Ubiquitin high affinity cyclic peptides and methods of use thereof

Abstract

The present invention is directed to a polypeptide which binds ubiquitin (Ub), e.g., Lysine 48 of Ub. Further provided are methods of using the polypeptide, such as for reducing deubiquitination activity of a cell, and for treating cancer in a subject in need thereof.

Description

UBIQUITIN HIGH AFFINITY CYCLIC PEPTIDES AND METHODS OF USETHEREOFREFERENCE TO AN ELECTRONIC SEQUENCE LISTING

[0001] The contents of the electronic sequence listing (TECH-P-0296-PCT.xml; size: 5,410 bytes; and date of creation: 22 December 2024) is herein incorporated by reference in its entirety.CROSS-REFERENCE TO RELATED APPLICATIONS

[0002] The application claims the benefit of priority of U.S. Provisional Patent Application No. 63 / 623,267, titled "UBIQUITIN HIGH AFFINITY CYCLIC PEPTIDES AND METHODS OF USE THEREOF", filed January 21, 2024, the contents of which are incorporated herein by reference in their entirety.FIELD OF INVENTION

[0003] The present invention is in the field of peptide engineering and drug screening.BACKGROUND OF THE INVENTION

[0004] The initial and obligatory step in ubiquitin (Ub) signaling is the ATP-dependent modification of the protein substrate by Ub or poly Ub chains. The formation of poly Ub chains is achieved by the collaborative action of three enzymes, known as El, E2 and E3. The most studied Ub chain is the K48-linked chain, which is known to adopt a compact structure and target the modified protein to proteasomal degradation.

[0005] Ubiquitination is a major post-translational modification affecting many aspects of cell biology and has been linked to various diseases such as cancer. Several tumor suppressors or oncogenes involved in Ub conjugation and deconjugation pathways are altered in cancerous states, making the Ub system an excellent target for cancer therapy. In particular, the ubiquitin-proteasome system (UPS) has proven to be a valid target for anti-cancer drug development as exemplified by the approval of the small molecule Bortezomib, for the treatment of multiple myeloma and mantle cell lymphoma.

[0006] Another approach is targeting the Ub chain itself. This offers great potential for interfering with Ub signaling compared to targeting individual Ub-modifying enzymes. In this regard, the small molecules ‘ubistatins’ emerged from a chemical genetic screen and were found to bind mono Ub and K48-linked chains, and thereby impair recognition by the proteasome and inhibit protease degradation. However, ubistatins suffer from poor cell permeability, weak pM binding and poor chain specificity.

[0007] Targeting Ub chains of particular lengths and linkages may be advantageous and influence specific cellular processes. However, this represents a significant challenge for molecular recognition, given the number of possible Ub chains and the often-subtle differences in their structure and dynamics.

[0008] To this end, there is still a need for a molecule or a compound having specific binding affinity to mono Ub and particularly K48-linked chains, wherein the molecule or compound is capable of sufficiently penetrating a living cell.SUMMARY OF THE INVENTION

[0009] The present invention is directed to a polypeptide and methods of using same, such as for reducing deubiquitination activity of a cell or for ameliorating, or treating cancer in a subject in need thereof.

[0010] According to the first aspect, there is provided a polypeptide comprising an amino acid sequence selected from the group consisting of: FQYWOYATGVCR (SEQ ID NO: 1); FQYWOYATGVCRR (SEQ ID NO: 2); FQYWOYATGVCGR (SEQ ID NO: 3); and FQYWOYATGVCGRR (SEQ ID NO: 4).[Oi l] According to another aspect, there is provided a pharmaceutical composition comprising the polypeptide of the invention and at least one acceptable carrier.

[0012] According to another aspect, there is provided a method for reducing deubiquitination activity of a cell, the method comprising contacting the cell with an effective amount of a polypeptide comprising the amino acid sequence set forth in SEQ ID Nos: 1-4.

[0013] According to another aspect, there is provided a method for ameliorating or treating cancer in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of a polypeptide comprising the amino acid sequence set forth in SEQ ID Nos: 1-4.

[0014] In some embodiments, the polypeptide is a cyclic polypeptide.

[0015] In some embodiments, the at least one amino acid residue of the is methylated.

[0016] In some embodiments, the polypeptide comprises not more than 16 amino acid residues.

[0017] In some embodiments, the amino acid at position one is a D amino acid.

[0018] In some embodiments, the amino acid at position one is conjugated to a cyclizing molecule.

[0019] In some embodiments, the polypeptide is a cyclic polypeptide prepared using a cyclizing molecule comprising a halogen.

[0020] In some embodiments, the cyclizing molecule is selected from the group consisting of: chloracetyl chloride, 3 -chlorobenzoyl (3-ClBz), 4 -chlorobenzoyl (4-ClBz) or C12SAc.

[0021] In some embodiments, the polypeptide is characterized as having: cell penetration capability, ubiquitin (Ub) binding capability, or a combination thereof.

[0022] In some embodiments, the polypeptide has increased affinity to Ub compared to control.

[0023] In some embodiments, the control is a polypeptide consisting of the amino acid sequence set forth in SEQ ID NO: 5.

[0024] In some embodiments, the pharmaceutical composition is for use in treatment of cancer in a subject in need thereof.

[0025] In some embodiments, the administering is subcutaneously administering.

[0026] In some embodiments, the polypeptide: (i) binds Ub with an affinity KD of 0.05- 100 nM; (ii) comprises not more than 16 amino acid residues; or both (i) and (ii).

[0027] In some embodiments, the polypeptide has increased affinity to Ub compared to control.

[0028] In some embodiments, the Ub is a polymeric Ub.

[0029] In some embodiments, the Ub comprises Ub monomers linked at their K48 position (K48Ub).

[0030] In some embodiments, the polypeptide reduces deubiquitination activity of a cell by at least 30%.

[0031] In some embodiments, the polypeptide reduces proteasomal degradation rate of ubiquitinated proteins by at least 40%.

[0032] In some embodiments, the polypeptide has increased pro-apoptotic activity compared to control.

[0033] In some embodiments, the increased pro-apoptotic activity results in at least 20% more cell apoptosis compared to control.

[0034] Unless otherwise defined, all technical and / or scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the invention, exemplary methods and / or materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be necessarily limiting.

[0035] Further embodiments and the full scope of applicability of the present invention will become apparent from the detailed description given hereinafter. However, it should be understood that the detailed description and specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.BRIEF DESCRIPTION OF THE DRAWINGS

[0036] Fig. 1 includes general non-limiting schematic representations of the cyclic polypeptides of the invention.

[0037] Fig. 2 includes a vertical bar graph showing a comparative efficiency assay of the cyclic peptides of the invention in MM Is cell line, normalized to the control. Ub4a- CR (SEQ ID NO: 1); Ub4a-CRR (SEQ ID NO: 2); Ub4a-GR (SEQ ID NO: 3); and Ub4a-GRR (SEQ ID NO: 4).

[0038] Fig. 3 includes a vertical bar graph showing a comparative efficiency assay of the cyclic peptides of the invention in BTZ900 (a bortezomib resistant cell line),normalized to the control. Ub4a-CR (SEQ ID NO: 1); Ub4a-CRR (SEQ ID NO: 2);Ub4a-GR (SEQ ID NO: 3); and Ub4a-GRR (SEQ ID NO: 4).

[0039] Fig. 4 includes a graph showing a comparison between the Ub4a derivatives, the cyclic peptides of the invention: Ub4a-CR (SEQ ID NO: 1) and Ub4a-GRR (SEQ ID NO: 4), time dependent efficacy in MMls cell line, normalized to the control. Each cyclic peptide was applied in two concentrations: 2 pM, and 5 pM.

[0040] Fig. 5 includes a graph showing a comparison between the Ub4a derivatives, the cyclic peptides of the invention: Ub4a-CR (SEQ ID NO: 1) and Ub4a-GRR (SEQ ID NO: 4), time dependent efficacy in BTZ900 (a bortezomib resistant cell line), normalized to the control. Each cyclic peptide was applied in two concentrations: 2 pM, and 5 pM.

[0041] Fig. 6 includes a vertical bar graph showing Ub4a-GRR (SEQ ID NO: 4) efficacy in MM1S and BTZ900, bortezomib resistant cell line, normalized to the control. Ub4a- GRR (SEQ ID NO: 4) was applied in two concentrations: 5 pM, and 8 pM.

[0042] Fig. 7 includes a vertical bar graph showing a comparison between Ub4a (SEQ ID NO: 5) and its derivative, the cyclic peptide of the invention Ub4a-GRR (SEQ ID NO: 4) in their efficacy in MM1S cell line using 2 concentrations: 2 pM, and 5 pM, normalized to the control.

[0043] Fig. 8 includes a vertical bar graph showing a time dependent stability of Ub4a- GRR (SEQ ID NO: 4) in human plasma, as determined using high-performance liquid chromatography (HPLC).

[0044] Fig. 9 includes a vertical bar graph showing concentration related effect of CP- 15, a Ub K63 inhibitor (as described in Vamisetti et al., Nature Communications (2022)13:6174, during a 12-day treatment on MM1S cell viability.

[0045] Fig. 10 includes a graph showing changes in body weight of 20 female NOD / SCID administered with Ub4a-GRR (SEQ ID NO: 4) by intravenous bolus (IV) or subcutaneously (SC). Data plotted as the percentage of change, relative to the initial body weight (Day 1). Results represent means +SEM for all mice in each group.

[0046] Fig. 11 includes a graph showing the mean plasma concentration of Ub4a-GRR (SEQ ID NO: 4) after the following means of administration: IV bolus, SC, intraperitoneally (IP), and intramuscularly (IM).

[0047] Fig. 12 includes a graph showing the plasma concentration of Ub4a-GRR (SEQ ID NO: 4) after SC dosing at 10.0 mg / kg.

[0048] Fig. 13 includes a graph showing in-vivo effect of UB4a (SEQ ID NO: 5) on tumor volume calculated average and standard error of 10 mice, over the span of 40 days in SCID NOD type, implanted with MM tumors from the BTZ900 cell line. Three (3) different doses were administered daily: 2 mg / kg, 5 mg / kg, and lOmg / kg. Changes in tumor volume was compared to vehicle-injected mice (daily), and bortezomib (once a week).

[0049] Fig. 14 includes a graph showing in-vivo effect of UB4a-GRR (SEQ ID NO: 4) on tumor volume calculated average and standard error of 3 mice, over the span of 38 days in SCID NOD type, implanted with MM tumors from the BTZ900 cell line. Changes in tumor volume after treatment with 10 mg / ml was compared to untreated mice, and CP- 15 Ub K63 inhibitor.DETAILED DESCRIPTION OF THE INVENTION

[0050] The present invention is directed to a polypeptide and methods of using same, such as for reducing deubiquitination activity of a cell or for ameliorating, or treating cancer in a subject in need thereof. The present invention is based, in part, on the findings that cyclic polypeptides bind ubiquitin polymers with an affinity KD at a nanomolar level. The present invention is further based, in part, on the surprising finding that cyclic polypeptides are capable of penetrating into a cell and bind to polymeric ubiquitin in vivo.Polypeptides

[0051] According to some embodiments, the invention is directed to a polypeptide.

[0052] In some embodiments, the polypeptide is capable of penetrating a cell (e.g., a cancer cell), binding to ubiquitin, or combination thereof.

[0053] In some embodiments, a polypeptide of the invention comprises or consists of an amino acid sequence selected from: FQYWOYATGVCR (SEQ ID NO: 1); FQYWOYATGVCRR (SEQ ID NO: 2); FQYWOYATGVCGR (SEQ ID NO: 3); or FQYWOYATGVCGRR (SEQ ID NO: 4), or an analog thereof, having at least 80%, 90%, 95%, 97%, or 99% homology or identity thereto, or any value and range therebetween. In some embodiments, a polypeptide of the invention comprises orconsists of an amino acid sequence selected from: FQYWOYATGVCR (SEQ ID NO: 1); FQYWOYATGVCRR (SEQ ID NO: 2); FQYWOYATGVCGR (SEQ ID NO: 3); or FQYWOYATGVCGRR (SEQ ID NO: 4), or an analog thereof, having 80-100%, 90- 100%, 95-100%, 97-100%, or 99-100% homology or identity thereto. Each possibility represents a separate embodiment of the invention.

[0054] In some embodiments, a polypeptide of the invention comprises the amino acid sequence FQYWOYATGVCR (SEQ ID NO: 1), or an analog thereof, having 80-100%, 90-100%, 95-100%, 97-100%, or 99-100% homology or identity thereto. Each possibility represents a separate embodiment of the invention. In some embodiments, a polypeptide of the invention consists of the amino acid sequence FQYWOYATGVCR (SEQ ID NO: 1), or an analog thereof, having 80-100%, 90-100%, 95-100%, 97-100%, or 99-100% homology or identity thereto. Each possibility represents a separate embodiment of the invention.

