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Guillon J, Cohen A, Boudot C, Monic S, Savrimoutou S, Moreau S, Albenque-Rubio S, Lafon-Schmaltz C, Dassonville-Klimpt A, Mergny JL, Ronga L, Bernabeu de Maria M, Lamarche J, Lago CD, Largy E, Gabelica V, Moukha S, Dozolme P, Agnamey P, Azas N, Mullié C, Courtioux B, Sonnet P. Design, Synthesis, and Antiprotozoal Evaluation of New Promising 2,9- Bis[(substituted-aminomethyl)]-4,7-phenyl-1,10-phenanthroline Derivatives, a Potential Alternative Scaffold to Drug Efflux. Pathogens 2022; 11:1339. [PMID: 36422591 PMCID: PMC9699089 DOI: 10.3390/pathogens11111339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2023] Open
Abstract
A series of novel 2,9-bis[(substituted-aminomethyl)]-4,7-phenyl-1,10-phenanthroline derivatives was designed, synthesized, and evaluated in vitro against three protozoan parasites (Plasmodium falciparum, Leishmania donovani and Trypanosoma brucei brucei). Pharmacological results showed antiprotozoal activity with IC50 values in the sub and μM range. In addition, the in vitro cytotoxicity of these original molecules was assessed with human HepG2 cells. The substituted diphenylphenanthroline 1l was identified as the most potent antimalarial derivative with a ratio of cytotoxic to antiparasitic activities of 505.7 against the P. falciparum CQ-resistant strain W2. Against the promastigote forms of L. donovani, the phenanthrolines 1h, 1j, 1n and 1o were the most active with IC50 from 2.52 to 4.50 μM. The phenanthroline derivative 1o was also identified as the most potent trypanosomal candidate with a selectivity index (SI) of 91 on T. brucei brucei strain. FRET melting and native mass spectrometry experiments evidenced that the nitrogen heterocyclic derivatives bind the telomeric G-quadruplexes of P. falciparum and Trypanosoma. Moreover, as the telomeres of the parasites P. falciparum and Trypanosoma could be considered to be possible targets of this kind of nitrogen heterocyclic derivatives, their potential ability to stabilize the parasitic telomeric G-quadruplexes have been determined through the FRET melting assay and by native mass spectrometry.
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Affiliation(s)
- Jean Guillon
- Faculty of Pharmacy, University of Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Anita Cohen
- Faculty of Pharmacy, University of Aix-Marseille, IRD, AP-HM, SSA, VITROME, F-13005 Marseille, France
| | - Clotilde Boudot
- Faculty of Pharmacy, Institute of Neuroepidemiology and Tropical Neurology, University of Limoges, INSERM U1094, F-87025 Limoges, France
| | - Sarah Monic
- Faculty of Pharmacy, University of Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Solène Savrimoutou
- Faculty of Pharmacy, University of Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Stéphane Moreau
- Faculty of Pharmacy, University of Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Sandra Albenque-Rubio
- Faculty of Pharmacy, University of Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Camille Lafon-Schmaltz
- Faculty of Pharmacy, University of Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Alexandra Dassonville-Klimpt
- Faculty of Pharmacy, Agents Infectieux, Résistance et Chimiothérapie (AGIR), UR 4294, UFR de Pharmacie, University of Picardie Jules Verne, F-80037Amiens, France
| | - Jean-Louis Mergny
- Laboratoire d’Optique et Biosciences, Institut Polytechnique de Paris, Ecole Polytechnique, CNRS, INSERM, F- 91128 Palaiseau, France
| | - Luisa Ronga
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, F-64012 Pau, France
| | | | - Jeremy Lamarche
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, F-64012 Pau, France
| | - Cristina Dal Lago
- University of Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Eric Largy
- University of Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Valérie Gabelica
- University of Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Serge Moukha
- Centre de Recherche Cardio-thoracique de Bordeaux (CRCTB), UMR U1045 INSERM, PTIB-Hôpital Xavier Arnozan, F-33600 Pessac, France
- INRAE Bordeaux Aquitaine, F- 33140 Villenave-d’Ornon, France
| | - Pascale Dozolme
- Centre de Recherche Cardio-thoracique de Bordeaux (CRCTB), UMR U1045 INSERM, PTIB-Hôpital Xavier Arnozan, F-33600 Pessac, France
- INRAE Bordeaux Aquitaine, F- 33140 Villenave-d’Ornon, France
| | - Patrice Agnamey
- Faculty of Pharmacy, Agents Infectieux, Résistance et Chimiothérapie (AGIR), UR 4294, UFR de Pharmacie, University of Picardie Jules Verne, F-80037Amiens, France
| | - Nadine Azas
- Faculty of Pharmacy, University of Aix-Marseille, IRD, AP-HM, SSA, VITROME, F-13005 Marseille, France
| | - Catherine Mullié
- Faculty of Pharmacy, Agents Infectieux, Résistance et Chimiothérapie (AGIR), UR 4294, UFR de Pharmacie, University of Picardie Jules Verne, F-80037Amiens, France
| | - Bertrand Courtioux
- Faculty of Pharmacy, Institute of Neuroepidemiology and Tropical Neurology, University of Limoges, INSERM U1094, F-87025 Limoges, France
| | - Pascal Sonnet
- Faculty of Pharmacy, Agents Infectieux, Résistance et Chimiothérapie (AGIR), UR 4294, UFR de Pharmacie, University of Picardie Jules Verne, F-80037Amiens, France
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2
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Dobrovolná M, Bohálová N, Peška V, Wang J, Luo Y, Bartas M, Volná A, Mergny JL, Brázda V. The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation. Int J Mol Sci 2022; 23:8482. [PMID: 35955617 PMCID: PMC9369095 DOI: 10.3390/ijms23158482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022] Open
Abstract
G-quadruplexes (G4s) have been long considered rare and physiologically unimportant in vitro curiosities, but recent methodological advances have proved their presence and functions in vivo. Moreover, in addition to their functional relevance in bacteria and animals, including humans, their importance has been recently demonstrated in evolutionarily distinct plant species. In this study, we analyzed the genome of Pisum sativum (garden pea, or the so-called green pea), a unique member of the Fabaceae family. Our results showed that this genome contained putative G4 sequences (PQSs). Interestingly, these PQSs were located nonrandomly in the nuclear genome. We also found PQSs in mitochondrial (mt) and chloroplast (cp) DNA, and we experimentally confirmed G4 formation for sequences found in these two organelles. The frequency of PQSs for nuclear DNA was 0.42 PQSs per thousand base pairs (kbp), in the same range as for cpDNA (0.53/kbp), but significantly lower than what was found for mitochondrial DNA (1.58/kbp). In the nuclear genome, PQSs were mainly associated with regulatory regions, including 5'UTRs, and upstream of the rRNA region. In contrast to genomic DNA, PQSs were located around RNA genes in cpDNA and mtDNA. Interestingly, PQSs were also associated with specific transposable elements such as TIR and LTR and around them, pointing to their role in their spreading in nuclear DNA. The nonrandom localization of PQSs uncovered their evolutionary and functional significance in the Pisum sativum genome.
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Affiliation(s)
- Michaela Dobrovolná
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Vratislav Peška
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
| | - Jiawei Wang
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Yu Luo
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, CEDEX, 91405 Orsay, France
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
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3
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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:ph15030300. [PMID: 35337098 PMCID: PMC8953082 DOI: 10.3390/ph15030300] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [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.)
- Correspondence:
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Edwards-Smallbone J, Jensen AL, Roberts LE, Totañes FIG, Hart SR, Merrick CJ. Plasmodium falciparum GBP2 Is a Telomere-Associated Protein That Binds to G-Quadruplex DNA and RNA. Front Cell Infect Microbiol 2022; 12:782537. [PMID: 35273922 PMCID: PMC8902816 DOI: 10.3389/fcimb.2022.782537] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023] Open
Abstract
In the early-diverging protozoan parasite Plasmodium, few telomere-binding proteins have been identified and several are unique. Plasmodium telomeres, like those of most eukaryotes, contain guanine-rich repeats that can form G-quadruplex structures. In model systems, quadruplex-binding drugs can disrupt telomere maintenance and some quadruplex-binding drugs are potent anti-plasmodial agents. Therefore, telomere-interacting and quadruplex-interacting proteins may offer new targets for anti-malarial therapy. Here, we report that P. falciparum GBP2 is such a protein. It was identified via 'Proteomics of Isolated Chromatin fragments', applied here for the first time in Plasmodium. In vitro, PfGBP2 binds specifically to G-rich telomere repeats in quadruplex form and it can also bind to G-rich RNA. In vivo, PfGBP2 partially colocalises with the known telomeric protein HP1 but is also found in the cytoplasm, probably due to its affinity for RNA. Consistently, its interactome includes numerous RNA-associated proteins. PfGBP2 is evidently a multifunctional DNA/RNA-binding factor in Plasmodium.
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Affiliation(s)
- James Edwards-Smallbone
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Staffordshire, United Kingdom
| | - Anders L. Jensen
- Department of Pathology, Cambridge University, Cambridge, United Kingdom
| | - Lydia E. Roberts
- Department of Pathology, Cambridge University, Cambridge, United Kingdom
| | | | - Sarah R. Hart
- School of Medicine, Faculty of Medicine and Health Sciences, Keele University, Staffordshire, United Kingdom
| | - Catherine J. Merrick
- Department of Pathology, Cambridge University, Cambridge, United Kingdom,*Correspondence: Catherine J. Merrick,
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5
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Dumetz F, Chow EYC, Harris LM, Liew SW, Jensen A, Umar MI, Chung B, Chan TF, Merrick CJ, Kwok CK. G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum. Nucleic Acids Res 2021; 49:12486-12501. [PMID: 34792144 PMCID: PMC8643661 DOI: 10.1093/nar/gkab1095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/15/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022] Open
Abstract
G-quadruplexes are non-helical secondary structures that can fold in vivo in both DNA and RNA. In human cells, they can influence replication, transcription and telomere maintenance in DNA, or translation, transcript processing and stability of RNA. We have previously showed that G-quadruplexes are detectable in the DNA of the malaria parasite Plasmodium falciparum, despite a very highly A/T-biased genome with unusually few guanine-rich sequences. Here, we show that RNA G-quadruplexes can also form in P. falciparum RNA, using rG4-seq for transcriptome-wide structure-specific RNA probing. Many of the motifs, detected here via the rG4seeker pipeline, have non-canonical forms and would not be predicted by standard in silico algorithms. However, in vitro biophysical assays verified formation of non-canonical motifs. The G-quadruplexes in the P. falciparum transcriptome are frequently clustered in certain genes and associated with regions encoding low-complexity peptide repeats. They are overrepresented in particular classes of genes, notably those that encode PfEMP1 virulence factors, stress response genes and DNA binding proteins. In vitro translation experiments and in vivo measures of translation efficiency showed that G-quadruplexes can influence the translation of P. falciparum mRNAs. Thus, the G-quadruplex is a novel player in post-transcriptional regulation of gene expression in this major human pathogen.
