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Cheng J, Liang T, Xie XQ, Feng Z, Meng L. A new era of antibody discovery: an in-depth review of AI-driven approaches. Drug Discov Today 2024; 29:103984. [PMID: 38642702 DOI: 10.1016/j.drudis.2024.103984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 04/02/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
Given their high affinity and specificity for a range of macromolecules, antibodies are widely used in the treatment of autoimmune diseases, cancers, inflammatory diseases, and Alzheimer's disease (AD). Traditional experimental methods are time-consuming, expensive, and labor-intensive. Recent advances in artificial intelligence (AI) technologies provide complementary methods that can reduce the time and costs required for antibody design by minimizing failures and increasing the success rate of experimental tests. In this review, we scrutinize the plethora of AI-driven methodologies that have been deployed over the past 4 years for modeling antibody structures, predicting antibody-antigen interactions, optimizing antibody affinity, and generating novel antibody candidates. We also briefly address the challenges faced in integrating AI-based models with traditional antibody discovery pipelines and highlight the potential future directions in this burgeoning field.
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Affiliation(s)
- Jin Cheng
- School of Pharmacy, Jiangsu Vocational College of Medicine, Yancheng, 224005, China
| | - Tianjian Liang
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Li Meng
- School of Pharmacy, Jiangsu Vocational College of Medicine, Yancheng, 224005, China.
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2
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Yang YR, Han J, Perrett HR, Richey ST, Rodriguez AJ, Jackson AM, Gillespie RA, O'Connell S, Raab JE, Cominsky LY, Chopde A, Kanekiyo M, Houser KV, Chen GL, McDermott AB, Andrews SF, Ward AB. Immune memory shapes human polyclonal antibody responses to H2N2 vaccination. Cell Rep 2024; 43:114171. [PMID: 38717904 DOI: 10.1016/j.celrep.2024.114171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 03/25/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase 1 clinical trial investigating a ferritin nanoparticle vaccine displaying H2 hemagglutinin (HA) in H2-naive and H2-exposed adults enabled us to perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited. We temporally map the epitopes targeted by serum antibodies after vaccine prime and boost, revealing that previous H2 exposure results in higher responses to the variable HA head domain. In contrast, initial responses in H2-naive participants are dominated by antibodies targeting conserved epitopes. We use cryoelectron microscopy and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the HA head, including the receptor-binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses post-vaccination.
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Affiliation(s)
- Yuhe R Yang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Chinese Academy of Sciences Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailee R Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alesandra J Rodriguez
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Abigail M Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Sarah O'Connell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Julie E Raab
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Lauren Y Cominsky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Ankita Chopde
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Katherine V Houser
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Grace L Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA.
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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3
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Wossnig L, Furtmann N, Buchanan A, Kumar S, Greiff V. Best practices for machine learning in antibody discovery and development. Drug Discov Today 2024; 29:104025. [PMID: 38762089 DOI: 10.1016/j.drudis.2024.104025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/25/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
In the past 40 years, therapeutic antibody discovery and development have advanced considerably, with machine learning (ML) offering a promising way to speed up the process by reducing costs and the number of experiments required. Recent progress in ML-guided antibody design and development (D&D) has been hindered by the diversity of data sets and evaluation methods, which makes it difficult to conduct comparisons and assess utility. Establishing standards and guidelines will be crucial for the wider adoption of ML and the advancement of the field. This perspective critically reviews current practices, highlights common pitfalls and proposes method development and evaluation guidelines for various ML-based techniques in therapeutic antibody D&D. Addressing challenges across the ML process, best practices are recommended for each stage to enhance reproducibility and progress.
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Affiliation(s)
- Leonard Wossnig
- LabGenius Ltd, The Biscuit Factory, 100 Drummond Road, London SE16 4DG, UK; Department of Computer Science, University College London, 66-72 Gower St, London WC1E 6EA, UK.
| | - Norbert Furtmann
- R&D Large Molecules Research Platform, Sanofi Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Andrew Buchanan
- Biologics Engineering, R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Sandeep Kumar
- Computational Protein Design and Modeling Group, Computational Science, Moderna Therapeutics, 200 Technology Square, Cambridge, MA 02139, USA
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
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4
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Li D, Pucci F, Rooman M. Prediction of Paratope-Epitope Pairs Using Convolutional Neural Networks. Int J Mol Sci 2024; 25:5434. [PMID: 38791470 PMCID: PMC11121317 DOI: 10.3390/ijms25105434] [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: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Antibodies play a central role in the adaptive immune response of vertebrates through the specific recognition of exogenous or endogenous antigens. The rational design of antibodies has a wide range of biotechnological and medical applications, such as in disease diagnosis and treatment. However, there are currently no reliable methods for predicting the antibodies that recognize a specific antigen region (or epitope) and, conversely, epitopes that recognize the binding region of a given antibody (or paratope). To fill this gap, we developed ImaPEp, a machine learning-based tool for predicting the binding probability of paratope-epitope pairs, where the epitope and paratope patches were simplified into interacting two-dimensional patches, which were colored according to the values of selected features, and pixelated. The specific recognition of an epitope image by a paratope image was achieved by using a convolutional neural network-based model, which was trained on a set of two-dimensional paratope-epitope images derived from experimental structures of antibody-antigen complexes. Our method achieves good performances in terms of cross-validation with a balanced accuracy of 0.8. Finally, we showcase examples of application of ImaPep, including extensive screening of large libraries to identify paratope candidates that bind to a selected epitope, and rescoring and refining antibody-antigen docking poses.
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Affiliation(s)
- Dong Li
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (D.L.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (D.L.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (D.L.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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5
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Lei X, Li P, Abd El-Aty AM, Zhao J, Xu L, Gao S, Li J, Zhao Y, She Y, Jin F, Wang J, Zheng L, Hammock BD, Jin M. Generation of a highly specific recombinant full-length antibody for detecting ethirimol in fruit and environmental water. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134067. [PMID: 38513441 PMCID: PMC11062638 DOI: 10.1016/j.jhazmat.2024.134067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/03/2024] [Accepted: 03/16/2024] [Indexed: 03/23/2024]
Abstract
High-performance antibodies are core reagents for highly sensitive immunoassays. Herein, based on a novel hapten, a hybridoma secreting the high-affinity anti-ethirimol monoclonal antibody (mAb-14G5F6) was isolated with an IC50 value of 1.35 μg/L and cross-reactivity below 0.20% for 13 analogs. To further address the challenge of hybridoma preservation and antibody immortalization, a recombinant full-length antibody (rAb-14G5F6) was expressed using the HEK293(F) expression system based on the mAb-14G5F6 gene. The affinity, specificity, and tolerance of rAb-14G5F6, as characterized by indirect competitive enzyme-linked immunosorbent assay and noncompetitive surface plasmon resonance, exhibited high concordance with those of mAb-14G5F6. Further immunoassays based on rAb-14G5F6 were developed for irrigation water and strawberry fruit with limits of detection of 0.0066 and 0.036 mg/kg, respectively, recoveries of 80100%, and coefficients of variation below 10%. Furthermore, homology simulation and molecular docking revealed that GLU(L40), GLY(L107), GLY(H108), and ASP(H114) play important roles in forming hydrogen bonds and pi-anion ionic bonds between rAb-14G5F6 and ethirimol, resulting in the high specificity and affinity of rAb-14G5F6 for ethirimol, with a KD of 5.71 × 10-10 mol/L. Overall, a rAb specific for ethirimol was expressed successfully in this study, laying the groundwork for rAb-based immunoassays for monitoring fungicide residues in agricultural products and the environment.
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Affiliation(s)
- Xingmei Lei
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Peipei Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt; Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum 25240, Turkey
| | - Jing Zhao
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lingyuan Xu
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Song Gao
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jia Li
- Jinhua Miaozhidizhi Agricultural Technology Co., Ltd., Jinhua, Zhejiang 321000, China
| | - Yun Zhao
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongxin She
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fen Jin
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jing Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lufei Zheng
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bruce D Hammock
- Department of Entomology & Nematology and the UC Davis Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
| | - Maojun Jin
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Research Center of Quality Standards for Agro-Products, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
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6
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Besli N, Bulut Hİ, Onaran İ, Carmena-Bargueño M, Pérez-Sánchez H. Comparative assessment of different anti-CD147/Basigin 2 antibodies as a potential therapeutic anticancer target by molecular modeling and dynamic simulation. Mol Divers 2024:10.1007/s11030-024-10832-w. [PMID: 38587771 DOI: 10.1007/s11030-024-10832-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024]
Abstract
Cluster of differentiation 147 (CD147) is an attractive target for anticancer therapy since it is pivotal in developing and progressing several of malignant tumors in the context of its high expression levels. Although anti-CD147 antibodies by different laboratories are designed for the Ig-like domains of CD147, there is a demand to provide priority among these anti-CD147 antibodies for developing of therapeutic anti-CD147 antibody before experimental validations. This study uses molecular docking and dynamic simulation techniques to compare the binding modes and affinities of nine antibody models against the Ig-like domains of CD147. After obtaining the model antibodies by homology modeling via Robetta, we predicted the CDRs of nine antibodies and the epitopes of CD147 to reach more accurate results for antigen affinity in molecular docking. Next, from HADDOCK 2.4., we meticulously handpicked the most superior model clusters (Z-Score: - 2.5 to - 1.2) and identified that meplazumab had higher affinities according to the success rate as the percentage of a scoring scale. We achieved stable simulations of CD147-antibody interaction. Our outcomes hold hypothetical importance for further experimental cancer research on the design and development of the relevant model antibodies.
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Affiliation(s)
- Nail Besli
- Department of Medical Biology, Hamidiye School of Medicine, University of Health Sciences, Istanbul, Turkey
| | - Halil İbrahim Bulut
- Faculty of Medicine, Medical Program, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - İlhan Onaran
- Department of Medical Biology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Miguel Carmena-Bargueño
- Computer Engineering Department, Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), UCAM Universidad Católica de Murcia, Guadalupe, Spain
| | - Horacio Pérez-Sánchez
- Computer Engineering Department, Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), UCAM Universidad Católica de Murcia, Guadalupe, Spain.
