# Patent

## Title
Cross-β structure comprising amyloid-binding proteins and methods for detection of the cross-β structure, for modulating cross-β structures fiber formation and modulating cross-β structure-mediated toxicity

## Abstract

The invention relates to the field of biochemistry, molecular biology, structural biology and medicine. More in particular, the invention relates to cross-β structures and the biological role of these cross-β structures. In one embodiment, the invention discloses a method for modulating extracellular protein degradation and/or protein clearance comprising modulating cross-β(beta) structure formation (and/or cross-β structure-mediated activity) of the protein present in the circulation.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a divisional of application Ser. No. 11/033,105, filed Jan. 10, 2005, pending, which is a continuation of PCT International Patent Application PCT/NL2003/000501, filed Jul. 8, 2003, designating the United States of America, corresponding to PCT International Publication WO 2004/004698 A3 (published in English on Jan. 15, 2004). The disclosure of each of the previously referenced patent applications referenced is hereby incorporated by reference in its entirety.


STATEMENT ACCORDING TO 37 C.F.R. §1.52(e)(5)
Sequence Listing Submitted on Compact Disc
Pursuant to 37 C.F.R. §1.52(e)(1)(iii), a compact disc containing an electronic version of the Sequence Listing has been submitted concomitant with this application, the contents of which are hereby incorporated by reference. A second compact disc is submitted and is an identical copy of the first compact disc. The discs are labeled “copy 1” and “copy 2,” respectively, and each disc contains one file entitled “sequence listing.txt” which is 16 KB and created on Sep. 4, 2007.
TECHNICAL FIELD
The invention relates to the fields of biotechnology, biochemistry, molecular biology, structural biology and medicine. More in particular, the invention relates to cross-β structure, their binding proteins and their biological roles.
BACKGROUND
An increasing body of evidence suggests that unfolding of globular proteins can lead to toxicity.1 Unfolded proteins can initiate protein aggregation and fibrillization by adopting a partially structured conformation. Such fibrillar aggregates can (slowly) accumulate in various tissue types and are associated with a variety of degenerative diseases. The term “amyloid” is used to describe these fibrillar deposits (or plaques). Diseases characterized by amyloids are referred to as amyloidosis and include Alzheimer disease (AD), light-chain amyloidosis, type II diabetes and spongiform encephalopathies. It has been found recently that toxicity is an inherent property of misfolded proteins. According to the present invention, this is the common mechanism for these conformational diseases.1 
A cross-β structure is a secondary structural element in peptides or proteins. A cross-β structure can be formed upon denaturation, proteolysis or unfolding of proteins.2 These secondary structure elements are typically absent in globular regions of proteins. The cross-β structure is found in amyloid fibers. Amyloid peptides or proteins are cytotoxic to cells. A cross-β structure includes stacked β-sheets. In a cross-β structure, the individual β-strands either run perpendicular to the long axis of a fibril or run in parallel to the long axis of a fibril. The direction of the stacking of the β-sheets in cross-β structures is perpendicular to the long fibril axis.
SUMMARY OF THE INVENTION
It is reported herein that glycation of proteins also induces the formation of the cross-β structure. These results, combined with existing literature information, indicate that a common structure is induced upon unfolding of globular proteins. Therefore, the present invention discloses a novel pathway involving a cross-β structure, which pathway will be called a “cross-β structure pathway.” This pathway includes several cross-β structure-binding proteins, including so-called multiligand receptors, and is involved in degradation and/or clearance of unwanted or destroyed (denatured) proteins. Also reported herein is the identification of novel cross-β-binding proteins that contain a cross-β structure-binding module. These findings support the identification of a cross-β structure pathway. Multiple aspects of this novel pathway are outlined below.
In one embodiment, the present invention discloses that proteolyzed, denatured, unfolded, glycated, oxidized, acetylated or otherwise structurally altered proteins adopt cross-β structures. Examples of known cross-β structure-forming proteins are all proteins that cause amyloidosis or proteins that are found in disease-related amyloid depositions, for example, but not restricted to, Alzheimer β-amyloid (Aβ) and Islet Amyloid PolyPeptide (IAPP). The present invention discloses that fibrin, glycated proteins (for example, glycated albumin and glycated hemoglobin), and endostatin are also capable of adopting a cross-β structure.
The invention furthermore discloses the identification of the formation of a cross-β structure as a signal for protein degradation and/or protein clearance.
The serine protease tissue plasminogen activator (tPA) induces the formation of plasmin through cleavage of plasminogen. Plasmin cleaves fibrin and this occurs during lysis of a blood clot. Although not essential for fibrinolysis in mice,3, 4 tPA has been recognized for its role in fibrinolysis for a long time.5, 6 Activation of plasminogen by tPA is stimulated by fibrin or fibrin fragments, but not by its precursor, fibrinogen.7-10 This can be in part explained by the strong binding of tPA to fibrin and weak binding to fibrinogen. The binding sites in fibrin and in tPA responsible for binding and activation of tPA have been mapped and studied in detail.8-21 However, the exact structural basis for the interaction of tPA with fibrin was unknown. In addition to fibrin and fibrin fragments, many other proteins have been described that are similarly capable of binding tPA and stimulating tPA-mediated plasmin formation.22-36 Like with fibrin and fibrin fragments, the exact nature of the interaction(s) between these ligands for tPA and tPA were not known. Moreover, it was unknown why and how all of these proteins, which lack primary sequence homology, bind tPA. The present invention discloses tissue-type plasminogen activator (tPA) as a protein capable of binding cross-β structures. Furthermore, the invention discloses the finger domain (also named fibronectin type I domain) and other comparable finger domains as a cross-β structure-binding module. The present invention further discloses that proteins which bind to these fingers will be typically capable of forming cross-β structures.
Since fibrin contains the cross-β structure, the present invention also discloses that the generation of cross-β structures plays a role in physiological processes. The invention discloses that the generation of cross-β structures is part of a signaling pathway, the “cross-β structure pathway,” that regulates protein degradation and/or protein clearance. Inadequate function of this pathway may result in the development of diseases, such as conformational diseases37 and/or amyloidosis.
The present invention furthermore discloses that the cross-β structure is a common denominator in ligands for multiligand receptors.38 The invention discloses, therefore, that multiligand receptors belong to the “cross-β structure pathway.”
The best studied example of a receptor for a cross-β structure is RAGE.39-44 Examples of ligands for RAGE are Aβ, protein-advanced glycation end-products (AGE) adducts (including glycated-BSA), amphoterin and S100. RAGE is a member of a larger family of multiligand receptors38 that includes several other receptors, some of which, including CD36, are known to bind cross-β structure-containing proteins (see also FIG. 1). At present, it is not clear what the exact nature of the structure or structures is in the ligands of these receptors that mediates the binding to these receptors. It is reported herein that glycation of proteins also induces the formation of a cross-β structure. Therefore, it is disclosed that all of these receptors form part of a mechanism to deal with the destruction and removal of unwanted or even damaging proteins or agents. These receptors play a role in recognition of infectious agents or cells, recognition of apoptotic cells and in internalization of protein complexes and/or pathogens. It is furthermore disclosed that all of these receptors recognize the same or similar structure, the cross-β structure, to respond to undesired molecules. It is shown herein that tPA binds cross-β structures, providing evidence that tPA belongs to the multiligand receptor family. As disclosed herein, tPA and the other multiligand receptors bind the cross-β structure and participate in the destruction of unwanted biomolecules. A prominent role of the protease tPA in the pathway lies in its ability to initiate a proteolytic cascade that includes the formation of plasmin. Proteolysis is likely to be essential for the degradation and subsequent removal of extracellular matrix components. The effect of tPA on the extracellular matrix will affect cell adhesion, cell migration, cell survival and cell death, through, for example, integrin-mediated processes. Based on these studies, strong evidence is provided that at least three other proteins, FXII (factor XII), hepatocyte growth factor activator (HGFa), and fibronectin, that contain one or more finger domain(s) are also part of the “cross-β structure pathway.”
The role of FXII is especially important, since it activates the intrinsic coagulation pathway. Activation of the intrinsic pathway, the resulting formation of vasoactive peptides, and the activation of other important proteins contribute to the process of protection and/or clearance of undesired proteins or agents. The “cross-β structure pathway” is modulated in many ways. Factors that regulate the pathway include modulators of synthesis and secretion, as well as modulators of activity. The pathway is involved in many physiological and pathological processes. Therefore, the invention furthermore provides a method for modulating extracellular protein degradation and/or protein clearance comprising modulating the activity of a receptor for cross-β structure-forming proteins. Examples of receptors for cross-β structure-forming proteins include RAGE, CD36, Low density lipoprotein-Related Protein (LRP), Scavenger Receptor B-1 (SR-B1), and SR-A. The invention discloses that FXII, HGFa and fibronectin are also receptors for cross-β structures.
The present invention discloses that tissue-type plasminogen activator (tPA) is a cross-β structure-binding protein, a multiligand receptor and a member of the “cross-β structure pathway.” The invention discloses that tPA mediates cross-β structure-induced cell dysfunction and/or cell toxicity. The invention discloses that tPA mediates, at least in part, cell dysfunction and/or toxicity through activation of plasminogen. The plasminogen-dependent effects are inhibited by B-type carboxypeptidase activity B and, thus, a role for carboxyterminal lysine residues in the cross-β structure pathway is disclosed.
The present invention relates, amongst others, to the structure(s) in fibrin and other proteins that bind tPA, to the binding domain in tPA, and to the pathway(s) regulated by this structure. The present invention discloses a presence of cross-β structures in proteins and peptides that are capable of binding tPA. The herein-disclosed results indicate a strong correlation between the presence of a cross-β structure and the ability of a molecule to bind tPA. Furthermore, the results indicate the presence of an amyloid structure in fibrin. This indicates that under physiological conditions, a cross-β structure can form, a phenomenon that has been previously unrecognized. The formation of cross-β structures has thus far only been associated with severe pathological disorders. tPA binds denatured proteins, which indicates that a large number of proteins, if not all proteins, can adopt a conformation containing cross-β structures or cross-β-like structure(s). Taken together, the formation of cross-β structures is likely to initiate and/or participate in a physiological cascade of events necessary to adequately deal with removal of unwanted molecules, i.e., misfolded proteins, apoptotic cells or even pathogens. FIG. 1 shows a schematic representation of the “cross-β structure pathway.” This pathway regulates the removal of unwanted biomolecules during several processes, including fibrinolysis, formation of neuronal synaptic networks, clearance of used, unwanted and/or destroyed (denatured) proteins, induction of apoptosis and clearance of apoptotic cells and pathogens. If insufficiently or incorrectly regulated or disbalanced, the pathway may lead to severe disease.
Thus, in a first embodiment, the invention discloses a method for modulating extracellular protein degradation and/or protein clearance comprising modulating cross-β(beta) structure formation (and/or cross-β structure-mediated activity) of the protein present in the circulation.
There are two major regular protein-folding patterns, which are known as the β(beta)-sheet and the a-helix. An antiparallel β-sheet is formed when an extended polypeptide chain folds back and forth upon itself; with each section of the chains running in the direction opposite to that of its immediate neighbors. This gives a structure held together by hydrogen bonds that connect the peptide bonds in neighboring chains. Regions of a polypeptide chain that run in the same direction form a parallel β-sheet. A cross-β structure is composed of stacked β-sheets. As disclosed herein, a broad range of proteins is capable of adopting a cross-β structure and, moreover, these cross-β structure-comprising proteins are all capable of binding and stimulating tPA, thus promoting destruction of unwanted or damaging proteins or agents.
An extracellular protein is typically defined as a protein present outside a cell or cells.
Protein degradation and/or protein clearance includes the breakdown and removal of unwanted proteins, for example, unwanted and/or destroyed (for example, denatured) proteins. Also included is the removal of unwanted biomolecules during several processes, including fibrinolysis, formation of neuronal synaptic networks, clearance of used, unwanted and/or destroyed (denatured) proteins, induction of apoptosis and clearance of apoptotic cells and pathogens.
The term “in the circulation” is herein defined as a circulation outside a cell or cells, for example, but not restricted to, the continuous movement of blood.
In yet another embodiment, the invention discloses a method for increasing extracellular protein degradation and/or protein clearance comprising increasing cross-β structure formation and/or cross-β structure-mediated activity of a protein present in the circulation. Increase of cross-β structure formation of a particular protein leads, for example, to activation of tPA, which, in turn, induces the formation of plasmin through cleavage of plasminogen and thus results in an increase in the degradation and/or protein clearance.
In one embodiment, the invention discloses a method for increasing extracellular protein degradation and/or protein clearance comprising providing a compound capable of increasing cross-β structure formation (and/or cross-β structure-mediated activity) of a protein present in the circulation. In another embodiment, the compound capable of increasing cross-β structure formation is glucose. Under certain circumstances, the addition of glucose to a protein leads to an irreversible, non-enzymatic glycation reaction in which predominantly a glucose molecule is attached to the free amino groups of lysine residues in a protein. In addition, N-termini and free amino groups of arginine residues are prone to glycation. It is disclosed herein within the experimental part that glycation leads to cross-β structure formation. Hence, the invention discloses a method for increasing extracellular protein degradation and/or protein clearance comprising providing a compound capable of increasing cross-β structure formation of the protein present in the circulation.
Other examples of compounds capable of increasing (or mimicking) cross-β structure formation in a protein are apolar solutions, urea (as disclosed herein within the experimental part), and ions (for example Zn2+). However, it is clear that there are also other ways to increase or mimic cross-β structure formation, for example, by denaturation, low pH, temperature, mutations or protein modification in general (for example, oxidation).
In addition to a method for increasing extracellular protein degradation and/or protein clearance comprising increasing cross-β structure formation of the protein present in the circulation via any of the above-described methods to degrade and/or remove, preferably, the protein which comprises the cross-β structure, it is also possible to degrade and/or remove a protein which does not comprise a cross-β structure. This is, for example, accomplished by providing a compound comprising a cross-β structure and a compound comprising tPA-like activity at or near the protein which needs to be degraded and/or removed. An example of a compound comprising a cross-β structure is fibrin or a fragment thereof comprising the cross-β structure. An example of a compound comprising tPA-like activity is tPA.
In another embodiment, the invention discloses a method for decreasing extracellular protein degradation and/or protein clearance comprising decreasing cross-β structure formation of the protein present in the circulation. For instance, the invention discloses a method for decreasing extracellular protein degradation and/or protein clearance comprising providing a compound capable of decreasing cross-β structure formation of the protein present in the circulation. Decreasing of cross-β structure formation is, for example, accomplished by shielding or blocking of the groups involved in the formation of a cross-β structure. Examples of compounds capable of decreasing cross-β structure formation are Congo red, antibodies, β-breakers, phosphonates, heparin, amino-guanidine or laminin.45 Yet another way to decrease cross-β structure formation in a protein is by removal of a glucose group involved in the glycation of the protein.
In yet another embodiment, the invention discloses a method for modulating extracellular protein degradation and/or protein clearance comprising modulating tPA or tPA-like activity. tPA induces the formation of plasmin through cleavage of plasminogen. Plasmin cleaves fibrin and this occurs during lysis of a blood clot. Activation of plasminogen by tPA is stimulated by fibrin or fibrin fragments, but not by its precursor fibrinogen. The term “tPA-like activity” is herein defined as a compound capable of inducing the formation of plasmin, possibly in different amounts, and/or other tPA-mediated activities. Preferably, tPA-like activity is modified such that it has a higher activity or affinity towards its substrate and/or a cofactor. This is, for example, accomplished by providing the tPA-like activity with multiple binding domains for cross-β structure-comprising proteins. Preferably, the tPA-like activity is provided with multiple finger domains. It is herein disclosed that the three-dimensional structures of the tPA finger domain and the fibronectin finger domains 4-5 reveal striking structural homology with respect to local charge-density distribution. Both structures contain a similar solvent-exposed stretch of five amino acid residues with alternating charge; for tPA, Arg7, Glu9, Arg23, Glu32, Arg30, and for fibronectin, Arg83, Glu85, Lys87, Glu89, Arg90, located at the fifth finger domain, respectively. The charged-residue alignments are located at the same side of the finger module. Hence, the tPA-like activity is provided with one or more extra finger domain(s) which comprise(s) ArgXGlu(X)13Arg(X)6ArgXGlu (SEQ ID NO: 1) or ArgXGluXLysXGluArg (SEQ ID NO: 2).
The activity of tPA and/or the tPA-mediated activation of plasminogen is increased by the binding to fibrin fragments or other protein fragments that have a lysine or an arginine at the carboxy-terminal end. B-type carboxypeptidases, including, but not limited to, carboxypeptidase B (CpB) or Thrombin Activatable Fibrinolysis Inhibitor (TAFI, also named carboxypeptidase U or carboxypeptidase R), are enzymes that cleave off carboxy-terminal lysine and arginine residues of fibrin fragments that would otherwise bind to tPA and/or plasminogen and stimulate plasmin formation.
In one embodiment, the invention discloses a method for increasing extracellular protein degradation and/or protein clearance comprising providing a compound capable of increasing tPA-like and/or tPA-mediated activity or activities. In another embodiment, the invention discloses a method for increasing extracellular protein degradation and/or protein clearance comprising providing a compound capable of increasing tPA-like activity, wherein the compound comprises a cross-β structure. In another embodiment, the invention discloses a method for increasing extracellular protein degradation and/or protein clearance comprising providing a compound capable of inhibiting B-type carboxypeptidase activity. In an additional embodiment, the compound comprises carboxypeptidase inhibitor (CPI) activity.
In yet another embodiment, the invention discloses a method for decreasing extracellular protein degradation and/or protein clearance comprising providing a compound capable of decreasing tPA-like activity. In one aspect, the invention discloses a method for decreasing extracellular protein degradation and/or protein clearance comprising providing a compound capable of decreasing tPA-like activity or tPA-mediated activity or activities, wherein the compound is a protein and/or a functional equivalent and/or a functional fragment thereof. For example, such a compound capable of decreasing tPA-like activity is an inhibitor of tPA or a substrate of tPA which binds and does not let go. Examples of a compound capable of decreasing tPA-like activity or tPA-mediated activity include, but are not limited to, lysine, arginine, e-amino-caproic acid or tranexamic acid, serpins (for example, neuroserpin, PAI-1), tPA-Pevabloc, antibodies that inhibit tPA-like activity or tPA-mediated activity or B-type carboxypeptidase(s). For example, providing lysine results in the prevention or inhibition of binding of a protein comprising a C-terminal lysine-residue to the Kringle domain of plasminogen. Hence, tPA activation is prevented or inhibited. Preferably, the compound capable of decreasing tPA-like activity or tPA-mediated activity or activities reduce the tPA-like activity or tPA-mediated activity or activities and, even more preferably, the tPA-like activity or tPA-mediated activity or activities is completely inhibited.
A functional fragment and/or a functional equivalent are typically defined as a fragment and/or an equivalent capable of performing the same function, possibly in different amounts. For example, a functional fragment of an antibody capable of binding to a cross-β structure would be the Fab′ fragment of the antibody.
In yet another embodiment, the invention discloses a method for modulating extracellular protein degradation and/or protein clearance comprising modulating an interaction between a compound comprising a cross-β structure and a compound comprising tPA-like activity. In another embodiment, the invention discloses a method for decreasing extracellular protein degradation and/or protein clearance comprising decreasing an interaction between a compound comprising a cross-β structure and a compound comprising tPA-like activity. Such a compound is, for example, a chemical, a proteinaceous substance or a combination thereof. In an additional embodiment, the invention discloses a method for decreasing extracellular protein degradation and/or protein clearance comprising providing a compound capable of decreasing an interaction between a compound comprising a cross-β structure and a compound comprising tPA-like activity. In one aspect, the invention discloses a method for decreasing extracellular protein degradation and/or protein clearance according to the invention, wherein the compound is a protein and/or a functional equivalent and/or a functional fragment thereof. In another aspect, the protein is an antibody and/or a functional equivalent and/or a functional fragment thereof.
Other examples are Congo red or Thioflavin. The invention also discloses a method for decreasing extracellular protein degradation and/or protein clearance comprising decreasing an interaction between a compound comprising a cross-β structure and a compound comprising tPA-like activity, wherein the interaction is decreased by providing a compound capable of competing with the interaction. More in particular, the compound capable of competing with the interaction comprises a finger domain and, even more particularly, the finger domain comprises a stretch of at least 5 amino acid residues with alternating charge, for example, ArgXGlu(X)13Arg(X)6ArgXGlu (SEQ ID NO: 1) or ArgXGluXLysXGluArg (SEQ ID NO: 2). In one aspect, the compound is fibronectin, FXII, HGFa or tPA.
In another embodiment, the invention also comprises a method for increasing extracellular protein degradation and/or protein clearance comprising increasing an interaction between a compound comprising a cross-β structure and a compound comprising tPA-like activity. This is, for example, accomplished by providing a compound capable of increasing an interaction between a compound comprising a cross-β structure and a compound comprising tPA-like activity. In one aspect, the compound capable of increasing an interaction between a compound comprising a cross-β structure and a compound comprising tPA-like activity is a protein and/or a functional equivalent and/or a functional fragment thereof. For example, an antibody which stabilizes the interaction between a compound comprising a cross-β structure and a compound comprising tPA-like activity, rendering the tPA-like activity in a continuous activated state, results in increased protein degradation and/or protein clearance. However, it is appreciated that increasing an interaction between a compound comprising a cross-β structure and a compound comprising tPA-like activity is also accomplished by mutations in either the compound comprising a cross-β structure or in the compound comprising tPA-like activity, like swapping of domains (for example, by providing the compound comprising tPA-like activity with other or more finger domains obtainable from tPA, fibronectin, FXII or HGFa), or by including binding domains of, for example, RAGE or CD36.
In yet another embodiment, the invention discloses a method for modulating extracellular protein degradation and/or protein clearance comprising modulating an interaction of a compound comprising tPA-like activity and the substrate of the activity. It is clear that there are multiple ways by which the interaction can either be increased or decreased. An increase in the interaction between a compound comprising tPA-like activity and the substrate of the activity is, for example, accomplished by providing the compound comprising tPA-like activity with a mutation or mutations which improve the affinity of the compound with tPA-like activity for its substrate.
In yet another embodiment, the invention discloses a method for removing cross-β structures from the circulation, using a compound comprising a cross-β structure-binding domain. In one aspect, the compound is tPA or the finger domain of tPA. It is clear that the invention also comprises other cross-β structure-binding domains, including, but not limited to, the finger domains of HGFa, FXII and fibronectin (SEQ ID NOs: 3-17). It is clear that the invention also comprises antibodies that bind cross-β structures.
The present invention further discloses the use of a novel strategy to prevent the formation of, or to decrease/diminish, (amyloid) plaques involved in a conformational disease, type II diabetes and/or aging (e.g., Alzheimer's disease). Plaques are typically defined as extracellular fibrillar protein deposits (fibrillar aggregates) and are characteristic of degenerative diseases. The “native” properties of the constituent amyloid proteins may vary: some are soluble oligomers in vivo (e.g., transthyretin in familial amyloid polyneuropathy), whereas others are flexible peptides (e.g., amyloid-b in Alzheimer's disease (AD)). The basic pathogenesis of conformational diseases, for example, neurodegenerative disorders (AD, prion disorders), is thought to be related to abnormal pathologic protein conformation, i.e., the conversion of a normal cellular and/or circulating protein into an insoluble, aggregated, β-structure-rich form which is deposited in the brain. These deposits are toxic and produce neuronal dysfunction and death. The formation of cross-β structures has thus far only been associated with severe pathological disorders. The results herein show that tPA and other receptors for cross-β structure-forming proteins can bind denatured proteins, indicating that a large number of proteins are capable of adopting a conformation containing cross-β or cross-β-like structures. Taken together, the formation of a cross-β structure initiates or participates in a physiological cascade of events necessary to adequately deal with removal of unwanted molecules, i.e., misfolded proteins, apoptotic cells or even pathogens. By increasing cross-β structure formation in a protein involved in a conformational disease, the pathway for protein degradation and/or protein clearance is activated and the protein is degraded, resulting in a decreasing plaque or, in another aspect, the plaque is completely removed. Hence, the effects of the conformational disease are diminished or, alternatively, completely abolished.
