Polypeptides containing γ-amino acids

• US 6,958,384 B2
• Filed: 03/14/2003
• Issued: 10/25/2005
• Est. Priority Date: 03/15/2002
• Status: Expired due to Fees

• Current Assignee: Wisconsin Alumni Research Foundation (University of Wisconsin System)
• Original Assignee: Wisconsin Alumni Research Foundation (University of Wisconsin System)
• Inventors: Lai, Jonathan R., Murray, Justin, Woll, Matthew G., Gellman, Samuel H.
• Primary Examiner(s): RUSSEL, JEFFREY E
• Application Number:
  US10/389,500
• Publication Number:
  US 20030211999A1
• Time in Patent Office: 956 Days
• Field of Search: 530/300, 530/332, 530/350
• US Class Current: 530/332
• CPC Class Codes: C07C 2601/08 the ring being saturated
• CPC Class Codes: C07C 271/24 with the nitrogen atom of at least one of the carbamate groups bound to a carbon atom of a ring other than a six-membered aromatic ring
• CPC Class Codes: C07D 207/16 Carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals
• CPC Class Codes: C07D 211/60 Carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals
• CPC Class Codes: G01N 2500/00 Screening for compounds of potential therapeutic value
• CPC Class Codes: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

Disclosed are polypeptide compounds containing at least one residue comprising a cyclically-constrained γ-amino acid residue. The compounds have the formula
where A is a hydrogen, hydroxy, amino- or carboxy-protecting group, Y is a single bond or a prolyl-containing linking group, and X and Y are γ-amino acid residues, provided that one of X or Y is a conformationally-restrained γ-amino acid residue, and “a,” “c,” and “d” are positive integers. The compounds find use as non-enzymatically degradable probes to mimic protein behavior in solution.

Claims

1. An unnatural polypeptide compound selected from the group consisting of:

wherein;

each Y is independently variable and is selected from the group consisting of a single bond or

wherein each R³ in Formula (ii) is independently variable and is selected from the group consisting of hydrogen, linear or branched C₁-C₆-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-C₁-C₆-alkyl, and mono- or bicyclic heteroaryl-C₁-C₆-alkyl;

each R⁴ in Formula (ii) is selected from the group of substituents as listed hereinbelow for R¹;

each X and each Z in Formula (i) is independently variable and is selected from the group consisting of γ

-amino acid residues, provided that at least one of X or Z is a substituted or unsubstituted cyclically-constrained γ

-amino acid residue independently selected from the group consisting of;

wherein R in Formula (iii), together with the carbons to which it is attached, independently defines a substituted or unsubstituted C₅ to C₁₀ 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 further wherein substituents on the cyclically-constrained γ

-amino acid residue of Formula (iii) are independently selected from the group consisting of linear or branched C₁-C₆-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-C₁-C₆-alkyl, mono- or bicyclic heteroaryl-C₁-C₆-alkyl, —

(CH₂)_n+1—

OR², —

(CH₂)_n+1—

SR², —

(CH₂)_n+1—

S(═

O)—

CH₂—

R², —

(CH₂)_n+1—

S(═

O)₂—

CH₂—

R², —

(CH₂)_n+1—

NR²R², —

(CH₂)_n+1—

NHC(═

O)R², —

(CH₂)_n+1—

NHS(═

O)₂—

CH₂—

R², —

(CH₂)_n+1—

O—

(CH₂)_m—

R¹, —

(CH₂)_n+1—

S—

(CH₂)_m—

R¹, —

(CH₂)_n+1—

S(═

O)—

(CH₂)_m—

R¹, —

(CH₂)_n+1—

S(═

O)₂—

(CH₂)_m—

R¹, —

(CH₂)_n+1—

NH—

(CH₂)_m—

R¹, —

(CH₂)_n+1—

N—

{(CH₂)_m—

R¹}₂, —

(CH₂)_n+1—

NHC(═

O)—

(CH₂)_n+1—

R¹, —

(CH₂)_n+1—

NHS(═

O)₂—

(CH₂)_m—

R¹;

