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Šprager E, Möller J, Lin Y, Reisinger V, Bratkovič T, Lunder M, Vašl J, Krajnc A. Identification of Acyl-Protein Thioesterase-1 as a Polysorbate-Degrading Host Cell Protein in a Monoclonal Antibody Formulation Using Activity-Based Protein Profiling. J Pharm Sci 2024; 113:2128-2139. [PMID: 38772451 DOI: 10.1016/j.xphs.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/23/2024]
Abstract
Polysorbate (PS) degradation in monoclonal antibody (mAb) formulations poses a significant challenge in the biopharmaceutical industry. PS maintains protein stability during drug product's shelf life but is vulnerable to breakdown by low-abundance residual host cell proteins (HCPs), particularly hydrolytic enzymes such as lipases and esterases. In this study, we used activity-based protein profiling (ABPP) coupled with mass spectrometry to identify acyl-protein thioesterase-1 (APT-1) as a polysorbate-degrading HCP in one case of mAb formulation with stability problems. We validated the role of APT1 by matching the polysorbate degradation fingerprint in the mAb formulation with that of a recombinant APT1 protein. Furthermore, we found an agreement between APT1 levels and PS degradation rates in the mAb formulation, and we successfully halted PS degradation using APT1-specific inhibitors ML348 and ML211. APT1 was found to co-purify with a specific mAb via hitchhiking mechanism. Our work provides a streamlined approach to identifying critical HCPs in PS degradation, supporting quality-by-design principles in pharmaceutical development.
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Affiliation(s)
- Ernest Šprager
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia; Novartis Technical Research & Development, Biologics Technical Development Mengeš, Novartis Pharmaceutical Manufacturing LLC, Slovenia
| | - Jens Möller
- Novartis Technical Research & Development, Analytical Characterization, Novartis Pharmaceutical Manufacturing GmbH, Kundl, Austria
| | - Yuhsien Lin
- Novartis Technical Research & Development, Analytical Characterization, Novartis Pharmaceutical Manufacturing GmbH, Kundl, Austria
| | - Veronika Reisinger
- Novartis Technical Research & Development, Analytical Characterization, Novartis Pharmaceutical Manufacturing GmbH, Kundl, Austria
| | - Tomaž Bratkovič
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Mojca Lunder
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Jožica Vašl
- Novartis Technical Research & Development, Biologics Technical Development Mengeš, Novartis Pharmaceutical Manufacturing LLC, Slovenia
| | - Aleksander Krajnc
- Novartis Technical Research & Development, Biologics Technical Development Mengeš, Novartis Pharmaceutical Manufacturing LLC, Slovenia.
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Dehghani A, Binder F, Zorn M, Feigler A, Fischer KI, Felix MN, Happersberger P, Reisinger B. Investigating pH Effects on Enzymes Catalyzing Polysorbate Degradation by Activity-Based Protein Profiling. J Pharm Sci 2024; 113:744-753. [PMID: 37758159 DOI: 10.1016/j.xphs.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/15/2023] [Accepted: 09/15/2023] [Indexed: 10/03/2023]
Abstract
Host cell proteins (HCPs) are process-related impurities that can negatively impact the quality of biotherapeutics. Some HCPs possess enzymatic activity and can affect the active pharmaceutical ingredient (API) or excipients such as polysorbates (PS). PSs are a class of non-ionic surfactants commonly used as excipients in biotherapeutics to enhance the stability of APIs. The enzyme activity of certain HCPs can result in the degradation of PSs, leading to particle formation and decreased shelf life of biotherapeutics. Identifying and characterizing these HCPs is therefore crucial. This study employed the Activity-Based Protein Profiling (ABPP) technique to investigate the effect of pH on the activity of HCPs that have the potential to degrade polysorbates. Two probes were utilized: the commercially available fluorophosphonate (FP)-Desthiobiotin probe and a probe based on the antiobesity drug, Orlistat. Over 50 HCPs were identified, showing a strong dependence on pH-milieu regarding their enzyme activity. These findings underscore the importance of accounting for pH variations in the ABPP method and other investigations of HCP activity. Notably, the Orlistat-based probe (OBP) enabled us to investigate the enzymatic activity of a wider range of HCPs, emphasizing the advantage of using more than one probe for ABPP. Finally, this study led to the discovery of previously unreported active enzymes, including three HCPs from the carboxylesterase enzyme family.
