WO2021181414A1

WO2021181414A1 - METHOD OF SEPARATING HIGH-MOLECULAR WEIGHT AGGREGATES OF AN Fc-FUSION PROTEIN

Info

Publication number: WO2021181414A1
Application number: PCT/IN2021/050232
Authority: WO
Inventors: Charles FRANKO; Shashank Mishra; Ravichandran Ramakrishnan; Gopinath GOVINDARAJAN; Krishna Prasad Chellapilla
Original assignee: Dr. Reddy’S Laboratories Limited
Priority date: 2020-03-11
Filing date: 2021-03-10
Publication date: 2021-09-16

Abstract

The present invention discloses a method for purification of fusion protein from the contaminants. The method disclosed describes a process for the reduction of high-molecular weight aggregates and non-covalent dimers of an Fc-fusion protein by hydrophobic-interaction chromatography without a preceding anion exchange chromatography step. The method also describes the use of mixed-mode chromatography for the reduction of high-molecular weight aggregates of the Fc-fusion protein.

Description

METHOD OF SEPARATING HIGH-MOLECULAR WEIGHT AGGREGATES OF

AN Fc-FUSION PROTEIN

FIELD OF INVENTION

The present invention relates to protein purification methods. In particular, disclosed is a method for purifying fusion proteins using chromatography.

BACKGROUND

Fc-fusion proteins are bioengineered polypeptides that join the crystallizable fragment (Fc) domain of an antibody with another biologically active protein domain to generate a molecule with unique structure-function properties and significant therapeutic potential. The gamma immunoglobulin (IgG) isotype is often used as the basis for generating Fc-fusion proteins because of favorable characteristics such as recruitment of effector function and increased plasma half-life. Given the range of proteins that can be used as fusion partners, Fc-fusion proteins have numerous biological and pharmaceutical applications, which has launched Fc- fusion proteins into the forefront of drug development.

Fc-fusion proteins can be commercially manufactured using platform upstream and downstream methods based for (monoclonal antibodies) mAbs. However, Fc-fusion proteins, receptor domains generally contain one or more glycosylation sites (both N- and O-linked) in contrast to single glycosylation site for mAbs. Also, the oligosaccharide structures are more varied and complex (complex and high mannose; bi-, tri- and tetra-antennary) in their receptor domains than IgG Fc (complex, bi-antennary) and can contain more sialic acid residues. The latter can shift the pi of Fc-fusion proteins into an acidic pH range and impart significantly more charge heterogeneity on them than that of the conventional mAbs. Hence, there are unique attributes of Fc-Fusion proteins that would require optimization or redesigning of the commercial process used for the manufacture of mAbs.

Chromatography is widely used and has become indispensable in purification of any protein, including Fc-fusion proteins. Combinations of different chromatographic techniques, such as affinity chromatography, ion-exchange chromatography, size-exclusion chromatography, hydrophobic interaction chromatography are generally employed for achieving high level of purity and removal of contaminants. However, while choosing any or combination of chromatography steps, several physicochemical conditions such as pH, temperature, buffer components and concentration, salt, chromatographic support, binding ligand, properties of the protein, such as hydrophobicity, need to the considered so as to have the protein in pure yet stable and functional form. One example of an Fc-fusion protein is abatacept, which exists as a covalent homodimer linked through an inter-chain disulfide bond. The linkage between the two monomers can, however, also be of non-covalent nature. This non-covalent interaction between two monomers can result in the formation of dimers which are unstable and hence should be removed from the purified composition of abatacept.

The objective of the present invention is to purify Fc-fusion protein from contaminants, such as high molecular weight (HMW) aggregates and non-covalent dimers arising from the cell culture process, using chromatography.

SUMMARY

The present invention discloses a method for purifying an Fc-Fusion protein from the contaminants, preferably high-molecular weight aggregates and non-covalently linked dimers, the method comprises use of hydrophobic interaction chromatography (HIC). The method disclosed in the invention leads to effective removal of the high-molecular weight aggregates and non-covalent dimers to yield a purified Fc-fusion protein composition.