In a further embodiment, the invention discloses the use of a compound capable of increasing cross-β structure formation for diminishing plaques involved in a conformational disease. In another embodiment, the invention discloses the use of a compound capable of binding to a cross-β structure for diminishing plaques and/or inhibiting cross-β structure-mediated toxicity involved in a conformational disease. In one use of the invention, the compound is a protein and/or a functional equivalent and/or a functional fragment thereof and, in another aspect, the protein is tPA, a finger domain, an antibody and/or a functional equivalent and/or a functional fragment thereof. Examples of such antibodies are 4B5 or 3H7.
In a yet further embodiment, the invention discloses the use of a compound capable of increasing tPA-like activity for diminishing plaques involved in a conformational disease. In one aspect, the tPA-like activity is modified such that it has a higher activity or affinity towards its substrate and/or cofactor. This is, for example, accomplished by providing the tPA-like activity with multiple binding domains for cross-β structure-comprising proteins. In another aspect, the binding domain comprises a finger domain and, in an additional aspect, the finger domain comprises a stretch of at least five amino acid residues with alternating charge, for example ArgXGlu(x)13Arg(X)6ArgXGlu (SEQ ID NO: 1) or ArgXGluXLysXGluArg (SEQ ID NO: 2). In an additional embodiment, the finger domain is derived from fibronectin, FXII, HGFa or tPA.
In yet another embodiment, the invention discloses the use of a compound capable of binding to a cross-β structure for the removal of cross-β structures. In one aspect, the compound is a protein and/or a functional equivalent and/or a functional fragment thereof. In an additional aspect, the compound comprises tPA or tPA-like activity and/or a functional equivalent and/or a functional fragment thereof. In a further embodiment, the functional fragment comprises a finger domain. In one embodiment, the finger domain comprises a stretch of at least five amino acid residues with alternating charge, for example, ArgXGlu(X)13Arg(X)6ArgXGlu (SEQ ID NO: 1) or ArgXGluXLysXGluArg (SEQ ID NO: 2). In yet an additional embodiment, the finger domain is derived from fibronectin, FXII, HGFa or tPA. In another embodiment, the protein is an antibody and/or a functional equivalent and/or a functional fragment thereof. With this use, the invention discloses, for example, a therapeutic method to remove cross-β structure-comprising proteins from, for example, the circulation, such as via extracorporeal dialysis. For example, a patient with sepsis is subjected to such use by dialysis of the blood of that patient through means which are provided with, for example, immobilized finger domains. One could, for example, couple the finger domains to a carrier or to the inside of the tubes used for dialysis. In this way, all cross-β structure-comprising proteins will be removed from the blood stream of the patient, thus, relieving patients of the negative effects caused by the cross-β structure-comprising proteins. Besides finger domain-comprising compounds, it is also possible to use other cross-β structure-binding compounds, like antibodies or Congo Red. It is also clear that the use could be applied in hemodialysis of kidney patients.
In yet another embodiment, the invention discloses the use of a compound capable of increasing or stabilizing an interaction of a compound comprising a cross-β structure and a compound comprising tPA-like activity for diminishing plaques involved in a conformational disease. Examples of a compound capable of increasing or stabilizing an interaction of a compound comprising a cross-β structure and a compound comprising tPA-like activity are given herein. In another use, the invention is used to treat the conformational disease Alzheimer or diabetes. It is clear that the invention not only discloses a use to decrease/diminish plaques involved in a conformational disease, but also that the onset of the disease can also be inhibited or even completely prevented. Examples of diseases which can be prevented and/or treated according to the invention are conformational disease, amyloidosis-type diseases, atherosclerosis, diabetes, bleeding, thrombosis, cancer, sepsis and other inflammatory diseases, Multiple Sclerosis, auto-immune diseases, disease associated with loss of memory or Parkinson and other neuronal diseases (epilepsy).
In another embodiment, the invention discloses the use of an antibody capable of recognizing a cross-β structure epitope for determining the presence of plaque involved in a conformational disease. In yet another embodiment, the invention discloses the use of a cross-β structure-binding domain (such as a finger domain from, for example, tPA) for determining the presence of a plaque involved in a conformational disease.
These uses of the invention provide a new diagnostic tool. It was not until the present invention that a universal b-structure epitope was disclosed and that a diagnostic assay could be based on the presence of the cross-β structure. Such use is particularly useful for diagnostic identification of conformational diseases or diseases associated with amyloid formation, such as Alzheimer or diabetes. It is clear that this diagnostic use is also useful for other diseases which involve cross-β structure formation, like all amyloidosis-type diseases, atherosclerosis, diabetes, bleeding, cancer, sepsis and other inflammatory diseases, Multiple Sclerosis, auto-immune diseases, disease associated with loss of memory or Parkinsons and other neuronal diseases (epilepsy). For example, one can use a finger domain (of, for example, tPA) and provide it with a label (radioactive, fluorescent, etc.). This labeled finger domain may be used either in vitro or in vivo for the detection of cross-β structure-comprising proteins and, thus, for determining the presence of a plaque involved in a conformational disease. One can, for example, use an ELISA assay to determine the amount of sepsis in a patient or one can localize a plaque involved in a conformational disease.
In yet another embodiment, the invention discloses a recombinant tPA comprising an improved cross-β structure-binding domain or multiple cross-β structure-binding domains. In one aspect, tPA is provided with multiple, possibly different, finger domains. A recombinant tPA comprising an improved cross-β structure-binding domain or multiple cross-β structure-binding domains is used for different purposes, for example, in a method for the improved treatment of thrombolysis or for the removal of cross-β structure-comprising proteins from the circulation of a patient in need thereof. Another use of a recombinant tPA comprising an improved cross-β structure-binding domain or multiple cross-β structure-binding domains is in diagnostic assays such as, for example, in a BSE detection kit or in imaging experiments. This imaging with a recombinant tPA comprising an improved cross-β structure-binding domain or multiple cross-β structure-binding domains is, for example, useful for detection of apoptosis. For example, labeled tPA, such as, but not limited to, radio-labeled tPA, is inoculated in an individual, followed by detection and localization of labeled tPA in the body. It is clear that recombinant tPA comprising a cross-β structure-binding domain or multiple cross-β structure-binding domains are also useful in therapeutic applications.
Because this invention has made clear that the cross-β structure is harmful when present in certain parts of the body, like the brain, for example, and the damage is effected by the combination of cross-β structures with tPA, a method is provided to inhibit cross-β structure-mediated effects comprising providing an effective amount of a protein comprising a finger domain to block the binding sites of the cross-β structure for tPA. Cross-β structure-mediated effects may even be further diminished by providing an effective amount of B-type carboxypeptidase activity to inhibit the tPA activity.
In another embodiment, the local cross-β structure-mediated effect can be used against tumors. To that effect, cross-β structure-mediated effects are locally induced to increase local cytotoxicity and/or fibrinolysis comprising locally administering an effective amount of cross-β structures and/or cross-β structure-inducing compounds in conjunction with tPA or a compound with tPA-like activity and/or CPI or a compound with CPI-like activity.
The present invention discloses in a further embodiment a method which is carried out ex vivo, e.g., by dialysis. According to this embodiment, the circulating fluid (blood) of a subject is brought in a system outside the body for clearing cross-β structures from the circulation. In one aspect, such a system is a flow-through system connected to the body circulation with an inlet and an outlet. The cross-β structures are cleared by binding to a cross-β binding compound as defined hereinbefore. It is very important that no elements, such as the cross-β binding compounds from the system, are brought into the subject's circulation. For that reason, among others, preferred systems are dialysis systems. The invention further discloses devices for carrying out methods as disclosed herein. Thus, the invention discloses a separation device for carrying out a method according to the invention wherein the apparatus comprises a system for transporting circulation fluids ex vivo, the system provided with means for connecting to a subject's circulation for entry into the system and return from the system to the subject's circulation, the system comprising a solid phase, the solid phase comprising at least one compound capable of binding cross-β structures. Compounds for binding cross-β structures have been disclosed herein. In one aspect, the device is a dialysis apparatus.
The invention also provides for detection of cross-β structures in samples. Such samples may be tissue samples, biopsies and the like, body fluid samples, such as blood, serum, liquor, CSF, urine, and the like. The invention thus discloses a method for detecting cross-β structures in a sample, comprising contacting the sample with a compound capable of binding cross-β structures, allowing for binding of cross-β structures to the compound and detecting the complex formed through binding.
Cross-β binding compounds have been defined hereinbefore. Detection of the complex or one of its constituents can be done through any conventional means involving antibodies or other specific binding compounds, further cross-β binding compounds, etc. Detection can be direct such as by labeling the complex or a binding partner for the complex or its constituents, or even by measuring a change in a physical or chemical parameter of the complex versus unbound material. It may also be indirect by further binding compounds provided with a label. A label may be a radioactive label, an enzyme, a fluorescent molecule, etc.
The invention further discloses devices for carrying out the diagnostic methods. Thus, the invention discloses a diagnostic device for carrying out a method according to the invention, comprising a sample container, a means for contacting the sample with a cross-β binding compound, a cross-β binding compound and a means for detecting bound cross-β structures. In one embodiment, the device comprises a means for separating unbound cross-β structures from bound cross-β structures which can be typically done by providing the cross-β binding compounds on a solid phase.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a schematic representation of the “cross-β structure pathway.” The cross-β structure is found in a number of proteins (1). The formation of a cross-β structure can be triggered by several physiological or pathological conditions and subsequently initiates a cascade of events, the “cross-β structure pathway.” Among the factors that trigger or regulate the formation of a cross-β structure within a given protein are: 1) the physicochemical properties of the protein, 2) proteolysis, 3) regulated post-translational modification, including cross-linking, oxidation, phosphorylation, glycosylation and glycation, 4) glucose, and 5) zinc. Certain mutations within the sequence of a protein are known to increase the ability of the protein to adopt a cross-β structure and form amyloid fibers. These mutations are often found in hereditary forms of amyloidosis, for example in AD. The present invention discloses multiple novel examples of proteins capable of adopting a cross-β structure. Several proteins are known to bind cross-β-containing proteins (2). These proteins are part of the herein disclosed signaling cascade (“cross-β structure pathway”) that is triggered upon formation of a cross-β structure. The “cross-β structure pathway” is modulated in many ways (3, 4, 5). Factors that regulate the pathway include modulators of synthesis and secretion including NO regulators, as well as modulators of activity, including protease inhibitors. The pathway is involved in many physiological and pathological processes including, but not limited to, atherosclerosis, diabetes, amyloidosis, bleeding, inflammation, multiple sclerosis, Parkinson's disease, sepsis, hemolytic uremic syndrome (7). Given the established role for tPA in long term potentiation, the “cross-β structure pathway” may also be involved in learning.
FIG. 2 illustrates a cross-β structure in fibrin. Panel A depicts Thioflavin T fluorescence of a fibrin clot. A fibrin clot was formed in the presence of Thioflavin T and fluorescence was recorded at indicated time points. Background fluorescence of buffer, Thioflavin T and a clot formed in the absence of Thioflavin T, was substracted. Panel B is a graph depicting circular dichroism analysis of fibrin-derived peptides 85, 86 and 87. Ellipticity (Dg.cm2/dmol) is plotted against wavelength (nm). The CD spectra demonstrates that peptides 85 and 86, but not peptide 87, contain β-sheets. Panel C shows that X-ray fiber diffraction analysis of peptide 85 reveals that the peptide forms cross-β sheets. Panel D is a graph showing plasminogen activation assay with fibrin peptides 85, 86 and 87. It is seen that peptides 85 and 86, both containing a cross-β structure, stimulate the formation of plasmin by tPA, whereas peptide 87, which lacks a cross-β structure, does not.
FIG. 3 is a set of graphs depicting binding of tPA, plasminogen and plasmin to Aβ. Aβ was coated onto plastic 96-well plates. Increasing concentrations of either (A) tPA or (B) plasmin(ogen) were allowed to bind to the immobilized peptide. After extensive washing, tPA and plasmin(ogen) binding was assessed by enzyme-linked immunosorbent assays using anti-tPA and anti-plasminogen antibodies. Binding of (C) tPA and (D) plasmin to Aβ in the presence of 50 mM ε-aminocaproic acid (ε-ACA) was assessed as in A and B.
FIG. 4 is a set of graphs illustrating stimulation of tPA-mediated plasmin formation by Aβ and synergistic stimulation of cell detachment by plasminogen and Aβ. Panel A depicts that plasminogen (200 μg/ml) and tPA (200 pM) were incubated with Aβ (5 μM) or control buffer. Samples were taken from the reaction mixture at the indicated periods of time and plasmin activity was measured by conversion of the chromogenic plasmin substrate S-2251 at 405 nm. Panel B shows that N1E-115 cells were differentiated and received the indicated concentrations of plasmin in the presence or absence of 25 μM Aβ. After 48 hours, the dead cells were washed away and the remaining adherent cells were stained with methylene blue. Plasmin cannot prevent Aβ-induced cell detachment. Panel C illustrates that N1E-115 cells were differentiated and received the indicated concentrations of plasminogen in the presence or absence of 10 μM Aβ. After 24 hours, cell detachment was assessed. Aβ or plasminogen alone does not affect cell adhesion, but cause massive cell detachment when added together. Panel D is an immunoblot analysis of plasmin formation and laminin degradation. Differentiated N1E-115 cells were treated with or without Aβ (10 μM) in the absence or presence of added plasminogen. Addition of Aβ results in the formation of plasmin (bottom panel) and in degradation of laminin (top panel).
FIG. 5 depicts graphs illustrating that carboxypeptidase B inhibits Aβ-stimulated tPA-mediated plasmin formation and cell detachment. Panel A shows that plasminogen (200 μg/ml) and tPA (200 pM) were incubated with Aβ (5 μM) or control buffer. Samples were taken from the reaction mixture at the indicated periods of time and plasmin activity was measured by conversion of the chromogenic plasmin substrate S-2251 at 405 nm. The reaction was performed in the absence or the presence of 50 μg ml−1 carboxypeptidase B (CpB) and in the absence or presence of 3.5 μM carboxypeptidase inhibitor (CPI). CpB greatly attenuates A-stimulated plasmin formation. Panel B shows that N1E-115 cells were differentiated and treated with Aβ (10 μM), plasminogen (Plg, 20 μg ml−1) and/or CpB (1 μM) as indicated. After 24 hours, the cells were photographed. Panel C illustrates that, subsequently, the cells were washed once with PBS and the remaining cells were quantified as percentage-adhered cells by methylene blue staining. In Panel D, the cells were treated as in Panels B and C and medium and cell fractions were collected and analyzed by Western blot using an anti-plasmin(ogen) antibody. Aβ stimulates plasmin formation that is inhibited by CpB.
FIG. 6 is a set of graphs illustrating that endostatin can form fibers comprising cross-β structure and stimulates plasminogen activation. In Panel A, TEM shows the formation of endostatin fibers. Panel B contains an X-ray analysis that reveals the presence of cross-β structure in precipitated (prec.) endostatin. Panel C is a plasminogen activation assay demonstrating the stimulating activity of cross-β structure-containing endostatin on tPA-mediated plasmin formation. Aβ is shown for comparison. Panel D is an analysis of endostatin-induced cell death by methylene blue staining. It is seen that only the precipitated form is capable of efficiently inducing cell death. Direct cell death, but not cell detachment, is protected in the presence of sufficient glucose. Buffer prec. indicates control buffer.
FIG. 7 is a graph showing that IAPP stimulates tPA-mediated plasminogen activation. Both full length (fl-hIAPP) and truncated amyloid core (Δ-hIAPP), but not mouse IAPP (Δ-mIAPP), stimulate tPA-mediated plasminogen activation.
FIG. 8 is a set of graphs illustrating glycated albumin: Thioflavin T and tPA binding, TEM images, X-ray fiber diffraction. Panel A is an ELISA showing binding of tPA to albumin-g6p. Panel B shows competition of tPA binding to albumin-g6p by Congo red as determined using ELISA. Panel C shows fluorescence measurements of Thioflavin T binding to albumin-g6p, which is incubated for two, four, or 23 weeks. Panel D shows that inhibition of the fluorescent signal is obtained upon incubation of 430 nM of albumin-g6p with 19 μM of Thioflavin T by tPA. Panels E and F illustrate that spectrophotometric analysis at 420 nm shows that increasing amounts of tPA result in a decrease of the specific absorbance obtained upon incubation of 500 nM of albumin-g6p with 10 μM of Thioflavin T. Panels G, H and I are electron micrographs showing (G) amorphous precipitates of four weeks glycated albumin-g6p, (H) bundles of fibrillar aggregates of 23 weeks incubated albumin-g6p, and (I) two weeks glycated albumin-g6p. Panel J is an X-ray scattering of albumin-g6p (23 weeks). Scattering intensities are color coded on a linear scale and decreases in the order white-grey-black. Scattering from amorphous control albumin is subtracted, as well as scattering from the capillary glass wall and from air. d-spacings and the direction of the fiber axis are given and preferred orientations are indicated with arrows. Panel K is radial scan of albumin control and albumin-g6p (23 weeks). Panel L is a radial scan of albumin-g6p (23 weeks), showing repeats originating from fibrous structure, after subtracting background scattering of amorphous precipitated albumin. d-spacings (in Å) are depicted above the peaks. Panel M contains tangential scans along the 20 scattering-angles corresponding to indicate d-spacings. The scans show that the 4.7 Å repeat, which corresponds to the hydrogen-bond distance within individual β-sheets, and the 6 Å repeat, are oriented perpendicular to the 2.3 Å repeat that runs parallel to the fiber axis. Panel N is a schematic drawing of the orientation of the cross-β structures in albumin-g6p (23 weeks) amyloid fibers.
FIG. 9 illustrates fibers formation of human hemoglobin. Panel A depicts binding of tPA to in vitro glycated Hb-g6p. Panel B is an electron micrograph showing in vitro glycated Hb, which aggregates in an amorphous and fibrous manner.
FIG. 10 shows that amyloid properties of albumin-AGE are introduced irrespective of the carbohydrate or carbohydrate derivative used for glycation. Panels A-I illustrate-Congo red fluorescence of air-dried albumin preparations. Fluorescence was measured with albumin incubated with buffer (Panel A) or with buffer and NaCNBH3 (Panel B), with amyloid core peptide of human IAPP(Panel C), Aβ (Panel D), with albumin incubated with g6p (Panel E), glucose (Panel F), fructose (Panel G), glyceraldehyde (Panel H), and glyoxylic acid (Panel I). Panel J shows that Thioflavin T-amyloid fluorescence was measured in solution with the indicated albumin preparations. Panels K and L show that binding of amyloid-binding serine protease tPA to albumin preparations was assayed using an ELISA set-up. In Panel K, binding of tPA to albumin-glucose, -fructose, -glyceraldehyde, -glyoxylic acid, and albumin-buffer controls is shown. In Panel L, binding of tPA to positive controls albumin-g6p, Aβ and IAPP is shown, as well as to albumin incubated with control buffer.
FIG. 11 illustrates analysis of Congo red and tPA binding to Aβ. Panel A shows binding of tPA to immobilized Aβ as measured using an ELISA. Panel B illustrates the influence of increasing concentrations of Congo red on binding of tPA to Aβ. In the ELISA, 10 μg ml−1 of Aβ (1-40) was coated and incubated with 40 nM of tPA and 0-100 μM of Congo red.
FIG. 12 illustrates binding of human FXII to amyloid peptides and proteins that contain the cross-β structure fold. Panels A and B show binding of FXII to prototype amyloid peptides hAβ (1-40) and human fibrin fragment α147-159 FP13, and albumin-AGE and Hb-AGE, that all contain cross-β structure, were tested in an ELISA. FXII does not bind to negative controls mouse A islet amyloid polypeptide (ΔmIAPP), albumin-control and Hb-control, all three lacking the amyloid-specific structure. kD's for hAβ (1-40), FP13, albumin-AGE and Hb-AGE are approximately 2, 11, 8 and 0.5 nM, respectively. Panels C and D depict that coated hAβ (1-40) was incubated with 2.5 nM FXII in binding buffer, in the presence of a concentration series of human recombinant tissue-type plasminogen activator (ACTILYSE®, full-length tPA), or RETEPLASE® (K2P-tPA). The f.l. tPA- and K2P-tPA concentration was, at maximum, 135 times the kD for tPA binding to hAβ (1-40) (50 nM). Panels E and F show that coated amyloid albumin-AGE was incubated with 15 nM FXII in binding buffer, in the presence of a concentration series of f.l. tPA or K2P-tPA. The tPA concentration was, at maximum, 150 times the kD for tPA binding to albumin-AGE (1 nM). Panel G illustrates that binding of FXII to hAβ (1-40) and the prototype amyloid human amylin fragment hΔIAPP was tested using dot blot analysis. 10 μg of the peptides that contain cross-β structure as well as the negative control peptide mΔIAPP and phosphate-buffered saline (PBS) were spotted in duplicate. FXII specifically bound to hAβ (1-40) as well as to hΔIAPP.
FIG. 13 illustrates that finger domains bind to amyloid (poly)peptides. Panel A depicts binding of tPA and K2-P tPA to albumin-g6p. Panel B shows binding of tPA and K2-P tPA to Aβ (1-40). The tPA antibody used for detection recognizes both tPA and K2-P-tPA with equal affinity (not shown). Panel C shows binding of tPA-F-GST and tPA to immobilized Aβ (1-40) and albumin-g6p. Control RPTPμ-GST does not bind Aβ or albumin-g6p. Panel D is a pull-down assay with insoluble Aβ fibers and tPA domains. Conditioned BHK medium from stably transfected cell lines expressing tPA F, F-EGF, EGF, F-EGF-K1 and K1 with a C-terminal GST tag, as well as the tag alone, was used. “Control,” medium before the pull-down, “Aβ,” washed amyloid Aβ pellet, after the pull-down, “Sup,” medium after extraction with Aβ. Samples were analyzed on Western blot using rabbit anti-GST antibody Z-5. Panels E-G are ELISA showing binding of tPA F-EGF-GST and f.l. recombinant tPA to amyloid Aβ (Panel E), FP13 (Panel F) and IAPP (Panel G). mΔIAPP was coated as non-amyloid negative control (Panel E). Peptides were immobilized on ELISA plates and overlayed with concentration series of tPA and F-EGF-GST. GST was used as a negative control. Binding was detected using rabbit anti-GST antibody Z-5. Panels H-M depict immunohistochemical analysis of binding of tPA F-EGF-GST to amyloid deposits in human brain inflicted by AD. Brain sections were overlayed with tPA F-EGF-GST (Panels H and J) or negative control GST (Panel L). The same sections were incubated with Congo red (Panels I, K and M) to locate amyloid deposits. Panels N and O are pull-down assays with insoluble Aβ fibers and finger domains. Recombinant F domains with a C-terminal GST tag were expressed by stably transfected BHK cells. “Control,” medium before the pull-down, “Aβ,” washed amyloid Aβ pellet, after the pull-down, “Sup,” medium after extraction with Aβ. Samples were analyzed on Western blot using rabbit anti-GST antibody Z-5.
FIG. 14 illustrates the finger module. Panel A is a schematic representation of the location of the finger domain in tPA, factor XII, HGFa and fibronectin (“FN”). Panel B is an alignment of the amino acid sequence of the finger domain of the respective proteins. Specifically: tPA, FXII, HGFa, FN F1, FN F2, FN F3, FN F4, FN F5, FN F6, FN F7, FN F8, FN F9, FN F10, FN F11, and FN F12 (SEQ ID NOs: 3-17 respectively). Panel C is a representation of the peptide backbone of the tPA finger domain and the fourth and fifth finger domain of FN. Conserved disulfide bonds are shown in ball and stick.
FIG. 15 shows that antibodies elicited against amyloid peptides cross-react with glycated proteins, and vice versa. Panels A-C are ELISA with immobilized g6p-glycated albumin-AGE:23 and Hb-AGE, their non-glycated controls (Panel A), Aβ (1-40) (Panel B), and IAPP and mΔIAPP (Panel C). For the Aβ ELISA, polyclonal anti-human vitronectin antibody α-hVn K9234 was used as a negative control. Panel D shows binding of α-AGE1 to immobilized Aβ (1-40) on an ELISA plate after pre-incubation of α-AGE 1 with IAPP fibers. Panel E is a pull-down assay with anti-AGE1 antibody and amyloid fibers of Aβ (16-22) (lanes 1-2), Aβ (1-40) (lanes 4-5) and IAPP (lanes 6-7). After pelleting and washing of the fibers, samples were boiled in non-reducing sample buffer and analyzed by SDS-PAGE. s=supernatant after amyloid extraction, p=amyloid pellet after extraction, m=molecular marker. Panels F and G depict that in an ELISA set-up, immobilized Aβ (1-40) (Panel F) and IAPP (Panel G) are co-incubated with tPA and 250 or 18 nM α-AGE1, respectively. Panel H shows that in an ELISA set-up binding of α-Aβ (1-42) H-43 to immobilized positive control Aβ (1-40), and to IAPP and albumin-AGE:23 is tested. Albumin-control:23 and mΔIAPP are used as negative controls. Panel I depicts binding of 100 nM α-Aβ (1-42) H-43 to IAPP, immobilized on an ELISA plate, in the presence of a concentration series of tPA. Panels J and K are ELISA showing binding of a polyclonal antibody in mouse serum elicited against albumin-AGE:23 and Aβ (1-40) (ratio 9:1) (“poab anti-amyloid”) and of a polyclonal antibody elicited against a control protein (“control serum”) to immobilized IAPP (Panel J) and albumin-AGE:23 (Panel K). Serum was diluted in PBS with 0.1% v/v Tween20. Panel L is an ELISA showing binding of mouse poab anti-amyloid serum to amyloid Aβ (1-40), hΔIAPP and fibrin fragment α148-160 FP13. Control serum with antibodies raised against an unrelated protein, buffer and immobilized non-amyloid mΔIAPP and fibrin fragment α148-157 FP10 were used as negative controls. Panel M is an immunohistochemical analysis of the binding of rabbit anti-AGE2 to a spherical amyloid plaque (arrow) in a section of a human brain afflicted by AD. Magnification 400×. Panel N is a Congo red fluorescence of the same section. Magnification 630×.
FIG. 16 illustrates that monoclonal anti-cross-β structure antibody 3H7 detects glycated hemoglobin, Aβ, IAPP and FP13. ELISA showing binding of mouse monoclonal anti-cross-β structure antibody 3H7 to (Panel A) glycated hemoglobin vs. control unglycated hemoglobin or (Panel B) Aβ, hIAPP, ΔmIAPP and fibrin fragment α148-160 FP13.
FIG. 17 is a sandwich ELISA for detection of amyloid albumin-AGE or amyloid hemoglobin in solution. Immobilized recombinant tPA on Exiqon protein Immobilizers was overlayed with albumin-AGE:23 solution or albumin-control:23 solution at the indicated concentrations. Bound amyloid structures were detected with anti-Aβ (1-42) H-43 (A).



