Polypeptide Ligands Containing Linkers

Abstract

There is provided herein a multivalent binding molecule and uses thereof. The molecule is useful in binding a target under certain conditions and releasing it under other conditions. The molecule has the general formula (1) of BM1-L-(BM2)n (1) wherein, BM1 is a binding moiety 1 having an affinity for site 1 on the target, BM2 is a binding moiety 2 having an affinity for a site other than site 1 on the target, n is 1 or greater, and L is a linker joining BM1 and BM2, said linker being adapted to respond to a change in its environment with a change in conformation and/or flexibility, wherein BM1 and BM2 may be the same or different and are selected such that in use each of the BM1 and BM2 existing separately has a lower binding affinity then the complex of BM1 and BM2 does when they are linked to form the molecule. BM2 may have a single binding region or multiple binding regions with affinity for the target. The binding affinity of BM1 or BM2 to the target alone is no more than ½ the binding affinity of the molecule of formula (1). The molecule of formula (1) can be constructed using an oligomeric or polymeric linker, such as a polypeptide sequence. Such molecules can be useful in the delayed release of drugs, in screening assays, for stabilizing enzymes such as proteases, and for controlling reactions such as blood clotting.

Description

FIELD OF THE INVENTION

The invention relates to the field of multivalent binding molecules containing polymeric linkers.

BACKGROUND TO THE INVENTION

Strategies of linking weak-binding molecular fragments together to produce a significantly stronger ligand molecule have been implemented in drug discovery. Tweezer-like molecules have also been designed recently in the area of host-guest chemistry to control the specific complexation of artificial receptors (hosts) with small molecules (guests). In these applications, the linking bridge is normally optimized and often rigidified to achieve maximal affinity of the bivalent molecule. Bivalent and polyvalent ligands have been reported that incorporate multiple copies of a single binding moeity on a polymer backbone.

It is an object of the invention to provide multivalent binding molecules containing linkers through which binding can be modulated.

SUMMARY OF THE INVENTION

There is disclosed herein an approach combining independent binding moieties in a single molecular structure, which couples binding affinity to an on/off or modulatable switch. This molecular organization provides responsiveness of the inherent ligand (effector/inhibitor) potency to an external triggering signal. A principle of such a molecular structure is the design of the ligand in a bivalent or otherwise multivalent fashion, termed “biomolecular tweezers”, which contain two or more binding moieties (or “heads”) linked by a structurally flexible bridge (FIG. 1). Each binding moiety in isolation preferably has only low-affinity and transient interactions with an intrinsic dissociation constant preferably less than 1 M for its specific binding site on a target biomacromolecule. When linked together, the resulting bivalent or multivalent ligand makes a substantially stable complex with the target, achieving enhancement of preferably at least two (2) fold in overall binding affinity as compared to the highest affinity of the constituent monovalent ligands. To achieve control of binding, a change (normally, decrease) in the flexibility of the linker can be induced by an external trigger to disrupt the molecule's ability to bind in a bivalent or multivalent high-affinity mode. Vise versa, removal of constraints imposed on the linker would preferably restore the high-affinity binding of the freed bivalent or multivalent ligand. Where the binding sites are known to occur in a defined spatial relationship, it may in some instances be desirable to select a linker which is substantially rigid in the environment in which binding is desired and has a conformation when rigid that places the ligands in preferred positions for binding.

In an embodiment of the invention there is provided a multivalent binding molecule and uses thereof. The molecule is useful in binding a target under certain conditions and releasing it under other conditions. The molecule has the general formula (I) of

BM1-L-(BM2)_n  (1)

wherein,

BM1 is a binding moiety 1 having an affinity for site 1 on the target,

BM2 is a binding moiety 2 having an affinity for a site other than site 1 on the target, n is 1 or greater, and

L is a linker joining BM1 and BM2, said linker being adapted to respond to a change in its environment with a change in conformation and/or flexibility,

wherein BM1 and BM2 may be the same or different, and when n>1, different BM2 moieties may have affinities for different binding sites on the target. BM1 and BM2 are selected such that in use each of the BM1 and BM2 existing separately has a lower binding affinity then the complex of BM1 and BM2 does when they are linked to form the molecule. BM1 and/or BM2 may each have a single binding region or multiple binding regions with affinity for the target. The binding affinity of BM1 or BM2 to the target alone is no more than ½ the binding affinity of the molecule of formula 1. The molecule of formula 1 can be constructed using an oligomeric or polymeric linker, such as a polypeptide sequence. Such molecules can be useful in the delayed release of drugs, in screening assays, for stabilizing enzymes such as proteases, and for controlling reactions such as blood clotting.In an embodiment of the invention there is provided a molecule of formula I wherein the amino acid sequence is selected from at least one of SEQ. ID. NO. 8, 12, 17, 24, 27, 28, 37-47, 48, 49, 50-56, 57, 58, 59-60, 124-126, 127, or 128.In an embodiment of the invention there is provided a molecule of formula I wherein BM1 comprises an amino acid sequence selected from: SEQ. ID. NO. 6, 9, 15, 19, 35, 68, 69-71, 72, 93, 92, 94-95, 116, 122 or linked sequences SEQ. ID. NO. 15 and SEQ. ID. NO. 16.In an embodiment of the invention there is provided a molecule of formula I wherein BM2 comprises an amino acid sequence selected from SEQ. ID. NO. 1, 20, 36, 96-99.In an embodiment of the invention there is provided a molecule of formula I comprising at least one amino acid sequence selected from SEQ. ID. NO. 2, 9, 10, 11, 13, 14, 16, 21, 22, 23, 25, 29, 32, 33, 34, 73, 74, 75, 76, 77, 78, 79, 80, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 100, 101, 102, 112, 115, 117, 119, 121, or 117, or an amino acid sequence at least 90% identical thereto.In an embodiment of the invention there is provided an isolated or substantially isolated amino acid sequence of no more than 100 amino acids, said sequence comprising a series of contiguous amino acids having at least 80%, 90% or 95% sequence identity to at least one of SEQ. ID. NO. 8, 12, 17, 24, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 128, 62, 63, 64, 65, 66, 67, 103, 104, 105, 106, 107, 108, 109, 110, 111, 118, 120, 123, 124, 125, 126, 127, 128, SEQ. ID. NO. 2, 9, 10, 11, 13, 14, 16, 21, 22, 23, 25, 29, 32, 33, 34, 73, 74, 75, 76, 77, 78, 79, 80, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 100, 101, 102, 112, 115, 117, 119, 121, 117, SEQ. 37, 38, 92, 93, 94, 95, 100, or 101. In an embodiment of the invention there is provided an isolated or substantially isolated nucleic acid sequence encoding one or more of the above amino acid sequences. In an embodiment of the invention there is provided a nucleic acid sequence substantially or completely complementary to at least one nucleic acid sequence described above. In an embodiment of the invention there is provided vectors comprising one or more of the nucleic acid sequence described above.In an embodiment of the invention there is provided a pharmaceutical composition comprising a molecule of formula 1 with a carrier. Also provided is a method of delivering a compound of interest for preferential release at a biological site of interest, comprising obtaining a molecule of formula 1 wherein BM1 and BM2 have binding affinities for the compound of interest and the linker is selected to undergo a conformational change in under conditions present or inducible at the biological site of interest so as to reduce multivalent binding f the compound by the molecule of formula 1 at the biological site of interest.In an embodiment of the invention there is provided a method to screen a population of molecules to identify a ligand of interest. The method comprises: a) selecting a target of interest with a known affinity for a component; b) selecting a second molecule having a known affinity for the component of step (b), the second molecule binding a different region of the component from the region bound by the target; c) connecting the target and the second molecule with a suitable linker to create a bivalent structure; d) monitoring binding of the bivalent structure to the component in the presence of ligands; and, e) identifying a ligand which reduces the level of bivalent binding.In an embodiment of the invention there is provided a method of assaying for the presence of a substance of concern in a sample. The method comprises: a) identifying a first target region known to be present on the substance of concern and less common within sample material which does not contain the substance; b) identifying a second target region known to be present on the substance of concern; c) obtaining a plurality of molecules comprising a first binding region having affinity for the first target region connected by way of a linker to a second binding region having affinity for the second target region, wherein the linker undergoes an assayable conformational change during the transition between bivalent and monovalent binding; d) combining molecules from step (c) with the sample; and e) assaying for bivalent binding.In an embodiment of the invention there is provided a method of identifying conditions affecting a structural characteristic of a polymeric molecule of interest. The method comprises: (a) obtaining a molecule according to claim 1 wherein the linker comprises the polymeric molecule of interest and binding moieties 1 and 2 are adapted to bind a known target when the linker has a first structural condition such that bivalent binding of binding moiety 1 and binding moiety 2 to the target causes a change in an assayable characteristic of the target; (b) permitting interaction between the molecule of step (a) and the target; (c) altering the conditions under which the interaction of step (b) occurs; and (d) assaying the effect of changes of conditions on the characteristic of the target.In an embodiment of the invention there is provided method to enhance the stability of an enzyme. The method comprises reducing functional activity of the enzyme by binding to it a molecule of formula 1 having first and second binding moieties with affinity for the enzyme. Also provided is this method with a further step of releasing bivalent binding of the molecule of formula 1 by inducing a change in the structure and/or flexibility of the linker so as to allow an increase in functional activity of the enzyme. In some instances the enzyme is a protease.In an embodiment of the invention there is provided a method of manufacture of a device capable of activation by an electromagnetic field. The method comprises: (a) obtaining a molecule of claim 1 wherein BM1 And BM2 bind to a target and L binds to an antidote which causes a change in the linker sufficient to reduce bivalent binding of the molecule to the target; (b) conjugating the antidote with a metal nanoparticle; (c) allowing interaction between the antidote and the target such that bivalent binding occurs. Also provided is a method of activating a device manufactured according to the method above comprising releasing the ligand by heating the metal nanoparticle by means of electromagnetic radiation.In an embodiment of the invention there is provided a method for the purification of a target. The method comprises: (a) immobilizing onto a solid support a molecule of claim 1 capable of binding to the target via BM1 and BM2; (b) allowing the target to bind the molecule of step (a); (c) eluting unbound materials; and, (d) eluting the target by inducing a condition which causes a change in structure and/or flexibility of the molecule of step (a) such that bivalent binding of the target by the molecule is reduced.

In an embodiment of the invention there is provided a method to obtain a molecule of formula 1 with high affinity to a protein target, said method comprising steps of: (a) obtaining at least two binding peptide moieties each having a binding affinity for a distinct binding site on the target based on already existing polypeptide ligands with high affinity; (b) establishing a weaker binding peptide moiety using NMR titration or NMR relaxation dispersion spectroscopy; (c) connecting the peptide moieties with a flexible linker; (d) increasing the bivalent affinity by sequence optimization of the weaker moiety by means of phage display.

In an embodiment of the invention there is provided a method to prolong the lifetime of a protease said method comprising the steps of: (a) Inhibiting the protease with a bivalent protease inhibitor containing a controllable linker; (b) Releasing and activating the protease with an appropriate linker-targeted antidote. In some instances the protease is thrombin. In some instances thrombin is a component of a fibrin sealant kit.

In an embodiment of the invention there is provided a method to detect an agent modifying the properties of the linker in a molecule of formula 1. The method comprises: (a) obtaining a multivalent ligand with the general structure of formula 1 having multivalent binding affinity for an enzyme catalyzing a detectable chemical reaction, for which the ligand is an inhibitor or an activator; (b) bringing the ligand and the enzyme in contact so as to form a complex with the ligand bound to the enzyme; and (c) carrying out an enzymatic assay of the complex wherein the course of the detectable enzymatic reaction is compared in the presence and absence of conditions modifying the properties of the linker in the bivalent ligand. In some instances the linker includes at least two residues, selected from the group of tyrosine; serine; threonine; histidine; phosphotyrosine; phosphoserine; phoshothreonine; and, phosphohistidine.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Depicts an embodiment of a biomolecular tweezer structure (A) in which a ligand is designed in a bivalent fashion, containing two binding moieties (“heads”), and linked by a structurally polymeric linker. (B) Depicts a proposed thermodynamic principle of linker-mediated control of bivalent ligands.

FIG. 2. Inhibition of fibrinogen clotting assays for embodiments of thrombin inhibitors of the general formula Bbs-R-(D-Pip)-linker-GDFEEIPEEYLQ. See further descriptions below:

FIG. 2 a. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-(GS)₂-GDFEEIPEEYLQ.

FIG. 2 b. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-(GS)₄-GDFEEIPEEYLQ.

FIG. 2 c. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-(GS)₆-GDFEEIPEEYLQ.

FIG. 2 d. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-(GS)_g-GDFEEIPEEYLQ.

FIG. 2 e. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-(GS)₁₀-GDFEEIPEEYLQ.

FIG. 2 f. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-(GS)₁₂-GDFEEIPEEYLQ.

FIG. 2 g. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-(GS)₁₄-GDFEEIPEEYLQ.

FIG. 2 h. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-Gly-Cys . . . Cys-(Gly-Ser)₈-Gly-DFEEIPEEYLQ.

FIG. 2 i. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-GTLDLNTPVDKTSN-GDFEEIPEEYLQ.

FIG. 2 j. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-GSGSGSGSGKGSGSGSGSGS-GDFEEIPEEYLQ.

FIG. 2 k. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-GSVVPRPQLHND-GDFEEIPEEYLQ.

FIG. 2 l. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-GSHAPRPQIHND-GDFEEIPEEYLQ.

FIG. 2 m. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-GHHLGGAKQAGDV-GDFEEIPEEYLQ.

FIG. 2 n. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-GYMESRADR-GDFEEIPEEYLQ.

FIG. 2 o. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-R-(D-Pip)-GQSHNR-GDFEEIPEEYLQ.

FIG. 3. Inhibition of fibrinogen clotting assays for embodiments of thrombin inhibitors of the general formula Bbs-R-(D-Pip)-G-(SPH(B)EKVSG)n-DFEEIPEEYLQ. See further descriptions below:

FIG. 3 a. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-Tyr-Glu-Lys-Val-Ser-Gly)-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln.

FIG. 3 b. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-Tyr(P)-Glu-Lys-Val-Ser-Gly)-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln.

FIG. 3 c. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-Tyr-Glu-Lys-Val-Ser-Gly)₂-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln.

FIG. 3 d. Inhibition of fibrinogen clotting by the thrombin inhibitor Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-Tyr(P)-Glu-Lys-Val-Ser-Gly)₂-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln.

FIG. 4. Inhibition of fibrinogen clotting assays for thrombin inhibitors of the general formula Bbs-R-(D-Pip)-G-(SPH(B)EKVSG)n-DFEEIPEEYLQ in the presence and absence of an SH2 domain from the Grb4 adaptor protein. See further descriptions below:

FIG. 4 a. Inhibition of fibrinogen clotting by the thrombin inhibitors Bbs-R-(D-Pip)-G-(SPH-B-EKVSG)₂-DFEEIPEEYLQ in the presence and absence of an SH2 domain from the Grb4 adaptor protein.

FIG. 4 b. Inhibition of fibrinogen clotting by the thrombin inhibitors Bbs-R-(D-Pip)-G-(SPH-B-EKVSG)-DFEEIPEEYLQ in the presence and absence of an SH2 domain from the Grb4 adaptor protein.

FIG. 5. Inhibition of fibrinogen clotting assays for thrombin inhibitor of the formula Bbs-R-(D-Pip)-GEQKLISEEDLG-DFEEIPEEYLQ in the presence and absence of the anti-c-myc antibody 9E10 (Sigma).

FIG. 6. Effect of calcium on the NMR spectra of calcium-binding linkers. See further descriptions below:

FIG. 6 a. Changes in the proton NMR spectra of Ac-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Glu-Phe-Glu-NH₂ upon the addition of CaCl₂.

FIG. 6 b. Changes in the proton NMR spectra of Ac-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Glu-Phe-Glu-NH₂ upon the addition of CaCl₂.

FIG. 6 c. Changes in the proton NMR spectra of Ac-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-NH₂ upon the addition of CaCl₂.

FIG. 6 d. Changes in the proton NMR spectra of Ac-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-NH₂ upon the addition of CaCl₂.

FIG. 6 e. Changes in the proton NMR spectra of Bbs-Arg-(D-Pip)-Gly-Cys . . . Cys-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln upon the addition of CaCl₂.

FIG. 6 f. Changes in the proton NMR spectra of Bbs-Arg-(D-Pip)-Gly-Cys . . . Cys-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln upon the addition of CaCl₂.

FIG. 7. Effect of calcium on the inhibition of the amidolydic activity of thrombin by Bbs-Arg-(D-Pip)-Gly-Cys . . . Cys-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln.

FIG. 8. Depicts the inhibition of fibrinogen clotting assays by mini-hirudin 1 and mini-hirudin 2. See further descriptions below:

FIG. 8 a. Inhibition of fibrinogen clotting by the thrombin inhibitor mini-hirudin 1.

FIG. 8 b. Inhibition of fibrinogen clotting by the thrombin inhibitor mini-hirudin 2.

FIG. 8 c. Inhibition of fibrinogen clotting by the thrombin inhibitor mini-hirudin 3.

FIG. 9. Amino acid sequences of the CaM-DTI and CaM-DTI2 protein(s).

FIG. 10. (A) Inhibition of the amidolydic activity of thrombin by CaM-DTI in the absence of Ca²⁺ (circle) and in the presence of 5 mM Ca²⁺ (square). (B) Inhibition of the amidolytic activity of thrombin by CaM-DTI2.

FIG. 11. Depicts a summary of the CRIB-containing peptide fragments and their hybrids.

FIG. 12. Depicts a bivalency model for two-site binding between extended CRIB peptides and Cdc42.

FIG. 13. Depicts fluorescence titration of sNBD-labeled and GMPPCP-loaded CaCdc42 (R150K) with different CRIB peptides.

FIG. 14. FIGS. 14A and 14B depict fluorescence titration assays of a SLAM-binding SH12 with an extended CRIB peptide containing the SLAM sequence as linker.

FIGS. 14C, 14D and 14E depict inhibition of fibrinogen clotting assays for a bivalent thrombin inhibitor containing the SLAM peptide sequence as linker.

FIG. 15. Depicts an embodiment of the preparation of conjugated stable complexes between Cdc42 and some extended CRIB peptides.

FIG. 15 b. Proton-15N NMR HSQC spectrum of the conjugated eCla4-CaCdc42 complex

FIG. 15 c. Proton-15N NMR HSQC spectrum of the conjugated eCst20-CaCdc42 complex

FIG. 15 d. Local dissociation of a bivalent ligand conjugated to the binding protein by a monovalent (L) molecule

FIG. 16. Depicts a utility of a bivalent polypeptide with a controllable polymeric linker in the fabrication of biomolecular devices remotely activatable by radio frequency magnetic fields (RFMF).

FIG. 16 b. Activation of a bivalent ligand by localized heating of the conjugated binding protein

FIG. 16 c. Activation of a bivalent ligand by localized heating of the linker moiety

FIG. 17. Is a schematic depiction of a utility of a bivalent polypeptide with a controllable polymeric linker in the dissection of cell-signaling pathways.