In particular, the method discloses the use of hydrophobic interaction chromatography in flow through mode using a linear butyl ligand for purifying an Fc-fusion protein composition from contaminants, preferably high-molecular weight aggregates and non-covalent dimers, thus obtaining a purified composition. Specifically, the inventive method discloses a HIC support / stationary phase with a linear butyl ligand for the purification of CTLA4-Ig fusion protein from its HMW aggregates and non-covalent dimers.

The method as disclosed herein is successful in a significant reduction of HMW aggregates, i.e., greater than 90% reduction in aggregates and 100% removal of non-covalent dimers are achieved by the method. The method disclosed in the invention is capable of being used at a commercial scale for controlling the level of HMW aggregates and non-covalent dimers and thus, in the manufacture of a purified composition of the said CTLA4-Ig fusion protein.

BRIEF DESCRIPTION OF DRAWINGS

Figure 1 shows the chromatography process flow chart for the evaluation of hexyl, octyl, phenyl and butyl ligands in flow-through mode for the development of the HIC step. Figure 2 shows the chromatography process flow chart for the evaluation of phenyl ligand in bind and elute mode for the development of the HIC step.

Figure 3 shows the chromatography process flow chart for optimization of the HIC step using butyl ligand in flow-through mode.

Figure 4 shows the chromatography process flow chart for the optimized HIC step using butyl ligand.

DETAILED DESCRIPTION OF THE INVENTION

Definitions

"Fc fusion protein" is a protein that contains an Fc region of an immunoglobulin is fused or linked to a heterologous polypeptide. The heterologous polypeptide fused to the Fc region may be a polypeptide from a protein other than an immunoglobulin protein. For instance, the heterologous polypeptide may be a ligand polypeptide, a receptor polypeptide, a hormone, cytokine, growth factor, an enzyme, or other polypeptide that is not a component of an immunoglobulin. Such Fc fusion proteins may comprise an Fc region fused to a receptor or fragment thereof or a ligand from a receptor including, but not limited to, any one of the following receptors: both forms of TNFR (referred to as p55 and p75), Interleukin-1 receptors types I and II (as described in EP Patent No. 0460846, US Patent No. 4,968,607, and US Patent No. 5,767,064, which are incorporated by reference herein in their entirety), Interleukin-2 receptor, Interleukin-4 receptor (as described in EP Patent No. 0 367 566 and US Patent No. 5,856,296, which are incorporated by reference herein in their entirety), Interleukin- 15 receptor, Interleukin- 17 receptor, Interleukin- 18 receptor, granulocyte- macrophage colony stimulating factor receptor, granulocyte colony stimulating factor receptor, receptors for oncostatin-M and leukemia inhibitory factor, receptor activator of NF-kappa B (RANK, as described in US Patent No. 6,271,349, which is incorporated by reference herein in its entirety), VEGF receptors, EGF receptor, FGF receptors, receptors for TRAIL (including TRAIL receptors 1,2,3, and 4), and receptors that comprise death domains, such as Fas or Apoptosis- Inducing Receptor (AIR). Fc fusion proteins also include peptibodies, such as those described in WO 2000/24782, which is hereby incorporated by reference in its entirety.

As used herein, CTLA4-Ig Fc-fusion refers to a protein that links the extracellular domain of human cytotoxic T-lymphocyte associated antigen 4 (CTLA4) to the modified Fc (hinge, CH2 and CH3 domains) region of human immunoglobulin G1. It is a homodimer of two polypeptide chains connected together through one disulfide bond in the CTLA4 domain. “High molecular weight aggregates” as referred herein encompasses association of at least two molecules of a product of interest, e.g., Fc-Fusion protein. The association of at least two molecules of a product of interest may arise by any means including, but not limited to, non- covalent interactions such as, e.g., charge-charge, hydrophobic and van der Waals interactions; and covalent interactions such as, e.g., disulfide interaction or nonreducible crosslinking. An aggregate can be a trimer, tetramer, or a multimer greater than a tetramer, etc. The term “protein aggregates,” includes any higher order species of the Fc-containing protein.

