Structure-Based Drug Design of Novel Inhibitors Targeting the Thiamine Biosynthesis Pathway in Bacteria

Abstract Current generation antibiotics are limited by poor target selectivity and are often mismanaged, leading to widespread antimicrobial resistance. The bacterial thiamine biosynthesis pathway offers compelling alternative since it is highly essential for bacterial survival and yet absent in humans. Genetic perturbations within pathway lead to documented auxotrophy and virulence defects, indicating low mutational tolerance within this pathway. Thiamine phosphate synthase is a key bottleneck enzyme performing the crucial role of coupling thiazole and pyrimidine moieties to form thiamine monophosphate. To develop a suitable inhibitor against it, a structure-based drug design pipeline was implemented. High-throughput virtual screening of nearly 1.5 million molecules provided sufficient exploration of chemical space. Further, R-group substitution was utilized for lead optimization. Structure-Activity Relationship analysis upon molecular mutants reveals patterns among R-group interactions to catalytic residues across various scaffolds. Additionally, ADMET screening and validation using molecular dynamics simulations resulted in a potent orally bioavailable broad-spectrum bactericidal molecule.