title: Validation of the AmpC β-lactamase binding site and identification of inhibitors with novel scaffolds.
abstract: AmpC β-lactamase confers resistance to β-lactam antibiotics in multiple Gram-negative bacteria. Therefore, identification of non-β-lactam compounds that inhibit the enzyme is considered crucial to the development of novel antibacterial therapies. Given the highly solvent-exposed active site, it is important to study the induced-fit movements and water-mediated interactions to improve docking accuracy and virtual screening enrichments in structure-based design of new AmpC inhibitors. Here, we tested multiple models of the AmpC binding site to investigate the importance of conserved water molecules and binding site plasticity on molecular docking. The results indicate that at least one conserved water molecule greatly improves the binding pose predictions and virtual screening enrichments of known noncovalent AmpC inhibitors. The best model was tested prospectively in the virtual screening of about 6 million commercially available compounds. Sixty-one chemically diverse top-scoring compounds were experimentally tested, which led to the identification of seven previously unknown inhibitors. These findings validate the essential features of the AmpC binding site for molecular recognition and are useful for further optimization of identified inhibitors.
authors.affiliation: Department of Applied Biology and Chemical Technology and State Key Laboratory of Chirosciences,  The Hong Kong Polytechnic University , Hung Hom, Kowloon, Hong Kong, P. R. China.
authors.forename: Fung-Yi
authors.initials: FY
authors.lastname: Chan
authors.forename: Marco A C
authors.initials: MA
authors.lastname: Neves
authors.forename: Ning
authors.initials: N
authors.lastname: Sun
authors.forename: Man-Wah
authors.initials: MW
authors.lastname: Tsang
authors.forename: Yun-Chung
authors.initials: YC
authors.lastname: Leung
authors.forename: Tak-Hang
authors.initials: TH
authors.lastname: Chan
authors.forename: Ruben
authors.initials: R
authors.lastname: Abagyan
authors.forename: Kwok-Yin
authors.initials: KY
authors.lastname: Wong
mesh_terms: D001426:Bacterial Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D016972:Enterobacter cloacae / Q000201:enzymology; D004789:Enzyme Activation / Q000187:drug effects; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D006801:Humans; D020128:Inhibitory Concentration 50; D008024:Ligands; D015394:Molecular Structure; D011485:Protein Binding / Q000187:drug effects; D054852:Small Molecule Libraries / Q000737:chemistry* / Q000494:pharmacology; D065093:beta-Lactamase Inhibitors; D001618:beta-Lactamases / Q000737:chemistry / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004791:Enzyme Inhibitors; D008024:Ligands; D054852:Small Molecule Libraries; D065093:beta-Lactamase Inhibitors; C048795:AmpC beta-lactamases; D001618:beta-Lactamases