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Guarra F, Colombo G. Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens. J Chem Theory Comput 2023; 19:5315-5333. [PMID: 37527403 PMCID: PMC10448727 DOI: 10.1021/acs.jctc.3c00513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Indexed: 08/03/2023]
Abstract
The design of new biomolecules able to harness immune mechanisms for the treatment of diseases is a prime challenge for computational and simulative approaches. For instance, in recent years, antibodies have emerged as an important class of therapeutics against a spectrum of pathologies. In cancer, immune-inspired approaches are witnessing a surge thanks to a better understanding of tumor-associated antigens and the mechanisms of their engagement or evasion from the human immune system. Here, we provide a summary of the main state-of-the-art computational approaches that are used to design antibodies and antigens, and in parallel, we review key methodologies for epitope identification for both B- and T-cell mediated responses. A special focus is devoted to the description of structure- and physics-based models, privileged over purely sequence-based approaches. We discuss the implications of novel methods in engineering biomolecules with tailored immunological properties for possible therapeutic uses. Finally, we highlight the extraordinary challenges and opportunities presented by the possible integration of structure- and physics-based methods with emerging Artificial Intelligence technologies for the prediction and design of novel antigens, epitopes, and antibodies.
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Affiliation(s)
- Federica Guarra
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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Bauer J, Rajagopal N, Gupta P, Gupta P, Nixon AE, Kumar S. How can we discover developable antibody-based biotherapeutics? Front Mol Biosci 2023; 10:1221626. [PMID: 37609373 PMCID: PMC10441133 DOI: 10.3389/fmolb.2023.1221626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/10/2023] [Indexed: 08/24/2023] Open
Abstract
Antibody-based biotherapeutics have emerged as a successful class of pharmaceuticals despite significant challenges and risks to their discovery and development. This review discusses the most frequently encountered hurdles in the research and development (R&D) of antibody-based biotherapeutics and proposes a conceptual framework called biopharmaceutical informatics. Our vision advocates for the syncretic use of computation and experimentation at every stage of biologic drug discovery, considering developability (manufacturability, safety, efficacy, and pharmacology) of potential drug candidates from the earliest stages of the drug discovery phase. The computational advances in recent years allow for more precise formulation of disease concepts, rapid identification, and validation of targets suitable for therapeutic intervention and discovery of potential biotherapeutics that can agonize or antagonize them. Furthermore, computational methods for de novo and epitope-specific antibody design are increasingly being developed, opening novel computationally driven opportunities for biologic drug discovery. Here, we review the opportunities and limitations of emerging computational approaches for optimizing antigens to generate robust immune responses, in silico generation of antibody sequences, discovery of potential antibody binders through virtual screening, assessment of hits, identification of lead drug candidates and their affinity maturation, and optimization for developability. The adoption of biopharmaceutical informatics across all aspects of drug discovery and development cycles should help bring affordable and effective biotherapeutics to patients more quickly.
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Affiliation(s)
- Joschka Bauer
- Early Stage Pharmaceutical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach/Riss, Germany
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
| | - Nandhini Rajagopal
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Priyanka Gupta
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Pankaj Gupta
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Andrew E. Nixon
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Sandeep Kumar
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
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Lee FS, Anderson AG, Olafson BD. Benchmarking TriadAb using targets from the second antibody modeling assessment. Protein Eng Des Sel 2023; 36:gzad013. [PMID: 37864287 DOI: 10.1093/protein/gzad013] [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: 05/05/2023] [Revised: 08/10/2023] [Indexed: 10/22/2023] Open
Abstract
Computational modeling and design of antibodies has become an integral part of today's research and development in antibody therapeutics. Here we describe the Triad Antibody Homology Modeling (TriadAb) package, a functionality of the Triad protein design platform that predicts the structure of any heavy and light chain sequences of an antibody Fv domain using template-based modeling. To gauge the performance of TriadAb, we benchmarked against the results of the Second Antibody Modeling Assessment (AMA-II). On average, TriadAb produced main-chain carbonyl root-mean-square deviations between models and experimentally determined structures at 1.10 Å, 1.45 Å, 1.41 Å, 3.04 Å, 1.47 Å, 1.27 Å, 1.63 Å in the framework and the six complementarity-determining regions (H1, H2, H3, L1, L2, L3), respectively. The inaugural results are comparable to those reported in AMA-II, corroborating with our internal bench-based experiences that models generated using TriadAb are sufficiently accurate and useful for antibody engineering using the sequence design capabilities provided by Triad.
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Bansia H, Ramakumar S. Homology Modeling of Antibody Variable Regions: Methods and Applications. Methods Mol Biol 2023; 2627:301-319. [PMID: 36959454 DOI: 10.1007/978-1-0716-2974-1_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Adaptive immunity specifically protects us from antigenic challenges. Antibodies are key effector proteins of adaptive immunity, and they are remarkable in their ability to recognize a virtually limitless number of antigens. Fragment variable (FV), the antigen-binding region of antibodies, can be split into two main components, namely, framework and complementarity determining regions. The framework (FR) consists of light-chain framework (FRL) and heavy-chain framework (FRH). Similarly, the complementarity determining regions (CDRs) comprises of light-chain CDRs 1-3 (CDRs L1-3) and heavy-chain CDRs 1-3 (CDRs H1-3). While FRs are relatively constant in sequence and structure across diverse antibodies, sequence variation in CDRs leading to differential conformations of CDR loops accounts for the distinct antigenic specificities of diverse antibodies. The conserved structural features in FRs and conformity of CDRs to a limited set of standard conformations allow for the accurate prediction of FV models using homology modeling techniques. Antibody structure prediction from its amino acid sequence has numerous important applications including prediction of antibody-antigen interaction interfaces and redesign of therapeutically and biotechnologically useful antibodies with improved affinity. This chapter summarizes the current practices employed in the successful homology modeling of antibody variable regions and the potential applications of the generated homology models.
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Affiliation(s)
- Harsh Bansia
- Department of Physics, Indian Institute of Science, Bengaluru, India.
- Advanced Science Research Center at The Graduate Center of the City University of New York, New York, NY, USA.
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Wilman W, Wróbel S, Bielska W, Deszynski P, Dudzic P, Jaszczyszyn I, Kaniewski J, Młokosiewicz J, Rouyan A, Satława T, Kumar S, Greiff V, Krawczyk K. Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery. Brief Bioinform 2022; 23:bbac267. [PMID: 35830864 PMCID: PMC9294429 DOI: 10.1093/bib/bbac267] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Antibodies are versatile molecular binders with an established and growing role as therapeutics. Computational approaches to developing and designing these molecules are being increasingly used to complement traditional lab-based processes. Nowadays, in silico methods fill multiple elements of the discovery stage, such as characterizing antibody-antigen interactions and identifying developability liabilities. Recently, computational methods tackling such problems have begun to follow machine learning paradigms, in many cases deep learning specifically. This paradigm shift offers improvements in established areas such as structure or binding prediction and opens up new possibilities such as language-based modeling of antibody repertoires or machine-learning-based generation of novel sequences. In this review, we critically examine the recent developments in (deep) machine learning approaches to therapeutic antibody design with implications for fully computational antibody design.
