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Tulika T, Pedersen RW, Rimbault C, Ahmadi S, Rivera‐de‐Torre E, Fernández‐Quintero ML, Loeffler JR, Bohn M, Ljungars A, Ledsgaard L, Voldborg BG, Ruso‐Julve F, Andersen JT, Laustsen AH. Phage display assisted discovery of a pH-dependent anti-α-cobratoxin antibody from a natural variable domain library. Protein Sci 2023; 32:e4821. [PMID: 37897425 PMCID: PMC10659949 DOI: 10.1002/pro.4821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/28/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023]
Abstract
Recycling IgG antibodies bind to their target antigen at physiological pH in the blood stream and release them upon endocytosis when pH levels drop, allowing the IgG antibodies to be recycled into circulation via FcRn-mediated cellular pathways, while the antigens undergo lysosomal degradation. This enables recycling antibodies to achieve comparable therapeutic effect at lower doses than their non-recycling counterparts. The development of such antibodies is typically achieved by histidine doping of their variable regions or by performing in vitro antibody selection campaigns utilizing histidine doped libraries. Both are strategies that may introduce sequence liabilities. Here, we present a methodology that employs a naïve antibody phage display library, consisting of natural variable domains, to discover antibodies that bind α-cobratoxin from the venom of Naja kaouthia in a pH-dependent manner. As a result, an antibody was discovered that exhibits a 7-fold higher off-rate at pH 5.5 than pH 7.4 in bio-layer interferometry experiments. Interestingly, no histidine residues were found in its variable domains, and in addition, the antibody showed pH-dependent binding to a histidine-devoid antigen mutant. As such, the results demonstrate that pH-dependent antigen-antibody binding may not always be driven by histidine residues. By employing molecular dynamics simulations, different protonation states of titratable residues were found, which potentially could be responsible for the observed pH-dependent antigen binding properties of the antibody. Finally, given the typically high diversity of naïve antibody libraries, the methodology presented here can likely be applied to discover recycling antibodies against different targets ab initio without the need for histidine doping.
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Affiliation(s)
- Tulika Tulika
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Rasmus W. Pedersen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Charlotte Rimbault
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Shirin Ahmadi
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | | | - Monica L. Fernández‐Quintero
- Center for Molecular Biosciences Innsbruck, Department of GeneralInorganic and Theoretical Chemistry, University of InnsbruckInnsbruckAustria
| | - Johannes R. Loeffler
- Center for Molecular Biosciences Innsbruck, Department of GeneralInorganic and Theoretical Chemistry, University of InnsbruckInnsbruckAustria
| | - Markus‐Frederik Bohn
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Anne Ljungars
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Line Ledsgaard
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Bjørn G. Voldborg
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Fulgencio Ruso‐Julve
- Department of PharmacologyUniversity of OsloOsloNorway
- Department of ImmunologyOslo University Hospital RikshospitaletOsloNorway
- Precision Immunotherapy AllianceUniversity of OsloOsloNorway
| | - Jan Terje Andersen
- Department of PharmacologyUniversity of OsloOsloNorway
- Department of ImmunologyOslo University Hospital RikshospitaletOsloNorway
- Precision Immunotherapy AllianceUniversity of OsloOsloNorway
| | - Andreas H. Laustsen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
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2
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Huhtinen O, Salbo R, Lamminmäki U, Prince S. Selection of biophysically favorable antibody variants using a modified Flp-In CHO mammalian display platform. Front Bioeng Biotechnol 2023; 11:1170081. [PMID: 37229492 PMCID: PMC10203562 DOI: 10.3389/fbioe.2023.1170081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023] Open
Abstract
Mammalian display enables the selection of biophysically favorable antibodies from a large IgG antibody library displayed on the plasma membrane of mammalian cells. We constructed and validated a novel mammalian display platform utilizing the commercially available Flp-In CHO cell line as a starting point. We introduced a single copy of a landing pad for Bxb1 integrase-driven recombinase-mediated cassette exchange into the FRT site of the Flp-In CHO line to facilitate the efficient single-copy integration of an antibody display cassette into the genome of the cell line. We then proceeded to demonstrate the ability of our platform to select biophysically favorable antibodies from a library of 1 × 106 displayed antibodies designed to improve the biophysical properties of bococizumab via randomization of problematic hydrophobic surface residues of the antibody. Enrichment of bococizumab variants via fluorescence-activated cell sorting selections was followed by next generation sequencing and thorough characterization of biophysical properties of 10 bococizumab variants that subsequently allowed attribution of the mutations to the biophysical properties of the antibody variants. The mammalian displayed variants exhibited reduced aggregation propensity and polyreactivity, while critically retaining its target binding thereby demonstrating the utility of this valuable tool.