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Affiliation(s)
- Alireza Dehghani
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, Biberach D-88397, Germany
| | - Florian Binder
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, Biberach D-88397, Germany
| | - Michael Zorn
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, Biberach D-88397, Germany
| | - Andreas Feigler
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, Biberach D-88397, Germany
| | - Kathrin Inge Fischer
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, Biberach D-88397, Germany
| | - Marius Nicolaus Felix
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, Biberach D-88397, Germany
| | - Peter Happersberger
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, Biberach D-88397, Germany
| | - Bernd Reisinger
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, Biberach D-88397, Germany.
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Ma S, Shi S, Xu B, Liu M, Xie L, Su Y, Li J, Liang Q, Ye S, Wang Y. Host serine protease ACOT2 assists DENV proliferation by hydrolyzing viral polyproteins. mSystems 2024; 9:e0097323. [PMID: 38112462 PMCID: PMC10804956 DOI: 10.1128/msystems.00973-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/12/2023] [Indexed: 12/21/2023] Open
Abstract
Dengue fever is a mosquito-borne tropical disease caused by the dengue virus (DENV). The replication of DENV relies on the processing of its genome-encoded polyprotein by both viral protease NS3 (NS3pro) and host proteases. However, the impact of host proteases on DENV proliferation is not well understood. In this study, we utilized fluorophosphonate-based probes (FPs) to investigate the up-regulation of host serine proteases during DENV infection in detail. Among the identified proteases, acyl-CoA thioesterase 2 (ACOT2), an enzyme that hydrolyzes acyl-CoA molecules to generate fatty acids and free CoA, exhibited cleavage activity against DENV polypeptide substrates. Enzymatic assays and virological experiments confirmed that ACOT2 contributes to DENV propagation during the replication stage by cleaving the viral polyprotein. Docking models provided insights into the binding pocket of viral polypeptides and the catalytic mechanism of ACOT2. Notably, this study is the first to demonstrate that ACOT2 functions as a serine protease to hydrolyze protein substrates. These findings offer novel insights into DENV infection, host response, as well as the potential development of innovative antiviral strategies.IMPORTANCEDENV, one of the major pathogens of Dengue fever, remains a significant public health concern in tropical and subtropical regions worldwide. How DENV efficiently hijacks the host and accesses its life cycle with delicate interaction remains to be elucidated. Here, we deconvoluted that the host protease ACOT2 assists the DENV replication and characterized the ACOT2 as a serine protease involved in the hydrolysis of the DENV polypeptide substrate. Our results not only further the understanding of the DENV life cycle but also provide a possibility for the usage of activity-based proteomics to reveal host-virus interactions.
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Affiliation(s)
- Sen Ma
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Sai Shi
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Binghong Xu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Meijun Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Lei Xie
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Yang Su
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China
| | - Jiachen Li
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Qinqin Liang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Yaxin Wang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
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Maier M, Weiß L, Zeh N, Schmieder-Todtenhaupt V, Dehghani A, Felix MN, Heinzelmann D, Lindner B, Schmidt M, Studts J, Schulz P, Reisinger B, Otte K, Franzreb M, Lakatos D, Fischer S. Illuminating a biologics development challenge: systematic characterization of CHO cell-derived hydrolases identified in monoclonal antibody formulations. MAbs 2024; 16:2375798. [PMID: 38984665 PMCID: PMC11238916 DOI: 10.1080/19420862.2024.2375798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/30/2024] [Indexed: 07/11/2024] Open
Abstract
Monoclonal antibodies (mAb) and other biological drugs are affected by enzymatic polysorbate (PS) degradation that reduces product stability and jeopardizes the supply of innovative medicines. PS represents a critical surfactant stabilizing the active pharmaceutical ingredients, which are produced by recombinant Chinese hamster ovary (CHO) cell lines. While the list of potential PS-degrading CHO host cell proteins (HCPs) has grown over the years, tangible data on industrially relevant HCPs are still scarce. By means of a highly sensitive liquid chromatography-tandem mass spectrometry method, we investigated seven different mAb products, resulting in the identification of 12 potentially PS-degrading hydrolases, including the strongly PS-degrading lipoprotein lipase (LPL). Using an LPL knockout CHO host cell line, we were able to stably overexpress and purify the remaining candidate hydrolases through orthogonal affinity chromatography methods, enabling their detailed functional characterization. Applying a PS degradation assay, we found nine mostly secreted, PS-active hydrolases with varying hydrolytic activity. All active hydrolases showed a serine-histidine-aspartate/glutamate catalytical triad. Further, we subjected the active hydrolases to pH-screenings and revealed a diverse range of activity optima, which can facilitate the identification of residual hydrolases during bioprocess development. Ultimately, we compiled our dataset in a risk matrix identifying PAF-AH, LIPA, PPT1, and LPLA2 as highly critical hydrolases based on their cellular expression, detection in purified antibodies, active secretion, and PS degradation activity. With this work, we pave the way toward a comprehensive functional characterization of PS-degrading hydrolases and provide a basis for a future reduction of PS degradation in biopharmaceutical drug products.