DETAILED DESCRIPTION OF THE INVENTION
The invention discloses (i) the identification of a “cross-β structure pathway,” (ii) the identification of multiligand receptors as being cross-β structure receptors, (iii) the identification of the finger domain as a cross-β-binding module and (iv) the identification of finger-containing proteins, including tPA, FXII, HGFa and fibronectin as part of the “cross-β structure pathway.”
This invention further discloses compounds not previously known to bind cross-β structure.
As disclosed herein, the invention describes compounds and methods for the detection and treatment of diseases associated with the excessive formation of a cross-β structure. Such diseases include known conformational diseases including Alzheimer disease and other types of amyloidosis. The present invention also discloses that other diseases not yet known to be associated with excessive formation of cross-β structures are also caused by excessive formation of cross-β structures. Such diseases include atherosclerosis, sepsis, diffuse intravascular coagulation, hemolytic uremic syndrome, preeclampsia, rheumatoid arthritis, autoimmune diseases, thrombosis and cancer.
According to the invention, the compound or means for binding the cross-β structure is a cross-β structure-binding molecule, such as a finger domain or a molecule containing one or more finger domains, or is a peptidomimetic analog of one or more finger domains. The compound can also be an antibody or a functional fragment thereof directed to the cross-β structure.
According to the invention, the compound or means for binding the cross-β structure may also be a multiligand receptor or fragment thereof. The compound may be, e.g., RAGE, CD36, Low density lipoprotein Related Protein (LRP), Scavenger Receptor B-1 (SR-B 1), SR-A, or a fragment of one of these proteins.
The finger domains, finger-containing molecules or antibodies may be human, mouse, rat or from any other species.
According to the invention, amino acids of the respective proteins may be replaced by other amino acids which may increase/decrease the affinity, the potency, bioavailability and/or half-life of the peptide. Alterations include conventional replacements (acid-acid, bulky-bulky and the like), introducing D-amino acids, making peptides cyclic, etc.
Further, the invention discloses compounds and methods:
1) for detecting the presence of the cross-β structure;
2) for inhibiting the formation of amyloid fibers;
3) for modulating cross-β structure-induced toxicity; and
4) for the removal of cross-β structure-containing molecules from the circulation.
This invention also discloses methods for preparing an assay to measure cross-β structure in sample solutions.
This invention also discloses methods for detecting cross-β structure in tissue samples or other samples obtained from living cells or animals.
This invention further discloses compounds and methods for preparing a composition for inhibiting cross-β structure fibers formation.
This invention still further discloses compounds and methods for preparing a composition for modulating cross-β structure-induced toxicity.
Abbreviations: Aβ, beta-amyloid peptide; AD, Alzheimer disease; AGE, advanced glycation end-products; CpB, carboxypeptidase B; COI (carboxypeptidase inhibitor); ELISA, enzyme-linked immunosorbent assay (ELISA); FN, fibronectin; F, finger or fibronectin type I domain; FXII, factor XII (Hageman factor); HGFa, hepatocyte growth factor activator; IAPP, islet amyloid polypeptide; PCR, polymerase chain reactions (PCR); RAGE, receptor for AGE; tPA, tissue-type plasminogen activator.
The invention discloses compounds and methods for the detection and treatment of diseases associated with the excessive formation of cross-β structure.
The cross-β structure can be part of an Aβ fibers or part of another amyloid fiber. The cross-β structure can also be present in denatured proteins.
The invention discloses methods to detect the cross-β structure. In one embodiment, a cross-β structure-binding compound or means for binding the cross-β structure such as a finger domain or a molecule comprising one or more finger modules, is bound or affixed to a solid surface, such as a microtiter plate. The solid surfaces useful in this embodiment would be known to one of skill in the art. For example, one embodiment of a solid surface is a bead, a column, a plastic dish, a plastic plate, a microscope slide, a nylon membrane, etc. After blocking, the surface is incubated with a sample. After removal of an unbound sample, bound molecules comprising the cross-β structure are subsequently detected using a second cross-β structure-binding compound, such as an anti-cross-β structure antibody or a molecule containing a finger module. The second cross-β structure compound is bound to a label such as an enzyme, i.e., peroxidase. The detectable label may also be a fluorescent label, a biotin, a digoxigenin, a radioactive atom, a paramagnetic ion, and a chemiluminescent label. It may also be labeled by covalent means such as chemical, enzymatic or other appropriate means with a moiety such as an enzyme or radioisotope. Portions of the above-mentioned compounds of the invention may be labeled by association with a detectable marker substance (e.g., radiolabeled with 125I or biotinylated) to provide reagents useful in detection and quantification of a compound or its receptor-bearing cells or its derivatives in solid tissue, and fluid samples such as blood, cerebral spinal fluid, urine or others. Such samples may also include serum used for tissue culture or medium used for tissue culture.
In another embodiment, the solid surface can be microspheres, for example, for agglutination tests.
In one embodiment, the compound containing a finger module is used to stain tissue samples. In one aspect, the compound or means for binding the cross-β structure is fused to a protein or peptide, such as glutathion-S-transferase. Alternatively, the compound is coupled to a label. The detectable label may be a fluorescent label, a biotin, a digoxigenin, a radioactive atom, a paramagnetic ion, or a chemiluminescent label. It may also be labeled by covalent means such as chemical, enzymatic or other appropriate means with a moiety such as an enzyme or radioisotope. Portions of the above-mentioned compounds of the invention may be labeled by association with a detectable marker substance (e.g., radiolabeled with 125I, 99mTc, 131I, chelated radiolabels, or biotinylated) to provide reagents useful in detection and quantification of a compound or its receptor-bearing cells or its derivatives in solid tissue, and fluid samples such as blood, cerebral spinal fluid or urine. The compound or means for binding the cross-β structure is incubated with the sample and after washing, is visualized with antibodies directed against the fused protein or polypeptide, such as glutathion-S-transferase.
In an embodiment, the sample is tissue from patients with or expected to suffer from a conformational disease. Alternatively, the tissue is derived from animals or from cells cultured in vitro.
The methods of the invention disclose a new diagnostic tool. It was not until the present invention that a universal β-structure epitope was disclosed and that a diagnostic assay could be based on the presence of the cross-β structure. Such use is particularly useful for diagnostic identification of conformational diseases or diseases associated with amyloid formation, such as Alzheimer or diabetes. It is clear that this diagnostic use is also useful for other diseases which involve cross-β structure formation, like all amyloidosis-type diseases, atherosclerosis, diabetes, bleeding, cancer, sepsis and other inflammatory diseases, Multiple Sclerosis, auto-immune diseases, disease associated with loss of memory or Parkinson and other neuronal diseases (epilepsy). For example, one can use a finger domain (of, for example, tPA) and provide it with a label (radioactive, fluorescent, etc.). This labeled finger domain may be used either in vitro or in vivo for the detection of cross-β structure-comprising proteins, hence, for determining the presence of a plaque involved in a conformational disease. One can use, for example, an ELISA assay to determine the amount of sepsis in a patient or one can localize a plaque involved in a conformational disease.
In another embodiment, this invention discloses a method for inhibiting the formation of amyloid fibers or to modulate cross-β structure-induced toxicity. The compound is a cross-β-binding module, such as a finger domain, a finger domain-containing molecule, a peptidomimetic analog, and/or an anti-cross-β structure antibody, and/or a multiligand receptor or a fragment thereof.
According to the invention, the inhibition of fiber formation has the consequence of decreasing the load of fibers.
The inhibition of fiber formation or modulating cross-β structure toxicity may also have the consequence of modulating cell death. The cell can be any cell, but may be a neuronal cell, an endothelial cell, or a tumor cell. The cell can be a human cell or a cell from any other species.
The cell may typically be present in a subject. The subject to which the compound is administered may be a mammal or a human.
The subject may be suffering from amyloidosis, from another conformational disease, from prion disease, from chronic renal failure and/or dialysis-related amyloidosis, from atherosclerosis, from cardiovascular disease, from autoimmune disease, or the subject may be obese. The subject may also be suffering from inflammation, rheumatoid arthritis, diabetes, retinopathy, sepsis, diffuse intravascular coagulation, hemolytic uremic syndrome, and/or preeclampsia. The diseases which may be treated or prevented with the methods of the present invention include, but are not limited to, diabetes, Alzheimer disease, senility, renal failure, hyperlipidemic atherosclerosis, neuronal cytotoxicity, Down's syndrome, dementia associated with head trauma, amyotrophic lateral sclerosis, multiple sclerosis, amyloidosis, an autoimmune disease, inflammation, a tumor, cancer, male impotence, wound healing, periodontal disease, neuropathy, retinopathy, nephropathy or neuronal degeneration.
The administration of compounds according to the invention may be constant or for a certain period of time. The compound may be delivered hourly, daily, weekly, monthly (e.g., in a time release form) or as a one time delivery. The delivery may also be continuous, e.g., intravenous delivery.
A carrier may also be used to deliver the compound to a subject. The carrier may be a diluent, an aerosol, an aqueous solution, a non-aqueous solution, or a solid carrier. This invention also discloses pharmaceutical compositions including therapeutically effective amounts of polypeptide compositions and compounds, together with suitable diluents, preservatives, solubilizers, emulsifiers, adjuvants and/or carriers. Such compositions may be liquids or lyophilized or otherwise dried formulations and include diluents of various buffer content (e.g., Tris-HCl, acetate, phosphate), pH and ionic strength, additives such as albumin or gelatin to prevent absorption to surfaces, detergents (e.g., Tween 20, Tween 80, Pluronic F68, bile acid salts), solubilizing agents (e.g., glycerol, polyethylene glycerol), antioxidants (e.g., ascorbic acid, sodium metabisulfite), preservatives (e.g., Thimerosal benzyl alcohol, parabens), bulking substances or tonicity modifiers (e.g., lactose, mannitol), covalent attachment of polymers such as polyethylene glycol to the compound, complexation with metal ions, or incorporation of the compound into or onto particulate preparations of polymeric compounds such as polylactic acid, polglycolic acid, hydrogels, etc, or onto liposomes, microemulsions, micelles, uni-lamellar or multi-lamellar vesicles, erythrocyte ghosts, or spheroplasts.
The administration of compounds according to the invention may comprise intralesional, intraperitoneal, intramuscular or intravenous injection; infusion; liposome-mediated delivery; topical, intrathecal, gingival pocket, per rectum, intrabronchial, nasal, oral, ocular or otic delivery. In a further embodiment, the administration includes intrabronchial administration, anal, intrathecal administration or transdermal delivery.
According to the invention, the compounds may be administered hourly, daily, weekly, monthly or annually. In another embodiment, the effective amount of the compound comprises from about 0.000001 mg/kg body weight to about 100 mg/kg body weight.
The compounds according to the invention may be delivered locally via a capsule which allows sustained release of the agent over a period of time. Controlled or sustained release compositions include formulation in lipophilic depots (e.g., fatty acids, waxes, oils). Also included in the invention are particulate compositions coated with polymers (e.g., poloxamers or poloxalenes) and the agent coupled to antibodies directed against tissue-specific receptors, ligands or antigens or coupled to ligands of tissue-specific receptors. Other embodiments of the compositions of the invention incorporate particulate forms protective coatings, protease inhibitors or permeation enhancers for various routes of administration, including parenteral, pulmonary, nasal and/or oral.
The effective amount of the compounds according to the invention may comprise 1 ng/kg body weight to about 1 gr/kg body weight. The actual effective amount will be based upon the size of the compound and its properties.
The activity of tPA and/or the tPA-mediated activation of plasminogen is increased by the binding to fibrin fragments or other protein fragments that have a lysine or an arginine at the carboxy-terminal end. B-type carboxypeptidases including, but not limited to, carboxypeptidase B (CpB) or Thrombin Activatable Fibrinolysis Inhibitor (TAFI, also named carboxypeptidase U or carboxypeptidase R), are enzymes that cleave off carboxy-terminal lysine and arginine residues of fibrin fragments that would otherwise bind to tPA and/or plasminogen and stimulate plasmin formation.
Because this invention has made clear that the cross-β structures are harmful when present in certain parts of the body like, for example, the brain and the damage is effected by the combination of cross-β structures with tPA, a method is disclosed to inhibit cross-β structure-mediated effects comprising providing an effective amount of a protein comprising a finger domain to block the binding sites of the cross-β structure for tPA. The cross-β structure-mediated effects may even be further diminished comprising providing an effective amount of B-type carboxypeptidase activity to inhibit the tPA activity.
The invention discloses the use of a compound capable of binding to a cross-β structure for the removal of cross-β structures. The compound or means for binding the cross-β structure is a cross-β-binding molecule, such a protein and/or a functional equivalent and/or a functional fragment thereof. In another aspect, the compound comprises a finger domain or a finger domain-containing molecule or a functional equivalent or a functional fragment thereof. In yet another aspect, the finger domain is derived from fibronectin, FXII, HGFa or tPA. It is clear that the invention also comprises antibodies that bind cross-β structures. In another embodiment, the protein is an antibody and/or a functional equivalent and/or a functional fragment thereof. With this use, the invention discloses, for example, a therapeutic method to remove cross-β structure-comprising proteins from, for example, the circulation, such as via extracorporeal dialysis. For example, a patient with sepsis is subjected to such use by dialysis of blood of the patient through means which are provided with, for example, immobilized finger domains. One could, for example, couple the finger domains to a solid surface or to the inside of the tubes used for dialysis. In this way, all cross-β structure-comprising proteins will be removed from the bloodstream of the patient, thus, relieving the patient of the negative effects caused by the cross-β structure-comprising proteins. Besides finger domain-comprising compounds, it is also possible to use other cross-β structure-binding compounds, like antibodies or soluble multiligand receptors. It is also clear that the use could be applied in hemodialysis of kidney patients.
As used herein, “finger” encompasses a sequence that fulfills the criteria outlined in FIG. 14. The sequence encompasses approximately 50 amino acids, containing four cysteine residues at distinct spacing. In one aspect, the finger domains of tPA, FXII, HGFa or fibronectin are used (SEQ ID NOs: 3-17). Alternatively, the “finger” may be a polypeptide analog or peptidomimetic with similar function, e.g., by having three-dimensional conformation. It is feasible that such analogs have improved properties.
EXAMPLES
Example 1
Reagents
Bovine serum albumin (BSA) fraction V pH 7.0 and D-glucose-6-phosphate di-sodium (g6p), D, L-glyceraldehyde, and chicken egg-white lysozyme were from ICN (Aurora, Ohio, USA). Rabbit anti-recombinant tissue-type plasminogen activator (tPA) 385R and mouse anti-recombinant tPA 374B were purchased from American Diagnostica (Veenendaal, The Netherlands). Anti-laminin (L9393) was from Sigma. Swine anti-rabbit immunoglobulins/HRP (SWARPO) and rabbit anti-mouse immunoglobulins/HRP (RAMPO) were from DAKO Diagnostics B.V. (The Netherlands). Alteplase (recombinant tissue-type plasminogen activator, tPA) was obtained from Boehringer-Ingelheim (Germany). Reteplase (Rapilysin), a recombinant mutant tPA containing only kringle 2 and the catalytic domain (K2P-tPA) was obtained from Roche, Hertfordshire, UK, and porcine pancreas carboxypeptidase B (CpB) was from Roche, Mannheim, Germany. Carboxypeptidase inhibitor (CPI) was from Calbiochem (La Jolla, Calif., USA). Tween 20 was purchased from Merck-Schuchardt (Hohenbrunn, Germany). Congo red was obtained from Aldrich (Milwaukee, Wis., USA). Thioflavin T and lyophilized human hemoglobin (Hb) were from Sigma (St. Louis, Mo., USA). Lyophilized human fibrinogen was from Kordia (Leiden, The Netherlands). Chromogenic plasmin substrate S-2251 was purchased from Chromogenix (Milan, Italy). Oligonucleotides were purchased from Sigma-Genosys (U.K.). Boro glass capillaries (0.5 mm Ø) were from Mueller (Berlin, Germany).
Example 2
Synthetic Peptides
Peptide Aβ (1-40), containing amino acids as present in the described human Alzheimer peptide (DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV) (SEQ ID NO: 18), fibrin peptides 85 (or FP13) (KRLEVDIDIKIRS) (SEQ ID NO: 19), 86 (or FP12) (KRLEVDIDIKIR) (SEQ ID NO: 20) and 87 (or FP10) (KRLEVDIDIK) (SEQ ID NO: 21), derived from the sequence of human fibrin(ogen) and the islet amyloid polypeptide (IAPP) peptide or derivatives (fl-hIAPP: KCNTATCATQRLANFLVHSSNNFGAILSSTNVGSNTY (SEQ ID NO: 22), ΔhIAPP(SNNFGAILSS) (SEQ ID NO:23), ΔmIAPP (SNNLGPVLPP) (SEQ ID NO: 24) were obtained from Pepscan, Inc. (The Netherlands) or from the peptide synthesis facility at the Netherlands Cancer Institute (NCI, Amsterdam, The Netherlands). The peptides were dissolved in phosphate buffered saline (PBS) to a final concentration of 1 mg ml−1 and stored for three weeks at room temperature (RT) to allow formation of fibers. During this period, the suspension was vortexed twice weekly. After three weeks, the suspension was stored at 4° C. Freeze-dried Aβ (1-40) from the NCI allowed to form cross-β structure in the same way. Cross-β structure formation was followed in time by examination of Congo red binding and green birefringence under polarized light.
Example 3
Congo Red Binding and Thioflavin T Fluorescence of a Fibrin Clot
For Thioflavin T-fluorescence measurements, 1 mg ml−1 of fibrinogen was incubated at 37° C. with 2 U ml−1 of factor IIa in 150 mM NaCl, 20 mM Tris-HCl pH 7.5, 10 mM CaCl2, 50 μM Thioflavin T. Background fluorescence of a clot was recorded in the absence of Thioflavin T and background Thioflavin T fluorescence was measured in the absence of factor IIa. Fluorescence was measured on a Hitachi F-4500 fluorescence spectrophotometer (Ltd., Tokyo, Japan), using Sarstedt REF67.754 cuvettes. Apparatus settings: excitation at 435 nm (slit 10 nm), emission at 485 nm (slit 10 nm), PMT voltage 950 V, measuring time 10 seconds, delay 0 seconds. For detection of Congo red binding, a fibrin clot was formed at room temperature as described above (Thioflavin T was omitted in the buffer). The clot was incubated with Congo red solution and washed according to the manufacturer's recommendations (Sigma Diagnostics, MO, USA). The clot was analyzed under polarized light.