FIG. 18. Depicts photographic data relating to the arrest of arterial bleeding facilitated by fibrin glue application.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

There is disclosed herein an approach combining independent binding moieties in a single molecular structure, which couples binding affinity to an on/off or modulatable switch. There is provided a molecule which contains two or more binding moieties (or “heads”) (FIG. 1) joined by a linker. Looking at the embodiment of FIG. 1, each binding moiety in isolation provides only moderate to weak binding affinity (typically up to hundreds of millimolar in dissociation constants) to its specific binding site on a biomolecular target as compared to binding affinity in a bivalent or multivalent complex. When linked together a resulting bivalent ligand binds to its target with a significantly increased affinity (in some instances at least about twice the affinity, in some instances at least about three times, in some instances at least about five times, in some instances at least about ten times.). A change in flexibility of the linker caused by its non-covalent binding to a linker-specific molecule, covalent modification of the linker, or ambient environmental change leads to a decrease or complete disruption of the molecule's ability to bind the target in a bivalent or multivalent mode (FIG. 1). Vise versa, removal of constraints imposed on the linker can restore the high-affinity binding of the freed bivalent ligand. From a thermodynamic point of view, binding of a linker-specific well-structured protein (labelled by “N”) confers on the polymeric linker a well-defined conformation enabling for the interaction, which substantially prevents the ligand from acting in a bivalent fashion (FIG. 1B). Each binding moiety in isolation preferably has only low-affinity and transient interactions with an intrinsic dissociation constant up to the high millimolar range for its specific binding site on a target biomacromolecule. When linked together, the resulting bivalent or multivalent molecule makes a substantially stable complex with the target, achieving enhancement of preferably a minimum of two (2) fold in overall binding affinity as compared to the highest affinity of the constituent monovalent ligands. In the design disclosed herein, a polymeric linker is preferably used, such that on one hand, it allows both binding heads to settle freely in their binding sites on a macromolecular target, thereby improving the stability of the complex upon simultaneous occupation of the two individual binding sites. The linker can also be optimized to be selectively responsive to each or a combination of external signals. Since the specifics of the molecular structure of the polymeric linker would not be crucial for the binding association between the bivalent ligand and the target, the linkers and the pairs of binding “heads” are in principle interchangeable, allowing for a number of practical applications. It would be apparent to one skilled in the art, in light of the disclosure herein, how to select a suitable linker and binding heads for a specific purpose.

Feasibility and generality of this approach are assured by the abundance of pharmaceutically important proteins with multiple or forming large binding surface areas, e.g. thrombin and Cdc42. In addition, many of these proteins bind unfolded polypeptides, the latter becoming structured only when in complex with target proteins. These target proteins in particular are suitable for binding bivalent/multivalent ligands or serve as switching or modulating devices through binding to the polymeric linkers in tweezer-like bivalent or multivalent ligands.

As used herein the term “polymeric linker” includes an oligomeric or a polymeric linker without a well-defined three-dimensional structure in the free state of a ligand. Such linkers are capable of connecting a variety of binding moieties and have sufficient length and flexibility to allow simultaneous binding of the individual moieties, enabling a higher binding affinity to the desired molecular target than the affinity of each moiety taken alone. As used herein, the term “controllable polymeric linker” refers to a polymeric linker which allows external control of its flexibility or conformation. The loss or decrease of flexibility or change in conformation of the linker preferably impedes simultaneous binding of the binding moieties, thus producing a reversing effect on the enhanced affinity. Accordingly, the linker will generally be chosen and optimized for the affinity-reversing external signal instead of being optimized to achieve the highest affinity of binding of the ligand to its target.

In an embodiment of the invention the controllable linker is a flexible peptide or peptide bound to another material. The linker will sometimes preferably also be a ligand to a well-structured macromolecular species, or an antidote. For example, many signaling proteins, or their subdomains are known to bind flexible peptides (Pawson and Linding, 2005, 1808-1814; Pawson and Nash, 2003, 445-452; Puntervoll and others, 2003, 3625-3630) conferring upon the latter a structure required for antidote effects. Once bound, such structured linkers will generally produce spatial orientation of binding moieties that will preclude simultaneous binding of the latter to the original target. Occasionally, the linkers may exhibit some molecular interactions with the targets. In some other cases, linker-bound antidotes may produce steric hindrance of their own with the targets in conflicts with a potential bivalent mode of ligand binding. In some cases, an antidote may bind to both the polymeric linker and to a binding moiety. These influences can make additional contributions to reversing the bivalent binding upon antidote complexation. Regardless, in all these cases the linker can still be optimized according to its interaction with the antidote to achieve the desired affinity-reversing effect.

Approaches taken in the Specific Examples

Tolerance of the bivalent mode of inhibition to the properties of the linking sequences is shown in the examples by a series of inhibitors of thrombin containing an active site binding moiety Bbs-Arg-(D-Pip)-Gly [H1, Bbs=4-tert-butyl-benzenesulfonyl, D-Pip=D-pipecolic acid, K_I in low μM range (Slon-Usakiewicz and others, 2000, 2384-2391)] and an exosite 1 binding moiety Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 1) derived from the C-terminal tail of hirudin (H2, K_I in low μM range). The H1 and H2 heads are linked by a variety of flexible sequences producing bivalent thrombin inhibitors with a general formula of Bbs-Arg-(D-Pip)-linker-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 2), where the linker is an amino acid sequence. With the wide range of linker lengths IC₅₀ values of the bivalent inhibitors in fibrinogen clotting assays catalyzed by thrombin remained between 0.3 and 3 nM (Table 1 and FIG. 2), which are sufficient for peptide-based antithrombotic agents, and much lower than the K₁ values of the constituent binding moieties. In these specific examples, the C-terminal portion of the bivalent peptides consisted of only natural amino acids and included the polymeric linker plus the H2 moiety [-linker-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln] (SEQ. ID. NO. 3), which can be produced using recombinant methods. Linking of the H1 moeity, containing unnatural amino acids, with the rest of the peptide was performed using standard disulfide coupling techniques. For example, peptides with amino acid sequences of Bbs-Arg-(D-Pip)-Gly-Cys (SEQ. ID. NO. 4) and Cys-(Gly-Ser)₈-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 5) were synthesized and purified. A product of disulfide-bonded linkage between peptides Bbs-Arg-(D-Pip)-Gly-Cys (SEQ. ID. NO. 6) and Cys-(Gly-Ser)₈-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 7) was tested for IC₅₀ in the fibrinogen clotting assay. It was established that the two-chain peptide was potent and therefore bivalent with an IC₅₀ of 1.1±0.2 nM (FIG. 2). A variety of amino acid sequences with high complexity, originating from naturally-occurring proteins, or binding to naturally-occurring macromolecules, was introduced between the two binding heads producing potent inhibitors. It is noted that the use of only natural amino acids is not essential and non-natural amino acids and chemically modified amino acids (natural or non-natural) are also specifically contemplated for use in the design of controllable bivalent peptides.

Looking at the results of FIG. 2, the assay employs bovine plasma fibrinogen dissolved at 0.1% in 50 mM Tris-Cl, 100 mM NaCl, 0.1% PEG-8000 at pH 7.6. Curves represent OD₄₂₀ time course after the addition of 0.6 nM thrombin in the presence of (♦) 0 nM; (◯) 0.5 nM; (□) 1 nM; (Δ) 1.5 nM; (⋄) 2.5 nM; () 3.75 nM; (▪) 6.25 nM; and (▴) 12.5 μM of the inhibitor with linker (GS)_n and n=2 (SEQ. ID. NO. 50) (a); n=4 (SEQ. ID. NO. 51) (b); n=6 (SEQ. ID. NO. 52) (c); n=8 (SEQ. ID. NO. 53) (d); n=10 (SEQ. ID. NO. 54) (e); and in the presence of (♦) 0 nM; (◯) 1 nM; (□) 2 nM; (Δ) 4 nM; (⋄) 6 nM; () 10 nM; (▪) 15 nM; and (▴) 25 nM of the inhibitor with linker (GS)_n and n=12 (SEQ. ID. NO. 55) (f); n=14 (SEQ. ID. NO. 56) (g), at 37° C. The onset clotting time was determined as an intersection of the baseline and the extrapolated linear portion of the OD change curve. Extracted IC₅₀ values are shown in Table 1. Curves (h) represent OD₄₂₀ time course in the presence of (▪) 0 nM; (◯) 1 nM; (□) 3 nM; (Δ) 5 nM; (⋄) 7 nM; and () 9 nM of a product of disulfide-bonded linkage between peptides Bbs-Arg-(D-Pip)-Gly-Cys and Cys-(Gly-Ser)₈-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 83), at 37° C. Curves (i) represent OD₄₂₀ time course in the presence of (A) 0 nM; (◯) 1 nM; (□) 2 nM; (Δ) 4 nM; (⋄) 6 nM; and () 15 nM of the inhibitor with linker GTLDLNTPVDKTSN (SEQ. ID. NO. 103), at 37° C. Curves (o) represent OD₄₂₀ time course in the presence of (◯) 0 nM; (□) 2 nM; (Δ) 4 nM; (⋄) 6 nM; () 8 nM; (▪) 10 nM; (▴) 12 nM; and (♦) 15 nM; of the inhibitor with linker GSGSGSGSGKGSGSGSGSGS (SEQ. ID. NO. 58) at 25° C. Curves (k) represent OD₄₂₀ time course in the presence of (◯) 0 nM; (□) 0.5 nM; (Δ) 1 nM; (⋄) 2 nM; () 3 nM; (▪) 4 nM; (▴) 5 nM; and (♦) 6 nM; of the inhibitor with linker GSVVPRPQLHND (SEQ. ID. NO. 105) at 37° C. Curves (l) represent OD₄₂₀ time course in the presence of (◯) 0 nM; (□) 0.25 nM; (Δ) 0.5 nM; (⋄) 1 nM; () 1.5 nM; (▪) 2 nM; and (▴) 2.5 nM; of the inhibitor with linker GSHAPRPQIHND (SEQ. ID. NO. 104) at 37° C. Curves (m) represent OD₄₂₀ time course in the presence of (◯) 0 nM; (□) 2 nM; (Δ) 4 nM; (⋄) 6 nM; () 8 nM; (▴) 10 nM; and (A) 12 nM; of the inhibitor with linker GHHLGGAKQAGDV (SEQ. ID. NO. 106) at 37° C. Curves (n) represent OD₄₂₀ time course in the presence of (◯) 0 nM; (□) 1 nM; (Δ) 2 nM; (⋄) 3 nM; () 4 nM; (▪) 5 nM; (▴) 6 nM; and (♦) 7 nM; of the inhibitor with linker GYMESRADR (SEQ. ID. NO. 107) at 37° C. Curves (o) represent OD₄₂₀ time course in the presence of (◯) 0 nM; (□) 4 nM; and (Δ) 8 nM; of the inhibitor with linker GQSHNR (SEQ. ID. NO. 108) at 37° C.

For some peptide-based linkers, modifications of amino acid side chains (such as tyrosine, serine or threonine phosphorylation by kinases, or dephosphorylation by phosphatases) will turn these peptides into binding ligands for signaling proteins and signaling protein subdomains or interrupt their specific interactions. The peptide sequence Cys-Pro-His-Tyr-Glu-Lys-Val-Ser-Gly (SEQ. ID. NO. 8) derived from the ephrinB cytoplasmic tail (ephrinB2_301-309) was used to link the H1 and H2 heads. The peptide is flexible and in its tyrosine-phosphorylated state binds an SH2 domain from the Grb4 adaptor protein with an affinity of 0.2 μM (Su, Xu, and Ni, 2004b, 1725-1736). Four peptides of a general formula Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-B-Glu-Lys-Val-Ser-Gly)n-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 9) were produced, wherein B was either tyrosine (Tyr) or O-phosphotyrosine (Tyr(P)), and n was 1 or 2. IC₅₀ of the inhibitors in the fibrinogen clotting assay were comparable and in the vicinity of 0.5-1 nM, except for the peptide with two phosphotyrosines which had an IC₅₀ of 18-20 nM (Table 1, FIG. 3).

Looking at the results of FIG. 3, the curves represent OD₄₂₀ time course after the addition of 0.6 nM thrombin in the presence of (♦) 0 nM; (◯) 1 nM; (□) 2 nM; (Δ) 4 nM; (⋄) 6 nM; () 10 nM; (▪) 15 nM; and (▴) 25 nM of inhibitor for n=1, B=Y (a); n=1, B=Y(P) (b); n=2, B=Y (c); n=2, B=Y(P) (d); at 25° C. Other experimental conditions were as used for the assays described in FIG. 2. Extracted IC₅₀ values are shown in Table 1.

To reverse the inhibitory potency of the peptides they were brought in contact with the SH2 domain in solution. Presence of the SH2 domain reversed the inhibitory potency of the Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-Tyr(P)-Glu-Lys-Val-Ser-Gly)n-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln peptide ((SEQ. ID. NO. 10), corresponding to (SEQ. ID. NO. 9) when B is Tyr (P)), but not that of Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-Tyr-Glu-Lys-Val-Ser-Gly)n-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln peptide ((SEQ. ID. NO. 11), corresponding to (SEQ. ID. NO. 9) when B is Tyr) (FIG. 4). The change in thrombin inhibitory activity upon binding of SH2 makes it useful in an assay for protein-to-peptide binding, which in some embodiments could be implemented in a high-throughput manner.

Looking at the results of FIG. 4, peptide inhibitors were designated in Table 1 as P3161 (n=2, B=Y); P3162 (n=2, B=Y(P)); P3169 (n=1, B=Y); and P3170 (n=1, B=Y(P)). The curves represent OD₄₂₀ time course after the addition of 0.6 nM thrombin in the presence of (a) (◯) 2 nM P3161; (□) 2 nM P3161, 3 μM SH2; (Δ) 50 nM P3162; (⋄) 50 nM P3162, 3 μM SH2; () no inhibitor, no SH2; (Δ) no inhibitor, 3 μM SH2; and (b) (◯) 1 nM P3169; (□) 1 nM P3169, 3 μM SH2; (Δ) 4 nM P3170; (⋄) 4 nM P3170, 3 μM SH2; () no inhibitor, no SH2; (▪) no inhibitor, 3 μM SH2. Other experimental conditions were as used for assays described in FIG. 3.

In another case a peptide linker Glu-Gln-Lys-Leu-Ile-Ser-Glu-Glu-Asp-Leu (also called the c-myc sequence, SEQ. ID NO. 12) known to bind an anti-c-myc antibody 9E10 with an affinity of approximately 0.5 μM (Hilpert at al. 2001, 803-806) was built into the bivalent thrombin inhibitor Bbs-Arg-(D-Pip)-Gly-Glu-Gln-Lys-Leu-Ile-Ser-Glu-Glu-Asp-Leu-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 13). The antibody 9E10 reversed the inhibitory potency of the inhibitor (FIG. 5).

Looking at the results of FIG. 5, the curves represent OD₄₂₀ time course in the presence (□,▪) or absence (◯,) of 150 nM of the inhibitor. Addition of ˜1.2 μM anti-c-myc antibody 9E10 (Sigma) only slightly slowed clotting of free thrombin (◯), but reversed the inhibitory effect of the inhibitor (□). Other experimental conditions were as used for assays described in FIG. 3.

In other cases, disulfide bonds can be formed or opened to rigidify or make the linkers more flexible. Limited specific proteolysis may turn a well-folded disulfide-bonded peptide into a polymeric linker, allowing for bivalent binding. In other instances amino acid side chain modifications producing two or more charged groups (as in the case of phosphorylation of an amino acid side chain) in the linker will generate electrostatic repulsion or attraction affecting the linker's flexibility and the end-to-end statistically average distance.

Incorporation of two phosphotyrosines in the polymeric linker of the peptide with the sequence Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-Tyr(P)-Glu-Lys-Val-Ser-Gly)₂-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln ((SEQ. ID. NO. 14), corresponding to (SEQ. ID. NO. 10) when n=2) produced a significant drop in inhibition potency as compared to the dephosphorylated analog (FIG. 3). The potency of the bivalent inhibitor generally depends on the phosphorylation state of the linker. Thus, kinase or phosphatase activities can be converted into serine protease (thrombin) activity in a coupled enzymatic assay in light of the disclosure herein. In such an assay, the linker preferably contains tyrosine, or other residues that can be phosphorylated or dephosphorylated after phosphorylation. Therefore, reversible and irreversible posttranslational modifications of the linker can be used as another mechanism of controlling ligand (inhibitor) affinity.

Some flexible peptides will bind metal ions specifically (FIG. 6). Organization of metal ion coordination sphere will change the flexibility of the peptides achieving the required affinity control. For example, a peptide Bbs-Arg-(D-Pip)-Gly-Cys . . . Cys-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 91) was prepared through coupling of two peptides, Bbs-Arg-(D-Pip)-Gly-Cys (SEQ. ID. NO. 15) and Cys-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 16) by means of a disulfide bond. The linker moiety of the bivalent peptide contains the sequence segment Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu (SEQ. ID. NO. 17) that binds calcium(II) with an affinity in the millimolar range. Calcium(II) addition altered inhibition of chromogenic substrate proteolysis by human α-thrombin observed in the presence of the peptide (FIG. 7).

Looking at the results in FIG. 6, panels a, b, c, d show changes in the proton NMR spectra of Ac-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Glu-Phe-Glu-NH₂ (SEQ. ID. NO. 109) (P3230, panels a, b) and Ac-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-NH₂ (SEQ. ID. NO. 110) (P3231, panels c, d) upon the addition to the initial ˜450 μL of the corresponding peptide in 20 mM sodium acetate-d₃ buffer, pH 5.5, containing 10% D₂O, of 1 μL (final CaCl₂ concentration ˜0.22 mM), additional 2 μL (final CaCl₂ concentration ˜0.66 mM), additional 10 μL (final CaCl₂ concentration ˜2.8 mM) of 100 mM CaCl₂, and additional 10 μL (final CaCl₂ concentration ˜23.9 mM) of 1 M CaCl₂. Panels e and f show changes in the proton NMR spectrum of a disulfide-linked peptide Bbs-Arg-(D-Pip)-Gly-Cys . . . Cys-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. No. 16) upon the addition to the initial volume of ˜450 μL of 1 μL (final CaCl₂ concentration ˜0.22 mM), additional 2 μL (final CaCl₂ concentration ˜0.66 mM) of 100 mM CaCl₂, and additional 10 μL (final CaCl₂ concentration ˜22.2 mM) of 1 M CaCl₂.

Looking at the results in FIG. 7, the effect was tested in the presence of two bivalent thrombin inhibitors, the calcium-binding Bbs-Arg-(D-Pip)-Gly-Cys . . . Cys-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. No. 16) (CaR), and control peptide Bbs-R-(D-Pip)-GSGSGSGS-GDFEEIPEEYLQ (SEQ. S10) (P3150). Curves represent OD₄₀₅ time course at 25° C. after the addition of 0.6 nM thrombin to 50 mM S-3266 (Chromogenics) in the clotting buffer, and in the presence of (◯) no inhibitors; (□) 150 nM CaR; (Δ) 150 nM CaR, 50 mM CaCl₂; (⋄) 150 nM CaR, 100 mM CaCl₂; () 2 nM P3150; (▪) 2 nM P3150, 50 mM CaCl₂; and (▴) 2 nM P3150, 100 mM CaCl₂.