[0055] In some embodiments, a polypeptide of the invention comprises the amino acid sequence FQYWOYATGVCRR (SEQ ID NO: 2), or an analog thereof, having 80- 100%, 90-100%, 95-100%, 97-100%, or 99-100% homology or identity thereto. Each possibility represents a separate embodiment of the invention. In some embodiments, a polypeptide of the invention consists of the amino acid sequence FQYWOYATGVCRR (SEQ ID NO: 2), or an analog thereof, having 80-100%, 90-100%, 95-100%, 97-100%, or 99-100% homology or identity thereto. Each possibility represents a separate embodiment of the invention.

[0056] In some embodiments, a polypeptide of the invention comprises the amino acid sequence FQYWOYATGVCGR (SEQ ID NO: 3), or an analog thereof, having 80- 100%, 90-100%, 95-100%, 97-100%, or 99-100% homology or identity thereto. Each possibility represents a separate embodiment of the invention. In some embodiments, a polypeptide of the invention consists of the amino acid sequence FQYWOYATGVCGR (SEQ ID NO: 3), or an analog thereof, having 80-100%, 90-100%, 95-100%, 97-100%, or 99-100% homology or identity thereto. Each possibility represents a separate embodiment of the invention.

[0057] In some embodiments, a polypeptide of the invention comprises the amino acid sequence FQYWOYATGVCGRR (SEQ ID NO: 4), or an analog thereof, having 80- 100%, 90-100%, 95-100%, 97-100%, or 99-100% homology or identity thereto. Eachpossibility represents a separate embodiment of the invention. In some embodiments, a polypeptide of the invention consists of the amino acid sequence FQYWOYATGVCGRR (SEQ ID NO: 4), or an analog thereof, having 80-100%, 90- 100%, 95-100%, 97-100%, or 99-100% homology or identity thereto. Each possibility represents a separate embodiment of the invention.

[0058] The terms “homology” or “identity”, as used interchangeably herein, refer to sequence identity between two amino acid sequences or two nucleic acid sequences, with identity being a stricter comparison. The phrases “percent identity or homology” and “% identity or homology” refer to the percentage of sequence identity found in a comparison of two or more amino acid sequences or nucleic acid sequences. Two or more sequences can be anywhere from 0-100% identical, or any value there between. Identity can be determined by comparing a position in each sequence that can be aligned for purposes of comparison to a reference sequence. When a position in the compared sequence is occupied by the same nucleotide base or amino acid, then the molecules are identical at that position. A degree of identity of amino acid sequences is a function of the number of identical amino acids at positions shared by the amino acid sequences. A degree of identity between nucleic acid sequences is a function of the number of identical or matching nucleotides at positions shared by the nucleic acid sequences. A degree of homology of amino acid sequences is a function of the number of amino acids at positions shared by the polypeptide sequences.

[0059] The following is a non-limiting example for calculating homology or sequence identity between two sequences (the terms are used interchangeably herein). The sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). The optimal alignment is determined as the best score using the GAP program in the GCG software package with a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frame shift gap penalty of 5. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percentage identity between the two sequences is a function of the number of identical positions shared by the sequences.

[0060] In some embodiments, % homology or identity as described herein are calculated or determined using the basic local alignment search tool (BLAST). In some embodiments, % homology or identity as described herein are calculated or determined using Blossum 62 scoring matrix.

[0061] As used herein, "O" standing for "Ornithine", refers to a non-proteinogenic amino acid that is known to be involved in the urea cycle, as would be apparent to a person of skill in the art.

[0062] In some embodiments, a polypeptide of the invention is linear or cyclic. In some embodiments, the peptide or polypeptide is a cyclic peptide or a cyclic polypeptide.

[0063] As defined herein, the amino acid sequence of a polypeptide of the invention (SEQ ID Nos: 1-4) is cited from its N-terminus to the C-terminus. In some embodiments, amino acid residue positioned at the N-terminus of a polypeptide is located at the first position of the polypeptide. In some embodiments, a cited position of a given amino acid residue within a cyclic polypeptide is referred to, based on the position of the amino acid residue in the linear form of the polypeptide.

[0064] In some embodiments, a cyclic polypeptide of the invention is characterized by having increased affinity to ubiquitin. In some embodiments, ubiquitin comprises dimeric ubiquitin, tetrameric ubiquitin, or both.

[0065] In some embodiments, a cyclic polypeptide of the invention having increased affinity to dimeric ubiquitin, tetrameric ubiquitin, or both, comprises or consists of the amino acid sequences set forth in SEQ ID Nos: 1-4.

[0066] In some embodiments, the cyclic polypeptide of the disclosed invention comprises not more than 16 amino acid residues. In some embodiments, not more than 16 amino acid residues comprises 8, 9, 10, 11, 12, 13, 14, or 15 amino acid residues, or any value and range therebetween. Each possibility represents a separate embodiment of the invention. In some embodiments, not more than 16 amino acid residues comprises 7-9, 8-11, 7-12, 10-13, 12-15, 8-14, 9-12, or 10-15 amino acid residues. Each possibility represents a separate embodiment of the invention.

[0067] In some embodiments, a polypeptide of the invention comprising or consisting of the amino acid sequences set forth in SEQ ID Nos: 1-4, further comprises a methylated amino acid residue.

[0068] In some embodiments, a polypeptide of the invention comprising or consisting of the amino acid sequence set forth in SEQ ID Nos: 1-4, is further functionalized such as by conjugation of a carbon chain to an amino acid residue at position 6 or 8, or both. In some embodiments, a carbon chain comprises one or more carbons. In some embodiments, a carbon chain comprising one or more carbons comprises at least 2, at least 3, at least 4, or at least five carbons, or any value and range therebetween. Each possibility represents a separate embodiment of the invention. In some embodiments, a carbon chain comprising one or more carbons comprises 2-3, 2-4, 2-5, 3-4, 3-5, or 4-5 carbons. Each possibility represents a separate embodiment of the invention. In some embodiments, amino acid residues of a polypeptide of the invention as mentioned above are functionalized by conjugation to a methyl group, ethyl group, propyl group, butyl group, or any combination thereof.

[0069] In some embodiments, a polypeptide of the invention is capable of binding ubiquitin (Ub). In some embodiments, a polypeptide of the invention has specific binding affinity to ubiquitin (Ub). As defined herein, the term "Ubiquitin" refers to the regulatory protein which is added to other proteins by means of post translational modification. In some embodiments, Ub is a polymeric Ub. In some embodiments, a polymeric Ub comprises at least 2, at least 3, at least 4, or at least 5 Ub monomers, or any value and range therebetween. Each possibility represents a separate embodiment of the invention. In some embodiments, a polymeric Ub comprises 2-3, 2-4, 2-5, 3-4, 3-5, or 4-5 Ub monomers. Each possibility represents a separate embodiment of the invention. In some embodiments, a Ub polymer comprises Ub monomers linked to one another at lysine (Lys) residue at position 48 (K48). In some embodiments, a polypeptide of the invention has greater binding affinity to polyK48Ub compared to polyK11Ub, or polyK63Ub. In some embodiments, a Ub is further conjugated to a protein. In some embodiments, a protein is posttranslationally modified by conjugation to a Ub monomer or polymer. In some embodiments, a Ub-conjugated protein is bound by a polypeptide of the invention at the Ub site. In some embodiments, a polypeptide of the invention reduces deubiquitination of a Ub-conjugated protein. In some embodiments, a polypeptide of the invention increases proteasomal degradation of a Ub-conjugated protein.

[0070] In some embodiments, a polypeptide of the invention is capable of binding to Ub in vitro, in vivo, ex vivo, or any combination thereof. In some embodiments, apolypeptide of the invention is capable of penetrating a cell. In some embodiments, the polypeptide requires no additional elements to penetrate a cell. In some embodiments, the polypeptide may be further formulated with other elements for enhancing cell penetration. In some embodiments, the polypeptide may be used as a carrier or vehicle to carry other elements into a cell.

[0071] In some embodiments, the present invention is directed to a cyclic polypeptide of 12-16 amino acids, capable of penetrating a cell and binding to Ub with affinity KD of 0.1-100 mM.

[0072] In some embodiments, a polypeptide of the invention has increased affinity to Ub compared to control. In some embodiments, increased affinity is by at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8- fold, at least 9-fold, or at least 10-fold greater compared to control, or any value and range therebetween. Each possibility represents a separate embodiment of the invention. In some embodiments, increased affinity is at least 5%, 10%, 20%, 35%, 50%, 65%, 75%, 85%, 90%, 99%, or 100% greater compared to control, or any value and range therebetween. Each possibility represents a separate embodiment of the invention. In some embodiments, increased affinity is by 1-5%, 4-10%, 8-20%, 25-35%, 30-50%, 45- 65%, 60-75%, 70-85%, 80-90%, 85-99%, or 95-100% compared to control. Each possibility represents a separate embodiment of the invention.

[0073] As used herein, "control" encompasses any baseline to which the binding affinity of a polypeptide of the invention to Ub is compared to. In some embodiments, a control is a protein having no Ub binding affinity. In some embodiments, a control is a protein having low Ub binding affinity. In some embodiments, a control is a protein known to have Ub binding capabilities, such as ubiquitin receptors and proteins comprising ubiquitin binding domains, non-limiting examples of which include, but are not limited to: Rabex-5, STAM1, STAM2, IsoT, EAP45, S5a / Rpnl0, Rpnl3, or any other protein known in the art. In some embodiments, a control is a polypeptide of the invention in its linear form. In some embodiments, a control is a polypeptide of the invention which is initially inactivated, such as by antibody neutralization, enzymatic digestion, denaturation, or other methodologies known in the art of protein inactivation, prior to incubation in an environment comprising Ub, in vitro or in vivo. In some embodiments, a control is a cyclic peptide. In some embodiments, a control is a peptide consisting of the amino acid sequence FQYWOYATGVCG (SEQ ID NO: 5). In some embodiments,a control is a peptide comprising the amino acid sequence FQYWOYATGVCG (SEQ ID NO: 5). In some embodiments, a control is CP- 15 (as described in Vamisetti et al., Nature Communications (2022)13:6174).

[0074] In some embodiments, a polypeptide of the invention has Ub binding affinity with KDof 0.05-1 nM, 0.5-5 nM, 1-10 nM, 5-15 nM, 10-20 nM, 15-30 nM, 20-40 nM, 35-50 nM, 45-60 nM, 55-70 nM, 65-80 nM, 75-90 nM, 85-95 nM, 90-120 nM, 100-500 nM, 250-750 nM, 0.7-1.5 pM, 1-5 pM, 4-10pM, 8-20 pM, or 15-40 pM. Each possibility represents a separate embodiment of the invention. In some embodiments, a polypeptide of the invention has Ub binding affinity with KD of 0.1 nM at most, 0.5 nM at most, 1 nM at most, 5 nM at most, 10 nM at most, 20 nM at most, 30 nM at most, 40 nM at most, 50 nM at most, 60 nM at most, 70 nM at most, 80 nM at most, 90 nM at most, 100 nM at most, 110 nM at most, 150 nM at most, 250 nM at most, 500 nM at most, 750 nM at most, 1,500 nM at most, 1 pM at most, 5 pM at most, 10 pM at most, 15 pM at most, 20 pM at most, or 30 pM at most, or any value and range therebetween. Each possibility represents a separate embodiment of the invention.

[0075] The present invention encompasses derivatives of the polypeptide of the invention. The term "derivative" or "chemical derivative" includes any chemical derivative of the polypeptide having one or more residues chemically derivatized by reaction of side chains or functional groups. Such derivatized molecules include, for example, those molecules in which free amino groups have been derivatized to form amine hydrochlorides, p-toluene sulfonyl groups, carbobenzoxy groups, t- butyloxycarbonyl groups, chloroacetyl groups or formyl groups. Free carboxyl groups may be derivatized to form salts, methyl and ethyl esters or other types of esters or hydrazides. Free hydroxyl groups may be derivatized to form O-acyl or O-alkyl derivatives. The imidazole nitrogen of histidine may be derivatized to form N-im- benzylhistidine. Also included as chemical derivatives are those peptides, which contain one or more naturally occurring amino acid derivatives of the twenty standard amino acid residues. For example: 4-hydroxyproline may be substituted for proline; 5- hydroxy lysine may be substituted for lysine; 3 -methylhistidine may be substituted for histidine; homoserine may be substituted or serine; and ornithine (O) may be substituted for lysine.

[0076] In addition, a peptide derivative can differ from the natural sequence of the peptide of the invention by chemical modifications including, but are not limited to,terminal-NH2 acylation, acetylation, or thioglycolic acid amidation, and by terminal- carboxlyamidation, e.g., with ammonia, methylamine, and the like. Peptides can be either linear, cyclic, or branched and the like, having any conformation, which can be achieved using methods known in the art.

[0077] As used herein, the terms “peptide”, "polypeptide" and "protein" are used interchangeably, and refer to a polymer of amino acid residues.