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7
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Paul R, Kasahara K, Sasaki J, Pérez JF, Matsunaga R, Hashiguchi T, Kuroda D, Tsumoto K. Unveiling the affinity-stability relationship in anti-measles virus antibodies: a computational approach for hotspots prediction. Front Mol Biosci 2024; 10:1302737. [PMID: 38495738 PMCID: PMC10941800 DOI: 10.3389/fmolb.2023.1302737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/11/2023] [Indexed: 03/19/2024] Open
Abstract
Recent years have seen an uptick in the use of computational applications in antibody engineering. These tools have enhanced our ability to predict interactions with antigens and immunogenicity, facilitate humanization, and serve other critical functions. However, several studies highlight the concern of potential trade-offs between antibody affinity and stability in antibody engineering. In this study, we analyzed anti-measles virus antibodies as a case study, to examine the relationship between binding affinity and stability, upon identifying the binding hotspots. We leverage in silico tools like Rosetta and FoldX, along with molecular dynamics (MD) simulations, offering a cost-effective alternative to traditional in vitro mutagenesis. We introduced a pattern in identifying key residues in pairs, shedding light on hotspots identification. Experimental physicochemical analysis validated the predicted key residues by confirming significant decrease in binding affinity for the high-affinity antibodies to measles virus hemagglutinin. Through the nature of the identified pairs, which represented the relative hydropathy of amino acid side chain, a connection was proposed between affinity and stability. The findings of the study enhance our understanding of the interactions between antibody and measles virus hemagglutinin. Moreover, the implications of the observed correlation between binding affinity and stability extend beyond the field of anti-measles virus antibodies, thereby opening doors for advancements in antibody research.
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Affiliation(s)
- Rimpa Paul
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
- Research Center of Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keisuke Kasahara
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Jiei Sasaki
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Jorge Fernández Pérez
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Ryo Matsunaga
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Takao Hashiguchi
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
- Research Center of Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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8
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Chiyyeadu A, Asgedom G, Bruhn M, Rocha C, Schlegel TU, Neumann T, Galla M, Vollmer Barbosa P, Hoffmann M, Ehrhardt K, Ha TC, Morgan M, Schoeder CT, Pöhlmann S, Kalinke U, Schambach A. A tetravalent bispecific antibody outperforms the combination of its parental antibodies and neutralizes diverse SARS-CoV-2 variants. Clin Immunol 2024; 260:109902. [PMID: 38218210 DOI: 10.1016/j.clim.2024.109902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The devastating impact of COVID-19 on global health shows the need to increase our pandemic preparedness. Recombinant therapeutic antibodies were successfully used to treat and protect at-risk patients from COVID-19. However, the currently circulating Omicron subvariants of SARS-CoV-2 are largely resistant to therapeutic antibodies, and novel approaches to generate broadly neutralizing antibodies are urgently needed. Here, we describe a tetravalent bispecific antibody, A7A9 TVB, which actively neutralized many SARS-CoV-2 variants of concern, including early Omicron subvariants. Interestingly, A7A9 TVB neutralized more variants at lower concentration as compared to the combination of its parental monoclonal antibodies, A7K and A9L. A7A9 also reduced the viral load of authentic Omicron BA.1 virus in infected pseudostratified primary human nasal epithelial cells. Overall, A7A9 displayed the characteristics of a potent broadly neutralizing antibody, which may be suitable for prophylactic and therapeutic applications in the clinics, thus highlighting the usefulness of an effective antibody-designing approach.
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Affiliation(s)
- Abhishek Chiyyeadu
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Girmay Asgedom
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany
| | - Cheila Rocha
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Tom U Schlegel
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Thomas Neumann
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Philippe Vollmer Barbosa
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Markus Hoffmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Katrin Ehrhardt
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Teng-Cheong Ha
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Clara T Schoeder
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Stefan Pöhlmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, United States of America.
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9
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Guo D, De Sciscio ML, Chi-Fung Ng J, Fraternali F. Modelling the assembly and flexibility of antibody structures. Curr Opin Struct Biol 2024; 84:102757. [PMID: 38118364 DOI: 10.1016/j.sbi.2023.102757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023]
Abstract
Antibodies are large protein assemblies capable of both specifically recognising antigens and engaging with other proteins and receptors to coordinate immune action. Traditionally, structural studies have been dedicated to antibody variable regions, but efforts to determine and model full-length antibody structures are emerging. Here we review the current knowledge on modelling the structures of antibody assemblies, focusing on their conformational flexibility and the challenge this poses to obtaining and evaluating structural models. Integrative modelling approaches, combining experiments (cryo-electron microscopy, mass spectrometry, etc.) and computational methods (molecular dynamics simulations, deep-learning based approaches, etc.), hold the promise to map the complex conformational landscape of full-length antibody structures.
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Affiliation(s)
- Dongjun Guo
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom; Randall Centre for Cell & Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, United Kingdom
| | - Maria Laura De Sciscio
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom; Department of Chemistry, Sapienza University of Rome, P.le A. Moro 5, Rome, 00185, Italy
| | - Joseph Chi-Fung Ng
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Franca Fraternali
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom.
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10
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Gomari MM, Arab SS, Balalaie S, Ramezanpour S, Hosseini A, Dokholyan NV, Tarighi P. Rational peptide design for targeting cancer cell invasion. Proteins 2024; 92:76-95. [PMID: 37646459 DOI: 10.1002/prot.26580] [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: 06/01/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023]
Abstract
Cell invasion is an important process in cancer progression and recurrence. Invasion and implantation of cancer cells from their original place to other tissues, by disabling vital organs, challenges the treatment of cancer patients. Given the importance of the matter, many molecular treatments have been developed to inhibit cancer cell invasion. Because of their low production cost and ease of production, peptides are valuable therapeutic molecules for inhibiting cancer cell invasion. In recent years, advances in the field of computational biology have facilitated the design of anti-cancer peptides. In our investigation, using computational biology approaches such as evolutionary analysis, residue scanning, protein-peptide interaction analysis, molecular dynamics, and free energy analysis, our team designed a peptide library with about 100 000 candidates based on A6 (acetyl-KPSSPPEE-amino) sequence which is an anti-invasion peptide. During computational studies, two of the designed peptides that give the highest scores and showed the greatest sequence similarity to A6 were entered into the experimental analysis workflow for further analysis. In experimental analysis steps, the anti-metastatic potency and other therapeutic effects of designed peptides were evaluated using MTT assay, RT-qPCR, zymography analysis, and invasion assay. Our study disclosed that the IK1 (acetyl-RPSFPPEE-amino) peptide, like A6, has great potency to inhibit the invasion of cancer cells.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saeed Balalaie
- Peptide Chemistry Research Institute, K. N. Toosi University of Technology, Tehran, Iran
| | - Sorour Ramezanpour
- Department of Chemistry, K. N. Toosi University of Technology, Tehran, Iran
| | - Arshad Hosseini
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Parastoo Tarighi
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
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11
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Zhang G, Su Z, Zhang T, Wu Y. Machine-learning-based Structural Analysis of Interactions between Antibodies and Antigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570397. [PMID: 38106177 PMCID: PMC10723427 DOI: 10.1101/2023.12.06.570397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Computational analysis of paratope-epitope interactions between antibodies and their corresponding antigens can facilitate our understanding of the molecular mechanism underlying humoral immunity and boost the design of new therapeutics for many diseases. The recent breakthrough in artificial intelligence has made it possible to predict protein-protein interactions and model their structures. Unfortunately, detecting antigen-binding sites associated with a specific antibody is still a challenging problem. To tackle this challenge, we implemented a deep learning model to characterize interaction patterns between antibodies and their corresponding antigens. With high accuracy, our model can distinguish between antibody-antigen complexes and other types of protein-protein complexes. More intriguingly, we can identify antigens from other common protein binding regions with an accuracy of higher than 70% even if we only have the epitope information. This indicates that antigens have distinct features on their surface that antibodies can recognize. Additionally, our model was unable to predict the partnerships between antibodies and their particular antigens. This result suggests that one antigen may be targeted by more than one antibody and that antibodies may bind to previously unidentified proteins. Taken together, our results support the precision of antibody-antigen interactions while also suggesting positive future progress in the prediction of specific pairing.
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Affiliation(s)
- Grace Zhang
- Staples High School, 70 North Avenue, Westport, CT 06880
| | - Zhaoqian Su
- Data Science Institute, Vanderbilt University, 1001 19th Ave S, Nashville, TN, 37212
| | - Tom Zhang
- California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
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12
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Jeon MY, Han JE, Lee DG, Cho YL, Jang JH, Lee J, Park JG, Kwon DH, Park SY, Kim W, Lee K, Kim JH, Lee NK. Novel sandwich immunoassay detects a shrimp AHPND-causing binary PirAB Vp toxin produced by Vibrio parahaemolyticus. Front Cell Infect Microbiol 2023; 13:1294801. [PMID: 38089817 PMCID: PMC10711049 DOI: 10.3389/fcimb.2023.1294801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction The binary PirA/PirB toxin expressed by Vibrio parahaemolyticus (PirABVp) is a virulent complex that causes acute hepatopancreatic necrosis disease (AHPND) in shrimps, affecting the global shrimp farming industry. AHPND is currently diagnosed by detecting pirA and pirB genes by PCR; however, several V. parahaemolyticus strains do not produce the two toxins as proteins. Thus, an immunoassay using antibodies may be the most effective tool for detecting toxin molecules. In this study, we report a sandwich ELISA-based immunoassay for the detection of PirABVp. Methods We utilized a single-chain variable fragment (scFv) antibody library to select scFvs against the PirA or PirB subunits. Phage display panning rounds were conducted to screen and identify scFv antibodies directed against each recombinant toxin subunit. Selected scFvs were converted into IgGs to develop a sandwich immunoassay to detect recombinant and bacterial PirABVp. Results Antibodies produced as IgG forms showed sub-nanomolar to nanomolar affinities (KD), and a pair of anti-PirA antibody as a capture and anti-PirB antibody as a detector showed a limit of detection of 201.7 ng/mL for recombinant PirABVp. The developed immunoassay detected PirABVp in the protein lysates of AHPND-causing V. parahaemolyticus (VpAHPND) and showed a significant detectability in moribund or dead shrimp infected with a VpAHPND virulent strain compared to that in non-infected shrimp. Discussion These results indicate that the developed immunoassay is a reliable method for diagnosing AHPND by detecting PirABVp at the protein level and could be further utilized to accurately determine the virulence of extant or newly identified VpAHPND in the global shrimp culture industry.