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Hsieh YC, Liao JM, Chuang KH, Ho KW, Hong ST, Liu HJ, Huang BC, Chen IJ, Liu YL, Wang JY, Tsai HL, Su YC, Wang YT, Cheng TL. A universal in silico V(D)J recombination strategy for developing humanized monoclonal antibodies. J Nanobiotechnology 2022; 20:58. [PMID: 35101043 PMCID: PMC8805405 DOI: 10.1186/s12951-022-01259-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/12/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Humanization of mouse monoclonal antibodies (mAbs) is crucial for reducing their immunogenicity in humans. However, humanized mAbs often lose their binding affinities. Therefore, an in silico humanization method that can prevent the loss of the binding affinity of mAbs is needed. METHODS We developed an in silico V(D)J recombination platform in which we used V(D)J human germline gene sequences to design five humanized candidates of anti-tumor necrosis factor (TNF)-α mAbs (C1-C5) by using different human germline templates. The candidates were subjected to molecular dynamics simulation. In addition, the structural similarities of their complementarity-determining regions (CDRs) to those of original mouse mAbs were estimated to derive the weighted interatomic root mean squared deviation (wRMSDi) value. Subsequently, the correlation of the derived wRMSDi value with the half maximal effective concentration (EC50) and the binding affinity (KD) of the humanized anti-TNF-α candidates was examined. To confirm whether our in silico estimation method can be used for other humanized mAbs, we tested our method using the anti-epidermal growth factor receptor (EGFR) a4.6.1, anti-glypican-3 (GPC3) YP9.1 and anti-α4β1 integrin HP1/2L mAbs. RESULTS The R2 value for the correlation between the wRMSDi and log(EC50) of the recombinant Remicade and those of the humanized anti-TNF-α candidates was 0.901, and the R2 value for the correlation between wRMSDi and log(KD) was 0.9921. The results indicated that our in silico V(D)J recombination platform could predict the binding affinity of humanized candidates and successfully identify the high-affinity humanized anti-TNF-α antibody (Ab) C1 with a binding affinity similar to that of the parental chimeric mAb (5.13 × 10-10). For the anti-EGFR a4.6.1, anti-GPC3 YP9.1, and anti-α4β1 integrin HP1/2L mAbs, the wRMSDi and log(EC50) exhibited strong correlations (R2 = 0.9908, 0.9999, and 0.8907, respectively). CONCLUSIONS Our in silico V(D)J recombination platform can facilitate the development of humanized mAbs with low immunogenicity and high binding affinities. This platform can directly transform numerous mAbs with therapeutic potential to humanized or even human therapeutic Abs for clinical use.
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Affiliation(s)
- Yuan-Chin Hsieh
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
- School of Medicine for International Students, I-Shou University, No.8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung, 82445, Taiwan
| | - Jun-Min Liao
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Kuo-Hsiang Chuang
- Graduate Institute of Pharmacognosy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
- Ph.D. Program for Clinical Drug Discovery From Botanical Herbs, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Kai-Wen Ho
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Shih-Ting Hong
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Hui-Ju Liu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Bo-Cheng Huang
- Institute of Biomedical Sciences, National Sun Yat-Sen University, 70 Lien-hai Road, Kaohsiung, 804, Taiwan
| | - I-Ju Chen
- School of Medicine, I-Shou University, No.8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung, 82445, Taiwan
| | - Yen-Ling Liu
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Jaw-Yuan Wang
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
- Department of Surgery, Faculty of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, No.100, Tzyou 1st Rd., Sanmin Dist., Kaohsiung, 80756, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Hsiang-Lin Tsai
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
- Department of Surgery, Faculty of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Yu-Cheng Su
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, No. 1001, Daxue Rd. East Dist., Hsin-Chu, 300, Taiwan
| | - Yen-Tseng Wang
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan.
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan.
| | - Tian-Lu Cheng
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan.
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan.
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Qu Y, Zhang X, Wang M, Sun L, Jiang Y, Li C, Wu W, Chen Z, Yin Q, Jiang X, Liu Y, Li C, Li J, Ying T, Li D, Zhan F, Wang Y, Guan W, Wang S, Liang M. Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Virol Sin 2021; 36:934-947. [PMID: 34224110 PMCID: PMC8255729 DOI: 10.1007/s12250-021-00409-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/06/2021] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has precipitated multiple variants resistant to therapeutic antibodies. In this study, 12 high-affinity antibodies were generated from convalescent donors in early outbreaks using immune antibody phage display libraries. Of them, two RBD-binding antibodies (F61 and H121) showed high-affinity neutralization against SARS-CoV-2, whereas three S2-target antibodies failed to neutralize SARS-CoV-2. Following structure analysis, F61 identified a linear epitope located in residues G446-S494, which overlapped with angiotensin-converting enzyme 2 (ACE2) binding sites, while H121 recognized a conformational epitope located on the side face of RBD, outside from ACE2 binding domain. Hence the cocktail of the two antibodies achieved better performance of neutralization to SARS-CoV-2. Importantly, these two antibodies also showed efficient neutralizing activities to the variants including B.1.1.7 and B.1.351, and reacted with mutations of N501Y, E484K, and L452R, indicated that it may also neutralize the recent India endemic strain B.1.617. The unchanged binding activity of F61 and H121 to RBD with multiple mutations revealed a broad neutralizing activity against variants, which mitigated the risk of viral escape. Our findings revealed the therapeutic basis of cocktail antibodies against constantly emerging SARS-CoV-2 variants and provided promising candidate antibodies to clinical treatment of COVID-19 patients infected with broad SARS-CoV-2 variants.
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Affiliation(s)
- Yuanyuan Qu
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xueyan Zhang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meiyu Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, 102629, China
- Peking Union Medical College, Beijing, 100730, China
| | - Lina Sun
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yongzhong Jiang
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430065, China
| | - Cheng Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wei Wu
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Zhen Chen
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
| | - Qiangling Yin
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xiaolin Jiang
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Yang Liu
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Chuan Li
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jiandong Li
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Tianlei Ying
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Dexin Li
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Faxian Zhan
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430065, China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, 102629, China
- Peking Union Medical College, Beijing, 100730, China
| | - Wuxiang Guan
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China.