[0078] The term "amino acid" as used herein means an organic compound containing both a basic amino group and an acidic carboxyl group. Included within this term are naturally occurring amino acids, modified, unusual, non-naturally occurring amino acids, as well as amino acids which are known to occur biologically in free or combined form but usually do not occur in proteins. Included within this term are modified and unusual amino acids, such as those disclosed in, for example, Roberts and Vellaccio (1983) The Peptides. 5: 342-429. Modified, unusual or non-naturally occurring amino acids include, but are not limited to, D-amino acids, hydroxylysine, 4-hydroxyproline, N-Cbz-protected aminovaleric acid (Nva), ornithine (O), aminooctanoic acid (Aoc), 2,4- diaminobutyric acid (Abu), homoarginine, norleucine (Nle), N-methylaminobutyric acid (MeB), 2-naphthylalanine (2Np), aminoheptanoic acid (Ahp), phenylglycine, [3- phenylproline, tert-leucine, 4-aminocyclohexylalanine (Cha), N-methyl-norleucine, 3,4- dehydroproline, N,N-dimethylaminoglycine, N-methylaminoglycine, 4- aminopipetdine-4-carboxylic acid, 6-aminocaproic acid, trans-4- (aminomethyl) - cyclohexanecarboxylic acid, 2-, 3-, and 4- (aminomethyl) - benzoic acid, 1- aminocyclopentanecarboxylic acid, 1 -aminocyclopropanecarboxylic acid, cyanopropionic acid, 2-benzyl-5- aminopentanoic acid, Norvaline (Nva), 4-O-methyl- threonine (TMe), 5-O-methyl-homoserine (hSM), tert-butyl- alanine (tBu), cyclopentylalanine (Cpa), 2-amino-isobutyric acid (Aib), N-methyl-glycine (MeG), N-methyl- alanine (MeA), N-methyl-phenylalanine (MeF), 2-thienyl-alanine (2Th), 3-thienyl- alanine (3Th), O-methyl-tyrosine (YMe), 3-Benzothienyl-alanine (Bzt) and D-alanine (DAI).

[0079] The term "amino acid residue" as used herein refers to the portion of an amino acid that is present in a peptide.

[0080] The term "peptide bond" means a covalent amide linkage formed by loss of a molecule of water between the carboxyl group of one ammo acid and the ammo group of a second ammo acid.

[0081] The terms "peptide", "polypeptide" and "protein" as used herein encompass native peptides, peptidomimetics (typically including non-peptide bonds or other synthetic modifications) and the peptide analogs peptoids and semi-peptoids or any combination thereof. In another embodiment, the terms “peptide”, "polypeptide" and "protein" apply to amino acid polymers in which at least one amino acid residue is an artificial chemical analog of a corresponding naturally occurring amino acid.

[0082] One of skill in the art will recognize that individual substitutions, deletions or additions to a peptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a conservatively modified variant where the alteration results in the substitution of an amino acid with a similar charge, size, and / or hydrophobicity characteristics, such as, for example, substitution of a glutamic acid (E) to an aspartic acid (D).

[0083] As used herein, the phrase "conservative substitution" also includes the use of a chemically derivatized residue in place of a non-derivatized residue provided that such peptide displays the requisite function as specified herein.

[0084] The peptide derivatives according to the principles of the present invention can also include side chain bond modifications, including but not limited to -CH2-NH-, - CH2-S-, -CH2-S=0, OC-NH-, -CH2-O-, -CH2-CH2-, S=C-NH-, and -CH=CH-, and backbone modifications such as modified peptide bonds. Peptide bonds (-CO-NH-) within the peptide can be substituted, for example, by N-methylated bonds (-N(CH3)- CO-); ester bonds (-C(R)H-C-O-O-C(R)H-N); ketomethylene bonds (-CO-CH2-); a-aza bonds (-NH-N(R)-CO-), wherein R is any alkyl group, e.g., methyl; carba bonds (-CH2- NH-); hydroxyethylene bonds (-CH(OH)-CH2-); thioamide bonds (-CS-NH); olefmic double bonds (-CH=CH-); and peptide derivatives (-N(R)-CH2-CO-), wherein R is the "normal" side chain, naturally presented on the carbon atom. These modifications can occur at one or more of the bonds along the peptide chain and even at several (e.g., 2-3) at the same time.

[0085] The invention further includes peptides and derivatives thereof, which can contain one or more D-isomer forms of the amino acids. Production of retro-inverso D-amino acid peptides where at least one amino acid and perhaps all amino acids are D- amino acids is well known in the art. When all of the amino acids in the peptide are D- amino acids, and the N- and C-terminals of the molecule are reversed, the result is a molecule having the same structural groups being at the same positions as in the L-amino acid form of the molecule. However, the molecule is more stable to proteolytic degradation and is therefore useful in many of the applications recited herein. Diastereomeric peptides may be highly advantageous over all L- or all D-amino acid peptides having the same amino acid sequence because of their higher water solubility, lower immunogenicity, and lower susceptibility to proteolytic degradation. The term "diastereomeric peptide" as used herein refers to a peptide comprising both L-amino acid residues and D-amino acid residues. The number and position of D-amino acid residues in a diastereomeric peptide of the preset invention may be variable so long as the peptide is capable of displaying the function of disclosed chimera of the invention.

[0086] According to one embodiment, the polypeptide of the invention may be synthesized or prepared by any method and / or technique known in the art for peptide synthesis. According to another embodiment, the polypeptide may be synthesized by a solid phase peptide synthesis method of Merrifield (see J. Am. Chem. Soc, 85:2149, 1964). According to another embodiment, the polypeptide of the invention can be synthesized using standard solution methods, which are well known in the art (see, for example, Bodanszky, M., Principles of Peptide Synthesis, Springer- Verlag, 1984).

[0087] In general, the synthesis methods comprise sequential addition of one or more amino acids or suitably protected amino acids to a growing peptide chain bound to a suitable resin. Normally, either the amino or carboxyl group of the first amino acid is protected by a suitable protecting group. The protected or derivatized amino acid can then be either attached to an inert solid support (resin) or utilized in solution by adding the next amino acid in the sequence having the complimentary (amino or carboxyl) group suitably protected, under conditions conductive for forming the amide linkage. The protecting group is then removed from this newly added amino acid residue and the next amino acid (suitably protected) is added, and so forth. After all the desired amino acids have been linked in the proper sequence, any remaining protecting groups are removed sequentially or concurrently, and the peptide chain, if synthesized by the solid phase method, is cleaved from the solid support to afford the final peptide.

[0088] In the solid phase peptide synthesis method, the alpha-amino group of the amino acid is protected by an acid or base sensitive group. Such protecting groups should have the properties of being stable to the conditions of peptide linkage formation, while being readily removable without destruction of the growing peptide chain. Suitable protecting groups are t-butyloxycarbonyl (BOC), benzyloxycarbonyl (Cbz), biphenylisopropyloxycarbonyl, t-amyloxycarbonyl, isobornyloxycarbonyl, (alpha, alpha)-dimethyl-3 ,5 dimethoxybenzyloxycarbonyl, o-nitrophenylsulfenyl, 2- cyano-t-butyloxycarbonyl, 9-fluorenylmethyloxycarbonyl (Fmoc) and the like. In the solid phase peptide synthesis method, the C-terminal amino acid is attached to a suitable solid support. Suitable solid supports useful for the above synthesis are those materials, which are inert to the reagents and reaction conditions of the stepwise condensationdeprotection reactions, as well as being insoluble in the solvent media used. Suitable solid supports are chloromethylpolystyrene-divinylbenzene polymer, hydroxymethyl- polystyrene-divinylbenzene polymer, and the like. The coupling reaction is accomplished in a solvent such as ethanol, acetonitrile, N,N-dimethylformamide (DMF), and the like. The coupling of successive protected amino acids can be carried out in an automatic polypeptide synthesizer as is well known in the art.

[0089] In another embodiment, a polypeptide of the invention may be synthesized such that one or more of the bonds, which link the amino acid residues of the peptide are nonpeptide bonds. In another embodiment, the non-peptide bonds include, but are not limited to, imino, ester, hydrazide, semicarbazide, and azo bonds, which can be formed by reactions well known to one skilled in the art.

[0090] The term "linker" refers to a molecule or macromolecule serving to connect different moieties of a peptide or a polypeptide. In one embodiment, a linker may also facilitate other functions, including, but not limited to, preserving biological activity, maintaining sub-units and domains interactions, and others.

[0091] In some embodiments, a polypeptide of the invention may be attached or linked to another molecule via a chemical linker. Chemical linkers are well known in the art and include, but are not limited to, dicyclohexylcarbodiimide (DCC), N- hydroxy succinimide (NHS), maleiimidobenzoyl-N-hydroxysuccinimide ester (MBS), N-ethyloxycarbonyl-2-ethyloxy- 1 ,2-dihydroquinoline (EEDQ), N -isobutyloxy - carbonyl-2-isobutyloxy-l,2-dihydroquinoline (IIDQ). In another embodiment, linkers may also be monomeric entities such as a single amino acid. In anotherembodiment, amino acids with small side chains are especially preferred, or a small polypeptide chain, or polymeric entities of several amino acids. In another embodiment, a polypeptide linker is fifteen amino acids long or less, ten amino acids long or less, or five amino acids long or less. In one embodiment, a linker may be a nucleic acid encoding a small polypeptide chain. In another embodiment, a linker encodes a polypeptide linker of fifteen amino acids long or less, ten amino acids long or less, or five amino acids long or less.

[0092] Recombinant technology may be used to express the polypeptide of the invention, and is well known in the art. In another embodiment, the linker may be a cleavable linker, resulting in cleavage of the polypeptide of the invention once delivered to the tissue or cell of choice. In such an embodiment, the cell or tissue would have endogenous (either naturally occurring enzyme or be recombinantly engineered to express the enzyme) or have exogenous (e.g., by injection, absorption or the like) enzyme capable of cleaving the cleavable linker.

[0093] In another embodiment, the linker may be biodegradable such that the polypeptide of the invention is further processed by hydrolysis and / or enzymatic cleavage inside cells. In one embodiment, tumor specifically-expressed proteases, can be used in the delivery of prodrugs of cytotoxic agents, with the linker being selective for a site-specific proteolysis. In some embodiments, a readily-cleavable group include acetyl, trimethylacetyl, butanoyl, methyl succinoyl, t-butyl succinoyl, ethoxycarbonyl, methoxycarbonyl, benzoyl, 3-aminocyclohexylidenyl, and the like.

[0094] According to another aspect, there is provided a polynucleotide encoding the polypeptide of the invention.

[0095] In another embodiment, the nucleic acid sequence encoding the polypeptide is at least 70%, or alternatively at least 80%, or alternatively at least 90%, or alternatively at least 95%, or alternatively at least 99% homologous to the nucleic acid sequence encoding the nucleic acid sequence of the polypeptides of the invention or a derivative thereof, or any value and range therebetween. Each possibility represents a separate embodiment of the invention.

[0096] In some embodiments, a polynucleotide molecule of the invention encodes a polypeptide comprising non-canonical amino acids.

[0097] In some embodiments, the polynucleotide of the invention is ligated into an expression vector, comprising a transcriptional control of a cis-regulatory sequence (e.g., promoter sequence). In some embodiments, the cis-regulatory sequence is suitable for directing constitutive expression of the polypeptide of the invention. In some embodiments, the cis-regulatory sequence is suitable for directing tissue- specific expression of the polypeptide of the invention. In some embodiments, the cis-regulatory sequence is suitable for directing inducible expression of the polypeptide of the invention.

[0098] The term “polynucleotide” refers to a nucleic acid (e.g., DNA or RNA) sequence that comprises coding sequences necessary for the production of a polypeptide. In one embodiment, a polynucleotide refers to a single or double stranded nucleic acid sequence which is isolated and provided in the form of an RNA sequence, a complementary polynucleotide sequence (cDNA), a genomic polynucleotide sequence and / or a composite polynucleotide sequences (e.g., a combination of the above).

[0099] In one embodiment, “complementary polynucleotide sequence” refers to a sequence, which results from reverse transcription of messenger RNA using a reverse transcriptase or any other RNA-dependent DNA polymerase. In one embodiment, the sequence can be subsequently amplified in vivo or in vitro using a DNA polymerase.

[0100] In one embodiment, “genomic polynucleotide sequence” refers to a sequence derived (or isolated) from a chromosome and, thus it represents a contiguous portion of a chromosome.

[0101] In one embodiment, “composite polynucleotide sequence” refers to a sequence, which is at least partially complementary and at least partially genomic. In one embodiment, a composite sequence can include some exonal sequences required to encode the polypeptide of the invention, as well as some intronic sequences interposing therebetween. In one embodiment, the intronic sequences can be of any source, including of other genes, and typically may include conserved splicing signal sequences. In one embodiment, intronic sequences include cis-acting expression regulatory elements.