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Affiliation(s)
- Min-Young Jeon
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Jee Eun Han
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Dong Gwang Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Young-Lai Cho
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ju-Hong Jang
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Jangwook Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Jong-Gil Park
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Do Hyung Kwon
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Seon Young Park
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon, Republic of Korea
| | - Wantae Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Kyunglee Lee
- Cetacean Research Institute, National Institute of Fisheries Science, Ulsan, Republic of Korea
| | - Ji Hyung Kim
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam, Republic of Korea
| | - Nam-Kyung Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, Republic of Korea
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13
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Wu H, Liu C, Yuan Q, Qiao Y, Ding Y, Duan L, Li W, Zhang M, Zhang X, Jiang Y, Lu J, Dong Z, Wang T, Liu K, Zhao J. A novel Fc-enhanced humanized monoclonal antibody targeting B7-H3 suppresses the growth of ESCC. Oncoimmunology 2023; 12:2282250. [PMID: 38126034 PMCID: PMC10732625 DOI: 10.1080/2162402x.2023.2282250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 11/07/2023] [Indexed: 12/23/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a prevalent malignant tumor of the digestive tract with a low 5-year survival rate due to the lack of effective treatment methods. Although therapeutic monoclonal antibodies (mAbs) now play an important role in cancer therapy, effective targeted mAbs are still lacking for ESCC. B7-H3 is highly expressed in a variety of tumors and has emerged as a promising therapeutic target. Several mAbs against B7-H3 have advanced to clinical trials, but their development has not yet been pursued for ESCC. Here, we developed a humanized and Fc-engineered anti-B7H3 mAb 24F-Hu-mut2 and systematically evaluated its anti-tumor activity in vitro and in vivo. The 24F-Hu-mut2 was humanized and modified in Fc fragment to obtain stronger antibody-dependent cell-mediated cytotoxicity(ADCC) activity and nanomolar affinity. Furthermore, both of ESCC cell-derived xenograft (CDX) and patient-derived xenograft (PDX) mice models indicated that 24F-Hu-mut2 displayed potent in vivo anti-tumor activity. In addition, a computational docking model showed that the mAb bound to IgC1 and IgC2 domain of B7-H3, which is closer to the cell membrane. Consistently, our ELISA results verified the binding of 24F-Hu-WT and IgC1 and IgC2. Our results indicate that 24F-Hu-mut2 has significant anti-ESCC activity both in vitro and in vivo, and this monoclonal antibody may be a promising antibody against ESCC and other B7-H3 overexpressing tumors.
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Affiliation(s)
- Huiting Wu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Provincial Cooperative Innovation Center for Cancer Chemo- prevention, Zhengzhou, China
| | - Chang Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Provincial Cooperative Innovation Center for Cancer Chemo- prevention, Zhengzhou, China
| | - Qiang Yuan
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Provincial Cooperative Innovation Center for Cancer Chemo- prevention, Zhengzhou, China
| | - Yan Qiao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Provincial Cooperative Innovation Center for Cancer Chemo- prevention, Zhengzhou, China
| | - Yongwei Ding
- Department of Pathophysiology, Shaoxing People Hospital, Shaoxing, China
| | - Lina Duan
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Provincial Cooperative Innovation Center for Cancer Chemo- prevention, Zhengzhou, China
| | - Wenjing Li
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Provincial Cooperative Innovation Center for Cancer Chemo- prevention, Zhengzhou, China
| | - Mengjia Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Provincial Cooperative Innovation Center for Cancer Chemo- prevention, Zhengzhou, China
| | - Xuhua Zhang
- The Affiliated Cancer Hospital, Zhengzhou University, Zhengzhou, China
| | - Yanan Jiang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Provincial Cooperative Innovation Center for Cancer Chemo- prevention, Zhengzhou, China
| | - Jing Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Provincial Cooperative Innovation Center for Cancer Chemo- prevention, Zhengzhou, China
| | - Ziming Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Provincial Cooperative Innovation Center for Cancer Chemo- prevention, Zhengzhou, China
| | - Tao Wang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
- The College of Nursing and Health, Zhengzhou University, Zhengzhou, China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Provincial Cooperative Innovation Center for Cancer Chemo- prevention, Zhengzhou, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, China
| | - Jimin Zhao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Provincial Cooperative Innovation Center for Cancer Chemo- prevention, Zhengzhou, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, China
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14
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Lecerf M, Lacombe RV, Dimitrov JD. Polyreactivity of antibodies from different B-cell subpopulations is determined by distinct sequence patterns of variable region. Front Immunol 2023; 14:1266668. [PMID: 38077343 PMCID: PMC10710144 DOI: 10.3389/fimmu.2023.1266668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023] Open
Abstract
An antibody molecule that can bind to multiple distinct antigens is defined as polyreactive. In the present study, we performed statistical analyses to assess sequence correlates of polyreactivity of >600 antibodies cloned from different B-cell types of healthy humans. The data revealed several sequence patterns of variable regions of heavy and light immunoglobulin chains that determine polyreactivity. The most prominent identified patterns were increased number of basic amino acid residues, reduced frequency of acidic residues, increased number of aromatic and hydrophobic residues, and longer length of CDR L1. Importantly, our study revealed that antibodies isolated from different B-cell populations used distinct sequence patterns (or combinations of them) for polyreactive antigen binding. Furthermore, we combined the data from sequence analyses with molecular modeling of selected polyreactive antibodies and demonstrated that human antibodies can use multiple pathways for achieving antigen-binding promiscuity. These data reconcile some contradictions in the literature regarding the determinants of antibody polyreactivity. Moreover, our study demonstrates that the mechanism of polyreactivity of antibodies evolves during immune response and might be tailored to specific functional properties of different B-cell compartments. Finally, these data can be of use for efforts in the development and engineering of therapeutic antibodies.
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Affiliation(s)
| | | | - Jordan D. Dimitrov
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
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15
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Sekar TV, Elghonaimy EA, Swancutt KL, Diegeler S, Gonzalez I, Hamilton C, Leung PQ, Meiler J, Martina CE, Whitney M, Aguilera TA. Simultaneous selection of nanobodies for accessible epitopes on immune cells in the tumor microenvironment. Nat Commun 2023; 14:7473. [PMID: 37978291 PMCID: PMC10656474 DOI: 10.1038/s41467-023-43038-z] [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: 02/16/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
In the rapidly advancing field of synthetic biology, there exists a critical need for technology to discover targeting moieties for therapeutic biologics. Here we present INSPIRE-seq, an approach that utilizes a nanobody library and next-generation sequencing to identify nanobodies selected for complex environments. INSPIRE-seq enables the parallel enrichment of immune cell-binding nanobodies that penetrate the tumor microenvironment. Clone enrichment and specificity vary across immune cell subtypes in the tumor, lymph node, and spleen. INSPIRE-seq identifies a dendritic cell binding clone that binds PHB2. Single-cell RNA sequencing reveals a connection with cDC1s, and immunofluorescence confirms nanobody-PHB2 colocalization along cell membranes. Structural modeling and docking studies assist binding predictions and will guide nanobody selection. In this work, we demonstrate that INSPIRE-seq offers an unbiased approach to examine complex microenvironments and assist in the development of nanobodies, which could serve as active drugs, modified to become drugs, or used as targeting moieties.
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Affiliation(s)
- Thillai V Sekar
- Department of Radiation Oncology, the University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Microbiology, Pondicherry University, Kalapet, Puducherry, India
| | - Eslam A Elghonaimy
- Department of Radiation Oncology, the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Katy L Swancutt
- Department of Radiation Oncology, the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sebastian Diegeler
- Department of Radiation Oncology, the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Isaac Gonzalez
- Department of Radiation Oncology, the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cassandra Hamilton
- Department of Radiation Oncology, the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter Q Leung
- Department of Radiation Oncology, the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Cristina E Martina
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Michael Whitney
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Todd A Aguilera
- Department of Radiation Oncology, the University of Texas Southwestern Medical Center, Dallas, TX, USA.
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16
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Fernández-Quintero ML, Pomarici ND, Fischer ALM, Hoerschinger VJ, Kroell KB, Riccabona JR, Kamenik AS, Loeffler JR, Ferguson JA, Perrett HR, Liedl KR, Han J, Ward AB. Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines. Antibodies (Basel) 2023; 12:67. [PMID: 37873864 PMCID: PMC10594513 DOI: 10.3390/antib12040067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Antibodies and other new antibody-like formats have emerged as one of the most rapidly growing classes of biotherapeutic proteins. Understanding the structural features that drive antibody function and, consequently, their molecular recognition is critical for engineering antibodies. Here, we present the structural architecture of conventional IgG antibodies alongside other formats. We emphasize the importance of considering antibodies as conformational ensembles in solution instead of focusing on single-static structures because their functions and properties are strongly governed by their dynamic nature. Thus, in this review, we provide an overview of the unique structural and dynamic characteristics of antibodies with respect to their antigen recognition, biophysical properties, and effector functions. We highlight the numerous technical advances in antibody structure prediction and design, enabled by the vast number of experimentally determined high-quality structures recorded with cryo-EM, NMR, and X-ray crystallography. Lastly, we assess antibody and vaccine design strategies in the context of structure and dynamics.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nancy D. Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna-Lena M. Fischer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Katharina B. Kroell
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Jakob R. Riccabona
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna S. Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James A. Ferguson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailee R. Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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17
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Boughter CT, Meier-Schellersheim M. An integrated approach to the characterization of immune repertoires using AIMS: An Automated Immune Molecule Separator. PLoS Comput Biol 2023; 19:e1011577. [PMID: 37862356 PMCID: PMC10619816 DOI: 10.1371/journal.pcbi.1011577] [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: 12/19/2022] [Revised: 11/01/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023] Open
Abstract
The adaptive immune system employs an array of receptors designed to respond with high specificity to pathogens or molecular aberrations faced by the host organism. Binding of these receptors to molecular fragments-collectively referred to as antigens-initiates immune responses. These antigenic targets are recognized in their native state on the surfaces of pathogens by antibodies, whereas T cell receptors (TCR) recognize processed antigens as short peptides, presented on major histocompatibility complex (MHC) molecules. Recent research has led to a wealth of immune repertoire data that are key to interrogating the nature of these molecular interactions. However, existing tools for the analysis of these large datasets typically focus on molecular sets of a single type, forcing researchers to separately analyze strongly coupled sequences of interacting molecules. Here, we introduce a software package for the integrated analysis of immune repertoire data, capable of identifying distinct biophysical differences in isolated TCR, MHC, peptide, antibody, and antigen sequence data. This integrated analytical approach allows for direct comparisons across immune repertoire subsets and provides a starting point for the identification of key interaction hotspots in complementary receptor-antigen pairs. The software (AIMS-Automated Immune Molecule Separator) is freely available as an open access package in GUI or command-line form.