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Affiliation(s)
- Franck Dumetz
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Eugene Yui-Ching Chow
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Lynne M Harris
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Anders Jensen
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Mubarak I Umar
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Betty Chung
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Ting Fung Chan
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Catherine J Merrick
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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Assis LHC, Andrade-Silva D, Shiburah ME, de Oliveira BCD, Paiva SC, Abuchery BE, Ferri YG, Fontes VS, de Oliveira LS, da Silva MS, Cano MIN. Cell Cycle, Telomeres, and Telomerase in Leishmania spp.: What Do We Know So Far? Cells 2021; 10:cells10113195. [PMID: 34831418 PMCID: PMC8621916 DOI: 10.3390/cells10113195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 12/18/2022] Open
Abstract
Leishmaniases belong to the inglorious group of neglected tropical diseases, presenting different degrees of manifestations severity. It is caused by the transmission of more than 20 species of parasites of the Leishmania genus. Nevertheless, the disease remains on the priority list for developing new treatments, since it affects millions in a vast geographical area, especially low-income people. Molecular biology studies are pioneers in parasitic research with the aim of discovering potential targets for drug development. Among them are the telomeres, DNA–protein structures that play an important role in the long term in cell cycle/survival. Telomeres are the physical ends of eukaryotic chromosomes. Due to their multiple interactions with different proteins that confer a likewise complex dynamic, they have emerged as objects of interest in many medical studies, including studies on leishmaniases. This review aims to gather information and elucidate what we know about the phenomena behind Leishmania spp. telomere maintenance and how it impacts the parasite’s cell cycle.
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Affiliation(s)
- Luiz H. C. Assis
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Débora Andrade-Silva
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Mark E. Shiburah
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Beatriz C. D. de Oliveira
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Stephany C. Paiva
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Bryan E. Abuchery
- DNA Replication and Repair Laboratory (DRRL), Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (B.E.A.); (Y.G.F.)
| | - Yete G. Ferri
- DNA Replication and Repair Laboratory (DRRL), Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (B.E.A.); (Y.G.F.)
| | - Veronica S. Fontes
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Leilane S. de Oliveira
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Marcelo S. da Silva
- DNA Replication and Repair Laboratory (DRRL), Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (B.E.A.); (Y.G.F.)
- Correspondence: (M.S.d.S.); (M.I.N.C.)
| | - Maria Isabel N. Cano
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
- Correspondence: (M.S.d.S.); (M.I.N.C.)
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7
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Soto-Sánchez J, Ospina-Villa JD. Current status of quinoxaline and quinoxaline 1,4-di-N-oxides derivatives as potential antiparasitic agents. Chem Biol Drug Des 2021; 98:683-699. [PMID: 34289242 DOI: 10.1111/cbdd.13921] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/19/2021] [Accepted: 06/26/2021] [Indexed: 11/29/2022]
Abstract
Parasitic diseases are a public health problem, especially in developing countries where millions of people are affected every year. Current treatments have several drawbacks: emerging resistance to the existing drugs, lack of efficacy, and toxic side effects. Therefore, new antiparasitic drugs are urgently needed to treat and control diseases that affect human health, such as malaria, Chagas disease, leishmaniasis, amebiasis, giardiasis schistosomiasis, and filariasis, among others. Quinoxaline is a compound containing a benzene ring and a pyrazine ring. The oxidation of both pyrazine ring nitrogens allows the obtention of quinoxaline 1,4-di-N-oxides (QdNOs) derivatives. By modifying the chemical structure of these compounds, it is possible to obtain a wide variety of biological properties. This review investigated the activity of quinoxaline derivatives and QdNOs against different protozoan parasites and helminths. We also cover the structure-activity relationship (SAR) and summarize the main findings related to their mechanisms of action from published works in recent years. However, further studies are needed to determine specific molecular targets. This review aims to highlight the new development of antiparasitic drugs with better pharmacological profiles than current treatments.
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Affiliation(s)
- Jacqueline Soto-Sánchez
- Sección de Estudios de Posgrado e Investigación, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, México
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Krafčík D, Ištvánková E, Džatko Š, Víšková P, Foldynová-Trantírková S, Trantírek L. Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy. Int J Mol Sci 2021; 22:6042. [PMID: 34205000 PMCID: PMC8199861 DOI: 10.3390/ijms22116042] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Recently, the 1H-detected in-cell NMR spectroscopy has emerged as a unique tool allowing the characterization of interactions between nucleic acid-based targets and drug-like molecules in living human cells. Here, we assess the application potential of 1H and 19F-detected in-cell NMR spectroscopy to profile drugs/ligands targeting DNA G-quadruplexes, arguably the most studied class of anti-cancer drugs targeting nucleic acids. We show that the extension of the original in-cell NMR approach is not straightforward. The severe signal broadening and overlap of 1H in-cell NMR spectra of polymorphic G-quadruplexes and their complexes complicate their quantitative interpretation. Nevertheless, the 1H in-cell NMR can be used to identify drugs that, despite strong interaction in vitro, lose their ability to bind G-quadruplexes in the native environment. The in-cell NMR approach is adjusted to a recently developed 3,5-bis(trifluoromethyl)phenyl probe to monitor the intracellular interaction with ligands using 19F-detected in-cell NMR. The probe allows dissecting polymorphic mixture in terms of number and relative populations of individual G-quadruplex species, including ligand-bound and unbound forms in vitro and in cellulo. Despite the probe's discussed limitations, the 19F-detected in-cell NMR appears to be a promising strategy to profile G-quadruplex-ligand interactions in the complex environment of living cells.
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Affiliation(s)
- Daniel Krafčík
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Eva Ištvánková
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Šimon Džatko
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavlína Víšková
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | | | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
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9
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Craven HM, Bonsignore R, Lenis V, Santi N, Berrar D, Swain M, Whiteland H, Casini A, Hoffmann KF. Identifying and validating the presence of Guanine-Quadruplexes (G4) within the blood fluke parasite Schistosoma mansoni. PLoS Negl Trop Dis 2021; 15:e0008770. [PMID: 33600427 PMCID: PMC7924807 DOI: 10.1371/journal.pntd.0008770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 03/02/2021] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
Schistosomiasis is a neglected tropical disease that currently affects over 250 million individuals worldwide. In the absence of an immunoprophylactic vaccine and the recognition that mono-chemotherapeutic control of schistosomiasis by praziquantel has limitations, new strategies for managing disease burden are urgently needed. A better understanding of schistosome biology could identify previously undocumented areas suitable for the development of novel interventions. Here, for the first time, we detail the presence of G-quadruplexes (G4) and putative quadruplex forming sequences (PQS) within the Schistosoma mansoni genome. We find that G4 are present in both intragenic and intergenic regions of the seven autosomes as well as the sex-defining allosome pair. Amongst intragenic regions, G4 are particularly enriched in 3´ UTR regions. Gene Ontology (GO) term analysis evidenced significant G4 enrichment in the wnt signalling pathway (p<0.05) and PQS oligonucleotides synthetically derived from wnt-related genes resolve into parallel and anti-parallel G4 motifs as elucidated by circular dichroism (CD) spectroscopy. Finally, utilising a single chain anti-G4 antibody called BG4, we confirm the in situ presence of G4 within both adult female and male worm nuclei. These results collectively suggest that G4-targeted compounds could be tested as novel anthelmintic agents and highlights the possibility that G4-stabilizing molecules could be progressed as candidates for the treatment of schistosomiasis.
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Affiliation(s)
- Holly M. Craven
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, United Kingdom
| | | | - Vasilis Lenis
- School of Health and Life Sciences, Teesside University, United Kingdom
| | - Nicolo Santi
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Daniel Berrar
- Data Science Laboratory, Tokyo Institute of Technology, Tokyo, Japan
| | - Martin Swain
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, United Kingdom
| | - Helen Whiteland
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, United Kingdom
| | - Angela Casini
- Department of Chemistry, Technical University of Munich, Germany
| | - Karl F. Hoffmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, United Kingdom
- * E-mail:
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10
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Gurung P, Gomes AR, Martins RM, Juranek SA, Alberti P, Mbang-Benet DE, Urbach S, Gazanion E, Guitard V, Paeschke K, Lopez-Rubio JJ. PfGBP2 is a novel G-quadruplex binding protein in Plasmodium falciparum. Cell Microbiol 2021; 23:e13303. [PMID: 33340385 DOI: 10.1111/cmi.13303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 11/27/2022]
Abstract
Guanine-quadruplexes (G4s) are non-canonical DNA structures that can regulate key biological processes such as transcription, replication and telomere maintenance in several organisms including eukaryotes, prokaryotes and viruses. Recent reports have identified the presence of G4s within the AT-rich genome of Plasmodium falciparum, the protozoan parasite causing malaria. In Plasmodium, potential G4-forming sequences (G4FS) are enriched in the telomeric and sub-telomeric regions of the genome where they are associated with telomere maintenance and recombination events within virulence genes. However, there is a little understanding about the biological role of G4s and G4-binding proteins. Here, we provide the first snapshot of G4-interactome in P. falciparum using DNA pull-down assay followed by LC-MS/MS. Interestingly, we identified ~24 potential G4-binding proteins (G4-BP) that bind to a stable G4FS (AP2_G4). Furthermore, we characterised the role of G-strand binding protein 2 (PfGBP2), a putative telomere-binding protein in P. falciparum. We validated the interaction of PfGBP2 with G4 in vitro as well as in vivo. PfGBP2 is expressed throughout the intra-erythrocytic developmental cycle and is essential for the parasites in the presence of G4-stabilising ligand, pyridostatin. Gene knockout studies showed the role of PfGBP2 in the expression of var genes. Taken together, this study suggests that PfGBP2 is a bona fide G4-binding protein, which is likely to be involved in the regulation of G4-related functions in these malarial parasites. In addition, this study sheds light on this understudied G4 biology in P. falciparum.
