A synthetic diterpene analogue inhibits mycobacterial persistence and biofilm formation by targeting (p)ppGpp synthetases

Alexander G Tkachenko; Natalya M Kashevarova; Roman Yu Sidorov; Larisa Yu Nesterova; Anna V Akhova; Ivan V Tsyganov; Vladimir Yu Vaganov; Sergei A Shipilovskikh; Aleksandr E Rubtsov; Andrei V Malkov

doi:10.1016/j.chembiol.2021.01.018

A synthetic diterpene analogue inhibits mycobacterial persistence and biofilm formation by targeting (p)ppGpp synthetases

Cell Chem Biol. 2021 Oct 21;28(10):1420-1432.e9. doi: 10.1016/j.chembiol.2021.01.018. Epub 2021 Feb 22.

Affiliations

¹ Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia; Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia. Electronic address: agtkachenko@iegm.ru.
² Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia.
³ Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia; Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia.
⁴ Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia.
⁵ Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia. Electronic address: rubtsov@psu.ru.
⁶ Department of Chemistry, Loughborough University Address: University Road, Loughborough, Leicestershire LE11 3TU, UK. Electronic address: a.malkov@lboro.ac.uk.

PMID: 33621482
DOI: 10.1016/j.chembiol.2021.01.018

Abstract

Bacterial persistence coupled with biofilm formation is directly associated with failure of antibiotic treatment of tuberculosis. We have now identified 4-(4,7-DiMethyl-1,2,3,4-tetrahydroNaphthalene-1-yl)Pentanoic acid (DMNP), a synthetic diterpene analogue, as a lead compound that was capable of suppressing persistence and eradicating biofilms in Mycobacterium smegmatis. By using two reciprocal experimental approaches - Δrel_Msm and ΔrelZ gene knockout mutations versus rel_Msm and relZ overexpression technique - we showed that both Rel_Msm and RelZ (p)ppGpp synthetases are plausible candidates for serving as targets for DMNP. In vitro, DMNP inhibited (p)ppGpp-synthesizing activity of purified Rel_Msm in a concentration-dependent manner. These findings, supplemented by molecular docking simulation, suggest that DMNP targets the structural sites shared by Rel_Msm, RelZ, and presumably by a few others as yet unidentified (p)ppGpp producers, thereby inhibiting persister cell formation and eradicating biofilms. Therefore, DMNP may serve as a promising lead for development of antimycobacterial drugs.

Keywords: (p)ppGpp synthetases; Rel(Msm); RelZ; biofilm formation; diterpene; mycobacteria; persistence; synthetic analogue; target.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Anti-Bacterial Agents / chemical synthesis
Anti-Bacterial Agents / metabolism
Anti-Bacterial Agents / pharmacology
Bacterial Proteins / antagonists & inhibitors
Bacterial Proteins / metabolism*
Binding Sites
Biofilms / drug effects*
Diterpenes / chemistry
Diterpenes / metabolism
Diterpenes / pharmacology*
Ligases / antagonists & inhibitors
Ligases / metabolism*
Microbial Sensitivity Tests
Molecular Docking Simulation
Mycobacterium smegmatis / drug effects
Mycobacterium smegmatis / enzymology*
Mycobacterium smegmatis / physiology
Protein Structure, Tertiary

Substances

Anti-Bacterial Agents
Bacterial Proteins
Diterpenes
guanosine pentaphosphate synthetase
Ligases