Title: 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 pathogen Mycobacterium tuberculosis (Mtb). The emergence of Rif-resistant (Rif^R) Mtb presents 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 Rif^R RNAPs, including the most prevalent clinical Rif^R RNAP substitution found in Mtb infected patients (S456>L of the β subunit). In this paper, we present structural and biochemical data demonstrating that Sor inhibits the wild-type Mtb RNAP by a similar mechanism as Rif: by preventing the translocation of very short RNAs. By contrast, Sor inhibits the RifR S456L 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 hasmore » 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.« less

Authors:

Lilic, Mirjana  ^[1];

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• Search DOE PAGES for ORCID "0000-0002-2669-3998"

Chen, James  ^[1];

• Search DOE PAGES for author "Chen, James"
• Search DOE PAGES for ORCID "0000-0002-2311-003X"

Boyaci, Hande ^[1]; Braffman, Nathaniel  ^[1];

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• Search DOE PAGES for ORCID "0000-0001-6563-984X"

Hubin, Elizabeth A. ^[1]; Herrmann, Jennifer ^[2]; Müller, Rolf  ^[2];

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• Search DOE PAGES for ORCID "0000-0002-1042-5665"

Mooney, Rachel ^[3]; Landick, Robert  ^[3];

• Search DOE PAGES for author "Landick, Robert"
• Search DOE PAGES for ORCID "0000-0002-5042-0383"

Darst, Seth A.  ^[1];

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• Search DOE PAGES for ORCID "0000-0002-8241-3153"

Campbell, Elizabeth A. ^[1]

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+ Show Author Affiliations

1. Rockefeller Univ., New York, NY (United States)
2. Saarland Univ., Saarbrücken (Germany); Center for Infection Research, Braunschweig (Germany)
3. Univ. of Wisconsin, Madison, WI (United States)

Publication Date:

Mon Nov 16 00:00:00 EST 2020

Research Org.:

Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Org.:

Simons Foundation; New York State Office of Science,Technology and Academic Research; National institutes of Health (NIH); National Institute of General Medical Sciences (NIGMS); Agouron Institute; USDOE Office of Science (SC); The Charles H. Revson Foundation

OSTI Identifier:

1763105

Grant/Contract Number:  

SF349247; GM103310; F00316; OD019994; 1S10RR027037; P41 GM103403; AC02-06CH11357; R01 GM114450; CEN5650030

Resource Type:

Accepted Manuscript

Journal Name:

Proceedings of the National Academy of Sciences of the United States of America

Additional Journal Information:

Journal Volume: 117; Journal Issue: 48; Journal ID: ISSN 0027-8424

Publisher:

National Academy of Sciences

Country of Publication:

United States

Language:

ENGLISH

Subject:

59 BASIC BIOLOGICAL SCIENCES; RNA polymerase; sorangicin A; cryo-electron microscopy; multidrug-resistant Mycobacterium tuberculosis; antibiotics