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Lin J, Xie M, Liu D, Gao Z, Zhao X, Ma H, Ding S, Li SM, Li S, Liu Y, Zhou F, Hu H, Chen T, Chen H, Xie M, Yang B, Cheng J, Ma M, Nan Y, Ju D. Characterization of light chain c-terminal extension sequence variant in one bispecific antibody. Front Chem 2022; 10:994472. [PMID: 36204149 PMCID: PMC9530627 DOI: 10.3389/fchem.2022.994472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Protein modifications such as post-translational modifications (PTMs) and sequence variants (SVs) occur frequently during protein biosynthesis and have received great attention by biopharma industry and regulatory agencies. In this study, an aberrant peak near light chain (LC) was observed in the non-reduced capillary electrophoresis sodium dodecyl sulfate (nrCE-SDS) electrophoretogram during cell line development of one bispecific antibody (BsAb) product, and the detected mass was about 944 Da higher than LC. The corresponding peak was then enriched by denaturing size-exclusion chromatography (SEC-HPLC) and further characterized by nrCE-SDS and peptide mapping analyses. De novo mass spectra/mass spectra (MS/MS) analysis revealed that the aberrant peak was LC related sequence variant, with the truncated C-terminal sequence “SFNR” (“GEC”deleted) linked with downstream SV40 promotor sequence “EAEAASASELFQ”. The unusual sequence was further confirmed by comparing with the direct synthetic peptide “SFNREAEAASASELFQ”. It was demonstrated by mRNA sequencing of the cell pool that the sequence variant was caused by aberrant splicing at the transcription step. The prepared product containing this extension variant maintained well-folded structure and good functional properties though the LC/Heavy chain (HC) inter-chain disulfide was not formed. Several control strategies to mitigate the risk of this LC related sequence variant were also proposed.
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Affiliation(s)
- Jun Lin
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, China
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Mengyu Xie
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Dan Liu
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Zhen Gao
- Genor Biopharma Co., Ltd., Shanghai, China
| | | | - Hongxia Ma
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Sheng Ding
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Shu mei Li
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Song Li
- Genor Biopharma Co., Ltd., Shanghai, China
| | | | - Fang Zhou
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Hao Hu
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Tao Chen
- Genor Biopharma Co., Ltd., Shanghai, China
| | - He Chen
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Min Xie
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Bo Yang
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Jun Cheng
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Mingjun Ma
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Yanyang Nan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, China
| | - Dianwen Ju
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, China
- *Correspondence: Dianwen Ju,
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Wong HE, Huang CJ, Zhang Z. Amino Acid Misincorporation Propensities Revealed through Systematic Amino Acid Starvation. Biochemistry 2018; 57:6767-6779. [DOI: 10.1021/acs.biochem.8b00976] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- H. Edward Wong
- Process Development, Amgen, Inc., 1 Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Chung-Jr Huang
- Process Development, Amgen, Inc., 1 Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Zhongqi Zhang
- Process Development, Amgen, Inc., 1 Amgen Center Drive, Thousand Oaks, California 91320, United States
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3
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Dutta S, Nandi N. Dynamics of the Active Sites of Dimeric Seryl tRNA Synthetase from Methanopyrus kandleri. J Phys Chem B 2015; 119:10832-48. [PMID: 25794108 DOI: 10.1021/jp511585w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Saheb Dutta
- Department
of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal 741235, India
| | - Nilashis Nandi
- Department
of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal 741235, India
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4
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Harris RP, Kilby PM. Amino acid misincorporation in recombinant biopharmaceutical products. Curr Opin Biotechnol 2014; 30:45-50. [PMID: 24922333 DOI: 10.1016/j.copbio.2014.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/16/2014] [Indexed: 11/28/2022]
Abstract
Microbial and mammalian host systems have been used extensively for the production of protein biotherapeutics. Generally these systems rely on the production of a specific gene sequence encoding one therapeutic product. Analysis of these protein products over many years has proven that this was not always the case, with multiple species of the intended product being produced due to amino acid misincorporation or mistranslation during biosynthesis of the protein. This review is the first to give a comprehensive overview of the occurrence and analysis of these misincorporations. Furthermore, using the latest data on misincorporation in native human proteins we explore potential considerations for producing a specification for misincorporation for the development of a human biotherapeutic protein product in a production environment.
