# Patent

## Title
Peptides having anti-inflammatory properties

## Abstract

Aspects of the present invention relate to peptides having anti-inflammatory activity, compositions containing one or more of the peptides, and use of the peptides to treat conditions associated with excessive inflammation in animals, particularly humans and other mammals.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
Pursuant to 35 U.S.C. §119 (e), this application claims the benefit of priority to U.S. Provisional Patent Application Ser. No. 62/063,909, filed Oct. 14, 2014, the disclosure of which application is hereby incorporated by reference herein in its entirety.


FIELD OF THE INVENTION
Aspects of the present invention relate to peptides having anti-inflammatory activity, compositions containing one or more of the peptides, and use of the peptides to treat conditions associated with excessive inflammation in animals, particularly humans and other mammals.
BACKGROUND OF THE INVENTION
Under normal conditions, inflammation is a process that helps an animal recover from injury. Acute inflammation is the initial response of a tissue to harmful stimuli. It involves a complex, highly regulated process that begins when cells present in the injured tissue, including macrophages, dendritic cells, histiocytes, Kupffer cells, and mastocytes, sense molecules associated with the injury and become activated. Upon activation, these cells release inflammatory mediators, such as vasodilators. The vasodilators induce increased blood flow and permeability of the blood vessels in the vicinity of the injury. This, in turn, results in the increased movement of plasma and leukocytes (including neutrophils and macrophages) from the blood into the injured tissue. Because inflammatory mediators are, in general, rapidly degraded, acute inflammation requires constant stimulation in order to be sustained. As a result, acute inflammation ends once the harmful stimulus is removed.
Various agents, including but not limited to bacteria, viruses, physical injury, chemical injury, cancer, chemotherapy, and radiation therapy, can, depending on the specific agent and the genetic makeup of the animal exposed to it, cause prolonged and excessive inflammation. Such inflammation, known as chronic inflammation, is believed to be a contributing factor to many widespread and debilitating diseases, including heart disease, cancer, respiratory disease, stroke, neurological diseases such as Alzheimer's disease, diabetes, and kidney disease. The result of chronic inflammation is the destruction of normal tissue and its replacement with collagen-rich connective tissue. Collagen-rich connective tissue, also known as scar tissue, exhibits diminished tissue function as compared to normal tissue. Persistent and prolonged formation of scar tissue, in turn, leads to fibrosis. Fibrosis is among the common symptoms of diseases affecting the lungs, skin, liver, heart, and bone marrow, and is a critical factor in diseases such as idiopathic pulmonary fibrosis, scleroderma, keloids, liver cirrhosis, myocardial fibrosis, diabetic kidney disease, myelodysplastic syndrome, and other disorders.
Studies of chronic inflammation and fibrosis have indicated that, regardless of the activating agent and the tissue affected, a common network of signaling proteins tend to function together to establish the pro-inflammatory state. This network of signaling proteins includes a number of different cytokines, cytokine receptors, transcription factors, and micro RNAs, including TGFβ, TGFβRII, and miRNA19b.
Despite growing knowledge about conditions that involve excessive inflammation, such as chronic inflammation and fibrosis, treatments for such conditions remain elusive. Many drugs and other substances have been shown to have anti-inflammatory activity, either in vitro or in vivo, but for many indications caused or potentiated by inflammation, there are still no therapies. In addition, many anti-inflammatory therapies are associated with harmful side effects. Thus, there remains a critical need to identify therapeutic agents that reduce inflammation without harmful side effects.
SUMMARY OF THE INVENTION
The present invention is based, in part, on the discovery of novel peptides that have powerful anti-inflammatory activities in vitro and in vivo. The present invention is also based, in part, on the discovery that peptides of the invention specifically bind to key functional regions on one or more signaling proteins, particularly pro-inflammatory cytokines, macrophage inhibition proteins, and histone regulation proteins. The present invention is also based, in part, on the discovery that the peptides of the invention are sufficiently stable in the circulation to allow for intravenous administration.
Accordingly, in one aspect, the invention provides a composition comprising an anti-inflammatory polypeptide. In certain embodiments, the anti-inflammatory polypeptide is 3 to 24 amino acids residues in length and includes a striapathic region consisting of alternating hydrophobic and hydrophilic modules. In certain embodiments, each hydrophilic module is made up of a sequence of one or more (e.g., 1-5, 1-4, 1-3) hydrophilic amino acid residues. In certain embodiments, each hydrophobic module is made up of a sequence of one or more (e.g., 1-5, 1-4, 1-3) hydrophobic amino acid residues.
In certain embodiments, the striapathic region of an anti-inflammatory peptide includes m hydrophilic modules and n hydrophobic modules, with m and n each being a positive integer. For example, in certain embodiments, the striapathic region includes two hydrophilic modules and two hydrophobic modules (2:2), two hydrophilic modules and three hydrophobic modules (2:3), three hydrophilic modules and two hydrophobic modules (3:2), three hydrophilic modules and three hydrophobic modules (3:3), three hydrophilic modules and four hydrophobic modules (3:4), or four hydrophilic modules and three hydrophobic modules (4:3).
In certain embodiments, the striapathic region of an anti-inflammatory polypeptide is at least 5, 6, 7, 8, 9, or 10 amino acid residues in length. In preferred embodiments, the length of the striapathic region is between 7 and 12 amino acid residues. In certain embodiments, the striapathic region makes up at least 25% of the length of the polypeptide. For example, in certain embodiments, the striapathic region comprises at least 30%, 35%, 40%, 45%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% of the length of the polypeptide.
In certain embodiments, the striapathic region of an anti-inflammatory polypeptide adopts a helical secondary structure. Examples of helical secondary structures include 310-helices, α-helices, π-helices, and poly-proline helices. In other embodiments, the striapathic region of an anti-inflammatory polypeptide adopts a beta-strand secondary structure. In preferred embodiments, the striapathic region of an anti-inflammatory polypeptides has an amphipathic conformation.
In certain embodiments, an anti-inflammatory polypeptide comprises, consists essentially of, or consists of a striapathic region having a sequence that conforms to any one of the structural formulas disclosed herein (e.g., any one of Formulas I-LIII). In certain embodiments, the anti-inflammatory polypeptide is one of the polypeptides listed in Tables 3-9. In other embodiments, the anti-inflammatory polypeptide has at least 70%, 80%, or 90% homology with any one of the polypeptides disclosed in Tables 3-9.
In certain embodiments, an anti-inflammatory polypeptide binds to at least one signaling protein. In preferred embodiments, the anti-inflammatory polypeptide binds to at least one signaling protein in vitro and/or in vivo, with sufficient affinity to modulate the activity of the signaling protein. Examples of signaling proteins that the anti-inflammatory polypeptides bind to include proteins that function as pro-inflammatory cytokines, proteins that inhibit macrophage activity, or protein that regulate histone function. In certain embodiments, the anti-inflammatory polypeptide binds to a protein target selected from the group consisting of NFkB class II proteins (e.g., Rel A, Rel B, cRel, NF-kB1, and NF-kB2), TGFβ, Notch receptors (e.g., Notch1), Wnt receptors (e.g., Wnt8R), TRAIL, EGFR, interleukin receptors (e.g., IL6R, IL10R), cyclin dependent kinases (e.g., CDK6), CD47, SIRP-α, transglutaminases (e.g., TGM2), LEGUMAIN, CD209, FAS, programmed cell death protein 1 (PD-1/CD279), mitogen-activated protein kinase kinase 7 (MKK7), ribonucleotide reductase (RNR), and histone methyl transferase. In preferred embodiments, the anti-inflammatory polypeptide binds to two, three, four, or more such signaling proteins. For example, in certain embodiments, an anti-inflammatory polypeptide binds to an NF-kB Class II protein (e.g., RelB) and at least one other signaling protein that functions as a pro-inflammatory cytokine, an inhibitor of macrophage activity, or a regulator of histone function. In preferred embodiments, the anti-inflammatory polypeptide binds to the NF-kB Class II protein and at least one other protein target, with sufficient binding affinity to each target to modulate the activity of both targets in vivo. In preferred embodiments, an anti-inflammatory polypeptide binds to the dimerization site of an NFkB Class II protein (e.g., RelB).
In certain embodiments, an anti-inflammatory polyeptides binds to a carrier protein in the blood (e.g., serum albumin).
In certain embodiments, an anti-inflammatory polypeptide is modified to include, for example, a linker, a carbohydrate, a lipid, or a polymer (e.g., PEG). In certain embodiments, a first anti-inflammatory polyeptide is linked to a second anti-inflammatory polypeptide so as to form a multimer, such as a dimer. In certain embodiments, the dimer is a homodimer. In other embodiments, the dimer is a heterodimer. In certain embodiments, the linker is a peptide linker. In preferred embodiments, the peptide linker forms a peptide bond with the C-terminus of the first anti-inflammatory polypeptide and a peptide bond with the N-terminus of the second anti-inflammatory polypeptide. In certain embodiments, the linker is a biodegradeable linker. In certain embodiments, the linker is a disulfide bond. In certain embodiments, the disulfide linkage is formed by a pair of cysteine residues (e.g., one cysteine residue from each of the polypeptides being linked).
In certain embodiments, the anti-inflammatory polypeptide is linked to a molecule other than another anti-inflammatory polypeptide. For example, the anti-inflammatory polypeptide can be linked to a label or a chemotherapeutic agent. In certain embodiments, the linker is a biodegradable linker. In certain embodiments, the linker is a di-sulfide bond (e.g., involving the sulfhydryl group of a cysteine residue located at the C-terminus or N-terminus of the anti-inflammatory polypeptide).
In another aspect, the invention provides pharmaceutical compositions that comprise an anti-inflammatory polypeptide and a pharmaceutically acceptable carrier. In certain embodiments, the pharmaceutical composition comprises a single type of anti-inflammatory polypeptide. In other embodiments, the pharmaceutical composition comprises a combination of two or more anti-inflammatory polypeptides. In preferred embodiments, the pharmaceutical composition is substantially free of blood proteins and/or metabolites found in the blood. In other embodiments, the pharmaceutical composition includes serum albumin (e.g., human serum albumin). In preferred embodiments, any serum albumin present in a pharmaceutical composition is recombinantly produced and/or substantially free of other blood proteins and/or metabolites found in the blood. In certain embodiments, the pharmaceutical composition comprises 1 mg to 1000 mg (e.g., 10 to 400 mg, 20 to 300 mg, or about 25 to 250 mg) of an anti-inflammatory polypeptide.
In another aspect, the invention provides methods of treating a subject by administering to the subject a composition (e.g., a pharmaceutical composition) comprising an anti-inflammatory polypeptide. In certain embodiments, the subject is an animal, such as a mammal (e.g., a human). In certain embodiments, the subject has elevated levels of inflammatory cytokines, is suffering from a chronic inflammatory condition, or is likely to develop a chronic inflammatory condition. In certain embodiments, the chronic inflammatory condition can be irritable bowel disease, ulcerative colitis, colitis, Crohn's disease, fibrosis, idiopathic pulmonary fibrosis, asthma, keratitis, arthritis, osteoarthritis, rheumatoid arthritis, an auto-immune disease, a feline or human immunodeficiency virus (FIV or HIV) infection, or cancer. In certain embodiments, the cancer is colon cancer, breast cancer, leukemia, lymphoma, ovarian cancer, prostate cancer, liver cancer, lung cancer, testicular cancer, cervical cancer, bladder cancer, endometrial cancer, kidney cancer, melanoma, or a cancer of the thyroid or brain. In certain embodiments, the composition is administered in combination with a chemotherapeutic agent, immunotherapeutic agent, and/or radiation therapy.
These and other features and advantages of the compositions and methods of the invention will be set forth or will become more fully apparent in the description that follows and in the appended claims. For example, suitable anti-inflammatory polypeptides may be identified by use of the Structural Algorithm described herein. Furthermore, features and advantages of the described compositions and methods may be learned by practicing the methods or will be obvious from the description.



BRIEF SUMMARY OF THE DRAWINGS
FIG. 1 depicts a structural model of human RelB, an NF-kB Class II protein.
FIG. 2 depicts a structural model of human RelB bound by RP-182.
FIG. 3 depicts a structural model of human RelB bound by RP-166.
FIG. 4 depicts a structural model of human RelB bound by RP-113.
FIG. 5 depicts a structural model of human RelB bound by RP-387.
FIG. 6 depicts a structural model of human RelB bound by RP-289.
FIG. 7 depicts a structural model of human RelB bound by NF-Contr2.
FIG. 8 depicts a structural model of human RelB bound by NF-Contr3.
FIG. 9 depicts structural models of polypeptides RP-182, RP-166, RP-113, and RP-289, with each model showing the polar and non-polar facial arc associated with the helices formed by the polypeptides.
FIG. 10 depicts structural models of polypeptides RP-387, NF-Contr2, and NF-Contr3, with each model showing the polar and non-polar amino acid residues. The facial arc associated with the helix formed by RP-387 is also shown.
FIG. 11 depicts a structural model of the binding pocket of the RelB dimerization domain.
FIG. 12 depicts a structural model of the binding pocket of the RelB dimerization domain bound by RP-183.
FIG. 13 depicts a structural model of histone methyl transferase enzyme bound by RP-182.
FIG. 14 depicts structural models of a CD47 dimer (left panel) and a CD47 dimer bound by RP-183.
FIG. 15 depicts structural models of a SIRP-α dimer (left panel) and a SIRP-α dimer bound by RP-183.
FIG. 16 depicts structural models of CD206 (left side) and CD206 bound by RP-182 (right side).
FIG. 17 depicts structural models of TGM2 (left side) and TGM2 bound by RP-182 (right side).
FIG. 18 depicts a structural model of human serum albumin bound by RP-183.
FIG. 19 shows PD-1-stained tumor cells from p53/KRAS mice treated with vehicle only (left panel) or treated with RP-182 (right panel). PD-1 expression is reduced in RP-182 treated mice.
FIG. 20 shows PD-L1-stained (left panels) and PD-L2-stained (right panels) tumor cells from p53/KRAS mice treated with vehicle only (top panel in each set) or treated with RP-182 (bottom panel in each set). PD-L1 and PD-L2 expression is reduced in RP-182 treated mice.
FIG. 21 shows MDA-MB-231 tumor volume in four cohorts of mice over time. Cohort 1: vehicle; Cohort 2: Gemcitabine treated; Cohort 3: RP-182 treated; Cohort 4: RP-182+Gemcitabine treated.
FIG. 22 shows C42B tumor volume in four cohorts of mice over time. Cohort 1: vehicle; Cohort 2: Docetaxel treated; Cohort 3: RP-182 treated; Cohort 4: RP-182+Docetaxel treated.



DETAILED DESCRIPTION OF THE INVENTION
The following description supplies specific details in order to provide a thorough understanding of the present invention. That said, to avoid obscuring aspects of the described anti-inflammatory polypeptides and related methods of treating a subject, well-known structures, materials, processes, techniques, and operations are not shown or described in detail. Additionally, the skilled artisan will understand that the described anti-inflammatory polypeptides and related methods of treating a subject can be implemented and used without employing these specific details. Indeed, the described anti-inflammatory polypeptides and methods can be placed into practice by modifying the illustrated polypeptides, compositions, and methods, and can be used in conjunction with other treatments, apparatuses, and techniques conventionally used in the industry.
As discussed above, the invention disclosed herein relates to immune-modulatory polypeptides, particularly peptides that have immunosuppressive properties, and methods of administering such immune-modulatory polypeptides to a subject, particularly a subject suffering from a medical condition associated with persistent inflammation or at risk developing such a medical condition.
The invention provides anti-inflammatory polypeptides, sometimes referred to as “RP peptides,” that satisfy the requirements of the Structural Algorithm described below. The invention also provides anti-inflammatory polypeptides that share a minimum degree of homology with any of the exemplary RP peptides disclosed herein. Thus, a peptide or polypeptide of the invention is an anti-inflammatory polypeptide that satisfies the Structural Algorithm described below or shares a minimum degree of homology with any of the exemplary RP peptides disclosed herein (e.g., in Tables 3-9).
The terms “peptide” and “polypeptide” are used synonymously herein to refer to polymers constructed from amino acid residues.
The term “amino acid residue,” as used herein, refers to any naturally occurring amino acid (L or D form), non-naturally occurring amino acid, or amino acid mimetic (such as a peptoid monomer).
The “length” of a polypeptide is the number of amino acid residues linked end-to-end that constitute the polypeptide, excluding any non-peptide linkers and/or modifications that the polypeptide may contain.
The term “striapathic region,” as used herein, refers to an alternating sequence of hydrophobic and hydrophilic modules. A “hydrophobic module” is made up of a peptide sequence consisting of one to five hydrophobic amino acid residues. Likewise, a hydrophilic module is made up of a peptide sequence consisting of one to five hydrophilic amino acid residues.
Hydrophobic amino acid residues are characterized by a functional group (“side chain”) that has predominantly non-polar chemical properties. Such hydrophobic amino acid residues can be naturally occurring (L or D form) or non-naturally occurring. Alternatively, hydrophobic amino acid residues can be amino acid mimetics characterized by a functional group (“side chain”) that has predominantly non-polar chemical properties. Conversely, hydrophilic amino acid residues are characterized by a functional group (“side chain”) that has predominantly polar (charged or uncharged) chemical properties. Such hydrophilic amino acid residues can be naturally occurring (L or D form) or non-naturally occurring. Alternatively, hydrophilic amino acid residues can be amino acid mimetics characterized by a functional group (“side chain”) that has predominantly polar (charged or uncharged) chemical properties. Examples of hydrophilic and hydrophobic amino acid residues are shown in Table 1, below. Suitable non-naturally occurring amino acid residues and amino acid mimetics are known in the art. See, e.g., Liang et al. (2013), “An Index for Characterization of Natural and Non-Natural Amino Acids for Peptidomimetics,” PLoS ONE 8(7):e67844.
Although most amino acid residues can be considered as either hydrophobic or hydrophilic, a few, depending on their context, can behave as either hydrophobic or hydrophilic. For example, due to their relatively weak non-polar characteristics, glycine, proline, and/or cysteine can sometimes function as hydrophilic amino acid residues. Conversely, due to their bulky, slightly hydrophobic side chains, histidine and arginine can sometimes function as hydrophobic amino acid residues.







TABLE 1







Hydrophobic and Hydrophilic Amino Acid Residues










Hydrophilic Residues (X)
Hydrophobic Residues (Y)







Arginine
Tryptophan



Histidine
Phenylalanine



Lysine
Tyrosine



Aspartic Acid
Isoleucine



Glutamic Acid
Leucine



Asparagine
Valine



Glutamine
Methionine



Pyrrolysine
Cysteine




Threonine




Serine




Alanine




Proline




Glycine




Selenocysteine




N-formylmethionine




Norleucine




Norvaline










The term “anti-inflammatory property,” as used herein, refers to any property of a polypeptide that can be evaluated in silico, in vitro, and/or in vivo, that reduces or inhibits, or would be expected to reduce or inhibit, a pro-inflammatory signal mediated by a protein target and/or reduces or inhibits inflammation in a subject.
Structural Algorithm
In its most basic form, the Structural Algorithm requires an anti-inflammatory peptide to have the following characteristics:
a length of 3 to 24 amino acid residues;
a striapathic region that comprises at least 25% of the length of the polypeptide; and
at least one anti-inflammatory property.
The anti-inflammatory peptide and/or its striapathic region can have a length that is greater than 3 amino acid residues and/or less than 24 amino acid residues. Thus, the requisite length of the polypeptide can be, for example, 3 to 20, 3 to 18, 3 to 16, 3 to 14, 3 to 12, 4 to 20, 4 to 18, 4 to 16, 4 to 14, 4 to 12, 5 to 20, 5 to 18, 5 to 16, 5 to 14, 5 to 12, 6 to 20, 6 to 18, 6 to 16, 6 to 14, 6 to 12, 7 to 20, 7 to 18, 7 to 16, 7 to 14, or in certain embodiments 7 to 12 amino acid residues. For an anti-inflammatory polypeptide that is longer than 12 amino acid residues, it can be advantageous to design a kink in the secondary structure (e.g., such as produced by a proline residue) such that the polypeptide has a striapathic region that is 12 or fewer amino acid residues in length. The striapathic region of an anti-inflammatory peptide can comprise at least 30%, 35%, 40%, 45%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% of the length of the polypeptide.
An anti-inflammatory polypeptide can have a striapathic region that includes at least two hydrophobic modules and one or more (e.g., two or three) hydrophilic modules. Alternatively, an anti-inflammatory polypeptide can have a striapathic region that includes at least three hydrophobic modules and two or more (e.g., three or four) hydrophilic modules; a striapathic region that includes at least two hydrophilic modules and one or more (e.g., two or three) hydrophilic modules; or a striapathic region that includes at least three hydrophilic modules and two or more (e.g., three or four) hydrophobic modules.
As discussed above, a striapathic region consists of alternating hydrophilic (Xm) and hydrophobic (Yn) modules. In this context, the subscripts m and n are positive integers that identify different modules. Each Xm module consists of a sequence according to the formula Xma-Xmb-Xmc-Xmd-Xme. Xma is selected from the group consisting of a naturally occurring hydrophilic amino acid, a non-naturally occurring hydrophilic amino acid, and a hydrophilic amino acid mimetic; and Xmb, Xmc, Xmd and Xme are each individually absent or selected from the group consisting of a naturally occurring hydrophilic amino acid, a non-naturally occurring hydrophilic amino acid, and a hydrophilic amino acid mimetic. Each Yn module consists of a sequence according to the formula Yna-Ynb-Ync-Ynd-Yne. Yna is selected from the group consisting of a naturally occurring hydrophobic amino acid, a non-naturally occurring hydrophobic amino acid, and a hydrophobic amino acid mimetic; Ynb, Ync, Ynd, and Yne are each individually absent or selected from the group consisting of a naturally occurring hydrophobic, a non-naturally occurring hydrophobic amino acid, and a hydrophobic amino acid mimetic.
In certain anti-inflammatory polypeptides, each Xm module consists of a sequence according to the formula Xma-Xmb-Xmc-Xmd or Xma-Xmb-Xmc. Similarly, in certain anti-inflammatory polypeptides, each Yn module consists of a sequence according to the formula Yna-Ynb-Ync-Ynd or Yna-Ynb-Ync.
Anti-inflammatory peptides can include a striapathic region corresponding to a formula selected from the group consisting of:

Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c  (Formula I);

Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c-X2a-Y3a-X3a  (Formula II);

X2a-Y3a-X3a-Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c  (Formula III);

X1a-X1b-X1c-Y2a-X2a-X2b-X2c  (Formula IV);

Y1a-X1a-X1b-X1c-Y2a-X2a-X2b-X2c-Y3a-X3a  (Formula V);

X1a-X1b-Y2a-Y2b-X2a-X2b  (Formula VI);

Y1a-X1a-X1b-Y2a-Y2b-X2a-X2b-Y3a  (Formula VII);

Y1a-X1a-X1b-Y2a-Y2b-X2a-X2b-Y3a-Y3b-X3a  (Formula VIII);

Y1a-Y1b-X1a-X1b-Y2a-Y2b-X2a-X2b-Y3a-Y3b  (Formula IX);

Y1a-Y1b-X1a-X1b-Y2a-Y2b-X2a-X2b-Y3a-X3a  (Formula X);

X1a-Y1a-X2a-X2b-Y2a-Y2b-X3a-X3b-Y3a-Y3b  (Formula XI);

X1a-Y1a-Y1b-X2a-X2b-Y2a-Y2b-X3a-X3b-Y3a  (Formula XII);

Y1a-X1a-X1b-Y2a-Y2b-X2a-X2b-X2c-Y3a-Y3b  (Formula XIII);

X1a-X1b-X1c-Y1a-Y1b-X2a-X2b-Y2a-Y2b-Y2c  (Formula XIV);

Y1a-Y1b-Y1c-X1a-X1b-Y2a-Y2b-X2a-X2b-X2c  (Formula XV);

Y1a-Y1b-X1a-X1b-X1c-Y2a-Y2b-X2a-X2b-Y3a  (Formula XVI);

Y1a-Y1b-X1a-X1b-Y2a-Y2b  (Formula XVII);

X1a-Y1a-Y1b-X2a-X2b-Y2a-Y2b-X3a  (Formula XVIII);

Y1a-Y1b-X1a-X1b-Y2a-Y2b-X2a-Y3a-Y3b-X3a  (Formula XIX);

X1a-Y1a-Y1b-X2a-Y2a-Y2b-X3a-X3b-Y3a-Y3b  (Formula XX);

Y1a-Y1b-X1a-X1b-Y2a-X2a-X2b-Y3a-Y3b  (Formula XXI);

X1a-Y1a-Y1b-X2a-X2b-X2c-Y2a-X3a-Y3a-Y3b  (Formula XXII);

Y1a-Y1b-X1a-Y2a-X2a-X2b-X2c-Y3a-Y3b-X3a  (Formula XXIII);

X1a-X1b-Y1a-X2a-Y2a-X3a-X3b  (Formula XXIV);

Y1a-Y1b-Y1c-X1a-X1b-Y2a-X2a-Y3a-X3a-X3b  (Formula XXV);

X1a-X1b-Y1a-X2a-Y2a-X3a-X3b-Y3a-Y3b-Y3c  (Formula XXVI);

X1a-X1b-X1c-Y1a-Y1b-Y1c  (Formula XXVII);

X1a-X1b-X1c-X1d-Y1a-Y1b-Y1c-Y1d  (Formula XXVIII);

Y1a-X1a-X1b-X1c-X1d-Y2a-Y2b-Y2c-Y2d-X2a  (Formula XXIX);

X1a-X1b-X1c-X1d-X1e-Y1a-Y1b-Y1c-Y1d-Y1e  (Formula XXX);

Y1a-Y1b-X1a-X1b-X1c-Y2a-Y2b-Y2c-X2a-X2b  (Formula XXXI);

X1a-Y1a-X2a-Y2a-X3a-X3b-X3c-Y3a-Y3b-Y3c  (Formula XXXII);

Y1a-Y1b-Y1c-X1a-X1b-X1c  (Formula XXXIII);

Y1a-Y1b-Y1c-Y1d-X1a-X1b-X1c-X1d  (Formula XXXIV);

X1a-Y1a-Y1b-Y1c-Y1d-X2a-X2b-X2c-X2d-Y2a  (Formula XXXV);

Y1a-Y1b-Y1c-Y1d-Y1e-X1a-X1b-X1c-X1d-X1e  (Formula XXXVI);

X1a-X1b-Y1a-Y1b-Y1c-X2a-X2b-X2c-Y2a-Y2b  (Formula XXXVII);

Y1a-Y1b-Y1c-X1a-X1a-X1c-Y2a-X2a-Y3a-X3a  (Formula XXXVIII);

Y1a-X1a-X1b-X1c-X1d-X1e-Y2a  (Formula XXXIX);

Y1a-X1a-X1b-X1c-X1d-X1e-Y2a-Y2b-Y2c-Y2d  (Formula XL);

Y1a-Y1b-X1a-X1b-X1c-X1d-X1e-Y2a-Y2b-Y2c  (Formula XLI);

Y1a-Y1b-Y1c-X1a-X1b-X1c-X1d-X1e-Y2a-Y2b  (Formula XLII);

Y1a-Y1b-Y1c-Y1e-X1a-X1b-X1c-X1d-X1e-Y2a  (Formula XLIII);

X1a-Y1a-Y1b-Y1c-Y1d-Y1e-X2a  (Formula XLIV);

X1a-Y1a-Y1b-Y1c-Y1d-Y1e-X2a-X2b-X2c-X2d  (Formula XLV);

X1a-X1b-Y1a-Y1b-Y1c-Y1d-Y1e-X2a-X2b-X2c  (Formula XLVI);

X1a-X1b-X1c-Y1a-Y1b-Y1c-Y1d-Y1e-X2a-X2b  (Formula XLVII);

X1a-X1b-X1c-X1d-Y1a-Y1b-Y1c-Y1d-Y1e-X2a  (Formula XLVIII);

Y1a-X1a-Y2a-X2a-Y3a-X3a  (Formula XLIX);

Y1a-Y1b-X1a-Y2a-Y2b-X2a-Y3a-Y3b-X3a-Y4a  (Formula L);

X1a-X1b-Y1a-Y1b-X2a-Y2a-Y2b-Y2c-Y2d  (Formula LI);

Y1a-Y1b-Y1c-Y1d-X1a-Y2a-Y2b-X2a-X2b  (Formula LII);

Y1a-Y1b-X1a-Y2a-Y2b-Y2c-X2b-Y3a-X3a-Y4a  (Formula LIII);

and

Y1a-X1a-Y2a-X2a-Y3a-Y3b-Y3c-X3a-Y4a-Y4b  (Formula LIV).

Typically, the striapathic region (or a portion thereof) of an anti-inflammatory polypeptide will have an amphipathic conformation (e.g., under physiological conditions). To be considered amphipathic, the striapathic region (or portion thereof) need not be in the amphipathic conformation at all times. Rather, it is sufficient that the amphipathic conformation be present at least 50%, 60%, 70%, 80%, or more of the time, or when the anti-inflammatory polypeptide is binding to a target molecule, such as an NF-kB Class II protein (e.g., Rel B). Often, the amphipathic conformation will be associated with a particular secondary structure, such as a helical structure. Thus, the striapathic region (or a portion thereof) of the anti-inflammatory polypeptide can have an amphipathic 310-helical conformation, an amphipathic α-helical conformation, an amphipathic π-helical conformation, or an amphipathic poly-proline helical conformation. Alternatively, the striapathic region (or a portion thereof) of the anti-inflammatory polypeptide can have an amphipathic β-strand conformation.
For anti-inflammatory peptides that comprise a striapathic region that includes or has an amphipathic helical conformation (e.g., 310-helical, α-helical, π-helical, or polyproline helical conformation), the hydrophobic surface (“side”) can have a facial arc of at least 100°. In certain embodiments, the facial arc of the hydrophobic surface or side is at least 125°, 150°, 175°, 200°, 225°, 250°, 275°, or 300°.
Anti-inflammatory polypeptides in certain embodiments have a striapathic region that has a relatively large hydrophobic volume. Accordingly, the striapathic region can optimally contain hydrophobic amino acid residues having a total side-chain volume of at least 600 cubic angstroms. In certain embodiments, the hydrophobic amino acid residues of the striapathic region have a hydrophobic side-chain volume of at least 650, 700, 750, 800, 850, 900, 950, 1000, or more cubic angstroms. Alternatively, or in addition, the striapathic region can be characterized by a ratio of the sum of the side-chain volume of hydrophobic amino acid residues to the sum of the side-chain volume of hydrophilic amino acid residues, wherein the ratio is at least 0.75 or higher. For example, the ratio can be at least 0.8, 0.85, 0.9, 0.95, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, or greater.
Because of the desirability of a striapathic region having a relatively large hydrophobic side-chain volume, it is generally preferable to include one or more (e.g., 2, 3, 4, 5, or more) large hydrophobic amino acid residues in the sequence of the striapathic region. Conversely, it is generally preferable to have two or fewer (e.g., 1 or 0) small hydrophobic amino acid residues in the sequence of the striapathic region. Examples of large hydrophobic amino acid residues include tryptophan, phenylalanine, and tyrosine. In addition, under certain circumstances, histidine or arginine can be considered a large hydrophobic amino acid residue. Examples of small hydrophobic residues include glycine, alanine, serine, cysteine, valine, threonine, and proline. Accordingly, an anti-inflammatory polypeptide can have a striapathic region that includes one or more (e.g., 2, 3, 4, 5, or more) hydrophobic residues selected from the group consisting of tryptophan, phenylalanine, and tyrosine. Alternatively, the anti-inflammatory polypeptide can have a striapathic region that includes one or more (e.g., 2, 3, 4, 5, or more) hydrophobic residues selected from (i) the group consisting of tryptophan, phenylalanine, tyrosine, and histidine, or (ii) the group consisting of tryptophan, phenylalanine, tyrosine, and arginine. In certain embodiments, the anti-inflammatory polypeptide has a striapathic region that includes two or fewer (e.g., 1 or 0) hydrophobic residues selected from the group consisting of glycine, alanine, serine, cysteine, valine, threonine, and proline. Alternatively, the anti-inflammatory polypeptide can have a striapathic region that includes no more than one hydrophobic residue selected from the group consisting of glycine, alanine, serine, cysteine, valine, threonine, and proline. In other alternatives, the anti-inflammatory polypeptide can have a striapathic region that includes no glycine residues, no alanine residues, no serine residues, no cysteine residues, no valine residues, no threonine residues, and/or no proline residues.
It is also preferable that an anti-inflammatory polypeptide have a striapathic region characterized by a moderate level of cationicity (i.e., a striapathic region that does not contain an excessive number of amino acid residues having positively charged side chains). Examples of amino acid residues having positively charged side groups (assuming physiological conditions) includes lysine, typically arginine, and sometimes histidine. Examples of amino acid residues having negatively charged side chains (assuming physiological conditions) include aspartic acid and glutamic acid. Examples of hydrophilic amino acid residues having uncharged side chains (assuming physiological conditions) include aspargine and glutamine. Accordingly, an anti-inflammatory polypeptide can have a striapathic region that includes five or fewer (e.g., 4, 3, 2) lysine residues. Alternatively, an anti-inflammatory polypeptide can have a striapathic region that includes five or fewer (e.g., 4, 3, 2) amino acid residues selected from the group consisting of lysine and arginine. In other alternatives, an anti-inflammatory polypeptide can have a striapathic region that includes five or fewer (e.g., 4, 3, 2) amino acid residues selected from the group consisting of lysine, arginine, and histidine. For anti-inflammatory polypeptides that have a striapathic region that includes one or more (e.g., two or more) positively charged amino acid residues, it can be advantageous for the striapathic region to also include some negatively charged or polar, uncharged amino acid residues. For example, the anti-inflammatory polypeptide can have a striapathic region that includes both positively and negatively charged amino acid residues, such that the net charge on the polypeptide is no more than +2 or +1 (e.g., the number of positively charged amino acid residues does not exceed the number of negatively charged amino acid residues by more than one or two). Alternatively, the anti-inflammatory polypeptide can have a striapathic region that includes both positively charged and polar, uncharged amino acid residues, such that the net charge on the polypeptide is no more than +2 or +1 (e.g., the number of positively charged amino acid residues does not exceed one or two). In other alternatives, the anti-inflammatory polypeptide can have a striapathic region that includes both positively charged, negatively charged, and hydrophilic uncharged charged amino acid residues, such that the net charge on the polypeptide is no more than +2.
To avoid certain undesired interactions between RP peptides and other molecules (whether another RP peptide, a metal ion, etc.) it can be advantageous to limit the number of certain types of amino acid residues in the polypeptide. For example, because cysteine residues form di-sulfide bonds under certain conditions (e.g., oxidative environments), it can be useful to limit the number of cysteine residues in a polypeptide of the invention to no more than one or two, or even none. Because histidine residues chelate metals under certain conditions (e.g., alkaline environments), it can be useful to limit the number of histidine residues in a polypeptide of the invention to no more than one or two, or even none. In addition, because proline residues tend to introduce kinks into secondary structure elements (e.g., α-helices and β-strands), it can be useful exclude proline residues in the striapathic region of a polypeptide of the invention, or limit their number to no more than one.
Class I Polypeptides
An anti-inflammatory polypeptide of the invention can be a Class I polypeptide. Class I polypeptides comprise, consist essentially of, or consist of a striapathic region that includes a sequence selected from the group of sequences defined by Formula I:

Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c  (Formula I).