—

(CH₂)_n—

OR, —

(CH₂)_n—

SR², —

(CH₂)_n—

S(═

O)—

CH₂—

R², —

(CH₂)_n—

S(═

O)₂—

CH₂—

R², —

(CH₂)_n—

NR²R², —

(CH₂)_n—

NHC(═

O)R², —

(CH₂)_n—

NHS(═

O)₂—

CH₂—

R², —

(CH₂)_n—

O—

(CH₂)_m—

R¹, —

(CH₂)_n—

S—

(CH₂)_m—

R¹, —

(CH₂)_n—

S(═

O)—

(CH₂)_m—

R¹, —

(CH₂)_n—

S(═

O)₂—

(CH₂)_m—

R¹, —

(CH₂)_n—

NH—

(CH₂)_m—

R¹, —

(CH₂)_n—

N—

{(CH₂)_m—

R¹}₂, —

(CH₂)_n—

NHC(═

O)—

(CH₂)_m—

R¹, and —

(CH₂)_n—

NHS(═

O)₂—

(CH₂)_m—

R¹;

wherein R² is independently selected from the group consisting of hydrogen, C₁-C₆-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-C₁-C₆-alkyl, and mono- or bicyclic heteroaryl-C₁-C₆-alkyl; and

wherein R¹ is selected from the group consisting of hydroxy, C₁-C₆-alkyloxy, aryloxy, heteroaryloxy, thio, C₁-C₆-alkylthio, C₁-C₆-alkylsulfinyl, C₁-C₆-alkylsulfonyl, arylthio, arylsulfinyl, arylsulfonyl, heteroarylthio, heteroarylsulfinyl, heteroarylsulfonyl, amino, mono- or di-C₁-C₆-alkylamino, mono- or diarylamino, mono- or diheteroarylamino, N-alkyl-N-arylamino, N-alkyl-N-heteroarylamino, N-aryl-N-heteroarylamino, aryl-C₁-C₆-alkylamino, carboxylic acid, carboxamide, mono- or di-C₁-C₆-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-C₁-C₆-alkylsulfonamide, mono- or diarylsulfonamide, mono- or diheteroarylsulfonamide, N-alkyl-N-arylsulfonamide, N-alkyl-N-heteroarylsulfonamide, N-aryl-N-heteroarylsulfonamide, urea; and

mono- di- or tri-substituted urea, wherein the subsitutent(s) is selected from the group consisting of C₁-C₆-alkyl, aryl, heteroaryl;

O-alkylurethane, O-arylurethane, and O-heteroarylurethane, and wherein m is an integer of from 2-6 and n is an integer of from 0-6;

wherein each “

A”

of Formula (i) is independently selected from the group consisting of hydrogen, hydroxy, an amino-terminus protecting group, and a carboxy-terminus protecting group;

wherein each of “

a,”

“

c,” and

“

d”

is an independently variable positive integer; and

salts thereof.

2. The compound of claim 1, wherein a+c≧

3.

3. The compound of claim 1, wherein Y is a single bond and a+c≧

3.

4. The compound of claim 1, wherein Y is:

and a+c≧

3.

5. The compound of claim 1, wherein Y is:

and a+c≧

3.

6. The compound of claim 1, wherein each R, together with the carbons to which it is attached, independently defines a substituted or unsubstituted C₅ to C₆ cycloalkyl, cycloalkenyl, or heterocycle moiety having a single nitrogen heteroatom.

7. The compound of claim 1, wherein each R, together with the carbons to which it is attached, independently defines an unsubstituted C₅ to C₆ cycloalkyl, cycloalkenyl, or heterocycle moiety having a single nitrogen heteroatom.