| | - Shiwen Wang
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Mifang Liang
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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Schneider C, Buchanan A, Taddese B, Deane CM. DLAB: deep learning methods for structure-based virtual screening of antibodies. Bioinformatics 2021; 38:377-383. [PMID: 34546288 PMCID: PMC8723137 DOI: 10.1093/bioinformatics/btab660] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/03/2021] [Accepted: 09/01/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Antibodies are one of the most important classes of pharmaceuticals, with over 80 approved molecules currently in use against a wide variety of diseases. The drug discovery process for antibody therapeutic candidates however is time- and cost-intensive and heavily reliant on in vivo and in vitro high throughput screens. Here, we introduce a framework for structure-based deep learning for antibodies (DLAB) which can virtually screen putative binding antibodies against antigen targets of interest. DLAB is built to be able to predict antibody-antigen binding for antigens with no known antibody binders. RESULTS We demonstrate that DLAB can be used both to improve antibody-antigen docking and structure-based virtual screening of antibody drug candidates. DLAB enables improved pose ranking for antibody docking experiments as well as selection of antibody-antigen pairings for which accurate poses are generated and correctly ranked. We also show that DLAB can identify binding antibodies against specific antigens in a case study. Our results demonstrate the promise of deep learning methods for structure-based virtual screening of antibodies. AVAILABILITY AND IMPLEMENTATION The DLAB source code and pre-trained models are available at https://github.com/oxpig/dlab-public. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Andrew Buchanan
- Antibody Discovery & Protein Engineering, R&D, AstraZeneca, Cambridge, CB2 0AA, UK
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Marrero Diaz de Villegas R, Seki C, Mattion NM, König GA. Functional and in silico Characterization of Neutralizing Interactions Between Antibodies and the Foot-and-Mouth Disease Virus Immunodominant Antigenic Site. Front Vet Sci 2021; 8:554383. [PMID: 34026880 PMCID: PMC8137985 DOI: 10.3389/fvets.2021.554383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/19/2021] [Indexed: 12/04/2022] Open
Abstract
Molecular knowledge of virus–antibody interactions is essential for the development of better vaccines and for a timely assessment of the spread and severity of epidemics. For foot-and-mouth disease virus (FMDV) research, in particular, computational methods for antigen–antibody (Ag–Ab) interaction, and cross-antigenicity characterization and prediction are critical to design engineered vaccines with robust, long-lasting, and wider response against different strains. We integrated existing structural modeling and prediction algorithms to study the surface properties of FMDV Ags and Abs and their interaction. First, we explored four modeling and two Ag–Ab docking methods and implemented a computational pipeline based on a reference Ag–Ab structure for FMDV of serotype C, to be used as a source protocol for the study of unknown interaction pairs of Ag–Ab. Next, we obtained the variable region sequence of two monoclonal IgM and IgG antibodies that recognize and neutralize antigenic site A (AgSA) epitopes from South America serotype A FMDV and developed two peptide ELISAs for their fine epitope mapping. Then, we applied the previous Ag–Ab molecular structure modeling and docking protocol further scored by functional peptide ELISA data. This work highlights a possible different behavior in the immune response of IgG and IgM Ab isotypes. The present method yielded reliable Ab models with differential paratopes and Ag interaction topologies in concordance with their isotype classes. Moreover, it demonstrates the applicability of computational prediction techniques to the interaction phenomena between the FMDV immunodominant AgSA and Abs, and points out their potential utility as a metric for virus-related, massive Ab repertoire analysis or as a starting point for recombinant vaccine design.
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Affiliation(s)
- Ruben Marrero Diaz de Villegas
- Instituto de Agrobiotecnología y Biología Molecular, Instituto Nacional de Tecnología Agropecuaria, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Cristina Seki
- Centro de Virología Animal, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Universidad Abierta Interamericana, Buenos Aires, Argentina
| | - Nora M Mattion
- Centro de Virología Animal, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Universidad Abierta Interamericana, Buenos Aires, Argentina
| | - Guido A König
- Instituto de Agrobiotecnología y Biología Molecular, Instituto Nacional de Tecnología Agropecuaria, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
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10
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Machine Learning Attempts for Predicting Human Subcutaneous Bioavailability of Monoclonal Antibodies. Pharm Res 2021; 38:451-460. [PMID: 33710513 DOI: 10.1007/s11095-021-03022-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/22/2021] [Indexed: 10/21/2022]
Abstract
PURPOSE One knowledge gap related to subcutaneous (SC) delivery is unpredictable and variable bioavailability. This study was aimed to develop machine learning methods to predict whether mAb's bioavailability was ≥70% or below, without completely knowing the mechanism and causality between inputs and outputs. METHODS A database of mAb SC products was built. The model training and validation were accomplished based on this database and a set of the inputs (product properties) were mapped to the output (bioavailability) using different machine learning algorithms. Dimensionality reduction was undertaken using principal component analysis (PCA). RESULTS The bioavailability of the mAb products being investigated varied from 35% to 90%. The tree-based methods, including random forest (RF), Adaptive Boost (AdaBoost), and decision tree (DT) presented the best predictability and generalization power on bioavailability classification. The models based on Multi-layer perceptron (MLP), Gaussian Naïve Bayes (GaussianNB), and k nearest neighbor (kNN) algorithms also provided acceptable prediction accuracy. CONCLUSION Machine learning could be a potential tool to predict mAb's bioavailability. Since all input features were acquired using theoretical calculations and predictions rather than experiments, the models may be particularly applicable to some early-stage research activities such as mAb molecule triage, design/optimization, mutant screening, molecule selection, and formulation design.
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Sivaccumar J, Sandomenico A, Vitagliano L, Ruvo M. Monoclonal Antibodies: A Prospective and Retrospective View. Curr Med Chem 2021; 28:435-471. [PMID: 32072887 DOI: 10.2174/0929867327666200219142231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Monoclonal Antibodies (mAbs) represent one of the most important classes of biotherapeutic agents. They are used to cure many diseases, including cancer, autoimmune diseases, cardiovascular diseases, angiogenesis-related diseases and, more recently also haemophilia. They can be highly varied in terms of format, source, and specificity to improve efficacy and to obtain more targeted applications. This can be achieved by leaving substantially unchanged the basic structural components for paratope clustering. OBJECTIVES The objective was to trace the most relevant findings that have deserved prestigious awards over the years, to report the most important clinical applications and to emphasize their latest emerging therapeutic trends. RESULTS We report the most relevant milestones and new technologies adopted for antibody development. Recent efforts in generating new engineered antibody-based formats are briefly reviewed. The most important antibody-based molecules that are (or are going to be) used for pharmacological practice have been collected in useful tables. CONCLUSION The topics here discussed prove the undisputed role of mAbs as innovative biopharmaceuticals molecules and as vital components of targeted pharmacological therapies.
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Affiliation(s)
- Jwala Sivaccumar
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
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12
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Norman RA, Ambrosetti F, Bonvin AMJJ, Colwell LJ, Kelm S, Kumar S, Krawczyk K. Computational approaches to therapeutic antibody design: established methods and emerging trends. Brief Bioinform 2020; 21:1549-1567. [PMID: 31626279 PMCID: PMC7947987 DOI: 10.1093/bib/bbz095] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/07/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Abstract
Antibodies are proteins that recognize the molecular surfaces of potentially noxious molecules to mount an adaptive immune response or, in the case of autoimmune diseases, molecules that are part of healthy cells and tissues. Due to their binding versatility, antibodies are currently the largest class of biotherapeutics, with five monoclonal antibodies ranked in the top 10 blockbuster drugs. Computational advances in protein modelling and design can have a tangible impact on antibody-based therapeutic development. Antibody-specific computational protocols currently benefit from an increasing volume of data provided by next generation sequencing and application to related drug modalities based on traditional antibodies, such as nanobodies. Here we present a structured overview of available databases, methods and emerging trends in computational antibody analysis and contextualize them towards the engineering of candidate antibody therapeutics.
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13
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Teraguchi S, Saputri DS, Llamas-Covarrubias MA, Davila A, Diez D, Nazlica SA, Rozewicki J, Ismanto HS, Wilamowski J, Xie J, Xu Z, Loza-Lopez MDJ, van Eerden FJ, Li S, Standley DM. Methods for sequence and structural analysis of B and T cell receptor repertoires. Comput Struct Biotechnol J 2020; 18:2000-2011. [PMID: 32802272 PMCID: PMC7366105 DOI: 10.1016/j.csbj.2020.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 02/07/2023] Open
Abstract
B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of BCR and TCR repertoires plays an important role in both basic immunology as well as in biotechnology. Because the repertoires are highly diverse, specialized software methods are needed to extract meaningful information from BCR and TCR sequence data. Here, we review recent developments in bioinformatics tools for analysis of BCR and TCR repertoires, with an emphasis on those that incorporate structural features. After describing the recent sequencing technologies for immune receptor repertoires, we survey structural modeling methods for BCR and TCRs, along with methods for clustering such models. We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. We also briefly discuss molecular dynamics in this context.
