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

Abstract

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

1 - 26 . (canceled) 
     
     
         27 . A composition comprising:
 directed sequence polymers (DSPs) having a length of between about 25 to 300 amino acids, wherein each of such DSPs comprises from between 1-15 cassettes,   wherein each DSP comprises at least one cassette that has a sequence of amino acid positions corresponding to each amino acid of a first base peptide sequence, wherein the first base peptide sequence is derived from an epitope of an antigen associated with an autoimmune disease and the amino acid of at least one position of the cassette varies within the DSPs of the composition, various DSPs having an amino acid selected from an original amino acid found at the corresponding amino acid position of the base peptide sequence, alanine (A), and optionally, at least one conserved substitution at each varied position,   wherein the relative molar amount of A is more than 10% and less than 90% of the total amino acid composition of the DSPs and wherein the composition has a complexity greater than 5×10 2  different DSPs.   
     
     
         28 . The composition of  claim 27 , wherein said DSP comprises cassettes, such cassettes comprising the amino acid sequences that are derived from the first base peptide sequence. 
     
     
         29 . The composition of  claim 27 , wherein said DSP comprises one or more cassettes, such cassettes comprising one or more cassettes having amino acid sequences that are derived from the first base peptide sequence and one or more cassettes having amino acid sequences that are derived from a second base peptide sequence of a second epitope. 
     
     
         30 . The composition of  claim 27 , wherein the first base peptide sequence is selected from SEQ ID NOS: 1-189. 
     
     
         31 . The composition of  claim 27 , wherein the autoimmune disease is selected from multiple sclerosis, systemic lupus erythematosus, type I diabetes mellitus, myasthenia gravis, rheumatoid arthritis, and pemphigus vulgaris. 
     
     
         32 . The composition of  claim 27 , wherein the amino acid sequence of the first base peptide sequence is a partial sequence of a protein selected from:
 (a) osteopontin, an HLA protein, myelin oligodendrite glycoprotein, myelin basic protein (MBP), proteolipid protein, and myelin associated glycoproteins, S100Beta, heat shock protein alpha, beta crystallin, myelin-associated oligodendrocytic basic protein (MOBP), 2′,3′ cyclic nucleotide 3′-phosphodiesterase;   (b) hsp60, hsp70, Ro60, La, SmD, and 70-kDa U1RNP;   (c) glutamic acid decarboxylase (GAD65), insulinoma-antigen 2 (IA-2), insulin;   (d) acetylcholine receptor (AChR) α-subunit and muscle-specific receptor tyrosine kinase (MuSK);   (e) type II collagen; and   (f) desmoglein 3 (Dsg3).   
     
     
         33 . The composition of  claim 27 , wherein the amino acid similarity is defined according to the similarity table shown in  FIG. 4 . 
     
     
         34 . The composition of  claim 27 , wherein the amino acid similarity is determined based on empirical data of known variants of the epitope. 
     
     
         35 . A method of treating an autoimmune disease by administering the directed sequence polymer (DSP) composition of  claim 27 , comprising administering to a subject in need thereof a dosing regimen of an effective amount of the DSP composition for the amelioration of said disease. 
     
     
         36 . The method according to  claim 35 , wherein the autoimmune disease is selected from multiple sclerosis, systemic lupus erythematosus, type I diabetes mellitus, myasthenia gravis, rheumatoid arthritis, and pemphigus vulgaris. 
     
     
         37 . (canceled) 
     
     
         38 . A composition comprising directed sequence polymers (DSPs) having a length of between about 25 to 300 amino acids, each DSP comprising from 1-15 cassettes,
 wherein each DSP comprises at least one cassette that has a sequence of amino acid positions corresponding to each amino acid of a first base peptide sequence, wherein the first base peptide sequence is an amino acid sequence of an epitope of an antigen associated with an autoimmune disease and the amino acid of at least one position of the cassette varies within the DSPs of the composition, various DSPs having an amino acid selected from an original amino acid found at the corresponding amino acid position of the base peptide sequence, alanine (A), and optionally, at least one conserved substitution at each varied position, and   wherein the relative molar amount of A is more than 10% and less than 90% of the total amino acid composition of the DSPs.   
     
     
         39 . A composition comprising directed sequence polymers (DSPs) manufactured by a process comprising:
 (1) selecting a first base peptide sequence, wherein the first base peptide sequence is an amino acid sequence of an epitope of an antigen associated with an autoimmune disease;   (2) synthesizing by solid phase peptide synthesis a first cassette of the DSPs, the cassette having a sequence of amino acid positions corresponding to each amino acid of the base peptide sequence,   wherein, for at least one amino acid position of the first cassette of the directed sequence polymers, an amino acid is added, said amino acid being randomly selected from a mixture of amino acids comprising the original amino acid found at that amino acid position, alanine (A), and, optionally, at least one conserved substitution,
 wherein the amino acids in the mixture are present in a fixed molar input ratio relative to each other, determined prior to starting synthesis, and 
 wherein the relative molar amount of A is more than 10% and less than 90% of the total amino acid concentration of the DSPs; 
   (3) optionally extending the length of the DSPs by at least one of
 (a) repeating step (2) for 2 to 15 cycles and elongating the DSP under the same condition; or 
 (b) repeating step (2) for 2 to 15 cycles and elongating the DSP, for each cycle, using a different input ratio of amino acids in the mixture; or 
 (c) repeating steps (1) and (2) for 2 to 15 cycles and elongating the DSP using cassettes based on more than one base peptide; or 
 (d) assembling 2 to 15 cassettes synthesized in a single cycle of step (2); or 
 (e) assembling 2 to 15 cassettes, the first cassette synthesized under one condition of step (2), and second and more cassettes synthesized under other conditions of step (2); and 
   (4) optionally further elongating the DSPs by repeating steps (2) and (3) for 2 to 15 cycles, wherein for each cycle a new cassette of the DSP is designed independently from any of the previous cassettes designated by previous cycles of step (2);   
       wherein the number of cycles selected in steps (3) and (4) is selected so that the final length of the DSP is about 25 to 300 amino acid residues. 
     
     
         40 . The composition of  claim 39 , wherein the composition has a complexity of greater than 5×10 2  different DSPs. 
     
     
         41 . A composition comprising directed sequence polymers (DSPs) manufactured by a process comprising:
 (1) selecting a first base peptide sequence, wherein the sequence is an amino acid sequence that is derived from an epitope of an antigen associated with an autoimmune disease;   (2) synthesizing by solid phase peptide synthesis a first cassette of the DSPs, the cassette having a sequence of amino acid positions corresponding to each amino acid of the base peptide sequence,   wherein, for at least one amino acid position of the first cassette of the directed sequence polymers, an amino acid is added, said amino acid being randomly selected from a mixture of amino acids comprising the original amino acid found at that amino acid position, alanine (A), and, optionally, at least one conserved substitution,
 wherein the amino acids in the mixture are present in a fixed molar input ratio relative to each other, determined prior to starting synthesis, and 
 wherein the relative molar amount of A is more than 10% and less than 90% of the total amino acid concentration of the DSPs; and 
   (3) optionally further extending the length of the DSPs by joining multiple cassettes in sequence;   wherein the number of cassettes in step (3) is selected so that the final length of the DSP is about 25 to 300 amino acid residues, and wherein the DSP composition has a complexity of greater than 5×10 2  different DSPs.