Heterogeneous foldamers containing α, β, and/or γ-amino acids
Disclosed are isolated, unnatural polypeptides containing cyclically-constrained β-amino acid residues and cyclically-constrained γ-amino acid residues. The compounds are unnatural and because they contain rotationally constrained residues that are not amenable to enzymatic degradation, the compounds are useful to probe protein-protein and other large molecule interactions.
1. An isolated, unnatural polypeptide compound of formula:
wherein:
each X and each Z is independently variable and is selected from the group consisting of α-amino acid residues, β-amino acid residues, and γ-amino acid residues, provided that at least one X or Z is an α-amino acid residue and at least another two of X or Z are two cyclically-constrained β-amino acid residues; and
wherein each cyclically-constrained β-amino acid residue is independently selected from the group consisting of:
wherein V and W are combined, together with the carbon atoms to which they are bonded, and independently define a substituted or unsubsituted, monocyclic or bicyclic C 3 -C 10 cycloalkyl, cycloalkenyl or heterocyclic ring having one or more N, O or S atom(s) as the heteroatom(s);
the substituents on carbon atoms of the rings being independently selected from the group consisting of linear, branched, or cyclic C 1 -C 6 -alkyl, alkenyl, alkynyl; mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, and mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl;
the substituents on nitrogen heteroatoms of the rings being independently selected from the group consisting of hydrogen, monocyclic or bicyclic C 1 -C 10 -alkyl, alkenyl, or alkynyl; mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl, —S(═O) 2 —R 17 , —C(═O)—R 17 , —S(═O) 2 —(CH 2 ) n+1 —R 18 , and —C(═O)—(CH 2 ) n —R 18 , where n = 1 to 6;
wherein R 17 is independently selected from the group consisting of hydrogen, monocyclic or bicyclic C 1 -C 10 -alkyl, alkenyl, or alkynyl; mono- or bicyclic aryl, mono -or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl; and
wherein R 18 is independently selected from the group consisting of hydroxy, linear, branched, or cyclic C 1 -C 6 -alkyl, alkenyl, or alkynyl; mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl; mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl; C 1 -C 6 -alkyloxy, aryloxy, heteroaryloxy, thio, C 1 -C 6 -alkylthio, C 1 -C 6 -alkylsulfinyl, C 1 -C 6 -alkylsulfonyl, arylthio, arylsulfinyl, arylsulfonyl, heteroarylthio, heteroarylsulfinyl, heteroarylsulfonyl, amino, mono- or di-C 1 -C 6 -alkylamino, mono- or diarylamino, mono- or diheteroarylamino, N-alkyl-N-arylamino, N-alkyl-N-heteroarylamino, N-aryl-N-heteroarylamino, aryl-C 