8. The compound of claim 1, wherein R, together with the carbons to which it is attached, defines a substituted C₅ to C₆ cycloalkyl, cycloalkenyl, or heterocycle moiety having a single nitrogen heteroatom;

and

substituents on the cycloalkyl, cylcloalkenyl, or heterocycle moieties are independently selected from the group consisting of linear or branched C₁-C₆-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-C₁-C₆-alkyl, mono- or bicyclic heteroaryl-C₁-C₆-alkyl, —

(CH₂)_n+1—

OR², —

(CH₂)_n+1—

SR², —

(CH₂)_n+1—

S(═

O)—

CH₂—

R², —

(CH₂)_n+1—

S(═

O)₂—

CH₂—

R², —

(CH₂)_n+1—

NR²R², —

(CH₂)_n+1—

NHC(═

O)R², —

(CH₂)_n+1—

NHS(═

O)₂—

CH₂—

R², —

(CH₂)_n+1—

O—

(CH₂)_m—

R¹, —

(CH₂)_n+1—

S—

(CH₂)_m—

R¹, —

(CH₂)_n+1—

S(═

O)—

(CH₂)_m—

R¹, —

(CH₂)_n+1—

S(═

O)₂—

(CH₂)_m—

R¹, —

(CH₂)_n+1—

NH—

(CH₂)_m—

R¹, —

(CH₂)_n+1—

N—

{(CH₂)_m—

R¹}₂, —

(CH₂)_n+1—

NHC(═

O)—

(CH₂)_n+1—

R¹, —

(CH₂)_n+1—

NHS(═

O)₂—

(CH₂)_m—

R¹, —

(CH₂)_n—

OR, —

(CH₂)_n—

SR², —

(CH₂)_n—

S(═

O)—

CH₂—

R², —

(CH₂)_n—

S(═

O)₂—

CH₂—

R², —

(CH₂)_n—

NR²R², —

(CH₂)_n—

NHC(═

O)R², —

(CH₂)_n—

NHS(═

O)₂—

CH₂—

R², —

(CH₂)_n—

O—

(CH₂)_m—

R¹, —

(CH₂)_nS—

(CH₂)_m—

R¹, —

(CH₂)_n—

S(═

O)—

(CH₂)_m—

R¹, —

(CH₂)_n—

S(═

O)₂—

(CH₂)_m—

R¹, —

(CH₂)_n—

NH—

(CH₂)_m—

R¹, —

(CH₂)_n—

N—

{(CH₂)_m—

R¹}₂, —

(CH₂)_n—

NHC(═

O)—

(CH₂)_m—

R¹, and —

(CH₂)_n—

NHS(═

O)₂—

(CH₂)_m—

R¹;

wherein R² is independently selected from the group consisting of hydrogen, C₁-C₆-alkyl, alkenyl, or alkynyl;

mono- or bicyclic aryl, mono- or bicyclic heteraryl having up to 5 heteroatoms selected from N, O, and S;

mono- or bicyclic aryl-C₁-C₆-alkyl, mono- or bicyclic heteroaryl-C₁-C₆-alkyl; and

wherein R¹ is selected from the group consisting of hydroxy, C₁-C₆-alkyloxy, aryloxy, heteroaryloxy, thio, C₁-C₆-alkylthio, C₁-C₆-alkylsulfinyl, C₁-C₆-alkylsulfonyl, arylthio, arylsulfinyl, arylsulfonyl, heteroarylthio, heteroarylsulfinyl, heteroarylsulfonyl, amino, mono- or di-C₁-C₆-alkylamino, mono- or diarylamino, mono- or diheteroarylamino, N-alkyl-N-arylamino, N-alkyl-N-heteroarylamino, N-aryl-N-heteroarylamino, aryl-C₁-C₆-alkylamino, carboxylic acid, carboxamide, mono- or di-C₁-C₆-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-C₁-C₆-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 C₁-C₆-alkyl, aryl, heteroaryl;

O-alkylurethane, O-arylurethane, and O-heteroarylurethane;

m is an integer of from 2-6 and n is an integer of from 0-6; and

salts thereof.