Example 4
Initial Preparation of Glycated Albumin, Hemoglobin (Hb) and Lysozyme
For preparation of advanced glycation end-product modified bovine serum albumin (albumin-g6p), 100 mg ml−1 of albumin was incubated with PBS containing 1 M of g6p and 0.05% m/v NaN3, at 37° C. in the dark. One albumin solution was glycated for two weeks, a different batch of albumin—was glycated for four weeks. Glycation was prolonged up to 23 weeks with part of the latter batch. Human Hb at 5 mg ml−1 was incubated for ten weeks at 37° C. with PBS containing 1 M of g6p and 0.05% m/v of NaN3. In Addition, a Hb solution of 50 mg ml−1 was incubated for eight weeks with the same buffer. For preparation of glyceraldehyde-modified albumin (albumin-glyceraldehyde) and chicken egg-white lysozyme (lysozyme-glyceraldehyde), filter-sterilized protein solutions of 15 mg ml−1 were incubated for two weeks with PBS containing 10 mM of glyceraldehyde. In controls, g6p or glyceraldehyde was omitted in the solutions. After incubations, albumin and lysozyme solutions were extensively dialyzed against distilled water and subsequently stored at −20° C. Protein concentrations were determined with Advanced protein-assay reagent ADV01 (Cytoskeleton, Denver, Colo., USA). Glycation was confirmed by measuring intrinsic-fluorescent signals from advanced glycation end-products; excitation wavelength 380 nm, emission wavelength 435 nm.
Example 5
Further Experiment Involving Glycation
For preparation of albumin-AGE, 100 mg ml−1 bovine serum albumin (fraction V, catalogue #A-7906, initial fractionation by heat shock, purity ≧98% (electrophoresis), remainder mostly globulins, Sigma-Aldrich, St. Louis, Mo., USA) was incubated at 37° C. in the dark, with phosphate-buffered saline (PBS, 140 mM sodium chloride, 2.7 mM potassium chloride, 10 mM disodium hydrogen phosphate, 1.8 mM potassium di-hydrogen phosphate, pH 7.3), 1 M D-glucose-6-phosphate disodium salt hydrate (anhydrous) (ICN, Aurora, Ohio, USA) and 0.055% (m/v) NaN3. Bovine albumin has 83 potential glycation sites (59 lysine and 23 arginine residues, N-terminus). Albumin was glycated for two weeks (albumin-AGE:2), four weeks (albumin-AGE:4) or 23 weeks (albumin-AGE:23). In controls, g6p was omitted. After incubation, solutions were extensively dialyzed against distilled water and subsequently stored at 4° C. Protein concentrations were determined with advanced protein-assay reagent ADV01 (Cytoskeleton, CO, USA). Alternatively, albumin was incubated for 86 weeks with 1 M g6p, 250 mM DL-glyceraldehyde (ICN, Aurora, Ohio, USA)/100 mM NaCNBH3, 1 M β-D-(−)-fructose (ICN, Aurora, Ohio, USA), 1 M D(+)-glucose (BDH, Poole, England), 500 mM glyoxylic acid monohydrate (ICN, Aurora, Ohio, USA)/100 mM NaCNBH3, and corresponding PBS and PBS/NaCNBH3 buffer controls. Glycation was confirmed (i) by observation of intense brown staining, (ii) by the presence of multimers on SDS-polyacrylamide gels, (iii) by assaying binding of AGE-specific antibodies moab anti-albumin-g6p 4B546 and poab anti-fibronectin-g6p (Ph. De Groot/I. Bobbink, UMC Utrecht; unpublished data), and (iv) by measuring intrinsic fluorescent signals from AGE (excitation wavelength 380 nm, emission wavelength 445 nm). Autofluorescent signals of albumin controls were less than 4% of the signals measured for albumin-AGE and were used for background corrections.
Example 6
Isolation of Hb from Human Erythrocytes
Human Hb was isolated from erythrocytes in EDTA-anticoagulated blood of three healthy individuals and of 16 diabetic patients. 100 μl of whole blood was diluted in 5 ml of physiological salt (154 mM NaCl), cells were gently spun down, and resuspended in 5 ml of physiological salt. After 16 hours incubation at room temperature, cells were again spun down. Pelleted cells were lysed by adding 2 ml of 0.1 M of boric acid, pH 6.5 and subsequently, cell debris was spun down. Supernatant was collected and stored at −20° C.
Example 7
Determination of GlycoHb Concentrations
Concentrations of glycated Hb, also named glycohemoglobin, or named HbAlc, in EDTA-blood of human healthy donors or diabetic patients, were determined using a turbidimetric inhibition immunoassay with hemolyzed whole blood, according to the manufacturer's recommendations (Roche Diagnostics, Mannheim, Germany). Standard deviations are 2.3% of the measured HbAlc concentrations.
Example 8
Binding of Congo Red to Glycated Albumin
Binding of Congo red to albumin-AGE glycated for 86 weeks with carbohydrates glucose, fructose and glucose-6-phosphate, or with carbohydrate derivatives glyceraldehyde and glyoxylic acid, was tested using air-dried samples. For this purpose, 5 μg albumin was applied to a glass cover slip and air dried. Samples were incubated with Congo red and subsequently washed according to the manufacturer's recommendations (Sigma Diagnostics, St Louis, Mo., USA). Pictures were taken on a Leica DMIRBE fluorescence microscope (Rijswijk, The Netherlands) using 596 nm and 620 nm excitation and emission wavelengths, respectively.
Example 9
Endostatin Preparations
Endostatin was purified from Escherichia coli essentially as described.47 In short, Bl21.DE3 bacteria expressing endostatin were lysed in a buffer containing 8 M urea, 10 mM Tris (pH 8.0), 10 mM imidazole and 10 mM β-mercapto-ethanol. Following purification over Ni2+-agarose, the protein sample was extensively dialyzed against H2O. During dialysis, endostatin precipitates as a fine white solid. Aliquots of this material were either stored at −80° C. for later use, or were freeze-dried prior to storage. Soluble endostatin produced in the yeast strain Pichia pastoris was kindly provided by Dr. Kim Lee Sim (EntreMed, Inc., Rockville, Mass., USA). Aggregated endostatin was prepared from soluble endostatin as follows. Soluble yeast endostatin was dialyzed overnight in 8 M urea and subsequently three times against H2O. Like bacterial endostatin, yeast endostatin precipitates as a fine white solid.
Example 10
Congo Red Staining
Freeze-dried bacterial endostatin was resuspended in either 0.1% formic acid (FA) or in dimethyl-sulfoxide and taken up in a glass capillary. The solvent was allowed to evaporate and the resulting endostatin material was stained with Congo red according to the manufacturer's protocol (Sigma Diagnostics, St. Louis, Mo., USA).
Example 11
Circular Dichroism Measurements
UV circular dichroism (CD) spectra of peptide and protein solutions (100 μml−1 in H2O) were measured on a JASCO J-810 CD spectropolarimeter (Tokyo, Japan). Averaged absorption spectra of five or ten single measurements from 190-240 nm or from 190-250 nm, for fibrin peptides 85, 86, 87 or for albumin, glycated albumin and human Aβ (16-22), respectively, are recorded. The CD spectrum of Aβ (16-22) was measured as a positive control. Aβ (16-22) readily adopts amyloid fiber conformation with cross-β structure when incubated in H2O45. For albumin and Aβ (16-22), relative percentage of the secondary structure elements present was estimated using k2d software.48 
Example 12
X-Ray Fiber Diffraction
Aggregated Endostatin was Solubilized in 0.1% FA, Lyophilized Fibrin Peptides were dissolved in H2O and glycated albumin was extensively dialyzed against water. Samples were taken up in a glass capillary. The solvent was allowed to evaporate over a period of several days. Capillaries containing the dried samples were placed on a Nonius kappaCCD diffractometer (Bruker-Nonius, Delft, The Netherlands). Scattering was measured using sealed tube MoKα radiation with a graphite monochromator on the CCD area detector during 16 hours. Scattering from air and the glass capillary wall were subtracted using in-house software (VIEW/EVAL, Dept. of Crystal- and Structural Chemistry, Utrecht University, The Netherlands).
Example 13
Transmission Electron Microscopy
Endostatin, hemoglobin and albumin samples were applied to 400 mesh specimen grids covered with carbon-coated collodion films. After five minutes, the drops were removed with filter paper and the preparations were stained with 1% methylcellulose and 1% uranyl acetate. After washing in H2O, the samples were dehydrated in a graded series of EtOH and hexanethyldisilazane. Transmission electron microscopy (TEM) images were recorded at 60 kV on a JEM-1200EX electron microscope (JEOL, Japan).
Example 14
Enzyme-Linked Immunosorbent Assay: Binding of tPA to Glycated Albumin, Hb and Aβ(1-40)
Binding of tPA to albumin-g6p (four-week and 23-week incubations), albumin-glyceraldehyde, control albumin, human Hb-g6p (ten-week incubation), Hb control, or to Aβ (1-40) was tested using an enzyme-linked immunosorbent assay (ELISA) set-up. Albumin-g6p and control albumin (2.5 μg ml−1 in coat buffer, 50 mM Na2CO3/NaHCO3 pH 9.6, 0.02% m/v NaN3, 50 μl/well) were immobilized for one hour at room temperature in 96-well protein Immobilizer plates (Exiqon, Vedbaek, Denmark). Aβ (1-40) (10 μg ml−1 in coat buffer) was immobilized for 75 minutes at room temperature in a 96-well peptide Immobilizer plate (Exiqon, Vedbaek, Denmark). Control wells were incubated with coat buffer only. After a wash step with 200 μl of PBS/0.1% v/v Tween 20, plates were blocked with 300 μl of PBS/1% v/v Tween 20, for two hours at room temperature while shaking. All subsequent incubations were performed in PBS/0.1% v/v Tween 20 for one hour at room temperature while shaking, with volumes of 50 μl per well. After each incubation, wells were washed five times with 200 μl of PBS/0.1% v/v Tween 20. Increasing amounts of f.l. tPA or K2-P tPA was added in triplicate to coated wells and to control wells. Antibody 385R and subsequently SWARPO, or antibody 374B and subsequently RAMPO, were added to the wells at a concentration of 1 μg ml−1. Bound peroxidase-labeled antibody was visualized using 100 μl of a solution containing 8 mg of ortho-phenylene-diamine and 0.0175% v/v of H2O2 in 20 ml of 50 mM citric acid/100 mM Na2HPO4 pH 50. Staining was stopped upon adding 50 μl of a 2-M H2SO4 solution. Absorbance was read at 490 nm on a Vmax kinetic microplate reader (Molecular Devices, Sunnyvale, Calif., USA).
Competition experiments were performed with 20 or 40 nM of tPA with, respectively, albumin-g6p or Aβ (1-40) and with increasing amounts of Congo red in PBS/0.08% v/v Tween 20/2% v/v EtOH.
Example 15
ELISA: Binding of tPA to Albumin-AGE
Binding of the cross-B structure marker tPA to albumin-AGE was tested using an ELISA setup. We showed that tPA binds to prototype amyloid peptides human Aβ (140) and human IAPP49 (this application). Therefore, we used tPA binding to these two peptides as positive control. The 86-week glycated samples and controls were coated to Greiner microlon plates (catalogue #655092, Greiner, Frickenhausen, Germany). Wells were blocked with Superblock (Pierce, Rockford, Ill., USA). All subsequent incubations were performed in PBS/0.1% (v/v) Tween 20 for one hour at room temperature while shaking, with volumes of 50 μl per well. After incubation, wells were washed five times with 300 μl PBS/0.1% (v/v) Tween 20. Increasing concentrations of tPA were added in triplicate to coated wells as well as to control wells. During tPA incubations of 86-week incubated samples, at least a 123,000 times molar excess of ε-amino caproic acid (εACA, 10 mM) was added to the solutions. εACA is a lysine analogue and is used to avoid potential binding of tPA to albumin via its kringle 2 domain.50 Monoclonal antibody 374b (American Diagnostica, Instrumentation laboratory, Breda, The Netherlands) and, subsequently, RAMPO (Dako diagnostics, Glostrup, Denmark) was added to the wells at a concentration of 0.3 μg ml−1. Bound peroxidase-labeled antibody was visualized using 100 μl of a solution containing 8 mg ortho-phenylene-diamine in 20 ml 50 mM citric acid/100 mM Na2HPO4 pH 5.0 with 0.0175% (v/v) H2O2. Staining was stopped upon adding 50 μl of a 2 M H2SO4 solution. Absorbance was read at 490 nm on a Vmax kinetic microplate reader (Molecular Devices, CA, USA). Background signals from non-coated control wells were substracted from corresponding coated wells.
Example 16
Thioflavin T Fluorescence of Glycated Albumin and Lysozyme, and tPA
Initially, for fluorescence measurements, 500 nM of albumin-g6p, albumin-glyceraldehyde, control albumin, lysozyme-glyceraldehyde, or control lysozyme were incubated with increasing amounts of Thioflavin T, in 50 mM of glycine-NaOH, pH 9. For blank readings, an identical Thioflavin T dilution range was prepared without protein or Thioflavin T was omitted in the protein solutions. Samples were prepared in triplicate.
Example 17
Thioflavin T Fluorescence
In further experiments, fluorescence measurements with albumin-g6p:2, albumin-g6p:4, albumin-g6p:23 and controls in 50 mM glycine-NaOH, pH 9 were incubated with increasing amounts of ThT (Sigma-Aldrich Chemie, Steinheim, Germany), a marker for amyloid cross-β structure.51 Albumin-AGE:4 concentration was 175 nM; other protein concentrations were 500 nM. For fluorescence measurements with 86-week glycated samples, 140 nM of protein was incubated with a fixed concentration of 20 μM ThT. Fluorescence was measured in triplicate on a Hitachi F-4500 fluorescence spectrophotometer (Ltd., Tokyo, Japan), after one hour incubation at room temperature. Excitation and emission wavelengths were 435 nm (slit 10 nm) and 485 nm (slit 10 nm), respectively. Background signals from buffer and protein solutions without ThT were substracted from corresponding measurements with protein solution incubated with ThT.
Example 18
Fluorescence: Competitive Binding of Thioflavin T and tPA to Albumin-g6p
A solution of 430 nM albumin-g6p and 19 μM of Thioflavin T was incubated with increasing amounts of tPA, for one hour at room temperature. For blank readings, albumin-g6p was omitted. Samples were prepared in four-fold in 50 mM glycine-NaOH pH 9. Emission measurements were performed as described above.
Example 19
Absorbance: Competitive Binding of Thioflavin T and tPA to Albumin-g6p
Albumin-g6p (500 nM) and Thioflavin T (10 μM) were incubated with increasing amounts of tPA, in 50 mM glycine-NaOH pH 9, for one hour at room temperature. Absorbance measurements were performed at the albumin-g6p Thioflavin T absorbance maximum at 420 nm. Samples were prepared in four-fold. For blank readings, albumin-g6p was omitted in the solutions. Absorbance was read in a quartz cuvette on a Pharmacia Biotech Ultrospec 3000 UV/visible spectrophotometer (Cambridge, England).
Example 20
Plasminogen Activation Assay
Plasminogen (200 μg ml−1) was incubated with tPA (200 pM) in the presence or the absence of a co-factor (5 μM of either endostatin, Aβ (1-40), or one the fibrin-derived peptides 85, 86 and 87). At the indicated time intervals, samples were taken and the reaction was stopped in a buffer containing 5 mM EDTA and 150 mM εACA. After collection of the samples, a chromogenic plasmin substrate S-2251 was added and plasmin activity was determined kinetically in a spectrophotometer at 37° C.
Example 21
N1E-115 Cell Culture and Differentiation
N1E-115 mouse neuroblastoma cells were routinely cultured in DMEM containing 5% FCS, supplemented with antibiotics. Cells were differentiated into post-mitotic neurons.52 The cells were exposed to Aβ (50 μg ml−1) for 24 hours in the presence or absence of 20 μg ml−1 plasminogen in the presence or absence of 50 μg ml−1 CpB. Cells were photographed, counted and lysed by the addition of 4× sample buffer (250 mM Tris pH 6.8, 8% SDS, 10% glycerol, 100 mM DTT, 0.01% w/v bromophenol blue) to the medium. The lysate, containing both adherent and floating (presumably dying and/or dead) cells, as well as the culture medium, were analyzed for the presence of plasminogen and plasmin, as well as for laminin, by Western blot analysis using specific antibodies against plasminogen (MoAb 3642, American Diagnostics), laminin (PoAb L9393, Sigma).
Example 22
Binding of Human Factor XII to Amyloid Peptides and Proteins that Contain the Cross-β Structure Fold
The binding of human FXII (Calbiochem, La Jolla, Calif., USA, catalogue #233490) to amyloid (poly)peptides was tested. Prototype amyloid peptides human amyloid-β (1-40) (hAβ (1-40)) and human fibrin fragment α147-159 FP13, and glucose-6-phosphate glycated bovine albumin (albumin-advanced glycation end product (AGE)) and glucose-6-phosphate glycated human hemoglobin (Hb-AGE), all containing cross-β structure, as well as negative controls mouse A islet amyloid polypeptide (ΔmIAPP), albumin-control and Hb-control, all three lacking the amyloid-specific structure, were coated to ELISA plates and overlayed with a concentration series of human factor XII. Binding of FXII was detected using a rabbit polyclonal anti-FXII antibody (Calbiochem, La Jolla, Calif., USA, catalogue #233504) and peroxidase-labeled swine anti-rabbit IgG. Wells were coated in triplicate. The FXII binding buffer included 10 mM HEPES pH 7.3, 137 mM NaCl, 11 mM D-glucose, 4 mM KCl, 1 mg ml−1 albumin, 50 μM ZnCl2, 0.02% (m/v) NaN3 and 10 mM ε-amino caproic acid (εACA). Lysine analogue εACA was added to avoid putative binding of FXII to cross-β structure via the FXII kringle domain. In addition, binding of FXII to hAβ (1-40) and the prototype amyloid human amylin fragment hΔIAPP was tested using dot blot analysis. 10 μg of the peptides that contain cross-β structure, as well as the negative control peptide mΔIAPP and phosphate-buffered saline (PBS) were spotted in duplicate onto methanol-activated nitrocellulose. Spots were subsequently incubated with 2 nM FXII in FXII buffer or with FXII buffer alone, anti-FXII antibody, and SWARPO. Binding of FXII was visualized by chemiluminescence upon incubation with enhanced luminol reagent (PerkinElmer Life Sciences, Boston, Mass., USA). To test whether FXII and tPA, which is known for its capacity to bind to polypeptides that contain the cross-β structure fold,49 bind to overlapping binding sites on amyloid (poly)peptides, competitive ELISAs were performed. Coated hAβ (1-40) or amyloid albumin-AGE were incubated with 2.5 nM or 15 nM FXII in binding buffer in the presence of a concentration series of human recombinant tissue-type plasminogen activator (ACTILYSE®, full-length tPA) or RETEPLASE® (K2P-tPA). RETEPLASE® is a truncated form of tPA that includes the second kringle domain and the protease domain. The f.l. tPA and K2P-tPA concentration was at maximum 135 times the kD for tPA binding to hAβ (1-40) (50 nM) or 150 times the kD for tPA binding to albumin-AGE (1 nM).
Example 23
Cloning Procedure
Cloning of the amino-terminal finger domain (F) of human tPA, residues Ser1-Ser50, preceded by the pro-peptide (residues Met-35-Arg-1) and a BglII restriction site, was performed by using PCR and standard recombinant DNA techniques. In brief, the pro-peptide finger region was amplified by PCR using 1 ng of plasmin Zp17,53 containing the cDNA encoding tPA as a template. Oligonucleotides used were 5′AAAAGTCGACAGCCGCCACCATGGATGCAATGAAGAGA (SEQ ID NO: 25) (1) and 3′AAAAGCGGCCGCCCACTTTTGACAGGCACTGAG (SEQ ID NO: 26) (2) comprising a SalI or a NotI restriction site, respectively (underlined). The PCR product was cloned in a SalI/NotI-digested expression vector, pMT2-GST.54 As a result, a construct is generated that contains a SalI restriction site, the coding sequence for the finger domain of tPA, a NotI and a KpnI restriction site, a thrombin cleavage-site (TCS), a glutathion-S-transferase (GST) tag and an EcoRI restriction site. The appropriate sequence of the construct was confirmed by sequence analysis. In a similar way, a construct consisting of the tPA F-EGF domains was prepared. Next, the constructs were ligated SalI-EcoRI in pGEM3Zf(−) (Promega, Madison, Wis., USA). The HindIII-SalI-tPA pro-peptide-BglII-F-NotI-KpnI-TCS-GST-EcoRI construct was used as a cloning cassette for preparation of constructs containing tPA K1, F-EGF-K1, EGF, as well as human hepatocyte growth factor activator F and F-EGF, human factor XII F and F-EGF, and human fibronectin F4, F5, F4-5 and F10-12. Subsequently, constructs were ligated HindIII-EcoRI in the pcDNA3 expression vector (Invitrogen, Breda, The Netherlands). In addition, the GST tag alone was cloned into pcDNA3, preceded by the tPA pro-peptide. Primers used for constructs were:










