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Kim DN, McNaughton AD, Kumar N. Leveraging Artificial Intelligence to Expedite Antibody Design and Enhance Antibody-Antigen Interactions. Bioengineering (Basel) 2024; 11:185. [PMID: 38391671 PMCID: PMC10886287 DOI: 10.3390/bioengineering11020185] [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: 12/30/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
This perspective sheds light on the transformative impact of recent computational advancements in the field of protein therapeutics, with a particular focus on the design and development of antibodies. Cutting-edge computational methods have revolutionized our understanding of protein-protein interactions (PPIs), enhancing the efficacy of protein therapeutics in preclinical and clinical settings. Central to these advancements is the application of machine learning and deep learning, which offers unprecedented insights into the intricate mechanisms of PPIs and facilitates precise control over protein functions. Despite these advancements, the complex structural nuances of antibodies pose ongoing challenges in their design and optimization. Our review provides a comprehensive exploration of the latest deep learning approaches, including language models and diffusion techniques, and their role in surmounting these challenges. We also present a critical analysis of these methods, offering insights to drive further progress in this rapidly evolving field. The paper includes practical recommendations for the application of these computational techniques, supplemented with independent benchmark studies. These studies focus on key performance metrics such as accuracy and the ease of program execution, providing a valuable resource for researchers engaged in antibody design and development. Through this detailed perspective, we aim to contribute to the advancement of antibody design, equipping researchers with the tools and knowledge to navigate the complexities of this field.
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Affiliation(s)
- Doo Nam Kim
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
| | - Andrew D McNaughton
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
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2
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Gonzalez KJ, Huang J, Criado MF, Banerjee A, Tompkins SM, Mousa JJ, Strauch EM. A general computational design strategy for stabilizing viral class I fusion proteins. Nat Commun 2024; 15:1335. [PMID: 38351001 PMCID: PMC10864359 DOI: 10.1038/s41467-024-45480-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: 04/04/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Many pathogenic viruses rely on class I fusion proteins to fuse their viral membrane with the host cell membrane. To drive the fusion process, class I fusion proteins undergo an irreversible conformational change from a metastable prefusion state to an energetically more stable postfusion state. Mounting evidence underscores that antibodies targeting the prefusion conformation are the most potent, making it a compelling vaccine candidate. Here, we establish a computational design protocol that stabilizes the prefusion state while destabilizing the postfusion conformation. With this protocol, we stabilize the fusion proteins of the RSV, hMPV, and SARS-CoV-2 viruses, testing fewer than a handful of designs. The solved structures of these designed proteins from all three viruses evidence the atomic accuracy of our approach. Furthermore, the humoral response of the redesigned RSV F protein compares to that of the recently approved vaccine in a mouse model. While the parallel design of two conformations allows the identification of energetically sub-optimal positions for one conformation, our protocol also reveals diverse molecular strategies for stabilization. Given the clinical significance of viruses using class I fusion proteins, our algorithm can substantially contribute to vaccine development by reducing the time and resources needed to optimize these immunogens.
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Affiliation(s)
- Karen J Gonzalez
- Institute of Bioinformatics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Jiachen Huang
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Miria F Criado
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, 36849, USA
| | - Avik Banerjee
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Stephen M Tompkins
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Jarrod J Mousa
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Eva-Maria Strauch
- Institute of Bioinformatics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, 30602, USA.
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, 30602, USA.
- Department of Medicine, School of Medicine, Washington University, St. Louis, MO, 63110, USA.
