecules having at least 50% sequence identity to a modified SPI produced according to the method of the invention. In another aspect, a functional equivalent may have 60%, 70%, 85%, 90%, 95%, 98%, 99% or more sequence identity to a modified SPI produced according to the method of the invention. Such functional equivalents preferably retain the enhanced ability to inhibit the target SP, as described previously.
The term “functional equivalents” also encompasses any polypeptide which comprises one or more conservative substitutions when compared to a modified SPI of the invention. In one aspect, the polypeptide comprises one or more conserved substitution. In another aspect, the polypeptide comprises two or more, three or more, four or more, or five or more conservative substitutions when compared to a modified SPI of the invention. A conserved substitution is an amino acid substitution wherein the characteristics of the substituted amino acid do not differ substantially from the amino acid which is normally found at that position. Conservative substitutions include the substitution of an acid amino acid for another acidic amino acid, a basic amino acid for another basic amino acid, an uncharged amino acid for another uncharged amino acid, a non-polar amino acid for another non-polar amino acid, a small amino acid for another small amino acid, or a bulky amino acid for another bulky amino acid. The acidic amino acids are aspartate and glutamate. The basic amino acids are arginine, histidine and lysine. The uncharged amino acids are asparagine, glutamine, serine, threonine, and tyrosine. The non-polar side chains are alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan, glycine, and cysteine. Within the category of non-polar amino acids, alanine, valine, leucine, isoleucine, and glycine are considered to be small amino acids, and praline, phenylalanine, methionine, and tryptophan are considered to be bulky amino acids.
In a further aspect, the invention includes a fragment of a SPI produced according to the method of the invention. In another aspect, the fragment may comprise 2 or more amino acids. In another aspect, the fragment may comprise 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, or 50 amino acids. In another aspect, the fragment may consist of 2 or more amino acids. In another aspect, the fragment may consist of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 1, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, or 50 amino acids. Such fragments retain the enhanced ability to inhibit the target SP, as described previously.
In another aspect, a functional equivalent may be a fusion protein, obtained, for example, by cloning a polynucleotide encoding a modified SPI of the invention or variant or fragment thereof in frame to the coding sequences for a heterologous protein sequence. The term “heterologous”, when used herein, is intended to designate any polypeptide other than the modified SPI or its functional equivalent. Examples of heterologous sequences, comprising the fusion proteins, either at N- or at C-terminus, are the following: extracellular domains of membrane-bound protein, immunoglobulin constant regions (Fc region), multimerization domains, domains of extracellular proteins, signal sequences, export sequences, or sequences allowing purification by affinity chromatography. Many of these heterologous sequences are commercially available in expression plasmids since these sequences are commonly included in the fusion proteins in order to provide additional properties without significantly impairing the specific biological activity of the protein fused to them (Terpe (2003)). Examples of such additional properties are a longer lasting half-life in body fluids, the extracellular localization, or an easier purification procedure as allowed by a tag such as a histidine or HA tag.
The heterologous protein may also be a marker domain. In one aspect, the marker domain may be a fluorescent tag, an epitope tag that allows purification by affinity binding, an enzyme tag that allows histochemical or fluorescent labelling, or a radiochemical tag. In another embodiment, the marker domain may be a radiochemical tag. Such fusion proteins will be useful as diagnostic tools.
Methods for the generation of fusion proteins are standard in the art and will be known to the skilled reader. For example, most general molecular biology, microbiology, recombinant DNA technology and immunological techniques can be found in Sambrook et al. (2000). Generally, fusion proteins may be most conveniently generated recombinantly from nucleic acid molecules in which two nucleic acid sequences are fused together in frame. These fusion proteins will be encoded by nucleic acid molecules that contain the relevant coding sequence of the fusion protein in question.
In one aspect, a functional equivalent of a modified SP according to the invention which may include any molecule which comprises a portion suitable for displacing one of the residues of the catalytic triad of the target SP. In one aspect, this molecule may be a protein molecule, and the portion suitable for displacing one of the residues of the catalytic triad may be an amino acid residue. It will be apparent to a person skilled in the art that this definition cannot encompass any residue individually, since the residue will require additional residues to be present in order to position the residue suitable for displacing one of the residues of the catalytic triad of the target SP in an orientation and location in which it is suitable for displacing one of the residues of the catalytic triad. In one aspect, the functional equivalent may include a histidine residue within a protein molecule, which is positioned and orientated in a manner suitable for displacing one of the residues of the catalytic triad of the target SP. The invention also includes synthetic analogs of the modified SPIs described above.
The fragment or functional equivalent of the modified SPI produced according to the method of the invention is capable of functioning as a SPI. By “capable of function as a SPI” is meant that the fragment or functional equivalent can inhibit the SP activity of a SP. In a further aspect, the fragment or functional equivalent may be capable of inhibiting the SP activity of the target SP.
It will be apparent to a person skilled in the art that a variety of assays may be used to assess whether the fragment or functional equivalent is capable of functioning as a SPI. By way of example, but not limitation, such an assay may be a SP amidolytic assay, as described above, wherein the formation of p-nitroaniline following incubation of the target SP with the modified SPI in the presence of S2238 is detected. The modified SPIs of the invention may have an IC50 of less than 30 nM, less than 25 nM, less than 20 nM, less than 15 nM, less than 14 nM, less than 13 nM, less than 12 nM, less than 11 nM, less than 10 nM, less than 9 nM, less than 8 nM, less than 7 nM, less than 6 nM, less than 5 nM, less than 4 nM, less than 3 nM, less than 2 nM or less than 1 nM when assessed in such a SP amidolytic assay. SPIs produced according to the method of the invention may have a Ki of less than less than 15 nM, less than 10 nM, less than 5 nM, less than 1 nM, less than 750 pM, less than 500 pM, less than 400 pM, less than 300 pM, less than 250 pM, less than 200 pM, less than 150 pM, less than 100 pM, less than 50 pM, less than 30 pM, less than 25 pM, less than 20 pM, less than 15 pM, less than 10 pM, less than 5 pM, less than 1 pM, or less than 100 pM when assessed in such a SP amidolytic assay.
In one aspect, the invention includes a nucleic acid molecule encoding a modified SPI produced according to the method of the invention. In another aspect, the invention includes a nucleic acid molecule having at least 50% sequence identity to a nucleic acid molecule encoding a modified SPI produced according to the method of the invention. In another aspect, the invention includes nucleic acid molecules having at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99% or more sequence identity to a nucleic acid molecule encoding a modified SPI produced according to the method of the invention. The invention also includes a fragment of a nucleic acid molecule encoding a modified SPI produced according to the method of the invention. In one aspect, the fragment may comprise 10 or more nucleotides. In another aspect, the fragment may comprise 12 or more, 14 or more, 16 or more, 18 or more, 10 or more, 25 or more, 30 or more, 40 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, or 100 or more nucleotides. Nucleic acid molecules according to the invention may be in any form, including double-stranded and single-stranded RNA, DNA, and cDNA.
In a further aspect, the invention includes an antisense nucleic acid molecule which hybridises under high stringency hybridisation conditions to a nucleic acid molecule according to the invention. High stringency hybridisation conditions are defined herein as overnight incubation at 42° C. in a solution comprising 50% formamide, 5×SSC (150 mM N NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5×Denhardts solution, 10% dextran sulphate, and 20 microgram/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1×SSC at approximately 65° C.
The invention also includes cloning and expression vectors comprising the nucleic acid molecules of the invention. Such expression vectors may comprise the appropriate transcriptional and translational control sequences, including but not limited to enhancer elements, promoter-operator regions, termination stop sequences, mRNA stability sequences, start and stop codons or ribosomal binding sites, linked in frame with the nucleic acid molecule(s) of the invention. Additionally, it may be convenient to cause the modified SPIs of the invention to be secreted from certain hosts. Accordingly, further components of such vectors may include nucleic acid sequences encoding secretion, signalling and processing sequences.
