Expanding the paradigm of glycopeptide antibiotic recognition through molecular dynamics simulations

Glycopeptide antibiotics (GPAs) canonically bind the terminus of peptidoglycan precursors. However, recent work suggests they can engage other targets. Keratinicyclin B (KCB), for example, is believed to bind the wall teichoic acid polysaccharide II (PSII). Although GPA-peptidoglycan interactions are well studied, the molecular determinants of KCB specificity remain unclear. Herein, we employ molecular dynamics and free-energy analysis to probe how scaffold variations, glycosylation patterns, and functional group modifications govern GPA recognition of canonical (peptidoglycan) and noncanonical (PSII) ligands. Our results demonstrate that features beyond the characteristic hydrogen bonding network, including steric preorganization, electrostatics, and binding site solvation, collectively shape the energetic landscape. Simulations of KCB-PSII variants reveal a layered recognition strategy in which PSII is stabilized by a secondary interface when the primary interface is disrupted. Together, these findings expand the paradigm of GPA recognition and provide a mechanistic framework for designing next-generation antibiotics.