1 -C 6 -alkylamino, carboxylic acid, carboxamide, mono- or di-C 1 -C 6 -alkylcarboxamide, mono- or diarylcarboxamide, mono- or diheteroarylcarboxamide, N-alkyl-N-arylcarboxamide, N-alkyl-N-heteroarylcarboxamide, N-aryl-N-heteroarylcarboxamide, sulfonic acid, sulfonamide, mono- or di-C 1 -C 6 -alkylsulfonamide, mono- or diarylsulfonamide, mono- or diheteroarylsulfonamide, N-alkyl-N-arylsulfonamide, N-alkyl-N-heteroarylsulfonamide, N-aryl-N-heteroarylsulfonamide, urea; mono- di- or tri-substituted urea, wherein the subsitutent(s) is selected from the group consisting of C 1 -C 6 -alkyl, aryl, heteroaryl; O-alkylurethane, O-arylurethane, and O-heteroarylurethane; and
wherein R 5 and R 6 are independently selected from the group consisting of hydrogen, hydroxy, linear, branched, or cyclic C 1 -C 16 -alkyl, alkenyl, or alkynyl; mono- or di-C 1 -C 16 alkylamino; mono- or bicyclic aryl; mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 16 -alkyl; mono- or bicyclic heteroaryl-C 1 -C 16 -alkyl; —(CH 2 ) 0-6 —OR 7 , —(CH 2 ) 0-6 —SR 7 , —(CH 2 ) 0-6 —S(═O)—CH 2 —R 7 , —(CH 2 ) 0-6 —S(═O) 2 —CH 2 —R 7 , —(CH 2 ) 0-6 —NR 7 R 7 , —(CH 2 ) 0-6 —NHC(═O)R 7 , —(CH 2 ) 0-6 —NHS(═O) 2 —CH 2 —R 7 , —(CH 2 ) 0-6 —C(═O)—OH, —(CH 2 ) 0-6 —C(═O)—OR 7 , —(CH 2 ) 0-6 —C(═O)—NH 2 , —(CH 2 ) 0-6 —C(═O)—NHR 7 , —(CH 2 ) 0-6 —C(═O)—N(R 7 ) 2 , —(CH 2 ) 0-6 —O—(CH 2 ) 2-6 —R 8 , —(CH 2 ) 0-6 —S—(CH 2 ) 2-6 —R 8 , —(CH 2 ) 0-6 —S(═O)—(CH 2 ) 2-6 —R 8 , —(CH 2 ) 0-6 —S(═O) 2 —(CH 2 ) 2-6 —R 8 , —(CH 2 ) 0-6 —NH—(CH 2 ) 2-6 —R 8 , —(CH 2 ) 0-6 —N—{(CH 2 ) 2-6 —R 8 } 2 , —(CH 2 ) 0-6 —NHC(═O)—(CH 2 ) 2-6 —R 8 , and —(CH 2 ) 0-6 —NHS(═O) 2 —(CH 2 ) 2-6 —R 8 ; wherein
R 7 is independently selected from the group consisting of hydrogen, C 1 -C 6 -alkyl, alkenyl, or alkynyl; mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl; and
R 8 is selected from the group consisting of hydroxy, C 1 -C 6 -alkyloxy, aryloxy, heteroaryloxy, thio, C 1 -C 6 -alkylthio, C 1 -C 6 -alkylsulfinyl, C 1 -C 6 -alkylsulfonyl, arylthio, arylsulfinyl, arylsulfonyl, heteroarylthio, heteroarylsulfinyl, heteroarylsulfonyl, amino, mono- or di-C 1 -C 6 -alkylamino, mono- or diarylamino, mono- or diheteroarylamino, N-alkyl-N-arylamino, N-alkyl-N-heteroarylamino, N-aryl-N-heteroarylamino, aryl-C 1 -C 6 -alkylamino, carboxylic acid, carboxamide, mono- or di-C 1 -C 6 -alkylcarboxamide, mono- or diarylcarboxamide, mono- or diheteroarylcarboxamide, N-alkyl-N-arylcarboxamide, N-alkyl-N-heteroarylcarboxamide, N-aryl-N-heteroarylcarboxamide, sulfonic acid, sulfonamide, mono- or di-C 1 -C 6 -alkylsulfonamide, mono- or diarylsulfonamide, mono- or diheteroarylsulfonamide, N-alkyl-N-arylsulfonamide, N-alkyl-N-heteroarylsulfonamide, N-aryl-N-heteroarylsulfonamide, urea; mono- di- or tri-substituted urea, wherein the subsitutent(s) is selected from the group consisting of C 1 -C 6 -alkyl, aryl, heteroaryl; O-alkylurethane, O-arylurethane, and O-heteroarylurethane; and
