Methods for designing and synthesizing directed sequence polymer compositions via the directed expansion of epitope permeability

Abstract

The instant invention comprises a process for the solid phase synthesis of directed epitope peptide mixtures useful in the modulation of unwanted immune responses, such process defined by a set of rules regarding the identity and the frequency of occurrence of amino acids that substitute a base or native amino acid of a known epitope. The resulting composition is a mixture of related peptides for therapeutic use.

Description

RELATED APPLICATIONS

[0001] This application claims the benefit of U.S. Provisional Application 60/792,085, filed Apr. 13, 2006.

FIELD OF INVENTION

[0002] This application provides methods of making improved compositions of immunomodulatory peptide mixtures and provides methods of modulating unwanted immune responses.

BACKGROUND OF THE INVENTION

[0003] Immunomodulation.

[0004] Many disease conditions are, at least in part, a result of an unwanted or excessive immune response within an organism. The rejection of a transplanted organ is axiomatic example of an unwanted immune response. The rejection of the graft is emblematic of a condition in which an organism's inability to control an immune response results in a pathology. In organ transplantation, the unwanted immune response that results in graft rejection is triggered by: (1) "direct recognition," where the T cells of the graft recipient recognize foreign major histocompatibility complex ("MHC") molecules on the graft tissue, already presenting some peptides, via their T-cell receptor ("TCR") directly, or "indirect recognition," where the recipient T cells recognize the antigenic determinants derived from the graft after the determinants are processed and presented by recipient MHC; (2) the generation of antibodies directed against the graft, more specifically, the human leukocyte antigens ("HLA") molecules present on the cells of the graft tissue, caused by the exposure of the recipient to the graft; and (3) binding of preformed anti-graft antibodies in the circulation of the recipient to the graft. Studies have shown that these immune responses are directed to three types of donor derived antigens: MHC (through direct or indirect recognition), minor histocompatibility antigens ("mH"), and organ derived antigens.

[0005] Successful transplantation depends on preventing the unwanted immune responses, inducing sustained chimerism. Sustained chimerism is a phenomenon in which the recipient develops tolerance for a foreign graft, enabling the grafted tissue to survive in the recipient without being subjected to immune responses. Under experimental conditions, sustained chimerism can be induced by peptides that are closely related to those that stimulate graft-rejecting immune responses, albeit for short periods of time. (B. Murphy et al., J. Am. Soc. Nephrol., 2003, 14:1053-1065; C. LeGuem, Trends Immunol., 2003, 24:633-638). The difficulty lies with the likelihood of the broadening of the offending epitopes via the process of epitope spreading (N. Suciu-Foca et al., Immunol. Rev., 1998, 164:241).

[0006] Transplant physicians have long recognized the need both to inhibit the immune response generated by the presence of what the recipient's immune system views as foreign, without also compromising the patient's ability to fight opportunistic infection. Currently, transplantation patients are often treated with immunosuppressive therapies that depress the overall immune response and reactivity in a patient. Immunosuppressive therapies attempt to attenuate the reaction of the body to an already-triggered immune response, and are accompanied by numerous undesirable side effects. Because of the significant undesirable side effects, a single immunosuppressant cannot be used continuously to treat a transplant recipient, and a course of treatment comprises using one immunosuppressant having one set of side effect, changing to second immunosuppressant with a different set of side effect, and to third, and so on, to limit the exposure of the recipient to each immunosuppressant and its side effects. For example, steroids such as prednisone or methylprednisone are powerful immunosuppressants but can induce cataracts, hyperglycemia, hirstutism, bruising, acne, bone growth suppression, and ulcerative oesophagitis. Long term use of steroids has also been associated with bone loss. Cyclosporin A (CsA), a widely used immunosuppressant, is nephrotoxic, and often replaced with tacrolimus (TAC) after a period of treatment. For the treatment of non-acute rejection, azathioprine is used, the side effect of which include leucopenia, anemia, fever, chills, nausea and vomiting. Regardless of what immunosuppressant is used, one of the most substantial side effects related to longer term treatment with immunosuppressives in addition to the general compromise of the immune system leaving the patient vulnerable to any type of infections, is the generation of transplant related malignancies such as Kaposi's sarcoma. There is a strong desire on the part of physician and patient to decrease or cease the use of these current front line therapies. (Pharmacotherapy: A pathophysiologic Approach, Fifth Edition. 2002, McGraw Hill.) It would be difficult to state that they have met the clinical goal of sustained chimerism without ongoing immunosuppressive therapy.

[0007] Immunomodulation, in contrast to immunosuppression, targets the cause of unwanted immune responses. Immunomodulation can be attempted in an antigen/epitope non-specific fashion by targeting the body's mechanism for immunity, or in an antigen/epitope specific manner. As an example of antigen/epitope non-specific treatment, therapies directly targeted at controlling T lymphocytes or their functions have been developed using biotechnological tools. The therapeutic agents useful for such treatment include Muromonab-CD3 (OKT3), antilymphocyte globulin (ALG), antithymocyte globulin (ATG), or interleukin-2 receptor monoclonal antibody ("mAb") daclizumab or basiliximab. Other agents include soluble CTLA-4, an anti-CD154 mAb; anti-CD11a; a humanized mAb which inhibits VLA-4; anti-CD2, 3, or 4 antibodies; and anti-CD152 antibodies (J. B. Matthews et al., Amer. J Transplantation, 2003, 3: 794-80). While all of these therapeutic agents may induce a state of non-responsiveness of the recipient's immune system to the transplanted tissue with a reduction in side effects, as compared to e.g. prednisone, the therapies still do not meet the clinical goal of sustained chimerism without ongoing immunosuppressive therapy, except for limited reports, such as immunosuppressive withdrawal after combination therapy of total lymphoid irradiation followed by ATG administration (S. Strober et al., Transplantation, 2004 Mar. 27; 77(6): 932-936). Further, these therapies also suffer from the unattractive side effects of compromised overall immune function.

[0008] In contrast to the antigen non-specific immunomodulatory approach, the immune system can also be retuned, or modulated in an antigen/epitope specific manner. Such a type of immunomodulation is the process of increasing or decreasing the immune system's ability to mount a response against a particular antigenic determinant through either the TCR's recognition of complexes formed by MHC and antigens, or through the B cell receptor's ("BCR") recognition of the epitope itself. Because of the specificity of the process toward a particular antigenic determinant and not toward the immune system as a whole, antigen specific immunomodulation has advantages such as fewer undesirable side effects compared to current treatment modalities such as immunosuppressive therapies, which affects the overall immune system.

[0009] Antigenic determinant-specific immunomodulatory treatments can help establish such sustained chimerism by inducing donor-specific tolerance in host T lymphocytes. Immunomodulation of the reaction toward any and all of these antigens help attenuate or alleviate graft rejection and establish sustained chimerism. Studies indicate that one mechanism of action of immunomodulation by certain immunomodulatory peptides may be through their binding to T cells that would otherwise bind to the donor-derived antigens and resulting in differential activation of T cell functions. This mechanism has been suggested to be centrally induced tolerance involving the thymus (G. Benichou et al. Immunol. Today, 1997, 18(2):67-72). The demonstration of achieving sustained chimerism without immunosuppressive treatment via induction of donor-specific tolerance in host T lymphocytes through immunomodulation was performed by a group of investigators who, using mice, induced tolerance to the subsequent graft by intrathymic injection of a series of determinants from 3M KCl-extracted donor MHC-- derived peptides. Two doses of anti-T cell antibody were given first to eliminate circulating T cells. Then eight peptide sequences extracted from the donor MHC were delivered in combination. The treated mice tolerated subsequent transplants. As a control, the investigators performed thymectomy, which caused graft rejection. The study is an example of importance of centrally-induced tolerance (T. Hamashima et al., Transplantation, 1994 Jul. 15; 58(1):105-7). Thus, designing appropriate peptides similar to T cell-stimulating antigens that bind to the T cells is beneficial to achieving sustained chimerism.

[0010] However, the difficulty lies with the likelihood of the broadening of the offending epitopes via the process of epitope spreading. (N. Suciu-Foca et al., Immunol. Rev. 1998, 164:241). Thus, in transplantation, the axiomatic example where certain immune response is unwanted, it is clear that, in the absence of the ability to modulate the relevant antigenic determinants over time, the only alternatives are non-specific immunomodulatory, or immunosuppressive therapies.

[0011] Other examples of unwanted immune responses are autoimmune diseases. One important contextual difference between autoimmune diseases and transplantation rejection is that the offending antigenic determinant(s) is/are generally more restricted and definable. While the trigger of an autoimmune disease is undefined and may be dictated by pre-existing and/or environmental factors, the direct causes of the pathological condition have been identified in many autoimmune diseases. An autoimmune disease results from an inappropriate immune response directed against a self antigen (an autoantigen), which is a deviation from the normal state of self-tolerance. Self-tolerance arises when the generation of T cells and B cells capable of reacting against autoantigens has been prevented or altered centrally by events that occur either in their early development or after maturation in the periphery. The cell surface proteins that play a central role in regulation of immune responses through their ability to bind and present processed peptides to T cells via the T cell receptor (TCR) are class I and class II MHC (J. B. Rothbard et al., Annu. Rev. Immunol., 1991, 9:527).

[0012] Thus, an attractive point of intervention for the amelioration of an autoimmune response is via the set of lymphocyte surface protein MHC molecules for example, HLA-DR, -DQ and -DP, themselves or in combination with the peptides they present. Different HLA alleles generate a diversity of responses via antigenic-determinant specificities by variable affinities for protein fragments found in the extra- and intra-cellular milieu because of differences in the amino acids which are directly involved in the binding of the peptides. There are large numbers of alternative or allelic forms within a mammalian population, but only a few of these allelic forms are associated with disease-related antigenic determinants. It is well understood to one with ordinary skill in the art the genomes of subjects affected with certain autoimmune diseases, for example MS and RA, are more likely to carry one or more such characteristic MHC class II alleles, to which that disease is linked. For example, HLA-DR2 (DRB1*1501) is associated with multiple sclerosis and HLA-DR1 (DRBI*0101) or HLA-DR4 (DRB1*0401) are associated with rheumatoid arthritis.

[0013] The disease-related antigenic determinants derive from proteins which have been described as being simply associated with an autoimmune response, or as being part of the pathogenesis of the disease process itself. There are highly conserved sequences within HLA that may play a role in either the generation or regulation of immunologic tolerance when processed into peptides and presented by intact HLA (reviewed in B. Murphy and A. M. Krensky, J. Am. Soc. Nephrol., 1999, 10:1346-55). A. Snijders et al. discuss one particular sequence (KDILEDERAAVDTYC) presented by HLA-DRB1 as being protective against rheumatoid arthritis, with the most relevant portion of the peptide being DERAA (J. Immunol., 2001, 166:4987-93), while others have promoted what is known as the `shared epitope hypothesis` (P. K. Gregersen et al., Arthritis Rheumatism 1987 November; 30(11):1205-13) where those individuals that carry HLA-DRB1 alleles having the sequence QKRAA are predisposed to rheumatoid arthritis. Other investigators have demonstrated that heat shock proteins (hsp) and the peptides derived from them can have immunomodulatory properties (S. M. Anderton et al., J. Exp. Med., 1995, 181:943-952; J. A. van Roon et al., J. Clin. Invest., 1997, 100:459-063). One peptide in particular, dubbed p277, derives from hsp60, VLGGGVALLRVIPALDSLTPANED, has demonstrated apparent activity in the context of Type I diabetes (I. Raz et al., Lancet, 2001, 358:1749-52). Further sources of epitope sequence may be derived from a pathogen-derived mimic of a sequence within mammalian MHC proteins such as the DNAjP1 peptide, or related peptides (QKRAAYDQYGHAAFE; Proc. Nat. Acad. Sci. USA, 101:4228-33; U.S. Pat. No. 6,989,146). Other proteins and the peptides that derive from them having disease association are: glutamate decarboxylase (GAD) with diabetes (M. A. Atkinson et al. J. Clin. Invest., 1994, 94:2125-29; D. B. Wilson J. Autoimmun., 2003, 20:199-201); myelin associated proteins such as myelin basic protein (MBP), myelin-associated glycoprotein (MAG), proteolipid protein (PLP), and myelin oligodendrite glycoprotein (MOG) with multiple sclerosis (reviewed in P. Fontoura et al., Int. Rev. Immunol., 2005, 24:415-46); Ro60, SmD and other ribonucleoprotein antigens with lupus (R. Pal, et al., J. Immunol., 2005, 175:7669-77; Seshmukh et al., J. Immunol., 2000, 164:6655-61; R. R. Singh, Mol. Immunol., 2004, 40:1137-45); or the acetylcholine receptor (AChR) with myasthenia gravis (MG) (S. L. Kirshner, et al. Scand. J. Immunol., 1996, 44:512-21); or desmoglein 3 (DsG3) with pemphigus vulgaris (PV) (Wucherpfennig et al., Proc. Nat. Acad. Sci. USA, 1995, 92:11935-9; Lin et al., J. Clin. Invest., 1997, 99:31-40; Veldman et al., J. Immunol., 2004 172:3883-92; Angelini et al., J. Translational Med., 2006, 4:43; U.S. Pat. No. 5,874,531; U.S. Pat. No. 7,084,247).

[0014] Despite the attraction of using HLA alleles and their associated antigenic determinants that have been linked to many autoimmune diseases as a point of intervention, therapeutic agents based on this knowledge have not been developed fully. Instead, a number of immunomodulatory therapeutic agents that are not specific to any particular antigenic determinant have been developed and being used to treat autoimmune diseases, including general anti-inflammatory drugs such as cyclooxygenase-2 (COX-2) inhibitors that can prevent formation of low molecular weight inflammatory compounds; inhibitors of a protein mediator of inflammation such as tumor necrosis factor (TNF), such as an anti-TNF specific monoclonal antibody or antibody fragment, or a soluble form of the TNF receptor that sequester TNF; and agents that target a protein on the surface of a T cell and generally prevent interaction with an antigen presenting cell (APC), for example by inhibiting the CD4 receptor or the cell adhesion receptor ICAM-1. However, these types of antigenic-determinant non-specific immunomodulatory therapeutic agents have residual immunosuppressive-like side-effects which diminish their attractiveness as chronic first line therapies. Additionally, compositions having natural folded proteins (such as antibodies) as therapeutic agents can encounter problems in production, formulation, storage, and delivery. Several of these problems necessitate delivery to the patient in a hospital setting.

[0015] Strategy for Creating Synthetic Therapeutic Peptides

[0016] Drug discovery can be generalized into two major elements, lead generation and lead optimization. The development and exploitation of combinatorial chemistry (CC) has seen the divergence of the uses of rational design versus random generation on a very fundamental level. On one side we find the use of CC to assist a researcher in the rational design of molecules. An example of which can be seen in the discovery of structure/activity relationships (SAR) between two or more active molecules of therapeutic interest. On the other side we find researchers using CC to define for them the design of new molecules discovered based on a specific activity. An example of which would be the generation of random libraries used in lead generation, whereby the lead is singled out and further optimized.

[0017] The level of expertise in the state of the art of combinatorial chemistry as applied to the synthesis of peptide libraries has risen, producing highly reliable and pure mixtures of peptides of great diversity. The use of these diverse peptide libraries has focused on lead generation and optimization. This strategy entails screening the vast numbers of individual peptide sequences in the library against a target of interest with the intention of defining a single, or limited set of peptides which demonstrate a particular activity. That single peptide, or the limited set of peptides, then become candidates which are modified to increase activity against the target. This process is schematically represented in FIG. 1A.

[0018] The challenge for practitioners in this art has been to deconvolute, or accurately define the single or limited set of peptides that were responsible for the observed activity. The difficulties associated with deconvolution have spawned great efforts on the part of practitioners to create synthesis methods which inherently increase the resolution of individual peptides, as well as the identity of individual amino acids within peptides.

[0019] In order to efficiently identify the target peptide from myriad of candidates presented by a library created by combinatorial chemistry, a variety of synthesis methods and approaches have been developed. These synthesis methods aim to provide a large number of candidates, and yet when a positive result is obtained, to quickly determine the identity of the peptide without having to laboriously isolate the positive species from the rest. The effort put forth by practitioners in this art in this regard is an indication of the industry-wide vision of the method's ultimate utility, which is to allow the random complexity of these libraries perform the screening process for the desired activity.

[0020] Examples of the resulting evolution of subtypes of combinatorial methods include: multiple synthesis, iterative synthesis, positional scanning, and one-compound-one-bead post assay identification design.

[0021] "Multiple synthesis" provides for any method whereby distinct compounds are synthesized simultaneously to create a library of isolated compounds. The identity of these compounds would be known from the rules of the synthesis. H. M. Greysen et al., Proc. Nat. Acad. Sci. USA, 1984, 81:3998, used the multiple synthesis method to identify peptides that bound to an antibody raised against VPI protein of foot-and-mouth disease virus. The investigators identified GDLQVL as the epitope recognized by the antibody. In this case the authors synthesized 108 overlapping peptides representing the VPI sequence on pins in a 96-well microplate array.

[0022] "Iterative synthesis/screening" involves methods of peptide synthesis which allow for a determination of the identity of individual residues within peptide sequences. An example of iterative synthesis can be seen in R. A. Houghten et al., Nature, 1991, 354:84-86, also to determine antibody binding epitopes. These investigators identified the sequence YPYDVPDYASLRS using an ELISA type assay format. The first library consisted of 324 pools of peptides with the first two residues fixed, which peptides can be shown as O.sub.1O.sub.2XXXX, wherein O1 and O2 are the fixed residues and X is randomly selected. The process identified DV as the fix residues. The next step was to do the same for position three, by synthesizing peptides that can be shown as DV O.sub.1XXX, wherein O1 again is a fixed residue. When the process identified which residue at the third position would elicit the desired binding, that residue was adopted as the unchanging third residue, and the fourth position was explored in a similar manner. The process continued until the native sequence DVPDYA was identified.

[0023] "Positional scanning" is a synthesis method producing complex mixtures of peptides that allows for the determination of the activity of each individual peptide. Based on the screening results, the derived peptide can then be separately synthesized for optimization. As seen in C. Pinilla et al., Biochem J., 1994, 301:847-853, positional scanning libraries were used to identify decapeptides which bound the same YPYDVPDYASLRS-binding antibody. In this case ten different libraries each containing 20 pools with a defined amino acid at each of the ten positions in the peptide. Fifteen peptides were identified.

[0024] Each of the above methods were also employed to identify enzyme substrates (J. H. Till et al., J. Biol. Chem., 1994, 269:7423-7428, J. Wu et al, Biochemistry, 1994, 33:14825-14833, W. Tegge et al., Biochemistry, 1995, 34:10569-10577), or enzyme inhibitors (M. Bastos et al., Proc. Nat. Acad. Sci. USA, 1995, 92:6738-6742, Meldal et al., Proc. Nat. Acad. Sci. USA, 1994, 91:3314-3318), R. A. Owens et al., Biomed Biophys. Re.s Commun., 1994, 181:402-408, J. Eichler. et al., Pept. Res., 1994, 7:300-7). These powerful tools allow investigators to rationally design combinatorial peptide libraries to identify a single species which has a desired activity.

[0025] As powerful and clear cut the identification of a specific peptide from a combinatorial library may be, it may only serve as a starting point and identification of a lead peptide that is not itself therapeutically useful. The identified epitope may be ignored by the immune system if it resembles a self protein or possibly exacerbate the very condition that the therapy aims to relieve. Such peptide is not directly therapeutically useful. However, one may create, based on such peptide, epitope reactive analogs that would act as modifiers of the unwanted immune response.

[0026] One such approach is creation of altered peptide ligands (APL). This approach is schematically represented in FIG. 1B. An APL is defined as an analog peptide which contains a small number of amino acid changes from the native immunogenic peptide ligand. Some of such APLs act as an antagonist to the T cell receptor, blocking the stimulating binding by the antigens causing the unwanted immune effect. Evabold et al., Proc. Nat. Acad. Sci. USA, 1994 Mar. 15; 91(6):2300-4. However, while recognition of the native response may induce an angonist like reaction, an APL might induce a partial agonist response, or induce a state of anergy in the reactive T cell population. In discussing APL in the context of allograft rejection therapy, Fairchild et al., Curr. Topics Peptide Protein Res., 2004, 6:237-44, note that an APL acting as an antagonist for one TCR, may become an agonist for another, complicating the rational design of an APL. Compounding the obstacle of the development of APL is the difficulty in translating a response developed in an animal system into human.

[0027] Despite these challenges, MPB83-99 (ENPVVHEFKNIVTPRTP) was made into an APL and placed into limited human trials by replacing the bold and underlined amino acid residues "E", "N", "E" and "K," resulting in a single peptide sequence consisting of AKPVVHLFANIVTPRTP, Kim et al. Clinical Immunology, 2002, 104:105-114. The authors describe the long term immune reactivity against the peptide, but the treatment has been deemed clinically ineffective by evaluation using MRI. Thus an APL, once identified, can be used as a therapeutic agent; however, its effectiveness may be limited in terms of clinical efficacy.

[0028] It has been observed for some time that in the course of development of multiple sclerosis, the reactive epitope does not stay constant. That is, the self recognition associated with the development of MS is a developmental process characterized by autoreactive diversity, plasticity, and instability, wherein the target epitope changes over time, typically from one epitope on a myelin proteolipid protein to one overlapping the amino acid residues but shifting by one or few amino acids to either side of the original epitope. The consequence of this phenomenon is that if an immunotherapeutic drug was targeted at the original epitope, over time, it becomes ineffective, not because of resistance to the mechanism of the drug, but simply because the target is no longer valid. J. Clin. Invest., 1997, 99:1682-1690.

[0029] A method conceived to make an investigational concept like a mixture of peptides into a drug is peptide dendrimer structures. Peptide dendrimers solve certain manufacturing issue of soluble peptide mixtures, in part by the promise of delivering to a patient a consistent ratio and quantity of each of the peptides in the mixture. This approach is schematically represented in FIG. 1C.

[0030] Dendrimers are diverse. They can range in size from 2 kDa to greater than 100 kDa. The design of dendrimers intends to mimic two traits of naturally occurring biological structures: a globular structure and polyvalency. As described in two comprehensive reviews (P. Niederhafier et al., J Peptide Sci. 11:757-788; K. Sadler and J. P. Tam, Rev. Mol. Biotechnol., 2002, 90:195-229), they are complex compounds that contain highly branched components organized in a radial or wedge-like fashion, and are intended to have an extensive three-dimensional structure. They have three distinct structural features: a central core surface functionalities and branching units that link the two. Peptide dendrimers are designed as vehicles for delivery of: RNA and DNA as gene expression therapeutics, biosensor systems as diagnostics, inhibitors of autoimmune diseases or cancer metastasis. The strategy behind each of these applications is to use the globular, polyvalent structure to amplify the ligand:substrate interaction (D. Zanini and R. Roy, J. Org. Chem., 1998, 63:3468-3491; J. Haensler and F. C. Szoka, Bioconjug Chem., 1993, 4:372-379).

[0031] Dendrimers have been made using amino, hydroxyl, carboxy, poly(propylenimine), silicone and polyamino amine cores (G. M. Dykes et al., J. Chem. Technol. Biotechnol., 2001, 76:903-918, P. Sadler and J. Jezek, Rev. Mol. Biotechnol., 2002, 80:195-229, and J. P. Tam, Methods Org. Chemistry, 2004, Vol E22d 129-168. Peptide dendrimers can be divided into three types: grafted peptide dendrimers, branching polyamino acids and multiple antigen peptides (MAPs).

[0032] The branching strategies in MAPs vary widely. The majority of first generation branches have used lysine. Second generation solid phase synthesis of MAPs has seen an interest in proline. The interest is said to come from both the properties of its secondary amine which decreases the reactivity during production, as well as its role in many cellular functions.

[0033] Simple MAPs have been synthesized using solid phase chemistry, with this type of synthesis strategy called divergent. Synthesis methods have been described which involves a two-step iterative reaction sequence producing concentric shells of dendritic beta-alanine units covalently linked in the second step to various functional groups (Kojima et al., Bioconjugate Chem., 2000, 11:910-17). These types of MAPs, which are synthesized using the divergent strategy, by necessity have simple branching schemes with few distinct members, as the purification and characterization are untenable with more complex MAPs. The end-product needs to be purified away from deletion compounds having similar characteristics to the end-product. Purifications have been described using gel filtration chromatography, reverse phase high-performance liquid chromatography (HPLC), or electromigration methods.

[0034] For complex MAPs, for example, those having a multiplicity of branching moieties, convergent synthesis is the preferred synthesis strategy. Convergent synthesis can be performed using either fragment condensation or ligation of the pre-purified fragments. There are many types of ligations: natural (true peptide bond created), thiol, hydrazone, or other. MAPs prepared using convergent synthesis strategies are easier to purify, as the end-product will look distinctly different from the reaction byproducts. HPLC was first used to purify convergent MAPs (J. C. Spetzler et al., Int. J. Pept. Protein Res., 1995, 45:78-85).

[0035] However, a high cost of manufacturing and the subsequent analytical development precludes this technology from being further currently developed commercially.

[0036] All of the above strategies, while recognizing the advantage of variations in the therapeutic peptide compositions, derive from the concept that there is one or more defined peptide sequence evoking a defined immunological response. These strategies have attempted to multiply and diversify modulatory peptides via the introduction of defined, single changes performed one at a time.

[0037] An entirely different approach which has evolved alongside the defined sequence peptide immunotherapy approach is the use of limited amino acid diversity, random epitope polymers. Random sequence polymers (RSP) can be described as a random order mixture of amino acid copolymers comprising two or more amino acid residues in various ratios, forming copolymers by random sequence bonding, preferably through peptide bonds, of these amino acid residues, which mixture is useful for invoking or attenuating certain immunological reactions when administered to a mammal. Because of the extensive diversity of the sequence mixture, a large number of therapeutically effective peptide sequences are likely included in the mixture. In addition, because of the additional peptides which may at any given time not be therapeutically effective, but may emerge as effective as the epitope shifting and spreading occurs, the therapeutic composition may remain effective over a time of dosing regimen. This approach is schematically represented in FIG. 1D.

[0038] Starting in 1959 (P. H. Maurer et al., J. Immunol., 1959, 83:193-7) to 1988, (J. L. Grun, and P. H. Maurer, Immunogenetics, 1988, 28(1): 61-3) Maurer and colleagues investigated the immune responses to poly glutamic acid and other random sequence polymers such as those consisting of tyrosine, glutamate and alanine (YEA), phenylalanine, glutamate and alanine (FEA), and phenylalanine, glutamate and lysine (FEK). Teitelbaum et al., Eur. J. Immunol., 1971, 1:242-8 was the initial report of work on random copolymer consisting of tyrosine, glutamate, alanine and lysine, that eventually culminated in an FDA approved therapy for multiple sclerosis using COP-1, described below. In 1978, Germain and Benacerraf, J. Exp. Medicine 148:1324-37, investigated suppressor T cell responses to YEA in what was to become Benacerrafs 1980 Nobel winning work on the role of MHC in the immune system and its relevance to alloreactivity (http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-le- cture.html).

[0039] Copolymer-1 (also known as Copaxone, glatiramer acetate, COP-1, or YEAK random copolymer), is used for the treatment of multiple sclerosis. Random copolymers are described in International PCT Publication Nos. WO 00/05250, WO 00/05249; WO 02/59143, WO 0027417, WO 96/32119, WO/2005/085323, in U.S. Patent Publication Nos. 2004/003888, 2002/005546, 2003/0004099, 2003/0064915 and 2002/0037848, in U.S. Pat. Nos. 6,514,938, 5,800,808 and 5,858,964.

SUMMARY OF THE INVENTION

[0040] The instant invention comprises a process for the solid phase synthesis of directed epitope peptide mixtures useful in the modulation of unwanted immune responses, such process defined by a set of rules regarding the identity and the frequency of occurrence of amino acids that substitute a base or native amino acid of a known epitope. A method of the instant invention uses a sequence of a known peptide epitope as a starting point. The amino acids that make up the epitope are sequentially modified via the introduction of different, related amino acids defined by a set of rules. The result is a mixture of related peptides useful in and of itself as a therapeutic, which is described herein as a composition comprising "directed-sequence polymers" or "DSP". Such composition is referred to as a "DSP composition." The method of synthesizing a DSP composition utilizes and maintains the natural order of amino acid residues of a defined peptide sequence of a specified length. Each amino acid position is subjected to change based on a defined set of rules. In a preferred embodiment the amino acids is substituted according to the methods seen in Table X of Kosiol et al., J Theoretical Biol., 2004, 228:97-106). Alternatively, amino acids can be changed in accordance with the exemplary substitutions described in PCT/US2004/032598, page 10-11. For the solid phase synthesis procedure of the instant invention, the mixture of amino acids for a given position in the peptide is defined by a ratio one to another. Prior to starting the synthesis, such ratio is determined for each position along the peptide. The resulting directed order peptide mixture comprises a multiplicity of related peptide sequences.

[0041] The length of a DSP can be one of the original defined sequence peptide or 30 lengths of the original defined sequence peptide. The length of the combined sequence can be between 25 and 300 amino acids.

[0042] The percentage of alanine as compared to all of the other amino acids in the DSP combined will always be greater than 10%, and will not exceed 90%. Preferably, the alanine percentage is between 20% and 80%. More preferably the percentage of alanine is between 40% and 75%. The complexity of the mixture is greater than 5.times.10.sup.2 different peptides. Preferably the complexity of the mixture is greater than 1.times.10.sup.10 different peptides. More preferably the complexity of the mixture is greater than 1.times.10.sup.15 different peptides.

[0043] In some embodiments, the base peptide sequence from which the DSP sequences are derived is selected from a group consisting of SEQ ID NO: 1 through _ depicted in Table I.