[0102] In some embodiments, a polynucleotide of the invention is prepared using PCR techniques, or any other method or procedure known to one of ordinary skill in the art.

[0103] In one embodiment, a polynucleotide of the invention is inserted into expression vectors (e.g., a nucleic acid construct) to enable expression of a recombinantpolypeptide. In one embodiment, the expression vector includes additional sequences which render this vector suitable for replication and integration in prokaryotes. In one embodiment, the expression vector includes additional sequences which render this vector suitable for replication and integration in eukaryotes. In one embodiment, the expression vector includes a shuttle vector which renders this vector suitable for replication and integration in both prokaryotes and eukaryotes. In some embodiments, cloning vectors comprise transcription and translation initiation sequences (e.g., promoters, enhancers) and transcription and translation terminators (e.g., polyadenylation signals).

[0104] In one embodiment, a variety of prokaryotic or eukaryotic cells can be used as host-expression systems to express the polypeptide of the invention. In some embodiments, these include, but are not limited to, microorganisms, such as bacteria transformed with a recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vector containing the polypeptide coding sequence; yeast transformed with recombinant yeast expression vectors containing the polypeptide coding sequence; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors, such as Ti plasmid, containing the polypeptide coding sequence.

[0105] In some embodiments, non-bacterial expression systems are used (e.g., mammalian expression systems) to express the polypeptide of the invention. In one embodiment, the expression vector is used to express the polynucleotide of the invention in mammalian cells.

[0106] In some embodiments, in bacterial systems, a number of expression vectors can be advantageously selected depending upon the use intended for the polypeptide expressed. In one embodiment, large quantities of polypeptide are desired. In one embodiment, vectors that direct the expression of high levels of the protein product, possibly as a fusion with a hydrophobic signal sequence, which directs the expressed product into the periplasm of the bacteria or the culture medium where the protein product is readily purified are desired. In one embodiment, certain fusion protein engineered with a specific cleavage site to aid in recovery of the polypeptide. In one embodiment, vectors adaptable to such manipulation include, but are not limited to, thepET series of E. coli expression vectors [Studier et al., Methods in Enzymol. 185:60-89 (1990)].

[0107] In one embodiment, yeast expression systems are used. In one embodiment, a number of vectors containing constitutive or inducible promoters can be used in yeast as disclosed in U.S. Pat. No. 5,932,447. In another embodiment, vectors which promote integration of foreign DNA sequences into the yeast chromosome are used.

[0108] In one embodiment, the expression vector may further include additional polynucleotide sequences that allow, for example, the translation of several proteins from a single mRNA such as an internal ribosome entry site (IRES).

[0109] In some embodiments, mammalian expression vectors include, but are not limited to, pcDNA3, pcDNA3.1 (±), pGL3, pZeoSV2(±), pSecTag2, pDisplay, pEF / myc / cyto, pCMV / myc / cyto, pCR3.1, pSinRep5, DH26S, DHBB, pNMTl, pNMT41, pNMT81, which are available from Invitrogen, pCI which is available from Promega, pMbac, pPbac, pBK-RSV and pBK-CMV which are available from Strategene, pTRES which is available from Clontech, and their derivatives.

[0110] In some embodiments, expression vectors containing regulatory elements from eukaryotic viruses such as retroviruses can be used. SV40 vectors include pSVT7 and pMT2. In some embodiments, vectors derived from bovine papilloma virus include pBV-lMTHA, and vectors derived from Epstein Bar virus include pHEBO, and p2O5. Other exemplary vectors include pMSG, pAV009 / A+, pMTO10 / A+, pMAMneo-5, baculovirus pDSVE, and any other vector allowing expression of proteins under the direction of the SV-40 early promoter, SV-40 later promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.

[0111] In some embodiments, recombinant viral vectors, which offer advantages such as lateral infection and targeting specificity, are used for in vivo expression of the polypeptide of the invention. In one embodiment, lateral infection is inherent in the life cycle of, for example, retrovirus and is the process by which a single infected cell produces many progeny virions that bud off and infect neighboring cells. In one embodiment, the result is that a large area becomes rapidly infected, most of which was not initially infected by the original viral particles. In one embodiment, the viral vectors that are produced are unable to spread laterally. In one embodiment, this characteristiccan be useful if the desired purpose is to introduce a specified gene into only a localized number of targeted cells.

[0112] Various methods can be used to introduce an expression vector into cells. Such methods are generally described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1989), Chang et al., Somatic Gene Therapy, CRC Press, Ann Arbor, Mich. (1995), Vega et al., Gene Targeting, CRC Press, Ann Arbor Mich. (1995), Vectors: A Survey of Molecular Cloning Vectors and Their Uses, Butterworths, Boston Mass. (1988) and Gilboa et at. [Biotechniques 4 (6): 504-512, 1986] and include, for example, stable or transient transfection, lipofection, electroporation and infection with recombinant viral vectors. In addition, see U.S. Pat. Nos. 5,464,764 and 5,487,992 for positive-negative selection methods.

[0113] In one embodiment, plant expression vectors are used. In one embodiment, the expression of a polypeptide coding sequence is driven by a number of promoters. In some embodiments, viral promoters such as the 35S RNA and 19S RNA promoters of CaMV [Brisson et al., Nature 310:511-514 (1984)], or the coat protein promoter to TMV [Takamatsu et al., EMBO J. 6:307-311 (1987)] are used. In another embodiment, plant promoters are used such as, for example, the small subunit of RUBISCO [Coruzzi et al., EMBO J. 3:1671-1680 (1984); and Brogli et al., Science 224:838-843 (1984)] or heat shock promoters, e.g., soybean hspl7.5-E or hspl7.3-B [Gurley et al., Mol. Cell. Biol. 6:559-565 (1986)]. In one embodiment, constructs are introduced into plant cells using Ti plasmid, Ri plasmid, plant viral vectors, direct DNA transformation, microinjection, electroporation and other techniques well known to the skilled artisan. See, for example, Weissbach & Weissbach [Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463 (1988)]. Other expression systems such as insects and mammalian host cell systems, which are well known in the art, can also be used by the present invention.

[0114] It will be appreciated that other than containing the necessary elements for the transcription and translation of the inserted coding sequence (encoding the polypeptide), the expression construct can also include sequences engineered to optimize stability, production, purification, yield or activity of the expressed polypeptide.

[0115] In some embodiments, transformed cells are cultured under effective conditions, which allow for the expression of high amounts of a recombinant polypeptide. In some embodiments, effective culture conditions include, but are not limited to, effective media, bioreactor, temperature, pH and oxygen conditions that permit protein production. In one embodiment, an effective medium refers to any medium in which a cell is cultured to produce a recombinant polypeptide of the present invention. In some embodiments, a medium typically includes an aqueous solution having assimilable carbon, nitrogen and phosphate sources, and appropriate salts, minerals, metals and other nutrients, such as vitamins. In some embodiments, the cells can be cultured in conventional fermentation bioreactors, shake flasks, test tubes, microtiter dishes and petri plates. In some embodiments, culturing is carried out at a temperature, pH and oxygen content appropriate for a recombinant cell. In some embodiments, culturing conditions are within the expertise of one of ordinary skill in the art.

[0116] In some embodiments, depending on the vector and host system used for production, resultant polypeptide of the invention either remains within the recombinant cell, secreted into the fermentation medium, secreted into a space between two cellular membranes, such as the periplasmic space in E. coli; or retained on the outer surface of a cell or viral membrane. In one embodiment, following a predetermined time in culture, recovery of the recombinant polypeptide is affected.

[0117] In one embodiment, the phrase “recovering the recombinant polypeptide” as used herein, refers to collecting the whole fermentation medium containing the polypeptide and need not imply additional steps of separation or purification.

[0118] In one embodiment, a polypeptide of the invention is purified using a variety of standard protein purification techniques, such as, but not limited to, affinity chromatography, ion exchange chromatography, filtration, electrophoresis, hydrophobic interaction chromatography, gel filtration chromatography, reverse phase chromatography, concanavalin A chromatography, chromatofocusing and differential solubilization.

[0119] In one embodiment, to facilitate recovery, the expressed coding sequence can be engineered to encode the polypeptide of the invention and fused cleavable moiety. In one embodiment, a fusion protein can be designed so that the polypeptide can be readily isolated by affinity chromatography; e.g., by immobilization on a column specific forthe cleavable moiety. In one embodiment, a cleavage site is engineered between the polypeptide and the cleavable moiety, and the polypeptide can be released from the chromatographic column by treatment with an appropriate enzyme or agent that specifically cleaves the fusion protein at this site [e.g., see Booth et al., Immunol. Lett. 19:65-70 (1988); and Gardella et al., J. Biol. Chem. 265:15854-15859 (1990)].

[0120] In one embodiment, the polypeptide of the invention is retrieved in “substantially pure” form that allows for the effective use of the protein in the applications described herein.

[0121] As used herein, the term “substantially pure” describes a peptide / polypeptide or other material which has been separated from its native contaminants. Typically, a monomeric peptide is substantially pure when at least about 60 to 75% of a sample exhibits a single peptide backbone. Minor variants or chemical modifications typically share the same peptide sequence. A substantially pure peptide can comprise over about 85 to 90% of a peptide sample, and can be over 95% pure, over 97% pure, or over about 99% pure, or any value and range therebetween. Each possibility represents a separate embodiment of the invention. Purity can be measured on a polyacrylamide gel, with homogeneity determined by staining. Alternatively, for certain purposes high resolution may be necessary and HPLC or a similar means for purification can be used. For most purposes, a simple chromatography column or polyacrylamide gel can be used to determine purity.

[0122] The term “purified” does not require the material to be present in a form exhibiting absolute purity, exclusive of the presence of other compounds. Rather, it is a relative definition. A peptide is in the “purified” state after purification of the starting material or of the natural material by at least one order of magnitude, 2 or 3, or 4 or 5 orders of magnitude.

[0123] In one embodiment, the polypeptide of the invention is substantially free of naturally-associated host cell components. The term “substantially free of naturally- associated host cell components” describes a peptide or other material which is separated from the native contaminants which accompany it in its natural host cell state. Thus, a peptide which is chemically synthesized or synthesized in a cellular system different from the host cell from which it naturally originates will be free from its naturally- associated host cell components.

[0124] In one embodiment, the polypeptide of the invention can also be synthesized using in vitro expression systems. In one embodiment, in vitro synthesis methods are well known in the art and the components of the system are commercially available. Non-limited example for in vitro system includes, but is not limited to in vitro translation, such as exemplified herein below.

[0125] In some embodiments, the polypeptide of the invention is cyclized. In some embodiments, the first amino acid residue of the N terminus of a polypeptide of the invention is conjugated to a cyclizing molecule. In some embodiments, the first amino acid residue of the polypeptide (positioned at the N terminus) and another amino residue of the polypeptide (positioned at the C terminus) are bound to one another, thereby resulting in a cyclic polypeptide. In some embodiments, the cyclizing molecule is bound to both the first amino acid residue and to another amino acid residue located at the C terminus. In some embodiments, the cyclizing molecule facilitates the binding of the first amino acid residue (of the N terminus) and the C terminal amino acid residue. In some embodiments, the cyclizing molecule is released upon binding of the first and the C terminal amino acid residue. In some embodiments, the cyclizing molecule is conjugated to both the first and the C terminal amino acid residue upon binding. In some embodiments, the first amino acid residue of the polypeptide (positioned at the N terminus) and a cysteine residue positioned at the C terminus of the polypeptide are bound to one another, thereby resulting in a cyclic polypeptide. In some embodiments, the cyclizing molecule is bound to both the first amino acid residue and to a cysteine amino acid residue located at the C terminus. In some embodiments, the cyclizing molecule facilitates the binding of the first amino acid residue (of the N terminus) and the C terminal cysteine amino acid residue. In some embodiments, the cyclizing molecule is released upon binding of the first and the C terminal amino acid residue. In some embodiments, the cyclizing molecule is conjugated to both the first amino acid residue of the polypeptide and the C terminal cysteine amino acid residue upon binding. In some embodiments, the cyclic polypeptide comprises a cyclizing molecule being bound to both the first amino acid residue positioned at the N terminus of the cyclic polypeptide and the cysteine residue located at the C terminus of the cyclic polypeptide.

[0126] As defined herein, a "C terminal amino acid residue" refers to an amino acid residue located in a position closer to the C terminal end of a linear polypeptide compared to the N terminal end of the polypeptide. In some embodiments, a C terminalamino acid residue is positioned 8 before last, 7 before last, 6 before last, 5 before last, 4 before last, 3 before last, 2 before last, 1 before last, or is the last amino acid residue in a linear polypeptide. Each possibility represents a separate embodiment of the invention. According to a non-limiting example, an amino acid residue at position 9 of a polypeptide comprising 16 amino acid residues is considered as a C terminal amino acid residue. A variety of methods are available for cyclizing a polypeptide (e.g., macrocyclization) as reviewed, for example by White and Yudin (2011). In some embodiments, the C terminal amino acid residue of the cyclic peptide of the invention is a cysteine.