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Affiliation(s)
- Olli Huhtinen
- Protein and Antibody Engineering, Orion Corporation, Turku, Finland
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Rune Salbo
- Protein and Antibody Engineering, Orion Corporation, Turku, Finland
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Stuart Prince
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
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3
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Ollier R, Fuchs A, Gauye F, Piorkowska K, Menant S, Ratnam M, Montanari P, Guilhot F, Phillipe D, Audrain M, Egesipe AL, Névoltris D, Seredenina T, Pfeifer A, Kosco-Vilbois M, Afroz T. Improved antibody pharmacokinetics by disruption of contiguous positive surface potential and charge reduction using alternate human framework. MAbs 2023; 15:2232087. [PMID: 37408314 DOI: 10.1080/19420862.2023.2232087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
Optimal pharmacokinetic (PK) properties of therapeutic monoclonal antibodies (mAbs) are essential to achieve the desired pharmacological benefits in patients. To accomplish this, we followed an approach comprising structure-based mAb charge engineering in conjunction with the use of relevant preclinical models to screen and select humanized candidates with PK suitable for clinical development. Murine mAb targeting TDP-43, ACI-5891, was humanized on a framework (VH1-3/VK2-30) selected based on the highest sequence homology. Since the initial humanized mAb (ACI-5891.1) presented a fast clearance in non-human primates (NHPs), reiteration of humanization on a less basic human framework (VH1-69-2/VK2-28) while retaining high sequence homology was performed. The resulting humanized variant, ACI-5891.9, presented a six-fold reduction in clearance in NHPs resulting in a significant increase in half-life. The observed reduced clearance of ACI-5891.9 was attributed not only to the overall reduction in isoelectric point (pI) by 2 units, but importantly to a more even surface potential. These data confirm the importance and contribution of surface charges to mAb disposition in vivo. Consistent low clearance of ACI-5891.9 in Tg32 mice, a human FcRn transgenic mouse model, further confirmed its utility for early assessment and prediction of human PK. These data demonstrate that mAb surface charge is an important parameter for consideration during the selection and screening of humanized candidates in addition to maintaining the other key physiochemical and target binding characteristics.
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Affiliation(s)
| | - Aline Fuchs
- Research, AC Immune SA, Lausanne, Switzerland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tariq Afroz
- Research, AC Immune SA, Lausanne, Switzerland
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4
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Dyson MR, Masters E, Pazeraitis D, Perera RL, Syrjanen JL, Surade S, Thorsteinson N, Parthiban K, Jones PC, Sattar M, Wozniak-Knopp G, Rueker F, Leah R, McCafferty J. Beyond affinity: selection of antibody variants with optimal biophysical properties and reduced immunogenicity from mammalian display libraries. MAbs 2021; 12:1829335. [PMID: 33103593 PMCID: PMC7592150 DOI: 10.1080/19420862.2020.1829335] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The early phase of protein drug development has traditionally focused on target binding properties leading to a desired mode of therapeutic action. As more protein therapeutics pass through the development pipeline; however, it is clear that non-optimal biophysical properties can emerge, particularly as proteins are formulated at high concentrations, causing aggregation or polyreactivity. Such late-stage "developability" problems can lead to delay or failure in traversing the development process. Aggregation propensity is also correlated with increased immunogenicity, resulting in expensive, late-stage clinical failures. Using nucleases-directed integration, we have constructed large mammalian display libraries where each cell contains a single antibody gene/cell inserted at a single locus, thereby achieving transcriptional normalization. We show a strong correlation between poor biophysical properties and display level achieved in mammalian cells, which is not replicated by yeast display. Using two well-documented examples of antibodies with poor biophysical characteristics (MEDI-1912 and bococizumab), a library of variants was created based on surface hydrophobic and positive charge patches. Mammalian display was used to select for antibodies that retained target binding and permitted increased display level. The resultant variants exhibited reduced polyreactivity and reduced aggregation propensity. Furthermore, we show in the case of bococizumab that biophysically improved variants are less immunogenic than the parental molecule. Thus, mammalian display helps to address multiple developability issues during the earliest stages of lead discovery, thereby significantly de-risking the future development of protein drugs.