“Non-covalent dimer” as used herein refers to the two monomeric polypeptides chains of abatacept connected together by non-covalent interactions.

The "composition" to be purified herein comprises the protein of interest and one or more contaminants. The composition may be "partially purified" (i.e., having been subjected to one or more purification steps) or may be obtained directly from a host cell or organism producing the antibody (e.g., the composition may comprise harvested cell culture fluid).

The term "load" herein refers to the composition loaded onto the chromatography material, i.e., HIC support or mixed mode chromatography (MMC) support. Preferably, the chromatography material is equilibrated with an equilibration buffer prior to loading the composition which is to be purified.

The term “Mixed Mode Chromatography” refers to a form of chromatography that uses a chromatographic support with at least two unique types of functional groups, each interacting with the molecule or protein of interest. Mixed mode chromatography generally uses ligands that have more than one type of interaction with target proteins and/or impurities. For example, a charge-charge type of interaction and/or a hydrophobic or hydrophilic type of interaction, or an electroreceptor-donor type interaction. In general, based on the difference in the total interaction, the target protein and one or more impurities can be separated under various conditions.

The term “flow-through mode” as used herein refers to that process wherein the target protein is not bound to the chromatographic support but instead obtained in the unbound or “flow- through” fraction during loading or post load wash of the chromatography support.

Aggregate concentration can be measured in a protein sample using Size Exclusion Chromatography (SEC), a well-known and widely accepted method in the art. Size exclusion chromatography uses a molecular sieving retention mechanism, based on differences in the hydrodynamic radii or differences in size of proteins. Large molecular weight aggregates cannot penetrate or only partially penetrate the pores of the stationary phase. Hence, the larger aggregates elute first and smaller molecules elute later, the order of elution being a function of the size.

Detailed description of the embodiments

The present invention discloses a method for purifying the Fc-Fusion proteins from the contaminants, the method comprises use of hydrophobic interaction chromatography.

In an embodiment, the method is used to obtain a purified composition of a CTLA4-Ig fusion protein using hydrophobic interaction chromatography.

In another embodiment, the method is used to obtain a purified composition of a CTLA4-Ig fusion protein by hydrophobic interaction chromatography, wherein the chromatographic medium has a straight butyl chain ligand attached to a hydrophilic base matrix.

In yet another embodiment, the method is used to obtain a purified composition of a CTLA4- Ig fusion protein by hydrophobic interaction chromatography, wherein the chromatographic support has a straight butyl chain ligand attached to a hydrophilic base matrix and the chromatography is operated in flow-through mode.

In yet another embodiment, the method is used to obtain a purified composition of a CTLA4- Ig fusion protein, the method comprising steps of hydrophobic interaction chromatography and mixed-mode chromatography, wherein the mixed mode chromatography follows the hydrophobic interaction chromatography.

In yet another embodiment, the method is used to obtain a purified composition of a CTLA4- Ig fusion protein, the method comprising steps of hydrophobic interaction chromatography and mixed-mode chromatography, wherein the mixed mode chromatography follows the hydrophobic interaction chromatography and wherein both the chromatographic steps are operated in flow-through mode.

In another embodiment, the method is used to obtain a purified composition of a CTLA4-Ig fusion protein, the method comprising steps of hydrophobic interaction chromatography and mixed-mode chromatography, wherein the mixed mode chromatography follows the hydrophobic interaction chromatography, and wherein both the chromatographic steps are operated in flow-through mode, and wherein the HIC chromatographic support has a straight butyl chain ligand attached to a hydrophilic base matrix.

In any of the above mentioned embodiments, the method is capable of significant removal of HMW aggregates and non-covalent dimers. In particular, greater than 90% reduction in the HMW aggregates level and 100% removal of non-covalent dimers are achieved by the method.

In any of the above mentioned embodiments the method is used to obtain a purified composition of a CTLA-Ig fusion protein, the method comprising hydrophobic interaction chromatography, wherein the HMW aggregate level is <1.5% and non-covalent dimers are below detectable limit (i.e., complete removal) in fusion protein composition obtained as the flow-through of the hydrophobic interaction chromatography.