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Affiliation(s)
- Pratima Gurung
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Ana Rita Gomes
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Rafael M Martins
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Stefan A Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Patrizia Alberti
- Laboratory Genome Structure and Instability, Muséum National d'Histoire Naturelle, CNRS UMR 7196, INSERM U 1154, Paris, France
| | - Diane-Ethna Mbang-Benet
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Serge Urbach
- BioCampus Montpellier, CNRS UMR 5203, IGF, Montpellier, France
| | - Elodie Gazanion
- Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Vincent Guitard
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Jose-Juan Lopez-Rubio
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
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11
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Bryan TM. G-Quadruplexes at Telomeres: Friend or Foe? Molecules 2020; 25:molecules25163686. [PMID: 32823549 PMCID: PMC7464828 DOI: 10.3390/molecules25163686] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/28/2022] Open
Abstract
Telomeres are DNA-protein complexes that cap and protect the ends of linear chromosomes. In almost all species, telomeric DNA has a G/C strand bias, and the short tandem repeats of the G-rich strand have the capacity to form into secondary structures in vitro, such as four-stranded G-quadruplexes. This has long prompted speculation that G-quadruplexes play a positive role in telomere biology, resulting in selection for G-rich tandem telomere repeats during evolution. There is some evidence that G-quadruplexes at telomeres may play a protective capping role, at least in yeast, and that they may positively affect telomere maintenance by either the enzyme telomerase or by recombination-based mechanisms. On the other hand, G-quadruplex formation in telomeric DNA, as elsewhere in the genome, can form an impediment to DNA replication and a source of genome instability. This review summarizes recent evidence for the in vivo existence of G-quadruplexes at telomeres, with a focus on human telomeres, and highlights some of the many unanswered questions regarding the location, form, and functions of these structures.
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Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
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12
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Gazanion E, Lacroix L, Alberti P, Gurung P, Wein S, Cheng M, Mergny JL, Gomes AR, Lopez-Rubio JJ. Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites. PLoS Genet 2020; 16:e1008917. [PMID: 32628663 PMCID: PMC7365481 DOI: 10.1371/journal.pgen.1008917] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 07/16/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
Mechanisms of transcriptional control in malaria parasites are still not fully understood. The positioning patterns of G-quadruplex (G4) DNA motifs in the parasite's AT-rich genome, especially within the var gene family which encodes virulence factors, and in the vicinity of recombination hotspots, points towards a possible regulatory role of G4 in gene expression and genome stability. Here, we carried out the most comprehensive genome-wide survey, to date, of G4s in the Plasmodium falciparum genome using G4Hunter, which identifies G4 forming sequences (G4FS) considering their G-richness and G-skewness. We show an enrichment of G4FS in nucleosome-depleted regions and in the first exon of var genes, a pattern that is conserved within the closely related Laverania Plasmodium parasites. Under G4-stabilizing conditions, i.e., following treatment with pyridostatin (a high affinity G4 ligand), we show that a bona fide G4 found in the non-coding strand of var promoters modulates reporter gene expression. Furthermore, transcriptional profiling of pyridostatin-treated parasites, shows large scale perturbations, with deregulation affecting for instance the ApiAP2 family of transcription factors and genes involved in ribosome biogenesis. Overall, our study highlights G4s as important DNA secondary structures with a role in Plasmodium gene expression regulation, sub-telomeric recombination and var gene biology.
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Affiliation(s)
- Elodie Gazanion
- MIVEGEC UMR IRD 224, CNRS 5290, Montpellier University, Montpellier, France
| | - Laurent Lacroix
- IBENS, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Patrizia Alberti
- "Structure and Instability of Genomes" laboratory, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, Paris, France
| | - Pratima Gurung
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
| | - Sharon Wein
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
| | - Mingpan Cheng
- ARNA Laboratory, IECB, CNRS UMR5320, INSERM U1212, Bordeaux University, Pessac, France
| | - Jean-Louis Mergny
- ARNA Laboratory, IECB, CNRS UMR5320, INSERM U1212, Bordeaux University, Pessac, France
- Institute of Biophysics of the Czech Academy of Sciences, Czech Republic
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, France
| | - Ana Rita Gomes
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
| | - Jose-Juan Lopez-Rubio
- MIVEGEC UMR IRD 224, CNRS 5290, Montpellier University, Montpellier, France
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
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13
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Gage HL, Merrick CJ. Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites. BMC Genomics 2020; 21:236. [PMID: 32183702 PMCID: PMC7077173 DOI: 10.1186/s12864-020-6625-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/26/2020] [Indexed: 11/25/2022] Open
Abstract
Background The Plasmodium genus of malaria parasites encodes several families of antigen-encoding genes. These genes tend to be hyper-variable, highly recombinogenic and variantly expressed. The best-characterized family is the var genes, exclusively found in the Laveranian subgenus of malaria parasites infecting humans and great apes. Var genes encode major virulence factors involved in immune evasion and the maintenance of chronic infections. In the human parasite P. falciparum, var gene recombination and diversification appear to be promoted by G-quadruplex (G4) DNA motifs, which are strongly associated with var genes in P. falciparum. Here, we investigated how this association might have evolved across Plasmodium species – both Laverania and also more distantly related species which lack vars but encode other, more ancient variant gene families. Results The association between var genes and G4-forming motifs was conserved across Laverania, spanning ~ 1 million years of evolutionary time, with suggestive evidence for evolution of the association occurring within this subgenus. In rodent malaria species, G4-forming motifs were somewhat associated with pir genes, but this was not conserved in the Laverania, nor did we find a strong association of these motifs with any gene family in a second outgroup of avian malaria parasites. Secondly, we compared two different G4 prediction algorithms in their performance on extremely A/T-rich Plasmodium genomes, and also compared these predictions with experimental data from G4-seq, a DNA sequencing method for identifying G4-forming motifs. We found a surprising lack of concordance between the two algorithms and also between the algorithms and G4-seq data. Conclusions G4-forming motifs are uniquely strongly associated with Plasmodium var genes, suggesting a particular role for G4s in recombination and diversification of these genes. Secondly, in the A/T-rich genomes of Plasmodium species, the choice of prediction algorithm may be particularly influential when studying G4s in these important protozoan pathogens.
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Affiliation(s)
- Hunter L Gage
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Catherine J Merrick
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge, CB2 1QP, UK.
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14
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Guillon J, Cohen A, Boudot C, Valle A, Milano V, Das RN, Guédin A, Moreau S, Ronga L, Savrimoutou S, Demourgues M, Reviriego E, Rubio S, Ferriez S, Agnamey P, Pauc C, Moukha S, Dozolme P, Nascimento SD, Laumaillé P, Bouchut A, Azas N, Mergny JL, Mullié C, Sonnet P, Courtioux B. Design, synthesis, and antiprotozoal evaluation of new 2,4-bis[(substituted-aminomethyl)phenyl]quinoline, 1,3-bis[(substituted-aminomethyl)phenyl]isoquinoline and 2,4-bis[(substituted-aminomethyl)phenyl]quinazoline derivatives. J Enzyme Inhib Med Chem 2020; 35:432-459. [PMID: 31899980 PMCID: PMC6968685 DOI: 10.1080/14756366.2019.1706502] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
A series of new 2,4-bis[(substituted-aminomethyl)phenyl]quinoline, 1,3-bis[(substituted-aminomethyl)phenyl]isoquinoline, and 2,4-bis[(substituted-aminomethyl)phenyl]quinazoline derivatives was designed, synthesised, and evaluated in vitro against three protozoan parasites (Plasmodium falciparum, Leishmania donovani, and Trypanosoma brucei brucei). Biological results showed antiprotozoal activity with IC50 values in the µM range. In addition, the in vitro cytotoxicity of these original molecules was assessed with human HepG2 cells. The quinoline 1c was identified as the most potent antimalarial candidate with a ratio of cytotoxic to antiparasitic activities of 97 against the P. falciparum CQ-sensitive strain 3D7. The quinazoline 3h was also identified as the most potent trypanosomal candidate with a selectivity index (SI) of 43 on T. brucei brucei strain. Moreover, as the telomeres of the parasites P. falciparum and Trypanosoma are possible targets of this kind of nitrogen heterocyclic compounds, we have also investigated stabilisation of the Plasmodium and Trypanosoma telomeric G-quadruplexes by our best compounds through FRET melting assays.