Vectors according to the invention include plasmids and viruses (including both bacteriophage and eukaryotic viruses), as well as other linear or circular DNA carriers, such as those employing transposable elements or homologous recombination technology. Many such vectors and expression systems will be apparent to a person skilled in the art. Particularly suitable viral vectors include baculovirus-, adenovirus- and vaccinia virus-based vectors.
Suitable hosts for recombinant expression include commonly used prokaryotic species, such as E. coli, or eukaryotic yeasts that can be made to express high levels of recombinant proteins and that can easily be grown in large quantities. Mammalian cell lines grown in vitro are also suitable, particularly when using virus-driven expression systems. Another suitable expression system is the baculovirus expression system that involves the use of insect cells as hosts. An expression system may also constitute host cells that have the DNA incorporated into their genome. Proteins, or protein fragments may also be expressed in vivo, for example in insect larvae or in mammalian tissues. A variety of techniques may be used to introduce vectors into prokaryotic or eukaryotic cells. Suitable transformation or transfection techniques are well described in the literature (Sambrook et al. (2000)). In eukaryotic cells, expression systems may either be transient (e.g. episomal) or permanent (chromosomal integration) according to the needs of the system.
The invention further includes the use of modified SPIs obtainable or obtained according to methods of the invention in therapy.
The uses and methods may also be performed using a modified SPI that is obtained by any means.
The invention includes a method of inhibiting a SP comprising administering to a subject a molecule of the invention.
By “molecule of the invention” is meant a modified SPI obtainable or obtained by a method of the invention, a nucleic acid encoding a modified SPI obtainable or obtained by a method of the invention, a vector comprising a nucleic acid encoding a modified SPI obtainable or obtained by a method of the invention, and a host cell containing a vector comprising a nucleic acid encoding a modified SPI obtainable or obtained by a method of the invention. A “molecule of the invention” also encompasses a modified SPI that is obtainable by the methods of the invention, but which is produced by any means. Accordingly, modified SPI molecules of the invention may be produced using any methodology known in the art, e.g., chemical peptide synthesis, solid-phase or solution-phase peptide synthesis, in vitro translation from a nucleic acid molecule encoding a modified SPI, or cell-based production methods employing prokaryotic or eukaryotic recombinant expression systems. In an exemplary embodiment, a “molecule of the invention” includes a polypeptide comprising a sequence set forth in any of SEQ ID NOs: 158-770. Such modified SPI molecules may be used in the methods of the invention, including any methods of treatment set forth herein.
The subject is generally an animal. The term “animal” encompasses any organism classified as a member of the animal kingdom. In general the animal is a mammal such as humans, cows, sheep, pigs, camels, horses, dogs, cats, monkeys, mice, rats, hamsters, and rabbits.
The method may involve administering the molecule of the invention in a therapeutically effective amount. The term “therapeutically effective amount” refers to the amount of compound needed to treat or ameliorate a targeted disease or condition. The term “prophylactically effective amount” used herein refers to the amount of compound needed to prevent a targeted disease or condition. The exact dosage will generally be dependent on the subject's status as the time of administration. Factors that may be taken into consideration when determining dosage include the severity of the disease state in the subject, the general health of the subject, the age, weight, gender, diet, time and frequency of administration, drug combinations, reaction sensitivities and the subject's tolerance or response to therapy. The precise amount can be determined by routine experimentation, but may ultimately lie with the judgement of the clinician or veterinarian. Generally, an effective dose will be from 0.01 mg/kg (mass of drug compared to mass of subject) to 50 mg/kg, preferably 0.05 mg/kg to 10 mg/kg. The molecule of the invention may be supplied in the form of a pharmaceutical composition in conjunction with a pharmaceutically acceptable carrier.
The term “pharmaceutically acceptable carrier”, as used herein, includes genes, polypeptides, antibodies, liposomes, polysaccharides, polylactic acids, polyglycolic acids and inactive virus particles or indeed any other agent provided that the excipient does not itself induce toxicity effects or cause the production of antibodies that are harmful to the individual receiving the pharmaceutical composition. Pharmaceutically acceptable carriers may additionally contain liquids such as water, saline, glycerol, ethanol or auxiliary substances such as wetting or emulsifying agents, pH buffering substances and the like. Excipients may enable the pharmaceutical compositions to be formulated into tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions to aid intake by the subject. A thorough discussion of pharmaceutically acceptable carriers is available in Remington's Pharmaceutical Sciences (Mack Pub. Co., N.J. 1991).
In one embodiment, the invention provides methods of treatment involving modified thrombin inhibitors obtainable or obtained by the methods of the invention.
The invention includes a method of treating a subject suffering from a coagulopathy or preventing a subject developing a coagulopathy comprising administering a modified thrombin inhibitor obtainable or obtained by a method of the invention.
The invention also includes a modified thrombin inhibitor obtainable or obtained by a method of the invention for use in the treatment of a subject suffering from a coagulopathy or the prevention of a subject developing a coagulopathy.
By “coagulopathy” is meant any disorder of blood coagulation.
Treatment when anticoagulation is desirable includes procedures involving percutaneous, transvascular or transorgan catheterisation for diagnostic or therapeutic reasons. Such procedures may include but are not confined to: coronary angioplasty; endovascular stent procedures; direct administration of thrombolytic agents via an arterial or venous catheter such as following stroke or coronary thrombosis; electrical cardioversion; placement of cardiac pacemaker leads; intravascular and intracardiac monitoring of pressure, gaseous saturation or other diagnostic parameters; radiological and other procedures involving percutaneous or transorgan catheterisation; to ensure the patency of long-term, indwelling, intravascular parentral nutritional catheters; to ensure the patency of vascular access ports whether long or short term.
Additional in vivo applications of the methods of the invention include emergency anticoagulation after a thromboembolic event including but not limited to: acute myocardial infarction; thrombotic stroke; deep venous thrombosis; thrombophlebitis; pulmonary embolism; embolic and micro-embolic episodes where the source may be the heart, atherosclerotic plaque, valvular or vascular prostheses or an unknown source; disseminated intravascular coagulation (DIC).
The methods of the invention may also be used to prevent coagulation during organ perfusion procedures such as during cardiopulmonary bypass, hepatic bypass and as an adjunct to organ transplantation. The massive thrombotic reaction precipitated by cardiac pulmonary bypass cannot fully be antagonised by indirect thrombin inhibitors such as heparin and its analogues (Edmunds & Colman (2006)).
Further instances when anticoagulation is desirable include during haemodialysis, haemofiltration or plasma exchange procedures. Anticoagulation may also be desirable during surgical procedures involving cross clamping of blood vessels in order to minimise the risk of coagulation in the distal circulation. Such procedures may include but are not confined to endarterectomy, insertion of vascular prostheses, repair of aortic and other arterial aneurysms.
Additionally, the methods and the modified thrombin inhibitors obtainable or obtained of the invention may be useful to induce anticoagulation in heparin-resistant subjects.
The methods and modified thrombin inhibitors obtainable or obtained by the methods of the invention may also be useful in the treatment or prevention of heparin-induced thrombocytopaenia. Such treatment may be administered to a subject with or at risk from HIT and with or without active thrombosis and may be administered until platelet counts have recovered to within the range of normal or until the risk of thrombosis has passed (Girolami & Girolami (2006), Lewis & Hursting (2007)). The molecules of the invention may be administered by any suitable route. Preferred routes of administration include intravenous, intramuscular or subcutaneous injection, oral administration, subligual administration and transdermal administration. The treatment may be continuously administered by intravenous infusion or as a single or repeated bolus injection. The molecules of the invention may be administered individually to a subject or may be administered in combination with other agents, drugs or hormones. For example, the molecules of the invention may be administered with oral anticoagulants such as coumarin derivatives until such time as the subject has become stabilised, following which the subject may be treated with the coumarin derivatives alone.
