Discovery of Potential Prolyl-tRNA Synthetase Allosteric Inhibitor Through Virtual Screening and In Vitro Assay against Plasmodium falciparum

Abstract

Objectives: This study aimed to identify novel antimalarial compounds based on allosteric inhibitor of prolyl-tRNA synthetase using hierarchical virtual screening. Materials and Methods: Pharmacophore model was designed initially, based on the structure-activity relationships data between several pyrazole-urea analogues and their IC50 enzymatic value. The model obtained was applied to screen ZINC15 database, after which followed by drug-likeness, toxicophore, and PAINS filter. The hit compounds were docked against P. falciparum prolyl-tRNA synthetase enzyme, using validated docking method. The resulting docking poses were ranked based on the docking score and re-evaluated based on the pharmacophore criteria. Top five compounds were obtained from this step and then evaluated using molecular dynamics simulation to verify its stability and hydrogen bond dynamics over 50 nanoseconds. MM-PBSA analysis was also performed to estimate their binding free energy. Ultimately, their potential bioactivity as antimalarial candidates have been verified against 3D7 strain. Results: The results showed that all five compounds obtained from virtual screening possess micromolar potency in vitro. Two compounds (ZINC 1029449 and ZINC1029453), yield high antimalarial activity (0.44 and 0.72 μM, respectively) Conclusions: Overall, the virtual screening approach has successfully produced lead compounds which can be further optimized to be antimalarial agents.