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Pérez-Soto M, Ramos-Soriano J, Peñalver P, Belmonte-Reche E, O'Hagan MP, Cucchiarini A, Mergny JL, Galán MC, López López MC, Thomas MDC, Morales JC. DNA G-quadruplexes in the genome of Trypanosoma cruzi as potential therapeutic targets for Chagas disease: Dithienylethene ligands as effective antiparasitic agents. Eur J Med Chem 2024; 276:116641. [PMID: 38971047 DOI: 10.1016/j.ejmech.2024.116641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/08/2024]
Abstract
Chagas disease is caused by the parasite Trypanosoma cruzi and affects over 7 million people worldwide. The two actual treatments, Benznidazole (Bzn) and Nifurtimox, cause serious side effects due to their high toxicity leading to treatment abandonment by the patients. In this work, we propose DNA G-quadruplexes (G4) as potential therapeutic targets for this infectious disease. We have found 174 PQS per 100,000 nucleotides in the genome of T. cruzi and confirmed G4 formation of three frequent motifs. We synthesized a family of 14 quadruplex ligands based in the dithienylethene (DTE) scaffold and demonstrated their binding to these identified G4 sequences. Several DTE derivatives exhibited micromolar activity against epimastigotes of four different strains of T. cruzi, in the same concentration range as Bzn. Compounds L3 and L4 presented remarkable activity against trypomastigotes, the active form in blood, of T. cruzi SOL strain (IC50 = 1.5-3.3 μM, SI = 25-40.9), being around 40 times more active than Bzn and displaying much better selectivity indexes.
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Affiliation(s)
- Manuel Pérez-Soto
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avenida Del Conocimiento, 17, Armilla, 18016 Granada, Spain
| | | | - Pablo Peñalver
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avenida Del Conocimiento, 17, Armilla, 18016 Granada, Spain
| | - Efres Belmonte-Reche
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada / Andalusian Regional Government, PTS Granada, Av. de La Ilustración, 114, 18016 Granada, Spain; Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain; Instituto de Investigación Biosanitaria Ibs.GRANADA, Hospital Virgen de Las Nieves, Granada, Spain
| | - Michael P O'Hagan
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Anne Cucchiarini
- Laboratoire d'optique et Biosciences, Ecole Polytechnique, Inserm U1182, CNRS UMR7645, Institut Polytechnique de Paris, Palaiseau, France
| | - Jean-Louis Mergny
- Laboratoire d'optique et Biosciences, Ecole Polytechnique, Inserm U1182, CNRS UMR7645, Institut Polytechnique de Paris, Palaiseau, France
| | - M Carmen Galán
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom.
| | - Manuel Carlos López López
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avenida Del Conocimiento, 17, Armilla, 18016 Granada, Spain.
| | - María Del Carmen Thomas
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avenida Del Conocimiento, 17, Armilla, 18016 Granada, Spain.
| | - Juan Carlos Morales
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avenida Del Conocimiento, 17, Armilla, 18016 Granada, Spain.
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2
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Gómez-Bra A, Gude L, Arias-Pérez MS. Synthesis, structural study and antitumor activity of novel alditol-based imidazophenanthrolines (aldo-IPs). Bioorg Med Chem 2024; 99:117563. [PMID: 38215623 DOI: 10.1016/j.bmc.2023.117563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024]
Abstract
A series of 1H-imidazo [4,5-f][1,10] phenanthroline derivatives functionalized at 2-position with chiral, and conformationally flexible polyhydroxy alkyl chains derived from carbohydrates (alditol-based imidazophenanthrolines, aldo-IPs) is presented herein. These novel glycomimetics showed relevant and differential cytotoxic activity against several cultured tumor cell lines (PC3, HeLa and HT-29), dependent on the nature and stereochemistry of the polyhydroxy alkyl chain. The mannose-based aldo-IP demonstrated the higher cytotoxicity in the series, substantially better than cisplatin metallo-drug in all cell lines tested, and better than G-quadruplex ligand 360A in HeLa and HT29 cells. Cell cycle experiments and Annexin V-PI assays revealed that aldo-IPs induce apoptosis in HeLa cells. Initial study of DNA interactions by DNA FRET melting assays proved that the aldo-IPs produce only a slight thermal stabilization of DNA secondary structures, more pronounced in the case of quadruplex DNA. Viscosity titrations with CT dsDNA suggest that the compounds behave as DNA groove binders, whereas equilibrium dialysis assays showed that the compounds bind CT with Ka values in the range 104-105 M-1. The aldo-IP derivatives were obtained with synthetically useful yields through a feasible one-pot multistep process, by aerobic oxidative cyclization of 1,10-phenanthroline-5,6-diamine with a selection of unprotected aldoses using (NH4)2SO4 as promoter.
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Affiliation(s)
- Ana Gómez-Bra
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28805-Alcalá de Henares, Madrid, Spain; Grupo DISCOBAC, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), Spain
| | - Lourdes Gude
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28805-Alcalá de Henares, Madrid, Spain; Grupo DISCOBAC, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), Spain.
| | - María-Selma Arias-Pérez
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28805-Alcalá de Henares, Madrid, Spain.