The invention further provides that the modified SPIs produced by the method of the invention may be used in diagnosis. Since these methods involve inhibiting SP activity specifically by interaction with the target SP, they can be used to detect the presence of the target SP and hence to diagnose conditions caused by SP accumulation, such as a fibrin or platelet thrombus, caused by an accumulation of thrombin. The invention therefore provides methods of diagnosing a condition caused by SP accumulation by administering a modified SPI of the invention as described above to a subject or to tissue isolated from a subject, and detecting the presence of said SPI or fragment or functional equivalent thereof, wherein the detection of said modified SPI or fragment or functional equivalent bound to the target SP is indicative of said disease or condition. The modified SPI or functional equivalent may be in the form of a fusion protein comprising a marker domain, as described in more detail above, to facilitate detection. In one aspect, the marker domain may be a radiochemical tag so that detection can be carried out using known imaging methods.
According to a further aspect of the invention, the in vivo method of the invention may be used to treat a malignant disease or a condition associated with malignant disease.
It has been recognised for decades that malignant disease is often associated with an increased tendency to thromboembolic episodes, caused by an increase in levels of the SP thrombin. Trousseau's syndrome, for example, is characterised by fleeting thrombophlebitis and underlying malignancy and thrombin inhibitors such as heparin have been used in its management (Varki (2007)). More recently it has become apparent that the generation of procoagulant factors including thrombin may be a cause rather than a result of certain aspects of malignant disease (Nierodzik & Karpatkin (2006)). There are many instances wherein it may be desirable to inhibit a SP and then neutralise such inhibition. By way of example, but not limitation, such inhibition and neuralisation may be advantageous during surgery, wherein target SP inhibition is required to prevent thrombin-induced coagulation whilst the surgery is taking place, and reversal of the inhibition is advantageous upon completion of the surgery in order to allow wound healing.
Where the SPI is a thrombin inhibitor, thrombin activity may be neutralised by the administration of a cationic peptide, e.g. protamine sulphate. Any of the methods of treatment relating to thrombin inhibition described herein may therefore describe the additional step of administering to the subject an amount of a cationic peptide to result in neutralisation of the thrombin inhibition. In one aspect, the amount of cationic peptide which is administered may be between 0.01 mg/ml and 1 mg/ml. In another aspect, the amount of cationic peptide which is administered may be 0.01 mg/ml or more, 0.02 mg/ml or more, 0.03 mg·ml or more, 0.04 mg/ml or more, 0.05 mg/ml or more, 0.06 mg/ml or more, 0.07 mg/ml or more, 0.08 mg/ml or more, 0.09 mg/ml or more, 0.1 mg/ml or more, 0.11 mg/ml or more, 0.12 mg/ml or more, 0.13 mg·ml or more, 0.14 mg/ml or more, 0.15 mg·ml or more, 0.16 mg/ml or more, 0.18 mg/ml or more, 0.19 mg/ml or more, 0.2 mg/ml or more, 0.3 mg·ml or more, 0.4 mg·ml or more, 0.5 mg·ml or more, or 1 mg/ml.
Various aspects and embodiments of the present invention will now be described in more detail by way of example. It will be appreciated that modification of detail may be made without departing from the scope of the invention.
(A) Thrombin-s-variegin complex structure. Thrombin A-chain backbone is coloured as light blue ribbon, B-chain backbone is coloured as white ribbon and s-variegin backbone and side chain atoms are showed as pink sticks.
(B) Thrombin-hirulog-1 complex structure (PDB: 2HGT). Hirulog-1 is coloured as red sticks.
(C) Thrombin-hirulog-3 complex structure (PDB: 1ABI). Hirulog-3 is coloured as yellow sticks.
(D) Thrombin-hirugen complex structure (PDB: 1HGT). Hirugen is coloured as green sticks.
(E) Thrombin-PPACK complex structure (PDB: 1PPB). PPACK is coloured as orange sticks.
(F) Wild-type, inhibitor- and Na+-free thrombin (PDB: 2AFQ). Structure represents ‘slow’ form thrombin and is without an inhibitor.
) and cleavage product of mass 2582 (representing C-terminal fragment MHKTAPPFDFEAIPEEYLDDES; MH22; SEQ ID NO: 3) (▪) was calculated by integrating the area under the peaks in RP-HPLC analysis. Cleavage proceeded faster at 37° C. than at room temperature (24° C.) (n=2, error bars represent S.D.).
(A) Results obtained by incubating s-variegin and thrombin at 37° C. Only 180 min was needed for complete cleavage.
(B) Results obtained by incubating s-variegin and thrombin at 24° C. 360 min was needed for ˜90% of cleavage.
(A) S-variegin was incubated with thrombin (3.33 nM) for up to 24 hours at room temperature and at various time points assayed for the ability to inhibit thrombin amidolytic activity on 100 μM S2238 (n=3, error bars represent S.D.).
(B) Similar experiments were carried out replacing s-variegin with EP25 (n=3, error bars represent S.D.).
Concentrations used for MH22 (▪) and s-variegin were 0.03 nM, 0.1 nM, 0.3 nM, 1 nM, 3 nM, 10 nM, 30 nM, 100 nM, 300 nM and 1000 nM. IC50 of inhibition are 11.46±0.71 nM and 8.25±0.45 nM, respectively (n=3, error bars represent S.D.). Concentrations used for hirulog-1 (▴) were 0.3 nM, 1 nM, 3 nM, 10 nM, 30 nM, 100 nM, 300 nM, 1000 nM, 3000 nM and 10000 nM. IC50 of inhibition is 72.6±3.9 nM (n=3, error bars represent S.D).
In the presence of variegin, thrombin binds to variegin (Ki-v is the inhibitory constant of variegin, shown as brown arrows) thus S2238 hydrolysis is inhibited competitively. Upon binding, thrombin cleaves variegin into MH22 (kc is the forward rate constant for cleavage, shown as a violet arrow).
MH22 remained bound to thrombin, acting as a classical non-competitive inhibitor of thrombin (Ki-m is the inhibitory constant of MH22). MH22 binds to free thrombin or S2238 bound thrombin with the same affinity, α=1, thus Ki-m=αKi−m (shown as red arrows). Similarly, Ks=αKs, binding of S2238 to thrombin is unaffected by MH22.
(A) Thrombin catalytic triad THis57, TAsp102 and TSer195 when unoccupied in the thrombin-hirugen structure (green) have the intact charge relay hydrogen bonding system. In the thrombin-s-variegin structure (pink), TSer195 Oγ is displaced by 1.10 Å (cyan arrow). The distance between THis57 Nε and TSer195 Oγ is 3.77 Å, thus a hydrogen bond is not formed and the charge relay system is broken.
(B) The displacement of TSer195 Oγ is due to an interaction between s-variegin (shown in gray) and the catalytic triad of thrombin. The vHis12 backbone N (donor) engaged TSer195 Oγ (acceptor) through a hydrogen bond (2.77 Å) while the vHis12 side chain Nδ (acceptor) could only contribute a weak hydrogen bond with TSer195 Oγ (donor) (3.68 Å). The vHis12 backbone N also forms a hydrogen bond with TGly193 backbone N and TCys42 Sγ via a water molecule (light blue). Thus, TSer195 Oγ is rendered a weak nucleophile, and incapable of attacking the backbone carbon of the substrate. Oxyanion hole formation is also disturbed due to the involvement of TGly193 backbone N in this hydrogen bond network.
(A) Thrombin has a deep canyon-like cleft (boxed) starting from active site, and extending to exosite-I.
(B) On the whole s-variegin (pink CPK model) fitted firmly at the bottom of the canyon-like cleft in an extended conformation, covering the catalytic pocket, prime subsites and exosite-I. The bottom of the cleft is composed of mainly apolar residues. The walls of the cleft are formed by the 60- and autolysis loops near the thrombin active site, along with the 34- and 70-loops at exosite-I.