wherein R 9 is selected from the group consisting of linear, branched, or cyclic C 1 -C 6 -alkyl, alkenyl, or alkynyl; mono- or di-C 1 -C 6 alkylamino, mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl, —(CH 2 ) 1-6 —OR 11 , —(CH 2 ) 1-6 —SR 11 , —(CH 2 ) 1-6 —S(═O)—CH 2 —R 11 , —(CH 2 ) 1-6 —S( ═O) 2 —CH 2 —R 11 , —(CH 2 ) 1-6 —NR 11 R 11 , —(CH 2 ) 1-6 —NHC(═O)R 11 , —(CH 2 ) 1-6 —NHS(═O) 2 —CH 2 —R 11 , —(CH 2 ) 0-6 —C(═O)—OH, —(CH 2 ) 0-6 —C(═O)—OR 11 , —(CH 2 ) 0-6 —C(═O)—NH 2 , —(CH 2 ) 0-6 —C(═O)—NHR 11 , —(CH 2 ) 0-6 —C(═O)—N(R 11 ) 2 , —(CH 2 ) 1-6 —O—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —S—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —S(═O)—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —S(═O) 2 —(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —NH—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —N—{(CH 2 ) 2-6 —R 12 } 2 , —(CH 2 ) 1-6 —NHC(═O)—(CH 2 ) 2-6 —R 12 , and —(CH 2 ) 1-6 —NHS(═O) 2 —(CH 2 ) 2-6 —R 12 ;
R 10 and R 13 are independently selected from the group consisting of hydrogen, linear, branched, or cyclic C 1 -C 6 -alkyl, alkenyl, or alkynyl; mono- or di-C 1 -C 6 alkylamino, mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl, —(CH 2 ) 1-6 —OR 11 , —(CH 2 ) 1-6 —SR 11 , —(CH 2 ) 1-6 —S(═O)—CH 2 —R 11 , —(CH 2 ) 1-6 —S(═O) 2 —CH 2 —R 11 , —(CH 2 ) 1-6 —NR 11 R 11 , —(CH 2 ) 1-6 —NHC(═O)R 11 , —(CH 2 ) 1-6 —NHS(═O) 2 —CH 2 —R 11 , —(CH 2 ) 0-6 —C(═O)—OH, —(CH 2 ) 0-6 —C(═O)—OR 11 , —(CH 2 ) 0-6 —C(═O)—NH 2 , —(CH 2 ) 0-6 —C(═O)—NHR 11 , —(CH 2 ) 0-6 —C(═O)—N(R 11 ) 2 , —(CH 2 ) 1-6 —O—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —S—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —S(═O)—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —S(═O) 2 —(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —NH—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —N—{(CH 2 ) 2-6 —R 12 } 2 , —(CH 2 ) 1-6 —NHC(═O)—(CH 2 ) 2-6 —R 12 , and —(CH 2 ) 1-6 —NHS(═O) 2 —(CH 2 ) 2-6 —R 12 ; wherein
R 11 is independently selected from the group consisting of hydrogen, C 1 -C 6 -alkyl, alkenyl, or alkynyl; mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl; and