Each of amino acid residues Y1a, Y1b, Y1c, Y2a, Y2b, and Y2c in Formula I can be selected from the group consisting of Phe (F), Trp (W), Tyr (Y), His (H), Leu (L), Cys (C), Met (M), Val (V), Ile (I), Pro (P), Thr (T), Ser (S), Ala (A), and Gly (G). In certain embodiments, at least 3, 4, 5, or 6 of amino acid residues Y1a, Y1b, Y1c, Y2a, Y2b, and Y2c in Formula I are selected from the group consisting of Phe (F), Trp (W), Tyr (Y), His (H), and Leu (L). In certain embodiments, at least 3, 4, 5, or 6 of amino acid residues Y1a, Y1b, Y1c, Y2a, Y2b, and Y2c in Formula I are selected from the group consisting of Phe (F), Trp (W), and Tyr (Y). In certain embodiments, less than two (and in certain embodiments 1 or none) of amino acid residues Y1a, Y1b, Y1c, Y2a, Y2b, and Y2c in Formula I are selected from the group consisting of Pro (P), Thr (T), Ser (S), Ala (A), and Gly (G).
The module Y1a-Y1b-Y1c in Formula I can have a sequence selected from the group consisting of Phe-Phe-Phe (FFF), Trp-Trp-Trp (WWW), Tyr-Tyr-Tyr (YYY), Leu-Leu-Leu (LLL), Cys-Cys-Cys (CCC), Met-Met-Met (MMM), Val-Val-Val (VVV), Ile-Ile-Ile (III). Alternatively, the module Y1a-Y1b-Y1c in Formula I can have a sequence selected from the group consisting of Pro-Pro-Pro (PPP), Thr-Thr-Thr (TTT), and Ala-Ala-Ala (AAA). In certain embodiments, module Y1a-Y1b-Y1c in Formula I has a sequence selected from the group consisting of Phe-Phe-Phe (FFF), Trp-Trp-Trp (WWW), Tyr-Tyr-Tyr (YYY), and combinations thereof (e.g., Phe-Phe-Trp (FFW), Phe-Trp-Trp (FWW), Trp-Phe-Trp (WFW), Trp-Trp-Phe (WWF), Phe-Phe-Tyr (FFY), Phe-Tyr-Tyr (FYY), Tyr-Phe-Tyr (YFY), Tyr-Tyr-Phe (YYF), Trp-Trp-Tyr (WWY), Trp-Tyr-Tyr (WYY), Tyr-Trp-Tyr (YWY), Tyr-Tyr-Trp (YYW), Phe-Trp-Tyr (FWY), Phe-Tyr-Trp (FYW), Trp-Phe-Tyr (WFY), Trp-Tyr-Phe (WYF), Tyr-Trp-Phe (YWF), or Tyr-Phe-Trp (YFW)).
The module Y2a-Y2b-Y2c in Formula I can have a sequence selected from the group consisting of Phe-Phe-Phe (FFF), Trp-Trp-Trp (WWW), Tyr-Tyr-Tyr (YYY), Leu-Leu-Leu (LLL), Cys-Cys-Cys (CCC), Met-Met-Met (MMM), Val-Val-Val (VVV), and Ile-Ile-Ile (III). Alternatively, the module Y2a-Y2b-Y2c in Formula I can have a sequence selected from the group consisting of Pro-Pro-Pro (PPP), Thr-Thr-Thr (TTT), and Ala-Ala-Ala (AAA). In certain embodiments, module Y2a-Y2b-Y2c in Formula I has a sequence selected from the group consisting of Phe-Phe-Phe (FFF), Trp-Trp-Trp (WWW), Tyr-Tyr-Tyr (YYY), and combinations thereof (e.g., Phe-Phe-Trp (FFW), Phe-Trp-Trp (FWW), Trp-Phe-Trp (WFW), Trp-Trp-Phe (WWF), Phe-Phe-Tyr (FFY), Phe-Tyr-Tyr (FYY), Tyr-Phe-Tyr (YFY), Tyr-Tyr-Phe (YYF), Trp-Trp-Tyr (WWY), Trp-Tyr-Tyr (WYY), Tyr-Trp-Tyr (YWY), Tyr-Tyr-Trp (YYW), Phe-Trp-Tyr (FWY), Phe-Tyr-Trp (FYW), Trp-Phe-Tyr (WFY), Trp-Tyr-Phe (WYF), Tyr-Trp-Phe (YWF), or Tyr-Phe-Trp (YFW)).
Thus, a Class I anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region having a sequence selected from the group consisting of FFF-X1a-FFF (SEQ ID NO: 1), WWW-X1a-WWW (SEQ ID NO: 2), YYY-X1a-YYY (SEQ ID NO: 3), and combinations thereof. Alternatively, a Class I anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region having a sequence selected from the group consisting of LLL-X1a-LLL (SEQ ID NO: 4), CCC-X1a-CCC (SEQ ID NO: 5), MMM-X1a-MMM (SEQ ID NO: 6), VVV-X1a-VVV (SEQ ID NO: 7), and III-X1a-III (SEQ ID NO: 8). In such peptides, X1a can be selected from the group consisting of Arg (R), His (H), and Lys (K); or X1a can be selected from the group consisting of Glu (E), Gln (Q), Asn (N), and Asp (D).
A Class I anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region having a sequence selected from the group of sequences defined by Formula II or the group of sequences defined by Formula III:

Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c-X2a-Y3a-X3a  (Formula II);

X2a-Y3a-X3a-Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c  (Formula III).

The Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c sequences defined by Formulas II and III can be any of the sequences described above in connection with Formula I. X2a and X3a in Formulas II and III can be each individually selected from the group consisting of Arg (R), His (H), Lys (K), Glu (E), Gln (Q), Asn (N), and Asp (D). Alternatively, X2a and X3a in Formulas II and III can be each individually selected from the group consisting of Arg (R), His (H), and Lys (K). In other alternatives, X2a and X3a in Formulas II and III can be each individually selected from the group consisting of Arg (R), His (H), Lys (K), and Gln (Q). In other alternatives, X2a and X3a in Formulas II and III can be each individually selected from the group consisting Glu (E), Gln (Q), Asn (N), and Asp (D). In other alternatives, X2a in Formulas II and III can be selected from the group consisting of Arg (R), His (H), and Lys (K), and X3a in Formulas II and III can be selected from the group consisting of Glu (E), Gln (Q), Asn (N), and Asp (D). Y3a in Formulas II and III can be selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), and Ile (I). In certain embodiments, Y3a in Formulas II and III is selected from the group consisting of Phe (F), Trp (W), Tyr (Y), and Leu (L).
The modules X2a-Y3a-X3a in Formulas II and III can be selected from the group consisting of EFQ, EFE, EFN, EFD, NFQ, NFE, NFN, NFD, QFQ, QFE, QFN, QFD, DFQ, DFE, DFN, DFD, EWQ, EWE, EWN, EWD, NWQ, NWE, NWN, NWD, QWQ, QWE, QWN, QWD, DWQ, DWE, DWN, DWD, EYQ, EYE, EFN, EYD, NYQ, NYE, NYN, NYD, QYQ, QYE, QYN, QYD, DYQ, DYE, DYN, DYD, ELQ, ELE, ELN, ELD, NLQ, NLE, NLN, NLD, QLQ, QLE, QLN, QLD, DLQ, DLE, DLN, DLD, RFR, RFQ, RFE, RFN, RFD, RWR, RWQ, RWE, RWN, and RWD.
A Class I anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region comprising, consisting essentially of, or consisting of a sequence selected from the group of sequences listed in Table 3, e.g., RP394, RP108-RP123, RP125-131, RP133, RP135-RP141, RP143-RP146, RP148-RP150, RP152-RP165, RP179, RP395, RP211, RP230, RP232, RP258, RP267, RP268, RP271, RP273, RP280-281, and RP287. In certain embodiments, the Class I anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region that comprises, consists essentially of, or consists of a sequence selected from the group of sequences consisting of RP113 (SEQ ID NO: 39), RP118 (SEQ ID NO: 44), and RP394 (SEQ ID NO: 33).
Class II Polypeptides
An anti-inflammatory polypeptide of the invention can be a Class II polypeptide. Class II anti-inflammatory polypeptides can comprise, consist essentially of, or consist of a striapathic region that includes a sequence selected from the group of sequences defined by Formula VII:

Y1a-X1a-X1b-Y2a-Y2b-X2a-X2b-Y3a  (Formula VII).

Amino acid residue Y2a in Formula VII can be selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), Ile (I), Pro (P), Thr (T), Ser (S), Ala (A), and Gly (G). In certain embodiments, amino acid residue Y2a in Formula VII is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y). Alternatively, amino acid residue Y2a in Formula VII can be selected from the group consisting of Leu (L), Cys (C), Met (M), Val (V), Ile (I).
Amino acid residue Y2b in Formula VII can be selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), Ile (I), Pro (P), Thr (T), Ser (S), Ala (A), and Gly (G). In certain embodiments, amino acid residue Y2b in Formula VII is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y). Alternatively, amino acid residue Y2b in Formula VII can be selected from the group consisting of Leu (L), Cys (C), Met (M), Val (V), Ile (I).
Amino acid residue X1b in Formula VII can be selected from the group consisting of Arg (R), Lys (K), and His (H). Alternatively amino acid residue X1b in Formula VII can be selected from the group consisting of Asn (N), Gln (Q), Asp (D), and Glu (E).
Amino acid residue X2a in Formula VII can be selected from the group consisting of Arg (R), Lys (K), and His (H). Alternatively, amino acid residue X2a can be selected from the group consisting of Asn (N), Gln (Q), Asp (D), and Glu (E).
The sequence X1b-Y2a-Y2b-X2a in Formula VII can be selected from the group consisting of Lys-Phe-Phe-Lys (KFFK; SEQ ID NO: 386), Lys-Trp-Trp-Lys (KWWK; SEQ ID NO: 387), Lys-Tyr-Try-Lys (KYYK; SEQ ID NO: 388), Lys-Phe-Trp-Lys (KFWK; SEQ ID NO: 389), Lys-Trp-Phe-Lys (KWFK; SEQ ID NO: 390), Lys-Phe-Tyr-Lys (KFYK; SEQ ID NO: 391), Lys-Tyr-Phe-Lys (KYFK; SEQ ID NO: 392), Lys-Trp-Tyr-Lys (KWYK; SEQ ID NO: 393), and Lys-Tyr-Trp-Lys (KYWK; SEQ ID NO: 394). Alternatively, the sequence X1b-Y2a-Y2b-X2a in Formula VII can be selected from the group consisting of Arg-Phe-Phe-Arg (RFFR; SEQ ID NO: 395), Arg-Trp-Trp-Arg (RWWR; SEQ ID NO: 396), Arg-Tyr-Try-Arg (RYYR; SEQ ID NO: 397), Arg-Phe-Trp-Arg (RFWR; SEQ ID NO: 398), Arg-Trp-Phe-Arg (RWFR; SEQ ID NO: 399), Arg-Phe-Tyr-Arg (RFYR; SEQ ID NO: 400), Arg-Tyr-Phe-Arg (RYFR; SEQ ID NO: 401), Arg-Trp-Tyr-Arg (RWYR; SEQ ID NO: 402), and Arg-Tyr-Trp-Arg (RYWR; SEQ ID NO: 403). In other alternatives, the sequence X1b-Y2a-Y2b-X2a in Formula VII can be selected from the group consisting of His-Phe-Phe-His (HFFH; SEQ ID NO: 404), His-Trp-Trp-His (HWWH; SEQ ID NO: 405), His-Tyr-Try-His (HYYH; SEQ ID NO: 406), His-Phe-Trp-His (HFWH; SEQ ID NO: 407), His-Trp-Phe-His (HWFH; SEQ ID NO: 408), His-Phe-Tyr-His (HFYH; SEQ ID NO: 409), His-Tyr-Phe-His (HYFH; SEQ ID NO: 410), His-Trp-Tyr-His (HWYH; SEQ ID NO: 411), and His-Tyr-Trp-His (HYWH;SEQ ID NO:132).
Amino acid residue X1a in Formula VII can be selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E). In certain embodiments, amino acid residue X1a is selected from the group consisting of Arg (R) and Gln (Q). In certain embodiments, amino acid residue X1a in Formula VII is Arg (R). Alternatively, amino acid residue X1a in Formula VII can be selected from the group consisting of Lys (K), Gln (Q), Glu (E), and Asn (N).
Amino acid resiude X2b in Formula VII can be selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E). In certain embodiments, amino acid residue X2b is selected from the group consisting of Arg (R) and Gln (Q). In certain embodiments, amino acid residue X2b in Formula VII is Arg (R). Alternatively, amino acid residue X2b in Formula VII can be selected from the group consisting of Lys (K), Gln (Q), Glu (E), and Asn (N).
Amino acid residue Y1a in Formula VII can be selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), Ile (I), Thr (T), Pro (P), Ser (S), Ala (A), and Gly (G). In certain embodiments, amino acid residue Y1a in Formula VII is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y). Alternatively, amino acid residue Y1a in Formula VII can be selected from the group consisting of Leu (L), Cys (C), Met (M), Val (V), Ile (I).
Amino acid residue Y3a in Formula VII can be selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), Ile (I), Thr (T), Pro (P), Ser (S), Ala (A), and Gly (G). In certain embodiments, amino acid residue Y3a in Formula VII is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y). Alternatively, amino acid residue Y3a in Formula VII can be selected from the group consisting of Leu (L), Cys (C), Met (M), Val (V), Ile (I).
Thus, a Class II anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region having a sequence selected from the group consisting of F-X1a-X1b-FF-X2a-X2b-F (SEQ ID NO: 9), F-X1a-X1b-FF-X2a-X2b-W (SEQ ID NO: 10), W-X1a-X1b-FF-X2a-X2b-F (SEQ ID NO: 11), F-X1a-X1b-FW-X2a-X2b-F (SEQ ID NO: 12), F-X1a-X1b-WF-X2a-X2b-F (SEQ ID NO: 13), F-X1a-X1b-WW-X2a-X2b-F (SEQ ID NO: 14), W-X1a-X1b-WW-X2a-X2b-F (SEQ ID NO: 15), F-X1a-X1b-WW-X2a-X2b-W (SEQ ID NO: 16), W-X1a-X1b-WW-X2a-X2b-W (SEQ ID NO: 17), F-X1a-X1b-FF-X2a-X2b-Y (SEQ ID NO: 18), Y-X1a-X1b-FF-X2a-X2b-F (SEQ ID NO: 19), F-X1a-X1b-FY-X2a-X2b-F (SEQ ID NO: 20), F-X1a-X1b-YF-X2a-X2b-F (SEQ ID NO: 21), F-X1a-X1b-YY-X2a-X2b-F (SEQ ID NO: 22), Y-X1a-X1b-YY-X2a-X2b-F (SEQ ID NO: 23), F-X1a-X1b-YY-X2a-X2b-Y (SEQ ID NO: 24), and Y-X1a-X1b-YY-X2a-X2b-Y (SEQ ID NO: 25), Y-X1a-X1b-YY-X2a-X2b-W (SEQ ID NO: 26), W-X1a-X1b-YY-X2a-X2b-Y (SEQ ID NO: 27), Y-X1a-X1b-YW-X2a-X2b-Y (SEQ ID NO: 28), Y-X1a-X1b-WY-X2a-X2b-Y (SEQ ID NO: 29), Y-X1a-X1b-WW-X2a-X2b-Y (SEQ ID NO: 30), W-X1a-X1b-WW-X2a-X2b-Y (SEQ ID NO: 31), and Y-X1a-X1b-WW-X2a-X2b-W (SEQ ID NO: 32). Amino acid residues X1a, X1b, X2a, and X2b in the foregoing sequences can be selected as discussed above.
A Class II anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region that further includes a first additional amino acid residue directly bound to amino acid residue Y1a of Formula VII. The first additional amino acid residue can be a hydrophobic amino acid residue (e.g., a residue selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), Ile (I), Thr (T), Pro (P), Ser (S), Ala (A), and Gly (G); a residue selected from the group consisting of Phe (F), Trp (W), and Tyr (Y); a residue selected from the group consisting of Phe (F), Trp (W), Tyr (Y), and Leu (L); or, a residue selected from the group consisting of Leu (L), Cys (C), Met (M), Val (V), and Be (I)). Alternatively, the first additional amino acid residue can be a hydrophilic amino acid residue (e.g., a residue selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E); a residue selected from the group consisting of Arg (R), Lys (K), and His (H); a residue selected from the group consisting Arg (R), Lys (K), His (H), and Gln (Q); or a residue selected from the group consisting of Asn (N), Gln (Q), Asp (D), and Glu (E)).
A Class II anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region that further includes a first additional amino acid residue directly bound to amino acid residue Y3a of Formula VII. The first additional amino acid residue can be a hydrophobic amino acid residue (e.g., a residue selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), Ile (I), Thr (T), Pro (P), Ser (S), Ala (A), and Gly (G); a residue selected from the group consisting of Phe (F), Trp (W), and Tyr (Y); a residue selected from the group consisting of Phe (F), Trp (W), Tyr (Y), and Leu (L); or, a residue selected from the group consisting of Leu (L), Cys (C), Met (M), Val (V), and Be (I)). Alternatively, the first additional amino acid residue can be a hydrophilic amino acid residue (e.g., a residue selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E); a residue selected from the group consisting of Arg (R), Lys (K), and His (H); a residue selected from the group consisting Arg (R), Lys (K), His (H), and Gln (Q); or a residue selected from the group consisting of Asn (N), Gln (Q), Asp (D), and Glu (E)).
A Class II anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region that further includes a first additional amino acid residue directly bound to amino acid residue Y1a of Formula VII and a second additional amino acid reside directly bound to amino acid residue Y3a of Formula VII. The first additional amino acid residue can be a hydrophobic amino acid residue and the second additional amino acid residue can be a hydrophilic amino acid residue. Alternatively, the first additional amino acid residue can be a hydrophilic amino acid residue and the second amino acid residue can be a hydrophobic amino acid residue. Regardless, the additional hydrophobic amino acid residue can be selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), Be (I), Thr (T), Pro (P), Ser (S), Ala (A), and Gly (G); and in certain embodiments from the group consisting of Phe (F), Trp (W), and Tyr (Y); and in additional embodiments from the group consisting of Phe (F). The additional hydrophilic amino acid residue can be selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E); and in certain embodiments, a residue selected from the group consisting of Arg (R), Lys (K), and His (H); or a residue selected from the group consisting of Asn (N), Gln (Q), Asp (D), and Glu (E).
A Class II anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region comprising, consisting essentially of, or consisting of a sequence selected from the group of sequences listed in Table 5, e.g., RP124, RP132, RP134, RP142, RP147, RP151, RP166-RP172, RP175, RP177, RP182, RP183, RP185, RP186, RP 424, RP190, RP194, RP198, RP199-RP202, RP204, RP206, RP207, RP209, RP210, RP212-RP216, RP218, RP219, RP425, RP225, RP227, RP233-RP239, RP398, RP241-RP247, RP250-RP256, RP426, RP427, RP285, and RP387. In certain embodiments, the Class II anti-inflammatory polypeptide comprises, consists essentially of, or consists of a striapathic region comprising, consisting essentially of, or consisting of a sequence selected from the group consisting of RP124 (SEQ ID NO: 106), RP166 (SEQ ID NO: 112), RP182 (SEQ ID NO: 121), and RP183 (SEQ ID NO: 122).
Class XII Polypeptides
An anti-inflammatory polypeptide of the invention can be a Class XII polypeptide. Class XII anti-inflammatory polypeptides can comprise, consist essentially of, or consist of a striapathic region that includes a sequence selected from the group of sequences defined by Formula XLIX:

Y1a-X1a-Y2a-X2a-Y3a-X3a  (Formula XLIX).

Amino acid residues Y1a, Y2a, and Y3a of Formula XLIX can be each independently selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Ile (I), Cys (C), Met (M), Val (V), Pro (P), Thr (T), Ser (S), Ala (A), and Gly (G). In certain embodiments, amino acid residues Y1a, Y2a, and Y3a of Formula XLIX are each independently selected from: the group consisting of Phe (F), Trp (W), and Tyr (Y); the group consisting of Phe (F), Trp (W), Tyr (Y), and Leu (L); or the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Ile (I), Cys (C), Met (M), Val (V), and Ala (A).
Amino acid residues X1a, X2a, and X3a of Formula XLIX can be each independently selected from the group consisting of Arg (R), Lys (K), His (H), Gln (Q), Glu (E), Asn (N), and Asp (D). In certain embodiments, amino acid residues X1a, X2a, and X3a are each independently selected from the group consisting of Arg (R), Lys (K), and His (H). Alternatively, amino acid residues X1a, X2a, and X3a are each independently selected from the group consisting of Arg (R), Lys (K), His (H), and Gln (Q).
A Class XII anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region that further includes a first additional amino acid residue. The first additional amino acid residue can be a hydrophilic amino acid residue directly bound to amino acid residue Y1a of Formula XLIX. Thus, the first additional amino acid residue can be, for example, a residue selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E); a residue selected from the group consisting of Arg (R), Lys (K), and His (H); a residue selected from the group consisting Arg (R), Lys (K), His (H), and Gln (Q); or a residue selected from the group consisting of Asn (N), Gln (Q), Asp (D), and Glu (E)). Alternatively, the first amino acid residue can be a hydrophobic amino acid residue directly bound to amino acid residue X3a of Formula XLIX. Thus, the first additional amino acid residue can be, for example, a residue selected from the group consisting of Phe (F), Trp (W), and Tyr (Y); a residue selected from the group consisting of Phe (F), Trp (W), Tyr (Y), and Leu (L); or a residue selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Ile (I), Cys (C), Met (M), Val (V), and Ala (A)).
A Class XII anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region that further includes first and second additional amino acid residues. The first additional amino acid residue can be a hydrophilic amino acid residue, as discussed above, which is directly bound to amino acid residue Y1a of Formula XLIX. The second additional amino acid residue can be directly bound to the first additional amino acid residue. Thus, the second additional amino acid residue can be a hydrophobic amino acid residue, e.g., a residue selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), Ile (I), Thr (T), Pro (P), Ser (S), Ala (A), and Gly (G); a residue selected from the group consisting of Phe (F), Trp (W), and Tyr (Y); a residue selected from the group consisting of Phe (F), Trp (W), Tyr (Y), and Leu (L); or, a residue selected from the group consisting of Leu (L), Cys (C), Met (M), Val (V), and Ile (I)). Alternatively, the second additional amino acid residue can be a hydrophobic amino acid residue directly bound to amino acid residue X3a of Formula XLIX, as discussed above.
A Class XII anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region that further includes first, second, and third additional amino acid residues. The first additional amino acid residue can be a hydrophilic amino acid residue which is directly bound to amino acid residue Y1a of Formula XLIX and the second additional amino acid residue can be a hydrophobic amino acid residue which is directly bound to the first additional amino acid residue, as discussed above. The third additional amino acid residue can be a hydrophilic amino acid residue that is directly bound to the second additional amino acid residue. Thus, the third additional amino acid residue can be, for example, a residue selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E); a residue selected from the group consisting of Arg (R), Lys (K), and His (H); a residue selected from the group consisting Arg (R), Lys (K), His (H), and Gln (Q); or a residue selected from the group consisting of Asn (N), Gln (Q), Asp (D), and Glu (E)). Alternatively, the third amino acid residue can be a hydrophobic amino acid residue directly bound to amino acid residue X3a of Formula XLIX. Thus, the third additional amino acid residue can be, for example, a residue selected from the group consisting of Phe (F), Trp (W), and Tyr (Y); a residue selected from the group consisting of Phe (F), Trp (W), Tyr (Y), and Leu (L); or a residue selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Ile (I), Cys (C), Met (M), Val (V), and Ala (A)).
A Class XII anti-inflammatory polypeptide can comprise, consist essentially of, or consist of a striapathic region that further includes four, five, six, or more additional amino acid residues. The additional amino acid residue can be added in a manner that continues the alternating patter of a hydrophobic amino acid residue followed by a hydrophilic amino acid residue followed by a hydrophobic amino acid residue, as shown in Formula XLIX. In this manner, Class XII anti-inflammatory polypeptides can be expanded to comprise, consist essentially of, or consist of a striapathic region having 10, 11, 12, or more amino acid residues.
An anti-inflammatory polypeptide of Class XII can comprise, consist essentially of, or consist of a striapathic region comprising, consisting essentially of, or consisting of a sequence selected from the group consisting of RP393, RP391, PR392, RP390, and RP389.
Class XIV Polypeptides
An anti-inflammatory polypeptide of the invention can be a Class XIV polypeptide. Class XIV anti-inflammatory polypeptides can comprise, consist essentially of, or consist of a striapathic region that includes a sequence selected from the group of sequences defined by any one of Formulas LI through LIV:

X1a-X1b-Y1a-Y1b-X2a-Y2a-Y2b-Y2c-Y2d  (Formula LI);

Y1a-Y1b-Y1c-Y1d-X1a-Y2a-Y2b-X2a-X2b  (Formula LII);

Y1a-Y1b-X1a-Y2a-Y2b-Y2c-X2b-Y3a-X3a-Y4a  (Formula LIII);

and

Y1a-X1a-Y2a-X2a-Y3a-Y3b-Y3c-X3a-Y4a-Y4b  (Formula LIV).

The striapathic region of a Class XIV polypeptide can include at least 3 (e.g., 3 to 6) proline amino acid residues. For example, amino acid residues Y1a, Y2a, and Y2b in Formula LI can be proline amino acid residues. Alternatively, amino acid residues Y1c, Y1d, and Y2b in Formula LII can be proline amino acid residues. In other alternatives, amino acid residues Y1a, Y2a, Y2b, Y2c, Y3a, and Y4a in Formula LIII can be proline amino acid residues. In still other alternatives, amino acid residues Y1a, Y2b, Y3a, Y3b, Y3c, and Y4b in Formula LIV can be proline amino acid residues.
Hydrophobic amino acid residues (e.g., Y1a, Y1b, Y1c, Y1d, Y2a, Y2b, Y2c, Y2d, Y3a, Y3b, Y3c, Y4a, and Y4b) not designated as proline residues in Formulas LI through LIV can be each individually selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), Ile (I), Thr (T), Pro (P), Ser (S), Ala (A), and Gly (G). In certain embodiments, such hydrophobic amino acid residues are each individually selected from: the group consisting of Phe (F), Trp (W), and Tyr (Y); the group consisting of Phe (F), Trp (W), Tyr (Y), and Leu (L); or, the group consisting of Leu (L), Cys (C), Met (M), Val (V), and Ile (I)).
Hydrophilic amino acid residues in Formulas LI through LIV (e.g., X1a, X1b, X2a, X2b, and X3a) can be each individually selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E). In certain embodiments, such hydrophilic amino acid residues are each individually selected from the group consisting of Arg (R), Lys (K), and His (H). Alternatively, such hydrophilic amino acid residues are each individually selected from: the group consisting of Arg (R), Lys (K), His (H), and Gln (Q); or the group consisting of Asn (N), Gln (Q), Asp (D), and Glu (E).
An anti-inflammatory polypeptide of Class XIV can comprise, consist essentially of, or consist of a striapathic region that comprises, consists essentially of, or consists of a sequence selected from the group consisting of RP449, RP450, RP448, RP447, RP452, RP451, RP444, RP441, RP446, RP445, RP442, and RP443.
Other Classes of Polypeptides
An anti-inflammatory polypeptide of the invention can be from any of Classes II through XI and XIII. Such anti-inflammatory polypeptides can comprise, consist essentially of, or consist of a striapathic region that includes a sequence selected from the group of sequences defined by any one of Formulas IV through XLVIII and L.
Hydrophobic amino acid residues in Formulas IV through XLVIII and L (e.g., Y1a, Y1b, Y1c, Y1d, Y1e, Y2a, Y2b, Y2c, Y2d, Y2e, Y3a, Y3b, Y3c, Y4a, and Y4b) can be each individually selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), Ile (I), Thr (T), Pro (P), Ser (S), Ala (A), and Gly (G). In certain embodiments, such hydrophobic amino acid residues are each individually selected from: the group consisting of Phe (F), Trp (W), and Tyr (Y); the group consisting of Phe (F), Trp (W), Tyr (Y), and Leu (L); or, the group consisting of Leu (L), Cys (C), Met (M), Val (V), and Ile (I)).
Hydrophilic amino acid residues in Formulas IV through XLVIII and L (e.g., X1a, X1b, X1c, X1d, X2a, X2b, X2c, X2d, X3a, X3b, X3c, X4a, and X4b) can be each individually selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E). In certain embodiments, such hydrophilic amino acid residues are each individually selected from the group consisting of Arg (R), Lys (K), and His (H). Alternatively, such hydrophilic amino acid residues are each individually selected from: the group consisting of Arg (R), Lys (K), His (H), and Gln (Q); or the group consisting of Asn (N), Gln (Q), Asp (D), and Glu (E).
An anti-inflammatory polypeptide of any one of Formulas IV through XLVIII and L can comprise, consist essentially of, or consist of a striapathic region that further includes a first additional amino acid residue directly bound to the first amino acid residue of the Formula (e.g., Y1a or X1a) or to the last amino acid residue in the formula. The first additional amino acid residue can be a hydrophilic amino acid residue (e.g., a residue selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E); a residue selected from the group consisting of Arg (R), Lys (K), and His (H); a residue selected from the group consisting Arg (R), Lys (K), His (H), and Gln (Q); or a residue selected from the group consisting of Asn (N), Gln (Q), Asp (D), and Glu (E)). Alternatively, the first additional amino acid residue can be a hydrophobic amino acid residue (e.g., a residue selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), Ile (I), Thr (T), Pro (P), Ser (S), Ala (A), and Gly (G); a residue selected from the group consisting of Phe (F), Trp (W), and Tyr (Y); a residue selected from the group consisting of Phe (F), Trp (W), Tyr (Y), and Leu (L); or, a residue selected from the group consisting of Leu (L), Cys (C), Met (M), Val (V), and Ile (I)).
An anti-inflammatory polypeptide of any one of Formulas IV through XLVIII and L can comprise, consist essentially of, or consist of a striapathic region that further includes first and second additional amino acid residues, with the first additional amino acid residue directly bound to the first amino acid residue of the Formula (e.g., Y1a or X1) or the last amino acid residue in the formula, and the second additional amino acid residue directly bound to the first amino acid residue in the formula, the last amino acid residue in the formula, or the first additional amino acid residue. The first additional amino acid residue can be a hydrophilic or hydrophobic amino acid residue, as discussed above. The second additional amino acid residue likewise can be a hydrophilic or hydrophobic amino acid residue, as discussed above.
An anti-inflammatory polypeptide of any one of Formulas IV through XLVIII and L can comprise, consist essentially of, or consist of a striapathic region that comprises, consists essentially of, or consists of a sequence selected from the group consisting of RP396, RP405, RP174, RP176, RP178, RP180-181, RP184, RP408, RP187, RP416, RP188, RP189, RP388, RP417, RP191-RP193, RP404, RP196, RP397, RP197, RP402, RP203, RP409, RP205, RP208, RP217, RP220-RP224, RP226, RP229, RP231, RP240, RP248, RP249, RP415, RP257, RP259-RP266, RP269, RP272, RP274, RP277-RP279, RP282, RP283, RP286, RP289, and RP414.
Variant Polypeptides
The exemplary anti-inflammatory polypeptide sequences shown in Tables 3-9 (below) are merely examples and are not the only anti-inflammatory polypeptides provided herein. Indeed, fragments and variants of the sequences of the disclosed peptides are within the scope of the invention.
A “fragment” of the invention includes at least 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 contiguous amino acid residues of a polypeptide disclosed herein (or up to one less than the number of amino acid residues in the subject polypeptide) and retains at least one anti-inflammatory property of the subject polypeptide. Thus, fragments of the invention include polypeptides that are missing one, two, three, four, or more amino acids from the N-terminus and/or the C-terminus relative to a polypeptide disclosed herein.
A “variant” of the invention is a polypeptide that is substantially similar to a polypeptide disclosed herein and retains at least one anti-inflammatory property of the subject polypeptide. Variants can include deletions (i.e., truncations) of one or more amino acid residues at the N-terminus or the C-terminus of a subject polypeptide disclosed herein; deletion and/or addition of one or more amino acid residues at one or more internal sites in the subject polypeptide disclosed herein; and/or substitution of one or more amino acid residues at one or more positions in the subject polypeptide disclosed herein. For subject polypeptides that are 12 amino acid residues in length or shorter, variant polypeptides can include three or fewer (e.g., two, one, or none) deleted amino acid residues, whether located internally, at the N-terminal end, and/or at the C-terminal end.
Accordingly, the invention further provides anti-inflammatory polypeptides that are at least 50% identical (e.g., at least 60%, 70%, 80%, 90%, or more) to any one of the anti-inflammatory polypeptides disclosed in Tables 3-9 and still retain at least one anti-inflammatory property. For example, the invention provides anti-inflammatory polypeptides that are 3 to 24 amino acids residues in length and comprise, consist essentially of, or consist of a striapathic region sharing at least 50% identity (e.g., at least 60%, 70%, 80%, 90%, or more identity) with a Class I anti-inflammatory polypeptide (e.g., any one of the sequences of Table 3). Such identity can be shared, for example, with RP-394 (SEQ ID NO: 33), RP-108 (SEQ ID NO: 34), RP-113 (SEQ ID NO: 39), RP-118 (SEQ ID NO: 44), RP-129 (SEQ ID NO: 54), or RP-179 (SEQ ID NO: 86). Alternatively, the invention provides anti-inflammatory polypeptides that are 3 to 24 amino acid residues in length and comprise, consist essentially of, or consist of a striapathic region sharing at least 50% identity (e.g., at least 60%, 70%, 80%, 90%, or more identity) with a Class II, Sub-class 1 anti-inflammatory polypeptide (e.g., any one of the sequences of Table 5). Such identity can be shared, for example, with RP-124 (SEQ ID NO: 106), RP-134 (SEQ ID NO: 108), RP-166 (SEQ ID NO: 112), RP-168 (SEQ ID NO: 114), RP-182 (SEQ ID NO: 121), or RP-183 (SEQ ID NO: 122). In other alternatives, the invention provides anti-inflammatory polypeptides that are 3 to 24 amino acid residues in length and comprise, consist essentially of, or consist of a striapathic region sharing at least 50% identity (e.g., at least 60%, 70%, 80%, 90%, or more identity) with any Class II through Class IX or Class XIII anti-inflammatory polypeptide (e.g., any one of the sequences of Table 6). In other alternatives, the invention provides anti-inflammatory polypeptides that are 3 to 24 amino acid residues in length and comprise, consist essentially of, or consist of a striapathic region sharing at least 50% identity (e.g., at least 60%, 70%, 80%, 90%, or more identity) with any Class VIII to Class XI anti-inflammatory polypeptide (e.g., any one of the sequences of Table 7). In other alternatives, the invention provides anti-inflammatory polypeptides that are 3 to 24 amino acid residues in length and comprise, consist essentially of, or consist of a striapathic region sharing at least 50% identity (e.g., at least 60%, 70%, 80%, 90%, or more identity) with a Class XII or Class XIV anti-inflammatory polypeptide (e.g., any one of the sequences of Table 8). In still other alternatives, the invention provides anti-inflammatory polypeptides that are 3 to 24 amino acid residues in length and comprise, consist essentially of, or consist of a striapathic region sharing at least 50% identity (e.g., at least 60%, 70%, 80%, 90%, or more identity) with any one of the combination sequences of Table 9.
The differences between the striapathic region of a homologous anti-inflammatory polypeptide and any one of the anti-inflammatory polypeptides of Tables 3-9 can include deletions, additions, and/or substitutions of amino acid residues, as discussed above. Substituted amino acid residues can be unrelated to the amino acid residue being replaced (e.g., unrelated in terms or hydrophobicity/hydrophilicity, size, charge, polarity, etc.), or the substituted amino acid residues can constitute similar, conservative, or highly conservative amino acid substitutions. As used herein, “similar,” “conservative,” and “highly conservative” amino acid substitutions are defined as shown in Table 2, below. The determination of whether an amino acid residue substitution is similar, conservative, or highly conservative is based exclusively on the side chain of the amino acid residue and not the peptide backbone, which may be modified to increase peptide stability, as discussed below.







TABLE 2







Classification of Amino Acid Substitutions













Highly



Similar
Conservative
Conservative


Amino Acid in
Amino Acid
Amino Acid
Amino Acid


Subject Polypeptide
Substitutions
Substitutions
Substitutions





Glycine (G)
A, S, N
A
n/a


Alanine (A)
S, G, T, V, C, P, Q
S, G, T
S


Serine (S)
T, A, N, G, Q
T, A, N
T, A


Threonine (T)
S, A, V, N, M
S, A, V, N
S


Cysteine (C)
A, S, T, V, I
A
n/a


Proline (P)
A, S, T, K
A
n/a


Methionine (M)
L, I, V, F
L, I, V
L, I


Valine (V)
I, L, M, T, A
I, L, M
I


Leucine (L)
M, I, V, F, T, A
M, I, V, F
M, I


Isoleucine (I)
V, L, M, F, T, C
V, L, M, F
V, L, M


Phenylalanine (F)
W, L, M, I, V
W, L
n/a


Tyrosine (Y)
F, W, H, L, I
F, W
F


Tryptophan (W)
F, L, V
F
n/a


Asparagine (N)
Q
Q
Q


Glutamine (Q)
N
N
N


Aspartic Acid (D)
E
E
E


Glutamic Acid (E)
D
D
D


Histidine (H)
R, K
R, K
R, K


Lysine (K)
R, H
R, H
R, H


Arginine (R)
KH
K, H
K, H









In certain embodiments, a variant polypeptide of the invention binds to two or more targets (e.g., pro-inflammatory targets). In some embodiments, a variant polypeptide binds to three, four, five, or more pro-inflammatory targets. For example, a variant polypeptide can bind to any combination of targets disclosed herein (e.g., an NF-kB Class II protein and human serum albumin (HSA)), as discussed below. Such binding can be based on in silico, in vitro, or in vivo data.
Modeling Polypeptide Binding to Target Molecules
The determination of whether a polypeptide has anti-inflammatory properties can be performed in silico. For example, the binding of a polypeptide (e.g., a polypeptide that has a length of 3 to 24 amino acid residues and includes a striapathic region comprising at least 25% of the length of the polypeptide) to a putative target molecule can be modeled in silico, using any of the numerous molecular modeling and docking platforms available in the art, to thereby assess whether the polypeptide is an anti-inflammatory polypeptide. The on-line ClusProTM algorithm, version 2.0 (developed at Boston University) is particularly useful for modeling the conformation of polypeptides and their binding to target molecules, such as signaling proteins, as described in the Examples set forth below. Modeling algorithms, such as the ClusProTM algorithm, that allow for docking of polypeptides on target molecules can be used, for example, to predict the binding energy associated with the polypeptide-target interaction. Such predictions provide reasonable estimates for the binding energies, but they are not necessarily equal to the binding energies that would be calculated by testing the polypeptides and protein targets in vitro. In that regard, the binding energies identified herein were all generated using the ClusProTM algorithm. Accordingly, absent indication to the contrary, any numerical reference to the binding energy associated with a peptide binding to a particular target is a reference to a binding energy determined by modeling the interaction using the ClusProTM algorithm.
As detailed in the Examples below, the exemplary RP peptides have been shown to interact with various signaling molecules associated with inflammation, including NF-kB Class II subunit RelB, TGFβ, Notch1, Wnt8R, TRAIL, IL6R, IL10R, EGFR, and CDK6, as well as other membrane associated signaling molecules, including CD206, CD47 and SIRP-α, translational modification protein transglutaminase 2 (TGM2), and histone modification enzyme histone methyl transferase (HMT). Upon folding of these protein targets to their normal 3-dimensional conformations, an amphipathic cleft is often generated that has high affinity for the immune-modulating peptides herein described.
For modeling interactions between potential anti-inflammatory polypeptides and NF-kB Class II subunits, any Class II subunit sequence can be used (e.g., RelA, RelB, cRel, NF-kB1, or NF-kB2). In certain embodiments, the Class II subunit sequence folds into a functional Class II subunit or a functional fragment thereof. The particular Class II subunit used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human NF-kB Class II subunit is selected if the intended subject is a human, a bovine NF-kB Class II subunit is selected if the intended subject is a cow, etc.). The NF-kB Class II subunit sequence used for modeling can be the human RelB sequence (NCBI Accession No. NP-006500), which is as follows:








(SEQ ID NO: 367)



MLRSGPASGPSVPTGRAMPSRRVARPPAAPELGALGSPDLSSLSLAVSRSTDELEIIDEYIKENG



 


FGLDGGQPGPGEGLPRLVSRGAASLSTVTLGPVAPPATPPPWGCPLGRLVSPAPGPGPQPHLVIT


 


EQPKQRGMRFRYECEGRSAGSILGESSTEASKTLPAIELRDCGGLREVEVTACLVWKDWPHRVHP


 


HSLVGKDCTDGICRVRLRPHVSPRHSFNNLGIQCVRKKEIEAAIERKIQLGIDPYNAGSLKNHQE


 














EPLPFTYLPRDHDSYGVDKKRKRGMPDVLGELNSSDPHGIESKRRKKKPAILDHFLPNHGSGPFL


 


PPSALLPDPDFFSGTVSLPGLEPPGGPDLLDDGFAYDPTAPTLFTMLDLLPPAPPHASAVVCSGG


 


AGAVVGETPGPEPLTLDSYQAPGPGDGGTASLVGSNMFPNHYREAAFGGGLLSPGPEAT.