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Affiliation(s)
- Shunsuke Teraguchi
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Dianita S. Saputri
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Mara Anais Llamas-Covarrubias
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Mexico
| | - Ana Davila
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Diego Diez
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Sedat Aybars Nazlica
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - John Rozewicki
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Hendra S. Ismanto
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Jan Wilamowski
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Jiaqi Xie
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Zichang Xu
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | | | - Floris J. van Eerden
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Songling Li
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Daron M. Standley
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
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14
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Karami Y, Rey J, Postic G, Murail S, Tufféry P, de Vries SJ. DaReUS-Loop: a web server to model multiple loops in homology models. Nucleic Acids Res 2020; 47:W423-W428. [PMID: 31114872 PMCID: PMC6602439 DOI: 10.1093/nar/gkz403] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/20/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023] Open
Abstract
Loop regions in protein structures often have crucial roles, and they are much more variable in sequence and structure than other regions. In homology modeling, this leads to larger deviations from the homologous templates, and loop modeling of homology models remains an open problem. To address this issue, we have previously developed the DaReUS-Loop protocol, leading to significant improvement over existing methods. Here, a DaReUS-Loop web server is presented, providing an automated platform for modeling or remodeling loops in the context of homology models. This is the first web server accepting a protein with up to 20 loop regions, and modeling them all in parallel. It also provides a prediction confidence level that corresponds to the expected accuracy of the loops. DaReUS-Loop facilitates the analysis of the results through its interactive graphical interface and is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/DaReUS-Loop/.
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Affiliation(s)
- Yasaman Karami
- Sorbonne Paris Cité, Université Paris Diderot, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France
| | - Julien Rey
- Sorbonne Paris Cité, Université Paris Diderot, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France
| | - Guillaume Postic
- Sorbonne Paris Cité, Université Paris Diderot, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France.,Institut Français de Bioinformatique (IFB), UMS 3601-CNRS, Université Paris-Saclay, Orsay, France
| | - Samuel Murail
- Sorbonne Paris Cité, Université Paris Diderot, CNRS UMR 8251, INSERM ERL U1133, Paris, France
| | - Pierre Tufféry
- Sorbonne Paris Cité, Université Paris Diderot, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France
| | - Sjoerd J de Vries
- Sorbonne Paris Cité, Université Paris Diderot, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France
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15
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Marks C, Deane CM. How repertoire data are changing antibody science. J Biol Chem 2020; 295:9823-9837. [PMID: 32409582 DOI: 10.1074/jbc.rev120.010181] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/28/2020] [Indexed: 12/13/2022] Open
Abstract
Antibodies are vital proteins of the immune system that recognize potentially harmful molecules and initiate their removal. Mammals can efficiently create vast numbers of antibodies with different sequences capable of binding to any antigen with high affinity and specificity. Because they can be developed to bind to many disease agents, antibodies can be used as therapeutics. In an organism, after antigen exposure, antibodies specific to that antigen are enriched through clonal selection, expansion, and somatic hypermutation. The antibodies present in an organism therefore report on its immune status, describe its innate ability to deal with harmful substances, and reveal how it has previously responded. Next-generation sequencing technologies are being increasingly used to query the antibody, or B-cell receptor (BCR), sequence repertoire, and the amount of BCR data in public repositories is growing. The Observed Antibody Space database, for example, currently contains over a billion sequences from 68 different studies. Repertoires are available that represent both the naive state (i.e. antigen-inexperienced) and that after immunization. This wealth of data has created opportunities to learn more about our immune system. In this review, we discuss the many ways in which BCR repertoire data have been or could be exploited. We highlight its utility for providing insights into how the naive immune repertoire is generated and how it responds to antigens. We also consider how structural information can be used to enhance these data and may lead to more accurate depictions of the sequence space and to applications in the discovery of new therapeutics.
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Affiliation(s)
- Claire Marks
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
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16
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Melarkode Vattekatte A, Shinada NK, Narwani TJ, Noël F, Bertrand O, Meyniel JP, Malpertuy A, Gelly JC, Cadet F, de Brevern AG. Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction. PeerJ 2020; 8:e8408. [PMID: 32185102 PMCID: PMC7061911 DOI: 10.7717/peerj.8408] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/16/2019] [Indexed: 12/28/2022] Open
Abstract
Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only three CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with their other important features, e.g., easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationship. In this study, sequence characteristics of VHH domains have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHH domains showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.
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Affiliation(s)
- Akhila Melarkode Vattekatte
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Faculté des Sciences et Technologies, Saint Denis, La Réunion, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Nicolas Ken Shinada
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Discngine SAS, Paris, France
| | - Tarun J Narwani
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Floriane Noël
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,PSL Research University, INSERM, UMR 932, Institut Curie, Paris, France.,Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Olivier Bertrand
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France
| | | | | | - Jean-Christophe Gelly
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,IBL, Paris, France
| | - Frédéric Cadet
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Faculté des Sciences et Technologies, Saint Denis, La Réunion, France.,Peaccel, Protein Engineering Accelerator, Paris, France
| | - Alexandre G de Brevern
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Faculté des Sciences et Technologies, Saint Denis, La Réunion, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,IBL, Paris, France
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17
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Ambrosetti F, Jiménez-García B, Roel-Touris J, Bonvin AMJJ. Modeling Antibody-Antigen Complexes by Information-Driven Docking. Structure 2019; 28:119-129.e2. [PMID: 31727476 DOI: 10.1016/j.str.2019.10.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/03/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
Antibodies are Y-shaped proteins essential for immune response. Their capability to recognize antigens with high specificity makes them excellent therapeutic targets. Understanding the structural basis of antibody-antigen interactions is therefore crucial for improving our ability to design efficient biological drugs. Computational approaches such as molecular docking are providing a valuable and fast alternative to experimental structural characterization for these complexes. We investigate here how information about complementarity-determining regions and binding epitopes can be used to drive the modeling process, and present a comparative study of four different docking software suites (ClusPro, LightDock, ZDOCK, and HADDOCK) providing specific options for antibody-antigen modeling. Their performance on a dataset of 16 complexes is reported. HADDOCK, which includes information to drive the docking, is shown to perform best in terms of both success rate and quality of the generated models in both the presence and absence of information about the epitope on the antigen.
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Affiliation(s)
- Francesco Ambrosetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00184 Rome, Italy; Faculty of Science - Chemistry, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Brian Jiménez-García
- Faculty of Science - Chemistry, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jorge Roel-Touris
- Faculty of Science - Chemistry, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexandre M J J Bonvin
- Faculty of Science - Chemistry, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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18
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Optimization of an Antibody Light Chain Framework Enhances Expression, Biophysical Properties and Pharmacokinetics. Antibodies (Basel) 2019; 8:antib8030046. [PMID: 31544852 PMCID: PMC6784111 DOI: 10.3390/antib8030046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 11/17/2022] Open
Abstract
Efficacy, safety, and manufacturability of therapeutic antibodies are influenced by their biopharmaceutical and biophysical properties. These properties can be optimized by library approaches or rationale protein design. Here, we employed a protein engineering approach to modify the variable domain of the light chain (VL) framework of an oxidized macrophage migration inhibitory factor (oxMIF)-specific antibody. The amendment of the antibody sequence was based on homology to human germline VL genes. Three regions or positions were identified in the VL domain—L1-4, L66, L79—and mutated independently or in combination to match the closest germline V gene. None of the mutations altered oxMIF specificity or affinity, but some variants improved thermal stability, aggregation propensity, and resulted in up to five-fold higher expression. Importantly, the improved biopharmaceutical properties translated into a superior pharmacokinetic profile of the antibody. Thus, optimization of the V domain framework can ameliorate the biophysical qualities of a therapeutic antibody candidate, and as result its manufacturability, and also has the potential to improve pharmacokinetics.
