Comparative Analysis of Steered Molecular Dynamics in Toxin Complexes and Evaluation of Drug k off for Antitoxin Drug Selection

Protein modeling and molecular dynamics (MD) simulations are crucial tools for understanding the functionality and interactions of these proteins. In this study, an exhaustive analysis was conducted to select the best cost-benefit system to be used as a selection method for molecules screening. Steered MD (SMD) simulations were performed with Shiga toxin type 2 (Stx2), an AB5-type toxin, with the purpose of calculating k off in three different complexes with previously selected drugs. The main goal of our group is to identify drugs with potential antitoxin activity. All calculations were performed on the Hypergator cluster (Research Computing, University of Florida). Several steered MD simulations were conducted to determine the optimal speed for the study, with a final selection of 2 Å/ns, resulting in a computational cost of 1.5 hours. Simultaneously, we observed the performance of the steered MD simulations of the Stx2(AB5)-drug and Stx2A1-drug complexes, where the Jarzynski average was 49.51 kJ/mol and 25.69 kJ/mol, respectively. Based on these results, we conducted 6 steered MD simulations for each Stx2-drug complex, obtaining the following Jarzynski average values: i) 49.51 (C20H19F2N3O5), ii) 30 (C23H27ClO7), iii) 27 (C15H16F6N3O+) kJ/mol. Drug i (C20H19F2N3O5) shows significant potential to form a complex with Stx2 in vitro and effectively inhibit its cytotoxic effect in vivo. We will continue the calculations by comparing other selected drugs with those studied so far. The aim is to select the best candidates for in vitro assays on cell cultures susceptible to Stx2, as well as to elucidate the molecular mechanism by which these drugs interact with the toxin.