The underlined sequence in human RelB (above) has been identified as the dimerization domain. The highlighted amino acid residues (Tyr-300, Leu-302, and His-332) are believed to be particularly important in the dimerization interaction.
An anti-inflammatory polypeptide can be identified based on its ability to bind (e.g., in silico) to the dimerization pocket of the Class II subunit and/or interfere with or block the ability of the Class II subunit to dimerize. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human RelB (SEQ ID NO: 367) selected from the group consisting of Leu-281, Ile-283, Cys-284, Glu-298, Tyr-300, Leu-301, Leu-302, Cys-303, Ile-311, Ser-312, Ala-329, Asp-330, Val-331, His-332, Gln-334, and Leu-371, or the equivalent amino acid residue(s) in a different human NF-kB Class II protein or an NF-kB Class II protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human RelB (SEQ ID NO: 367) selected from the group consisting of Glu-298, Tyr-300, Leu-302, Asp-330, Gln-334, and Leu-371 or the equivalent amino acid residue(s) in a different human NF-kB Class II protein or an NF-kB Class II protein of another species.
In certain embodiments, an anti-inflammatory polypeptide binds to human RelB (SEQ ID NO: 367) with an affinity of at least −650 kcal/mol, and in certain embodiments at least −700, −750, −800, −850, −900, −925, −950, −975, −1000, −1025, −1050, −1075, −1100, −1125, −1150, −1200 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and TGFβ, any TGFβ protein sequence can be used. The TGFβ sequence generally folds into a functional TGFβ protein or a functional fragment thereof. The TGFβ protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human TGFβ is selected if the intended subject is a human, a bovine TGFβ is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human TGFβ sequence (NCBI Acc. No. NP_000651.3), which is as follows:







(SEQ ID NO: 368)


MPPSGLRLLPLLLPLLWLLVLTPGRPAAGLSTCKTIDMELVKRKRIE


 


AIRGQILSKLRLASPPSQGEVPPGPLPEAVLALYNSTRDRVAGESAE


 


PEPEPEADYYAKEVTRVLMVETHNEIYDKFKQSTHSIYMFFNTSELR


 


EAVPEPVLLSRAELRLLRLKLKVEQHVELYQKYSNNSWRYLSNRLLA


 


PSDSPEWLSFDVTGVVRQWLSRGGEIEGFRLSAHCSCDSRDNTLQVD


 


INGFTTGRRGDLATIHGMNRPFLLLMATPLERAQHLQSSRHRRALDT


 


NYCFSSTEKNCCVRQLYIDFRKDLGWKWIHEPKGYHANFCLGPCPYI


 


WSLDTQYSKVLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRKPKV


 


EQLSNMIVRSCKCS.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the receptor binding site on TGFβ and/or interfere with or block the ability of TGFβ to bind to its receptor. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human TGFβ (SEQ ID NO: 368) selected from the group consisting of Arg-25, Gly-29, Trp-30, Lys-31, Trp-32, Ile-33, His-34, Tyr-91, Val-92, Val-93, Gly-94, Arg-95, Lys-96, and Pro-97, or the equivalent amino acid residue(s) in a TGFβ protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human TGFβ (SEQ ID NO: 368) selected from the group consisting of Leu-20, Ile-22, Phe-24, Asp-27, Leu-28, Trp-30, Trp-32, Tyr-39, Phe-43, Pro-80, Leu-83, Leu-101 and Ser-112, or the equivalent amino acid residue(s) in a TGFβ protein of another species. In other alternatives, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human TGFβ (SEQ ID NO: 368) selected from the group consisting of Asp-27, Leu-28, Trp-30, and Trp-32, or the equivalent amino acid residue(s) in a TGFβ protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human TGFβ (SEQ ID NO: 368) with an affinity of at least −650 kcal/mol, and in certain embodiments at least −700, −750, −800, −850, −900, −925, −950, −975, −1000, −1025, −1050 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and Notch1, any Notch1 protein sequence can be used. The Notch1 sequence used for modeling generally folds into a functional Notch1 protein or a calcium-binding fragment thereof. The Notch1 sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human Notch1 is selected if the intended subject is a human, a bovine Notch1 is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human Notch1 sequence (GenBank Acc. No. AAG33848.1), which is as follows:







(SEQ ID NO: 369)


MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACV


 


CGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFS


 


GPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPGWSGKSCQQA


 


DPCASNPCANGGQCLPFEASYICHCPPSFHGPTCRQDVNECGQKPRL


 


CRHGGTCHNEVGSYRCVCRATHTGPNCERPYVPCSPSPCQNGGTCRP


 


TGDVTHECACLPGFTGQNCEENIDDCPGNNCKNGGACVDGVNTYNCP


 


CPPEWTGQYCTEDVDECQLMPNACQNGGTCHNTHGGYNCVCVNGWTG


 


EDCSENIDDCASAACFHGATCHDRVASFYCECPHGRTGLLCHLNDAC


 


ISNPCNEGSNCDTNPVNGKAICTCPSGYTGPACSQDVDECSLGANPC


 


EHAGKCINTLGSFECQCLQGYTGPRCEIDVNECVSNPCQNDATCLDQ


 


IGEFQCMCMPGYEGVHCEVNTDECASSPCLHNGRCLDKINEFQCECP


 


TGFTGHLCQYDVDECASTPCKNGAKCLDGPNTYTCVCTEGYTGTHCE


 


VDIDECDPDPCHYGSCKDGVATFTCLCRPGYTGHHCETNINECSSQP


 


CRLRGTCQDPDNAYLCFCLKGTTGPNCEINLDDCASSPCDSGTCLDK


 


IDGYECACEPGYTGSMCNSNIDECAGNPCHNGGTCEDGINGFTCRCP


 


EGYHDPTCLSEVNECNSNPCVHGACRDSLNGYKCDCDPGWSGTNCDI


 


NNNECESNPCVNGGTCKDMTSGIVCTCREGFSGPNCQTNINECASNP


 


CLNKGTCIDDVAGYKCNCLLPYTGATCEVVLAPCAPSPCRNGGECRQ


 


SEDYESFSCVCPTAGAKGQTCEVDINECVLSPCRHGASCQNTHGXYR


 


CHCQAGYSGRNCETDIDDCRPNPCHNGGSCTDGINTAFCDCLPGFRG


 


TFCEEDINECASDPCRNGANCTDCVDSYTCTCPAGFSGIHCENNTPD


 


CTESSCFNGGTCVDGINSFTCLCPPGFTGSYCQHVVNECDSRPCLLG


 


GTCQDGRGLHRCTCPQGYTGPNCQNLVHWCDSSPCKNGGKCWQTHTQ


 


YRCECPSGWTGLYCDVPSVSCEVAAQRQGVDVARLCQHGGLCVDAGN


 


THHCRCQAGYTGSYCEDLVDECSPSPCQNGATCTDYLGGYSCKCVAG


 


YHGVNCSEEIDECLSHPCQNGGTCLDLPNTYKCSCPRGTQGVHCEIN


 


VDDCNPPVDPVSRSPKCFNNGTCVDQVGGYSCTCPPGFVGERCEGDV


 


NECLSNPCDARGTQNCVQRVNDFHCECRAGHTGRRCESVINGCKGKP


 


CKNGGTCAVASNTARGFICKCPAGFEGATCENDARTCGSLRCLNGGT


 


CISGPRSPTCLCLGPFTGPECQFPASSPCLGGNPCYNQGTCEPTSES


 


PFYRCLCPAKFNGLLCHILDYSFGGGAGRDIPPPLIEEACELPECQE


 


DAGNKVCSLQCNNHACGWDGGDCSLNFNDPWKNCTQSLQCWKYFSDG


 


HCDSQCNSAGCLFDGFDCQRAEGQCNPLYDQYCKDHFSDGHCDQGCN


 


SAECEWDGLDCAEHVPERLAAGTLVVVVLMPPEQLRNSSFHFLRELS


 


RVLHTNVVFKRDAHGQQMIFPYYGREEELRKHPIKRAAEGWAAPDAL


 


LGQVKASLLPGGSEGGRRRRELDPMDVRGSIVYLEIDNRQCVQASSQ


 


CFQSATDVAAFLGALASLGSLNIPYKIEAVQSETVEPPPPAQLHFMY


 


VAAAAFVLLFFVGCGVLLSRKRRRQHGQLWFPEGFKVSEASKKKRRE


 


PLGEDSVGLKPLKNASDGALMDDNQNEWGDEDLETKKFRFEEPVVLP


 


DLDDQTDHRQWTQQHLDAADLRMSAMAPTPPQGEVDADCMDVNVRGP


 


DGFTPLMIASCSGGGLETGNSEEEEDAPAVISDFIYQGASLHNQTDR


 


TGETALHLAARYSRSDAAKRLLEASADANIQDNMGRTPLHAAVSADA


 


QGVFQILIRNRATDLDARMHDGTTPLILAARLAVEGMLEDLINSHAD


 


VNAVDDLGKSALHWAAAVNNVDAAVVLLKNGANKDMQNNREETPLFL


 


AAREGSYETAKVLLDHFANRDITDHMDRLPRDIAQERMHHDIVRLLD


 


EYNLVRSPQLHGAPLGGTPTLSPPLCSPNGYLGSLKPGVQGKKVRKP


 


SSKGLACGSKEAKDLKARRKKSQDGKGCLLDSSGMLSPVDSLESPHG


 


YLSDVASPPLLPSPFQQSPSVPLNHLPGMPDTHLGIGHLNVAAKPEM


 


AALGGGGRLAFETGPPRLSHLPVASGTSTVLGSSSGGALNFTVGGST


 


SLNGQCEWLSRLQSGMVPNQYNPLRGSVAPGPLSTQAPSLQHGMVGP


 


LHSSLAASALSQMMSYQGLPSTRLATQPHLVQTQQVQPQNLQMQQQN


 


LQPANIQQQQSLQPPPPPPQPHLGVSSAASGHLGRSFLSGEPSQADV


 


QPLGPSSLAVHTILPQESPALPTSLPSSLVPPVTAAQFLTPPSQHSY


 


SSPVDNTPSHQLQVPEHPFLTPSPESPDQWSSSSPHSNVSDWSEGVS


 


SPPTSMQSQIARIPEAFK.






An anti-inflammatory polypeptide can be identified based on its ability to bind to the calcium-binding site on Notch1 and/or interfere with or block the ability of Notch1 to bind to calcium. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human Notch1 (SEQ ID NO: 369) selected from the group consisting of Phe-1520, Gln-1523, Arg-1524, Glu-1526, Ala-1553, Glu-1556, Trp-1557, Cys-1562, His-1602, Arg-1684, Gln-1685, Cys-1686, Ser-1691, Cys-1693, Phe-1694, and Phe-1703, or the equivalent amino acid residue(s) in a Notch1 protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human Notch1 (SEQ ID NO: 369) selected from the group consisting of Phe-1520, Trp-1557, Cys-1562, and Phe-1703, or the equivalent amino acid residue(s) in a Notch1 protein of another species.
In certain embodiments, a polypeptide of the invention binds to human Notch1 (SEQ ID NO: 369) with an affinity of at least −650 kcal/mol, and in certain embodiments at least −700, −750, −800, −850, −900, −925, −950, −975, −1000, −1025, −1050, −1075 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and Wnt8R, any Wnt8R protein sequence can be used. The Wnt8R sequence used for modeling generally folds into a functional Wnt8R protein or a Wnt8-binding fragment thereof. The Wnt8R protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human Wnt8R is selected if the intended subject is a human, a bovine Wnt8R is selected if the intended subject is a cow, etc.). The sequence used for modeling can be, for example, the bovine Wnt8R sequence (NCBI Acc. No. XP_005214377.1), which is as follows:







(SEQ ID NO: 370)


MEWGYLLEVTSLLAALALLQRSSGAAAASAKELACQEITVPLCKGIG


 


YNYTYMPNQFNHDTQDEAGLEVHQFWPLVEIQCSPDLKFFLCSMYTP


 


ICLEDYKKPLPPCRSVCERAKAGCAPLMRQYGFAWPDRMRCDRLPEQ


 


GNPDTLCMDYNRTDLTTAASSVDGDPVAGICYVGNQSLDNLLGFVLA


 


PLVIYLFIGTMFLLAGFVSLFRIRSVIKQQGGPTKTHKLEKLMIRLG


 


LFTVLYTVPAAVVVACLFYEQHNRPRWEATHNCPCLRDLQPDQARRP


 


DYAVFMLKYFMCLVVGITSGVWVWSGKTLESWRALCTRCCWASKGAG


 


AAGAGAAGGGPGGGGPGAGGGGGPGAGGAGSLYSDVSTGLTWRSGTA


 


SSVSYPKQMPLSQV.






An anti-inflammatory polypeptide can be identified based on its ability to bind to a Wnt ligand-binding site on Wnt8R and/or interfere with or block the ability of Wnt8R to bind to a Wnt ligand (e.g., Wnt8). For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of bovine Wnt8R (SEQ ID NO: 370) selected from the group consisting of Tyr-52, Gln-56, Phe-57, Asn-58, Met-91, Tyr-100, Lys-101, Pro-103, Pro-105, Pro-106, Arg-137 and Asp-145, or the equivalent amino acid residue(s) in a Wnt8R protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of bovine Wnt8R (SEQ ID NO: 370) selected from the group consisting of Tyr-52, Phe-57, Tyr-100, and Asp-145, or the equivalent amino acid residue(s) in a Wnt8R protein of another species.
In certain embodiments, a polypeptide of the invention binds to bovine Wnt8R (SEQ ID NO: 370) with an affinity of at least −600 kcal/mol, and in certain embodiments at least −650, −700, −750, −800, −850, −875, −900, −925, −950, −975 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and TRAIL, any TRAIL protein sequence can be used. The TRAIL sequence used for modeling in certain embodiments folds into a function TRAIL protein or a functional fragment thereof. The TRAIL protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human TRAIL is selected if the intended subject is a human, a bovine TRAIL is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human TRAIL sequence (GenBank Acc. No. EAW78466.1), which is as follows:







(SEQ ID NO: 371)


KEKQQNISPLVRERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRK


 


INSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIK


 


ENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSKDAEYGLYSIYQ


 


GGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the receptor binding site on TRAIL and/or interfere with or block the ability of TRAIL to bind to its receptor. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human TRAIL (SEQ ID NO: 371) selected from the group consisting of Arg-130, Arg-158, Ser-159, Gly-160, His-161, Phe-163, Tyr-189, Arg-189, Gln-193, Glu-195, Glu-236, Tyr-237, Leu-239, Asp-267, Asp-269, His-270, and Glu-271, or the equivalent amino acid residue(s) in a TRAIL protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human TRAIL (SEQ ID NO: 371) selected from the group consisting of Ala-123, His-161, Ser-162, Phe-163, Tyr-183, Tyr-185, Tyr-243, His-270, Glu-271, Phe-274, Phe-278, Leu-279, and Val-280, or the equivalent amino acid residue(s) in a TRAIL protein of another species. In other alternatives, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human TRAIL (SEQ ID NO: 371) selected from the group consisting of Phe-163, Tyr-243, Glu-271, and Phe-278, or the equivalent amino acid residue(s) in a TRAIL protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human TRAIL (SEQ ID NO: 371) with an affinity of at least −650 kcal/mol, and in certain embodiments at least −700, −750, −800, −850, −900, −925, −950, −975, −1000, −1025, −1050 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and IL6R, any IL6R protein sequence can be used. The IL6R sequence used for modeling generally folds into a functional IL6R protein or a IL6-binding fragment thereof. The IL6R protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human IL6R is selected if the intended subject is a human, a bovine IL6R is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human IL6R sequence (NCBI Acc. No. NP_786943.1), which is as follows:







(SEQ ID NO: 372)


MLTLQTWLVQALFIFLTTESTGELLDPCGYISPESPVVQLHSNFTAV


 


CVLKEKCMDYFHVNANYIVWKTNHFTIPKEQYTIINRTASSVTFTDI


 


ASLNIQLTCNILTFGQLEQNVYGITIISGLPPEKPKNLSCIVNEGKK


 


MRCEWDGGRETHLETNFTLKSEWATHKFADCKAKRDTPTSCTVDYST


 


VYFVNIEVWVEAENALGKVTSDHINFDPVYKVKPNPPHNLSVINSEE


 


LSSILKLTWTNPSIKSVIILKYNIQYRTKDASTWSQIPPEDTASTRS


 


SFTVQDLKPFTEYVFRIRCMKEDGKGYWSDWSEEASGITYEDNIASF.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the IL6-binding site on IL6R and/or interfere with or block the ability of IL6R to bind to its ligand, IL6. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human IL6R (SEQ ID NO: 372) selected from the group consisting of Glu-163, Gly-164, Phe-168, Gln-190, Phe-229, Tyr-230, Phe-279 and Gln-281, or the equivalent amino acid residue(s) in a IL6R protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human IL6R (SEQ ID NO: 372) selected from the group consisting of Leu-108, Glu-140, Pro-162, Phe-229, Tyr-230, and Phe-279, or the equivalent amino acid residue(s) in a IL6R protein of another species. In other alternatives, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human IL6R (SEQ ID NO: 372) selected from the group consisting of Glu-140, Phe-229, Tyr-230, Phe-279, or the equivalent amino acid residue(s) in a IL6R protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human IL6R (SEQ ID NO: 372) with an affinity of at least −600 kcal/mol, and in certain embodiments at least −650, −700, −750, −800, −850, −900, −925, −950, −975, −1000, −1025, −1050 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and IL10R, any appropriate IL10R protein sequence can be used. The IL10R sequence used for modeling generally folds into a functional IL10R protein or a IL10-binding fragment thereof. The IL10R protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human IL10R is selected if the intended subject is a human, a bovine IL10R is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human IL10R sequence (NCBI Acc. No. NP_001549.2), which is as follows:







(SEQ ID NO: 373)


MLPCLVVLLAALLSLRLGSDAHGTELPSPPSVWFEAEFFHHILHWTP


 


IPNQSESTCYEVALLRYGIESWNSISNCSQTLSYDLTAVTLDLYHSN


 


GYRARVRAVDGSRHSNWTVTNTRFSVDEVTLTVGSVNLEIHNGFILG


 


KIQLPRPKMAPANDTYESIFSHFREYEIAIRKVPGNFTFTHKKVKHE


 


NFSLLTSGEVGEFCVQVKPSVASRSNKGMWSKEECISLTRQYFTVTN


 


VIIFFAFVLLLSGALAYCLALQLYVRRRKKLPSVLLFKKPSPFIFIS


 


QRPSPETQDTIHPLDEEAFLKVSPELKNLDLHGSTDSGFGSTKPSLQ


 


TEEPQFLLPDPHPQADRTLGNREPPVLGDSCSSGSSNSTDSGICLQE


 


PSLSPSTGPTWEQQVGSNSRGQDDSGIDLVQNSEGRAGDTQGGSALG


 


HHSPPEPEVPGEEDPAAVAFQGYLRQTRCAEEKATKTGCLEEESPLT


 


DGLGPKFGRCLVDEAGLHPPALAKGYLKQDPLEMTLASSGAPTGQWN


 


QPTEEWSLLALSSCSDLGISDWSFAHDLAPLGCVAAPGGLLGSFNSD


 


LVTLPLISSLQSSE.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the IL10-binding site on IL10R and/or interfere with or block the ability of IL10R to bind to its ligand, IL10. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human IL10R (SEQ ID NO: 373) selected from the group consisting of Tyr-43, Ile-45, Glu-46, Asp-61, Asn-73, Arg-76, Asn-94, Arg-96, Phe-143, Ala-189, Ser-190, and Ser-191, or the equivalent amino acid residue(s) in a IL6R protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human IL10R (SEQ ID NO: 373) selected from the group consisting of Leu-41, Arg-42, Tyr-43, Ile-45, Glu-46, Ser-47, Trp-48, Arg-76, and Arg-78, or the equivalent amino acid residue(s) in a IL10R protein of another species. In other alternatives, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human IL10R (SEQ ID NO: 373) selected from the group consisting of Tyr-43, Ile-45, Glu-46, Trp-48, or the equivalent amino acid residue(s) in a IL10R protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human IL10R (SEQ ID NO: 373) with an affinity of at least −600 kcal/mol, and in certain embodiments at least −650, −700, −750, −775, −800, −825, −850, −875, −900 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and EGFR, any EGFR protein sequence can be used. The EGFR sequence used for modeling generally folds into a functional EGFR protein or a ligand-binding fragment thereof. The EGFR protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human EGFR is selected if the intended subject is a human, a bovine EGFR is selected if the intended subject is a cow, etc.). Alternatively, the sequence used for modeling can be the drosophila EGFR sequence (GenBank Acc. No. AAR85273.1), which is as follows:







(SEQ ID NO: 374)


KICIGTKSRLSVPSNKEHHYRNLRDRYTNCTYVDGNLELTWLPNENL


 


DLSFLDNIREVTGYILISHVDVKKVVFPKLQIIRGRTLFSLSVEEEK


 


YALFVTYSKMYTLEIPDLRDVLNGQVGFHNNYNLCHMRTIQWSEIVS


 


NGTDAYYNYDFTAPERECPKCHESCTHGCWGEGPKNCQKFSKLTCSP


 


QCAGGRCYGPKPRECCHLFCAGGCTGPTQKDCIACKNFFDEGVCKEE


 


CPPMRKYNPTTYVLETNPEGKYAYGATCVKECPGHLLRDNGACVRSC


 


PQDKMDKGGECVPCNGPCPKTCPGVTVLHAGNIDSFRNCTVIDGNIR


 


ILDQTFSGFQDVYANYTMGPRYIPLDPERLEVFSTVKEITGYLNIEG


 


THPQFRNLSYFRNLETIHGRQLMESMFAALAIVKSSLYSLEMRNLKQ


 


ISSGSVVIQHNRDLCYVSNIRWPAIQKEPEQKVWVNENLRADLCEKN


 


GTICSDQCNEDGCWGAGTDQCLNCKNFNFNGTCIADCGYISNAYKFD


 


NRTCKICHPECRTCNGAGADHCQECVHVRDGQHCVSECPKNKYNDRG


 


VCRECHATCDGCTGPKDTIGIGACTTCNLAIINNDATVKRCLLKDDK


 


CPDGYFWEYVHPQEQGSLKPLAGRAVCRKCHPLCELCTNYGYHEQ.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the ligand-binding site on EGFR and/or interfere with or block the ability of at least one ligand to bind to EGFR. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of drosophila EGFR (SEQ ID NO: 374) selected from the group consisting of Leu-10, Thr-40, Trp-41, Asp-48, Phe-51, Leu-63, His-66, Asp-68, Leu-88, and Tyr-101, or the equivalent amino acid residue(s) in a EGFR protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of drosophila EGFR (SEQ ID NO: 374) selected from the group consisting of Trp-41, Asp-48, Phe-51, Asp-68, and Tyr-101, or the equivalent amino acid residue(s) in a EGFR protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to drosophila EGFR (SEQ ID NO: 374) with an affinity of at least −650 kcal/mol, and in certain embodiments at least −700, −750, −800, −850, −900, −925, −950, −975, −1000, −1025, −1050 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and CDK6, any CDK6 protein sequence can be used. The CDK6 sequence used for modeling generally folds into a functional CDK6 protein or a functional fragment thereof. The CDK6 protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human CDK6 is selected if the intended subject is a human, a bovine CDK6 is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human CDK6 sequence (NCBI Acc. No. NP_001250.1), which is as follows:







(SEQ ID NO: 375)


MEKDGLCRADQQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRV


 


QTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDRETKL


 


TLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLDFLHSHRV


 


VHRDLKPQNILVTSSGQIKLADFGLARIYSFQMALTSVVVTLWYRAP


 


EVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILDVI


 


GLPGEEDWPRDVALPRQAFHSKSAQPIEKFVTDIDELGKDLLLKCLT


 


FNPAKRISAYSALSHPYFQDLERCKENLDSHLPPSQNTSELNTA.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the active site on CDK6 and/or interfere with or block the kinase activity of CDK6 or the ability of CDK6 to phosphorylate one or more CDK6 substrates. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human CDK6 (SEQ ID NO: 375) selected from the group consisting of Val-142, Arg-144, Asp-145, Ser-171, Val-180, Val-181, Leu-183, Arg-186, Val-190, Gln-193, Tyr-196, and Val-200, or the equivalent amino acid residue(s) in a CDK6 protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human CDK6 (SEQ ID NO: 375) selected from the group consisting of Asp-145, Val-180, and Tyr-196, or the equivalent amino acid residue(s) in a CDK6 protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human CDK6 (SEQ ID NO: 375) with an affinity of at least −600 kcal/mol, and in certain embodiments at least −650, −700, −750, −800, −850, −900, −925, −950, −975, −1000, −1025, −1050 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and histone methyl transferase (HMT), any HMT protein sequence can be used. The HMT sequence used for modeling generally folds into a functional HMT protein or a functional fragment thereof. The HMT protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human HMT is selected if the intended subject is a human, a bovine HMT is selected if the intended subject is a cow, etc.). The sequence used for modeling can be, for example, the Paramecium bursaria Chlorella virus 1 HMT sequence (NCBI Acc. No. NP_048968.1), which is as follows:







(SEQ ID NO: 376)


MFNDRVIVKKSPLGGYGVFARKSFEKGELVEECLCIVRHNDDWGTAL


 


EDYLFSRKNMSAMALGFGAIFNHSKDPNARHELTAGLKRMRIFTIKP


 


IAIGEEITISYGDDYWLSRPRLTQN.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the active site on HMT and/or interfere with or block the methyl transferase activity of HMT or the ability of HMT to methylate histone substrates. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of Paramecium bursaria HMT (SEQ ID NO: 376) selected from the group consisting of Asn-69, His-70, Ser-71, Lys-72, Asp-73, Pro-74, and Asn-75, or the equivalent amino acid residue(s) in a HMT protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of Paramecium bursaria HMT (SEQ ID NO: 376) selected from the group consisting of Tyr-16, Glu-48, Tyr-50, Leu-51, Phe-52, and Asn-69, or the equivalent amino acid residue(s) in a HMT protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to Paramecium bursaria HMT (SEQ ID NO: 376) with an affinity of at least −600 kcal/mol, and in certain embodiments at least −650, −700, −750, −800, −850, −900, −925, −950, −975, −1000, −1025, −1050 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and CD47, any CD47 protein sequence can be used. The CD47 sequence used for modeling generally folds into a functional CD47 protein or a SIRP-α-binding portion thereof. The CD47 protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human CD47 is selected if the intended subject is a human, a bovine CD47 is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human CD47 sequence (NCBI Acc. No. XP_005247966.1), which is as follows:







(SEQ ID NO: 377)


MWPLVAALLLGSACCGSAQLLFNKTKSVEFTFCNDTVVIPCFVTNME


 


AQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKG


 


DASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYRVVSWFSPNE


 


NILIVIFPIFAILLFWGQFGIKTLKYRSGGMDEKTIALLVAGLVITV


 


IVIVGAILFVPGEYSLKNATGLGLIVTSTGILILLHYYVFSTAIGLT


 


SFVIAILVIQVIAYILAVVGLSLCIAACIPMHGPLLISGLSILALAQ


 


LLGLVYMKFVE.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the SIRP-α-binding site on HMT and/or interfere with or block the binding of CD47 to SIRP-α. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of CD47 (SEQ ID NO: 377) selected from the group consisting of Glu-29, Ala-30, Glu-35, Val-36, Tyr-37, Lys-39, Thr-49, Asp-51, Glu-97, Thr-99, Leu-101, Thr-102, Arg-103, Glu-104, and Glu-106, or the equivalent amino acid residue(s) in a CD47 protein of another species. In certain embodiments, the anti-inflammatory polypeptide can bind to at least one amino acid residue of CD47 (SEQ ID NO: 377) selected from the group consisting of Glu-29, Glu-35, Lys-39, Glu-97, Leu-101, Thr-102, Arg-103, Glu-104, and Glu-106, or the equivalent amino acid residue(s) in a CD47 protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human CD47 (SEQ ID NO: 377) selected from the group consisting of Tyr-16, Glu-48, Tyr-50, Leu-51, Phe-52, and Asn-6 Tyr-37, Thr-49, Phe-50, Asp-51, Ala-53, Glu-97, Val-98, Glu-100, Leu-101, Thr-102, Glu-104, Glu-106, Gly-107, or the equivalent amino acid residue(s) in a CD47 protein of another species. In certain embodiments, the anti-inflammatory polypeptide can bind to at least one amino acid residue of CD47 (SEQ ID NO: 377) selected from the group consisting of Tyr-37, Glu-97, Glu-100, Leu-101, Glu-104, Glu-106, or the equivalent amino acid residue(s) in a CD47 protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human CD47 (SEQ ID NO: 377) with an affinity of at least −550 kcal/mol, and in certain embodiments at least −600, −650, −675, −700, −725, −750, −775, −800 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and SIRP-α, any SIRP-α protein sequence can be used. The SIRP-α sequence used for modeling generally folds into a functional SIRP-α protein or a CD47-binding fragment thereof. The SIRP-α protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human SIRP-α is selected if the intended subject is a human, a bovine SIRP-α is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human SIRP-α sequence (GenBank Acc. No. AAH26692.1), which is as follows:







(SEQ ID NO: 378)


MEPAGPAPGRLGPLLCLLLAASCAWSGVAGEEELQVIQPDKSVSVAA


 


GESAILHCTVTSLIPVGPIQWFRGAGPARELIYNQKEGHFPRVTTVS


 


ESTKRENMDFSISISNITPADAGTYYCVKFRKGSPDTEFKSGAGTEL


 


SVRAKPSAPVVSGPAARATPQHTVSFTCESHGFSPRDITLKWFKNGN


 


ELSDFQTNVDPVGESVSYSIHSTAKVVLTREDVHSQVICEVAHVTLQ


 


GDPLRGTANLSETIRVPPTLEVTQQPVRAENQVNVTCQVRKFYPQRL


 


QLTWLENGNVSRTETASTVTENKDGTYNWMSWLLVNVSAHRDDVKLT


 


CQVEHDGQPAVSKSHDLKVSAHPKEQGSNTAAENTGSNERNIYIVVG


 


VVCTLLVALLMAALYLVRIRQKKAQGSTSSTRLHEPEKNAREITQVQ


 


SLDTNDITYADLNLPKGKKPAPQAAEPNNHTEYASIQTSPQPASEDT


 


LTYADLDMVHLNRTPKQPAPKPEPSFSEYASVQVPRK.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the HMT-binding site on SIRP-α and/or interfere with or block the binding of SIRP-α to HMT. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of SIRP-α (SEQ ID NO: 378) selected from the group consisting of Leu-30, Gln-37, Gln-52, Lys-53, Ser-66, Thr-67, Arg-69, Met-72, Phe-74, Lys-96 and Asp-100, or the equivalent amino acid residue(s) in a SIRP-α protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human SIRP-α (SEQ ID NO: 378) selected from the group consisting of Tyr-50, Gln-52, Pro-58, Ser-66, Thr-67, and Ser-77, or the equivalent amino acid residue(s) in a SIRP-α protein of another species. In certain embodiments, the anti-inflammatory polypeptide can bind to at least one amino acid residue of SIRP-α (SEQ ID NO: 378) selected from the group consisting of Tyr-50, Gln-52, Ser-66, and Thr-67, or the equivalent amino acid residue(s) in a SIRP-α protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human SIRP-α (SEQ ID NO: 378) with an affinity of at least −600 kcal/mol, and in certain embodiments at least −650, −700, −750, −800, −825, −850, −875, −900, −925, −950, −975, −1000 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and CD206, any CD206 protein sequence can be used. The CD206 sequence used for modeling generally folds into a functional CD206 protein or a mannose-binding fragment thereof. The CD206 protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human CD206 is selected if the intended subject is a human, a bovine CD206 is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human CD206 sequence (NCBI Acc. No. NP_002429.1), which is as follows:







(SEQ ID NO: 379)


MRLPLLLVFASVIPGAVLLLDTRQFLIYNEDHKRCVDAVSPSAVQTA


 


ACNQDAESQKFRWVSESQIMSVAFKLCLGVPSKTDWVAITLYACDSK


 


SEFQKWECKNDTLLGIKGEDLFFNYGNRQEKNIMLYKGSGLWSRWKI


 


YGTTDNLCSRGYEAMYTLLGNANGATCAFPFKFENKWYADCTSAGRS


 


DGWLWCGTTTDYDTDKLFGYCPLKFEGSESLWNKDPLTSVSYQINSK


 


SALTWHQARKSCQQQNAELLSITEIHEQTYLTGLTSSLTSGLWIGLN


 


SLSFNSGWQWSDRSPFRYLNWLPGSPSAEPGKSCVSLNPGKNAKWEN


 


LECVQKLGYICKKGNTTLNSFVIPSESDVPTHCPSQWWPYAGHCYKI


 


HRDEKKIQRDALTTCRKEGGDLTSIHTIEELDFIISQLGYEPNDELW


 


IGLNDIKIQMYFEWSDGTPVTFTKWLRGEPSHENNRQEDCVVMKGKD


 


GYWADRGCEWPLGYICKMKSRSQGPEIVEVEKGCRKGWKKHHFYCYM


 


IGHTLSTFAEANQTCNNENAYLTTIEDRYEQAFLTSFVGLRPEKYFW


 


TGLSDIQTKGTFQWTIEEEVRFTHWNSDMPGRKPGCVAMRTGIAGGL


 


WDVLKCDEKAKFVCKHWAEGVTHPPKPTTTPEPKCPEDWGASSRTSL


 


CFKLYAKGKHEKKTWFESRDFCRALGGDLASINNKEEQQTIWRLITA


 


SGSYHKLFWLGLTYGSPSEGFTWSDGSPVSYENWAYGEPNNYQNVEY


 


CGELKGDPTMSWNDINCEHLNNWICQIQKGQTPKPEPTPAPQDNPPV


 


TEDGWVIYKDYQYYFSKEKETMDNARAFCKRNFGDLVSIQSESEKKF


 


LWKYVNRNDAQSAYFIGLLISLDKKFAWMDGSKVDYVSWATGEPNFA


 


NEDENCVTMYSNSGFWNDINCGYPNAFICQRHNSSINATTVMPTMPS


 


VPSGCKEGWNFYSNKCFKIFGFMEEERKNWQEARKACIGFGGNLVSI


 


QNEKEQAFLTYHMKDSTFSAWTGLNDVNSEHTFLWTDGRGVHYTNWG


 


KGYPGGRRSSLSYEDADCVVIIGGASNEAGKWMDDTCDSKRGYICQT


 


RSDPSLTNPPATIQTDGFVKYGKSSYSLMRQKFQWHEAETYCKLHNS


 


LIASILDPYSNAFAWLQMETSNERVWIALNSNLTDNQYTWTDKWRVR


 


YTNWAADEPKLKSACVYLDLDGYWKTAHCNESFYFLCKRSDEIPATE


 


PPQLPGRCPESDHTAWIPFHGHCYYIESSYTRNWGQASLECLRMGSS


 


LVSIESAAESSFLSYRVEPLKSKTNFWIGLFRNVEGTWLWINNSPVS


 


FVNWNTGDPSGERNDCVALHASSGFWSNIHCSSYKGYICKRPKIIDA


 


KPTHELLTTKADTRKMDPSKPSSNVAGVVIIVILLILTGAGLAAYFF


 