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19
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Krokhotin A, Du H, Hirabayashi K, Popov K, Kurokawa T, Wan X, Ferrone S, Dotti G, Dokholyan NV. Computationally Guided Design of Single-Chain Variable Fragment Improves Specificity of Chimeric Antigen Receptors. MOLECULAR THERAPY-ONCOLYTICS 2019; 15:30-37. [PMID: 31650023 PMCID: PMC6804740 DOI: 10.1016/j.omto.2019.08.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/24/2019] [Indexed: 01/24/2023]
Abstract
Chimeric antigen receptor (CAR)-T cell-based immunotherapy of malignant disease relies on the specificity and association constant of single-chain variable fragments (scFvs). The latter are synthesized from parent antibodies by fusing their light (VL) and heavy (VH)-chain variable domains into a single chain using a flexible linker peptide. The fusion of VL and VH domains can distort their relative orientation, thereby compromising specificity and association constant of scFv, and reducing the lytic efficacy of CAR-T cells. Here, we circumvent the complications of domains' fusion by designing scFv mutants that stabilize interaction between scFv and its target, thereby rescuing scFv efficacy. We employ an iterative approach, based on structural modeling and mutagenesis driven by computational protein design. To demonstrate the power of this approach, we use the scFv derived from an antibody specific to a human leukocyte antigen A2 (HLA-A2)-HER2-derived peptide complex. Whereas the parental antibody is highly specific to its target, the scFv showed reduced specificity. Using our approach, we design mutations into scFvs that restore specificity of the original antibody.
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Affiliation(s)
- Andrey Krokhotin
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hongwei Du
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Koichi Hirabayashi
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Konstantin Popov
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tomohiro Kurokawa
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xinhui Wan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Soldano Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Gianpietro Dotti
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nikolay V Dokholyan
- Departments of Pharmacology and Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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20
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Lepore R, Olimpieri PP, Messih MA, Tramontano A. PIGSPro: prediction of immunoGlobulin structures v2. Nucleic Acids Res 2019; 45:W17-W23. [PMID: 28472367 PMCID: PMC5570210 DOI: 10.1093/nar/gkx334] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 04/19/2017] [Indexed: 01/14/2023] Open
Abstract
PIGSpro is a significant upgrade of the popular PIGS server for the prediction of the structure of immunoglobulins. The software has been completely rewritten in python following a similar pipeline as in the original method, but including, at various steps, relevant modifications found to improve its prediction accuracy, as demonstrated here. The steps of the pipeline include the selection of the appropriate framework for predicting the conserved regions of the molecule by homology; the target template alignment for this portion of the molecule; the selection of the main chain conformation of the hypervariable loops according to the canonical structure model, the prediction of the third loop of the heavy chain (H3) for which complete canonical structures are not available and the packing of the light and heavy chain if derived from different templates. Each of these steps has been improved including updated methods developed along the years. Last but not least, the user interface has been completely redesigned and an automatic monthly update of the underlying database has been implemented. The method is available as a web server at http://biocomputing.it/pigspro.
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Affiliation(s)
- Rosalba Lepore
- Department of Physics, Sapienza University, Piazzale Aldo Moro 500-184 Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy
| | - Pier P Olimpieri
- Department of Physics, Sapienza University, Piazzale Aldo Moro 500-184 Rome, Italy
| | - Mario A Messih
- Department of Physics, Sapienza University, Piazzale Aldo Moro 500-184 Rome, Italy
| | - Anna Tramontano
- Department of Physics, Sapienza University, Piazzale Aldo Moro 500-184 Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy
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21
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Miura K, Tsuji Y, Mitsui H, Oshima T, Noshi Y, Arisawa Y, Okano K, Okano T. THETA system allows one-step isolation of tagged proteins through temperature-dependent protein-peptide interaction. Commun Biol 2019; 2:207. [PMID: 31240245 PMCID: PMC6572768 DOI: 10.1038/s42003-019-0457-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/09/2019] [Indexed: 11/09/2022] Open
Abstract
Tools to control protein-protein interactions by external stimuli have been extensively developed. For this purpose, thermal stimulation can be utilized in addition to light. In this study, we identify a monoclonal antibody termed C13 mAb, which shows an approximately 480-fold decrease in the affinity constant at 37 °C compared to that at 4 °C. Next, we apply this temperature-dependent protein-peptide interaction for one-step protein purifications. We term this THermal-Elution-based TAg system as the THETA system, in which gel-immobilized C13 mAb-derived single-chain variable fragment (scFv) (termed THETAL) is able to bind with proteins tagged by C13 mAb-epitope(s) (THETAS) at 4 °C and thermally release at 37-42 °C. Moreover, to reveal the temperature-dependent interaction mechanism, molecular dynamics simulations are performed along with epitope mapping experiments. Overall, the high specificity and reversibility of the temperature-dependent features of the THETA system will support a wide variety of future applications such as thermogenetics.
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Affiliation(s)
- Kota Miura
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, Waseda University, TWIns, Wakamatsucho 2-2, Shinjuku-Ku, Tokyo 162-8480 Japan
| | - Yusuke Tsuji
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, Waseda University, TWIns, Wakamatsucho 2-2, Shinjuku-Ku, Tokyo 162-8480 Japan
| | - Hiromasa Mitsui
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, Waseda University, TWIns, Wakamatsucho 2-2, Shinjuku-Ku, Tokyo 162-8480 Japan
| | - Takuya Oshima
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, Waseda University, TWIns, Wakamatsucho 2-2, Shinjuku-Ku, Tokyo 162-8480 Japan
| | - Yosei Noshi
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, Waseda University, TWIns, Wakamatsucho 2-2, Shinjuku-Ku, Tokyo 162-8480 Japan
| | - Yudai Arisawa
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, Waseda University, TWIns, Wakamatsucho 2-2, Shinjuku-Ku, Tokyo 162-8480 Japan
| | - Keiko Okano
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, Waseda University, TWIns, Wakamatsucho 2-2, Shinjuku-Ku, Tokyo 162-8480 Japan
| | - Toshiyuki Okano
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, Waseda University, TWIns, Wakamatsucho 2-2, Shinjuku-Ku, Tokyo 162-8480 Japan
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22
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Leem J, Deane CM. High-Throughput Antibody Structure Modeling and Design Using ABodyBuilder. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 1851:367-380. [PMID: 30298409 DOI: 10.1007/978-1-4939-8736-8_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Antibodies are proteins of the adaptive immune system; they can be designed to bind almost any molecule, and are increasingly being used as biotherapeutics. Experimental antibody design is an expensive and time-consuming process, and computational antibody design methods can now be used to help develop new therapeutics and diagnostics. Within the design pipeline, accurate antibody structure modeling is essential, as it provides the basis for antibody-antigen docking, binding affinity prediction, and estimating thermal stability. Ideally, models should be rapidly generated, allowing the exploration of the breadth of antibody space. This allows methods to replicate the natural processes of antibody diversification (e.g., V(D)J recombination and somatic hypermutation), and cope with large volumes of data that are typical of next-generation sequencing datasets. Here we describe ABodyBuilder and PEARS, algorithms that build and mutate antibody model structures. These methods take ~30 s to generate a model antibody structure.
