In silico discovery of thioglycoside analogues as donor-site inhibitors of glycosyltransferase LgtC

Abstract The growing prevalence of multidrug-resistant Gram-negative pathogens highlights the urgent need for therapeutic strategies that complement traditional antibiotics by targeting essential virulence pathways. Glycosyltransferase LgtC, a key enzyme in lipooligosaccharide (LOS) biosynthesis, represents an attractive target for antivirulence approaches because of its essential role in bacterial immune evasion and pathogenicity. In this work, we employed an integrated in silico pipeline to identify thioglycoside analogs structurally related to the metabolic decoys FucSBn and BacSBn, evaluating their potential to hit the UDP-galactose donor pocket of LgtC. A similarity-based screening in PubChem, followed by ADME–Tox filtering yield 18 candidate analogs. Molecular docking using AutoDock-GPU revealed several candidates, most notably C-5 (− 8.36 kcal/mol) and C-18 (− 8.13 kcal/mol), to bind favorably within the donor site, showing more negative mean scoring values than natural donor UDP-α-D-galactose (− 6.74 kcal/mol). Redocking of the natural ligand reproduced the crystallographic pose, supporting the reliability of the docking protocol. To assess dynamic behavior, 100 ns molecular dynamics simulations (AMBER14) were performed for each complex. The top-scoring analogs maintained stable binding poses, with RMSD values of ~ 2.0–3.0 Å and preserved donor-like hydrogen-bond networks complemented by π-stacking and sulfur-mediated contacts. These interaction patterns suggest that the thioglycoside analogs may occupy the donor site in a manner compatible with competitive binding. While docking and MD describe different aspects of ligand recognition, several trends observed in docking, such as the favorable binding scores of C-5 and C-18, are broadly consistent with their ability to maintain stable poses during MD. Based on this consistency and scoring, the thioglycoside scaffolds C-5, C-14, and C-18 emerge as computationally prioritized candidates for subsequent biochemical testing against LgtC. Furthermore, these scaffolds offer a mechanistic basis and putative starting points for future structure-based optimization of thioglycoside analogs aimed at disrupting LOS biosynthesis in multidrug-resistant Gram-negative bacteria.