[0044] In other embodiments, such base peptide sequence is an epitope relevant to the pathology of an autoimmune disease selected from the group consisting of multiple sclerosis, systemic lupus erythematosus, type I diabetes mellitus, myasthenia gravis, rheumatoid arthritis, and pemphigus vulgaris. More particularly, the base peptide sequence is a partial sequence of a protein selected from the group consisting of: (a) osteopontin, an HLA protein, myelin oligodendrite glycoprotein, myelin basic protein (MBP), proteolipid protein, and myelin associated glycoproteins, S100Beta, heat shock protein alpha, beta crystallin, myelin-associated oligodendrocytic basic protein (MOBP), 2',3' cyclic nucleotide 3'-phosphodiesterase; (b) hsp60, hsp70, Ro60, La, SmD, and 70-kDa U1RNP; (c) glutamic acid decarboxylase (GAD65), insulinoma-antigen 2 (IA-2), insulin; (d) acetylcholine receptor (AChR) .alpha.-subunit and muscle-specific receptor tyrosine kinase (MuSK); (e) type II collagen; and (f) desmoglein 3 (Dsg3)

[0045] One aspect of the present invention is a pharmaceutical composition comprising a DSP composition, optionally as a pharmaceutically acceptable salt. In a preferred embodiment, such pharmaceutical composition comprising a DSP composition, when administered to a subject, causes a favorable modification of an unwanted immune response in the subject desirous of such an effect.

[0046] Another aspect of the present invention is a method of treating unwanted immune response by administering a DSP composition to a subject in need thereof. In preferred embodiments, the subject is in need of such administration because of acute inflammation, rheumatoid arthritis, transplant rejection, asthma, inflammatory bowel disease, uveitis, restenosis, multiple sclerosis, psoriasis, wound healing, lupus erythematosus, pemphigus vulgaris, and any other autoimmune or inflammatory disorder that can be recognized by one of ordinary skill in the art. In other embodiments, the subject is in need of such administration because of Host versus Graft Disease (HVGD) or Graft versus Host Disease (GVHD), in the case of organ transplantation.

BRIEF DESCRIPTION OF THE DRAWINGS

[0047] FIG. 1A-D is a schematic depicting methodologies for designing synthetic peptide-based therapeutics. Panel A: how a peptide library is used for epitope discovery; Panel B: conceptual steps for generating Altered Peptide Ligand-based therapeutic; Panel C: a schematic of a dendrimer for multi-valent peptide presentation; Panel D: random sequence polymer generation.

[0048] FIG. 2 is a schematic for conceptual steps for generating Directed Sequence Polymers.

[0049] FIG. 3 shows the steps for preparing Directed Sequence Polymers.

[0050] FIG. 4 shows the preferred defined substitutive rules for directed expansion of epitope permeability.

[0051] FIG. 5 shows a generic rule structure and ranges of substitutions of DSP synthesis.

[0052] FIG. 6 shows an example of the application of the DSP Synthesis Rules using a mock-source peptide.

[0053] FIG. 7A-B shows an example of the application of the DSP Synthesis Rules using myelin basic protein (a.a. residues 83-99) as a source peptide.

[0054] FIG. 8A-C shows examples of the application of the DSP Synthesis Rules using an HLA-derived peptide and an HLA mimic-derived peptide as source peptides.

[0055] FIG. 9A-B shows an example of the application of the DSP Synthesis Rules using a GAD65-derived epitope peptide as a source peptide and applying an emprirically determined substitution rule.

DETAILED DESCRIPTION OF THE INVENTION

[0056] It has previously been shown that mixtures of related peptides may be therapeutically more effective than a single peptide. Lustgarten et al., J. Immunol. 2006, 176: 1796-1805; Quandt et al., Molec. Immunol. 2003, 40: 1075-1087. The effectiveness of a peptide mixture as opposed to a single peptide is the likelihood of interaction with the broadening of the offending epitopes via the process of epitope spreading. (Immunol. Rev. 1998, 164:241) Therefore, to increase and maintain the effectiveness, these previous treatment modalities have been modified. For example, a therapeutic composition based on an APL may include multiple peptides created by the APL method in combination with the original peptide, or other APLs. Fairchild et al., Curr. Topics Peptide & Protein Res. 6, 2004. Each APL would have a defined sequence, but the therapeutic composition may be a mixture of APLs with more than one sequence. A reverse example involving conceptually similar altered peptide ligands involves an inventor's attempt to reduce the amount of variation created by pathogens to avoid immune recognition (viral alteration of immunogenic eptitopes over time, eg the creation of altered peptide ligands), by using the very changes created by the pathogen in an epitope sequence to create a limited diversity pool of peptides potentially useful in vaccinations (U.S. Pat. No. 7,118,874).

[0057] There have also been approaches to improving RSP, most notably upon COP-1. One can be seen in the work originated by Strominger et al. (WO/2003/029276) and developed further by Rasmussen et al. (US 2006/0194725) using RSP consisting of the amino acids Y,F,A, and K. Other than the change in amino acid content, the differences between the composition reside in the length (YFAK is shorter than COP-1), and alanine content (YFAK is suggested to have between 60-80% alanine, compared to _% of COP-1), which show as differences in the animal model data (YFAK has better efficacy in EAE, the animal model of multiple sclerosis). Regarding the alanine content, Maurer (Pinchuck and Maurer, J Exp Med 122(4), 673-9, 1965) described how an EAK polymer with higher alanine content (10-60 mole percent) produced "better antigens", and Rasumussen et al. demonstrated that a YFAK input ratio of 1:1:1:1 was not effective in eliciting a recall response as compared to a YFAK preparation with an input ratio of 1:1:10:6.

[0058] Another attempt at improving upon COP-1 is described in WO/2005/032482 (the '482 publication). One interpretation of the '482 publication is that it is an attempt to make a more specific COP-1 by limiting the amount of diversity via the generation of `therapeutic ordered peptides` for the treatment of multiple sclerosis. The '482 publication builds degenerate peptide sequences based not on actual peptide sequences, but on motifs. A preferred motif is [EYYK], which is quite similar to the amino acid composition of COP-1 (YEAK). The rationale for this motif teaches that the relative value placed on the inclusion of alanine as seen in the Maurer publication and Rasmussen et al. application discussed above is of a lesser importance The motifs are used as is, or can be altered by amino acid substitutions (defined on page 10-11 of the '482 publication). Much of the invention hinges on the presence of a D-amino acid at the amino terminal of the motif.

[0059] Yet another attempt at improving upon COP-1 is disclosed in WO/2005/074579 (the '579 publication). The application describes complex peptide mixtures containing A,E,K and Y of a length from 8-100 residues long. The disclosure contains preferred embodiments where the mixture also comprises AEKY, FLMY, IMQV, KRILV, FILMV, FWEF, EK, AEK, AKY, ANY, AINV, ASV, YEFW,Y, EFIVWY, EFKQ, AEKQ, AKQY, ANQY, AGNSY, AGINSV, AIQSV, IKRSVY, KHRV, HKR, PI, A, E, K, AE, AK, AY, EY, KY, AEY, EKY. The disclosure also contains diversity constraining mechanisms of defining amino acids at certain positions rather than being chosen by the random nature of the synthesis rules. The disclosure provides for a ratio of amino acids one to another for the AEKY mixture as being similar to COP-1 at 1:1:6:3 YEAK.

[0060] The drawback of the these approaches is the undefined nature of what is effective in each motif, and quite possibly a large proportion of the peptides in the mixture may be inactive, lowering the concentration of the active components, or worse, adversely stimulating the immune system. Additionally, these compounds are difficult to manufacture and to obtain consistency from lot to lot.

[0061] Still another attempt at improving upon COP-1 can be seen in Strominger's efforts to design distinct, single 15mer peptide sequences who's amino acid composition resembles that of COP-1 and COP-1 related random sequence polymers. These single sequence fixed peptides were designed to increase an ability to compete for HLA-DR2 binding with the native myelin basic protein (MBP) peptide 85-99 (Stem et al., roc. Nat. Acad. Sci. USA, 102:1620-25). The drawback of this technology lies in the very nature of the attempt to determine discrete substitutes for the randomness that COP-1 encompasses.

[0062] The instant invention draws out the most useful properties of the previous treatment modalities yet removes the limitations of each. The instant invention utilizes: (1) the specific immunologic relevance of a defined epitope peptide, (2) the modulatory properties of an APL, (3) the multivalency of MAPs, (4) and the alanine content from RSP to generate a directed expansion via alteration and degeneration of epitope permeability that forms a complex yet directed peptide library useful for delivery as a therapeutic. The approach is schematically represented in FIG. 2.

[0063] The instant invention relates to a "Directed Sequence Polymer" (DSP). A DSP is a peptide having a sequence derived from a base peptide sequence, which may be but not limited to a native epitope associated with an unwanted immune response. A DSP has one or more amino acid residue that differs from that of the base peptide sequence, the substitution of which is determined by a defined rule. A DSP composition comprising multiple DSPs is synthesized by applying a set of synthesis rules that define the amino acid variations and the ratio of occurrence of introduction of such amino acid residues at any given position of the sequence to the base peptide sequence. Thus, a DSP is not synthesized as a single peptide, but is always synthesized as part of a composition comprising multiple related DSPs, the overall mixture of which is reproducible and consistent with the rules of synthesis that were applied. The schematic for the steps for creating a DSP composition, starting from the choice of a base peptide, is shown in FIG. 3.

I. Base Peptide Sequences

[0064] To create a meaningful DSP composition, one first needs to define the base peptide sequence to derive the DSPs from. The base peptide sequences can be derived in many ways. A peptide sequence useful for this purpose is a peptide sequence related to immune response in a mammal. These peptide sequences are, for example, partial sequences of certain heat shock proteins as an epitope, HLA derived peptide ligand sequences, organ-derived peptide sequences, and empirically derived peptide sequences, such as through screening of library created by a combinatory chemistry. Heat Shock Protein-derived base peptide sequences.

[0065] A source of epitope sequence may be derived from heat shock proteins of any source or with the pathogen-derived mimic of a sequence within a mammalian heat shock protein (hsp). Mammalian heat shock proteins such as HSP-60 (Swiss-Prot primary accession number P10809), HSP-70 (Swiss-Prot primary accession number P08107), HSP-90 alpha (Swiss-Prot accession number P07900), HSP-90 beta (Swiss-Prot accession number P08238), or any protein having 75% homology to each are examples. Bacterial homologues of mammalian heat shock proteins include mycobacterial hsp65 (belonging to the hsp60 family)

[0066] Heat shock proteins as cellular chaperones that are known to be upregulated in response to stress signals have a high degree of potential pathophysiological disease mechanism involvement. Hsp, the peptides that derive from them, and their cross-species mimics have been implicated in central nervous system disease such as schizophrenia and multiple sclerosis (Schwarz et al., Am. J. Psychiatry, 1999, 156:1103-4; Battistine et al., Mol. Medicine, 1995, 1:554-62), atherosclerosis (Benagiano, et al., J. Immunol., 2005, 174:6509-17), rheumatoid arthritis (Anderton et al., J. Exp. Med., 1995, 181:943-52; van Roon et al., J. Clin. Invest., 1997, 100:459-63; Quintana et al., J. Immunol., 2003, 171:3533-41), systemic lupus erythematosus (Minota et al., J. Exp. Med., 1988, 168:1475-80), and diabetes (Raz et al., Lancet 358:1749-53).

HLA Derived Base Peptide Sequences

[0067] Immunologically relevant in a transplantation setting, HLA represent a large percentage of proteins to which recipient antibodies are directed. The gene products of HLA are seen to function as transplantation antigens. For example, studies analyzing the occurrence of acute graft versus host disease (GVHD) in relation to mismatched HLA alleles implicate the roles of HLA-DRB1 and HLA-DQB1 disparity between the donor and the recipient of a graft. Petersdorf et al., Proc. Nat. Acad. Sci. USA, 1996, 93: 15358-15363. Conversely, multiple examples of MHC-derived peptides have been reported as useful for immunotherapy. A study indicates that a large percentage of peptides bound to MHC on resting antigen presenting cells are MHC derived, leading to postulation that, other than functioning as stabilizers for the MHC heterodimers, these peptides may have roles in immunomodulation by competing with antigenic peptides, thereby increasing the threshold for antigenic stimulation. Murphy et al., J. Am. Soc. Nephrol., 2003, 14:1053-1065. Peptides derived from Class II MHC are indeed reported to act as T-cell regulatory factors. (LeGuem, Trends Immunol., 2003, 24:633-638). Further, synthetic peptides from a conserved region of class II MHC was able to mediate APC apoptosis and T cell hyporesponsiveness. Murphy, ibid. Elsewhere, a peptide derived from the predicted alpha helical domain of class II bound to I-Ak and inhibited antigen-dependent T-cell activation. Williams et al., Immunol. Res., 1992, 11:11-23. Peptides derived from Class I MHC are reported to exert effects on the immune system through various mechanisms, such as anergy, deletion, immune deviation, cell cycle prevention, disruption of antigen presentation, and inhibition of T cell activation. Murphy and Krensky, J. Am. Soc. Nephrol., 1999, 10:1346-1355.

[0068] Therefore, attenuating the immunological response to MHC is expected to reduce the severity and occurrence of GVHD. The above examples in the art showed the immunomodulatory effects using peptides having various contiguous amino acid sequences of HLA molecules. DSP based on the amino acid composition of HLA are expected to overcome such shortcomings and function as broadly relevant immunomodulators.

[0069] In an embodiment of the present invention, one or more epitopes comprising a mature HLA molecule are incorporated into the DSP. In another embodiment, one or more epitopes comprising the beta sheet of HLA are incorporated into the DSP. Synthetic peptides derived from the beta sheet of HLA-B7 have been shown to be immunodominant T-cell epitopes regulating alloresponses in GVHD. Freese and Zavazava (2002) Blood 99:3286-3292. These HLA-B7 derived allopeptides interfered with T cell mediated cytotoxicity targeted to HLA-B7 in vitro, and HLA-A2 derived allopeptides interfered with the cytotoxicity targeted to HLA-A2 in vitro, indicating allospecificity of these peptides.

[0070] Examples of amino acid compositions of HLA are provided herein. Known amino acid sequences of HLA proteins were obtained from GenBank and Swiss-Prot/trEMBL and were analyzed by using the ProtScale functions of ExPASy found at http://ca.expasy.org/cgi-bin/protscale.pl. Exemplary HLA sequences are GenBank Accession No. AAA36281, AAC02715, P01903 (alpha chain precursor), AAA17992, AAA59622 (heavy chain precursor), and AAA76608.

Organ Derived Base Peptide Sequences

[0071] A further category of derivation epitopes that may be useful for inducing tolerance are antigens derived from an organ to be transplanted itself. "Organ derived epitopes," as defined herein, are: peptide epitopes comprising organ-specific proteins. These proteins are potentially important as antigens in a context of organ transplant. For example, it has been shown that donor allopeptides are continuously shed from grafts, resulting in indirect recognition of such donor allopeptides by the recipient T cells. This results in chronic organ transplant rejection and prevents sustained chimerism. For example, in cardiac allografts, chronic rejection is manifested as a diffuse and accelerated form of atherosclerosis, termed cardiac allograft vasculopathy. Lee et al. Proc. Nat. Acad. Sci. USA, 2001, 98: 3276-3281. Perhaps invoking the similar mechanism as that used by the MHC derived peptides, peptides derived from the transplanted organ may induce sustained chimerism by preventing the stimulation of immune response by the transplantation. The suppression of immunologic reaction to such allopeptide may contribute to preventing chronic rejection and aid to achieve sustained chimerism.

[0072] Hence, in another embodiment of the present invention, one or more epitopes comprising the organ-derived proteins of the organ subject to transplantation.

[0073] Other relevant organ-derived DSP may include the epitopes of proteins considered to be organ-specific. A DSP suitable for alleviating the immune reaction to transplantation of an organ and promoting sustained chimerism is designed based on the epitopes of organ-specific proteins for the organ being transplanted.

[0074] Liver: Organ specific antigens for liver includes bile salt export pump (GenBank accession number O95342), which is considered to be predominantly expressed on liver cells.

[0075] Heart: An example of a protein found specifically in heart is Atrial natriuteric peptide-converting enzyme (pro-ANP-converting enzyme) (Corin) (Heart specific serine proteinase ATC2) (Swiss-Prot Accession No. Q9Y5Q5).

[0076] Pancreas: An example of an organ-specific protein for human pancreas is carboxypeptidase B1 (GenBank Accession No. 32880163).

[0077] Kidney: An example of an organ-specific protein for kidney is chloride channel ClC-6c (GenBank Accession No. 1770380).

[0078] Spleen: An example of spleen specific protein is Spleen tyrosine kinase (SYK) (Swiss-Prot Accession No. P43405).

[0079] Lung: An example of lung specific protein is Plunc (Palate lung and nasal epithelium clone protein) (Lung specific X protein)(GenBank Accession No. 9801236).

Empirically Derived Base Peptide Sequences

[0080] As described in the above sections, peptide sequences with some significance to a disease state or an adverse reaction may be identified through experimental investigation of a relevant epitope. These sequences may include non-naturally occurring peptide sequences that proved to be useful in treating a disease or a condition, an example found in the international patent application publication WO 2006/031727, U.S. Pat. No. 6,930,168 and the related scientific publication Stem et al., Proc. Nat. Acad. Sci. USA, 2005, 102:1620-25.

[0081] Further, epitopes are empirically determined by identifying candidate sequences by positional scanning of synthetic combinatorial peptide libraries (see, for example, D. Wilson et al., above; R. Houghten et al., above; Hernandez et al., Eur J. Immunol., 2004, 34:2331-41), or by making overlapping peptide sequences of the entire protein of interest, and testing those peptides for immune reactivity (using, for example, any readout assay useful for such purposes, described in Current Protocols in Immunology Edited by John E Coligan, Ada M Kruisbeek, David H Margulies, Ethan M Shevach, Warren Strober NIH, John Wiley & Sons) in an in vitro or in vivo assay system appropriate for the disease and species the epitope is sought for. For example, for the design of a multiple sclerosis drug, an example of an appropriate system uses cells that derive from human subjects with MS.

[0082] After identifying a candidate epitope, a probable set of additional related epitopes are generated using modeling and prediction algorithms described in readily available references, for example WO 2000/042559, align and analyze the predicted binding of these probable epitopes using available prediction methods described in, for example, WO 2005/103679, WO 2002/073193 and WO 99/45954. Selecting from the peptides having the highest predicted activity/binding, take 40% of the predicted sequences and acquire the percentage of any given amino acid at each position. Use those percentages to create the rules for amino acid incorporation into a DSP synthesis.

Other Sources of Base Peptide Sequences

[0083] In addition to methodology and results described in the above sections, epitope sequences may be used as base peptide sequences, that are identified and included in the Immune Epitope Database, (available at http://www.immuneepitope.org/home.do, led by Alex Sette funded by the National Institute of Allergy and Infectious Diseases of the National Institute of Health, USA) or any sequences identified by processes performed and disclosed by commercial entities such as Mixtures Sciences of San Diego, or by Algonomics of Ghent Belgium.

[0084] Examples of epitopes identified as part of a naturally occurring, full length protein or synthetic peptides that were identified to have similar activities as such epitopes are shown in the table below.

TABLE-US-00001 TABLE I Examples of epitopes Source/ Representative Original SEQ ID Disease Peptide Sequence Protein Residue Number ref NO: Myasthenia KSYCEIIVTHFPFDEQNCSMK AChR a125-163, a256-269 35 1 gravis LGTWTYDGSVVATNPESD MKSDQESNNAAAEWKYVAM AChR a386-411, h 35 2 VMDHILL Rheumatoid FKGEQGPK Type II 263-270 38 3 Arthritis Collagen PKGQTGEBGIAGFKGEQGPK Type II 251-270 38 4 Collagen GEBGIAGFKGEQGPKGEBGP Type II 256-276 38 5 A Collagen Multiple EVGELSRGKLYSLGNGRWM CNPase 343-373 5 6 sclerosis LTLAKNMEVRAI GNGRWMLTLAKNMEVRAIFT CNPase 356-388 5 7 GYYGKGKPVPTQG ASQKRPSQRH MBP 1-10 8 LSRFSWGAEGQRPGFGYGG MBP 111-129 5 9 ASDYKSAHKGFKGVD MBP 131-145 10 ASDYKSAHKGLKGVDAQGTL MBP 131-155 5 11 SKIFK KYLATASTMDHARHGFLPRH MBP 13-32 5 12 KGFKGVDAQGTLSKI MBP 139-153 49 13 AQGTLSKIFKLGGRDSRSGS MBP 146-170 5 14 P-MARR GTLSKIFKLGGRDSR MBP 148-162 49 15 SHGRTQDENPWHFFK MBP 76-91 49 16 YGRTQDENPVVHFFKNIVTP MBP 80-103 49 17 RTPPP ENPVVHFFKNIVTPRTP MBP 83-99 5 18 DENPVVHFFKNIVTPRTPP MBP 84-102 49 19 ENPVVHFFKNIVTPR MBP 85-99 49 20 VVHFFKNIVTPRTPPPSQGK MBP 86-105 49 21 EKAKYEAYKAAAAAA Empirical 1 205 FSIHCCPPFTFNNSKKEIV MOBP 21-39 5 22 FLNSKKEIVDRKYSICKSG MOBP 31-49 5 23 CQFRVIGPRHPIRALVGDEV MOG 1-20 5 24 PIRALVGDEVELPCRISPGK MOG 11-30 5 25 ELPCRISPGKNATGMEVGWY MOG 21-40 5 26 MEVGWYRPPFSRVVHLYRN MOG 35-55 5 27 GK HSLGKWLGHPDKF PLP 139-151 28 HCLGKWLGHPDKFVGI PLP 139-154 5 29 NTWTTCQSIAFPSKTSASIG PLP 178-197 5 30 SKTSASIGSLCADARMYGVL PLP 190-209 5 31 GFYTTGAVRQIFGDYKTT PLP 89-106 5 32 Penphigus REWVKFAKPCRE Dsg3 49-60 8 33 vulgaris QATQKITYRISGVGIDQ Dsg3 78-94 45 34 PFGIFVVDKNTGDINIT Dsg3 96-112 45 35 HLNSKIAFKIVSQEPAG Dsg3 189-205 45 36 GTPMFLLSRNTGEVRTL Dsg3 205-221 45 37 QCECNIKVKDVNDNFPM Dsg3 250-266 45 38 SVKLSIAVKNKAEFHQS Dsg3 342-358 45 39 NVREGIAFRPASKTFTV Dsg3 376-392 45 40 RDSTFIVNKTITAEVLA Dsg3 483-499 45 41 SARTLNNRYTGPYTF Dsg3 512-526 48 42 QSGTMRTRHSTGGTN Dsg3 762-786 48 43 Insulin AALGIGTDSVILIKCDERGK GAD65 10 44 Dependent Diabetes AFTSEHSHFSLKKGAAALGI GAD65 10 45 ATHQDIDFLIEEIERLGQDL GAD65 10 46 AVRPLWVRME GAD65 46 47 AYVRPLWVRME GAD65 46 48 CGRHVDVFKLWLMWRAKGT GAD65 10 49 TG DERGKMIPSDLERRILEAKQ GAD65 10 50 DICKKYKIWMHVDAAWGGGLL GAD65 10 51 MS DMVGLAADWLTSTANTNMFT GAD65 10 52 EEILMHCQTTLKYAIKTGHP GAD65 10 53 ELLQEYNWELADQPQNLEEIL GAD65 10 54 M ERANSVTWNPHKMMGVPLQ GAD65 10 55 C EYGTTMVSYQPLGDKVNFFR GAD65 10 56 EYLYNIIKNREGYEMVFDGK GAD65 10 57 EYVTLKKMREIIGWPGGSGD GAD65 10 58 GGSGDGIFSPGGAISNMYAM GAD65 10 59 GLLMSRKHKWKLSGVERANS GAD65 10 60 GSGDSENPGTARAWCQVAQK GAD65 10 61 FTG HATDLLPACDGERPTLAFLQ GAD65 10 62 IPPSLRTLEDNEERMSRLSK GAD65 10 63 KGTTGFEAHVDKCLELAEYL GAD65 10 64 YN KHYDLSYDTGDKALQCGRHV GAD65 10 65 KPCSCSKVDVNYAFLHATDL GAD65 10 66 KTGHPRYFNQLSTGLDMVGL GAD65 10 67 KVAPVIKARMME GAD65 46 68 KVAPVWVARMME GAD65 46 69 KVAPVWVRME GAD65 46 70 LAFLQDVMNILLQYVVKSFDR GAD65 10 71 S LEAKQKGFVPFLVSATAGTT GAD65 10 72 LLYGDAEKPAESGGSQPPRA GAD65 10 73 LSKVAPVIKARMMEYG GAD65 526-541 46 74 MASPGSGFWSFGSEDGSGDS GAD65 10 75 NMYAMMIARFKMFPEVKEKG GAD65 10 76 PEVKEKGMAALPRLIAFTSE GAD65 10 77 QHRPLWVRME GAD65 46 78 QKFTGGIGIGNKLCALLYGD GAD65 10 79 QNCNQMHASYLFQQDKHYD GAD65 10 80 L QPPRAAARKAACACDQKPC GAD65 10 81 SC RTRPLWVRME GAD65 46 82 RVLPLWVRME GAD65 46 83 SFDRSTKVIDFHYPNELLQE GAD65 10 84 SRLSKVAPVIKARMMEYGTT GAD65 524-543 46 85 TAGTTVYGAFDPLLAVADICK K GAD65 10 86 TNMFTYEIAPVFVLLEYVTL GAD65 10 87 VFDGKPQHTMVCKWYIPPSL GAD65 10 88 VNFFRMVISMPAATHQDIDF GAD65 10 89 VPLQCSALLVREEGLMQNCNQ GAD65 10 90 YTLPLWVRME GAD65 46 91 systemic lupus QCSDISTKQMFKAVSEVCRI human 101-125 28 92 erythematosus PTHL Ro60 ETEKLLKYLEAVEKVKRTRDE human 221-245 28 93 LEVI Ro60 KARIHPFHILIALETYKTGH hRo60 316-335 15 94 FKTVEPTGKRFLLAVDVSAS human 361-385 28 95 MNQRV Ro60 MNQRVLGSILNASTVAAAMCI human 381-405 28 96 KALDA Ro60 PCPVTTDMTLQQVLMAMSQI human 421-445 28 97 PAGGT Ro60 PAGGTDCSLPMIWAQKTNTP hRo60 441-465 15 98 ADVFI KTNTPADVFIVFTDNETFAG human 456-475 28 99 Ro60 MAALEAKICHQIEYYF La/SSB 10-25 20 100 DEYKNDVKNRSVYIKGFPTD La/SSB 102-127 20 101 ATLDDI RSVYIKGFPTDATLDD La/SSB 111-126 20 102 TLDDIKEWLEDKGQVL La/SSB 123-138 20 103 WLEDKGQVLNIQMRRT La/SSB 130-145 20 104 KGQVLNIQMRRTLHKAFKGSI La/SSB 134-169 20 105 FVVFDSIESAKKFVE MRRTLHKAFKGSIFVV La/SSB 142-157 20 106 SIFVVFDSIESAKKFV La/SSB 153-168 20 107 VVFDSIESAKKFVETP La/SSB 156-171 20 108 SIESAKKFVETPGQKY La/SSB 160-175 20 109 TDLLILFKDDYFAKKNE La/SSB 178-194 20 110 ILFKDDYFAKKNEERK La/SSB 182-197 20 111 CHQIEYYFGDFNLPRDKFLK La/SSB 18-37 20 112 EEDAEMKSLEEKIGCL La/SSB 218-233 20 113 LEEKIGCLLKFSGDLD La/SSB 226-241 20 114 YYFGDFNLPRDKFLKE La/SSB 23-38 20 115 SNHGEIKWIDFVRGAK La/SSB 254-269 20 116 GEIKWIDFVRGAKEGI La/SSB 257-272 20 117 ALKGKAKDANNGLNQLR La/SSB 282-297 20 118 FNLPRDKFLKEQIKLD La/SSB 28-43 20 119 AKDANNGNLQLRNKEV La/SSB 286-301 20 120 LQLRNKEVTWELVEGE La/SSB 294-309 20 121 NKEVTWELVEGEVEKE La/SSB 298-313 20 122 EGEVEKEALKKIIEDQ La/SSB 307-322 20 123 EKEALKKIIEDQQESL La/SSB 311-326 20 124 RDKFLKEQIKLDEGWV La/SSB 32-47 20 125 GKGKGNKAAQPGSGKG La/SSB 338-353 20 126 GSKGKGKVQFQGKKTK La/SSB 349-363 20 127 FQGKKTKFASDDEHDE La/SSB 357-372 20 128 DENGATGPVKRAREET La/SSB 377-389 20 129 EETDKEEPASKQQKTE La/SSB 387-402 20 130 GWVPLEIMIKFNRLNRLTTDF La/SSB 45-67 20 131 NV PLEIMIKFNRLNRLTT La/SSB 48-63 20 132 IMIKFNRLNRLTTDFN La/SSB 51-66 20 133 KFNRLNRLTTDFNVIV La/SSB 54-69 20 134 DFNVIVEALSKSKAEL La/SSB 64-79 20 135 LSKSKAELMEISEDKT La/SSB 72-87 20 136 SKAELMEISEDKTKIR La/SSB 75-90 20 137 RRSPSKPLPEVTDEY La/SSB 89-104 20 138 PSKPLPEVTDEYKNDV La/SSB 93-108 20 139 KFGADARALMLQGVDLLADA human 31-50 34 140 HSP60 autoimmunity LKVGLQVVAVKAPGF human 291-305 12 141 in general HSP60 GGAVFGEEGLTLNLE human 321-335 12 142 HSP60 TLNLEDVQPHDLGKV human 331-345 12 143 HSP60 VGAATEIEMKEKKDR human 381-395 12 144 HSP60 VGGTSDVEVNEKKDR human 406-420 12 145 HSP60 IVLGGGCALLRCIPA human 436-450 12 146 HSP60 VLGGGVALLRVIPALDSLTPA human 437-460 36 147 NED HSP60 GCALLRCIPALDSLT human 441-455 12 148 HSP60 RCIPALDSLTPANED human 446-460 12 149 HSP60 EIIKRTLKIPAMTIA human 446-480 12 150 HSP60 VEKIMQSSSEVGYDA human 491-505 12 151 HSP60 MAGDFVNMVEKGIID human 506-520 12 152 HSP60 VNMVEKGIIDPTKVV human 511-525 12 153 HSP60 VAVTMGPKGRTVIIE human 51-65 12 154 HSP60 KGIIDPTKVVRTALL human 516-530 12 155 HSP60 PTKWRTALLDAAGV human 521-535 12 156 HSP60 ASLLTTAEWVTEIP human 536-550 12 157 HSP60 GETRKVKAH HLA-A2 62-70 18 158 RKVKAHSQTHRVDLG HLA-A2 65-79 18 159 RVDLGTLRGYYNQSE HLA-A2 75-89 18 160 DGRLLRGHDQYAYDG HLA-B7 106-120 18 161 GPEYWDRNTQIYKA HLA-B7 56-69 18 162 WDRNTQIYKAQAQTDR HLA-B7 60-75 18 163 RNTQIYKAQ HLA-B7 62-70 18 164 RESLRNLRGYYNQSE HLA-B7 75-89 18 165 GSHTLQSMYGCDVGP HLA-B7 91-105 18 166 LNEDLRSWTAAD HLA-B7 150-161 19 167 LNEDLRSWTAABTAA HLA-B7 150-164 19 168 DKGQVLNIQ HLA-DQ2 133-142 20 169 LEDKGQVLNIQMRR HLA-DQ2 131-144 20 170 AFKGSIFVVFDSIE HLA-DQ2 149-162 20 171 ESAKKFVET HLA-DQ2 162-170 20 172 IESAKKFVETPGQK HLA-DQ2 161-174 20 173 AKDANNGNLQLR HLA-DQ2 286-297 20 174 EALKKIIED HLA-DQ2 311-324 20 175 EQIKLDEGW HLA-DQ2 36-47 20 176 LKEQIKLDEGWV HLA-DQ2 36-47 20 177 AELMEISED HLA-DQ2 75-87 20 178 SKAELMEISEDKT HLA-DQ2 75-87 20 179 KGSIFWFD HLA- 149-162 20 180 DQ2, DQ7 AKDANNGNLQLRNK HLA 286-299 20 181 DQ2,

DQ7 DANNGNLQL HLA- 288-299 20 182 DQ2, DQ7 IVEALSKSKAEL HLA 66-80 20 183 DQ2, DQ7 AFKGSIFVVFDSI HLA-DQ7 149-161 20 184 GSIFVVFDSIESAK HLA-DQ7 152-165 20 185 IFWFDSIESAKKF HLA-DQ7 154-167 20 186 WFDSIESA HLA-DQ7 154-167 20 187 ELMEISEDKTKIR HLA-DQ7 78-90 20 188 EALYLVCGE HLA-DQ8 35-47 20 189

II. Rules of Synthesis for Directed Sequence Polymers

[0085] Steps in the creation of a DSP sequentially encompass the following

[0086] (a) Identify a protein having known or believed association with a pathology.

