Engineered polypeptide conjugates and methods for making thereof using transglutaminase

1. An engineered Fc-containing polypeptide conjugate comprising the formula: (Fc-containing polypeptide)-T-A, wherein T is an acyl donor glutamine-containing tag engineered at a specific site or comprises an endogenous glutamine (Q) made reactive by the Fc-containing polypeptide engineering; wherein A is an amine donor agent; wherein the amine donor agent is site-specifically conjugated to the acyl donor glutamine-containing tag or the endogenous glutamine at a carboxyl terminus, an amino terminus, or at an another site in the Fc-containing polypeptide, wherein the acyl donor glutamine-containing tag consists of an amino acid sequence selected from the group consisting of LLQGG (SEQ ID NO:2), LSLSQG (SEQ ID NO:4), GGGLLQGG (SEQ ID NO:5), GLLQG (SEQ ID NO:6), LLQ, GSPLAQSHGG (SEQ ID NO:7), GLLQGGG (SEQ ID NO:8), GLLQGG (SEQ ID NO:9), GLLQ (SEQ ID NO:10), LLQLLQGA (SEQ ID NO:47), LLQGA (SEQ ID NO:48), LLQYQGA (SEQ ID NO:49), LLQGSG (SEQ ID NO:50), LLQYQG (SEQ ID NO:51), LLQLLQG (SEQ ID NO:52), SLLQG (SEQ ID NO:53), LLQLQ (SEQ ID NO:54), LLQLLQ (SEQ ID NO:55), and LLQGR (SEQ ID NO:56).

2. The engineered Fc-containing polypeptide conjugate of claim 1 , wherein the acyl donor glutamine-containing tag is not spatially adjacent to a reactive Lys in the Fc-containing polypeptide.

3. The engineered Fc-containing polypeptide conjugate of claim 1 , wherein the Fc-containing polypeptide comprises an amino acid modification at the last amino acid position in the carboxyl terminus relative to a wild-type Fc-containing polypeptide at the same position.

4. The engineered Fc-containing polypeptide conjugate of claim 1 , wherein the Fc-containing polypeptide conjugate comprises a full length antibody heavy chain and an antibody light chain.

5. The engineered Fc-containing polypeptide conjugate of claim 4 , wherein the acyl donor glutamine-containing tag is located at the carboxyl terminus of a heavy chain, a light chain, or both the heavy chain and the light chain.

6. The engineered Fc-containing polypeptide conjugate of claim 5 , wherein the acyl donor glutamine-containing tag comprises a first acyl donor glutamine-containing tag and a second acyl donor glutamine-containing tag, wherein the first acyl donor glutamine-containing tag is located at the carboxyl terminus of the heavy chain, and the second acyl donor glutamine-containing tag is located elsewhere at the another site on the Fc-containing polypeptide.

7. The engineered Fc-containing polypeptide conjugate of claim 4 , wherein the acyl donor glutamine-containing tag is located at the Fc-containing polypeptide at the amino terminus of a heavy chain, a light chain, or both the heavy chain and the light chain.

8. The engineered Fc-containing polypeptide conjugate of claim 1 , wherein the Fc-containing polypeptide comprises an antibody, wherein the antibody is a monoclonal antibody, a polyclonal antibody, a human antibody, a humanized antibody, a chimeric antibody, a bispecific antibody, a minibody, or an antibody fragment.

9. The engineered Fc-containing polypeptide conjugate of claim 8 , wherein the antibody is an IgG.

10. The engineered Fc-containing polypeptide conjugate of claim 9 , wherein effector function of the IgG decreases no greater than about 2-fold relative to a wild type IgG.

11. The engineered Fc-containing polypeptide conjugate of claim 1 , wherein the amine donor agent comprises the formula: X—Y—Z, wherein X is an amine donor unit; Y is a linker; and Z is an agent moiety.

12. The engineered Fc-containing polypeptide conjugate of claim 11 , wherein the amine donor unit-linker (X—Y) is selected from the group consisting of Ac-Lys-Gly, aminocaproic acid, Ac-Lys-β-Ala, amino-PEG2-C2, amino-PEG3-C2, amino-PEG6-C2, Ac-Lys-Val-Cit-PABC, aminocaproyl-Val-Cit-PABC, putrescine, and Ac-Lys-putrescine.

13. The engineered Fc-containing polypeptide conjugate of claim 11 , where in the agent moiety is a cytotoxic agent.

14. The engineered Fc-containing polypeptide conjugate of claim 13 , wherein the cytotoxic agent is selected from the group consisting of an anthracycline, an auristatin, a dolastatin, a duocarmycin, an enediyne, a geldanamycin, a maytansine, a puromycin, a taxane, a vinca alkaloid, SN-38, a tubulysin, a hemiasterlin, and stereoisomers, isosteres, analogs, or derivatives thereof.

15. The engineered Fc-containing polypeptide conjugate of claim 11 , wherein the amine donor agent is selected from the group consisting of Alexa 488 cadaverine, 5-FITC cadaverine, Alexa 647 cadaverine, Alexa 350 cadaverine, 5-carboxytetramethylrhodamine (5-TAMRA) cadaverine, 5-fluorescein amidite (5-FAM) cadaverine, sulforhodamine (SR) 101 cadaverine, 5,6-TAMRA cadaverine, 5-FAM lysine, Ac-LysGly-monomethyl auristatin D (MMAD), amino-PEG3-C2-MMAD, amino-PEG6-C2-MMAD, amino-PEG3-C2-amino-nonanoyl-MMAD, aminocaproyl-Val-Cit-p-aminobenzyloxycarbonyl (PABC)-MMAD, Ac-Lys-Val-Cit-PABC-MMAD, aminocaproyl-MMAD, Ac-Lys-β-Ala-MMAD, amino-PEG2-C2-monomethyl auristatin E (MMAE), aminocaproyl-MMAE, amino-PEG3-C2-MMAE, aminocaproyl-monomethyl auristatin F (MMAF), Aminocaproyl-Val-Cit-PABC-MMAE, aminocaproyl-Val-Cit-PABC-MMAF, putrescinyl-geldanamycin, and Ac-Lys-putrescinyl-geldanamycin.

16. The engineered Fc-containing polypeptide conjugate of claim 15 , wherein the amine donor agent is amino-PEG6-C2-MMAD or aminocaproyl-Val-Cit-PABC-MMAD.

17. The engineered Fc-containing polypeptide conjugate of claim 11 , wherein the amine donor unit-linker (X—Y) is a branched unit and the agent moiety comprises at least about 2 agent moieties, wherein the agent moiety can be the same or different.

18. A pharmaceutical composition comprising the engineered Fc-containing polypeptide conjugate of claim 1 , and a pharmaceutically acceptable excipient.

19. The engineered Fc-containing polypeptide conjugate of claim 1 , wherein the acyl donor glutamine-containing tag engineering or the Fc-containing polypeptide engineering is not an amino acid substitution from asparagine (Asn) to glutamine (Gln) at position 297 of a human IgG.