(C) Thrombin residues that interfaced with s-variegin are coloured according to their positions: catalytic pocket—blue; 60-loop—red; autolysis loop—cyan; 34-loop—yellow; 70-loop—green; bottom of the cleft—orange. A ball and stick model of s-variegin is shown in pink.
(D) s-variegin interacts with thrombin through specific side-chain contacts. All but five residues (vPhe18, vAsp19, vAla22, vGlu26 and vTyr27, all coloured white) on s-variegin have their side chains buried in the interface with thrombin.
(A) EP21 (0.3 nM, 1 nM, 3 nM, 10 nM, 30 nM, 100 nM, 300 nM, 1000 nM, 3000 nM and 10000 nM) inhibition of thrombin (1.65 nM) amidolytic activity with S2238 (100 μM) showed a pre-incubation time-dependent shift due to slow binding. The IC50 values were 176.9±6.8 nM without pre-incubation (solid line) and 16.2±2.9 nM with 20 min pre-incubation (dotted line) (n=3, error bars represent S.D.).
(B) Progression curves (not shown) of thrombin (1.65 nM) inhibition by different concentrations of EP21 (18.8 nM, 25 nM, 37.5 nM, 50 nM, 75 nM, 100 nM and 150 nM) at 100 μM S2238 were fitted to the equation P=Vft+(Vi−Vf)(1−e−kt)/k+Po describing a slow binding inhibitor to obtain a k value for each concentration of EP21 used. A plot of k against EP21 concentration (solid line) is a hyperbolic curve described by the equation k=K4+K3It/[It+Ki′(1+S/Km)] and hence was fitted to the equation to obtain a Ki′ of 1.66±0.36 nM, representing the dissociation constant of initial collision complex EI. The overall inhibitory constant (Ki) was calculated from the equation Kt=Ki′[K4/(K3+K4)] as 0.315±0.024 nM (n=3, error bars represent S.D.).
(A) The ability of MH18 (0.1 nM, 0.3 nM, 1 nM, 3 nM, 10 nM, 30 nM, 100 nM, 300 nM, 1000 nM, 3000 nM and 10000 nM) to inhibit amidolytic activity of thrombin (1.65 nM) was assayed in 100 μM S2238. Dose-response curves are independent of pre-incubation time. IC50 values were 10.9±1.2 nM without pre-incubation (solid line) and 11.7±1.9 nM after 20 min pre-incubation (dotted line) (n=3, error bars represent S.D.). (B) Since MH18 behaved as a fast and tight-binding inhibitor, thrombin (1.65 nM) inhibition was tested with 0.39 nM, 0.78 nM, 1.56 nM, 3.13 nM, 6.25 nM, 12.5 nM, 25 nM, 50 nM, 100 nM and 200 nM of MH18 at 100 μM of S2238 (solid line). The apparent inhibitory constant (Ki′) obtained by fitting data to the equation Vs=(Vo/2Et) {[(Ki′+It−Et)2+4Ki′Et]1/2−(Ki′+It−Et)} was 14.9±3.5 nM. The inhibitory constant (Ki) was calculated to be 14.9±3.5 nM based on equations Ki′=(S+Km)/[(Km/Kt)+(S/αKi)] and Ki′=Ki (n=3, error bars represent S.D.).
(A) Dose-response curves of thrombin (1.65 nM) inhibition by DV24 (0.1 nM, 0.3 nM, 1 nM, 3 nM, 10 nM, 30 nM, 100 nM, 300 nM, 1000 nM and 3000 nM) in 100 μM S2238 showed a right shift with increased pre-incubation time due to cleavage. IC50 values were 7.49±0.28 nM without pre-incubation (solid line) and 10.07±0.60 nM with 20 min pre-incubation (dotted line) (n=3, error bars represent S.D.).
(B) Since DV24 behaved as a fast and tight-binding inhibitor, thrombin (1.65 nM) inhibition was tested with 0.39 nM, 0.78 nM, 1.56 nM, 3.13 nM, 6.25 nM, 12.5 nM, 25 nM, 50 nM, 100 nM and 200 nM of DV24 at 100 μM of S2238 (solid line). The apparent inhibitory constant (Ki′) obtained by fitting data to the equation Vs=(Vo/2Et) {[(Ki′+It−Et)2+4Ki′Et]1/2−(Ki′−Et)} was 9.74±0.91 nM. The inhibitory constant (Ki) was calculated to be 0.306±0.029 nM based on the equation Ki′=Ki(1+S/Km) (n=3, error bars represent S.D.).
(A) Dose-response curves of thrombin (1.65 nM) inhibition by DV24K10R (0.1 nM, 0.3 nM, 1 nM, 3 nM, 10 nM, 30 nM, 100 nM, 300 nM, 1000 nM and 3000 nM) in 100 μM S2238 showed a right shift with increased pre-incubation time due to cleavage. IC50 values were 6.98±0.76 nM without pre-incubation (solid line) and 12.01±0.41 nM after 20 min pre-incubation (dotted line) (n=3, error bars represent S.D.).
(B) Since DV24K10R behaved as a fast and tight-binding inhibitor, thrombin (1.65 nM) inhibition was tested with 0.39 nM, 0.78 nM, 1.56 nM, 3.13 nM, 6.25 nM, 12.5 nM, 25 nM, 50 nM, 100 nM and 200 nM of DV24K10R at 100 μM of S2238 (solid line). The apparent inhibitory constant (Ki′) obtained by fitting data to the equation Vs=(Vo/2Et) {[(Ki′+It−Et)2+4Ki′Et]1/2−(Ki′+It−Et)} was 8.27±0.85 nM. The inhibitory constant (Ki) is calculated to be 0.259±0.015 nM based on equation (4) (n=3, error bars represent S.D.).
(A) Dose-response curves of thrombin (1.65 nM) inhibition by DV23 (0.1 nM, 0.3 nM, 1 nM, 3 nM, 10 nM, 30 nM, 100 nM, 300 nM, 1000 nM and 3000 nM) in 100 μM S2238 showed a right shift with increased pre-incubation time due to cleavage. IC50 were 45.4±1.6 nM without pre-incubation (solid line) and 77.8±6.1 nM after 20 min pre-incubation (dotted line) (n=3, error bars represent S.D.).
(B) Thrombin (1.65 nM) inhibition was tested with 3.91 nM, 7.81 nM, 15.6 nM, 31.3 nM, 62.5 nM, 125 nM, 250 nM and 500 nM of DV23 at 100 μM of S2238. The apparent inhibitory constant (Ki′) obtained by fitting data to the equation Vs=(Vo/2Et) {[(Ki′+It−Et)2+4Ki′Et]1/2−(Ki′+It−Et)} was 69.6±7.8 nM. The inhibitory constant (Ki) was calculated to be 2.19±0.23 nM based on the equation Ki′=Ki′=(1+S/Km) (n=3, error bars represent S.D.).
(A) DV23K10R (0.1 nM, 0.3 nM, 1 nM, 3 nM, 10 nM, 30 nM, 100 nM, 300 nM, 1000 nM and 3000 nM) inhibited thrombin (1.65 nM) in the presence of 100 μM S2238. Loss of activity after cleavage was rapid, indicated by the strong right shift of dose-response curve. IC50 values were 12.9±1.0 nM without pre-incubation (solid line) and 101.9±1.2 nM after 20 min pre-incubation (dotted line) (n=3, error bars represent S.D.).
(B) Thrombin (1.65 nM) inhibition was tested with 3.91 nM, 7.81 nM, 15.6 nM, 31.3 nM, 62.5 nM, 125 nM, 250 nM and 500 nM of DV23K10R at 100 μM of S2238 (solid line). The apparent inhibitory constant (Ki′) obtained by fitting data to the equation Vs=(Vo/2Et) {[(Ki′+It−Et)2+4Ki′Et]1/2−(Ki′+It−Et)} was 19.1±1.9 nM. The inhibitory constant (Ki) was calculated to be 0.600±0.010 nM based on the equation Ki′=Ki(1+S/Km) (n=3, error bar represents S.D.).
