Lipoteichoic acid synthase (LtaS) is a key enzyme for the cell wall biosynthesis of Gram-positive bacteria. Gram-positive bacteria that lack lipoteichoic acid (LTA) exhibit impaired cell division and growth defects. Thus, LtaS appears to be an attractive anti-microbial target. The pharmacology around LtaS remains largely unexplored with only two small molecule LtaS inhibitors reported, namely 'compound 1771' and the Congo Red dye. Structure-based drug discovery effort against LtaS remained unattempted due to the lack of an inhibitor-bound structure of LtaS. To address this, we combined the use of molecular docking technique with molecular dynamics (MD) simulation to model a plausible binding mode of compound 1771 to the extracellular catalytic domain of LtaS (eLtaS). The model was validated using alanine mutagenesis studies combined with isothermal titration calorimetry (ITC). Additionally, lead optimization driven by our computational model resulted in an improved version of compound 1771, namely compound 4 which showed greater
affinity for binding to eLtaS than compound 1771 in biophysical assays. Compound 4 reduced lipoteichoic acid (LTA) production in S. aureus dose-dependently, induced aberrant morphology as seen for LTA-deficient bacteria and significantly reduced bacteria titres in the lung of mice infected with S. aureus. Analysis of our MD simulation trajectories revealed possible formation of a transient cryptic pocket in eLtaS. Virtual screening against the cryptic pocket led to the identification of a new class of inhibitors that could potentiate β-lactams against methicillin-resistant S. aureus. Our overall workflow and data should encourage further drug design campaign against LtaS. Lastly, our work reinforces the
importance of considering protein conformational flexibility to a successful virtual screening endeavour.