R 12 is selected from the group consisting of hydroxy, C 1 -C 6 -alkyloxy, aryloxy, heteroaryloxy, thio, C 1 -C 6 -alkylthio, C 1 -C 6 -alkylsulfinyl, C 1 -C 6 -alkylsulfonyl, arylthio, arylsulfinyl, arylsulfonyl, heteroarylthio, heteroarylsulfinyl, heteroarylsulfonyl, amino, mono- or di-C 1 -C 6 -alkylamino, mono- or diarylamino, mono- or diheteroarylamino, N-alkyl-N-arylamino, N-alkyl-N-heteroarylamino, N-aryl-N-heteroarylamino, aryl-C 1 -C 6 -alkylamino, carboxylic acid, carboxamide, mono- or di-C 1 -C 6 -alkylcarboxamide, mono- or diarylcarboxamide, mono- or diheteroarylcarboxamide, N-alkyl-N-arylcarboxamide, N-alkyl-N-heteroarylcarboxamide, N-aryl-N-heteroarylcarboxamide, sulfonic acid, sulfonamide, mono- or di-C 1 -C 6 -alkylsulfonamide, mono- or diarylsulfonamide, mono- or diheteroarylsulfonamide, N-alkyl-N-arylsulfonamide, N-alkyl-N-heteroarylsulfonamide, N-aryl-N-heteroarylsulfonamide, urea; mono- di- or tri-substituted urea, wherein the subsitutent(s) is selected from the group consisting of C 1 -C 6 -alkyl, aryl, heteroaryl; O-alkylurethane, O-arylurethane, and O-heteroarylurethane;
R 14 is selected from the group consisting of hydrogen, linear, branched, or cyclic C 1 -C 6 -alkyl, alkenyl, or alkynyl; mono- or di-C 1 -C 6 alkylamino, mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl, —S(═O) 2 —(CH 2 ) 1-6 —R 11 , —C(═O)R 11 , —S(═O) 2 —(CH 2 ) 2-6 R 12 , and —C(═O)—(CH 2 ) 1-6 —R 12 ; wherein R 11 and R 12 are as defined above;
R 15 and R 16 are selected from the group listed above for R 10 and R 13 , and are further selected from the group consisting of hydroxy, C 1 -C 6 -alkyloxy, aryloxy, heteroaryloxy, thio, C 1 -C 6 -alkylthio, C 1 -C 6 -alkylsulfinyl, C 1 -C 6 -alkylsulfonyl, arylthio, arylsulfinyl, arylsulfonyl, heteroarylthio, heteroarylsulfinyl, heteroarylsulfonyl, amino, mono- or di-C 1 -C 6 -alkylamino, mono- or diarylamino, mono- or diheteroarylamino, N-alkyl-N-arylamino, N-alkyl-N-heteroarylamino, N-aryl-N-heteroarylamino, aryl-C 1 -C 6 -alkylamino, carboxylic acid, carboxamide, mono- or di-C 1 -C 6 -alkylcarboxamide, mono- or diarylcarboxamide, mono- or diheteroarylcarboxamide, N-alkyl-N-arylcarboxamide, N-alkyl-N-heteroarylcarboxamide, N-aryl-N-heteroarylcarboxamide, sulfonic acid, sulfonamide, mono- or di-C 1 -C 6 -alkylsulfonamide, mono- or diarylsulfonamide, mono- or diheteroarylsulfonamide, N-alkyl-N-arylsulfonamide, N-alkyl-N-heteroarylsulfonamide, N-aryl-N-heteroarylsulfonamide, urea; mono- di- or tri-substituted urea, wherein the subsitutent(s) is selected from the group consisting of C 1 -C 6 -alkyl, aryl, heteroaryl; O-alkylurethane, O-arylurethane, and O-heteroarylurethane and
each “Y” is a single bond; and
“A” is independently selected from the group consisting of hydrogen and an amino-terminus protecting group, and “A′” is selected from the group consisting of hydroxy and a carboxy-terminus protecting group; and
each “a,” “c,” and “d” is an independently variable positive integer, and wherein “a”+“c”>3; or
salts thereof.