Similar experiments were conducted with the peptides at their IC90 concentrations (dotted lines): 167 nM for s-variegin (□), 224 nM for MH22 (◯) and 13.6 nM for DV24K10RYsulf (Δ). Higher concentrations of protamine sulphate are needed for reversal of all three peptides. s-variegin and MH22 are again neutralized to the same extent, while it is more difficult to neutralize DV24K10RYsulf. Therefore, the peptides acidic C-terminal residues are most likely responsible for protamine sulphate binding. This invention is further illustrated by the following examples which should not be construed as limiting. The contents of all references, patents and published patent applications cited throughout this application are incorporated herein by reference.
The following examples and definitions of parameters are used throughout the examples:
V=(VmaxS)/(S+Km)
where V is the initial rate of reaction, S is the concentration of substrate S2238 and Km is the Michaelis-Menten constant of substrate for the enzyme (thrombin).
y=A
2+(A1−A2)/[1+(x/x0)H]
where y is percentage of inhibition, A2 is right horizontal asymptote, A1 is left horizontal asymptote, x is log 10 of inhibitor concentration, x0 is point of inflection and H is the slope of the curve. IC50 was calculated by substituting ‘50’ into y.
V
s=(Vo/2Et){[(Ki′+It−Et)2+4Ki′Et]1/2−(Ki′+It−Et)}
where Vs is steady state velocity in the presence of inhibitor, Vo is velocity observed in the absence of inhibitor, Et is total enzyme concentration, It is total inhibitor concentration and Ki′ is apparent inhibitory constant.
K
i
′=K
i(1+S/Km)
where Ki′ increases linearly with S, K; is the inhibitory constant, S is the concentration of substrate and Km is the Michaelis-Menten constant for S2238.
K
i′=(S+Km)/[(Km/Ki)+(S/αKi)]
where α is the modifying constant of the inhibitor on the affinity of the enzyme for its substrate, and likewise the effect of the substrate on the affinity of the enzyme for the inhibitor. α<1 when binding of one supported the other, α>1 when binding of one impedes the other and when α=1, binding of one has no effect on the other. For a mixed-type non-competitive inhibitor, α is either <1 or >1.
K
i
′=K
i
where Ki′ remained constant with increasing S, K; is the inhibitory constant, S is the concentration of substrate S2238 and Km is the Michaelis-Menten constant for S2238
P=V
f
t+(Vi−Vf)(1−e−kt)k+Po
k=K
4
+K
3
I
t
/[I
t
+K
i′(1+S/Km)]
wherein Ki is the overall inhibitory constant.
K
i
=K
i
′[K
4/(K3+K4)]
where P is the amount of product formed, P. the is initial amount of product, Vf is final steady state velocity, Vi is initial velocity, t is time, and k is apparent first-order rate constant.
4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES), HEPES sodium salt and polyethylene glycol (PEG) 8000 were from Sigma Aldrich (St. Louis, Mo., USA). Crystallization trays and grease were purchased from Hampton Research (Aliso Viejo, Calif., USA).
All peptides used in the studies were synthesized using solid phase peptide synthesis methods on an Applied Biosystems Pioneer Model 433A Peptide Synthesizer (Foster City, Calif., USA). The synthesized peptides were assembled on support resins pre-loaded with respective C-terminal amino acids, which cleaves to release peptides with free carboxylic acid at the C-terminus. Fmoc groups of amino acids were removed by 20% v/v piperidine in DMF and coupled using HATU/DIPEA in situ neutralization chemistry. Cleavage of synthesized peptides from resins and side chain protection groups were typically carried out using a cocktail of TFA/1,2-ethanedithiol/thioanisole/water (90:4:4:2% v/v) at room temperature for 2 h. Cleaved peptides were precipitated with cold diethyl ether. Precipitated peptides were dissolved in either water or 0.1% TFA and lyophilized before purification.
Synthetic crude peptides were purified to homogeneity by RP-HPLC on ÄKTA™ purifier system (GE Healthcare, Uppsala, Sweden) with SunFire™ C18 (100 Å, 5 μm; 250 mm×10 mm) (Waters, Milford, Mass.) column. Typically peptides were eluted using an optimized linear elution gradient created by a combination of two solvents (solvent A: 0.1% TFA in water and solvent B: 0.1% TFA and 80% acetonitrile in water).
Of special note are peptides containing sulphotyrosine (DV24Ysulf, DV24K10RYsulf and MH18Ysulf), of which the sulphate groups are acid labile. Cleavage of these peptides was carried out with 90% aqueous TFA on ice for 5 h as previously described (Kitagawa et al., 2001). Purification of the peptides containing sulphotyrosine (DV24Ysulf, DV24K10R Ysulf and MH18Ysulf and phosphotyrosine (DV24Yphos and DV24K10R Yphos) were performed with solvent containing 0.1% FA as ion pairing agent instead of TFA. The sulphate moiety on Tyr27 is unstable during ionization in mass spectrometry analysis, thus non-sulphated masses were observed. Identification of sulphated peptides was on the basis of: (1) non-sulphated masses of the peptides; (2) as opposed to tyrosine residue that absorbs UV at 280 nm, sulphotyrosine residue does not; and (3) sulphated and non-sulphated peptides do not co-elute in RP-HPLC.
Two different sources of thrombin—recombinant α-thrombin (based on human α-thrombin sequence) and human plasma derived thrombin, both were generous gifts from the Chemo-Sero-Therapeutic Research Institute (KAKETSUKEN, Japan). Recombinant α-thrombin was desalted with the HiTrap™ Desalting Column (GE Healthcare, Uppsala, Sweden) in 20 mM ammonium bicarbonate (NH4HCO3) and lyophilized before being used for crystallization. Human plasma derived thrombin was used to assay thrombin inhibitory activities of the peptides.
The reported crystallization conditions that were used to crystallized thrombin-hirugen and thrombin-hirulog-1 complexes of human α-thrombin (Skrzypczak-Jankun et al., 1991) were modified and optimized. Lyophilized s-variegin was dissolved in 50 mM HEPES buffer (pH 7.4) containing 375 mM NaCl to a concentration of 8.34 μM (3 mg/ml). Desalted, lyophilized recombinant α-thrombin was subsequently dissolved in the s-variegin solution to a final concentration of 5.56 μM (20 mg/ml). The amount of s-variegin in this mixture was 1.5-fold in excess of thrombin. Crystallization of the thrombin-s-variegin complex was achieved using the hanging drop vapor diffusion method. Typically, 1 μl of protein solution was mixed with 1 μl of precipitant buffer (100 mM HEPES buffer pH 7.4, containing 20 to 25% (w/v) PEG 8000) and were equilibrated against 1 ml of precipitant buffer at 4° C. Crystals appeared after approximately four weeks and were harvested for data collection two weeks later. The entire process for setting up, growing and harvesting of crystals were performed in cold room (4° C.) as the crystals are unstable at room temperature.
Prior to data collection, crystals were briefly soaked in a cryoprotectant solution containing the mother liquor, supplemented with 25% (v/v) glycerol, and flash cooled at 100 K in nitrogen (gas) cold stream (Cryostream cooler, Oxford Cryosystem, Oxford, United Kingdom). Synchrotron data were measured at the Beamline X29 (National Synchrotron Light Source, Brookhaven, USA). Data sets were collected (Table 1) using the Quantum 4-CCD detector. The diffraction data were processed using the program HKL2000 (Otwinowski and Minor, 1997). The crystal belonged to the monoclinic space group C2 and diffracted up to 2.7 Å resolution with a=124.66 Å, b=50.83 Å, c=61.54 Å and V=385390.59 A3 Da-1 and corresponded to a solvent content of 59.09%.
