In Silico Design of Blinatumomab: A conventional Bispecific T Cell Engager for Targeted Immunotherapy

Blinatumomab is an FDA-approved bispecific T Cell engager(BiTE) that binds CD3 on T cells and CD19 on B cells, redirecting cytotoxic T cell activity to malignant B cells. Blinatumomab has achieved clinical success in treating B-cell acute lymphoblastic leukemia(B-ALL), however, the structural and functional optimization of BiTE molecules remains be active research. In this study, we design and report the de novo in silico design of a functional Blinatumomab molecule using computational modeling techniques, followed by molecular dynamics (MD) simulations to evaluate its structural stability, flexibility, and binding interactions. Using available crystal structures of anti-CD3, anti-CD19 single-chain variable fragments(scFvs), and flexible linkers, we engineered a full bispecific T cell engager in silico. The resulting 3D structure was energy-minimized and put through MD simulations in a solvated environment in order to retrieve conformation stability and inter-domain interactions. Parameters like root mean square deviation(RMSD), root mean square fluctuation(RMSF), radius of gyration, and hydrogen bond persistence were additionally monitored from the MD simulations. To further assess the structure, we calculate the free energy of folding and binding using MM/PBSA methods. These energy profiles provided domain stability and interchain interactions. Developing a valid computation model of a BiTE molecule is useful for additional testing in comparison to in vivo and clinical lab tests for improving BiTE Immunotherapy. Computational models are cost-effective and enable faster testing, optimization, and screening prior to in vivo experimental synthesis.