1
|
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.
Collapse
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
| |
Collapse
|
2
|
Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| |
Collapse
|
3
|
Xuan TF, Liu J, Wang ZQ, Chen WM, Lin J. Fluorescent Detection of the Ubiquitous Bacterial Messenger 3',5' Cyclic Diguanylic Acid by Using a Small Aromatic Molecule. Front Microbiol 2020; 10:3163. [PMID: 31993044 PMCID: PMC6970945 DOI: 10.3389/fmicb.2019.03163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/31/2019] [Indexed: 12/28/2022] Open
Abstract
3′,5′ Cyclic diguanylic acid (c-di-GMP) has been shown to play a central role in the regulation of bacterial physiological processes such as biofilm formation and virulence production, and is regarded as a potential target for the development of anti-infective drugs. A method for the facile detection of the bacterial level of cellular c-di-GMP is required to explore the details of c-di-GMP signaling and design drugs on the basis of this pathway. Current methods of c-di-GMP detection have limited sensitivity or difficultly in probe preparation. Herein a new fluorescent probe is reported for the detection of c-di-GMP at concentrations as low as 500 nM. The probe was developed on the basis of the G-quadruplex formation of c-di-GMP induced by aromatic molecules. When used on crude bacterial cell lysates, it can effectively distinguish between the low c-di-GMP levels of bacteria in plankton and the high c-di-GMP levels in biofilm. The method described here is simple, inexpensive, sensitive, and suitable for practical applications involving the rapid detection of cellular c-di-GMP levels in vitro after simple bacterial lysis and filtration.
Collapse
Affiliation(s)
- Teng-Fei Xuan
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China
| | - Jun Liu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China
| | - Zi-Qiang Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China
| | - Wei-Min Chen
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China
| | - Jing Lin
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China
| |
Collapse
|
4
|
Kim KT, Kim HW, Moon D, Rhee YM, Kim BH. (DNS)C: a fluorescent, environmentally sensitive cytidine derivative for the direct detection of GGG triad sequences. Org Biomol Chem 2014; 11:5605-14. [PMID: 23846401 DOI: 10.1039/c3ob41222a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With the goal of developing a fluorescent nucleoside sensitive to its environment, in this study we synthesized (DNS)C, a novel modified 2'-deoxycytidine bearing a 5-(dimethylamino)naphthalene-1-sulfonyl (dansyl) moiety at the N4 position, and tested its properties in monomeric and oligomeric states. (DNS)C undergoes intramolecular photoinduced electron transfer between its dansyl and cytosine units, resulting in remarkable changes in fluorescence that depend on the choice of solvent. In addition, the fluorescence behavior and thermal stability of oligonucleotides containing (DNS)C are dependent on the nature of the flanking and neighboring bases. Notably, (DNS)C exhibits fluorescence enhancement only in fully matched duplex DNA containing a GGG triad sequence. The environmental sensitivity of (DNS)C can be exploited as a fluorescence tool for monitoring the interactions of DNA with other biomolecules, including DNA, RNA, and proteins.
Collapse
Affiliation(s)
- Ki Tae Kim
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | | | | | | | | |
Collapse
|
5
|
Musumeci D, Oliviero G, Roviello GN, Bucci EM, Piccialli G. G-quadruplex-forming oligonucleotide conjugated to magnetic nanoparticles: synthesis, characterization, and enzymatic stability assays. Bioconjug Chem 2012; 23:382-91. [PMID: 22239558 DOI: 10.1021/bc200305t] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present work, we report the conjugation of superparamagnetic nanoparticles to a fluorescently labeled oligodeoxyribonucleotide (ODN) able to fold into stable unimolecular guanine quadruple helix under proper ion conditions by means of its thrombin-binding aptamer (TBA) sequence. The novel modified ODN, which contained a fluorescent dU(Py) unit at 3'-end and a 12-amino-dodecyl spacer (C(12)-NH(2)) at 5' terminus, was characterized by ESI-MS and optical spectroscopy (UV, CD, fluorescence), and analyzed by RP-HPLC chromatography and electrophoresis. From CD and fluorescence experiments, we verified that dU(Py) and C(12)-NH(2) incorporation does not interfere with the conformational stability of the G-quadruplex. Subsequently, the conjugation of the pyrene-labeled ODN with the magnetite particles was performed, and the ODN-conjugated nanoparticles were studied through optical spectroscopy (UV, CD, fluorescence) and by enzymatic and chemical assays. We found that the nanoparticles enhanced the stability of the TBA ODN to enzymatic degradation. Finally, we evaluated the amount of the TBA-conjugated nanoparticles immobilized on a magnetic separator in view of the potential use of the nanosystem for the magnetic capture of thrombin from complex mixtures.