In any of the above mentioned embodiments the method is used to obtain a purified composition of a CTLA-Ig fusion protein, the method comprising hydrophobic interaction chromatography and mixed mode chromatography, wherein the HMW aggregate level is <1.0% and non-covalent dimers are below detectable limit (i.e., complete removal) in fusion protein composition obtained as the flow-through of the mixed-mode chromatography.

In any of the above mentioned embodiments, the chromatographic medium used in hydrophobic interaction chromatography is preferably Capto™ Butyl.

In any of the above mentioned embodiments, the buffer used for hydrophobic interaction chromatography is Tris buffer and the salt used is ammonium sulphate. In any of the above embodiments, the buffer solution used for mixed-mode chromatography is phosphate buffer.

In any of the above mentioned embodiments, the method comprises use of one or more chromatographic steps before HIC chromatography, wherein the preceding chromatography does not comprise an ion exchange chromatography step. In particular, the polishing steps may be selected from ion exchange chromatography, hydrophobic interaction chromatography, hydrophobic charge induction chromatography, mixed-mode chromatography.

In any of the above mentioned embodiments, the method comprises use of one or more polishing chromatography steps after HIC chromatography. In particular, the polishing steps may be selected from ion exchange chromatography, hydrophobic ion exchange chromatography, hydrophobic charge induction chromatography, mixed-mode chromatography.

In any of the above mentioned embodiments, the method employs use of one or more steps such as viral inactivation, filtration and diafiltration. These steps may be interspersed between the chromatographic steps or the after all the chromatographic steps.

In any of the above mentioned embodiments, the purity of the fusion protein composition is more than 95%.

In any of the above mentioned embodiments, the fusion protein is CTLA4-Ig fusion protein.

In any of the above mentioned embodiments, the fusion protein is abatacept.

The invention is more fully understood by reference to the following examples. These examples should not, however, be construed as limiting the scope of the invention.

EXAMPLES

Example 1 : Evaluation of Octyl HIC ligand

CTLA4-IgG fusion protein was cloned and expressed in a Chinese Hamster Ovary cell line and the cell culture broth containing the expressed fusion protein was harvested, clarified and subjected to protein- A affinity chromatography. The eluate from protein- A affinity chromatography was subjected to low-pH incubation and depth filtration, and the eluate was loaded onto an Octyl ligand. Details of the salts used for evaluation are listed in Table 1. Column chromatography conditions are listed in Table 2 and buffer details are captured in Table 3. The loading and post-load washing steps were fractionated 1 column volume (CV) each, and representative pools were analysed by SEC-UPLC for non-covalent dimer content and SEC-HPLC for HMW aggregate content.

able 1 : Salts used for evaluation of octyl ligand

Table 2: Chromatography conditions used for the evaluation of octyl ligand

Table 3 : Buffer details for octyl ligand evaluation

Table 4 shows the %HMW and %non-covalent dimer data for HIC load and HIC flow through

evaluation

Example 2: Evaluation of Hexyl ligand

CTLA4-IgG fusion protein was cloned and expressed in a Chinese Hamster Ovary cell line and the cell culture broth containing the expressed fusion protein was harvested, clarified and subjected to protein- A affinity chromatography. The eluate from protein-A affinity chromatography was subjected to low-pH incubation and depth filtration, and the eluate was loaded onto a Hexyl ligand. Details of the salts used for evaluation are listed in Table 5. Column chromatography conditions are listed in Table 6 and buffer details are captured in Table 7. The loading and post-load washing steps were fractionated 1 CV each, and representative pools were analysed by SEC-UPLC for non-covalent dimer content and SEC-HPLC for HMW aggregate content.

