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Miller NL, Clark T, Raman R, Sasisekharan R. Learned features of antibody-antigen binding affinity. Front Mol Biosci 2023; 10:1112738. [PMID: 36895805 PMCID: PMC9989197 DOI: 10.3389/fmolb.2023.1112738] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/18/2023] [Indexed: 02/23/2023] Open
Abstract
Defining predictors of antigen-binding affinity of antibodies is valuable for engineering therapeutic antibodies with high binding affinity to their targets. However, this task is challenging owing to the huge diversity in the conformations of the complementarity determining regions of antibodies and the mode of engagement between antibody and antigen. In this study, we used the structural antibody database (SAbDab) to identify features that can discriminate high- and low-binding affinity across a 5-log scale. First, we abstracted features based on previously learned representations of protein-protein interactions to derive 'complex' feature sets, which include energetic, statistical, network-based, and machine-learned features. Second, we contrasted these complex feature sets with additional 'simple' feature sets based on counts of contacts between antibody and antigen. By investigating the predictive potential of 700 features contained in the eight complex and simple feature sets, we observed that simple feature sets perform comparably to complex feature sets in classification of binding affinity. Moreover, combining features from all eight feature-sets provided the best classification performance (median cross-validation AUROC and F1-score of 0.72). Of note, classification performance is substantially improved when several sources of data leakage (e.g., homologous antibodies) are not removed from the dataset, emphasizing a potential pitfall in this task. We additionally observe a classification performance plateau across diverse featurization approaches, highlighting the need for additional affinity-labeled antibody-antigen structural data. The findings from our present study set the stage for future studies aimed at multiple-log enhancement of antibody affinity through feature-guided engineering.
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Affiliation(s)
- Nathaniel L Miller
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas Clark
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Rahul Raman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ram Sasisekharan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
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2
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Tiper I, Kourout M, Lanning B, Fisher C, Konduru K, Purkayastha A, Kaplan G, Duncan R. Tracking ebolavirus genomic drift with a resequencing microarray. PLoS One 2022; 17:e0263732. [PMID: 35143574 PMCID: PMC8830711 DOI: 10.1371/journal.pone.0263732] [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: 07/02/2021] [Accepted: 01/25/2022] [Indexed: 11/17/2022] Open
Abstract
Filoviruses are emerging pathogens that cause acute fever with high fatality rate and present a global public health threat. During the 2013–2016 Ebola virus outbreak, genome sequencing allowed the study of virus evolution, mutations affecting pathogenicity and infectivity, and tracing the viral spread. In 2018, early sequence identification of the Ebolavirus as EBOV in the Democratic Republic of the Congo supported the use of an Ebola virus vaccine. However, field-deployable sequencing methods are needed to enable a rapid public health response. Resequencing microarrays (RMA) are a targeted method to obtain genomic sequence on clinical specimens rapidly, and sensitively, overcoming the need for extensive bioinformatic analysis. This study presents the design and initial evaluation of an ebolavirus resequencing microarray (Ebolavirus-RMA) system for sequencing the major genomic regions of four Ebolaviruses that cause disease in humans. The design of the Ebolavirus-RMA system is described and evaluated by sequencing repository samples of three Ebolaviruses and two EBOV variants. The ability of the system to identify genetic drift in a replicating virus was achieved by sequencing the ebolavirus glycoprotein gene in a recombinant virus cultured under pressure from a neutralizing antibody. Comparison of the Ebolavirus-RMA results to the Genbank database sequence file with the accession number given for the source RNA and Ebolavirus-RMA results compared to Next Generation Sequence results of the same RNA samples showed up to 99% agreement.
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Affiliation(s)
- Irina Tiper
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Moussa Kourout
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Bryan Lanning
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Carolyn Fisher
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Krishnamurthy Konduru
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | | | - Gerardo Kaplan
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Robert Duncan
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
- * E-mail:
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Tit-Oon P, Tharakaraman K, Artpradit C, Godavarthi A, Sungkeeree P, Sasisekharan V, Kerdwong J, Miller NL, Mahajan B, Khongmanee A, Ruchirawat M, Sasisekharan R, Fuangthong M. Prediction of the binding interface between monoclonal antibody m102.4 and Nipah attachment glycoprotein using structure-guided alanine scanning and computational docking. Sci Rep 2020; 10:18256. [PMID: 33106487 PMCID: PMC7588459 DOI: 10.1038/s41598-020-75056-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/21/2020] [Indexed: 11/08/2022] Open
Abstract
Nipah Virus (NiV) has been designated as a priority disease with an urgent need for therapeutic development by World Health Organization. The monoclonal antibody m102.4 binds to the immunodominant NiV receptor-binding glycoprotein (GP), and potently neutralizes NiV, indicating its potential as a therapeutic agent. Although the co-crystal structure of m102.3, an m102.4 derivative, in complex with the GP of the related Hendra Virus (HeV) has been solved, the structural interaction between m102.4 and NiV is uncharacterized. Herein, we used structure-guided alanine-scanning mutagenesis to map the functional epitope and paratope residues that govern the antigen-antibody interaction. Our results revealed that the binding of m102.4 is mediated predominantly by two residues in the HCDR3 region, which is unusually small for an antibody-antigen interaction. We performed computational docking to generate a structural model of m102.4-NiV interaction. Our model indicates that m102.4 targets the common hydrophobic central cavity and a hydrophilic rim on the GP, as observed for the m102.3-HeV co-crystal, albeit with Fv orientation differences. In summary, our study provides insight into the m102.4-NiV interaction, demonstrating that structure-guided alanine-scanning and computational modeling can serve as the starting point for additional antibody reengineering (e.g. affinity maturation) to generate potential therapeutic candidates.