[0127] In some embodiments, a cyclizing molecule comprises one or more halogen atoms selected from the group consisting of: Fluoride (F), Chlorine (Cl), Bromide (Br), Iodine (I) and Astatine (At), or any combination thereof. Non-limiting examples for a cyclizing molecule comprising a halogen include, but are not limited to: chloracetyl chloride, 3 -chlorobenzoyl (3-ClBz), 4 -chlorobenzoyl (4-ClBz) or ChSAc. In one embodiment, a cyclizing molecule comprising a halogen group is conjugated to the first amino acid residue of a polypeptide's N terminus and nucleophilicaly attacks a thiol group of a cysteine residue located at the C terminal end of the polypeptide, thereby resulting in a cyclic polypeptide.

[0128] In some embodiments, the polypeptide of the invention is characterized by increased solubility compared to a control. In some embodiments, solubility is in vitro solubility, in vivo solubility, ex vivo solubility, or any combination thereof. In some embodiments, the polypeptide of the invention is characterized by increased solubility in serum, plasma, blood, whole blood, or any combination thereof, compared to control. In some embodiments, the polypeptide is characterized by reduced toxicity to a subject administered therewith, compared to a control. In some embodiments, administered is intravenously administered. In some embodiments, the polypeptide of the invention is characterized by increased solubility, increased apoptotic activity, and reduced toxicity, compared to a control. In some embodiments, the polypeptide of the invention is SEQ ID NO: 5, and the control comprises SEQ ID NO: 5, CP-15, or both.Compositions

[0129] In some embodiments, the present invention is directed to a composition comprising a polypeptide comprising or consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, or any combination thereof.

[0130] According to another embodiment, the invention provides a pharmaceutical composition comprising as an active ingredient the polypeptide of the present invention, and pharmaceutically acceptable carrier and / or diluents. In some embodiments, the pharmaceutical composition facilitates administration of a compound to an organism. According to another embodiment, the invention provides a pharmaceutical composition comprising as an active ingredient a therapeutically effective amount of the polypeptide of the invention.

[0131] In another embodiment, the pharmaceutical composition of the invention may be formulated in the form of a pharmaceutically acceptable salt of the polypeptides of the present invention or their analogs, or derivatives thereof. In another embodiment, pharmaceutically acceptable salts include those salts formed with free amino groups such as salts derived from non-toxic inorganic or organic acids such as hydrochloric, phosphoric, acetic, oxalic, tartaric acids, and the like, and those salts formed with free carboxyl groups such as salts derived from non-toxic inorganic or organic bases such as sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.

[0132] As used herein, the term "carrier" refers to a diluent, adjuvant, excipient, or vehicle with which the therapeutic compound is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like, polyethylene glycols, glycerin, propylene glycol or other synthetic solvents. Water is a preferred carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene glycol, water, ethanol and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents such as acetates, citrates or phosphates. Antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid orsodium bisulfite; and agents for the adjustment of tonicity such as sodium chloride or dextrose are also envisioned. The carrier may comprise, in total, from about 0.1% to about 99.99999% by weight of the pharmaceutical compositions presented herein.

[0133] As used herein, the term "pharmaceutically acceptable" means suitable for administration to a subject, e.g., a human. For example, the term "pharmaceutically acceptable" can mean approved by a regulatory agency of the Federal or a state government or listed in the U. S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans.

[0134] In another embodiment, the compositions of the invention take the form of solutions, suspensions, emulsions, tablets, pills, capsules, powders, gels, creams, ointments, foams, pastes, sustained-release formulations and the like. In another embodiment, the compositions of the invention can be formulated as a suppository, with traditional binders and carriers such as triglycerides, microcrystalline cellulose, gum tragacanth or gelatin. Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Examples of suitable pharmaceutical carriers are described in: Remington's Pharmaceutical Sciences" by E.W. Martin, the contents of which are hereby incorporated by reference herein. Such compositions will contain a therapeutically effective amount of the polypeptide of the invention, preferably in a substantially purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the subject.

[0135] According to an embodiment of the invention, pharmaceutical compositions contain 0.1-95% of the polypeptide(s) of the invention, derivatives, or analogs thereof. According to another embodiment of the invention, pharmaceutical compositions contain 1-70% of the polypeptide(s). According to another embodiment of the invention, the composition or formulation to be administered may contain a quantity of polypeptide(s), according to embodiments of the invention in an amount effective to treat the condition or disease of the subject being treated.

[0136] An embodiment of the invention relates to a polypeptide of the invention, presented in unit dosage form and prepared by any of the methods well known in the art of pharmacy. In an embodiment of the invention, the unit dosage form is in the form of a tablet, capsule, lozenge, wafer, patch, ampoule, vial or pre-filled syringe. In addition,in vitro assays may optionally be employed to help identify optimal dosage ranges. The precise dose to be employed in the formulation will also depend on the route of administration, and the nature of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. Effective doses can be extrapolated from dose-response curves derived from in-vitro or in-vivo animal model test bioassays or systems.

[0137] According to one embodiment, the compositions of the invention are administered in the form of a pharmaceutical composition comprising at least one of the active components of this invention (the cyclic polypeptide) together with a pharmaceutically acceptable carrier or diluent. In another embodiment, the compositions of this invention can be administered either individually or together in any conventional oral, parenteral or transdermal dosage form. In some embodiments, the pharmaceutical composition further comprises at least one anticancer agent such as a chemotherapeutic agent. In some embodiments, the pharmaceutical composition is adopted for combined administration with an anticancer therapy such as chemotherapy, radiotherapy, immunotherapy, hormonal therapy, toxin therapy or surgery.

[0138] As used herein, the terms “administering”, “administration”, and like terms refer to any method which, in sound medical practice, delivers a composition containing an active agent to a subject in such a manner as to provide a therapeutic effect.

[0139] Depending on the location of the tissue of interest, the polypeptide of the invention can be administered in any manner suitable for the provision of the polypeptides to cells within the tissue of interest. Thus, for example, a composition containing the polypeptide of the invention can be introduced, for example, into the systemic circulation, which will distribute the peptide to the tissue of interest. Alternatively, a composition can be applied topically to the tissue of interest (e.g., injected, or pumped as a continuous infusion, or as a bolus within a tissue, applied to all or a portion of the surface of the skin, etc.).

[0140] In some embodiments, the pharmaceutical compositions comprising the polypeptide are administered via oral, rectal, vaginal, topical, nasal, ophthalmic, transdermal, subcutaneous, intramuscular, intraperitoneal or intravenous routes of administration. The route of administration of the pharmaceutical composition will depend on the disease or condition to be treated. Suitable routes of administrationinclude, but are not limited to, parenteral injections, e.g., intradermal, intravenous, intramuscular, intralesional, subcutaneous, intrathecal, and any other mode of injection as known in the art. Although the bioavailability of peptides administered by other routes can be lower than when administered via parenteral injection, by using appropriate formulations it is envisaged that it will be possible to administer the compositions of the invention via transdermal, oral, rectal, vaginal, topical, nasal, inhalation and ocular modes of treatment. In addition, it may be desirable to introduce the pharmaceutical compositions of the invention by any suitable route, including intraventricular and intrathecal injection; intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir. Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer.

[0141] For topical application, a polypeptide of the invention, derivative, analog or a fragment thereof can be combined with a pharmaceutically acceptable carrier so that an effective dosage is delivered, based on the desired activity. The carrier can be in the form of, for example, and not by way of limitation, an ointment, cream, gel, paste, foam, aerosol, suppository, pad or gelled stick.

[0142] For oral applications, the pharmaceutical composition may be in the form of tablets or capsules, which can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose; a disintegrating agent such as alginic acid, Primogel, or com starch; a lubricant such as magnesium stearate; or a glidant such as colloidal silicon dioxide. When the dosage unit form is a capsule, it can contain, in addition to materials of the above type, a liquid carrier such as fatty oil. In addition, dosage unit forms can contain various other materials which modify the physical form of the dosage unit, for example, coatings of sugar, shellac, or other enteric agents. The tablets of the invention can further be film coated.

[0143] For purposes of parenteral administration, solutions in sesame or peanut oil or in aqueous propylene glycol can be employed, as well as sterile aqueous solutions of the corresponding water-soluble salts. Such aqueous solutions may be suitably buffered, if necessary, and the liquid diluent first rendered isotonic with sufficient saline or glucose. These aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal injection purposes.

[0144] According to some embodiments, the polypeptide of the invention, can be delivered in a controlled release system. In another embodiment, an infusion pump can be used to administer the peptide such as the one that is used, for example, for delivering insulin or chemotherapy to specific organs or tumors. In another embodiment, the peptide of the invention is administered in combination with a biodegradable, biocompatible polymeric implant, which releases the peptide over a controlled period of time at a selected site. Examples of preferred polymeric materials include, but are not limited to, poly anhydrides, polyorthoesters, polyglycolic acid, polylactic acid, polyethylene vinyl acetate, copolymers and blends thereof (See, Medical applications of controlled release, Langer and Wise (eds.), 1974, CRC Pres., Boca Raton, Fla., the contents of which are hereby incorporated by reference in their entirety). In yet another embodiment, a controlled release system can be placed in proximity to a therapeutic target, thus requiring only a fraction of the systemic dose.

[0145] The presently described peptide may also be contained in artificially created structures such as liposomes, ISCOMS, slow-releasing particles, and other vehicles which increase the half-life of the peptides or polypeptides in serum. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. Liposomes for use with the presently described peptides are formed from standard vesicle-forming lipids which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally determined by considerations such as liposome size and stability in the blood. A variety of methods are available for preparing liposomes as reviewed, for example, by Coligan, J. E. et al, Current Protocols in Protein Science, 1999, John Wiley & Sons, Inc., New York, and see also U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.

[0146] The compositions also include incorporation of the active material into or onto particulate preparations of polymeric compounds such as polylactic acid, polglycolic acid, hydrogels, etc., or onto liposomes, microemulsions, micelles, unilamellar or multilamellar vesicles, erythrocyte ghosts, or spheroplasts. Such compositions will influence the physical state, solubility, stability, rate of in vivo release, and rate of in vivo clearance.

[0147] In one embodiment, depending on the severity and responsiveness of the condition to be treated, dosing can be of a single or a plurality of administrations, withcourse of treatment lasting from several days to several weeks or until cure is affected or diminution of the disease state is achieved.

[0148] In some embodiments, the polypeptide is administered in a therapeutically safe and effective amount. As used herein, the term “safe and effective amount” refers to the quantity of a component which is sufficient to yield a desired therapeutic response without undue adverse side effects (such as toxicity, irritation, or allergic response) commensurate with a reasonable benefit / risk ratio when used in the presently described manner. In another embodiment, a therapeutically effective amount of the polypeptide is the amount of the polypeptide necessary for the in vivo measurable expected biological effect. The actual amount administered, and the rate and time-course of administration, will depend on the nature and severity of the condition being treated. Prescription of treatment, e.g., decisions on dosage, timing, etc., is within the responsibility of general practitioners or specialists, and typically takes account of the disorder to be treated, the condition of the individual patient, the site of delivery, the method of administration and other factors known to practitioners. Examples of techniques and protocols can be found in Remington: The Science and Practice of Pharmacy, 21st Ed., Lippincott Williams & Wilkins, Philadelphia, Pa., (2005). In some embodiments, preparation of effective amount or dose can be estimated initially from in vitro assays. In one embodiment, a dose can be formulated in animal models and such information can be used to more accurately determine useful doses in humans.

[0149] In one embodiment, toxicity and therapeutic efficacy of the active ingredients described herein can be determined by standard pharmaceutical procedures in vitro, in cell cultures or experimental animals. In one embodiment, the data obtained from these in vitro and cell culture assays and animal studies can be used in formulating a range of dosage for use in human. In one embodiment, the dosages vary depending upon the dosage form employed and the route of administration utilized. In one embodiment, the exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. [See e.g., Fingl, et al., (1975) "The Pharmacological Basis of Therapeutics", Ch. 1 p.l].

[0150] Pharmaceutical compositions containing the presently described polypeptide as the active ingredient can be prepared according to conventional pharmaceutical compounding techniques. See, for example, Remington's Pharmaceutical Sciences, 18th Ed., Mack Publishing Co., Easton, Pa. (1990). See also, Remington: The Science andPractice of Pharmacy, 21st Ed., Lippincott Williams & Wilkins, Philadelphia, Pa. (2005).

[0151] In one embodiment, compositions including the preparation of the present invention formulated in a compatible pharmaceutical carrier are prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.

