Ligase fusion proteins and application thereof

1. A process

for preparing a conjugate of formula (III):

wherein the process comprises contacting T and formula (IV) with a ligase unit to catalyze conjugation of T and formula (IV),

wherein the ligase unit comprises a ligase fusion protein immobilized to a support comprising a ligase which is a sortase and a Halo tag;

wherein the ligase fusion protein has an isoelectric point (pI) that is lower than that of the ligase from which the ligase fusion protein is derived;

wherein T comprises a protein, a peptide, an antibody, or an antibody fragment, which is modified to have either a recognition motif of the ligase donor substrate or a recognition motif of the ligase acceptor substrate;

L comprises a linker, which comprises the other of the recognition motif of the ligase donor substrate and the recognition motif of the ligase acceptor substrate;

P comprises a payload;

z is an integer of 1-20; and

t is an integer of 1-20.

2. The process according to claim 1 , wherein at least one of T and formula (IV) comprise one or more impurities.

3. The process according to claim 1 , wherein a harvested clarified cell culture fluid (HCCF) comprises T.

4. The process according to claim 1 , wherein the ligase unit comprises a sortase A.

5. The process according to claim 1 , wherein the support comprises a haloalkyl linker such that the ligase fusion protein is immobilized on the support through covalent interaction between the haloalkyl linker and the Halo tag.

6. The process according to claim 1 , further comprising the steps of

(1) subjecting T to one or more chromatography steps to remove one or more impurities prior to contacting T with formula (IV), and/or

(2) subjecting formula (IV) to one or more chromatography steps to remove one or more impurities prior to contacting formula (IV) with T, and/or

(3) subjecting the conjugate obtained, to one or more chromatography steps to remove one or more impurities.

7. The process according to claim 6 , wherein the chromatography step is independently selected from affinity chromatography, hydrophobic interaction chromatography, ion exchange chromatography, and a combination thereof.

8. The process according to claim 7 , wherein at least one of steps (1)-(3) comprises an affinity chromatography.

9. The process according to claim 7 , wherein T comprises an Fc fragment,

steps (1) and (2) do not exist, and step (3) comprises the steps in any order:

(3a-1): Protein A affinity chromatography;

(3a-2): anion exchange chromatography; and

(3a-3): cation exchange chromatography;

or

step (1) or step (2) comprises a Protein A affinity chromatography, and step (3) comprises the steps in any order:

(3b-1): anion exchange chromatography; and

(3b-2): cation exchange chromatography;

or

step (1) or step (2) comprises a Protein A affinity chromatography, and step (3) comprises the steps in any order:

(3c-1): Protein A affinity chromatography;

(3c-2): anion exchange chromatography; and

(3c-3): cation exchange chromatography.

10. The process according to claim 7 , wherein

the affinity chromatography is performed in bind-and-elute mode; and/or

the ion exchange chromatography is performed in bind-and-elute mode or flow-through mode.

11. The process according to claim 1 , wherein the process is performed in batch mode, semi-continuous mode or continuous mode.

12. The process according to claim 6 , wherein at least one of, the conjugation and steps (1)-(3) is performed in semi-continuous mode or continuous mode.

13. The process according to claim 1 , wherein

the ligase is a sortase A; and/or

the recognition motif of the ligase donor substrate is LPXTGJ; and/or

the recognition motif of the ligase acceptor substrate is G n , wherein G is glycine (Gly), and n is an integer of 3-10;

X is any natural or unnatural amino acid;

J is absent, or is an amino acid fragment comprising 1-10 amino acids, wherein each amino acid is independently any natural or unnatural amino acid.

14. The process according to claim 1 , wherein the conjugate has the structure selected from the following formulae (3), (3′), (5) and (5′):

wherein n is an integer of 3-10;

x is OH, NH 2 or Gly;

Toxin represents a cytotoxin;

Lk is L 1 -L 2 -L 3 ;

L 1 and L 3 are each independently selected from the group consisting of:

—CH 2 —, —NH—, —(CO)—, —NH(CO)—, —(CO)NH—; and combination of a C1-4 alkylene with one of the following groups: —CH 2 —, —NH—, —(CO)—, —NH(CO)—, —(CO)NH—;

L 2 is absent or is a C 7-34 alkylene, and wherein one or more (—CH 2 —) structures in the alkylene is optionally replaced by —O—;

L 1 , L 2 and L 3 are each optionally and independently substituted with 1, 2 or 3 substituents selected from [[—OR1[[—OR 1 and —NR 1 R 2 ;

R 1 and R 2 are each independently selected from the group consisting of hydrogen, —C 1-6 alkyl, —(CO)—C 1-6 alkyl and —S(═O) 2 —C 1-6 alkyl;

Y is absent or selected from the group consisting of a cleavable sequence, spacer Sp1, and a combination thereof;

the cleavable sequence comprises an amino acid sequence which can be cleaved by an enzyme, and the cleavable sequence comprises 1-10 amino acids; and

Sp1 is selected from the group consisting of a spacer sequence containing 1-20 amino acids, PAB, and a combination thereof.