[0087] (b) Select from within the protein a peptide or peptides, each having a fixed sequence, that are associated with the pathology and immunologically relevant. If no peptides have been described, then peptides useful in the treatment of the pathology of interest are created. One exemplary method is to create a library of peptides that collectively span the entire length of the protein of interest. This may be done by, for example, partial endopeptidase digestion or by peptide synthesis. The library is screened for immunologically relevant peptides using appropriate detection methods such as binding affinity determination using antibodies detected in the sera of patients with the target pathology. The peptides may be further examined for immunogenicity useful for the treatment of the pathology in an in vitro or in vivo experimental system.

[0088] (c) the amino acid substitutions are decided based on either of two sets of rules, defined or empirical and are set forth below;

[0089] (d) Solid phase synthesis of DSP according to the rules is performed, and pharmaceutically acceptable formulation the DSP is delivered as a therapeutic.

[0090] The rules of synthesis for a composition comprising DSPs are outlined below. Briefly, a DSP may be envisioned as a polypeptide having a defined length that is either the same length as or multiples of the length of the base peptide sequence. For each residue position of the base peptide sequence, one or more substitute residue is defined. The rule of synthesis defines the ratio among the original base peptide residue for that position, the first substitute residue, the second substitute residue, the third substitute residue, and an alanine, to occupy any given residue position.

[0091] The substitute residues are defined according either: (1) to a rational comparison and finding of similarities of relevant characteristics of the original residue with those of the substitute residue or (2) to a comparison of reported experimental results on the relative activities of actual peptides having slight variations from the base sequence. The substitute residues defined in either of these two approaches are termed "conserved substitution" herein.

[0092] An example of a rational comparison and findings of similarity is the methods described by Kosiol et al., J. Theoretical Biol., 2004, 228:97-106. Amino acids are grouped together in a matrix, referred therein as PAM replacement matrix. FIG. 4 is a table showing the amino acid similarity and grouping, according to Kosiol, based on the characteristics of the residues such as size, charge, hydrophobicity, etc., as shown in Table X of the reference. In FIG. 4, amino acids grouped together are considered interchangeable, with high likelihood of retaining characteristics common among the group,

[0093] A comparison of experimental results showing the relative activities of peptides having slight variations from the base sequence can also be used as a basis for the rule for substitution. The sequences of the peptides responsible for observed changes are aligned and the type and percent presence of the new amino acid are noted. If there is more than one amino acid substitution at any given position of the peptide, the frequency of occurrence of an amino acid and the magnitude of activity change compared to the original sequence are taken into account to determine the order of prevalent substitution. Examples of the overall process leading up to the rule generation for DSP synthesis can be found using libraries (Molec. Immunol. 40:1047-1055; Molec. Immunol. 40:1063-74; J Autoimmunity 20:199-201; and J Immunol 163:6424-34), by making altered peptide ligands of overlapping peptides representing the entire protein of interest (Atkinson et al., J. Clin. Invest. 94:2125-29; Meini et al., J. Clin. Invest. 92:2633-43) or de novo (U.S. Pat. Nos. 7,058,515; 6,376,246; 6,368,861; 7,024,312; 6,376,246; 7,024,312; 6,961,664; 6,917,882). Briefly, a cellular material of interest is chosen as the assay system to rank the immunoreactivity of the peptides to be interrogated. Such an assay system can be either an in vitro or in vivo system, and can comprise adaptive or innate immune reactivity. Readouts for the assay system can be the up- or down-regulation of the status of the activation state of a protein, a change in the localization of a protein, the expression of the mRNA encoding for the protein, the relative concentration of a protein, changes in the generation of specific cell types, changes in cellular phenotype, changes in cellular activation, changes in cell number, changes in organ size or function, changes in animal behavior or phenotype. Once the assay or assays are performed the results are analyzed to determine the prevalence of any particular amino acid as a conserved substitution. If more than three residues in a given position within the peptide sequence are identified as generating a change in immunologic function, the top three residues first by frequency of representation in the interrogated peptides, and second by the magnitude of changes elicited. Once chosen, the relative amounts of the residues are defined. As depicted in FIG. 5, each cassette, "y", has a set of amino acid ratios one to another that have a range of about 0-100 for the base (a), the primary change (b), the secondary change (c), and the tertiary change (d), whereas alanine (e) has a ratio of about 5-1000. The rules for the DSP synthesis continue with the combination of the cassettes in the order prescribed. The same block can be repeated either sequentially or separated by another block. On either side of the cassette sequence are N- and C-terminal modifiers. The number of cassettes is dictated by the requirements of the end length of the DSP which is required to be longer than 25 amino acids and shorter than 300 amino acids.

[0094] As described in FIG. 6, the instant invention envisions multiple epitopes to be defined as separate cassettes and synthesized sequentially. Cassette ratios within the same DSP may have different ratios of amino acids. Further, if there is less than three non-alanine amino acid substitutions, the percentage of the `missing` substitution is added to the base sequence. Further, a cassette may be placed in any order with multiple appearances in the overall DSP synthesis. The N- and C-terminal Modifications reside prior to and after the entirety of the DSP cassettes respectively. As seen in FIG. 7A, a single base peptide sequence may have more than one ratio defined as a separate cassette in this example y.sub.1, y.sub.2, and y.sub.3. The individual cassettes can be placed in any order with multiple appearances in the overall DSP synthesis as seen in FIG. 7B. The synthesis rules seen in FIGS. 8A and 8B describe a DSP of the instant invention having portions of a single base peptide sequence with more than one ratio defined as a separate cassette.

[0095] FIG. 9 demonstrates how the instant invention envisions empirically derived ratios of amino acids at a particular position. The example uses data derived from a T cell activation assay using diabetogenic T cells derived from transgenic NOD.BCD2.5 mice (J. Immunol. 166:908-17; J Autoimmunity 20:199-201). The cells re interrogated with a combinatorial decamer library which resulted in a number of different peptides with inhibitory activity. The peptides with the highest activity were used to generate the amino acids at each position, as well as the ratio of different amino acids one to another.

[0096] A cassette may be repeated more than once. After a desired number of multiples of the cassette, if the desired length of the DSP is not yet reached, the DSP sequence is further defined by applying the same process, possibly using different ratio among the original, substitute, second substitute, and alanine residues.

[0097] N or C-terminal DSP modifiers may be added to the synthesis rules. The purpose of such modifiers include but are not limited to enhancing binding to specific proteins as in the case of RDG-based amino acid sequences (U.S. Pat. Nos. 5,773,412; 5,770,565) used as targeting moieties, or peptides that are known to bind to a wide array of HLA-DR species, such as AKAVAAWTLK AAA (U.S. App. Pub. No. 2006/0018915) as a DR-targeting moiety. Such modifiers may include moieties which enhance complexation to delivery systems including sustained release delivery systems. Modifiers can be resorbable matrix constructs/synthesizable backbones such as PLGA. Modifiers can be protease resistant moieties such as D-amino acids.

[0098] Thus, for any given base peptide sequence, a set of synthesis rules is applied to yield a composition comprising reproducible, consistent mixture of DSPs.

III. Peptide Synthesis Methods

[0099] Any known solid phase synthesis appropriate for peptide synthesis may be used to synthesize a composition comprising DSPs, for example as originally described by Merrifield (J. Am. Chem. Soc., 1963, 85:2149) and any variation thereof. More specifically, the synthesis is done in multiple steps by the Solid Phase Peptide Synthesis (SPPS) approach using Fmoc protected amino acids. SPPS is based on sequential addition of protected amino acid derivatives, with side chain protection where appropriate, to a polymeric support (bead). The base-labile Fmoc group is used for N-protection. After removing the protecting group (via piperidine hydrolysis) the next amino acid mixture is added using a coupling reagent (TBTU). After the final amino acid is coupled, the N-terminus is acetylated.

[0100] The resulting peptides (attached to the polymeric support through its C-terminus) are cleaved with TFA to yield the crude peptide. During this cleavage step, all of the side chains protecting groups are also cleaved. After precipitation with diisopropyl ether, the solid is filtered and dried. The resulting peptides are analyzed and stored at 2-8.degree. C.

[0101] Additionally, any peptide synthesis method that allows synthesis incorporating more than one amino acid species at a controlled ratio in any given position of the peptide sequence is suitable for use with this invention. Further, as described below, DSPs may be peptidomimetics or include unnatural or modified amino acid, necessitating the adaptation to allow addition of such chemical species to the polymers synthesized up to that point.

[0102] The synthesis may include unnatural amino acids, or amino acid analogs. In some embodiments, the DSPs are comprised of naturally occurring and synthetic derivatives, for example, selenocysteine. Amino acids further include amino acid analogs. An amino acid "analog" is a chemically related form of the amino acid having a different configuration, for example, an isomer, or a D-configuration rather than an L-configuration, or an organic molecule with the approximate size and shape of the amino acid, or an amino acid with modification to the atoms that are involved in the peptide bond, so as to be protease resistant when polymerized in a polypeptide.

[0103] The DSPs for use in the present invention can be composed of L- or D-amino acids or mixtures thereof. As is known by those of skill in the art, L-amino acids occur in most natural proteins. However, D-amino acids are commercially available and can be substituted for some or all of the amino acids used to make DSPs of the present invention. The present invention contemplates DSPs containing both D- and L-amino acids, as well as DSPs consisting essentially of either L- or D-amino acids.

[0104] In certain embodiments, the DSPs of the present invention include such linear DSPs that are further modified by substituting or appending different chemical moieties. In one embodiment, such modification is at a residue location and in an amount sufficient to inhibit proteolytic degradation of the DSPs in a subject. For example, the amino acid modification may be the presence in the sequence of at least one proline residue; the residue is present in at least one of carboxy- and amino termini; further, the proline can be present within four residues of at least one of the carboxy- and amino-termini. Further, the amino acid modification may be the presence of a D-amino acid.

[0105] In certain embodiments, the subject DSPs is a peptidomimetic. Peptidomimetics are compounds based on, or derived from, peptides and proteins. The DSP peptidomimetics of the present invention typically can be obtained by structural modification of one or more native amino acid residues, e.g., using one or more unnatural amino acids, conformational restraints, isosteric replacement, and the like. The subject peptidomimetics constitute the continuum of structural space between peptides and non-peptide synthetic structures.

[0106] Such peptidomimetics can have such attributes as being non-hydrolyzable (e.g., increased stability against proteases or other physiological conditions which degrade the corresponding peptide DSPS), increased specificity and/or potency. For illustrative purposes, peptide analogs of the present invention can be generated using, for example, benzodiazepines (e.g., see Freidinger et al. in "Peptides: Chemistry and Biology," G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substituted gamma lactam rings (Garvey et al. in "Peptides: Chemistry and Biology," G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988, p123), C-7 mimics (Huffman et al. in "Peptides: Chemistry and Biology," G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988, p. 105), keto-methylene pseudopeptides (Ewenson et al. J. Med. Chem., 1986, 29:295; and Ewenson et al. in "Peptides: Structure and Function (Proceedings of the 9th American Peptide Symposium)," Pierce Chemical Co. Rockland, Ill., 1985), .beta.-turn dipeptide cores (Nagai et al., Tetrahedron Lett., 1985 26:647; and Sato et al. J. Chem. Soc. Perkin Trans., 1986, 1:1231), .beta.-aminoalcohols (Gordon et al. Biochem. Biophys. Res. Commun., 1985, 126:419; and Dann et al. Biochem. Biophys. Res. Commun., 1986, 134:71), diaminoketones (Natarajan et al. Biochem. Biophys. Res. Commun., 1984, 124:141), and methyleneamino-modified (Roark et al. in "Peptides: Chemistry and Biology," G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988, p134). Also, see generally, Session III: Analytic and synthetic methods, in "Peptides: Chemistry and Biology," G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988.

[0107] The molecular weight of a DSP composition can be adjusted during polypeptide synthesis or after the DSPs have been synthesized. To adjust the molecular weight during polypeptide synthesis, the synthetic conditions or the amounts of amino acids are adjusted so that synthesis stops when the polypeptide reaches the approximate length which is desired. After synthesis, polypeptides with the desired molecular weight can be obtained by any available size selection procedure, such as chromatography of the polypeptides on a molecular weight sizing column or gel, and collection of the molecular weight ranges desired. The present polypeptides can also be partially hydrolyzed to remove high molecular weight species, for example, by acid or enzymatic hydrolysis, and then purified to remove the acid or enzymes.

[0108] In one embodiment, the DSPs with a desired molecular weight may be prepared by a process which includes reacting a protected polypeptide with hydrobromic acid to form a trifluoroacetyl-polypeptide having the desired molecular weight profile. The reaction is performed for a time and at a temperature which is predetermined by one or more test reactions. During the test reaction, the time and temperature are varied and the molecular weight range of a given batch of test polypeptides is determined. The test conditions which provide the optimal molecular weight range for that batch of polypeptides are used for the batch. Thus, a trifluoroacetyl-polypeptide having the desired molecular weight profile can be produced by a process which includes reacting the protected polypeptide with hydrobromic acid for a time and at a temperature predetermined by test reaction. The trifluoroacetyl-polypeptide with the desired molecular weight profile is then further treated with an aqueous piperidine solution to form a low toxicity polypeptide having the desired molecular weight.

[0109] In one preferred embodiment, a test sample of protected polypeptide from a given batch is reacted with hydrobromic acid for about 10-50 hours at a temperature of about 20-28.degree. C. The best conditions for that batch are determined by running several test reactions. For example, in one embodiment, the protected polypeptide is reacted with hydrobromic acid for about 17 hours at a temperature of about 26.degree. C.

IV. Pharmaceutical Composition

[0110] One aspect of the present invention is a pharmaceutical composition comprising a DSP composition. As described below in the method of treatment as an aspect of this invention, the DSP composition produced by the process of the invention is useful in treatment of unwanted immune response, such as autoimmune diseases and transplantation rejection in a subject.

[0111] The DSPs of the present invention may be administered to the subject as a composition which comprises a pharmaceutically effective amount of DSPs and an acceptable carrier and/or excipients. A pharmaceutically acceptable carrier includes any solvents, dispersion media, or coatings that are physiologically compatible. Preferably, the carrier is suitable for oral, rectal, transmucosal (including by inhalation), parenteral, intravenous, intramuscular, intraperitoneal, intradermal, transdermal, topical, or subcutaneous administration. One exemplary pharmaceutically acceptable carrier is physiological saline. Other pharmaceutically acceptable carriers and their formulations are well-known and generally described in, for example, Remington's Pharmaceutical Science (18.sup.th Ed., ed. Gennaro, Mack Publishing Co., Easton, Pa., 1990). Various pharmaceutically acceptable excipients are well-known in the art and can be found in, for example, Handbook of Pharmaceutical Excipients (4.sup.th ed., Ed. Rowe et al. Pharmaceutical Press, Washington, D.C.). The composition can be formulated as a solution, microemulsion, liposome, capsule, tablet, or other suitable forms. The active component which comprises the copolymer may be coated in a material to protect it from inactivation by the environment prior to reaching the target site of action. The pharmaceutical compositions of the present invention are preferably sterile and non-pyrogenic at the time of delivery, and are preferably stable under the conditions of manufacture and storage. When desirable, the composition further comprises components to enhance stability, permeability, and/or bioavailability, such as particulate forms protective coatings, protease inhibitors or permeation enhancers for various routes of administration, including parenteral, pulmonary, nasal and oral.

[0112] For oral administration, the pharmaceutical preparation may be in liquid form, for example, solutions, syrups or suspensions, or may be presented as a drug product for reconstitution with water or other suitable vehicle before use. Such liquid preparations may be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g., almond oil, oily esters, or fractionated vegetable oils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid). The pharmaceutical compositions may take the form of, for example, tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g., pre-gelatinized maize starch, polyvinyl pyrrolidone or hydroxypropyl methylcellulose); fillers (e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc or silica); disintegrants (e.g., potato starch or sodium starch glycolate); or wetting agents (e.g., sodium lauryl sulfate). The tablets may be coated by methods well-known in the art.

[0113] In one embodiment, the oral composition is enterically-coated. Use of enteric coatings is well known in the art. For example, Lehman (1971) teaches enteric coatings such as Eudragit S and Eudragit L. The Handbook of Pharmaceutical Excipients, 2.sup.nd Ed., also teaches Eudragit S and Eudragit L applications. One Eudragit which may be used in the present invention is L30D55. Preparations for oral administration may be suitably formulated to give controlled release of the active compound.

[0114] The compositions may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides.

[0115] For administration by inhalation, the compositions for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin, for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

[0116] The compositions may be formulated for administration by injection, e.g., by bolus injection or continuous infusion in a parenteral, intravenous, intraperitoneal, intramuscular, or subcutaneous manner. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Alternatively, the active ingredient may be in powder form for reconstitution with a suitable vehicle, e.g., sterile pyrogen free water, before use.

[0117] In a preferred embodiment, compositions comprising DSP compositions are formulated in accordance with routine procedures as pharmaceutical compositions adapted for intravenous administration to human beings. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline, with the intervals between administrations being greater than 24 hours, 32 hours, or more preferably greater than 36 or 48 hours. Where the composition is administered by injection, an ampoule of sterile water or saline for injection can be provided so that the ingredients may be mixed prior to administration.

[0118] In other embodiments of the present invention, the pharmaceutical compositions are regulated-release or sustained release formulations. DSP compositions of the present invention may be admixed with biologically compatible polymers or matrices which control the release rate of the copolymers into the immediate environment. Controlled or sustained release compositions include formulation in lipophilic depots (e.g., fatty acids, waxes, oils). One embodiment of sustained release formulations is transdermal patches.

[0119] In some embodiments of the present invention, pharmaceutical compositions comprise DSPs formulated with oil and emulsifier to form water-in-oil microparticles and/or emulsions. The oil may be any non-toxic hydrophobic material liquid at ambient temperature to about body temperature, such as edible vegetable oils including safflower oil, soybean oil, corn oil, and canola oil; or mineral oil. Chemically defined oil substance such as lauryl glycol may also be used. The emulsifier useful for this embodiment includes Span 20 (sorbitan monolaurate) and phosphatidylcholine. In some embodiments, a DSP composition is prepared as an aqueous solution and is prepared into an water-in-oil emulsion dispersed in 95 to 65% oil such as mineral oil, and 5 to 35% emulsifier such as Span 20. In another embodiment of the invention, the emulsion is formed with alum rather than with oil and emulsifier. These emulsions and microparticles reduce the speed of uptake of DSPs, and achieve controlled delivery.

[0120] In another embodiment, the controlled and/or sustained delivery is achieved by implantable medical devices coated with sustained-release formulations, or implantable pharmaceutical formulation suitable for sustained-release of the active components.

[0121] In some embodiments of the invention, pharmaceutical compositions comprise a set of nucleic acid vectors encoding a DSP composition, which is expressed as polypeptides within a subject. The vectors may comprise transcription- and/or translation-controlling elements such that the timing and level of the DSPs composition produced may be regulated.

[0122] In some embodiments, the vectors also comprise one or more additional coding sequences, which encodes a therapeutically beneficial polypeptide or a second, different composition of DSPs that is not a member of the first DSP composition. In alternative embodiments, a pharmaceutical composition comprises one or more vectors, each encoding either: the DNA sequences for the DSPs of a first DSP composition, or the DNA sequences for the DSPs of a second DSPs composition or a therapeutically beneficial polypeptide, that is not a member of the first DSP composition. Such therapeutically beneficial polypeptide may be, for example, an immunomodulatory cytokine or a growth factor.

[0123] Some embodiments of the invention are pharmaceutical compositions for targeted delivery of the DSP composition of the invention. In such embodiments, a pharmaceutical composition comprises a DSP composition that is complexed with a targeting moiety. The targeting moiety allows localized delivery of the DSP composition to a desired location or microenvironment within the subject. A targeting moiety include, and may be selected from, the group comprising a chemical group or functionality such as biotin or simple sugars, a single or double stranded DNA sequence of various lengths, a single or double stranded RNA sequence of various lengths, a peptide of various lengths, an antibody including single chain antibodies, Fab', or modified antibodies, a lipid, or a glycolipid. More than one of such moiety may be used at the same time in combination. For examples of targeting moieties, see U.S. Pat. No. 6,268,488; U.S. Appl. Pub. No. 2003/0190676; and see, for example, www.covx.com/tech_creating.html.

[0124] In one embodiment of the invention, the complex has characteristics of a prodrug, causing the DSP composition to exhibit no pharmaceutical activity of the present invention until the dissolution of the complex in the subject. In another embodiment, the complex does not affect the activity of the DSP composition.

[0125] Any methods generally known to one skilled in the art may be used to produce a complex of the instant invention and a targeting moiety. The target moiety may be complexed to the DSPs by a chemical bond, which may be covalent, ionic, hydrophobic, or van der Waals force, directly or through another chemical entity. Alternatively, the target moiety may be co-localized with the DSPs through common medium such as a biocompatible resin within which the DSP composition is included. The manner of forming a complex is chosen also based on the active state of the instant invention while existing in the combination and whether a permanent complex or a transitory complex is desired.

[0126] In some embodiments, the pharmaceutical compositions also include additional therapeutically active agents. Such additional ingredient can be at least an additional DSP composition that binds to a different target, an antibody which binds to an unwanted inflammatory molecule or cytokine such as interleukin-6, interleukin-8, granulocyte macrophage colony stimulating factor, and tumor necrosis factor-.alpha.; an enzyme inhibitor such as a protease inhibitor aprotinin or a cyclooxygenase inhibitor; an antibiotic such as amoxicillin, rifampicin, erythromycin; an antiviral agent such as acyclovir; a steroidal anti-inflammatory such as a glucocorticoid; a non-steroidal anti-inflammatory such as aspirin, ibuprofen, or acetaminophen; or a non-inflammatory cytokine such as interleukin-4 or interleukin-10. Other cytokines and growth factors such as interferon-.beta., tumor necrosis factors, antiangiogenic factors, erythropoietins, thrombopoietins, interleukins, maturation factors, chemotactic protein, and their variants and derivatives that retain similar physiological activities may also be used as an additional ingredient.

[0127] Further, a form of vitamin D that is or becomes biologically active within the body of the subject receiving such form of vitamin D may also be used as an additional ingredient. The two main forms of vitamin D are: vitamin D3 or cholecalciferol, which is formed in the skin after exposure to sunlight or ultraviolet light, and ergocalciferol or vitamin D2 which is obtained by irradiation of plants or plant materials or foods. The differences are situated in the side chain. Vitamin D3 may be obtained from natural sources such as fatty fish such as herring and mackerel. In the body, two other forms of vitamin D3 can be found. Vitamin D3 is hydroxylated in the liver into 25-hydroxyvitamin D3 (25(OH)D), and subsequently in the kidney into 1,25-dihydroxyvitamin D3 (1,25(OH)2D), which is the active metabolite that stimulates the calcium absorption from the gut (Feldman et al., 2005). When 1,25(OH)2D is sufficiently available, 24,25-dihydroxyvitamin D (24,25(OH)2D) is formed in the kidney, which is further catabolized.

[0128] Another class of therapeutically active agents useful as an additional agent is immune boosters which increases the production of common lymphoid precursors (CLPs) from the multilineage potential cells. An example of such agent is PBI-1402 developed by ProMetic in Quebec, Canada.

[0129] In some embodiments, the additional active therapeutically active agent is selected from the group consisting of anti-psoriasis creams, Sulfasalazine, glucocorticoids, propylthiouracil, methimazole, I.sup.131, insulin, IFN-.beta.1a, IFN-.beta.1b, glucocorticoids, ACTH, avonex, azathiopurine, cyclophosphamide, UV-B, PUVA, methotrexate, calcipitriol, cyclophosphamide, OKT3, FK-506, cyclosporin A, azathioprine, and mycophenolate mofetil.

[0130] Another class of therapeutic agents that are useful to combine with the DSP composition of the invention is anti-obesity drugs, for example Lipitor. Anti-obesity drugs include P-3 agonists, CB-1 antagonists, appetite suppressants, such as, for example, sibutramine (Meridia), and lipase inhibitors, such as, for example, or list at (Xenical). The subject copolymers may also be used in methods of the invention in combination with drugs commonly used to treat lipid disorders in diabetic patients. Such drugs include, but are not limited to, HMG-CoA reductase inhibitors, nicotinic acid, bile acid sequestrants, and fibric acid derivatives. Polypeptides of the invention may also be used in combination with anti-hypertensive drugs, such as, for example, .beta.-blockers, cathepsin S inhibitors and ACE inhibitors. Examples of .beta.-blockers are: acebutolol, bisoprolol, esmolol, propanolol, atenolol, labetalol, carvedilol, and metoprolol. Examples of ACE inhibitors are: captopril, enalapril, lisinopril, benazepril, fosinopril, ramipril, quinapril, perindopril, trandolapril, and moexipril.

[0131] In a specific embodiment, the disease to be treated by administration of the pharmaceutical composition of the invention is selected from the group consisting of multiple sclerosis, type-I diabetes, Hashimoto's thyroiditis, Crohn's disease, rheumatoid arthritis, systemic lupus erythematosus (SLE), gastritis, autoimmune hepatitis, hemolytic anemia, autoimmune hemophilia, autoimmune lymphoproliferative syndrome (ALPS), autoimmune uveoretinitis, glomerulonephritis, Guillain-Barre syndrome, psoriasis, myasthenia gravis, autoimmune encephalomyelitis, Goodpasture's syndrome, Grave's disease, paraneoplastic pemphigus, autoimmune thrombocytopenic purpura, scleroderma with anti-collagen antibodies, mixed connective tissue disease, pernicious anemia, polymyositis, idiopathic Addison's disease, autoimmune-associated infertility, bullous pemphigoid, Sjogren's syndrome, idiopathic myxedema and colitis.