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Affiliation(s)
| | | | | | | | - Johanna L Syrjanen
- WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory , NY, USA
| | | | | | | | | | | | - Gordana Wozniak-Knopp
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences , Vienna, Austria
| | - Florian Rueker
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences , Vienna, Austria
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5
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Wang B, Gallolu Kankanamalage S, Dong J, Liu Y. Optimization of therapeutic antibodies. Antib Ther 2021; 4:45-54. [PMID: 33928235 PMCID: PMC7944496 DOI: 10.1093/abt/tbab003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/15/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
In this review, we have summarized the current landscape of therapeutic antibody optimization for successful development. By engineering antibodies with display technology, computer-aided design and site mutagenesis, various properties of the therapeutic antibody candidates can be improved with the purpose of enhancing their safety, efficacy and developability. These properties include antigen binding affinity and specificity, biological efficacy, pharmacokinetics and pharmacodynamics, immunogenicity and physicochemical developability features. A best-in-class strategy may require the optimization of all these properties to generate a good therapeutic antibody.
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Affiliation(s)
- Bo Wang
- Ab Studio, Inc. Hayward, CA 94545, USA
| | | | | | - Yue Liu
- Ab Studio, Inc. Hayward, CA 94545, USA
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6
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Jacobsen FW, Stevenson R, Li C, Salimi-Moosavi H, Liu L, Wen J, Luo Q, Daris K, Buck L, Miller S, Ho SY, Wang W, Chen Q, Walker K, Wypych J, Narhi L, Gunasekaran K. Engineering an IgG Scaffold Lacking Effector Function with Optimized Developability. J Biol Chem 2016; 292:1865-1875. [PMID: 27994062 DOI: 10.1074/jbc.m116.748525] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 12/11/2016] [Indexed: 01/12/2023] Open
Abstract
IgG isotypes can differentially bind to Fcγ receptors and complement, making the selection of which isotype to pursue for development of a particular therapeutic antibody important in determining the safety and efficacy of the drug. IgG2 and IgG4 isotypes have significantly lower binding affinity to Fcγ receptors. Recent evidence suggests that the IgG2 isotype is not completely devoid of effector function, whereas the IgG4 isotype can undergo in vivo Fab arm exchange leading to bispecific antibody and off-target effects. Here an attempt was made to engineer an IgG1-based scaffold lacking effector function but with stability equivalent to that of the parent IgG1. Care was taken to ensure that both stability and lack of effector function was achieved with a minimum number of mutations. Among the Asn297 mutants that result in lack of glycosylation and thus loss of effector function, we demonstrate that the N297G variant has better stability and developability compared with the N297Q or N297A variants. To further improve the stability of N297G, we introduced a novel engineered disulfide bond at a solvent inaccessible location in the CH2 domain. The resulting scaffold has stability greater than or equivalent to that of the parental IgG1 scaffold. Extensive biophysical analyses and pharmacokinetic (PK) studies in mouse, rat, and monkey further confirmed the developability of this unique scaffold, and suggest that it could be used for all Fc containing therapeutics (e.g. antibodies, bispecific antibodies, and Fc fusions) requiring lack of effector function or elimination of binding to Fcγ receptors.
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Affiliation(s)
- Frederick W Jacobsen
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320.
| | - Riki Stevenson
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Cynthia Li
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Hossein Salimi-Moosavi
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Ling Liu
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Jie Wen
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Quanzhou Luo
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Kristine Daris
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Lynette Buck
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Sterling Miller
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Shu-Yin Ho
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Wei Wang
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Qing Chen
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Kenneth Walker
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Jette Wypych
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Linda Narhi
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320
| | - Kannan Gunasekaran
- From the Biologics Optimization-Therapeutic Discovery, Clinical Immunology, and Process Development, Amgen Inc., Thousand Oaks, California 91320.
