Biosynthetically generated pyrroline-carboxy-lysine and site specific protein modifications via chemical derivatization of pyrroline-carboxy-lysine and pyrrolysine residues

1. A compound having the structure of Formula (II):

R 1 -(BB) n -R 2   (II)

wherein:

R 1 is H or an amino terminus modification group;

R 2 is OH or a carboxy terminus modification group;

n is an integer from 1 to 5000;

each BB is independently selected from an amino acid residue, a pyrrolysine analogue amino acid residue having the structure of Formula (D-1), and a pyrrolysine analogue amino acid residue having the structure of Formula (F 1):

wherein:

R 5 is selected from H, —OH, —NO 2 , halo, C 1-8 alkyl, halo-substituted-C 1-8 alkyl, hydroxy-substituted-C 1-8 alkyl, aryl, heteroaryl, heterocycloalkly or cycloalkyl and -LX 1 ;

R 6 is H or C 1 alkyl;

A is a phenyl optionally substituted with 1 to 3 substituents independently selected from —OH, —NO 2 , halo, C 1-8 alkyl, halo-substituted-C 1-8 alkyl, hydroxy-substituted-C 1-8 alkyl, aryl, heteroaryl, heterocycloalkly, or cycloalkyl and -LX 1 ;

L is selected from a bond, C 1-8 alkylene, halo-substituted-C 1-8 alkylene, hydroxy-substituted-C 1-8 alkylene, C 2-8 alkenylene, halo-substituted-C 2-8 alkenylene, hydroxy-substituted-C 2-8 alkenylene,

 —O(CR 11 R 12 ) k —, —S(CR 11 R 12 ) k , —S(O) k (CR 11 R 12 ) k —, —O(CR 11 R 12 ) k —NR 11 C(O)—, —O(CR 11 R 12 ) k C(O)NR 11 —, —C(O)—, —C(O)(CR 11 R 12 ) k —, —C(S)—, —C(S)(CR 11 R 12 ) k —, —C(O)NR 11 —, —NR 11 C(O)—, —NR 11 (CR 11 R 12 ) k —, —CONR 11 (CR 11 R 12 ) k —, —N(R 11 )CO(CR 11 R 12 ) k —, —C(O)NR 11 (CR 11 R 12 ) k —, —NR 11 C(O)CR 11 R 12 ) k —, where each R 11 and R 12 are independently H, C 1-8 alkyl, halo-substituted-C 1-8 alkyl, or hydroxy-substituted-C 1-8 alkyl, and k is an integer from 1 to 12, and

X 1 is selected from a water-soluble polymer, a polyalkylene glycol, a poly(ethylene glycol), a derivative of poly(ethylene glycol), a sugar, a lipid, a cytotoxic compound, an affinity label, a peptide, a protein, an antibody or antibody fragment, a carbohydrate, a DNA, a RNA, phosphorothioate-modified DNA, a saccharide, a disaccharide, an oligosaccharide, a polysaccharide, a spin label, a fluorophore, a radioactive moiety a photocaged moiety, biotin, a biotin analogue, a TLR2 agonist, a TLR4 agonist, a TLR7 agonist, a TLR9 agonist, a TLR8 agonist, a T-cell epitope, a phospho-lipid, a LPS-like molecule, an immunogenic hapten, an immune response potentiator, a solid support, —CH 2 CH 2 —(OCH 2 CH 2 O) p —OX 2 , —O—(CH 2 CH 2 O) p CH 2 CH 2 —X 2 , and any combination thereof, wherein p is 1 to 10,000 and X 2 is H, a C 1-8 alkyl, a protecting group or a terminal functional group, and

wherein:

at least one BB in the compound of Formula (II) is a pyrrolysine analogue amino acid residue having the structure of Formula (D-1).