[0132] The invention further provides a kit comprising (i) a composition comprising a DSP composition or DNA delivery vehicle comprising DNA encoding DSPs and (ii) instructions for administering the composition to a subject in need thereof at intervals greater than 24 hours, more preferably greater than 36 hours, for the treatment of a disease, such as an autoimmune disease. In one embodiment, the autoimmune disorder is multiple sclerosis. In a preferred embodiment, the DSP composition is formulated in dosages for administration of greater than about 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or any intervening interval thereof. In another embodiment of the kits described herein, the instructions indicate that the DSP is to be administered every about 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or any interval in between. Kits may comprise additional components, such as packaging, instructions, and one or more apparatuses for the administration of the copolymer, such as a hypodermic syringe

V. Methods of Treatment

[0133] The instant invention provides for a further improvement on the need to improve the effectiveness of peptide immunotherapies. The improvement takes form in an ability to dynamically administer the compound based on the ability of the compound to achieve sustained chimerism, or immune regulation--either active or passive, while generating either a T.sub.H1 immune posture, or a T.sub.H2 immune posture, and while producing anti-compound antibodies at either a low or a high level. Dynamic administration of random sequence copolymer is comprised of any combination of dose, regimen, route of administration, and/or formulation. This dynamic immunomodulation provides for increased effectiveness at any of the multiple stages of a disease within a particular patient, as well as the ability to treat multiple, pathogenic antigenic-determinant unrelated diseases more effectively.

[0134] The invention provides methods for the treatment or prevention of a disease in a subject, preferably in a human, which subject is afflicted with or is suspected to be afflicted with the disease. Another embodiment of the present invention is a method for prophylactically treating a subject at risk of developing e.g., an autoimmune disease by administering a DSP composition. A subject at risk is identified by, for example, determining the genetic susceptibility to an autoimmune disease by testing for alleles of HLA that are associated with such autoimmune disease, and/or based on familial history, or other genetic markers that correlate with such autoimmune disease. Alternatively, the subject at risk is a subject that is scheduled to have or has had organ transplantation. Such prophylactic treatment may additionally comprise a DSP composition that binds to a second HLA molecule associated with the disease or condition to be treated. The second HLA molecule may be a HLA-DQ or HLA-DR molecule.

[0135] One aspect of the invention provides methods of treating or preventing a disease, the method comprising administering to said subject a dosing regimen of an effective amount of a DSP composition for the amelioration of a disease treatable with the DSP composition, said effective amount delivered to said subject at time intervals greater than 24 hours, 36 hours, or more preferably greater than 48 hours. A related aspect of the invention provides a method for the treatment of a subject in need thereof, comprising administering to said subject a dosing regimen of an effective amount of a DSP composition for the amelioration of a disease treatable with the DSP composition, said effective amount delivered to the subject using a sustained-release formulation which administers the DSP composition over a period of at least 2 days, at least 4 days, or at least 6 days, wherein the effective amount is an amount that is effective if delivered daily.

[0136] In a specific embodiment, the method of the invention is effective in treating a disease selected from the group consisting of multiple sclerosis, type-I diabetes, Hashimoto's thyroiditis, Crohn's disease, rheumatoid arthritis, systemic lupus erythematosus (SLE), gastritis, autoimmune hepatitis, hemolytic anemia, autoimmune hemophilia, autoimmune lymphoproliferative syndrome (ALPS), autoimmune uveoretinitis, glomerulonephritis, Guillain-Barre syndrome, psoriasis, myasthenia gravis, autoimmune encephalomyelitis, Goodpasture's syndrome, Grave's disease, paraneoplastic pemphigus, autoimmune thrombocytopenic purpura, scleroderma with anti-collagen antibodies, mixed connective tissue disease, pernicious anemia, polymyositis, idiopathic Addison's disease, autoimmune-associated infertility, bullous pemphigoid, Sjogren's syndrome, idiopathic myxedema and colitis.

[0137] In some embodiments, the disease of the methods of the present invention is mediated by T-cells, and in particular T.sub.H1 cells or cells with T.sub.H1 immune posture, or is a disease which is exacerbated by an excess of inflammatory cytokines. In one aspect the application relates to methods of modulating an immune response by administering a composition comprising a DSP composition as described above. In some embodiments, the disease include, without limitation, acute inflammation, rheumatoid arthritis, transplant rejection, asthma, inflammatory bowel disease, uveitis, restenosis, multiple sclerosis, psoriasis, wound healing, lupus erythematosus, allergies, atopic dermatitis, and neuroprotection and any other autoimmune or inflammatory disorder that can be recognized by one of ordinary skill in the art.

[0138] A preferred embodiment of the invention is a method for treating a disease treatable by administering to a subject in need thereof a composition comprising a DSP composition wherein the disease is selected from the group consisting of allergies, asthma, atopic dermatitis, and neuroprotection. The invention is not limited to any particular DSP composition or mode of administration.

[0139] One aspect of the invention provides methods of modulating the immune response for preventing, treating, or attenuating, Host versus Graft Disease (HVGD) or Graft versus Host Disease (GVHD), in the case of organ transplantation, and in preventing, treating, or attenuating autoimmune disorders, by administering a composition comprising a DSP composition as described above. Thus, in another aspect this application relates to methods of inducing sustained chimerism in case of organ transplantation. Additionally, the present application relates to methods of selectively inhibiting T-cell response to a graft, consequently, increasing the chances of survival of the graft.

[0140] Transplantation systems such as organ transplantations and bone marrow reconstitution have become important and effective therapies for many life threatening diseases. However, immune rejection is still the major barrier for successful transplantation. This is manifested in functional deterioration and graft rejection in the case of organ transplantation (host-versus-graft disease, or HVGD. Another manifestation of pathological immune reactivity is GVHD that occurs in approximately 30% of bone marrow recipients. Up to half of those patients who develop GVHD may succumb to this process. This high morbidity and mortality has led to continuous interest in the possibility of controlling or preventing GVHD. Clinicopathologically, two forms of GVHD have been recognized. Acute GVHD develops within the first 3 months after bone marrow transplantation and features disorders of skin, liver and gastrointestinal tract. Chronic GVHD is a multi-organ autoimmune-like disease emerging from 3 months up to 3 years post-transplantation and shares features common to naturally occurring autoimmune disorders, like systemic lupus erythematosus (SLE) and scleroderma. The methods described herein may be used to treat both acute and chronic GVHD.

[0141] In a specific embodiment of the methods described herein, the DSP composition based on applicable organ-derived or HLA-derived native peptide sequences may be used for prevention and treatment of GVHD in all cases of organ transplantation that develop GVHD. A particularly suitable application of the present invention is in allogeneic bone marrow transplantation. A treatment regimen may comprise administrations of the random copolymer at intervals greater than 24, 30, 36, 42, or 48 hours, for up to 60 days, starting from 2 days prior to the graft. Other immunosuppressive drugs, such as cyclosporine, methotrexate and prednisone, may be administered with the DSP composition.

[0142] The method of the invention may also be applied to the prevention and treatment of GVHD in the course of bone marrow transplantation in patients suffering from diseases curable by bone marrow transplantation, including leukemias, such as acute lymphoblastic leukemia (ALL), acute nonlymphoblastic leukemia (ANLL), acute myelocytic leukemia (AML) and chronic myelocytic leukemia (CML), severe combined immunodeficiency syndromes (SCID), osteopetrosis, aplastic anemia, Gaucher's disease, thalassemia and other congenital or genetically-determined hematopoietic or metabolic abnormalities.

[0143] One aspect of the invention is the administration of a DSP composition to a subject in need there of, as described above, in combination with other therapeutic agents that are effective in treating the conditions that are treated by administration of the DSP, or conditions that accompany or occur concurrently with the conditions that are treated by administration of the DSP. The additional therapeutically active agents may treat the same or related disease as the DSP composition, or may be intended to treat an undesirable side effect of administration of the DSP composition, such as to reduce swelling at a site of intradermal injection. Alternatively, the other therapeutic agents enhance the activity of DSP compositions. Such additional therapeutic agents are, by way of example, antibodies, cytokines, growth factors, enzyme inhibitors, antibiotics, antiviral agents, anti-inflammatory including steroids, immune boosters, antimetabolites, soluble cytokine receptors, and vitamin D or agents that increase the level of circulating vitamin D. Additional therapeutically active agents also include copolymers which bind to a HLA molecule associated with the disease such as Copolymer-1, or another DSP composition. The HLA molecule may be an HLA-DQ molecule or an HLA-DR molecule. The enzyme inhibitor may be a protease inhibitor or a cyclooxygenase inhibitor. Examples of the therapeutically active agents to be administered in conjunction with the DSP composition are recited in Section IV, "Pharmaceutical Composition" section, though the administration of these agents are not limited to co-administration as a single composition. The additional therapeutic agents may be administered before, concomitantly with, or after the administration of the DSP composition, at such time that the effect of the additional therapeutic agents and the effect of the DSP composition overlap at some time point.

[0144] In particular, the method of present invention further comprises administering to said subject an anti-lymphocyte therapies. In such embodiments, the DSP composition of the present invention are administered to a patient with an autoimmune disease following an anti-lymphocyte therapy (e.g., anti-T cell or anti-B cell). In one embodiment, anti-T cell therapies may use antibodies, such as Campath-1H.RTM. (alemtuzumab; anti-CD52), OKT3 (anti-CD3), thymoglobulin (anti-thymocytic globulins), or anti-IL2R antibodies (e.g., daclizumab and basiliximab). Alternatively, anti-T cell therapies may use chemotherapy agents such as fludarabine, external-beam radiation therapy (XRT), and cyclophosphamide. In one embodiment, the anti-lymphocyte therapy agent selected from the group consisting of a polyclonal antibody or a monoclonal antibody. In certain embodiments, the polyclonal antibody is antithymocyte gamma globulin (ATGAM). In other embodiment, the antibody is a monoclonal antibody selected from the group consisting of alemtuzumab (Campath.RTM.), muromonab (OKT.RTM.3), daclizumab, and basiliximab. In another embodiment, the method of the invention comprises administering to said subject an anti B-cell therapy. In one embodiment, the anti-B-cell therapy anti CD-20 antibody such as the antibody Rituxan (Rituximab). The dosage of the above additional treatments to be administered to a subject varies with the precise nature of the condition being treated and the recipient of the treatment. The scaling of dosages for human administration can be performed according to art-accepted practices. For example, the dose for Campath-1H.RTM. will generally be in the range 1 to about 100 mg for an adult patient, usually administered daily for a period between 1 and 30 days. The preferred daily dose is 1 to 10 mg per day although in some instances larger doses of up to 40 mg per day may be used (see, e.g., U.S. Pat. No. 6,120,766). Although not wishing to be bound by any particular mechanism or theory, it is believed that such combination therapy can enhance the therapeutic efficacy without any potential long-term toxicity. To illustrate, Campath-1H.RTM. is introduced in a patient for initial induction immunosuppression. Then, the patient is administered a copolymer of the present invention in the absence of Campath-1H.RTM.

[0145] In a preferred embodiment, the DSP composition of the present invention can be administered with a form of vitamin D that is or becomes biologically active within the body of the subject receiving such form of vitamin D. The classical role of vitamin D that of an involvement in the regulation of calcium homeostasis. After the discovery of a vitamin D receptor (VDR) on peripheral blood mononuclear cells, interest in its role in the etiopathogenesis of certain autoimmune diseases increased. Vitamin D deficiency has been shown in increase susceptibility to experimental models of multiple sclerosis (MS), while vitamin D treatment suppressed these experimental models of MS. Further studies have shown that limiting the VDR signaling on T cells increases Th1 effector cells, while augmenting VDR signaling increases T regulatory cells. Thus, any increase in Vitamin D during the course of immunomodulatory therapy, such as those described herein, would have a potentially synergistic effect leading to increased efficacy of treatment as the vitamin D will assist in increasing the regulatory component of the treatment, while the peptide based immunotherapy will provide an epitope specific direction to the adaptive immune response

[0146] In particular, for the role vitamin D plays in immunological phenomena, see M. T. Cantorna, Progress in Biophys. Molec. Biol. 2006 September; 92(1):60-4. Epub 2006 Feb. 28.) and Spach and Hayes, J. Immunol. 2005, 175:4199-4126.

[0147] In one embodiment of the methods described herein, the route of administration can be oral, intraperitoneal, transdermal, subcutaneous, by intravenous or intramuscular injection, by inhalation, topical, intralesional, or by infusion; liposome-mediated delivery; intrathecal, gingival pocket, rectal, intravaginal, intrabronchial, nasal, transmucosal, intestinal, ocular or otic delivery, or any other methods known in the art as one skilled in the art may easily perceive. Administration can be systemic or local. In the event more than one DSP composition is being administered to a subject during the same or overlapping time period, such additional therapeutic agent may be administered by a route different from that for the administration of the DSP composition.

[0148] In general, an embodiment of the invention is to administer a suitable dose of a therapeutic DSP composition that will be the lowest effective dose to produce a therapeutic effect, for example, mitigating symptoms. The therapeutic DSP compositions are preferably administered at a dose per subject, which corresponds to a dose per day of at least about 2 mg, at least about 5 mg, at least about 10 mg, or at least about 20 mg as appropriate minimal starting dosages, or about x mg, wherein x is an integer between 1 and 20. In one embodiment of the methods described herein, a dose of about 0.01 to about 500 mg/kg can be administered. In general, the effective dosage of the DSP composition of the present invention is about 50 to about 400 micrograms of the composition per kilogram of the subject per day. In one specific embodiment, the equivalent dosage per day, regardless of the frequency with which the doses are administered, is from about 5 to 100, or more preferably, from about 10 to 40, or more preferably about 20 mg/day. In another specific embodiment, each individual dosage in the treatment regimen is from about 5 to 100, or more preferably from about 10 to 40, or more preferably about 20 mg/dose.

[0149] However, it is understood by one skilled in the art that the dose of the DSP composition of the invention will vary depending on the subject and upon the particular route of administration used. It is routine in the art to adjust the dosage to suit the individual subjects. Additionally, the effective amount may be based upon, among other things, the size of the DSPs, the biodegradability of the DSPs, the bioactivity of the DSPs and the bioavailability of the DSPs. If the DSPs does not degrade quickly, such as is expected when the DSPs comprise unnatural amino acids or are peptidomimetics, is bioavailable and highly active, a smaller amount will be required to be effective. The actual dosage suitable for a subject can easily be determined as a routine practice by one skilled in the art, for example a physician or a veterinarian given a general starting point. For example, the physician or veterinarian could start doses of the DSP composition of the invention employed in the pharmaceutical composition at a level lower than that required in order to achieve the desired therapeutic effect, and increase the dosage with time until the desired effect is achieved. The dosage of the DSP composition may either be increased in the event the patient does not respond significantly to current dosage levels, or the dose may be decreased if an alleviation of the symptoms of the disorder or disease state is observed, or if the disorder or disease state has been ablated, or if an unacceptable side effects are seen with the starting dosage.

[0150] In one embodiment, a therapeutically effective amount of the DSP composition is administered to the subject in a treatment regimen comprising intervals of at least 36 hours, or more preferably 48 hours, between dosages. In another embodiment, the DSP composition is administered at intervals of at least 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or the equivalent amount of days. In some embodiments, the DSP composition is administered every other day, while in other embodiments it is administered weekly. If two different DSP compositions, or DSP composition with another therapeutic agent, are administered to the subject, such administration may take place at the same time, such as simultaneously, or essentially at the same time, such as in succession. Alternatively, their administration may be staggered. For example, two DSP compositions which are each administered every 48 hours may both be administered on the same days, or one may be administered one day and the other on the next day and so on in an alternating fashion.

[0151] Treatment regimens with longer dosing intervals, consequently often with lower total exposure of DSPs, are expected to induce lower titers of antibodies against DSPs themselves, while still inducing desired protective effects. Such reduction of neutralizing antibodies are desirable because it is considered likely to help DSP compositions to retain its effectiveness without being neutralized, and it is associated with reduced risk of anaphylactic shocks, providing safer treatments of diseases. Longer interval regimens are also desirable in treatment of some of the diseases, because they strengthen the bias for T.sub.H2 responses, which is considered to be the mode of action for the treatment of these diseases by DSPs.

[0152] In other embodiments, the DSP composition is administered in a treatment regimen which comprises at least one uneven time interval, wherein at least one of the time intervals is at least 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or the equivalent amount of days.

[0153] In one embodiment, the DSP composition is administered to be subject at least three times during a treatment regimen, such that there are at least two time intervals between administrations. These intervals may be denoted I.sub.1 and I.sub.2. If the DSP composition is administered four times, then there would be an additional interval between the third and fourth administrations, I.sub.3, such that the number of intervals for a given number "n" of administrations is n-1. Accordingly, in one embodiment, at least one of the time intervals between administrations is greater than about 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours. In another embodiment, at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 95% of the total number n-1 of time intervals are at least about 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours.

[0154] In yet another embodiment, the average time interval between administrations ((I.sub.1+I.sub.2+ . . . +I.sub.n-1)/n-1) is at least 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or at least two weeks.

[0155] In another embodiment, the dosage regimen consists of two or more different interval sets. For example, a first part of the dosage regimen is administered to a subject daily, every other day, or every third day, for example, at about 22 mg copolymer/m.sup.2 body surface area of the subject, wherein the subject is a human. In some embodiment of the invention, the dosing regimen starts with dosing the subject every other day, every third day, weekly, biweekly, or monthly. The dosage for administration every other day or every third day may be up to about 65 mg/m.sup.2 and 110 mg/m.sup.2 respectively. For a dosing regimen comprising dosing of the random copolymer every week, the dose comprises up to about 500 mg/m.sup.2, and for a dosing regimen comprising dosing of the random copolymer every two weeks or every month, up to 1.5 g/m.sup.2 may be administered. The first part of the dosing regimen may be administered for up to 30 days, for example, 7, 14, 21, or 30 days. A subsequent second part of the dosing regimen with a different, longer interval administration with usually lower exposure (step-down dosage), administered weekly, every 14 days, or monthly may optionally follow, for example, at 500 mg/m.sup.2 body surface area weekly, up to maximum of about 1.5 g/m.sup.2 body surface area, continuing for 4 weeks up to two years, for example, 4, 6, 8, 12, 16, 26, 32, 40, 52, 63, 68, 78, or 104 weeks. Alternatively, if the disease goes into remission or generally improves, the dosage may be maintained or kept at lower than maximum amount, for example, at 140 mg/m.sup.2 body surface area weekly. If, during the step-down dosage regimen, the disease condition relapses, the first dosage regimen may be resumed until effect is seen, and the second dosing regimen may be implemented. This cycle may be repeated multiple times as necessary.

[0156] In other embodiments of the invention, any of the methods of the invention may be practiced using sustained release formulation comprising a DSP composition. When administering a DSP composition of the invention using a sustained release formula, the overall exposure to the DSP is generally lower than in bolus administration. For example, a first part of the dosage regimen is administered to a subject daily, every other day, or every third day, for example, at about 22 mg DSP/m.sup.2 body surface area of the subject, wherein the subject is a human. In some embodiment of the invention, the dosing regimen uses sustained release formula, dosing the subject every other day, every third day, weekly, biweekly, or monthly so that the copolymer is released during the interval. The dosage for administration every other day or every third day may be up to about 35 mg/m.sup.2 and 65 mg/m.sup.2 respectively. For a dosing regimen comprising dosing of the DSP composition every week, the dose comprises up to about 140 mg/m.sup.2, and for a dosing regimen comprising dosing of the DSP composition every two weeks or every month, up to 750 mg/m.sup.2 may be administered. The first part of the dosing regimen may be administered for up to 30 days, for example, 7, 14, 21, or 30 days. A subsequent second part of the dosing regimen with a different, longer interval administration with usually lower exposure (step-down dosage), administered weekly, every 14 days, or monthly may optionally follow, for example, at 140 mg/m.sup.2 body surface area weekly, up to maximum of about 1.5 g/m.sup.2 body surface area, continuing for 4 weeks up to two years, for example, 4, 6, 8, 12, 16, 26, 32, 40, 52, 63, 68, 78, or 104 weeks. Alternatively, if the disease goes into remission or generally improves, the dosage may be maintained or kept at lower than maximum amount, for example, at 140 mg/m.sup.2 body surface area weekly. If, during the step-down dosage regimen, the disease condition relapses, the first dosage regimen may be resumed until effect is seen, and the second dosing regimen may be implemented. This cycle may be repeated multiple times as necessary.

[0157] For such sustained release administration, such method comprises applying a sustained-release transdermal patch or implanting a sustained-release capsule or a coated implantable medical device so that a therapeutically effective dose of the copolymer of the present invention is delivered at defined time intervals to a subject of such a method. The DSP composition of the subject invention may be delivered via a capsule which allows regulated-release of the DSPs over a period of time. Controlled or sustained-release compositions include formulation in lipophilic depots (e.g., fatty acids, waxes, oils). Also comprehended by the invention are particulate compositions coated with polymers (e.g., poloxamers or poloxamines). In certain embodiments, a source of a DSP composition is stereotactically provided within or proximate to the area of autoimmune attack, for example, near the pancreas for the treatment of IDDM.

[0158] An improvement in the symptoms of a subject afflicted with a disease as a result of administration of the DSP composition may be noted by a decrease in frequency of recurrences of episodes of the disease symptoms, by decrease in severity of symptoms, and by elimination of recurrent episodes for a period of time after the start of administration. A therapeutically effective dosage preferably reduces symptoms and frequency of recurrences by at least about 20%, for example, by at least about 40%, by at least about 60%, and by at least about 80%, or by about 100% elimination of one or more symptoms, or elimination of recurrences of the autoimmune disease, relative to untreated subjects. The period of time can be at least about one month, at least about six months, or at least about one year.

[0159] For example, an improvement in the symptoms of a subject afflicted with arthritis or any other autoimmune disorder which results in inflammation of the joints may be noted by a reduction in edema of one or more joints, by a reduction in inflammation in one or more joints, or by an increase in mobility in one or more joints. A therapeutically effective dosage preferably reduces joint inflammation and edema and improves mobility by at least about 20%, more preferably by at least about 40%, even more preferably by at least about 60%, and even still more preferably by at least about 80%, relative to untreated subjects.

DEFINITIONS

[0160] The term "associated with" means "coexistent with" or "in correlation with." The term does not necessarily indicate causal relationship, though such relationship may exist.

[0161] The term "binding" refers to a direct association between two molecules, due to, for example, covalent, electrostatic, hydrophobic, ionic and/or hydrogen-bond interactions under physiological conditions, and including interactions such as salt bridges and water bridges.

[0162] The term "HLA molecule" means any class II major histocompatibility complex glycoproteins.

[0163] The term "immunomodulation" means the process of increasing or decreasing the immune system's ability to mount a response against a particular antigenic determinant through the T-cell receptor ("TCR")'s recognition of complexes formed by major histocompatibility complex ("MHC") and antigens.

[0164] The term "immunosuppression" means the depression of immune response and reactivity in recipients of organ or bone marrow allotransplants.

[0165] The term "MHC activity" refers to the ability of an MHC molecule to stimulate an immune response, e.g., by activating T cells. An inhibitor of MHC activity is capable of suppressing this activity, and thus inhibits the activation of T cells by MHC. In preferred embodiments, a subject inhibitor selectively inhibits activation by a particular class II MHC isotype or allotype. Such inhibitors may be capable of suppressing a particular undesirable MHC activity without interfering with all MHC activity in an organism, thereby selectively treating an unwanted immune response in an animal, such as a mammal, preferably a human, without compromising the animal's immune response in general.

[0166] The term "organ-specific protein" or "organ-specific antigen" means proteins that are expressed predominantly or exclusively by cells comprising a certain organ.

[0167] The term "patient" refers to an animal, preferably a mammal, including humans as well as livestock and other veterinary subjects.

[0168] The terms "peptide", "polypeptide" and "protein" are used interchangeably herein. These terms refer to unmodified amino acid chains, and also include minor modifications, such as phosphorylations, glycosylations and lipid modifications. The terms "peptide" and "peptidomimetic" are not mutually exclusive and include substantial overlap.

[0169] A "peptidomimetic" includes any modified form of an amino acid chain, such as a phosphorylation, capping, fatty acid modification and including unnatural backbone and/or side chain structures. As described below, a peptidomimetic comprises the structural continuum between an amino acid chain and a non-peptide small molecule. Peptidomimetics generally retain a recognizable peptide-like polymer unit structure. Thus, a peptidomimetic may retain the function of binding to a HLA protein forming a complex which activates autoreactive T cells in a patient suffering from an autoimmune disease.

[0170] The term "amino acid residue" is known in the art. In general the abbreviations used herein for designating the amino acids and the protective groups are based on recommendations of the IUPAC-IUB Commission on Biochemical Nomenclature (see Biochemistry (1972) 11:1726-1732). In certain embodiments, the amino acids used in the application of this invention are those naturally occurring amino acids found in proteins, or the naturally occurring anabolic or catabolic products of such amino acids which contain amino and carboxyl groups. Particularly suitable amino acid side chains include side chains selected from those of the following amino acids: glycine, alanine, valine, cysteine, leucine, isoleucine, serine, threonine, methionine, glutamic acid, aspartic acid, glutamine, asparagine, lysine, arginine, proline, histidine, phenylalanine, tyrosine, and tryptophan.

[0171] The term "amino acid residue" further includes analogs, derivatives and congeners of any specific amino acid referred to herein, as well as C-terminal or N-terminal protected amino acid derivatives (e.g. modified with an N-terminal or C-terminal protecting group). For example, the present invention contemplates the use of amino acid analogs wherein a side chain is lengthened or shortened while still providing a carboxyl, amino or other reactive precursor functional group for cyclization, as well as amino acid analogs having variant side chains with appropriate functional groups). For instance, the subject compound can include an amino acid analog such as, for example, cyanoalanine, canavanine, djenkolic acid, norleucine, 3-phosphoserine, homoserine, dihydroxy-phenylalanine, 5-hydroxytryptophan, 1-methylhistidine, 3-methylhistidine, diaminopimelic acid, ornithine, or diaminobutyric acid. Other naturally occurring amino acid metabolites or precursors having side chains which are suitable herein will be recognized by those skilled in the art and are included in the scope of the present invention.

[0172] Most of the amino acids used in the DSPs of the present invention may exist in particular geometric or stereoisomeric forms. In preferred embodiments, the amino acids used to form the subject DSPs are (L)-isomers, although (D)-isomers may be included in the DSPs such as at non-anchor positions or in the case of peptidomimetic versions of the DSPs.

[0173] "Prevent", as used herein, means to delay or preclude the onset of, for example, one or more symptoms, of a disorder or condition.

[0174] "Treat", as used herein, means at least lessening the severity or ameliorating the effects of, for example, one or more symptoms, of a disorder or condition.

[0175] "Treatment regimen" as used herein, encompasses therapeutic, palliative and prophylactic modalities of administration of one or more compositions comprising one or more DSP compositions. A particular treatment regimen may last for a period of time at a particular dosing pattern, which will vary depending upon the nature of the particular disease or disorder, its severity and the overall condition of the patient, and may extend from once daily, or more preferably once every 36 hours or 48 hours or longer, to once every month or several months.

[0176] The terms "structure-activity relationship" or "SAR" refer to the way in which altering the molecular structure of drugs alters their interaction with a receptor, enzyme, etc.

[0177] The practice of the present invention will employ, where appropriate and unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, virology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are described in the literature. See, for example, Molecular Cloning: A Laboratory Manual, 3rd Ed., ed. by Sambrook and Russell (Cold Spring Harbor Laboratory Press: 2001); the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Using Antibodies, Second Edition by Harlow and Lane, Cold Spring Harbor Press, New York, 1999; Current Protocols in Cell Biology, ed. by Bonifacino, Dasso, Lippincott-Schwartz, Harford, and Yamada, John Wiley and Sons, Inc., New York, 1999; and PCR Protocols, ed. by Bartlett et al., Humana Press, 2003; PHARMACOLOGY A Pathophysiologic Approach Edited by Josehp T. DiPiro, Robert Talbert, Gary, Yee, Gary Matzke, Barbara Wells, and L. Michael Posey. 5th edition 2002 McGraw Hill; Pathologic Basis of Disease. Ramzi Cotran, Vinay Kumar, Tucker Collins. 6th Edition 1999. Saunders.

EXAMPLE 1

Preparation of a DSP Composition from Fictitious Base Peptides

[0178] For ease of understanding, as an illustration, preparation of a DSP composition deriving from two fictitious peptide sequences, representing a known epitope, is described and shown in the table depicted in FIG. 6. In this illustration, the cassettes consist of five amino acids each, (x1, x2, x3, x4, x5=THMCE in y.sub.1 and PWKNA in y.sub.2). THMCE is defined as having an input ratio of a=7, b=1, c=1, d=1, e=10. PWKNA is defined as having an input ratio of a=1, b=3, c=3, d=3, e=20. For synthesis, the identity of group of amino acids occupying each amino acid position for each peptide is determined using the preferred method of amino acid substitution described by Kosiol et al., J Theoretical Biol. 228:97-106, 2004, as shown in FIG. 4 (or less preferably an equivalent means of systematically altering amino acids), and the overall ratio of amino acids that occupy each of such positions in the resulting collective DSP composition is given above. Each cassette, y.sub.1 and y.sub.2, will twice be repeated two times, generating an order of y.sub.1 y.sub.1 y.sub.2 y.sub.2 y.sub.1 y.sub.1 y.sub.2 y.sub.2. N.sub.n are the number of times the sequence within the cassette is to be repeated, and in our fictitious example N=2. MN can be any type of modifying moiety. MN must be amenable to solid phase synthesis methods. For this fictitious example, a modifying moiety of amino acids that would target the DSP to a certain location within a subject is chosen, such as an RGD-based sequence motif on a particular integrin such as alphaVbeta3. In this example the C-terminal modifier will also be an RGD-based motif, but comprised of D-amino acids.

[0179] The DSP composition as described above is prepared using a solid phase peptide synthesis method as described elsewhere in this disclosure.

EXAMPLE 2

Preparation of a DSP Composition from MBP(83-99)

[0180] Myelin basic protein is implicated in the pathology of multiple sclerosis, and several epitopes have been identified and proven to be relevant in the disease symptoms and progression. One such epitope spans amino acid residues 83 to 99 of myelin basic protein (MBP(83-99). COP-1 is thought to target the same binding pocket of HLA as MBP(83-99) does. A DSP composition is defined and prepared using MBP (83-99) as the base peptide sequence.