YKKRRVHLPQEGAFENTLYFNSQSSPGTSDMKDLVGNIEQNEHSVI.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the mannose-binding site on CD206 and/or interfere with or block the binding of SIRP-mannose to CD206. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of CD206 (SEQ ID NO: 379) selected from the group consisting of Glu-725, Tyr-729, Glu-733, Asn-747, and Asp-748, or the equivalent amino acid residue(s) in a CD206 protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human CD206 (SEQ ID NO: 379) selected from the group consisting of Phe-708, Thr-709, Trp-710, Pro-714. Glu-719, Asn-720, Trp-721, Ala-722, Glu-725, Tyr-729, Glu-733, Asn-747, Asp-748, Ser-1691, Cys-1693, Phe-1694, and Phe-1703, or the equivalent amino acid residue(s) in a CD206 protein of another species. In certain embodiments, the anti-inflammatory polypeptide can bind to at least one amino acid residue of CD206 (SEQ ID NO: 379) selected from the group consisting of Phe-708, Trp-710, Trp-721, Glu-725, Tyr-729, Glu-733, or the equivalent amino acid residue(s) in a CD206 protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human CD206 (SEQ ID NO: 379) with an affinity of at least −650 kcal/mol, and in certain embodiments at least −700, −750, −800, −850, −900, −925, −950, −975, −1000, −1025, −1050 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and TGM2, any TGM2 protein sequence can be used. The TGM2 sequence used for modeling generally folds into a functional TGM2 protein or acyl-transferase catalytic fragment thereof. The TGM2 protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human TGM2 is selected if the intended subject is a human, a bovine TGM2 is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human TGM2 sequence (GenBank Acc. No. AAB95430.1), which is as follows:







(SEQ ID NO: 380)


MMDASKELQVLHIDFLNQDNAVSHHTWEFQTSSPVFRRGQVFHLRLV


 


LNQPLQSYHQLKLEFSTGPNPSIAKHTLVVLDPRTPSDHYNWQATLQ


 


NESGKEVTVAVTSSPNAILGKYQLNVKTGNHILKSEENILYLLFNPW


 


CKEDMVFMPDEDERKEYILNDTGCHYVGAARSIKCKPWNFGQFEKNV


 


LDCCISLLTESSLKPTDRRDPVLVCRAMCAMMSFEKGQGVLIGNWTG


 


DYEGGTAPYKWTGSAPILQQYYNTKQAVCFGQCWVFAGILTTVLRAL


 


GIPARSVTGFDSAHDTERNLTVDTYVNENGEKITSMTHDSVWNFHVW


 


TDAWMKRPDLPKGYDGWQAVDATPQERSQGVFCCGPSPLTAIRKGDI


 


FIVYDTRFVFSEVNGDRLIWLVKMVNGQEELHVISMETTSIGKNIST


 


KAVGQDRRRDITYEYKYPEGSSEERQVMDHAFLLLSSEREHRRPVKE


 


NFLHMSVQSDDVLLGNSVNFTVILKRKTAALQNVNILGSFELQLYTG


 


KKMAKLCDLNKTSQIQGQVSEVTLTLDSKTYINSLAILDDEPVIRGF


 


IIAEIVESKEIMASEVFTSFQYPEFSIELPNTGRIGQLLVCNCIFKN


 


TLAIPLTDVKFSLESLGISSLQTSDHGTVQPGETIQSQIKCTPIKTG


 


PKKFIVKLSSKQVKEINAQKIVLITK.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the active site on TGM2 and/or interfere with or block the acyl-transferase activity of TGM2. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of TGM2 (SEQ ID NO: 380) selected from the group consisting of Cys-277, His-335, and Asp-358, or the equivalent amino acid residue(s) in a TGM2 protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human TGM2 (SEQ ID NO: 380) with an affinity of at least −650 kcal/mol, and in certain embodiments at least −700, −750, −800, −850, −900, −925, −950, −975, −1000, −1025, −1050 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and serum albumin, any serum albumin protein sequence can be used. The serum albumin sequence used for modeling generally folds into a functional serum albumin protein or a functional fragment thereof. The serum albumin protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human serum albumin (HSA) is selected if the intended subject is a human, a bovine serum albumin (BSA) is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human serum albumin (HSA) sequence (NCBI Acc. No. NP_000468.1), which is as follows:







(SEQ ID NO: 381)


DAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVT


 


EFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQ


 


EPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYE


 


IARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDE


 


GKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLV


 


TDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKP


 


LLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGM


 


FLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDE


 


FKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTL


 


VEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVS


 


DRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLS


 


EKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDK


 


ETCFAEEGKKLVAASQAALGL.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to HSA under physiological conditions (e.g., in the blood stream).
In certain embodiments, an anti-inflammatory polypeptide can bind to HSA (SEQ ID NO: 381) with an affinity of at least −650 kcal/mol, and in certain embodiments at least −700, −750, −800, −850, −900, −925, −950, −975, −1000, −1025, −1050 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
In certain embodiments, an anti-inflammatory polypeptide binds to two or more targets (e.g., pro-inflammatory targets). In some embodiments, an anti-inflammatory polypeptide binds to three, four, five, or more pro-inflammatory targets. For example, an anti-inflammatory polypeptide can bind to any combination of targets disclosed herein. Such binding can be based on in silico, in vitro, or in vivo data. Thus, an anti-inflammatory polypeptide can bind to two or more NF-kB Class II subunits (e.g., RelB and at least one other NF-kB Class II subunit, such as RelA, cRel, NF-kB1, or NF-kB2). Alternatively (or in addition), an anti-inflammatory polypeptide can bind to an NF-kB Class II subunit (e.g., RelB) and at least one other signaling molecule (e.g., at least one signaling molecule selected from the group consisting of TGFβ, Notch1, Wnt8R, TRAIL, IL6R, IL10R, EGFR, CDK6, CD206, CD47, SIRP-α, HMT, and TGM2). For example, an anti-inflammatory polypeptide can bind to an NF-kB Class II subunit (e.g., RelB) and at least one signaling molecule selected from the group consisting of TGFβ, Notch1, Wnt8R, TRAIL, IL6R, IL10R, EGFR, and CDK6. Alternatively, an anti-inflammatory polypeptide can bind to an NF-kB Class II subunit (e.g., RelB) and at least one signaling molecule selected from the group consisting of CD206, CD47, SIRP-α, and TGM2. In other alternatives, an anti-inflammatory polypeptide can bind to an NF-kB Class II subunit (e.g., RelB) and HMT. In other alternatives, an anti-inflammatory polypeptide can bind to at least one signaling molecule selected from the group consisting of TGFβ, Notch1, Wnt8R, TRAIL, IL6R, IL10R, EGFR, and CDK6, and at least one signaling molecule selected from the group consisting of CD206, CD47, SIRP-α, and TGM2. In other alternatives, an anti-inflammatory polypeptide can bind to at least one signaling molecule selected from the group consisting of TGFβ, Notch1, Wnt8R, TRAIL, IL6R, IL10R, EGFR, and CDK6, and also bind to HMT. In still other embodiments, an anti-inflammatory polypeptide can bind to an NF-kB Class II subunit (e.g., RelB), at least one signaling molecule selected from the group consisting of TGFβ, Notch1, Wnt8R, TRAIL, IL6R, IL10R, EGFR, and CDK6, at least one signaling molecule selected from the group consisting of CD206, CD47, SIRP-α, and TGM2, and also HMT. In certain embodiments, an anti-inflammatory polypeptide binds to two or more pro-inflammatory targets and also serum albumin (e.g., human serum albumin).
For modeling interactions between potential anti-inflammatory polypeptides and LEGUMAIN, any LEGUMAIN protein sequence can be used. The LEGUMAIN sequence used for modeling generally folds into a functional LEGUMAIN protein or a functional fragment thereof. The LEGUMAIN protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human LEGUMAIN is selected if the intended subject is a human, a bovine LEGUMAIN is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human LEGUMAIN sequence (GenBank Acc. No. AAH03061.1).








(SEQ ID NO: 413)










 


IVVMMYDDIAYSEDNPTPGIVINRPNGTDVYQGVPKDYTGEDVTPQNFLAVLRGDAEAVKGIGSG


 














HTNTSHVMQYGNKTISTMKVMQFQGMKRKASSPVPLPPVTHLDLTPSPDVPLTIMKRKLMNTNDL


 


EESRQLTEEIQRHLDARHLIEKSVRKIVSLLAASEAEVEQLLSERAPLTGHSCYPEALLHFRTHC


 


FNWHSPTYEYALRHLYVLVNLCEKPYPLHRIKLSMDHVCLGHY.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the active site on LEGUMAIN and/or interfere with or block the ability of LEGUMAIN to bind to its target. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human LEGUMAIN (SEQ ID NO: 137) selected from the group consisting of Asn-44, Arg-46, His-159, Glu-189, Cys-191, Ser-217, Ser-218 and Asp-233, or the equivalent amino acid residue(s) in a LEGUMAIN protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human LEGUMAIN (SEQ ID NO: 137) selected from the group consisting of Asn-44, Glu-189 and Asp-233, or the equivalent amino acid residue(s) in a LEGUMAIN protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human LEGUMAIN (SEQ ID NO: 137) with an affinity of at least −600 kcal/mol, and in certain embodiments at least −650, −700, −750, −800, −850, −900, −925, −950 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and CD209, any CD209 protein sequence can be used. The CD209 sequence used for modeling generally folds into a functional CD209 protein or a functional fragment thereof. The CD209 protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human CD209 is selected if the intended subject is a human, a bovine CD209 is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human CD209 sequence (GenBank Acc. No. NP_001138366.1).








(SEQ ID NO: 414)



MSDSKEPRLQQLGLLVSKVPSSISQEQSRQDAIYQNLTQLKAAVGELSEKSKLQEIYQELTQLKA



 


AVGELPEKSKLQEIYQELTRLKAAVGELPEKSKLQEIYQELTWLKAAVGELPEKSKMQEIYQELT


 


RLKAAVGELPEKSKQQEIYQELTRLKAAVGELPEKSKQQEIYQELTRLKAAVGELPEKSKQQEIY


 


QELTQLKAAVERLCHPCPWEWTFFQGNCYFMSNSQRNWHDSITACKEVGAQLVVIKSAEEQNFLQ


 








NLAKFWICKKSAASCSRDEEQFLSPAPATPNPPPA






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the active site on CD209 and/or interfere with or block the ability of CD209 to bind to its receptor. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human CD209 (SEQ ID NO: 140) selected from the group consisting of Phe-269, Glu-280, Glu-303, Asn-305, Asn-306, Glu-310, Asp-311, Ser-316, Gly-317, Asn-321 and Lys-324 or the equivalent amino acid residue(s) in a CD209 protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human CD209 (SEQ ID NO: 140) selected from the group consisting of Phe-269, Glu-280, Glu-303, Glu-310, Asp-311, Asn-321 and Lys-324, or the equivalent amino acid residue(s) in a CD209 protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human CD209 (SEQ ID NO: 140) with an affinity of at least −600 kcal/mol, and in certain embodiments at least −650, −700, −750, −800, −850, −900, −925, −950, −1,000, −1,050 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and FAS, any FAS protein sequence can be used. The FAS sequence used for modeling generally folds into a functional FAS protein or a functional fragment thereof. The FAS protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human FAS is selected if the intended subject is a human, a bovine FAS is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human FAS sequence (NCBI Reference Sequence: NP_000034.1).








(SEQ ID NO: 415)



MLGIWTLLPLVLTSVARLSSKSVNAQVTDINSKGLELRKTVTTVETQNLEGLHHDGQFCHKPCPP



 


GERKARDCTVNGDEPDCVPCQEGKEYTDKAHFSSKCRRCRLCDEGHGLEVEINCTRTQNTKCRCK


 


PNFFCNSTVCEHCDPCTKCEHGIIKECTLTSNTKCKEEGSRSNLGWLCLLLLPIPLIVWVKRKEV


 














NFRNEIQSLV.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the active site on FAS and/or interfere with or block the ability of FAS to bind to its ligand. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human FAS (SEQ ID NO: 152) selected from the group consisting of Lys-251, Lys-296, Lys-299, Leu-303, Leu-306, Ala-307, Glu-308, Lys-309, Gln-311, Ile-314, Leu-315, Asp-317, Ile-318 and Thr-319, or the equivalent amino acid residue(s) in a FAS protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human FAS (SEQ ID NO: 152) selected from the group consisting of Lys-296, Lys-299, Leu-306, Ala-307, Glu-308, Ile-314, Leu-315, Asp-317 and Ile-318, or the equivalent amino acid residue(s) in a FAS protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human FAS (SEQ ID NO: 152) with an affinity of at least −600 kcal/mol, and in certain embodiments at least −650, −700, −750, −800, −850, −900, −925, −950 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
Programmed cell death protein 1, also known as PD-1 and CD279 (cluster of differentiation 279), is a protein that in humans is encoded by the PDCD1 gene. PD-1 is a cell surface receptor that belongs to the immunoglobulin superfamily and is expressed on T cells and pro-B cells. PD-1 binds two ligands, PD-L1 and PD-L2. PD-1, functioning as an immune checkpoint plays an important role in down regulating the immune system by preventing the activation of T-cells, which in turn reduces autoimmunity and promotes self-tolerance. The inhibitory effect of PD-1 is accomplished through a dual mechanism of promoting apoptosis (programmed cell death) in antigen specific T-cells in lymph nodes while simultaneously reducing apoptosis in regulatory T cells (suppressor T cells).
For modeling interactions between potential anti-inflammatory polypeptides and PD-1, any PD-1 protein sequence can be used. The PD-1 sequence used for modeling generally folds into a functional PD-1 protein or a functional fragment thereof. The PD-1 protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human PD-1 is selected if the intended subject is a human, a bovine PD-1 is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human PD-1 sequence (Locus: XP_006712636.1).








(SEQ ID NO: 416)
















KAQIKESLRAELRVTERRAEVPTAHPSPSPRPAGQFQTLVVGVVGGLLGSLVLLVWVLAVICSRA


 


ARG.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the active site on PD-1 and/or interfere with or block the ability of PD-1 to bind to its receptor. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human PD-1 (SEQ ID NO: 159) selected from the group consisting of Val-64, Asn-66, Tyr-68, Met-70, Thr-76, Lys-78, Thr-120, Leu-122, Ala-125, Ser-127, or the equivalent amino acid residue(s) in a PD-1 protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human PD-1 (SEQ ID NO: 159) selected from the group consisting of Tyr-68, Met-70, Lys-78 and Leu-122, or the equivalent amino acid residue(s) in a PD-1 protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human PD-1 (SEQ ID NO: 159) with an affinity of at least −600 kcal/mol, and in certain embodiments at least −650, −700, −750, −800, −850, −900, −925, −950, −1,000 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
Dual specificity mitogen-activated protein kinase kinase 7, also known as MAP kinase kinase 7 or MKK7, is an enzyme that in humans is encoded by the MAP2K7 gene. This protein is a member of the mitogen-activated protein kinase kinase family. The MKK7 protein exists as six different isoforms with three possible N-termini (α, β, and γ isoforms) and two possible C-termini (1 and 2 isoforms). MKK7 is involved in signal transduction mediating the cell responses to proinflammatory cytokines, and environmental stresses. This kinase specifically activates MAPK8/JNK1 and MAPK9/JNK2, and this kinase itself is phosphorylated and activated by MAP kinase kinase kinases including MAP3K1/MEKK1, MAP3K2/MEKK2, MAP3K3/MEKK5, and MAP4K2/GCK.
For modeling interactions between potential anti-inflammatory polypeptides and MKK7, any MKK7 protein sequence can be used. The MKK7 sequence used for modeling generally folds into a functional MKK7 protein or a functional fragment thereof. The MKK7 protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human MKK7 is selected if the intended subject is a human, a bovine MKK7 is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the human MKK7 sequence (NCBI Reference Sequence: NP_001284484.1).








(SEQ ID NO: 417)



MAASSLEQKLSRLEAKLKQENREARRRIDLNLDISPQRPRPIIVITLSPAPAPSQRAALQLPLAN



 


DGGSRSPSSESSPQHPTPPARPRHMLGLPSTLFTPRSMESIEIDQKLQEIMKQTGYLTIGGQRYQ


 




















ISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKL


 


LEHSFIKRYETLEVDVASWFKDVMAKTESPRTSGVLSQPHLPFFR.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the active site on MKK7 and/or interfere with or block the ability of MKK7 to bind to its receptor. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human MKK7 (SEQ ID NO: 166) selected from the group consisting of Met-142, Val-150, Lys-152, Lys-165, Met-212, Met-215, Thr-217, Lys-221, Leu-266, Cys-276 and Asp-277, or the equivalent amino acid residue(s) in a MKK7 protein of another species. Alternatively, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human MKK7 (SEQ ID NO: 166) selected from the group consisting of Met-142, Val-150, Lys-165, Met-212, Met-215, Leu-266 and Asp-277, or the equivalent amino acid residue(s) in a MKK7 protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human MKK7 (SEQ ID NO: 166) with an affinity of at least −600 kcal/mol, and in certain embodiments at least −650, −700, −750, −800, −850, −900, −925, −950, −1,000 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
For modeling interactions between potential anti-inflammatory polypeptides and ribonucleotide reductase (RNR), any RNR protein sequence can be used. The RNR sequence used for modeling generally folds into a functional RNR protein or a functional fragment thereof. The RNR protein sequence used for modeling can be selected based on the type of subject that the anti-inflammatory polypeptide is intended to treat (e.g., a human RNR is selected if the intended subject is a human, a bovine RNR is selected if the intended subject is a cow, etc.). The sequence used for modeling can be the yeast RNR sequence (GenBank: AJV34160.1).








(SEQ ID NO: 418)



MYVYKRDGRKEPVQFDKITARISRLCYGLDPKHIDAVKVTQRIISGVYEGVTTIELDNLAAETCA



 


YMTTVHPDYATLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDK


 


LNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETYNLMSL


 


KYYTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGS


 


YIAGTNGTSNGLIPMIRVFNNTARYVDQGGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRA


 


RDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWY


 








TSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLR


 


LPFDSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDW


 








DLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVYIDQSHSLNLF


 


LRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQAASAAIQFTIDQKIADQATENVADISNLKRPSYM


 


PSSASYAASDFVPAAVTANATIPSLDSSSEASREASPAPTGSHSLTKGMAELNVQESKVEVPEVP


 


APTKNEEKAAPIVDDEETEFDIYNSKVIACAIDNPEACEMCSG.






An anti-inflammatory polypeptide can be identified, for example, based on its ability to bind to the active site on RNR and/or interfere with or block the ability of RNR to bind to its receptor. For example, the anti-inflammatory polypeptide can bind to at least one amino acid residue of human RNR (SEQ ID NO: 168) selected from the group consisting of Asn-426, Leu-427, Cys-428, Glu-430, Met-606, Pro-608 and Ala-610, or the equivalent amino acid residue(s) in a RNR protein of another species.
In certain embodiments, an anti-inflammatory polypeptide can bind to human RNR (SEQ ID NO: 168) with an affinity of at least −600 kcal/mol, and in certain embodiments at least −650, −700, −750, −800, −850, −900, −925, −950, −1,000 kcal/mol, or greater. The requisite binding affinity can correspond to a binding affinity that can be detected in vitro or in vivo. Alternatively, the requisite binding affinity can correspond to a binding affinity that can be detected in silico, e.g., using the ClusProTM algorithm.
Excluded Polypeptides
Compositions of the invention optionally exclude polypeptides that satisfy the Structural Algorithm described herein which may have been known in the art prior to the filing of the present application. Various publications have discussed synthetic and naturally occurring anti-inflammatory polypeptides and/or polypeptides having a striapathic sequence including, for example, US Patent Application Nos. 2012/0270770 and 2003/0109452, and U.S. Pat. No. 6,559,281. Accordingly, one or more polypeptides and/or uses of such polypeptides described in such publications can be excluded from the scope of the presently disclosed composition and/or methods. For example, peptide RP-398 (SEQ ID NO: 155) is optionally excluded from compositions disclosed herein and/or methods of using such compositions. Moreover, any of the polypeptides disclosed in Tables 3-9, below, can be optionally excluded from compositions disclosed herein and/or methods of using such compounds.
Linked Anti-Inflammatory Polypeptide Combinations
The invention further includes any two anti-inflammatory polypeptides which have been linked together. The linkage can be formed by a peptide linker, such as a Gly-Gly-Gly (GGG), Gly-Gly-Gly-Arg (GGGR; SEQ ID NO: 412), Gly-Pro-Gly (GPG), or Gly-Pro-Gly-Arg (GPGR; SEQ ID NO: 413) sequence, that links the C-terminal end of a first anti-inflammatory polypeptide to the N-terminal end of a second anti-inflammatory polypeptide. Alternatively, the linkage can be a peptoid linker (e.g., a poly N-substituted version of any of the foregoing peptide linkers), a polymer containing g-amino acids (e.g., corresponding to any of the foregoing peptide linkers), or a non-peptide, chemical linker. The linked anti-inflammatory polypeptides can be any of the polypeptides disclosed herein (e.g., in Tables 3-9), and can include the same polypeptide being linked to form a homodimer or different polypeptides being linked to form a heterodimer. Techniques for linking peptides via peptide and non-peptide linkers are well known in the art, and the inventive polypeptide combinations are intended to encompass all such linkages.
Anti-inflammatory polypeptides can be linked to another molecule via a biodegradable linkage, such as a disulfide bond. The disulfide bond can be mediated by the sulfhydryl group of a cysteine residue found in the anti-inflammatory polypeptide and a sulfhydryl group in the other molecule. The cysteine residue can be, e.g., located at either the C-terminal or N-terminal end of anti-inflammatory polypeptide. Specific examples include RP-433 (FAKKFAKKFKC, SEQ ID NO: 384) and RP-434 (KFRKAFKRFFC; SEQ ID NO: 385), though any of the peptides disclosed herein could be similarly modified. Using a disulfide linkage of this sort, polypeptides of the invention can be conveniently linked to various types of useful molecules. For example, the linkage can be with another anti-inflammatory polypeptide (which optionally includes a C-terminal or N-terminal cysteine residue), a fluorescent label (e.g., Dylight 350), a chemotherapeutic agent (e.g., a taxol derivative formed by adding a sulfhydral group to an appropriate site on the taxol ring structure, followed by oxidation with a cysteine-containing peptide of the invention), or the like.
Linked anti-inflammatory polypeptides (e.g., homo- or heterodimers) can bind to a target molecule (e.g., a target protein, such as a pro-inflammatory signaling protein) with a binding energy that is greater than that of either monomer polypeptide alone. Thus, for example, the energy of binding of linked anti-inflammatory polypeptides to an NF-kB Class II protein (e.g., RelB) can be at least −700 kcal/mol, and in certain embodiments at least −750, −800, −900, −1000, −1100, −1200, −1250, −1300, −1350, −1400, −1425, −1450, −1475, −1500, −1525, −1550, −1575, −1600 kcal/mol, or greater. The energy of binding can be determined, e.g., in silico, in vitro, or in vivo, using methods well-known in the art (e.g., using the ClusProTM algorithm).
Modified Polypeptides
Embodiments of the invention include the modification of any of the anti-inflammatory polypeptides of the invention, by chemical or genetic means. Examples of such modification include construction of peptides of partial or complete sequence with non-natural amino acids and/or natural amino acids in L or D forms. For example, any of the peptides disclosed herein and any variants thereof could be produced in an all-D form. Furthermore, polypeptides of the invention can be modified to contain carbohydrate or lipid moieties, such as sugars or fatty acids, covalently linked to the side chains or the N- or C-termini of the amino acids. In addition, the polypeptides of the invention can be modified to enhance solubility and/or half-life upon being administered. For example, polyethylene glycol (PEG) and related polymers have been used to enhance solubility and the half-life of protein therapeutics in the blood. Accordingly, the polypeptides of the invention can be modified by PEG polymers and the like. Polypeptides of the invention can also be modified to contain sulfur, phosphorous, halogens, metals, etc. And amino acid mimics can be used to produce polypeptides of the invention (e.g., having a structure based on the Structural Algorithm or a structure similar to any of the anti-inflammatory polypeptides disclosed herein). In certain embodiments, polypeptides of the invention that include amino acid mimics have enhanced properties, such as resistance to degradation. For example, polypeptides of the invention can include one or more (e.g., all) peptoid monomers.
Compositions
Compositions of the invention include an anti-inflammatory polypeptide that satisfies the structural algorithm described herein. For example, the anti-inflammatory polypeptide can have a striapathic region having a sequence that conforms with any one of Formulas I-LIV. In particular, the anti-inflammatory polypeptide can be any of the polypeptides listed in Table 3-9, or a fragment or variant thereof. Typically, the anti-inflammatory polypeptide included in the compositions of the invention will be a synthetic polypeptide (e.g., made by chemical synthesis and/or produced recombinantly).
The compositions of the invention can include a single anti-inflammatory polypeptide, or combinations thereof. The compositions can be substantially free of proteins and other polypeptides that do not satisfy the structural algorithm disclosed herein. As used herein, the term “substantially free of proteins and other polypeptides” means that less than 5% of the protein content of the composition is made up of proteins and other polypeptides that are not an anti-inflammatory polypeptide of the invention. A composition that is substantially free of non-anti-inflammatory polypeptides of the invention can have less than 4%, 3%, 2% , 1%, 0.5%, 0.1%, 0.05%, 0.01%, or less of proteins or other polypeptides that do not satisfy the structural algorithm disclosed herein. Thus, the compositions can be substantially free of blood proteins, such as serum albumin, globulins, fibrinogen, and clotting factors. Alternatively, the compositions can be substantially free of globulins, fibrinogen, and clotting factors, but can include purified or recombinantly produced serum albumin.
The compositions of the invention in certain embodiments contain an anti-inflammatory polypeptide that is not naturally found in a human or other mammal or animal. However, compositions of the invention can include an anti-inflammatory polypeptide that is naturally found in a human or other mammal or animal, provided that the composition is substantially free of biological molecules (such as non-anti-inflammatory polypeptides, nucleic acids, lipids, carbohydrates, and metabolites) that are associated with the anti-inflammatory polypeptide in vivo or co-purify with the anti-inflammatory polypeptide. As used herein, the term “substantially free of biological molecules” means that less than 5% of the dry weight of the composition is made up of biological molecules that are not anti-inflammatory polypeptides. A composition that is substantially free of such biological molecules can have less than 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, 0.01%, or less of biological molecules that are not anti-inflammatory polypeptides. Thus, for example, the composition can be substantially free of biological molecules that are abundant in the blood, such the proteins discussed above, fatty acids, cholesterol, non-protein clotting factors, metabolites, and the like. In addition, the composition can be substantially free of cells, including red blood cells, white blood cells, and platelets, and cell fragments.
The compositions of the invention can include at least 1 mg (e.g., at least 5, 10, 20, 30, 40, 50, 75, 100, 150, 200, 250, 300, 400, 500, 600, 700, 800, 900, 1000 mg, or more) of anti-inflammatory polypeptide. Thus, for example, the compositions can include an amount of anti-inflammatory polypeptide equal to about 1 mg to about 1000 mg (e.g., about 5 mg to about 900 mg, about 5 mg to about 800 mg, about 5 mg to about 700 mg, about 5 mg to about 600 mg, about 10 mg to about 500 mg, about 10 mg to about 400 mg, about 10 mg to about 300 mg, about 10 mg to about 250 mg, about 10 mg to about 200 mg, about 10 mg to about 150 mg, about 10 mg to about 100 mg, about 50 mg to about 500 mg, about 50 mg to about 400 mg, about 50 mg to about 300 mg, about 50 mg to about 250 mg, about 50 mg to about 200 mg, about 50 mg to about 150 mg, about 50 mg to about 100 mg, about 75 mg to about 500 mg, about 75 mg to about 400 mg, about 75 mg to about 300 mg, about 75 mg to about 250 mg, about 75 mg to about 200 mg, about 75 mg to about 150 mg, about 75 mg to about 100 mg, about 100 mg to about 500 mg, about 100 mg to about 400 mg, about 100 mg to about 300 mg, about 100 mg to about 250 mg, about 100 mg to about 200 mg, or any other range containing two of the foregoing endpoints).
The compositions of the invention can include a solution that contains at least 1 mg/ml (e.g., at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 mg/ml or more) of an anti-inflammatory polypeptide. Thus, for example, the compositions can include a solution having an anti-inflammatory polypeptide concentration of about 1 mg/ml to about 1000 mg/ml (e.g., about 5 mg/ml to about 900 mg/ml, about 5 mg/ml to about 800 mg/ml, about 5 mg/ml to about 700 mg/ml, about 5 mg/ml to about 600 mg/ml, about 5 mg/ml to about 500 mg/ml, about 10 mg/ml to about 500 mg/ml, about 10 mg/ml to about 400 mg/ml, about 10 mg/ml to about 300 mg/ml, about 10 mg/ml to about 250 mg/ml, about 10 mg/ml to about 200 mg/ml, about 10 mg/ml to about 150 mg/ml, about 10 mg/ml to about 100 mg/ml, about 50 mg/ml to about 500 mg/ml, about 50 mg/ml to about 400 mg/ml, about 50 mg/ml to about 300 mg/ml, about 50 mg/ml to about 250 mg/ml, about 50 mg/ml to about 200 mg/ml, about 50 mg/ml to about 150 mg/ml, about 50 mg/ml to about 100 mg/ml, about 75 mg/ml to about 500 mg/ml, about 75 mg/ml to about 400 mg/ml, about 75 mg/ml to about 300 mg/ml, about 75 mg/ml to about 250 mg/ml, about 75 mg/ml to about 200 mg/ml, about 75 mg/ml to about 150 mg/ml, about 75 mg/ml to about 100 mg/ml, about 100 mg/ml to about 500 mg/ml, about 100 mg/ml to about 400 mg/ml, about 100 mg/ml to about 300 mg/ml, about 100 mg/ml to about 250 mg/ml, about 100 mg/ml to about 200 mg/ml, about 10 mg/ml to about 150 mg/ml, or any other range containing two of the foregoing endpoints).
The compositions of the invention include pharmaceutical compositions. Such pharmaceutical compositions can comprise one or more anti-inflammatory polypeptides and a pharmaceutically acceptable carrier. Pharmaceutical compositions can further include a protein other than an anti-inflammatory polypeptide of the invention and/or a chemotherapeutic agent. The other protein can be a therapeutic agent, such as a therapeutic antibody. The therapeutic protein or antibody can have anti-inflammatory properties or other properties that the anti-inflammatory polypeptides of the invention augment or are augmented by. Alternatively, the other protein can be a carrier protein, such as serum albumin (e.g., HSA). The serum albumin (e.g., HAS, BSA, etc.) can be purified or recombinantly produced. By mixing the anti-inflammatory polypeptide(s) in the pharmaceutical composition with serum album, the anti-inflammatory polypeptides can be effectively “loaded” onto the serum albumin, allowing a greater amount of anti-inflammatory polypeptide to be successfully delivered to a site of inflammation. The chemotherapeutic agent can be, for example, an anti-cancer chemotherapeutic agent. Such chemotherapeutic agents include, but are not limited to, Gemcitabine, Docetaxel, Bleomycin, Erlotinib, Gefitinib , Lapatinib, Imatinib, Dasatinib, Nilotinib, Bosutinib, Crizotinib, Ceritinib, Trametinib, Bevacizumab, Sunitinib, Sorafenib, Trastuzumab, Ado-trastuzumab emtansine, Rituximab, Ipilimumab, Rapamycin, Temsirolimus, Everolimus, Methotrexate, Doxorubicin, Abraxane, Folfirinox, Cisplatin, Carboplatin, 5-fluorouracil, Teysumo, Paclitaxel, Prednisone, Levothyroxine, and Pemetrexed.
Methods
The anti-inflammatory polypeptides of the invention provide powerful tools for reducing inflammation and/or treating conditions associated with excessive inflammation (whether acute or chronic). As used herein, the terms “treat,” “treating,” and similar words shall mean stabilizing, reducing the symptoms of, preventing the occurrence of, or curing a medical condition.
Accordingly, the invention provides methods of reducing the expression level and/or activity of at least one (e.g., 2, 3, 4, 5, or more) pro-inflammatory cytokine(s) at a site of inflammation in a subject. The methods include administering an anti-inflammatory polypeptide of the invention (or, for example, a pharmaceutical composition comprising an anti-inflammatory polypeptide) to the subject. The pro-inflammatory cytokine can be selected from the group consisting of NF-kB, TNF α, IL-1, IL-6, IL-8, IL-12, IL-17, IL-23, MCP-1, MMP-1, and MMP-9. The reduction can be a reduction of at least 10% (e.g., 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, or more) in the expression or activity of the cytokine.
The invention also provides methods of inhibiting an increase in the expression level and/or activity of at least one (e.g., 2, 3, 4, 5, or more) pro-inflammatory cytokine(s) at a potential site of inflammation in a subject. The methods include administering an anti-inflammatory polypeptide of the invention (or, for example, a pharmaceutical composition comprising an anti-inflammatory polypeptide) to the subject. The pro-inflammatory cytokine can be selected from the group consisting of NF-kB, TNFα, IL-1, IL-6, IL-8, IL-12, IL-17, IL-23, MCP-1, MMP-1, and MMP-9. The methods can inhibit increased cytokine expression and/or activity by limiting such increases to no more than 20% (e.g., 15%, 12.5%, 10%, 7.5%, 5%, 4%, 3%, 2%, 1%, or less).
The invention also provides a method of treating or preventing a condition associated with chronic inflammation. The condition associated with chronic inflammation can be irritable bowel disease, ulcerative colitis, colitis, Crohn's disease, idiopathic pulmonary fibrosis, asthma, keratitis, arthritis, osteoarthritis, rheumatoid arthritis, auto-immune diseases, a feline or human immunodeficiency virus (FIV or HIV) infection, cancer, age-related inflammation and/or stem cell dysfunction (e.g., age-related increases in Nlrp3 expression, age-related elevation of SOCS3 in muscle stem cells, etc.), graft-versus-host disease (GVHD), keloids, scleroderma, obesity, diabetes, diabetic wounds, other chronic wounds, atherosclerosis, multiple sclerosis, Parkinson's disease, Alzheimer's disease, macular degeneration, gout, gastric ulcers, gastritis, mucositis, toxoplasmosis, and chronic viral or microbial infections (e.g., such as chronic bacterial or protozoan infections). The methods includes administering an anti-inflammatory polypeptide of the invention (or, for example, a pharmaceutical composition comprising an anti-inflammatory polypeptide) to a subject suffering from or likely to develop the condition.
The invention also provides methods of treating or preventing fibrosis. The fibrosis can be, for example, pulmonary fibrosis, dermal fibrosis, hepatic fibrosis, renal fibrosis, or fibrosis caused by ionizing radiation. The methods include administering an anti-inflammatory polypeptide of the invention (or, for example, a pharmaceutical composition comprising an anti-inflammatory polypeptide) to a subject suffering from or likely to develop fibrosis.
The invention also provides methods of treating cancer. The cancer can be colon cancer, breast cancer, leukemia, lymphoma, ovarian cancer, prostate cancer, liver cancer, lung cancer, testicular cancer, cervical cancer, bladder cancer, endometrial cancer, kidney cancer, melanoma, cancers of the thyroid or brain, or ophthalmic cancer. The methods include administering an anti-inflammatory polypeptide of the invention (or, for example, a pharmaceutical composition comprising an anti-inflammatory polypeptide) to a subject suffering from cancer.
For any of the foregoing methods, the subject can be an animal, such as a domesticated animal (e.g., a horse, cow, pig, goat, sheep, rabbit, chicken, turkey, duck, etc.), a pet (e.g., a dog, cat, rabbit, hamster, gerbil, bird, fish, etc.), a lab animal (e.g., a mouse, rat, monkey, chimpanzee, owl, fish, etc.), a zoo animal (e.g., a gorilla, orangutan, chimpanzee, monkey, elephant, camel, zebra, boar, lion, tiger, giraffe, bear, bird, etc.), a wild animal (e.g., a deer, wolf, mountain lion, bird, etc.), or a human.
In conjunction with any of the foregoing methods, the anti-inflammatory polypeptide(s) can be administered at a dose and frequency that depends on the type of animal, the size of the animal, and the condition being treated. Typically, the anti-inflammatory polypeptide is administered daily (or every other day, or weekly), in an amount between about 1 mg and about 1000 mg (e.g., about 5 mg to about 900 mg, about 5 mg to about 800 mg, about 5 mg to about 700 mg, about 5 mg to about 600 mg, about 10 mg to about 500 mg, about 10 mg to about 400 mg, about 10 mg to about 300 mg, about 10 mg to about 250 mg, about 10 mg to about 200 mg, about 10 mg to about 150 mg, about 10 mg to about 100 mg, about 50 mg to about 500 mg, about 50 mg to about 400 mg, about 50 mg to about 300 mg, about 50 mg to about 250 mg, about 50 mg to about 200 mg, about 50 mg to about 150 mg, about 50 mg to about 100 mg, about 75 mg to about 500 mg, about 75 mg to about 400 mg, about 75 mg to about 300 mg, about 75 mg to about 250 mg, about 75 mg to about 200 mg, about 75 mg to about 150 mg, about 75 mg to about 100 mg, about 100 mg to about 500 mg, about 100 mg to about 400 mg, about 100 mg to about 300 mg, about 100 mg to about 250 mg, about 100 mg to about 200 mg, or any other range containing two of the foregoing endpoints). The daily dose can be administered once during the day, or broken up into smaller doses that are taken at multiple time points during the day. For a human (and other similarly-sized mammals), a dose of 5 mg/kg every other day can be administered. The anti-inflammatory polypeptide can be administered for a fixed period of time (e.g., for 2-3 weeks), at intervals (e.g., administer polypeptide for 2-3 weeks, wait 2-3 weeks, then repeat the cycle), or until such time as the pro-inflammatory cytokine levels have been reduced or stabilized, the chronic inflammatory condition or fibrosis has ameliorated, or the cancer has gone into remission.
The administration of the anti-inflammatory polypeptides (or pharmaceutical compositions comprising such polypeptides) in conjunction with any of the foregoing methods can be performed intravenously, intraperitoneally, parenteral, orthotopically, subcutaneously, topically, nasally, orally, sublingually, intraocularly, by means of an implantable depot, using nanoparticle-based delivery systems, microneedle patch, microspheres, beads, osmotic or mechanical pumps, and/or other mechanical means.
In conjunction with any of the foregoing methods, the anti-inflammatory polypeptides (or pharmaceutical compositions comprising such polypeptides) can be administered in combination with another drug designed to reduce or prevent inflammation, treat or prevent chronic inflammation or fibrosis, or treat cancer. In each case, the anti-inflammatory polypeptide can be administered prior to, at the same time as, or after the administration of the other drug. For the treatment of cancer, the anti-inflammatory polypeptide(s) can be administered in combination with a chemotherapeutic agent selected from the group consisting of steroids, anthracyclines, thyroid hormone replacement drugs, thymidylate-targeted drugs, Chimeric Antigen Receptor/T cell therapies, and other cell therapies. Specific chemotherapeutic agents include, for example, Gemcitabine, Docetaxel, Bleomycin, Erlotinib, Gefitinib, Lapatinib, Imatinib, Dasatinib, Nilotinib, Bosutinib, Crizotinib, Ceritinib, Trametinib, Bevacizumab, Sunitinib, Sorafenib, Trastuzumab, Ado-trastuzumab emtansine, Rituximab, Ipilimumab, Rapamycin, Temsirolimus, Everolimus, Methotrexate, Doxorubicin, Abraxane, Folfirinox, Cisplatin, Carboplatin, 5-fluorouracil, Teysumo, Paclitaxel, Prednisone, Levothyroxine, and Pemetrexed.
Alternatively, for the methods of treating cancer, the anti-inflammatory polypeptide(s) (or pharmaceutical compositions comprising such polypeptides) can be administered in combination with radiation therapy. Again, the anti-inflammatory polypeptide(s) can be administered prior to, or after the administration of the radiation therapy.
Any of the foregoing methods of the invention further include a step of assessing the efficacy of the therapeutic treatment. Because the anti-inflammatory polypeptides of the invention have a demonstrable ability to reduce tissue inflammation and suppress the excessive production of inflammatory mediators such as IL-1, IL-6, IL-12, and TNFα, both in tissues and in serum (data not shown), the efficacy of the therapeutic treatment can be assessed by measuring the levels of such cytokines (e.g., in the serum) to determine whether the levels have responded appropriately to the treatment. Depending on the cytokine levels, the dosage of anti-inflammatory polypeptide(s) can be adjusted up or down, as needed.
EXAMPLES
Example 1
Peptide Designs
Polypeptides were designed in silico to include a striapathic region of alternating Xm and Yn modules, with each Xm module having one to five hydrophilic amino acid residues and each Yn module having one to five hydrophobic residues.
Initial designs focused on polypeptides consisting of a striapathic region having a total length of around 10 amino acid residues, with each Xm module having one or two hydrophilic amino acid residues and each Yn module having one or two hydrophobic residues, and with the ratio of hydrophobic to hydrophilic amino acid residues being around 1:1. Such polypeptides were predicted to have an amphipathic, helical secondary structure, with a hydrophobic surface on one side of the helix and a hydrophilic surface on the opposite side of the helix.
Additional peptide designs were subsequently generated that maintained a total length of around 10 amino acid residues, but expanded the number of possible amino acid residues in a hydrophilic or hydrophobic module from two to three and varied the hydrophobic to hydrophilic ratio. For example, larger hydrophobic modules having three hydrophobic amino acid residues were coupled with shorter hydrophilic modules having one hydrophilic amino acid residue, giving rise to polypeptides predicted to have a stronger hydrophobic character. Such peptides were predicted to maintain an amphipathic, helical secondary structure, but have a larger hydrophobic surface on one side of the helix and a correspondingly smaller hydrophilic surface on the other side. Similarly, larger hydrophilic modules having three hydrophilic amino acid residues were coupled with shorter hydrophobic modules having one hydrophobic amino acid residue, giving rise to peptides having a stronger hydrophilic character. Such peptides were also predicted to maintain an amphipathic, helical secondary structure, but have a larger hydrophilic surface on one side of the helix and a correspondingly smaller hydrophobic surface on the other side.
Other peptide designs included: polypeptides having modules of four or five hydrophilic amino acid residues and/or four or five hydrophobic; polypeptides having a total length of around 10 amino acid residues but lacking hydrophobic amino acid residues; polypeptides having hydrophilic and hydrophobic modules each consisting of a single amino acid residue; and proline-rich polypeptides. Finally, larger polypeptides comprising two of the smaller peptide designs were also generated.
Exemplary polypeptides designed as described above are presented in Tables 3-9, below. To provide greater clarity into the types of polypeptides that have been developed, the peptides have been organized into Classes. Typically, the striapathic region of a specific Class of polypeptides shares a common sequence of hydrophobic and hydrophilic modules that is at least six or seven amino acid residues long. However, because the data indicates that polypeptides that have the same sequence but reversed N-terminal to C-terminal orientation have surprisingly similar anti-inflammatory activities, efforts have been made to keep such polypeptides in the same Class. Accordingly, some polypeptides have been grouped into the same Class even though the common sequence of hydrophobic and hydrophilic modules is less than six amino acid residues long. In addition, some of the polypeptides could have been grouped differently because they contain the common sequence of hydrophobic and hydrophilic modules of more than one Class. Thus, while providing a helpful framework for organizing the polypeptides around structural and functional similarities, the classification system does not capture all aspects of the relationships between different polypeptides.
Table 3 presents various Class I polypeptides, which have a striapathic region that includes a sequence corresponding to Formula I (i.e., Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c). Two different types of Class I polypeptides are presented in Table 3: peptides that have a striapathic region consisting of a sequence corresponding to Formula II (i.e., Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c-X2a-Y3a-X3a); and peptide that have a striapathic region consisting of a sequence corresponding to Formula III (i.e., X2a-Y3a-X3a-Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c). In addition, a peptide having a striapathic region having a sequence corresponding to Formula I, but not Formulas II or III, is presented.







