Computational elucidation and validation of the three-dimensional structure of humanized aldolase catalytic antibody...

Catalytic antibodies are immunoglobulin proteins that are capable of catalyzing multiple reactions with diverse substrates. Aldolase catalytic antibody 38C2 catalyzes aldol and retro-aldol reactions via an enamine mechanism. Therefore, 38C2 has a high potential to be used in prodrug activation, and it is currently developed for selective chemotherapy. For medical applications, its humanization is essential, and therefore, the understanding of the three-dimensional (3D) spatial atomistic structure of 38C2 is mandatory. In this study, it was attempted to construct the 3D atomic structure of humanized abzyme 38C2 using computational methods. A homology modeled structure was simulated for 100 ns with classical molecular dynamics simulations for its dynamics stability. The accuracy of the constructed model was further evaluated with various theoretical methods. The binding of four selected natural substrates to the constructed structure was studied in detail to further validate the model. Finally, to evaluate the reaction readiness of the constructed protein, the first step of the catalytic reaction has been successfully carried out with QST3/IRC calculations using the DFT/B3LYP-6-31G level of theory in the presence of extracted catalytic residues with the preserved coordinates in implicit water. Hence, the reaction readiness of the proposed protein structure, along with all the other validation tests, strongly proves that the modeled structure has high accuracy. This study, therefore, sheds new light on the structure, mechanism of action and applications of the 38C2 abzyme by constructing and validating its full 3D atomistic model. Further, this highly reliable modeled structure will expedite and facilitate future 38C2-based drug discovery.Communicated by Ramaswamy H. Sarma.