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Affiliation(s)
- Robert P Harris
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks RG42 6EY, UK.
| | - Peter M Kilby
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks RG42 6EY, UK
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Feeney L, Carvalhal V, Yu XC, Chan B, Michels DA, Wang YJ, Shen A, Ressl J, Dusel B, Laird MW. Eliminating tyrosine sequence variants in CHO cell lines producing recombinant monoclonal antibodies. Biotechnol Bioeng 2013; 110:1087-97. [PMID: 23108857 DOI: 10.1002/bit.24759] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/08/2012] [Indexed: 12/21/2022]
Abstract
Amino acid sequence variants are defined as unintended amino acid sequence changes that contribute to product variation with potential impact to product safety, immunogenicity, and efficacy. Therefore, it is important to understand the propensity for sequence variant (SV) formation during the production of recombinant proteins for therapeutic use. During the development of clinical therapeutic products, several monoclonal antibodies (mAbs) produced from Chinese Hamster Ovary (CHO) cells exhibited SVs at low levels (≤3%) in multiple locations throughout the mAbs. In these examples, the cell culture process depleted tyrosine, and the tyrosine residues in the recombinant mAbs were replaced with phenylalanine or histidine. In this work, it is demonstrated that tyrosine supplementation eliminated the tyrosine SVs, while early tyrosine starvation significantly increased the SV level in all mAbs tested. Additionally, it was determined that phenylalanine is the amino acid preferentially misincorporated in the absence of tyrosine over histidine, with no other amino acid misincorporated in the absence of tyrosine, phenylalanine, and histidine. The data support that the tyrosine SVs are due to mistranslation and not DNA mutation, most likely due to tRNA(Tyr) mischarging due to the structural similarities between tyrosine and phenylalanine.
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Affiliation(s)
- Lauren Feeney
- Department of Late Stage Cell Culture, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080-4990, USA
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Kim SK, Li Y, Park C, Abrol R, Goddard WA. Prediction of the three-dimensional structure for the rat urotensin II receptor, and comparison of the antagonist binding sites and binding selectivity between human and rat receptors from atomistic simulations. ChemMedChem 2010; 5:1594-608. [PMID: 20683923 PMCID: PMC3517062 DOI: 10.1002/cmdc.201000175] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Indexed: 11/11/2022]
Abstract
Urotensin-II (U-II) has been shown to be the most potent mammalian vasoconstrictor known. Thus, a U-II antagonist might be of therapeutic value in a number of cardiovascular disorders. However, interspecies variability of several nonpeptidic ligands complicates the interpretation of in vivo studies of such antagonists in preclinical animal disease models. ACT058362 is a selective antagonist for the human U-II receptor (hUT2R) with a reported K(d) value of approximately 4 nM in a molecular binding assay, but it is reported to bind weakly to rat UT2R (rUT2R), with a K(d) value of approximately 1 500 nM. In contrast, the arylsulphonamide SB706375 is a selective antagonist against both hUT2R (K(d)= approximately 9 nM) and rUT2R (K(d)= approximately 21 nM). To understand the species selectivity of the UT2R, we investigated the binding site of ACT058362 and SB706375 in both hUT2R and rUT2R to explain the dramatically lower (approximately 400-fold) affinity of ACT058362 for rUT2R and the similar affinity (approximately 10 nM) of SB706375 for both UT2Rs. These studies used MembStruk and MSCDock to predict the UT2R structure and the binding site of ACT058362 and SB706375. Based on binding energies, we found two binding modes each with D130(3.32) as the crucial anchoring point (Ballesteros-Weinstein numbering given in superscript). We predict that ACT058362 (an aryl-amine-aryl or ANA ligand) binds in the transmembrane (TM) 3456 region, while SB706375 (an aryl-aryl-amine or AAN ligand) binds in the TM 1237 region. These predicted sites explain the known differences in binding of the ANA ligand to rat and human receptors, while explaining the similar binding of the AAN compound to rat and human receptors. Moreover the predictions explain currently available structure-activity relationship (SAR) data. To further validate the predicted binding sites of these ligands in hUT2R and rUT2R, we propose several mutations that would help define the structural origins of differential responses between UT2R of different species, potentially indicating novel UT2R antagonists with cross-species high affinity.
