Structure-based approach for binding site identification on AmpC -lactamase

â-Lactamases are the most widespread resistance mechanism to â-lactam antibiotics and are an increasing menace to public health. Several â-lactamase structures have been determined, making this enzyme an attractive target for structure-based drug design. To facilitate inhibitor design for the class C â-lactamase AmpC, binding site “hot spots ” on the enzyme were identified using experimental and computational approaches. Experimentally, X-ray crystal structures of AmpC in complexes with four boronic acid inhibitors and a higher resolution (1.72 Å) native apo structure were determined. Along with previously determined structures of AmpC in complexes with five other boronic acid inhibitors and four â-lactams, consensus binding sites were identified. Computationally, the programs GRID, MCSS, and X-SITE were used to predict potential binding site hot spots on AmpC. Several consensus binding sites were identified from the crystal structures. An amide recognition site was identified by the interaction between the carbonyl oxygen in the R1 side chain of â-lactams and the atom Nä2 of the conserved Asn152. Surprisingly, this site also recognizes the aryl rings of arylboronic acids, appearing to form quadrupole-dipole interactions with Asn152. The highly conserved “oxyanion ” hole defines a site that recognizes both carbonyl and hydroxyl groups. A hydroxyl binding site was identifie