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Affiliation(s)
- Jean Guillon
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Anita Cohen
- IRD, AP-HM, SSA, VITROME, Aix-Marseille University, Marseille, France
| | - Clotilde Boudot
- INSERM U1094, Tropical Neuroepidemiology, Institute of Neuroepidemiology and Tropical Neurology, Université de Limoges, Limoges, France
| | - Alessandra Valle
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Vittoria Milano
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Rabindra Nath Das
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Aurore Guédin
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Stéphane Moreau
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Luisa Ronga
- PREM UMR5254 - UPPA/CNRS, Technopole Hélioparc, Université de Pau, Pau, France
| | - Solène Savrimoutou
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Maxime Demourgues
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Elodie Reviriego
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Sandra Rubio
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Sandie Ferriez
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Patrice Agnamey
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Cécile Pauc
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Serge Moukha
- Université de Bordeaux, Laboratoire de Toxicologie et d'Hygiène Appliquée - INRA, UFR des Sciences Pharmaceutiques, Bordeaux, France
| | - Pascale Dozolme
- Université de Bordeaux, Laboratoire de Toxicologie et d'Hygiène Appliquée - INRA, UFR des Sciences Pharmaceutiques, Bordeaux, France
| | - Sophie Da Nascimento
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Pierre Laumaillé
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Anne Bouchut
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Nadine Azas
- IRD, AP-HM, SSA, VITROME, Aix-Marseille University, Marseille, France
| | - Jean-Louis Mergny
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France.,Institut Curie, Université Paris-Saclay, CNRS-UMR 9187, INSERM U1196, Université Paris-Saclay, Orsay, France.,Institute of Biophysics of the CAS, Brno, Czech Republic
| | - Catherine Mullié
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Pascal Sonnet
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Bertrand Courtioux
- INSERM U1094, Tropical Neuroepidemiology, Institute of Neuroepidemiology and Tropical Neurology, Université de Limoges, Limoges, France
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15
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Parasitic Protozoa: Unusual Roles for G-Quadruplexes in Early-Diverging Eukaryotes. Molecules 2019; 24:molecules24071339. [PMID: 30959737 PMCID: PMC6480360 DOI: 10.3390/molecules24071339] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 12/17/2022] Open
Abstract
Guanine-quadruplex (G4) motifs, at both the DNA and RNA levels, have assumed an important place in our understanding of the biology of eukaryotes, bacteria and viruses. However, it is generally little known that their very first description, as well as the foundational work on G4s, was performed on protozoans: unicellular life forms that are often parasitic. In this review, we provide a historical perspective on the discovery of G4s, intertwined with their biological significance across the protozoan kingdom. This is a history in three parts: first, a period of discovery including the first characterisation of a G4 motif at the DNA level in ciliates (environmental protozoa); second, a period less dense in publications concerning protozoa, during which DNA G4s were discovered in both humans and viruses; and third, a period of renewed interest in protozoa, including more mechanistic work in ciliates but also in pathogenic protozoa. This last period has opened an exciting prospect of finding new anti-parasitic drugs to interfere with parasite biology, thus adding new compounds to the therapeutic arsenal.
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16
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Claessens A, Harris LM, Stanojcic S, Chappell L, Stanton A, Kuk N, Veneziano-Broccia P, Sterkers Y, Rayner JC, Merrick CJ. RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics. PLoS Genet 2018; 14:e1007490. [PMID: 29965959 PMCID: PMC6044543 DOI: 10.1371/journal.pgen.1007490] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 07/13/2018] [Accepted: 06/13/2018] [Indexed: 11/18/2022] Open
Abstract
The malaria parasite Plasmodium falciparum has evolved an unusual genome structure. The majority of the genome is relatively stable, with mutation rates similar to most eukaryotic species. However, some regions are very unstable with high recombination rates, driving the generation of new immune evasion-associated var genes. The molecular factors controlling the inconsistent stability of this genome are not known. Here we studied the roles of the two putative RecQ helicases in P. falciparum, PfBLM and PfWRN. When PfWRN was knocked down, recombination rates increased four-fold, generating chromosomal abnormalities, a high rate of chimeric var genes and many microindels, particularly in known 'fragile sites'. This is the first identification of a gene involved in suppressing recombination and maintaining genome stability in Plasmodium. By contrast, no change in mutation rate appeared when the second RecQ helicase, PfBLM, was mutated. At the transcriptional level, however, both helicases evidently modulate the transcription of large cohorts of genes, with several hundred genes-including a large proportion of vars-showing deregulated expression in each RecQ mutant. Aberrant processing of stalled replication forks is a possible mechanism underlying elevated mutation rates and this was assessed by measuring DNA replication dynamics in the RecQ mutant lines. Replication forks moved slowly and stalled at elevated rates in both mutants, confirming that RecQ helicases are required for efficient DNA replication. Overall, this work identifies the Plasmodium RecQ helicases as major players in DNA replication, antigenic diversification and genome stability in the most lethal human malaria parasite, with important implications for genome evolution in this pathogen.
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Affiliation(s)
- Antoine Claessens
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Medical Research Council Unit The Gambia, Fajara, Banjul, The Gambia
| | - Lynne M. Harris
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Slavica Stanojcic
- University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier, France
| | - Lia Chappell
- Malaria Programme, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Adam Stanton
- School of Computing and Mathematics, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Nada Kuk
- University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier, France
| | - Pamela Veneziano-Broccia
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Yvon Sterkers
- University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier, France
- CNRS 5290 - IRD 224 - University of Montpellier (UMR “MiVEGEC”), Montpellier, France
- University Hospital Centre (CHU), Department of Parasitology-Mycology, Montpellier, France
| | - Julian C. Rayner
- Malaria Programme, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
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17
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G-Quadruplex DNA Motifs in the Malaria Parasite Plasmodium falciparum and Their Potential as Novel Antimalarial Drug Targets. Antimicrob Agents Chemother 2018; 62:AAC.01828-17. [PMID: 29311059 DOI: 10.1128/aac.01828-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/20/2017] [Indexed: 01/06/2023] Open
Abstract
G-quadruplexes are DNA or RNA secondary structures that can be formed from guanine-rich nucleic acids. These four-stranded structures, composed of stacked quartets of guanine bases, can be highly stable and have been demonstrated to occur in vivo in the DNA of human cells and other systems, where they play important biological roles, influencing processes such as telomere maintenance, DNA replication and transcription, or, in the case of RNA G-quadruplexes, RNA translation and processing. We report for the first time that DNA G-quadruplexes can be detected in the nuclei of the malaria parasite Plasmodium falciparum, which has one of the most A/T-biased genomes sequenced and therefore possesses few guanine-rich sequences with the potential to form G-quadruplexes. We show that despite this paucity of putative G-quadruplex-forming sequences, P. falciparum parasites are sensitive to several G-quadruplex-stabilizing drugs, including quarfloxin, which previously reached phase 2 clinical trials as an anticancer drug. Quarfloxin has a rapid initial rate of kill and is active against ring stages as well as replicative stages of intraerythrocytic development. We show that several G-quadruplex-stabilizing drugs, including quarfloxin, can suppress the transcription of a G-quadruplex-containing reporter gene in P. falciparum but that quarfloxin does not appear to disrupt the transcription of rRNAs, which was proposed as its mode of action in both human cells and trypanosomes. These data suggest that quarfloxin has potential for repositioning as an antimalarial with a novel mode of action. Furthermore, G-quadruplex biology in P. falciparum may present a target for development of other new antimalarial drugs.
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18
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Belmonte-Reche E, Martínez-García M, Guédin A, Zuffo M, Arévalo-Ruiz M, Doria F, Campos-Salinas J, Maynadier M, López-Rubio JJ, Freccero M, Mergny JL, Pérez-Victoria JM, Morales JC. G-Quadruplex Identification in the Genome of Protozoan Parasites Points to Naphthalene Diimide Ligands as New Antiparasitic Agents. J Med Chem 2018; 61:1231-1240. [PMID: 29323491 PMCID: PMC6148440 DOI: 10.1021/acs.jmedchem.7b01672] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
G-quadruplexes
(G4) are DNA secondary structures that take part
in the regulation of gene expression. Putative G4 forming sequences
(PQS) have been reported in mammals, yeast, bacteria, and viruses.
Here, we present PQS searches on the genomes of T. brucei,
L. major, and P. falciparum. We found telomeric
sequences and new PQS motifs. Biophysical experiments showed that
EBR1, a 29 nucleotide long highly repeated PQS in T. brucei, forms a stable G4 structure. G4 ligands based on carbohydrate conjugated
naphthalene diimides (carb-NDIs) that bind G4’s including hTel
could bind EBR1 with selectivity versus dsDNA. These ligands showed
important antiparasitic activity. IC50 values were in the
nanomolar range against T. brucei with high selectivity
against MRC-5 human cells. Confocal microscopy confirmed these ligands
localize in the nucleus and kinetoplast of T. brucei suggesting they can reach their potential G4 targets. Cytotoxicity
and zebrafish toxicity studies revealed sugar conjugation reduces
intrinsic toxicity of NDIs.
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Affiliation(s)
- Efres Belmonte-Reche
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Marta Martínez-García
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Aurore Guédin
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), 2 Rue Robert Escarpit, 33607 Pessac, France
| | - Michela Zuffo
- Department of Chemistry, University of Pavia , Via Taramelli 10, 27100 Pavia, Italy
| | - Matilde Arévalo-Ruiz
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Filippo Doria
- Department of Chemistry, University of Pavia , Via Taramelli 10, 27100 Pavia, Italy
| | - Jenny Campos-Salinas
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Marjorie Maynadier
- Dynamique des Interactions Membranaires Normales et Pathologiques, CNRS UMR 5235, Université de Montpellier, 34095 Montpellier, France
| | - José Juan López-Rubio
- CNRS, 5290, IRD 224, University of Montpellier (UMR "MiVEGEC"), INSERM, 34394 Montpellier, France
| | - Mauro Freccero
- Department of Chemistry, University of Pavia , Via Taramelli 10, 27100 Pavia, Italy
| | - Jean-Louis Mergny
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), 2 Rue Robert Escarpit, 33607 Pessac, France.,Institute of Biophysics , AS CR, v.v.i. Kralovopolska 135, 612 65 Brno, Czech Republic
| | - José María Pérez-Victoria
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
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19
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Guillon J, Cohen A, Das RN, Boudot C, Gueddouda NM, Moreau S, Ronga L, Savrimoutou S, Basmaciyan L, Tisnerat C, Mestanier S, Rubio S, Amaziane S, Dassonville-Klimpt A, Azas N, Courtioux B, Mergny JL, Mullié C, Sonnet P. Design, synthesis, and antiprotozoal evaluation of new 2,9-bis[(substituted-aminomethyl)phenyl]-1,10-phenanthroline derivatives. Chem Biol Drug Des 2018; 91:974-995. [PMID: 29266861 DOI: 10.1111/cbdd.13164] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/04/2017] [Accepted: 12/07/2017] [Indexed: 01/06/2023]
Abstract
A series of new 2,9-bis[(substituted-aminomethyl)phenyl]-1,10-phenanthroline derivatives was synthesized, and the compounds were screened in vitro against three protozoan parasites (Plasmodium falciparum, Leishmania donovani, and Trypanosoma brucei brucei). Biological results showed antiparasitic activity with IC50 values in the μm range. The in vitro cytotoxicity of these molecules was assessed by incubation with human HepG2 cells; for some derivatives, cytotoxicity was observed at significantly higher concentrations than antiparasitic activity. The 2,9-bis[(substituted-aminomethyl)phenyl]-1,10-phenanthroline 1h was identified as the most potent antimalarial candidate with ratios of cytotoxic-to-antiparasitic activities of 107 and 39 against a chloroquine-sensitive and a chloroquine-resistant strain of P. falciparum, respectively. As the telomeres of the parasite P. falciparum are the likely target of this compound, we investigated stabilization of the Plasmodium telomeric G-quadruplexes by our phenanthroline derivatives through a FRET melting assay. The ligands 1f and 1m were noticed to be more specific for FPf8T with higher stabilization for FPf8T than for the human F21T sequence.