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Affiliation(s)
- Soo-Kyung Kim
- Materials and Process Simulation Center (MC 139-74), California Institute of Technology, Pasadena, CA 91125, USA, Fax: (+1)626-585-0918
| | - Youyong Li
- Materials and Process Simulation Center (MC 139-74), California Institute of Technology, Pasadena, CA 91125, USA, Fax: (+1)626-585-0918
| | | | - Ravinder Abrol
- Materials and Process Simulation Center (MC 139-74), California Institute of Technology, Pasadena, CA 91125, USA, Fax: (+1)626-585-0918
| | - William A. Goddard
- Materials and Process Simulation Center (MC 139-74), California Institute of Technology, Pasadena, CA 91125, USA, Fax: (+1)626-585-0918
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7
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Armen RS, Schiller SM, Brooks CL. Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl-tRNA synthetase enzymes. Proteins 2010; 78:1926-38. [PMID: 20310065 DOI: 10.1002/prot.22706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Orthogonal aminoacyl-tRNA synthetase/tRNA pairs from archaea have been evolved to facilitate site specific in vivo incorporation of unnatural amino acids into proteins in Escherichia coli. Using this approach, unnatural amino acids have been successfully incorporated with high translational efficiency and fidelity. In this study, CHARMM-based molecular docking and free energy calculations were used to evaluate rational design of specific protein-ligand interactions for aminoacyl-tRNA synthetases. A series of novel unnatural amino acid ligands were docked into the p-benzoyl-L-phenylalanine tRNA synthetase, which revealed that the binding pocket of the enzyme does not provide sufficient space for significantly larger ligands. Specific binding site residues were mutated to alanine to create additional space to accommodate larger target ligands, and then mutations were introduced to improve binding free energy. This approach was used to redesign binding sites for several different target ligands, which were then tested against the standard 20 amino acids to verify target specificity. Only the synthetase designed to bind Man-alpha-O-Tyr was predicted to be sufficiently selective for the target ligand and also thermodynamically stable. Our study suggests that extensive redesign of the tRNA synthatase binding pocket for large bulky ligands may be quite thermodynamically unfavorable.