Collapse
Affiliation(s)
- Domenica Musumeci
- Dipartimento di Chimica delle Sostanze Naturali, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
| | | | | | | | | |
Collapse
|
6
|
Lee IJ, Park M, Joo T, Kim BH. Using fluorescence changes of F1U units at terminal and mid-loop positions to probe i-motif structures. ACTA ACUST UNITED AC 2012; 8:486-90. [DOI: 10.1039/c1mb05343d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
7
|
Lee IJ, Kim BH. Monitoring i-motif transitions through the exciplex emission of a fluorescent probe incorporating two PyA units. Chem Commun (Camb) 2012; 48:2074-6. [DOI: 10.1039/c1cc16497j] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
8
|
Nakayama S, Kelsey I, Wang J, Roelofs K, Stefane B, Luo Y, Lee VT, Sintim HO. Thiazole orange-induced c-di-GMP quadruplex formation facilitates a simple fluorescent detection of this ubiquitous biofilm regulating molecule. J Am Chem Soc 2011; 133:4856-64. [PMID: 21384923 DOI: 10.1021/ja1091062] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Recently, there has been an explosion of research activities in the cyclic dinucleotides field. Cyclic dinucleotides, such as c-di-GMP and c-di-AMP, have been shown to regulate bacterial virulence and biofilm formation. c-di-GMP can exist in different aggregate forms, and it has been demonstrated that the polymorphism of c-di-GMP is influenced by the nature of cation that is present in solution. In previous work, polymorphism of c-di-GMP could only be demonstrated at hundreds of micromolar concentrations of the dinucleotide, and it has been a matter of debate if polymorphism of c-di-GMP exists under in vivo conditions. In this Article, we demonstrate that c-di-GMP can form G-quadruplexes at low micromolar concentrations when aromatic molecules such as thiazole orange template the quadruplex formation. We then use this property of aromatic molecule-induced G-quadruplex formation of c-di-GMP to design a thiazole orange-based fluorescent detection of this important signaling molecule. We determine, using this thiazole orange assay on a crude bacterial cell lysate, that WspR D70E (a constitutively activated diguanylate cyclase) is functional in vivo when overexpressed in E. Coli . The intracellular concentration of c-di-GMP in an E. Coli cell that is overexpressed with WspR D70E is very high and can reach 2.92 mM.
Collapse
Affiliation(s)
- Shizuka Nakayama
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 658] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| |
Collapse
|
10
|
Lee IJ, Yi JW, Kim BH. Probe for i-motif structure and G-rich strands using end-stacking ability. Chem Commun (Camb) 2009:5383-5. [PMID: 19724792 DOI: 10.1039/b908624b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We suggest a novel method for probing human i-motif structure based on a pi-stacking interaction between a base pair of two cytosines and a non-polar aromatic fluorophore, PyA, at the end position.
Collapse
Affiliation(s)
- Il Joon Lee
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | | | | |
Collapse
|
11
|
Bang EK, Kim BH. Synthesis of hairpin siRNA using 18β-glycyrrhetinic acid derivative as a loop motif. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.03.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
|
12
|
Seo YJ, Lee IJ, Kim BH. Homoadenine signalling system for SNP typing. MOLECULAR BIOSYSTEMS 2008; 5:235-7. [PMID: 19225612 DOI: 10.1039/b821543j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a homoadenine-based fluorescent probing system containing two pyrene-modified deoxyadenosine units for SNP typing in homoadenine and homothymine.
Collapse
Affiliation(s)
- Young Jun Seo
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Korea
| | | | | |
Collapse
|