[0181] The methods and rules to define the identity of amino acids for each position of the resulting peptides are described above in Example 1. The actual application of such rules are illustrated in the tables of FIG. 8A-B. As with Example 1, the DSP composition is synthesized using a solid phase peptide synthesis method.

[0182] The following references are exemplary sources of epitopes useful as base peptide sequences. Numbers to the left are the reference numbers of Table I. [0183] 1 U.S. Pat. No. 6,930,168--issued Aug. 16, 2005 to Strominger et al. [0184] 2 U.S. Pat. No. 7,118,874--issued Oct. 10, 2006 to Torres [0185] 3 U.S. Publ. No.: 2006/0045888A1--published Mar. 2, 2006 to Punnonen et al. [0186] 4 WO 2005/032482--published Apr. 14, 2005 in the name of Bayhill Therapeutics, Inc. [0187] 5 WO 2005/074579--published Aug. 18, 2005 in the name of Mixture Sciences, Inc. [0188] 6 WO 2006/031727--published Mar. 23, 2006 in the name of President and Fellows of Harvard College [0189] 7 ANDERTON, S., et al., "Activation of T Cells Recognizing Self 60-kD Heat Shock Protein Can Protect Against Experimental Arthritis", J. Exp. Med. Vol. 181, 943-952 (1995). [0190] 8 ANGELINI, G., et al. "Preliminary Data on Pemphigus Vulgaris Treatment by a Proteomics-defined peptide: a case report", Journal of Translational Medicine", 4:43, 1-7 (2006). [0191] 9 ATASSI, M Z, et al., "On the initial trigger of myasthenia gravis and suppression of the disease by antibodies against the MHC peptide region involved in the presentation of a pathogenic T-cell epitope", Crit. Rev Immunol. 21(1-3): 1-27 (2001) (Abstract). [0192] 10 ATKINSON, M., et al., "Cellular immunity to a determinant common to glutamate decarboxylase and coxsackie virus in insulin dependent diabetes", J Clin Invest., Vol. 94, 2125-2129 (1994). [0193] 11 BENACERRAF, B., "The role of MHC gene products in immune regulation and its relevance to alloreactivity", Nobel Lecture, Harvard Medical School, 597-623 (1980). [0194] 12 BENAGIANO, M., et al., "Human 60-kDa heat shock protein is a target autoantigen of T cells derived form atherosclerotic plaques", The Journal of Immunology, 174: 6509-6517, (2005). [0195] 13 BIAN, H., etl al., "The use of bioinformatics for identifying class II-restricted T-cell epitopes", Methods 29, 299-309, (2003) [0196] 14 BOOG, C., et al., "Two monoclonal antibodies generated against human hsp60 show reactivity with synovial membranes of patients with juvenile chronic arthritis", J. Exp. Med., Vol. 175, 1805-1810, (1992). [0197] 15 DESHMUKH, U., et al., "Ro60 peptides induce antibodies to similar epitopes shared among lupus-related autoantigens", The Journal of Immunology, 164: 6655-6661 (2000). [0198] 16 EREZ-ALON, N., et al., Immunity to p53 induced by an idiotypic network of anti-p53 antibodies: generation of sequence-specific anti-DNA antibodies and protection form tumor metastasis", Cancer Research, 58, 5447-5452 (1998). [0199] 17 FRANCIS, J., et al., "Peptide-based vaccination: where do we stand", Curr Opin Allergy Clin Immunol 5:537-543 (2005). [0200] 18 FREESE, A., et al., "HLA-B7 B-pleated sheet-derived synthetic peptides are immunodominant T-cell epitopes regulating alloresponces", Blood, Vol. 99, No. 9, 3286-3292 (2002). [0201] 19 GODKINS, A., et al., "Use of eluted peptide sequence data to identify the binding characteristics of peptides to the insulin-dependent diabetes susceptibility allele HLA-DQ8 (DQ 3.2)", International Immunology, Vol. 9, No. 6, pp 905-911, (1997) [0202] 20 KOSMOPOULOU, A., "T-cell Epitopes of the La/SSB Autoantigen: Prediction Based on the Homology Modeling of HLA-DQ2/DQ7 with the Insulin-B Peptide/HLA-DQ8 Complex", Journal of Computational Chemistry, Vol 27, No. 9, pp 1033-1044, (2006) [0203] 21 LIN, M., et al., "Development and Characterization of Desmoglein-3 Specific T Cells from Patients and Pemphigus Vulgaris", J. Clin. Invest., Vol. 99, No. 1, 31-40 (1997). [0204] 22 LIN, Q., et al., "Genetic dissection of the effects of stimulatory and inhibitory IgG Fc receptors on murine lupus", The Journal of Immunology, 177: 1646-1655 (2006). [0205] 23 LU, Y., et al., "Identification of Kinectin as a Novel Behcet's Disease Autoantigen", Arthritis Res. Ther. 2005; 7(5):R1133-R1139, (2005), [0206] 24 MAYNARD, J., et al., "Structure of an Autoimmune T Cell Receptor Complexed with Class II Peptide-MHC: Insights into MHC Bias and Antigen Specificity", Immunity, Vol. 22, 81-92 (2005). [0207] 25 MEINL, E., et al., "Genetic dissection of the effects of stimulatory and inhibitory IgG Fc receptors on murine lupus", J. Clin. Invest., Vol. 92, 2633-2643 (1993). [0208] 26 MINOTA, S., et al., "Autoantibodies to the constitutive 73-kD member of the hsp70 family of heat shock proteins in systemic lupus erythematosus", J. Exp. Med., Vol. 168, 1475-1480 (1988). [0209] 27 MULLER, R., et al. "IgG reactivity against non-conformational NH.sub.2-terminal epitopes of the desmoglein 3 ectodomain relates to clinical activity and phenotype of pemphigus vularis", Experimental Dermatology, 15: pp. 606-614, (2006) [0210] 28 PAL, R., et al., "Evidence for multiple shared antigenic determinants within Ro60 and other Lupus-related ribonucleoprotein autoantigens in human autoimmune responses", The Journal of Immunology, 175: 7669-7677 (2005). [0211] 29 PAPASSAVAS, A. C., "HLA peptide-mediated strategies for 29 modulation of cellular and humoral immune responses in transplantation", Current Pharmacogenomics, Vol. 1, No. 1, 17-36 (2003). [0212] 30 PEDOTTI, R., et al., "Severe anaphylactic reactions to glutamic acid 30 decarboxylase (GAD) self peptides in NOD mice that spontaneously develop autoimmune type 1 diabetes mellitus", BMC Immunology, 4:2 (2003). [0213] 31 PINCHUK, P., et al., "Antigenicity of polypeptides (poly alpha amino acids)", Microbiology Department, New Jersey College of Medicine and Dentistry, 673-679 (1965). [0214] 32 PINILLA, C., et al., "Advances in the use of synthetic combinatorial chemistry: Mixture-based libraries", Nature Medicine, Vol. 9, No. 1, pp. 118-126, (2003). [0215] 33 QUANDT, J. S. et al., "Peptidic complex mistures as therapeutic agents in CNS autoimmunity", Molecular Immunology, 40:1075-1087, (2004). [0216] 34 QUINTANA, F., et al., "DNA fragments of the human 60-kDa heat shock protein (HSP60) vaccinate against adjuvant arthritis: identification of a regulatory HSP60 peptide", The Journal of Immunology, 171: 3533-3541 (2003). [0217] 35 RAGJEB, et. al., "Myasthenia gravis patients, but not healthy subjects, recognize epitopes that are unique to the epsilon-subunit of the acetylcholine receptor." J. Neuroimmunol. 2005 February; 159(1-2): 137-45. Epub 2004 Nov. 23 [0218] 36 RAZ, R., et al., "B-cell function in new-onset type diabetes and immunomodulation with heat-shock protein peptide (DiaPep27): a randomised, double-blind, phase II trial", The Lancet, Vol. 358, 1749-1753 (2001). [0219] 37 ROSLONIEC, E., et al., "HLA-DR1 (DRB1*0101) and DR4 (DRB1*0401) Use the Same Anchor Residues for Binding an Immunodominant Peptide Derived from Human Type II Collagen", The Journal of Immunology, 168:253-259, (2002) [0220] 38 SAKURAI, Y. et al., "Analog Peptides of type II collagen can suppress arthritis in HLA-DR4 (DRB1*0401) transgenic mice", Arthritis Research & Therapy, 8:R150, (2006) [0221] 39 SCHWARZ, M., et al., "Antibodies to heat shock proteins in schizophrenic patients: Implications for the mechanism of the disease", Am J Psychiatry 156:7, 1103-1104 (1999). [0222] 40 SEKIGUCHI, M., et al., "Dominant Autoimmune Epitopes Recognized by Pemphigus Antibodies Map to the N-Terminal.Adhesive Region of Desmogleins", The Journal of Immunology, 167:5439-5448 (2001). [0223] 41 STERN, Joel N. H., et al., "Peptide 15-mers of defined sequence that substitute for random amino acid copolymers in amelioration of experimental autoimmune encephalomyelitis", PNAS, 102:5, (2005) [0224] 42 ULMANSKY, R., et al., "Resistance to adjuvant arthritis is due to protective antibodies against heat shock protein surface epitopes and the induction of IL-10 secretion", The Journal of Immunology, 168: 6463-6469 (2002). [0225] 43 VAN ROON, J., et al., "Stimulation of suppressive T cell responses by human but not bacterial 60-kD heat-shock protein in synovial fluid of patients with rheumatoid arthritis", J. Clin. Invest., Vol. 1100, No. 2, 459-463 (1997). [0226] 44 VELDMAN, C., et al., "Detection of Low Avidity Desmoglein 3-reactive T cells in pemphigus vulgaris using HLA-DR-beta*0402 tetramers", Clinical Immunology, 1-8 (2006) [0227] 45 VELDMAN, C., et al., "T Cell Recognition of Desmoglein 3 peptides in Patients with Pemphigus Vulgaris and Healthy Individuals", The Journal of Immunology, 172: 3883-3892 (2004). [0228] 46 WILSON, D., "GAD-about BDC2.5: Peptides that stimulate BDC2.5 T cells and inhibit IDDM", Journal of Autoimmunity 20, 199-201 (2003). [0229] 47 WILSON, D. et al, "Specificity and degeneracy of T cells", Molecular Immunology 40:1047-1055, (2004) [0230] 48 WUCHERPFENNIG, K., et al., "Structural basis for major histocompatibility complex (MHC)-- linked susceptibility to autoimmunity: Charged residues of a single MHC binding pocket confer selective presentation of self-peptides in pemphigus vulgaris", Proc. Natl. Acad. Sci. USA, Vol. 92, 11935-11939 (1995). [0231] 49 WUCHERPFENNIG, K., et al., "Structural requirements for binding of an immunodominant myelin basic protein peptide to DR2 isotypes and for its recognition by human T cell clones" J. Exp. Med., Vol. 179, 279-290 (1994). [0232] 50 YURASOV, S., et al., "Persistent expression of autoantibodies in SLE patients in remission", The Journal of Experimental Medicine", Vol. 203, No. 10, 2255-2261 (2006).

[0233] The contents of any patents, patent applications, patent publications, or scientific articles referenced anywhere in this application are herein incorporated in their entirety.

TABLE-US-00002 Sequence Listings in addition to Table I SEQ ID NO: 190 HSP-60 (human): MLRLPTVFRQ MRPVSRVLAP HLTRAYAKDV KFGADARALM LQGVDLLADA VAVTMGPKGR TVIIEQSWGS PKVTKDGVTV AKSIDLKDKY KNIGAKLVQD VANNTNEEAG DGTTTATVLA RSIAKEGFEK ISKGANPVEI RRGVMLAVDA VIAELKKQSK PVTTPEEIAQ VATISANGDK EIGNIISDAM KKVGRKGVIT VKDGKTLNDE LEIIEGMKFD RGYISPYFIN TSKGQKCEFQ DAYVLLSEKK ISSIQSIVPA LEIANAHRKP LVIIAEDVDG EALSTLVLNR LKVGLQVVAV KAPGFGDNRK NQLKDMAIAT GGAVFGEEGL TLNLEDVQPH DLGKVGEVIV TKDDANLLKG KGDKAQIEKR IQEIIEQLDV TTSEYEKEKL NERLAKLSDG VAVLKVGGTS DVEVNEKKDR VTDALNATRA AVEEGIVLGG GCALLRCIPA LDSLTPANED QKIGIEIIKR TLKIPAMTIA KNAGVEGSLI VEKIMQSSSE VGYDAMAGDF VNMVEKGIID PTKVVRTALL DAAGVASLLT TAEVVVTEIP KEEKDPGMGA MGGMGGGMGG GMF SEQ ID NO: 191 HSP-70 (human): MAKAAAIGID LGTTYSCVGV FQHGKVEIIA NDQGNRTTPS YVAFTDTERL IGDAAKNQVA LNPQNTVFDA KRLIGRKFGD PVVQSDMKHW PFQVINDGDK PKVQVSYKGE TKAFYPEEIS SMVLTKMKEI AEAYLGYPVT NAVITVPAYF NDSQRQATKD AGVIAGLNVL RIINEPTAAA IAYGLDRTGK GERNVLIFDL GGGTFDVSIL TIDDGIFEVK ATAGDTHLGG EDFDNRLVNH FVEEFKRKHK KDISQNKRAV RRLRTACERA KRTLSSSTQA SLEIDSLFEG IDFYTSITRA RFEELCSDLF RSTLEPVEKA LRDAKLDKAQ IHDLVLVGGS TRIPKVQKLL QDFFNGRDLN KSINPDEAVA YGAAVQAAIL MGDKSENVQD LLLLDVAPLS LGLETAGGVM TALIKRNSTI PTKQTQIFTT YSDNQPGVLI QVYEGERAMT KDNNLLGRFE LSGIPPAPRG VPQIEVTFDI DANGILNVTA TDKSTGKANK ITITNDKGRL SKEEIERMVQ EAEKYKAEDE VQRERVSAKN ALESYAFNMK SAVEDEGLKG KISEADKKKV LDKCQEVISW LDANTLAEKD EFEHKRKELE QVCNPIISGL YQGAGGPGPG GFGAQGPKGG SGSGPTIEEV D SEQ ID NO: 192 HSP-90 alpha (human): PEETQTQDQP MEEEEVETFA FQAEIAQLMS LIINTFYSNK EIFLRELISN SSDALDKIRY ESLTDPSKLD SGKELHINLI PNKQDRTLTI VDTGIGMTKA DLINNLGTIA KSGTKAFMEA LQAGADISMI GQFGVGFYSA YLVAEKVTVI TKHNDDEQYA WESSAGGSFT VRTDTGEPMG RGTKVILHLK EDQTEYLEER RIKEIVKKHS QFIGYPITLF VEKERDKEVS DDEAEEKEDK EEEKEKEEKE SEDKPEIEDV GSDEEEEKKD GDKKKKKKIK EKYIDQEELN KTKPIWTRNP DDITNEEYGE FYKSLTNDWE DHLAVKHFSV EGQLEFRALL FVPRRAPFDL FENRKKKNNI KLYVRRVFIM DNCEELIPEY LNFIRGVVDS EDLPLNISRE MLQQSKILKV IRKNLVKKCL ELFTELAEDK ENYKKFYEQF SKNIKLGIHE DSQNRKKLSE LLRYYTSASG DEMVSLKDYC TRMKENQKHI YYITGETKDQ VANSAFVERL RKHGLEVIYM IEPIDEYCVQ QLKEFEGKTL VSVTKEGLEL PEDEEEKKKQ EEKKTKFENL CKIMKDILEK KVEKVVVSNR LVTSPCCIVT STYGWTANME RIMKAQALRD NSTMGYMAAK KHLEINPDHS IIETLRQKAE ADKNDKSVKD LVILLYETAL LSSGFSLEDP QTHANRIYRM IKLGLGIDED DPTADDTSAA VTEEMPPLEG DDDTSRMEEV D SEQ ID NO: 193 HSP-90 beta (human): PEEVHHGEEE VETFAFQAEI AQLMSLIINT FYSNKEIFLR ELISNASDAL DKIRYESLTD PSKLDSGKEL KIDIIPNPQE RTLTLVDTGI GMTKADLINN LGTIAKSGTK AFMEALQAGA DISMIGQFGV GFYSAYLVAE KVVVITKHND DEQYAWESSA GGSFTVRADH GEPIGRGTKV ILHLKEDQTE YLEERRVKEV VKKHSQFIGY PITLYLEKER EKEISDDEAE EEKGEKEEED KDDEEKPKIE DVGSDEEDDS GKDKKKKTKK IKEKYIDQEE LNKTKPIWTR NPDDITQEEY GEFYKSLTND WEDHLAVKHF SVEGQLEFRA LLFIPRRAPF DLFENKKKKN NIKLYVRRVF IMDSCDELIP EYLNFIRGVV DSEDLPLNIS REMLQQSKIL KVIRKNIVKK CLELFSELAE DKENYKKFYE AFSKNLKLGI HEDSTNRRRL SELLRYHTSQ SGDEMTSLSE YVSRMKETQK SIYYITGESK EQVANSAFVE RVRKRGFEVV YMTEPIDEYC VQQLKEFDGK SLVSVTKEGL ELPEDEEEKK KMEESKAKFE NLCKLMKEIL DKKVEKVTIS NRLVSSPCCI VTSTYGWTAN MERIMKAQAL RDNSTMGYMM AKKHLEINPD HPIVETLRQK AEADKNDKAV KDLVVLLFET ALLSSGFSLE DPQTHSNRIY RMIKLGLGID EDEVAAEEPN AAVPDEIPPL EGDEDASRME EVD SEQ ID NO: 194 GAD65 (human) MASPGSGFWS FGSEDGSGDS ENPGTARAWC QVAQKFTGGI GNKLCALLYG DAEKPAESGG SQPPRAAARK AACACDQKPC SCSKVDVNYA FLHATDLLPA CDGERPTLAF LQDVMNILLQ YVVKSFDRST KVIDFHYPNE LLQEYNWELA DQPQNLEEIL MHCQTTLKYA IKTGHPRYFN QLSTGLDMVG LAADWLTSTA NTNMFTYEIA PVFVLLEYVT LKKMRETTGW PGGSGDGIFS PGGAISNMYA MMIARFKMFP EVKEKGMAAL PRLIAFTSEH SHFSLKKGAA ALGIGTDSVI LIKCDERGKM IPSDLERRIL EAKQKGFVPF LVSATAGTTV YGAFDPLLAV ADICKKYKIW MHVDAAWGGG LLMSRKHKWK LSGVERANSV TWNPHKMMGV PLQCSALLVR EEGLMQNCNQ MHASYLFQQD KHYDLSYDTG DKALQCGRHV DVFKLWLMWR AKGTTGFEAH VDKCLELAEY LYNIIKNREG YEMVFDGKPQ HTNVCFWYIP PSLRTLEDNE ERMSRLSKVA PVIKARNMEY GTTMVSYQPL GDKVNFFRMV ISNPAATHQD IDELIEEIER LGQDL SEQ ID NO: 195 Ro60 (human) MEESVNQMQP LNEKQIANSQ DGYVWQVTDM NRLHRFLCFG SEGGTYYIKE QKLGLENAEA LIRLIEDGRG CEVIQEIKSF SQEGRTTKQE PMLFALAICS QCSDISTKQA AFKAVSEVCR IPTHLFTFIQ FKKDLKESMK CGMWGRALRK AIADWYNEKG GMALALAVTK YKQRNGWSHK DLLRLSHLKP SSEGLAIVTK YITKGWKEVH ELYKEKALSV ETEKLLKYLE AVEKVKRTRD ELEVIHLIEE HRLVREHLLT NHLKSKEVWK ALLQEMPLTA LLRNLGKMTA NSVLEPGNSE VSLVCEKLCN EKLLKKARIH PFHILTALET YKTGHGLRGK LKWRPDEEIL KALDAAFYKT FKTVEPTGKR FLLAVDVSAS MNQRVLGSIL NASTVAAAMC MVVTRTEKDS YVVAFSDEMV PCPVTTDMTL QQVLMAMSQI PAGGTDCSLP MIWAQKTNTP ADVFIVFTDN ETFAGGVHPA IALREYRKKM DIPAKLIVCG MTSNGFTIAD PDDRALQNTL LNKSF SEQ ID NO: 196 HLA DQ2 ALPHA CHAIN VADHVASYGV NLYQSYGPSG QYTHEFDGDE QFYVDLGRKE TVWCLPELRQ FRGFDPQFAL TNIAVLKHNL NSLIKRSNST AATNEVPEVT VFSKSPVTLG QPNTLICLVD NIFPPVVNIT WLTNGHSVTE GVSETTFLSK SDHSFFKISY LTLLPSAEES YDCKVEHWGL DKPLLKHWEP E SEQ ID NO: 197 HLA DQ2 BETA CHAIN SPEDEVYQFK GMCYFTNGTE RVRLVSRSIY NREEIVRFDS DVGEFRAVTL LGLPAAEYWN SQKDILERKR AAVDRVCRHN YQLELRTTLQ RRVEPTVTIS PSRTEALNHH NLLVCSVTDF YPAQIKVRWF RKDQEETAGV VSTPLIRNGD WTFQILVMLE MTPQRGDVYT CHVEHPSLQS PITVEWRAQS SEQ ID NO: 198 HLA DQ7 ALPHA CHAIN VADHVASYGV NLYQSYGPSG QYTHEFDGDE QFYVDLGRKE TVWCLPELRQ FRGFDPQFAL TNIAVLKHNL NSLIKRSNST AATNEVPEVT VFSKSPVTLG QPNTLICLVD NIFPPVVNIT WLTNGHSVTE GVSETTFLSK SDHSFFKISY LTLLPSAEES YDCKVEHWGL DKPLLKHWEP E SEQ ID NO: 199 HLA DQ7 BETA CHAIN SPEDFVYQFK AMCYFTNGTE RVYVTRYIYN REEYARFDSD VEVYRAVTPL GPPDAEYWNS QKEVLERTRA ELDTVCRHNY QLELRTTLQR RVEPTVTISP SRTEALNHHN LLVCSVTDFY PAQIKVRWFR NDQEETTGVV STPLIRNGDW TFQILVMLEM TPQHGDVYTC HVEHPSLQNP ITVEWRAQS SEQ ID NO: 200 HLA DQS ALPHA CHAIN VADHVASYGV NLYQSYGPSG QYSHEFDGDE EFYVDLERKE TVWQLPLFRR FRRFDPQFAL TNIAVLKHNL NIVIKRSNST AATNEVPEVT VFSKSPVTLG QPNTLICLVD NIFPPVVNIT WLSNGHSVTE GVSETSFLSK SDHSFFKISY LTFLPSDDEI YDCKVEHWGL DEPLLKHWEP E SEQ ID NO: 201 HLA DQ8 BETA CHAIN SPEDFVYQFK GMCYFTNGTE RVRLVTRYIY NREEYARFDS DVGVYRAVTP LGPPAAEYWN SQKEVLERTR AELDTVCRHN YQLELRTTLQ RRVEPTVTIS PSRTEALNHH NLLVCSVTDF YPAQIKVRWF RNDQEETTAG VVSTPLIRNG DWTFQILVML EMTPQRGDVY TCHVEHPSLQ NPIIVEWRAQ S SEQ ID NO: 202 Human myelin oligodendrocyte glycoprotein (MOG) QFRVIGPRHP IRALVGDEVE LPCRISPGKN ATGMEVGWYR PPFSRVVHLY RNGKDQDGDQ APEYRGRTEL LKDAIGEGKV TLRIRNVRFS DEGGFTCFFR DHSYQEEAAM ELKVEDPFYW VSPGVLVLLA VLPVLLLQIT VGLVFLCLQY RLRGKLRAEI ENLHRTFGQF LEELRNPF SEQ ID NO: 203 Human Myelin-associated oligodendrocyte basic protein MSQKPAKEGP RLSKNQKYSE HFSIHCCPPF TFLNSKKEIV DRKYSICKSG CFYQKKEEDW ICCACQKTRL KRKIRPTPKK K SEQ ID NO: 204 HUMAN DESMOGLEIN 3 PREPROPROTEIN MMGLFPRTTG ALAIFVVVIL VHGELRIETK GQYDEEEMTM QQAKRRQKRE WVKFAKPCRE GEDNSKRNPI AKITSDYQAT QKITYRISGV GIDQPPFGIF VVDKNTGDIN ITAIVDREET PSFLITCRAL NAQGLDVEKP LILTVKILDI NDNPPVFSQQ IFMGEIEENS ASNSLVMILN ATDADEPNHL NSKIAFKIVS QEPAGTPMFL LSRNTGEVRT LTNSLDREQA SSYRLVVSGA DKDGEGLSTQ CECNIKVKDV NDNFPMFRDS QYSARIEENI LSSELLRFQV TDLDEEYTDN WLAVYFFTSG NEGNWFEIQT DPRTNEGILK VVKALDYEQL QSVKLSIAVK NKAEFHQSVI SRYRVQSTPV TIQVINVREG IAFRPASKTF TVQKGISSKK LVDYILGTYQ AIDEDTNKAA SNVKYVMGRN DGGYLMIDSK TAEIKFVKNM NRDSTFIVNK TITAEVLAID EYTGKTSTGT VYVRVPDFND NCPTAVLEKD AVCSSSPSVV VSARTLNNRY TGPYTFALED QPVKLPAVWS ITTLNATSAL LRAQEQIPPG VYHISLVLTD SQNNRCEMPR SLTLEVCQCD NRGICGTSYP TTSPGTRYGR PHSGRLGPAA IGLLLLGLLL LLLAPLLLLT CDCGAGSTGG VTGGFIPVPD GSEGTIHQWG IEGAHPEDKE ITNICVPPVT ANGADFMESS EVCTNTYARG TAVEGTSGME MTTKLGAATE SGGAAGFATG TVSGAASGFG AATGVGICSS GQSGTMRTRH STGGTNKDYA DGAISMNFLD SYFSQKAFAC AEEDDGQEAN DCLLIYDNEG ADATGSPVGS VGCCSFIADD LDDSFLDSLG PKFKKLAEIS LGVDGEGKEV QPPSKDSGYG IESCGHPIEV QQTGFVKCQT LSGSQGASAL STSGSVQPAV SIPDPLQHGN YLVTETYSAS GSLVQPSTAG FDPLLTQNVI VTERVICPIS SVPGNLAGPT QLRGSHTMLC TEDPCSRLI

