Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor

Scott S. Walker, David Degen, Elliott Nickbarg, Donna Carr, Aileen Soriano, Mihir Mandal, Ronald E. Painter, Payal Sheth, Li Xiao, Xinwei Sher, Nicholas Murgolo, Jing Su, David B. Olsen, Richard H. Ebright, Katherine Young

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

The growing prevalence of drug resistant bacteria is a significant global threat to human health. The antibacterial drug rifampin, which functions by inhibiting bacterial RNA polymerase (RNAP), is an important part of the antibacterial armamentarium. Here, in order to identify novel inhibitors of bacterial RNAP, we used affinity-selection mass spectrometry to screen a chemical library for compounds that bind to Escherichia coli RNAP. We identified a novel small molecule, MRL-436, that binds to RNAP, inhibits RNAP, and exhibits antibacterial activity. MRL-436 binds to RNAP through a binding site that differs from the rifampin binding site, inhibits rifampin-resistant RNAP derivatives, and exhibits antibacterial activity against rifampin-resistant strains. Isolation of mutants resistant to the antibacterial activity of MRL-436 yields a missense mutation in codon 622 of the rpoC gene encoding the RNAP β′ subunit or a null mutation in the rpoZ gene encoding the RNAP ω subunit, confirming that RNAP is the functional cellular target for the antibacterial activity of MRL-436, and indicating that RNAP β′ subunit residue 622 and the RNAP ω subunit are required for the antibacterial activity of MRL-436. Similarity between the resistance determinant for MRL-436 and the resistance determinant for the cellular alarmone ppGpp suggests a possible similarity in binding site and/or induced conformational state for MRL-436 and ppGpp.

Original languageEnglish (US)
Pages (from-to)1346-1352
Number of pages7
JournalACS chemical biology
Volume12
Issue number5
DOIs
StatePublished - May 19 2017

Fingerprint

DNA-Directed RNA Polymerases
Mass spectrometry
Mass Spectrometry
Rifampin
Bacterial RNA
Gene encoding
Binding Sites
Small Molecule Libraries
Missense Mutation
Codon
Pharmaceutical Preparations
Escherichia coli
Genes
Bacteria
Health
Derivatives

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Medicine

Cite this

Walker, S. S., Degen, D., Nickbarg, E., Carr, D., Soriano, A., Mandal, M., ... Young, K. (2017). Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor. ACS chemical biology, 12(5), 1346-1352. https://doi.org/10.1021/acschembio.6b01133
Walker, Scott S. ; Degen, David ; Nickbarg, Elliott ; Carr, Donna ; Soriano, Aileen ; Mandal, Mihir ; Painter, Ronald E. ; Sheth, Payal ; Xiao, Li ; Sher, Xinwei ; Murgolo, Nicholas ; Su, Jing ; Olsen, David B. ; Ebright, Richard H. ; Young, Katherine. / Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor. In: ACS chemical biology. 2017 ; Vol. 12, No. 5. pp. 1346-1352.
@article{65b121784ba248d88740f72f66935e9a,
title = "Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor",
abstract = "The growing prevalence of drug resistant bacteria is a significant global threat to human health. The antibacterial drug rifampin, which functions by inhibiting bacterial RNA polymerase (RNAP), is an important part of the antibacterial armamentarium. Here, in order to identify novel inhibitors of bacterial RNAP, we used affinity-selection mass spectrometry to screen a chemical library for compounds that bind to Escherichia coli RNAP. We identified a novel small molecule, MRL-436, that binds to RNAP, inhibits RNAP, and exhibits antibacterial activity. MRL-436 binds to RNAP through a binding site that differs from the rifampin binding site, inhibits rifampin-resistant RNAP derivatives, and exhibits antibacterial activity against rifampin-resistant strains. Isolation of mutants resistant to the antibacterial activity of MRL-436 yields a missense mutation in codon 622 of the rpoC gene encoding the RNAP β′ subunit or a null mutation in the rpoZ gene encoding the RNAP ω subunit, confirming that RNAP is the functional cellular target for the antibacterial activity of MRL-436, and indicating that RNAP β′ subunit residue 622 and the RNAP ω subunit are required for the antibacterial activity of MRL-436. Similarity between the resistance determinant for MRL-436 and the resistance determinant for the cellular alarmone ppGpp suggests a possible similarity in binding site and/or induced conformational state for MRL-436 and ppGpp.",
author = "Walker, {Scott S.} and David Degen and Elliott Nickbarg and Donna Carr and Aileen Soriano and Mihir Mandal and Painter, {Ronald E.} and Payal Sheth and Li Xiao and Xinwei Sher and Nicholas Murgolo and Jing Su and Olsen, {David B.} and Ebright, {Richard H.} and Katherine Young",
year = "2017",
month = "5",
day = "19",
doi = "10.1021/acschembio.6b01133",
language = "English (US)",
volume = "12",
pages = "1346--1352",
journal = "ACS Chemical Biology",
issn = "1554-8929",
publisher = "American Chemical Society",
number = "5",

