In silico proof of principle of machine learning-based antibody design at unconstrained scale

MAbs. 2022 Jan-Dec;14(1):2031482. doi: 10.1080/19420862.2022.2031482.

Abstract

Generative machine learning (ML) has been postulated to become a major driver in the computational design of antigen-specific monoclonal antibodies (mAb). However, efforts to confirm this hypothesis have been hindered by the infeasibility of testing arbitrarily large numbers of antibody sequences for their most critical design parameters: paratope, epitope, affinity, and developability. To address this challenge, we leveraged a lattice-based antibody-antigen binding simulation framework, which incorporates a wide range of physiological antibody-binding parameters. The simulation framework enables the computation of synthetic antibody-antigen 3D-structures, and it functions as an oracle for unrestricted prospective evaluation and benchmarking of antibody design parameters of ML-generated antibody sequences. We found that a deep generative model, trained exclusively on antibody sequence (one dimensional: 1D) data can be used to design conformational (three dimensional: 3D) epitope-specific antibodies, matching, or exceeding the training dataset in affinity and developability parameter value variety. Furthermore, we established a lower threshold of sequence diversity necessary for high-accuracy generative antibody ML and demonstrated that this lower threshold also holds on experimental real-world data. Finally, we show that transfer learning enables the generation of high-affinity antibody sequences from low-N training data. Our work establishes a priori feasibility and the theoretical foundation of high-throughput ML-based mAb design.

Keywords: Generative machine learning; antibody design; epitope; paratope.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antibodies, Monoclonal / chemistry
  • Antigen-Antibody Reactions*
  • Binding Sites, Antibody
  • Epitopes
  • Machine Learning*

Substances

  • Antibodies, Monoclonal
  • Epitopes

Grant support

This was work was funded by the Leona M. and Harry B. Helmsley Charitable Trust (#2019PG-T1D011, to VG), UiO World-Leading Research Community (to VG), UiO:LifeScience Convergence Environment Immunolingo (to VG, GKS, and IHH), EU Horizon 2020 iReceptorplus (#825821) (to VG), a Research Council of Norway FRIPRO project (#300740, to VG), a Research Council of Norway IKTPLUSS project (#311341, to VG and GKS), a Norwegian Cancer Society Grant (#215817, to VG), and Stiftelsen Kristian Gerhard Jebsen (K.G. Jebsen Coeliac Disease Research Centre) (to GKS).