TABLE 3 







Class I Polypeptides













RelB






Binding E

SEQ


RP #
Sequence
(kCal/mol)
Formula
ID NO:














394
NFNFFFRFFF
−1,286.6
III
33


 


108
WWWRWWWEWQ
−1,278.0
II
34


 


109
EFNFFFRFFF
−1,247.7
III
35


 


110
DFEFFFRFFF
−1,232.0
III
36


 


111
QFEFFFRFFF
−1,226.8
III
37


 


112
EFEFFFRFFF
−1,216.0
III
38


 


113
FFFRFFFEFQ
−1,208.9
II
39


 


114
FFFRFFFEFE
−1,176.3
II
40


 


115
FFFRFFFEFD
−1,172.3
II
41


 


116
FFFRFFFNFE
−1,162.6
II
42


 


117
FFFRFFFDFE
−1,147.7
II
43


 


118
FFFRFFFNFN
−1,139.9
II
44


 


119
FFFHFFFEFQ
−1,135.4
II
45


 


120
FFFHFFFNFE
−1,126.4
II
46


 


121
FFFHFFFEFN
−1,126.4
II
47


 


122
EFNFFFHFFF
−1,125.1
III
48


 


123
FFFRFFFEFN
−1,124.5
II
49


 


125
FFFHFFFEFE
−1,115.4
II
50


 


126
QFEFFFHFFF
−1,114.4
III
51


 


127
FFFHFFFEFD
−1,114.3
II
52


 


128
FFFHFFFDFE
−1,111.4
II
53


 


129
YYYRYYYEYQ
−1,110.2
II
54


 


130
NFEFFFHFFF
−1,109.1
III
55


 


131
FFFKFFFKFE
−1,107.0
II
56


 


133
EFDFFFRFFF
−1,103.4
III
57


 


135
FFFHFFFDFD
−1,102.4
II
58


 


136
FFFHFFFNFN
−1,100.4
II
59


 


137
FFFRFFFDFD
−1,100.3
II
60


 


138
FFFKFFFKFN
−1,098.2
II
61


 


139
FFFKFFFEFE
−1,095.1
II
62


 


140
FFFEFFFKFE
−1,091.8
II
63


 


141
FFFQFFFQFQ
−1,088.8
II
64


 


143
FFFKFFFQFQ
−1,084.4
II
65


 


144
FFFKFFFNFN
−1,083.5
II
66


 


145
FFFNFFFNFN
−1,083.3
II
67


 


146
FFFKFFFEFQ
−1,082.6
II
68


 


148
FFFKFFFKFQ
−1,080.0
II
69


 


149
FFFKFFFQFK
−1,079.6
II
70


 


150
FFFKFFFKFD
−1,077.4
II
71


 


152
FFFKFFFDFD
−1,074.5
II
72


 


153
FFFNFFFKFN
−1,074.2
II
73


 


154
FFFDFFFDFD
−1,073.5
II
74


 


155
FFFKFFFEFK
−1,073.3
II
75


 


156
FFFKFFFDFK
−1,072.6
II
76


 


157
FFFEFFFEFE
−1,070.8
II
77


 


158
FFFDFFFKFD
−1,070.7
II
78


 


159
FFFKFFFKFK
−1,070.7
II
79


 


160
FFFEFFFKFK
−1,069.7
II
80


 


161
FFFQFFFKFK
−1,069.6
II
81


 


162
FFFKFFFNFK
−1,069.2
II
82


 


163
FFFNFFFKFK
−1,066.7
II
83


 


164
FFFQFFFKFQ
−1,062.5
II
84


 


165
FFFDFFFKFK
−1,061.9
II
85


 


179
LLLRLLLELQ
−966.7
II
86


 


395
FVFKFVFKFV
−917.2
I
87


 


211
CCCRCCCECQ
−818.2
II
88


 


230
MMMRMMMEMQ
−774.6
II
89


 


232
VVVRVVVEVQ
−771.6
II
90


 


258
IIIRIIIEIQ
−699.2
II
91


 


267
GGGRGGGEGQ
−640.4
II
92


 


268
PPPRPPPEPQ
−627.1
II
93


 


271
TTTRTTTETQ
−614.4
II
94


 


273
AAARAAAEAQ
−609.4
II
95


 


280
AAAKAAAKAA
−556.0
II
96


 


281
AAAEAAAEAE
−541.6
II
97


 


287
SSSRSSSESQ
−499.3
II
98









Table 4 presents some quasi-Class I polypeptides. These peptides include a sequence similar to the striapathic sequence of Formula II (i.e., Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c-X2a-Y3a-X3a), but the hydrophobic amino acid residues have all been replaced with a particular hydrophilic amino acid residue.







TABLE 4 







Quasi-Class I Polypeptides













RelB






Binding E

SEQ


RP #
Sequence
(kCal/mol)
Formula
ID NO:














173
HHHRHHHEHQ
−1,002.2
II*
 99


 


195
RRRRRRRERQ
−855.2
II*
100


 


275
QQQRQQQEQQ
−575.6
II*
101


 


276
EEEREEEEEQ
−569.5
II*
102


 


284
NNNRNNNENQ
−522.7
II*
103


 


288
DDDRDDDEDQ
−463.6
II*
104


 


290
KKKRKKKEKQ
−423.7
II*
105





*These peptides do not comply with the sequence requirements of Formula II, but instead represent an “all hydrophilic” variation on the sequence requirements of Formula II.






Table 5 presents various Class II, Sub-class 1 polypeptides. The presented peptides have a striapathic region consisting of a sequence corresponding to Formula X (i.e., Y1a-Y1b-X1a-X1b-Y2a-Y2b-X2a-X2b-Y3a-X3a), or a striapathic region consisting of a sequence corresponding to Formula XI (i.e., X1a-Y1a-X2a-X2b-Y2a-Y2b-X3a-X3b-Y3a-Y3b).







TABLE 5 







Class II, Sub-class 1 Polypeptides













RelB






Binding E

SEQ


RP #
Sequence
(kCal/mol)
Formula
ID NO:














124
FFQKFFKRWR
−1,121.3
X
106


 


132
FFRKFFKRFR
−1,104.8
X
107


 


134
RFRKFFKRFF
−1,103.3
XI
108


 


142
RFRKFFKQFF
−1,085.5
XI
109


 


147
FFQKFFKRFR
−1,080.3
X
110


 


151
RWRKFFKQFF
−1,077.0
XI
111


 


166
FFEHFWKEFN
−1,044.8
X
112


 


167
FFQHFWKQFN
−1,024.9
X
113


 


168
QFNHFFKEFF
−1,022.8
XI
114


 


169
FFDKFFHDFQ
−1,014.2
X
115


 


170
QFDHFFKDFF
−1,011.9
XI
116


 


171
FFEKFFHNFQ
−1,009.9
X
117


 


172
NFEKWFHEFF
−1,007.9
XI
118


 


175
LFRRAFKQLD
−989.5
X
119


 


177
NFQKWFHQFF
−976.3
XI
120


 


182
KFRKAFKRFF
−944.8
XI
121


 


183
FFRKFAKRFK
−933.2
X
122


 


185
FFKKFFKKFK
−920.6
X
123


 


186
KFKKFFKKFF
−919.6
XI
124


 


424
KARKAFKRFF
−910.2
XI
125


 


190
WVKDAMQHLD
−888.7
X
126


 


194
FFKKFAKKFK
−859.1
X
127


 


198
FAEKFFKNFK
−850.4
X
128


 


199
KFNKFFKEAF
−847.1
XI
129


 


200
FAKQFFNKFK
−846.0
X
130


 


201
KFNKAFKQAF
−837.8
XI
131


 


202
KFNKAFKQAF
−837.8
XI
132


 


204
FAQKFFKDFK
−835.9
X
133


 


206
FAEEFAEEFE
−823.1
X
134


 


207
KFKKFFKKAF
−820.7
XI
135


 


209
KFKNFFQKAF
−819.1
XI
136


 


210
KFKNFFQKAF
−819.1
XI
137


 


212
FAKQFANKFK
−817.9
X
138


 


213
KFKNAFQKAF
−815.2
XI
139


 


214
KFKNAFQKAF
−815.2
XI
140


 


215
FAKKFFKKFK
−814.0
X
141


 


216
KFKKAFKKFF
−811.2
XI
142


 


218
FAEKFAEKFE
−807.6
X
143


 


219
DLHQMADKVW
−807.6
XI
144


 


425
KARKAAKRFF
−800.3
XI
145


 


225
FAKNFAKKFK
−794.0
X
146


 


227
FAEKFAKNFK
−786.6
X
147


 


233
KFKKAFKKAF
−771.2
XI
148


 


234
FAKNFAKNFK
−769.8
X
149


 


235
FAKEFAKEFE
−768.9
X
150


 


236
KFDKAFKQAF
−766.2
XI
151


 


237
KFDKAFKQAF
−766.2
XI
152


 


238
FAEKFAKKFK
−765.1
X
153


 


239
FAEKFAEKFK
−764.2
X
154


 


398
FAKKFAKKFK
−760.3
X
155


 


241
FAKNFAKNFN
−758.7
X
156


 


242
FAQKFAKNFK
−758.6
X
157


 


243
FANNFANNFN
−755.2
X
158


 


244
FANNFANNFN
−755.2
X
159


 


245
FANKFANKFN
−754.0
X
160


 


246
FANKFAKKFK
−752.2
X
161


 


247
FAQKFAKDFK
−750.7
X
162


 


250
FAKEFAKEFK
−745.7
X
163


 


251
FANKFANKFK
−739.7
X
164


 


252
KFDKFFKQAF
−739.1
XI
165


 


253
KFDKFFKQAF
−739.1
XI
166


 


254
KFNKAFKEAF
−738.4
XI
167


 


255
KFNKAFKEAF
−738.4
XI
168


 


256
FAKEFAKKFK
−702.8
X
169


 


426
KARKAAKRAF
−634.5
XI
170


 


427
KARKAAKRAA
−578.1
XI
171


 


285
AAEEAAEEAE
−511.6
X
172


 


387
AAKKAAKKAK
−301.6
X
173









Table 6 presents polypeptides that fall into a variety of different Classes, including: Class II peptides (having a striapathic region that includes a sequence corresponding to any of Formulas VI to XVI); Class II, Sub-class 2 (having a striapathic region that includes a sequence corresponding to Formulas VIII and XII); Class II, Sub-class 3 (having a striapathic region that includes a sequence corresponding to Formula IX); Class II, Sub-class 4 (having a striapathic region that includes a sequence corresponding to Formulas XIV and XV); Class II, Sub-class 5 (having a striapathic region that includes a sequence corresponding to Formulas XIII and XVI); Class III peptides (having a striapathic region that includes a sequence corresponding to any of Formulas XVII to XX); Class III, Sub-class 1 peptides (having a striapathic region that includes a sequence corresponding to Formulas XIX or XX); Class IV peptides (having a striapathic region that includes a sequence corresponding to Formulas IV and V); Class V peptides (having a striapathic region that includes a sequence corresponding to Formula XXI); Class VI peptides (having a striapathic region that includes a sequence corresponding to Formulas XXII and XXIII); Class VII peptides (having a striapathic region that includes a sequence corresponding to any of Formulas XXIV to XXVI); Class VIII peptides (having a striapathic region that includes a sequence corresponding to any of Formulas XXVII to XXXII); Class VIII, Sub-class 3 and 4 peptides (having a striapathic region that includes a sequence corresponding to Formulas XXXI and XXXII, respectively); Class IX peptides (having a striapathic region that includes a sequence corresponding to any of Formulas XXXIII to XXXVIII); Class IX, Sub-class 3 and 4 peptides (having striapathic regions that include a sequence corresponding to Formulas XXXVII and XXXVIII, respectively); and Class XIII (having a striapathic region that includes a sequence corresponding to Formula L). Because polypeptides of Class VIII, Sub-class 3 and Class IX, Sub-class 3 share the same sequence of hydrophobic and hydrophilic modules, but reversed N-terminal to C-terminal orientation, they could have been grouped into the same Class and Sub-class. Similarly, because polypeptides of Class VIII, Sub-class 4 and Class IX, Sub-class 4 share the same sequence of hydrophobic and hydrophilic modules, but reversed N-terminal to C-terminal orientation, they could have been grouped into the same Class and Sub-class.







TABLE 6 







Class II to Class IX and Class XIII Polypeptides













RelB






Binding E




RP #
Sequence
(kCal/mol)
Formula
SEQ ID NO:














396
FVKFVKFVKF
−1,039.7
L
174


 


405
KRKAFRKFFF
−1,026.6
XIV
175


 


174
LHKMYNQVW
−1,000.2
VII
176


 


176
WVQNYMKHL
−979.3
VII
177


 


178
RLVEMMRQIW
−972.2
XX
178


 


180
FLKRLLQEI
−955.9
VII
179


 


181
LRLLHRLL
−950.2
XVII
180


 


184
WVRDSMKHL
−925.6
VII
181


 


408
KFFRKKFRFA
−917.4
XXII
182


 


187
WVQRVVEKFL
−906.4
IX
183


 


416
AFFRRFKFKK
−904.1
XXV
184


 


188
LFKEVVRQVW
−902.9
IX
185


 


189
MDKIYDQVWK
−893.3
VIII
186


 


388
FVKKFVKKFV
−891.9
X
187


 


417
KKFKFRRFFA
−888.8
XXVI
188


 


191
WVRDVVRSMD
−874.1
XIX
189


 


192
ELSNIYERVW
−872.4
XX
190


 


193
WIQRMMEVLR
−866.9
XIX
191


 


404
FFFKRFAKRK
−856.7
XV
192


 


196
LHKMSDRVW
−852.4
VII
193


 


197
WVREYINSLE
−851.2
XIX
195


 


402
FFKKRFAFRK
−851.0
XXXI
196


 


203
KWVQDYIKDM
−837.0
XII
197


 


409
AFRFKKRFFK
−832.7
XXIII
198


 


205
LLRHLLRL
−830.0
XVII
199


 


208
WIKKLLESSQ
−819.7
XIX
200


 


217
DMSRVVDRVW
−810.4
XX
201


 


220
FEEEFEEEFE
−804.8
V
202


 


221
WVKNSINHL
−803.7
VII
203


 


222
LTKKGRRFC
−799.7
XXI
204


 


223
IEQLLRKLF
−796.8
VII
205


 


224
LHNISNKVW
−794.5
VII
206


 


226
CFRRGKKTL
−786.7
XXI
207


 


229
IVRRADRAAV
−781.5
XXI
208


 


231
TVERFKNLS
−771.8
XXI
209


 


240
QSSELLKKIW
−761.9
XX
210


 


248
SLNKFREVT
−750.5
XXI
211


 


249
LIKQIVKKLF
−750.5
IX
212


 


397
FAKKFAKKF
−739.3
VII
194


 


415
KKKFFF
−706.8
XXVII
213


 


257
LYKKIIKKLL
−699.8
IX
214


 


259
FKKKFKKKFK
−686.5
V
215


 


260
VAARDARRVI
−684.6
XXI
216


 


261
FLKKVIQKIL
−679.4
IX
217


 


262
LIKEIIKQVM
−668.4
IX
218


 


263
LLKKIIKKYL
−666.7
IX
219


 


264
AFFEEEAEFE
−652.2
XXXVIII
220


 


265
KKWVQDSMK
−650.1
XVIII
221


 


266
NFANKVQEVA
−644.1
XXI
222


 


269
AVEQVKNAFN
−621.1
XXI
223


 


272
MVQKIIEKIL
−613.1
IX
224


 


274
KMSDQVWKK
−595.9
XVIII
225


 


277
MVKKIIEKM
−569.2
VII
226


 


278
ALKKQVIKKI
−559.1
XVI
227


 


279
IKKIVQKKLA
−556.7
XIII
228


 


282
AFFKKKAKFK
−537.6
XXXVIII
229


 


283
MKEIIKVM
−533.1
VII
230


 


286
AEEEAEEEAE
−504.4
V
231


 


289
AKKKAKKKAK
−431.6
V
232


 


414
KKKAAA
0.0
XXVII
233









Table 7 presents polypeptide of Classes VIII through XI. All of the peptides presented in Table 7 have a striapathic region that includes a hydrophilic module having four or five hydrophilic amino acid residues and/or a hydrophobic module having four or five hydrophobic amino acid residues. Class VIII, Sub-class 1 peptides have a striapathic region that includes a sequence corresponding to Formulas XXVIII or XXIX; Class VIII, Sub-class 2 peptides have a striapathic region that includes a sequence corresponding to Formula XXX; Class IX, Sub-class 1 peptides have a striapathic region that includes a sequence corresponding to Formulas XXXIV or XXXV; Class IX, Sub-class 2 peptides have a striapathic region that includes a sequence corresponding to Formula XXXVI; Class X peptides have a striapathic region that includes a sequence corresponding to any of Formulas XXXIX to XLIII; and Class XI peptides have a striapathic region that includes a sequence corresponding to any of Formulas XLIV to XLVIII. Because polypeptides of Class VIII, Sub-class 1 and Class IX, Sub-class 1 share the same sequence of hydrophobic and hydrophilic modules, but reversed N-terminal to C-terminal orientation, they could have been grouped into the same Class and Sub-class. Similarly, because polypeptides of Class VIII, Sub-class 2 and Class IX, Sub-class 2 share the same sequence of hydrophobic and hydrophilic modules, but reversed N-terminal to C-terminal orientation, they could have been grouped into the same Class and Sub-class.







TABLE 7 







Class VIII to XI Polypeptides













RelB






Binding E




RP #
Sequence
(kCal/mol)
Formula
SEQ ID NO:














406
KRKKRFAFFF
−993.5
XXX
234


 


422
RKRKFFAFFK
−948.2
XLVIII
235


 


407
FFFAFRKKRK
−914.7
XXXVI
236


 


400
FRKKRFAFFK
−900.5
XXIX
237


 


419
FFFRRKKKFA
−881.9
XLII
238


 


401
KFFAFRKKRF
−880.1
XXXV
239


 


423
KFFAFFKRKR
−877.1
XLV
240


 


411
KKKKKFFFFF
−863.7
XXX
241


 


418
AFKKKRRFFF
−854.1
XLI
242


 


428
KRKKRAAFFF
−842.0
XXX
243


 


420
KKFFAFFRKR
−840.2
XLVI
244


 


421
RKRFFAFFKK
−835.5
XLVII
245


 


429
KRKKRAAAFF
−758.1
XXX
246


 


413
KKKKFFFF
−715.8
XXVIII
247


 


430
KRKKRAAAAF
−676.7
XXX
248


 


270
KKKAFFFAKK
−614.4
XLVII
249


 


431
KRKKRAAAAA
−544.9
XXX
250


 


410
KKKKKAAAAA
−385.3
XXX
251


 


412
KKKKAAAA
−382.8
XXVIII
252









Table 8 presents polypeptides of Class XII and Class XIV. Class XII peptides have a striapathic region that includes a sequence corresponding to Formula XLIX (i.e., Y1a-X1a-Y2a-X2a-Y3a-X3a). Class XII peptides are predicted to adopt a beta-strand secondary structure. Class XIV peptides are proline-rich peptides that have a striapathic region that includes a sequence corresponding to one of Formulas LI-LIV.







TABLE 8 







Beta-Strand and Proline-Rich Polypeptides













RelB






Binding E




RP #
Sequence
(kCal/mol)
Formula
SEQ ID NO:














393
FKFKFKFKF
−1,193.2
XLIX
253


 


391
FRFKFKFR
−1,190.8
XLIX
254


 


392
RFQFKFRF
−1,170.3
XLIX
255


 


390
FRFKFKF
−1,083.3
XLIX
256


 


389
FRFKFA
−1,009.8
XLIX
257


 


449
RRFPRPPFF
−1,116.8
LI
258


 


450
FFPPRPFRR
−1,100.0
LII
259


 


448
LYPPRPFRR
−1,059.3
LII
260


 


447
RRIPRPPYL
−1,050.5
LI
261


 


452
PFRPPPRPRF
−1,012.2
LIII
262


 


451
PRPRPPPRFF
−1,002.1
LIV
263


 


444
FFPPKPFKK
−954.8
LII
264


 


441
KKIPKPPYL
−922.1
LI
265


 


446
PFKPPPKPKP
−882.3
LIII
266


 


445
PKPKPPPKFP
−866.3
LIV
267


 


442
LYPPKPIKK
−846.6
LII
268


 


443
KKFPKPPFF
−802.8
LI
269









Table 9 presents fusion peptides, which include combinations of Class I, Class II, and/or Class III peptides linked together by a peptide bond and, optionally, a short peptide linker (e.g., a tri-glycine (GGG) linker).







TABLE 9







Peptide Combinations












RelB














Binding E

SEQ


RP #
Sequence
(kCal/mol)
Formula
ID NO:














292
EFEFFFRFFFGGGEFEFFFRFFF
−1,606.1
III + III
270


 


293
QFEFFFRFFFGGGQFEFFFRFFF
−1,602.0
III + III
271


 


294
DFEFFFRFFFGGGDFEFFFRFFF
−1,591.8
III + III
272


 


295
EFNFFFRFFFGGGEFNFFFRFFF
−1,591.8
III + III
273


 


296
FFFRFFFEFQFFFRFFFEFQ
−1,511.6
II + II
274


 


297
FFFRFFFEFQGGGFFFRFFFEFQ
−1,511.5
II + II
275


 


298
RWRKFFKRFFQFEFFFRFFF
−1,505.2
 XI + III
276


 


299
RWRKFFKRFFGGGFFFRFFFNFN
−1,501.3
XI + II
277


 


300
RFRKFFKRFFQFEFFFRFFF
−1,486.0
 XI + III
278


 


301
RFRKFFKRFFGGGFFFRFFFNFN
−1,485.0
XI + II
279


 


302
RWRKFFKRFFGGGFFFRFFFEFQ
−1,479.6
XI + II
280


 


303
RFRKFFKRFFGGGFFFRFFFEFQ
−1,476.8
XI + II
281


 


304
EFEFFFRFFFEFEFFFRFFF
−1,476.0
III + III
282


 


305
RWRKFFKRFFNFNFFFRFFF
−1,474.2
 XI + III
283


 


306
QFEFFFRFFFQFEFFFRFFF
−1,467.0
III + III
284


 


307
RWRKFFKRFFGGGNFNFFFRFFF
−1,464.2
 XI + III
285


 


308
EFNFFFRFFFEFNFFFRFFF
−1,460.5
III + III
286


 


309
RFRKFFKRFFNFNFFFRFFF
−1,458.4
 XI + III
287


 


310
FFRKFFKRFRGGGNFNFFFRFFF
−1,447.1
  X + III
288


 


311
RFRKFFKRFFGGGNFNFFFRFFF
−1,432.1
 XI + III
289


 


312
DFEFFFRFFFDFEFFFRFFF
−1,430.0
III + III
290


 


313
RWRKFFKRFFFFFRFFFEFQ
−1,427.4
XI + II
291


 


314
RFRKFFKRFFFFFRFFFEFQ
−1,425.6
XI + II
292


 


315
FFRKFFKRFRGGGFFFRFFFNFN
−1,420.6
 X + II
293


 


316
FFRKFFKRWRGGGFFFRFFFNFN
−1,417.5
 X + II
294


 


317
RFRKFFKRFFFFFRFFFNFN
−1,406.6
XI + II
295


 


318
FFRKFFKRFRFFFRFFFEFQR
−1,402.0
 X + II
296


 


291
FFEHFWKEFNGGGNFQKWFHQFF
−1,401.6
 X + XI
297


 


319
FFRKFFKRWRQFEFFFRFFF
−1,400.7
  X + III
298


 


320
RWRKFFKRFFFFFRFFFNFN
−1,397.9
XI + II
299


 


321
NFQKWFHQFFGGGFFEHFWKEFN
−1,396.0
XI + X 
300


 


322
FFRKFFKRWRGGGNFNFFFRFFF
−1,394.4
  X + III
301


 


323
FFRKFFKRWRFFFRFFFEFQR
−1,394.3
 X + II
302


 


324
FFRKFFKRWRNFNFFFRFFF
−1,393.7
  X + III
303


 


325
FFRKFFKRFRGGGFFFRFFFEFQR
−1,386.8
 X + II
304


 


326
FFRKFFKRFRQFEFFFRFFF
−1,382.8
  X + III
305


 


327
FFRKFFKRFRNFNFFFRFFF
−1,378.2
  X + III
306


 


328
RFRKFFKRFFGGGQFEFFFRFFF
−1,368.5
 XI + III
307


 


329
FFRKFFKRWRGGGFFFRFFFEFQR
−1,354.5
 X + II
308


 


330
FFRKFFKRFRGGGQFEFFFRFFF
−1,352.8
  X + III
309


 


331
FFRKFFKRWRGGGQFEFFFRFFF
−1,352.2
  X + III
310


 


332
RWRKFFKRFFGGGQFEFFFRFFF
−1,349.8
 XI + III
311


 


333
QFNHFFKEFGGGQFNHFFKEFF
−1,340.0
VII + XI 
312


 


334
FFRKFFKRFRFFFRFFFNFN
−1,337.5
 X + II
313


 


335
FFRKFFKRWRFFFRFFFNFN
−1,337.0
 X + II
314


 


336
FFEHFWKEFNGGGFFEHFWKEFN
−1,325.5
X + X
315


 


337
FFEHFWKEFGGGNFQKWFHQFF
−1,324.8
VII + XI 
316


 


338
NFQKWFHQFGGGFFEHFWKEFN
−1,317.9
VII + X  
317


 


339
FFEHFWKEFNGGGLHKMYNQVW
−1,315.4
  X + VII
318


 


340
NFQKWFHQFFGGGNFQKWFHQFF
−1,309.9
XI + XI
319


 


341
FAKKFAKKFKGGGNFQKWFHQFF
−1,308.3
 X + XI
320


 


342
FFEKFFHNFQGGGFFEKFFHNFQ
−1,304.6
X + X
321


 


343
FFQHFWKQFNGGGFFQHFWKQFN
−1,300.2
X + X
322


 


344
NFQKWFHQFFNFQKWFHQFF
−1,293.5
XI + XI
323


 


345
FAKKFAQKFKGGGNFQKWFHQFF
−1,291.9
 X + XI
324


 


346
FAKKFAKKFKGGGQFEFFFRFFF
−1,290.9
  X + III
325


 


347
QFNHFFKEFQFNHFFKEFF
−1,279.8
VII + XI 
326


 


348
FAKKFAKKFKGGGDFEFFFRFFF
−1,278.4
  X + III
327


 


349
FFEHFWKEFNGGGWVQNYMKHL
−1,268.8
  X + VII
328


 


350
FAKKFAKKFKQFEFFFRFFF
−1,268.5
  X + III
329


 


351
FFQHFWKQFNFFQHFWKQFN
−1,263.2
X + X
330


 


352
FFEHFWKEFNFFEHFWKEFN
−1,251.5
X + X
331


 


353
NFEKWFHEFFNFEKWFHEFF
−1,247.0
XI + XI
332


 


354
FAKKFAKKFKGGGQFNHFFKEFF
−1,244.6
 X + XI
333


 


355
NFEKWFHEFFGGGNFEKWFHEFF
−1,241.4
XI + XI
334


 


356
FAKKFAKKFKGGGFFFRFFFEFQ
−1,237.9
 X + II
335


 


357
FAKKFAKKFKDFEFFFRFFF
−1,235.3
  X + III
336


 


358
QFNHFFKEFFGGGQFNHFFKEFF
−1,230.0
XI + XI
337


 


359
FAKKFAKKFKGGGEFEFFFRFFF
−1,221.7
  X + III
338


 


360
FAKKFAKKFKGGGEFNFFFRFFF
−1,221.0
  X + III
339


 


361
FAKKFAKKFKGGGNFEKWFHEFF
−1,212.3
 X + XI
340


 


362
FAKKFAKKFKGGGFFEKFFHNFQ
−1,210.8
X + X
341


 


363
QFNHFFKEFFQFNHFFKEFF
−1,208.6
XI + XI
342


 


364
FFEKFFHNFQFFEKFFHNFQ
−1,207.5
X + X
343


 


365
FAKKFAKKFKEFEFFFRFFF
−1,204.2
  X + III
344


 


366
FAKKFAKKFKEFNFFFRFFF
−1,187.6
  X + III
345


 


367
FAKKFAKKFKFFEHFWKEFN
−1,168.1
X + X
346


 


368
FAKKFAKKFKFFFRFFFEFQ
−1,166.4
 X + II
347


 


369
FAKKFAKKFKLHKMYNQVW
−1,159.5
  X + VII
348


 


370
FAKKFAKKFKGGGFFEHFWKEFN
−1,140.4
X + X
349


 


371
FAKKFAKKFKGGGWVQNYMKHL
−1,130.4
  X + VII
350


 


372
FAKKFAKKFKNFQKWFHQFF
−1,126.1
 X + XI
351


 


373
FAKKFAKKFKFFQHFWKQFN
−1,119.8
X + X
352


 


374
FAKKFAKKFKGGGFFQHFWKQFN
−1,119.6
X + X
353


 


375
FAKKFAKKFKWVQNYMKHL
−1,119.2
  X + VII
354


 


376
FAKKFAKKFKQFNHFFKEFF
−1,108.3
 X + XI
355


 


377
FAKKFAKKFKGGGLHKMYNQVW
−1,100.3
  X + VII
356


 


378
FAKKFAKKFKNFEKWFHEFF
−1,081.4
 X + XI
357


 


379
FAKKFAKKFKFFEKFFHNFQ
−1,046.8
X + X
358


 


380
FAKKFAKKFKGGGAFFKKKAKFK
−950.9
      X + XXXVIII
359


 


381
AFFKKKAKFKGGGAFFKKKAKFK
−935.5
XXXVIII + XXXVIII
360


 


382
KFKKAFKKAFKFKKAFKKAF
−925.2
XI + XI
361


 


383
KFKKAFKKAFGGGKFKKAFKKAF
−923.8
XI + XI
362


 


384
FAKKFAKKFKGGGFAKKFAKKFK
−909.2
X + X
363


 


385
FAKKFAKKFKAFFKKKAKFK
−839.9
      X + XXXVIII
364


 


228
PSRKSMEKSVAKLLNKIAKSEP
−782.4
   IX + XVIII
365


 


386
AFFKKKAKFKAFFKKKAKFK
−716.0
XXXVIII + XXXVIII
366









In each of Tables 3-9, the RP# is a randomly assigned designation used to identify specific peptide sequences. The “Binding E” (see column 3 in each of the Tables) corresponds to a predicted measure of the energy released when individual peptides bind to the protein dimerization domain of RelB, an NFkB Class II protein (see Example 2, below).
Example 2
Predicted Binding of Peptides to Rel B
To identify peptides having anti-inflammatory activity, the NF-kB complex was selected as a target, since it is known to be a key component in the signaling pathways that regulate inflammation. Dimerization of NF-kB (either homologous or heterologous), which is mediated by the dimerization domains found in NF-kB Class II proteins (e.g., RelA, RelB, cRel, NF-kB1, and NF-kB2), is essential for activation of the NF-kB complex and its generation of pro-inflammatory signals. Accordingly, peptide designs were selected for their ability to specifically bind to the dimerization domain of RelB (NCBI Acc. No. NP_033072.2), with the goal that such binding would inhibit NF-kB dimerization and activation.
Peptide binding to the dimerization domain of Rel B was evaluated in silico, using the web-based ClusProTM algorithm developed at Boston University. The ClusProTM algorithm filters docked conformations between a protein target and a putative ligand and determines surface complementarity, ranking the conformations based on their clustering properties. The free energy filters select complexes with the lowest desolvation and electrostatic energies. Clustering is then used to smooth the local minima and to select the ones with the broadest energy wells, a property associated with the free energy at the binding site. Using this method, it is possible to evaluate the affinity a ligand possesses for a particular target, whereupon the ligands can be ranked and then tested for biological activity in vitro or in vivo.
The binding energies calculated by the ClusProTM algorithm are shown for each of the peptides in Tables 3-9, in the third columns of the tables. In each of Tables 3-9, the peptides are ranked according to the calculated RelB binding energy, from highest to lowest binding energy. The RelB binding energies were used to explore the structure-function relationship of the peptides, particularly with regard to (i) increasing or decreasing hydrophobicity, (ii) positive/negative charge density, and (iii) altering the arc of the hydrophobic and hydrophilic faces of the peptides. The peptides shown in Table 10 (below) will be used to illustrate the results of the study.







