Selective inhibition of Mycobacterium tuberculosis GpsI unveils a novel strategy to target the RNA metabolism.

Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.

Mycobacterium tuberculosis*/enzymology ; Mycobacterium tuberculosis*/drug effects ; Mycobacterium tuberculosis*/genetics ; Bacterial Proteins*/antagonists & inhibitors ; Bacterial Proteins*/metabolism ; Bacterial Proteins*/chemistry ; Bacterial Proteins*/genetics ; Enzyme Inhibitors*/pharmacology ; Enzyme Inhibitors*/chemistry ; Antitubercular Agents*/pharmacology ; Antitubercular Agents*/chemistry ; RNA*/metabolism; Cryoelectron Microscopy ; Mycobacterium smegmatis/genetics ; Mycobacterium smegmatis/enzymology ; Mycobacterium smegmatis/drug effects ; Binding Sites ; Models, Molecular

Polyribonucleotide nucleotidyl-transferases (PNPases) play a critical role in the degradation of mRNA. The mycobacterial PNPase, guanosine penta-phosphate synthase I (GpsI), is an essential enzyme in Mycobacterium tuberculosis (Mtb), collaborating with endoribonucleases and helicases to process RNA. In this study, we identify GpsI as a novel and underexplored drug target. The inhibitor 1-(4'-(2-phenyl-5-(trifluoromethyl) oxazole-4-carboxamido)-[1,1'-biphenyl]-4-caroxamido) cyclopentane-1-carboxylic acid (X1), discovered through a whole-cell screening, specifically inhibits GpsI activity in biochemical assays. Biochemical and physiological analyses of engineered GpsI variants and recombinant Mycobacterium smegmatis pinpoint amino acids 328 and 527 as critical residues for the selective activity of X1 against Mtb complex. High-resolution cryo-electron microscopy analysis of the ternary GpsI-X1-poly(A) complex elucidates the drug-binding pocket, providing insight into its mechanism of action. This study introduces a potent inhibitor targeting the underexplored Mtb-GpsI and offers a molecular explanation for its selective specificity.
(© The Author(s) 2025. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Protein Sci. 2018 Jan;27(1):293-315. (PMID: 29067766)
Nucleic Acids Res. 2019 Jun 20;47(11):5892-5905. (PMID: 30957850)
J Comput Chem. 2004 Oct;25(13):1605-12. (PMID: 15264254)
Antimicrob Agents Chemother. 2022 Feb 15;66(2):e0151021. (PMID: 34930031)
Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):11966-71. (PMID: 11035800)
Antimicrob Agents Chemother. 1994 Apr;38(4):805-11. (PMID: 8031050)
Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):531-544. (PMID: 29872004)
Science. 2005 Jan 14;307(5707):223-7. (PMID: 15591164)
Lancet. 1993 Mar 13;341(8846):647-50. (PMID: 8095569)
Electrophoresis. 2000 Nov;21(17):3740-56. (PMID: 11271494)
Mol Cell Proteomics. 2011 Jan;10(1):M110.002527. (PMID: 21030493)
Nature. 1992 Aug 13;358(6387):591-3. (PMID: 1501713)
mSystems. 2019 Jun 25;4(4):. (PMID: 31239393)
RNA. 2008 Nov;14(11):2361-71. (PMID: 18812438)
Infect Genet Evol. 2024 Sep;123:105645. (PMID: 39067582)
Structure. 2000 Nov 15;8(11):1215-26. (PMID: 11080643)
Lancet Infect Dis. 2019 Feb;19(2):e40-e50. (PMID: 30337260)
Antimicrob Agents Chemother. 2024 Aug 7;68(8):e0053524. (PMID: 39007560)
Sci Rep. 2018 Jun 22;8(1):9539. (PMID: 29934571)
Wiley Interdiscip Rev RNA. 2016 Mar-Apr;7(2):241-58. (PMID: 26750178)
Trans R Soc Trop Med Hyg. 2016 Mar;110(3):163-72. (PMID: 26884496)
Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844)
RNA. 2021 Jun 4;:. (PMID: 34088850)
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501. (PMID: 20383002)
Arch Biochem Biophys. 2024 Apr;754:109917. (PMID: 38395123)
Antimicrob Agents Chemother. 2015 Sep;59(9):5316-23. (PMID: 26100695)
Cell. 2021 Aug 19;184(17):4579-4592.e24. (PMID: 34297925)
Antimicrob Agents Chemother. 2017 Jun 27;61(7):. (PMID: 28438933)
PLoS Pathog. 2011 Sep;7(9):e1002251. (PMID: 21980284)
Curr Opin Pharmacol. 2018 Oct;42:81-94. (PMID: 30144650)
Int J Infect Dis. 2022 Nov;124 Suppl 1:S20-S25. (PMID: 35342000)
J Mol Biol. 2009 May 29;389(1):17-33. (PMID: 19327365)
mBio. 2017 Jan 17;8(1):. (PMID: 28096490)
N Engl J Med. 2022 Sep 1;387(9):810-823. (PMID: 36053506)
J Clin Tuberc Other Mycobact Dis. 2021 Nov 05;25:100285. (PMID: 34816020)
Microbiol Immunol. 2005;49(11):1003-7. (PMID: 16301812)
Sci Rep. 2015 Jan 26;5:8028. (PMID: 25619596)
Open Biol. 2012 Apr;2(4):120028. (PMID: 22724061)
FEMS Microbiol Rev. 2010 Sep;34(5):883-923. (PMID: 20659169)
Protein Sci. 2023 Nov;32(11):e4792. (PMID: 37774136)
J Mol Med (Berl). 2019 Nov;97(11):1601-1613. (PMID: 31728550)
J Antimicrob Chemother. 2017 Feb;72(2):376-384. (PMID: 27999011)

P41 GM103311 United States GM NIGMS NIH HHS; R01 GM129325 United States GM NIGMS NIH HHS; Switzerland SNSF_ Swiss National Science Foundation; 3632001500 Federal Office of Public Health; 2022_050 JPIAMR; 310030_197699/1 Switzerland SNSF_ Swiss National Science Foundation

0 (Bacterial Proteins)
0 (Enzyme Inhibitors)
0 (Antitubercular Agents)
63231-63-0 (RNA)

Date Created: 20250618 Date Completed: 20250618 Latest Revision: 20250630

20250630

PMC12203904

10.1093/nar/gkaf529

40530695