tPA F-EGF





3′AAAAGCGGCCGCGTGGCCCTGGTATCTATTTC
(SEQ ID NO: 27)
(3) and (1)


 


PA EGF


5′AAAAGAGATCTGTGCCTGTCAAAAGTTGC
(SEQ ID NO: 28)
(4) and (2)


 


tPA K1


5′AAAAGAGATCTGATACCAGGGCCACGTGCTAC
(SEQ ID NO: 29)
(5)


3′AAAAGCGGCCGCCCGTCACTGTTTCCCTCAGAGCA
(SEQ ID NO: 30)
(6)


 


tPA F-EGF-K1




(1) and (6)


 


GST tag


(1)
(SEQ ID NO: 31)
(7)


and


 


AAAAGCGGCCGCCTGGCTCCTCTTCTGAATC


 


Fibronectin F4


5′TGCAAGATCTATAGCTGAGAAGTGTTTTGAT
(SEQ ID NO: 32)
(8)


3′GATGCGGCCGCCCTGTATTCCTAGAAGTGCAAGTG
(SEQ ID NO: 33)
(9)


 


Fibronectin F5


5′TGCAAGATCTACTTCTAGAAATAGATGCAAC
(SEQ ID NO: 34)
(10)


3′TGATGCGGCCGCCCCACAGAGGTGTGCCTCTC
(SEQ ID NO: 35)
(11)


 


Fibronectin F4-5




(8) and (11)


 


Fibronectin F10-12


5′AAAAAAGATCTAACCAACCTACGGATGACTC
(SEQ ID NO: 36)
(12)


3′AAAAAAGGTACCGACTGGGTTCACCCCCAGGT
(SEQ ID NO: 37)
(13)


 


factor XII F


5′GAAACAAGATCTCAGAAAGAGAAGTGCTTTGA
(SEQ ID NO: 38)
(14)


3′ACGGGCGGCCGCCCGGCCTGGCTGGCCAGCCGCT
(SEQ ID NO: 39)
(15)


 


factor XII F-EGF


5′AAAAAAGATCTCAGAAAGAGAAGTGCTTTGA
(SEQ ID NO: 40)
(16)


3′AAAAAGGTACCGGCTTGCCTTGGTGTCCACG
(SEQ ID NO: 41)
(17)


 


HGFa F


5′GCAAGAAGATCTGGCACAGAGAAATGCTTTGA
(SEQ ID NO: 42)
(18)


3′AAGGGCGGCCGCCCAGCTGTATGTCGGGTGCCTT
(SEQ ID NO: 43)
(19)


 


HGFa F-EGF


5′AAAAAAGATCTGGCACAGAGAATGCTTTGA
(SEQ ID NO: 44)
(20)


3′AAAAAGGTACCGCTCATCAGGCTCGATGTTG
(SEQ ID NO: 45)
(21)