TABLE 10 







Predicted Binding of Select Peptides to RelB













RelB






Binding E




RP #
Sequence
(kCal/mol)*
Formula
SEQ ID NO:














RP−182
KFRKAFKRFF
−944.8
XI
121


 


RP−166
FFEHFWKEFN
−1,044.8
X
112


 


RP−113
FFFRFFFEFQ
−1,208.9
II
39


 


RP−289
AKKKAKKKAK
−431.6
V
232


 


RP−387
AAKKAAKKAK
−338.3
X
173


 


NF-CONTR2
IESKRRKKKP
−476.6
N/A
382


 


NF-CONTR3
APGPGDGGTA
−621.1
N/A
383





*The lower the energy value, the greater affinity the ligand possesses for the binding site on the target protein.






A structural model of the RelB subunit of NF-kB is shown in FIG. 1. Amino acids with the dimerization site are shaded to indicate their hydrophobic or hydrophilic character. In particular, the amino acid residues colored light grey are hydrophilic, while the amino acid residues colored dark grey are hydrophobic. Given the distinct locations of the hydrophilic and hydrophobic amino acid residues within the binding pocket of the dimerization domain, it is evident that striapathic peptides having an amphipathic secondary structure have the potential to bind site-specifically to the dimerization domain binding pocket.
The secondary structure of RP-182 (SEQ ID NO: 121) and its binding to RelB (SEQ ID NO: 367) is modeled in FIG. 2. As can be seen in the panels on the right, RP-182's predicted secondary structure has distinct hydrophobic and hydrophilic sides that comprise approximately equal facial arcs (see also FIG. 9) and are of high volume. Overall, the structure of RP-182 possesses high hydrophobicity and high cationicity (with a total of five cationic amino acid residues). These characteristics of RP-182 are summarized in Table 11, below. Based on the structural modeling, RP-182 binds with high affinity to the RelB dimerization domain binding pocket, with an estimated binding energy of −944.8 kcal/mol.
The secondary structure of RP-166 (SEQ ID NO: 112) and its binding to RelB (SEQ ID NO: 367) is modeled in FIG. 3. As can be seen in the panels on the right, RP-166's predicted secondary structure also has distinct hydrophobic and hydrophilic sides that comprise approximately equal facial arcs (see also FIG. 9). These characteristics are not surprising, as the striapathic region of RP-166 has a modular structure that is identical (albeit reversed) to that of RP-182's (compare Formulas X and XI). As with RP-182, the hydrophobic and hydrophilic surfaces of RP-166 are of high volume, but RP-166 has a greater ratio of hydrophobic volume to hydrophilic volume as compared to RP-182. In addition, the cationicity of RP-166 is significantly reduced relative to that of RP-182, since RP-166 has an equal number of cationic amino acid residues and anionic amino acid residues. These characteristics of RP-166 are summarized in Table 11, below. Based on the structural modeling, RP-166 binds to the RelB dimerization domain binding pocket with even higher affinity than RP-182, having an estimated binding energy of −1,044.8 kcal/mol.
The secondary structure of RP-113 (SEQ ID NO: 39) and its binding to RelB (SEQ ID NO: 367) is modeled in FIG. 4. As can be seen in the panels on the right, RP-113's predicted secondary structure also has distinct hydrophobic and hydrophilic sides, but the hydrophobic side comprises a much larger facial arc than the hydrophilic side. As shown in FIG. 9, the facial arc of the polar side of RP-113 is only 60°, while the facial arc of the non-polar side is 300°. Consistent with this shift toward a larger hydrophobic surface, RP-113 has a larger hydrophobic volume than either RP-182 or RP-166, as well as a significantly larger ratio of hydrophobic to hydrophilic volume. See Table 11, below. Like RP-166, the cationicity of RP-113 is significantly reduced relative to that of RP-182, since RP-113 has an equal number of cationic amino acid residues and anionic amino acid residues. Based on the structural modeling, RP-113 binds to the RelB dimerization domain binding pocket with one of the highest affinities predicted for the peptides of the invention, having an estimated binding energy of −1,208.9 kcal/mol.
The secondary structure of RP-387 (SEQ ID NO: 173) and its binding to RelB (SEQ ID NO: 367) is modeled in FIG. 5. As can be seen in the panels on the right, RP-387's predicted secondary structure has distinct hydrophobic and hydrophilic sides. However, in contrast to RP-113, the hydrophilic side of RP-387 comprises a much larger facial arc than the hydrophobic side. As shown in FIG. 10, the facial arc of the polar side of RP-387 is 245°, while the facial arc of the non-polar side is 115°. Consistent with this shift toward a larger hydrophilic surface, RP-387 has a smaller hydrophobic volume than any of RP-182, RP-166, and RP-113, as well as a significantly smaller ratio of hydrophobic to hydrophilic volume. See Table 11, below. With regard to cationicity, RP-387 is similar to RP-182, having a total of five cationic amino acid residues. Based on the structural modeling, RP-387 binds to the RelB dimerization domain binding pocket, but is does so relatively poorly, having an estimated binding energy of only −338.3 kcal/mol.
The secondary structure of RP-289 (SEQ ID NO: 232) and its binding to RelB (SEQ ID NO: 367) is modeled in FIG. 6. As can be seen in the panels on the right, RP-289's predicted secondary structure has distinct hydrophobic and hydrophilic sides. However, RP-289's hydrophobic side is one of the smallest of the peptides screened. As shown in FIG. 9, the facial arc of the polar side of RP-289 is 290°, while the facial arc of the non-polar side is only 70°. Of the peptides listed in Table 11, RP-289 has the smallest hydrophobic volume and the smallest ratio of hydrophobic to hydrophilic volume. RP-289 also has the highest cationicity of the peptides listed in Table 11, having a total of seven cationic amino acid residues. Based on the structural modeling, RP-289 binds to the RelB dimerization domain, though comparatively much more weakly than RP-182, RP-166, and RP-113, having an estimated binding energy of only −431.6 kcal/mol.
Tables 10 and 11 also identify two control peptides, NF-CONTR2 and NF-CONTR3, which are fragments of the RelB subunit of NF-kB. The sequences of NF-CONTR2 and NF-CONTR3 do not conform to any of structural Formulas I-LIII. The secondary structure of NF-CONTR2 (SEQ ID NO: 382) and its binding to RelB (SEQ ID NO: 367) is modeled in FIG. 7. The secondary structure of NF-CONTR3 (SEQ ID NO: 383) and its binding to RelB (SEQ ID NO: 367) is modeled in FIG. 8. Neither peptide is predicted to adopt a clearly amphipathic secondary structure throughout the length of the peptide. Moreover, although the ClusProTM algorithm identifies a binding interaction between each of NF-CONTR2 and NF-CONTR3 and RelB, the binding energies are not very strong and neither peptide displays a preference for binding to the RelB dimerization domain binding pocket.







TABLE 11 







Physical Characteristics of Select Peptides


























HPB







SEQ
RelB




Vol/







ID
Binding


HPL
HPB
HPL
tH
tH
tH HPB/


RP#
Sequence
NO:
Energy
(+)
(−)
Vol
Vol
Vol
HPL
HPB
tH HPL





















182
KFRKAFKRFF
121
−944.8
6
1
696.9
659.8
0.95
−50.8
16.4
−0.32


 


166
FFEHFWKEFN
112
−1,044.8
3
3
637.7
775.0
1.22
−33.0
16.7
−0.51


 


113
FFFRFFFEFQ
 39
−1,208.9
2
2
414.5
1030.4
2.49
−23.5
25.9
−1.10


 


289
AKKKAKKKAK
232
−431.6
8
1
896.8
213.3
0.24
−61.6
4.8
−0.08


 


387
AAKKAAKKAK
173
−338.3
6
1
640.5
355.5
0.55
−44.0
8.0
−0.18


 


NF-C2
IESKRRKKKP
382
−476.6
7
2
954.9
297.4
0.31
−66.8
3.5
−0.05


 


NF-C3
APGPGDGGTA
383
−621.1
1
1
115.1
665.7
5.78
−9.2
8.0
−0.87





*Binding energies are in kcal/mol.


Volumes are in cubic angstroms.


HPL means hydrophilic; HPB means hydrophobic.


“tH” is the total hydrophobicity (in kcal/mol), as defined by Engleman et al. (1986), “Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins,” Annu. Rev. Biophys. Bioeng. 15: 321−53.






FIGS. 1 through 10 and Table 11 reveal some important aspects of the structure-function relationship for the peptides of the invention. First, all of the peptides that are predicted to bind the RelB dimerization domain binding pocket have an amphipathic secondary structure. Second, greater hydrophobic volume, a greater ratio of hydrophobic to hydrophilic volume, and a greater hydrophobic arc are all associated with increased affinity for the binding pocket of the RelB dimerization domain. Third, increased cationicity is associated with decreased binding affinity for the binding pocket of the RelB dimerization domain.
Table 4, which lists some “all hydrophilic” variants of the Class I peptides, appears to potentially refute the conclusion that increased cationicity is associated with decreased binding affinity for the binding pocket of the RelB dimerization domain. In each of the peptides in Table 4, the hydrophobic residues of a Class I, Formula II peptide have been replaced with a single type of hydrophilic residue. Significantly, RP-173 (HHHRHHHEHQ; SEQ ID NO: 99) and RP-195 (RRRRRRRERQ; SEQ ID NO: 100) both have a high affinity for the binding pocket of the RelB dimerization domain (−1,002.2 and −855.2 kcal/mol, respectively), despite have eight amino acid residues that generally have a cationic charge in solution. Because both histidine and arginine have large side chains, a potential explanation for their high RelB binding affinities is that the uncharged hydrocarbon groups in the side chains provide some hydrophobicity that would otherwise have been lost by switching from a hydrophobic residue to a hydrophilic residue. In addition, when bound to RelB, some of the histidine and arginine residues may adopt an uncharged state. Table 4 therefore sheds further light on the structure-function relationship of the peptides of the invention by indicating that histidine and arginine can function in a quasi-hydrophobic capacity, at least with regard to the binding affinities of peptides for the RelB dimerization domain binding pocket. Accordingly, in some peptides of the invention, it can be energetically advantageous to place a histidine or arginine adjacent to a hydrophobic module that is made up of one or two hydrophobic amino acid residues.
Example 3
RelB Amino Acid Residues Involved in Peptide Binding
A model of the amino acid residues that line the binding pocket of the RelB dimerization domain is shown in FIG. 11. The model shows that Glu-298, Asp-330, and His-332 are key hydrophilic amino acid residues that line the binding pocket, while Tyr-300, Leu-301, Leu-302, and Leu-371 are important hydrophobic residues. The same model, with the addition of a stick diagram of the RP-182 peptide (SEQ ID NO: 121) is shown in FIG. 12. The dotted lines in FIG. 12 show ionic bonds between (1) Lys-7 of RP-183 and Asp-330 of RelB, and (2) Lys-4 of RP-183 and Glu-298 of RelB. Further stabilizing the interaction is an intra-ionic bond formed between Arg-8 of RP-183 and the carboxy terminal Lys-10 of RP-183. In addition to the ionic binds, there are numerous Van der Waals interactions. For the sake of clarity, only that of Phe-9 of RP-182 with Leu-371 of Rel-B is shown. However, the other hydrophobic amino acid residues on the hydrophobic face of RP-183 interact with the hydrophobic “floor” of the cleft of dimerization site of Rel-B.
An analysis of the ionic and Van der Waals interactions involved with the binding of different peptides of the invention has revealed that the peptides bind to a subset of the RelB amino acid residues selected from the group consisting of Leu-281, Ile-283, Cys-284, Glu-298, Tyr-300, Leu-301, Leu-302, Cys-303, Ile-311, Ser-312, Ala-329, Asp-330, Val-331, His-332, Gln-334, and Leu-371. See Table 13, below. Tyr-300, Leu-302, and His-332 are designated in the literature as being critical for dimerization. The amino acids most critical to binding by peptides of the invention include Glu-298, Tyr-300, Leu-302, Asp-330, Gln-334, and Leu-371.
Example 4
Binding of Peptides to Protein Targets Other Than RelB
A subset of the peptides shown in Tables 3-9 were further evaluated in silico to determine whether they bind to signaling proteins involved in the inflammatory response other than RelB. In doing so, it was discovered the dimerization cleft of the RelB subunit of NF-kB has structural parallels in a number of other signaling molecules. Consistent with these structural parallels, the peptides of the invention are predicted (by the ClusProTM algorithm) to bind with high affinity to important signaling molecules in the inflammatory cascade, including: TGFβ (NCBI Acc. No. NP_000651.3; SEQ ID NO: 368); Notch1 (GenBank Acc. No. AAG33848.1; SEQ ID NO: 369); Wnt8R (NCBI Acc. No. XP_005214377.1; SEQ ID NO: 370); TRAIL (GenBank Acc. No. EAW78466.1; SEQ ID NO: 371); IL6R (NCBI Acc. No. NP_786943.1; SEQ ID NO: 372); IL10R (NCBI Acc. No. NP_001549.2; SEQ ID NO: 373); EGFR (GenBank Acc. No. AAR85273.1; SEQ ID NO: 374); and CDK6 (NCBI Acc. No. NP_001250.1; SEQ ID NO: 375). Representative peptides of the invention and the predicted binding energies between the peptides and each of these signaling molecules is shown in Tables 12A and 12B, below.







TABLE 12A 







Predicted Binding of Select Peptides to Different Inflammatory Targets
















SEQ ID







RP#
Sequence
NO:
RelB
TGFβ
NOTCH1
WNT8R
TRAIL

















185
FFKKFFKKFK
123
−920.6
−880.1
−817.7
−747.2
−904.5


 


186
KFKKFFKKFF
124
−919.6
−846.0
−887.7
−739.1
−884.3


 


183
FFRKFAKRFK
122
−933.2
−878.9
−890.8
−763.1
−938.8


 


182
KFRKAFKRFF
121
−944.8
−851.8
−1,096.3
−733.7
−938.8


 


118
FFFRFFFNFN
44
−1,139.9
−1,074.7
−1,032.4
−990.9
−995.4


 


394
NFNFFFRFFF
33
−1,286.6
−1,002.6
−1,059.6
−971.2
−943.8


 


389
FRFKFA
257
−1,009.8
−878.4
−846.4
−804.5
−916.8


 


390
FRFKFKF
256
−1,083.3
−933.2
−1,005.3
−871.0
−1,014.4


 


391
FRFKFKFR
254
−1,190.8
−987.5
−1,005.4
−897.9
−1,049.2


 


392
RFQFKFRF
255
−1,170.3
−943.2
−923.1
−853.8
−1,039.6


 


387
AAKKAAKKAK
173
−301.6
−397.7
−385.5
−394.9
−397.7





*All binding affinities are in kcal/mol.













TABLE 12A 







Predicted Binding of Select Peptides to Different Inflammatory Targets












SEQ ID















RP#
Sequence
NO:
RelB
EGFR
IL6R
IL10R
CDK6

















185
FFKKFFKKFK
123
−920.6
−785.4
−747.5
−756.3
−753.9


 


186
KFKKFFKKFF
124
−919.6
−866.3
−755.0
−742.0
−718.1


 


183
FFRKFAKRFK
122
−933.2
−795.6
−696.7
−738.6
−783.0


 


182
KFRKAFKRFF
121
−944.8
−853.8
−784.5
−785.9
−781.5


 


118
FFFRFFFNFN
44
−1,139.9
−1,039.4
−1,074.8
−881.4
−1,020.8


 


394
NFNFFFRFFF
33
−1,286.6
−1,061.4
−1,069.9
−850.8
−1,075.3


 


389
FRFKFA
257
−1,009.8
−896.0
−812.3
−779.2
−900.5


 


390
FRFKFKF
256
−1,083.3
−1,036.3
−952.2
−876.2
−861.1


 


391
FRFKFKFR
254
−1,190.8
−1,024.9
−957.6
−882.3
−899.9


 


392
RFQFKFRF
255
−1,170.3
−1,010.4
−1,052.3
−901.7
−870.0


 


387
AAKKAAKKAK
173
−301.6
−395.9
−342.0
−338.1
−351.4









The data reveals that the strength of binding to RelB is highly correlated with the strength of binding to the various inflammatory targets. In other words, peptides that are predicted to bind with high affinity to RelB are likewise predicted to bind with high affinity to TGFβ, Notch1, Wnt8R, TRAIL, EGFR, IL6R, and IL10R.
A closer evaluation of the predicted binding interactions between the peptides of the invention and each of TGFβ, Notch1, Wnt8R, TRAIL, EGFR, IL6R, and IL10R reveals that the peptides not only bind with high affinity, but also bind to functionally critical sites on the targets. For example, peptides of the invention are predicted to bind to the receptor-binding site on TGFβ, the calcium-binding site on Notch1, the Wnt8-binding site on Wnt8R, the receptor-binding site on TRAIL, the IL6-binding site on IL6R, the IL10-binding site on IL10R, and the general ligand-binding site on EGFR. A non-exhaustive list of amino acid residues in each of these targets that are bound by the peptides of the invention is shown in Table 13.







TABLE 13







Amino Acid Residues in Target Proteins Contacted by Peptides of the Invention











SEQ ID




Target
NO:
AA Residue Contacts
Most Critical AAs





RelB
367
Leu-281, Ile-283, Cys-284, Glu-298, Tyr-300,
Glu-298, Tyr-300, Leu-302,




Leu-301, Leu-302, Cys-303, Ile-311, Ser-312,
Asp-330, Gln-334, Leu-371




Ala-329, Asp-330, Val-331, His-332, Gln-334,




Leu-371


TGFβ
368
Leu-20, Ile-22, Phe-24, Asp-27, Leu-28, Trp-30,
Asp-27, Leu-28, Trp-30,




Trp-32, Tyr-39, Phe-43, Pro-80, Leu-83, Leu-101,
Trp-32




Ser-112


Notch1
369
Phe-1520, Gln-1523, Arg-1524, Glu-1526,
Phe-1520, Trp-1557,




Ala-1553, Glu-1556, Trp-1557, Cys-1562, His-1602,
Cys-1562, Phe-1703




Arg-1684, Gln-1685, Cys-1686, Ser-1691, Cys-1693,




Phe-1694, Phe-1703


Wnt8R
370
Tyr-52, Gln-56, Phe-57, Asn-58, Met-91, Tyr-100,
Tyr-52, Phe-57, Tyr-100,




Lys-101, Pro-103, Pro-105, Pro-106, Arg-137,
Asp-145




Asp-145


TRAIL
371
Ala-123, His-161, Ser-162, Phe-163, Tyr-183,
Phe-163, Tyr-243, Glu-271,




Tyr-185, Tyr-243, His-270, Glu-271, Phe-274,
Phe-278




Phe-278, Leu-279, Val-280


IL6R
372
Leu-108, Glu-140, Pro-162, Phe-229, Tyr-230,
Glu-140, Phe-229, Tyr-230,




Phe-279
Phe-279


IL10R
373
Leu-41, Arg-42, Tyr-43, Ile-45, Glu-46, Ser-47,
Tyr-43, Ile-45, Glu-46,




Trp-48, Arg-76, Arg-78
Trp-48


EGFR
374
Leu-10, Thr-40, Trp-41, Asp-48, Phe-51, Leu-63,
Trp-41, Asp-48, Phe-51,




His-66, Asp-68, Leu-88, Tyr-101
Asp-68, Tyr-101,


CDK6
375
Val-142, Arg-144, Asp-145, Ser-171, Val-180,
Asp-145, Val-180, Tyr-196




Val-181, Leu-183, Arg-186, Val-190, Gln-193,




Tyr-196, Val-200


HMT
376
Tyr-16, Glu-48, Tyr-50, Leu-51, Phe-52, Asn-69
Tyr-16, Glu-48, Tyr-50,





Leu-51, Phe-52, Asn-69


CD47
377
Tyr-37, Thr-49, Phe-50, Asp-51, Ala-53, Glu-97,
Tyr-37, Glu-97, Glu-100,




Val-98, Glu-100, Leu-101, Thr-102, Glu-104,
Leu-101, Glu-104, Glu-106




Glu-106, Gly-107


SIRP-α
378
Tyr-50, Gln-52, Pro-58, Ser-66, Thr-67, Ser-77
Tyr-50, Gln-52, Ser-66,





Thr-67


CD206
379
Phe-708, Thr-709, Trp-710, Pro-714. Glu-719,
Phe-708, Trp-710, Trp-721,




Asn-720, Trp-721, Ala-722, Glu-725, Tyr-729,
Glu-725, Tyr-729,




Glu-733, Asn-747, Asp-748, Ser-1691, Cys-1693,
Glu-733




Phe-1694, Phe-1703


TGM2
380
Cys-277, His-335, Asp-358
Cys-277, His-335, Asp-358









Given the large number of immunologically important signaling proteins that are targeted by the peptides of the invention, the data suggests that the peptides act in a pleiotropic manner, making many different interactions that sum together to create a broad anti-inflammatory response. This may make possible a reduction in disease conditions without the toxicity observed in the use of more highly-targeted chemotherapeutic agents.
Example 5
Binding of Peptides to Histone Modifying Enzymes and Ribonuclease Reductase
A number of the peptides of the invention were observed to share structural characteristics of the N-terminal regions of histones. Accordingly, representative peptides were evaluated in silico for their ability to bind to histone modification enzymes. In this manner, it was discovered that the peptides of the invention have high binding affinity for histone methyl transferase (HMT)(NCBI Acc. No. NP_048968.1; SEQ ID NO: 376), binding close to the active site of the enzyme. Predicted binding energies of select peptides of the invention for HMT, calculated using the ClusProTM algorithm, are shown in Table 14. Again, the predicted binding energies correlate well with the predicted energies for binding RelB.







TABLE 14 







Binding Affinities of Select Peptides to


HMT, MKK7, and RNR













SEQ ID




RP#
Sequence
NO:
RelB
HMT














185
FFKKFFKKFK
123
−920.6
−846.4


 


186
KFKKFFKKFF
124
−919.6
−795.7


 


183
FFRKFAKRFK
122
−933.2
−839.4


 


182
KFRKAFKRFF
121
−944.8
−826.6


 


118
FFFRFFFNFN
44
−1,139.9
−1,000.2


 


394
NFNFFFRFFF
33
−1,286.6
−998.4


 


389
FRFKFA
257
−1,009.8
−836.8


 


390
FRFKFKF
256
−1,083.3
−906.6


 


391
FRFKFKFR
254
−1,190.8
−949.2


 


392
RFQFKFRF
255
−1,170.3
−962.2


 


387
AAKKAAKKAK
173
−301.6
−334.5





*All binding affinities are in kcal/mol.






A model of Histone Methyl Transferase (HMT) bound by RP-182 is shown in FIG. 13. The orange amino acids are the active site of the histone methyl transferase enzyme. Inhibition of methyl transferase activity by RP-182 is expected since RP-182 binds to at least one residue of the active site, in a manner that appears to obstruct access to the active site. A non-exhaustive list of amino acid residues in HMT that are bound by the peptides of the invention is shown in Table 13, above.
Peptides of the invention are also observed to display strong predicted affinities to MAP kinase kinase 7 (MKK7; SEQ ID NO: 166), a member of the mitogen-activated protein kinase kinase family involved in signal transduction mediating cell responses to proinflammatory cytokines, and therefore likely involved in peptides' anti-inflammatory activity. The predicted affinity of e.g. RP-182 for MKK7 is −738.2 kcals/mol.
In addition, peptides of the invention were observed to display substantial predicted affinities to ribonuclease reductase (RNR; SEQ ID NO: 168) also known as ribonucleoside diphosphate reductase. This is an enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides. Deoxyribonucleotides in turn are used in the synthesis of DNA. The reaction catalyzed by RNR is strictly conserved in all living organisms. Furthermore, RNR plays a critical role in regulating the total rate of DNA synthesis, so that DNA to cell mass is maintained at a constant ratio during cell division and DNA repair. A somewhat unusual feature of the RNR enzyme is that it catalyzes a reaction that proceeds via a free radical mechanism of action. The substrates for RNR are ADP, GDP, CDP and UDP. dTDP (deoxythymidine diphosphate) is synthesized by another enzyme (thymidylate kinase) from dTMP (deoxythymidine monophosphate). The predicted affinity of e.g. RP-182 for RNR is −814.0 kcals/mol.
Example 6
Binding of Peptides to Targets Associated with Macrophage Activation
Peptides of the invention are also predicted to interact with several proteins relevant to macrophage activity and apoptosis, properties associated with inflammation and with tumor genesis and metastasis. Targets identified to date include CD47, SIRP-α, CD206, TGM2, LEGUMAIN, DC-SIGN, CSF1, CSF1R, and IL34.
CD47 (or “Cluster of Differentiation 47”), also known as integrin associated protein (IAP), is a transmembrane protein that belongs to the immunoglobulin superfamily. CD47 protein partners with membrane-bound cellular adhesion receptors known as integrins and also binds the ligands thrombospondin-1 (TSP-1) and signal-regulatory protein alpha (SIRP-α). CD47 is involved in a range of cellular processes, including apoptosis, proliferation, adhesion, and migration. Furthermore, it plays a key role in immune and angiogenic responses. CD47 is expressed in many types of human cells and has been found to be overexpressed in many different types of tumors. The overexpression of CD47 has received considerable attention as a possible protective agent for human cancers. By binding to SIRP-α on the surface of macrophages, CD47 is believed to send a “don't eat me” signal that disables the macrophages from attacking the cancer cell.
CD206 and TGM2 have likewise been identified as potentially important regulators of macrophage activity. CD206 is a C-type lectin, primarily present on the surface of macrophages and dendritic cells. It is the first member of a family of endocytic receptors that includes Endo180 (CD280), M-type PLA2R, and DEC-205 (CD205). The receptor recognizes terminal mannose, N-acetylglucosamine, and fucose residues that make up glycans, which are attached to proteins found on the surface of some microorganisms. Accordingly, the CD206 receptor appears to play a role in both the innate and adaptive immune systems. In addition, tumor-associated macrophages may use CD206 to ingest collagen, yielding degradation products capable of nourishing both themselves and tumor cells, and weakening collagen binding of tumor cells so as to encourage metastasis.
TGM2 belongs to a family of enzymes that catalyze the calcium-dependent translational modification of proteins. The family members are found both intracellularly and extracellularly. TGM2 is unique in the family because of its multi-functionality and specialized structure, which includes four distinct domains: an N-terminal β-sandwich that contains fibronectin and integrin binding sites; a catalytic core that contains the catalytic triad for acyl-transfer reactions (Cys-277, His-335, and Asp-358); and two C-terminal β-barrel domains, with the second having a phospholipase-binding sequence. TGM2 has been implicated as a regulator of extracellular matrix functions, including cell adhesion and migration, cellular growth and differentiation, apoptosis, tumor growth, and wound healing. Although TGM2 is ubiquitously expressed, it is most highly expressed in M2 macrophages. Furthermore, increased TGM2 levels are associated with scleroderma, lung and kidney fibrosis, worsening symptoms for diabetes, arthritis, and EAE, and poor outcomes in a number of different cancers, all of which can be linked to M2 macrophages.
Predicted binding energies of select peptides of the invention for CD47 (NCBI Acc. No. XP_005247966.1; SEQ ID NO: 377), SIRP-α (GenBank Acc. No. AAH26692.1; SEQ ID NO: 378), CD206 (NCBI Acc. No. NP_002429.1; SEQ ID NO: 379), and TGM2 (GenBank Acc. No. AAB95430.1; SEQ ID NO: 380) calculated using the ClusProTM algorithm, are shown in Table 15. As with the other targets discussed above, the predicted binding energies correlate well with the predicted energies for binding RelB.
LEGUMAIN is a protein that in humans is encoded by the LGMN gene. This gene encodes a cysteine protease, legumain that has a strict specificity for hydrolysis of asparaginyl bonds. This enzyme may be involved in the processing of bacterial peptides and endogenous proteins for MHC class II presentation in the lysosomal/endosomal systems. Enzyme activation is triggered by acidic pH and appears to be autocatalytic. Protein expression occurs after monocytes differentiate into dendritic cells. A fully mature, active enzyme is produced following lipopolysaccharide expression in mature dendritic cells. Overexpression of this gene may be associated with the majority of solid tumor types. LEGUMAIN is also overexpressed in M2 macrophages, and inhibition of its activity by the disclosed peptides is expected to downregulate M2-activated macrophages.
DC-SIGN (Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin) also known as CD209 (Cluster of Differentiation 209) is a protein that in humans is encoded by the CD209 gene. DC-SIGN is a C-type lectin receptor present on the surface of both macrophages and dendritic cells. DC-SIGN on macrophages recognizes and binds to mannose type carbohydrates, a class of pathogen associated molecular patterns PAMPs commonly found on viruses, bacteria and fungi. This binding interaction activates phagocytosis. On myeloid and pre-plasmacytoid dendritic cells DC-SIGN mediates dendritic cell rolling interactions with blood endothelium and activation of CD4+ T cells, as well as recognition of pathogen haptens. DC-SIGN is significantly overexpressed in M2 macrophages, and inhibition of its activity by the disclosed peptides is expected to downregulate M2-activated macrophages.







TABLE 15 







Binding Affinities of Select Peptides to CD47, SIRP-α, CD206, and TGM2
















SEQ ID







RP#
Sequence
NO:
RelB
SIRP-α
CD47
CD206
TGM2

















185
FFKKFFKKFK
123
−920.6
−799.2
−639.3
−807.1
−827.2


 


186
KFKKFFKKFF
124
−919.6
−711.8
−637.4
−881.3
−885.3


 


183
FFRKFAKRFK
122
−933.2
−834.2
−658.1
−786.7
−860.7


 


182
KFRKAFKRFF
121
−944.8
−733.1
−723.1
−844.5
−869.1


 


118
FFFRFFFNFN
44
−1,139.9
−805.2
−751.5
−1,048.7
n/a


 


394
NFNFFFRFFF
33
−1,286.6
−854.2
−751.5
−986.6
n/a


 


389
FRFKFA
257
−1,009.8
−934.6
−688.3
−861.9
n/a


 


390
FRFKFKF
256
−1,083.3
−887.2
−783.5
−978.1
n/a


 


391
FRFKFKFR
254
−1,190.8
−932.1
−790.1
−941.3
n/a


 


392
RFQFKFRF
255
−1,170.3
−982.5
−792.1
−981.6
n/a


 


387
AAKKAAKKAK
173
−301.6
−392.3
−308.7
−416.6
n/a





*All binding affinities are in kcal/mol.






FIG. 14 (left panel) shows a model of the ecto-domain of a CD47 dimer (top view) (SEQ ID NO: 377), with light grey- and dark grey-colored surfaces representing the polar and non-polar amino acids, respectively, that are involved in the binding of CD47 to the SIRP-α receptor. FIG. 14 (right panel) is a model of the ecto-domain of the CD47 dimer when bound by RP-183 (SEQ ID NO: 121). Based on this predicted interaction between RP-183 and CD47, peptides of the invention are expected to block the interaction between CD47 and SIRP-α.
FIG. 15 shows a model of a SIRP-α dimer (SEQ ID NO: 378), with light grey and dark grey-colored surfaces representing the polar and non-polar amino acids involved in its binding to CD47 (see left-most dimer). In a slightly-skewed view of the same SIRP-α dimer bound by RP-183 (SEQ ID NO: 122) (see right-most dimer), it can be seen that RP-183 binds tightly to the amino acids involved in binding to the CD47 receptor. It therefore appears that RP-183 (and other peptides of the invention) block the interaction between CD47 and SIRP-α by two distinct mechanisms, binding to the corresponding binding sites in both CD47 and SIRP-α. Thus, predicted activities associated with the peptides of the invention include thwarting of an important defense mechanism for cancer cells.
Peptides of the invention are also predicted to block key sites on the CD206 receptor subunit. FIG. 16 shows a model of CD206 (SEQ ID NO: 379) bound by RP-182 (SEQ ID NO: 121). The dark grey-colored tyrosine residue on the bend region of CD206 (left-most molecule) forms a planar, hydrophobic stacking interactions with the mannose ligands on the surface of target cells. The light grey colored amino acids are acidic residues that help chelate the required calcium ion necessary for stable interactions with the mannose receptor. The RP-182 peptide (seen in mesh on the right-most molecule) blocks activity by interacting with both of these key sites on the receptor subunit. Peptides of the invention are therefore expected to reduce the viability of M2 macrophages, which has been experimentally confirmed (as set forth below).
Furthermore, peptides of the invention are predicted to block the active site of TGM2. FIG. 17 (left panel) shows a model of TGM2 (SEQ ID NO: 380) with the active site residues highlighted in dark grey. FIG. 17 (right panel) shows the same model of TGM2 bound by RP-182 (SEQ ID NO: 121), which is colored light grey. As can be seen, RP-182 is predicted to bind to TGM2 in a manner that completely covers the active site, thereby obstructing substrate access and inhibiting TGM2 function. Significantly, decreased levels of TGM2 is associated with reduced NF-kB activation, so the interaction of the polypeptides of the invention with TGM2 would appear to reinforce and/or augment their suppression of NF-kB activity.
Non-exhaustive lists of specific amino acid residues in CD47, SIRP-α, CD206, and TGM2 that are bound by the peptides of the invention are shown in Table 13, above.
Example 7
Binding of Peptides to Checkpoint Inhibitors and Related Targets
It has also been observed that peptides of the present invention display substantial affinity to checkpoint inhibitor proteins and their ligands. Such proteins, including cytotoxic T-lymphocyte antigen 4 (CTLA-4), PD-1, and other inhibitory coreceptors, expressed on the surface of effector immune cells, when activated appear to exhaust the activity of the immune cells, serving as immune checkpoints in order to prevent uncontrolled immune reactions. Tumor cells often express ligands to the checkpoint inhibitors, e.g. PD-L1 and PD-L2, attenuating the capacity of the immune system to attack the tumor.
In particular, programmed cell death protein 1, also known as PD-1 and CD279 (cluster of differentiation 279), is a protein that in humans is encoded by the PDCD1 gene. PD-1 is a cell surface receptor that belongs to the immunoglobulin superfamily and is expressed on T cells and pro-B cells. PD-1 binds two ligands, PD-L1 and PD-L2. PD-1, functioning as an immune checkpoint plays an important role in downregulating the immune system by preventing the activation of T-cells, which in turn reduces autoimmunity and promotes self-tolerance. The inhibitory effect of PD-1 is accomplished through a dual mechanism of promoting apoptosis (programmed cell death) in antigen specific T-cells in lymph nodes while simultaneously reducing apoptosis in regulatory T cells (suppressor T cells).
Programmed death-ligand 1 (PD-L1) also known as cluster of differentiation 274 (CD274) or B7 homolog 1 (B7-H1) is a protein that in humans is encoded by the CD274 gene. Programmed death-ligand 1 (PD-L1) is a 40 kDa type 1 transmembrane protein that has been speculated to play a major role in suppressing the immune system during particular events such as pregnancy, tissue allografts, autoimmune disease and other disease states such as hepatitis. Normally the immune system reacts to foreign antigens where there is some accumulation in the lymph nodes or spleen that triggers a proliferation of antigen-specific CD8+ T cell. The formation of PD-1 receptor/PD-L1 or B7.1 receptor/PD-L1 ligand complex transmits an inhibitory signal which reduces the proliferation of these CD8+ T cells at the lymph nodes and supplementary to that PD-1 is also able to control the accumulation of foreign antigen specific T cells in the lymph nodes through apoptosis which is further mediated by a lower regulation of the gene Bcl-2.
As illustrations of the binding of peptides of the present invention with checkpoint inhibitors and their ligands, the predicted affinity of RP-182 to PD-1 is −742.9, and that of RP-621 is −1,008.8. The affinity of RP-182 to PD-L1 is −677.4, and that of RP-621 to PD-L1 is −1,010.6. As with inflammatory targets, there is a striking correlation among predicted affinities to several other checkpoint inhibitors and their ligands, as well as other proteins known to play a role in modulating the immune apparatus. These include: TIM-1 (believed to play a role in T-helper cell development: predicted affinity to RP-182, -850.1); CTLA-4 (checkpoint inhibitor: predicted affinity to RP-182, −663.2); ADORA2a (modulates activity of neutrophils and mast cells: predicted affinity to RP-182, −938.7); OX40 (secondary co-stimulatory immune checkpoint: predicted affinity to RP-182, −759.9); IDO (immune checkpoint: predicted affinity to RP-182, −934.0); LAG-3 (immune checkpoint receptor: predicted affinity to RP-182, −873.1); CD73 (enzyme limiting T cell activity through adenosine receptor signaling: predicted affinity of CD73-I to RP-182, −808.7; predicted affinity of CD73-II to RP-182, −949.1); Arginase-1 (blocks activity of cytotoxic T lymphocytes: predicted affinity to RP-182, −984.2); Colony Stimulating Factor 1 (blockade shown to upregulate checkpoint molecules, as well as reprogramming macrophage responses; predicted affinity of CSF1 to RP-182, −854.7; predicted affinity of CSF1D to RP-182, −847.1; predicted affinity of CSF1R to RP-182, −774.1); and IL34 (also activates CSF1R; predicted affinity to RP-182, −828.5).
Example 8
Binding of Peptides to MKK7
Dual specificity mitogen-activated protein kinase kinase 7, also known as MAP kinase kinase 7 or MKK7, is an enzyme that in humans is encoded by the MAP2K7 gene. This protein is a member of the mitogen-activated protein kinase kinase family. The MKK7 protein exists as six different isoforms with three possible N-termini (α, β, and γ isoforms) and two possible C-termini (1 and 2 isoforms). MKK7 is involved in signal transduction mediating the cell responses to proinflammatory cytokines, and environmental stresses. This kinase specifically activates MAPK8/JNK1 and MAPK9/JNK2, and this kinase itself is phosphorylated and activated by MAP kinase kinase kinases including MAP3K1/MEKK1, MAP3K2/MEKK2, MAP3K3/MEKK5, and MAP4K2/GCK.
Example 9
Binding of Peptides to Serum Albumin
It is well-known that the most abundant protein in the circulation is serum albumin. It is also known that solid tumors will take up serum albumin into their cells (through the process of pinocytosis) and use it as an energy source. Therefore, peptides of the invention were evaluated in silico for their ability to bind to human serum albumin (HSA)(NCBI Acc. No. NP_000468.1; SEQ ID NO: 381). It was discovered that peptides of the invention have the capacity to bind to HSA with high affinity. Predicted binding energies of select peptides of the invention for binding to HSA are shown in Table 16, below.