Table 5: Salt used for evaluation of hexyl ligand

Table 6: Chromatography conditions used for the evaluation of hexyl ligand

Table 7 : Buffer details for hexyl ligand evaluation

evaluation Example 3 : Evaluation of Phenyl ligand in Bind and Elute mode

CTLA4-IgG fusion protein was cloned and expressed in a Chinese Hamster Ovary cell line and the cell culture broth containing the expressed fusion protein was harvested, clarified and subjected to protein- A affinity chromatography. The eluate from protein- A affinity chromatography was subjected to low-pH incubation and depth filtration, and the eluate was loaded onto a Phenyl ligand. Details of the salts used for evaluation are listed in Table 9. Column chromatography conditions are listed in Table 10 and buffer details are captured in Table 11. The loading and post-load washing steps were fractionated 1 CV each, and representative pools were analysed by SEC-UPLC for non-covalent dimer content and SEC- HPLC for HMW aggregate content.

Table 9: Salt used for evaluation of phenyl ligand in bind and elute mode

Table 10: Chromatography conditions used for the evaluation of phenyl ligand in bind and elute mode

Table 11 : Buffer details for phenyl ligand evaluation in bind and elute mode

ligand evaluation in bind and elute mode

Example 4: Evaluation of Phenyl ligand in Flow-through mode

CTLA4-IgG fusion protein was cloned and expressed in a Chinese Hamster Ovary cell line and the cell culture broth containing the expressed fusion protein was harvested, clarified and subjected to protein- A affinity chromatography. The eluate from protein-A affinity chromatography was subjected to low-pH incubation and depth filtration, and the eluate was loaded onto a Phenyl ligand. Details of the salts used for evaluation are listed in Table 13. Column chromatography conditions are listed in Table 14 and buffer details are captured in Table 15. The loading and post-load washing steps were fractionated 1 CV each, and representative pools were analysed by SEC-UPLC for non-covalent dimer content and SEC- HPLC for HMW aggregate content.

Table 13: Salt used for evaluation of phenyl ligand in flow-through mode

Table 14: Chromatography conditions used for the evaluation of phenyl ligand in flow-through mode

Table 15: Buffer details for phenyl ligand evaluation in flow-through mode

ligand evaluation in flow-through mode

Example 5: Evaluation of Butyl ligand in Flow-through mode CTLA4-IgG fusion protein was cloned and expressed in a Chinese Hamster Ovary cell line and the cell culture broth containing the expressed fusion protein was harvested, clarified and subjected to protein- A affinity chromatography. The eluate from protein-A affinity chromatography was subjected to low-pH incubation and depth filtration, and the eluate was loaded onto a Butyl ligand. Details of the salts used for evaluation are listed in Table 17. Column chromatography conditions are listed in Table 18 and buffer details are captured in Table 19. The loading and post-load washing steps were fractionated 1 CV each, and representative pools were analysed by SEC-UPLC for non-covalent dimer content and SEC- HPLC for HMW aggregate content.

Table 17: Salts used for evaluation of butyl ligand in flow-through mode

Table 18: Chromatography conditions used for the evaluation of butyl ligand in flow-through mode

Table 19: Buffer details for butyl ligand evaluation in flow-through mode

evaluation in flow-through mode Example 6: Optimization of HIC step using Butyl ligand

CTLA4-IgG fusion protein was cloned and expressed in a Chinese Hamster Ovary cell line and the cell culture broth containing the expressed fusion protein was harvested, clarified and subjected to protein- A affinity chromatography. The eluate from protein-A affinity chromatography was subjected to low-pH incubation and depth filtration, and the eluate was loaded onto a Butyl ligand. Details of the salts used for evaluation are listed in Table 21. Column chromatography conditions are listed in Table 22 and buffer details are captured in Table 23. The loading and post-load washing steps were fractionated 1 CV each, and representative pools were analysed by SEC-UPLC for non-covalent dimer content and SEC- HPLC for HMW aggregate content.