15. The process according to claim 14 , wherein Y does not exist, and the conjugate has the structure selected from the following formulae (4), (4′), (6) and (6′):

16. A process for the preparation of a conjugate, comprising contacting a ligase unit with a linker-payload intermediate and T to catalyze the conjugation reaction between T and the linker-payload intermediate to obtain the conjugate,

wherein the ligase unit comprises a ligase fusion protein immobilized to a support comprising a ligase which is a sortase and a Halo tag;

wherein the ligase fusion protein has an isoelectric point (pI) that is lower than that of the ligase from which the ligase fusion protein is derived;

wherein the linker-payload intermediate has the structure of formula (IV-1-5) or (IV-1-5′), the conjugate has the structure of formula (5) or (5′), and the formulae (IV-1-5), (IV-1-5′), (5) and (5′) are as follows

wherein T a protein, a peptide, an antibody, or an antibody fragment, which is optionally modified to have the recognition motif of the ligase donor substrate;

n is an integer of 3-10; and

Toxin represents a cytotoxin.

17. The process according to claim 16 , wherein the linker-payload intermediate of formula (IV-1-5) has the structure of formula (IV-1-6), the linker-payload intermediate of formula (IV-1-5′) has the structure of formula (IV-1-6′), the conjugate of formula (5) has the structure of formula (6), and the conjugate of formula (5′) has the structure of formula (6′), and the formulae (IV-1-6), (IV-1-6′), (6) and (6′) are as follows

18. The process according to claim 5 , wherein the haloalkane linker is a chloroalkane linker produced by a chloroalkyl substrate having the structure of formula (I-1):

wherein u is an integer of 1 to 20, v is an integer of 0 to 20, and w is an integer of 1 to 19.

19. The process according to claim 1 , wherein the ligase fusion protein comprises a ligase, a Halo tag, and optionally a linker peptide, wherein the ligase, the Halo tag, and optionally the linker peptide are fused by a covalent bond, wherein the ligase is a sortase A comprising the amino acid sequence of SEQ ID NO:27 or an amino acid sequence having a sequence identity of at least 85% thereto, and wherein the ligase has an isoelectric point (pI) of about 7.5 to about 10.0, the Halo tag has an isoelectric point of about 4.5 to about 5.0, and the pI of the ligase fusion protein is about 2.0 to about 4.5 pH units lower than that of the ligase.

20. The process according to claim 19 , wherein the Halo tag comprises the amino acid sequence of SEQ ID NO: 28 or an amino acid sequence having a sequence identity of at least about 85% thereto.

21. The process according to claim 19 , wherein the pI of the ligase fusion protein is about 4.5 to about 6.5.

22. The process according to claim 21 , wherein the pI of the ligase fusion protein is about 5.0 to about 6.0.

23. The process according to claim 19 , wherein the ligase fusion protein comprises the amino acid sequence of SEQ ID NO: 29.

24. The process according to claim 16 , wherein the support comprises a haloalkyl linker such that the ligase fusion protein is immobilized on the support through covalent interaction between the haloalkyl linker and the Halo tag, wherein the haloalkane linker is a chloroalkane linker produced by a chloroalkyl substrate having the structure of formula (I-1):

wherein u is an integer of 1 to 20, v is an integer of 0 to 20, and w is an integer of 1 to 19.

25. The process according to claim 24 , wherein the ligase fusion protein comprises a ligase, a Halo tag, and optionally a linker peptide, wherein the ligase, the Halo tag, and optionally the linker peptide are fused by a covalent bond, wherein the ligase is a sortase A comprising the amino acid sequence of SEQ ID NO:27 or an amino acid sequence having a sequence identity of at least 85% thereto, and wherein the ligase has an isoelectric point (pI) of about 7.5 to about 10.0, the Halo tag has an isoelectric point of about 4.5 to about 5.0, and the pI of the ligase fusion protein is about 2.0 to about 4.5 pH units lower than that of the ligase.

26. The process according to claim 25 , wherein the ligase fusion protein comprises the amino acid sequence of SEQ ID NO: 29.

27. The process according to claim 15 , wherein the conjugate has the structure selected from the following formulae (6) and (6′):

28. The process according to claim 26 , wherein the conjugate has the structure selected from the following formulae (6) and (6′):