Polypeptides containing only natural amino acids can also be used as starting points for the generation of a bivalent ligand with a controllable linker. In order to design a ligand with a controllable linker, at least two binding heads of adequate affinities to two distinct sites on a target should preferably be known. The binding heads can be discovered through ab initio screening or minimization of structurally or functionally characterized polypeptide interactions with its target. Outlining minimal regions of polypeptides capable of binding to their macromolecular targets (“hot spots”) may produce a set of at least two peptide sequences, interacting with distinct sites on the target surface. Determination of minimal binding regions (“hot spots”) can be carried out using spectroscopic (e.g. NMR spectroscopy) or recombinant (e.g. alanine scan) methods. Through minimization of hirudin two peptides were designed having sequences of Val-Arg-Phe-Thr-Asp-Gly-Glu-Gly-Thr-Pro-Lys-Pro-Gln-Ser-His-Asn-Asp-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (mini-hirudin 1) (SEQ. ID. NO. 22) and Ile-Arg-Phe-Thr-Asp-Gly-Glu-Gly-Thr-Pro-Asn-Pro-Glu-Ser-His-Asn-Asn-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (mini-hirudin 2) (SEQ. ID. NO. 23) incorporating N-terminal and C-terminal moieties believed to interact with the active site and exosite I of thrombin, respectively. These peptides displayed high potencies for thrombin inhibition with IC₅₀ of 33±3 μM (mini-hirudin 1) and 14±1 nM (mini-hirudin 2), indicating a bivalent mode of binding (FIG. 8). The modular character of interaction was further confirmed when a candidacidal peptide known to bind laminarin (Polonelli, L.; and others, 2003, 6205-6212), in other words, the peptide of the sequence -Ala-Lys-Val-Thr-Met-Thr-Cys-Ser-Ala-Ser-(SEQ. ID. NO. 24), was inserted as a linker into mini-hirudin 2 to give mini-hirudin 3 with a sequence of Ile-Arg-Phe-Thr-Asp-Gly-Ala-Lys-Val-Thr-Met-Thr-Cys-Ser-Ala-Ser-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 25). The peptide was shown to preserve high affinity of binding to thrombin, with an IC₅₀ of 10±1 nM (FIG. 8).

Looking at the results in FIG. 8, curves (a) represent OD₄₂₀ time course in the presence of (◯) 0 μM; (□) 10 nM; (Δ) 30 nM; (⋄) 50 nM; () 70 nM; and (▪) 100 nM of mini-hirudin 1 at 37° C. Curves (b) represent OD₄₂₀ time course in the presence of (◯) 0 nM; (□) 4 nM; (Δ) 8 nM; (⋄) 12 nM; () 20 nM; (▪) 30 nM; (▴) 50 nM; and (♦) 100 nM of mini-hirudin 2 at 37° C. Curves (c) represent OD₄₂₀ time course in the presence of (◯) 0 nM; (□) 2.15 nM; (Δ) 4.3 nM; (⋄) 8.6 nM; () 17.2 nM; and (▪) 43 nM of mini-hirudin3 at 37° C. Other experimental conditions are as used for assays shown in FIG. 2.

The peptide with a sequence of Trp-Asp-Pro-Arg-Pro-Gln-Arg-His-Asn-Asp-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 18) is a bivalent molecule with a K_I of 17 nM for thrombin inhibition. The peptide can be decomposed into two moieties, an active site binding moiety, Trp-Asp-Pro-Arg-Pro-Gln-Arg-His (SEQ. ID. NO. 19), and an exosite-1 binding moiety, Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 20). A thrombin inhibitor was prepared with the sequence of Trp-Asp-Pro-Arg-Pro-Gln-Arg-His-(CamCKK)-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 21), designated as CaM-DTI, where CamCKK is a protein with calcium-binding properties (see for example Truong, 2001, 1069-1073). The sequence of the CaM-DTI molecule is shown in FIG. 9. As depicted in FIG. 9, the sequence includes at the N-terminus a binding moiety (bold) to the thrombin active site, a binding moiety (italic bold) to the exosite-1 of thrombin at the C-terminus, and a calcium-responsive protein linker. CaM-DTI was prepared with a recombinant DNA approach. Potency of thrombin inhibition by CaM-DTI was determined by an amidolytic assay. Upon the addition of 5 mM Ca²⁺, an increase in apparent K_I from 480 nM (no calcium) to 2200 nM (Ca²⁺) was observed (FIG. 10).

In another case, the small GTPase Cdc42 binds with high-affinities to the ˜40-residue extended CRIB domains of the Candida Cla4 and Step 20 kinases (K_D=20˜50 nM) (the latter also known as Cst20). When subjected to NMR relaxation dispersion analysis (Tolkatchev, Xu, and Ni, 2003b, 12432-12442), these complexes exhibit no responses, as expected for a tight binding complex. The full-length CRIB domains were decomposed into two peptide fragments (FIG. 11): (i) mCla4 (mCst20) including the consensus CRIB motif, and (ii) cCla4 (cCst20) which comprises residues directly to the C-terminus of the minimal CRIB sequence. Looking at FIG. 11, the extended CRIB fragments (eCRIBs) comprise the CRIB motif, plus ˜20 residues to the C-terminus and exhibit high-affinity binding to CaCdc42. These sequences were dissected into two fragments: the minimal CRIB (mCRIB), mCla4 and mCst20, and the C-terminal CRIB (cCRIB), cCla4 and cCst20. In order to construct a bivalent peptide ligand for Candida Cdc42 (CaCdc42) with a suitable linker, the binding affinities of these component peptides derived from the CRIB domains of Candida Cla4 and Step 20 were determined. For this purpose, a CaCdc42 expression vector encoding the R150K mutation was constructed and the sequence of the R150K CaCdc42 mutant (Table 4) was verified by DNA sequencing.

FIG. 12 depicts a bivalency model for two-site binding between extended CRIB peptides and Cdc42. This dissectional strategy is used to analyse the interaction of the CRIB fragments with CaCdc42 (A). The m and c represent the mCRIB and the cCRIB fragments, respectively, as defined in FIG. 11. Dissociation constants and corresponding Gibbs free energies are indicated according to the reaction coordinate. (B) depicts the bivalent binding mode of covalently-linked CRIB sub-fragments with Cdc42. The mCRIB and cCRIB sequences are assumed to have the same “intrinsic” binding affinities after linkage. An additional factor C_eff is introduced together with the cooperativity factors, C₁₂ and c₂₁ to define the partial dissociation constants of the individual dissociation steps. The thermodynamic dissociation constant representing complete dissociation of the extended “bivalent” CRIB peptide can be deduced following microscopic equilibria from either one of the two dissociation pathways.

FIG. 13 shows binding isotherms obtained following the CRIB-induced changes in the sNBD fluorescence of the CaCdc42 (R150K) protein. All the titration curves could be best fitted to a simple bimolecular binding model. The average apparent K_d values for different CRIB peptides are summarized in Table 2. As expected, the extended CRIB (eCRIB) fragments exhibited the strongest affinities to CaCdc42 in the low nanomolar range. The mCRIB fragments containing the consensus CRIB sequence, ISXPXXFXHXXHVGXD (SEQ. ID. NO. 26) (Burbelo, P. D., Drechsel, D., and Hall, A., 1995, 29071-29074), also had moderately strong binding affinities in micromolar concentrations, but clearly, as seen previously for the human PAK homologues (Rudolph, M. G., Bayer, P., Abo, A., Kuhlmann, J., Vetter, I. R., and Wittinghofer, A., 1998, 18067-18076; Thompson, G., Owen, D., Chalk, P. A., and Lowe, P. N., 1998, 7885-7891), require extra residues to retain stronger binding to Cdc42. The cCRIB peptides exhibited much weaker affinities to the CaCdc42 protein. The K_d value of cCla4 for binding to CaCdc42 is in a high micromolar concentration (275 μM). An even weaker binding (K_d=1160 μM) was observed between cCst20 and CaCdc42 with the current fluorescence titration strategy.

Looking at the results of FIG. 13, one micromolar concentration of sNBD-labeled, and GMPPCP-loaded CaCdc42 (R150K) was titrated with the indicated amounts of CRIB fragments shown in FIG. 11. (A) eCla4 (open circle) and eCst20 (open triangle); (B) mCla4 (open circle) and mCst20 (open triangle), and (C) cCla4 (open circle), cCst20 (open triangle), cCla4 in the presence of 50 μM mCla4 (filled circle) and cCst20 in the presence of 50 μM mCst20 (filled triangle). Solid lines represent fits of the data to a bimolecular association model.

Fluorescence measurements were used to substantiate and quantify the effects of cross-titrations observed by NMR (Table 2). The affinity of the Cla4 peptide fragments for CaCdc42 was not significantly affected by the addition of the cognate peptide. In contrast, the affinities of the Cst20 peptide fragments preincubated with CaCdc42 exhibited a dramatic enhancement in binding for CaCdc42 by ˜5.5-fold, upon addition of the cognate Cst20 peptide (Table 2). Thus, upon addition of mCst20 to the cCst20/CaCdc42 complex, the affinity of cCst20 for CaCdc42 increased from a K_d of 1160 μM to 207 μM (Table 2 and FIG. 13c). Similarly, mCst20 affinity for CaCdc42 increased from 0.43 μM to 0.081 μM when cCst20 was added to a preincubated mCst20/CaCdc42 complex. These results strongly suggest that the eCst20 and eCla4 peptides exhibit different mechanisms for binding CaCdc42, in which long eCst20 peptide utilizes a cooperative mechanism for high-affinity interaction while eCla4 does not.

Modular nature of interactions of m- and c-CRIB fragments is emphasized by the binding affinities of hybrid peptides incorporating m- and c-CRIBs from different molecular species. Both mCla4-cCst20 and mCst20-P-cCla4 constructs (FIG. 11) displayed affinities of the same order of magnitude as the original eCRIB peptides (Table 2). Moreover, incorporation of -Ser-Gly-Ser-Gly-(SEQ. ID. NO. 27) and -Arg-Lys-Ser-Leu-Thr-Ile-Tyr-Ala-Gln-Val-Gln-Lys-(SEQ. ID. NO. 28), in other words the SLAM peptide sequence (Li et al and Pawson, Curr. Biol. 9, 1355-1362, 1999) as linkers into the eCla4 sequence preserved a bivalent mode of binding.

In addition to bivalent binding to CaCdc42, the eCla4-SLAM peptide (FIG. 11 and Table 2) also preserved the binding capacity of the SLAM linker peptide to the SH2 domain derived from the SAP protein (Table 4). FIG. 14A and FIG. 14B depict the competition binding of SAP-SH2 and CaCdc42 to the polypeptide eCla4-SLAM. FIG. 14A shows the effect of including SAP-SH2 at various concentrations on the binding affinity of eCla4-SLAM to CaCdc42 R150K. The concentration of CaCdc42 R150K is 1 μM. FIG. 14B shown that the apparent dissociation constant for the Cdc42-eCla4 complex is a function of the concentration of added SAP-SH2

The SLAM sequence, i.e. the peptide of SEQ.ID.NO.28 can also be used as a linker moiety with a bivalent thrombin molecule. FIGS. 14C, 14D and 14E depict inhibition of fibrinogen clotting assays by the thrombin inhibitor Bbs-Arg-dPip-Gly-Arg-Lys-Ser-Leu-Thr-Ile-Tyr-Ala-Gln-Val-Gln-Lys-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 102) in the presence and absence of an SH2 domain from the SAP protein (SAP-SH2). This thrombin inhibitor is designated as P3291. The curves represent OD₄₂₀ time course after the addition of 0.6 nM thrombin in the presence of (C) (◯) 0 nM P3291; (□) 10 nM P3291; (Δ) 15 nM P3291; (⋄) 20 nM P3291; () 30 nM P3291; (▪) 40 nM P3291; (▴) 50 nM P3291; (♦) 60 nM P3291; (D) (◯) 0 nM P3291, 0 μM SAP-SH2; (□) 0 nM P3291, 5 μM SAP-SH2; (Δ) 25 nM P3291, 0 μM SAP-SH2; (⋄) 25 nM P3291, 5 μM SAP-SH2; (E) (◯) 0 nM P3291, 0 μM SAP-SH2; (□) 0 nM P3291, 10 μM SAP-SH2; (Δ) 25 nM P3291, 0 μM SAP-SH2; (⋄) 25 nM P3291, 10 μM SAP-SH2. Other experimental conditions were as used in assays described in FIG. 3.

Generally, linkers are elongate oligomeric or polymeric molecules adapted to permit strong covalent attachment or strong electrostatic binding of at least two moieties, wherein the moieties spaced apart along said linker. Linkers are preferably “modulatable linkers”, in other words, linkers which undergo a change in flexibility and/or conformation in response to a defined environmental condition such as pH, temperature, proteolysis, chemical modification, magnetic field, local concentration of one or more molecules or complexes. Examples of temperature-sensitive linkers include polypeptides containing the elastin repeats (Urry, 1997, 11007-11028), specifically the (VPGVG)₁₉-VPGV (SEQ. ID. NO. 118) peptide which is producible by recombinant DNA methods (McPherson and others, 1992, 347-352). Other examples of peptide linkers responsive to protein binding including short linear peptide motifs known for cell compartment targeting, protein-protein interactions, and regulation by post-translation modifications (Puntervoll and others, 2003, 3625-3630; Diella and others, 2004, 79).

Introduction of a long oligomeric or polymeric linker between two binding heads may reduce the affinity beyond the point where the bivalent ligand is no longer switchable for a desired application. This is particularly true if one of the binding moieties is significantly weaker than the other, as is the case for the CaM-DTI and CaM-DTI2 proteins (FIG. 10) (see Table 2 for other examples). In addition, long oligomeric linkers are often more flexible, giving rise to significantly larger statistical distances spanning any given covalent spacing (Bright, Woolf and Hoh, 2001, 131-173). In this case the observed affinity is approximately equal to the monovalent affinity of the stronger binding moiety, in other words, the bivalent increase in affinity is lost. One can remedy this situation by optimizing the binding affinities of the individual heads through combinatorial library selection.

A strategy to improve the binding affinity of polypeptide ligands consisting of natural amino acids is to utilize phage display optimization. If one of the binding moieties is sufficiently strong, phage-displayed peptides need to be randomized only in the vicinity of the other binding moiety. The reappearing bivalency allows strong affinity of the ligand and the corresponding polypeptide sequences will be readily selected from a medium-sized phage library. Alternatively or additionally, NMR relaxation dispersion techniques can be used to identify an appropriate candidate from a fragment library for subsequent linkage to the other binding moiety. The advantage of this new NMR-based approach lies in its ability to provide both the molecular structure (identity) and ranking of the dissociation kinetics of hit fragments. Such an NMR-based screening can also be applied to molecules that are either natural polypeptides or other chemical entities available only through chemical synthesis.

In addition, if more than two distinct sites interacting with their specific ligands are known on a target surface, one can design an inhibitor containing more than two binding heads and link them with two or more controllable linkers, identical or different.

Production of polypeptides containing multiple binding moieties and controllable linkers can be achieved either through chemical peptide synthesis or using recombinant methods. Additional opportunities are provided by the possibilities to conjugate peptide fragments using thiol, primary amine or carboxyl chemistries. In light of the disclosure herein, one skilled in the art could readily produce such polypeptides. For example, thiol chemistry is particularly effective for coupling oligonucleotides to peptides (Lin and others, 1995, 11044-11048) in the fabrication of biomolecular devices containing oligonucleotides as linkers (FIG. 16C).

Molecular species and methods of the invention can be used in a number of screening methods. In some instances the recorded compound (“readout”) is preferably chromogenic or fluorogenic. For example, some commercially available substrates for thrombin are based on p-nitroaniline (chromogenic) or on 6-amino-1-naphthalenesulfonamide (fluorogenic). The presence of an inhibitor impedes development of color or fluorescence in an assay that can be readily performed in a 96-well plate and recorded by a plate-reader. If the inhibitor contains a linker sensitive to a certain type of specific peptide-protein molecular interaction, the presence of linker-binding protein can be identified in a 96-well plate format. Alternatively, the same 96-well plate format can be used for the identification of an enzymatic activity (e.g. performed by such enzymes as phosphatases or kinases) changing the ability of the linker to bind a known protein or altering flexibility of the linker. In this regard, binding or enzymatic activities are converted and recorded in the activities or changes in the activities of the target protein (e.g. thrombin). As such, it will be complementary to fluorescence-based methods (UK patent Application, GB 2375538) that have limitations in dynamic-range imposed by specific conformational changes (Truong and others, 2001, 1069-1073).

FIG. 15 depicts the concept of covalent conjugations between tweezer-like polypeptides and the binding proteins. FIG. 15A is a model for a conjugated complex of CaCdc42 and an eCRIB via a polymeric linker. FIG. 15B depicts resonance assignment of the ¹H-¹⁵N HSQC spectra for Candida Cla4-eCRIB in a conjugated complex with CaCdc42. The resonance peaks have the same pattern as those in the non-covalent complex. However, the conjugated complex is significantly more stable (>3 months) than the non-covalent one (<one week). FIG. 15C shows the ¹H-¹⁵N HSQC spectrum for Candida Cst20-eCRIB in a conjugated complex with CaCdc42. FIG. 15D shows the potential application of a stable conjugated complex for discovering stronger and specific binders. The dissociation of the tethered bivalent polypeptide can be detected by use of NMR relaxation and H/D exchange experiments using the assigned H-¹⁵N HSQC spectrum of the conjugated protein (see FIGS. 15B and 15C).

Certain polypeptides are known to undergo folding or unfolding transitions upon changes of pH, ionic strength or temperature. Inhibitors incorporating these flexible peptides as linkers will be affected in their potency by the corresponding environmental changes. In an embodiment of the invention, the controllable linker is a well-folded and structured biomolecule, whose rigid three-dimensional structure prevents the binding of the bivalent ligand in the high-affinity mode. Defined three-dimensional structure of the biomolecule can be denatured by a variety of environmental effects such as changes in pH, temperature, proteolysis, chemical modifications and localized electromagnetic irradiation. Such a denaturation will render the linker moiety flexible, thereby providing the linker moiety with suitable physicochemical properties for bivalent ligand binding to its target.

Bivalent polypeptides at the generic level are responsive to signals that modulate the physicochemical properties of the linker moiety (FIG. 1). When the linker is responsive to binding, e.g. of a protein or of an oligonucleotide, or other biomolecules, the active concentration of the linker binding molecule can generally be reduced through denaturation, e.g. by use of radio-wave (or radio-frequency magnetic field, RFMF) induced biomolecular heating (Hamad-Schifferli and others, 2002, 152-155). Such a reduction in concentration of the activity-reversing protein will be accompanied by the reactivation of the inhibited target protein, a phenomenon governed by thermodynamic principles (FIG. 1B).

FIG. 16 depicts three scenarios by which the bivalent polypeptides can be used to fabricate biomolecular devices sensitive to electromagnetic irradiation. FIG. 16A shows a generally inactive complex produced by the binding of the linker moiety of a bivalent peptide to a linker-specific protein. The linker-binding protein is in addition conjugated to a heat-transducing nanoparticle, which in the illustrated case is a gold nanoparticle as described previously (Hamad-Schifferli and others, 2002, 152-155). Upon electromagnetic (RF fields) irradiation, the linker-binding (antidote) protein will be denatured upon heating, leading to release and activation of the bivalent polypeptide. FIG. 16B depicts the construction of a covalent conjugate of the bivalent polypeptide with a heat-transducing antidote protein. The bivalent polypeptide is more efficiently inactivated in a covalent conjugate as a result of intramolecular effects. RF irradiation will lead to local release of the bivalent peptide, in a way suitable for target binding through bivalent interactions (FIG. 1). FIG. 16C depicts an extension of the fabrication procedure illustrated in FIG. 16B. In this scenario, the linker moiety itself confers the antidote effect, in that the linker can fold into a defined three-dimensional structure with geometry not suitable for bivalent binding of the attached monovalent ligands. Presence of RF fields will denature the structure of the linker moiety, thereby creating a polymeric linker conformation suitable for bivalency effects. In this regard, the CaM-DTI proteins (FIG. 9) can be attached to a gold nanoparticle or a magnetic nanoparticle (MNPs) and RF irradiation is expected to enhance thrombin inhibitory activity of a MNP-conjugated CaM-DTI protein.