2. An isolated, unnatural polypeptide compound of formula:
wherein:
each X and each Z is independently variable and is selected from the group consisting of α-amino acid residues, β-amino acid residues, and γ-amino acid residues, provided that at least one X or Z is an α-amino acid residue and at least another two of X or Z are two cyclically-constrained residues, the two cyclically-constrained residues being cyclically-constrained β-amino acid residues or cyclically -constrained γ-amino acid residues, or one cyclically-constrained β-amino acid residue and one cyclically-constrained γ-amino acid residue; and
wherein the cyclically-constrained β-amino acid residues are selected from the group consisting of:
wherein V and W are combined, together with the carbon atoms to which they are bonded, and independently define a substituted or unsubsituted, monocyclic or bicyclic C 3 -C 10 cycloalkyl, cycloalkenyl or heterocyclic ring having one or more N, O or S atom(s) as the heteroatom(s);
the substituents on carbon atoms of the rings being independently selected from the group consisting of linear, branched, or cyclic C 1 -C 6 -alkyl, alkenyl, alkynyl; mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, and mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl
the substituents on nitrogen heteroatoms of the rings being independently selected from the group consisting of hydrogen, monocyclic or bicyclic C 1 -C 10 -alkyl, alkenyl, or alkynyl; mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl, —S(═O) 2 —R 17 , —C(═O)—R 17 , —S(═O) 2 —(CH 2 ) n+1 —R 18 , and —C(═O)—(CH 2 ) n —R 18 , where n=1 to 6;
wherein R 17 is independently selected from the group consisting of hydrogen, monocyclic or bicyclic C 1 -C 10 -alkyl, alkenyl, or alkynyl; mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl; and
wherein R 18 is independently selected from the group consisting of hydroxy, linear, branched, or cyclic C 1 -C 6 -alkyl, alkenyl, or alkynyl; mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl; mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl; C 1 -C 6 -alkyloxy, aryloxy, heteroaryloxy, thio, C 1 -C 6 -alkylthio, C 1 -C 6 -alkylsulfinyl, C 1 -C 6 -alkylsulfonyl, arylthio, arylsulfinyl, arylsulfonyl, heteroarylthio, heteroarylsulfinyl, heteroarylsulfonyl, amino, mono- or di-C 1 -C 6 -alkylamino, mono- or diarylamino, mono- or diheteroarylamino, N-alkyl-N-arylamino, N-alkyl-N-heteroarylamino, N-aryl-N-heteroarylamino, aryl-C 1 -C 6 -alkylamino, carboxylic acid, carboxamide, mono- or di-C 1 -C 6 -alkylcarboxamide, mono- or diarylcarboxamide, mono- or diheteroarylcarboxamide, N-alkyl-N-arylcarboxamide, N-alkyl-N-heteroarylcarboxamide, N-aryl-N-heteroarylcarboxamide, sulfonic acid, sulfonamide, mono- or di-C 1 -C 6 -alkylsulfonamide, mono- or diarylsulfonamide, mono- or diheteroarylsulfonamide, N-alkyl-N-arylsulfonamide, N-alkyl-N-heteroarylsulfonamide, N-aryl-N-heteroarylsulfonamide, urea; mono- di- or tri-substituted urea, wherein the subsitutent(s) is selected from the group consisting of C 1 -C 6 -alkyl, aryl, heteroaryl; O-alkylurethane, O-arylurethane, and O-heteroarylurethane; and