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Affiliation(s)
- Jinwoo Leem
- Department of Statistics, University of Oxford, Oxford, UK
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23
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Long X, Jeliazkov JR, Gray JJ. Non-H3 CDR template selection in antibody modeling through machine learning. PeerJ 2019; 7:e6179. [PMID: 30648015 PMCID: PMC6330961 DOI: 10.7717/peerj.6179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/28/2018] [Indexed: 12/13/2022] Open
Abstract
Antibodies are proteins generated by the adaptive immune system to recognize and counteract a plethora of pathogens through specific binding. This adaptive binding is mediated by structural diversity in the six complementary determining region (CDR) loops (H1, H2, H3, L1, L2 and L3), which also makes accurate structural modeling of CDRs challenging. Both homology and de novo modeling approaches have been used; to date, the former has achieved greater accuracy for the non-H3 loops. The homology modeling of non-H3 CDRs is more accurate because non-H3 CDR loops of the same length and type can be grouped into a few structural clusters. Most antibody-modeling suites utilize homology modeling for the non-H3 CDRs, differing only in the alignment algorithm and how/if they utilize structural clusters. While RosettaAntibody and SAbPred do not explicitly assign query CDR sequences to clusters, two other approaches, PIGS and Kotai Antibody Builder, utilize sequence-based rules to assign CDR sequences to clusters. While the manually curated sequence rules can identify better structural templates, because their curation requires extensive literature search and human effort, they lag behind the deposition of new antibody structures and are infrequently updated. In this study, we propose a machine learning approach (Gradient Boosting Machine [GBM]) to learn the structural clusters of non-H3 CDRs from sequence alone. The GBM method simplifies feature selection and can easily integrate new data, compared to manual sequence rule curation. We compare the classification results using the GBM method to that of RosettaAntibody in a 3-repeat 10-fold cross-validation (CV) scheme on the cluster-annotated antibody database PyIgClassify and we observe an improvement in the classification accuracy of the concerned loops from 84.5% ± 0.24% to 88.16% ± 0.056%. The GBM models reduce the errors in specific cluster membership misclassifications when the involved clusters have relatively abundant data. Based on the factors identified, we suggest methods that can enrich structural classes with sparse data to further improve prediction accuracy in future studies.
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Affiliation(s)
- Xiyao Long
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Jeliazko R Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States of America
| | - Jeffrey J Gray
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States of America.,Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States of America.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States of America.,Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, United States of America
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24
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Li S, Wilamowski J, Teraguchi S, van Eerden FJ, Rozewicki J, Davila A, Xu Z, Katoh K, Standley DM. Structural Modeling of Lymphocyte Receptors and Their Antigens. Methods Mol Biol 2019; 2048:207-229. [PMID: 31396940 DOI: 10.1007/978-1-4939-9728-2_17] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Structural modeling plays a key role in protein function prediction on a genome-wide scale. For B and T lymphocyte receptors, the critical functional question is: which antigens and epitopes are targeted? With emerging B cell receptor (BCR) and T cell receptor (TCR) sequencing methods improving in both breadth and depth, there is a growing need for methods that can help answer this question. Since lymphocyte-antigen recognition depends on complementarity, structural modeling is likely to play an important role in understanding antigen specificity and affinity. In the case of BCRs, such modeling methods have a long history in the study and design of antibodies. However, for TCRs there are relatively few publicly available modeling tools, and, to our knowledge, none that incorporate interaction between TCRs and peptide-MHC (pMHC) complexes. Here, we provide a web-based tool, ImmuneScape ( https://sysimm.org/immune-scape/ ), to carry out TCR-pMHC modeling as a first step toward structure-based function prediction.
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Affiliation(s)
- Songling Li
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Jan Wilamowski
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shunsuke Teraguchi
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | | | - John Rozewicki
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Ana Davila
- Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Zichang Xu
- Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kazutaka Katoh
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Daron M Standley
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan. .,Immunology Frontier Research Center, Osaka University, Osaka, Japan.
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25
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Bekker GJ, Ma B, Kamiya N. Thermal stability of single-domain antibodies estimated by molecular dynamics simulations. Protein Sci 2018; 28:429-438. [PMID: 30394618 PMCID: PMC6319760 DOI: 10.1002/pro.3546] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/03/2018] [Accepted: 10/28/2018] [Indexed: 12/20/2022]
Abstract
Single‐domain antibodies (sdAbs) function like regular antibodies, however, consist of only one domain. Because of their low molecular weight, sdAbs have advantages with respect to production and delivery to their targets and for applications such as antibody drugs and biosensors. Thus, sdAbs with high thermal stability are required. In this work, we chose seven sdAbs, which have a wide range of melting temperature (Tm) values and known structures. We applied molecular dynamics (MD) simulations to estimate their relative stability and compared them with the experimental data. High‐temperature MD simulations at 400 K and 500 K were executed with simulations at 300 K as a control. The fraction of native atomic contacts, Q, measured for the 400 K simulations showed a fairly good correlation with the Tm values. Interestingly, when the residues were classified by their hydrophobicity and size, the Q values of hydrophilic residues exhibited an even better correlation, suggesting that stabilization is correlated with favorable interactions of hydrophilic residues. Measuring the Q value on a per‐residue level enabled us to identify residues that contribute significantly to the instability and thus demonstrating how our analysis can be used in a mutant case study.
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Affiliation(s)
- Gert-Jan Bekker
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Benson Ma
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo, Japan
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26
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Bandehpour M, Ahangarzadeh S, Yarian F, Lari A, Farnia P. In silicoevaluation of the interactions among two selected single chain variable fragments (scFvs) and ESAT-6 antigen ofMycobacterium tuberculosis. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1142/s0219633617500699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nowadays antibody engineering is an important approach in the design and manufacture of therapeutic and diagnostic antibodies. The study of interactions between antibodies and antigens is the critical step in the design of antibodies with desirable properties. Computational docking is a useful tool for structural characterization of bimolecular interactions. Docking is the process of predicting bound conformations and binding enthalpy of antibody–antigen complexes. In this study, the three-dimensional structures of two ribosome displayed-selected scFv antibodies were constructed by Kotai Antibody Builder. By using ClusPro 2.0 web server, the ESAT-6 antigen (a tuberculosis-specific antigen) structure was docked to both scFv models to obtain the structures of the binding complexes and molecular dynamics (MD) simulations were performed using GROMACS 4.5.3 package. By analyzing of the ESAT-scFv complexes, important amino acids involved in antigen–antibody interactions were identified which were Asn164 in VL3, Ser164 in VL7 and Asn55 in VH7. All three amino acids belonged to the CDRs. In conclusion, results achieved from this bioinformatics study can help in the design and development of novel antibodies with improved affinities for tuberculosis diagnosis.
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Affiliation(s)
- Mojgan Bandehpour
- Cellular & Molecular Biology Research Center Shahid Beheshti, University of Medical Sciences, Tehran, Iran
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahrzad Ahangarzadeh
- Cellular & Molecular Biology Research Center Shahid Beheshti, University of Medical Sciences, Tehran, Iran
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Yarian
- Cellular & Molecular Biology Research Center Shahid Beheshti, University of Medical Sciences, Tehran, Iran
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arezou Lari
- Systems Biomedicine, Pasteur Institute of Iran, Tehran, Iran
| | - Poopak Farnia
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Mycobacteriology Research Centre (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
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27
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Kovaltsuk A, Krawczyk K, Galson JD, Kelly DF, Deane CM, Trück J. How B-Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data. Front Immunol 2017; 8:1753. [PMID: 29276518 PMCID: PMC5727015 DOI: 10.3389/fimmu.2017.01753] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/27/2017] [Indexed: 12/24/2022] Open
Abstract
Next-generation sequencing of immunoglobulin gene repertoires (Ig-seq) allows the investigation of large-scale antibody dynamics at a sequence level. However, structural information, a crucial descriptor of antibody binding capability, is not collected in Ig-seq protocols. Developing systematic relationships between the antibody sequence information gathered from Ig-seq and low-throughput techniques such as X-ray crystallography could radically improve our understanding of antibodies. The mapping of Ig-seq datasets to known antibody structures can indicate structurally, and perhaps functionally, uncharted areas. Furthermore, contrasting naïve and antigenically challenged datasets using structural antibody descriptors should provide insights into antibody maturation. As the number of antibody structures steadily increases and more and more Ig-seq datasets become available, the opportunities that arise from combining the two types of information increase as well. Here, we review how these data types enrich one another and show potential for advancing our knowledge of the immune system and improving antibody engineering.