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Affiliation(s)
- Jean Guillon
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Anita Cohen
- Laboratory of Parasitology, UMR-MD3, Faculty of Pharmacy, Aix-Marseille University, Marseille, France
| | - Rabindra Nath Das
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Clotilde Boudot
- INSERM U1094, Tropical Neuroepidemiology, Limoges, France.,Institute of Neuroepidemiology and Tropical Neurology, Université de Limoges, Limoges, France
| | - Nassima Meriem Gueddouda
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Stéphane Moreau
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Luisa Ronga
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Solène Savrimoutou
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Louise Basmaciyan
- Laboratory of Parasitology, UMR-MD3, Faculty of Pharmacy, Aix-Marseille University, Marseille, France
| | - Camille Tisnerat
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Sacha Mestanier
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Sandra Rubio
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Sophia Amaziane
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Alexandra Dassonville-Klimpt
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressouces, UMR CNRS 7378, UFR de Pharmacie, Université de Picardie Jules Verne, Amiens, France
| | - Nadine Azas
- Laboratory of Parasitology, UMR-MD3, Faculty of Pharmacy, Aix-Marseille University, Marseille, France
| | - Bertrand Courtioux
- INSERM U1094, Tropical Neuroepidemiology, Limoges, France.,Institute of Neuroepidemiology and Tropical Neurology, Université de Limoges, Limoges, France
| | - Jean-Louis Mergny
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France.,Institute of Biophysics of the CAS, v.v.i., Brno, Czech Republic
| | - Catherine Mullié
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressouces, UMR CNRS 7378, UFR de Pharmacie, Université de Picardie Jules Verne, Amiens, France
| | - Pascal Sonnet
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressouces, UMR CNRS 7378, UFR de Pharmacie, Université de Picardie Jules Verne, Amiens, France
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20
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Das RN, Chevret E, Desplat V, Rubio S, Mergny JL, Guillon J. Design, Synthesis and Biological Evaluation of New Substituted Diquinolinyl-Pyridine Ligands as Anticancer Agents by Targeting G-Quadruplex. Molecules 2017; 23:molecules23010081. [PMID: 29301210 PMCID: PMC6017375 DOI: 10.3390/molecules23010081] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 12/20/2017] [Accepted: 12/29/2017] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes (G4) are stacked non-canonical nucleic acid structures found in specific G-rich DNA or RNA sequences in the human genome. G4 structures are liable for various biological functions; transcription, translation, cell aging as well as diseases such as cancer. These structures are therefore considered as important targets for the development of anticancer agents. Small organic heterocyclic molecules are well known to target and stabilize G4 structures. In this article, we have designed and synthesized 2,6-di-(4-carbamoyl-2-quinolyl)pyridine derivatives and their ability to stabilize G4-structures have been determined through the FRET melting assay. It has been established that these ligands are selective for G4 over duplexes and show a preference for the parallel conformation. Next, telomerase inhibition ability has been assessed using three cell lines (K562, MyLa and MV-4-11) and telomerase activity is no longer detected at 0.1 μM concentration for the most potent ligand 1c. The most promising G4 ligands were also tested for antiproliferative activity against the two human myeloid leukaemia cell lines, HL60 and K562.
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Affiliation(s)
- Rabindra Nath Das
- Université de Bordeaux, ARNA laboratory, INSERM U1212, UMR CNRS 5320, UFR des Sciences Pharmaceutiques, 33076 Bordeaux CEDEX, France.
| | - Edith Chevret
- Université de Bordeaux, INSERM U1053, Cutaneous Lymphoma Oncogenesis Team, 33076 Bordeaux CEDEX, France.
| | - Vanessa Desplat
- Université de Bordeaux, INSERM U1035, Cellules souches hématopoïétiques normales et leucémiques, UFR des Sciences Pharmaceutiques, 33076 Bordeaux CEDEX, France.
| | - Sandra Rubio
- Université de Bordeaux, ARNA laboratory, INSERM U1212, UMR CNRS 5320, UFR des Sciences Pharmaceutiques, 33076 Bordeaux CEDEX, France.
| | - Jean-Louis Mergny
- Université de Bordeaux, ARNA laboratory, INSERM U1212, UMR CNRS 5320, UFR des Sciences Pharmaceutiques, 33076 Bordeaux CEDEX, France.
- Institute of Biophysics of the CAS, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Jean Guillon
- Université de Bordeaux, ARNA laboratory, INSERM U1212, UMR CNRS 5320, UFR des Sciences Pharmaceutiques, 33076 Bordeaux CEDEX, France.
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21
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Anas M, Sharma R, Dhamodharan V, Pradeepkumar PI, Manhas A, Srivastava K, Ahmed S, Kumar N. Investigating Pharmacological Targeting of G-Quadruplexes in the Human Malaria Parasite. Biochemistry 2017; 56:6691-6699. [DOI: 10.1021/acs.biochem.7b00964] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mohammad Anas
- Parasitology
Division, CSIR-Central Drug Research Institute, Lucknow 226031, Uttar Pradesh, India
| | - Richa Sharma
- Parasitology
Division, CSIR-Central Drug Research Institute, Lucknow 226031, Uttar Pradesh, India
| | - V. Dhamodharan
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - P. I. Pradeepkumar
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Ashan Manhas
- Parasitology
Division, CSIR-Central Drug Research Institute, Lucknow 226031, Uttar Pradesh, India
| | - Kumkum Srivastava
- Parasitology
Division, CSIR-Central Drug Research Institute, Lucknow 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Delhi, India
| | - Shakil Ahmed
- Molecular
and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Delhi, India
| | - Niti Kumar
- Parasitology
Division, CSIR-Central Drug Research Institute, Lucknow 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Delhi, India
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22
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Malaria parasites possess a telomere repeat-binding protein that shares ancestry with transcription factor IIIA. Nat Microbiol 2017; 2:17033. [PMID: 28288093 DOI: 10.1038/nmicrobiol.2017.33] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/09/2017] [Indexed: 12/19/2022]
Abstract
Telomere repeat-binding factors (TRFs) are essential components of the molecular machinery that regulates telomere function. TRFs are widely conserved across eukaryotes and bind duplex telomere repeats via a characteristic MYB-type domain. Here, we identified the telomere repeat-binding protein PfTRZ in the malaria parasite Plasmodium falciparum, a member of the Alveolate phylum for which TRFs have not been described so far. PfTRZ lacks an MYB domain and binds telomere repeats via a C2H2-type zinc finger domain instead. In vivo, PfTRZ binds with high specificity to the telomeric tract and to interstitial telomere repeats upstream of subtelomeric virulence genes. Conditional depletion experiments revealed that PfTRZ regulates telomere length homeostasis and is required for efficient cell cycle progression. Intriguingly, we found that PfTRZ also binds to and regulates the expression of 5S rDNA genes. Combined with detailed phylogenetic analyses, our findings identified PfTRZ as a remote functional homologue of the basic transcription factor TFIIIA, which acquired a new function in telomere maintenance early in the apicomplexan lineage. Our work sheds unexpected new light on the evolution of telomere repeat-binding proteins and paves the way for dissecting the presumably divergent mechanisms regulating telomere functionality in one of the most deadly human pathogens.
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23
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Guillon J, Cohen A, Gueddouda NM, Das RN, Moreau S, Ronga L, Savrimoutou S, Basmaciyan L, Monnier A, Monget M, Rubio S, Garnerin T, Azas N, Mergny JL, Mullié C, Sonnet P. Design, synthesis and antimalarial activity of novel bis{N-[(pyrrolo[1,2-a]quinoxalin-4-yl)benzyl]-3-aminopropyl}amine derivatives. J Enzyme Inhib Med Chem 2017; 32:547-563. [PMID: 28114821 PMCID: PMC6445168 DOI: 10.1080/14756366.2016.1268608] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Novel series of bis- and tris-pyrrolo[1,2-a]quinoxaline derivatives 1 were synthesized and tested for in vitro activity upon the intraerythrocytic stage of W2 and 3D7 Plasmodium falciparum strains. Biological results showed good antimalarial activity with IC50 in the μM range. In attempting to investigate the large broad-spectrum antiprotozoal activities of these new derivatives, their properties toward Leishmania donovani were also investigated and revealed their selective antiplasmodial profile. In parallel, the in vitro cytotoxicity of these molecules was assessed on the human HepG2 cell line. Structure–activity relationships of these new synthetic compounds are discussed here. The bis-pyrrolo[1,2-a]quinoxalines 1n and 1p were identified as the most potent antimalarial candidates with selectivity index (SI) of 40.6 on W2 strain, and 39.25 on 3D7 strain, respectively. As the telomeres of the parasite could constitute an attractive target, we investigated the possibility of targeting Plasmodium telomeres by stabilizing the Plasmodium telomeric G-quadruplexes through a FRET melting assay by our new compounds.