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3
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Asarnow D, Becker VA, Bobe D, Dubbledam C, Johnston JD, Kopylov M, Lavoie NR, Li Q, Mattingly JM, Mendez JH, Paraan M, Turner J, Upadhye V, Walsh RM, Gupta M, Eng ET. Recent advances in infectious disease research using cryo-electron tomography. Front Mol Biosci 2024; 10:1296941. [PMID: 38288336 PMCID: PMC10822977 DOI: 10.3389/fmolb.2023.1296941] [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: 09/19/2023] [Accepted: 12/07/2023] [Indexed: 01/31/2024] Open
Abstract
With the increasing spread of infectious diseases worldwide, there is an urgent need for novel strategies to combat them. Cryogenic sample electron microscopy (cryo-EM) techniques, particularly electron tomography (cryo-ET), have revolutionized the field of infectious disease research by enabling multiscale observation of biological structures in a near-native state. This review highlights the recent advances in infectious disease research using cryo-ET and discusses the potential of this structural biology technique to help discover mechanisms of infection in native environments and guiding in the right direction for future drug discovery.
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Affiliation(s)
- Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Vada A. Becker
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States
| | - Daija Bobe
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Charlie Dubbledam
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Jake D. Johnston
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States
| | - Mykhailo Kopylov
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Nathalie R. Lavoie
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, MA, United States
| | - Qiuye Li
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Jacob M. Mattingly
- Department of Chemistry, College of Arts and Sciences, Emory University, Atlanta, GA, United States
| | - Joshua H. Mendez
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Mohammadreza Paraan
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Jack Turner
- European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Viraj Upadhye
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Richard M. Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology and Harvard Medical School, Boston, MA, United States
| | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
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4
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Mitra D, Afreen S, Das Mohapatra PK, Abdalla M. Inhibition of respiratory syncytial virus by Daclatasvir and its derivatives: synthesis of computational derivatives as a new drug development. J Biomol Struct Dyn 2024:1-23. [PMID: 38217429 DOI: 10.1080/07391102.2023.2300408] [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: 08/08/2023] [Accepted: 11/23/2023] [Indexed: 01/15/2024]
Abstract
The most common cause of respiratory tract illness in newborns and young children is the respiratory syncytial virus (RSV). There is no approved vaccination or specific antiviral medication for RSV infections. Here, an attempt has been made to explore the potential of currently marketed drugs as well as their probable derivatives to improve the possibility of developing stronger medications against RSV. From the 100 synthetic drug compounds library, the best drug molecule was identified through drug-likeness properties, toxicity, molecular docking and molecular dynamics simulations. Molecular Mechanics Generalized Born Surface Area (MM-GBSA) was also a method that was applied in this study. Daclatasvir showed the highest binding energy and appeared as the best drug to inhibit matrix protein and a fusion protein of RSV. Based on Daclatasvir, 40 computational derivatives were made. D28, D34 and D40 showed far better results than the actual drug. Changes in lipophilicity character increase the binding energy of derivatives. Molecular dynamic simulations showed their non-deviated, non-fluctuated and stable complex formation with target proteins. The high number of amino acid contacts throughout the trajectory increases the stability and effectiveness of derivatives. The key to producing a novel medicine to eradicate RSV is provided by derivatives. Daclatasvir will be employed as a potential RSV inhibitor up until that point.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, India
| | - Shagufta Afreen
- CAS Key laboratory of Biobased material, Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences, Qingdao, PR China
| | | | - Mohnad Abdalla
- Research Institute of Pediatrics, Children's Hospital Affiliated to Shandong University (Jinan Children's Hospital), Jinan, PR China
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Guerrini G, Mehn D, Fumagalli F, Gioria S, Pedotti M, Simonelli L, Bianchini F, Robbiani DF, Varani L, Calzolai L. Analytical Ultracentrifugation Detects Quaternary Rearrangements and Antibody-Induced Conformational Selection of the SARS-CoV-2 Spike Trimer. Int J Mol Sci 2023; 24:14875. [PMID: 37834322 PMCID: PMC10573103 DOI: 10.3390/ijms241914875] [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: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Analytical ultracentrifugation (AUC) analysis shows that the SARS-CoV-2 trimeric Spike (S) protein adopts different quaternary conformations in solution. The relative abundance of the "open" and "close" conformations is temperature-dependent, and samples with different storage temperature history have different open/close distributions. Neutralizing antibodies (NAbs) targeting the S receptor binding domain (RBD) do not alter the conformer populations; by contrast, a NAb targeting a cryptic conformational epitope skews the Spike trimer toward an open conformation. The results highlight AUC, which is typically applied for molecular mass determination of biomolecules as a powerful tool for detecting functionally relevant quaternary protein conformations.
