Development of fluorinated ripostatins as RNA-polymerase inhibitors and potential atibiotics

• Applicant: Dr. Evgeny V. Prusov
• Subject Area: Organic Molecular Chemistry - Synthesis and Characterisation
• Term: from 2011 to 2019
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 204291117

In the previous phase of this project we developed a highly convergent and flexible synthetic strategy towards the molecular architecture of ripostatin A and ripostatin B. With the help of this stategy we generated several stabilized analogues of ripostatins and evaluated their biological activity in RNA-polymerase assays and in bacterial cultures. For this purpose, a collaboration with the group of Prof. Dr. Ebright from Waksman Institute for Microbiology, USA was established. The fluorinated analogs of ripostatin B showed activity comparable to that of natural products while exhibiting substantially improved stability. Additionally, inhibitory action on the RNA-polymerase of the Mycobacterium tuberculosis was observed for these analogues. The Ebright group also obtained a crystal structure of difluoripostatin B-RNA-polymerase complex, which confirmed the Switch region as the binding site of the ligand. These results show that difluororipostatins are promising leads for the further development as potential antibiotics and the exploration of their biomedical potential should be continued. Therefore, the main goals of the project are to gain the additional knowledge regarding structure-activity relationships of macrolactone and side chain modified ripostatins and to generate RNA-polymerase inhibitors with MIC values in the single digit nanomolar range. In this regard, we plan to develop an improved synthetic route to difluroripostatin analogues, which would allow a rapid introduction of various heterocycle-containing side chains to the existing macrolactone core. In conjunction with these studies, the investigation of the catalytic asymmetric additions of difluro-substituted Weinreb amide synthones to aldehydes will be performed in order to provide the access to the important building blocks for the construction of macrolactone ring of difluororipostatin. We also aim to investigate the substitution of exocyclic carboxylic acid with carbamate and tetrazole moieties in the ripostatin B molecule since its binding conformation resembles closely that of myxopyronin, and thus, additional interaction with the binding site can be created. Taking advantage of the information from the now available crystal structure of difluoripostatin B-RNA-polymerase complex, the application of the computational docking methods for the virtual screening of potential analogues will be attempted.

• DFG Programme: Research Grants