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Affiliation(s)
- Christopher T. Boughter
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Martin Meier-Schellersheim
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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18
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Yang YR, Han J, Perrett HR, Richey ST, Jackson AM, Rodriguez AJ, Gillespie RA, O’Connell S, Raab JE, Cominsky LY, Chopde A, Kanekiyo M, Houser KV, Chen GL, McDermott AB, Andrews SF, Ward AB. Immune memory shapes human polyclonal antibody responses to H2N2 vaccination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554525. [PMID: 37781590 PMCID: PMC10541104 DOI: 10.1101/2023.08.23.554525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in H2-naïve and H2-exposed adults. Therefore, we could perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited after H2 vaccination. We temporally map the epitopes targeted by serum antibodies after first and second vaccinations and show previous H2 exposure results in higher responses to the variable head domain of hemagglutinin while initial responses in H2-naïve participants are dominated by antibodies targeting conserved epitopes. We use cryo-EM and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the hemagglutinin head including the receptor binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses.
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Affiliation(s)
- Yuhe R. Yang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Chinese Academy of Sciences Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Hailee R. Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sara T. Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Abigail M. Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Alesandra J. Rodriguez
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Rebecca A. Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Sarah O’Connell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Julie E. Raab
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Lauren Y. Cominsky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Ankita Chopde
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Katherine V. Houser
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Grace L. Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Sarah F. Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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19
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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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20
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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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21
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Han W, Chen N, Xu X, Sahil A, Zhou J, Li Z, Zhong H, Gao E, Zhang R, Wang Y, Sun S, Cheung PPH, Gao X. Predicting the antigenic evolution of SARS-COV-2 with deep learning. Nat Commun 2023; 14:3478. [PMID: 37311849 DOI: 10.1038/s41467-023-39199-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 05/31/2023] [Indexed: 06/15/2023] Open
Abstract
The relentless evolution of SARS-CoV-2 poses a significant threat to public health, as it adapts to immune pressure from vaccines and natural infections. Gaining insights into potential antigenic changes is critical but challenging due to the vast sequence space. Here, we introduce the Machine Learning-guided Antigenic Evolution Prediction (MLAEP), which combines structure modeling, multi-task learning, and genetic algorithms to predict the viral fitness landscape and explore antigenic evolution via in silico directed evolution. By analyzing existing SARS-CoV-2 variants, MLAEP accurately infers variant order along antigenic evolutionary trajectories, correlating with corresponding sampling time. Our approach identified novel mutations in immunocompromised COVID-19 patients and emerging variants like XBB1.5. Additionally, MLAEP predictions were validated through in vitro neutralizing antibody binding assays, demonstrating that the predicted variants exhibited enhanced immune evasion. By profiling existing variants and predicting potential antigenic changes, MLAEP aids in vaccine development and enhances preparedness against future SARS-CoV-2 variants.
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Affiliation(s)
- Wenkai Han
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ningning Chen
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Xinzhou Xu
- Department of Chemical Pathology, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Adil Sahil
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Juexiao Zhou
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Zhongxiao Li
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Huawen Zhong
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Elva Gao
- The KAUST School, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | | | - Yu Wang
- Syneron Technology, Guangzhou, 510000, China
| | - Shiwei Sun
- Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peter Pak-Hang Cheung
- Department of Chemical Pathology, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China.
- Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China.
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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22
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Desta IT, Kotelnikov S, Jones G, Ghani U, Abyzov M, Kholodov Y, Standley DM, Beglov D, Vajda S, Kozakov D. The ClusPro AbEMap web server for the prediction of antibody epitopes. Nat Protoc 2023; 18:1814-1840. [PMID: 37188806 PMCID: PMC10898366 DOI: 10.1038/s41596-023-00826-7] [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: 12/31/2021] [Accepted: 01/19/2023] [Indexed: 05/17/2023]
Abstract
Antibodies play an important role in the immune system by binding to molecules called antigens at their respective epitopes. These interfaces or epitopes are structural entities determined by the interactions between an antibody and an antigen, making them ideal systems to analyze by using docking programs. Since the advent of high-throughput antibody sequencing, the ability to perform epitope mapping using only the sequence of the antibody has become a high priority. ClusPro, a leading protein-protein docking server, together with its template-based modeling version, ClusPro-TBM, have been re-purposed to map epitopes for specific antibody-antigen interactions by using the Antibody Epitope Mapping server (AbEMap). ClusPro-AbEMap offers three different modes for users depending on the information available on the antibody as follows: (i) X-ray structure, (ii) computational/predicted model of the structure or (iii) only the amino acid sequence. The AbEMap server presents a likelihood score for each antigen residue of being part of the epitope. We provide detailed information on the server's capabilities for the three options and discuss how to obtain the best results. In light of the recent introduction of AlphaFold2 (AF2), we also show how one of the modes allows users to use their AF2-generated antibody models as input. The protocol describes the relative advantages of the server compared to other epitope-mapping tools, its limitations and potential areas of improvement. The server may take 45-90 min depending on the size of the proteins.
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Affiliation(s)
- Israel T Desta
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - George Jones
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Usman Ghani
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | | | - Daron M Standley
- Department of Genome Informatics, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.
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23
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Qiu T, Zhang L, Chen Z, Wang Y, Mao T, Wang C, Cun Y, Zheng G, Yan D, Zhou M, Tang K, Cao Z. SEPPA-mAb: spatial epitope prediction of protein antigens for mAbs. Nucleic Acids Res 2023:7175357. [PMID: 37216611 DOI: 10.1093/nar/gkad427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Identifying the exact epitope positions for a monoclonal antibody (mAb) is of critical importance yet highly challenging to the Ab design of biomedical research. Based on previous versions of SEPPA 3.0, we present SEPPA-mAb for the above purpose with high accuracy and low false positive rate (FPR), suitable for both experimental and modelled structures. In practice, SEPPA-mAb appended a fingerprints-based patch model to SEPPA 3.0, considering the structural and physic-chemical complementarity between a possible epitope patch and the complementarity-determining region of mAb and trained on 860 representative antigen-antibody complexes. On independent testing of 193 antigen-antibody pairs, SEPPA-mAb achieved an accuracy of 0.873 with an FPR of 0.097 in classifying epitope and non-epitope residues under the default threshold, while docking-based methods gave the best AUC of 0.691, and the top epitope prediction tool gave AUC of 0.730 with balanced accuracy of 0.635. A study on 36 independent HIV glycoproteins displayed a high accuracy of 0.918 and a low FPR of 0.058. Further testing illustrated outstanding robustness on new antigens and modelled antibodies. Being the first online tool predicting mAb-specific epitopes, SEPPA-mAb may help to discover new epitopes and design better mAbs for therapeutic and diagnostic purposes. SEPPA-mAb can be accessed at http://www.badd-cao.net/seppa-mab/.
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Affiliation(s)
- Tianyi Qiu
- School of Life Sciences, Fudan University, Shanghai 200092, China
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lu Zhang
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zikun Chen
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yuan Wang
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Tiantian Mao
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Caicui Wang
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yewei Cun
- School of Life Sciences, Fudan University, Shanghai 200092, China
| | - Genhui Zheng
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Deyu Yan
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Mengdi Zhou
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Kailin Tang
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhiwei Cao
- School of Life Sciences, Fudan University, Shanghai 200092, China
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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24
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Dzimianski JV, Han J, Sautto GA, O'Rourke SM, Cruz JM, Pierce SR, Ecker JW, Carlock MA, Nagashima KA, Mousa JJ, Ross TM, Ward AB, DuBois RM. Structural insights into the broad protection against H1 influenza viruses by a computationally optimized hemagglutinin vaccine. Commun Biol 2023; 6:454. [PMID: 37185989 PMCID: PMC10126545 DOI: 10.1038/s42003-023-04793-3] [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: 03/17/2023] [Accepted: 03/31/2023] [Indexed: 05/17/2023] Open
Abstract
Influenza virus poses an ongoing human health threat with pandemic potential. Due to mutations in circulating strains, formulating effective vaccines remains a challenge. The use of computationally optimized broadly reactive antigen (COBRA) hemagglutinin (HA) proteins is a promising vaccine strategy to protect against a wide range of current and future influenza viruses. Though effective in preclinical studies, the mechanistic basis driving the broad reactivity of COBRA proteins remains to be elucidated. Here, we report the crystal structure of the COBRA HA termed P1 and identify antigenic and glycosylation properties that contribute to its immunogenicity. We further report the cryo-EM structure of the P1-elicited broadly neutralizing antibody 1F8 bound to COBRA P1, revealing 1F8 to recognize an atypical receptor binding site epitope via an unexpected mode of binding.
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Affiliation(s)
- John V Dzimianski
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Giuseppe A Sautto
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Sara M O'Rourke
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Joseph M Cruz
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Spencer R Pierce
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Jeffrey W Ecker
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Michael A Carlock
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Kaito A Nagashima
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Jarrod J Mousa
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| | - Ted M Ross
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rebecca M DuBois
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
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25
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Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL, Gray JJ, Sauna ZE. Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus. Heliyon 2023; 9:e15032. [PMID: 37035348 PMCID: PMC10069166 DOI: 10.1016/j.heliyon.2023.e15032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
The human infectious disease COVID-19 caused by the SARS-CoV-2 virus has become a major threat to global public health. Developing a vaccine is the preferred prophylactic response to epidemics and pandemics. However, for individuals who have contracted the disease, the rapid design of antibodies that can target the SARS-CoV-2 virus fulfils a critical need. Further, discovering antibodies that bind multiple variants of SARS-CoV-2 can aid in the development of rapid antigen tests (RATs) which are critical for the identification and isolation of individuals currently carrying COVID-19. Here we provide a proof-of-concept study for the computational design of high-affinity antibodies that bind to multiple variants of the SARS-CoV-2 spike protein using RosettaAntibodyDesign (RAbD). Well characterized antibodies that bind with high affinity to the SARS-CoV-1 (but not SARS-CoV-2) spike protein were used as templates and re-designed to bind the SARS-CoV-2 spike protein with high affinity, resulting in a specificity switch. A panel of designed antibodies were experimentally validated. One design bound to a broad range of variants of concern including the Omicron, Delta, Wuhan, and South African spike protein variants.