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Affiliation(s)
| | - Konrad Krawczyk
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Jacob D Galson
- Division of Immunology and the Children's Research Center, University Children's Hospital, University of Zürich, Zürich, Switzerland
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Johannes Trück
- Division of Immunology and the Children's Research Center, University Children's Hospital, University of Zürich, Zürich, Switzerland
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28
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Sangha AK, Dong J, Williamson L, Hashiguchi T, Saphire EO, Crowe JE, Meiler J. Role of Non-local Interactions between CDR Loops in Binding Affinity of MR78 Antibody to Marburg Virus Glycoprotein. Structure 2017; 25:1820-1828.e2. [PMID: 29153506 PMCID: PMC5718948 DOI: 10.1016/j.str.2017.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 08/17/2017] [Accepted: 10/23/2017] [Indexed: 11/17/2022]
Abstract
An atomic-detail model of the Marburg virus glycoprotein in complex with a neutralizing human monoclonal antibody designated MR78 was constructed using Phenix.Rosetta starting from a 3.6Å crystallographic density map. The Asp at T6 in the HCDR3's bulged torso cannot form the canonical salt bridge as position T2 lacks an Arg or Lys residue. It instead engages in a hydrogen bond interaction with a Tyr contributed by the HCDR1 loop. This inter-CDR loop interaction stabilizes the bulged conformation needed for binding to the viral glycoprotein: a Tyr to Phe mutant displays a binding affinity reduced by a factor of at least 10. We found that 5% of a database of 465 million human antibody sequences has the same residues at T2 and T6 positions in HCDR3 and Tyr in HCDR1 that could potentially form this Asp-Tyr interaction, and that this interaction might contribute to a non-canonical bulged torso conformation.
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Affiliation(s)
- Amandeep K Sangha
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Jinhui Dong
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lauren Williamson
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Takao Hashiguchi
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Erica Ollmann Saphire
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA.
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29
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Marks C, Deane C. Antibody H3 Structure Prediction. Comput Struct Biotechnol J 2017; 15:222-231. [PMID: 28228926 PMCID: PMC5312500 DOI: 10.1016/j.csbj.2017.01.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/24/2017] [Accepted: 01/27/2017] [Indexed: 01/20/2023] Open
Abstract
Antibodies are proteins of the immune system that are able to bind to a huge variety of different substances, making them attractive candidates for therapeutic applications. Antibody structures have the potential to be useful during drug development, allowing the implementation of rational design procedures. The most challenging part of the antibody structure to experimentally determine or model is the H3 loop, which in addition is often the most important region in an antibody's binding site. This review summarises the approaches used so far in the pursuit of accurate computational H3 structure prediction.
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Affiliation(s)
- C. Marks
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford OX1 3LB, United Kingdom
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30
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Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL, Gray JJ. Modeling and docking of antibody structures with Rosetta. Nat Protoc 2017; 12:401-416. [PMID: 28125104 DOI: 10.1038/nprot.2016.180] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe Rosetta-based computational protocols for predicting the 3D structure of an antibody from sequence (RosettaAntibody) and then docking the antibody to protein antigens (SnugDock). Antibody modeling leverages canonical loop conformations to graft large segments from experimentally determined structures, as well as offering (i) energetic calculations to minimize loops, (ii) docking methodology to refine the VL-VH relative orientation and (iii) de novo prediction of the elusive complementarity determining region (CDR) H3 loop. To alleviate model uncertainty, antibody-antigen docking resamples CDR loop conformations and can use multiple models to represent an ensemble of conformations for the antibody, the antigen or both. These protocols can be run fully automated via the ROSIE web server (http://rosie.rosettacommons.org/) or manually on a computer with user control of individual steps. For best results, the protocol requires roughly 1,000 CPU-hours for antibody modeling and 250 CPU-hours for antibody-antigen docking. Tasks can be completed in under a day by using public supercomputers.
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Affiliation(s)
- Brian D Weitzner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeliazko R Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nicholas Marze
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Daisuke Kuroda
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Analytical and Physical Chemistry, Showa University School of Pharmacy, Tokyo, Japan
| | - Rahel Frick
- Centre for Immune Regulation, Department of Biosciences, University of Oslo, Oslo, Norway.,Centre for Immune Regulation, Department of Immunology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Jared Adolf-Bryfogle
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA.,Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Naireeta Biswas
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Roland L Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA.,Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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31
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Nishigami H, Kamiya N, Nakamura H. Revisiting antibody modeling assessment for CDR-H3 loop. Protein Eng Des Sel 2016; 29:477-484. [PMID: 27515703 PMCID: PMC5081041 DOI: 10.1093/protein/gzw028] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 06/14/2016] [Accepted: 06/14/2016] [Indexed: 02/05/2023] Open
Abstract
The antigen-binding site of antibodies, also known as complementarity-determining region (CDR), has hypervariable sequence properties. In particular, the third CDR loop of the heavy chain, CDR-H3, has such variability in its sequence, length, and conformation that ordinary modeling techniques cannot build a high-quality structure. At Stage 2 of the Second Antibody Modeling Assessment (AMA-II) held in 2013, the model structures of the CDR-H3 loops were submitted by the seven modelers and were critically assessed. After our participation in AMA-II, we rebuilt one of the long CDR-H3 loops with 13 residues (A52 antibody) by a more precise method, using enhanced conformational sampling with the explicit water model, as compared to our previous method employed at AMA-II. The current stable models obtained from the free energy landscape at 300 K include structures similar to the X-ray crystal structures. Those models were not built in our previous work at AMA-II. The current free energy landscape suggested that the CDR-H3 loop structures in the crystal are not stable in solution, but they are stabilized by the crystal packing effect.
