β-lactam antibiotics, such as penicillin, are among the most commonly prescribed group of antibiotics. These antibiotics are characterized by a four-membered β-lactam ring in their molecular structure, and they act by binding to transpeptidase enzymes found exclusively in bacteria, also called penicillin binding proteins (PBPs). Once the β-lactam binds to this target, bacterial cell wall biosynthesis is disrupted and the bacteria lyse and die.
Unfortunately, due to the heavy use of these antibiotics, bacteria developed mechanisms that can render β-lactams inactive and lead to resistance. Antibiotic resistance in humans and in animals poses a serious public health threat and is a growing health concern worldwide. One mechanism for bacterial resistance to β-lactam antibiotics is the production of a β-lactamase enzyme that hydrolyzes the β-lactam ring of the antibiotic, making the antibiotic ineffective against its target, the bacterial cell wall transpeptidase. Currently, there are four recognized classes of β-lactamases (A-D) classified by their unique mechanism for destroying β-lactam antibiotics. Classes A, C and D act by a serine based mechanism for destruction which involves a two-step acylation/ deacylation reaction. Despite their increasing clinical importance, class D β-lactamases are among the least understood. To date, about 250 known class D β-lactamases have been identified. OXA-1 is a member of the noncarbapenem- hydrolyzing subgroup of the class D β-lactamases and the first discovered.
β-lactamase inhibitors were created in an effort to combat these resistance enzymes. Due to the similarities in structures of both the β-lactam antibiotic substrate and the inhibitor, bacteria have rapidly evolved to develop mechanisms to resist the inhibitors as well. Unfortunately, the common clinical β-lactamase inhibitors do not often inhibit class D β-lactamases. Therefore, the major goal to studying the class D β-lactamase OXA-1 is to discover a competitive inhibitor that does not have a structure similar to β-lactam compounds because bacteria would not be able to quickly evolve to develop mechanisms to resist these non-β-lactam molecules.
The discovery of a novel inhibitor for an enzyme target is a challenging task. We have chosen a structure-based approach using DOCK, a molecular docking program. DOCK computationally predicts binding conformations of a database of small molecules within a target site on the enzyme. The ZINC database of commercially available compounds was used in our docking calculations and allowed for millions of small compounds to be screened against the target OXA- 1 active site. Compounds were ranked by favorable interaction energies, and the top compounds in the list suggested possibilities for potential inhibitors. In part, interaction energies are calculated based on the size and shape of the molecule, as well as the non-covalent interactions between the molecule and OXA-1 active site. The top hits, or compounds most likely to inhibit based on their docking score, were experimentally tested.
Structure-based docking led to the identification of several novel leads that inhibit OXA-1 β-lactamase. So far, 13 compounds from the lead-like subset have been ordered and tested experimentally for inhibition of OXA-1. Of the 13 compounds tested, five inhibited OXA- 1 with a Ki < 1 mM. Optimization of a novel series of OXA-1 inhibitors is currently underway.
*This scholar and faculty mentor have requested that only an abstract be published.