Structure-Based Discovery of a Novel, Noncovalent Inhibitor of AmpC β-Lactamase

Abstract

beta-lactamases are the most widespread resistance mechanisms to beta-lactam antibiotics, and there is a pressing need for novel, non-beta-lactam drugs. A database of over 200,000 compounds was docked to the active site of AmpC beta-lactamase to identify potential inhibitors. Fifty-six compounds were tested, and three had K(i) values of 650 microM or better. The best of these, 3-[(4-chloroanilino)sulfonyl]thiophene-2-carboxylic acid, was a competitive noncovalent inhibitor (K(i) = 26 microM), which also reversed resistance to beta-lactams in bacteria expressing AmpC. The structure of AmpC in complex with this compound was determined by X-ray crystallography to 1.94 A and reveals that the inhibitor interacts with key active-site residues in sites targeted in the docking calculation. Indeed, the experimentally determined conformation of the inhibitor closely resembles the prediction. The structure of the enzyme-inhibitor complex presents an opportunity to improve binding affinity in a novel series of inhibitors discovered by structure-based methods.

Hierarchical Docking of Databases of Multiple Ligand Conformations

“…For flexible molecules that can adopt many conformations, the method increases selectivity for ligands, improves sampling near the native binding modes, and does so at little computational cost. In our own lab, we now use this hierarchical method regularly, and it has lead to the discovery of new ligands in several targets [41][42][43][44].…”

Structure-based Discovery of Antagonists of Nuclear Receptor LRH-1

“…We attribute the success in the discovery of LRH-1-specific inhibitors to an efficient screening strategy, which combined high throughput computer-assisted search for compounds with preferred structural characteristics with the following in vitro direct binding and functional assays for compound selection and validation. Such combinations of the protein-centric computational approaches with experimental verifications of the top-ranked hits have proven to be successful for identification of specific ligands for different protein targets in the past (53)(54)(55)(56)(57).…”

Three Decades of β-Lactamase Inhibitors

“…Inhibitors with a sulfonamide core and varied substituents were developed by structure-based optimization (351,413). This non-␤-lactam design approach is intended to avoid both hydrolysis by ␤-lactamases and the upregulation of ␤-lactamases induced by some ␤-lactam-based inhibitors.…”

“…This non-␤-lactam design approach is intended to avoid both hydrolysis by ␤-lactamases and the upregulation of ␤-lactamases induced by some ␤-lactam-based inhibitors. Starting from a map of binding "hot spots" developed from crystal structures of 13 different ligands in complex with the E. coli AmpC ␤-lactamase, 200,000 commercially available small molecules were docked into the active site of the enzyme by computer simulation (351,352). Based on these results, lead compounds were screened in vitro, and the molecule with the highest affinity (26 M) was crystallized in complex with the AmpC (PDB 1L2S) (Fig.…”