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Affiliation(s)
- Jean Guillon
- a ARNA Laboratory , University Bordeaux, UFR des Sciences Pharmaceutiques , Bordeaux , France.,b INSERM U1212, UMR CNRS 5320, ARNA Laboratory , Bordeaux , France
| | - Anita Cohen
- c UMR-MD3, Faculty of Pharmacy , Aix-Marseille University, Laboratory of Parasitology , Marseille , France
| | - Nassima Meriem Gueddouda
- a ARNA Laboratory , University Bordeaux, UFR des Sciences Pharmaceutiques , Bordeaux , France.,b INSERM U1212, UMR CNRS 5320, ARNA Laboratory , Bordeaux , France
| | - Rabindra Nath Das
- a ARNA Laboratory , University Bordeaux, UFR des Sciences Pharmaceutiques , Bordeaux , France.,b INSERM U1212, UMR CNRS 5320, ARNA Laboratory , Bordeaux , France
| | - Stéphane Moreau
- a ARNA Laboratory , University Bordeaux, UFR des Sciences Pharmaceutiques , Bordeaux , France.,b INSERM U1212, UMR CNRS 5320, ARNA Laboratory , Bordeaux , France
| | - Luisa Ronga
- a ARNA Laboratory , University Bordeaux, UFR des Sciences Pharmaceutiques , Bordeaux , France.,b INSERM U1212, UMR CNRS 5320, ARNA Laboratory , Bordeaux , France
| | - Solène Savrimoutou
- a ARNA Laboratory , University Bordeaux, UFR des Sciences Pharmaceutiques , Bordeaux , France.,b INSERM U1212, UMR CNRS 5320, ARNA Laboratory , Bordeaux , France
| | - Louise Basmaciyan
- c UMR-MD3, Faculty of Pharmacy , Aix-Marseille University, Laboratory of Parasitology , Marseille , France
| | - Alix Monnier
- a ARNA Laboratory , University Bordeaux, UFR des Sciences Pharmaceutiques , Bordeaux , France.,b INSERM U1212, UMR CNRS 5320, ARNA Laboratory , Bordeaux , France
| | - Myriam Monget
- a ARNA Laboratory , University Bordeaux, UFR des Sciences Pharmaceutiques , Bordeaux , France.,b INSERM U1212, UMR CNRS 5320, ARNA Laboratory , Bordeaux , France
| | - Sandra Rubio
- a ARNA Laboratory , University Bordeaux, UFR des Sciences Pharmaceutiques , Bordeaux , France.,b INSERM U1212, UMR CNRS 5320, ARNA Laboratory , Bordeaux , France
| | - Timothée Garnerin
- d Université de Picardie Jules Verne, Laboratoire de Glycochimie , des Antimicrobiens et des Agroressouces, UMR CNRS 7378, UFR de Pharmacie , Amiens , France
| | - Nadine Azas
- c UMR-MD3, Faculty of Pharmacy , Aix-Marseille University, Laboratory of Parasitology , Marseille , France
| | - Jean-Louis Mergny
- a ARNA Laboratory , University Bordeaux, UFR des Sciences Pharmaceutiques , Bordeaux , France.,b INSERM U1212, UMR CNRS 5320, ARNA Laboratory , Bordeaux , France
| | - Catherine Mullié
- d Université de Picardie Jules Verne, Laboratoire de Glycochimie , des Antimicrobiens et des Agroressouces, UMR CNRS 7378, UFR de Pharmacie , Amiens , France
| | - Pascal Sonnet
- d Université de Picardie Jules Verne, Laboratoire de Glycochimie , des Antimicrobiens et des Agroressouces, UMR CNRS 7378, UFR de Pharmacie , Amiens , France
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24
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Bhartiya D, Chawla V, Ghosh S, Shankar R, Kumar N. Genome-wide regulatory dynamics of G-quadruplexes in human malaria parasite Plasmodium falciparum. Genomics 2016; 108:224-231. [PMID: 27789319 DOI: 10.1016/j.ygeno.2016.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 11/17/2022]
Abstract
The AT-rich genome of P. falciparum has uniquely localized G-rich stretches that have propensity to form G-quadruplexes. However, their global occurrence and potential biological roles in the parasite are poorly explored. Our genome-wide analysis revealed unique enrichment of quadruplexes in P. falciparum genome which was remarkably different from other Plasmodium species. A distinct predominance of quadruplexes was observed in nuclear and organellar genes that participate in antigenic variation, pathogenesis, DNA/RNA regulation, metabolic and protein quality control processes. Data also suggested association of quadruplexes with SNPs and DNA methylation. Furthermore, analysis of steady state mRNA (RNA-seq) and polysome-associated mRNA (Ribosome profiling) data revealed stage-specific differences in translational efficiency of quadruplex harboring genes. Taken together, our findings hint towards existence of regulatory dynamics associated with quadruplexes that may modulate translational efficiency of quadruplex harboring genes to provide survival advantage to the parasite against host immune response and antimalarial drug pressure.
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Affiliation(s)
- Deeksha Bhartiya
- ICMR-Institute of Cytology and Preventive Oncology, Noida 201301, Uttar Pradesh, India
| | - Vandna Chawla
- CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Sourav Ghosh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road Campus, Delhi 110020, India
| | - Ravi Shankar
- CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India
| | - Niti Kumar
- CSIR-Central Drug Research Institute, Lucknow 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India.
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25
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Kotera N, Granzhan A, Teulade-Fichou MP. Comparative study of affinity and selectivity of ligands targeting abasic and mismatch sites in DNA using a fluorescence-melting assay. Biochimie 2016; 128-129:133-7. [PMID: 27523781 DOI: 10.1016/j.biochi.2016.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/08/2016] [Indexed: 11/29/2022]
Abstract
Recently, several families of small-molecule ligands have been developed to selectively target DNA pairing defects, such as abasic sites and mismatched base pairs, with the aim to interfere with the DNA repair and the template function of the DNA. However, the affinity and selectivity (with respect to well-matched DNA) of these ligands has barely been evaluated in a systematic way. Herein, we report a comparative study of binding affinity and selectivity of a representative panel of 16 ligands targeting abasic sites and a T-T mismatch in DNA, using a fluorescence-monitored melting assay. We demonstrate that bisintercalator-type macrocyclic ligands are characterized by moderate affinity but exceptionally high selectivity with respect to well-matched DNA, whereas other reported ligands show either modest selectivity or rather low affinity in identical conditions.
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Affiliation(s)
- Naoko Kotera
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France
| | - Anton Granzhan
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France.
| | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France
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26
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Gama S, Rodrigues I, Mendes F, Santos IC, Gabano E, Klejevskaja B, Gonzalez-Garcia J, Ravera M, Vilar R, Paulo A. Anthracene-terpyridine metal complexes as new G-quadruplex DNA binders. J Inorg Biochem 2016; 160:275-86. [PMID: 27267415 DOI: 10.1016/j.jinorgbio.2016.04.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/15/2016] [Accepted: 04/03/2016] [Indexed: 12/21/2022]
Abstract
The formation of quadruple-stranded DNA induced by planar metal complexes has particular interest in the development of novel anticancer drugs. This is especially relevant for the inhibition of telomerase, which plays an essential role in cancer cell immortalization and is overexpressed in ca. 85-90% of cancer cells. Moreover, G-quadruplexes also exist in other locations in the human genome, namely oncogene promoter regions, and it has been hypothesized that they play a regulatory role in gene transcription. Herein we report a series of new anthracene-containing terpyridine ligands and the corresponding Cu(II) and Pt(II) complexes, with different linkers between the anthracenyl moiety and the terpyridine chelating unit. The interaction of these ligands and metal complexes with different topologies of DNA was studied by several biophysical techniques. The Pt(II) and Cu(II) complexes tested showed affinity for quadruplex-forming sequences with a good selectivity over duplex DNA. Importantly, the free ligands do not have significant affinity for any of the DNA sequences used, which shows that the presence of the metal is essential for high affinity (and selectivity). This effect is more evident in the case of the Pt(II) complexes. Moreover, the presence of a longer linker between the chelating terpyridine unit and the anthracene moiety enhances the interaction with G-quadruplex-forming sequences. We further evaluated the ability of the Cu(II) complexes to interact with, and stabilize G-quadruplex containing regions in oncogene promoters via a polymerase stop assay. These studies indicated that the metal complexes are able to induce G-quadruplex formation and stop polymerase activity.
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Affiliation(s)
- Sofia Gama
- Centro de Ciências e Tecnologias Nucleares (C(2)TN), Instituto Superior Técnico, Universidade de Lisboa, Portugal.
| | - Inês Rodrigues
- Centro de Ciências e Tecnologias Nucleares (C(2)TN), Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Filipa Mendes
- Centro de Ciências e Tecnologias Nucleares (C(2)TN), Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Isabel C Santos
- Centro de Ciências e Tecnologias Nucleares (C(2)TN), Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Elisabetta Gabano
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale "Amedeo Avogadro", Alessandria, Italy
| | - Beata Klejevskaja
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | | | - Mauro Ravera
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale "Amedeo Avogadro", Alessandria, Italy
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - António Paulo
- Centro de Ciências e Tecnologias Nucleares (C(2)TN), Instituto Superior Técnico, Universidade de Lisboa, Portugal
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Zheng C, Liu Y, Liu Y, Qin X, Zhou Y, Liu J. Dinuclear ruthenium complexes display loop isomer selectivity to c-MYC DNA G-quadriplex and exhibit anti-tumour activity. J Inorg Biochem 2016; 156:122-32. [DOI: 10.1016/j.jinorgbio.2016.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 12/30/2015] [Accepted: 01/07/2016] [Indexed: 12/18/2022]
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Saintomé C, Amrane S, Mergny JL, Alberti P. The exception that confirms the rule: a higher-order telomeric G-quadruplex structure more stable in sodium than in potassium. Nucleic Acids Res 2016; 44:2926-35. [PMID: 26762980 PMCID: PMC4824101 DOI: 10.1093/nar/gkw003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/31/2015] [Indexed: 11/14/2022] Open
Abstract
DNA and RNA guanine-quadruplexes (G4s) are stabilized by several cations, in particular by potassium and sodium ions. Generally, potassium stabilizes guanine-quartet assemblies to a larger extent than sodium; in this article we report about a higher-order G4 structure more stable in sodium than in potassium. Repeats of the DNA GGGTTA telomeric motif fold into contiguous G4 units. Using three independent approaches (thermal denaturation experiments, isothermal molecular-beacon and protein-binding assays), we show that the (GGGTTA)7GGG sequence, folding into two contiguous G4 units, exhibits an unusual feature among G4 motifs: despite a lower thermal stability, its sodium conformation is more stable than its potassium counterpart at physiological temperature. Using differential scanning calorimetry and mutated sequences, we show that this switch in the relative stability of the sodium and potassium conformations (occurring around 45°C in 100 mM cation concentration) is the result of a more favorable enthalpy change upon folding in sodium, generated by stabilizing interactions between the two G4 units in the sodium conformation. Our work demonstrates that interactions between G4 structural domains can make a higher-order structure more stable in sodium than in potassium, even though its G4 structural domains are individually more stable in potassium than in sodium.