Sequence CWU 1

1

240139PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 1Lys Ser Tyr Cys Glu Ile Ile Val Thr His Phe Pro Phe Asp Glu Gln1 5 10 15Asn Cys Ser Met Lys Leu Gly Thr Trp Thr Tyr Asp Gly Ser Val Val20 25 30Ala Thr Asn Pro Glu Ser Asp35226PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 2Met Lys Ser Asp Gln Glu Ser Asn Asn Ala Ala Ala Glu Trp Lys Tyr1 5 10 15Val Ala Met Val Met Asp His Ile Leu Leu20 2538PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 3Phe Lys Gly Glu Gln Gly Pro Lys1 5420PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 4Pro Lys Gly Gln Thr Gly Glu Asx Gly Ile Ala Gly Phe Lys Gly Glu1 5 10 15Gln Gly Pro Lys20521PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 5Gly Glu Asx Gly Ile Ala Gly Phe Lys Gly Glu Gln Gly Pro Lys Gly1 5 10 15Glu Asx Gly Pro Ala20631PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 6Glu Val Gly Glu Leu Ser Arg Gly Lys Leu Tyr Ser Leu Gly Asn Gly1 5 10 15Arg Trp Met Leu Thr Leu Ala Lys Asn Met Glu Val Arg Ala Ile20 25 30733PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 7Gly Asn Gly Arg Trp Met Leu Thr Leu Ala Lys Asn Met Glu Val Arg1 5 10 15Ala Ile Phe Thr Gly Tyr Tyr Gly Lys Gly Lys Pro Val Pro Thr Gln20 25 30Gly810PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 8Ala Ser Gln Lys Arg Pro Ser Gln Arg His1 5 10919PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 9Leu Ser Arg Phe Ser Trp Gly Ala Glu Gly Gln Arg Pro Gly Phe Gly1 5 10 15Tyr Gly Gly1015PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 10Ala Ser Asp Tyr Lys Ser Ala His Lys Gly Phe Lys Gly Val Asp1 5 10 151125PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 11Ala Ser Asp Tyr Lys Ser Ala His Lys Gly Leu Lys Gly Val Asp Ala1 5 10 15Gln Gly Thr Leu Ser Lys Ile Phe Lys20 251220PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 12Lys Tyr Leu Ala Thr Ala Ser Thr Met Asp His Ala Arg His Gly Phe1 5 10 15Leu Pro Arg His201315PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 13Lys Gly Phe Lys Gly Val Asp Ala Gln Gly Thr Leu Ser Lys Ile1 5 10 151425PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 14Ala Gln Gly Thr Leu Ser Lys Ile Phe Lys Leu Gly Gly Arg Asp Ser1 5 10 15Arg Ser Gly Ser Pro Met Ala Arg Arg20 251515PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 15Gly Thr Leu Ser Lys Ile Phe Lys Leu Gly Gly Arg Asp Ser Arg1 5 10 151616PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 16Ser His Gly Arg Thr Gln Asp Glu Asn Pro Val Val His Phe Phe Lys1 5 10 151725PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 17Tyr Gly Arg Thr Gln Asp Glu Asn Pro Val Val His Phe Phe Lys Asn1 5 10 15Ile Val Thr Pro Arg Thr Pro Pro Pro20 251817PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 18Glu Asn Pro Val Val His Phe Phe Lys Asn Ile Val Thr Pro Arg Thr1 5 10 15Pro1919PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 19Asp Glu Asn Pro Val Val His Phe Phe Lys Asn Ile Val Thr Pro Arg1 5 10 15Thr Pro Pro2015PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 20Glu Asn Pro Val Val His Phe Phe Lys Asn Ile Val Thr Pro Arg1 5 10 152120PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 21Val Val His Phe Phe Lys Asn Ile Val Thr Pro Arg Thr Pro Pro Pro1 5 10 15Ser Gln Gly Lys202219PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 22Phe Ser Ile His Cys Cys Pro Pro Phe Thr Phe Asn Asn Ser Lys Lys1 5 10 15Glu Ile Val2319PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 23Phe Leu Asn Ser Lys Lys Glu Ile Val Asp Arg Lys Tyr Ser Ile Cys1 5 10 15Lys Ser Gly2420PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 24Cys Gln Phe Arg Val Ile Gly Pro Arg His Pro Ile Arg Ala Leu Val1 5 10 15Gly Asp Glu Val202520PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 25Pro Ile Arg Ala Leu Val Gly Asp Glu Val Glu Leu Pro Cys Arg Ile1 5 10 15Ser Pro Gly Lys202620PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 26Glu Leu Pro Cys Arg Ile Ser Pro Gly Lys Asn Ala Thr Gly Met Glu1 5 10 15Val Gly Trp Tyr202721PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 27Met Glu Val Gly Trp Tyr Arg Pro Pro Phe Ser Arg Val Val His Leu1 5 10 15Tyr Arg Asn Gly Lys202813PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 28His Ser Leu Gly Lys Trp Leu Gly His Pro Asp Lys Phe1 5 102916PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 29His Cys Leu Gly Lys Trp Leu Gly His Pro Asp Lys Phe Val Gly Ile1 5 10 153020PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 30Asn Thr Trp Thr Thr Cys Gln Ser Ile Ala Phe Pro Ser Lys Thr Ser1 5 10 15Ala Ser Ile Gly203120PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 31Ser Lys Thr Ser Ala Ser Ile Gly Ser Leu Cys Ala Asp Ala Arg Met1 5 10 15Tyr Gly Val Leu203218PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 32Gly Phe Tyr Thr Thr Gly Ala Val Arg Gln Ile Phe Gly Asp Tyr Lys1 5 10 15Thr Thr3312PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 33Arg Glu Trp Val Lys Phe Ala Lys Pro Cys Arg Glu1 5 103417PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 34Gln Ala Thr Gln Lys Ile Thr Tyr Arg Ile Ser Gly Val Gly Ile Asp1 5 10 15Gln3517PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 35Pro Phe Gly Ile Phe Val Val Asp Lys Asn Thr Gly Asp Ile Asn Ile1 5 10 15Thr3617PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 36His Leu Asn Ser Lys Ile Ala Phe Lys Ile Val Ser Gln Glu Pro Ala1 5 10 15Gly3717PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 37Gly Thr Pro Met Phe Leu Leu Ser Arg Asn Thr Gly Glu Val Arg Thr1 5 10 15Leu3817PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 38Gln Cys Glu Cys Asn Ile Lys Val Lys Asp Val Asn Asp Asn Phe Pro1 5 10 15Met3917PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 39Ser Val Lys Leu Ser Ile Ala Val Lys Asn Lys Ala Glu Phe His Gln1 5 10 15Ser4017PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 40Asn Val Arg Glu Gly Ile Ala Phe Arg Pro Ala Ser Lys Thr Phe Thr1 5 10 15Val4117PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 41Arg Asp Ser Thr Phe Ile Val Asn Lys Thr Ile Thr Ala Glu Val Leu1 5 10 15Ala4215PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 42Ser Ala Arg Thr Leu Asn Asn Arg Tyr Thr Gly Pro Tyr Thr Phe1 5 10 154315PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 43Gln Ser Gly Thr Met Arg Thr Arg His Ser Thr Gly Gly Thr Asn1 5 10 154420PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 44Ala Ala Leu Gly Ile Gly Thr Asp Ser Val Ile Leu Ile Lys Cys Asp1 5 10 15Glu Arg Gly Lys204520PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 45Ala Phe Thr Ser Glu His Ser His Phe Ser Leu Lys Lys Gly Ala Ala1 5 10 15Ala Leu Gly Ile204620PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 46Ala Thr His Gln Asp Ile Asp Phe Leu Ile Glu Glu Ile Glu Arg Leu1 5 10 15Gly Gln Asp Leu204710PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 47Ala Val Arg Pro Leu Trp Val Arg Met Glu1 5 104811PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 48Ala Tyr Val Arg Pro Leu Trp Val Arg Met Glu1 5 104921PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 49Cys Gly Arg His Val Asp Val Phe Lys Leu Trp Leu Met Trp Arg Ala1 5 10 15Lys Gly Thr Thr Gly205020PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 50Asp Glu Arg Gly Lys Met Ile Pro Ser Asp Leu Glu Arg Arg Ile Leu1 5 10 15Glu Ala Lys Gln205123PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 51Asp Ile Cys Lys Lys Tyr Lys Ile Trp Met His Val Asp Ala Ala Trp1 5 10 15Gly Gly Gly Leu Leu Met Ser205220PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 52Asp Met Val Gly Leu Ala Ala Asp Trp Leu Thr Ser Thr Ala Asn Thr1 5 10 15Asn Met Phe Thr205320PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 53Glu Glu Ile Leu Met His Cys Gln Thr Thr Leu Lys Tyr Ala Ile Lys1 5 10 15Thr Gly His Pro205422PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 54Glu Leu Leu Gln Glu Tyr Asn Trp Glu Leu Ala Asp Gln Pro Gln Asn1 5 10 15Leu Glu Glu Ile Leu Met205520PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 55Glu Arg Ala Asn Ser Val Thr Trp Asn Pro His Lys Met Met Gly Val1 5 10 15Pro Leu Gln Cys205620PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 56Glu Tyr Gly Thr Thr Met Val Ser Tyr Gln Pro Leu Gly Asp Lys Val1 5 10 15Asn Phe Phe Arg205720PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 57Glu Tyr Leu Tyr Asn Ile Ile Lys Asn Arg Glu Gly Tyr Glu Met Val1 5 10 15Phe Asp Gly Lys205820PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 58Glu Tyr Val Thr Leu Lys Lys Met Arg Glu Ile Ile Gly Trp Pro Gly1 5 10 15Gly Ser Gly Asp205920PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 59Gly Gly Ser Gly Asp Gly Ile Phe Ser Pro Gly Gly Ala Ile Ser Asn1 5 10 15Met Tyr Ala Met206020PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 60Gly Leu Leu Met Ser Arg Lys His Lys Trp Lys Leu Ser Gly Val Glu1 5 10 15Arg Ala Asn Ser206123PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 61Gly Ser Gly Asp Ser Glu Asn Pro Gly Thr Ala Arg Ala Trp Cys Gln1 5 10 15Val Ala Gln Lys Phe Thr Gly206220PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 62His Ala Thr Asp Leu Leu Pro Ala Cys Asp Gly Glu Arg Pro Thr Leu1 5 10 15Ala Phe Leu Gln206320PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 63Ile Pro Pro Ser Leu Arg Thr Leu Glu Asp Asn Glu Glu Arg Met Ser1 5 10 15Arg Leu Ser Lys206422PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 64Lys Gly Thr Thr Gly Phe Glu Ala His Val Asp Lys Cys Leu Glu Leu1 5 10 15Ala Glu Tyr Leu Tyr Asn206520PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 65Lys His Tyr Asp Leu Ser Tyr Asp Thr Gly Asp Lys Ala Leu Gln Cys1 5 10 15Gly Arg His Val206620PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 66Lys Pro Cys Ser Cys Ser Lys Val Asp Val Asn Tyr Ala Phe Leu His1 5 10 15Ala Thr Asp Leu206720PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 67Lys Thr Gly His Pro Arg Tyr Phe Asn Gln Leu Ser Thr Gly Leu Asp1 5 10 15Met Val Gly Leu206812PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 68Lys Val Ala Pro Val Ile Lys Ala Arg Met Met Glu1 5 106912PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 69Lys Val Ala Pro Val Trp Val Ala Arg Met Met Glu1 5 107010PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 70Lys Val Ala Pro Val Trp Val Arg Met Glu1 5 107122PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 71Leu Ala Phe Leu Gln Asp Val Met Asn Ile Leu Leu Gln Tyr Val Val1 5 10 15Lys Ser Phe Asp Arg Ser207220PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 72Leu Glu Ala Lys Gln Lys Gly Phe Val Pro Phe Leu Val Ser Ala Thr1 5 10 15Ala Gly Thr Thr207320PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 73Leu Leu Tyr Gly Asp Ala Glu Lys Pro Ala Glu Ser Gly Gly Ser Gln1 5 10 15Pro Pro Arg Ala207416PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 74Leu Ser Lys Val Ala Pro Val Ile Lys Ala Arg Met Met Glu Tyr Gly1 5 10 157520PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 75Met Ala Ser Pro Gly Ser Gly Phe Trp Ser Phe Gly Ser Glu Asp Gly1 5 10 15Ser Gly Asp Ser207620PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 76Asn Met Tyr Ala Met Met Ile Ala Arg Phe Lys Met Phe Pro Glu Val1 5 10 15Lys Glu Lys Gly207720PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 77Pro Glu Val Lys Glu Lys Gly Met Ala Ala Leu Pro Arg Leu Ile Ala1 5 10 15Phe Thr Ser Glu207810PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 78Gln His Arg Pro Leu Trp Val Arg Met Glu1 5 107920PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 79Gln Lys Phe Thr Gly Gly Ile Gly Ile Gly Asn Lys Leu Cys Ala Leu1 5 10 15Leu Tyr Gly Asp208020PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 80Gln Asn Cys Asn Gln Met His Ala Ser Tyr Leu Phe Gln Gln Asp Lys1 5 10 15His Tyr Asp Leu208121PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 81Gln Pro Pro Arg Ala Ala Ala Arg Lys Ala Ala Cys Ala Cys Asp Gln1 5 10 15Lys Pro Cys Ser Cys208210PRTArtificial SequenceDescription of

Artificial Sequence Synthetic peptide 82Arg Thr Arg Pro Leu Trp Val Arg Met Glu1 5 108310PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 83Arg Val Leu Pro Leu Trp Val Arg Met Glu1 5 108420PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 84Ser Phe Asp Arg Ser Thr Lys Val Ile Asp Phe His Tyr Pro Asn Glu1 5 10 15Leu Leu Gln Glu208520PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 85Ser Arg Leu Ser Lys Val Ala Pro Val Ile Lys Ala Arg Met Met Glu1 5 10 15Tyr Gly Thr Thr208622PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 86Thr Ala Gly Thr Thr Val Tyr Gly Ala Phe Asp Pro Leu Leu Ala Val1 5 10 15Ala Asp Ile Cys Lys Lys208720PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 87Thr Asn Met Phe Thr Tyr Glu Ile Ala Pro Val Phe Val Leu Leu Glu1 5 10 15Tyr Val Thr Leu208820PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 88Val Phe Asp Gly Lys Pro Gln His Thr Met Val Cys Lys Trp Tyr Ile1 5 10 15Pro Pro Ser Leu208920PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 89Val Asn Phe Phe Arg Met Val Ile Ser Met Pro Ala Ala Thr His Gln1 5 10 15Asp Ile Asp Phe209021PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 90Val Pro Leu Gln Cys Ser Ala Leu Leu Val Arg Glu Glu Gly Leu Met1 5 10 15Gln Asn Cys Asn Gln209110PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 91Tyr Thr Leu Pro Leu Trp Val Arg Met Glu1 5 109225PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 92Gln Cys Ser Asp Ile Ser Thr Lys Gln Ala Ala Phe Lys Ala Val Ser1 5 10 15Glu Val Cys Arg Ile Pro Thr His Leu20 259325PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 93Glu Thr Glu Lys Leu Leu Lys Tyr Leu Glu Ala Val Glu Lys Val Lys1 5 10 15Arg Thr Arg Asp Glu Leu Glu Val Ile20 259420PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 94Lys Ala Arg Ile His Pro Phe His Ile Leu Ile Ala Leu Glu Thr Tyr1 5 10 15Lys Thr Gly His209525PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 95Phe Lys Thr Val Glu Pro Thr Gly Lys Arg Phe Leu Leu Ala Val Asp1 5 10 15Val Ser Ala Ser Met Asn Gln Arg Val20 259626PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 96Met Asn Gln Arg Val Leu Gly Ser Ile Leu Asn Ala Ser Thr Val Ala1 5 10 15Ala Ala Met Cys Ile Lys Ala Leu Asp Ala20 259725PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 97Pro Cys Pro Val Thr Thr Asp Met Thr Leu Gln Gln Val Leu Met Ala1 5 10 15Met Ser Gln Ile Pro Ala Gly Gly Thr20 259825PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 98Pro Ala Gly Gly Thr Asp Cys Ser Leu Pro Met Ile Trp Ala Gln Lys1 5 10 15Thr Asn Thr Pro Ala Asp Val Phe Ile20 259920PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 99Lys Thr Asn Thr Pro Ala Asp Val Phe Ile Val Phe Thr Asp Asn Glu1 5 10 15Thr Phe Ala Gly2010016PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 100Met Ala Ala Leu Glu Ala Lys Ile Cys His Gln Ile Glu Tyr Tyr Phe1 5 10 1510126PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 101Asp Glu Tyr Lys Asn Asp Val Lys Asn Arg Ser Val Tyr Ile Lys Gly1 5 10 15Phe Pro Thr Asp Ala Thr Leu Asp Asp Ile20 2510216PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 102Arg Ser Val Tyr Ile Lys Gly Phe Pro Thr Asp Ala Thr Leu Asp Asp1 5 10 1510316PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 103Thr Leu Asp Asp Ile Lys Glu Trp Leu Glu Asp Lys Gly Gln Val Leu1 5 10 1510416PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 104Trp Leu Glu Asp Lys Gly Gln Val Leu Asn Ile Gln Met Arg Arg Thr1 5 10 1510536PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 105Lys Gly Gln Val Leu Asn Ile Gln Met Arg Arg Thr Leu His Lys Ala1 5 10 15Phe Lys Gly Ser Ile Phe Val Val Phe Asp Ser Ile Glu Ser Ala Lys20 25 30Lys Phe Val Glu3510616PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 106Met Arg Arg Thr Leu His Lys Ala Phe Lys Gly Ser Ile Phe Val Val1 5 10 1510716PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 107Ser Ile Phe Val Val Phe Asp Ser Ile Glu Ser Ala Lys Lys Phe Val1 5 10 1510816PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 108Val Val Phe Asp Ser Ile Glu Ser Ala Lys Lys Phe Val Glu Thr Pro1 5 10 1510916PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 109Ser Ile Glu Ser Ala Lys Lys Phe Val Glu Thr Pro Gly Gln Lys Tyr1 5 10 1511017PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 110Thr Asp Leu Leu Ile Leu Phe Lys Asp Asp Tyr Phe Ala Lys Lys Asn1 5 10 15Glu11116PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 111Ile Leu Phe Lys Asp Asp Tyr Phe Ala Lys Lys Asn Glu Glu Arg Lys1 5 10 1511220PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 112Cys His Gln Ile Glu Tyr Tyr Phe Gly Asp Phe Asn Leu Pro Arg Asp1 5 10 15Lys Phe Leu Lys2011316PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 113Glu Glu Asp Ala Glu Met Lys Ser Leu Glu Glu Lys Ile Gly Cys Leu1 5 10 1511416PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 114Leu Glu Glu Lys Ile Gly Cys Leu Leu Lys Phe Ser Gly Asp Leu Asp1 5 10 1511516PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 115Tyr Tyr Phe Gly Asp Phe Asn Leu Pro Arg Asp Lys Phe Leu Lys Glu1 5 10 1511616PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 116Ser Asn His Gly Glu Ile Lys Trp Ile Asp Phe Val Arg Gly Ala Lys1 5 10 1511716PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 117Gly Glu Ile Lys Trp Ile Asp Phe Val Arg Gly Ala Lys Glu Gly Ile1 5 10 1511817PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 118Ala Leu Lys Gly Lys Ala Lys Asp Ala Asn Asn Gly Leu Asn Gln Leu1 5 10 15Arg11916PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 119Phe Asn Leu Pro Arg Asp Lys Phe Leu Lys Glu Gln Ile Lys Leu Asp1 5 10 1512016PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 120Ala Lys Asp Ala Asn Asn Gly Asn Leu Gln Leu Arg Asn Lys Glu Val1 5 10 1512116PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 121Leu Gln Leu Arg Asn Lys Glu Val Thr Trp Glu Leu Val Glu Gly Glu1 5 10 1512216PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 122Asn Lys Glu Val Thr Trp Glu Leu Val Glu Gly Glu Val Glu Lys Glu1 5 10 1512316PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 123Glu Gly Glu Val Glu Lys Glu Ala Leu Lys Lys Ile Ile Glu Asp Gln1 5 10 1512416PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 124Glu Lys Glu Ala Leu Lys Lys Ile Ile Glu Asp Gln Gln Glu Ser Leu1 5 10 1512516PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 125Arg Asp Lys Phe Leu Lys Glu Gln Ile Lys Leu Asp Glu Gly Trp Val1 5 10 1512616PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 126Gly Lys Gly Lys Gly Asn Lys Ala Ala Gln Pro Gly Ser Gly Lys Gly1 5 10 1512716PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 127Gly Ser Lys Gly Lys Gly Lys Val Gln Phe Gln Gly Lys Lys Thr Lys1 5 10 1512816PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 128Phe Gln Gly Lys Lys Thr Lys Phe Ala Ser Asp Asp Glu His Asp Glu1 5 10 1512916PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 129Asp Glu Asn Gly Ala Thr Gly Pro Val Lys Arg Ala Arg Glu Glu Thr1 5 10 1513016PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 130Glu Glu Thr Asp Lys Glu Glu Pro Ala Ser Lys Gln Gln Lys Thr Glu1 5 10 1513123PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 131Gly Trp Val Pro Leu Glu Ile Met Ile Lys Phe Asn Arg Leu Asn Arg1 5 10 15Leu Thr Thr Asp Phe Asn Val2013216PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 132Pro Leu Glu Ile Met Ile Lys Phe Asn Arg Leu Asn Arg Leu Thr Thr1 5 10 1513316PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 133Ile Met Ile Lys Phe Asn Arg Leu Asn Arg Leu Thr Thr Asp Phe Asn1 5 10 1513416PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 134Lys Phe Asn Arg Leu Asn Arg Leu Thr Thr Asp Phe Asn Val Ile Val1 5 10 1513516PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 135Asp Phe Asn Val Ile Val Glu Ala Leu Ser Lys Ser Lys Ala Glu Leu1 5 10 1513616PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 136Leu Ser Lys Ser Lys Ala Glu Leu Met Glu Ile Ser Glu Asp Lys Thr1 5 10 1513716PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 137Ser Lys Ala Glu Leu Met Glu Ile Ser Glu Asp Lys Thr Lys Ile Arg1 5 10 1513815PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 138Arg Arg Ser Pro Ser Lys Pro Leu Pro Glu Val Thr Asp Glu Tyr1 5 10 1513916PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 139Pro Ser Lys Pro Leu Pro Glu Val Thr Asp Glu Tyr Lys Asn Asp Val1 5 10 1514020PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 140Lys Phe Gly Ala Asp Ala Arg Ala Leu Met Leu Gln Gly Val Asp Leu1 5 10 15Leu Ala Asp Ala2014115PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 141Leu Lys Val Gly Leu Gln Val Val Ala Val Lys Ala Pro Gly Phe1 5 10 1514215PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 142Gly Gly Ala Val Phe Gly Glu Glu Gly Leu Thr Leu Asn Leu Glu1 5 10 1514315PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 143Thr Leu Asn Leu Glu Asp Val Gln Pro His Asp Leu Gly Lys Val1 5 10 1514415PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 144Val Gly Ala Ala Thr Glu Ile Glu Met Lys Glu Lys Lys Asp Arg1 5 10 1514515PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 145Val Gly Gly Thr Ser Asp Val Glu Val Asn Glu Lys Lys Asp Arg1 5 10 1514615PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 146Ile Val Leu Gly Gly Gly Cys Ala Leu Leu Arg Cys Ile Pro Ala1 5 10 1514724PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 147Val Leu Gly Gly Gly Val Ala Leu Leu Arg Val Ile Pro Ala Leu Asp1 5 10 15Ser Leu Thr Pro Ala Asn Glu Asp2014815PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 148Gly Cys Ala Leu Leu Arg Cys Ile Pro Ala Leu Asp Ser Leu Thr1 5 10 1514915PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 149Arg Cys Ile Pro Ala Leu Asp Ser Leu Thr Pro Ala Asn Glu Asp1 5 10 1515015PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 150Glu Ile Ile Lys Arg Thr Leu Lys Ile Pro Ala Met Thr Ile Ala1 5 10 1515115PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 151Val Glu Lys Ile Met Gln Ser Ser Ser Glu Val Gly Tyr Asp Ala1 5 10 1515215PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 152Met Ala Gly Asp Phe Val Asn Met Val Glu Lys Gly Ile Ile Asp1 5 10 1515315PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 153Val Asn Met Val Glu Lys Gly Ile Ile Asp Pro Thr Lys Val Val1 5 10 1515415PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 154Val Ala Val Thr Met Gly Pro Lys Gly Arg Thr Val Ile Ile Glu1 5 10 1515515PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 155Lys Gly Ile Ile Asp Pro Thr Lys Val Val Arg Thr Ala Leu Leu1 5 10 1515615PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 156Pro Thr Lys Val Val Arg Thr Ala Leu Leu Asp Ala Ala Gly Val1 5 10 1515715PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 157Ala Ser Leu Leu Thr Thr Ala Glu Val Val Val Thr Glu Ile Pro1 5 10 151589PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 158Gly Glu Thr Arg Lys Val Lys Ala His1 515915PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 159Arg Lys Val Lys Ala His Ser Gln Thr His Arg Val Asp Leu Gly1 5 10 1516015PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 160Arg Val Asp Leu Gly Thr Leu Arg Gly Tyr Tyr Asn Gln Ser Glu1 5 10 1516115PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 161Asp Gly Arg Leu Leu Arg Gly His Asp Gln Tyr Ala Tyr Asp Gly1 5 10 1516214PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 162Gly Pro Glu Tyr Trp Asp Arg Asn Thr Gln Ile Tyr Lys Ala1 5 1016316PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 163Trp Asp Arg Asn Thr Gln Ile Tyr Lys Ala Gln Ala Gln Thr Asp Arg1 5 10 151649PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 164Arg Asn Thr Gln Ile Tyr Lys

