The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase

Abstract

Rifampicin (Rif) is a first-line therapeutic used to treat the infectious disease tuberculosis (TB), which is caused by the pathogenMycobacterium tuberculosis(Mtb). The emergence of Rif-resistant (RifR)Mtbpresents a need for new antibiotics. Rif targets the enzyme RNA polymerase (RNAP). Sorangicin A (Sor) is an unrelated inhibitor that binds in the Rif-binding pocket of RNAP. Sor inhibits a subset of RifRRNAPs, including the most prevalent clinical RifRRNAP substitution found inMtbinfected patients (S456>L of the β subunit). Here, we present structural and biochemical data demonstrating that Sor inhibits the wild-typeMtbRNAP by a similar mechanism as Rif: by preventing the translocation of very short RNAs. By contrast, Sor inhibits the RifRS456L enzyme at an earlier step, preventing the transition of a partially unwound promoter DNA intermediate to the fully opened DNA and blocking the template-strand DNA from reaching the active site in the RNAP catalytic center. By defining template-strand blocking as a mechanism for inhibition, we provide a mechanistic drug target in RNAP. Our finding that Sor inhibits the wild-type and mutant RNAPs through different mechanisms prompts future considerations for designing antibiotics against resistant targets. Also, we show that Sor has a better pharmacokinetic profile than Rif, making it a suitable starting molecule to design drugs to be used for the treatment of TB patients with comorbidities who require multiple medications.

Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model

“…Importantly, these findings highlight the importance of β-lobe during transcription initiation, which open opportunities to the development of antibiotics that target β-lobe. Interestingly, a recent cryo-EM study suggests that an antibiotic, Sorangicin, may inhibit the bacterial transcription via affecting the movement of β-lobe through allosteric interactions (73).…”

Natural products lysobactin and sorangicin A show in vitro activity against Mycobacterium abscessus complex

“…36,37 Like RIF and RFB, SOR inhibits bacterial transcription via binding to the RpoB subunit of wildtype RNAP but in M. tuberculosis, SOR was shown to prevent promoter DNA unwinding specifically in RIF R mutants. 27,38 Importantly, SOR maintained activity against E. coli and M. tuberculosis rpoB mutants despite being resistant to RIF. This has important implications for the treatment of M. tuberculosis as RIF is a front-line agent and for the treatment of M. abscessus since the activity of RFB has recently been explored.…”

A Rifampicin-resistant (rpoB) Mutation in Pseudomonas Stutzeri Leads to Enhance the Biosynthesis of Secondary Metabolites and Nitrogen Fixation to Adapt Against Harsh Environments

“…Consecutively, the highest nitrogenase activity was determined at 7h interval in rifr mutant D521V that was of 2176.58 nmole ethylene/h/mg proteins and at the same time the lowest was of 1061 ethylene/h/mg protein in I614T. The antibiotic rif is binding to RNA polymerase β subunit within the DNA/RNA channel and acts as an inhibitor blocking the elongation of RNA [8,22], but there were no nitrogenase inhibitory effects among the studied strains in respect of nitrogen xation.…”