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Affiliation(s)
- Carole Saintomé
- Structure et Instabilité des Génomes, Sorbonne Universités, Muséum national d'Histoire naturelle, Inserm U 1154, CNRS UMR 7196, Paris, France UPMC (Université Pierre et Marie Curie) Université Paris 6, UFR 927, Paris, France
| | - Samir Amrane
- Université de Bordeaux, ARNA Laboratory, Bordeaux, France IECB (Institut Européen de Chimie et Biologie), Inserm U 869, Pessac, France
| | - Jean-Louis Mergny
- Université de Bordeaux, ARNA Laboratory, Bordeaux, France IECB (Institut Européen de Chimie et Biologie), Inserm U 869, Pessac, France
| | - Patrizia Alberti
- Structure et Instabilité des Génomes, Sorbonne Universités, Muséum national d'Histoire naturelle, Inserm U 1154, CNRS UMR 7196, Paris, France
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Abstract
DNA can form several secondary structures besides the classic double helix: one that has received much attention in recent years is the G-quadruplex (G4). This is a stable four-stranded structure formed by the stacking of quartets of guanine bases. Recent work has convincingly shown that G4s can form in vivo as well as in vitro and can affect both replication and transcription of DNA. They also play important roles at G-rich telomeres. Now, a spate of exciting reports has begun to reveal roles for G4 structures in virulence processes in several important microbial pathogens of humans. Interestingly, these come from a range of kingdoms—bacteria and protozoa as well as viruses—and all facilitate immune evasion in different ways. In particular, roles for G4s have been posited in the antigenic variation systems of bacteria and protozoa, as well as in the silencing of at least two major human viruses, human immunodeficiency virus (HIV) and Epstein-Barr virus (EBV). Although antigenic variation and the silencing of latent viruses are quite distinct from one another, both are routes to immune evasion and the maintenance of chronic infections. Thus, highly disparate pathogens can use G4 motifs to control DNA/RNA dynamics in ways that are relevant to common virulence phenotypes. This review explores the evidence for G4 biology in such processes across a range of important human pathogens.
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Hernández-Rivas R, Herrera-Solorio AM, Sierra-Miranda M, Delgadillo DM, Vargas M. Impact of chromosome ends on the biology and virulence of Plasmodium falciparum. Mol Biochem Parasitol 2013; 187:121-8. [PMID: 23354131 DOI: 10.1016/j.molbiopara.2013.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Revised: 01/15/2013] [Accepted: 01/17/2013] [Indexed: 11/15/2022]
Abstract
In recent years, many studies have focused on heterochromatin located at chromosome ends, which plays an important role in regulating gene expression in many organisms ranging from yeast to humans. Similarly, in the protozoan Plasmodium falciparum, which is the most virulent human malaria parasite, the heterochromatin present in telomeres and subtelomeric regions exerts a silencing effect on the virulence gene families located therein. Studies addressing P. falciparum chromosome ends have demonstrated that these regions participate in other functions, such as the formation of the T-loop structure, the replication of telomeric regions, the regulation of telomere length and the formation of telomeric heterochromatin. In addition, telomeres are involved in anchoring chromosome ends to the nuclear periphery, thereby playing an important role in nuclear architecture and gene expression regulation. Here, we review the current understanding of chromosome ends, the proteins that bind to these regions and their impact on the biology and virulence of P. falciparum.
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Affiliation(s)
- Rosaura Hernández-Rivas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del, Instituto Politécnico Nacional (IPN), Apartado postal 14-740, 07360 México, D.F., Mexico.
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31
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Doria F, Nadai M, Folini M, Scalabrin M, Germani L, Sattin G, Mella M, Palumbo M, Zaffaroni N, Fabris D, Freccero M, Richter SN. Targeting loop adenines in G-quadruplex by a selective oxirane. Chemistry 2012; 19:78-81. [PMID: 23212868 DOI: 10.1002/chem.201203097] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Indexed: 11/06/2022]
Abstract
Caught in the oxirane: Naphthalene diimides conjugated to a quinone methide and an oxirane have been synthesized and investigated as selective DNA G-quadruplex alkylating agents. The oxirane derivative generates a stable adduct with a G-quadruplex and shows selective alkylation of the loop adenines, as illustrated.
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Affiliation(s)
- Filippo Doria
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia (Italy)
| | - Matteo Nadai
- Dipartimento di Medicina Molecolare, Università di Padova, via Gabelli 63, 35121 Padua, Italy
| | - Marco Folini
- Dipartimento di Oncologia Sperimentale e Medicina Molecolare, Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. Amadeo 42,20133 Milano, Italy
| | - Matteo Scalabrin
- The RNA Institute of University at Albany (SUNY), Albany, New York
| | - Luca Germani
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia (Italy)
| | - Giovanna Sattin
- Dipartimento di Medicina Molecolare, Università di Padova, via Gabelli 63, 35121 Padua, Italy
| | - Mariella Mella
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia (Italy)
| | - Manlio Palumbo
- Department of Pharmaceutical and Pharmacological Sciences, Università di Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Nadia Zaffaroni
- Dipartimento di Oncologia Sperimentale e Medicina Molecolare, Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. Amadeo 42,20133 Milano, Italy
| | - Daniele Fabris
- The RNA Institute of University at Albany (SUNY), Albany, New York
| | - Mauro Freccero
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia (Italy)
| | - Sara N Richter
- Dipartimento di Medicina Molecolare, Università di Padova, via Gabelli 63, 35121 Padua, Italy
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32
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Stefan L, Bertrand B, Richard P, Le Gendre P, Denat F, Picquet M, Monchaud D. Assessing the Differential Affinity of Small Molecules for Noncanonical DNA Structures. Chembiochem 2012; 13:1905-12. [DOI: 10.1002/cbic.201200396] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Indexed: 01/19/2023]
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33
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Nikan M, Patrick BO, Sherman JC. Crystal Structure of a Template-Assembled Synthetic G-Quadruplex. Chembiochem 2012; 13:1413-5. [DOI: 10.1002/cbic.201200262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Indexed: 01/24/2023]
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34
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Fluorescence and Electrochemical Recognition of Nucleosides and DNA by A Novel Luminescent Bioprobe Eu(lll) -TNB. J Fluoresc 2012; 22:971-92. [DOI: 10.1007/s10895-011-1036-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 12/28/2011] [Indexed: 12/11/2022]
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35
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36
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37
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Vuong S, Stefan L, Lejault P, Rousselin Y, Denat F, Monchaud D. Identifying three-way DNA junction-specific small-molecules. Biochimie 2011; 94:442-50. [PMID: 21884749 DOI: 10.1016/j.biochi.2011.08.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 08/14/2011] [Indexed: 11/26/2022]
Abstract
Three-way junction DNA (TWJ-DNA, also known as 3WJ-DNA) is an alternative secondary DNA structure comprised of three duplex-DNAs that converge towards a single point, termed the branch point. This point is characterized by unique geometrical properties that make its specific targeting by synthetic small-molecules possible. Such a targeting has already been demonstrated in the solid state but not thoroughly biophysically investigated in solution. Herein, a set of simple biophysical assays has been developed to identify TWJ-specific small-molecule ligands; these assays, inspired by the considerable body of work that has been reported to characterize the interactions between small-molecules and other higher-order DNA (notably quadruplex-DNA), have been calibrated with a known non-specific DNA binder (the porphyrin TMPyP4) and validated via the study of a small series of triazacyclononane (TACN) derivatives (metal-free or not) and the identification of a fairly-affinic and exquisitely TWJ-selective candidate (a TACN-quinoline construct named TACN-Q).
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Affiliation(s)
- Sophie Vuong
- Institut de Chimie Moléculaire de l'Université de Bourgogne, CNRS UMR5260, 9 Avenue Alain Savary, 21000 Dijon, France
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38
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Collie GW, Parkinson GN. The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem Soc Rev 2011; 40:5867-92. [PMID: 21789296 DOI: 10.1039/c1cs15067g] [Citation(s) in RCA: 461] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The intriguing structural diversity in folded topologies available to guanine-rich nucleic acid repeat sequences have made four-stranded G-quadruplex structures the focus of both basic and applied research, from cancer biology and novel therapeutics through to nanoelectronics. Distributed widely in the human genome as targets for regulating gene expression and chromosomal maintenance, they offer unique avenues for future cancer drug development. In particular, the recent advances in chemical and structural biology have enabled the construction of bespoke selective DNA based aptamers to be used as novel therapeutic agents and access to detailed structural models for structure based drug discovery. In this critical review, we will explore the important underlying characteristics of G-quadruplexes that make them functional, stable, and predictable nanoscaffolds. We will review the current structural database of folding topologies, molecular interfaces and novel interaction surfaces, with a consideration to their future exploitation in drug discovery, molecular biology, supermolecular assembly and aptamer design. In recent years the number of potential applications for G-quadruplex motifs has rapidly grown, so in this review we aim to explore the many future challenges and highlight where possible successes may lie. We will highlight the similarities and differences between DNA and RNA folded G-quadruplexes in terms of stability, distribution, and exploitability as small molecule targets. Finally, we will provide a detailed review of basic G-quadruplex geometry, experimental tools used, and a critical evaluation of the application of high-resolution structural biology and its ability to provide meaningful and valid models for future applications (255 references).
