Exploring the potential of structure-based deep learning approaches for T cell receptor design

• Published in: PLoS computational biology 2024-09, Vol.20 (9), p.e1012489
• Main Authors: Ribeiro-Filho, Helder V, Jara, Gabriel E, Guerra, João V S, Cheung, Melyssa, Felbinger, Nathaniel R, Pereira, José G C, Pierce, Brian G, Lopes-de-Oliveira, Paulo S
• Format: Article
• Language: English
• Subjects: Antigen receptors, T cell; Biology and Life Sciences; Computer and Information Sciences; Immunotherapy; Machine learning; Medicine and Health Sciences; Methods; Protein engineering; Protein research; Proteins; Receptors; Research and Analysis Methods; Structure; T cells
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1012489

Deep learning methods, trained on the increasing set of available protein 3D structures and sequences, have substantially impacted the protein modeling and design field. These advancements have facilitated the creation of novel proteins, or the optimization of existing ones designed for specific functions, such as binding a target protein. Despite the demonstrated potential of such approaches in designing general protein binders, their application in designing immunotherapeutics remains relatively underexplored. A relevant application is the design of T cell receptors (TCRs). Given the crucial role of T cells in mediating immune responses, redirecting these cells to tumor or infected target cells through the engineering of TCRs has shown promising results in treating diseases, especially cancer. However, the computational design of TCR interactions presents challenges for current physics-based methods, particularly due to the unique natural characteristics of these interfaces, such as low affinity and cross-reactivity. For this reason, in this study, we explored the potential of two structure-based deep learning protein design methods, ProteinMPNN and ESM-IF1, in designing fixed-backbone TCRs for binding target antigenic peptides presented by the MHC through different design scenarios. To evaluate TCR designs, we employed a comprehensive set of sequence- and structure-based metrics, highlighting the benefits of these methods in comparison to classical physics-based design methods and identifying deficiencies for improvement.