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Affiliation(s)
- Roger S Armen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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Guo D, Gao A, Michels DA, Feeney L, Eng M, Chan B, Laird MW, Zhang B, Yu XC, Joly J, Snedecor B, Shen A. Mechanisms of unintended amino acid sequence changes in recombinant monoclonal antibodies expressed in Chinese Hamster Ovary (CHO) cells. Biotechnol Bioeng 2010; 107:163-71. [DOI: 10.1002/bit.22780] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Yu XC, Borisov OV, Alvarez M, Michels DA, Wang YJ, Ling V. Identification of Codon-Specific Serine to Asparagine Mistranslation in Recombinant Monoclonal Antibodies by High-Resolution Mass Spectrometry. Anal Chem 2009; 81:9282-90. [DOI: 10.1021/ac901541h] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- X. Christopher Yu
- Protein Analytical Chemistry, Genentech, South San Francisco, California 94080-4990
| | - Oleg V. Borisov
- Protein Analytical Chemistry, Genentech, South San Francisco, California 94080-4990
| | - Melissa Alvarez
- Protein Analytical Chemistry, Genentech, South San Francisco, California 94080-4990
| | - David A. Michels
- Protein Analytical Chemistry, Genentech, South San Francisco, California 94080-4990
| | - Yajun Jennifer Wang
- Protein Analytical Chemistry, Genentech, South San Francisco, California 94080-4990
| | - Victor Ling
- Protein Analytical Chemistry, Genentech, South San Francisco, California 94080-4990
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Wen D, Vecchi MM, Gu S, Su L, Dolnikova J, Huang YM, Foley SF, Garber E, Pederson N, Meier W. Discovery and investigation of misincorporation of serine at asparagine positions in recombinant proteins expressed in Chinese hamster ovary cells. J Biol Chem 2009; 284:32686-94. [PMID: 19783658 DOI: 10.1074/jbc.m109.059360] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Misincorporation of amino acids in proteins expressed in Escherichia coli has been well documented but not in proteins expressed in mammalian cells under normal recombinant protein production conditions. Here we report for the first time that Ser can be incorporated at Asn positions in proteins expressed in Chinese hamster ovary cells. This misincorporation was discovered as a result of intact mass measurement, peptide mapping analysis, and tandem mass spectroscopy sequencing. Our analyses showed that the substitution was not related to specific protein molecules or DNA codons and was not site-specific. We believe that the incorporation of Ser at sites coded for Asn was due to mischarging of tRNA(Asn) rather than to codon misreading. The rationale for substitution of Asn by Ser and not by other amino acids is also discussed. Further investigation indicated that the substitution was due to the starvation for Asn in the cell culture medium and that the substitution could be limited by using the Asn-rich feed. These observations demonstrate that the quality of expressed proteins should be closely monitored when altering cell culture conditions.
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Affiliation(s)
- Dingyi Wen
- Biogen Idec Inc., 14 Cambridge Center, Cambridge, Massachusetts 02412, USA.
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11
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Li Y, Zhu F, Vaidehi N, Goddard WA. Prediction of the 3D structure and dynamics of human DP G-protein coupled receptor bound to an agonist and an antagonist. J Am Chem Soc 2007; 129:10720-31. [PMID: 17691773 PMCID: PMC2535578 DOI: 10.1021/ja070865d] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prostanoids play important physiological roles in the cardiovascular and immune systems and in pain sensation in peripheral systems through their interactions with eight G-protein coupled receptors. These receptors are important drug targets, but development of subtype specific agonists and antagonists has been hampered by the lack of 3D structures for these receptors. We report here the 3D structure for the human DP G-protein coupled receptor (GPCR) predicted by the MembStruk computational method. To validate this structure, we use the HierDock computational method to predict the binding mode for the endogenous agonist (PGD2) to DP. Based on our structure, we predicted the binding of different antagonists and optimized them. We find that PGD2 binds vertically to DP in the TM1237 region with the alpha chain toward the extracellular (EC) region and the omega chain toward the middle of the membrane. This structure explains the selectivity of the DP receptor and the residues involved in the predicted binding site correlate very well with available mutation experiments on DP, IP, TP, FP, and EP subtypes. We report molecular dynamics of DP in explicit lipid and water and find that the binding of the PGD2 agonist leads to correlated rotations of helices of TM3 and TM7, whereas binding of antagonist leads to no such rotations. Thus, these motions may be related to the mechanism of activation.
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Affiliation(s)
- Youyong Li
- Materials and Process Simulation Center (MC 139-74), California Institute of Technology, Pasadena CA 91125
| | - Fangqiang Zhu
- Materials and Process Simulation Center (MC 139-74), California Institute of Technology, Pasadena CA 91125
| | | | - William A. Goddard
- Materials and Process Simulation Center (MC 139-74), California Institute of Technology, Pasadena CA 91125
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