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3
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Monti L, Di Antonio M. G-Quadruplexes as Key Transcriptional Regulators in Neglected Trypanosomatid Parasites. Chembiochem 2023; 24:e202300265. [PMID: 37146230 PMCID: PMC10946822 DOI: 10.1002/cbic.202300265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/07/2023]
Abstract
G-quadruplexes (G4s) are nucleic acid secondary structures that have been linked to the functional regulation of eukaryotic organisms. G4s have been extensively characterised in humans and emerging evidence suggests that they might also be biologically relevant for human pathogens. This indicates that G4s might represent a novel class of therapeutic targets for tackling infectious diseases. Bioinformatic studies revealed a high prevalence of putative quadruplex-forming sequences (PQSs) in the genome of protozoans, which highlights their potential roles in regulating vital processes of these parasites, including DNA transcription and replication. In this work, we focus on the neglected trypanosomatid parasites, Trypanosoma and Leishmania spp., which cause debilitating and deadly diseases across the poorest populations worldwide. We review three examples where G4-formation might be key to modulate transcriptional activity in trypanosomatids, providing an overview of experimental approaches that can be used to exploit the regulatory roles and relevance of these structures to fight parasitic infections.
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Affiliation(s)
- Ludovica Monti
- Chemistry Department, Imperial College LondonMolecular Sciences Research Hub82 Wood LaneW12 0BZLondonUK
| | - Marco Di Antonio
- Chemistry Department, Imperial College LondonMolecular Sciences Research Hub82 Wood LaneW12 0BZLondonUK
- The Francis Crick Institute1 Midland RoadNW1 1ATLondonUK
- The Institute of Chemical BiologyMolecular Sciences Research Hub82 Wood LaneW12 0BZLondonUK
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Structure-Activity Relationship studies on divalent naphthalene diimide G quadruplex ligands with anticancer and antiparasitic activity. Bioorg Med Chem 2022; 71:116946. [DOI: 10.1016/j.bmc.2022.116946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/18/2022]
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Mendes E, Aljnadi IM, Bahls B, Victor BL, Paulo A. Major Achievements in the Design of Quadruplex-Interactive Small Molecules. Pharmaceuticals (Basel) 2022; 15:300. [PMID: 35337098 PMCID: PMC8953082 DOI: 10.3390/ph15030300] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022] Open
Abstract
Organic small molecules that can recognize and bind to G-quadruplex and i-Motif nucleic acids have great potential as selective drugs or as tools in drug target discovery programs, or even in the development of nanodevices for medical diagnosis. Hundreds of quadruplex-interactive small molecules have been reported, and the challenges in their design vary with the intended application. Herein, we survey the major achievements on the therapeutic potential of such quadruplex ligands, their mode of binding, effects upon interaction with quadruplexes, and consider the opportunities and challenges for their exploitation in drug discovery.
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Affiliation(s)
- Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
| | - Israa M. Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bruno L. Victor
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
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Ramos-Soriano J, Galan MC. Photoresponsive Control of G-Quadruplex DNA Systems. JACS AU 2021; 1:1516-1526. [PMID: 34723256 PMCID: PMC8549047 DOI: 10.1021/jacsau.1c00283] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Indexed: 05/14/2023]
Abstract
G-quadruplex (G4) oligonucleotide secondary structures have recently attracted significant attention as therapeutic targets owing to their occurrence in human oncogene promoter sequences and the genome of pathogenic organisms. G4s also demonstrate interesting catalytic activities in their own right, as well as the ability to act as scaffolds for the development of DNA-based materials and nanodevices. Owing to this diverse range of opportunities to exploit G4 in a variety of applications, several strategies to control G4 structure and function have emerged. Interrogating the role of G4s in biology requires the delivery of small-molecule ligands that promote its formation under physiological conditions, while exploiting G4 in the development of responsive nanodevices is normally achieved by the addition and sequestration of the metal ions required for the stabilization of the folded structure. Although these strategies prove successful, neither allows the system in question to be controlled externally. Meanwhile, light has proven to be an attractive means for the control of DNA-based systems as it is noninvasive, can be delivered with high spatiotemporal precision, and is orthogonal to many chemical and biological processes. A plethora of photoresponsive DNA systems have been reported to date; however, the vast majority deploy photoreactive moieties to control the stability and assembly of duplex DNA hybrids. Despite the unique opportunities afforded by the regulation of G-quadruplex formation in biology, catalysis, and nanotechnology, comparatively little attention has been devoted to the design of photoresponsive G4-based systems. In this Perspective, we consider the potential of photoresponsive G4 assemblies and examine the strategies that may be used to engineer these systems toward a variety of applications. Through an overview of the main developments in the field to date, we highlight recent progress made toward this exciting goal and the emerging opportunities that remain ripe for further exploration in the coming years.
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Affiliation(s)
- Javier Ramos-Soriano
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - M Carmen Galan
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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Oshchepkov AS, Reznichenko O, Xu D, Morozov BS, Granzhan A, Kataev EA. Dye-functionalized phosphate-binding macrocycles: from nucleotide to G-quadruplex recognition and "turn-on" fluorescence sensing. Chem Commun (Camb) 2021; 57:10632-10635. [PMID: 34581337 DOI: 10.1039/d1cc04096k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel strategy to design "turn-on" fluorescent receptors for G-quadruplexes of DNA is presented, which relies on the connection of phosphate binding macrocycles (PBM) with naphthalimide dyes. A new PBM-dye family was synthesized and evaluated in terms of binding and detection of nucleotides and DNA G-quadruplexes of different topologies.
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Affiliation(s)
- Aleksandr S Oshchepkov
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany. .,Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Oksana Reznichenko
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, Bât. 110, Centre Universitaire Paris Sud, F-91405 Orsay, France
| | - Dan Xu
- Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Boris S Morozov
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany. .,Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, Bât. 110, Centre Universitaire Paris Sud, F-91405 Orsay, France
| | - Evgeny A Kataev
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany. .,CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, Bât. 110, Centre Universitaire Paris Sud, F-91405 Orsay, France
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