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7
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Geoghegan JC, Fleming R, Damschroder M, Bishop SM, Sathish HA, Esfandiary R. Mitigation of reversible self-association and viscosity in a human IgG1 monoclonal antibody by rational, structure-guided Fv engineering. MAbs 2016; 8:941-50. [PMID: 27050875 DOI: 10.1080/19420862.2016.1171444] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Undesired solution behaviors such as reversible self-association (RSA), high viscosity, and liquid-liquid phase separation can introduce substantial challenges during development of monoclonal antibody formulations. Although a global mechanistic understanding of RSA (i.e., native and reversible protein-protein interactions) is sufficient to develop robust formulation controls, its mitigation via protein engineering requires knowledge of the sites of protein-protein interactions. In the study reported here, we coupled our previous hydrogen-deuterium exchange mass spectrometry findings with structural modeling and in vitro screening to identify the residues responsible for RSA of a model IgG1 monoclonal antibody (mAb-C), and rationally engineered variants with improved solution properties (i.e., reduced RSA and viscosity). Our data show that mutation of either solvent-exposed aromatic residues within the heavy and light chain variable regions or buried residues within the heavy chain/light chain interface can significantly mitigate RSA and viscosity by reducing the IgG's surface hydrophobicity. The engineering strategy described here highlights the utility of integrating complementary experimental and in silico methods to identify mutations that can improve developability, in particular, high concentration solution properties, of candidate therapeutic antibodies.
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Affiliation(s)
- James C Geoghegan
- a Department of Antibody Discovery and Protein Engineering , MedImmune , Gaithersburg , MD , USA
| | - Ryan Fleming
- a Department of Antibody Discovery and Protein Engineering , MedImmune , Gaithersburg , MD , USA
| | - Melissa Damschroder
- a Department of Antibody Discovery and Protein Engineering , MedImmune , Gaithersburg , MD , USA
| | - Steven M Bishop
- b Department of Formulation Sciences , MedImmune , Gaithersburg , MD , USA
| | - Hasige A Sathish
- b Department of Formulation Sciences , MedImmune , Gaithersburg , MD , USA
| | - Reza Esfandiary
- b Department of Formulation Sciences , MedImmune , Gaithersburg , MD , USA
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8
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Liu Y, Caffry I, Wu J, Geng SB, Jain T, Sun T, Reid F, Cao Y, Estep P, Yu Y, Vásquez M, Tessier PM, Xu Y. High-throughput screening for developability during early-stage antibody discovery using self-interaction nanoparticle spectroscopy. MAbs 2013; 6:483-92. [PMID: 24492294 DOI: 10.4161/mabs.27431] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The discovery of monoclonal antibodies (mAbs) that bind to a particular molecular target is now regarded a routine exercise. However, the successful development of mAbs that (1) express well, (2) elicit a desirable biological effect upon binding, and (3) remain soluble and display low viscosity at high concentrations is often far more challenging. Therefore, high throughput screening assays that assess self-association and aggregation early in the selection process are likely to yield mAbs with superior biophysical properties. Here, we report an improved version of affinity-capture self-interaction nanoparticle spectroscopy (AC-SINS) that is capable of screening large panels of antibodies for their propensity to self-associate. AC-SINS is based on concentrating mAbs from dilute solutions around gold nanoparticles pre-coated with polyclonal capture (e.g., anti-Fc) antibodies. Interactions between immobilized mAbs lead to reduced inter-particle distances and increased plasmon wavelengths (wavelengths of maximum absorbance), which can be readily measured by optical means. This method is attractive because it is compatible with dilute and unpurified mAb solutions that are typical during early antibody discovery. In addition, we have improved multiple aspects of this assay for increased throughput and reproducibility. A data set comprising over 400 mAbs suggests that our modified assay yields self-interaction measurements that are well-correlated with other lower throughput assays such as cross-interaction chromatography. We expect that the simplicity and throughput of our improved AC-SINS method will lead to improved selection of mAbs with excellent biophysical properties during early antibody discovery.
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Affiliation(s)
- Yuqi Liu
- Protein Analytics; Adimab; Lebanon, NH USA
| | | | - Jiemin Wu
- Center for Biotechnology & Interdisciplinary Studies; Isermann Dept. of Chemical & Biological Engineering; Rensselaer Polytechnic Institute; Troy, NY USA
| | - Steven B Geng
- Center for Biotechnology & Interdisciplinary Studies; Isermann Dept. of Chemical & Biological Engineering; Rensselaer Polytechnic Institute; Troy, NY USA
| | - Tushar Jain
- Computational Biology; Adimab; Palo Alto, CA USA
| | | | | | - Yuan Cao
- Protein Analytics; Adimab; Lebanon, NH USA
| | | | - Yao Yu
- Protein Analytics; Adimab; Lebanon, NH USA
| | | | - Peter M Tessier
- Center for Biotechnology & Interdisciplinary Studies; Isermann Dept. of Chemical & Biological Engineering; Rensselaer Polytechnic Institute; Troy, NY USA
| | - Yingda Xu
- Protein Analytics; Adimab; Lebanon, NH USA
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