Stereoselective synthesis and mechanistic studies of boron-containing antibacterials and beta-lactamase inhibitors

Beta-Lactamases are bacterial enzymes that degrade Beta-lactam antibiotics, the most widely prescribed class of antibiotics worldwide. Their clinical efficacy is threatened by serine-Beta-lactamases (SBLs; Classes A, C and D) and metallo-Beta-lactamases (MBLs; Class B), two mechanistically divergent groups of bacterial enzymes used for hydrolytic inactivation of Beta-lactam antibiotics. While there are currently several marketed SBL inhibitors, a clinically useful MBL inhibitor is yet to be developed. This project aims to prolong the clinical utility of Beta-lactam antibiotics through the discovery and development of novel boron-containing small molecules that inhibit Beta-lactamases, thereby limiting the degradation of Beta-lactams. Recently, boron-based molecules have attracted a great deal of scientific attention and are one of the most promising and exciting classes of broad-spectrum Beta-lactamase inhibitors due to the unique and attractive physiochemical properties of boron. This project explores the versatile chemistry of boron through the synthesis of diverse (a)cyclic boronates inspired by natural products and derived from computational analyses. Project Aims: i. To optimise asymmetric synthetic routes towards existing boronate scaffolds (e.g. VNRX-5133) and to develop new robust routes towards novel boron-containing and hydrolytically stable MBL, SBL and PBP inhibitors; ii. To understand and study the effects of varied bicyclic ring sizes (6-5, 6-6 or larger), hybridization states (sp2 or sp3) and structural configurations (closed or open) of cyclic boronates on the inhibition of SBLs, MBLs and PBPs; iii. To investigate why cyclic boronates are not able to effectively inhibit PBPs; iv.To carry out mechanistic studies on the dynamic centre and relate this equilibrium to enzyme binding/inhibition. Results Summary: Asymmetric synthesis of bicyclic boronate VNRX-5133 (Taniborbactam) and other (a)cyclic boronates. Optimised stereoselective synthesis of VNRX- 5133 has been successfully completed, following extensive method development/optimisation efforts. Strenuous efforts towards other novel bicyclic boronate analogues have also been made, some are still in progress. Results from this work have been thus far published in several peer-reviewed publications. NMR investigations of boronate binding/conformation. By crystallography, unexpected tricyclic inhibitor form of VNRX-5133 was observed. 1H/11B NMR studies are in-progress to try verify the relevance of this form in solution, as well to study the pH-dependent conformations of this and other related boronates, in order to try to develop an in-depth understanding of how this class of compounds behaves both in solution (at different pHs) and when engaged with a biological target. Fragment-based boron work: a library of bicyclic boronates (6-5/6-6 ring systems) has been synthesised and tested for inhibition against a panel of SBLs and MBLs. Several crystal structure of these fragments with various beta-lactamases have been obtained through collaborative research efforts. Additionally, a fragment-based drug design (FBDD) approach was used for in silico design of several boron-containing small molecules have been synthesised, and these will be validated once series is completed. Mechanistic studies on enzymes for TB. Stereoselective synthesis of bacterial cell-wall component is in-progress, which has the potential to be used in developed enzyme assays.
This project falls within the following EPSRC research areas: Research infrastructure (Synthetic Organic Chemistry) and Healthcare Technologies (Chemical Biology and Biological Chemistry).