De novo design methods hold the promise of reducing the time and cost of antibody discovery while enabling the facile and precise targeting of predetermined epitopes. Here, we describe a fragment-based method for the com-binatorial design of antibody binding loops and their grafting onto antibody scaffolds. We designed and tested six single-domain antibodies targeting different epitopes on three antigens, including the receptor-binding do-main of the SARS-CoV-2 spike protein. Biophysical characterization showed that all designs are stable and bind their intended targets with affinities in the nanomolar range without in vitro affinity maturation. We further dis-cuss how a high-resolution input antigen structure is not required, as similar predictions are obtained when the input is a crystal structure or a computer-generated model. This computational procedure, which readily runs on a laptop, provides a starting point for the rapid generation of lead antibodies binding to preselected epitopes.

Fragment-based computational design of antibodies targeting structured epitopes / M. Aguilar Rangel, A. Bedwell, E. Costanzi, R.J. Taylor, R. Russo, G.J.L. Bernardes, S. Ricagno, J. Frydman, M. Vendruscolo, P. Sormanni. - In: SCIENCE ADVANCES. - ISSN 2375-2548. - 8:45(2022 Nov 11), pp. eabp9540.1-eabp9540.14. [10.1126/sciadv.abp9540]

Fragment-based computational design of antibodies targeting structured epitopes

E. Costanzi;R. Russo;S. Ricagno;
2022

Abstract

De novo design methods hold the promise of reducing the time and cost of antibody discovery while enabling the facile and precise targeting of predetermined epitopes. Here, we describe a fragment-based method for the com-binatorial design of antibody binding loops and their grafting onto antibody scaffolds. We designed and tested six single-domain antibodies targeting different epitopes on three antigens, including the receptor-binding do-main of the SARS-CoV-2 spike protein. Biophysical characterization showed that all designs are stable and bind their intended targets with affinities in the nanomolar range without in vitro affinity maturation. We further dis-cuss how a high-resolution input antigen structure is not required, as similar predictions are obtained when the input is a crystal structure or a computer-generated model. This computational procedure, which readily runs on a laptop, provides a starting point for the rapid generation of lead antibodies binding to preselected epitopes.
Settore BIO/10 - Biochimica
PRIN202022SRICA_01 - Protein misfolding in AL amyloidosis: from fibrillar deposits to soluble toxicity - RICAGNO, STEFANO - PRIN2020 - PRIN bando 2020 - 2022
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/945481
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