TABLE 16 







Binding Affinities of Select Peptides to Human


Serum Albumin (HSA)













SEQ ID




RP#
Sequence
NO:
RelB
HSA














185
FFKKFFKKFK
123
−920.6
−880.2


 


186
KFKKFFKKFF
124
−919.6
−850.5


 


183
FFRKFAKRFK
122
−933.2
−860.1


 


182
KFRKAFKRFF
121
−944.8
−789.0


 


118
FFFRFFFNFN
44
−1,139.9
−1,064.7


 


394
NFNFFFRFFF
33
−1,286.6
−1,016.5


 


389
FRFKFA
257
−1,009.8
−904.8


 


390
FRFKFKF
256
−1,083.3
−1,046.0


 


391
FRFKFKFR
254
−1,190.8
−1,021.9


 


392
RFQFKFRF
255
−1,170.3
−1,037.4


 


387
AAKKAAKKAK
173
−301.6
−410.7





*All binding affinities are in kcal/mol.






FIG. 18 is a model of HSA (shown in green) bound by RP-183 (blue). The computational modeling has identified a number of possible peptide binding sites on HSA. Therefore, it is believed that a single HSA molecule is able to bind to multiple peptides of the invention. The binding interaction between peptides of the invention and HSA suggest that HSA could be used as an in vivo carrier of the peptides. In this manner, HSA could protect the peptides from degradation in the blood and carry the peptides to sites of action, such as sites of inflammation and/or cancer cells, thereby increasing the efficacy of the peptides.
Example 10
In Vitro Modulation of NF-kB Activity
NF-kB activity was monitored using the a 3T3-L1 preadipocyte cell line stably transformed with a Nfkb-RE/GFP construct, as described in Shen et al. (2013), “Adipocyte reporter assays: Application for identification of anti-inflammatory and antioxidant properties of mangosteen xanthones,” Mol. Nutr. Food Res. 00:1-9, the entire contents of which are incorporated herein by reference. NF-kB expressing adipocyte reporter cells were plated in DMEM in wells of a 24-well plate, at a seeding density of 5×104. On the second and third days post-plating, test peptides were individually added to the wells to a final concentration of 0.01 μM. The test peptides included RP-398 (SEQ ID NO: 155), and RP-185 (SEQ ID NO: 123). On day 4 post-plating, lipopolysaccharide was added to the medium to a final concentration of 20 ng/ml. Finally, on day 5 post-plating, the cells were harvested and a fluorescence assay performed to detect GFP expression levels.
In this experiment, NF-kB expression was reduced approximately 58% relative to control cells that were not exposed to RP-398 or RP-185 peptide.
Example 11
In Vivo Modulation of Macrophage Activity
A frequently observed phenotype associated with tumor genesis and metastasis is the polarization of macrophage cells into the “M2” transition state, in which they are in an inflammatory state. Such macrophages are among those designated as “tumor-associated macrophages” (TAMs). To determine whether the peptides of the invention could influence macrophage polarization, the following experiment was performed.
Primary bone marrow cells were collected from male C57BL/6J (The Jackson Laboratory, Bar Harbor, Me.). Mouse bone marrow macrophages were differentiated in vitro from the primary bone marrow cells by culturing in Dulbecco's minimal essential medium (DMEM) with 10% FBS and 30 ng/ml murine M-CSF (colony stimulating factor) for 6 days. At day 7, macrophages were plated into 12-well plates and cultured in DMEM (10% FBS) with (i) IL-4 peptide (20 ng/mL), (ii) INF-γ (10 ng/mL), or (iii) neither IL-4 nor INF-γ for 24 hours. After 24 hours, the media was replaced with pure DMEM and the cells were cultured for an additional 48 hours. The resulting macrophages were (i) M2-polarized, (ii) M1-polarized, or (iii) undifferentiated, respectively.
A macrophage sample containing approximately 70,000 undifferentiated macrophages per ml was incubated for 72 hours with 100 nM RP-182 (SEQ ID NO: 121). Following the incubation, a count of viable cells revealed that there were 68,000 cells per ml. Similarly, incubating M1-polarized macrophages for 72 hours with 100 nM RP-182 resulted in a viable cell count of 68,000 cells per ml. Thus, the RP-182 had little effect on the viability of M1 macrophages. In contrast, incubating M2-polarized macrophages for 72 hours with 100 nM RP-182 resulted in a viable cell count of only 20,000 cells per ml. The results indicate that RP-182 reduces the viability of M2 macrophages.
Example 12
Downregulation of Checkpoint Inhibitors and Ligands
Based on their predicted affinity to checkpoint inhibitors (e.g. PD-1) and their ligands (e.g. PD-L1 and PD-L2), the polypeptides of the invention were also evaluated to determine whether the concentration of these proteins in treated tissue would be downregulated in vivo. In one experiment, tumors in transgenic p53/KRAS mice were allowed to grow to approximately 100 m3 in volume, and the animals were then treated daily subcu for one week with either vehicle only, or 10 mg/kg RP-182, following which the animals were sacrificed and the tumors resected, formalin-fixed, and stained with antibodies to PD-1 (FIG. 19), PD-L1 and PD-L2 (FIG. 20). It is clear from the figures that both the checkpoint inhibitor PD-1 and each of its ligands PD-L1 and PD-L2 are significantly downregulated in vivo in tissue treated with peptides of the present disclosure.
Example 13
Suppression of Tumor Growth
The polypeptides of the invention were also tested for their effect on tumor growth in a mouse model of non-metastatic breast cancer. MCF-7 human non-metastatic breast cancer cells were cultured at 37° C., 5% CO2 in normal growth media. Cells were harvested at 80% to 90% confluence. Immune compromised athymic nude mice (J:NU) were divided into 2 groups (9 animals per group). All mice were injected with  ̃4.5×106 MCF-7 cells which had been stained with VIVO Tracker 680 and suspended in 200 μl of PBS/Matrigel mixture. Cells were injected subcutaneously on the dorsal surface of treated animals using a 22 gauge needle fitted with a 500 μl syringe.
Animals were designated vehicle and peptide treated. The peptide treated animals were treated with the RP-397 polypeptide (SEQ ID NO: 194). Freshly prepared RP-397 peptide was dissolved in sterile saline at a concentration of 100 μM and was used to treat the animals in the peptide group. Vehicle treated animals were injected with saline buffer alone. All treatments were injected into the tumor mass two times weekly for 5 weeks using a 271⁄2 gauge needle fitted with a 1 ml syringe. Animal weights and tumor volumes were measured 3 times weekly and the fluorescence labeling was followed by VIVO Tracker 680 and IVIS Imaging. The results are shown in Table 17, below.







TABLE 17







Suppression of Tumor Growth Using RP-397












Avg. Tumor
Rate of Tumor
Body Weight
Body Weight



Weight
Growth
Before
After















Vehicle
1.5 g
63
25.2
30.2


RP-397
0.75 g*
 20*
25.1
30.1





The rate of tumor growth was measured in mm3/day. The “*” denotes a statistically significant difference from the vehicle control.






The data shows that polypeptides of the invention can suppress tumor growth in vivo.
Example 14
Administering Peptides in Combination with Chemotherapy
Given the significant role of inflammation in tumor genesis and metastasis, as well as the known association of M2 macrophage activity with tumor development, it was anticipated that the administration of peptides of the invention could positively influence the outcomes of cancer treatment.
To test this theory, cohorts of immunocompromised (“nude”) mice were injected with  ̃5×106 human triple-negative breast cancer cells (MDA-MB-231) under the upper left teat. Following this administration, one cohort received only vehicle; two of the cohorts received the chemotherapeutic agent Gemcitabine, at a q4d dose of 40 mg/kg of body weight. One of these cohorts also received RP-182 (SEQ ID NO: 121) at a daily dose of 5 mg/kg body weight; and a fourth cohort received only RP-182 at a daily dose of 5 mg/kg body weight. Beginning on day 32 of the study, in the Gemcitabine+RP-182 cohort, concentrations of RP-182 were increased to 20 mg/kg body weight. Tumor volume was assessed at various time points following initial cell administration (FIG. 21). After 50 days, the mice were sacrificed.
The data demonstrates that, as compared to treatment with Gemcitabine alone, combined treatment with Gemcitabine and polypeptides of the invention resulted in reductions in mean tumor volume. When RP-182 concentration was increased to 20 mg/kg body weight, the increase in tumor volume was essentially halted.
In a second experiment, xenografts of C42B prostate cancer cells were introduced into four cohorts of mice, and the tumors allowed to grow to approximately 100 m3 before treatment. One cohort was treated only with vehicle; a second with Docetaxel at 2.5 mg/kg body weight administered weekly; a third with RP-182 administered daily subcu at 10 mg/kg body weight; and a fourth with both Docetaxel at 2.5 mg/kg weekly and RP-182 at 10 mg/kg daily. Tumor volume was assessed at various time points following initial cell administration (FIG. 22); after 27 days, the mice were sacrificed. Similarly, the administration of RP-182 plus Docetaxel resulted in decreases in mean tumor volume compared to Docetaxel alone.
It is anticipated that the peptides of the invention will produce synergistic effects when administered with chemotherapeutic agents other than Gemcitabine and Docetaxel, as well as checkpoint inhibitor therapies and other immunotherapies. In particular, the peptides of the invention may be particularly useful when used in conjunction with recently-developed CAR-T (chimeric antigen receptor/T cell) therapies. Such therapies, while destroying tumor cells, create a very high systemic burden of dead cell material, overstimulating the immune system and creating a “cytokine storm” which can be fatal to the patient.
EMBODIMENTS
The following embodiments are provided to illustrate aspects of the present invention.
1. An anti-inflammatory composition comprising a peptide, wherein the peptide is 3 to 24 amino acid residues in length and comprises a striapathic region consisting of alternating Xm and Yn modules, wherein m and n are positive integers that identify different modules, wherein each Xm module consists of a sequence according to the formula Xma-Xmb-Xmc-Xmd-Xme, wherein Xma is selected from the group consisting of a naturally occurring hydrophilic amino acid, a non-naturally occurring hydrophilic amino acid, and a hydrophilic amino acid mimetic, and wherein Xmb, Xmc, Xmd and Xme are each individually absent or selected from the group consisting of a naturally occurring hydrophilic amino acid, a non-naturally occurring hydrophilic amino acid, and a hydrophilic amino acid mimetic, wherein each Yn module consists of a sequence according to the formula Yna-Ynb-Ync-Ynd-Yne, wherein Yna is selected from the group consisting of a naturally occurring hydrophobic amino acid, a non-naturally occurring hydrophobic amino acid, and a hydrophobic amino acid mimetic, and wherein Ynb, Ync, Ynd, and Yne are each individually absent or selected from the group consisting of a naturally occurring hydrophobic, a non-naturally occurring hydrophobic amino acid, and a hydrophobic amino acid mimetic, and wherein the peptide binds to the dimerization site on a NFkB Class II protein.
2. The anti-inflammatory composition of embodiment 1, wherein each Xm module consists of a sequence according to the formula Xma-Xmb-Xmc-Xmd, and each Yn module consists of a sequence according to the formula Yna-Ynb-YncYnd.
3. The anti-inflammatory composition of embodiment 1, wherein each Xm module consists of a sequence according to the formula Xma-Xmb-Xmc, and each Yn module consists of a sequence according to the formula Yna-Ynb-Ync.
4. The anti-inflammatory composition of any one of embodiments 1 to 3, wherein the peptide also binds to human serum albumin.
5. The anti-inflammatory composition of any one of embodiments 1 to 4, wherein the striapathic region of the peptide contains at least two Xm modules (X1, X2, and X3) and at least two Yn modules (Y1, Y2, and Y3).
6. The anti-inflammatory composition of any one of embodiments 1 to 5, wherein the striapathic region of the peptide contains at least seven amino acid residues.
7. The anti-inflammatory composition of any one of embodiments 1 to 6, wherein the striapathic region of the peptide has a length of 7 to 12 amino acid residues.
8. The anti-inflammatory composition of any one of embodiments 1 to 7, wherein the striapathic region of the peptide constitutes at least 25% of the length of the peptide.
9. The anti-inflammatory composition of any one of embodiments 1 to 8, wherein the striapathic region of the peptide has an amphipathic conformation under physiological conditions.
10. The anti-inflammatory composition of embodiment 9, wherein the striapathic region of the peptide has an amphipathic 310-helical conformation, an amphipathic α-helical conformation, or an amphipathic π-helical conformation when bound to the NFkB Class II protein.
11. The anti-inflammatory composition of embodiment 10, wherein the amphipathic 310-helical, α-helical, or π-helical conformation includes a hydrophobic portion having a facial arc of at least 100°.
12. The anti-inflammatory composition of any one of embodiments 1 to 11, wherein the striapathic region contains hydrophobic amino acid residues having a total volume of at least 650 cubic angstroms.
13. The anti-inflammatory composition of any one of embodiments 1 to 12, wherein the striapathic region is characterized by a ratio of the sum of the volume of hydrophobic amino acid residues to the sum of the volume of hydrophilic amino acid residues, wherein the ratio is at least 0.75 or higher.
14. The anti-inflammatory composition of embodiment 9, wherein the striapathic region of the peptide comprises at least one proline residue and adopts an amphipathic conformation that includes a proline-rich helix.
15. The anti-inflammatory composition of embodiment 9, wherein the striapathic region of the peptide adopts an amphipathic beta-strand conformation.
16. The anti-inflammatory composition of any one of embodiments 1 to 13, wherein the striapathic region includes a sequence selected from the group of sequences defined by Formula I: Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c (Formula I).
17. The anti-inflammatory composition of embodiment 16, wherein the module Y1a-Y1b-Y1c has a sequence selected from the group consisting of Phe-Phe-Phe (FFF), Trp-Trp-Trp (WWW), Tyr-Tyr-Tyr (YYY), Leu-Leu-Leu (LLL), Cys-Cys-Cys (CCC), Met-Met-Met (MMM), Val-Val-Val (VVV), and Ile-Ile-Ile (III).
18. The anti-inflammatory composition of embodiment 16, wherein the module Y1a-Y1b-Y1c has a sequence selected from the group consisting of Phe-Phe-Phe (FFF), Trp-Trp-Trp (WWW), and Tyr-Tyr-Tyr (YYY).
19. The anti-inflammatory composition of any one of embodiments 16 to 18, wherein the module Y2a-Y2b-Y2c has a sequence selected from the group consisting of Phe-Phe-Phe (FFF), Trp-Trp-Trp (WWW), Tyr-Tyr-Tyr (YYY), Leu-Leu-Leu (LLL), Cys-Cys-Cys (CCC), Met-Met-Met (MMM), Val-Val-Val (VVV), and Ile-Ile-Ile (III).
20. The anti-inflammatory composition of any one of embodiments 16 to 18, wherein the module Y2a-Y2b-Y2c has a sequence selected from the group consisting of Phe-Phe-Phe (FFF), Trp-Trp-Trp (WWW), and Tyr-Tyr-Tyr (YYY).
21. The anti-inflammatory composition of embodiment 16, wherein the striapathic region includes a sequence selected from the group consisting of FFF-X1a-FFF (SEQ ID NO: 1), WWW-X1a-WWW (SEQ ID NO: 2), and YYY-X1a-YYY (SEQ ID NO: 3).
22. The anti-inflammatory composition of embodiment 16, wherein the sequence of the three modules is selected from the group consisting of LLL-X1a-LLL (SEQ ID NO: 4), CCC-X1a-CCC (SEQ ID NO: 5), MMM-X1a-MMM (SEQ ID NO: 6), VVV-X1a-VVV (SEQ ID NO: 7), and III-X1a-III (SEQ ID NO: 8).
23. The anti-inflammatory composition of any one of embodiments 16 to 22, wherein X1a is selected from the group consisting of Arg (R), His (H), and Lys (K).
24. The anti-inflammatory composition of any one of embodiments 16 to 22, wherein X1a is selected from the group consisting of Glu (E), Gln (Q), Asn (N), and Asp (D).
25. The anti-inflammatory composition of any one of embodiments 16 to 24, wherein the striapathic region includes a sequence selected from the group of sequences defined by Formula II or the group of sequences defined by Formula III: Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c-X2a-Y3a-X3a (Formula II); X2a-Y3a-X3a-Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c (Formula III).
26. The anti-inflammatory composition of embodiment 25, wherein X2a and X3a are each individually selected from the group consisting of Arg (R), His (H), Lys (K), Glu (E), Gln (Q), Asn (N), and Asp (D).
27. The anti-inflammatory composition of embodiment 25, wherein X2a and X3a are each individually selected from the group consisting of Glu (E), Gln (Q), Asn (N), and Asp (D).
28. The anti-inflammatory composition of any one of embodiments 25 to 27, wherein Y3a is selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), and Be (I).
29. The anti-inflammatory composition of any one of embodiments 25 to 27, wherein Y3a is selected from the group consisting of Phe (F), Trp (W), Tyr (Y), and Leu (L).
30. The anti-inflammatory composition of embodiment 25, wherein the sequence of X2a-Y3a-X3a is selected from the group consisting of EFQ, EFE, EFN, EFD, NFQ, NFE, NFN, NFD, QFQ, QFE, QFN, QFD, DFQ, DFE, DFN, DFD, EWQ, EWE, EWN, EWD, NWQ, NWE, NWN, NWD, QWQ, QWE, QWN, QWD, DWQ, DWE, DWN, DWD, EYQ, EYE, EFN, EYD, NYQ, NYE, NYN, NYD, QYQ, QYE, QYN, QYD, DYQ, DYE, DYN, DYD, ELQ, ELE, ELN, ELD, NLQ, NLE, NLN, NLD, QLQ, QLE, QLN, QLD, DLQ, DLE, DLN, DLD, RFR, RFQ, RFE, RFN, RFD, RWR, RWQ, RWE, RWN, and RWD.
31. The anti-inflammatory composition of embodiment 25, wherein the striapathic region comprises, consists essentially of, or consists of a sequence selected from the group consisting of RP394, RP108-RP123, RP125-131, RP133, RP135-RP141, RP143-RP146, RP148-RP150, RP152-RP165, RP179, RP395, RP211, RP230, RP232, RP258, RP267, RP268, RP271, and RP273.
32. The anti-inflammatory composition of embodiment 25, wherein the striapathic region comprises, consists essentially of, or consists of a sequence selected from the group consisting of RP113 (SEQ ID NO: 39), RP118 (SEQ ID NO: 44), and RP394 (SEQ ID NO: 33).
33. The anti-inflammatory composition of any one of embodiments 1 to 13, wherein the striapathic region includes a sequence selected from the group of sequences defined by Formula VII: Y1a-X1a-X1b-Y2a-Y2b-X2a-X2b-Y3a (Formula VII).
34. The anti-inflammatory composition of embodiment 33, wherein Y2a is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y).
35. The anti-inflammatory composition of embodiment 33, wherein Y2a is selected from the group consisting of Leu (L), Cys (C), Met (M), Val (V), Ile (I), and Ala (A).
36. The anti-inflammatory composition of any one of embodiments 33 to 35, wherein Y2b is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y).
37. The anti-inflammatory composition of any one of embodiments 33 to 35, wherein Y2b is selected from the group consisting of Leu (L), Cys (C), Met (M), Val (V), Ile (I), and Ala (A).
38. The anti-inflammatory composition of any one of embodiments 33 to 37, wherein X1b is selected from the group consisting of Arg (R), Lys (K), and His (H).
39. The anti-inflammatory composition of any one of embodiments 33 to 37, wherein X1b is selected from the group consisting of Asn (N), Gln (Q), Asp (D), and Glu (E).
40. The anti-inflammatory composition of any one of embodiments 33 to 39, wherein X2a is selected from the group consisting of Arg (R), Lys (K), and His (H).
41. The anti-inflammatory composition of any one of embodiments 33 to 39, wherein X2a is selected from the group consisting of Asn (N), Gln (Q), Asp (D), and Glu (E).
42. The anti-inflammatory composition of embodiment 33, wherein the sequence X1b-Y2a-Y2b-X2a is selected from the group consisting of Lys-Phe-Phe-Lys (KFFK; SEQ ID NO: 386), Lys-Trp-Trp-Lys (KWWK; SEQ ID NO: 387), Lys-Tyr-Try-Lys (KYYK; SEQ ID NO: 388), Lys-Phe-Trp-Lys (KFWK; SEQ ID NO: 389), Lys-Trp-Phe-Lys (KWFK; SEQ ID NO: 390), Lys-Phe-Tyr-Lys (KFYK; SEQ ID NO: 391), Lys-Tyr-Phe-Lys (KYFK; SEQ ID NO: 392), Lys-Trp-Tyr-Lys (KWYK; SEQ ID NO: 393), and Lys-Tyr-Trp-Lys (KYWK; SEQ ID NO: 394).
43. The anti-inflammatory composition of embodiment 33, wherein the sequence X1b-Y2a-Y2b-X2a is selected from the group consisting of Arg-Phe-Phe-Arg (RFFR; SEQ ID NO: 395), Arg-Trp-Trp-Arg (RWWR; SEQ ID NO: 396), Arg-Tyr-Try-Arg (RYYR; SEQ ID NO: 397), Arg-Phe-Trp-Arg (RFWR; SEQ ID NO: 398), Arg-Trp-Phe-Arg (RWFR; SEQ ID NO: 399), Arg-Phe-Tyr-Arg (RFYR; SEQ ID NO: 400), Arg-Tyr-Phe-Arg (RYFR; SEQ ID NO: 401), Arg-Trp-Tyr-Arg (RWYR; SEQ ID NO: 402), and Arg-Tyr-Trp-Arg (RYWR; SEQ ID NO: 403).
44. The anti-inflammatory composition of embodiment 33, wherein the sequence X1b-Y2a-Y2bl-X2a is selected from the group consisting of His-Phe-Phe-His (HFFH; SEQ ID NO: 404), His-Trp-Trp-His (HWWH; SEQ ID NO: 405), His-Tyr-Try-His (HYYH; SEQ ID NO: 406), His-Phe-Trp-His (HFWH; SEQ ID NO: 407), His-Trp-Phe-His (HWFH; SEQ ID NO: 408), His-Phe-Tyr-His (HFYH; SEQ ID NO: 409), His-Tyr-Phe-His (HYFH; SEQ ID NO: 410), His-Trp-Tyr-His (HWYH; SEQ ID NO: 411), and His-Tyr-Trp-His (HYWH; SEQ ID NO: 132).
45. The anti-inflammatory composition of any one of embodiments 33 to 44, wherein X1a is selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E).
46. The anti-inflammatory composition of any one of embodiments 33 to 44, wherein X1a is selected from the group consisting of Arg (R) and Gln (Q).
47. The anti-inflammatory composition of any one of embodiments 33 to 46, wherein X2b is selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E).
48. The anti-inflammatory composition of any one of embodiments 33 to 46, wherein X2b is selected from the group consisting of Arg (R) and Gln (Q).
49. The anti-inflammatory composition of any one of embodiments 33 to 48, wherein Y1a is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y).
50. The anti-inflammatory composition of any one of embodiments 33 to 48, wherein Y1a is selected from the group consisting of Leu (L), Cys (C), Met (M), Val (V), Ile (I), and Ala (A).
51. The anti-inflammatory composition of any one of embodiments 33 to 50, wherein Y3a is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y).
52. The anti-inflammatory composition of any one of embodiments 33 to 50, wherein Y3a is selected from the group consisting of Leu (L), Cys (C), Met (M), Val (V), Ile (I), and Ala (A).
53. The anti-inflammatory composition of embodiment 33, wherein the striapathic region includes a sequence selected from the group consisting of F-X1a-X1b-FF-X2a-X2b-F (SEQ ID NO: 9), F-X1a-X1b-FF-X2a-X2b-W (SEQ ID NO: 10), W-X1a-X1b-FF-X2a-X2b-F (SEQ ID NO: 11), F-X1a-X1b-FW-X2a-X2b-F (SEQ ID NO: 12), F-X1a-X1b-WF-X2a-X2b-F (SEQ ID NO: 13), F-X1a-X1b-WW-X2a-X2b-F (SEQ ID NO: 14), W-X1a-X1b-WW-X2a-X2b-F (SEQ ID NO: 15), F-X1a-X1b-WW-X2a-X2b-W (SEQ ID NO: 16), W-X1a-X1b-WW-X2a-X2b-W (SEQ ID NO: 17), F-X1a-X1b-FF-X2a-X2b-Y (SEQ ID NO: 18), Y-X1a-X1b-FF-X2a-X2b-F (SEQ ID NO: 19), F-X1a-X1b-FY-X2a-X2b-F (SEQ ID NO: 20), F-X1a-X1b-YF-X2a-X2b-F (SEQ ID NO: 21), F-X1a-X1b-YY-X2a-X2b-F (SEQ ID NO: 22), Y-X1a-X1b-YY-X2a-X2b-F (SEQ ID NO: 23), F-X1a-X1b-YY-X2a-X2b-Y (SEQ ID NO: 24), and Y-X1a-X1b-YY-X2a-X2b-Y (SEQ ID NO: 25), Y-X1a-X1b-YY-X2a-X2b-W (SEQ ID NO: 26), W-X1a-X1b-YY-X2a-X2b-Y (SEQ ID NO: 27), Y-X1a-X1b-YW-X2a-X2b-Y (SEQ ID NO: 28), Y-X1a-X1b-WY-X2a-X2b-Y (SEQ ID NO: 29), Y-X1a-X1b-WW-X2a-X2b-Y (SEQ ID NO: 30), W-X1a-X1b-WW-X2a-X2b-Y (SEQ ID NO: 31), and Y-X1a-X1b-WW-X2a-X2b-W (SEQ ID NO: 32).
54. The anti-inflammatory composition of embodiment 53, wherein X1a, X1b, X2a, and X2b are each independently selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E).
55. The anti-inflammatory composition of embodiment 53 or 54, wherein X1b and X2a are each independently selected from the group consisting of Arg (R), Lys (K), and His (H).
56. The anti-inflammatory composition of any one of embodiments 33 to 55, wherein the striapathic region includes a first additional amino acid residue directly bound to Y1a of Formula VII, wherein the first additional amino acid residue is a hydrophobic amino acid residue.
57. The anti-inflammatory composition of embodiment 56, wherein the first additional amino acid residue is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y).
58. The anti-inflammatory composition of any one of embodiments 33 to 55, wherein the striapathic region includes a first additional amino acid residue directly bound to Y3a of Formula VII, wherein the first additional amino acid residue is a hydrophobic amino acid residue.
59. The anti-inflammatory composition of embodiment 58, wherein the first additional amino acid residue is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y).
60. The anti-inflammatory composition of any one of embodiments 33 to 55, wherein the striapathic region includes a first additional amino acid residue directly bound to Y1a of Formula VII, wherein the first additional amino acid residue is a hydrophilic amino acid residue.
61. The anti-inflammatory composition of embodiment 60, wherein the first additional amino acid residue is selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E).
62. The anti-inflammatory composition of any one of embodiments 33 to 55, wherein the striapathic region includes a first additional amino acid residue directly bound to Y3a of Formula VII, wherein the first additional amino acid residue is a hydrophilic amino acid residue.
63. The anti-inflammatory composition of embodiment 62, wherein the first additional amino acid residue is selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E).
64. The anti-inflammatory composition of 56, 57, 60, or 61, wherein the striapathic region includes a second additional amino acid residue directly bound to Y3a of Formula VII, wherein the second additional amino acid residue is a hydrophobic amino acid residue.
65. The anti-inflammatory composition of embodiment 64, wherein the second additional amino acid residue is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y).
66. The anti-inflammatory composition of 58, 59, 62, or 63, wherein the striapathic region includes a second additional amino acid residue directly bound to Y1a of Formula VII, wherein the second additional amino acid residue is a hydrophilic amino acid residue.
67. The anti-inflammatory composition of embodiment 66, wherein the second additional amino acid residue is selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E).
68. The anti-inflammatory composition of embodiment 33, wherein the striapathic region comprises, consists essentially of, or consists of a sequence selected from the group consisting of RP124, RP132, RP134, RP142, RP147, RP151, RP166-RP172, RP175, RP177, RP182, RP183, RP185, RP186, RP 424, RP190, RP194, RP198, RP199-RP202, RP204, RP206, RP207, RP209, RP210, RP212-RP216, RP218, RP219, RP425, RP225, RP227, RP233-RP239, RP398, RP241-RP247, RP250-RP256, and RP426.
69. The anti-inflammatory composition of embodiment 33, wherein the striapathic region comprises, consists essentially of, or consists of a sequence selected from the group consisting of RP124 (SEQ ID NO: 106), RP166 (SEQ ID NO: 112), RP182 (SEQ ID NO: 121), and RP183 (SEQ ID NO: 122).
70. The anti-inflammatory composition of any one of embodiments 1 to 15, wherein the striapathic region includes a sequence selected from the group of sequences defined by any one of Formulas I-XLVIII and L: Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c (Formula I); Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c-X2a-Y3a-X3a (Formula II); X2a-Y3a-X3a-Y1a-Y1b-Y1c-X1a-Y2a-Y2b-Y2c (Formula III); X1a-X1b-X1c-Y2a-X2a-X2b-X2c (Formula IV); Y1a-X1a-X1b-X1c-Y2a-X2a-X2b-X2c-Y3a-X3a (Formula V); X1a-X1b-Y2a-Y2b-X2a-X2b (Formula VI); Y1a-X1a-X1b-Y2a-Y2b-X2a-X2b-Y3a (Formula VII); Y1a-X1a-X1b-Y2a-Y2b-X2a-X2b-Y3a-Y3b-X3a (Formula VIII); Y1a-Y1b-X1a-X1b-Y2a-Y2b-X2a-X2b-Y3a-Y3b (Formula IX); Y1a-Y1b-X1a-X1b-Y2a-Y2b-X2a-X2b-Y3a-X3a (Formula X); X1a-Y1a-X2a-X2b-Y2a-Y2b-X3a-X3b-Y3a-Y3b (Formula XI); X1a-Y1a-Y1b-X2a-X2b-Y2a-Y2b-X3a-X3b-Y3a (Formula XII); Y1a-X1a-X1b-Y2a-Y2b-X2a-X2b-X2c-Y3a-Y3b (Formula XIII); X1a-X1b-X1c-Y1a-Y1b-X2a-X2b-Y2a-Y2b-Y2c (Formula XIV); Y1a-Y1b-Y1c-X1a-X1b-Y2a-Y2b-X2a-X2b-X2c (Formula XV); Y1a-Y1b-X1a-X1b-X1c-Y2a-Y2b-X2a-X2b-Y3a (Formula XVI); Y1a-Y1b-X1a-X1b-Y2a-Y2b (Formula XVII); X1a-Y1a-Y1b-X2a-X2b-Y2a-Y2b-X3a (Formula XVIII); Y1a-Y1b-X1a-X1b-Y2a-Y2b-X2a-Y3a-Y3b-X3a (Formula XIX); X1a-Y1a-Y1b-X2a-Y2a-Y2b-X3a-X3b-Y3a-Y3b (Formula XX); Y1a-Y1b-X1a-X1b-Y2a-X2a-X2b-Y3a-Y3b (Formula XXI); X1a-Y1a-Y1b-X2a-X2b-X2c-Y2a-X3a-Y3a-Y3b (Formula XXII); Y1a-Y1b-X1a-Y2a-X2a-X2b-X2c-Y3a-Y3b-X3a (Formula XXIII); X1a-X1b-Y1a-X2a-Y2a-X3a-X3b (Formula XXIV); Y1a-Y1b-Y1c-X1a-X1b-Y2a-X2a-Y3a-X3a-X3b (Formula XXV); X1a-X1b-Y1a-X2a-Y2a-X3a-X3b-Y3a-Y3b-Y3c (Formula XXVI); X1a-X1b-X1c-Y1a-Y1b-Y1c (Formula XXVII); X1a-X1b-X1c-X1d-Y1a-Y1b-Y1c-Y1d (Formula XXVIII); Y1a-X1a-X1b-X1c-X1d-Y2a-Y2b-Y2c-Y2d-X2a (Formula XXIX); X1a-X1b-X1c-X1d-X1e-Y1a-Y1b-Y1c-Y1d-Y1e (Formula XXX); Y1a-Y1b-X1a-X1b-X1c-Y2a-Y2b-Y2c-X2a-X2b (Formula XXXI); X1a-Y1a-X2a-Y2a-X3a-X3b-X3c-Y3a-Y3b-Y3c (Formula XXXII); Y1a-Y1b-Y1c-X1a-X1b-X1c (Formula XXXIII); Y1a-Y1b-Y1c-Y1d-X1a-X1b-X1c-X1d (Formula XXXIV); X1a-Y1a-Y1b-Y1c-Y1d-X2a-X2b-X2c-X2d-Y2a (Formula XXXV); Y1a-Y1b-Y1c-Y1d-Y1e-X1a-X1b-X1c-X1d-X1e (Formula XXXVI); X1a-X1b-Y1a-Y1b-Y1c-X2a-X2b-X2c-Y2a-Y2b (Formula XXXVII); Y1a-Y1b-Y1c-X1a-X1a-X1c-Y2a-X2a-Y3a-X3a (Formula XXXVIII); Y1a-X1a-X1b-X1c-X1d-X1e-Y2a (Formula XXXIX); Y1a-X1a-X1b-X1c-X1d-X1e-Y2a-Y2b-Y2c-Y2d (Formula XL); Y1a-Y1b-X1a-X1b-X1c-X1d-X1e-Y2a-Y2b-Y2c (Formula XLI); Y1a-Y1b-Y1c-X1a-X1b-X1c-X1d-X1e-Y2a-Y2b (Formula XLII); Y1a-Y1b-Y1c-Y1e-X1a-X1b-X1c-X1d-X1e-Y2a (Formula XLIII); X1a-Y1a-Y1b-Y1c-Y1d-Y1e-X2a (Formula XLIV); X1a-Y1a-Y1b-Y1c-Y1d-Y1e-X2a-X2b-X2c-X2d (Formula XLV); X1a-X1b-Y1a-Y1b-Y1c-Y1d-Y1e-X2a-X2b-X2c (Formula XLVI); X1a-X1b-X1c-Y1a-Y1b-Y1c-Y1d-Y1e-X2a-X2b (Formula XLVII); X1a-X1b-X1c-X1d-Y1a-Y1b-Y1c-Y1d-Y1e-X2a (Formula XLVIII); and Y1a-Y1b-X1a-Y2a-Y2b-X2a-Y3a-Y3b-X3a-Y4a (Formula L).
71. The anti-inflammatory composition of embodiment 70, wherein Y1a, Y1b, Y1c, Y2a, Y2b, Y2c, Y3a, Y3b, and Y3c are each individually selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Cys (C), Met (M), Val (V), Ile (I), and Ala (A).
72. The anti-inflammatory composition of embodiment 70, wherein Y1a, Y1b, Y1c, Y2a, Y2b, Y2c, Y3a, Y3b, and Y3c are each individually selected from the group consisting of Phe (F), Trp (W), and Tyr (Y).
73. The anti-inflammatory composition of any one of embodiments 70 to 72, wherein X1a, X1b, X1c, X2a, X2b, X2c, X3a, and X3b are each individually selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E).
74. The anti-inflammatory composition of any one of embodiments 70 to 73, wherein X1a, X1b, X1c, X2a, X2b, X2c, X3a, and X3b are each individually selected from the group consisting of Arg (R), Lys (K), His (H), and Gln (Q).
75. The anti-inflammatory composition of any one of embodiments 70 to 74, wherein the striapathic region includes a first additional amino acid residue directly bound to the N-terminal end of any one of Formulas I-XLVIII and L, wherein the first additional amino acid residue is a hydrophobic amino acid residue.
76. The anti-inflammatory composition of embodiment 70, wherein the first additional amino acid residue is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y).
77. The anti-inflammatory composition of any one of embodiments 70 to 74, wherein the striapathic region includes a first additional amino acid residue directly bound to the C-terminal end of any one of Formulas I-XLVIII and L, wherein the first additional amino acid residue is a hydrophobic amino acid residue.
78. The anti-inflammatory composition of embodiment 77, wherein the first additional amino acid residue is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y).
79. The anti-inflammatory composition of any one of embodiments 70 to 74, wherein the striapathic region includes a first additional amino acid residue directly bound to the N-terminal end of any one of Formulas I-XLVIII and L, wherein the first additional amino acid residue is a hydrophilic amino acid residue.
80. The anti-inflammatory composition of embodiment 79, wherein the first additional amino acid residue is selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E).
81. The anti-inflammatory composition of any one of embodiments 70 to 74, wherein the striapathic region includes a first additional amino acid residue directly bound to the C-terminal end of any one of Formulas I-XLVIII and L, wherein the first additional amino acid residue is a hydrophilic amino acid residue.
82. The anti-inflammatory composition of embodiment 81, wherein the first additional amino acid residue is selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E).
83. The anti-inflammatory composition of any one of embodiments 75, 76, 79, or 80, wherein the striapathic region includes a second additional amino acid residue directly bound to the C-terminal end of any one of Formulas I-XLVIII and L, wherein the second additional amino acid residue is a hydrophobic amino acid residue.
84. The anti-inflammatory composition of embodiment 83, wherein the second additional amino acid residue is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y).
85. The anti-inflammatory composition of any one of embodiments 77, 78, 81, or 82, wherein the striapathic region includes a second additional amino acid residue directly bound to the N-terminal end of any one of Formulas I-XLVIII and L, wherein the second additional amino acid residue is a hydrophilic amino acid residue.
86. The anti-inflammatory composition of embodiment 81, wherein the second additional amino acid residue is selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E).
87. The anti-inflammatory composition of embodiment 70, wherein the striapathic region comprises, consists essentially of, or consists of a sequence selected from the group consisting of RP396, RP405, RP174, RP176, RP178, RP180-181, RP184, RP408, RP187, RP416, RP188, RP189, RP388, RP417, RP191-RP193, RP404, RP196, RP397, RP197, RP402, RP203, RP409, RP205, RP208, RP217, RP220-RP224, RP226, RP229, RP231, RP240, RP248, RP249, RP415, RP257, RP259-RP266, RP269, RP272, RP406, RP422, RP407, RP400, RP419, RP401, RP423, RP411, RP418, RP428, RP420, RP421, RP429, RP413, RP430, RP270.
88. The anti-inflammatory composition of any one of embodiments 1 to 9 or 15, wherein the striapathic region includes a sequence selected from the group of sequences defined by Formula XLIX:

Y1a-X1a-Y2a-X2a-Y3a-X3a  (Formula XLIX).