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Affiliation(s)
- Hiroshi Nishigami
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871, Japan
- Present address: Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | - Narutoshi Kamiya
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871, Japan
- Advanced Institute for Computational Science, RIKEN, QBiC Building B, 6-2-4, Furuedai, Suita, Osaka 565-0874, Japan
- Present address: Graduate School of Simulation Studies, University of Hyogo, 7-1-28, Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871, Japan
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32
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Shimba N, Kamiya N, Nakamura H. Model Building of Antibody–Antigen Complex Structures Using GBSA Scores. J Chem Inf Model 2016; 56:2005-2012. [DOI: 10.1021/acs.jcim.6b00066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Noriko Shimba
- Device
Research Laboratory, Advanced Research Division, Panasonic Corporation, 3-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan
| | - Narutoshi Kamiya
- Advanced
Institute for Computational Science, RIKEN, QBiC Building B, 6-2-4 Furuedai, Suita, Osaka 565-0874, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruki Nakamura
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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33
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Leem J, Dunbar J, Georges G, Shi J, Deane CM. ABodyBuilder: Automated antibody structure prediction with data-driven accuracy estimation. MAbs 2016; 8:1259-1268. [PMID: 27392298 PMCID: PMC5058620 DOI: 10.1080/19420862.2016.1205773] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Computational modeling of antibody structures plays a critical role in therapeutic antibody design. Several antibody modeling pipelines exist, but no freely available methods currently model nanobodies, provide estimates of expected model accuracy, or highlight potential issues with the antibody's experimental development. Here, we describe our automated antibody modeling pipeline, ABodyBuilder, designed to overcome these issues. The algorithm itself follows the standard 4 steps of template selection, orientation prediction, complementarity-determining region (CDR) loop modeling, and side chain prediction. ABodyBuilder then annotates the 'confidence' of the model as a probability that a component of the antibody (e.g., CDRL3 loop) will be modeled within a root-mean square deviation threshold. It also flags structural motifs on the model that are known to cause issues during in vitro development. ABodyBuilder was tested on 4 separate datasets, including the 11 antibodies from the Antibody Modeling Assessment-II competition. ABodyBuilder builds models that are of similar quality to other methodologies, with sub-Angstrom predictions for the 'canonical' CDR loops. Its ability to model nanobodies, and rapidly generate models (∼30 seconds per model) widens its potential usage. ABodyBuilder can also help users in decision-making for the development of novel antibodies because it provides model confidence and potential sequence liabilities. ABodyBuilder is freely available at http://opig.stats.ox.ac.uk/webapps/abodybuilder .
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Affiliation(s)
- Jinwoo Leem
- a Department of Statistics , University of Oxford , Oxford , UK
| | - James Dunbar
- a Department of Statistics , University of Oxford , Oxford , UK.,b Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg , Germany
| | - Guy Georges
- b Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich , Penzberg , Germany
| | - Jiye Shi
- c Informatics Department , UCB Pharma , Slough , UK
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34
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Yang HT, Yang H, Chiang JH, Wang SJ. Translating genomic sequences into antibody efficacy and safety against influenza toward clinical trial outcomes: a case study. Drug Discov Today 2016; 21:1664-1671. [PMID: 27319290 DOI: 10.1016/j.drudis.2016.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/26/2016] [Accepted: 06/07/2016] [Indexed: 11/18/2022]
Abstract
Antibodies (Abs) are regarded as a newly emerging form of therapeutics that can provide passive protection against influenza. Although the application of genomics in clinics has increased dramatically, the number of therapeutics available for the treatment of many diseases remains insufficient. To translate genomics into medicines, we established a computational workflow to reconstruct 3D structures of hemagglutinin [HA, antigen (Ag)] and Ab for modeling Ab-HA interactions, based on their protein sequences. This platform was capable of testing the validity of bioinformatics predictions against viral neutralization titers for four Abs: CH65, CR8020, C05, and 5J8. By considering off-target effects, CR8020, the only successful candidate in clinical trials, was prospectively identified. Our approach could facilitate the discovery of Ab drugs against infectious diseases.
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Affiliation(s)
- Hsih-Te Yang
- Institute of Medical Informatics, Department of Computer Science and Information Engineering, National Cheng Kung University, Taiwan; Institute of Oral Medicine, National Cheng Kung University College of Medicine, Taiwan.
| | - Hong Yang
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Jung-Hsien Chiang
- Institute of Medical Informatics, Department of Computer Science and Information Engineering, National Cheng Kung University, Taiwan
| | - Shih-Jon Wang
- Department of Bioscience Technology, Chang Jung Christian University, Taiwan
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35
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Dunbar J, Krawczyk K, Leem J, Marks C, Nowak J, Regep C, Georges G, Kelm S, Popovic B, Deane CM. SAbPred: a structure-based antibody prediction server. Nucleic Acids Res 2016; 44:W474-8. [PMID: 27131379 PMCID: PMC4987913 DOI: 10.1093/nar/gkw361] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/24/2016] [Indexed: 01/17/2023] Open
Abstract
SAbPred is a server that makes predictions of the properties of antibodies focusing on their structures. Antibody informatics tools can help improve our understanding of immune responses to disease and aid in the design and engineering of therapeutic molecules. SAbPred is a single platform containing multiple applications which can: number and align sequences; automatically generate antibody variable fragment homology models; annotate such models with estimated accuracy alongside sequence and structural properties including potential developability issues; predict paratope residues; and predict epitope patches on protein antigens. The server is available at http://opig.stats.ox.ac.uk/webapps/sabpred.
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Affiliation(s)
- James Dunbar
- Department of Statistics, Oxford Protein Informatics Group, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, 82377, Penzberg, Germany
| | - Konrad Krawczyk
- Department of Statistics, Oxford Protein Informatics Group, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Jinwoo Leem
- Department of Statistics, Oxford Protein Informatics Group, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Claire Marks
- Department of Statistics, Oxford Protein Informatics Group, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Jaroslaw Nowak
- Department of Statistics, Oxford Protein Informatics Group, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Cristian Regep
- Department of Statistics, Oxford Protein Informatics Group, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Guy Georges
- Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, 82377, Penzberg, Germany
| | - Sebastian Kelm
- Informatics Department, UCB Pharma, 208 Bath Road, Slough, SL1 3WE, UK
| | - Bojana Popovic
- Antibody Discovery and Protein Engineering, Medimmune Ltd, Granta Park, Cambridge, CB21 6GH, UK
| | - Charlotte M Deane
- Department of Statistics, Oxford Protein Informatics Group, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
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Klausen MS, Anderson MV, Jespersen MC, Nielsen M, Marcatili P. LYRA, a webserver for lymphocyte receptor structural modeling. Nucleic Acids Res 2015; 43:W349-55. [PMID: 26007650 PMCID: PMC4489227 DOI: 10.1093/nar/gkv535] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/09/2015] [Indexed: 01/22/2023] Open
Abstract
The accurate structural modeling of B- and T-cell receptors is fundamental to gain a detailed insight in the mechanisms underlying immunity and in developing new drugs and therapies. The LYRA (LYmphocyte Receptor Automated modeling) web server (http://www.cbs.dtu.dk/services/LYRA/) implements a complete and automated method for building of B- and T-cell receptor structural models starting from their amino acid sequence alone. The webserver is freely available and easy to use for non-specialists. Upon submission, LYRA automatically generates alignments using ad hoc profiles, predicts the structural class of each hypervariable loop, selects the best templates in an automatic fashion, and provides within minutes a complete 3D model that can be downloaded or inspected online. Experienced users can manually select or exclude template structures according to case specific information. LYRA is based on the canonical structure method, that in the last 30 years has been successfully used to generate antibody models of high accuracy, and in our benchmarks this approach proves to achieve similarly good results on TCR modeling, with a benchmarked average RMSD accuracy of 1.29 and 1.48 Å for B- and T-cell receptors, respectively. To the best of our knowledge, LYRA is the first automated server for the prediction of TCR structure.
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Affiliation(s)
- Michael Schantz Klausen
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mads Valdemar Anderson
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Morten Nielsen
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Paolo Marcatili
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
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Abstract
Antibodies recognize their cognate antigens in a precise and effective way. In order to do so, they target regions of the antigenic molecules that have specific features such as large exposed areas, presence of charged or polar atoms, specific secondary structure elements, and lack of similarity to self-proteins. Given the sequence or the structure of a protein of interest, several methods exploit such features to predict the residues that are more likely to be recognized by an immunoglobulin. Here, we present two methods (BepiPred and DiscoTope) to predict linear and discontinuous antibody epitopes from the sequence and/or the three-dimensional structure of a target protein.
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Affiliation(s)
- Morten Nielsen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Paolo Marcatili
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark.
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