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Affiliation(s)
- Nancy E. Hernandez
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research U.S. FDA, Silver Spring, MD, USA
| | - Wojciech Jankowski
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research U.S. FDA, Silver Spring, MD, USA
| | - Rahel Frick
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Simon P. Kelow
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
- Dept. of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph H. Lubin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ USA
| | - Vijaya Simhadri
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research U.S. FDA, Silver Spring, MD, USA
| | | | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Roland L. Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jeffrey J. Gray
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Zuben E. Sauna
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research U.S. FDA, Silver Spring, MD, USA
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26
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Chen L, Lu J, Yue J, Wang R, Du P, Yu Y, Guo J, Wang X, Jiang Y, Cheng K, Yang Z, Zheng T. A humanized anti-human adenovirus 55 monoclonal antibody with good neutralization ability. Front Immunol 2023; 14:1132822. [PMID: 37006289 PMCID: PMC10060833 DOI: 10.3389/fimmu.2023.1132822] [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: 12/28/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
BackgroundHuman adenovirus type 55 (HAdV55) has a re-emerged as pathogen causing an acute respiratory disease presenting as a severe lower respiratory illness that can cause death. To date, there is no HAdV55 vaccine or treatment available for general use.MethodsHerein, a monoclonal antibody specific for HAdV55, mAb 9-8, was isolated from an scFv-phage display library derived from mice immunized with the purified inactived-HAdV55 virions. By using ELISA and a virus micro-neutralization assay, we evaluated the binding and neutralizing activity of mAb 9-8 following humanization. Western blotting analysis and antigen-antibody molecular docking analysis were used to identify the antigenic epitopes that the humanized monoclonal antibody 9-8-h2 recognized. After that, their thermal stability was determined.ResultsMAb 9-8 showed potent neutralization activity against HAdV55. After humanization, the humanized neutralizing monoclonal antibody (9-8-h2) was identified to neutralize HAdV55 infection with an IC50 of 0.6050 nM. The mAb 9-8-h2 recognized HAdV55 and HAdV7 virus particles, but not HAdV4 particles. Although mAb 9-8-h2 could recognize HAdV7, it could not neutralize HAdV7. Furthermore, mAb 9-8-h2 recognized a conformational neutralization epitope of the fiber protein and the crucial amino acid residues (Arg 288, Asp 157, and Asn 200) were identified. MAb 9-8-h2 also showed favorable general physicochemical properties, including good thermostability and pH stability.ConclusionsOverall, mAb 9-8-h2 might be a promising molecule for the prevention and treatment of HAdV55.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Tao Zheng
- *Correspondence: Tao Zheng, ; Zhixin Yang,
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27
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Li T, Li Y, Zhu X, He Y, Wu Y, Ying T, Xie Z. Artificial intelligence in cancer immunotherapy: Applications in neoantigen recognition, antibody design and immunotherapy response prediction. Semin Cancer Biol 2023; 91:50-69. [PMID: 36870459 DOI: 10.1016/j.semcancer.2023.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Cancer immunotherapy is a method of controlling and eliminating tumors by reactivating the body's cancer-immunity cycle and restoring its antitumor immune response. The increased availability of data, combined with advancements in high-performance computing and innovative artificial intelligence (AI) technology, has resulted in a rise in the use of AI in oncology research. State-of-the-art AI models for functional classification and prediction in immunotherapy research are increasingly used to support laboratory-based experiments. This review offers a glimpse of the current AI applications in immunotherapy, including neoantigen recognition, antibody design, and prediction of immunotherapy response. Advancing in this direction will result in more robust predictive models for developing better targets, drugs, and treatments, and these advancements will eventually make their way into the clinical setting, pushing AI forward in the field of precision oncology.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yupeng Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyi Zhu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Yao He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yanling Wu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Tianlei Ying
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China.
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China; Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China.
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28
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Nadaradjane AA, Diharce J, Rebehmed J, Cadet F, Gardebien F, Gelly JC, Etchebest C, de Brevern AG. Quality assessment of V HH models. J Biomol Struct Dyn 2023; 41:13287-13301. [PMID: 36752327 DOI: 10.1080/07391102.2023.2172613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023]
Abstract
Heavy Chain Only Antibodies are specific to Camelid species. Despite the lack of the light chain variable domain, their heavy chain variable domain (VH) domain, named VHH or nanobody, has promising potential applications in research and therapeutic fields. The structural study of VHH is therefore of great interest. Unfortunately, considering the huge amount of sequences that might be produced, only about one thousand of VHH experimental structures are publicly available in the Protein Data Bank, implying that structural model prediction of VHH is a necessary alternative to obtaining 3D information besides its sequence. The present study aims to assess and compare the quality of predictions from different modelling methodologies. Established comparative & homology modelling approaches to recent Deep Learning-based modelling strategies were applied, i.e. Modeller using single or multiple structural templates, ModWeb, SwissModel (with two evaluation schema), RoseTTAfold, AlphaFold 2 and NanoNet. The prediction accuracy was evaluated using RMSD, TM-score, GDT-TS, GDT-HA and Protein Blocks distance metrics. Besides the global structure assessment, we performed specific analyses of Frameworks and CDRs structures. We observed that AlphaFold 2 and especially NanoNet performed better than the other evaluated softwares. Importantly, we performed molecular dynamics simulations of an experimental structure and a NanoNet predicted model of a VHH in order to compare the global structural flexibility and local conformations using Protein Blocks. Despite rather similar structures, substantial differences in dynamical properties were observed, which underlies the complexity of the task of model evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aravindan Arun Nadaradjane
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Joseph Rebehmed
- Department of Computer Science and Mathematics, Lebanese, American University, Beirut, Lebanon
| | - Frédéric Cadet
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
- Artificial Intelligence Department, PEACCEL, Paris, France
| | - Fabrice Gardebien
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
| | - Jean-Christophe Gelly
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Catherine Etchebest
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Alexandre G de Brevern
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
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29
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Boorla VS, Chowdhury R, Ramasubramanian R, Ameglio B, Frick R, Gray JJ, Maranas CD. De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD). Proteins 2023; 91:196-208. [PMID: 36111441 PMCID: PMC9538105 DOI: 10.1002/prot.26422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/17/2022] [Accepted: 09/06/2022] [Indexed: 01/11/2023]
Abstract
The continued emergence of new SARS-CoV-2 variants has accentuated the growing need for fast and reliable methods for the design of potentially neutralizing antibodies (Abs) to counter immune evasion by the virus. Here, we report on the de novo computational design of high-affinity Ab variable regions (Fv) through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike receptor binding domain (RBD) protein using the software tool OptMAVEn-2.0. Subsequently, we carried out computational affinity maturation of the designed variable regions through amino acid substitutions for improved binding with the target epitope. Immunogenicity of designs was restricted by preferring designs that match sequences from a 9-mer library of "human Abs" based on a human string content score. We generated 106 different antibody designs and reported in detail on the top five that trade-off the greatest computational binding affinity for the RBD with human string content scores. We further describe computational evaluation of the top five designs produced by OptMAVEn-2.0 using a Rosetta-based approach. We used Rosetta SnugDock for local docking of the designs to evaluate their potential to bind the spike RBD and performed "forward folding" with DeepAb to assess their potential to fold into the designed structures. Ultimately, our results identified one designed Ab variable region, P1.D1, as a particularly promising candidate for experimental testing. This effort puts forth a computational workflow for the de novo design and evaluation of Abs that can quickly be adapted to target spike epitopes of emerging SARS-CoV-2 variants or other antigenic targets.
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Affiliation(s)
- Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park. PA 16802
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park. PA 16802
| | | | - Brandon Ameglio
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Rahel Frick
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park. PA 16802,Corresponding author:
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30
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Boron VA, Martin ACR. abYpap: improvements to the prediction of antibody VH/VL packing using gradient boosted regression. Protein Eng Des Sel 2023; 36:gzad021. [PMID: 38015984 PMCID: PMC10719492 DOI: 10.1093/protein/gzad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/08/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
The Fv region of the antibody (comprising VH and VL domains) is the area responsible for target binding and thus the antibody's specificity. The orientation, or packing, of these two domains relative to each other influences the topography of the Fv region, and therefore can influence the antibody's binding affinity. We present abYpap, an improved method for predicting the packing angle between the VH and VL domains. With the large data set now available, we were able to expand greatly the number of features that could be used compared with our previous work. The machine-learning model was tuned for improved performance using 37 selected residues (previously 13) and also by including the lengths of the most variable 'complementarity determining regions' (CDR-L1, CDR-L2 and CDR-H3). Our method shows large improvements from the previous version, and also against other modeling approaches, when predicting the packing angle.
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Affiliation(s)
- Veronica A Boron
- Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Andrew C R Martin
- Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
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31
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Lusiany T, Xu Z, Saputri DS, Ismanto HS, Nazlica SA, Standley DM. Structural Modeling of Adaptive Immune Responses to Infection. Methods Mol Biol 2023; 2552:283-294. [PMID: 36346598 DOI: 10.1007/978-1-0716-2609-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Antibody and TCR modeling are becoming important as more and more sequence data becomes available to the public. One of the pressing questions now is how to use such data to understand adaptive immune responses to disease. Infectious disease is of particular interest because the antigens driving such responses are often known to some extent. Here, we describe tips for gathering data and cleaning it for use in downstream analysis. We present a method for high-throughput structural modeling of antibodies or TCRs using Repertoire Builder and its extensions. AbAdapt is an extension of Repertoire Builder for antibody-antigen docking from antibody and antigen sequences. ImmuneScape is a corresponding extension for TCR-pMHC 3D modeling. Together, these pipelines can help researchers to understand immune responses to infection from a structural point of view.
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Affiliation(s)
- Tina Lusiany
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Zichang Xu
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Dianita S Saputri
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hendra S Ismanto
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | | | - Daron M Standley
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
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32
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Yang YX, Wang P, Zhu BT. Binding affinity prediction for antibody-protein antigen complexes: A machine learning analysis based on interface and surface areas. J Mol Graph Model 2023; 118:108364. [PMID: 36356467 DOI: 10.1016/j.jmgm.2022.108364] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022]
Abstract
Specific antibodies can bind to protein antigens with high affinity and specificity, and this property makes them one of the best protein-based therapeutics. Accurate prediction of antibody‒protein antigen binding affinity is crucial for designing effective antibodies. The current predictive methods for protein‒protein binding affinity usually fail to predict the binding affinity of an antibody‒protein antigen complex with a comparable level of accuracy. Here, new models specific for antibody‒antigen binding affinity prediction are developed according to the different types of interface and surface areas present in antibody‒antigen complex. The contacts-based descriptors are also employed to construct or train different models specific for antibody‒protein antigen binding affinity prediction. The results of this study show that (i) the area-based descriptors are slightly better than the contacts-based descriptors in terms of the predictive power; (ii) the new models specific for antibody‒protein antigen binding affinity prediction are superior to the previously-used general models for predicting the protein‒protein binding affinities; (iii) the performances of the best area-based and contacts-based models developed in this work are better than the performances of a recently-developed graph-based model (i.e., CSM-AB) specific for antibody‒protein antigen binding affinity prediction. The new models developed in this work would not only help understand the mechanisms underlying antibody‒protein antigen interactions, but would also be of some applicable utility in the design and virtual screening of antibody-based therapeutics.
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Affiliation(s)
- Yong Xiao Yang
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Pan Wang
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China; Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Bao Ting Zhu
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China; Shenzhen Bay Laboratory, Shenzhen, 518055, China.