Ala Gln1 516515PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 165Arg Glu Ser Leu Arg Asn Leu Arg Gly Tyr Tyr Asn Gln Ser Glu1 5 10 1516615PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 166Gly Ser His Thr Leu Gln Ser Met Tyr Gly Cys Asp Val Gly Pro1 5 10 1516712PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 167Leu Asn Glu Asp Leu Arg Ser Trp Thr Ala Ala Asp1 5 1016815PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 168Leu Asn Glu Asp Leu Arg Ser Trp Thr Ala Ala Asx Thr Ala Ala1 5 10 151699PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 169Asp Lys Gly Gln Val Leu Asn Ile Gln1 517014PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 170Leu Glu Asp Lys Gly Gln Val Leu Asn Ile Gln Met Arg Arg1 5 1017114PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 171Ala Phe Lys Gly Ser Ile Phe Val Val Phe Asp Ser Ile Glu1 5 101729PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 172Glu Ser Ala Lys Lys Phe Val Glu Thr1 517314PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 173Ile Glu Ser Ala Lys Lys Phe Val Glu Thr Pro Gly Gln Lys1 5 1017412PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 174Ala Lys Asp Ala Asn Asn Gly Asn Leu Gln Leu Arg1 5 101759PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 175Glu Ala Leu Lys Lys Ile Ile Glu Asp1 51769PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 176Glu Gln Ile Lys Leu Asp Glu Gly Trp1 517712PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 177Leu Lys Glu Gln Ile Lys Leu Asp Glu Gly Trp Val1 5 101789PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 178Ala Glu Leu Met Glu Ile Ser Glu Asp1 517913PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 179Ser Lys Ala Glu Leu Met Glu Ile Ser Glu Asp Lys Thr1 5 101809PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 180Lys Gly Ser Ile Phe Val Val Phe Asp1 518114PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 181Ala Lys Asp Ala Asn Asn Gly Asn Leu Gln Leu Arg Asn Lys1 5 101829PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 182Asp Ala Asn Asn Gly Asn Leu Gln Leu1 518312PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 183Ile Val Glu Ala Leu Ser Lys Ser Lys Ala Glu Leu1 5 1018413PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 184Ala Phe Lys Gly Ser Ile Phe Val Val Phe Asp Ser Ile1 5 1018514PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 185Gly Ser Ile Phe Val Val Phe Asp Ser Ile Glu Ser Ala Lys1 5 1018614PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 186Ile Phe Val Val Phe Asp Ser Ile Glu Ser Ala Lys Lys Phe1 5 101879PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 187Val Val Phe Asp Ser Ile Glu Ser Ala1 518813PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 188Glu Leu Met Glu Ile Ser Glu Asp Lys Thr Lys Ile Arg1 5 101899PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 189Glu Ala Leu Tyr Leu Val Cys Gly Glu1 5190573PRTHomo sapiens 190Met Leu Arg Leu Pro Thr Val Phe Arg Gln Met Arg Pro Val Ser Arg1 5 10 15Val Leu Ala Pro His Leu Thr Arg Ala Tyr Ala Lys Asp Val Lys Phe20 25 30Gly Ala Asp Ala Arg Ala Leu Met Leu Gln Gly Val Asp Leu Leu Ala35 40 45Asp Ala Val Ala Val Thr Met Gly Pro Lys Gly Arg Thr Val Ile Ile50 55 60Glu Gln Ser Trp Gly Ser Pro Lys Val Thr Lys Asp Gly Val Thr Val65 70 75 80Ala Lys Ser Ile Asp Leu Lys Asp Lys Tyr Lys Asn Ile Gly Ala Lys85 90 95Leu Val Gln Asp Val Ala Asn Asn Thr Asn Glu Glu Ala Gly Asp Gly100 105 110Thr Thr Thr Ala Thr Val Leu Ala Arg Ser Ile Ala Lys Glu Gly Phe115 120 125Glu Lys Ile Ser Lys Gly Ala Asn Pro Val Glu Ile Arg Arg Gly Val130 135 140Met Leu Ala Val Asp Ala Val Ile Ala Glu Leu Lys Lys Gln Ser Lys145 150 155 160Pro Val Thr Thr Pro Glu Glu Ile Ala Gln Val Ala Thr Ile Ser Ala165 170 175Asn Gly Asp Lys Glu Ile Gly Asn Ile Ile Ser Asp Ala Met Lys Lys180 185 190Val Gly Arg Lys Gly Val Ile Thr Val Lys Asp Gly Lys Thr Leu Asn195 200 205Asp Glu Leu Glu Ile Ile Glu Gly Met Lys Phe Asp Arg Gly Tyr Ile210 215 220Ser Pro Tyr Phe Ile Asn Thr Ser Lys Gly Gln Lys Cys Glu Phe Gln225 230 235 240Asp Ala Tyr Val Leu Leu Ser Glu Lys Lys Ile Ser Ser Ile Gln Ser245 250 255Ile Val Pro Ala Leu Glu Ile Ala Asn Ala His Arg Lys Pro Leu Val260 265 270Ile Ile Ala Glu Asp Val Asp Gly Glu Ala Leu Ser Thr Leu Val Leu275 280 285Asn Arg Leu Lys Val Gly Leu Gln Val Val Ala Val Lys Ala Pro Gly290 295 300Phe Gly Asp Asn Arg Lys Asn Gln Leu Lys Asp Met Ala Ile Ala Thr305 310 315 320Gly Gly Ala Val Phe Gly Glu Glu Gly Leu Thr Leu Asn Leu Glu Asp325 330 335Val Gln Pro His Asp Leu Gly Lys Val Gly Glu Val Ile Val Thr Lys340 345 350Asp Asp Ala Met Leu Leu Lys Gly Lys Gly Asp Lys Ala Gln Ile Glu355 360 365Lys Arg Ile Gln Glu Ile Ile Glu Gln Leu Asp Val Thr Thr Ser Glu370 375 380Tyr Glu Lys Glu Lys Leu Asn Glu Arg Leu Ala Lys Leu Ser Asp Gly385 390 395 400Val Ala Val Leu Lys Val Gly Gly Thr Ser Asp Val Glu Val Asn Glu405 410 415Lys Lys Asp Arg Val Thr Asp Ala Leu Asn Ala Thr Arg Ala Ala Val420 425 430Glu Glu Gly Ile Val Leu Gly Gly Gly Cys Ala Leu Leu Arg Cys Ile435 440 445Pro Ala Leu Asp Ser Leu Thr Pro Ala Asn Glu Asp Gln Lys Ile Gly450 455 460Ile Glu Ile Ile Lys Arg Thr Leu Lys Ile Pro Ala Met Thr Ile Ala465 470 475 480Lys Asn Ala Gly Val Glu Gly Ser Leu Ile Val Glu Lys Ile Met Gln485 490 495Ser Ser Ser Glu Val Gly Tyr Asp Ala Met Ala Gly Asp Phe Val Asn500 505 510Met Val Glu Lys Gly Ile Ile Asp Pro Thr Lys Val Val Arg Thr Ala515 520 525Leu Leu Asp Ala Ala Gly Val Ala Ser Leu Leu Thr Thr Ala Glu Val530 535 540Val Val Thr Glu Ile Pro Lys Glu Glu Lys Asp Pro Gly Met Gly Ala545 550 555 560Met Gly Gly Met Gly Gly Gly Met Gly Gly Gly Met Phe565 570191641PRTHomo sapiens 191Met Ala Lys Ala Ala Ala Ile Gly Ile Asp Leu Gly Thr Thr Tyr Ser1 5 10 15Cys Val Gly Val Phe Gln His Gly Lys Val Glu Ile Ile Ala Asn Asp20 25 30Gln Gly Asn Arg Thr Thr Pro Ser Tyr Val Ala Phe Thr Asp Thr Glu35 40 45Arg Leu Ile Gly Asp Ala Ala Lys Asn Gln Val Ala Leu Asn Pro Gln50 55 60Asn Thr Val Phe Asp Ala Lys Arg Leu Ile Gly Arg Lys Phe Gly Asp65 70 75 80Pro Val Val Gln Ser Asp Met Lys His Trp Pro Phe Gln Val Ile Asn85 90 95Asp Gly Asp Lys Pro Lys Val Gln Val Ser Tyr Lys Gly Glu Thr Lys100 105 110Ala Phe Tyr Pro Glu Glu Ile Ser Ser Met Val Leu Thr Lys Met Lys115 120 125Glu Ile Ala Glu Ala Tyr Leu Gly Tyr Pro Val Thr Asn Ala Val Ile130 135 140Thr Val Pro Ala Tyr Phe Asn Asp Ser Gln Arg Gln Ala Thr Lys Asp145 150 155 160Ala Gly Val Ile Ala Gly Leu Asn Val Leu Arg Ile Ile Asn Glu Pro165 170 175Thr Ala Ala Ala Ile Ala Tyr Gly Leu Asp Arg Thr Gly Lys Gly Glu180 185 190Arg Asn Val Leu Ile Phe Asp Leu Gly Gly Gly Thr Phe Asp Val Ser195 200 205Ile Leu Thr Ile Asp Asp Gly Ile Phe Glu Val Lys Ala Thr Ala Gly210 215 220Asp Thr His Leu Gly Gly Glu Asp Phe Asp Asn Arg Leu Val Asn His225 230 235 240Phe Val Glu Glu Phe Lys Arg Lys His Lys Lys Asp Ile Ser Gln Asn245 250 255Lys Arg Ala Val Arg Arg Leu Arg Thr Ala Cys Glu Arg Ala Lys Arg260 265 270Thr Leu Ser Ser Ser Thr Gln Ala Ser Leu Glu Ile Asp Ser Leu Phe275 280 285Glu Gly Ile Asp Phe Tyr Thr Ser Ile Thr Arg Ala Arg Phe Glu Glu290 295 300Leu Cys Ser Asp Leu Phe Arg Ser Thr Leu Glu Pro Val Glu Lys Ala305 310 315 320Leu Arg Asp Ala Lys Leu Asp Lys Ala Gln Ile His Asp Leu Val Leu325 330 335Val Gly Gly Ser Thr Arg Ile Pro Lys Val Gln Lys Leu Leu Gln Asp340 345 350Phe Phe Asn Gly Arg Asp Leu Asn Lys Ser Ile Asn Pro Asp Glu Ala355 360 365Val Ala Tyr Gly Ala Ala Val Gln Ala Ala Ile Leu Met Gly Asp Lys370 375 380Ser Glu Asn Val Gln Asp Leu Leu Leu Leu Asp Val Ala Pro Leu Ser385 390 395 400Leu Gly Leu Glu Thr Ala Gly Gly Val Met Thr Ala Leu Ile Lys Arg405 410 415Asn Ser Thr Ile Pro Thr Lys Gln Thr Gln Ile Phe Thr Thr Tyr Ser420 425 430Asp Asn Gln Pro Gly Val Leu Ile Gln Val Tyr Glu Gly Glu Arg Ala435 440 445Met Thr Lys Asp Asn Asn Leu Leu Gly Arg Phe Glu Leu Ser Gly Ile450 455 460Pro Pro Ala Pro Arg Gly Val Pro Gln Ile Glu Val Thr Phe Asp Ile465 470 475 480Asp Ala Asn Gly Ile Leu Asn Val Thr Ala Thr Asp Lys Ser Thr Gly485 490 495Lys Ala Asn Lys Ile Thr Ile Thr Asn Asp Lys Gly Arg Leu Ser Lys500 505 510Glu Glu Ile Glu Arg Met Val Gln Glu Ala Glu Lys Tyr Lys Ala Glu515 520 525Asp Glu Val Gln Arg Glu Arg Val Ser Ala Lys Asn Ala Leu Glu Ser530 535 540Tyr Ala Phe Asn Met Lys Ser Ala Val Glu Asp Glu Gly Leu Lys Gly545 550 555 560Lys Ile Ser Glu Ala Asp Lys Lys Lys Val Leu Asp Lys Cys Gln Glu565 570 575Val Ile Ser Trp Leu Asp Ala Asn Thr Leu Ala Glu Lys Asp Glu Phe580 585 590Glu His Lys Arg Lys Glu Leu Glu Gln Val Cys Asn Pro Ile Ile Ser595 600 605Gly Leu Tyr Gln Gly Ala Gly Gly Pro Gly Pro Gly Gly Phe Gly Ala610 615 620Gln Gly Pro Lys Gly Gly Ser Gly Ser Gly Pro Thr Ile Glu Glu Val625 630 635 640Asp192731PRTHomo sapiens 192Pro Glu Glu Thr Gln Thr Gln Asp Gln Pro Met Glu Glu Glu Glu Val1 5 10 15Glu Thr Phe Ala Phe Gln Ala Glu Ile Ala Gln Leu Met Ser Leu Ile20 25 30Ile Asn Thr Phe Tyr Ser Asn Lys Glu Ile Phe Leu Arg Glu Leu Ile35 40 45Ser Asn Ser Ser Asp Ala Leu Asp Lys Ile Arg Tyr Glu Ser Leu Thr50 55 60Asp Pro Ser Lys Leu Asp Ser Gly Lys Glu Leu His Ile Asn Leu Ile65 70 75 80Pro Asn Lys Gln Asp Arg Thr Leu Thr Ile Val Asp Thr Gly Ile Gly85 90 95Met Thr Lys Ala Asp Leu Ile Asn Asn Leu Gly Thr Ile Ala Lys Ser100 105 110Gly Thr Lys Ala Phe Met Glu Ala Leu Gln Ala Gly Ala Asp Ile Ser115 120 125Met Ile Gly Gln Phe Gly Val Gly Phe Tyr Ser Ala Tyr Leu Val Ala130 135 140Glu Lys Val Thr Val Ile Thr Lys His Asn Asp Asp Glu Gln Tyr Ala145 150 155 160Trp Glu Ser Ser Ala Gly Gly Ser Phe Thr Val Arg Thr Asp Thr Gly165 170 175Glu Pro Met Gly Arg Gly Thr Lys Val Ile Leu His Leu Lys Glu Asp180 185 190Gln Thr Glu Tyr Leu Glu Glu Arg Arg Ile Lys Glu Ile Val Lys Lys195 200 205His Ser Gln Phe Ile Gly Tyr Pro Ile Thr Leu Phe Val Glu Lys Glu210 215 220Arg Asp Lys Glu Val Ser Asp Asp Glu Ala Glu Glu Lys Glu Asp Lys225 230 235 240Glu Glu Glu Lys Glu Lys Glu Glu Lys Glu Ser Glu Asp Lys Pro Glu245 250 255Ile Glu Asp Val Gly Ser Asp Glu Glu Glu Glu Lys Lys Asp Gly Asp260 265 270Lys Lys Lys Lys Lys Lys Ile Lys Glu Lys Tyr Ile Asp Gln Glu Glu275 280 285Leu Asn Lys Thr Lys Pro Ile Trp Thr Arg Asn Pro Asp Asp Ile Thr290 295 300Asn Glu Glu Tyr Gly Glu Phe Tyr Lys Ser Leu Thr Asn Asp Trp Glu305 310 315 320Asp His Leu Ala Val Lys His Phe Ser Val Glu Gly Gln Leu Glu Phe325 330 335Arg Ala Leu Leu Phe Val Pro Arg Arg Ala Pro Phe Asp Leu Phe Glu340 345 350Asn Arg Lys Lys Lys Asn Asn Ile Lys Leu Tyr Val Arg Arg Val Phe355 360 365Ile Met Asp Asn Cys Glu Glu Leu Ile Pro Glu Tyr Leu Asn Phe Ile370 375 380Arg Gly Val Val Asp Ser Glu Asp Leu Pro Leu Asn Ile Ser Arg Glu385 390 395 400Met Leu Gln Gln Ser Lys Ile Leu Lys Val Ile Arg Lys Asn Leu Val405 410 415Lys Lys Cys Leu Glu Leu Phe Thr Glu Leu Ala Glu Asp Lys Glu Asn420 425 430Tyr Lys Lys Phe Tyr Glu Gln Phe Ser Lys Asn Ile Lys Leu Gly Ile435 440 445His Glu Asp Ser Gln Asn Arg Lys Lys Leu Ser Glu Leu Leu Arg Tyr450 455 460Tyr Thr Ser Ala Ser Gly Asp Glu Met Val Ser Leu Lys Asp Tyr Cys465 470 475 480Thr Arg Met Lys Glu Asn Gln Lys His Ile Tyr Tyr Ile Thr Gly Glu485 490 495Thr Lys Asp Gln Val Ala Asn Ser Ala Phe Val Glu Arg Leu Arg Lys500 505 510His Gly Leu Glu Val Ile Tyr Met Ile Glu Pro Ile Asp Glu Tyr Cys515 520 525Val Gln Gln Leu Lys Glu Phe Glu Gly Lys Thr Leu Val Ser Val Thr530 535 540Lys Glu Gly Leu Glu Leu Pro Glu Asp Glu Glu Glu Lys Lys Lys Gln545 550 555 560Glu Glu Lys Lys Thr Lys Phe Glu Asn Leu Cys Lys Ile Met Lys Asp565 570 575Ile Leu Glu Lys Lys Val Glu Lys Val Val Val Ser Asn Arg Leu Val580 585 590Thr Ser Pro Cys Cys Ile Val Thr Ser Thr Tyr Gly Trp Thr Ala Asn595 600 605Met Glu Arg Ile Met Lys Ala Gln Ala Leu Arg Asp Asn Ser Thr Met610 615 620Gly Tyr Met Ala Ala Lys Lys His Leu Glu Ile Asn Pro Asp His Ser625 630 635 640Ile Ile Glu Thr Leu Arg Gln Lys Ala Glu Ala Asp Lys Asn Asp Lys645 650 655Ser Val Lys Asp Leu Val Ile Leu Leu Tyr Glu Thr Ala Leu Leu Ser660 665 670Ser Gly Phe Ser Leu Glu Asp Pro Gln Thr His Ala Asn Arg Ile Tyr675 680 685Arg Met Ile Lys Leu Gly Leu Gly Ile Asp Glu Asp Asp Pro Thr Ala690 695 700Asp Asp Thr Ser Ala Ala Val Thr Glu Glu Met Pro Pro Leu Glu Gly705 710 715 720Asp Asp Asp Thr Ser Arg Met Glu Glu Val Asp725 730193723PRTHomo sapiens 193Pro Glu Glu Val His His Gly Glu Glu Glu Val Glu Thr Phe Ala Phe1 5 10 15Gln Ala Glu Ile Ala Gln Leu Met Ser Leu Ile Ile Asn Thr Phe Tyr20 25 30Ser Asn Lys Glu Ile Phe Leu Arg Glu Leu Ile Ser Asn Ala Ser Asp35 40 45Ala Leu Asp Lys Ile Arg Tyr Glu Ser Leu Thr Asp Pro Ser Lys Leu50 55 60Asp Ser Gly Lys Glu

Leu Lys Ile Asp Ile Ile Pro Asn Pro Gln Glu65 70 75 80Arg Thr Leu Thr Leu Val Asp Thr Gly Ile Gly Met Thr Lys Ala Asp85 90 95Leu Ile Asn Asn Leu Gly Thr Ile Ala Lys Ser Gly Thr Lys Ala Phe100 105 110Met Glu Ala Leu Gln Ala Gly Ala Asp Ile Ser Met Ile Gly Gln Phe115 120 125Gly Val Gly Phe Tyr Ser Ala Tyr Leu Val Ala Glu Lys Val Val Val130 135 140Ile Thr Lys His Asn Asp Asp Glu Gln Tyr Ala Trp Glu Ser Ser Ala145 150 155 160Gly Gly Ser Phe Thr Val Arg Ala Asp His Gly Glu Pro Ile Gly Arg165 170 175Gly Thr Lys Val Ile Leu His Leu Lys Glu Asp Gln Thr Glu Tyr Leu180 185 190Glu Glu Arg Arg Val Lys Glu Val Val Lys Lys His Ser Gln Phe Ile195 200 205Gly Tyr Pro Ile Thr Leu Tyr Leu Glu Lys Glu Arg Glu Lys Glu Ile210 215 220Ser Asp Asp Glu Ala Glu Glu Glu Lys Gly Glu Lys Glu Glu Glu Asp225 230 235 240Lys Asp Asp Glu Glu Lys Pro Lys Ile Glu Asp Val Gly Ser Asp Glu245 250 255Glu Asp Asp Ser Gly Lys Asp Lys Lys Lys Lys Thr Lys Lys Ile Lys260 265 270Glu Lys Tyr Ile Asp Gln Glu Glu Leu Asn Lys Thr Lys Pro Ile Trp275 280 285Thr Arg Asn Pro Asp Asp Ile Thr Gln Glu Glu Tyr Gly Glu Phe Tyr290 295 300Lys Ser Leu Thr Asn Asp Trp Glu Asp His Leu Ala Val Lys His Phe305 310 315 320Ser Val Glu Gly Gln Leu Glu Phe Arg Ala Leu Leu Phe Ile Pro Arg325 330 335Arg Ala Pro Phe Asp Leu Phe Glu Asn Lys Lys Lys Lys Asn Asn Ile340 345 350Lys Leu Tyr Val Arg Arg Val Phe Ile Met Asp Ser Cys Asp Glu Leu355 360 365Ile Pro Glu Tyr Leu Asn Phe Ile Arg Gly Val Val Asp Ser Glu Asp370 375 380Leu Pro Leu Asn Ile Ser Arg Glu Met Leu Gln Gln Ser Lys Ile Leu385 390 395 400Lys Val Ile Arg Lys Asn Ile Val Lys Lys Cys Leu Glu Leu Phe Ser405 410 415Glu Leu Ala Glu Asp Lys Glu Asn Tyr Lys Lys Phe Tyr Glu Ala Phe420 425 430Ser Lys Asn Leu Lys Leu Gly Ile His Glu Asp Ser Thr Asn Arg Arg435 440 445Arg Leu Ser Glu Leu Leu Arg Tyr His Thr Ser Gln Ser Gly Asp Glu450 455 460Met Thr Ser Leu Ser Glu Tyr Val Ser Arg Met Lys Glu Thr Gln Lys465 470 475 480Ser Ile Tyr Tyr Ile Thr Gly Glu Ser Lys Glu Gln Val Ala Asn Ser485 490 495Ala Phe Val Glu Arg Val Arg Lys Arg Gly Phe Glu Val Val Tyr Met500 505 510Thr Glu Pro Ile Asp Glu Tyr Cys Val Gln Gln Leu Lys Glu Phe Asp515 520 525Gly Lys Ser Leu Val Ser Val Thr Lys Glu Gly Leu Glu Leu Pro Glu530 535 540Asp Glu Glu Glu Lys Lys Lys Met Glu Glu Ser Lys Ala Lys Phe Glu545 550 555 560Asn Leu Cys Lys Leu Met Lys Glu Ile Leu Asp Lys Lys Val Glu Lys565 570 575Val Thr Ile Ser Asn Arg Leu Val Ser Ser Pro Cys Cys Ile Val Thr580 585 590Ser Thr Tyr Gly Trp Thr Ala Asn Met Glu Arg Ile Met Lys Ala Gln595 600 605Ala Leu Arg Asp Asn Ser Thr Met Gly Tyr Met Met Ala Lys Lys His610 615 620Leu Glu Ile Asn Pro Asp His Pro Ile Val Glu Thr Leu Arg Gln Lys625 630 635 640Ala Glu Ala Asp Lys Asn Asp Lys Ala Val Lys Asp Leu Val Val Leu645 650 655Leu Phe Glu Thr Ala Leu Leu Ser Ser Gly Phe Ser Leu Glu Asp Pro660 665 670Gln Thr His Ser Asn Arg Ile Tyr Arg Met Ile Lys Leu Gly Leu Gly675 680 685Ile Asp Glu Asp Glu Val Ala Ala Glu Glu Pro Asn Ala Ala Val Pro690 695 700Asp Glu Ile Pro Pro Leu Glu Gly Asp Glu Asp Ala Ser Arg Met Glu705 710 715 720Glu Val Asp194585PRTHomo sapiens 194Met Ala Ser Pro Gly Ser Gly Phe Trp Ser Phe Gly Ser Glu Asp Gly1 5 10 15Ser Gly Asp Ser Glu Asn Pro Gly Thr Ala Arg Ala Trp Cys Gln Val20 25 30Ala Gln Lys Phe Thr Gly Gly Ile Gly Asn Lys Leu Cys Ala Leu Leu35 40 45Tyr Gly Asp Ala Glu Lys Pro Ala Glu Ser Gly Gly Ser Gln Pro Pro50 55 60Arg Ala Ala Ala Arg Lys Ala Ala Cys Ala Cys Asp Gln Lys Pro Cys65 70 75 80Ser Cys Ser Lys Val Asp Val Asn Tyr Ala Phe Leu His Ala Thr Asp85 90 95Leu Leu Pro Ala Cys Asp Gly Glu Arg Pro Thr Leu Ala Phe Leu Gln100 105 110Asp Val Met Asn Ile Leu Leu Gln Tyr Val Val Lys Ser Phe Asp Arg115 120 125Ser Thr Lys Val Ile Asp Phe His Tyr Pro Asn Glu Leu Leu Gln Glu130 135 140Tyr Asn Trp Glu Leu Ala Asp Gln Pro Gln Asn Leu Glu Glu Ile Leu145 150 155 160Met His Cys Gln Thr Thr Leu Lys Tyr Ala Ile Lys Thr Gly His Pro165 170 175Arg Tyr Phe Asn Gln Leu Ser Thr Gly Leu Asp Met Val Gly Leu Ala180 185 190Ala Asp Trp Leu Thr Ser Thr Ala Asn Thr Asn Met Phe Thr Tyr Glu195 200 205Ile Ala Pro Val Phe Val Leu Leu Glu Tyr Val Thr Leu Lys Lys Met210 215 220Arg Glu Ile Ile Gly Trp Pro Gly Gly Ser Gly Asp Gly Ile Phe Ser225 230 235 240Pro Gly Gly Ala Ile Ser Asn Met Tyr Ala Met Met Ile Ala Arg Phe245 250 255Lys Met Phe Pro Glu Val Lys Glu Lys Gly Met Ala Ala Leu Pro Arg260 265 270Leu Ile Ala Phe Thr Ser Glu His Ser His Phe Ser Leu Lys Lys Gly275 280 285Ala Ala Ala Leu Gly Ile Gly Thr Asp Ser Val Ile Leu Ile Lys Cys290 295 300Asp Glu Arg Gly Lys Met Ile Pro Ser Asp Leu Glu Arg Arg Ile Leu305 310 315 320Glu Ala Lys Gln Lys Gly Phe Val Pro Phe Leu Val Ser Ala Thr Ala325 330 335Gly Thr Thr Val Tyr Gly Ala Phe Asp Pro Leu Leu Ala Val Ala Asp340 345 350Ile Cys Lys Lys Tyr Lys Ile Trp Met His Val Asp Ala Ala Trp Gly355 360 365Gly Gly Leu Leu Met Ser Arg Lys His Lys Trp Lys Leu Ser Gly Val370 375 380Glu Arg Ala Asn Ser Val Thr Trp Asn Pro His Lys Met Met Gly Val385 390 395 400Pro Leu Gln Cys Ser Ala Leu Leu Val Arg Glu Glu Gly Leu Met Gln405 410 415Asn Cys Asn Gln Met His Ala Ser Tyr Leu Phe Gln Gln Asp Lys His420 425 430Tyr Asp Leu Ser Tyr Asp Thr Gly Asp Lys Ala Leu Gln Cys Gly Arg435 440 445His Val Asp Val Phe Lys Leu Trp Leu Met Trp Arg Ala Lys Gly Thr450 455 460Thr Gly Phe Glu Ala His Val Asp Lys Cys Leu Glu Leu Ala Glu Tyr465 470 475 480Leu Tyr Asn Ile Ile Lys Asn Arg Glu Gly Tyr Glu Met Val Phe Asp485 490 495Gly Lys Pro Gln His Thr Asn Val Cys Phe Trp Tyr Ile Pro Pro Ser500 505 510Leu Arg Thr Leu Glu Asp Asn Glu Glu Arg Met Ser Arg Leu Ser Lys515 520 525Val Ala Pro Val Ile Lys Ala Arg Met Met Glu Tyr Gly Thr Thr Met530 535 540Val Ser Tyr Gln Pro Leu Gly Asp Lys Val Asn Phe Phe Arg Met Val545 550 555 560Ile Ser Asn Pro Ala Ala Thr His Gln Asp Ile Asp Phe Leu Ile Glu565 570 575Glu Ile Glu Arg Leu Gly Gln Asp Leu580 585195525PRTHomo sapiens 195Met Glu Glu Ser Val Asn Gln Met Gln Pro Leu Asn Glu Lys Gln Ile1 5 10 15Ala Asn Ser Gln Asp Gly Tyr Val Trp Gln Val Thr Asp Met Asn Arg20 25 30Leu His Arg Phe Leu Cys Phe Gly Ser Glu Gly Gly Thr Tyr Tyr Ile35 40 45Lys Glu Gln Lys Leu Gly Leu Glu Asn Ala Glu Ala Leu Ile Arg Leu50 55 60Ile Glu Asp Gly Arg Gly Cys Glu Val Ile Gln Glu Ile Lys Ser Phe65 70 75 80Ser Gln Glu Gly Arg Thr Thr Lys Gln Glu Pro Met Leu Phe Ala Leu85 90 95Ala Ile Cys Ser Gln Cys Ser Asp Ile Ser Thr Lys Gln Ala Ala Phe100 105 110Lys Ala Val Ser Glu Val Cys Arg Ile Pro Thr His Leu Phe Thr Phe115 120 125Ile Gln Phe Lys Lys Asp Leu Lys Glu Ser Met Lys Cys Gly Met Trp130 135 140Gly Arg Ala Leu Arg Lys Ala Ile Ala Asp Trp Tyr Asn Glu Lys Gly145 150 155 160Gly Met Ala Leu Ala Leu Ala Val Thr Lys Tyr Lys Gln Arg Asn Gly165 170 175Trp Ser His Lys Asp Leu Leu Arg Leu Ser His Leu Lys Pro Ser Ser180 185 190Glu Gly Leu Ala Ile Val Thr Lys Tyr Ile Thr Lys Gly Trp Lys Glu195 200 205Val His Glu Leu Tyr Lys Glu Lys Ala Leu Ser Val Glu Thr Glu Lys210 215 220Leu Leu Lys Tyr Leu Glu Ala Val Glu Lys Val Lys Arg Thr Arg Asp225 230 235 240Glu Leu Glu Val Ile His Leu Ile Glu Glu His Arg Leu Val Arg Glu245 250 255His Leu Leu Thr Asn His Leu Lys Ser Lys Glu Val Trp Lys Ala Leu260 265 270Leu Gln Glu Met Pro Leu Thr Ala Leu Leu Arg Asn Leu Gly Lys Met275 280 285Thr Ala Asn Ser Val Leu Glu Pro Gly Asn Ser Glu Val Ser Leu Val290 295 300Cys Glu Lys Leu Cys Asn Glu Lys Leu Leu Lys Lys Ala Arg Ile His305 310 315 320Pro Phe His Ile Leu Ile Ala Leu Glu Thr Tyr Lys Thr Gly His Gly325 330 335Leu Arg Gly Lys Leu Lys Trp Arg Pro Asp Glu Glu Ile Leu Lys Ala340 345 350Leu Asp Ala Ala Phe Tyr Lys Thr Phe Lys Thr Val Glu Pro Thr Gly355 360 365Lys Arg Phe Leu Leu Ala Val Asp Val Ser Ala Ser Met Asn Gln Arg370 375 380Val Leu Gly Ser Ile Leu Asn Ala Ser Thr Val Ala Ala Ala Met Cys385 390 395 400Met Val Val Thr Arg Thr Glu Lys Asp Ser Tyr Val Val Ala Phe Ser405 410 415Asp Glu Met Val Pro Cys Pro Val Thr Thr Asp Met Thr Leu Gln Gln420 425 430Val Leu Met Ala Met Ser Gln Ile Pro Ala Gly Gly Thr Asp Cys Ser435 440 445Leu Pro Met Ile Trp Ala Gln Lys Thr Asn Thr Pro Ala Asp Val Phe450 455 460Ile Val Phe Thr Asp Asn Glu Thr Phe Ala Gly Gly Val His Pro Ala465 470 475 480Ile Ala Leu Arg Glu Tyr Arg Lys Lys Met Asp Ile Pro Ala Lys Leu485 490 495Ile Val Cys Gly Met Thr Ser Asn Gly Phe Thr Ile Ala Asp Pro Asp500 505 510Asp Arg Ala Leu Gln Asn Thr Leu Leu Asn Lys Ser Phe515 520 525196181PRTHomo sapiens 196Val Ala Asp His Val Ala Ser Tyr Gly Val Asn Leu Tyr Gln Ser Tyr1 5 10 15Gly Pro Ser Gly Gln Tyr Thr His Glu Phe Asp Gly Asp Glu Gln Phe20 25 30Tyr Val Asp Leu Gly Arg Lys Glu Thr Val Trp Cys Leu Pro Glu Leu35 40 45Arg Gln Phe Arg Gly Phe Asp Pro Gln Phe Ala Leu Thr Asn Ile Ala50 55 60Val Leu Lys His Asn Leu Asn Ser Leu Ile Lys Arg Ser Asn Ser Thr65 70 75 80Ala Ala Thr Asn Glu Val Pro Glu Val Thr Val Phe Ser Lys Ser Pro85 90 95Val Thr Leu Gly Gln Pro Asn Thr Leu Ile Cys Leu Val Asp Asn Ile100 105 110Phe Pro Pro Val Val Asn Ile Thr Trp Leu Thr Asn Gly His Ser Val115 120 125Thr Glu Gly Val Ser Glu Thr Thr Phe Leu Ser Lys Ser Asp His Ser130 135 140Phe Phe Lys Ile Ser Tyr Leu Thr Leu Leu Pro Ser Ala Glu Glu Ser145 150 155 160Tyr Asp Cys Lys Val Glu His Trp Gly Leu Asp Lys Pro Leu Leu Lys165 170 175His Trp Glu Pro Glu180197190PRTHomo sapiens 197Ser Pro Glu Asp Phe Val Tyr Gln Phe Lys Gly Met Cys Tyr Phe Thr1 5 10 15Asn Gly Thr Glu Arg Val Arg Leu Val Ser Arg Ser Ile Tyr Asn Arg20 25 30Glu Glu Ile Val Arg Phe Asp Ser Asp Val Gly Glu Phe Arg Ala Val35 40 45Thr Leu Leu Gly Leu Pro Ala Ala Glu Tyr Trp Asn Ser Gln Lys Asp50 55 60Ile Leu Glu Arg Lys Arg Ala Ala Val Asp Arg Val Cys Arg His Asn65 70 75 80Tyr Gln Leu Glu Leu Arg Thr Thr Leu Gln Arg Arg Val Glu Pro Thr85 90 95Val Thr Ile Ser Pro Ser Arg Thr Glu Ala Leu Asn His His Asn Leu100 105 110Leu Val Cys Ser Val Thr Asp Phe Tyr Pro Ala Gln Ile Lys Val Arg115 120 125Trp Phe Arg Asn Asp Gln Glu Glu Thr Ala Gly Val Val Ser Thr Pro130 135 140Leu Ile Arg Asn Gly Asp Trp Thr Phe Gln Ile Leu Val Met Leu Glu145 150 155 160Met Thr Pro Gln Arg Gly Asp Val Tyr Thr Cys His Val Glu His Pro165 170 175Ser Leu Gln Ser Pro Ile Thr Val Glu Trp Arg Ala Gln Ser180 185 190198181PRTHomo sapiens 198Val Ala Asp His Val Ala Ser Tyr Gly Val Asn Leu Tyr Gln Ser Tyr1 5 10 15Gly Pro Ser Gly Gln Tyr Thr His Glu Phe Asp Gly Asp Glu Gln Phe20 25 30Tyr Val Asp Leu Gly Arg Lys Glu Thr Val Trp Cys Leu Pro Glu Leu35 40 45Arg Gln Phe Arg Gly Phe Asp Pro Gln Phe Ala Leu Thr Asn Ile Ala50 55 60Val Leu Lys His Asn Leu Asn Ser Leu Ile Lys Arg Ser Asn Ser Thr65 70 75 80Ala Ala Thr Asn Glu Val Pro Glu Val Thr Val Phe Ser Lys Ser Pro85 90 95Val Thr Leu Gly Gln Pro Asn Thr Leu Ile Cys Leu Val Asp Asn Ile100 105 110Phe Pro Pro Val Val Asn Ile Thr Trp Leu Thr Asn Gly His Ser Val115 120 125Thr Glu Gly Val Ser Glu Thr Thr Phe Leu Ser Lys Ser Asp His Ser130 135 140Phe Phe Lys Ile Ser Tyr Leu Thr Leu Leu Pro Ser Ala Glu Glu Ser145 150 155 160Tyr Asp Cys Lys Val Glu His Trp Gly Leu Asp Lys Pro Leu Leu Lys165 170 175His Trp Glu Pro Glu180199189PRTHomo sapiens 199Ser Pro Glu Asp Phe Val Tyr Gln Phe Lys Ala Met Cys Tyr Phe Thr1 5 10 15Asn Gly Thr Glu Arg Val Tyr Val Thr Arg Tyr Ile Tyr Asn Arg Glu20 25 30Glu Tyr Ala Arg Phe Asp Ser Asp Val Glu Val Tyr Arg Ala Val Thr35 40 45Pro Leu Gly Pro Pro Asp Ala Glu Tyr Trp Asn Ser Gln Lys Glu Val50 55 60Leu Glu Arg Thr Arg Ala Glu Leu Asp Thr Val Cys Arg His Asn Tyr65 70 75 80Gln Leu Glu Leu Arg Thr Thr Leu Gln Arg Arg Val Glu Pro Thr Val85 90 95Thr Ile Ser Pro Ser Arg Thr Glu Ala Leu Asn His His Asn Leu Leu100 105 110Val Cys Ser Val Thr Asp Phe Tyr Pro Ala Gln Ile Lys Val Arg Trp115 120 125Phe Arg Asn Asp Gln Glu Glu Thr Thr Gly Val Val Ser Thr Pro Leu130 135 140Ile Arg Asn Gly Asp Trp Thr Phe Gln Ile Leu Val Met Leu Glu Met145 150 155 160Thr Pro Gln His Gly Asp Val Tyr Thr Cys His Val Glu His Pro Ser165 170 175Leu Gln Asn Pro Ile Thr Val Glu Trp Arg Ala Gln Ser180 185200181PRTHomo sapiens 200Val Ala Asp His Val Ala Ser Tyr Gly Val Asn Leu Tyr Gln Ser Tyr1 5 10 15Gly Pro Ser Gly Gln Tyr Ser His Glu Phe Asp Gly Asp Glu Glu Phe20 25 30Tyr Val Asp Leu Glu Arg Lys Glu Thr Val Trp Gln Leu Pro Leu Phe35 40 45Arg Arg Phe Arg Arg Phe Asp Pro Gln Phe Ala Leu Thr Asn Ile Ala50 55 60Val Leu Lys His Asn Leu Asn Ile Val Ile Lys Arg Ser Asn Ser Thr65 70 75 80Ala Ala Thr Asn Glu Val Pro Glu Val Thr Val Phe Ser Lys Ser Pro85 90 95Val Thr Leu Gly Gln Pro Asn Thr Leu Ile Cys Leu Val Asp Asn Ile100 105 110Phe Pro Pro Val Val Asn Ile Thr Trp Leu Ser Asn Gly His Ser Val115 120 125Thr Glu Gly Val