wherein R 5 and R 6 are independently selected from the group consisting of hydrogen, hydroxy, linear, branched, or cyclic C 1 -C 16 -alkyl, alkenyl, or alkynyl; mono- or di-C 1 -C 16 alkylamino; mono- or bicyclic aryl; mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 16 -alkyl; mono- or bicyclic heteroaryl-C 1 -C 16 -alkyl; —(CH 2 ) 0-6 —OR 7 , —(CH 2 ) 0-6 —SR 7 , —(CH 2 ) 0-6 —S(═O)—CH 2 —R 7 , —(CH 2 ) 0-6 —S(═O) 2 —CH 2 —R 7 , —(CH 2 ) 0-6 —NR 7 R 7 , —(CH 2 ) 0-6 —NHC(═O)R 7 , —(CH 2 ) 0-6 —NHS(═O) 2 —CH 2 —R 7 , —(CH 2 ) 0-6 —C(═O)—OH, —(CH 2 ) 0-6 —C(═O)—OR 7 , —(CH 2 ) 0-6 —C(═O)—NH 2 , —(CH 2 ) 0-6 —C(═O)—NHR 7 , —(CH 2 ) 0-6 —C(═O)—N(R 7 ) 2 , —(CH 2 ) 0-6 —O—(CH 2 ) 2-6 —R 8 , —(CH 2 ) 0-6 —S—(CH 2 ) 2-6 —R 8 , —(CH 2 ) 0-6 —S(═O)—(CH 2 ) 2-6 —R 8 , —(CH 2 ) 0-6 —S(═O) 2 —(CH 2 ) 2-6 —R 8 , —(CH 2 ) 0-6 —NH—(CH 2 ) 2-6 —R 8 , —(CH 2 ) 0-6 —N—{(CH 2 ) 2-6 —R 8 } 2 , —(CH 2 ) 0-6 —NHC(═O)—(CH 2 ) 2-6 —R 8 , and —(CH 2 ) 0-6 —NHS(═O) 2 —(CH 2 ) 2-6 —R 8 ; wherein
R 7 is independently selected from the group consisting of hydrogen, C 1 -C 6 -alkyl, alkenyl, or alkynyl; mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl; and
R 8 is selected from the group consisting of hydroxy, C 1 -C 6 -alkyloxy, aryloxy, heteroaryloxy, thio, C 1 -C 6 -alkylthio, C 1 -C 6 -alkylsulfinyl, C 1 -C 6 -alkylsulfonyl, arylthio, arylsulfinyl, arylsulfonyl, heteroarylthio, heteroarylsulfinyl, heteroarylsulfonyl, amino, mono- or di-C 1 -C 6 -alkylamino, mono- or diarylamino, mono- or diheteroarylamino, N-alkyl-N-arylamino, N-alkyl-N-heteroarylamino, N-aryl-N-heteroarylamino, aryl-C 1 -C 6 -alkylamino, carboxylic acid, carboxamide, mono- or di-C 1 -C 6 -alkylcarboxamide, mono- or diarylcarboxamide, mono- or diheteroarylcarboxamide, N-alkyl-N-arylcarboxamide, N-alkyl-N-heteroarylcarboxamide, N-aryl-N-heteroarylcarboxamide, sulfonic acid, sulfonamide, mono- or di-C 1 -C 6 -alkylsulfonamide, mono- or diarylsulfonamide, mono- or diheteroarylsulfonamide, N-alkyl-N-arylsulfonamide, N-alkyl-N-heteroarylsulfonamide, N-aryl-N-heteroarylsulfonamide, urea; mono- di- or tri-substituted urea, wherein the subsitutent(s) is selected from the group consisting of C 1 -C 6 -alkyl, aryl, heteroaryl; O-alkylurethane, O-arylurethane, and O-heteroarylurethane;
wherein R 9 is selected from the group consisting of linear, branched, or cyclic C 1 -C 6 -alkyl, alkenyl, or alkynyl; mono- or di-C 1 -C 6 alkylamino, mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl, —(CH 2 ) 1-6 —OR 11 , —(CH 2 ) 1-6 —SR 11 , —(CH 2 ) 1-6 —S(═O)—CH 2 —R 11 , —(CH 2 ) 1-6 —S(═O) 2 —CH 2 —R 11 , —(CH 2 ) 1-6 —NR 11 R 11 , —(CH 2 ) 1-6 —NHC(═O)R 11 , —(CH 2 ) 1-6 —NHS(═O) 2 —CH 2 —R 11 , —(CH 2 ) 0-6 —C(═O)—OH, —(CH 2 ) 0-6 —C(═O)—OR 11 , —(CH 2 ) 0-6 —C(═O)—NH 2 , —(CH 2 ) 0-6 —C(═O)—NHR 11 , —(CH 2 ) 0-6 —C(═O)—N(R 11 ) 2 , —(CH 2 ) 1-6 —O—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —S—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —S(═O)—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —S(═O) 2 —(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —NH—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —N—{(CH 2 ) 2-6 —R 12 } 2 , —(CH 2 ) 1-6 —NHC(═O)—(CH 2 ) 2-6 —R 12 , and —(CH 2 ) 1-6 —NHS(═O) 2 —(CH 2 ) 2-6 —R 12 ; and