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Affiliation(s)
- Phanthakarn Tit-Oon
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Kannan Tharakaraman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Abhinav Godavarthi
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
- Yale University, New Haven, CT, 06520, USA
| | - Pareenart Sungkeeree
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Varun Sasisekharan
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Jarunee Kerdwong
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Nathaniel Loren Miller
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bhuvna Mahajan
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Amnart Khongmanee
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Mathuros Ruchirawat
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Ram Sasisekharan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Mayuree Fuangthong
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand.
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4
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Wassenaar TM, Wanchai V, Buzard GS, Ussery DW. In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks. Front Microbiol 2019; 10:857. [PMID: 31080442 PMCID: PMC6497787 DOI: 10.3389/fmicb.2019.00857] [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: 01/15/2019] [Accepted: 04/03/2019] [Indexed: 11/13/2022] Open
Abstract
To achieve maximum transmission chain tracking in the current Ebola outbreak, whole genome sequencing (WGS) has been proposed to provide optimal information. However, WGS remains a costly and time-intensive procedure that is poorly suited for the large numbers of samples being generated, especially under severe time and work-environment constraints as in the present DRC outbreak. To better prepare for future outbreaks, where an apparent single outbreak may actually represent overlapping outbreaks caused by independent variants, and where rapid identification of emerging new transmission chains will be essential, a more practical method would be to amplify and sequence genomic areas that reveal the highest information to differentiate EBOV variants. We have identified four highly informative polymorphism PCR sequencing targets, suitable for rapid tracing of transmission chains and identification of new sources of Ebola outbreaks, an approach which will be far more practical in the field than WGS.
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Affiliation(s)
- Trudy M Wassenaar
- Molecular Microbiology and Genomics Consultants, Zotzenheim, Germany
| | - Visanu Wanchai
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | | | - David W Ussery
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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Wong YH, Kumar A, Liew CW, Tharakaraman K, Srinivasaraghavan K, Sasisekharan R, Verma C, Lescar J. Molecular basis for dengue virus broad cross-neutralization by humanized monoclonal antibody 513. Sci Rep 2018; 8:8449. [PMID: 29855525 PMCID: PMC5981469 DOI: 10.1038/s41598-018-26800-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 05/21/2018] [Indexed: 12/18/2022] Open
Abstract
Dengue is a widespread viral disease with 3.6 billion people at risk worldwide. Humanized monoclonal antibody (mAb) 513, currently undergoing clinical trials in Singapore, targets an epitope on the envelope protein domain III exposed at the surface of the viral particle. This antibody potently neutralizes all four dengue virus serotypes in a humanized mouse model that recapitulates human dengue infection, without signs of antibody-mediated enhancement of the disease. The crystal structure of single-chain variable fragment (scFv) 513 bound to the envelope protein domain III from dengue virus serotype 4 was used as a template to explore the molecular origins of the broader cross-reactivity and increased in vivo potency of mAb 513, compared to the parent murine mAb 4E11, using molecular dynamics simulations and network analyses. These two methods are a powerful complement to existing structural and binding data and detail specific interactions that underpin the differential binding of the two antibodies. We found that a Glu at position H55 (GluH55) from the second Complementarity Determining Region of the Heavy chain (CDR-H2) which corresponds to Ala in 4E11, is a major contributor to the enhancement in the interactions of mAb 513 compared to 4E11. Importantly, we also validate the importance of GluH55 using site-directed mutagenesis followed by isothermal titration calorimetry measurements.
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Affiliation(s)
- Yee Hwa Wong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.,Nanyang Institute of Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Akshita Kumar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.,Infectious Diseases Interdisciplinary Research group, Singapore MIT Alliance for Research & Technology, Singapore, Singapore.,Bioinformatics Institute, ASTAR, 30 Biopolis Street, #07-01 Matrix, 138671, Singapore, Singapore
| | - Chong Wai Liew
- Nanyang Institute of Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, Singapore, 636921, Singapore
| | | | - Kannan Srinivasaraghavan
- Bioinformatics Institute, ASTAR, 30 Biopolis Street, #07-01 Matrix, 138671, Singapore, Singapore
| | - Ram Sasisekharan
- Department of Biological engineering MIT, Cambridge, United Kingdom.,Infectious Diseases Interdisciplinary Research group, Singapore MIT Alliance for Research & Technology, Singapore, Singapore
| | - Chandra Verma
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. .,Bioinformatics Institute, ASTAR, 30 Biopolis Street, #07-01 Matrix, 138671, Singapore, Singapore.
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. .,Infectious Diseases Interdisciplinary Research group, Singapore MIT Alliance for Research & Technology, Singapore, Singapore. .,Nanyang Institute of Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, Singapore, 636921, Singapore.
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