Example 24
Transient Expression of tPA-F-GST in 293T Cells
Initially, 293T cells were grown in RPMI1640 medium (Invitrogen, Scotland, U.K.) supplemented with 5% v/v fetal calf-serum, penicillin, streptomycin and guanidine, to 15% confluency. Cells were transiently transfected using Fugene-6, according to the manufacturer's recommendations (Roche, Ind., USA). pMT2-tPA-F-GST containing the tPA fragment, or a control plasmid, pMT2-RPTPμ-GST, containing the extracellular domain of receptor-like protein tyrosine phosphatase μ (RPTPμ)54 were transfected, and medium was harvested after 48 hours transfection. Expression of tPA-F-GST and RPTPμ-GST in 293T medium was verified by immunoblotting. Collected samples were run out on SDS-PAA gels after the addition of 2× sample buffer. Gels were blotted on nitrocellulose membranes. Membranes were blocked in 1% milk (Nutricia) and incubated with primary monoclonal anti-GST antibody 2F354 and secondary HRP-conjugated rabbit anti-mouse IgG (RAMPO). The blots were developed using Western Lightning Chemiluminescence Reagent Plus (PerkinElmer Life Sciences, MA, USA).
Example 25
Stable Expression of Finger Constructs in BHK Cells
Baby hamster kidney cells were seeded in DMEM/NUT mix F-12 (HAM) medium (Invitrogen, U.K.) supplemented with 5% v/v fetal calf-serum (FCS), penicillin, streptomycin and guanidine, to 1% confluency. Cells were stably transfected by using the Ca3(PO4)2-DNA precipitation method. After 24 hours, medium was supplemented with 1 mg ml−1 geneticin G-418 sulphate (Gibco, U.K.). Medium with G-418 was refreshed several times during ten days to remove dead cells. After this period of time, stable single colonies were transferred to new culture flasks and cells were grown to confluency. Expression of constructs was verified by immunoblotting. Collected samples were run out on SDS-PAA gels after the addition of 2× sample buffer. Gels were blotted on nitrocellulose membranes. Membranes were blocked in 5% milk (Nutricia) with 1.5% m/v BSA and incubated with primary monoclonal anti-GST antibody (Santa Cruz Biotechnology, Santa Cruz, Calif., USA, catalogue #Z-5), and secondary HRP-conjugated rabbit anti-mouse IgG (RAMPO). The blots were developed using Western Lightning Chemiluminescence Reagent Plus (PerkinElmer Life Sciences, MA, USA). Stable clones were grown in the presence of 250 μg ml−1 G-418. For pull-down experiments, conditioned medium with 5% FCS of stable clones that produce constructs of interest was used. For purification purposes, cells of a stable clone of tPA F-EGF-GST were transferred to triple-layered culture flasks and grown in medium with 0.5% v/v Ultroser G (ITK Diagnostics, Uithoorn, The Netherlands). Medium was refreshed every three to four days. TPA F-EGF-GST was isolated from the medium on a Glutathione Sepharose 4B (Amersham Biosciences, Uppsala, Sweden) column and eluted with 100 mM reduced glutathione (Roche Diagnostics, Mannheim, Germany). Purity of the construct was checked with SDS-PAGE followed by Coomassie staining or Western blotting. From these analyses, it is clear that some GST is present in the preparation. Purified tPA F-EGF-GST was dialyzed against PBS and stored at −20° C.
Example 26
Purification of GST-Tagged tPA-F-GST and RPTPμ-GST
Medium was concentrated twenty-fold using Nanosep 10KΩ centrifugal devices (Pall Gelman Laboratory, MI, USA) and incubated with glutathione coupled to Sepharose 4B, according to the manufacturer's recommendations (Pharmacia Biotech, Uppsala, Sweden). Bound constructs were washed with PBS and eluted with 10 mM of glutathione in 50 mM Tris-HCl pH 8.0. Constructs were stored at −20° C., before use.
Example 27
Amyloid Pull-Down
Conditioned medium of BHK cells expressing GST-tagged tPA F, F-EGF, EGF, K1, F-EGF-K1, FXII F, HGFa F, Fn F4, Fn F5, Fn F4-5 and GST was used for amyloid binding assays. At first, constructs were adjusted to approximately equal concentration using Western blots. Qualitative binding of the recombinant fragments were evaluated using a “pull-down” assay. To this end, the recombinantly made fragments were incubated with either Aβ or IAPP fibrils. Since these peptides form insoluble fibers, unbound proteins can be easily removed from the fibers following centrifugation. The pellets containing the bound fragments were subsequently washed several times. Bound fragments were solubilized in SDS-sample buffer and analyzed by PAGE, as were unbound proteins in the supernatant fraction and starting material. The gels were analyzed using immunoblotting analysis with the anti-GST antibody Z-5.
Example 28
Amyloid ELISA with tPA F-EGF-GST
In order to define the affinity of the purified tPA F-EGF-GST recombinant protein, ELISAs were performed with immobilized amyloid (poly)peptides and non-amyloid control ΔmIAPP. Twenty-five μg ml−1 of Aβ, FP13, IAPP or ΔmIAPP was immobilized on Exiqon peptide immobilizer plates. A concentration series of tPA F-EGF-GST in the presence of excess εACA was added to the wells and binding was assayed using anti-GST antibody Z-5. As a control, GST (Sigma-Aldrich, St. Louis, Mo., USA, catalogue #G-5663) was used at the same concentrations.
Example 29
Immunohistochemistry: Binding of tPA F-EGF to Human AD Brain
Paraffin brain sections of a human inflicted with AD was a kind gift of Prof. Slootweg (Dept. of Pathology, UMC Utrecht). Sections were deparaffinized in a series of xylene-ethanol. Endogenous peroxidases were blocked with methanol/1.5% H2O2 for 15 minutes. After rinsing in H2O, sections were incubated with undiluted formic acid for ten minutes, followed by incubation in PBS for five minutes. Sections were blocked in 10% HPS in PBS for 15 minutes. Sections were exposed for two hours with 7 nM of tPA F-EGF-GST or GST in PBS/0.3% BSA. After three wash steps with PBS, sections were overlayed with 200 ng ml−1 anti-GST antibody Z-5, for one hour. After washing, ready-to-use goat anti-rabbit Powervision (Immunologic, Duiven, The Netherlands, catalogue #DPVR-55AP) was applied and incubated for one hour. After washing, sections were stained for ten minutes with 3,3′-diamino benzidine (Sigma-Aldrich, St Louis, Mo., USA, catalogue #D-5905), followed by hematoxylin staining for ten seconds. After washing with H2O, sections were incubated with Congo red according to the manufacturer's recommendations (Sigma Diagnostics, St Louis, Mo., USA). Sections were cleared in xylene and mounted with D.P.X. Mounting Medium (Nustain, Nottingham, U.K.). Analysis of sections was performed on a Leica DMIRBE fluorescence microscope (Rijswijk, The Netherlands). Fluorescence of Congo red was analyzed using an excitation wavelength of 596 nm and an emission wavelength of 620 nm.
Example 30
ELISA: Binding of tPA-F-GST and RPTPμ-GST to Human Ab (1-40) and Glycated Albumin
Binding of tPA-F-GST and RPTPμ-GST to fibrous amyloids human Aβ (1-40) and albumin-g6p was assayed with an ELISA. In brief, human Aβ (1-40), albumin-g6p, or buffer only, were coated on a peptide I Immobilizer or a protein I Immobilizer, respectively. Wells were incubated with the purified GST-tagged constructs or control medium and binding was detected using primary anti-GST monoclonal antibody 2F3 and RAMPO. The wells were also incubated with 500 mM of tPA in the presence of 10 mM of εACA. Binding of tPA is independent of the lysyl binding site located at the kringle 2 domain. Binding of tPA was measured using primary antibody 374B and RAMPO. Experiments were performed in triplicate and blank readings of non-coated wells were substracted.
Example 31
Anti-AGE Antibodies
Antibodies against glucose-6-phosphate glycated bovine serum albumin were elicited in rabbits using standard immunization schemes. Anti-AGE1 was obtained after immunization with two-week glycated albumin-AGE (Prof. Dr. Ph.G. de Groot/Dr. I. Bobbink; unpublished data). The antibody was purified from serum using a Protein G column. Anti-AGE2 was developed by Davids Biotechnologie (Regensburg, Germany). After immunization with albumin-AGE:23, antibodies were affinity purified on human Aβ (1-40) conjugated to EMD Epoxy-activated beads (Merck, Darmstadt, Germany). Polyclonal mouse anti-AGE antibody was obtained after immunization with albumin-AGE:23 and human Aβ (1-40) in a molar ratio of 9:1. Polyclonal serum was obtained using standard immunization procedures, which were performed by the Academic Biomedical Cluster Hybridoma Facility (Utrecht University, The Netherlands). Subsequently, monoclonal antibodies were generated using standard procedures.
Example 32
ELISA: Binding of Antibodies Against Amyloid Peptides or Glycated Protein to Protein-AGE and Amyloid Fibers
For ELISAs, amyloid compounds were immobilized on Exiqon peptide or protein Immobilizers (Vedbaek, Denmark), as described before. Anti-AGE antibodies and commercially available anti-Aβ (1-42) H-43 (Santa Cruz Biotechnology, Santa Cruz, Calif., USA) were diluted in PBS with 0.1% v/v Tween 20. Rabbit anti-human vitronectin K9234 was a kind gift of Dr. H. de Boer (UMC Utrecht) and was used as a negative control. For ELISAs with mouse polyclonal anti-albumin-AGE/Aβ, control serum with antibody elicited against an unrelated protein was used. Binding of mouse polyclonal anti-albumin-AGE/Aβ was performed using a dilution series of serum in PBS/0.1% Tween 20. For competitive binding assays with IAPP, anti-AGE1 was pre-incubated with varying IAPP concentrations. The IAPP fibers were spun down and the supernatant was applied in triplicate to wells of an ELISA plate coated with Aβ. Competitive binding assays with multiligand cross-β structure binding serine protease tPA were performed in a slightly different way. Coated Aβ and IAPP are overlayed with an anti-AGE1 or anti-Aβ (1-42) H-43 concentration related to the kD, together with a concentration series of tPA. A 107-104 times molar excess of lysine analogue εACA (10 mM) was present in the binding buffer in order to avoid binding of tPA to lysine residues of Aβ and IAPP, which would be independent of the presence of amyloid structures.
Example 33
Pull-Down Assay with Amyloid Peptides and Rabbit Anti-AGE1 Antibody
Anti-AGE1 was incubated with amyloid aggregates of Aβ (16-22), Aβ (1-40) and IAPP. After centrifugation, pellets were washed three times with PBS/0.1% Tween 20, dissolved in non-reducing sample buffer (1.5% (n/v) sodium dodecyl sulphate, 5% (v/v) glycerol, 0.01% (m/v) bromophenol blue, 30 mM Tris-HCl pH 6.8). Supernatant after pelleting of the amyloid fibers was diluted 1:1 with 2× sample buffer. Samples were applied to a polyacrylamide gel and after Western blotting, anti-AGE1 was detected with SWARPO.
Example 34
Immunohistochemical Analysis of the Binding of Anti-AGE2 to an Amyloid Plaque in a Section of a Human Brain Inflicted by AD
Rabbit anti-AGE2, affinity purified on an Aβ column, was used for assaying binding properties towards amyloid plaques in brain sections of a human with AD. The procedure was performed essentially as described above. To avoid eventual binding of 11 μg ml−1 anti-AGE2 to protein-AGE adducts or to human albumin in the brain section, 300 nM of g6p-glycated dipeptide Gly-Lys was added to the binding buffer, together with 0.3% m/v BSA. After the immunohistochemical stain, the section was stained with Congo red.
Example 35
Sandwich ELISA for Detection of Amyloid Albumin-AGE in Solution
For detection of amyloid cross-β structure in solutions, the sandwich ELISA approach was used. Actilyse tPA was immobilized at a concentration of 10 μg ml−1 to wells of a 96-wells protein Immobilizer plate (Exiqon, Vedbaek, Denmark). Concentration series of albumin-AGE:23 and albumin-control:23 were added to the tPA-coated wells, as well as to non-coated control wells. Binding of amyloid structures was detected upon incubation with 1 μg ml−1 anti-Aβ (1-42) H-43 (Santa Cruz Biotechnology, Santa Cruz, Calif., USA) and subsequently 0.3 μg ml−1 SWARPO, followed by ortho-phenylene-diamine/H2O2/H2SO4 stain.
Example 36
Cross-β Structure is Present in Fibrin and in Synthetic Peptides Derived from Fibrin
It has been demonstrated herein that a fibrin clot stains with Congo red (not shown) and exhibits Thioflavin T fluorescence (FIG. 2, Panel A), indicative of the presence of amyloid structure in a fibrin clot. Using Congo red staining (not shown), circular dichroism measurements and X-ray diffraction analysis, it was shown that synthetic peptides derived from the sequence of fibrin adopt cross-β structure (FIG. 2, Panels B and C). These peptides were previously found to possess tPA-binding and tPA-activating properties.18 The presence of cross-β structure in these peptides was found to correlate with the ability to stimulate tPA-mediated plasminogen activation (FIG. 2, Panel D).
These data provide evidence for physiological occurrence/relevance for formation of cross-β structure and the role of this structural element in binding of tPA to fibrin.
Example 37
Aβ Contains Cross-β Structure, Binds Plasmin(Ogen) and tPA, Stimulates Plasminogen Activation, Induces Matrix Degradation and Induces Cell Detachment that is Aggravated by Plasminogen and Inhibited by CpB
To test whether tPA, plasminogen and plasmin bind Aβ, solid-phase binding assays were performed. Aβ was coated onto plastic 96-well plates and binding of the peptide to either plasmin(ogen) or to tPA was assessed by overlaying the coated peptide with increasing concentrations of either tPA, plasminogen or plasmin. Binding was assessed using specific antibodies to either plasmin(ogen) or to tPA by performing ELISA. FIG. 3, Panel A, shows that tPA binds to Aβ with a kD of about 7 nM, similar to the kD of tPA binding to fibrin.55 In contrast, No detectable binding of plasminogen to Aβ was found (FIG. 3, Panel B). However, activated plasminogen (plasmin) does bind to Aβ and does so with a kD of 47 nM. The fact that (active) plasmin, but not (inactive) plasminogen, binds to Aβ suggests that plasmin activity and, hence, the generation of free lysines, is important for binding of plasmin to Aβ. To test this, use was made of the lysine analogue ε-aminocaproic acid (εACA) and binding of plasmin and tPA to Aβ was tested in its presence. It is shown herein that the binding of plasmin to Aβ is completely abolished in the presence of εACA (FIG. 3, Panel D). In contrast, εACA has no effect on the tPA-Aβ interaction (FIG. 3, Panel C). Thus, it was concluded that plasmin binds to free lysines that were generated during the incubation period, presumably via its lysine-binding Kringle domain(s). In line with this, the kD of plasminogen Kringle domain binding to free lysines in fibrin is similar to the kD for plasmin binding to Aβ.
The kinetics of plasminogen activation in the absence and the presence of Aβ was investigated. As has been published before by Kingston et al.,24 it was found that Aβ potently stimulates the activation of plasminogen by tPA (FIG. 4, Panel A). However, it was found that the reaction proceeds with second-order, rather than with first-order, kinetics. The possibility was considered that the generation of free lysines during the reaction was causing this phenomenon (see below). tPA-mediated plasmin generation has been implicated in neuronal cell death caused by ischemia or by excitotoxic amino acids. Recent data suggest that plasmin can degrade Aβ and thereby prevents Aβ toxicity.56, 57It was found that 48 hours following the addition of Aβ to a culture of differentiated N1E-115 cells, the majority of cells had died and detached from the matrix (not shown). When added together with Aβ, plasmin (up to 100 mM) was unable to ameliorate Aβ-induced cell detachment. Even prolonged pre-incubations of Aβ with 100 nM plasmin did not affect Aβ-induced cell detachment (FIG. 4, Panel B). Subsequently, the possibility was considered that plasmin generation may potentiate rather than inhibit Aβ-induced cell detachment and survival. To test this, N1E-115 cells were exposed to suboptimal concentrations of Aβ and low concentrations of plasminogen for 24 hours. In the absence of Aβ, plasminogen had no effect on cell adhesion (FIG. 4, Panel C). However, plasminogen had a dramatic potentiating effect on Aβ-induced cell detachment. The minimal levels of plasminogen that were required to potentiate Aβ-induced cell detachment (10-20 μg/ml) were well below those found in human plasma (250 pg/ml). Plasmin-mediated degradation of the extracellular matrix molecule laminin precedes neuronal detachment and cell death in ischemic brain. Whether Aβ-stimulated plasmin generation leads to laminin degradation was tested. Cell detachment was accompanied by degradation of the extracellular matrix protein laminin (FIG. 4, Panel D).
The possibility was considered that the generation of free lysines during Aβ-stimulated plasmin formation was responsible for the observed second-order kinetics. To test this, use was made of carboxypeptidase B (CpB), an enzyme that cleaves of C-terminal lysine and arginine residues, and the CpB-inhibitor CPI. FIG. 5, Panel A, shows that in the presence of CpB, the generation of plasmin was greatly diminished. Furthermore, this effect depends on CpB activity as it was abolished by co-incubation with CPI. FIG. 5, Panel A, also shows that CpB did not completely abolish Aβ-stimulated plasmin generation, but that the reaction proceeded with slow first-order kinetics. These data suggest that the (plasmin-mediated) generation of free lysines during the reaction is essential for efficient Aβ-stimulated plasmin generation, presumably by supporting plasminogen and tPA binding through interaction with their respective Kringle domains. A similar dependency on the generation of C-terminal lysines has been shown for efficient fibrin-mediated plasmin generation.58 These results show that Aβ-stimulated plasmin formation is regulated by carboxypeptidase B in vitro. Thus, if cell detachment is the result of plasmin generation, CpB may affect Aβ-induced cell detachment and/or viability. It is shown herein that cell detachment induced by plasminogen and Aβ is completely prevented by co-incubation with CpB (FIG. 5, Panels B and C). This was accompanied by a complete inhibition of Aβ-stimulated plasmin formation, both in the medium and on the cells (FIG. 5, Panel D).
Example 38
Endostatin can Form Amyloid Fibers Comprising Cross-β Structure
Using Congo red staining (not shown), X-ray diffraction analysis and TEM, the presence of cross-β structure in aggregated endostatin from Escherichia coli, as well as from Pichia pastoris, and the ability of endostatin to form amyloid fibrils (FIG. 6, Panels A and B) has been demonstrated. It was found that bacterial endostatin produced reflection lines at 4.7 Å (hydrogen-bond distance), as well as at 10-11 Å (inter-sheet distance). The reflection lines showed maximal intensities at opposite diffraction angles. The fiber axis, with its 4.7 Å hydrogen bond repeat distance, was oriented along the vertical capillary axis. This implies that inter-sheet distance of 10-11 Å is perpendicular to these hydrogen bonds. This is consistent with the protein being a cross-β sheet conformation with a cross-β structure. Intramolecular sheets in a globular protein cannot cause a diffraction pattern that is ordered in this way. From the amount of background scattering, it follows that only part of the protein takes part in cross-β structure formation. It was found that the presence of cross-β structures in endostatin correlates with its ability to stimulate tPA-mediated plasminogen activation (FIG. 6, Panel C) and correlates with neuronal cell death (FIG. 6, Panel D).
Herein, it is demonstrated that endostatin is an example of a denatured protein that is able to stimulate the suggested cross-β pathway.
Example 39
IAPP Binds tPA and Stimulates tPA-Mediated Plasminogen Activation
Amyloid deposits of IAPP are formed in the pancreas of type II diabetic patients.59 IAPP can cause cell death in vitro and is, therefore, thought to contribute to destruction of β-cells that is seen in vivo, which leads to insufficient insulin production. IAPP forms fibers comprising cross-β structure.60 
Whether IAPP could stimulate tPA-mediated plasminogen activation was tested (FIG. 7). Indeed, similar to Aβ, IAPP enhanced the formation of plasmin by tPA.
Example 40
Glycated Albumin Binds Thioflavin T and tPA, and Aggregates as Amyloid Fibers Comprising Cross-β Structure
It has been demonstrated that glycation of several proteins can induce or increase the ability of these proteins to bind tPA and stimulate tPA-mediated plasmin formation.22, 61 It is shown herein that glycation of albumin with g6p not only confers high-affinity tPA binding to albumin (FIG. 8, Panel A), but also leads to its ability to bind Thioflavin T (FIG. 8, Panel C). Binding of tPA competed with Congo red (FIG. 8, Panel B). In addition, binding of Thioflavin T to glycated albumin competed with tPA (FIG. 8, Panels D and E). The fact that Congo red and/or Thioflavin T and tPA competed with each other illustrates that they have either the same or overlapping binding sites.
Analyses with TEM of the g6p-modified albumin preparations revealed that after a four-week incubation, amorphous albumin aggregates are formed (FIG. 8, Panel G), which exhibits a CD spectrum indicative for the presence of 7% of the albumin amino acid residues in β-sheet (Table I). Prolonged incubation up to 23 weeks resulted in a switch to highly ordered sheet-like fibrous structures, with a length of approximately 500 nm and a diameter ranging from about 50 to 100 nm (FIG. 8, Panel H). These fibers showed an increase to 19% β-sheet when analyzed with CD spectropolarimetry (Table I). Albumin from a different batch that was glycated in the same way already showed bundles of fibrous aggregates after a two-week period of incubation (FIG. 8, Panel I), whereas an increase in β-sheet content was not detected with CD spectropolarimetry (Table I). In each bundle, about ten separate linear 3-5-nm-wide fibers with a length of 200-300 nm can be were identified. On top of each bundle, regularly distributed spots are were seen with a diameter of approximately 5 nm. These spots may be accounted for by globular albumin molecules that are bound to the fibers or, alternatively, that are partly incorporated in the fibers. Aggregates were absent in control albumin (not shown) and no β-sheets were measured using CD spectropolarimetry (Table I). The fibrous structures obtained after two-week and 23-week periods of glycation enhance enhanced the fluorescence of Thioflavin T (ThT) in a similar way, whereas the amorphous precipitates obtained after four weeks hardly increased the fluorescent signal.
