Abstract

Discovery of Novel Dual ATP-Competitive Inhibitors of DNA Gyrase and Topoisomerase IV inspired by Marine Natural Compounds

Danijel Kikelj, Professor, University of Ljubljana

Bacterial DNA gyrase and topoisomerase IV are heterotetrameric proteins consisting of two GyrA or ParC subunits involved in DNA binding, and two GyrB or ParE subunits which bind ATP. They are validated targets in the discovery of antibacterial drugs but inhibitors of their ATP-binding subunits GyrB and ParE, have so far not reached the clinical use. Growing resistance against the fluoroquinolones that target the GyrA/ParC subunits, limits their therapeutic use and requires the search for novel inhibitors targeting the GyrB/ParE ATP-binding sites. The attractiveness of these two enzymes for antibacterial drug discovery is evidenced by several recent publications and patent applications on bacterial DNA gyrase and topoIV inhibitors.1 Recently, we have realized that the 4,5-dibromo-1H-pyrrole-2-carboxamide moiety, present in Agelas oroides marine sponge alkaloid oroidin, is a suitable group for binding to the hydrophobic pocket of the Escherichia coli GyrB ATP-binding site.2 Optimization of initial low micromolar hits based on the 4,5,6,7-tetrahydrobenzo[1,2-d]thiazole scaffold resulted in a series of low nanomolar E. coli and submicromolar Staphylococcus aureus DNA gyrase inhibitors possessing micromolar inhibitory activity against E. coli and S. aureus topoIV. These compounds also displayed modest antibacterial activity against Gram positive S. aureus and Enterococcus faecalis, while they were found to be efflux pump substrates in E. coli, which most likely leads to their inactivity against Gram negative bacterial strains.2 Replacement of the 4,5,6,7-tetrahydrobenzo[1,2-d]thiazole skeleton by the benzothiazole scaffold3 resulted in almost equipotent E. coli DNA gyrase inhibitors some of which possessed balanced dual DNA gyrase/topoIV inhibitory activities. High resolution crystal structure of the E. coli GyrB in complex with a benzothiazole inhibitor gave insight into its interactions within the ATP-binding site and provided basis for further structure-based optimization. Starting from the 4,5,6,7-tetrahydrobenzo[1,2-d]thiazole series of E. coli DNA gyrase inhibitors, a new structural class of N-phenylpyrrolamides was designed and, through several optimisation cycles, led to low nanomolar E. coli DNA gyrase inhibitors. The binding mode of this structural class to the ATP-binding site of E. coli GyrB was revealed by a high-resolution crystal structure of the enzyme in complex with a N-phenyl-4,5-dibromopyrrolamide-based inhibitor.4,5 Potent bacterial DNA gyrase inhibition, observed antibacterial activity and available structural information highlight these structural classes of DNA gyrase and topoisomerase IV inhibitors as promising starting points for their structure-based optimization to achieve improved antibacterial activity.