[0152] In one embodiment, compositions of the invention are presented in a pack or dispenser device, such as an FDA approved kit, which contains one or more unit dosages forms containing the active ingredient. In one embodiment, the pack, for example, comprises metal or plastic foil, such as a blister pack. In one embodiment, the pack or dispenser device is accompanied by instructions for administration. In one embodiment, the pack or dispenser is accommodated by a notice associated with the container in a form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the compositions or human or veterinary administration. Such notice, in one embodiment, is labeling approved by the U.S. Food and Drug Administration for prescription drugs or of an approved product insert.Methods of use

[0153] According to another aspect, there is provided a method for reducing deubiquitination activity of a cell, comprising contacting the cell with a cyclic polypeptide comprising an amino acid sequence as set forth in SEQ ID Nos: 1-4.

[0154] According to another aspect, there is provided a method for inducing or increasing apoptosis rate of a cell, comprising contacting the cell with a cyclic polypeptide comprising an amino acid sequence as set forth in SEQ ID Nos: 1-4.

[0155] According to another aspect, there is provided a method for ameliorating or treating cancer or pre-malignancy in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a cyclic polypeptide comprising an amino acid sequence as set forth in SEQ ID Nos: 1-4.

[0156] In some embodiments, the present invention is directed to a method for treating, ameliorating, reducing and / or preventing a condition associated with increased deubiquitination activity of a cell in a subject in need thereof, the method comprising the step of: administering to the subject a pharmaceutical composition comprising atherapeutically effective amount of a cyclic polypeptide comprising an amino acid sequence as set forth in SEQ ID Nos: 1-4.

[0157] In some embodiments, the present invention is directed to a method for treating, ameliorating, reducing and / or preventing a condition associated with increased proliferation activity of a cell in a subject in need thereof, the method comprising the step of: administering to the subject a pharmaceutical composition comprising a therapeutically effective amount of a cyclic polypeptide comprising an amino acid sequence as set forth in SEQ ID Nos: 1-4.

[0158] In some embodiments, there present invention is directed to a method for treating, ameliorating, reducing and / or preventing a condition associated with increased apoptosis-resistance activity of a cell in a subject in need thereof, the method comprising the step of: administering to the subject a pharmaceutical composition comprising a therapeutically effective amount of a cyclic polypeptide comprising an amino acid sequence as set forth in SEQ ID Nos: 1-4.

[0159] In some embodiments, the condition associated with: increased deubiquitination activity of a cell, increased proliferation activity of a cell, increased apoptosis-resistance activity of a cell, or any combination thereof, comprises cancer.

[0160] In some embodiments, a method for treating or ameliorating a cancer in a subject in need thereof according to the present invention, comprises administering to the subject any one of: (i) the polypeptide of the invention; or (ii) the pharmaceutical composition of the invention.

[0161] In some embodiments, the treating comprises reducing any one of: the volume, size, weight, or any combination thereof, of a tumor in a subject. In some embodiments, the treating comprises reducing the volume of a tumor in a subject. In some embodiments, reducing is compared to a control. In some embodiments, reducing is by at least 50%, 60%, 70%, 80%, 90%, 95%, 99%, or any value and range therebetween, compared to a control. In some embodiments, reducing is by 50-100%, 60-100%, 70- 100%, 80-100%, 90-100%, 95-100%, or 99-100%, compared to a control. Each possibility represents a separate embodiment of the invention.

[0162] In some embodiments, a control comprises an untreated subject afflicted with cancer. In some embodiments, a control comprises a subject administered with CP-15 ora composition comprising thereof. In some embodiments, a control comprises a subject administered with Ub4a (SEQ ID NO: 5) or a composition comprising thereof.

[0163] In another embodiment, the polypeptide of the invention or a composition comprising the thereof is for use in treatment, amelioration, reduction, and / or prevention of cancer or pre-malignancy condition in a subject in need thereof. In some embodiments, the composition comprises an effective amount of a polypeptide for use in the treatment or prevention of cancer or pre-malignancy condition in a subject in need thereof. In some embodiments, a composition comprises a therapeutically effective amount of a polypeptide, comprising or consisting of an amino acid sequence selected from SEQ ID Nos.: 1-4, is for use in the treatment or prevention of cancer or pre- malignancy condition in the subject in need thereof. In some embodiments, the composition further comprises at least one anticancer agent such as a chemotherapeutic agent. In some embodiments, the composition is adopted for use in combination with an anticancer therapy such as chemotherapy, radiotherapy, immunotherapy, hormonal therapy, toxin therapy or surgery.

[0164] In some embodiments, a composition of the invention comprises an effective amount of the polypeptide for the preparation of a medicament for the treatment, amelioration, reduction, or prevention of a disease associated with increased cell proliferation, deubiquitination activity, apoptosis-resistance activity, or a combination thereof, in a subject in need thereof. In some embodiments, the invention is directed to a use of a composition comprising an effective amount of a polypeptide, comprising or consisting of an amino acid sequence selected from SEQ ID Nos.: 1-4 in the preparation of a medicament for the treatment of a disease associated with increased cell proliferation, deubiquitination activity, or a combination thereof, in a subject in need thereof.

[0165] In one embodiment, the polypeptide of the invention is provided to the subject per se. In one embodiment, one or more (e.g., "a plurality") of the polypeptides of the invention are provided to the subject per se. In one embodiment, the polypeptide of the invention is provided to the subject as part of a pharmaceutical composition where it is mixed with a pharmaceutically acceptable carrier. In one embodiment, one or more of the polypeptides of the invention are provided to the subject as part of a pharmaceutical composition where they are mixed with a pharmaceutically acceptable carrier.

[0166] In some embodiments, the disease associated with increased cell deubiquitination activity, increased cell proliferation activity, increased apoptosisresistance activity, or a combination thereof, is cancer.

[0167] As used herein the terms "cancer" or "pre-malignancy" refer to diseases associated with cell proliferation. Non-limiting types of cancer include carcinoma, sarcoma, lymphoma, leukemia, blastoma and germ cells tumors. In one embodiment, carcinoma refers to tumors derived from epithelial cells including but not limited to breast cancer, prostate cancer, lung cancer, pancreas cancer, and colon cancer. In one embodiment, sarcoma refers of tumors derived from mesenchymal cells including but not limited to sarcoma botryoides, chondrosarcoma, Ewing's sarcoma, malignant hemangioendothelioma, malignant schwannoma, osteosarcoma and soft tissue sarcomas. In one embodiment, lymphoma refers to tumors derived from hematopoietic cells that leave the bone marrow and tend to mature in the lymph nodes including but not limited to Hodgkin lymphoma, non-Hodgkin lymphoma, multiple myeloma and immunoproliferative diseases. In one embodiment, leukemia refers to tumors derived from hematopoietic cells that leave the bone marrow and tend to mature in the blood including but not limited to acute lymphoblastic leukemia, chronic lymphocytic leukemia, acute myelogenous leukemia, chronic myelogenous leukemia, hairy cell leukemia, T-cell prolymphocytic leukemia, large granular lymphocytic leukemia and adult T-cell leukemia. In one embodiment, blastoma refers to tumors derived from immature precursor cells or embryonic tissue including but not limited to hepatoblastoma, medulloblastoma, nephroblastoma, neuroblastoma, pancreatoblastoma, pleuropulmonary blastoma, retinoblastoma and glioblastoma-multiforme. In one embodiment, germ cell tumors refer to tumors derived from germ cells including but not limited to germinomatous or seminomatous germ cell tumors (GGCT, SGCT) and nongerminomatous or nonseminomatous germ cell tumors (NGGCT, NSGCT). In one embodiment, germinomatous or seminomatous tumors include but are not limited to germinoma, dysgerminoma and seminoma. In one embodiment, nongerminomatous or non-seminomatous tumors refers to pure and mixed germ cells tumors including but not limited to embryonal carcinoma, endodermal sinus tumor, choriocarcinoma, tearoom, polyembryoma, gonadoblastoma and teratocarcinoma.

[0168] As used herein, "cancer or pre-malignant cell proliferation" is a molecular process which further to increased cell proliferation rates requires increaseddeubiquitination activity. In some embodiments, the method of the present invention is directed to reducing deubiquitination activity. In some embodiments, reducing deubiquitination activity results in increased proteasomal activity. In some embodiments, reducing deubiquitination activity results in increased protein degradation. In some embodiments, reducing deubiquitination activity further reduces drug resistance. In some embodiments, a cancerous cell has increased deubiquitination activity compared to a non-cancerous cell or a benign cell. In another embodiment, reducing deubiquitination activity reduces viability of a cancerous cell. In some embodiments, reducing deubiquitination activity increases apoptosis rates in or of a cancerous cell. In some embodiments, increasing cell apoptosis results in reduced cell viability.

[0169] In some embodiments, the terms "reduce" or "reducing" used in the abovementioned embodiments (such as for deubiquitination activity of a cell, proteasomal degradation of ubiquitinated proteins, cell viability, or others), are by at least 10%, by at least 20%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 80%, by at least 90%, or by at least 100% compared to control, or any value and range therebetween. Each possibility represents a separate embodiment of the invention. In some embodiments, reducing is by 1-5%, 4-10%, 8- 20%, 15-30%, 25-40%, 35-55%, 50-70%, 60-80%, 75-90%, 90-99%, or 95-100% compared to control. Each possibility represents a separate embodiment of the invention. In some embodiments, reducing is by at least 2-fold, by at least 3-fold, by at least 5-fold, by at least 10-fold, by at least 15 -fold, by at least 20-fold, by at least 40-fold, by at least 75-fold, by at least 100-fold, by at least 150-fold, by at least 200-fold, by at least 500- fold, or by at least 1,000-fold compared to control, or any value and range therebetween. Each possibility represents a separate embodiment of the invention.

[0170] The terms "inhibiting", "reducing" and "decreasing" are interchangeable.

[0171] In some embodiments, the term "increase" or "increasing" used in the abovementioned embodiments (such as for pro-apoptotic activity, cell apoptosis rate, or others), is by at least 10%, by at least 20%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 80%, by at least 90%, or by at least 100% compared to control, or any value and range therebetween. Each possibility represents a separate embodiment of the invention. In some embodiments, increasing is by 1-5%, 4-10%, 8-20%, 15-30%, 25-40%, 35-55%, 50-70%, 60-80%, 75-90%, 90-99%, or 95-100% compared to control. Each possibility represents a separate embodiment of the invention. In some embodiments, increasing is by at least 2-fold, by at least 3 -fold, by at least 5-fold, by at least 10-fold, by at least 15-fold, by at least 20- fold, by at least 40-fold, by at least 75-fold, by at least 100-fold, by at least 150-fold, by at least 200-fold, by at least 500-fold, or by at least 1,000-fold compared to control, or any value and range therebetween. Each possibility represents a separate embodiment of the invention.

[0172] In some embodiments, a polypeptide of the invention reduces cell viability with a half maximal inhibitory concentration (IC50) of 0.01-1 nM, 0.05-2 nM, 1-5 nM, 4-10 nM, 5-50 nM, 10-100 nM, 50-250 nM, 200-750 nM, 0.5-1.5 pM, 1-3 pM, 2-4 pM, 3-6 pM, 4-7 pM, 5-8 pM, 6-9 pM, 8-12 pM, 10-13 pM, 12-14 pM, 11-15 pM, 13-17 pM, 16-19 pM, 15-20 pM, 14-22 pM, 20-25 pM, or 26-35 pM. Each possibility represents a separate embodiment of the invention.

[0173] In some embodiments, ubiquitination / deubiquitination kinetics or dynamics, are detected by any assay known to in the art, including immune- as says, western-blot, immune-histochemistry, and the like, such as for detectingK48Ub. In some embodiments, protein degradation and proteasomal activity are detected by any acceptable method, including immune- as says, western-blot, immune -histochemistry, pulse-chase assay, and the like, all of which are well known to one of ordinary skill in the art.

[0174] The term "subject" as used herein refers to an animal, more particularly to nonhuman mammals and human organism. Non-human animal subjects may also include prenatal forms of animals, such as, e.g., embryos or fetuses. Non-limiting examples of non-human animals include: horse, cow, camel, goat, sheep, dog, cat, non-human primate, mouse, rat, rabbit, hamster, guinea pig, pig. In one embodiment, the subject is a human. Human subjects may also include fetuses. In one embodiment, a subject in need thereof is a subject afflicted with and / or at risk of being afflicted with a condition associated with increased cell proliferation, deubiquitination activity, or combination thereof.

[0175] As used herein, the terms “treatment” or “treating” of a disease, disorder, or condition encompasses alleviation of at least one symptom thereof, a reduction in the severity thereof, or inhibition of the progression thereof. Treatment need not mean that the disease, disorder, or condition is totally cured. To be an effective treatment, a usefulcomposition herein needs only to reduce the severity of a disease, disorder, or condition, reduce the severity of symptoms associated therewith, or provide improvement to a patient or subject’s quality of life.

