?-lactams, like penicillin and the cephalosporins, are the most widely prescribed class of antibiotics in clinical use today. In response to their extensive use and misuse, resistance has developed and is now one of the most pressing public health crises of the 21st century. Many resistant bacteria express ?-lactamase enzymes. These enzymes hydrolyze the defining lactam ring, rendering them inactive toward their original target, the transpeptidases that crosslink the bacterial cell wall. ?-lactamases are categorized into four, distinct classes (A, B, C, and D) based on sequence similarity and mechanism of action. In an effort to overcome resistance, inhibitors have been developed to block the activity of these enzymes. Of particular concern are the class D ?-lactamases, or oxacillinases (OXAs), which are not inhibited by classic ?-lactam-based inhibitors, like clavulanic acid, and are able to hydrolyze several of the most potent ?-lactams in clinical use (the oxyimino cephalosporins and the carbapenems). In part, resistance derives from the structural similarity of the inhibitors to te ?-lactams themselves: both contain a ?-lactam ring. Therefore an urgent need exists for novel inhibitors that do not resemble the ?-lactam substrates. However, most structure-based design efforts rely on modification of existing ?-lactam antibiotics. Our strategy uses a consensus map of binding sites present on the enzyme and pairs this with molecular docking to discover novel inhibitors for the class D ?-lactamases. We identified two classes of inhibitors using this approach. The first are non-covalent fragments that were identified via molecular docking, and the second are reversible, covalent boronic acid transition state analogs. Both classes provide an excellent starting point for optimization of these compounds into viable leads with desired drug-like properties. With X-ray crystal structures of class D ?-lactamases in complexes with molecules from each class now in hand, we are poised to develop these compounds into the first clinical inhibitors for class D ?-lactamases.