The structure of thrombin-s-variegin complex was solved by the molecular replacement method using the MolRep program (Vagin and Teplyakov, 2000). The coordinates of thrombin-hirulog-3 structure (PDB code 1ABI) (Qiu et al., 1992) were used as a search model. The rotation search located one thrombin-peptide complex molecule in the asymmetric unit. The rigid body refinement after determining the translation components gave a correlation coefficient of 0.60 and R=0.48. The resultant electron density map was of good quality. The Fourier and difference Fourier maps clearly showed electron density for s-variegin. Several cycles of map fitting using the program O version 7.0 (Jones et al., 1991) and refinement using the program CNS version 1.1 (Brunger et al., 1998) led to convergence of R-values. The crystallographic and refinement statistics are given in Table 1. The correctness of stereochemistry of the model was verified using PROCHECK (Laskowsi et al., 1993). Online server PISA (Krissinel and Henrick, 2007) was used to analyze the protein (
aRsym = Σhkl Σl [|Ii (hkl) − <I(hkl)>|]/Σhkl I(hkl)
bRwork = Σ|Fobs − Fcalc|/Σ|Fobs| where Fcalc and Fobs are the calculated and observed structure factor amplitudes, respectively.
cRfree = as for Rwork, but for 8.0% of the total reflections chosen at random and omitted from refinement.
Materials, thrombin, methods of synthesis, purification and mass spectrometry analysis of peptides are as described for Example 1.
Peptides were incubated with recombinant α-thrombin at both room temperature in 50 mM Tris buffer (pH 7.4) containing 100 mM NaCl and 1 mg/ml BSA. Reaction mixtures without thrombin were set up as control. After various incubation times, the reactions were quenched with 0.1% TFA buffer (pH 1.8) and loaded onto a SunFire™ C18 column attached to an ÄKTA™ purifier. New peaks other than those present in the chromatogram of both control reaction mixture and 0 min incubation were identified as cleavage products and subjected to ESI-MS to verify their masses. The peaks were integrated to calculate the area under the peaks and the relative percentage of each peak to determine the extent of cleavage.
Variegin is hypothesized to canonically bind thrombin active site, and it is therefore thought that it may be cleaved by thrombin which is similar to other serine protease inhibitors (Witting et al., 1992; Bode and Huber, 1992). Therefore we examined the cleavage of s-variegin by thrombin and its effects on peptides activities. RP-HPLC analysis showed that s-variegin was indeed cleaved by thrombin at both 37° C. and room temperature (˜25° C.). At 0 min of incubation, only peaks corresponding to full-length s-variegin and thrombin were present. Two new peaks of cleavage products appeared and increased with longer incubation times (
To test if variegin cleavage product is indeed responsible for its prolonged activity, the C-terminal fragment of cleavage (MHKTAPPFDFEAIPEEYLDDES; MH22; SEQ ID NO: 3) was synthesized. This fragment was selected primarily because preliminary data from thrombin-variegin structure obtained by X-ray diffraction suggested that MH22 binds to thrombin after cleavage.
The inhibitory Constant Ki of MH22
The inhibitory constant, Ki of MH22 was determined using S2238 as substrate. MH22 is a fast and tight binding inhibitor. Apparent inhibitory constants, Ki′ were determined in the presence of different concentrations of S2238 using the equation Vs=(Vo/2Et) {[(Ki′+It−Et)2+4Ki′Et]1/2−(Ki′+It−Et)}. Unlike s-variegin which has Ki′ increases linearly with increasing concentrations of S2238 (as shown by the equation Ki′=Ki(1+S/Km)), MH22 Ki′ values remained constant with changes in S2238 concentrations. This behaviour of the curve fits an equation that describes non-competitive inhibition where α=1 (using the equation Ki′=(S+Km)/[(Km/Ki)+(S/αKi)]) and hence, Ki′=Ki (as shown by the equation Ki′=Ki). Fitting the Ki′ values by linear regression derived a value of 14.11±0.29 nM for Ki (
MH22 inhibited thrombin amidolytic activity at equimolar concentration (˜15%) and progress curves of inhibition showed that steady state equilibrium was achieved upon mixing. Thus, similar to s-variegin, MH22 is a fast and tight-binding inhibitor. Dose-response curve showed IC50 value of 11.46±0.71 nM (
MH22 was shown to non-competitively inhibit thrombin. Typically, a non-competitive inhibitor binds at a site away from the enzyme active site and allosterically inhibits the active site function. However, the MHKT tetrapeptide is immediately after the scissile bond. Intuitively, binding of this segment to thrombin is likely to be within the active site. The substrate used in the experiments, S2238, has a chemical structure of D-Phe-Pipecolyl-Arg-pNA, with its Arg side chain inserted into thrombin S1 subsite and cleavage occurs between Arg-pNA. With the pNA moiety also occupying the S1′ in the immediate proximity of scissile bond during amidolysis, its presence should theoretically interfere with binding of MH22 to the same site. In such a case, a should be >1 (using the equation Ki′=(S+Km)/[(Km/Ki)+(S/αKi)]) and the plot of Ki′ against substrate concentrations should increase in a hyperbolic manner with increasing concentration of substrate (Copeland, 2000). This type of non-competitive inhibition is usually termed ‘mixed inhibition’. However, under our experimental conditions, the apparent inhibitory constant, Ki′, remained strictly constant with changes in substrate concentrations. Thus, MH22 act as a classical non-competitive inhibitor—binding to both free thrombin and thrombin-substrate complex with the same affinity (
Thirteen new variegin variants were designed based on the thrombin-s-variegin structure as well as background information available on thrombin interactions. The general approach was to first optimize the length of variegin before optimizing several key positions on variegin to obtain maximum interaction with thrombin (
Activities of s-variegin (SEQ ID NO: 1), EP25 (SEQ ID NO: 6), MH22 (SEQ ID NO: 3) and hirulog-1 (SEQ ID NO: 14) were assayed by their abilities to inhibit thrombin amidolytic activity on S2238.
The activity of each peptide was determined by the inhibition of recombinant α-thrombin amidolytic activity assayed using the chromogenic substrate S2238. All assays were performed in 96-well microtiter plates in 50 mM Tris buffer (pH 7.4) containing 100 mM NaCl and 1 mg/ml BSA at room temperature. Typically, 100 μl of peptide and 100 μl of recombinant α-thrombin were pre-incubated for different durations before the addition of 100 μl of S2238. Details of each experiment are described along with the graphs representing the results obtained. The rates of formation of colored product pNA were followed at 405 nm for 10 min with a SPECTRAMax Plus microplate spectrophotometer. Percentage inhibition was calculated by taking the rate of increase in absorbance in the absence of inhibitor as 0%. Dose-response curves were fitted using Origin software to calculate IC50 values with the following logistic sigmoidal equation: y=A2+(A1−A2)/[1+(x/x0)H], where y is percentage of inhibition, A2 is right horizontal asymptote, A1 is left horizontal asymptote, x is log 10 of inhibitor concentration, x0 is point of inflection and H is the slope of the curve. IC50 was calculated by substituting ‘50’ into y.
Effects of pre-incubation times (hence cleavage) on thrombin inhibitory activities of peptides were performed with the same assay, varying pre-incubation times and/or concentrations of BSA. For experiments to ascertain integrity of thrombin exosite-I during extended incubation time, parallel sets of assay were performed with or without addition of freshly prepared inhibitors after 28 h of pre-incubation. All data obtained were fitted using Origin software to the y=A2+(A1−A2)/[1+(x/x0)H] equation for calculation of IC50 values and to the equations:
V
s=(Vo/2Et){[(Ki′+It−Et)2+4Ki′Et]1/2−(Ki′+It−Et)} for tight binding inhibition;
K
i
′=K
i(1+S/Km) for competitive inhibition;
K
i′ (S+Km)/[(Km/Ki)+(S/αKt)] for non-competitive inhibition;
K
i
′=K
t for classical non-competitive inhibition;
P=V
f
t+(Vi−Vf)(1−e−kt)/k+Po for slow-binding inhibition;
k=K
4
+K
3
I
t
/[I
t
+K
i′(1+S/Km)] for calculation of the dissociation constant; and
K
i
=K
i
′[K
4/(K3+K4)] for calculation of the overall inhibitory constant.