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33
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Neamtu A, Mocci F, Laaksonen A, Barroso da Silva FL. Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants. Colloids Surf B Biointerfaces 2023; 221:112986. [PMID: 36375294 PMCID: PMC9617679 DOI: 10.1016/j.colsurfb.2022.112986] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/13/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022]
Abstract
A highly efficient and robust multiple scales in silico protocol, consisting of atomistic Molecular Dynamics (MD), coarse-grain (CG) MD, and constant-pH CG Monte Carlo (MC), has been developed and used to study the binding affinities of selected antigen-binding fragments of the monoclonal antibody (mAbs) CR3022 and several of its here optimized versions against 11 SARS-CoV-2 variants including the wild type. Totally 235,000 mAbs structures were initially generated using the RosettaAntibodyDesign software, resulting in top 10 scored CR3022-like-RBD complexes with critical mutations and compared to the native one, all having the potential to block virus-host cell interaction. Of these 10 finalists, two candidates were further identified in the CG simulations to be the best against all SARS-CoV-2 variants. Surprisingly, all 10 candidates and the native CR3022 exhibited a higher affinity for the Omicron variant despite its highest number of mutations. The multiscale protocol gives us a powerful rational tool to design efficient mAbs. The electrostatic interactions play a crucial role and appear to be controlling the affinity and complex building. Studied mAbs carrying a more negative total net charge show a higher affinity. Structural determinants could be identified in atomistic simulations and their roles are discussed in detail to further hint at a strategy for designing the best RBD binder. Although the SARS-CoV-2 was specifically targeted in this work, our approach is generally suitable for many diseases and viral and bacterial pathogens, leukemia, cancer, multiple sclerosis, rheumatoid, arthritis, lupus, and more.
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Affiliation(s)
- Andrei Neamtu
- Department of Physiology, "Grigore T. Popa" University of Medicine and Pharmacy of Iasi, Str. Universitatii nr. 16, 700051 Iasi, România; TRANSCEND Centre - Regional Institute of Oncology (IRO) Iasi, Str. General Henri Mathias Berthelot, Nr. 2-4 Iași, România
| | - Francesca Mocci
- University of Cagliari, Department of Chemical and Geological Sciences, Campus Monserrato, SS 554 bivio per Sestu, 09042 Monserrato, Italy
| | - Aatto Laaksonen
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, PetruPoni Institute of Macromolecular Chemistry Aleea Grigore Ghica-Voda, 41 A, 700487 Iasi, Romania; University of Cagliari, Department of Chemical and Geological Sciences, Campus Monserrato, SS 554 bivio per Sestu, 09042 Monserrato, Italy; Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden; State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing 210009, PR China; Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Fernando L Barroso da Silva
- Universidade de São Paulo, Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. café, s/no - campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA.
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34
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Katoh H, Komura D, Furuya G, Ishikawa S. Immune repertoire profiling for disease pathobiology. Pathol Int 2023; 73:1-11. [PMID: 36342353 PMCID: PMC10099665 DOI: 10.1111/pin.13284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/20/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Lymphocytes consist of highly heterogeneous populations, each expressing a specific cell surface receptor corresponding to a particular antigen. Lymphocytes are both the cause and regulator of various diseases, including autoimmune/allergic diseases, lifestyle diseases, neurodegenerative diseases, and cancers. Recently, immune repertoire sequencing has attracted much attention because it helps obtain global profiles of the immune receptor sequences of infiltrating T and B cells in specimens. Immune repertoire sequencing not only helps deepen our understanding of the molecular mechanisms of immune-related pathology but also assists in discovering novel therapeutic modalities for diseases, thereby shedding colorful light on otherwise tiny monotonous cells when observed under a microscope. In this review article, we introduce and detail the background and methodology of immune repertoire sequencing and summarize recent scientific achievements in association with human diseases. Future perspectives on this genetic technique in the field of histopathological research will also be discussed.
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Affiliation(s)
- Hiroto Katoh
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Genta Furuya
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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35
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Thorsteinson N, Comeau SR, Kumar S. Structure-Based Optimization of Antibody-Based Biotherapeutics for Improved Developability: A Practical Guide for Molecular Modelers. Methods Mol Biol 2023; 2552:219-235. [PMID: 36346594 DOI: 10.1007/978-1-0716-2609-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A great effort to avoid known developability risks is now more often being made earlier during the lead candidate discovery and optimization phase of biotherapeutic drug development. Predictive computational strategies, used in the early stages of antibody discovery and development, to mitigate the risk of late-stage failure of antibody candidates, are highly valuable. Various structure-based methods exist for accurately predicting properties critical to developability, and, in this chapter, we discuss the history of their development and demonstrate how they can be used to filter large sets of candidates arising from target affinity screening and to optimize lead candidates for developability. Methods for modeling antibody structures from sequence and detecting post-translational modifications and chemical degradation liabilities are also discussed.
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Affiliation(s)
- Nels Thorsteinson
- Scientific Services Manager, Biologics, Chemical Computing Group ULC, Montreal, QC, Canada
| | - Stephen R Comeau
- Computational Biochemistry and Bioinformatics Group, Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA
| | - Sandeep Kumar
- Computational Biochemistry and Bioinformatics Group, Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA.
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36
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Peng HP, Yang AS. Computational Analysis of Antibody Paratopes for Antibody Sequences in Antibody Libraries. Methods Mol Biol 2023; 2552:437-445. [PMID: 36346607 DOI: 10.1007/978-1-0716-2609-2_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To ensure the functionalities of the antibodies in phage-displayed synthetic antibody libraries, we use computational method to evaluate the designs of the antibody libraries. The computational methodologies developed in our lab for designing antibody library provide rich information on the function of the designed antibody sequences-adequate antibody designs for a specific antigen type should have predicted paratopes for the antigen type. This computational assessment of the designed antibody sequences helps eliminate non-functional designs before proceeding to construct the library designs in the wet lab. As such, only reasonable antibody designs are constructed for antibody discoveries.
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Affiliation(s)
- Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
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37
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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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38
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Bahnan W, Happonen L, Khakzad H, Kumra Ahnlide V, de Neergaard T, Wrighton S, André O, Bratanis E, Tang D, Hellmark T, Björck L, Shannon O, Malmström L, Malmström J, Nordenfelt P. A human monoclonal antibody bivalently binding two different epitopes in streptococcal M protein mediates immune function. EMBO Mol Med 2022; 15:e16208. [PMID: 36507602 PMCID: PMC9906385 DOI: 10.15252/emmm.202216208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
Group A streptococci have evolved multiple strategies to evade human antibodies, making it challenging to create effective vaccines or antibody treatments. Here, we have generated antibodies derived from the memory B cells of an individual who had successfully cleared a group A streptococcal infection. The antibodies bind with high affinity in the central region of the surface-bound M protein. Such antibodies are typically non-opsonic. However, one antibody could effectively promote vital immune functions, including phagocytosis and in vivo protection. Remarkably, this antibody primarily interacts through a bivalent dual-Fab cis mode, where the Fabs bind to two distinct epitopes in the M protein. The dual-Fab cis-binding phenomenon is conserved across different groups of M types. In contrast, other antibodies binding with normal single-Fab mode to the same region cannot bypass the M protein's virulent effects. A broadly binding, protective monoclonal antibody could be a candidate for anti-streptococcal therapy. Our findings highlight the concept of dual-Fab cis binding as a means to access conserved, and normally non-opsonic regions, regions for protective antibody targeting.
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Affiliation(s)
- Wael Bahnan
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Hamed Khakzad
- Equipe Signalisation Calcique et Infections MicrobiennesÉcole Normale Supérieure Paris‐SaclayGif‐sur‐YvetteFrance,Institut National de la Santé et de la Recherche Médicale (INSERM) U1282Gif‐sur‐YvetteFrance,Present address:
Université de Lorraine, Inria, LORIANancyFrance
| | - Vibha Kumra Ahnlide
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Therese de Neergaard
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Sebastian Wrighton
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Oscar André
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Eleni Bratanis
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Di Tang
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Thomas Hellmark
- Department of Clinical Sciences Lund, Division of NephrologyLund UniversityLundSweden
| | - Lars Björck
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Oonagh Shannon
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Lars Malmström
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Pontus Nordenfelt
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
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39
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Cohen T, Halfon M, Carter L, Sharkey B, Jain T, Sivasubramanian A, Schneidman-Duhovny D. Multi-state modeling of antibody-antigen complexes with SAXS profiles and deep-learning models. Methods Enzymol 2022; 678:237-262. [PMID: 36641210 DOI: 10.1016/bs.mie.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Antibodies are an established class of human therapeutics. Epitope characterization is an important part of therapeutic antibody discovery. However, structural characterization of antibody-antigen complexes remains challenging. On the one hand, X-ray crystallography or cryo-electron microscopy provide atomic resolution characterization of the epitope, but the data collection process is typically long and the success rate is low. On the other hand, computational methods for modeling antibody-antigen structures from the individual components frequently suffer from a high false positive rate, rarely resulting in a unique solution. Recent deep learning models for structure prediction are also successful in predicting protein-protein complexes. However, they do not perform well for antibody-antigen complexes. Small Angle X-ray Scattering (SAXS) is a reliable technique for rapid structural characterization of protein samples in solution albeit at low resolution. Here, we present an integrative approach for modeling antigen-antibody complexes using the antibody sequence, antigen structure, and experimentally determined SAXS profiles of the antibody, antigen, and the complex. The method models antibody structures using a novel deep-learning approach, NanoNet. The structures of the antibodies and antigens are represented using multiple 3D conformations to account for compositional and conformational heterogeneity of the protein samples that are used to collect the SAXS data. The complexes are predicted by integrating the SAXS profiles with scoring functions for protein-protein interfaces that are based on statistical potentials and antibody-specific deep-learning models. We validated the method via application to four Fab:EGFR and one Fab:PCSK9 antibody:antigen complexes with experimentally available SAXS datasets. The integrative approach returns accurate predictions (interface RMSD<4Å) in the top five predictions for four out of five complexes (respective interface RMSD values of 1.95, 2.18, 2.66 and 3.87Å), providing support for the utility of such a computational pipeline for epitope characterization during therapeutic antibody discovery.
