Cyclic amino acid molecules and methods of preparing the same

1. A process to produce a cyclic molecule comprising reacting an amino acid molecule, having an amino terminus and a carboxyl terminus, with an isocyanide and a compound having formula (Ia) and/or (Ib):

wherein:

R 1 , R 2 , R 3 , are independently selected from H; lower alkyl; alkenyl; heterocycle; cyckoalkyl; esters of the formula —C(O)OR* wherein R* is selected from alkyl and aryl; amides of the formula —C(O)NR**R***, wherein R** and R*** are independently selected from alkyl and aryl; —CH 2 C(O)R, wherein R is selected from —OH, lower alkyl, aryl, -lower alkyl-aryl, or —NR a R b , where R a and R b are independently selected from H, lower alkyl, aryl or -lower alkyl-aryl; —C(O)R c , wherein R c is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl-OR d , wherein R d is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents; and

the aldehyde component thereof may optionally be in its bisulfite adduct form; and

the amino acid molecule is an amino acid, a linear peptide or a salt of the foregoing, provided that if the amino acid molecule is a linear peptide, the compound having formula (Ia) and/or (Ib) comprises an aziridine chiral center proximal to the aldehyde with matching stereochemistry to the carbon atom proximal to the amino terminus of the peptide;

wherein the cyclic molecule is of formula (II):

wherein Z is an amino terminus of an amino acid;

—C═O—C is the carboxy terminus of an amino acid;

L, along with Z and —C═O— is an amino acid or peptide; and

R″ is an optionally substituted amide.

2. The process of claim 1 , wherein if L, along with Z and —C═O— is an amino acid then the amino terminus is a primary amino group or a secondary amino group but when L, along with Z and —C═O— is a linear peptide, then the amino terminus is a secondary amino group.

3. The process of claim 1 , wherein any one of R 1 -R 3 is H.

4. The process of claim 1 , wherein each of R 1 -R 3 is H.

5. The process of claim 1 , wherein R 2 and R 3 are both H.

6. The process of claim 5 , wherein R 1 is CH 2 OTBDMS or CH 2 i Pr.

7. The process of claim 1 wherein the amino acid molecule is a linear peptide.

8. The process of claim 7 , wherein the amino terminus amino acid of the linear peptide is selected from the group consisting of proline and an amino acid with an amino group substituted with NHBn, NHCH 2 CH 2 SO 2 Ph or NHCH 2 CH 2 CN.

9. The process of claim 1 wherein the amino acid molecule is a D or L amino acid selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine.

10. The process of claim 1 wherein the amino acid molecule is an alpha-amino acid.

11. The process of claim 1 wherein the amino acid molecule is a beta-amino acid.

12. The process of claim 1 wherein the amino acid molecule is a gamma-amino acid.

13. The process of claim 1 wherein the isocyanide is selected from the group consisting of: (S)-(−)-α-Methylbenzyl isocyanide; 1,1,3,3,-Tetramethylbutyl isocyanide; 1-Pentyl isocyanide; 2,6-Dimethylphenyl isocyanide; 2-Morpholinoethyl isocyanide; 2-Naphthyl isocyanide; 2-Pentyl isocyanide; 4-Methoxyphenyl isocyanide; Benzyl isocyanide; Cutyl isocyanide; Cyclohexyl isocyanide; Isopropyl isocyanide; p-Toluenesulfonylmethyl isocyanide; Phenyl isocyanide dichloride; tert-Butyl isocyanide;(Trimethylsilyl)methyl isocyanide; 1H-Benzotriazol-1-ylmethyl isocyanide; 2-Chloro-6-methylphenyl isocyanide; Di-tert-butyl 2-isocyanosuccinate; tert-Butyl 2-isocyano-3-methylbutyrate; tert-Butyl 2-isocyano-3-phenylpropionate; tert-Butyl 2-isocyanopropionate; and tert-butyl 3-isocyanopropionate.

14. The process of claim 1 wherein the isocyanide is tert-Butyl isocyanide.

15. The process of claim 1 wherein the process is conducted in a non-nucleophilic reaction medium.

16. The process of claim 15 wherein the non-nucleophilic reaction medium is trifluoroethanol.

17. The process of claim 15 wherein the non-nucleophilic reaction medium is HFIP mixed with water.

18. The process of claim 1 , wherein amino acid molecule is an amino acid and the process is conducted in water.

19. The process of claim 1 wherein the peptide is between 2 and 30 amino acids in length.

20. A cyclic molecule of formula (II):

wherein,

R 1 , R 2 and R 3 are independently selected from H; lower alkyl; aryl; heteroaryl; alkenyl; heterocycle; esters of the formula —C(O)OR* wherein R* is selected from alkyl and aryl; amides of the formula —C(O)NR**R***, wherein R** and R*** are independently selected from alkyl and aryl; —CH 2 C(O)R, wherein R is selected from —OH, lower alkyl, aryl, -loweralkyl-aryl, or —NR a R b , where R a and R b are independently selected from H, lower alkyl, aryl or -loweralkyl-aryl; —C(O)R c , wherein R c is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl-OR d , wherein R d is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents,

Z is an amino terminus of an amino acid;

—C═O— is the carboxy terminus of an amino acid;

L, along with Z and —C═O— is an amino acid or peptide and R″ is an optionally substituted amide.

