Computational investigation of the catalytic mechanism and dynamics of Staphylococcus aureus glycosyltransferase towards development of novel antibiotics

Bacterial glycosyltransferases of the GT51 family are key enzymes in the bacterial cell wall synthesis. Inhibiting cell wall synthesis is a very effective approach for development of antibiotics, as this can lead to either bacteriostatic or bactericidal effects. However, drug development focused on bacterial transglycosylase has been hampered due to little being know about its structure and reaction mechanism. We have addressed this issue by computationally investigating the S. aureus monoglycosyltransferase enzyme, which is one of the main catalysts for peptidoglycan synthesis in S. aureus. Using molecular dynamics simulations, it was possible to gain new insights on the dynamics of the protein and the binding mode of the natural substrate, lipid II. The function of the different protein domains was explored this way, as well as the function of metal ions in facilitating catalysis. It was also found that the binding mode of the natural substrate appears to be different from the commonly proposed binding mode, and that lipid II subunits bind a shared pocket between the flexible flap domain and motif 3. Following these findings, a detailed study of the catalytic mechanism using hybrid quantum mechanics/molecular mechanics provided further insight on the functionality of the protein. One particular mechanism was discovered in which lipid II linkage is catalyzed by a metal-bound hydroxyl ion. With newfound structural information, the binding mode of existing drug-like inhibitors was reevaluated. Through molecular dynamics simulations, a new binding mode was proposed and provided the basis for an extensive virtual screening campaign in which molecular docking was combined with umbrella sampling calculations. The campaign did not lead to the discovery of novel inhibitors, but have paved the way for future virtual screening campaigns. With advancements in X-ray crystallography and cryogenic electron microscopy, high resolution structures of glycosyltransferases in complex with inhibitors should become available. With these new structures, virtual screening campaigns augmented by fragment screening methodologies could very well lead to novel, high potency inhibitors of Staphylococcus aureus glycosyltransferase which could be further developed into novel antibiotics.

Publication year:2021

Keywords:Doctoral thesis

Accessibility:Open