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Affiliation(s)
- Giuditta Guerrini
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Dora Mehn
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Francesco Fumagalli
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Sabrina Gioria
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Filippo Bianchini
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Davide F. Robbiani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luigi Calzolai
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
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Gonzalez KJ, Huang J, Criado MF, Banerjee A, Tompkins S, Mousa JJ, Strauch EM. A general computational design strategy for stabilizing viral class I fusion proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532924. [PMID: 36993551 PMCID: PMC10055117 DOI: 10.1101/2023.03.16.532924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Many pathogenic viruses, including influenza virus, Ebola virus, coronaviruses, and Pneumoviruses, rely on class I fusion proteins to fuse viral and cellular membranes. To drive the fusion process, class I fusion proteins undergo an irreversible conformational change from a metastable prefusion state to an energetically more favorable and stable postfusion state. An increasing amount of evidence exists highlighting that antibodies targeting the prefusion conformation are the most potent. However, many mutations have to be evaluated before identifying prefusion-stabilizing substitutions. We therefore established a computational design protocol that stabilizes the prefusion state while destabilizing the postfusion conformation. As a proof of concept, we applied this principle to the fusion protein of the RSV, hMPV, and SARS-CoV-2 viruses. For each protein, we tested less than a handful of designs to identify stable versions. Solved structures of designed proteins from the three different viruses evidenced the atomic accuracy of our approach. Furthermore, the immunological response of the RSV F design compared to a current clinical candidate in a mouse model. While the parallel design of two conformations allows identifying and selectively modifying energetically less optimized positions for one conformation, our protocol also reveals diverse molecular strategies for stabilization. We recaptured many approaches previously introduced manually for the stabilization of viral surface proteins, such as cavity-filling, optimization of polar interactions, as well as postfusion-disruptive strategies. Using our approach, it is possible to focus on the most impacting mutations and potentially preserve the immunogen as closely as possible to its native version. The latter is important as sequence re-design can cause perturbations to B and T cell epitopes. Given the clinical significance of viruses using class I fusion proteins, our algorithm can substantially contribute to vaccine development by reducing the time and resources needed to optimize these immunogens.
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Affiliation(s)
- Karen J Gonzalez
- Institute of Bioinformatics, Franklin College of Arts and Sciences, University of Georgia; Athens, GA 30602, USA
| | - Jiachen Huang
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia; Athens, GA 30602, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia; Athens, GA 30602, USA
| | - Miria F Criado
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia; Athens, GA 30602, USA
- Department of Pathobiology, Auburn University; Auburn, AL 36849, USA
| | - Avik Banerjee
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia; Athens, GA 30602, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia; Athens, GA 30602, USA
| | - Stephen Tompkins
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia; Athens, GA 30602, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia; Athens, GA 30602, USA
| | - Jarrod J Mousa
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia; Athens, GA 30602, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia; Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia; Athens, GA 30602, USA
| | - Eva-Maria Strauch
- Institute of Bioinformatics, Franklin College of Arts and Sciences, University of Georgia; Athens, GA 30602, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia; Athens, GA 30602, USA
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia; Athens, GA 30602, USA
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7
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Russell CJ, Govorkova EA. Novel Vaccines and Drugs That Target the Surface Glycoproteins of Influenza Viruses, RSV, Parainfluenza Viruses, and SARS-CoV-2. Viruses 2022; 14:1160. [PMID: 35746631 PMCID: PMC9229051 DOI: 10.3390/v14061160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Newly emerging and seasonal respiratory viruses have a great impact on public health[...]