In an embodiment of the invention, the linker moiety is an oligonucleotide, to which is attached covalently two weak-binding monovalent ligands. The oligonucleotide linker is in addition labeled by a gold or magnetic nanoparticle for inductive coupling to and activation by an external field. Specifically, Bbs-Arg-(dPip)-Gly-Cys (SEQ.ID.NO.15) is to be coupled using thiol chemistry to the 3′ or 5′ end of a single-stranded DNA (e.g. the DNA-I molecule or 5′-TAGCGATACTGCGTGGGTTGGGGCGGGTAGGGCCAGCAGTCTCGT-3′ of Lin et al and Jayasena (Lin and others, 1995, 11044-11048) or 5′-GCGCCCTAAACTGGTGGT*GGAATGCGTCATGAGGGCGC-3′ of Hamad-Schifferl et al and Jacobson (Hamad-Schifferli and others, 2002, 152-155). The other end of the DNA molecule will be attached covalently with a peptide containing the sequence Asp-Phe-Glu-Gly-Ile-Pro-Glu-Glu-Tyr-Gln. Denaturation of the single-stranded DNA hairpin should activate the bivalent functionality of the attached peptides for high-affinity thrombin inhibition in the presence of an RF magnetic field (FIG. 16C).

In some cases molecular species and methods of the invention can be used to specifically dissect, interrupt or initiate biological pathways. One can design a bivalent ligand with a trigger to release its target at a certain location and/or at a specific time. The ligand/target pair can be delivered together or separately using known methods of extra or intracellular delivery including protein expression from an oligonucleotide template. Alternatively, the target can occur naturally, outside or inside the cell, e.g. the GTPase of the Rho-family, Cdc42 (FIG. 15). The triggering molecular device can be a delivered molecule or a naturally occurring molecule. The triggering molecular device can be a molecular process (for example, catalytic phosphorylation, dephosphorylation, or specific proteolysis). The triggering molecular device can be localized and/or produced and initiated at a certain time point. For example, a bivalent CRIB-based ligand of Cdc42 can be delivered into the cell to arrest the action of membrane-anchored Cdc42 (FIG. 15). The inhibitory action of intracellularly-delivered and membrane-localized CRIB peptides can be reversed by the binding of the linker portion (i.e. the SLAM segment of eCla4-SLAM in FIG. 11 and Table 2) to an SH2 domain. The affinity of the SH2-linker interaction is relatively weak, with a thermodynamic dissociation constant in the micromolar range (˜1 μM, see FIGS. 14A and 14B). Therefore, the SH2 domain (i.e. the antidote) is to be conjugated to the surface a nanoparticle for affinity enhancement through multivalent presentation. Vice versa, the complexes of the CRIB peptides with the SH2 molecules conjugated to metal or magnetic nanoparticles (MNPs) can be disrupted by radio-wave induced heating of MNPs, as reported previously (Jordan and others, 1999, 413-419; Hamad-Schifferli and others, 2002, 152-155; also see FIG. 16).

FIG. 17 depicts schematically the use of a bivalent polypeptide with a controllable polymeric linker in the examination of cell-signaling pathways. In the embodiment of FIG. 17, a bivalent CRIB polypeptide is to be delivered into the cytoplasmic space of a cell, specifically for associations with the cytoplasmic face of the cell membrane. As such, the CRIB peptide (e.g. the eCla4 peptide containing the -Arg-Lys-Ser-Leu-Thr-Ile-Tyr-Ala-Gln-Val-Gln-Lys-sequence (SEQ. ID. NO. 28), or eCla4-SLAM (FIG. 11 and Table 2) will inhibit the membrane-anchored Cdc42 for its interactions with downstream effector proteins. This inhibitory action can be reversed by the delivery of an SH2 domain (i.e. the antidote or “A”) with specific binding to the linker portion. For affinity enhancement, the SH2 domain antidote can be conjugated to the surface of a nanoparticle for multivalent presentation. A metal or magnetic nanoparticle (MNPs) is used here since these nanoparticles can transduce radio-frequency waves into heat (for both metal and magnetic nanoparticles, see also FIG. 16) or can be used as contrast agents (magnetic nanoparticles) in magnetic resonance imaging (MRI) applications.

In light of the disclosures provided herein, it should be apparent to ones skilled in the art that Cdc42 inhibition can be achieved by any number of suitable polypeptides (see for example Pirone, Carter and Burbelo, Trends in Genetics 17, 370-373, 2001) containing sequences homologous to the extended CRIB sequences derived from Candida albicans Cla4 and Cst20 proteins (FIG. 11). In these applications, monovalent CRIB fragments will be identified following the same procedures as used for Candida proteins (FIGS. 11-13). Such peptide fragments will then be reassembled into bivalent polypeptides, containing as linkers either the SLAM sequence (SEQ.ID.NO.28) or other linear peptide motifs (Puntervoll and others, 2003, 3625-3630; Diella and others, 2004, 79) depending on the applications. Furthermore, all the bivalent peptides including eCla4-SLAM (FIG. 11 and Table 2) are preferably prepared in palmitoylated forms, which enable intracellular delivery and localization to the cytoplasmic face of the cell membrane (Covic et al, and Kuliopulos, Proc. Natl. Acad. Sci. 99, 643, 2002).

Molecular species and methods of the invention can also be used to design new molecules for pharmaceutical intervention. Medical intervention in case of an injury to an internal organ requires a strategy to seal the wound. Fibrin sealant is found to be effective and can be used safely on vital organs. It is thus widely used as a bioactive hemostat in cases of both superficial and internal injury. The formulation that is commercially available (e.g. Tisseel VH Fibrin Sealant, Baxter) consists of two components: thrombin and fibrinogen. When both components are reconstituted and mixed thrombin catalyses the conversion of fibrinogen to fibrin, which in turn forms a fibrin scaffold or sealant. One of the limitations of the present formulation is that once reconstituted, thrombin proteolytically degrades itself. In light of the disclosure herein there is provided a new formulation, wherein the proteolytic activity of thrombin is inhibited by a stimuli-responsive bivalent inhibitor e.g. Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-Tyr(P)-Glu-Lys-Val-Ser-Gly)n-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (P3170) (SEQ. ID. NO. 29) with a controllable polymeric linker binding to an SH2 domain (FIG. 4). In the new formulation of fibrin glue, thrombin and inhibitor can be premixed and will stay substantially inactive (and stable) for a reasonable period of time until exposed to SH2.

The middle auricular artery of eight rabbits was cut transversely with a scalpel. Two rabbits were left untreated to measure the bleeding time. The Tisseel fibrin glue (one fresh sample, one incubated overnight at 37° C.) was applied to the wound of two other rabbits. The fibrin glue containing inhibitor-stabilized thrombin component, “Thrombin 4”, was applied to another pair of rabbits immediately after activation with SH2. SH2-activated fibrin glue with the P3170 inhibitor was able to seal the wound at around ˜5 minutes (FIG. 18).

Looking at FIG. 18, the top panel shows arterial bleeding from a rabbit ear 5 minutes after the transversal cut was made. Left bottom panel shows an arrest of the bleeding 1′47″ after a commercial Tisseel preparation was applied to the fresh cut according to the manufacturer's procedure. Right bottom panel shows an arrest of bleeding 5 minutes after an inhibited and reactivated commercial Tisseel preparation was applied to the fresh cut according to the manufacturer's instructions. Thrombin inhibition was achieved by the addition of 8 nM of P3170 to the reconstituted “Thrombin 4” component of the Tisseel product. Thrombin activation was achieved by the inclusion of concentrated SH2 solution in the fibrinogen component of Tisseel to a final concentration of 12 μM.

In light of the disclosures provided herein, it will be apparent to one skilled in the art that other forms of fibrin sealants can be formulated. In particular, bivalent thrombin inhibitors with Ca⁺⁺-sensitive linkers can be used to inactivate (and stabilize) thrombin. The inactivated thrombin can in turn be reactivated upon contact with the bleeding wounds, wherein the fresh blood contains Ca⁺⁺ ions in millimolar concentrations. As well, the SH2-binding linker can be replaced by linker peptides with specific binding to other components of the blood, e.g. to integrin receptors on platelet surfaces (i.e. peptides P3234 and P3238 of Table 1, or SEQ. ID. NO. 88 and SEQ. ID. NO. 90), to fibrinogen itself (i.e. peptide P3236, Table 1 or SEQ. ID. NO. 89), to prothrombin (see the next section) and even to human serum albumin. One peptide sequence to use for the latter can be Leu-Ile-Glu-Asp-Ile-Cys-Leu-Pro-Arg-Trp-Gly-Cys-Leu-Trp-Glu-Asp (SEQ. ID. NO. 111), which is derived from panning a phage library against human serum albumin (Dennis and others, 2002, 35035-35043). One bivalent thrombin inhibitor containing an albumin-binding linker will have the sequence of Bbs-Arg-(D-Pip)-Gly-Leu-Ile-Glu-Asp-Ile-Cys-Leu-Pro-Arg-Trp-Gly-Cys-Leu-Trp-Glu-Asp-Gly-Asp-Phe-Gln-Gln-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 112). One can envision a bivalent thrombin inhibitor of the formula Bbs-Arg-dPip-Gly-(Val-Pro-Gly-Val-Gly)₂₀-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln, (SEQ. ID. NO. 119) containing as linker a temperature responsive elastin-repeat peptide Gly-(Val-Pro-Gly-Val-Gly)₁₉-Val-Pro-Gly-Val (SEQ. ID. NO. 120) (McPherson and others, 1992, 347-352). An analogue of this peptide suitable for recombinant production will have the formula of Ile-Arg-Phe-Thr-Asp-Gly-Glu-Gly-(Val-Pro-Gly-Val-Gly)₂₀-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Leu-Gln (SEQ. ID. NO. 121) with the Bbs-Arg-dPip-Gly (SEQ. ID. NO. 122) moiety replaced by Ile-Arg-Phe-Thr-Asp-Gly-Glu-Gly (SEQ. ID. NO. 116) for binding to the thrombin active site. Other thrombin inhibitors can also be constructed that contain as linkers with specific binding to other blood-borne proteins. For example, these peptide sequences and binding proteins can be selected from the database of linear peptide motifs as published previously (Puntervoll and others, 2003, 3625-3630). The different means of thrombin inhibition and re-activation can be combined to address specific requirements for the properties of new fibrin sealants.

In another case bivalent thrombin inhibitors were generated, which can bind to (and be neutralized by) prothrombin. One clinical application of such inhibitors is in the formulation of new fibrin sealants using inactivated thrombin that can be reactivated by prothrombin (vide supra). Another clinical application of this type of inhibitors is to display potency of thrombin inhibition only at a location with low prothrombin concentration due to its binding to prothrombinase and rapid turnover into thrombin (e.g. localized to the site of an atherosclerotic plaque). C-termini of the inhibitors contain hirudin residues 55-65, a fragment known to bind proexosite I of prothrombin with low affinity (Ni, F., Ning, Q., Jackson, C. M., and Fenton, J. W., 1993, 16899-16902; Anderson, P. J.; Nesset, A.; Dharmawardana, K. R.; and Bock, P. E., 2000, 16428-16434; Tolkatchev, Xu and Ni, 2003, JACS 12432-12442). A linker is engineered to provide additional contacts with prothrombin and confer much stronger specific affinity of the inhibitor to prothrombin. A phage-displayed peptide library was designed and constructed (preparation of the library is described in Su, Z.; Vinogradova, A.; Koutychenko, A.; Tolkatchev, D.; and Ni, F., 2004a, 647-657). The library was panned against prothrombin immobilized on the bottom of a MaxiSorp plate well. Panning enhanced growth of two phage species containing displayed sequences Gly-Ser-Val-Val-Pro-Arg-Pro-Gln-Leu-His-Asn-Asp-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 30) and Gly-Ser-His-Ala-Pro-Arg-Pro-Gln-Ile-His-Asn-Asp-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 31). Discovered sequences were used to construct two bivalent thrombin inhibitors, Bbs-Arg-(D-Pip)-Gly-Ser-Val-Val-Pro-Arg-Pro-Gln-Leu-His-Asn-Asp-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 32) and Bbs-Arg-(D-Pip)-Gly-Ser-His-Ala-Pro-Arg-Pro-Gln-Ile-His-Asn-Asp-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 33). Measured IC₅₀ were 1.1 and 0.6 nM, respectively, indicating the bivalent nature of inhibitor interaction with thrombin was retained (FIG. 2, Table 1). Further improvement of the linker includes panning against phage-displayed peptide library with four randomized residues in the sequence Gly-Ser-Val-Val-Pro-Asn-Xxx-Xxx-Leu-Xxx-Xxx-Asp-Gly-Asp-Phe-Glu-Glu-Ee-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 34). Specifically, bio-panning of new phage libraries against prothrombin will expand the sequence hits from the two sequences shown (i.e. SEQ. ID. NO. 30 and SEQ. ID. NO. 31), leading to bivalent peptides with adequate binding affinities to prothrombin. These new prothrombin-binding polypeptides are conjugated through their N-termini to the Bbs-Arg-(D-Pip) (SEQ. ID. NO. 68) moiety to create high-affinity bivalent inhibitors of thrombin, as demonstrated with peptides Bbs-Arg-(D-Pip)-Gly-Ser-Val-Val-Pro-Arg-Pro-Gln-Leu-His-Asn-Asp-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 32) and Bbs-Arg-(D-Pip)-Gly-Ser-His-Ala-Pro-Arg-Pro-Gln-Ile-His-Asn-Asp-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 33). Ultimately, a dual-affinity polypeptide is to be selected from this process. In other words, one can generate polypeptides with high-affinity bivalent binding of and inhibition against thrombin and at the same time with suitable binding affinities to prothrombin and whose thrombin-binding potency can be neutralized by circulating concentrations of prothrombin (in the range of a few micromolar in normal plasma).

In an embodiment of the invention, there is provided a method for the purification of a target protein, e.g. thrombin, prothrombin, Cdc42, or any other protein for which a bivalent and retractable polypeptide ligand is designed. The bivalent polypeptide will be immobilized on a solid support for use as an affinity absorbent for the targeted protein. The absorbed protein can be eluted using molecular agents or temperature, which upon contact with the affinity matrix will inactivate the bivalent ligand and release the absorbed protein. In light of the disclosures provided here in, it will be apparent to ones skilled in the art what detailed procedures will need to be followed for the above-mentioned applications.

SPECIFIC EXAMPLES

Example 1

A tolerance of the bivalent mode of inhibition to the amino acid composition of the linker moeity on a series of bivalent inhibitors of thrombin with an active site binding moiety Bbs-Arg-(D-Pip)-Gly (H1, Bbs=4-tert-butyl-benzenesulfonyl, D-Pip=D-pipecolic acid, K_I in low μM range (SEQ. ID. NO. 35) (Slon-Usakiewicz and others, 2000, 2384-2391) and an exosite 1 binding moiety Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln ((SEQ. ID. NO. 36), H2, K_I in low μM range) derived from the C-terminal tail of hirudin was demonstrated. The peptides were synthesized using standard Fmoc chemistry. Crude peptides were purified by HPLC using a reversed-phase C₁₈ Vydac column and a linear 10-45% or 20-45% acetonitrile gradient in 0.1% trifluoroacetic acid (TFA). Peptides were freeze-dried and their identity was confirmed by ion-spray mass spectrometry. Clotting assays were carried out by use of the protocols described previously (DiMaio and others, 1990, 21698-21703; Witting and others, 1992, 737-743). The assay employs bovine plasma fibrinogen dissolved at 0.1% in 50 mM Tris-Cl, 100 mM NaCl, 0.1% PEG-8000 at pH 7.6 (i.e. the clotting buffer). Each assay mixture contained a certain concentration of the peptide, and the reaction was started by the addition of human thrombin to a final concentration of 0.6-1.2 nM. Optical absorbance increase at 420 nm caused by fibrin clot formation was measured at 25° C. or 37° C. using the Spectramax plate reader. The onset clotting time was determined as an intersection of the baseline and the extrapolated linear portion of the OD change curve. The concentration of a peptide needed to double the clotting time was defined as IC₅₀ (DiMaio and others, 1990, 21698-21703). Kinetic amidolytic curves were obtained in clotting buffer at 25° C. using eight inhibitor concentrations and three to five concentrations of the chromogenic substrate S-2238 (Chromogenix) (DiMaio and others, 1990, 21698-21703). Inhibition constants were extracted from Lineweaver-Burk equation by using weighted linear regression. Errors in K_i determination were estimated by using Monte-Carlo sampling with 1-3% variance of the experimental points. Peptide concentrations were determined spectrophotometrically using predicted extinction coefficients at 278 nm (Gill and von Hippel, 1989, 319-326).

With a wide range of linker lengths and compositions IC₅₀ of the bivalent inhibitors in a fibrinogen clotting assay remained in low-nanomolar range (Table 1, and FIG. 2), values sufficiently low for peptide-based antithrombotic pharmaceutical compounds (Witting and others, 1992, 737-743), and much lower than the K_I values of the constituent binding moieties (Slon-Usakiewicz and others, 2000, 2384-2391). In every case an improvement in IC₅₀ as compared with that of the H2 moiety confirmed the bivalent mode of the polypeptide-thrombin interaction. The C-terminal portion of the peptide consisting of only natural amino acids and including the polymeric linker plus the H2 moiety ((Gly-Ser)n-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln) (SEQ. ID. NO, 113) can be produced using recombinant methods. Linking of the H1, containing unnatural amino acids, with the rest of the peptide can be performed using standard coupling techniques. We synthesized and purified peptides with amino acid sequences Bbs-Arg-(D-Pip)-Gly-Cys (SEQ. ID. NO. 4) and Cys-(Gly-Ser)₈-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 5). They were linked together by thiol oxidation in 2% ammonium acetate buffer, pH 8.6, over a period of 2 days. Resulting products were separated by reversed-phase HPLC and their identity was established by ion-spray mass spectroscopy. A product of disulfide bond linkage between peptides Bbs-Arg-(D-Pip)-Gly-Cys (SEQ. ID. NO. 4) and Cys-(Gly-Ser)₈-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 5) (corresponding to SEQ. ID. NO. 83) was tested for IC₅₀ in the clotting assay. We established that the two-chain peptide was potent and therefore bivalent with an IC₅₀ of 1.1±0.2 nM (FIG. 2). Another disulfide-linked bivalent thrombin inhibitor (corresponding to SEQ. ID. NO. 91) was prepared in the same fashion from two peptides Bbs-Arg-(D-Pip)-Gly-Cys (SEQ. ID. NO. 4) an d Cys-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 114).

