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Ciaco S, Aronne R, Fiabane M, Mori M. The Rise of Bacterial G-Quadruplexes in Current Antimicrobial Discovery. ACS OMEGA 2024; 9:24163-24180. [PMID: 38882119 PMCID: PMC11170735 DOI: 10.1021/acsomega.4c01731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024]
Abstract
Antimicrobial resistance (AMR) is a silent critical issue that poses several challenges to health systems. While the discovery of novel antibiotics is currently stalled and prevalently focused on chemical variations of the scaffolds of available drugs, novel targets and innovative strategies are urgently needed to face this global threat. In this context, bacterial G-quadruplexes (G4s) are emerging as timely and profitable targets for the design and development of antimicrobial agents. Indeed, they are expressed in regulatory regions of bacterial genomes, and their modulation has been observed to provide antimicrobial effects with translational perspectives in the context of AMR. In this work, we review the current knowledge of bacterial G4s as well as their modulation by small molecules, including tools and techniques suitable for these investigations. Finally, we critically analyze the needs and future directions in the field, with a focus on the development of small molecules as bacterial G4s modulators endowed with remarkable drug-likeness.
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Affiliation(s)
- Stefano Ciaco
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Rossella Aronne
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Martina Fiabane
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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Lemke C, Roach K, Ortega T, Tantillo DJ, Siegel JB, Peters RJ. Investigation of Acid–Base Catalysis in Halimadienyl Diphosphate Synthase Involved in Mycobacterium tuberculosis Virulence. ACS BIO & MED CHEM AU 2022; 2:490-498. [PMID: 36281298 PMCID: PMC9585517 DOI: 10.1021/acsbiomedchemau.2c00023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The devastating human
pathogenMycobacterium tuberculosis (Mtb)
is able to parasitize phagosomal compartments within alveolar
macrophage cells due, in part, to the activity of its cell-surface
lipids. Prominent among these is 1-tuberculosinyl-adenosine (1-TbAd),
a derivative of the diterpenoid tuberculosinyl (halima-5,13-dienyl)
diphosphate produced by the class II diterpene cyclase encoded by
Rv3377c, termed here MtHPS. Given the demonstrated ability of 1-TbAd
to act as a virulence factor for Mtb and the necessity for Rv3377c
for its production, there is significant interest in MtHPS activity.
Class II diterpene cyclases catalyze a general acid–base-mediated
carbocation cascade reaction initiated by protonation of the terminal
alkene in the general diterpenoid precursor (E,E,E)-geranylgeranyl diphosphate and terminated by deprotonation of the
final cyclized (and sometimes also rearranged) intermediate. Here,
structure-guided mutagenesis was applied to characterize the various
residues contributing to activation of the enzymatic acid, as well
as identify the enzymatic base in MtHPS. Particularly given the ability
of conservative substitution for the enzymatic base (Y479F) to generate
an alternative product (labda-7,13-dienyl diphosphate) via deprotonation
of an earlier unrearranged intermediate, further mutational analysis
was carried out to introduce potential alternative catalytic bases.
The results were combined with mechanistic molecular modeling to elucidate
how these mutations affect the catalytic activity of this important
enzyme. This not only provided detailed structure–function
insight into MtHPS but also further emphasized the inert nature of
the active site of MtHPS and class II diterpene cyclases more generally.
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Affiliation(s)
- Cody Lemke
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Kristin Roach
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Teresa Ortega
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Justin B. Siegel
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California-Davis, Davis, California 95616, United States
- Genome Center, University of California-Davis, Davis, California 95616, United States
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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