The design and synthesis of bacterial RNAP inhibitors

The increasing occurrence of multi drug resistant bacterial infections has underlined the urgent need for the development of new and more potent antibiotics. Bacterial RNA polymerase (RNAP) is a validated target that allows efficacy and selective toxicity. Unfortunately the efficacy of clinically used RNAP inhibitors (rifamycins) is threatened by the emergence of bacterial resistance. The recent identification of the binding region of myxopyronin (Myx), a natural product antibiotic, coupled with the availability of crystal structural data, offers the possibility of using a ligand- and structure-based design approach for the identification of new drug-like RNA polymerase inhibitors. Validation studies of different docking algorithms were performed on the available X-ray co-crystal structures of Thermus thermophilus RNAP and several ligand- and structure-based virtual screening protocols on the Myx binding region were applied to identify hits for SAR-based exploration. A combined ligand- and structure-based protocol identified two compounds which showed selective inhibitory activity towards E. coli RNAP in the micromolar range of concentration. A SAR expansion programme based upon one of these active molecules was conducted via the synthesis of a chemical library of acylhydrazones in order to identify the factors determining potency and to validate the putative binding mode. Similarity-based virtual screening and docking studies were also applied to explore the close chemical space of the initial hit and to prioritize the synthesis of analogs. Some of the designed compounds showed better inhibitory activity than the initial hit and moreover, one derivative possessed moderate activity towards S. aureus SH1000. A structure-based virtual screening protocol was then conducted on an in-house chemical database, applying a preliminary library filtering approach based on physico-chemical descriptors. The identification of a hit active in the micromolar range of concentration underlined the predictive power of this approach and offered useful ideas for future RNAP inhibitor design.