Example 2

We made use of an amino acid sequence Cys-Pro-His-Tyr-Glu-Lys-Val-Ser-Gly (SEQ. ID. NO. 8) derived from the cytoplasmic tail of the cell-surface anchored ligand ephrin B2 (ephrinB2_301-309) to link the H1 and H2 moeities. The peptide is known to be flexible and in its tyrosine-phosphorylated state to bind SH2 domain from Grb4 with an affinity of 0.2 μM (Su, Xu, and Ni, 2004b, 1725-1736). We produced four peptides of a general formula Bbs-R-(D-Pip)-Gly-(Ser-Pro-His-B-Glu-Lys-Val-Ser-Gly)n-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 9), wherein B was either tyrosine (Tyr) or phosphotyrosine (Tyr(P)), and n was 1 or 2. The peptides were synthesized and their identity confirmed as outlined in Example 1. IC₅₀ of the inhibitors in the thrombin-clotting assay were comparable and in the vicinity of 0.5-1 nM, except for the peptide with two phosphotyrosines whose IC₅₀ was 18-20 nM (Table 2, FIG. 3). Incorporation of two phosphotyrosines in the linker resulted in a significant drop in the inhibition potency. Given the fact that the potency of the bivalent inhibitor Bbs-R-(D-Pip)-Gly-(Ser-Pro-His-B-Glu-Lys-Val-Ser-Gly)₂-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 115) depends on the phosphorylation state of the linker, a coupling with enzymatic assay translating activity of kinase or phosphatase into serine protease activity such as that of thrombin can be developed.

Example 3

An alternative way to reverse the inhibitory potency of the peptides with a general formula Bbs-R-(D-Pip)-Gly-(Ser-Pro-His-B-Glu-Lys-Val-Ser-Gly)n-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 9), wherein B was either tyrosine (Tyr) or phosphotyrosine (Tyr(P)), and n was 1 or 2, is to bring them in contact with SH2 domain in solution. SH2 domain of Grb4 was prepared as follows. The DNA sequences encoding the Grb4 SH2 domain was deduced from the amino acid sequences of murine Grb4 protein using the codon preference of Escherichia coli. The synthetic gene was amplified by PCR from six pairs of overlapping synthetic primers containing the two restriction sites of NcoI and BamHI for the SH2 domain at its two ends. The double-digested DNA fragment of SH2 was subcloned into the pET3215 expression vector, which was modified from pET32 and pET15 vectors (Novagen, Madison, Wis., USA), removing the original fusion carrier in the pET32 vector. In order to facilitate protein purification, a His-tag with six histidine residues was placed at the N-terminus of the SH2 domain linked with a thrombin cleavage sequence. The expression construct was confirmed by DNA sequencing and transformed into the E. coli BL21(DE3) expression host. The SH2 protein was expressed at 37° C. The cells were harvested four hours after induction with isopropyl thio-β-D-galactoside at OD₆₀₀=0.8. Protein purification was performed under denaturing conditions with Ni-nitriloacetic acid agarose beads (Qiagen) in the presence of 20 mM 2-mercaptoethanol at pH values of 8.0, 6.3, 5.9 and 4.5 for the binding, two washing, and eluting steps, respectively. Protein fractions were analyzed using SDS PAGE. Fractions containing SH2 domain were collected and refolded by dialyzing 2 3 times against a large volume of 50 mM sodium phosphate buffer containing 20 mM 2-mercaptoethanol (pH 6.8) at 4° C. The pellet was removed by centrifugation and the supernatant was concentrated by ultrafiltration (Millipore, Bedford, Mass., USA). Protein concentration was determined spectrophotometrically at 280 nm with a calculated extinction coefficient of 12210 M⁼¹cm⁼¹.

Influence of SH2 on inhibitory potency of the four peptides was tested in the clotting assay. Clotting time in the presence or absence of each of the inhibitors, presence and absence of 3 μM SH2 (inhibitor antidote), and equal amount of thrombin (0.6 nM) was measured at 22° C. The peptide Bbs-R-(D-Pip)-Gly-(Ser-Pro-His-Tyr-Glu-Lys-Val-Ser-Gly)-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 80) was used at a concentration of 1 nM, the peptide Bbs-R-(D-Pip)-Gly-(Ser-Pro-His-Tyr(P)-Glu-Lys-Val-Ser-Gly)-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 82) was used at a concentration of 4 nM, the peptide Bbs-R-(D-Pip)-Gly-(Ser-Pro-His-Tyr-Glu-Lys-Val-Ser-Gly)₂-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 81) was used at a concentration of 2 nM, and the peptide Bbs-R-(D-Pip)-Gly-(Ser-Pro-His-Tyr(P)-Glu-Lys-Val-Ser-Gly)₂-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 14) was used at a concentration of 50 nM. Interaction of the SH2 domain with phosphotyrosine-containing inhibitors reversed the inhibitory potency of the Bbs-R-(D-Pip)-Gly-(Ser-Pro-His-Tyr(P)-Glu-Lys-Val-Ser-Gly)n-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 29) (n=1,2) peptides, but not that of Bbs-K-(D-Pip)-Gly-(Ser-Pro-His-Tyr-Glu-Lys-Val-Ser-Gly)n-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 11) (n=1,2) peptides (FIG. 4). The change in thrombin activity upon binding of SH2 is a basis for developing an assay for protein-to-peptide binding, which can be realized in a high-throughput manner.

A linker known to bind to a specific antibody may be used to perform as a switchable polymeric linker if the antibody is introduced into the activity assay. A peptide with a formula Bbs-R-(D-Pip)-Gly-Glu-Gln-Lys-Leu-Ile-Ser-Glu-Glu-Asp-Leu-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 13) was prepared and tested for its ability to inhibit thrombin and be neutralized by a commercially available anti-c-myc antibody, known to bind to the peptide with a sequence Glu-Gln-Lys-Leu-Ile-Ser-Glu-Glu-Asp-Leu (SEQ. ID. NO. 12). The peptide was present in the clotting assay at a concentration of 150 nM, and thrombin—at a concentration of 0.6 nM. In the absence of the neutralizing antibody clotting onset time was delayed from approximately 100 s to approximately 530 s (FIG. 5). Addition of anti-c-myc antibody 9E10 (Sigma) in the stock buffer provided by the supplier to the final concentration of 1.2 μM reversed the inhibitory effect of the inhibitor to the clotting onset time of approximately 230 s. The effect of the control on thrombin activity in the absence of the inhibitor was very small (FIG. 5).

Example 4

An inhibitor with a linker known to bind specific metal ions will be affected by the presence of these ions in solution. Two peptides homologous to the calcium-binding loop of troponin C were designed and established that they bind calcium ions in solution. The peptides have the following sequences—Ac-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Glu-Phe-Glu-NH₂ (P3230) (SEQ. ID. NO. 109) and Ac-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-NH₂ (P3231) (SEQ. ID. NO. 110). The peptides were synthesized, purified and their identity was confirmed as described in Example 1. They were tested for calcium binding by use of NMR. For this both freeze-dried peptides were reconstituted at a concentration of approximately 0.5 mM in 20 mM sodium acetate-d₃ buffer, pH 5.5, containing 10% D₂O. Proton spectra of the peptides were recorded at 800 MHz, 15° C., before and after addition of increasing amounts of 0.1 and 1 M stock solutions of CaCl₂ in the same buffer. FIGS. 6a,b,c,d show changes in the proton NMR spectra of these two peptides upon the addition to the initial volume of ˜450 μL of 1 μL (final CaCl₂ concentration ˜0.22 mM), additional 2 μL (final CaCl₂ concentration ˜0.66 mM), additional 10 μL (final CaCl₂ concentration ˜2.8 mM) of 100 mM CaCl₂, and additional 10 μL (final CaCl₂ concentration ˜23.9 mM) of 1 M CaCl₂. The changes in the spectra confirm binding of calcium with affinity in mM range.

One of the two designed peptides was used to construct a calcium-responsive bivalent thrombin inhibitor. The disulfide-linked bivalent thrombin inhibitor (corresponding to SEQ. ID. NO. 91) prepared by cross-oxidation of cysteine thiol groups from two peptides Bbs-Arg-(D-Pip)-Gly-Cys (SEQ. ID. NO. 4) and Cys-Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 114) (preparation described in Example 1) was tested for its ability to bind calcium and inhibit amidolytic reaction in the presence and absence of calcium. FIGS. 6e,f show changes in the proton NMR spectrum of this peptide upon the addition to the initial volume of 450 μL of 1 μL (final CaCl₂ concentration ˜0.22 mM), additional 2 μL (final CaCl₂ concentration ˜0.66 mM) of 100 mM CaCl₂, and additional 10 μL (final CaCl₂ concentration ˜22.2 mM) of 1 M CaCl₂. The changes in the spectra confirm binding of calcium and the peptide with affinity in mM range.

Samples tested for inhibition potency contained in the clotting buffer 0.6 nM thrombin, 50 μM chromogenic substrate S-3266 (Chromogenix), and either no inhibitors or 2 nM of P3150, or 150 nM of the calcium-responsive disulfide-linked bivalent thrombin inhibitor. The time course of reactions is displayed in FIG. 7. Upon addition of increasing concentrations of calcium (50 and 100 mM) to the inhibitor incorporating calcium-binding linker, the potency of the latter is decreased. The same amounts of calcium produce no visible effect on the potency of control peptide P3150.

Example 5

Two peptides with sequences Val-Arg-Phe-Thr-Asp-Gly-Glu-Gly-Thr-Pro-Lys-Pro-Gln-Ser-His-Asn-Asp-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 22) (mini-hirudin 1) and Ile-Arg-Phe-Thr-Asp-Gly-Glu-Gly-Thr-Pro-Asn-Pro-Glu-Ser-His-Asn-Asn-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 23) (mini-hirudin 2) were designed incorporating N-terminal and C-terminal moieties presumably interacting with the active site and exosite I of thrombin. We found that they displayed high affinity to thrombin with IC₅₀ of 33±3 nM (mini-hirudin 1) and 14±1 nM (mini-hirudin 2) indicating a bivalent mode of binding (FIG. 8). The modular character of interaction was further implied when a candidacidal peptide known to bind laminarin (Polonelli, L.; and others, 2003, 6205-6212), or -Ala-Lys-Val-Thr-Met-Thr-Cys-Ser-Ala-Ser- (SEQ. ID. NO. 24), was inserted as a linker into the minihirudin-2 to give minihirudin-3 with a sequence of Ile-Arg-Phe-Thr-Asp-Gly-Ala-Lys-Val-Thr-Met-Thr-Cys-Ser-Ala-Ser-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 25). The peptide exhibited high affinity of binding to thrombin, with IC₅₀ of 10±1 nM (FIG. 8), confirming the presence of bivalent interactions.

Example 6

A peptide with a sequence of Trp-Asp-Pro-Arg-Pro-Gln-Arg-His-Asn-Asp-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 18) is a bivalent inhibitor of thrombin with a K_I of 17 nM (subject of another patent application). The peptide is built of two moieties, an active site binding moiety, Trp-Asp-Pro-Arg-Pro-Gln-Arg-His (SEQ. ID. NO. 19), and an exosite-1 binding moiety, Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 20). We prepared a bivalent thrombin inhibitor with the sequence Trp-Asp-Pro-Arg-Pro-Gln-Arg-His-(CamCKK)-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 21), designated as CaM-DTI, where CamCKK is a protein linker with a calcium-responsive property (Truong and others, 2001, 1069-1073). Another potentially bivalent thrombin inhibitor was derived from CaM-DTI, where the active-site targeting moiety Trp-Asp-Pro-Arg-Pro-Asn-Arg-His (SEQ. ID. NO. 18) of CaM-DTI was replaced by the sequence Ile-Arg-Phe-Thr-Asp-Gly-Glu-Gly (SEQ. ID. NO. 116) in mini-hirudins 1 and 3. In other words, this bivalent peptide incorporating the CamCKK linker was built from an N-terminal module, Ile-Arg-Phe-Thr-Asp- (SEQ. ID. NO. 72), and the exosite-1 binding moiety, Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 20). CaM-DTI2 has the sequence Ile-Arg-Phe-Thr-Asp-Gly-Glu-Gly-(CamCKK)-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 117). This new generation of CaM-DTI was named Cam-DTI2. The sequences of the thrombin inhibitors CaM-DTI and CaM-DTI2 are shown in FIG. 9. Both CaM-DTI and CaM-DTI2 were prepared by use of a recombinant DNA approach. Typically, the proteins were expressed and purified by a standard procedure using Ni-NTA agarose affinity chromatographic column (Qiagen). The N-terminal tag was removed by digesting the sample with enterokinase with a subsequent passage through a Ni-NTA agarose affinity chromatographic column. 20 mM EDTA was added into the flow-through and the sample was desalted on a PD-10 column. The final purification was carried out with ion-exchange chromatography on a Mono-S column. Purity was confirmed by SDS-PAGE. Final samples were essentially Ca²⁺-free.

Thrombin inhibition potencies of CaM-DTI and CaM-DTI2 were determined by an amidolytic assay. Kinetics of thrombin-catalyzed hydrolysis of the chromogenic substrates S-2238 or S-2366 (Chromogenix) was followed by absorbance at 405 nm on a SpectraMax plate reader thermostated at 37° C. The concentration of the substrate was 400 μM. Inhibition assays were performed in the clotting buffer with a certain fixed concentration of α-thrombin (˜0.3 nM) such that linear progress curves were observed within at least 15 min in the absence of the inhibition. The total volume of the reaction mixture was 200 μl. Reactions were initiated by addition of the chromogenic substrate to the wells containing thrombin and a certain concentration of CaM-DTI premixed for less than 2 min. The concentration of CaM-DTI ranged from 25 nM to 2.5 μM. Kinetics data from initial rate experiments were used to construct Lineweaver-Burke plot; i.e. the relationship of (substrate concentration)⁻¹ versus (initial velocity)⁻¹ which were analysed by linear regression with MicroCal Origin 6.0 program (MicroCal, Md.). The K_i values of the inhibitors were determined using the equation K_i=[I]/{(SL_o/SL₁)−1}, where [I] is the inhibitor concentration, SL_o is the slope of the reaction in the absence of inhibitors, and SL₁ is the slope of the reaction in the presence of the inhibitor.

Upon the addition of 5 mM Ca²⁺ an increase in inhibition constant for CaM-DTI was observed from 480 nM (calcium-free sample) to 2200 nM (calcium-loaded sample) (FIG. 10A). The CaM-DTI2 protein also inhibited the thrombin active site (FIG. 10B), but this inhibition was not affected by the presence of Ca²⁺ upon concentration of 5 mM.

FIG. 10B depicts the kinetics of thrombin-catalyzed hydrolysis of the chromogenic S-2366 (Chromogenix). Thrombin inhibition potency of CaM-DTI2 was determined by amidolytic assay. Kinetics of thrombin-catalyzed hydrolysis of the chromogenic substrate S-2366 (Chromogenix) was followed by absorbance at 405 nm on a SpectraMax plate reader at 25° C. The concentration of the substrate S-2366 was 50 μM. Inhibition assays were performed in the clotting buffer with a certain fixed concentration of α-thrombin (˜0.6 nM). The total volume of the reaction mixture was 200 μl. Reactions were initiated by the addition of the chromogenic substrate to the wells containing thrombin in the presence of 4.2 μM and 8.4 μM CaM-DTI2. Curves represent OD₄₀₅ time course after the addition of 0.6 nM thrombin in the presence of (◯) 0 nM; (Δ) 4.2 μM; and (□) 8.4 M CaM-DTI2. Inhibition of the amidolytic reaction confirming the bivalent mode of binding as shown for CaM-DTI in FIG. 10A.

Example 7

Cdc42 binds tightly to the ˜40-residue extended CRIB domains of Candida Cla4 and Step 20. When subjected to NMR relaxation dispersion analysis (Tolkatchev, Xu, and Ni, 2003b, 12432-12442), these complexes exhibit no responses, as expected for a tight binding complex.

We over-expressed two peptide fragments of the extended CRIB regions from the Candida Cla4 and Candida Step 20 (or Cst20) kinases (FIG. 11): (i) mCla4 (mCst20) including the consensus CRIB motif, and (ii) cCla4 (cCst20) which comprises residues directly to the C-terminus of the minimal CRIB sequence. All the peptides described in the example were prepared via a recombinant technique as described previously (Gizachew, D. and Oswald, R. E., 2001, 14368-14375; Osborne, M. J., and others, 2003, 317-326). The identity of the final products was verified by mass spectrometry.

Cdc42 constructs were prepared as follows. DNA fragments encoding the Cdc42 protein (residues 1-178) of Candida albicans SC5314 were amplified from the genomic DNA by a standard PCR reaction using the pfu polymerase. Through PCR reactions, two restriction sites, Nde I and BamH I, were generated in the 5′-end and 3′-end, respectively. A stop codon, TAG, was placed immediately after the codon for residue 178. The PCR fragment was subcloned into pET-15b (Novagen, Madison, Wis.) and the resulting construct was defined as pCaCdc42Δ13 (Stevens & Ni, unpublished data). A CaCdc42 expression vector encoding the R150K mutation was performed using the QuickChange Site-directed Mutegenesis Kit (Stratagene, La Jolla, Calif.). The sequences of the wild-type and R150K mutant CaCdc42 (Table 4) vectors were verified by DNA sequencing.

Wild type and mutant CaCdc42 proteins were expressed in the E. coli BL21 strain as hexa-histidine fusion proteins. Cells expressing CaCdc42 were grown in LB media. Cells were harvested from 1 L culture by centrifugation at 8000 g for 30 min and re-suspended in 50 mL of lysis buffer (20 mM Tris-HCl, pH 8.0, 500 mM NaCl, 10 mM imidazole, 5 mM MgCl₂, 100 μM GDP, 2 μg/ml aprotinin, leupeptin and pepstatin, and 10 μg/mL benzamidine and PMSF). The collected cells were treated with lysozyme (1 mg/mL) for 30 min on ice, followed by sonication for 4 min and subsequent addition of DNase at 2 μg/ml. The insoluble fraction was removed by centrifugation at 10,000 g for 30 min. The supernatant was mixed with Ni-NTA agarose beads (Qiagen, Mississauga, ON) by rocking for one hour and then washed extensively in a column with a washing buffer (20 mM Tris-HCl, pH 8.0, 500 mM NaCl, 15 mM imidazole, 5 mM MgCl₂). The fusion protein was eluted with the wash buffer (50 mL) except that the concentration of imidazole was 200 mM. The protein sample was buffer-exchanged extensively using CentriPrep YM10 to remove imidazole.

The non-hydrolyzable GTP analogues, GMPPNP or GMPPCP (Sigma, St-Louis, Mich.) were used to produce the activated, but stable nucleotide-loaded form of CaCdc42. In this work, no differences were observed for the two GTP analogues-loaded forms of Cdc42 in NMR and fluorescence experiments except that the lifetime of the complex with GMPPCP is longer than that with GMPPNP. Nucleotide exchange was facilitated by incubating CaCdc42 with a 5- to 10-fold molar excess of the non-hydrolyzable GTP analogue in the presence of 10 mM EDTA. To this mixture, 100 units of alkaline phosphatase beads were added and the mixture was gently shaken on ice for 3 hrs. The alkaline phosphatase beads were removed by filtration, followed by the addition of MgCl₂ to a final concentration of 15 mM. The excess unbound nucleotides were removed using a PD-10 gel filtration column (Amersham Bioscience, Piscataway, N.J.).