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Affiliation(s)
- Melanie Maier
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Linus Weiß
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach an der Riss, Germany
| | - Nikolas Zeh
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | | | - Alireza Dehghani
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Marius Nicolaus Felix
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Daniel Heinzelmann
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Benjamin Lindner
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Moritz Schmidt
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Joey Studts
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Patrick Schulz
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Bernd Reisinger
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Kerstin Otte
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach an der Riss, Germany
| | - Matthias Franzreb
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Daniel Lakatos
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Simon Fischer
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
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Doyle M, Barnes A, Larson NR, Liu H, Yi L. Development of UPLC-UV-ELSD Method for Fatty Acid Profiling in Polysorbate 80 and Confirmation of the Presence of Conjugated Fatty Acids by Mass Spectrometry, UV Absorbance and Proton Nuclear Magnetic Resonance Spectroscopy. J Pharm Sci 2023; 112:2393-2403. [PMID: 37295606 DOI: 10.1016/j.xphs.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Polysorbate 80 (PS80), a chemical substance composed of sorbitol, ethylene glycol, and fatty acids, is commonly used in pharmaceutical drug products to stabilize formulations. However, recent studies have demonstrated that PS80 may hydrolyze over time and the released free fatty acids (FFAs) may lead to particle formation. Naming conventions of fatty acids in current pharmacopeia and in products' certificates of analysis (CoA) of PS80 do not typically distinguish between isomeric species of fatty acids in PS80. Thus, methods to fully characterize the fatty acid species present in PS80 raw materials are needed to enhance quality control strategies of pharmaceuticals using PS80. Here, extended effort is taken to characterize fatty acids in hydrolyzed PS80 raw materials and elucidate the identities of isomeric fatty acid species. In this work, a method was developed and optimized for separation and detection of fatty acids in alkaline hydrolyzed PS80 raw materials using ultra performance liquid chromatography (UPLC) with ultra-violet (UV) detection and evaporative light scattering detection (ELSD). Fatty acids not specified in the current pharmacopeias were detected in PS80 raw material by the developed LC-UV-ELSD method including conjugated forms of linoleic and linolenic fatty acid species. Their identities were orthogonally confirmed by retention time agreement with analytical standards, accurate mass by high resolution mass spectrometry, UV absorbance, and proton nuclear magnetic resonance spectroscopy. The detected conjugated fatty acids are theoretically more hydrophobic and less soluble than their unconjugated counterparts and may increase the propensity of PS80 to form particles upon hydrolysis. This work highlights the need for better quality control of PS80 raw material, as it may eventually play a critical role in product quality of therapeutic proteins.
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Affiliation(s)
- Michael Doyle
- Analytical Development, Biogen Inc., 5000 Davis Drive, RTP, NC, 27709, United States of America
| | - Adam Barnes
- Analytical Development, Biogen Inc., 5000 Davis Drive, RTP, NC, 27709, United States of America
| | - Nicholas R Larson
- Analytical Development, Biogen Inc., 225 Binney Street, Cambridge, MA, 02142, United States of America
| | - Haiyan Liu
- Analytical Development, Biogen Inc., 5000 Davis Drive, RTP, NC, 27709, United States of America
| | - Linda Yi
- Analytical Development, Biogen Inc., 5000 Davis Drive, RTP, NC, 27709, United States of America.
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