Table 21:

flow-through mode

Table 22: Chromatography conditions used for the optimization of HIC step using Butyl ligand in flow-through mode

Table 23: Buffer details for optimization of HIC step using butyl ligand in flow-through mode

optimization of HIC step using Butyl ligand in flow-through mode Example 7: Scale-up of HIC step using Butyl ligand

CTLA4-IgG fusion protein was cloned and expressed in a Chinese Hamster Ovary cell line and the cell culture broth containing the expressed fusion protein was harvested, clarified and subjected to protein- A affinity chromatography. The eluate from protein-A affinity chromatography was subjected to low-pH incubation and depth filtration, and the eluate was loaded onto a Butyl ligand. Column chromatography conditions are listed in Table 25 and buffer details are captured in Table 26. Fractionation of the flow-through was done based on UV signal, and representative fractions were analyzed by Capillary Electrophoresis - Sodium dodecyl sulphate (CE-SDS) for Non-covalent dimer content and SEC-HPLC for HMW aggregate content.

Table 25 : Chromatography conditions used for the scale-up of HIC step using Butyl ligand in flow through mode

Table 26: Buffer details for optimization of HIC step using butyl ligand in flow-through mode

Table 27: non-covalent dimer data for HIC load and HIC flow-through for scale-up of HIC step using butyl ligand in flow-through mode

The HIC flow-through fraction comprising the protein of interest was loaded onto the CHT support after diafiltration in 10 mM phosphate buffer comprising 15 mM NaCl, pH 7.5. Mixed mode chromatography was operated in flow-through mode. The chromatographic details are listed in Table 28 and the %HMW and %non-covalent dimer data are shown in Table 29.

Table 28: Chromatography parameters for mixed mode chromatography using CHT support

Table 29: %HMW and %non-covalent dimer data for MMC load and MMC flow-through

Claims

1. A method for purifying a CTLA4-Ig Fc-fusion protein from a composition comprising the target protein, high-molecular weight aggregates and non-covalent dimers by hydrophobic interaction chromatography, the method comprising steps of: a. loading the composition comprising the target protein, high-molecular weight aggregates and non-covalent dimers using a buffer solution onto a chromatography material that has a hydrophilic base matrix attached to a butyl ligand; b. allowing the high-molecular weight aggregates and non-covalent dimers in the composition loaded in step (a) to bind to the chromatography material; c. washing the chromatography material with a buffer solution to obtain a fraction of the composition which remains unbound to and flows through the chromatography material; and d. recovering the target protein from the fraction of the composition obtained in step (c), wherein the composition obtained in step (d) is substantially free from high- molecular weight aggregates, as measured by size exclusion chromatography, and completely free from non-covalent dimers, as measured by capillary electrophoresis.

2. A method for purifying a CTLA4-Ig Fc-fusion protein from a composition comprising the target protein, high-molecular weight aggregates and non-covalent dimers, the method comprising steps of: a. loading the composition comprising the target protein, high-molecular weight aggregates and non-covalent dimers using a buffer solution onto a chromatography material that has a hydrophilic base matrix attached to a butyl ligand; b. allowing the high-molecular weight aggregates and non-covalent dimers in the composition loaded in step (a) to bind to the chromatography material; c. washing the chromatography material with a buffer solution to obtain a fraction of the composition which remains unbound to and flows through the chromatography material; d. recovering the target protein from the fraction of the composition obtained in step (c), e. optionally diafiltering the composition obtained in step (d), f. loading the composition obtained in step (d) or step (e) onto a chromatography material having a mixed-mode ligand, g. allowing the high-molecular weight aggregates in the composition loaded in step (f) to bind to the said chromatography material, h. obtaining a fraction of the composition which remains unbound to and flows through the said chromatography material; and i. recovering the target protein from the fraction of the composition obtained in step (h), wherein the composition obtained in step (d) is substantially free from high-molecular weight aggregates, as measured by size exclusion chromatography, and completely free from non-covalent dimers, as measured by capillary electrophoresis.

3. The method as claimed in claim 1 or claim 2, wherein the buffer solution comprises Tris and ammonium sulphate.

4. The method as claimed in claim 1, wherein the butyl ligand attached to the hydrophilic base matrix is a straight-chain butyl ligand.

5. The method as claimed in claim 2, wherein there is a reduction of more than 90% high-molecular weight aggregates in the composition obtained in step (i) as compared to the composition loaded in step (a).

6. The method as claimed in claiml or claim 2, wherein the CTLA4-Ig Fc-fusion protein is abatacept.