[0176] As used herein, the term “prevention” of a disease, disorder, or condition encompasses the delay, prevention, suppression, or inhibition of the onset of a disease, disorder, or condition. As used in accordance with the presently described subject matter, the term "prevention" relates to a process of prophylaxis in which a subject is exposed to the presently described peptides prior to the induction or onset of the disease / disorder process. This could be done where an individual has a genetic pedigree indicating a predisposition toward occurrence of the disease / disorder to be prevented. For example, this might be true of an individual whose ancestors show a predisposition toward certain types of, for example, inflammatory disorders. The term "suppression" is used to describe a condition wherein the disease / disorder process has already begun but obvious symptoms of the condition have yet to be realized. Thus, the cells of an individual may have the disease / disorder, but no outside signs of the disease / disorder have yet been clinically recognized. In either case, the term prophylaxis can be applied to encompass both prevention and suppression. Conversely, the term "treatment" refers to the clinical application of active agents to combat an already existing condition whose clinical presentation has already been realized in a patient.

[0177] As used herein, the term "condition" includes anatomic and physiological deviations from the normal that constitute an impairment of the normal state of the living animal or one of its parts, that interrupts or modifies the performance of the bodily functions.

[0178] Any concentration ranges, percentage range, or ratio range recited herein are to be understood to include concentrations, percentages or ratios of any integer within that range and fractions thereof, such as one tenth and one hundredth of an integer, unless otherwise indicated.

[0179] Any number range recited herein relating to any physical feature, such as polymer subunits, size or thickness, are to be understood to include any integer within the recited range, unless otherwise indicated.

[0180] As used herein, the terms “subject” or “individual” or “animal” or “patient” or “mammal,” refers to any subject, particularly a mammalian subject, for whom therapy is desired, for example, a human.

[0181] In the discussion unless otherwise stated, adjectives such as “substantially” and “about” modifying a condition or relationship characteristic of a feature or features of an embodiment of the invention, are understood to mean that the condition or characteristic is defined to within tolerances that are acceptable for operation of the embodiment for an application for which it is intended. Unless otherwise indicated, the word “or” in the specification and claims is considered to be the inclusive “or” rather than the exclusive or, and indicates at least one of, or any combination of items it conjoins.

[0182] It should be understood that the terms “a” and “an” as used above and elsewhere herein refer to “one or more” of the enumerated components. It will be clear to one of ordinary skill in the art that the use of the singular includes the plural unless specifically stated otherwise. Therefore, the terms “a”, “an” and “at least one” are used interchangeably in this application.

[0183] For purposes of better understanding the present teachings and in no way limiting the scope of the teachings, unless otherwise indicated, all numbers expressing quantities, percentages or proportions, and other numerical values used in the specification and claims, are to be understood as being modified in all instances by the term “about.” Accordingly, unless indicated to the contrary, the numerical parameters set forth in the following specification and attached claims are approximations that may vary depending upon the desired properties sought to be obtained. At the very least, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques.

[0184] In the description and claims of the present application, each of the verbs, “comprise”, “include”, and “have” and conjugates thereof, are used to indicate that the object or objects of the verb are not necessarily a complete listing of components, elements or parts of the subject or subjects of the verb.

[0185] Other terms as used herein are meant to be defined by their well-known meanings in the art.

[0186] Additional objects, advantages, and novel features of the present invention will become apparent to one ordinarily skilled in the art upon examination of the following examples, which are not intended to be limiting. Additionally, each of the various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below finds experimental support in the following examples.

[0187] It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub -combination or as suitable in any other described embodiment of the invention. Certain features described in the context of various embodiments are not to be considered essential features of those embodiments unless the embodiment is inoperative without those elements.EXAMPLES

[0188] Generally, the nomenclature used herein, and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, "Molecular Cloning: A laboratory Manual" Sambrook et al., (1989); "Current Protocols in Molecular Biology" Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., "Current Protocols in Molecular Biology", John Wiley and Sons, Baltimore, Maryland (1989); Perbal, "A Practical Guide to Molecular Cloning", John Wiley & Sons, New York (1988); Watson et al., "Recombinant DNA", Scientific American Books, New York; Birren et al. (eds.) "Genome Analysis: A Laboratory Manual Series", Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; "Cell Biology: A Laboratory Handbook", Volumes I-III Cellis, J. E., ed. (1994); "Culture of Animal Cells - A Manual of Basic Technique" by Freshney, Wiley- Liss, N. Y. (1994), Third Edition; "Current Protocols in Immunology" Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), "Basic and Clinical Immunology" (8th Edition), Appleton & Lange, Norwalk, CT (1994); Mishell and Shiigi (eds), "Strategies for Protein Purification and Characterization - A Laboratory Course Manual" CSHLPress (1996); all of which are incorporated by reference. Other general references are provided throughout this document.Materials and MethodsSurface Plasmon Resonance ( SPR )

[0189] The interactions between cyclic peptides and e.g.,UbiK48Ub2 andK48Ub4, are determined using BIACORE T100 instrument (GE healthcare) equipped with a biotin CAPture kit Series S chip. The buffer in all experiments contains 50 mM HEPES, pH 7.3, 150 mM NaCl, 0.05% Tween20, 2 mM DTT with 0.2% DMSO. Biotinylated Ubi,K48Ub2 andK48Ub4 are loaded to approximately equal molar amounts on the SPR chip, and various concentrations of cyclic peptides are flowed over at 100 pL / sec for 120 sec, before initiation of dissociation by flowing buffer over at 100 pL / sec for further 700 sec. Traces are fit to the simplest, two-state model for binding. Association is fit to a single exponential assuming pseudo-first order conditions, whereas the dissociation trace is fit to single exponential plus a drift term.In vitro deubiquitination assay

[0190] In vitro deubiquitination reactions are performed in a Tris buffer (50 mM TRIS, 1 mM TCEP, pH 7.7), containing 2 pMK48Ub2 / 4, then the specific DUB (50 mM Tris, 0.5 mM EDTA, 1 mM TCEP and 0.5 mg / ml ovalbumin, pH 7.5) is added. The reaction mixtures are incubated at 37 °C and at the indicated time points the reactions are stopped by taking aliquots and mixed them with 3x sample buffer and boiling. The same amounts are loaded on 14% SDS-PAGE, electro-blotted to nitrocellulose membrane and probed with an anti-Ub antibody. Bands are quantified with Image Quant LAS 4000 (GE Healthcare).In vitro proteasome degradation assay

[0191] Twelve and a half (12.5) pL: 5.3 pM of synthetic HA-a-globin-K48-linked tetra- Ub and 150 nM proteasome (Enzo) are incubated in the presence of 2 mM ATP, 40 mM Tris, 2 mM DTT and 5 mM MgCh, at 37 °C for 50 min. The reactions are stopped by the addition of 3x sample buffer. The reactions are loaded on 10% SDS-PAGE, electroblotted to nitrocellulose membrane and probed with a rabbit anti-HA antibody. Quantification is carried out using the ECL camera software (Fuji).Radioactive pulse and chase

[0192] For the assay of inhibitions of protein synthesis, cells are incubated with DMSO, ribosomal inhibitor cycloheximide (CHX), or polypeptides of the invention (SEQ ID Nos: 1-4). After 4 hours, media are replaced with medium containing35S -methionine and cysteine (20 pCi) and cells are pulsed for 4 hours. Plates are extensively washed with ice-cold PBS and proteins are extracted from cells using trichloroacetic acid (TCA) precipitation. The radioactive readings are measured using a scintillation counter.

[0193] For degradation-inhibition assays, cells are labeled with35S -methionine and cysteine (20 pCi) for 16 hours, followed by a chase in cold medium for 4 hours, in the presence of DMSO, proteasome inhibitor MG132, or polypeptides of the invention (SEQ ID Nos: 1-4). Media are then collected, and amino acids are extracted using TCA precipitation. Radioactive readings are measured using a scintillation counter.Cell intake of the polypeptides of the invention

[0194] HeLa cells are seeded on glass -bottomed (#1.5) 96-well dish and are incubated in the presence of either DMSO or Fluorescein-5-Maleimide-polypeptide of the invention (SEQ ID Nos: 1-4) for the indicated times. Medium is then aspired, and fresh medium is added to the wells. Live cell imaging is carried out using Zeiss LSM-700 confocal microscope equipped with an environmental control module.Cell viability assays and kinetic experiments

[0195] In order to assess the effect of the cyclic peptides on Hela cells, toxicity is determined using the MTT assay. Equal amounts of cells (8,000 cells / well) are plated in 96-well plates in triplicate. After 24 hours, attached cells are exposed to increasing concentrations of the cyclic peptides for another 24 hours. Thereafter, 10 pL of 12 mM MTT (Vybrant® MTT Cell Proliferation Assay Kit, ThermoFisher) are added per well according to the manufacturer's protocol and incubated for 4 hours at 37 °C. This is followed by the addition of 100 pL of SDS-HC1 solution, thorough mixing and incubated for 4 hours at 37 °C. Optical density is recorded at 590 nm with a reference measurement at 630 nm. Half maximal inhibitory concentration (IC50) values are defined as the concentrations that correspond to a reduction of cell growth by 50% when compared to values of untreated control cells and depicted as means of relative activity ± standard deviation.Fluorescence-activated cell sorting (FACS) analysis

[0196] Induction of apoptosis in Hela cells by treatment with cyclic peptides are determined after 24- and 48-hours incubation in a dose dependent manner, using annexin V-FITC apoptosis detection kit (BD Biosciences) according to the manufacturer's protocol. Two (2) x 105cells / well are seeded in 6-well plates and treated with an inhibitor for 24 / 48 hours in a dose dependent manner. The increase in fluorescence, which indicates the apoptosis level in the treated cells, is monitored using flow cytometry and compared to untreated cells containing DMSO as a negative control and MG132 as a positive control.EXAMPLE 1De novo cyclic peptides tightly bind K48-linked Ub chains

[0197] To test the binding and specificity of the polypeptides of the invention, each is prepared by chemical synthesis for Surface Plasmon Resonance (SPR) analysis. Each peptide is flowed over Ubi,K48Ub2 andK48Ub2 immobilized on SPR chips, and KD values are calculated. Binding to Ubi for any of the peptides is not expected.EXAMPLE 2Cyclic peptide protection of Ub chains against DUB cleavage in vitro

[0198] The inventors further examine the effect of the cyclic peptides on two DUBs: OTUB1, a K48-linkage chain specific DUB, and USP2, which cleaves most Ub chains without specificity, using K48-linked di- and tetra-Ub chains as substrates. Inhibition of cleavage by OTUB 1 or USP2 is quantified.EXAMPLE 3Cyclic peptide prevention of ubiquitinated proteins from proteasomal degradation

[0199] The inventors examine whether the binding of cyclic peptides to K48-Ub chains prevents the recognition by the proteasome and inhibits the degradation of proteins tagged with these Ub chains. To test this, the inventors incubate a a-globin-K48 -linked tetra-Ub and 26S proteasome, with or without the polypeptides of the invention, and monitor proteasomal degradation.EXAMPLE 4Cyclic peptides entrance into cancer cells

[0200] In order to assess the feasibility of using the polypeptides of the invention in cultured cells, the inventors test whether the examined polypeptides are able to cross the cellular membrane of human cells. The inventors synthesize the polypeptides of the invention being labeled with fluorescein and use live cell imaging to monitor and determined their entrance into HeLa cells, USOS osteosarcoma cells, and U87 primary glioblastoma cells.EXAMPLE 5Polypeptides of the invention promote accumulation of Ub-conjugates

[0201] Under basal conditions, the levels of Ub-conjugates reflect a dynamic steady state between the enzymatic bindings of Ub to proteins on the one hand, with the removal of conjugated Ub moieties by DUBs, and subsequent degradation by the proteasome, on the other. The inventors text in vitro whether the cyclic polypeptides of the invention protect Ub-chains from cleavage by DUBs, and also prevent recognition by the proteasome. Both effects are predicted to prevent degradation, and lead to the accumulation of proteins tagged with K48-Ub chains in cells. The inventors monitor the cellular level of Ub-conjugates in cells upon treatment with the polypeptides of the invention and determine elevation / reduction in Ub-conjugates following treatment with the cyclic polypeptides of the invention. A similar effect is predicted to be observed when treating cells with the direct proteasome inhibitor MG132.

