Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3).

Abstract

Fidaxomicin is an antibacterial drug in clinical use for treatment of Clostridium difficile diarrhea. The active ingredient of fidaxomicin, lipiarmycin A3 (Lpm), functions by inhibiting bacterial RNA polymerase (RNAP). Here we report a cryo-EM structure of Mycobacterium tuberculosis RNAP holoenzyme in complex with Lpm at 3.5-Å resolution. The structure shows that Lpm binds at the base of the RNAP "clamp." The structure exhibits an open conformation of the RNAP clamp, suggesting that Lpm traps an open-clamp state. Single-molecule fluorescence resonance energy transfer experiments confirm that Lpm traps an open-clamp state and define effects of Lpm on clamp dynamics. We suggest that Lpm inhibits transcription by trapping an open-clamp state, preventing simultaneous interaction with promoter -10 and -35 elements. The results account for the absence of cross-resistance between Lpm and other RNAP inhibitors, account for structure-activity relationships of Lpm derivatives, and enable structure-based design of improved Lpm derivatives.

• Authors: Wei Lin, Kalyan Das, David Degen, Abhishek Mazumder, Diego Duchi, Dongye Wang, Yon W Ebright, Richard Y Ebright, Elena Sineva, Matthew Gigliotti, Aashish Srivastava, Sukhendu Mandal, Yi Jiang, Yu Liu, Ruiheng Yin, Zhening Zhang, Edward T Eng, Dennis Thomas, Stefano Donadio, Haibo Zhang, Changsheng Zhang, Achillefs N Kapanidis, Richard H Ebright
• Journal: Molecular cell (Mol Cell) Vol. 70 Issue 1 Pg. 60-71.e15 (04 05 2018) ISSN: 1097-4164 [Electronic] United States
• PMID: 29606590 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)
• Copyright: Copyright © 2018 Elsevier Inc. All rights reserved.

Chemical References

• Anti-Bacterial Agents
• Bacterial Proteins
• DNA-Directed RNA Polymerases
• Fidaxomicin

Topics

• Anti-Bacterial Agents (chemistry, metabolism, pharmacology)
• Bacterial Proteins (antagonists & inhibitors, metabolism, ultrastructure)
• Binding Sites
• Cryoelectron Microscopy
• DNA-Directed RNA Polymerases (antagonists & inhibitors, metabolism, ultrastructure)
• Drug Design
• Drug Resistance, Bacterial (genetics)
• Escherichia coli (drug effects, enzymology, genetics, ultrastructure)
• Fidaxomicin (chemistry, metabolism, pharmacology)
• Fluorescence Resonance Energy Transfer
• Gene Expression Regulation, Bacterial (drug effects)
• Models, Molecular
• Mutation
• Mycobacterium tuberculosis (drug effects, enzymology, genetics, ultrastructure)
• Protein Binding
• Protein Conformation
• Single Molecule Imaging
• Staphylococcus aureus (drug effects, enzymology, genetics)
• Structure-Activity Relationship
• Transcription, Genetic (drug effects)