9. The compound of claim 1, wherein each R, together with the carbons to which it is attached, independently defines a substituted or unsubstituted cyclopentyl, substituted or unsubstituted cyclohexyl, unsubstituted or N-substituted piperidinyl, or unsubstituted or N-substituted pyrrolidinyl.

10. The compound of claim 1, wherein at least one of X or Z is a cyclically-constrained γ

-amino acid residue independently selected from the group consisting of;

11. The compound of claim 1, wherein at least one of X or Z is a cyclically-constrained γ

-amino acid residue independently selected from the group consisting of;

12. The compound of claim 1, wherein at least one of X or Z is a cyclically-constrained γ

-amino acid residue selected from the group consisting of;

13. The compound of claim 1, wherein at least one of X or Z is a cyclically-constrained γ

-amino acid residue selected from the group consisting of;

14. The compound of claim 13, wherein each R, together with the carbons to which it is attached, independently defines a substituted or unsubstituted C₅ to C₆ cycloalkyl, cycloalkenyl, or heterocycle moiety having a single nitrogen heteroatom.

15. The compound of claim 13, wherein each R, together with the carbons to which it is attached, independently defines an unsubstituted C₅ to C₆ cycloalkyl, cycloalkenyl, or heterocycle moiety having a single nitrogen heteroatom.

16. The compound of claim 13, wherein each R, together with the carbons to which it is attached, independently defines a substituted or unsubstituted cyclopentyl, substituted or unsubstituted cyclohexyl, unsubstituted or N-substituted piperidinyl, or unsubstituted or N-substituted pyrrolidinyl.

17. The compound of claim 1, wherein at least one of X or Z is a cyclically-constrained γ

-amino acid residue independently selected from the group consisting of;

18. The compound of claim 17, wherein each R, together with the carbons to which it is attached, independently defines a substituted or unsubstituted C₅ to C₆ cycloalkyl, cycloalkenyl, or heterocycle moiety having a single nitrogen heteroatom.

19. The compound of claim 17, wherein each R, together with the carbons to which it is attached, independently defines an unsubstituted C₅ to C₆ cycloalkyl, cycloalkenyl, or heterocycle moiety having a single nitrogen heteroatom.

20. The compound of claim 17, wherein each R, together with the carbons to which it is attached, independently defines a substituted or unsubstituted cyclopentyl, substituted or unsubstituted cyclohexyl, unsubstituted or N-substituted piperidinyl, or unsubstituted or N-substituted pyrrolidinyl.

21. The compound of claim 1, wherein at least one of X or Z is a cyclically-constrained γ

-amino acid residue independently selected from the group consisting of;

22. The compound of claim 21, wherein each R, together with the carbons to which it is attached, independently defines a substituted or unsubstituted C₅ to C₆ cycloalkyl, cycloalkenyl, or heterocycle moiety having a single nitrogen heteroatom.

23. The compound of claim 21, wherein each R, together with the carbons to which it is attached, independently defines an unsubstituted C₅ to C₆ cycloalkyl, cycloalkenyl, or heterocycle moiety having a single nitrogen heteroatom.

24. The compound of claim 21, wherein each R, together with the carbons to which it is attached, independently defines a substituted or unsubstituted cyclopentyl, substituted or unsubstituted cyclohexyl, unsubstituted or N-substituted piperidinyl, or unsubstituted or N-substituted pyrrolidinyl.

25. The compound of claim 1, wherein when Y is a single bond, one of the “

A”

moieties is a hydrogen or a amino-terminus protecting group, and the other of the “

A”

moieties is a hydroxy or a carboxy-terminus protecting group; and

when Y is not a single bond, both of the “

A”

moieties are hydrogens or amino-terminus protecting groups.

26. A method of probing, 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,

(a) introducing to the reaction an unnatural polypeptide compound according to claim 1; and

then

(b) quantifying any 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.