The lack of electron densities for the four s-variegin C-terminal residues [v(29DDES32)] in the complex structure indicated that these four residues are unlikely to interact strongly with thrombin. Further, these residues were not present in hirulogs or hirugen. Considering the vast differences between C-terminal conformations of s-variegin and hirulog/hirugen, it would be interesting to examine the role of these residues. Two truncation variants, EP21 (SEQ ID NO: 8) and MH18 (SEQ ID NO: 9), corresponded to EP25 and MH22 respectively but lacking those four C-terminal residues, were designed and characterized. Since EP25 and s-variegin binds to thrombin with the same affinity, C-terminal truncation variant of s-variegin was not synthesized. Progress curves of thrombin inhibition by EP21 (SEQ ID NO: 8) showed two-phase equilibria in the absence of pre-incubation, typical of a slow binding inhibitor. EP21 activity was dependent on pre-incubation time. IC50 decreased from 176.9±6.8 nM (without pre-incubation) to 16.2±2.9 nM (after 20 min pre-incubation) (
MH18 (SEQ ID NO: 9) inhibited thrombin amidolytic activity at equimolar concentration (˜15%) and steady state equilibrium was achieved upon mixing. Thus, MH18 is a fast, tight-binding inhibitor for thrombin. Dose-response curves showed IC50 values of 10.9±1.2 nM (without pre-incubation) and 11.7±1.9 nM (after 20 min pre-incubation) (
Inhibition of Thrombin Amidolytic Activity by DV24
Our earlier data showed that the seven N-terminal residues of variegin are responsible for its fast binding kinetics; when removed, the binding characteristics changed from fast to slow without loss in affinity (data not shown). We then postulated that the highly basic thrombin exosite-II could help to steer variegin N-terminus residues (which contains two negatively charged residues in its sequence 1 SDQGDVA7) into an optimal orientation close to the active site allowing rapid formation of short-range interactions. Since thrombin exosite-II is located about 10 Å away from the active site (Page et al., 2005), this distance could theoretically be covered by at least three N-terminal residues in an extended conformation. In order to produce a peptide that retained the fast-binding property, we designed and characterized a peptide extending EP21 by three residues at the N-terminus. One out of the two acidic N-terminal residues, vAsp5, is present in this variant, which is named DV24 (SEQ ID NO: 10).
Instead of the two-phase equilibria usually observed for slow binding inhibitor, DV24 (SEQ ID NO: 10) progress curves of thrombin inhibition were similar to s-variegin—reaching steady state equilibrium upon mixing. Thus, DV24 is a fast and tight-binding inhibitor. Activity of DV24 decreased with increasing pre-incubation time due to cleavage by thrombin. Dose-response curves showed IC50 values of 7.49±0.28 nM (without pre-incubation) and 10.07±0.60 nM (after 20 min pre-incubation) (
One difference between variegin and other thrombin substrates/inhibitors is the presence of Lys in the P1 position of the scissile bond. Typically, Arg is found in this position for thrombin substrates. The electrostatic interaction between the side chain guanidinium group of Arg and the side chain carboxylate group of TAsp 189 in the S1 subsite is usually preferred. In contrast, P1 Lys usually interacts with Asp 189 through a water molecule (Perona and Craik, 1995), resulting in reduced affinity and specificity (Vindigni et al., 1997). The absence of electron density for residues before the scissile bond [v(1SDQGDVAEPK10)] in the thrombin-s-variegin structure probably implies the lack of strong affinity for thrombin within this segment. Therefore, using DV24 as template sequence, the P1 residue Lys10 was replaced by Arg in a new variant named DV24K10R (SEQ ID NO: 11).
IC50 obtained for DV24K10R is 6.98±0.76 nM without pre-incubation, which is similar to IC50 of DV24 (7.49±0.28 nM). However, IC50 for DV24K10R is 12.01±0.41 nM after 20 min pre-incubation, slightly higher than that of DV24 (10.07±0.60 nM). It is likely that cleavage of the peptide proceeds faster with the presence of P1 Arg (
The phenyl group of VPhe20 is inserted into an apolar cavity in thrombin and interacts with TPhe34 by π-π stacking. This interaction is also present in hirulog, hirugen and hirudin complex structures and marks the start of the C-terminal segment—DFEA(E)IPEEYL—where s-variegin and hirulog/hirugen are almost identical. In s-variegin, there are nine residues present in between the P1 Lys residue and the Phe [V(11 MHKTAPPFD19)]. However, in hirulog-⅓, the same distance is spanned by only eight residues (4PGGGGNGD11). Analysis of the thrombin-s-variegin structure showed that vPro16 and vPro17 induced a kink in its backbone, causing a slight bend upwards, away from thrombin. This in turn caused a displacement of vPhe18 and vAsp19 by about 3.16 Å and 1.70 Å from their corresponding residues in hirulog-3—Gly10 and Asp11—as measured by distances between their Cα atoms (
Both DV23 and DV23K10R showed decrease in activities compared to their templates. DV23 IC50 values are 45.4±1.6 nM (without pre-incubation) and 77.8±6.1 nM (after 20 min pre-incubation) (
Of the 17 observed s-variegin residues, selected few N-terminal residues are of special interest. The thrombin-s-variegin structure was compared with thrombin-hirugen structure (PDB: 1HGT) as they shared one common characteristic—both occupy the exosite-I but not the non-prime subsites of active site (since N-terminal cleavage fragment of s-variegin is not present). Of the three catalytic residues (THis57, TAsp102 and TSer195), the most striking difference was with the Oγ atom of TSer195. In the thrombin-s-variegin structure, TSer195 Oγ is displaced by 1.1 Å. As a result, the hydrogen bond with NE of THis57 (which should be part of the catalytic charge relay system) is absent in the thrombin-s-variegin structure. The distance between the two atoms increased to 3.77 Å (
No other major structural changes are observed around the active site cleft, including the non-prime subsites (occupied by substrates residues N-terminal to the scissile bond) and Na+binding loop. This indicates that C-terminal cleavage fragment of s-variegin (MH22; SEQ ID NO: 3) does not affect binding affinities of small peptidyl substrates, such as S2238. This observation supports the classical non-competitive inhibition observed for MH22. As shown in
In addition to the extensive network of hydrogen bonds, other interactions between s-variegin P2′ to P5′ (vHis12, vLys13, vThr14 and vAla15) with thrombin further anchored this moiety in the prime subsites of thrombin. Extensive interface contacts between vHis12 to vAla15 of s-variegin and thrombin surface formed by residues in 60-loop, autolysis loop and 34-loop was observed (
Thrombin-s-variegin binding in exosite-I is mainly driven by hydrophobic interactions. On the whole s-variegin fitta firmly into the canyon-like cleft extending from the thrombin active site to exosite-I (
In contrast to the apolar nature of the bottom of canyon-like cleft, the top surfaces of these loops, especially the 70-loop, are dominated by positively-charged residues. These basic residues include TArg35, TLys36, TArg73, TArg75, TLys81, TArg77A, TLys 109, TLys110 and TLys149E, forming a positively-charged entrance over the apolar canyon-like cleft. Despite the presence of multiple acidic residues in s-variegin C-terminus (vAsp19, vGlu21, vGlu25 and vGlu26), only one ion pair is formed between vGlu21 and TArg75. Interestingly, in hirulog, hirugen and hirudin structures the analogous Glu makes an ion pair with TArg75 of a 2-fold symmetry-related molecule (Rydel et al., 1990; Skrzypczak-Jankun et al., 1991; Qiu et al., 1992).