89. The anti-inflammatory composition of embodiment 88, wherein Y1a, Y2a, and Y3a are each independently selected from the group consisting of Phe (F), Trp (W), Tyr (Y), Leu (L), Ile (I), Cys (C), and Met (M).
90. The anti-inflammatory composition of embodiment 88, wherein Y1a, Y2a, and Y3a are each independently selected from the group consisting of Phe (F), Trp (W), and Tyr(Y).
91. The anti-inflammatory composition of any one of embodiments 88 to 90, wherein X1a, X2a, and X3a are each independently selected from the group consisting of Arg (R), Lys (K), His (H), Gln (Q), Glu (E), Asn (N), and Asp (D).
92. The anti-inflammatory composition of any one of embodiments 88 to 90, wherein X1a, X2a, and X3a are each independently selected from the group consisting of Arg (R), Lys (K), and His (H).
93. The anti-inflammatory composition of any one of embodiments 88 to 92, wherein the striapathic region includes a first additional amino acid residue directly bound to Y1a of Formula XLIX, wherein the first additional amino acid residue is a hydrophilic amino acid residue.
94. The anti-inflammatory composition of embodiment 93, wherein the first additional amino acid residue is selected from the group consisting of Arg (R), Lys (K), His (H), Asn (N), Gln (Q), Asp (D), and Glu (E).
95. The anti-inflammatory composition of embodiment 93, wherein the first additional amino acid residue is selected from the group consisting of Arg (R), Lys (K), and His (H).
96. The anti-inflammatory composition of any one of embodiments 88 to 92, wherein the striapathic region includes a first additional amino acid residue directly bound to X3a of Formula XLIX, wherein the first additional amino acid residue is a hydrophobic amino acid residue.
97. The anti-inflammatory composition of embodiment 96, wherein the first additional amino acid residue is selected from the group consisting of Phe (F), Trp (W), (Tyr), Leu (L), Ile (I), Cys (C), and Met (M).
98. The anti-inflammatory composition of embodiment 96, wherein the first additional amino acid residue is selected from the group consisting of Phe (F), Trp (W), and (Tyr).
99. The anti-inflammatory composition of any one of embodiments 93 to 95, wherein the striapathic region includes a second additional amino acid residue directly bound to X3a of Formula XLIX, wherein the second additional amino acid residue is a hydrophobic amino acid residue.
100. The anti-inflammatory composition of embodiment 99, wherein the second additional amino acid residue is selected from the group consisting of Phe (F), Trp (W), (Tyr), Leu (L), Ile (I), Cys (C), and Met (M).
101. The anti-inflammatory composition of embodiment 99, wherein the second additional amino acid residue is selected from the group consisting of Phe (F), Trp (W), and Tyr (Y).
102. An anti-inflammatory composition comprising a peptide, wherein the peptide is 3 to 24 amino acids residues in length and comprises a striapathic region having at least 70% identity with the sequence NFNFFFRFFF (RP394, SEQ ID NO: 33), wherein the peptide binds to the dimerization site on a NFkB Class II protein.
103. The anti-inflammatory composition of embodiment 102, wherein the peptide also binds to human serum albumin.
104. The anti-inflammatory composition of embodiment 102 or 103, wherein the differences between the striapathic region of the peptide and the sequence NFNFFFRFFF (SEQ ID NO: 33) are limited to conservative or highly conservative amino acid substitutions.
105. The anti-inflammatory composition of embodiment 102 or 103, wherein the striapathic region of the peptide differs from the sequence NFNFFFRFFF (SEQ ID NO: 33) by substitution of one or more of the phenylalanine (F) residues with an amino acid residue selected from the group consisting of Trp (W), Tyr (Y), His (H), and Leu (L).
106. The anti-inflammatory composition of embodiment 102 or 103, wherein the striapathic region of the peptide differs from the sequence NFNFFFRFFF (SEQ ID NO: 33) by the deletion of one, two, or three amino acids.
107. The anti-inflammatory composition of embodiment 106, wherein the deleted amino acids are located at the N-terminal end, the C-terminal end, or both ends of the sequence NFNFFFRFFF (SEQ ID NO: 33).
108. An anti-inflammatory composition comprising a peptide, wherein the peptide is 3 to 24 amino acids residues in length and comprises a striapathic region having at least 70% identity with the sequence FFFRFFFNFN (RP118, SEQ ID NO: 44), wherein the peptide binds to the dimerization site on a NFkB Class II protein.
109. The anti-inflammatory composition of embodiment 108, wherein the peptide also binds to human serum albumin.
110. The anti-inflammatory composition of embodiment 108 or 109, wherein the differences between the striapathic region of the peptide and the sequence FFFRFFFNFN (SEQ ID NO: 44) are limited to conservative or highly conservative amino acid substitutions.
111. The anti-inflammatory composition of embodiment 108 or 109, wherein the striapathic region of the peptide differs from the sequence FFFRFFFNFN (SEQ ID NO: 44) by substitution of one or more of the phenylalanine (F) residues with an amino acid residue selected from the group consisting of Trp (W), Tyr (Y), His (H), and Leu (L).
112. The anti-inflammatory composition of embodiment 108 or 109, wherein the striapathic region of the peptide differs from the sequence FFFRFFFNFN (SEQ ID NO: 44) by the deletion of one, two, or three amino acids.
113. The anti-inflammatory composition of embodiment 112, wherein the deleted amino acids are located at the N-terminal end, the C-terminal end, or both ends of the sequence FFFRFFFNFN (SEQ ID NO: 44).
114. An anti-inflammatory composition comprising a peptide, wherein the peptide is 3 to 24 amino acids residues in length and comprises a striapathic region having at least 70% identity with the sequence FFRKFAKRFK (RP183, SEQ ID NO: 122), wherein the peptide binds to the dimerization site on a NFkB Class II protein.
115. The anti-inflammatory composition of embodiment 114, wherein the peptide also binds to human serum albumin.
116. The anti-inflammatory composition of embodiment 114 or 115, wherein the differences between the striapathic region of the peptide and the sequence FFRKFAKRFK (SEQ ID NO: 122) are limited to conservative or highly conservative amino acid substitutions.
117. The anti-inflammatory composition of embodiment 114 or 115, wherein the striapathic region of the peptide differs from the sequence FFRKFAKRFK (SEQ ID NO: 122) by substitution of one or more of the phenylalanine (F) residues with an amino acid residue selected from the group consisting of Trp (W), Tyr (Y), and Leu (L).
118. The anti-inflammatory composition of embodiment 114 or 115, wherein the striapathic region of the peptide differs from the sequence FFRKFAKRFK (SEQ ID NO: 122) by the deletion of one, two, or three amino acids.
119. The anti-inflammatory composition of embodiment 118, wherein the deleted amino acids are located at the N-terminal end, the C-terminal end, or both ends of the sequence FFRKFAKRFK (SEQ ID NO: 122).
120. An anti-inflammatory composition comprising a peptide, wherein the peptide is 3 to 24 amino acids residues in length and comprises a striapathic region having at least 70% identity with the sequence KFRKAFKRFF (RP182, SEQ ID NO: 121), wherein the peptide binds to the dimerization site on a NFkB Class II protein.
121. The anti-inflammatory composition of embodiment 120, wherein the peptide also binds to human serum albumin.
122. The anti-inflammatory composition of embodiment 120 or 121, wherein the differences between the striapathic region of the peptide and the sequence KFRKAFKRFF (SEQ ID NO: 121) are limited to conservative or highly conservative amino acid substitutions.
123. The anti-inflammatory composition of embodiment 120 or 121, wherein the striapathic region of the peptide differs from the sequence KFRKAFKRFF (SEQ ID NO: 121) by substitution of one or more of the phenylalanine (F) residues with an amino acid residue selected from the group consisting of Trp (W), Tyr (Y), and Leu (L) .
124. The anti-inflammatory composition of embodiment 120 or 121, wherein the striapathic region of the peptide differs from the sequence KFRKAFKRFF (SEQ ID NO: 121) by the deletion of one, two, or three amino acids.
125. The anti-inflammatory composition of embodiment 124, wherein the deleted amino acids are located at the N-terminal end, the C-terminal end, or both ends of the sequence KFRKAFKRFF (SEQ ID NO: 121).
126. The anti-inflammatory composition of any one of embodiments 1 to 125, wherein the peptide binds to the dimerization site on Rel B (SEQ ID NO: 367) with a binding energy of at least −650 kcal/mol.
127. The anti-inflammatory composition of any one of embodiments 1 to 126, wherein the peptide binds to the dimerization site on Rel B (SEQ ID NO: 367) and directly contacts at least one amino acid residue of Rel B selected from the group consisting of Glu 298, Tyr-300, Leu-301, Leu-302, Asp-330, His-332, and Leu-371.
128. The anti-inflammatory composition of embodiment 127, wherein the peptide, when bound to the dimerization site on Rel B, forms an ionic bond with Asp-330, forms an ionic bond with His-332, and/or makes a hydrophobic contact with Leu-371.
129. The anti-inflammatory composition of any one of embodiments 1 to 128, wherein the peptide binds to at least one signaling molecule selected from the group consisting of TGFβ (SEQ ID NO: 368), Notch1 (SEQ ID NO: 369), Wnt8R (SEQ ID NO: 370), TRAIL (SEQ ID NO: 371), IL6R (SEQ ID NO: 372), IL10R (SEQ ID NO: 373), EGFR (SEQ ID NO: 374), CDK6 (SEQ ID NO: 375), Histone Methyl Transferase (HMT) (SEQ ID NO: 376), CD47 (SEQ ID NO: 377), SIRP-α (SEQ ID NO: 378), CD206 (SEQ ID NO: 379), TGM2 (SEQ ID NO: 380); LEGUMAIN (SEQ ID NO: 137), CD209 (SEQ ID NO: 140), FAS (SEQ ID NO: 152), PD-1 (SEQ ID NO: 159), MKK7 (SEQ ID NO: 166), and RNR (SEQ ID NO: 168).
130. The anti-inflammatory composition of embodiment 129, wherein the peptide binds to TGFβ (SEQ ID NO: 368) with a binding energy of at least −650 kcal/mol.
131. The anti-inflammatory composition of embodiment 129 or 130, wherein the peptide binds to TGFβ (SEQ ID NO: 368) and directly contacts at least one amino acid residue of TGFβ selected from the group consisting of Leu-20, Ile-22, Phe-24, Asp-27, Leu-28, Trp-30, Trp-32, Tyr-39, Phe-43, Pro-80, Leu-83, Leu-101, and Ser-112.
132. The anti-inflammatory composition of any one of embodiments 129 to 131, wherein the peptide binds to Notch1 (SEQ ID NO: 369) with a binding energy of at least −650 kcal/mol.
133. The anti-inflammatory composition of any one of embodiments 120 to 123, wherein the peptide binds to Notch (SEQ ID NO: 369) and directly contacts at least one amino acid residue of Notch selected from the group consisting of Phe-1520, Gln-1523, Arg-1524, Glu-1526, Ala-1553, Glu-1556, Trp-1557, Cys-1562, His-1602, Arg-1684, Gln-1685, Cys-1686, Ser-1691, Cys-1693, Phe-1694, and Phe-1703.
134. The anti-inflammatory composition of any one of embodiments 129 to 133, wherein the peptide binds to Wnt8R (SEQ ID NO: 370) with a binding energy of at least −600 kcal/mol.
135. The anti-inflammatory composition of any one of embodiments 129 to 134, wherein the peptide binds to Wnt8R (SEQ ID NO: 370) and directly contacts at least one amino acid residue of Wnt8R selected from the group consisting of Tyr-52, Gln-56, Phe-57, Asn-58, Met-91, Tyr-100, Lys-101, Pro-103, Pro-105, Pro-106, Arg-137, and Asp-145.
136. The anti-inflammatory composition of any one of embodiments 129 to 135, wherein the peptide binds to TRAIL (SEQ ID NO: 371) with a binding energy of at least −650 kcal/mol.
137. The anti-inflammatory composition of any one of embodiments 120 to 127, wherein the peptide binds to TRAIL (SEQ ID NO: 371) and directly contacts at least one amino acid residue of TRAIL selected from the group consisting of Arg-130, Arg-158, Ser-159, Gly-160, His-161, Phe-163, Tyr-189, Arg-189, Gln-193, Glu-195, Glu-236, Tyr-237, Leu-239, Asp-267, Asp-269, His-270, and Glu-271.
138. The anti-inflammatory composition of any one of embodiments 129 to 137, wherein the peptide binds to IL6R (SEQ ID NO: 372) with a binding energy of at least −600 kcal/mol.
139. The anti-inflammatory composition of any one of embodiments 129 to 138, wherein the peptide binds to IL6R (SEQ ID NO: 372) and directly contacts at least one amino acid residue of IL6R selected from the group consisting of Glu-163, Gly-164, Phe-168, Gln-190, Phe-229, Tyr-230, Phe-279, and Gln-281.
140. The anti-inflammatory composition of any one of embodiments 129 to 139, wherein the peptide binds to IL10R (SEQ ID NO: 373) with a binding energy of at least −600 kcal/mol.
141. The anti-inflammatory composition of any one of embodiments 129 to 140, wherein the peptide binds to IL10R (SEQ ID NO: 373) and directly contacts at least one amino acid residue of IL10R selected from the group consisting of Tyr-43, Ile-45, Glu-46, Asp-61, Asn-73, Arg-76, Asn-94, Arg-96, Phe-143, Ala-189, Ser-190, and Ser-191.
142. The anti-inflammatory composition of any one of embodiments 129 to 141, wherein the peptide binds to EGFR (SEQ ID NO: 374) with a binding energy of at least −650 kcal/mol.
143. The anti-inflammatory composition of any one of embodiments 129 to 142, wherein the peptide binds to EGFR (SEQ ID NO: 374) and directly contacts at least one amino acid residue of EGFR selected from the group consisting of Leu-10, Thr-40, Trp-41, Leu-63, His-66, Asp-68, Leu-88, Tyr-101, Asp-48, and Phe-51.
144. The anti-inflammatory composition of any one of embodiments 129 to 143, wherein the peptide binds to CDK6 (SEQ ID NO: 375) with a binding energy of at least −600 kcal/mol.
145. The anti-inflammatory composition of any one of embodiments 129 to 144, wherein the peptide binds to CDK6 (SEQ ID NO: 375) and directly contacts at least one amino acid residue of CDK6 selected from the group consisting of Val-142, Arg-144, Asp-145, Ser-171, Val-180, Val-181, Leu-183, Arg-186, Val-190, Gln-193, Tyr-196, and Val-200.
146. The anti-inflammatory composition of any one of embodiments 129 to 145, wherein the peptide binds to histone methyl transferase (HMT) (SEQ ID NO: 376) with a binding energy of at least −600 kcal/mol.
147. The anti-inflammatory composition of any one of embodiments 129 to 146, wherein the peptide binds to HMT (SEQ ID NO: 376) and directly contacts at least one amino acid residue of HMT selected from the group consisting of Asn-69, His-70, Ser-71, Lys-72, Asp-73, Pro-74, and Asn-75.
148. The anti-inflammatory composition of any one of embodiments 129 to 147, wherein the peptide binds to the SIRP-α binding site on CD47 (SEQ ID NO: 377) with a binding energy of at least −550 kcal/mol.
149. The anti-inflammatory composition of any one of embodiments 129 to 148, wherein the peptide binds to CD47 (SEQ ID NO: 377) and directly contacts at least one amino acid residue of CD47 selected from the group consisting of Glu-29, Ala-30, Glu-35, Val-36, Tyr-37, Lys-39, Thr-49, Asp-51, Glu-97, Thr-99, Leu-101, Thr-102, Arp-103, Glu-104, and Glu-106.
150. The anti-inflammatory composition of any one of embodiments 129 to 149, wherein the peptide binds to the CD47 binding site on SIRP-α (SEQ ID NO: 378) with a binding energy of at least −600 kcal/mol.
151. The anti-inflammatory composition of any one of embodiments 129 to 150, wherein the peptide binds to SIRP-α (SEQ ID NO: 378) and directly contacts at least one amino acid residue of SIRP-a selected from the group consisting of Leu-30, Gln-37, Gln-52, Lys-53, Ser-66, Thr-67, Arg-69, Met-72, Phe-74, Lys-96, and Asp-100.
152. The anti-inflammatory composition of any one of embodiments 129 to 151, wherein the peptide binds to CD206 (SEQ ID NO: 379) with a binding energy of at least −650 kcal/mol.
153. The anti-inflammatory composition of any one of embodiments 129 to 152, wherein the peptide binds to CD206 (SEQ ID NO: 379) and directly contacts at least one amino acid residue of CD206 selected from the group consisting of Glu-725, Tyr-729, Glu-733, Asn-747, and Asp-748.
154. The anti-inflammatory composition of any one of embodiments 129 to 153, wherein the peptide binds to TGM2 (SEQ ID NO: 380) with a binding energy of at least −650 kcal/mol.
155. The anti-inflammatory composition of any one of embodiments 129 to 154, wherein the peptide binds to TGM2 (SEQ ID NO: 380) and directly contacts at least one amino acid residue of TGM2 selected from the group consisting of Cys-277, His-335, and Asp-358.
156. The anti-inflammatory composition of any one of embodiments 129 to 155, wherein the peptide binds to LEGUMAIN (SEQ ID NO: 137) with a binding energy of at least −600 kcal/mol.
157. The anti-inflammatory composition of any one of embodiments 129 to 156, wherein the peptide binds to LEGUMAIN (SEQ ID NO: 137) and directly contacts at least one amino acid residue of LEGUMAIN selected from the group consisting of Asn-44, Arg-46, His-159, Glu-189, Cys-191, Ser-217, Ser-218 and Asp-233.
158. The anti-inflammatory composition of any one of embodiments 129 to 157, wherein the peptide binds to CD209 (SEQ ID NO: 140) with a binding energy of at least −600 kcal/mol.
159. The anti-inflammatory composition of any one of embodiments 129 to 158, wherein the peptide binds to CD209 (SEQ ID NO: 140) and directly contacts at least one amino acid residue of CD209 selected from the group consisting of Phe-269, Glu-280, Glu-303, Asn-305, Asn-306, Glu-310, Asp-311, Ser-316, Gly-317, Asn-321 and Lys-324.
160. The anti-inflammatory composition of any one of embodiments 129 to 159, wherein the peptide binds to FAS (SEQ ID NO: 152) with a binding energy of at least −600 kcal/mol.
161. The anti-inflammatory composition of any one of embodiments 129 to 160, wherein the peptide binds to FAS (; SEQ ID NO: 152) and directly contacts at least one amino acid residue of FAS selected from the group consisting of Lys-251, Lys-296, Lys-299, Leu-303, Leu-306, Ala-307, Glu-308, Lys-309, Gln-311, Ile-314, Leu-315, Asp-317, Ile-318 and Thr-319.
162. The anti-inflammatory composition of any one of embodiments 129 to 161, wherein the peptide binds to PD-1 (SEQ ID NO: 159) with a binding energy of at least −600 kcal/mol.
163. The anti-inflammatory composition of any one of embodiments 129 to 162, wherein the peptide binds to PD-1 (SEQ ID NO: 159) and directly contacts at least one amino acid residue of PD-1 selected from the group consisting of Val-64, Asn-66, Tyr-68, Met-70, Thr-76, Lys-78, Thr-120, Leu-122, Ala-125, and Ser-127.
164. The anti-inflammatory composition of any one of embodiments 129 to 163, wherein the peptide binds to MKK7 (SEQ ID NO: 166) with a binding energy of at least −600 kcal/mol.
165. The anti-inflammatory composition of any one of embodiments 129 to 164, wherein the peptide binds to MKK7 (SEQ ID NO: 166) and directly contacts at least one amino acid residue of MKK7 selected from the group consisting of Met-142, Val-150, Lys-152, Lys-165, Met-212, Met-215, Thr-217, Lys-221, Leu-266, Cys-276 and Asp-277.
166. The anti-inflammatory composition of any one of embodiments 129 to 165, wherein the peptide binds to RNR (SEQ ID NO: 168) with a binding energy of at least −600 kcal/mol.
167. The anti-inflammatory composition of any one of embodiments 129 to 166, wherein the peptide binds to RNR (SEQ ID NO: 168) and directly contacts at least one amino acid residue of RNR selected from the group consisting of Asn-426, Leu-427, Cys-428, Glu-430, Met-606, Pro-608 and Ala-610.
168. The anti-inflammatory composition of any one of embodiments 1 to 167, wherein the peptide binds to human serum albumin (HSA) (SEQ ID NO: 381) with a binding energy of at least −650 kcal/mol.
169. The anti-inflammatory composition of any one of embodiments 1 to 168, wherein the peptide comprises a striapathic region that is composed exclusively of D-form amino acid residues.
170. The anti-inflammatory composition of any one of embodiments 1 to 169, wherein the peptide is in solution at a concentration of about 0.1 mg/ml to about 100 mg/ml.
171. The anti-inflammatory composition of any one of embodiments 1 to 170, wherein the composition contains about 1 mg to about 500 mg of the peptide.
172. The anti-inflammatory composition of embodiment 158 or 171, wherein the composition is substantially free of protein other than the peptide.
173. An anti-inflammatory composition comprising a first peptide as defined in any one of embodiments 1 to 171 in combination with a second peptide as defined in any one of embodiments 1 to 171, wherein the first and second peptides can have the same sequence or different sequences.
174. The anti-inflammatory composition of embodiment 173, wherein the first and second peptides are linked together by a peptide bond, a peptide linker, or a non-peptide linker.
175. The anti-inflammatory composition of embodiment 173, wherein the first and second peptides are linked together by a peptide linker, wherein the peptide linker has a sequence selected from the group consisting of Gly-Gly-Gly (GGG), Gly-Gly-Gly-Arg (GGGR; SEQ ID NO: 412), Gly-Pro-Gly (GPG), and Gly-Pro-Gly-Arg (GPGR; SEQ ID NO: 413).
176. The anti-inflammatory composition of embodiment 174 or 175, wherein the linked first and second peptides bind to the dimerization site on Rel B (SEQ ID NO: 367) with a binding energy of at least −700 kcal/mol.
177. The anti-inflammatory composition of any one of embodiments 1 to 171 and embodiments 173 to 176, further comprising serum albumin.
178. The anti-inflammatory composition of embodiment 177, wherein the composition is substantially free of blood proteins other than serum albumin.
179. A pharmaceutical composition comprising the anti-inflammatory composition of any one of embodiments 1 to 178, and a pharmaceutically acceptable carrier.
180. The pharmaceutical composition of embodiment 179, wherein the composition comprises a chemotherapeutic agent.
181. A method of treating a condition associated with chronic inflammation, the method comprising administering a composition according to any one of embodiments 1 to 180 to a subject suffering from the condition.
182. The method of embodiment 181, wherein the condition is selected from the group consisting of irritable bowel disease, ulcerative colitis, colitis, Crohn's disease, idiopathic pulmonary fibrosis, asthma, keratitis, arthritis, osteoarthritis, rheumatoid arthritis, auto-immune diseases, a feline or human immunodeficiency virus (FIV or HIV) infection, and cancer.
183. The method of embodiment 181 or 182, wherein the subject is a mammal.
184. The method of any one of embodiments 181 to 183, wherein the subject is a human.
185. The method of any one of embodiments 181 to 184, wherein the anti-inflammatory composition is administered in a dosage that includes between about 1 mg and about 500 mg of peptide.
186. The method of any one of embodiments 181 to 185, wherein the anti-inflammatory composition is administered intravenously, intraperitoneally, parenteral, orthotopically, subcutaneously, topically, nasally, by means of an implantable depot, using nanoparticle-based delivery systems, microneedle patch, microspheres, beads, osmotic or mechanical pumps, and/or other mechanical means.
187. The method of any one of embodiments 181 to 186, wherein the anti-inflammatory composition is administered in conjunction with another drug known to be effective in treating the condition.
188. The method of embodiment 187, wherein the anti-inflammatory composition is administered prior to, at the same time as, or after the administration of the other drug.
189. A method of treating fibrosis in a subject, the method comprising administering a composition according to any one of embodiments 1 to 180 to the subject.
190. The method of embodiment 189, wherein the fibrosis is selected from the group consisting of pulmonary fibrosis, dermal fibrosis, hepatic fibrosis, renal fibrosis, and fibrosis caused by ionizing radiation.
191. The method of embodiment 189 or 190, wherein the subject is a mammal.
192. The method of any one of embodiments 189 to 191, wherein the subject is a human.
193. The method of any one of embodiments 189 to 192, wherein the anti-inflammatory composition is administered in a dosage that includes between about 1 mg and about 500 mg of peptide.
194. The method of any one of embodiments 189 to 193, wherein the anti-inflammatory composition is administered intravenously, intraperitoneally, parenteral, orthotopically, subcutaneously, topically, nasally, by means of an implantable depot, using nanoparticle-based delivery systems, microneedle patch, microspheres, beads, osmotic or mechanical pumps, and/or other mechanical means.
195. The method of any one of embodiments 189 to 194, wherein the anti-inflammatory composition is administered in conjunction with another drug known to be effective in treating fibrosis.
196. The method of embodiment 195, wherein the anti-inflammatory composition is administered prior to, at the same time as, or after the administration of the other drug.
197. A method of reducing pro-inflammatory cytokine levels in a subject suffering from a chronic inflammatory condition, the method comprising administering a composition according to any one of embodiments 1 to 180 to the subject.
198. The method of embodiment 197, wherein the chronic inflammatory condition is selected from the group consisting of irritable bowel disease, ulcerative colitis, colitis, Crohn's disease, idiopathic pulmonary fibrosis, asthma, keratitis, arthritis, osteoarthritis, rheumatoid arthritis, auto-immune diseases, a feline or human immunodeficiency virus (FIV or HIV) infection, and cancer.
199. The method of embodiment 197 or 198, wherein the method reduces the level of at least one cytokine selected from group consisting of NF-kB, TNFα, IL1, IL6, IL12, MMP-1, MMP-9, MCP-1, IL8, IL17, and IL23.
200. The method of embodiment 199, wherein the level of the at least one cytokine is reduced by at least 10%.
201. The method of any one of embodiments 197 to 200, wherein the subject is a mammal.
202. The method of any one of embodiments 197 to 201, wherein the subject is a human.
203. The method of any one of embodiments 197 to 202, wherein the anti-inflammatory composition is administered in a dosage that includes between about 1 mg and about 500 mg of peptide.
204. The method of any one of embodiments 197 to 203, wherein the anti-inflammatory composition is administered intravenously, intraperitoneally, parenteral, orthotopically, subcutaneously, topically, nasally, by means of an implantable depot, using nanoparticle-based delivery systems, microneedle patch, microspheres, beads, osmotic or mechanical pumps, and/or other mechanical means.
205. The method of any one of embodiments 197 to 204, wherein the anti-inflammatory composition is administered in conjunction with another drug known to be effective in treating the chronic inflammatory condition that the subject is suffering from.
206. The method of embodiment 205, wherein the anti-inflammatory composition is administered prior to, at the same time as, or after the administration of the other drug.
207. A method of treating cancer in a subject, the method comprising administering an anti-inflammatory composition according to any one of embodiments 1 to 180 to the subject.
208. The method of embodiment 207, wherein the cancer is selected from the group consisting of colon cancer, and breast cancer.
209. The method of embodiment 207 or 208, wherein the anti-inflammatory composition is administered in conjunction with a chemotherapeutic agent or cell therapy.
210. The method of embodiment 209, wherein the chemotherapeutic agent or cell therapy is selected from the group consisting of steroids, anthracyclines, thyroid hormone replacement drugs, thymidylate-targeted drugs, checkpoint inhibitor drugs, Chimeric Antigen Receptor/T cell therapies, and other cell therapies.
211. The method of embodiment 209, wherein the chemotherapeutic agent is selected from the group consisting of Gemcitabine, Docetaxel, Bleomycin, Erlotinib, Gefitinib, Lapatinib, Imatinib, Dasatinib, Nilotinib, Bosutinib, Crizotinib, Ceritinib, Trametinib, Bevacizumab, Sunitinib, Sorafenib, Trastuzumab, Ado-trastuzumab emtansine, Rituximab, Ipilimumab, Rapamycin, Temsirolimus, Everolimus, Methotrexate, Doxorubicin, Abraxane, Folfirinox, Cisplatin, Carboplatin, 5-fluorouracil, Teysumo, Paclitaxel, Prednisone, Levothyroxine, and Pemetrexed.
212. The method of any one of embodiments 209 to 211, wherein the anti-inflammatory composition is administered prior to, at the same time as, or after the administration of the chemotherapeutic agent or cell therapy.
213. The method of embodiment 207 or 208, wherein the anti-inflammatory composition is administered in conjunction with radiation therapy.
214. The method of embodiment 213, wherein the anti-inflammatory composition is administered prior to, or after the administration of the radiation therapy.
215. The method of any one of embodiments 207 to 214, wherein the subject is a mammal.
216. The method of any one of embodiments 207 to 215, wherein the subject is a human.
217. The method of any one of embodiments 207 to 216, wherein the anti-inflammatory composition is administered in a dosage that includes between about 1 mg and about 500 mg of peptide.
218. The method of any one of embodiments 207 to 217, wherein the anti-inflammatory composition is administered intravenously, intraperitoneally, parenteral, orthotopically, subcutaneously, nasally, by means of an implantable depot, using nanoparticle-based delivery systems, microneedle patch, microspheres, beads, osmotic or mechanical pumps, and/or other mechanical means.

## Claims

1. An anti-inflammatory composition comprising a peptide, wherein the peptide comprises one of the amino acid sequences selected from the group consisting of: SEQ ID NO: 121, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 120.

2. The anti-inflammatory composition of claim 1, wherein the peptide binds to the dimerization site on a NFkB Class II protein.

3. The anti-inflammatory composition of claim 1, wherein the peptide binds to human serum albumin.

4. The anti-inflammatory composition of claim 1, wherein the peptide consists essentially of one of the amino acid sequences selected from the group consisting of: SEQ ID NO: 121, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 120.

5. The anti-inflammatory composition of claim 1, wherein the peptide comprises the amino acid sequence of SEQ ID NO:121.

6. The anti-inflammatory composition of claim 1, wherein the peptide consists essentially of the amino acid sequence of SEQ ID NO:121.

7. The anti-inflammatory composition of claim 2, wherein the peptide binds to the dimerization site on Rel B (SEQ ID NO: 367) and wherein:
(i) the peptide binds with a binding energy of at least −650 kcal/mol;
(ii) the peptide directly contacts at least one amino acid residue of Rel B selected from the group consisting of Glu 298, Tyr-300, Leu-301, Leu-302, Asp-330, His-332, and Leu-371; or
(iii) the peptide, when bound to the dimerization site on Rel B, forms an ionic bond with Asp-330, forms an ionic bond with His-332, and/or makes a hydrophobic contact with Leu-371.

8. The anti-inflammatory composition of claim 1, wherein the peptide binds to CD206 (SEQ ID NO: 379) and wherein:
(i) the peptide binds to the mannose-binding site on CD206 and/or interferes with or blocks the binding of SIRP-mannose to CD206;
(ii) the peptide binds with a binding energy of at least −650 kcal/mol; or
(iii) the peptide directly contacts at least one amino acid residue of CD206 selected from the group consisting of Phe-708, Thr-709, Trp-710, Pro-714. Glu-719, Asn-720, Trp-721, Ala-722, Glu-725, Tyr-729, Glu-733, Asn-747, Asp-748, Ser-1691, Cys-1693, Phe-1694, and Phe-1703.

9. The anti-inflammatory composition of claim 1, wherein the peptide binds to at least one signaling molecule selected from the group consisting of TGFβ (SEQ ID NO: 368), Notch1 (SEQ ID NO: 369), Wnt8R (SEQ ID NO: 370), TRAIL (SEQ ID NO: 371), IL6R (SEQ ID NO: 372), IL10R (SEQ ID NO: 373), EGFR (SEQ ID NO: 374), CDK6 (SEQ ID NO: 375), Histone Methyl Transferase (HMT) (SEQ ID NO: 376), CD47 (SEQ ID NO: 377), SIRP-α (SEQ ID NO: 378), CD206 (SEQ ID NO: 379), TGM2 (SEQ ID NO: 380); LEGUMAIN (SEQ ID NO: 413), CD209 (SEQ ID NO: 414), FAS (SEQ ID NO: 415), PD-1 (SEQ ID NO: 416), MKK7 (SEQ ID NO: 417), and RNR (SEQ ID NO: 418).

10. The anti-inflammatory composition of claim 1, wherein the composition further comprises a second peptide, wherein the second peptide comprises one of the amino acid sequences selected from the group consisting of: SEQ ID NO: 121, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 120, wherein the first and second peptides can have the same or different sequences.

11. The anti-inflammatory composition of claim 10, wherein the first and second peptides are linked together by a peptide bond, a peptide linker, or a non-peptide linker.

12. The anti-inflammatory composition of claim 1, wherein the composition is free of protein other than the peptide.

13. A pharmaceutical composition comprising the anti-inflammatory composition of claim 1 and a pharmaceutically acceptable carrier.

14. The pharmaceutical composition of claim 13, wherein the composition further comprises a chemotherapeutic agent.

15. The pharmaceutical composition of claim 13, wherein the composition further comprises a Chimeric Antigen Receptor/T Cell therapy.

16. The pharmaceutical composition of claim 14, wherein the chemotherapeutic agent is selected from the group consisting of Gemcitabine, Docetaxel, Bleomycin, Erlotinib, Gefitinib, Lapatinib, Imatinib, Dasatinib, Nilotinib, Bosutinib, Crizotinib, Ceritinib, Trametinib, Bevacizumab, Sunitinib, Sorafenib, Trastuzumab, Ado-trastuzumab emtansine, Rituximab, Ipilimumab, Rapamycin, Temsirolimus, Everolimus, Methotrexate, Doxorubicin, Abraxane, Folfirinox, Cisplatin, Carboplatin, 5-fluorouracil, Teysumo, Paclitaxel, Prednisone, Levothyroxine, and Pemetrexed.

17. A method of treating a condition associated with chronic inflammation, the method comprising administering a pharmaceutical composition according to claim 13 to a subject suffering from the condition.

18. The method of claim 17, wherein the condition is selected from the group consisting of: irritable bowel disease, ulcerative colitis, colitis, Crohn's disease, idiopathic pulmonary fibrosis, asthma, keratitis, arthritis, osteoarthritis, rheumatoid arthritis, auto-immune diseases, a feline or human immunodeficiency virus (FIV or HIV) infection, cancer, pulmonary fibrosis, dermal fibrosis, hepatic fibrosis, renal fibrosis, and fibrosis caused by ionized radiation.

19. The method of claim 17, wherein the subject is a mammal.

20. The method of claim 19, wherein the subject is a human.

21. The method of claim 17, wherein the method reduces the level of at least one pro-inflammatory cytokine selected from group consisting of TNFα, IL1, IL6, IL12, MMP-1, MMP-9, MCP-1, IL8, IL17, and IL23.

22. The method of claim 21, wherein the level of the at least one cytokine is reduced by at least 10%.

23. The pharmaceutical composition of claim 13, wherein the anti-inflammatory composition comprises a peptide comprising the amino acid sequence of SEQ ID NO:121.

24. The pharmaceutical composition of claim 13, wherein the anti-inflammatory composition comprises a peptide consisting essentially of the amino acid sequence of SEQ ID NO:121.

25. The method of claim 17, wherein the wherein the anti-inflammatory composition comprises a peptide comprising the amino acid sequence of SEQ ID NO:121.

26. The method of claim 17, wherein the anti-inflammatory composition comprises a peptide consisting essentially of the amino acid sequence of SEQ ID NO:121.