R 10 and R 13 are independently selected from the group consisting of hydrogen, linear, branched, or cyclic C 1 -C 6 -alkyl, alkenyl, or alkynyl; mono- or di-C 1 -C 6 alkylamino, mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl, —(CH 2 ) 1-6 —OR 11 , —(CH 2 ) 1-6 —SR 11 , —(CH 2 ) 1-6 —S(═O)—CH 2 —R 11 , —(CH 2 ) 1-6 —S(═O) 2 —CH 2 —R 11 , —(CH 2 ) 1-6 —NR 11 R 11 , —(CH 2 ) 1-6 —NHC(═O)R 11 , —(CH 2 ) 1-6 —NHS(═O) 2 —CH 2 —R 11 , —(CH 2 ) 0-6 —C(═O)—OH, —(CH 2 ) 0-6 —C(═O)—OR 11 , —(CH 2 ) 0-6 —C(═O)—NH 2 , —(CH 2 ) 0-6 —C(═O)—NHR 11 , —(CH 2 ) 0-6 —C(═O)—N(R 11 ) 2 , —(CH 2 ) 1-6 —O—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —S—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —S(═O)—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —S(═O) 2 —(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —NH—(CH 2 ) 2-6 —R 12 , —(CH 2 ) 1-6 —N—{(CH 2 ) 2-6 —R 12 } 2 , —(CH 2 ) 1-6 —NHC(═O)—(CH 2 ) 2-6 —R 12 , and —(CH 2 ) 1-6 —NHS(═O) 2 —(CH 2 ) 2-6 —R 12 ; wherein
R 11 is independently selected from the group consisting of hydrogen, C 1 -C 6 -alkyl, alkenyl, or alkynyl; mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl; and
R 12 is selected from the group consisting of hydroxy, C 1 -C 6 -alkyloxy, aryloxy, heteroaryloxy, thio, C 1 -C 6 -alkylthio, C 1 -C 6 -alkylsulfinyl, C 1 -C 6 -alkylsulfonyl, arylthio, arylsulfinyl, arylsulfonyl, heteroarylthio, heteroarylsulfinyl, heteroarylsulfonyl, amino, mono- or di-C 1 -C 6 -alkylamino, mono- or diarylamino, mono- or diheteroarylamino, N-alkyl-N-arylamino, N-alkyl-N-heteroarylamino, N-aryl-N-heteroarylamino, aryl-C 1 -C 6 -alkylamino, carboxylic acid, carboxamide, mono- or di-C 1 -C 6 -alkylcarboxamide, mono- or diarylcarboxamide, mono- or diheteroarylcarboxamide, N-alkyl-N-arylcarboxamide, N-alkyl-N-heteroarylcarboxamide, N-aryl-N-heteroarylcarboxamide, sulfonic acid, sulfonamide, mono- or di-C 1 -C 6 -alkylsulfonamide, mono- or diarylsulfonamide, mono- or diheteroarylsulfonamide, N-alkyl-N-arylsulfonamide, N-alkyl-N-heteroarylsulfonamide, N-aryl-N-heteroarylsulfonamide, urea; mono- di- or tri-substituted urea, wherein the subsitutent(s) is selected from the group consisting of C 1 -C 6 -alkyl, aryl, heteroaryl; O-alkylurethane, O-arylurethane, and O-heteroarylurethane;
R 14 is selected from the group consisting of hydrogen, linear, branched, or cyclic C 1 -C 6 -alkyl, alkenyl, or alkynyl; mono- or di-C 1 -C 6 alkylamino, mono- or bicyclic aryl, mono- or bicyclic heteroaryl having up to 5 heteroatoms selected from N, O, and S; mono- or bicyclic aryl-C 1 -C 6 -alkyl, mono- or bicyclic heteroaryl-C 1 -C 6 -alkyl, —S(═O) 2 —(CH 2 ) 1-6 —R 11 , —C(═O)R 11 , —S(═O) 2 —(CH 2 ) 2-6 R 12 , and —C(═O)—(CH 2 ) 1-6 —R 12 ; wherein R 11 and R 12 are as defined above;