This interaction was suggested to happen within the same thrombin-inhibitor pair in solution although structurally it was not observed (Rydel et al., 1990). In our structure, the TArg75 side chain is rotated by 96.8° about Cγ compared to TArg75 of hirulog-3 to facilitate the electrostatic interaction with vGlu21, providing structural evidence for the existent of the predicted interaction. Similarly, in hirulog-⅓ and hirugen structures, only one ion pair can be observed. However, this interaction is between TArg73 and an Asp corresponds to vAsp19. Formation of an equivalent ion pair in the thrombin-s-variegin structure was not possible as vAsp19 side chain points in an opposite direction into the solvent. This change in side chain orientation is most likely due to the kink in s-variegin backbone which is induced by Pro16-Pro17.
At the end of the canyon-like cleft is a relatively flatter surface formed by thrombin residues TAsp63-TIle68 and TLys81-TLeu85. Despite being present in close proximity, s-variegin C-terminal residues vPro24 to vLeu28 stacked loosely on top of this surface with two of the side chains (vGlu26 and vTyr27) pointing into the solvent (
Adult zebrafish and zebrafish larvae were maintained in Department of Biological Sciences, University of North Texas, Denton, Tex., USA.
Synthesis, purification and mass spectrometry analysis of all peptides followed the procedures described in Example 1.
The zebrafish breeding tank was assembled with two 1 L tanks. The bottom of one tank was cut off and placed onto a sterilized mesh. This tank was subsequently inserted into a second tank with intact bottom. A pair of zebrafish was then placed into the breeding tank at the end of a light cycle. The mesh served to isolate the pair of zebrafish in the top tank. Within the first 2 hours of the next light cycle, the fish begin to spawn and eggs collect at the bottom of the breeding tank under the protection of the mesh. After removal of fish, water in the breeding tank was filtered through a brine shrimp net which retains the eggs. The net was immediately inverted over a Petri dish containing E3 media (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4 and 10-5% methylene blue), releasing the eggs and other contaminating materials such as feces. The eggs were subsequently transferred into fresh E3 media with a plastic Pasteur pipette. This cleaning step was repeated twice before the eggs were transferred into a new tank and maintained at 28.5° C. for hatching.
Larvae at 4 days-post-fertilization (dpf) were used to determine in vivo activities of peptides in venous thrombosis model. Intravenous microinjections of peptides were performed using Nanoject II (Drummond, Broomall, Pa., USA) with glass injection needles (3.5-in. capillaries) pulled on a vertical pipette puller (Knopf, Tujunga, Calif.). The tips of the pulled needles were clipped using small scissors and filled with 500 μM of peptides dissolved in phosphate buffered solution (PBS). 10 nl of peptides or PBS were injected into the larvae circulation through the posterior (caudal) cardinal vein.
Each larvae injected with peptides were placed in 0.5 ml of distilled water added with 6 μl of 10 mM Tricaine solution for anesthetization. To this water containing larvae equal volume of 1% low-melt agarose solution (maintained at 35° C. in a water bath) was added. The mixture (with anesthetized larvae) was poured onto a glass microscopic slide within a rectangular rubber gasket to mount the larvae flat on their side in agarose.
Laser ablation of larvae veins were performed with pulsed nitrogen laser light pumped through coumarin 440 dye (445 nm) (MicroPoint Laser system, Photonic Instrument, St Charles, Ill., USA) at 10 pulses/second with laser intensity setting at 10. Accuracy of the laser was tested before ablations. Laser ablation of each larva was carried out 20 min after microinjection of the peptide. Glass slides were placed under Optipnot phase-contrast fluorescence microscope (Nikon, Melville, N.Y., USA). The larvae were viewed with 20× lens (10× eyepiece) to locate the site for laser ablations, which was five somites towards the caudal end from the anal pore (data not shown). Laser beam aimed at the caudal vein within the ablation site was triggered for 3 s. The process was recorded using a digital camera attached to a video home system (VHS) recorder and a monitor. Thrombus formation following vein injury due to laser ablation was monitored and the time taken for complete occlusion of injured vein was recorded.
Five inhibitors were selected as representative peptides to test for their antithrombotic effects in vivo using venous thrombosis model of zebrafish larvae. They are: (1) s-variegin (the full-length sequence of native variegin; a fast, tight-binding competitive inhibitor; Ki=0.318±0.020 nM; SEQ ID NO: 1); (2) EP25 (without seven N-terminal residues, has similar affinity to thrombin, but it is a slow binding inhibitor; Ki=0.370±0.11 nM; SEQ ID NO: 6) (3) MH22 (the cleavage product that is a fast and tight-binding, non-competitive inhibitor; Ki=14.11±0.29 nM; SEQ ID NO: 3); (4) DV24K10RYsulf (a peptide with potent in vitro activity; Ki=0.0420±0.0061 nM; SEQ ID NO: 16); and (5) hirulog-1 (a fast, tight-binding, competitive inhibitor currently in the market; Ki=2.94±0.12 nM; SEQ ID NO: 14). Hirulog-1 was used as positive control of the experiments.
All five peptides were injected into the zebrafish larvae circulation through the posterior (caudal) cardinal vein at a single dose (500 μM, 10 nl). Antithrombotic effects of the peptides are measured by the abilities of all peptides to delay time-to-occlusion (TTO) of caudal vein after laser ablation. After laser ablation, control TTO of a wild-type 4 dpf larva is about 21 s (Jagadeeswaran et al., 2006). Typically, if thrombus formation is inhibited (due to either an antithrombotic agent or genetic defect), TTO can be delayed up to 150 s, beyond which complete occlusion will not occur (Seongcheol Kim, personal communication). Therefore, the dose for injection (500 μM, 10 nl) was carefully selected based on a few preliminary experiments such that a definite TTO can be obtained for most, if not all, of the peptides (data not shown).
Zebrafish larvae injected with the same volume of PBS have a TTO (mean±S.D.) of 19.0±3.2 s (
The ability of protamine sulphate to neutralise inhibition of thrombin amidolytic activity by the peptides was assayed using the chromogenic substrate S2238. Protamine is a mixture of highly cationic peptides originally extracted from fish sperm nuclei. Protamine sulphate is clinically used for the reversal of anticoagulant effect of heparin by binding to the anionic heparin molecules (Schulman and Bijsterveld, 2007). Variegin has several acidic residues at its C-terminus which could be the target for protamine sulphate. This option was first explored since there are ample clinical experiences for protamine sulphate administration.
All assays were performed in 96-well microtiter plates in 50 mM Tris buffer (pH 7.4) containing 100 mM NaCl and 1 mg/ml BSA at room temperature. Typically, 100 μl of peptide and 100 μl of protamine sulphate were pre-incubated for 10 min before the addition of 50 μl of human plasma derived thrombin. 50 μl of S2238 were added to initiate the reaction. The rates of formation of coloured product pNA were followed at 405 nm for 10 min with SPECTRAMax Plus microplate spectrophotometer (Molecular Devices, Sunnyvale, Calif., USA). Percentages of inhibition in the presence and absence of protamine sulphate were compared for calculation of percentages of reversal. Fixed concentrations of s-variegin, DV24K10RYsulf and MH22 (at their respective IC50 and IC90) were incubated with various concentrations of protamine sulfate before assaying their residual thrombin inhibitory activities. Protamine sulfate reversed the effects of all three peptides dose-dependently (
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| Number | Date | Country | Kind |
|---|---|---|---|
| 0907698.5 | May 2009 | GB | national |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/GB10/00889 | 5/5/2010 | WO | 00 | 2/21/2012 |
| Number | Date | Country | |
|---|---|---|---|
| 61250412 | Oct 2009 | US |