X-ray fiber diffraction analyses revealed that albumin-g6p (23 weeks) comprises a significant amount of crystalline fibers (FIG. 8, Panels J and L), whereas diffraction patterns of albumin-g6p (2 weeks) and albumin-g6p (4 weeks) showed features originating from amorphous precipitated globular protein very similar to the patterns obtained for albumin controls (FIG. 8, Panel K). For albumin-g6p (23 weeks), the 4.7 Å repeat corresponds to the characteristic hydrogen-bond distance between β-strands in β-sheets. The 2.3 and 3.3 Å repeats have a preferred orientation perpendicular to the 4.7 Å repeat (FIG. 8, Panel M). Combining the 2.3 and 3.3 Å repeats suggests that the fiber axis is oriented perpendicular to the direction of the hydrogen bonds, with a repeat of 6.8 Å. This dimension corresponds to the length of two peptide bonds and indicates that β-strands run parallel to the fiber axis. This implies that the albumin-g6p (23 weeks) structure is composed of cross-β structure consisting of packed β-sheets of hydrogen-bonded chains (FIG. 8, Panel N). A similar orientation is found in amyloid fibrils of the first predicted α-helical region of PrPc.62 When the a-axis is 9.4 Å, or alternatively 4.7 Å, and the c-axis is 6.8 Å, the 2.5 and 6.0 Å repeats can only be indexed as (h k l). This implies a highly ordered b-axis repeat corresponding to the inter β-sheet distance. With a-axis and c-axis of 4.7 or 9.4 Å and 6.8 Å, respectively, the strong 3.8 Å repeat should be indexed as (2 0 1) or (1 0 1). Considering all observations, it is clear that the albumin-g6p fibers (23 weeks) are built up by cross-β structures, a characteristic feature of amyloid fibrils.
These results show that due to incubation and/or modification with sugar moieties, cross-β structures in albumin are formed that are able to support tPA binding.
Example 41
Glycation of Hemoglobin Induces tPA Binding and Fiber Formation
Incubation of human hemoglobin with g6p resulted in high-affinity tPA binding (FIG. 9, Panel A). Amorphous aggregated Hb-g6p adducts including fibrils were observed with TEM (FIG. 9, Panel B), whereas control Hb did not aggregate (not shown). Human Hb of diabetes mellitus patients had the tendency to form fibrillar aggregates once more than 12.4% of the Hb is glycated (Table II).
Example 42
Amyloid Albumin is Formed Irrespective of the Original Carbohydrate (Derivative)
From the above-listed observations, it is clear that modification of —NH2 groups of albumin with g6p induces formation of amyloid cross-β structure. The next question addressed was whether triggering of refolding of globular albumin into an amyloid fold was a restricted property of g6p, or whether amyloid formation occurs irrespective of the original carbohydrate or carbohydrate derivative used for AGE formation. Albumin solutions were incubated for 86 weeks at 37° C. with 1 M g6p, 250 mM DL-glyceraldehyde/100 mM NaCNBH3, 1 M β-D-(−)-fructose, 1 M D(+)-glucose, 500 mM glyoxylic acid/100 mM NaCNBH3, and corresponding PBS and PBS/NaCNBH3 buffer controls. Glyceraldehyde and glyoxylic acid are carbohydrate derivatives that are precursors of AGE in Maillard reactions.63, 64 After 86 weeks, albumin-glyceraldehyde and albumin-fructose were light-yellow/brown suspensions. Controls were colorless and clear solutions. Albumin-glucose and albumin-glyoxylic acid were clear light-yellow to light-brown solutions. Albumin-g6p:86 was a clear and dark brown solution. AGE formation was confirmed by autofluorescence measurements using AGE-specific excitation/emission wavelengths (not shown), binding of moab anti-AGE 4B5 (not shown) and binding of poab anti-AGE (not shown). As expected, albumin-glyoxylic acid did not show an autofluorescent signal due to the fact that (mainly) non-fluorescent carboxymethyl-lysine (CML) adducts are formed.63 
The autofluorescence data and the binding of AGE-specific antibodies listed above show that various carbohydrates and carbohydrate derivatives led to similar AGE structures. Using g6p as the starting point for AGE formation, it is shown that albumin adopted amyloid properties similar to those observed in the well-studied fibrils of Aβ and IAPP. Therefore, the presence of amyloid structures in the albumin-AGE adducts obtained with alternative carbohydrates and derivatives was tested for. Fluorescence of albumin-AGE—ThT solutions (FIG. 10, Panel J) and of air-dried albumin-AGE preparations that were incubated with Congo red (FIG. 10, Panels A-I) was measured. Incubation of albumin with glyceraldehyde, glucose or fructose resulted in an increased fluorescent signal of ThT (FIG. 10, Panel J). After subtraction of background signals of ThT and buffer, no specific amyloid—ThT fluorescence was measured for albumin-glyoxylic acid and buffer controls. Albumin-g6p, albumin-glyceraldehyde and albumin-fructose gave a Congo red fluorescent signal similar to the signals of Aβ and IAPP (FIG. 10, Panels C-E, G and H). With albumin-glucose, a uniformly distributed pattern of fluorescent precipitates was observed (FIG. 10, Panel F). With albumin-glyoxylic acid and buffer controls, hardly any staining is observed (FIG. 10, Panels A, B and I). These ThT and Congo red fluorescence data show that, in addition to albumin-g6p, albumin-glyceraldehyde, albumin-glucose and albumin-fructose have amyloid-like properties. To further substantiate these findings, binding of amyloid-specific serine protease tPA in an ELISA was tested for. The enzyme bound specifically to albumin-g6p, albumin-glyceraldehyde, albumin-glucose and albumin-fructose (FIG. 10, Panels K and L) and to positive controls Aβ and IAPP, as was shown before.49 No tPA binding was observed for albumin-glyoxylic acid and buffer controls.
From the ThT, Congo red and tPA data, it is clear that inducing amyloid properties in albumin is not an exclusive property of g6p. Apparently, a spectrum of carbohydrates and carbohydrate derivatives comprising g6p, glucose, fructose, glyceraldehyde, and likely more, has the capacity to trigger the switch from a globular native fold to the amyloid cross-β structure fold upon their covalent binding to albumin.
Example 43
Analysis of Congo Red Binding and tPA Binding to Aβ
It has been demonstrated that Aβ bound tPA and Congo red. It was shown that the binding of tPA to Aβ competed with Congo red (FIG. 11). These results support the findings herein that structures in Aβ, fibrin and glycated albumin are similar and are able to mediate the binding to tPA.
Example 44
Binding of Human FXII to Amyloid Peptides and Proteins that Contain the Cross-β Structure Fold
The graphs in FIG. 12 show that FXII binds specifically to all amyloid compounds tested. kDs for hAβ (1-40), FP13, albumin-AGE and Hb-AGE are approximately 2, 11, 8 and 0.5 nM, respectively. The data obtained with the competitive FXII—tPA ELISA show that tPA efficiently inhibits binding of FXII to amyloid (poly)peptides (FIG. 12). From these data, it is concluded that FXII and f.l. tPA compete for overlapping binding sites on hAβ (1-40). K2P-tPA did not inhibit FXII binding. Binding of FXII to albumin-AGE was also effectively abolished by tPA but not by K2P-tPA, similar to what was observed for hAβ (1-40). This indicates that FXII may bind in a similar manner to hAβ (1-40) and albumin-AGE. In addition, these data show that the first three domains of tPA (finger, EGF-like, kringle 1) seem to be involved in the inhibitory effect of f.l. tPA on interactions between FXII and amyloid hAβ (1-40) or albumin-AGE. Using a dot-blot assay, binding of FXII to spotted amyloid hΔIAPP and hAβ (1-40) was tested. No binding of FXII was observed for negative controls PBS and mΔIAPP (FIG. 12). However, FXII specifically bound to hAβ (1-40), in agreement with an earlier report,65 as well as to hΔIAPP (FIG. 12). These data, together with the ELISA data shown in FIG. 12, Panels A-F, suggest that FXII can bind to polypeptides that do not share amino acid sequence homology, but which do share the cross-β structure fold. This is in accordance with the recent data on interactions between tPA and polypeptides that contain the amyloid-specific fold.
Example 45
Binding of tPA to the Cross-β Structure-Containing Molecules, Aβ and Glycated Albumin Requires the Presence of an N-Terminal Region in tPA, which Contains the Finger Domain
Several domains in tPA have been shown to mediate binding to fibrin or fibrin fragments.12, 53, 66, 67 However, it is unknown which domain of tPA is needed for binding to Aβ or other cross-β structure-containing molecules. It is shown that a mutated tPA, termed reteplase, which lacks the N-terminal finger, EGF and kringle 1 domain (K2-tPA), is unable to bind cross-βstructure-comprising molecules (FIG. 13, Panels A and B). These results suggest that the N-terminal region is required for binding of tPA to fibers comprising cross-β structure.
Example 46
Expression and Purification of tPA-F-GST and RPTP-GST
Purification of the GST-tagged constructs tPA-F-GST and RPTPμ-GST(control) from 293T medium using glutathione coupled to Sepharose 4B beads resulted in single bands of approximately 35 kDa and 150 kDa, respectively (not shown). Traces of BSA, originating from the FCS used in the medium, were also present.
Example 47
ELISA: Binding of tPA-F-GST and RPTP-GST to Human Aβ (1-40) and Glycated Albumin
In the ELISA, control tPA bound to both human Aβ (1-40) and albumin-g6p in the presence of excess εACA (FIG. 13, Panel C). This shows that in the assay used, tPA is capable of binding to fibrous amyloids in a kringle 2-independent manner. The tPA-F domain bound to human Aβ (1-40) and to albumin-g6p, whereas no binding was observed with RPTPμ-GST. Therefore, binding observed with tPA-F-GST is specific and does not originate from the GST tag. This result points to the tPA finger domain as a specific domain designed by nature for binding to cross-β-structured amyloid fibers.
cDNA constructs in pcDNA3 of the F, F-EGF, EGF, F-EGF-K1 and K1 fragments of human tPA was prepared. Recombinant proteins with a C-terminal GST tag were expressed in BHK cells and secreted to the medium. Medium from BHK cells expressing the GST tag alone was used as a control. Conditioned medium was used for pull-down assays using Aβ and IAPP fibrils, followed by Western blot analyses. Efficient binding to Aβ was evident for all three tPA mutants that contain the finger domain, i.e., F-GST, F-EGF-GST and F-EGF-K1-GST (FIG. 13, Panel D). The K1-GST and EGF-GST constructs, as well as the GST tag alone, remain in the supernatant after Aβ incubation. A similar pattern was obtained after IAPP pull-downs (not shown).
Binding of purified tPA F-EGF-GST, recombinant f.l. Actilyse tPA and a GST control to immobilized amyloid fibrin fragment α148-160 FP13, amyloid IAPP and to non-amyloid mΔIAPP control was compared (FIG. 13, Panels E-G). Full-length tPA and tPA F-EGF-GST bind to all three amyloid peptides; for Aβ kDs for tPA and F-EGF are 2 and 2 nM, respectively; for FP13, 5 and 2 nM; for IAPP, 2 and 13 nM. No binding to non-amyloid mΔIAPP was observed (FIG. 13, Panel E). GST did not bind to FP13 and IAPP, while some binding is detected to Aβ. This may reflect the small fraction of GST that bound to Aβ in the pull-down assay (FIG. 13, Panel D).
With immunohistochemical analysis, binding of the purified recombinant tPA F-EGF-GST construct to paraffin sections of human brain inflicted by AD was tested. Presence of amyloid depositions was confirmed by the Dept. of Pathology (UMC Utrecht) using standard techniques. In the experiments, these amyloid depositions were located using Congo red fluorescence (FIG. 13, Panels I, K and M). In FIG. 13, Panels H-K, it is clearly seen that areas that are positive for Congo red binding coincides with areas that are positive for tPA F-EGF-GST binding. Control stain with GST did not show specific binding of the tag alone (FIG. 13, Panels L and M).
At present, based on sequential and structural homology, next to tPA, three proteins are known that contain one or more finger domains, i.e., HGFa (one F domain), FXII (one F domain), Fn (one stretch of six F domains, two stretches of three F domains). From the above-listed results, it was concluded that the F domain of tPA (SEQ ID NO: 3) plays a crucial role in binding of tPA to amyloid peptides or polypeptides. It was hypothesized that the finger domain could be a general cross-β structure-binding module. Presently, four proteins, tPA, FXII, HGFa and fibronectin, are known that contain a finger motif. FIG. 14, Panel A, schematically depicts the localization of the finger module in the respective proteins. FIG. 14, Panel B, shows an alignment of the human amino acid sequences of the finger domains in these four proteins. (SEQ ID NOs: 3-17). FIG. 14, Panel C, shows a schematic representation of the three-dimensional structure of the finger domain of tPA (SEQ ID NO: 3), and of the fourth and fifth finger domain of fibronectin (SEQ ID NOs: 9 and 10). To test the hypothesis that finger domains in general bind amyloid, the F domains of HGFa (SEQ ID NO: 5) and FXII (SEQ ID NO: 4), as well as the fourth and fifth F domain of Fn (SEQ ID NOs: 9 and 10), which are known for their capacity to bind to fibrin,68 were cloned. Using a pull-down assay, it was shown that Fn F4-GST and Fn F4-5-GST, as well as FXII F-GST and HGFa F-GST, specifically bind to Aβ (FIG. 13, Panels M and N) and IAPP (not shown). Fn F5-GST bound to Aβ to some extent, however, it was extracted less efficiently from the medium and seemed to be partly released during the washing procedure of the amyloid pellet (FIG. 13, Panel M). No construct was left in the medium after extraction of positive control tPA F-EGF-GST, whereas no negative control GST was detected in the pellet fraction (not shown). These data show that binding to amyloid peptides or polypeptides is not a unique capacity of the tPA F domain (SEQ ID NO: 3), yet a more general property of the F domains tested. Moreover, these data indicate that observed binding of FXII to amyloid (poly)peptides, as shown in FIG. 13, Panels A and H, and by Shibayama et al.,65 is regulated via the F domain.
Example 48
Amyloid-Binding Domain of tPA
The finger domain of tPA has been shown to be of importance for high-affinity binding to fibrin.12, 66 The present results using RETEPLASE® (K2-P tPA) and F-tPA, F-EGF-tPA and F-EGF-K1-tPA, indicate an important role for the N-terminal finger domain of tPA in binding to stimulatory factors other than fibrin. Thus far, all of these factors bind Congo red and contain cross-β structure. Furthermore, the binding site of fibronectin for fibrin has been mapped to the finger domain tandem F4-F5.68 It has been demonstrated that plasminogen activation by full-length tPA, in the presence of fibrin fragment FCB2, can be inhibited by fibronectin.69 Taken together, these observations suggest that tPA and fibronectin compete, via their finger domain, for the same or overlapping binding sites on fibrin. The data now shows that the F4-5 domains of Fn (SEQ ID NOs: 9 and 10) bind to amyloid Aβ.
Example 49
Binding of Anti-AGE Antibodies to Amyloid (Poly)Peptides and Binding of Anti-Aβ to Protein-AGE Adducts
Recently, O'Nuallain and Wetzel70 showed that antibodies elicited against a peptide with amyloid characteristics can bind to any other peptide with similar amyloid properties, irrespective of amino acid sequence. Based on these data and on the observations that tissue-type plasminogen activator and factor XII can bind to a family of sequence-unrelated polypeptides that share the amyloid-specific cross-β structure fold, a broader class of proteins can display affinity towards this structural unit, rather than towards a linear or conformational epitope, built up by specific amino acid residues. This prompted the question as to whether antibodies elicited against albumin-AGE, that contain the amyloid cross-β structure fold, also display the broad-range specificity towards any (poly)peptide which bears this cross-β structure fold.
In an ELISA set-up, α-AGE1, which was elicited against g6p-glycated albumin-AGE, bound to amyloid albumin-AGE:23 (Kd=66 nM) and Hb-AGE:32 (Kd=20 nM), as well as to Aβ (1-40) (Kd=481 nM) and IAPP (Kd=18 nM) (FIG. 15, Panels A-C). Negative controls were non-glycated albumin and Hb, non-amyloid peptide mouse ΔIAPP for IAPP and polyclonal anti-human vitronectin antibody α-hVn K9234 for Aβ. To test whether the same fraction of α-AGE1 binds to IAPP and Aβ, the antibody was pre-incubated with IAPP fibrils, followed by pelleting of the fibrils, together with the possible amyloid-binding fraction of α-AGE1. Binding of α-AGE1, left in the supernatant, to Aβ (1-40) was reduced (FIG. 15, Panel D). This indicates that the same fraction of a-AGE1 bound to IAPP and Aβ (1-40). With a pull-down assay, the binding of anti-AGE1 to amyloid peptides in an alternative way was assessed. After incubation of anti-AGE1 solutions with amyloid fibrils Aβ (16-22) (FIG. 15, Panel E, lanes 1-2), Aβ (1-40) (FIG. 15, Panel E, lanes 4-5), and IAPP (FIG. 15, Panel E; lanes 6-7), and subsequent pelleting of the amyloid fibrils, the supernatant was completely depleted from α-AGE1 by Aβ (16-22). With IAPP, approximately 50% of the antibody is found in the amyloid fraction, whereas less antibody is pelleted with Aβ (1-40). These data obtained in a complementary way, again show that anti-AGE1 can bind to amyloid peptides, which share no amino-acid sequence homology with albumin-AGE:23, though which share the cross-β structure fold. In addition, the observation that binding of tPA to amyloid peptides inhibited binding of anti-AGE1, also indicates that anti-AGE1, like tPA, binds bound to the cross-β structure fold (FIG. 15, Panels F and G). The observation that tPA reduces anti-AGE 1 binding to Aβ to a lesser extent than the reduction seen with IAPP, is putatively related to the higher number of anti-AGE1-binding sites on coated Aβ, when, compared with IAPP (see FIG. 15, Panels B and C), and to the higher affinity of tPA for IAPP (kD=6 nM) than for Aβ (kD=46 nM), when using Exiqon ELISA plates (not shown). The binding data together suggest that anti-AGE1 binds to this amyloid fold, irrespective of the (poly)peptide that bears the cross-β structure fold, which identifies anti-AGE1 as a member of the class of multiligand cross-β structure-binding proteins.
Based on the above-listed results obtained with anti-AGE1, testing was done as to whether commercially available rabbit anti-human Aβ (1-42) H-43 also displays broad-range specificity towards any (poly)peptide with unrelated amino acid sequence, although with amyloid characteristics. Indeed, with an ELISA, it was shown that H-43 not only binds to Aβ (1-40), but also to IAPP and albumin-AGE (FIG. 15, Panel H). In addition, binding of H-43 to immobilized IAPP was effectively diminished by tPA (FIG. 15, Panel I). These observations together show that anti-Aβ (1-42) H-43 can bind to other amyloid (poly)peptides in a way similar to multiligand cross-β structure-binding protein tPA.
ELISAs with polyclonal mouse anti-albumin-AGE/Aβ showed that the antibody not only binds to these antigens, but that it specifically binds to other amyloid peptides than those used for immunization (FIG. 15, Panels J-L). Similar to the rabbit anti-AGE1 antibody and anti-Aβ (1-42) H-43, anti-albumin-AGE/Aβ displayed affinity for the amyloid peptides tested, irrespective of amino acid sequence. This suggests that also mouse anti-albumin-AGE/Aβ is a multiligand amyloid-binding antibody.
Based on the amyloid-binding characteristics of anti-AGE1, anti-Aβ (1-42) H-43 and anti-albumin-AGE/Aβ, the amyloid-binding fraction of anti-AGE2, which is elicited against albumin-AGE:23, with Aβ fibrils irreversibly coupled to a column, was purified. This fraction was used for immunohistochemical analysis of a human brain section that is inflicted by Alzheimer's disease. In FIG. 15, Panel M, it is clearly seen that the antibody binds bound specifically to the spherical amyloid deposition, indicated by the Congo red fluorescence shown in FIG. 15, Panel N.
The finding that anti-amyloid and anti-AGE antibodies display affinity for a broad range of sequentially unrelated (poly)peptides as long as the cross-β structure fold is present, is in agreement with the recently published data by O'Nuallain and Wetzel70 and Kayed et al.71 From several older reports in literature, it can be distilled that anti-cross-β antibodies can be obtained. For example, cross-reactive antibodies against fibrin and Aβ and against Aβ and hemoglobin are described.72, 73 It is indicated herein that fibrinogen and hemoglobin-AGE adopt the cross-β structure fold, which suggests that the cross-reactivity observed for anti-Aβ antibodies was, in fact, binding of anti-cross-β structure antibodies to similar structural epitopes on Aβ, fibrinogen and hemoglobin.
Based on the results with the poly-clonal anti-AGE and amyloid antibodies, it was hypothesized that anti-cross-β structure antibodies could be obtained. Therefore, the spleen of mice immunized with glycated BSA and Aβ was fused with myeloma cells. Subsequently, potential anti-cross-β structure antibodies were selected by examining binding of hybridoma-produced antibodies to glycated hemoglobin and IAPP. Using this procedure, a monoclonal antibody 3H7 was isolated that recognizes glycated hemoglobin, as well as several peptides that contain the cross-β structure (FIG. 16). No binding was observed to unglycated hemoglobin or a synthetic peptide that does not form amyloid fibers (mΔIAPP).
Example 50
Sandwich ELISA: Fishing Amyloid Structures from Solution
Using a sandwich ELISA approach with coated tPA that was overlayed with amyloid albumin-AGE:23 in solution, followed by detection with broad-range anti-Aβ (1-42) H-43 (FIG. 17), cross-β structure-containing proteins in solution were detected.
It is herein disclosed that the three-dimensional structures of the tPA finger domain74, 75 and the fibronectin finger domains 4-575, 76 reveal striking structural homology with respect to local charge-density distribution. Both structures contain a similar solvent-exposed stretch of five amino acid residues with alternating charge; for tPA, Arg7, Glu9, Arg23, Glu32, Arg30; and for fibronectin, Arg83, Glu85, Lys87, Glu89, Arg90, located at the fifth finger domain, respectively. The charged-residue alignments are located at the same side of the finger module. These alignments may be essential for fibrin binding.
Based on the observations, results and the herein-disclosed similarities, it was shown that the same binding sites for tPA became present in all proteins that bound and activated tPA and that this binding site comprises a cross-β structure.
Taken together, the data shows that a cross-β structure is a physiological relevant quarternary structure element in which appearance is tightly regulated and in which occurrence induces a normal physiological response, i.e., the removal of unwanted biomolecules. To the knowledge of the inventors, the existence of a general system, which is termed “cross-β structure pathway,” to remove unwanted biomolecules is herein disclosed for the first time. The results show that this mechanism is fundamental to nature and controls many physiological processes to protect organisms from induced damage or from accumulating useless or denatured biomolecules. If deregulated, by whatever means, this system may cause severe problems. On the other hand, if properly used, this system may be applicable for inducing cell death in specific target cells, like, for example, tumor cells.
Tables







