Computational discovery of binding mode of anti-TRBC1 antibody and predicted key amino acids of TRBC1.

Jirakrit Saetang, Surasak Sangkhathat, Nawaphat Jangphattananont, Wannakorn Khopanlert, Jakrawadee Julamanee, Varomyalin Tipmanee

Scientific reports 2022 Feb 02

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Peripheral T-cell lymphoma (PTCL) is a type of non-Hodgkin lymphoma that progresses aggressively with poor survival rate. CAR T cell targeting T-cell receptor β-chain constant domains 1 (TRBC1) of malignant T cells has been developed recently by using JOVI.1 monoclonal antibody as a template. However, the mode of JOVI.1 binding is still unknown. This study aimed to investigate the molecular interaction between JOVI.1 antibody and TRBC1 by using computational methods and molecular docking. Therefore, the TRBC protein crystal structures (TRBC1 and TRBC2) as well as the sequences of JOVI.1 CDR were chosen as the starting materials. TRBC1 and TRBC2 epitopes were predicted, and molecular dynamic (MD) simulation was used to visualize the protein dynamic behavior. The structure of JOVI.1 antibody was also generated before the binding mode was predicted using molecular docking with an antibody mode. Epitope prediction suggested that the N3K4 region of TRBC1 may be a key to distinguish TRBC1 from TCBC2. MD simulation showed the major different surface conformation in this area between two TRBCs. The JOVI.1-TRBC1 structures with three binding modes demonstrated JOVI.1 interacted TRBC1 at N3K4 residues, with the predicted dissociation constant (Kd) ranging from 1.5 × 108 to 1.1 × 1010 M. The analysis demonstrated JOVI.1 needed D1 residues of TRBC1 for the interaction formation to N3K4 in all binding modes. In conclusion, we proposed the three binding modes of the JOVI.1 antibody to TRBC1 with the new key residue (D1) necessary for N3K4 interaction. This data was useful for JOVI.1 redesign to improve the PTCL-targeting CAR T cell. © 2022. The Author(s).

Citation

Jirakrit Saetang, Surasak Sangkhathat, Nawaphat Jangphattananont, Wannakorn Khopanlert, Jakrawadee Julamanee, Varomyalin Tipmanee. Computational discovery of binding mode of anti-TRBC1 antibody and predicted key amino acids of TRBC1. Scientific reports. 2022 Feb 02;12(1):1760