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Affiliation(s)
- Tomer Cohen
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Matan Halfon
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lester Carter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, United States
| | - Beth Sharkey
- High-Throughput Expression, Adimab LLC, Lebanon, NH, United States
| | - Tushar Jain
- Computational Biology, Adimab LLC, Palo Alto, CA, United States
| | | | - Dina Schneidman-Duhovny
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
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40
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Antibody CDR amino acids underlying the functionality of antibody repertoires in recognizing diverse protein antigens. Sci Rep 2022; 12:12555. [PMID: 35869245 PMCID: PMC9307644 DOI: 10.1038/s41598-022-16841-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
Antibodies recognize protein antigens with exquisite specificity in a complex aqueous environment, where interfacial waters are an integral part of the antibody–protein complex interfaces. In this work, we elucidate, with computational analyses, the principles governing the antibodies’ specificity and affinity towards their cognate protein antigens in the presence of explicit interfacial waters. Experimentally, in four model antibody–protein complexes, we compared the contributions of the interaction types in antibody–protein antigen complex interfaces with the antibody variants selected from phage-displayed synthetic antibody libraries. Evidently, the specific interactions involving a subset of aromatic CDR (complementarity determining region) residues largely form the predominant determinant underlying the specificity of the antibody–protein complexes in nature. The interfacial direct/water-mediated hydrogen bonds accompanying the CDR aromatic interactions are optimized locally but contribute little in determining the epitope location. The results provide insights into the phenomenon that natural antibodies with limited sequence and structural variations in an antibody repertoire can recognize seemingly unlimited protein antigens. Our work suggests guidelines in designing functional artificial antibody repertoires with practical applications in developing novel antibody-based therapeutics and diagnostics for treating and preventing human diseases.
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Sun D, Sun M, Zhang J, Lin X, Zhang Y, Lin F, Zhang P, Yang C, Song J. Computational tools for aptamer identification and optimization. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Dănăilă VR, Avram S, Buiu C. The applications of machine learning in HIV neutralizing antibodies research-A systematic review. Artif Intell Med 2022; 134:102429. [PMID: 36462896 DOI: 10.1016/j.artmed.2022.102429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 09/03/2022] [Accepted: 10/13/2022] [Indexed: 12/14/2022]
Abstract
Machine learning algorithms play an essential role in bioinformatics and allow exploring the vast and noisy biological data in unrivaled ways. This paper is a systematic review of the applications of machine learning in the study of HIV neutralizing antibodies. This significant and vast research domain can pave the way to novel treatments and to a vaccine. We selected the relevant papers by investigating the available literature from the Web of Science and PubMed databases in the last decade. The computational methods are applied in neutralization potency prediction, neutralization span prediction against multiple viral strains, antibody-virus binding sites detection, enhanced antibodies design, and the study of the antibody-induced immune response. These methods are viewed from multiple angles spanning data processing, model description, feature selection, evaluation, and sometimes paper comparisons. The algorithms are diverse and include supervised, unsupervised, and generative types. Both classical machine learning and modern deep learning were taken into account. The review ends with our ideas regarding future research directions and challenges.
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Affiliation(s)
- Vlad-Rareş Dănăilă
- Department of Automatic Control and Systems Engineering, Politehnica University of Bucharest, 313 Splaiul Independenţei, Bucharest 060042, Romania.
| | - Speranţa Avram
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, Bucharest 050095, Romania.
| | - Cătălin Buiu
- Department of Automatic Control and Systems Engineering, Politehnica University of Bucharest, 313 Splaiul Independenţei, Bucharest 060042, Romania.
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Wu C, Guo D. Computational Docking Reveals Co-Evolution of C4 Carbon Delivery Enzymes in Diverse Plants. Int J Mol Sci 2022; 23:ijms232012688. [PMID: 36293547 PMCID: PMC9604239 DOI: 10.3390/ijms232012688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Proteins are modular functionalities regulating multiple cellular activities in prokaryotes and eukaryotes. As a consequence of higher plants adapting to arid and thermal conditions, C4 photosynthesis is the carbon fixation process involving multi-enzymes working in a coordinated fashion. However, how these enzymes interact with each other and whether they co-evolve in parallel to maintain interactions in different plants remain elusive to date. Here, we report our findings on the global protein co-evolution relationship and local dynamics of co-varying site shifts in key C4 photosynthetic enzymes. We found that in most of the selected key C4 photosynthetic enzymes, global pairwise co-evolution events exist to form functional couplings. Besides, protein-protein interactions between these enzymes may suggest their unknown functionalities in the carbon delivery process. For PEPC and PPCK regulation pairs, pocket formation at the interactive interface are not necessary for their function. This feature is distinct from another well-known regulation pair in C4 photosynthesis, namely, PPDK and PPDK-RP, where the pockets are necessary. Our findings facilitate the discovery of novel protein regulation types and contribute to expanding our knowledge about C4 photosynthesis.
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Parzych EM, Du J, Ali AR, Schultheis K, Frase D, Smith TRF, Cui J, Chokkalingam N, Tursi NJ, Andrade VM, Warner BM, Gary EN, Li Y, Choi J, Eisenhauer J, Maricic I, Kulkarni A, Chu JD, Villafana G, Rosenthal K, Ren K, Francica JR, Wootton SK, Tebas P, Kobasa D, Broderick KE, Boyer JD, Esser MT, Pallesen J, Kulp DW, Patel A, Weiner DB. DNA-delivered antibody cocktail exhibits improved pharmacokinetics and confers prophylactic protection against SARS-CoV-2. Nat Commun 2022; 13:5886. [PMID: 36202799 PMCID: PMC9537531 DOI: 10.1038/s41467-022-33309-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/07/2022] [Indexed: 11/09/2022] Open
Abstract
Monoclonal antibody therapy has played an important role against SARS-CoV-2. Strategies to deliver functional, antibody-based therapeutics with improved in vivo durability are needed to supplement current efforts and reach underserved populations. Here, we compare recombinant mAbs COV2-2196 and COV2-2130, which compromise clinical cocktail Tixagevimab/Cilgavimab, with optimized nucleic acid-launched forms. Functional profiling of in vivo-expressed, DNA-encoded monoclonal antibodies (DMAbs) demonstrated similar specificity, broad antiviral potency and equivalent protective efficacy in multiple animal challenge models of SARS-CoV-2 prophylaxis compared to protein delivery. In PK studies, DNA-delivery drove significant serum antibody titers that were better maintained compared to protein administration. Furthermore, cryo-EM studies performed on serum-derived DMAbs provide the first high-resolution visualization of in vivo-launched antibodies, revealing new interactions that may promote cooperative binding to trimeric antigen and broad activity against VoC including Omicron lineages. These data support the further study of DMAb technology in the development and delivery of valuable biologics.
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Affiliation(s)
- Elizabeth M Parzych
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | - Jianqiu Du
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Ali R Ali
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | | | - Drew Frase
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | | | - Jiayan Cui
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Neethu Chokkalingam
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | - Nicholas J Tursi
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | | | - Bryce M Warner
- Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Ebony N Gary
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | - Yue Li
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | - Jihae Choi
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | - Jillian Eisenhauer
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | - Igor Maricic
- Inovio Pharmaceuticals, Plymouth Meeting, PA, 19462, USA
| | - Abhijeet Kulkarni
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | - Jacqueline D Chu
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | - Gabrielle Villafana
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | - Kim Rosenthal
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Kuishu Ren
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Joseph R Francica
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Sarah K Wootton
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Pablo Tebas
- University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Darwyn Kobasa
- Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
| | | | - Jean D Boyer
- Inovio Pharmaceuticals, Plymouth Meeting, PA, 19462, USA
| | - Mark T Esser
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Jesper Pallesen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Dan W Kulp
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | - Ami Patel
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA
| | - David B Weiner
- The Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, 19104, USA.
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Jang JH, Kim S, Kim SG, Lee J, Lee DG, Jang J, Jeong YS, Song DH, Min JK, Park JG, Lee MS, Han BS, Son JS, Lee J, Lee NK. A Sensitive Immunodetection Assay Using Antibodies Specific to Staphylococcal Enterotoxin B Produced by Baculovirus Expression. BIOSENSORS 2022; 12:bios12100787. [PMID: 36290925 PMCID: PMC9599101 DOI: 10.3390/bios12100787] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/30/2022]
Abstract
Staphylococcal enterotoxin B (SEB) is a potent bacterial toxin that causes inflammatory stimulation and toxic shock, thus it is necessary to detect SEB in food and environmental samples. Here, we developed a sensitive immunodetection system using monoclonal antibodies (mAbs). Our study is the first to employ a baculovirus expression vector system (BEVS) to produce recombinant wild-type SEB. BEVS facilitated high-quantity and pure SEB production from suspension-cultured insect cells, and the SEB produced was characterized by mass spectrometry analysis. The SEB was stable at 4 °C for at least 2 years, maintaining its purity, and was further utilized for mouse immunization to generate mAbs. An optimal pair of mAbs non-competitive to SEB was selected for sandwich enzyme-linked immunosorbent assay-based immunodetection. The limit of detection of the immunodetection method was 0.38 ng/mL. Moreover, it displayed higher sensitivity in detecting SEB than commercially available immunodetection kits and retained detectability in various matrices and S. aureus culture supernatants. Thus, the results indicate that BEVS is useful for producing pure recombinant SEB with its natural immunogenic property in high yield, and that the developed immunodetection assay is reliable and sensitive for routine identification of SEB in various samples, including foods.
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Affiliation(s)
- Ju-Hong Jang
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
- Department of Biomolecular Science, Korea Research Institute of Bioscience and Biotechnology, School of Bioscience, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea
| | - Sungsik Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Seul-Gi Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
- Department of Biomolecular Science, Korea Research Institute of Bioscience and Biotechnology, School of Bioscience, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea
| | - Jaemin Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Dong-Gwang Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Jieun Jang
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
- Department of Biomolecular Science, Korea Research Institute of Bioscience and Biotechnology, School of Bioscience, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea
| | - Young-Su Jeong
- Agency for Defense Development, 488 Bugyuseoung-daero, Daejeon 34060, Korea
| | - Dong-Hyun Song
- Agency for Defense Development, 488 Bugyuseoung-daero, Daejeon 34060, Korea
| | - Jeong-Ki Min
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
- Department of Biomolecular Science, Korea Research Institute of Bioscience and Biotechnology, School of Bioscience, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea
| | - Jong-Gil Park
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Moo-Seung Lee
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Baek-Soo Han
- Biodefense Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Jee-Soo Son
- iNtRON Biotechnology, 137 Sagimakgol-ro, Jungwon-gu, Seongnam-si 13202, Korea
| | - Jangwook Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
- Department of Biomolecular Science, Korea Research Institute of Bioscience and Biotechnology, School of Bioscience, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea
- Correspondence: (J.L.); (N.-K.L.); Tel.: +82-42-860-4123 (J.L.); +82-42-860-4117 (N.-K.L.)
| | - Nam-Kyung Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
- Correspondence: (J.L.); (N.-K.L.); Tel.: +82-42-860-4123 (J.L.); +82-42-860-4117 (N.-K.L.)