R 15 and R 16 are selected from the group listed above for R 10 and R 13 , and are further selected from the group consisting of hydroxy, C 1 -C 6 -alkyloxy, aryloxy, heteroaryloxy, thio, C 1 -C 6 -alkylthio, C 1 -C 6 -alkylsulfinyl, C 1 -C 6 -alkylsulfonyl, arylthio, arylsulfinyl, arylsulfonyl, heteroarylthio, heteroarylsulfinyl, heteroarylsulfonyl, amino, mono- or di-C 1 -C 6 -alkylamino, mono- or diarylamino, mono- or diheteroarylamino, N-alkyl-N-arylamino, N-alkyl-N-heteroarylamino, N-aryl-N-heteroarylamino, aryl-C 1 -C 6 -alkylamino, carboxylic acid, carboxamide, mono- or di-C 1 -C 6 -alkylcarboxamide, mono- or diarylcarboxamide, mono- or diheteroarylcarboxamide, N-alkyl-N-arylcarboxamide, N-alkyl-N-heteroarylcarboxamide, N-aryl-N-heteroarylcarboxamide, sulfonic acid, sulfonamide, mono- or di-C 1 -C 6 -alkylsulfonamide, mono- or diarylsulfonamide, mono- or diheteroarylsulfonamide, N-alkyl-N-arylsulfonamide, N-alkyl-N-heteroarylsulfonamide, N-aryl-N-heteroarylsulfonamide, urea; mono- di- or tri-substituted urea, wherein the subsitutent(s) is selected from the group consisting of C 1 -C 6 -alkyl, aryl, heteroaryl; O-alkylurethane, O-arylurethane, and O-heteroarylurethane; and
wherein the cyclically-constrained γ-amino acid residues are selected from the group consisting of:
wherein R, together with the carbons to which it is attached, and further together with the β-position carbon in the γ-amino acid backbone where appropriate, independently defines a substituted or unsubstituted, monocyclic or bicyclic C 3 to C 10 cycloalkyl, cycloalkenyl, or heterocycle moiety, the heterocycle moiety having 1, 2, or 3 heteroatoms selected from the group consisting of N, S, and O; and
each “Y” is a single bond; and
“A” is independently selected from the group consisting of hydrogen and an amino-terminus protecting group, and “A′ ” is selected from the group consisting of hydroxy and a carboxy-terminus protecting group; and
each “a,” “c,” and “d” is an independently variable positive integer, and wherein “a”+“c”>3; or
salts thereof.
3. The compound of claim 2 , wherein at least one of X or Z is a cyclically-constrained β-amino acid residue wherein V and W, and the carbon atoms to which they are bonded, define a substituted or unsubstituted C 4 to C 6 cycloalkyl, cycloalkenyl, or heterocyclic ring having one nitrogen atom as the sole heteratom.
4. The compound of claim 2 , wherein at least one of X or Z is a cyclically-constrained β-amino acid residue wherein V and W, and the carbon atoms to which they are bonded, define a substituted or unsubstituted cyclopentyl, cyclohexyl, pyrrolidinyl, or piperdinyl ring.
5. A method of disrupting or mimicking binding interactions between two protein molecules or fragments thereof, the method comprising:
in an in vivo, in vitro, or ex vivo reaction between the two proteins or fragments thereof,
(a) introducing to the reaction an unnatural polypeptide compound according to claim 1 ; and then
(b) quantifying the effect of the added compound from step (a) on thermodynamic or kinetic parameters of the binding interaction between the two protein molecules or fragments thereof.