REVIEW article

Front. Immunol.

Sec. Vaccines and Molecular Therapeutics

Volume 16 - 2025 | doi: 10.3389/fimmu.2025.1571371

Applying computational protein design to therapeutic antibody discovery - current state and perspectives

Provisionally accepted
Weronika BielskaWeronika Bielska1,2Igor JaszczyszynIgor Jaszczyszyn2,3Paweł DudzicPaweł Dudzic2Bartosz JanuszBartosz Janusz2Dawid ChomiczDawid Chomicz2Sonia WrobelSonia Wrobel2Victor GreiffVictor Greiff4,5Ryan FeehanRyan Feehan6Jared Adolf-BryfogleJared Adolf-Bryfogle6Konrad KrawczykKonrad Krawczyk2*
  • 1Medical University of Lodz, Łódź, Poland
  • 2NaturalAntibody, Kraków, Lesser Poland, Poland
  • 3Medical University of Warsaw, Warsaw, Masovian, Poland
  • 4Department of Immunology, University of Oslo, Oslo, Norway
  • 5Imprint Labs, LLC, New York, United States
  • 6Janssen Pharmaceuticals, Inc., Titusville, New Jersey, United States

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Machine learning applications in protein sciences have ushered in a new era for designing molecules in silico. Antibodies, which currently form the largest group of biologics in clinical use, stand to benefit greatly from this shift. Despite the proliferation of these protein design tools, their direct application to antibodies is often limited by the unique structural biology of these molecules. We note that multiple methods attempting antibody design focus on the discovery of an antigen-specific antibody. Here, we review the current computational methods for antibody design, focusing on binder discovery, contextualizing their role in the drug discovery process.

Keywords: Antibody discovery, AlphaFold 2, machine learning, Drug Discovery, therapeutic antibodies, Protein design

Received: 05 Feb 2025; Accepted: 24 Apr 2025.

Copyright: © 2025 Bielska, Jaszczyszyn, Dudzic, Janusz, Chomicz, Wrobel, Greiff, Feehan, Adolf-Bryfogle and Krawczyk. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Konrad Krawczyk, NaturalAntibody, Kraków, Lesser Poland, Poland

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

Supplementary Material