In order to construct a bivalent peptide ligand for Candida Cdc42 (CaCdc42) (with a suitable linker) (FIG. 12), the binding affinities of component peptides derived from the CRIB domains of Candida Cla4 and Step 20 were determined. Residue K150 of the R150K CaCdc42 mutant was covalently modified with the fluorescent probe, sNBD (Molecular Probes, Eugene, Oreg.), essentially as described by Nomanbhoy and Cerione (Nomanbhoy, T. and Cerione, R. A., 1999, 15878-15884.). The stoichiometry of the fluorescent probe per protein molecule was estimated at 1.13, based on protein concentration determined with ε_280nm=13,610 M⁻¹ cm⁻¹ (Gill, S. C. and von Hippel, P. H., 1989, 319-326), and using the absorbance of the sNBD moiety of 463 μm=22,000 M⁻¹ cm⁻¹. Interaction of the CRIB peptides with sNBD-labeled CaCdc42 was monitored using extrinsic fluorescence measurements with a Hitachi F-2500 fluorescence spectrophotometer. Samples of sNBD-labeled, activated CaCdc42 were added in the assay buffer (50 mM phosphate, pH 6.8, 50 mM NaCl and 5 mM MgCl₂) to a cuvette being continuously stirred. The protein concentration was 1 μM. Individual CRIB peptide dissolved in the same assay buffer was added drop-wise to the cuvette. The mixture was excited at 488 nm with an excitation slit width of 5 nm. The emission spectra were scanned from 510 nm to 590 nm. The fluorescence emission intensity at the emission maximum 545 nm was determined from each spectrum and the final value was obtained by averaging the values from five scans of the same sample. Control titration experiments were performed by adding the same volume of buffer instead of peptide. Each set of the titration data was repeated three times.

FIG. 13 shows binding isotherms obtained following the CRIB-induced changes in the sNBD fluorescence of the CaCdc42 (R150K) protein. The K_d values for the binding of the CRIB peptides to sNBD-labeled activated CaCdc42 were determined by fitting the fluorescence titration data to a simple bimolecular association model as described by Leonard et al (Leonard, D. A., and others, 1997, 1173-1180). The association between CaCdc42 (P) and a CRIB peptide (L) can be described by the following equation

$P+L\underset{k_{\mathrm{off}}}{\overset{k_{\mathrm{on}}}{\leftrightarrow }}P·L$

The fluorescence intensity (F) is related to the dissociation constant, K_d as follows,

$F=F_0+\left(F_t-F_0\right)\left[\frac{\left(K_d+L_T+P_T\right)-\sqrt{{\left(K_d+L_T+P_T\right)}^2-4P_TL_T}}{2P_T}\right]$

where F₀ and F_t are the fluorescence intensities at the starting and end points of the titration, respectively. PT is the total concentration of sNBD-labeled activated CaCdc42 and L_T is the total concentration of the CRIB peptide at any point in the titration. Fitting of the data was carried out using the computer program Microcal Origin™ 6.0 (Northampton, Mass.). Average K_d values were determined from multiple independent measurements.

The average apparent K_d values for different CRIB peptides are summarized in Table 2. As expected, the extended CRIB (eCRIB) fragments exhibited the strongest affinities of binding to CaCdc42 in the low nanomolar range. The mCRIB fragments containing the consensus CRIB sequence, ISXPXXFXHXXHVGXD (SEQ. ID. NO. 26) (Burbelo, P. D., Drechsel, D., and Hall, A., 1995, 29071-29074), also had moderately strong binding affinities in micromolar concentrations, but clearly, as seen previously for the human PAK homologues (Rudolph, M. G., Bayer, P., Abo, A., Kuhlmann, J., Vetter, I. R., and Wittinghofer, A., 1998, 18067-18076; Thompson, G., Owen, D., Chalk, P. A., and Lowe, P. N., 1998, 7885-7891), require extra residues to retain stronger binding to Cdc42. The cCRIB peptides exhibited much weaker affinities to the CaCdc42 protein. The K_d value of cCla4 for binding to CaCdc42 is in a high micromolar concentration (275 μM). An even weaker binding (K_d=1160 μM) was observed between cCst20 and CaCdc42 with the current fluorescence titration strategy.

Fluorescence measurements of cross-titrations were used to quantify allosteric effects (Table 2). The affinity of the Cla4 peptide fragments for CaCdc42 was not significantly affected by the addition of the cognate peptide. In contrast, the affinities of the Cst20 peptide fragments preincubated with CaCdc42 exhibited a dramatic enhancement in binding for CaCdc42 by ˜5.5-fold, upon addition of the cognate Cst20 peptide (Table 2). Thus, upon addition of mCst20 to the cCst20/CaCdc42 complex, the affinity of cCst20 for CaCdc42 increased from a K_d of 1160 μM to 207 μM (Table 2 and FIG. 13c). Similarly, mCst20 affinity for CaCdc42 increased from 0.43 μM to 0.081 μM when cCst20 was added to a preincubated mCst20/CaCdc42 complex. These results strongly suggest that the eCst20 and eCla4 peptides exhibit different mechanisms for binding CaCdc42, in which long eCst20 peptide utilizes a cooperative mechanism for high-affinity interaction while eCla4 does not.

Modular nature of interactions of m- and c-CRIB fragments is confirmed by the binding affinities of hybrid peptides incorporating m- and c-CRIBs from different molecular species. Both mCla4-cCst20 and mCst20-P-cCla4 constructs (FIG. 11) displayed affinities of the same order of magnitude as the original eCRIB peptides (Table 2). Moreover, incorporation of -Ser-Gly-Ser-Gly- (SEQ. ID. NO. 27) and -Arg-Lys-Ser-Leu-Thr-Ile-Tyr-Ala-Gln-Val-Gln-Lys-(SEQ. ID. NO. 28) linkers (FIG. 11) into the eCla4 sequence preserved a bivalent mode of binding, since the affinity of the chimeric peptide was significantly stronger than those of H1 and H2 heads (Table 2).

Example 8

The dissociation constant (K_i) for the interaction between SAP-SH2 and the eCla4-SLAM peptide was obtained by fitting fluorescence titration data (FIGS. 14A and 14B) using the following equation

$K_d^{\mathrm{app}}=K_d+\frac{K_d}{K_i}\left[{\mathrm{SH}}_2\right]$

where, K_d^app, K_d are the apparent dissociation constants between CaCdc42 and eCla4-SLAM in the presence or absence of SAP-SH2, respectively. K_i is the dissociation constant for the binding interaction between SAP-SH2 and the linker portion (i.e. the SLAM sequence of eCla4-SLAM). The value of K_i determined from these experiments is 362 μM, indicating that the SLAM sequence in the eCla4-SLAM peptide preserved the binding affinity to SAP-SH2 (Li et al and Pawson, Curr. Biol. 9, 1355-1362, 1999).

A peptide of the sequence Bbs-Arg-dPip-Gly-Arg-Lys-Ser-Leu-Thr-Ile-Tyr-Ala-Gln-Val-Gln-Lys-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (SEQ. ID. NO. 102), was synthesized and purified which contains as linker the SLAM sequence with specific binding to SAP-SH2 in the absence of tyrosine phosphorylation (Li et al and Pawson, Curr. Biol. 9, 1355-1362, 1999). The peptide was added at the concentrations of 10, 15, 20, 30, 40, 50 and 60 nM to 0.6 nM thrombin in the clotting buffer. Optical absorbance increase at 420 nm caused by fibrin clot formation was measured at 25° C. using the Spectramax plate reader. The onset clotting time was determined as an intersection of the baseline and the extrapolated linear portion of the OD change curve. The concentration of the peptide needed to double the clotting time was defined as IC₅₀. The peptide is found to be a potent inhibitor of thrombin with IC₅₀=7±1 nM (FIG. 14C). Also, to the clotting buffer containing 0.6 nM thrombin and 25 nM of the inhibitor were added 5 and 10 μM SAP-SH2 from the stock solution of 116 μM SAP-SH2 in 10 mM 2-[N-Morpholino]ethanesulfonic buffer (MES) at pH 5.0. The clotting assays serving as control experiments included thrombin+inhibitor, thrombin+SAPSH2, and thrombin alone. FIGS. 14D and 14E shows the course of the optical absorbance changes at 420 nm, and at 25° C., demonstrating the reversal of thrombin inhibition by SAP-SH2.

Example 9

The tweezer-like bivalent ligands can be attached to the protein target, either chemically or through recombinant techniques. We used the recombinant approach to conjugate Candida albicans Cdc42 (CaCdc42) with the full-length CRIB peptides from Candida Cla4 and Step 20 (FIG. 11). A model for a conjugated complex of CaCdc42 and the eCRIBs via a polymeric linker is displayed in FIG. 15a. Resonance assignments of the ¹H-¹⁵N HSQC spectra for Candida Cla4-eCRIB in a conjugated complex with CaCdc42 are displayed in FIG. 15b. The resonance peaks of the Cla4-eCRIB have the same pattern as those in the non-covalent complex. However, the conjugated complex is more stable (>3 months) than the non-covalent one (<one week). The ¹H-¹⁵N HSQC spectrum of Candida Cst20-eCRIB in a conjugated complex with CaCdc42 is shown in FIG. 15c. One potential application of the stably-conjugated complex is for discovering stronger and specific binding molecules to Cdc42 is outlined in FIG. 15d. More specifically, NMR techniques such as relaxation and H/D exchange can be used to detect the dissociation of a conjugated bivalent ligand by competing monovalent small molecules.

Example 10

Molecular species and methods of invention can also be used to design new molecules for pharmaceutical intervention. Medical intervention in case of an injury to an internal organ requires a strategy to seal the wound. Fibrin sealant is found to be effective and can be used safely on vital organs. It is thus widely used as a bioactive hemostat in cases of internal injury. The formulation that is commercially available (e.g. Tisseel VH Fibrin Sealant, Baxter) contains two major components: thrombin and fibrinogen. When both components are reconstituted and mixed thrombin catalyses the conversion of fibrinogen to fibrin, which in turn forms a fibrin scaffold or sealant. One of the limitations of the present formulation is that once reconstituted, thrombin proteolytically degrades itself.

Thus, there is provided herein a new formulation, wherein the proteolytic activity of thrombin is inhibited by a specific bivalent inhibitor Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-Tyr(P)-Glu-Lys-Val-Ser-Gly)-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln (P3170) (SEQ. ID. NO. 82) with a controllable polymeric linker binding to SH2 domain (FIG. 4). Therefore in the modified formulation, thrombin and inhibitor can be premixed and will stay inactive (and stable) until exposed to SH2.

The middle auricular artery of eight rabbits was cut transversely with a scalpel. Two rabbits were left untreated to measure the bleeding time. A commercial source of fibrin glue (one fresh sample, one incubated overnight at 37° C.) was applied to the wound of two other rabbits. The fibrin glue containing inhibitor-stabilized thrombin component, “Thrombin 4”, was applied to another pair of rabbits immediately after activation with SH2. The fibrin glue containing inhibitor-stabilized and highly purified human α-thrombin (Haemotologics), replacing the “Thrombin 4” component from the Tisseel kit, was applied to the last pair of rabbits immediately after SH2 activation. The final table of applied formulations employed in the example was as follows:

	Left ear	Right ear
Group 1- R1	Bleeding rabbit (no sealant)
Group 1- R2	Bleeding rabbit (no sealant)
Group 2- R1	Syringe (1) - 250 μL	Syringe (1) - 250 μL
	Commercial Tisseel	Commercial Tisseel solution,
	solution, prepared fresh	prepared fresh
	Syringe (2) - 250 μL	Syringe (2) - 250 μL Tisseel
	Tisseel “Thrombin 4”	“Thrombin 4” solution,
	solution, prepared fresh	prepared the night before and
		incubated o/n at 37 C.
Group 2- R2	Same sample as above	Same sample as above
Group 3- R1	Syringe (1) - 250 μL	Syringe (1) - 250 μL
	Commercial Tisseel	Commercial Tisseel solution,
	solution, prepared fresh +	prepared fresh + SH2 to 12
	SH2 to 12 μM	μM concentration.
	concentration.
	Syringe (2) - 250 μL	Syringe (2) - 250 μL Tisseel
	Tisseel “Thrombin 4”	“Thrombin 4” solution,
	solution + P3170 to 8 nM	prepared the night before and
	concentration, prepared the	incubated o/n at 37 C.
	night before and incubated
	o/n at 37 C.
Group 3- R2	Same sample as above	Same sample as above
Group 4- R1	Syringe (1) - 250 μL	Syringe (1) - 250 μL
	Commercial Tisseel	Commercial Tisseel solution,
	solution, prepared fresh +	prepared fresh + SH2 to 12
	SH2 to 12 μM	μM concentration.
	concentration.
	Syringe (2) - 250 μL “α-	Syringe (2) - 250 μL “α-
	thrombin (10−5)” solution +	thrombin (10−5)” solution,
	P3170 to 8 nM	prepared the night before and
	concentration, prepared the	incubated o/n at 37 C.
	night before and incubated
	o/n at 37 C.
Group 4- R2	Same sample as above	Same sample as above

SH2-activated fibrin glue with P3170 inhibitor was able to seal the wound after ˜5 minutes (FIG. 18).

In an embodiment of the invention there is provided a multivalent binding molecule and uses thereof. The molecule is useful in binding a target under certain conditions and releasing it under other conditions. The molecule has the general formula (1) of

BM1-L-(BM2)_n  (1)

wherein,

BM1 is a binding moiety 1 having an affinity for site 1 on the target,

BM2 is a binding moiety 2 having an affinity for a site other than site 1 on the target, n is 1 or greater, and

L is a linker joining BM1 and BM2, said linker being adapted to respond to a change in its environment with a change in conformation and/or flexibility,

wherein BM1 and BM2 may be the same or different, and when n>1, different BM2 moieties may have affinities for different binding sites on the target. BM1 and BM 2 are selected such that in use each of the BM1 and BM2 existing separately has a lower binding affinity then the complex of BM1 and BM2 does when they are linked to form the molecule. In some instances the ligand is a polypeptide. In some instances the ligand is covalently attached to its target. In some instances the target is a protein, and the ligand is attached to its protein target by means of recombinant conjugation. In some instances the linkers are modified by means of binding to a biomolecule. In some instances the linkers are modified by means of covalent modification. In some instances the linkers are modified by means of a local environment change. In some instances the linker binds to an antibody. In some instances the linker binds to an SH2 domain. In some instances the linker binds to Cdc42. In some instances the linker binds to prothrombin. In some instances the linker binds to metal ion. In some instances the linker binds to calcium. In some instances the linker binds to a cell surface. In some instances the linker sequence contains at least two residues, selected from the group of tyrosine; serine; threonine; histidine; phosphotyrosine; phosphoserine; phoshothreonine; phosphohistidine.

In some instances the linker sequence is selected from the group consisting of

In some instances the FL sequence is selected from the group consisting of

-(Gly-Ser)2-;
-(Gly-Ser)4-;
-(Gly-Ser)6-;
-(Gly-Ser)8-;
-(Gly-Ser)10-;
-(Gly-Ser)12-;
-(Gly-Ser)14-;
-Gly-Cys...Cys-(Gly-Ser)8-;
-(Gly-Ser)4-Gly-Lys-(Gly-Ser)5-Ser-Pro-His-Tyr-
Glu-Lys-Val-Ser-Gly
-(Ser-Pro-His-Tyr-Glu-Lys-Val-Ser-Gly)2-;
-Ser-Pro-His-Tyr(P)-Glu--Lys-Val-Ser-Gly-;
-(Ser-Pro-His-Tyr(P)Glu-Lys-Val-Ser-Gly)2-;
-Pro-His-Tyr-Glu-Lys-Val-Ser-;
-Pro-His-Tyr-Glu-Lys-Val-Ser-Gly-Ser-Pro-His-Tyr-
Glu-Lys-Val-Ser-;
-Pro-His-Tyr(P)-Glu-Lys-Val-Ser-;
-Pro-His-Tyr(P)-Glu-Lys-Val-Ser-Gly-Ser-Pro-His-
Tyr(P)-Glu-Lys-Val-Ser-;

wherein Tyr(P) is O-phosphotyrosine;In some instances the FL sequence is selected from the group consisting of -Ser-Val-Val-Pro-Asn-Aaa-Bbb-Leu-Ccc-Ddd-Asp-;wherein Aaa, Bbb, Ccc, and Ddd—natural amino acids;

In some instances the molecule is a thrombin inhibitor;

In some instances the BM1 sequence is selected from the group consisting of:

Bbs-Arg-(D-Pip);
Bbs-Arg-(D-Pip)-Gly;

where Bbs is 4-tert-butylbenzenesulfonyl, D-Pip is D-pipecolic acid;

In some instances the BM1 sequence is a subsequence from an amino acid sequence selected from the group consisting of

Val-Arg-Phe-Thr-Asp-Gly-Glu-Gly-Thr-Pro-Lys;
Val-Arg-Phe-Thr-Asp;
Ile-Arg-Phe-Thr-Asp-Gly-Glu-Gly-Thr-Pro-Asn;
Ile-Arg-Phe-Thr-Asp;
Trp-ASp-Pro-Arg-Pro-Gln-Arg-His;

In some instances the BM2 amino acid sequence is selected from the group consisting of:

Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln;
Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln;

In some instances the molecule is selected from the group consisting of:

where Bbs is 4-tert-butylbenzenesulfonyl, D-Pip is D-pipecolic acid; Tyr(P) is O-phosphorylated tyrosine;

In some instances the molecule is

WDPRPQRHADQLTEEQIAEFKEAFSLFDKGDGTITTKELGTVMRSLGQNP
TEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTGGVKLIPSWTTVIL
VKSMLRKRSFGNPFGGDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLG
EKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAKDFEEIPEEYLQ;

In some instances the molecule is a ligand of Cdc42;

In some instances the BM1 sequence is a subsequence from an amino acid sequence selected from the group consisting of

Gly-Gly-Asn-Ser-Gly-Val-Ser-Gly-Pro-Ile-Asn-Phe-
Thr-His-Lys-Val-His-Val-Gly-Phe-Asp-Pro-Ala-Ser;
Gly-Gly-Asn-Ser-Gly-Val-Ser-Gly-Pro-Ile-Asn-Phe-
Thr-His-Lys-Val-His-Val-Gly-Phe-Asp;
Glu-Val-Asn-Ile-Lys-Ile-Ser-Thr-Pro-Phe-Asn-Ala-
Lys-His-Leu-Ala-His-Val-Gly-Ile-Asp-ASp-Asn-Gly;
Glu-Val-Asn-Ile-Lys-Ile-Ser-Thr-Pro-Phe-Asn-Ala-
Lys-His-Leu-Ala-His-Val-Gly-Ile-Asp;

In some instances the BM2 sequence is a subsequence from an amino acid sequence selected from the group consisting of

Gly-Asn-Phe-Thr-Gly-Leu-Pro-Asp-Thr-Trp-Lys-Ser-
Leu-Leu-Gln-His-Ser-Lys-Ile-Thr;
Asn-Phe-Thr-Gly-Leu-Pro-Asp-Thr-Trp-Lys-Ser-Leu-
Leu-Gln-His-Ser-Lys-Ile-Thr;
Gly-Ser-Tyr-Thr-Gly-Leu-Pro-Ile-Glu-Trp-Glu-Arg-
Leu-Leu-Ser-Ala-Ser-Gly-Ile-Thr;
Ser-Tyr-Thr-Gly-Leu-Pro-Ile-Glu-Trp-Glu-Arg-Leu-
Leu-Ser-Ala-Ser-Gly-Ile-Thr;

In some instances the molecule is selected from the group consisting of:

Gly-Gly-Asn-Ser-Gly-Val-Ser-Gly-Pro-Ile-Asn-Phe-
Thr-His-Lys-Val-His-Val-Gly-Phe-Asp-Ser-Gly-Ser-
Gly-Asn-Phe-Thr-Gly-Leu-Pro-Asp-Thr-Trp-Lys-Ser-
Leu-Leu-Gln-His-Ser-Lys-Ile-Thr;
Gly-Gly-Asn-Ser-Gly-Val-Ser-Gly-Pro-Ile-Asn-Phe-
Thr-His-Lys-Val-His-Val-Gly-Phe-Asp-Arg-Lys-Ser-
Leu-Thr-Ile-Tyr-Ala-Gln-Val-Gln-Lys-Asn-Phe-Thr-
Gly-Leu-Pro-Asp-Thr-Trp-Lys-Ser-Leu-Leu-Gln-His-
Ser-Lys-Ile-Thr;

In an embodiment of the invention there is provided a method to obtain the polypeptide molecule according to claim 3 with high affinity to a protein target, said method comprising steps of:

• • a) Identification of two binding peptide moieties to two different binding sites of the target based on already existing polypeptide ligands with high affinity;
  • b) Establishing a weaker binding peptide moiety using NMR titration or NMR relaxation dispersion spectroscopy;
  • c) Connecting the peptide moieties with a polymeric linker;
  • d) Increasing the bivalent affinity by sequence optimization of the weaker moiety by means of phage display;

In an embodiment of the invention there is provided a method to prolong the lifetime of reconstituted autocatalytic protease said method comprising the steps of

• • a) Inhibiting the protease with a bivalent protease inhibitor containing a controllable linker,
  • b) Releasing and activating the protease with an appropriate linker-targeted antidote;

In some instances the protease is thrombin.