[0202] In order to directly measure the effect of the polypeptides of the invention on proteolysis, the inventors employ radiolabeling of cellular proteins, followed by a chase experiment in the presence of either the effect of the polypeptides of the invention or the proteasome inhibitor MG132. When compared to non-treated cells, or ones treated with DMSO, protein breakdown in cells treated with the polypeptides of the invention is predicted to be markedly reduced, with similar rates of degradation as being observed in the presence of MG132. A dose-dependent effect on cellular protein degradation is also suggested. The inventors validate the inhibitory effect on protein breakdown with known proteasomal substrates, the proteins p53, and p27, bona fide substrates of the UPS. In the presence of the polypeptides of the invention, accumulation of both p53 and p27 over time is predicted, up to similar levels to the ones in the presence of MG132.EXAMPLE 6Cyclic polypeptides of the invention induce apoptosis

[0203] The inventors further examine whether the polypeptides of the invention inhibit cell growth and induce apoptosis in cancer cells. To test this, HeLa cells are treated with each cyclic peptide and cell viability is assessed using an MTT assay. The inventors forecast that the polypeptides of the invention effectively suppress cell growth. The effect of the cyclic peptides of the invention on apoptosis is evaluated using FACS analysis. An increase in apoptosis after 24 h and 48 h treatment is forecasted for the polypeptides of the invention, similarly to the direct proteasome inhibitor MG 132.EXAMPLE 7Ub4a derivatives synthesis, and activity assays

[0204] In order to enhance peptide efficacy, new novel structures and derivates of Ub4a were created addressing the issue of its challenging solubility which may be a factor in its cell permeability and hence efficacy. To this end, new structures working in the same mechanism of action of Ub4a (SEQ ID NO: 5) yet with enhanced solubility and / or activity were designed.

[0205] For this purpose, variations of Ub4a (SEQ ID NO: 5) with the addition of Arginine (R) and Glycine (G) were designed and synthesized. Four (4) Ub4a derivatives were synthesized herein: Ub4a-CR: FQYWOYATGVCR (SEQ ID NO: 1); Ub4a-CRR: FQYWOYATGVCRR (SEQ ID NO: 2); Ub4a-GR: FQYWOYATGVCGR (SEQ ID NO: 3); and Ub4a-GRR: FQYWOYATGVCGRR (SEQ ID NO: 4) (Fig. 1).

[0206] A comparison between the 4 different Ub4a derivatives efficacy was tested on 2 cell lines, MM1S and BTZ900, using an Annexin-PI apoptosis assay after an incubation for a period of 14 days with the 8 pM and 5 pM peptides.

[0207] The results shown in Figs. 2-3 indicate a better apoptotic response in MM IS after incubation with Ub4a-CR (SEQ ID NO: 2) and Ub4a-GRR (SEQ ID NO: 4), while in BTZ900 a lower viability was observed following incubation with Ub4a-CR (SEQ ID NO: 2) and Ub4a-GRR (SEQ ID NO: 4). In light of these results, more experiments were performed using Ub4a-CR (SEQ ID NO: 2) and Ub4a-GRR SEQ ID NO: 4).

[0208] A time dependent response was studied on both multiple myeloma (MM) cell lines, MM1S and BTZ900, examining Ub4a-CR (SEQ ID NO: 2) and Ub4a-GRR (SEQID NO: 4) effect on cell viability after incubation for 5 and 10 days with 2 |aM and 5 |iM peptide.

[0209] Both Figs. 4-6 show that Ub4a-GRR (SEQ ID NO: 4) has induced a significantly higher negative effect on cell viability.

[0210] To ensure that the modifications had improved peptide efficacy, a comparison between the effect of Ub4a (SEQ ID NO: 5) and Ub4a-GRR (SEQ ID NO: 4) on cell viability after 8 days of incubation of MM1S and BTZ900 cell lines with 5 pM or 2 pM was performed. The results surprisingly showed that Ub4a-GRR (SEQ ID NO: 4) demonstrated an increase of efficacy compared to Ub4a (Fig. 7).

[0211] Moreover, the stability of Ub4a-GRR (SEQ ID NO: 4) in human plasma was studied by incubating Ub4a-GRR (SEQ ID NO: 4) in human plasma in a concentration of 0.5 mg / ml for 1 hr in 37 °C. Then, peptide extraction was performed by precipitating plasma proteins in cold Aceton in -20 °C for 1 hr. Then, samples were centrifuged in 14,000 RPM for 10 min. The supernatant was collected and tested using HPLC. By comparison Ub4a-GRR (SEQ ID NO: 4) peak to a control of Ub4a-GRR diluted in 5%DMSO in water that undergone the same incubation and extraction method, Ub4a- GRR recovery and stability in plasma was performed. A stability for at least 8 hr was observed (Fig. 8).

[0212] In order to calculate the half maximal effective concentration (ECso), the concentration related response was studied by examining cell viability after treatment with different concentrations for 12 days. The calculation of ECso was performed according to the results demonstrated in Fig. 9, which was found to be approximately 0.44. To this end, the ECso of the ‘parent peptide’, Ub4a (SEQ ID NO: 5), was found to be greater than 3 pM (data not shown). Therefore, it was concluded that Ub4a-GRR is likely an improved derivative of Ub4a, at least in terms of inhibitory activity.

[0213] Given the afore-mentioned promising in vitro efficacy data, and improved effect / activity compared to the ‘parent peptide’, Ub4a (SEQ ID NO: 5), it was essential to evaluate the safety profile of Ub4a-GRR (SEQ ID NO: 4) to ensure its suitability for further development. This experiment provides critical insights into the potential toxicities associated with Ub4a-GRR and help identify any dose-limiting toxicities.

[0214] Therefore, a maximum tolerated dose (MTD) experiment was conducted. The primary objective of the MTD experiment was to determine the highest dose of Ub4a-GRR (SEQ ID NO: 4) which can be safely administered without causing severe / adverse effects. Establishing the MTD is a crucial step in the drug development process, as it helps define the dosage range for subsequent preclinical and clinical studies.

[0215] For this study, a total of 20 female NOD / SCID mice were utilized and divided into six groups of one, three or six animals per each group. Treatment group were treated with Ub4a-GRR for 5 days, then morbidity and mortality observations were performed as well as evaluating body weight, and food consumption. Then, on day 6, animals were scarified, and gross necropsy were undergone for the detection of abnormalities.

[0216] The changes in body weight are presented in Fig. 10. According to the results, the MTD was not reached, as Ub4a-GRR did not cause any apparent damage at any of the tested doses (5-45 mg / kg SC and 0.5-2 mg / kg IV).

[0217] According to the results presented in Fig. 11, the pharmacokinetic profile of Ub4a-GRR was evaluated following intravenous (IV) bolus, subcutaneous (SC), intraperitoneal (IP), and intramuscular (IM) dosing.

[0218] Notably, SC route of administration demonstrated a distinct advantage, as it was the only administration route where the compound remained detectable beyond 8 hours, suggesting prolonged systemic exposure and extended half-life (Figs. 10-11). Given this extended duration and favorable profile, SC administration seems like a preferred route for further in-vivo investigation. Moreover, due to rapid absorption, twice-daily SC dosing of Ub4a-GRR (SEQ ID NO: 4) may be optimal for maintaining adequate plasma levels over time.

[0219] Further, anti-cancer effect(s) of the polypeptide of the invention was examined in vivo. Briefly, UB4a (SEQ ID NO: 5) was administered to mice with MM tumors resistant to bortezomib. Mice of the SCID NOD type, were implanted with MM tumors from the BTZ900 cell line, each group of 10 mice received a different treatment. UB4a treated group, received three different doses of UB4a (2, 5, and 10 mg / kg) intramuscularly daily for 40 days. Tumor volume changes were monitored throughout the study to assess the treatment's impact on tumor growth. The results were compared to a vehicle control and Bortezomib treated group. The results show a significant tumor growth inhibition after 22 days, wherein a decrease in tumor volume of up to 44% was observed after 40 days of treatment with the Ub4a peptide (SEQ ID NO: 5; Fig. 13).

[0220] Further, a study using comparable negative control as described above (Fig. 13), was conducted, examining the in-vivo effect of UB4a-GRR (SEQ ID NO: 4) in KMS- 12-BM-BPR subcutaneous multiple myeloma tumor model in female NSG mice (MM tumors resistant to bortezomib). A group of 3 mice received 2 mg / ml dose subcutaneously (SC) daily. Tumor volume changes were monitored throughout the study to assess the treatment's impact on tumor growth. Results were compared to an untreated group, which indicate a significant inhibition in tumor growth after 10 days from dosing initiation, and a decrease in tumor volume of up to 63% after 24 days of treatment (Fig. 14). Further, a second control group including CP-15, a known inhibitor capable of binding to Ub K63 (as described in Vamisetti et al., Nature Communications (2022)13:6174), was also applied. The results show that CP-15 activity was comparable to the untreated control, both of which were found to be substantially inferior compared to Ub4a-GRR (Fig. 14). Further, plasma solubility of CP- 15 was found to be rather low (data not shown). Moreover, pharmacokinetic studies in vivo (in mice) showed that CP- 15 was lethal following intravenous injection, with no detectable levels in plasma (data not shown). Subsequent in vitro studies revealed that CP 15 precipitates in plasma, likely contributing to its poor pharmacokinetic profile.

[0221] These results highlight the significant improvement posed by the Ub4a-GRR peptide over its predecessor UB4a, as well as over other suitable controls, e.g., CP-15, in-vivo.

[0222] While certain features of the invention have been illustrated and described herein, many modifications, substitutions, changes, and equivalents will now occur to those of ordinary skill in the art. It is, therefore, to be understood that the appended claims are intended to cover all such modifications and changes as fall within the true spirit of the invention.

Claims

CLAIMSWhat is claimed is:

1. A polypeptide comprising an amino acid sequence selected from the group consisting of: FQYWOYATGVCR (SEQ ID NO: 1); FQYWOYATGVCRR (SEQ ID NO: 2); FQYWOYATGVCGR (SEQ ID NO: 3); and FQYWOYATGVCGRR (SEQ ID NO: 4).

2. The polypeptide of claim 1, wherein at least one amino acid residue of said polypeptide is methylated.

3. The polypeptide of claim 1 or 2, wherein said polypeptide comprises not more than 16 amino acid residues.

4. The polypeptide of any one of claims 1 to 3, wherein the amino acid at position one is a D amino acid.

5. The polypeptide of any one of claims 1 to 4, wherein the amino acid at position one is conjugated to a cyclizing molecule.

6. The polypeptide of any one of claims 1 to 5, wherein said polypeptide is a cyclic polypeptide prepared using a cyclizing molecule comprising a halogen.

7. The polypeptide of claim 6, wherein said cyclizing molecule is selected from the group consisting of: chloracetyl chloride, 3 -chlorobenzoyl (3-ClBz), 4 -chlorobenzoyl (4-ClBz) or C12SAc.

8. The polypeptide of any one of claims 1 to 7, being characterized as having: cell penetration capability, ubiquitin (Ub) binding capability, or a combination thereof.

9. The polypeptide of claim 8, having increased affinity to Ub compared to control.

10. The polypeptide of claim 9, wherein said control is a polypeptide consisting of the amino acid sequence set forth in SEQ ID NO: 5.

11. The polypeptide of any one of claims 1 to 10, being a cyclic polypeptide.

12. A pharmaceutical composition comprising the polypeptide of any one of claims 1 to 11 and at least one acceptable carrier.

13. The pharmaceutical composition of claim 12, for use in treatment of cancer in a subject in need thereof.

14. A method for reducing deubiquitination activity of a cell, the method comprising contacting the cell with an effective amount of a polypeptide comprising the amino acid sequence set forth in SEQ ID Nos: 1-4.

15. A method for ameliorating or treating cancer in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of a polypeptide comprising the amino acid sequence set forth in SEQ ID Nos: 1-4.

16. The method of claim 15, wherein said administering is subcutaneously administering.

17. The method of claim 15 or 16, wherein said administering comprises multiple administrations.

18. The method of claim 17, wherein said multiple administrations comprise at least two administrations, being 4 to 12 hours apart.

19. The method of claim 17 or 18, wherein said multiple administrations comprise at least two administrations being 4 to 10 hours apart.

20. The method of any one of claims 14 to 19, wherein said polypeptide: (i) binds Ub with an affinity KD of 0.05-100 nM; (ii) comprises not more than 16 amino acid residues; or both (i) and (ii).

21. The method of any one of claims 14 to 20, wherein the amino acid at position one of said polypeptide is a D amino acid.

22. The method of any one of claims 14 to 21, wherein the amino acid at position one of said polypeptide is conjugated to a cyclizing molecule.

23. The method of any one of claims 14 to 22, wherein said polypeptide is a cyclic polypeptide being prepared using a cyclizing molecule comprising a halogen.

24. The method of claim 23, wherein said cyclizing molecule is selected from the group consisting of: chloracetyl chloride, 3 -chlorobenzoyl (3-ClBz), 4 -chlorobenzoyl (4-ClBz) or ChSAc.

25. The method of any one of claims 14 to 24, wherein said polypeptide has: cell penetrating capability, Ub binding capability, or a combination thereof.

26. The method of any one of claims 14 to 25, wherein said polypeptide has increased affinity to Ub compared to control.

27. The method of any one of claims 20 to 26, wherein said Ub is a polymeric Ub.

28. The method of claim 26, wherein said polymeric Ub comprises Ub monomers linked at their K48 position (K48Ub).

29. The method of claim 28, wherein said polypeptide has increased pro-apoptotic activity compared to control.

30. The method of any one of claims 14 to 29, wherein said polypeptide is a cyclic polypeptide.

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