Ser Glu Thr Ser Phe Leu Ser Lys Ser Asp His Ser130 135 140Phe Phe Lys Ile Ser Tyr Leu Thr Phe Leu Pro Ser Asp Asp Glu Ile145 150 155 160Tyr Asp Cys Lys Val Glu His Trp Gly Leu Asp Glu Pro Leu Leu Lys165 170 175His Trp Glu Pro Glu180201191PRTHomo sapiens 201Ser Pro Glu Asp Phe Val Tyr Gln Phe Lys Gly Met Cys Tyr Phe Thr1 5 10 15Asn Gly Thr Glu Arg Val Arg Leu Val Thr Arg Tyr Ile Tyr Asn Arg20 25 30Glu Glu Tyr Ala Arg Phe Asp Ser Asp Val Gly Val Tyr Arg Ala Val35 40 45Thr Pro Leu Gly Pro Pro Ala Ala Glu Tyr Trp Asn Ser Gln Lys Glu50 55 60Val Leu Glu Arg Thr Arg Ala Glu Leu Asp Thr Val Cys Arg His Asn65 70 75 80Tyr Gln Leu Glu Leu Arg Thr Thr Leu Gln Arg Arg Val Glu Pro Thr85 90 95Val Thr Ile Ser Pro Ser Arg Thr Glu Ala Leu Asn His His Asn Leu100 105 110Leu Val Cys Ser Val Thr Asp Phe Tyr Pro Ala Gln Ile Lys Val Arg115 120 125Trp Phe Arg Asn Asp Gln Glu Glu Thr Thr Ala Gly Val Val Ser Thr130 135 140Pro Leu Ile Arg Asn Gly Asp Trp Thr Phe Gln Ile Leu Val Met Leu145 150 155 160Glu Met Thr Pro Gln Arg Gly Asp Val Tyr Thr Cys His Val Glu His165 170 175Pro Ser Leu Gln Asn Pro Ile Ile Val Glu Trp Arg Ala Gln Ser180 185 190202178PRTHomo sapiens 202Gln Phe Arg Val Ile Gly Pro Arg His Pro Ile Arg Ala Leu Val Gly1 5 10 15Asp Glu Val Glu Leu Pro Cys Arg Ile Ser Pro Gly Lys Asn Ala Thr20 25 30Gly Met Glu Val Gly Trp Tyr Arg Pro Pro Phe Ser Arg Val Val His35 40 45Leu Tyr Arg Asn Gly Lys Asp Gln Asp Gly Asp Gln Ala Pro Glu Tyr50 55 60Arg Gly Arg Thr Glu Leu Leu Lys Asp Ala Ile Gly Glu Gly Lys Val65 70 75 80Thr Leu Arg Ile Arg Asn Val Arg Phe Ser Asp Glu Gly Gly Phe Thr85 90 95Cys Phe Phe Arg Asp His Ser Tyr Gln Glu Glu Ala Ala Met Glu Leu100 105 110Lys Val Glu Asp Pro Phe Tyr Trp Val Ser Pro Gly Val Leu Val Leu115 120 125Leu Ala Val Leu Pro Val Leu Leu Leu Gln Ile Thr Val Gly Leu Val130 135 140Phe Leu Cys Leu Gln Tyr Arg Leu Arg Gly Lys Leu Arg Ala Glu Ile145 150 155 160Glu Asn Leu His Arg Thr Phe Gly Gln Phe Leu Glu Glu Leu Arg Asn165 170 175Pro Phe20381PRTHomo sapiens 203Met Ser Gln Lys Pro Ala Lys Glu Gly Pro Arg Leu Ser Lys Asn Gln1 5 10 15Lys Tyr Ser Glu His Phe Ser Ile His Cys Cys Pro Pro Phe Thr Phe20 25 30Leu Asn Ser Lys Lys Glu Ile Val Asp Arg Lys Tyr Ser Ile Cys Lys35 40 45Ser Gly Cys Phe Tyr Gln Lys Lys Glu Glu Asp Trp Ile Cys Cys Ala50 55 60Cys Gln Lys Thr Arg Leu Lys Arg Lys Ile Arg Pro Thr Pro Lys Lys65 70 75 80Lys204999PRTHomo sapiens 204Met Met Gly Leu Phe Pro Arg Thr Thr Gly Ala Leu Ala Ile Phe Val1 5 10 15Val Val Ile Leu Val His Gly Glu Leu Arg Ile Glu Thr Lys Gly Gln20 25 30Tyr Asp Glu Glu Glu Met Thr Met Gln Gln Ala Lys Arg Arg Gln Lys35 40 45Arg Glu Trp Val Lys Phe Ala Lys Pro Cys Arg Glu Gly Glu Asp Asn50 55 60Ser Lys Arg Asn Pro Ile Ala Lys Ile Thr Ser Asp Tyr Gln Ala Thr65 70 75 80Gln Lys Ile Thr Tyr Arg Ile Ser Gly Val Gly Ile Asp Gln Pro Pro85 90 95Phe Gly Ile Phe Val Val Asp Lys Asn Thr Gly Asp Ile Asn Ile Thr100 105 110Ala Ile Val Asp Arg Glu Glu Thr Pro Ser Phe Leu Ile Thr Cys Arg115 120 125Ala Leu Asn Ala Gln Gly Leu Asp Val Glu Lys Pro Leu Ile Leu Thr130 135 140Val Lys Ile Leu Asp Ile Asn Asp Asn Pro Pro Val Phe Ser Gln Gln145 150 155 160Ile Phe Met Gly Glu Ile Glu Glu Asn Ser Ala Ser Asn Ser Leu Val165 170 175Met Ile Leu Asn Ala Thr Asp Ala Asp Glu Pro Asn His Leu Asn Ser180 185 190Lys Ile Ala Phe Lys Ile Val Ser Gln Glu Pro Ala Gly Thr Pro Met195 200 205Phe Leu Leu Ser Arg Asn Thr Gly Glu Val Arg Thr Leu Thr Asn Ser210 215 220Leu Asp Arg Glu Gln Ala Ser Ser Tyr Arg Leu Val Val Ser Gly Ala225 230 235 240Asp Lys Asp Gly Glu Gly Leu Ser Thr Gln Cys Glu Cys Asn Ile Lys245 250 255Val Lys Asp Val Asn Asp Asn Phe Pro Met Phe Arg Asp Ser Gln Tyr260 265 270Ser Ala Arg Ile Glu Glu Asn Ile Leu Ser Ser Glu Leu Leu Arg Phe275 280 285Gln Val Thr Asp Leu Asp Glu Glu Tyr Thr Asp Asn Trp Leu Ala Val290 295 300Tyr Phe Phe Thr Ser Gly Asn Glu Gly Asn Trp Phe Glu Ile Gln Thr305 310 315 320Asp Pro Arg Thr Asn Glu Gly Ile Leu Lys Val Val Lys Ala Leu Asp325 330 335Tyr Glu Gln Leu Gln Ser Val Lys Leu Ser Ile Ala Val Lys Asn Lys340 345 350Ala Glu Phe His Gln Ser Val Ile Ser Arg Tyr Arg Val Gln Ser Thr355 360 365Pro Val Thr Ile Gln Val Ile Asn Val Arg Glu Gly Ile Ala Phe Arg370 375 380Pro Ala Ser Lys Thr Phe Thr Val Gln Lys Gly Ile Ser Ser Lys Lys385 390 395 400Leu Val Asp Tyr Ile Leu Gly Thr Tyr Gln Ala Ile Asp Glu Asp Thr405 410 415Asn Lys Ala Ala Ser Asn Val Lys Tyr Val Met Gly Arg Asn Asp Gly420 425 430Gly Tyr Leu Met Ile Asp Ser Lys Thr Ala Glu Ile Lys Phe Val Lys435 440 445Asn Met Asn Arg Asp Ser Thr Phe Ile Val Asn Lys Thr Ile Thr Ala450 455 460Glu Val Leu Ala Ile Asp Glu Tyr Thr Gly Lys Thr Ser Thr Gly Thr465 470 475 480Val Tyr Val Arg Val Pro Asp Phe Asn Asp Asn Cys Pro Thr Ala Val485 490 495Leu Glu Lys Asp Ala Val Cys Ser Ser Ser Pro Ser Val Val Val Ser500 505 510Ala Arg Thr Leu Asn Asn Arg Tyr Thr Gly Pro Tyr Thr Phe Ala Leu515 520 525Glu Asp Gln Pro Val Lys Leu Pro Ala Val Trp Ser Ile Thr Thr Leu530 535 540Asn Ala Thr Ser Ala Leu Leu Arg Ala Gln Glu Gln Ile Pro Pro Gly545 550 555 560Val Tyr His Ile Ser Leu Val Leu Thr Asp Ser Gln Asn Asn Arg Cys565 570 575Glu Met Pro Arg Ser Leu Thr Leu Glu Val Cys Gln Cys Asp Asn Arg580 585 590Gly Ile Cys Gly Thr Ser Tyr Pro Thr Thr Ser Pro Gly Thr Arg Tyr595 600 605Gly Arg Pro His Ser Gly Arg Leu Gly Pro Ala Ala Ile Gly Leu Leu610 615 620Leu Leu Gly Leu Leu Leu Leu Leu Leu Ala Pro Leu Leu Leu Leu Thr625 630 635 640Cys Asp Cys Gly Ala Gly Ser Thr Gly Gly Val Thr Gly Gly Phe Ile645 650 655Pro Val Pro Asp Gly Ser Glu Gly Thr Ile His Gln Trp Gly Ile Glu660 665 670Gly Ala His Pro Glu Asp Lys Glu Ile Thr Asn Ile Cys Val Pro Pro675 680 685Val Thr Ala Asn Gly Ala Asp Phe Met Glu Ser Ser Glu Val Cys Thr690 695 700Asn Thr Tyr Ala Arg Gly Thr Ala Val Glu Gly Thr Ser Gly Met Glu705 710 715 720Met Thr Thr Lys Leu Gly Ala Ala Thr Glu Ser Gly Gly Ala Ala Gly725 730 735Phe Ala Thr Gly Thr Val Ser Gly Ala Ala Ser Gly Phe Gly Ala Ala740 745 750Thr Gly Val Gly Ile Cys Ser Ser Gly Gln Ser Gly Thr Met Arg Thr755 760 765Arg His Ser Thr Gly Gly Thr Asn Lys Asp Tyr Ala Asp Gly Ala Ile770 775 780Ser Met Asn Phe Leu Asp Ser Tyr Phe Ser Gln Lys Ala Phe Ala Cys785 790 795 800Ala Glu Glu Asp Asp Gly Gln Glu Ala Asn Asp Cys Leu Leu Ile Tyr805 810 815Asp Asn Glu Gly Ala Asp Ala Thr Gly Ser Pro Val Gly Ser Val Gly820 825 830Cys Cys Ser Phe Ile Ala Asp Asp Leu Asp Asp Ser Phe Leu Asp Ser835 840 845Leu Gly Pro Lys Phe Lys Lys Leu Ala Glu Ile Ser Leu Gly Val Asp850 855 860Gly Glu Gly Lys Glu Val Gln Pro Pro Ser Lys Asp Ser Gly Tyr Gly865 870 875 880Ile Glu Ser Cys Gly His Pro Ile Glu Val Gln Gln Thr Gly Phe Val885 890 895Lys Cys Gln Thr Leu Ser Gly Ser Gln Gly Ala Ser Ala Leu Ser Thr900 905 910Ser Gly Ser Val Gln Pro Ala Val Ser Ile Pro Asp Pro Leu Gln His915 920 925Gly Asn Tyr Leu Val Thr Glu Thr Tyr Ser Ala Ser Gly Ser Leu Val930 935 940Gln Pro Ser Thr Ala Gly Phe Asp Pro Leu Leu Thr Gln Asn Val Ile945 950 955 960Val Thr Glu Arg Val Ile Cys Pro Ile Ser Ser Val Pro Gly Asn Leu965 970 975Ala Gly Pro Thr Gln Leu Arg Gly Ser His Thr Met Leu Cys Thr Glu980 985 990Asp Pro Cys Ser Arg Leu Ile99520515PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 205Glu Lys Ala Lys Tyr Glu Ala Tyr Lys Ala Ala Ala Ala Ala Ala1 5 10 1520615PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 206Lys Asp Ile Leu Glu Asp Glu Arg Ala Ala Val Asp Thr Tyr Cys1 5 10 152075PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 207Asp Glu Arg Ala Ala1 52085PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 208Gln Lys Arg Ala Ala1 520915PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 209Gln Lys Arg Ala Ala Tyr Asp Gln Tyr Gly His Ala Ala Phe Glu1 5 10 152106PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 210Gly Asp Leu Gln Val Leu1 521113PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 211Tyr Pro Tyr Asp Val Pro Asp Tyr Ala Ser Leu Arg Ser1 5 102126PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 212Asp Val Pro Asp Tyr Ala1 521317PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 213Glu Asn Pro Val Val His Glu Phe Lys Asn Ile Val Thr Pro Arg Thr1 5 10 15Pro21417PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 214Ala Lys Pro Val Val His Leu Phe Ala Asn Ile Val Thr Pro Arg Thr1 5 10 15Pro2154PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 215Tyr Phe Ala Lys12164PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 216Glu Tyr Tyr Lys12174PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 217Tyr Glu Ala Lys12184PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 218Ala Glu Lys Tyr12194PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 219Phe Leu Met Tyr12204PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 220Ile Met Gln Val12215PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 221Lys Arg Ile Leu Val1 52225PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 222Phe Ile Leu Met Val1 52234PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 223Phe Trp Glu Phe12244PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 224Ala Ile Asn Val12254PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 225Tyr Glu Phe Trp12266PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 226Glu Phe Ile Val Trp Tyr1 52274PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 227Glu Phe Lys Gln12284PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 228Ala Glu Lys Gln12294PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 229Ala Lys Gln Tyr12304PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 230Ala Asn Gln Tyr12315PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 231Ala Gly Asn Ser Tyr1 52326PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 232Ala Gly Ile Asn Ser Val1 52335PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 233Ala Ile Gln Ser Val1 52346PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 234Ile Lys Arg Ser Val Tyr1 52354PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 235Lys His Arg Val123613PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 236Ala Lys Ala Val Ala Ala Trp Thr Leu Lys Ala Ala Ala1 5 102375PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 237Thr His Met Cys Glu1 52385PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 238Pro Trp Lys Asn Ala1 52394PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 239Arg Gly Asp Ser124010PRTArtificial SequenceDescription of Artificial Sequence Synthetic peptide 240Tyr Val Arg Pro Leu Trp Val Arg Met Glu1 5 10

Claims

1. A process for manufacturing a composition comprising directed sequence polymers (DSPs) useful for the amelioration of an unwanted immune response, comprising the steps of: (1) selecting a first base peptide sequence, wherein the sequence is an amino acid sequence of an epitope of an antigen associated with the autoimmune disease; (2) synthesizing by solid phase peptide synthesis a first cassette of the DSPs, wherein, for each amino acid position of the first cassette of the directed sequence polymers, an amino acid is incorporated into a DSP, such amino acid randomly selected from a mixture of amino acids consisting of: (i) an amino acid found at the corresponding position in said first peptide sequence, such amino acid present in the pool at a relative molar concentration of a0; (ii) a primary replacement of the amino acid found at the said position in said selected amino acid sequence, said primary replacement defined according to amino acid similarity, such primary replacement amino acid present in the mixture at a relative molar concentration of a1; (iii) a secondary replacement, if applicable, of the amino acid found at the said position in said selected amino acid sequence, said secondary replacement defined according to amino acid similarity, such secondary replacement amino acid present in the mixture at a relative molar concentration of a2; (iv) a tertiary replacement, if applicable, of the amino acid found at the said position in said selected amino acid sequence, said tertiary replacement defined according to tertiary amino acid similarity, such tertiary replacement amino acid present in the mixture at a relative molar concentration of a3; and (v) A: alanine, present in the mixture at a fixed relative molar concentration A, wherein the amino acids in the mixture are present in a fixed molar input ratio relative to each other, determined prior to starting synthesis, wherein the relative molar amount of A is more than 50% of the total amino acid concentration of the DSPs, and each of a0 and a1 is within the range of 0.05-50%, each of a2 and a3 is within the range of 0-50%, and wherein a0+a1+a2+a3=100-A; (3) extending the length of the DSPs by (a) repeating step (2) for 2 to 15 cycles and elongating the DSP under the same condition; (b) repeating step (2) for 2 to 15 cycles and elongating the DSP, for each cycle, using a different input ratio of amino acids in the mixture; (c) repeating steps (1) and (2) for 2 to 15 cycles and elongating the DSP using cassettes based on more than one base peptide; or (d) assembling 2 to 15 cassettes synthesized in a single cycle of step (2); or (e) assembling 2 to 15 cassettes, the first cassette synthesized under one condition of step (2), and second and more cassettes synthesized under a second condition of step (2); (4) optionally further elongating the DSPs by repeating steps (2) and (3) for 2 to 15 cycles, wherein for each cycle a new cassette of the DSP is designed independently from the any of the previous cassettes designated by previous cycles of step (2); wherein the number of cycles selected in steps (3) and (4) is selected so that the final length of the DSP is about 25 to 300 amino acid residues.

2. The process according to claim 1, wherein the amino acid sequence of the epitope is selected from a group consisting of SEQ ID NO: 1 through 189 depicted in Table I.

3. The process according to claim 1, wherein the unwanted immune response derives from a host's attempted rejection of a transplanted organ.

4. The process according to claim 1, wherein the unwanted immune response is an autoimmune disease.

5. The process according to claim 4, wherein the autoimmune disease is selected from the group consisting of multiple sclerosis, systemic lupus erythematosus, type I diabetes mellitus, myasthenia gravis, rheumatoid arthritis, and pemphigus vulgaris.

6. The process according to claim 5, wherein the autoimmune disease is multiple sclerosis.

7. The process according to claim 5, wherein the autoimmune disease is systemic lupus erythematosus.

8. The process according to claim 5, wherein the autoimmune disease is type I diabetes mellitus.

9. The process according to claim 5, wherein the autoimmune disease is myasthenia gravis.

10. The process according to claim 5, wherein the autoimmune disease is rheumatoid arthritis.

11. The process according to claim 5, wherein the autoimmune disease is pemphigus vulgaris.

12. The process according to claim 6, wherein the amino acid sequence of the epitope is a partial sequence of a protein selected from the group consisting of osteopontin, an HLA protein, myelin oligodendrite glycoprotein, myelin basic protein (MBP), proteolipid protein, and myelin associated glycoproteins, S100Beta, heat shock protein alpha, beta crystallin, myelin-associated oligodendrocytic basic protein (MOBP), and 2',3' cyclic nucleotide 3'-phosphodiesterase.

13. The process according to claim 6, wherein the amino acid sequence of the epitope is selected from the group consisting of SEQ ID NO: 6-32.

14. The process according to claim 7, wherein the amino acid sequence of the epitope is a partial sequence of a protein selected from hsp60, hsp70, Ro60, La, SmD, and 70-kDa U I RNP.

15. The process according to claim 7, wherein the amino acid sequence of the epitope is selected from the group consisting of SEQ ID NO: 92-140.

16. The process according to claim 8, wherein the amino acid sequence of the epitope is a partial sequence of a protein selected from the group consisting of hsp60, glutamic acid decarboxylase (GAD65), insulinoma-antigen 2 (IA-2), and insulin.

17. The process according to claim 8, wherein the amino acid sequence of the amino acid sequence of the epitope is selected from the group consisting of SEQ ID NO: 44-91.

18. The process according to claim 9, wherein the amino acid sequence of the epitope is a partial sequence of a protein selected from the group consisting of acetylcholine receptor (AChR) .alpha.-subunit and muscle-specific receptor tyrosine kinase (MuSK).

19. The process according to claim 9, wherein the amino acid sequence of the epitope is selected from the group consisting of SEQ ID NO: 1-2.

20. The process according to claim 10, wherein the amino acid sequence of the epitope is a partial sequence of a protein selected from the group consisting of type II collagen and hsp60.

21. The process according to claim 10, wherein the amino acid sequence of the epitope is selected from the group consisting of SEQ ID NO: 3-5.

22. The process according to claim 11, wherein the amino acid sequence of the epitope is a partial sequence of a protein selected from the group consisting of desmoglein 3 (Dsg3).

23. The process according to claim 11, wherein the amino acid sequence of the epitope is selected from the group consisting of SEQ ID NO: 33-43.

24. The process according to claim 1, wherein the amino acid similarity is defined according to the similarity table shown in FIG. 4.

25. A process for manufacturing a composition comprising directed sequence polymers (DSPs) useful for the amelioration of an unwanted immune response, comprising the steps of: (1) selecting a first base peptide sequence, wherein the sequence is an amino acid sequence of an epitope of an antigen associated with the autoimmune disease; (2) synthesizing by solid phase peptide synthesis a first cassette of the DSPs, wherein, for each amino acid position of the first cassette of the directed sequence polymers, an amino acid is incorporated into a DSP, such amino acid randomly selected from a mixture of amino acids consisting of: (i) an amino acid found at the corresponding position in said first peptide sequence, such amino acid present in the pool at a relative molar concentration of a0; (ii) a primary replacement of the amino acid found at the said position in said selected amino acid sequence, said primary replacement being the most prevalent conserved substitution, such primary replacement amino acid present in the mixture at a relative molar concentration of a1; (iii) a secondary replacement, if applicable, of the amino acid found at the said position in said selected amino acid sequence, said secondary replacement being the second most prevalent conserved substitution, such secondary replacement amino acid present in the mixture at a relative molar concentration of a2; (iv) a tertiary replacement, if applicable, of the amino acid found at the said position in said selected amino acid sequence, said tertiary replacement being the third most prevalent conserved substitution, such tertiary replacement amino acid present in the mixture at a relative molar concentration of a3; and (v) A: alanine, present in the mixture at a fixed relative molar concentration A, wherein the amino acids in the mixture are present in a fixed molar input ratio relative to each other, determined prior to starting synthesis, wherein the relative molar amount of A is more than 50% of the total amino acid concentration of the DSPs, and each of a0 and a1 is within the range of 0.05-50%, each of a2 and a3 is within the range of 0-50%, and wherein a0+a1+a2+a3=100-A; (3) extending the length of the DSPs by (a) repeating step (2) for 2 to 15 cycles and elongating the DSP under the same condition; (b) repeating step (2) for 2 to 15 cycles and elongating the DSP, for each cycle, using a different input ratio of amino acids in the mixture; (c) repeating steps (1) and (2) for 2 to 15 cycles and elongating the DSP using cassettes based on more than one base peptide; or (d) assembling 2 to 15 cassettes synthesized in a single cycle of step (2); or (e) assembling 2 to 15 cassettes, the first cassette synthesized under one condition of step (2), and second and more cassettes synthesized under a second condition of step (2); (4) optionally further elongating the DSPs by repeating steps (2) and (3) for 2 to 15 cycles, wherein for each cycle a new cassette of the DSP is designed independently from the any of the previous cassettes designated by previous cycles of step (2); wherein the number of cycles selected in steps (3) and (4) is selected so that the final length of the DSP is about 25 to 300 amino acid residues, and wherein the conserved substitution is determined based on empirical data of known variants of the epitope.

26. A composition comprising directed sequence polymers (DSPS) manufactured by the process according to claim 1.

27. A composition comprising: directed sequence polymers (DSPs) having a length of between about 25 to 300 amino acids, wherein each of such DSPs comprises between 2-15 cassettes, each block comprising between 8-30 amino acids; wherein each cassette is derived from a first base peptide sequence, wherein the sequence is an amino acid sequence of an epitope of an antigen associated with an autoimmune disease and the amino acid at each position of the cassette is selected from the group consisting of: (i) an amino acid, a0, found at the corresponding position in a first base peptide sequence; (ii) a primary replacement, if applicable, of the amino acid, a1, found at the said position in said selected amino acid sequence, said primary replacement defined according to amino acid similarity; (iii) a secondary replacement, if applicable, of the amino acid, a3, found at the said position in said selected amino acid sequence, said secondary replacement defined according to amino acid similarity; (iv) a tertiary replacement, if applicable, of the amino acid, a4, found at the said position in said selected amino acid sequence, said tertiary replacement defined according to amino acid similarity; and (v) A: alanine; wherein the amino acids in the mixture are present in a fixed molar ratio relative to each other, wherein the relative molar amount of A is at least 20% of the total amino acid comprising the DSPs.

28. The composition of claim 27, wherein said DSP comprises cassettes, such cassettes comprising the amino acid sequences that are derived from the first base peptide sequence.

29. The composition of claim 27, wherein said DSP comprises one or more cassettes, such cassettes comprising one or more cassettes having amino acid sequences that are derived from the first base peptide sequence and one or more cassettes having amino acid sequences that are derived from a second base peptide sequence of a second epitope.

30. The composition of claim 27, wherein the first base peptide sequence is selected from SEQ ID NO: 1-189.

31. The composition of claim 27, wherein the autoimmune disease is selected from the group consisting of multiple sclerosis, systemic lupus erythematosus, type I diabetes mellitus, myasthenia gravis, rheumatoid arthritis, and pemphigus vulgaris.

32. The composition of claim 27, wherein the amino acid sequence of the first base peptide sequence is a partial sequence of a protein selected from the group consisting of: (a) osteopontin, an HLA protein, myelin oligodendrite glycoprotein, myelin basic protein (MBP), proteolipid protein, and myelin associated glycoproteins, S100Beta, heat shock protein alpha, beta crystallin, myelin-associated oligodendrocytic basic protein (MOBP), 2',3' cyclic nucleotide 3'-phosphodiesterase; (b) hsp60, hsp70, Ro60, La, SmD, and 70-kDa U1RNP; (c) glutamic acid decarboxylase (GAD65), insulinoma-antigen 2 (IA-2), insulin; (d) acetylcholine receptor (AChR) .alpha.-subunit and muscle-specific receptor tyrosine kinase (MuSK); (e) type II collagen; and (f) desmoglein 3 (Dsg3)

33. The composition of claim 27, wherein the amino acid similarity is defined according to the similarity table shown in FIG. 4.

34. The composition of claim 27, wherein the amino acid similarity is determined based on empirical data of known variants of the epitope.

35. A method of treating an autoimmune disease by administering a directed sequence polymer (DSP) composition, comprising administering to a subject in need thereof a dosing regimen of an effective amount of a DSP composition for the amelioration of said disease, wherein the DSP composition is selected from any one of claims 24 to 30.

36. The method according to claim 35, wherein the autoimmune disease is selected from the group consisting of multiple sclerosis, systemic lupus erythematosus, type I diabetes mellitus, myasthenia gravis, rheumatoid arthritis, and pemphigus vulgaris.

37. Use of a composition according to any one of claims 26 to 34 for the manufacturer of a medicament for the treatment of an autoimmune disease.