2. The compound of claim 1 , wherein ring A is a phenyl substituted with -LX 1 .

3. The compound of claim 1 , wherein each BB is independently selected from an amino acid residue, a pyrrolysine analogue amino acid residue having the structure of Formula (D-2);

wherein,

R 5 is selected from H, —OH, —NO 2 , halo, C 1-8 alkyl, halo-substituted-C 1-8 alkyl, hydroxy-substituted-C 1-8 alkyl, aryl, heteroaryl, heterocycloalkly or cycloalkyl and -LX 1 ;

R 6 is H or C 1 alkyl;

when present each R 7 is independently selected from —OH, —NO 2 , halo, C 1-8 alkyl, halo-substituted-C 1-8 alkyl, hydroxy-substituted-C 1-8 alkyl, aryl, heteroaryl, heterocycloalkly, or cycloalkyl and -LX 1 ;

L is selected from a bond, C 1-8 alkylene, halo-substituted-C 1-8 alkylene, hydroxy-substituted-C 1-8 alkylene, C 2-8 alkenylene, halo-substituted-C 2-8 alkenylene, hydroxy-substituted-C 2-8 alkenylene,

 —O(CR 11 R 12 ) k —, —S(CR 11 R 12 ) k , —S(O) k (CR 11 R 12 ) k —, —O(CR 11 R 12 ) k —NR 11 C(O)—, —O(CR 11 R 12 ) k C(O)NR 11 —, —C(O)—, —C(O)(CR 11 R 12 ) k —, —C(S)—, —C(S)(CR 11 R 12 ) k —, —C(O)NR 11 —, —NR 11 C(O)—, —NR 11 (CR 11 R 12 ) k —, —CONR 11 (CR 11 R 12 ) k —, —N(R 11 )CO(CR 11 R 12 ) k —, —C(O)NR 11 (CR 11 R 12 ) k —, —NR 11 C(O)CR 11 R 12 ) k —, where each R 11 and R 12 are independently H, C 1-8 alkyl, halo-substituted-C 1-8 alkyl, or hydroxy-substituted-C 1-8 alkyl, and k is an integer from 1 to 12, and

X 1 is selected from a water-soluble polymer, a polyalkylene glycol, a poly(ethylene glycol), a derivative of poly(ethylene glycol), a sugar, a lipid, a cytotoxic compound, an affinity label, a peptide, a protein, an antibody or antibody fragment, a carbohydrate, a DNA, a RNA, phosphorothioate-modified DNA, a saccharide, a disaccharide, an oligosaccharide, a polysaccharide, a spin label, a fluorophore, a radioactive moiety, a photocaged moiety, biotin, a biotin analogue, a TLR2 agonist, a TLR4 agonist, a TLR7 agonist, a TLR9 agonist, a TLR8 agonist, a T-cell epitope, a phospho-lipid, a LPS-like molecule, an immunogenic hapten, an immune response potentiator, a solid support, —CH 2 CH 2 —(OCH 2 CH 2 O) p —OX 2 , —O—(CH 2 CH 2 O) p CH 2 CH 2 —X 2 , and any combination thereof, wherein p is 1 to 10,000 and X 2 is H, a C 1-8 alkyl, a protecting group or a terminal functional group.

4. The compound of claim 3 , wherein R 7 is -LX 1 .

5. The compound of claim 1 , wherein X 1 is a sugar, a polyethylene glycol, a fluorophore, an immunomodulator, a ribonucleic acid (RNA), a deoxyribonucleic acid (DNA), a protein, a peptide, a biotin, a phospholipid, a TLR7 agonist, an immunogenic hapten, a T-cell epitope, a lipid, a carbohydrate, phosphorothioate-modified DNA, a saccharide, a disaccharide, an oligosaccharide, a polysaccharide, a spin label, an immune response potentiator, a cytotoxic compound or a solid support.

6. The compound of claim 5 , wherein L is a poly(alkyleneglycol), a poly(ethyleneglycol), C 1-8 alkylene, halo-substituted-C 1-8 alkylene, hydroxy-substituted-C 1-8 alkylene,

7. The compound of claim 6 , wherein R 6 is H.