Discovery of AI-2 Quorum Sensing Inhibitors Targeting the LsrK/HPr Protein-Protein Interaction Site by Molecular Dynamics Simulation, Virtual Screening, and Bioassay Evaluation

• Published in: Pharmaceuticals (Basel, Switzerland) Vol. 16; no. 5; p. 737
• Main Authors: Xu, Yijie, Zeng, Chunlan, Wen, Huiqi, Shi, Qianqian, Zhao, Xu, Meng, Qingbin, Li, Xingzhou, Xiao, Junhai
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 12.05.2023; MDPI
• Subjects: AI-2; Analysis; antibacterial agents; Antibiotics; Bacteria; Bacterial infections; Binding sites; Bioassays; Biofilms; Complications and side effects; Crystal structure; Decomposition; Dosage and administration; Drug resistance; Drug resistance in microorganisms; Drug therapy; Energy; Genes; Glucose; Gram-positive bacteria; Hydrogen bonds; LsrK; Methods; Molecular dynamics; Motility; Multidrug resistant organisms; Patient outcomes; Phosphorylation; Prevention; Proteins; Quorum sensing; Simulation; virtual screening; Virulence; China; AI-2; quorum sensing; LsrK; quorum sensing inhibitors; virtual screening; antibacterial agents; HPr; molecular dynamics
• ISSN: 1424-8247; 1424-8247
• DOI: 10.3390/ph16050737

Quorum sensing (QS) is a cell-to-cell communication mechanism that regulates bacterial pathogenicity, biofilm formation, and antibiotic sensitivity. Among the identified quorum sensing, AI-2 QS exists in both Gram-negative and Gram-positive bacteria and is responsible for interspecies communication. Recent studies have highlighted the connection between the phosphotransferase system (PTS) and AI-2 QS, with this link being associated with protein-protein interaction (PPI) between HPr and LsrK. Here, we first discovered several AI-2 QSIs targeting the LsrK/HPr PPI site through molecular dynamics (MD) simulation, virtual screening, and bioassay evaluation. Of the 62 compounds purchased, eight compounds demonstrated significant inhibition in LsrK-based assays and AI-2 QS interference assays. Surface plasmon resonance (SPR) analysis confirmed that the hit compound 4171-0375 specifically bound to the LsrK-N protein (HPr binding domain, KD = 2.51 × 10 M), and therefore the LsrK/HPr PPI site. The structure-activity relationships (SARs) emphasized the importance of hydrophobic interactions with the hydrophobic pocket and hydrogen bonds or salt bridges with key residues of LsrK for LsrK/HPr PPI inhibitors. These new AI-2 QSIs, especially 4171-0375, exhibited novel structures, significant LsrK inhibition, and were suitable for structural modification to search for more effective AI-2 QSIs.