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Ahmad B, Choi S. Unraveling the Tomaralimab Epitope on the Toll-like Receptor 2 via Molecular Dynamics and Deep Learning. ACS OMEGA 2022; 7:28226-28237. [PMID: 35990491 PMCID: PMC9386714 DOI: 10.1021/acsomega.2c02559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Tomaralimab (OPN-305) is the first humanized immunoglobulin G4 monoclonal antibody against TLR2 and is designed to prevent inflammation that is driven by inappropriate or excessive activation of innate immune pathways. Here, we constructed a homology model of Tomaralimab and its complex with TLR2 at different mapped epitopes and unraveled their behavior at the atomistic level. Furthermore, we predicted a novel epitope (leucine-rich region 9-12) near the lipopeptide-binding site that can be targeted and studied for the utility of therapeutic antibodies. A geometric deep learning algorithm was used to envisage Tomaralimab binding affinity changes upon mutation. There was a significant difference in binding affinity for Tomaralimab following epitope-mutated alanine substitutions of Val266, Pro294, Arg295, Asn319, Pro326, and His372. Using deep learning-based ΔΔG prediction, we computationally contrasted human TLR2-TLR2, TLR2-TLR1, and TLR2-TLR6 dimerization. These results reveal the mechanism that underlies Tomaralimab binding to TLR2 and should help to design structure-based mimics or bispecific antibodies that can be used to inhibit both lipopeptide-binding and TLR2 dimerization.
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Affiliation(s)
- Bilal Ahmad
- Department
of Molecular Science and Technology, Ajou
University, Suwon 16499, Korea
- S&K
Therapeutics, Ajou University
Campus Plaza 418, 199 Worldcup-ro, Yeongtong-gu, Suwon 16502, Korea
| | - Sangdun Choi
- Department
of Molecular Science and Technology, Ajou
University, Suwon 16499, Korea
- S&K
Therapeutics, Ajou University
Campus Plaza 418, 199 Worldcup-ro, Yeongtong-gu, Suwon 16502, Korea
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47
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França RKADO, Silva JM, Rodrigues LS, Sokolowskei D, Brigido MM, Maranhão AQ. New Anti-Flavivirus Fusion Loop Human Antibodies with Zika Virus-Neutralizing Potential. Int J Mol Sci 2022; 23:ijms23147805. [PMID: 35887153 PMCID: PMC9321016 DOI: 10.3390/ijms23147805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 02/04/2023] Open
Abstract
Zika virus infections exhibit recurrent outbreaks and can be responsible for disease complications such as congenital Zika virus syndrome. Effective therapeutic interventions are still a challenge. Antibodies can provide significant protection, although the antibody response may fail due to antibody-dependent enhancement reactions. The choice of the target antigen is a crucial part of the process to generate effective neutralizing antibodies. Human anti-Zika virus antibodies were selected by phage display technology. The antibodies were selected against a mimetic peptide based on the fusion loop region in the protein E of Zika virus, which is highly conserved among different flaviviruses. Four rounds of selection were performed using the synthetic peptide in two strategies: the first was using the acidic elution of bound phages, and the second was by applying a competing procedure. After panning, the selected VH and VL domains were determined by combining NGS and bioinformatic approaches. Three different human monoclonal antibodies were expressed as scFvs and further characterized. All showed a binding capacity to Zika (ZIKV) and showed cross-recognition with yellow fever (YFV) and dengue (DENV) viruses. Two of these antibodies, AZ1p and AZ6m, could neutralize the ZIKV infection in vitro. Due to the conservation of the fusion loop region, these new antibodies can potentially be used in therapeutic intervention against Zika virus and other flavivirus illnesses.
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Affiliation(s)
- Renato Kaylan Alves de Oliveira França
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
| | - Jacyelle Medeiros Silva
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
| | - Lucas Silva Rodrigues
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
| | - Dimitri Sokolowskei
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Biology, University of Brasilia, Brasilia 70910-900, Brazil
| | - Marcelo Macedo Brigido
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
- Graduation Program in Molecular Biology, University of Brasilia, Brasilia 70910-900, Brazil
- III-Immunology Investigation Institute–CNPq-MCT, São Paulo 05403-000, Brazil
- Correspondence:
| | - Andrea Queiroz Maranhão
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
- Graduation Program in Molecular Biology, University of Brasilia, Brasilia 70910-900, Brazil
- III-Immunology Investigation Institute–CNPq-MCT, São Paulo 05403-000, Brazil
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Magi Meconi G, Sasselli IR, Bianco V, Onuchic JN, Coluzza I. Key aspects of the past 30 years of protein design. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:086601. [PMID: 35704983 DOI: 10.1088/1361-6633/ac78ef] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Proteins are the workhorse of life. They are the building infrastructure of living systems; they are the most efficient molecular machines known, and their enzymatic activity is still unmatched in versatility by any artificial system. Perhaps proteins' most remarkable feature is their modularity. The large amount of information required to specify each protein's function is analogically encoded with an alphabet of just ∼20 letters. The protein folding problem is how to encode all such information in a sequence of 20 letters. In this review, we go through the last 30 years of research to summarize the state of the art and highlight some applications related to fundamental problems of protein evolution.
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Affiliation(s)
- Giulia Magi Meconi
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | - Ivan R Sasselli
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | | | - Jose N Onuchic
- Center for Theoretical Biological Physics, Department of Physics & Astronomy, Department of Chemistry, Department of Biosciences, Rice University, Houston, TX 77251, United States of America
| | - Ivan Coluzza
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Bld. Martina Casiano, UPV/EHU Science Park, Barrio Sarriena s/n, 48940 Leioa, Spain
- Basque Foundation for Science, Ikerbasque, 48009, Bilbao, Spain
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49
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Liu H, Wu W, Sun G, Chia T, Cao L, Liu X, Guan J, Fu F, Yao Y, Wu Z, Zhou S, Wang J, Lu J, Kuang Z, Wu M, He L, Shao Z, Wu D, Chen B, Xu W, Wang Z, He K. Optimal target saturation of ligand-blocking anti-GITR antibody IBI37G5 dictates FcγR-independent GITR agonism and antitumor activity. Cell Rep Med 2022; 3:100660. [PMID: 35732156 PMCID: PMC9245059 DOI: 10.1016/j.xcrm.2022.100660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/26/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022]
Abstract
Glucocorticoid-induced tumor necrosis factor receptor (GITR) is a co-stimulatory receptor and an important target for cancer immunotherapy. We herein present a potent FcγR-independent GITR agonist IBI37G5 that can effectively activate effector T cells and synergize with anti-programmed death 1 (PD1) antibody to eradicate established tumors. IBI37G5 depends on both antibody bivalency and GITR homo-dimerization for efficient receptor cross-linking. Functional analyses reveal bell-shaped dose responses due to the unique 2:2 antibody-receptor stoichiometry required for GITR activation. Antibody self-competition is observed after concentration exceeded that of 100% receptor occupancy (RO), which leads to antibody monovalent binding and loss of activity. Retrospective pharmacokinetics/pharmacodynamics analysis demonstrates that the maximal efficacy is achieved at medium doses with drug exposure near saturating GITR occupancy during the dosing cycle. Finally, we propose an alternative dose-finding strategy that does not rely on the traditional maximal tolerated dose (MTD)-based paradigm but instead on utilizing the RO-function relations as biomarker to guide the clinical translation of GITR and similar co-stimulatory agonists.
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Affiliation(s)
- Huisi Liu
- Department of Immunology, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Weiwei Wu
- Department of Pharmacology and Preclinical Studies, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Gangyu Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Tiongsun Chia
- Department of Immunology, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Lei Cao
- Department of Pharmacology and Preclinical Studies, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Xiaodan Liu
- Department of Immunology, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Jian Guan
- Department of Immunology, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Fenggen Fu
- Department of Antibody Discovery and Protein Engineering, Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Ying Yao
- Department of Pharmacology and Preclinical Studies, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Zhihai Wu
- Department of Antibody Discovery and Protein Engineering, Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Shuaixiang Zhou
- Department of Antibody Discovery and Protein Engineering, Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Jie Wang
- Department of Pharmacology and Preclinical Studies, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Jia Lu
- Department of Pharmacology and Preclinical Studies, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Zhihui Kuang
- Department of Pharmacology and Preclinical Studies, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Min Wu
- Department of Pharmacology and Preclinical Studies, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Luan He
- Department of Immunology, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Zhiyuan Shao
- Department of Antibody Discovery and Protein Engineering, Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Dongdong Wu
- Department of Pharmacology and Preclinical Studies, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Bingliang Chen
- Department of Pharmacology and Preclinical Studies, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Wenqing Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhizhi Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Kaijie He
- Department of Immunology, Innovent Guoqing Academy, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China.
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Akpinaroglu D, Ruffolo JA, Mahajan SP, Gray JJ. Simultaneous prediction of antibody backbone and side-chain conformations with deep learning. PLoS One 2022; 17:e0258173. [PMID: 35704640 PMCID: PMC9200299 DOI: 10.1371/journal.pone.0258173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 05/24/2022] [Indexed: 11/20/2022] Open
Abstract
Antibody engineering is becoming increasingly popular in medicine for the development of diagnostics and immunotherapies. Antibody function relies largely on the recognition and binding of antigenic epitopes via the loops in the complementarity determining regions. Hence, accurate high-resolution modeling of these loops is essential for effective antibody engineering and design. Deep learning methods have previously been shown to effectively predict antibody backbone structures described as a set of inter-residue distances and orientations. However, antigen binding is also dependent on the specific conformations of surface side-chains. To address this shortcoming, we created DeepSCAb: a deep learning method that predicts inter-residue geometries as well as side-chain dihedrals of the antibody variable fragment. The network requires only sequence as input, rendering it particularly useful for antibodies without any known backbone conformations. Rotamer predictions use an interpretable self-attention layer, which learns to identify structurally conserved anchor positions across several species. We evaluate the performance of the model for discriminating near-native structures from sets of decoys and find that DeepSCAb outperforms similar methods lacking side-chain context. When compared to alternative rotamer repacking methods, which require an input backbone structure, DeepSCAb predicts side-chain conformations competitively. Our findings suggest that DeepSCAb improves antibody structure prediction with accurate side-chain modeling and is adaptable to applications in docking of antibody-antigen complexes and design of new therapeutic antibody sequences.
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Affiliation(s)
- Deniz Akpinaroglu
- Department of Bioengineering, University of California, Merced, CA, United States of America
| | - Jeffrey A. Ruffolo
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, United States of America
| | - Sai Pooja Mahajan
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, United States of America
| | - Jeffrey J. Gray
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, United States of America
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, United States of America
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