21. The cyclic molecule of claim 20 , wherein if L, along with Z and —C═O—is an amino acid then the amino terminus is a primary amino group or a secondary amino group but when L, along with Z and —C═O— is a linear peptide, then the amino terminus is a secondary amino group.

22. The process of claim 1 , wherein the concentration of the amino acid molecule is at least at 0.002M.

23. The process of claim 1 , wherein the concentration of the amino acid molecule is between 0.002M to 0.2M.

24. The process of claim 1 , wherein the concentration of the amino acid molecule is at least 0.1M.

25. The process of claim 1 , wherein the concentration of the amino acid molecule is around 0.2M.

26. The cyclic molecule of claim 20 , wherein the molecule is a compound having the following formula:

wherein Ph is a phenyl group and t Bu is a tent-butyl group.

27. The cyclic molecule of claim 20 , wherein any one of R 1 -R 3 is H.

28. The cyclic molecule of claim 20 , wherein R 1 -R 3 are H.

29. The cyclic molecule of claim 27 , wherein R 2 and R 3 are H.

30. The cyclic molecule of claim 29 , wherein R 1 is CH 2 OTBDMS or CH 2 i Pr.

31. The cyclic molecule of claim 20 , wherein L, along with Z and —C═O— is a linear peptide.

32. The cyclic molecule of claim 31 , wherein the amino terminus amino acid of the linear peptide is selected from the group consisting of proline and an amino acid with an amino group substituted with NHBn, NHCH 2 CH 2 SO 2 Ph or NHCH 2 CH 2 CN.

33. The cyclic molecule of claim 20 , wherein L, along with Z and —C═O— is a D- or L- amino acid selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine.

34. The cyclic molecule of claim 20 wherein L, along with Z and —C═O— is an alpha-amino acid.

35. The cyclic molecule of claim 20 wherein L, along with Z and —C═O— is a beta-amino acid.

36. The cyclic molecule of claim 20 wherein L, along with Z and —C═O— is a gamma-amino acid.

37. The cyclic molecule of claim 20 , wherein R″ is tert-Butyl amide.

38. The cyclic molecule of claim 20 , wherein —Z-L —C═O— is a peptide consisting of 2 amino acids.

39. The cyclic molecule of claim 20 , wherein —Z-L —C═O— is a peptide consisting of 3 amino acids.

40. The cyclic molecule of claim 22 , wherein —Z-L —C═O— is a peptide consisting of 4 amino acids.

41. The cyclic molecule of claim 20 , wherein —Z-L —C═O— is a peptide consisting of 5 amino acids.

42. The cyclic molecule of claim 20 , wherein —Z-L —C═O— is a peptide consisting of 6 amino acids.

43. The cyclic molecule of claim 20 , wherein —Z-L —C═O— is a peptide consisting of 7 amino acids.

44. The cyclic molecule of claim 22 , wherein —Z-L —C═O— is a peptide consisting of 8 amino acids.

45. The cyclic molecule of claim 22 , wherein —Z-L —C═O— is a peptide consisting of 9 amino acids.

46. A process for producing a cyclic molecule of formula (III)

comprising reacting an amino acid molecule, having an amino terminus and a carboxyl terminus, with an isocyanide and a compound of formula (Ia) and/or (Ib)

thereby forming a cyclic molecule of formula II :

and subsequently reacting the cyclic molecule of formula (II) with a compound of formula Y—H under conditions effective to form the cyclic molecule of formula (III);

wherein

R 1 , R 2 , and R 3 are independently selected from H; lower alkyl; alkenyl; heterocycle; cyckoalkyl; esters of the formula —C(O)OR* wherein R* is selected from alkyl and aryl; amides of the formula —C(O)NR**R***, wherein R** and R*** are independently selected from alkyl and aryl; —CH 2 C(O)R, wherein R is selected from —OH, lower alkyl, aryl, -lower alkyl-aryl, or —NR a R b , where R a and R b are independently selected from H, lower alkyl, aryl or -lower alkyl-aryl; —C(O)R c , wherein R c , is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl —OR d , wherein R d is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents; and

the aldehyde component thereof may optionally be in its bisulfite adduct form; and

the amino acid molecule is an amino acid, a linear peptide or a salt of the foregoing, provided that if the amino acid molecule is a linear peptide, the compound having formula (Ia) and/or (Ib) comprises an aziridine chiral center proximal to the aldehyde with matching stereochemistry to the carbon atom proximal to the amino terminus of the peptide;

Z is an amino terminus of an amino acid;

—C═O— is the carboxy terminus of an amino acid;

L, along with Z and —C ═O— is an amino acid or peptide

R″ is an optionally substituted amide; and

Y—H comprises a nucleophilic moiety.

47. The process according to claim 46 , wherein Y is a fluorescent moiety.