Vertical Multi-Target Design of Potential Staphylococcus aureus Respiratory Inhibitors: A Systematic in Silico Fragment-Based Approach

Multi-target drug design has emerged as a promising strategy to overcome the limitations of single-target drugs, particularly in combating infectious diseases that develop resistance through different mechanisms. Enzymes in the Menaquinone (MK) biosynthesis pathway of Staphylococcus aureus represent attractive targets for this approach, as they catalyze the sequential steps in the pathway, each of which processes a substrate intermediate that contains a thioester-coenzyme A or dicarboxylate moiety. Therefore, this acts as a vertical targeting strategy where multiple enzymes within the same pathway can be inhibited simultaneously. In this study, we provide the first systematic approach for vertical multi-target design. We used an in silico fragment-based approach to match the structural features of the active sites and identify common pharmacophoric elements, and screen for compounds that can simultaneously inhibit target enzymes within the MK pathway. Common fragments across the targets were identified through multi-target docking, and built compounds were prioritized using a geometric mean-based multi-target activity score. Structure-based pharmacophore modeling revealed a conserved Donor-Hydrophobic-Ring-Ring motif across all active sites. Molecular dynamics simulations supported the stability and multi-target potential of the identified compounds.