In some instances thrombin is a component of a fibrin sealant kit.

Thus, it will be apparent that there has been provided herein multivalent binding molecules containing linkers through which binding can be modulated.

TABLE 1
IC50 and K1 va1ues of thrombin inhibitors of the series
Bbs-R-(D-Pip)-linker-GDFEEIPEEYLQ (SEQ. ID. NO. 2).
		KI, nM	IC50, nM
	linker	(25° C.)	(37° C.)	FIG.
P3149,	GSGS		9.7 ± 0.7	2a
SEQ. ID. NO. 73	(SEQ. ID. NO. 50)
P3150,	GSGSGSGS	0.5 ± 0.2	0.5 ± 0.1	2b
SEQ. ID. NO. 74	(SEQ. ID. NO. 51)
P3151,	GSGSGSGSGSGS	0.6 ± 0.1	0.5 ± 0.1	2c
SEQ. ID. NO. 75	(SEQ. ID. NO. 52)
P3152,	GSGSGSGSGSGSGSGS	1.3 ± 0.3	0.7 ± 0.1	2d
SEQ. ID. NO. 76	(SEQ. ID. NO. 53)
P3153	GSGSGSGSGSGSGSGSGSGS	2.0 ± 0.3	1.0 ± 0.1	2e
SEQ. ID. NO. 77	(SEQ. ID. NO. 54)
P3160,	GSGSGSGSGGSGSGSGSGSGSGS	4.6 ± 0.8	2.8 ± 0.1	2f
SEQ. ID. NO. 78	(SEQ. ID. NO. 55)
P3159,	GSGSGSGSGSGSGSGSGSGSGSGSGSGS	6.7 ± 1.9	3.5 ± 0.2	2g
SEQ. ID. NO. 79	(SEQ. ID. NO. 56)
P3172-P3165,	Gly-Cys...Cys-GSGSGSGSGSGSGSGS		1.1 ± 0.2	2h
SEQ. ID. NO. 83	(SEQ. ID. NO. 57)
P3169,	GSPHYEKVS	1.0 ± 0.2	0.4	3a
SEQ. ID. NO. 80	(SEQ. ID. NO. 123)		(25° C.)
	Ligand of an SH2 domain from
	Grb4, dephosphorylated
P3170,	GSPH(Y(P))EKVS	1.5 ± 0.4	0.7	3b
SEQ. ID. NO. 82	(SEQ. ID. NO. 124)		(25° C.)
	Ligand of an SH2 domain from
	Grb4, phosphorylated
P3161,	GSPHYEKVSGSPHYEKVS		0.7	3c
SEQ. ID. NO. 81	(SEQ. ID. NO. 125)		(25° C.)
	Tandem of two peptide ligands
to SH2 from Grb4,
	dephosphorylated
P3162,	GSPH(Y(P))EKVSGSPH(Y(P))EKVS		19 ± 1	3d
SEQ. ID. NO. 14	(SEQ. ID. NO. 126)		(25° C.)
	Tandem of two peptide ligands
	to SH2 from Grb4,
	phosphorylated
P3174,	GSGSGSGSGKGSGSGSGSGS		1.6 ± 0.9	2j
SEQ. ID. NO. 84	(SEQ. ID. NO. 58)		(25° C.)
	Lys in the midd1e of a
	long GS repeat linker
P3181,	GTLDLNTPVDKTSN		1.9 ± 0.2	2i
SEQ. ID. NO. 85	(SEQ. ID. NO. 103)
	C5a receptor peptide
P3182,	GEQKLISEEDL	66 ± 13	~25
SEQ. ID. NO. 13	(SEQ. ID. NO. 123)
	c-myc peptide
P3209,	GSVVPRPQLHND		1.1	2k
SEQ. ID. NO. 32	(SEQ. ID. NO. 105)
	Prothrombin-binding
	linker 1 (VV)
P3210,	GSHAPRPQIHND		0.6	2l
SEQ. ID. NO. 33	(SEQ. ID. NO. 104)
	Prothrombin-binding
	linker 2 (HA)
P3234,	GHHLGGAKQAGDV		3.9 ± 0.8	2m
SEQ. ID. NO. 88	(SEQ. ID. NO. 106)
	Fibrinogen γ-chain 400-411,
	integrin specific
P3236,	GYMESRADR		1.0 ± 0.5	2n
SEQ. ID. NO. 89	(SEQ. ID. NO. 107)
	Fibrinogen antagonist, also
	targets the fibrinogen-
	integrin interaction
P3238,	GQSHNR		21	2o
SEQ. ID. NO. 90	(SEQ. ID. NO. 108)
	Linkers conferring a RGDF
	sequence, with potentia1
	binding to an integrin
	receptor
3243-3255,	Gly-Cys...Cys-DKNADGWIDN			7
SEQ. ID. NO. 91	(SEQ. ID. NO. 48)
	Calcium-binding linker
P3291,	GRKSLTIYAQVQK		7 ± 1
SEQ. ID. NO. 102	(SEQ. ID. NO. 128)
	SLAM peptide
	(ligand for SAP-SH2)

TABLE 2
Dissociation constants for binding of Candida CRIB
fragments to CaCdc42 measured by fluorescence titration.
Peptide	mCla4	mCst20	cCla4	cCst20	eCla4	eCst20
Kdm	4.2 ± 0.15	0.43 ± 0.03	275 ± 9	1160 ±	0.025 ±	0.046 ±
(μM)				106	0.002	0.002
	mCla4	mCst20	cCla4	cCst20
Peptide	(+cCla4)	(+cSt20)	(+mCla4)	(+mCst20)
Kdm	4.1 ± 0.13	0.081 ± 0.002	311 ± 12	207 ± 10
(μM)
	mCla4-	mCst20-	mCst20-		eCla4-
Peptide	cCst20	cCla4	P-cCla4	eCla4-SG	SLAM
Kdm	0.031 ±	2.64 ± 0.20	0.093 ± 0.01	0.067 ±	0.127 ± 0.07
(μM)	0.002			0.008

TABLE 3
SEQ. ID. NO. SEQUENCE
SEQ. ID. NO. Gly-Asp-Phe-Glu-Glu-Ile-Glu-Glu-
1            Tyr-Leu-Gln
SEQ. ID. No. Bbs-Arg-(D-Pip)-linker-Gly-Asp-Phe-
2            Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. [-linker-Gly-Asp-Phe-Glu-Glu-Ile-Pro-
3            Glu-Glu-Tyr-Leu-Gln]
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Cys
4
SEQ. ID. NO. Cys-(Gly-Ser)8-Gly-Asp-Phe-Glu-Glu-
5            Ile-Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Cys
6
SEQ. ID. NO. Cys-(Gly-Ser)8-Gly-Asp-Phe-Glu-Glu-
7            Ile-Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Cys-Pro-His-Tyr-Glu-Lys-Val-Ser-Gly
8
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-B-
9            Glu-Lys-Val-Ser-Gly)n-Asp-Phe-Glu-
             Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-
10           Tyr(P)-Glu-Lys-Val-Ser-Gly)n-Asp-Phe-
             Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-Tyr-
11           Glu-Lys-Val-Ser-Gly)n-Asp-Phe-Glu-
             Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Glu-Gln-Lys-Leu-Ile-Ser-Glu-Glu-Asp-
12           Leu
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Glu-Gln-Lys-Leu-
13           Ile-Ser-Glu-Glu-Asp-Leu-Gly-Asp-Phe-
             Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-
14           Tyr(P)-Glu-Lys-Val-Ser-Gly)2-Asp-Phe-
             Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Cys . . .
15
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Cys . . . Cys-Asp-
16           Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-Asn-
             Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-
             Tyr-Leu-Gln
SEQ. ID. NO. Asp-Lys-Asn-Ala-Asp-Gly-Trp-Ile-Asp-
17           Asn-Gly-Asp-Phe-Glu
SEQ. ID. NO. Trp-Asp-Pro-Arg-Pro-Gln-Arg-His-Asn-
18           Asp-Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-
             Glu-Tyr-Leu-Gln
SEQ. ID. NO. Trp-Asp-Pro-Arg-Pro-Gln-Arg-His
19
SEQ. ID. NO. Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-
20           Leu-Gln
SEQ. ID. NO. Trp-Asp-Pro-Arg-Pro-Gln-Arg-His-
21           (CamCKK)-Asp-Phe-Glu-Glu-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Val-Arg-Phe-Thr-Asp-Gly-Glu-Gly-Thr-
22           Pro-Lys-Pro-Gln-Ser-His-Asn-Asp-Gly-
             Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-
             Leu-Gln (mini-hirudin 1)
SEQ. ID. NO. Ile-Arg-Phe-Thr-Asp-Gly-Glu-Gly-Thr-
23           Pro-Asn-Pro-Glu-Ser-His-Asn-Asn-Gly-
             Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-
             Leu-Gln (mini-hirudin 2)
SEQ. ID. NO. Ala-Lys-Val-Thr-Met-Thr-Cys-Ser-Ala-
24           Ser-
SEQ. ID. NO. Ile-Arg-Phe-Thr-Asp-Gly-Ala-Lys-Val-
25           Thr-Met-Thr-Cys-Ser-Ala-Ser-Gly-Asp-
             Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-
             Gln
SEQ. ID. NO. ISXPXXFXHXXHVGXD
26
SEQ. ID. NO. -Ser-Gly-Ser-Gly-
27
SEQ. ID. NO. -Arg-Lys-Ser-Leu-Thr-Ile-Tyr-Ala-Gln-
28           Val-Gln-Lys-
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-(Ser-Pro-His-
29           Tyr(P)-Glu-Lys-Val-Ser-Gly)n-Asp-Phe-
             Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Gly-Ser-Val-Val-Pro-Arg-Pro-Gln-Gln-Leu-
30           His-Asn-Asp-Gly-Asp-Phe-Glu-Glu-Ile-
             Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Gly-Ser-His-Ala-Pro-Arg-Pro-Gln-Ile-
31           His-Asn-Asp-Gly-Asp-Phe-Glu-Glu-Ile-
             Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Ser-Val-Val-Pro-
32           Arg-Pro-Gln-Leu-His-Asn-Asp-Gly-Asp-
             Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-
             Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Ser-His-Ala-Pro-
33           Arg-Pro-Gln-Ile-His-Asn-Asp-Gly-Asp-
             Phe-Glu-Glu-Ile-Pro-Glu-Glu-Tyr-Leu-
             Gln
SEQ. ID. NO. Gly-Ser-Val-Val-Pro-Asn-Xxx-Xxx-Leu-
34           Xxx-Xxx-Asp-Gly-Asp-Phe-Glu-Glu-Ile-
             Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly (H1, Bbs = 4-tert-
35           butyl-benzenesulfonyl, D-Pip = D-
             pipecolic acid, KI in low μM range
SEQ. ID. NO. Gly-Asp-Phe-Glu-Glu-Ile-Pro-Glu-Glu-
36           Tyr-Leu-Gln
SEQ. ID. NO. -Gly-Gly-Asn-Ser-Gly-Val-
37           Ser-Gly-Pro-Ile-Asn-Phe-Thr-
             His-Lys-Val-His-Val-Gly-Phe-
             Asp-Pro-Ala-Ser-Gly-Asn-Phe-
             Thr-Gly-Leu-Pro-Asp-Thr-Trp-
             Lys-Ser-Leu-Leu-Gln-His-Ser-
             Lys-Ile-Thr-
SEQ. ID. NO. -Glu-Val-Asn-Ile-Lys-Ile-
38           Ser-Thr-Pro-Phe-Asn-Ala-Lys-
             His-Leu-Ala-His-Val-Gly-Ile-
             Asp-Asp-Asn-Gly-Ser-Tyr-Thr-
             Gly-Leu-Pro-Ile-Glu-Trp-Glu-
             Arg-Leu-Leu-Ser-Ala-Ser-Gly-
             Ile-Thr-;
SEQ. ID. NO. -Thr-Leu-Asp-Leu-Asn-Thr-
39           Pro-Val-Asp-Lys-Thr-Ser-Asn-
SEQ. ID. NO. -Ser-Val-Val-Pro-Arg-Pro-
40           Gln-Leu-His-Asn-Asp-
SEQ. ID. NO. -Ser-His-Ala-Pro-Arg-Pro-
41           Gln-Ile-His-Asn-Asp-
SEQ. ID. NO. -Asn-Gly-Arg-Lys-Ile-Cys-
42           Leu-Asp-Leu-Gln-Ala-Pro-Leu-
             Tyr-Lys-Lys-Ile-Ile-Lys-Lys-
             Leu-Leu-Glu-Ser-
SEQ. ID. NO. -Asn-Gly-Arg-Lys-Ile-Cys-
43           Leu-Glu-Leu-Arg-Ala-Pro-Leu-
             Tyr-Lys-Lys-Ile-Ile-Lys-Lys-
             Leu-Leu-Glu-Ser-
SEQ. ID. NO. -His-His-Leu-Gly-Gly-Ala-
44           Lys-Gln-Ala-Gly-Asp-Val-
SEQ. ID. NO. -Tyr-Met-Glu-Ser-Arg-Ala-
45           Asp-Arg-
SEQ. ID. NO. -Gln-Ser-His-Asn-Arg-
46
SEQ. ID. NO.47
SEQ. ID. NO.48
             Asn-Ala-Asp-Gly-Trp-Ile-Asp-
             Asn-
SEQ. ID. NO. -Asp-Lys-Asn-Ala-Asp-Gly-
49           Trp-Ile-Asp-Asn-Gly-Glu-Phe-
             Glu-
SEQ. ID. NO. -(Gly-Ser)2-
50
SEQ. ID. NO. -(Gly-Ser)4-
51
SEQ. ID. NO. -(Gly-Ser)6-
52
SEQ. ID. NO. -(Gly-Ser)8-
53
SEQ. ID. No. -(Gly-Ser)10-
54
SEQ. ID. NO. -(Gly-Ser)12-
55
SEQ. ID. NO. -(Gly-Ser)14-
56
SEQ. ID. NO. -Gly-Cys . . . Cys-(Gly-Ser)8-
57
SEQ. ID. NO. -(Gly-Ser)4-Gly-Lys-(Gly-
58           Ser)5-
SEQ. ID. NO. -Ser-Pro-His-Tyr-Glu-Lys-
59           Val-Ser-Gly-
SEQ. ID. NO. -(Ser-Pro-His-Tyr-Glu-Lys-
60           Val-Ser-Gly)2-
SEQ. ID. NO. -Ser-Pro-His-Tyr(P)-Glu-Lys-
61           Val-Ser-Gly-
SEQ. ID. NO. -(Ser-Pro-His-Tyr(P)-Glu-
62           Lys-Val-Ser-Gly)2-
SEQ. ID. NO. -Pro-His-Tyr-Glu-Lys-Val-
63           Ser-
SEQ. ID. NO. -Pro-His-Tyr-Glu-Lys-Val-
64           Ser-Gly-Ser-Pro-His-Tyr-Glu-
             Lys-Val-Ser-
SEQ. ID. NO. -Pro-His-Tyr(P)-Glu-Lys-Val-
65           Ser-
SEQ. ID. NO. -Pro-His-Tyr(P)-Glu-Lys-Val-
66           Ser-Gly-Ser-Pro-His-Tyr(P)-
             Glu-Lys-Val-Ser-
SEQ. ID. NO. -Ser-Val-Val-Pro-Asn-Aaa-
67           Bbb-Leu-Ccc-Ddd-Asp-
SEQ. ID. NO. Bbs-Arg-(D-Pip)
68
SEQ. ID. NO. Val-Arg-Phe-Thr-Asp-Gly-Glu-
69           Gly-Thr-Pro-Lys
SEQ. ID. NO. Val-Arg-Phe-Thr-Asp
70
SEQ. ID. NO. Ile-Arg-Phe-Thr-Asp-Gly-Glu-
71           Gly-Thr-Pro-Asn
SEQ. ID. NO. Ile-Arg-Phe-Thr-Asp
72
SEQ. ID. NO. Bbs-Arg-(D-Pip)-(Gly-Ser)2-
73           Gly-Asp-Phe-Glu-Glu-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-(Gly-Ser)4-
74           Gly-Asp-Phe-Glu-Glu-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-(Gly-Ser)6-
75           Gly-Asp-Phe-Glu-Glu-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-(Gly-Ser)8-
76           Gly-Asp-Phe-Glu-Glu-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-(Gly-Ser)10-
77           Gly-Asp-Phe-Glu-Glu-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-(Gly-Ser)12-
78           Gly-Asp-Phe-Glu-Glu-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-(Gly-Ser)14-
79           Gly-Asp-Phe-Glu-Glu-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Ser-Pro-
80           His-Tyr-Glu-Lys-Val-Ser-Gly-
             Asp-Phe-Glu-Glu-Ile-Pro-Glu-
             Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-(Ser-
81           Pro-His-Tyr-Glu-Lys-Val-Ser-
             Gly)2-Asp-Phe-Glu-Glu-Ile-
             Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Ser-Pro-
82           His-Tyr(P)-Glu-Lys-Val-Ser-
             Gly-Asp-Phe-Glu-Glu-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-
83
             Asp-Phe-Glu-Glu-Ile-Pro-Glu-
             Glu-Tyr-Leu-Gln;
SEQ. ID. NO. Bbs-Arg-(D-Pip)-(Gly-Ser)4-
84           Gly-Lys-(Gly-Ser)5-Gly-Asp-
             Phe-Glu-Glu-Ile-Pro-Glu-
             Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Thr-
85           Leu-Asp-Leu-Asn-Thr-Pro-
             Val-Asp-Lys-Thr-Ser-Asn-
             Gly-Asp-Phe-Glu-Glu-Ile-
             Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Asn-
86           Gly-Arg-Lys-Ile-Cys-Leu-
             Asp-Leu-Gln-Ala-Pro-Leu-
             Tyr-Lys-Lys-Ile-Ile-Lys-
             Lys-Leu-Leu-Glu-Ser-Gly-
             Asp-Phe-Glu-Glu-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Asn-
87           Gly-Arg-Lys-Ile-Cys-Leu-
             Glu-Leu-Arg-Ala-Pro-Leu-
             Tyr-Lys-Lys-Ile-Ile-Lys-
             Lys-Leu-Leu-Glu-Ser-Gly-
             Asp-Phe-Glu-Glu-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-His-
88           His-Leu-Gly-Gly-Ala-Lys-
             Gln-Ala-Gly-Asp-Val-Gly-
             Asp-Phe-Glu-Glu-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Tyr-
89           Met-Glu-Ser-Arg-Ala-Asp-
             Arg-Gly-Asp-Phe-Glu-Glu-
             Ile-Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Gln-
90           Ser-His-Asn-Arg-Gly-Asp-
             Phe-Glu-Glu-Ile-Pro-Glu-
             Glu-Tyr-Leu-Gln
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-(Cys)-
91           COOH
             Asp-Lys-Asn-Ala-Asp-Gly-
             Trp-Ile-Asp-Asn-Gly-Asp-
             Phe-Glu-Glu-Ile-Pro-Glu-
             Glu-Tyr-Leu-Gln
SEQ. ID. NO. Gly-Gly-Asn-Ser-Gly-Val-Ser-
92           Gly-Pro-Ile-Asn-Phe-Thr-His-
             Lys-Val-His-Val-Gly-Phe-Asp-
             Pro-Ala-Ser
SEQ. ID. NO. Gly-Gly-Asn-Ser-Gly-Val-Ser-
93           Gly-Pro-Ile-Asn-Phe-Thr-His-
             Lys-Val-His-Val-Gly-Phe-Asp
SEQ. ID. NO. Glu-Val-Asn-Ile-Lys-Ile-Ser-
94           Thr-Pro-Phe-Asn-Ala-Lys-His-
             Leu-Ala-His-Val-Gly-Ile-Asp-
             Asp-Asn-Gly
SEQ. ID. NO. Glu-Val-Asn-Ile-Lys-Ile-Ser-
95           Thr-Pro-Phe-Asn-Ala-Lys-His-
             Leu-Ala-His-Val-Gly-Ile-Asp
SEQ. ID. NO. Gly-Asn-Phe-Thr-Gly-Leu-Pro-
96           Asp-Thr-Trp-Lys-Ser-Leu-Leu-
             Gln-His-Ser-Lys-Ile-Thr
SEQ. ID. NO. Asn-Phe-Thr-Gly-Leu-Pro-Asp-
97           Thr-Trp-Lys-Ser-Leu-Leu-Gln-
             His-Ser-Lys-Ile-Thr
SEQ. ID. NO. Gly-Ser-Tyr-Thr-Gly-Leu-Pro-
98           Ile-Glu-Trp-Glu-Arg-Leu-Leu-
             Ser-Ala-Ser-Gly-Ile-Thr
SEQ. ID. NO. Ser-Tyr-Thr-Gly-Leu-Pro-Ile-
99           Glu-Trp-Glu-Arg-Leu-Leu-Ser-
             Ala-Ser-Gly-Ile-Thr
SEQ. ID. NO. Gly-Gly-Asn-Ser-Gly-Val-Ser-
100          Gly-Pro-Ile-Asn-Phe-Thr-His-
             Lys-Val-His-Val-Gly-Phe-Asp-
             Ser-Gly-Ser-Gly-Asn-Phe-Thr-
             Gly-Leu-Pro-Asp-Thr-Trp-Lys-
             Ser-Leu-Leu-Gln-His-Ser-Lys-
             Ile-Thr
SEQ. ID. NO. Gly-Gly-Asn-Ser-Gly-Val-Ser-
101          Gly-Pro-Ile-Asn-Phe-Thr-His-
             Lys-Val-His-Val-Gly-Phe-Asp-
             Arg-Lys-Ser-Leu-Thr-Ile-Tyr-
             Ala-Gln-Val-Gln-Lys-Asn-Phe-
             Thr-Gly-Leu-Pro-Asp-Thr-Trp-
             Lys-Ser-Leu-Leu-Gln-His-Ser-
             Lys-Ile-Thr
SEQ. ID. NO. Bbs-R-dPip-Gly-Arg-Lys-Ser-
102          Leu-Thr-Ile-Tyr-Ala-Gln-Val-
             Gln-Lys-Gly-Asp-Phe-Glu-Glu-
             Ile-Pro-Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. Gly-Thr-Leu-Asp-Leu-Asn-Thr-
103          Pro-Val-Asp-Lys-Thr-Ser-Asn-
SEQ. ID. NO. Gly-Ser-His-Ala-Pro-Arg-Pro-
104          Gln-Ile-His-Asn-Asp-
SEQ. ID. NO. Gly-Ser-Val-Val-Pro-Arg-Pro-
105          Gln-Leu-His-Asn-Asp-
SEQ. ID. NO. Gly-His-His-Leu-Gly-Gly-Ala-
106          Lys-Gln-Ala-Gly-Asp-Val-
SEQ. ID. NO. Gly-Tyr-Met-Glu-Ser-Arg-Ala-
107          Asp-Arg-
SEQ. ID. NO. Gly-Gln-Ser-His-Asn-Arg-
108
SEQ. ID. NO. Ac-Asp-Lys-Asn-Ala-Asp-Gly-
109          Trp-Ile-Asp-Asn-Gly-Glu-Phe-
             Glu-NH2
SEQ. ID. NO. Ac-Asp-Lys-Asn-Ala-Asp-Gly-
110          Trp-Ile-Asp-Asn-Gly-Asp-Phe-
             Glu-NH2
SEQ. ID. NO. Leu-Ile-Glu-Asp-Ile-Cys-Leu-
111          Pro-Arg-Trp-Gly-Cys-Leu-Trp-
             Glu-Asp
SEQ. ID. NO. Bbs-Arg-(D-Pip)-Gly-Leu-Ile-
112          Glu-Asp-Ile-Cys-Leu-Pro-Arg-
             Trp-Gly-Cys-Leu-Trp-Glu-Asp-
             Gly-Asp-Phe-Gln-Gln-Ile-Pro-
             Glu-Glu-Tyr-Leu-Gln
SEQ. ID. NO. ((Gly-Ser)n-Gly-Asp-Phe-Glu-
113          Glu-Ile-Pro-Glu-Glu-Tyr-Leu-
             Gln)
SEQ. ID. NO. Cys-Asp-Lys-Asn-Ala-Asp-Gly-
114          Trp-Ile-Asp-Asn-Gly-Asp-Phe-
             Glu-Glu-Ile-Pro-Glu-Glu-Tyr-
             Leu-Gln
SEQ. ID. NO. Bbs-R-(D-Pip)-Gly-(Ser-Pro-
115          His-B-Glu-Lys-Val-Ser-Gly)2-
             Asp-Phe-Glu-Glu-Ile-Pro-Glu-
             Glu-Tyr-Leu-Gln
SEQ. ID. NO. Ile-Arg-Phe-Thr-Asp-Gly-Glu-
116          Gly
SEQ. ID. NO. Ile-Arg-Phe-Thr-Asp-Gly-Glu-
117          Gly-(CamCKK)-Asp-Phe-Glu-
             Glu-Ile-Pro-Glu-Glu-Tyr-Leu-
             Gln
SEQ. ID. NO. (Val-Pro-Gly-Val-Gly)19-Val-
118          Pro-Gly-Val
SEQ. ID. NO. Bbs-Arg-dPip-Gly-(Val-Pro-
119          Gly-Val-Gly)20-Asp-Phe-Glu-
             Glu-Ile-Pro-Glu-Glu-Tyr-Leu-
             Gln
SEQ. ID. NO. Gly-(Val-Pro-Gly-Val-Gly)19-
120          Val-Pro-Gly-Val
SEQ. ID. NO. Ile-Arg-Phe-Thr-Asp-Gly-Glu-
121          Gly-(Val-Pro-Gly-Val-Gly)20-
             Asp-Phe-Glu-Glu-Ile-Pro-Glu-
             Glu-Leu-Gln
SEQ. ID. NO. Bbs-Arg-dPip-Gly
122
SEQ. ID. NO. Gly-Ser-Pro-His-Tyr-Glu-Lys-
123          Val-Ser
SEQ. ID. NO. Gly-Ser-Pro-His-Tyr(P)-Glu-
124          Lys-Val-Ser
SEQ. ID. NO. Gly-Ser-Pro-His-Tyr-Glu-Lys-
125          Val-Ser-Gly-Ser-Pro-His-Tyr-
             Glu-Lys-Val-Ser
SEQ. ID. NO. Gly-Ser-Pro-His-Tyr(P)-Glu-
126          Lys-Val-Ser-Gly-Ser-Pro-His-
             Tyr(P)-Glu-Lys-Val-Ser
SEQ. ID. NO. Gly-Glu-Gln-Lys-Leu-Ile-Ser-
127          Glu-Glu-Asp-Leu
SEQ. ID. NO. Gly-Arg-Lys-Ser-Leu-Thr-Ile-
128          Tyr-Ala-Gln-Val-Gln-Lys
SEQ. ID. NO. -Ser-Pro-His-Tyr(P)-Glu-Lys-
129          Val-Ser-Gly-
SEQ. ID. NO. GGNSGFPGPI NFTHKVHVGF
130          DRKSLTIYAQ VQKNFTGLPD
             TWKSLLQHSK IT
SEQ. ID. NO. YGRKKRRQRR RGGNSGFPGP
131          INFTHKVHVG FDRKSLTIYA
             QVQKNFTGLP
SEQ. ID. NO. GSSHHHHHHSSFNPRGSWYY
132          GNVTRHQAECALNERGVEGDFLIRDSE
             SSPSDFSVSLKASGRNKHFKVQL
             VDSVYCIGQRRFHSMDELVEHYKKAP
             IFTSEHGEKLYLVRALQ
SEQ. ID. NO. GSSHHHHHHSSFNPRGSD
133          AVAVYHGKISRETGEKLLLATGLDG
             SYLLRDSESVPGVYCLCVLYHGYI
             YTYRVSQTETGSWSAETAPGVHKRYF
             RKIKNLISAFQKPDQGIVIPLQVPVEK
SEQ. ID. NO. GSSHHHHHHSSGLVPRGSHMQTIKCVV
134          VGDGAVGKTCLLISYTTSKFPA
             DYVPTVFDNYAVTVMIGDEPFTLGLF
             DTAGQEDYDRLRPLSYPSTDV
             FLVCFSVISPASFENVKEKWFPEVHHH
             CPGVPIIIVGTQTDLRNDDVI
             LQRLHRQKLSPITQEQGEKLAKELKA
             VKYVECSALTQRGLKTVFDEAIVAALE