}

Walker, SS, Degen, D, Nickbarg, E, Carr, D, Soriano, A, Mandal, M, Painter, RE, Sheth, P, Xiao, L, Sher, X, Murgolo, N, Su, J, Olsen, DB, Ebright, RH & Young, K 2017, 'Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor', ACS chemical biology, vol. 12, no. 5, pp. 1346-1352. https://doi.org/10.1021/acschembio.6b01133

Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor. / Walker, Scott S.; Degen, David; Nickbarg, Elliott; Carr, Donna; Soriano, Aileen; Mandal, Mihir; Painter, Ronald E.; Sheth, Payal; Xiao, Li; Sher, Xinwei; Murgolo, Nicholas; Su, Jing; Olsen, David B.; Ebright, Richard H.; Young, Katherine.

In: ACS chemical biology, Vol. 12, No. 5, 19.05.2017, p. 1346-1352.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor

AU - Walker, Scott S.

AU - Degen, David

AU - Nickbarg, Elliott

AU - Carr, Donna

AU - Soriano, Aileen

AU - Mandal, Mihir

AU - Painter, Ronald E.

AU - Sheth, Payal

AU - Xiao, Li

AU - Sher, Xinwei

AU - Murgolo, Nicholas

AU - Su, Jing

AU - Olsen, David B.

AU - Ebright, Richard H.

AU - Young, Katherine

PY - 2017/5/19

Y1 - 2017/5/19

N2 - The growing prevalence of drug resistant bacteria is a significant global threat to human health. The antibacterial drug rifampin, which functions by inhibiting bacterial RNA polymerase (RNAP), is an important part of the antibacterial armamentarium. Here, in order to identify novel inhibitors of bacterial RNAP, we used affinity-selection mass spectrometry to screen a chemical library for compounds that bind to Escherichia coli RNAP. We identified a novel small molecule, MRL-436, that binds to RNAP, inhibits RNAP, and exhibits antibacterial activity. MRL-436 binds to RNAP through a binding site that differs from the rifampin binding site, inhibits rifampin-resistant RNAP derivatives, and exhibits antibacterial activity against rifampin-resistant strains. Isolation of mutants resistant to the antibacterial activity of MRL-436 yields a missense mutation in codon 622 of the rpoC gene encoding the RNAP β′ subunit or a null mutation in the rpoZ gene encoding the RNAP ω subunit, confirming that RNAP is the functional cellular target for the antibacterial activity of MRL-436, and indicating that RNAP β′ subunit residue 622 and the RNAP ω subunit are required for the antibacterial activity of MRL-436. Similarity between the resistance determinant for MRL-436 and the resistance determinant for the cellular alarmone ppGpp suggests a possible similarity in binding site and/or induced conformational state for MRL-436 and ppGpp.

AB - The growing prevalence of drug resistant bacteria is a significant global threat to human health. The antibacterial drug rifampin, which functions by inhibiting bacterial RNA polymerase (RNAP), is an important part of the antibacterial armamentarium. Here, in order to identify novel inhibitors of bacterial RNAP, we used affinity-selection mass spectrometry to screen a chemical library for compounds that bind to Escherichia coli RNAP. We identified a novel small molecule, MRL-436, that binds to RNAP, inhibits RNAP, and exhibits antibacterial activity. MRL-436 binds to RNAP through a binding site that differs from the rifampin binding site, inhibits rifampin-resistant RNAP derivatives, and exhibits antibacterial activity against rifampin-resistant strains. Isolation of mutants resistant to the antibacterial activity of MRL-436 yields a missense mutation in codon 622 of the rpoC gene encoding the RNAP β′ subunit or a null mutation in the rpoZ gene encoding the RNAP ω subunit, confirming that RNAP is the functional cellular target for the antibacterial activity of MRL-436, and indicating that RNAP β′ subunit residue 622 and the RNAP ω subunit are required for the antibacterial activity of MRL-436. Similarity between the resistance determinant for MRL-436 and the resistance determinant for the cellular alarmone ppGpp suggests a possible similarity in binding site and/or induced conformational state for MRL-436 and ppGpp.

UR - http://www.scopus.com/inward/record.url?scp=85019589272&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85019589272&partnerID=8YFLogxK

U2 - 10.1021/acschembio.6b01133

DO - 10.1021/acschembio.6b01133

M3 - Article

C2 - 28323406

AN - SCOPUS:85019589272

VL - 12

SP - 1346

EP - 1352

JO - ACS Chemical Biology

JF - ACS Chemical Biology

SN - 1554-8929

IS - 5

ER -