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Affiliation(s)
- Charles J. Russell
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Elena A. Govorkova
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
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White JM, Schiffer JT, Bender Ignacio RA, Xu S, Kainov D, Ianevski A, Aittokallio T, Frieman M, Olinger GG, Polyak SJ. Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses. mBio 2021; 12:e0334721. [PMID: 34933447 PMCID: PMC8689562 DOI: 10.1128/mbio.03347-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The world was unprepared for coronavirus disease 2019 (COVID-19) and remains ill-equipped for future pandemics. While unprecedented strides have been made developing vaccines and treatments for COVID-19, there remains a need for highly effective and widely available regimens for ambulatory use for novel coronaviruses and other viral pathogens. We posit that a priority is to develop pan-family drug cocktails to enhance potency, limit toxicity, and avoid drug resistance. We urge cocktail development for all viruses with pandemic potential both in the short term (<1 to 2 years) and longer term with pairs of drugs in advanced clinical testing or repurposed agents approved for other indications. While significant efforts were launched against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in vitro and in the clinic, many studies employed solo drugs and had disappointing results. Here, we review drug combination studies against SARS-CoV-2 and other viruses and introduce a model-driven approach to assess drug pairs with the highest likelihood of clinical efficacy. Where component agents lack sufficient potency, we advocate for synergistic combinations to achieve therapeutic levels. We also discuss issues that stymied therapeutic progress against COVID-19, including testing of agents with low likelihood of efficacy late in clinical disease and lack of focus on developing virologic surrogate endpoints. There is a need to expedite efficient clinical trials testing drug combinations that could be taken at home by recently infected individuals and exposed contacts as early as possible during the next pandemic, whether caused by a coronavirus or another viral pathogen. The approach herein represents a proactive plan for global viral pandemic preparedness.
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Affiliation(s)
- Judith M. White
- University of Virginia, Department of Cell Biology, Charlottesville, Virginia, USA
- University of Virginia, Department of Microbiology, Charlottesville, Virginia, USA
| | - Joshua T. Schiffer
- University of Washington, Division of Allergy and Infectious Diseases, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Rachel A. Bender Ignacio
- University of Washington, Division of Allergy and Infectious Diseases, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Shuang Xu
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Denis Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Institute of Technology, University of Tartu, Tartu, Estonia
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Aleksandr Ianevski
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, Oslo, Norway
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Stephen J. Polyak
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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Abernathy ME, Dam KMA, Esswein SR, Jette CA, Bjorkman PJ. How Antibodies Recognize Pathogenic Viruses: Structural Correlates of Antibody Neutralization of HIV-1, SARS-CoV-2, and Zika. Viruses 2021; 13:2106. [PMID: 34696536 PMCID: PMC8537525 DOI: 10.3390/v13102106] [Citation(s) in RCA: 7] [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: 09/16/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
The H1N1 pandemic of 2009-2010, MERS epidemic of 2012, Ebola epidemics of 2013-2016 and 2018-2020, Zika epidemic of 2015-2016, and COVID-19 pandemic of 2019-2021, are recent examples in the long history of epidemics that demonstrate the enormous global impact of viral infection. The rapid development of safe and effective vaccines and therapeutics has proven vital to reducing morbidity and mortality from newly emerging viruses. Structural biology methods can be used to determine how antibodies elicited during infection or vaccination target viral proteins and identify viral epitopes that correlate with potent neutralization. Here we review how structural and molecular biology approaches have contributed to our understanding of antibody recognition of pathogenic viruses, specifically HIV-1, SARS-CoV-2, and Zika. Determining structural correlates of neutralization of viruses has guided the design of vaccines, monoclonal antibodies, and small molecule inhibitors in response to the global threat of viral epidemics.
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Affiliation(s)
- Morgan E. Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (M.E.A.); (K.-M.A.D.); (C.A.J.)
| | - Kim-Marie A. Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (M.E.A.); (K.-M.A.D.); (C.A.J.)
| | - Shannon R. Esswein
- David Geffen School of Medicine at University of California, Los Angeles, CA 90095, USA;
| | - Claudia A. Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (M.E.A.); (K.-M.A.D.); (C.A.J.)
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (M.E.A.); (K.-M.A.D.); (C.A.J.)
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