TABLE I







Percentage β-sheet, as calculated front CD spectra












Incubation time




Sample‡
(weeks)
β-sheet (%)†















Aβ (16-22)

100



Albumin-glyceraldehyde
2
0



Albumin control
2
0



Albumin-g6p
2
0



Albumin-g6p
4
7



Albumin control
23
0



Albumin-g6p
23
19







‡Two-weeks incubated albumin was from a different batch than four- and 23-weeks incubated albumin.



†Percentage of amino acid residues in β-sheets are given.













TABLE II







Correlation between HbA1c concentrations


and Hb fiber formation in vitro








Healthy controls
Diabetes mellitus patients












sample
[HbA1c] (%)‡
Fibers†
sample
[HbA1c] (%)‡
Fibers†















1
5.6
−
1
5.5
−


2
5.9
−
2
5.8
−


3
6.2
−
3
5.8
−





4
10.7
−





5
11.3
−





6
11.6
−





7
12.4
+





8
12.5
−





9
12.5
−





10
12.6
+





11
12.7
−





12
12.8
−





13
13.3
+





14
13.7
+





15
14.8
+





16
15.3
+





‡The HbA1c concentration is given as a percentage of the total amount of Hb present in erythrocytes of diabetes mellitus patients and of healthy controls. The s.d. is 2.3% of the values given.


†Presence of fibers as determined with TEM.






REFERENCES


    1. Bucciantini M., Giannoni E., Chiti F., et al. Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature 2002; 416:507-511.
    2. Rochet J. C., Lansbury P. T., Jr. Amyloid fibrillogenesis: themes and variations. Curr. Opin. Struct. Biol. 2000; 10:60-68.
    3. Carmeliet P., Bouche A., De Clercq C., et al. Biological effects of disruption of the tissue-type plasminogen activator, urokinase-type plasminogen activator, and plasminogen activator inhibitor-1 genes in mice. Ann. N.Y. Acad. Sci. 1995; 748:367-381.
    4. Carmeliet P., Collen D. Genetic analysis of the plasminogen and coagulation system in mice. Haemostasis 1996; 26 Suppl. 4:132-153.
    5. Collen D., Lijnen H. R. Molecular basis of fibrinolysis, as relevant for thrombolytic therapy. Thromb. Haemost. 1995; 74:167-171.
    6. Lijnen H. R., Collen D. Mechanisms of physiological fibrinolysis. Baillieres Clin. Haematol. 1995; 8:277-290.
    7. Bosma P. J., Rijken D. C., Nieuwenhuizen W. Binding of tissue-type plasminogen activator to fibrinogen fragments. Eur. J. Biochem. 1988; 172:399-404.
    8. Grailhe P., Nieuwenhuizen W., Angles-Cano B. Study of tissue-type plasminogen activator binding sites on fibrin using distinct fragments of fibrinogen. Eur. J. Biochem. 1994; 219:961-967.
    9. Nieuwenhuizen W. Fibrin-mediated plasminogen activation. Ann. N.Y. Acad. Sci. 2001; 936:237-246.
    10. Yakovlev S., Makogonenko E., Kurochkina N., Nieuwenhuizen W., Ingham K., Medved L. Conversion of fibrinogen to fibrin: mechanism of exposure of tPA- and plasminogen-binding sites. Biochemistry 2000; 39:15730-15741.
    11. Bakker A. H., Weening-Verhoeff E. J., Verheijen J. H. The role of the lysyl binding site of tissue-type plasminogen activator in the interaction with a forming fibrin clot. J. Biol. Chem. 1995; 270:12355-12360.
    12. de Munk G. A., Caspers M. P., Chang G. T., Pouwels P. H., Enger-Valk B. E., Verheijen J. H. Binding of tissue-type plasminogen activator to lysine, lysine analogues, and fibrin fragments. Biochemistry 1989; 28:7318-7325.
    13. Fleury V., Loyau S., Lijnen H. R., Nieuwenhuizen W., Angles-Cano B. Molecular assembly of plasminogen and tissue-type plasminogen activator on an evolving fibrin surface. Eur. J. Biochem. 1993; 216:549-556.
    14. Haddeland U., Sletten K., Bennick A., Nieuwenhuizen W., Brosstad F. Aggregated, conformationally changed fibrinogen exposes the stimulating sites for t-PA-catalysed plasminogen activation. Thromb. Haemost. 1996; 75:326-331.
    15. Hasan A. A., Chang W. S., Budzynski A. Z. Binding of fibrin fragments to one-chain and two-chain tissue-type plasminogen activator. Blood 1992; 79:2313-2321.
    16. Nieuwenhuizen W., Vermond A., Voskuilen M., Traas D. W., Verheijen J. H. Identification of a site in fibrin(ogen) which is involved in the acceleration of plasminogen activation by tissue-type plasminogen activator. Biochim. Biophys. Acta. 1983; 748:86-92.
    17. Nieuwenhuizen W., Schielen W. J., Yonekawa O., Tesser G. I., Voskuilen M. Studies on the localization and accessibility of sites in fibrin which are involved in the acceleration of the activation of plasminogen by tissue-type plasminogen activator. Adv. Exp. Med. Biol. 1990; 281:83-91.
    18. Nieuwenhuizen W. Sites in fibrin involved in the acceleration of plasminogen activation by t-PA. Possible role of fibrin polymerisation. Thromb. Res. 1994; 75:343-347.
    19. Schielen W. J., Adams H. P., Voskuilen M., Tosser G. I., Nieuwenhuizen W. The sequence A alpha-(154-159) of fibrinogen is capable of accelerating the t-PA catalysed activation of plasminogen. Blood Coagul. Fibrinolysis 1991; 2:465-470.
    20. Tsurupa G., Medved L. Identification and characterization of novel tPA- and plasminogen-binding sites within fibrin(ogen) alpha C-domains. Biochemistry 2001; 40:801-808.
    21. Yonekawa O., Voskuilen M., Nieuwenhuizen W. Localization in the fibrinogen gamma-chain of a new site that is involved in the acceleration of the tissue-type plasminogen activator-catalysed activation of plasminogen. Biochem J. 1992; 283 (Pt 1):187-191.
    22. Bobbink I. W., Tekelenburg W. L., Sixma J. J., de Boer H. C., Banga J. D., de Groot P. G. Glycated proteins modulate tissue-plasminogen activator-catalyzed plasminogen activation. Biochem. Biophys. Res. Commun. 1997; 240:595-601.
    23. Hu G. F., Riordan J. F. Angiogenin enhances actin acceleration of plasminogen activation. Biochem. Biophys. Res. Commun. 1993; 197:682-687.
    24. Kingston I. B., Castro M. J., Anderson S. In vitro stimulation of tissue-type plasminogen activator by Alzheimer amyloid beta-peptide analogues. Nat. Med. 1995; 1:138-142.
    25. Lind S. E., Smith C. J. Actin accelerates plasmin generation by tissue plasminogen activator. J. Biol. Chem. 1991; 266:17673-17678.
    26. Machovich R., Owen W. G. Denatured proteins as cofactors for plasminogen activation. Arch. Biochem. Biophys. 1997; 344:343-349.
    27. Machovich R., Ajtai K., Kolev K., Owen W. G. Myosin as cofactor and substrate in fibrinolysis. FEBS Lett. 1997; 407:93-96.
    28. Machovich R., Komorowicz E., Kolev K., Owen W. G. Facilitation of plasminogen activation by denatured prothrombin. Thromb. Res. 1999; 94:389-394.
    29. Parkkinen J., Hacker J., Korhonen T. K. Enhancement of tissue plasminogen activator-catalyzed plasminogen activation by Escherichia coli S. fimbriae associated with neonatal septicaemia and meningitis. Thromb. Haemost. 1991; 65:483-486.
    30. Parkkinen J., Rauvala H. Interactions of plasminogen and tissue plasminogen activator (t-PA) with amphoterin. Enhancement of t-PA-catalyzed plasminogen activation by amphoterin. J. Biol. Chem. 1991; 266:16730-16735.
    31. Pryzdial E. L., Bajzar L., Nesheim M. E. Prothrombinase components can accelerate tissue plasminogen activator-catalyzed plasminogen activation. J. Biol. Chem. 1995; 270:17871-17877.
    32. Radcliffe R., Heinze T. Stimulation of tissue plasminogen activator by denatured proteins and fibrin clots: a possible additional role for plasminogen activator? Arch. Biochem. Biophys. 1981; 211:750-761.
    33. Sheng S., Truong B., Fredrickson D., Wu R., Pardee A. B., Sager R. Tissue-type plasminogen activator is a target of the tumor suppressor gene maspin. Proc. Natl. Acad. Sci. U.S. A. 1998; 95:499-504.
    34. Silverstein R. L., Leung L. L., Harpel P. C., Nachman R. L. Complex formation of platelet thrombospondin with plasminogen. Modulation of activation by tissue activator. J. Clin. Invest. 1984; 74:1625-1633.
    35. Stack S., Gonzalez-Gronow M., Pizzo S. V. Regulation of plasminogen activation by components of the extracellular matrix. Biochemistry 1990; 29:4966-4970.
    36. Wada H., Kumeda Y., Ogasawara Z., et al. Stimulation of tissue type plasminogen activator by leukaemic cell homogenates. Blood Coagul. Fibrinolysis 1993; 4:591-597.
    37. Carrell R. W., Gooptu B. Conformational changes and disease—serpins, prions and Alzheimer's. Curr. Opin. Struct. Biol. 1998; 8:799-809.
    38. Krieger M., Stern D. M. Series introduction: multiligand receptors and human disease. J. Clin. Invest. 2001; 108:645-647.
    39. Schmidt A. M., Yan S. D., Wautier J. L., Stern D. Activation of receptor for advanced glycation end products: a mechanism for chronic vascular dysfunction in diabetic vasculopathy and atherosclerosis. Circ. Res. 1999; 84:489-497.
    40. Schmidt A. M., Yan S. D., Yan S. F., Stern D. M. The biology of the receptor for advanced glycation end products and its ligands. Biochim. Biophys. Acta. 2000; 1498:99.111.
    41. Schmidt A. M., Hofmann M., Taguchi A., Yan S. D., Stern D. M. RAGE: a multiligand receptor contributing to the cellular response in diabetic vasculopathy and inflammation. Semin. Thromb. Hemost. 2000; 26:485-493.
    42. Schmidt A. M., Yan S. D., Yan S. F., Stern D. M. The multiligand receptor RAGE as a progression factor amplifying immune and inflammatory responses. J. Clin. Invest. 2001; 108:949-955.
    43. Weldon D. T., Maggio J. E., Mantyh P. W. New insights into the neuropathology and cell biology of Alzheimer's disease. Geriatrics 1997; 52 Suppl. 2:S13-S16.
    44. Yan S. D., Roher A., Chaney M., Zlokovic B., Schmidt A. M., Stern D. Cellular cofactors potentiating induction of stress and cytotoxicity by amyloid beta-peptide. Biochim. Biophys. Acta. 2000; 1502:145-157.
    45. Balbach J. J., Ishii Y., Antzutkin O. N., et al. Amyloid fibril formation by A beta 16-22, a seven-residue fragment of the Alzheimer's beta-amyloid peptide, and structural characterization by solid state NMR. Biochemistry 2000; 39:13748-13759.


46. Bobbink I. W., de Boer H. C., Tekelenburg W. L., Banga J. D., de Groot P. G. Effect of extracellular matrix glycation on endothelial cell adhesion and spreading: involvement of vitronectin. Diabetes 1997; 46:87-93.

    47. Boehm T., Folkman J., Browder T., O'Reilly M. S. Anti-angiogenic therapy of experimental cancer does not induce acquired drug resistance. Nature 1997; 390:404-407.
    48. Andrade M. A., Chacon P., Merelo J. J., Moran F. Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network. Protein Eng. 1993; 6:383-390.
    49. Kranenburg O., Bouma B., Kroon-Batenburg L. M., et al. Tissue-type plasminogen activator is a multiligand cross-beta structure receptor. Curr. Biol. 2002; 12:1833-1839.
    50. van Zonneveld A. J., Veerman H., Pannekoek H. On the interaction of the finger and the kringle-2 domain of tissue-type plasminogen activator with fibrin. Inhibition of kringle-2 binding to fibrin by epsilon-amino caproic acid. J. Biol. Chem. 1986; 261:14214-14218.
    51. LeVine H., III. Quantification of beta-sheet amyloid fibril structures with thioflavin T. Methods Enzymol. 1999; 309:274-284.
    52. Kranenburg O., Scharnhorst V., Van der Eb A. J., Zantema A. Inhibition of cyclin-dependent kinase activity triggers neuronal differentiation of mouse neuroblastoma cells. J. Cell. Biol. 1995; 131:227-234.
    53. Johannessen M., Diness V., Pingel K., et al. Fibrin affinity and clearance of t-PA deletion and substitution analogues. Thromb. Haemost. 1990; 63:54-59.
    54. Gebbink M. F., Zondag G. C., Koningstein G. M., Feiken E., Wubbolts R. W., Moolenaar W. H. Cell surface expression of receptor protein tyrosine phosphatase RPTP mu is regulated by cell-cell contact. J. Cell. Biol. 1995; 131:251-260.
    55. Stewart R. J., Fredenburgh J. C., Weitz J. I. Characterization of the interactions of plasminogen and tissue and vampire bat plasminogen activators with fibrinogen, fibrin, and the complex of D-dimer non-covalently linked to fragment E. J. Biol. Chem. 1998; 273:18292-18299.
    56. Tucker H. M., Kihiko M., Caldwell J. N., et al. The plasmin system is induced by and degrades amyloid-beta aggregates. J. Neurosci. 2000; 20:3937-3946.
    57. Tucker H. M., Kihiko-Ehmann M., Wright S., Rydel R. E., Estus S. Tissue plasminogen activator requires plasminogen to modulate amyloid-beta neurotoxicity and deposition. J. Neurochem. 2000; 75:2172-2177.
    58. Redlitz A., Tan A. K., Eaton D. L., Plow E. F. Plasma carboxypeptidases as regulators of the plasminogen system. J. Clin. Invest. 1995; 96:2534-2538.
    59. Hayden M. R., Tyagi S. C. “A” is for amylin and amyloid in type 2 diabetes mellitus. J.O.P. 2001; 2:124-139.
    60. Moriarty D. F., Raleigh D. P. Effects of sequential proline substitutions on amyloid formation by human amylin 20-29. Biochemistry 1999; 38:1811-1818.
    61. Saishoji T., Higashi T., Ikeda K., et al. Advanced glycation end products stimulate plasminogen activator activity via GM-CSF in RAW 264.7 cells. Biochem. Biophys. Res. Commun. 1995; 217:278-285.
    62. Nguyen J. T., Inouye H., Baldwin M. A., et al. X-ray diffraction of scrapie prion rods and PrP peptides. J. Mol. Biol. 1995; 252:412-422.
    63. Motomiya Y., Oyama N., Iwamoto H., Uchimura T., Maruyama I. N epsilon-(carboxymethyl)lysine in blood from maintenance hemodialysis patients may contribute to dialysis-related amyloidosis. Kidney Int. 1998; 54:1357-1366.
    64. Sady C., Jiang C. L., Chellan P., et al. Maillard reactions by alpha-oxoaldehydes: detection of glyoxal-modified proteins. Biochim. Biophys. Acta. 2000; 1481:255-264.
    65. Shibayama Y., Joseph K., Nakazawa Y., Ghebreihiwet B., Peerschke E. I., Kaplan A. P. Zinc-dependent activation of the plasma kinin-forming cascade by aggregated beta amyloid protein. Clin. Immunol. 1999; 90:89-99.
    66. Bennett W. F., Paoni N. F., Keyt B. A., et al. High resolution analysis of functional determinants on human tissue-type plasminogen activator. J. Biol. Chem. 1991; 266:5191-5201.
    67. Horrevoets A. J., Smilde A., de Vries C., Pannekoek H. The specific roles of finger and kringle 2 domains of tissue-type plasminogen activator during in vitro fibrinolysis. J. Biol. Chem. 1994; 269:12639-12644.
    68. Matsuka Y. V., Medved L. V., Brew S. A., Ingham K. C. The NH2-terminal fibrin-binding site of fibronectin is formed by interacting fourth and fifth finger domains. Studies with recombinant finger fragments expressed in Escherichia coli. J. Biol. Chem. 1994; 269:9539-9546.
    69. Beckmann R., Geiger M., de Vries C., Pannekoek H., Binder B. R. Fibronectin decreases the stimulatory effect of fibrin and fibrinogen fragment FCB-2 on plasmin formation by tissue plasminogen activator. J. Biol. Chem. 1991; 266:2227-2232.
    70. O'Nuallain B., Wetzel R. Conformational Abs recognizing a generic amyloid fibril epitope. Proc. Natl. Acad. Sci. U.S.A. 2002; 99:1485-1490.
    71. Kayed R., Head E., Thompson J. L., et al. Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science 2003; 300:486-489.
    72. Cutler P., Brown F., Camilleri P., et al. The recognition of haemoglobin by antibodies raised for the immunoassay of beta-amyloid. FEBS Lett. 1997; 412:341-345.
    73. Stern R. A., Trojanowski J. Q., Lee V. M. Antibodies to the beta-amyloid peptide cross-react with conformational epitopes in human fibrinogen subunits from peripheral blood. FEBS Lett. 1990; 264:43-47.
    74. Downing A. K., Driscoll P. C., Harvey T. S., et al. Solution structure of the fibrin binding finger domain of tissue-type plasminogen activator determined by 1H nuclear magnetic resonance. J. Mol. Biol. 1992; 225:821-833.
    75. Smith B. O., Downing A. K., Driscoll P. C., Dudgeon T. J., Campbell I. D. The solution structure and backbone dynamics of the fibronectin type I and epidermal growth factor-like pair of modules of tissue-type plasminogen activator. Structure 1995; 3:823-833.
    76. Williams M. J., Phan I., Harvey T. S., Rostagno A., Gold L. I., Campbell I. D. Solution structure of a pair of fibronectin type 1 modules with fibrin binding activity. J. Mol. Biol. 1994; 235:1302-1311.

## Claims

1. A method for diminishing plaques comprising cross-β structures involved in a disease in a subject, the method comprising administering, to a subject in need thereof, a compound able to directly bind to a cross-β structure in a protein in the subject, for the purpose of allowing the subject to remove the cross-β structure, so as to diminish plaques in the subject, wherein said compound is a peptide consisting of a finger domain.