TABLE 4
Full sequences of recombinant
peptides and proteins
1. eCla4-SLAM
GGNSGFPGPI NFTHKVHVGF DRKSLTIYAQ VQKNFTGLPD
TWKSLLQHSK IT
(SEQ. ID. NO. 130)
2. TAT-eCla4-SLAM:
YGRKKRRQRR RGGNSGFPGP INFTHKVHVG FDRKSLTIYA
QVQKNFTGLP DTWKSLLQHS KIT
(SEQ. ID. NO. 131)
3. Grb4-SH2
GSSHHHHHHSSFNPRGSWYYGNVTRHQAECALNERGVEGDFLIRDSESSP
SDFSVSLKASGRNKHFKVQLVDSVYCIGQRRFHSMDELVEHYKKAP IFT
SEHGEKLYLVRALQ
(SEQ. ID. NO. 132)
4. SAP-SH2:
GSSHHHHHH SSFNPRGSD AVAVYHGKISR ETGEKLLLATGLDG
SYLLRDSESVPGVYCLC VLYHGYI YTYRVSQT ETGSWSAE
TAPGVHKRYF RKIKNLI SAFQ KPDQGI VIPLQYPVEK
(SEQ. ID. NO. 133)
5. CaCdc42 (R150K)
GSSHHHHHHS SGLVPRGSH MQTIKCVV VGDGAVG KTCLLISY
TTSKFPA DYVPTVF DNYAVT VMIGDE PFTLGLF DTAGQED
YDRLRPL SYPSTDV FLVCFSV ISPASF ENVKEKW FPEVHHH
CPGVPII IVGTQTD LRNDDVI LQRLHRQ KLSPIT QEQGEKLA
KELKA VKYVEC SALTQRGLKT VFDEA IVAALE
(SEQ. ID. NO. 134)
6. CaM-DTI:
WDPRPQRHADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQN
PTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTGGVKLIPSWTTVI
LVKSMLRKRSFGNPFGGDSEEEIREAFRVFDKDGNGYISAAELRHVMTNL
GEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAKDFEEIPEEYLQ
(SEQ. ID. NO. 21)
7. CaM-DTI2:
IRFTDGEGADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQN
PTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDNGGVKLIPSWTTVI
LVKSMLRKRSFGNPFGGDSEEEIREAFRVFDKDGNGYIRAAELRHVMTNL
GEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAKDFEEIPEEYLQ
(SEQ. ID. NO. 117)

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Claims

1. A molecule comprised of a structure useful in binding a target, said molecule having the general formula (1) of BM1-L-BM2  (1)

2. The molecule of claim 1 wherein the binding affinity of BM1 or BM2 alone is no more than ½ the binding affinity of the molecule.

3. The molecule of claim 1 wherein the linker is an oligomeric or polymeric linker.

4. The molecule of claim 1 wherein the linker comprises an amino acid sequence.

5. The molecule of claim 4 wherein the amino acid sequence is selected from at least one of SEQ. D. NO. 8, 12, 17, 24, 27, 28, 37-47, 48, 49, 50-56, 57, 58, 59-60, 124-126, 127, or 128.

6. The molecule of claim 1 wherein BM1 comprises an amino acid sequence selected from: SEQ. ID. NO. 6, 9, 15, 19, 35, 68, 69-71, 72, 93, 92, 94-95, 116, 122 or linked sequences SEQ. ID. NO. 15 and SEQ. ID. NO. 16.

7. The molecule of claim 1 wherein BM2 comprises an amino acid sequence selected from SEQ. ID. NO. 1, 20, 36, 96-99.

8. The molecule of claim 1 comprising at least one amino acid sequence selected from SEQ. ID. NO. 2, 9, 10, 11, 13, 14, 16, 21, 22, 23, 25, 29, 32, 33, 34, 73, 74, 75, 76, 77, 78, 79, 80, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 100, 101, 102, 112, 115, 117, 119, 121, or 117.

9. The molecule of claim 1, said sequence comprising a series of contiguous amino acids having at least 90% sequence identity to at least one of SEQ. ID. NO. 8, 12, 17, 24, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 63, 64, 65, 66, 67, 103, 104, 105, 106, 107, 108, 109, 110, 111, 118, 120, 123, 124, 125, 126, 127, or 128.

10. A nucleic acid sequence encoding the amino acid sequence of claim 9.

11. An amino acid sequence having at least 95% sequence identity to at least one of SEQ. ID. NO. 2, 9, 10, 11, 13, 14, 16, 21, 22, 23, 25, 29, 32, 33, 34, 73, 74, 75, 76, 77, 78, 79, 80, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 100, 101, 102, 112, 115, 117, 119, 121, or 117.

12. A nucleic acid sequence encoding the amino acid sequence of claim 11.

13. A pharmaceutical composition comprising a molecule of claim 1 with a carrier.

14. (canceled)

15. A method to screen a population of molecules to identify a ligand of interest, said method comprising: a) selecting a target of interest with a known affinity for a component;b) selecting a second molecule having a known affinity for the component of step (b); said second molecule binding a different region of the component from the region bound by the target;c) connecting the target and the second molecule with a suitable linker to create a bivalent structure;d) monitoring binding of the bivalent structure to the component in the presence of ligands;e) identifying a ligand which reduces the level of bivalent binding.

16. The method of claim 15 wherein the linker selected is one which undergoes an assayable conformation change during the transition between bivalent and monovalent binding, such that this conformation change can be readily assayed.

17-18. (canceled)

19. A method of assaying for the presence of a substance of concern in a sample, said method comprising: a) identifying a first target region known to be present on the substance of concern and less common within sample material which does not contain the substance;b) identifying a second target region known to be present on the substance of concern;c) obtaining a plurality of molecules comprising a first binding region having affinity for the first target region connected by way of a linker to a second binding region having affinity for the second target region, wherein the linker undergoes an assayable conformational change during the transition between bivalent and monovalent binding;d) combining molecules from step (c) with the sample; ande) assaying for bivalent binding.

20-21. (canceled)

22. The molecule of claim 1 wherein the linker is a controllable flexible linker.

23. The molecule of claim 22 wherein the linker contains a specific binding site for a binding molecule.

24. The molecule of claim 23 wherein the linker contains at least one amino acid which is a substrate for a kinase or phosphatase.

25. The molecule of claim 24 wherein the linker conformation is modulated by SH2 binding.

26. The molecule of claim 22 wherein the linker contains a specific binding site for an antibody.

27. The molecule of claim 26 wherein the antibody is a monoclonal antibody.

28. The molecule of claim 27 wherein the specific binding site is SEQ. ID. NO. 12 and the antibody is 9E10.

29. The molecule of claim 22 wherein the linker contains residues capable of forming disulfide bonds with each other.

30. The molecule of claim 22 wherein the linker has an affinity for a metal.

31. The molecule of claim 30 wherein the linker comprises SEQ. ID. NO. 17 and the metal ion is a calcium ion.

32. The molecule of claim 30 wherein the linker comprises SEQ. ID. NO. 21 and the metal is calcium.

33. The molecule of claim 22 wherein the linker undergoes a folding transition in response to a change in pH.

34. The molecule of claim 22 wherein the linker undergoes a folding transition in response to a change in ionic strength.

35. The molecule of claim 22 wherein the linker undergoes a folding transition in response to a change in temperature.

36-38. (canceled)

39. A molecule of claim 1 comprising at least one of SEQ. 37, 38, 92, 93, 94, 95, 100, or 101.

40. The polypeptide sequence of claim 39 further comprising at least one of SEQ. ID. NO. 96, 97, 98 or 99.

41. The molecule of claim 1 wherein the linker has a metal and/or magnetic nanoparticle conjugated to it.

42. (canceled)

43. The molecule of claim 1 wherein bivalent binding of the molecule causes the linker to undergo a change in fluorescent, chromogenic, or chiral properties.

44-46. (canceled)

47. A kit comprising a polypeptide comprising SEQ. ID. NO. 29 together with SH2 and thrombin.

48-50. (canceled)

51. The molecule of claim 1 wherein the linker has an affinity for prothrombin.

52. The molecule of claim 1 comprising at least one of SEQ. ID. NO. 32 and 33.

53. A kit comprising: (a) a controllable polymeric linker having a first end and a second end; and(b) instructions for the conjugation of a binding moiety to the first and second end of the linker.

54. The kit of claim 53 wherein the linker is designed to undergo a structural change in response to a change in physical environment.

55-61. (canceled)

62. A method for the purification of a target, said method comprising: a) immobilizing onto a solid support a molecule of claim 1 capable of binding to the target via BM1 and BM2;b) allowing the target to bind the molecule of step (a)c) eluting unbound materials;d) eluting the target by inducing a condition which causes a change in structure and/or flexibility of the molecule of step (a) such that bivalent binding of the target by the molecule is reduced.

63. The molecule of claim 1 covalently attached to the target at a point in addition to BM1 or BM2.

64. The molecule of claim 63 wherein the molecule is covalently attached to its target.

65. The molecule of claim 65 wherein the molecule is attached to its target by means of recombinant conjugation.

66. The method of claim 15, wherein a change in linker structure or flexibility is assayable by nuclear magnetic resonance, surface plasmon resonance, and/or H/D exchange.

67. The method of claim 15, wherein the linker is selected to undergo a structural change assayable by a change in fluorescence, optical chiral properties or absorbance properties.