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Affiliation(s)
- Gavin W Collie
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, UK WC1N 1AX
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39
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Bertrand H, Granzhan A, Monchaud D, Saettel N, Guillot R, Clifford S, Guédin A, Mergny J, Teulade‐Fichou M. Recognition of G‐Quadruplex DNA by Triangular Star‐Shaped Compounds: With or Without Side Chains? Chemistry 2011; 17:4529-39. [DOI: 10.1002/chem.201002810] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 01/03/2011] [Indexed: 12/12/2022]
Affiliation(s)
- Hélène Bertrand
- Institut Curie, Centre de Recherche, CNRS UMR176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay (France), Fax: (+33) 169075381
| | - Anton Granzhan
- Institut Curie, Centre de Recherche, CNRS UMR176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay (France), Fax: (+33) 169075381
| | - David Monchaud
- Institut Curie, Centre de Recherche, CNRS UMR176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay (France), Fax: (+33) 169075381
- Current address: Institut de Chimie Moléculaire, CNRS UMR5260, Université de Bourgogne (ICMUB), Faculté des Sciences Mirande, 9, Avenue Alain Savary, 21000 Dijon (France)
| | - Nicolas Saettel
- Institut Curie, Centre de Recherche, CNRS UMR176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay (France), Fax: (+33) 169075381
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, CNRS UMR8182, Université Paris Sud XI, Bât. 420, 91405 Orsay (France)
| | - Sarah Clifford
- Département de chimie minérale, analytique et appliquée Université de Genève, quai Ernest‐Ansermet 30, 1211 Genève 4 (Switzerland)
| | - Aurore Guédin
- Laboratoire des Régulations et Dynamique du Génome, INSERM U565, CNRS UMR5153, Muséum National d'Histoire Naturelle, 43, Rue Cuvier, 75005 Paris (France)
- INSERM U869, Université de Bordeaux, Institut Européen de Chimie et Biologie, 2, Rue Robert Escarpit, 33607 Pessac (France)
| | - Jean‐Louis Mergny
- Laboratoire des Régulations et Dynamique du Génome, INSERM U565, CNRS UMR5153, Muséum National d'Histoire Naturelle, 43, Rue Cuvier, 75005 Paris (France)
- INSERM U869, Université de Bordeaux, Institut Européen de Chimie et Biologie, 2, Rue Robert Escarpit, 33607 Pessac (France)
| | - Marie‐Paule Teulade‐Fichou
- Institut Curie, Centre de Recherche, CNRS UMR176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay (France), Fax: (+33) 169075381
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Abstract
In most eukaryotes, telomeric DNA consists of repeats of a short motif that includes consecutive guanines and may hence fold into G-quadruplexes. Budding yeasts have telomeres composed of longer repeats and show variation in the degree of repeat homogeneity. Although telomeric sequences from several organisms have been shown to fold into G-quadruplexes in vitro, surprisingly, no study has been dedicated to the comparison of G-quadruplex folding and stability of known telomeric sequences. Furthermore, to our knowledge, folding of yeast telomeric sequences into intramolecular G-quadruplexes has never been investigated. Using biophysical and biochemical methods, we studied sequences mimicking about four repetitions of telomeric motifs from a variety of organisms, including yeasts, with the aim of comparing the G-quadruplex folding potential of telomeric sequences among eukaryotes. G-quadruplex folding did not appear to be a conserved feature among yeast telomeric sequences. By contrast, all known telomeric sequences from eukaryotes other than yeasts folded into G-quadruplexes. Nevertheless, while G(3)T(1-4)A repeats (found in a variety of organisms) and G(4)T(2,4) repeats (found in ciliates) folded into stable G-quadruplexes, G-quadruplexes formed by repetitions of G(2)T(2)A and G(2)CT(2)A motifs (found in many insects and in nematodes, respectively) appeared to be in equilibrium with non-G-quadruplex structures (likely hairpin-duplexes).
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Affiliation(s)
- Phong Lan Thao Tran
- INSERM, U565, Acides Nucléiques: Dynamique, Ciblage et Fonctions Biologiques, Muséum National d'Histoire Naturelle, CNRS, UMR7196, Département de Régulations, Développement et Diversité Moléculaire, 43 rue Cuvier, CP26, Paris Cedex 5 -75231, France
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Xu H, Gao S, Yang Q, Pan D, Wang L, Fan C. Amplified fluorescent recognition of g-quadruplex folding with a cationic conjugated polymer and DNA intercalator. ACS APPLIED MATERIALS & INTERFACES 2010; 2:3211-3216. [PMID: 21028820 DOI: 10.1021/am1006854] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The single stranded DNA (ssDNA) with G-rich sequence can fold into G-quadruplex via intramolecular hydrogen-bonding interaction in the presence of ligand. This structure conversion can be specifically detected by a fluorescence method based on different interaction between SYBR Green I (SG) and various DNA structures. SG is proved to intercalate into G-quadruplex and results in high fluorescence intensity, which can be further amplified by 6-fold through fluorescence resonance energy transfer (FRET) from a water-soluble cationic conjugated polymer (CCP) to SG due to the high affinity of positively charged CCP to negatively charged rigid G-quadruplex, whereas it is not performed for ssDNA in the absence of K(+). As a result, the ssDNA/SG/CCP complex can be used to detect potassium ions with improved selectivity in a label-free and cost-effective manner.
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Affiliation(s)
- Hui Xu
- School of Chemistry and Material Sciences, Ludong University, Yantai 264025, China
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42
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Bencini A, Lippolis V. 1,10-Phenanthroline: A versatile building block for the construction of ligands for various purposes. Coord Chem Rev 2010. [DOI: 10.1016/j.ccr.2010.04.008] [Citation(s) in RCA: 288] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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43
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Mauritz JMA, Esposito A, Tiffert T, Skepper JN, Warley A, Yoon YZ, Cicuta P, Lew VL, Guck JR, Kaminski CF. Biophotonic techniques for the study of malaria-infected red blood cells. Med Biol Eng Comput 2010; 48:1055-63. [PMID: 20661776 DOI: 10.1007/s11517-010-0668-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 07/11/2010] [Indexed: 12/23/2022]
Abstract
Investigation of the homeostasis of red blood cells upon infection by Plasmodium falciparum poses complex experimental challenges. Changes in red cell shape, volume, protein, and ion balance are difficult to quantify. In this article, we review a wide range of optical techniques for quantitative measurements of critical homeostatic parameters in malaria-infected red blood cells. Fluorescence lifetime imaging and tomographic phase microscopy, quantitative deconvolution microscopy, and X-ray microanalysis, are used to measure haemoglobin concentration, cell volume, and ion contents. Atomic force microscopy is briefly reviewed in the context of these optical methodologies. We also describe how optical tweezers and optical stretchers can be usefully applied to empower basic malaria research to yield diagnostic information on cell compliance changes upon malaria infection. The combined application of these techniques sheds new light on the detailed mechanisms of malaria infection providing potential for new diagnostic or therapeutic approaches.
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Affiliation(s)
- Jakob M A Mauritz
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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Monchaud D, Granzhan A, Saettel N, Guédin A, Mergny JL, Teulade-Fichou MP. "One ring to bind them all"-part I: the efficiency of the macrocyclic scaffold for g-quadruplex DNA recognition. J Nucleic Acids 2010; 2010. [PMID: 20725629 PMCID: PMC2915875 DOI: 10.4061/2010/525862] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 02/18/2010] [Indexed: 01/01/2023] Open
Abstract
Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the “standard” B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. Stimulated by the pioneering studies on the cationic porphyrin TMPyP4 and the natural product telomestatin, follow-up studies have developed, rapidly leading to a large diversity of macrocyclic structures with remarkable-quadruplex binding properties and biological activities. In this review we summarize the current state of the art in detailing the three main categories of quadruplex-binding macrocycles described so far (telomestatin-like polyheteroarenes, porphyrins and derivatives, polyammonium cyclophanes), and in addressing both synthetic issues and biological aspects.
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Affiliation(s)
- David Monchaud
- Section Recherche, Institut Curie, CNRS UMR176, Centre Universitaire Paris XI, Batiment 110, 91405 Orsay, France
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45
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Granzhan A, Monchaud D, Saettel N, Guédin A, Mergny JL, Teulade-Fichou MP. "One Ring to Bind Them All"-Part II: Identification of Promising G-Quadruplex Ligands by Screening of Cyclophane-Type Macrocycles. J Nucleic Acids 2010; 2010. [PMID: 20725622 PMCID: PMC2915812 DOI: 10.4061/2010/460561] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 02/10/2010] [Indexed: 11/30/2022] Open
Abstract
A collection of 26 polyammonium cyclophane-type macrocycles with a large structural diversity has been screened for G-quadruplex recognition. A two-step selection procedure based on the FRET-melting assay was carried out enabling identification of macrocycles of high affinity (ΔT1/2 up to 30°C) and high selectivity for the human telomeric G-quadruplex. The four selected hits possess sophisticated architectures, more particularly the presence of a pendant side-arm as well as the existence of a particular topological arrangement appear to be strong determinants of quadruplex binding. These compounds are thus likely to create multiple contacts with the target that may be at the origin of their high selectivity, thereby suggesting that this class of macrocycles offers unique advantages for targeting G-quadruplex-DNA.
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Affiliation(s)
- Anton Granzhan
- Section Recherche, Institut Curie, CNRS UMR176, Centre Universitaire Paris XI, Bat. 110, 91405 Orsay, France
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Piazza A, Boulé JB, Lopes J, Mingo K, Largy E, Teulade-Fichou MP, Nicolas A. Genetic instability triggered by G-quadruplex interacting Phen-DC compounds in Saccharomyces cerevisiae. Nucleic Acids Res 2010; 38:4337-48. [PMID: 20223771 PMCID: PMC2910037 DOI: 10.1093/nar/gkq136] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
G-quadruplexes are nucleic acid secondary structures for which many biological roles have been proposed but whose existence in vivo has remained elusive. To assess their formation, highly specific G-quadruplex ligands are needed. Here, we tested Phen-DC3 and Phen-DC6, two recently released ligands of the bisquinolinium class. In vitro, both compounds exhibit high affinity for the G4 formed by the human minisatellite CEB1 and inhibit efficiently their unwinding by the yeast Pif1 helicase. In vivo, both compounds rapidly induced recombination-dependent rearrangements of CEB1 inserted in the Saccharomyces cerevisiae genome, but did not affect the stability of other tandem repeats lacking G-quadruplex forming sequences. The rearrangements yielded simple-deletion, double-deletion or complex reshuffling of the polymorphic motif units, mimicking the phenotype of the Pif1 inactivation. Treatment of Pif1-deficient cells with the Phen-DC compounds further increased CEB1 instability, revealing additional G4 formation per cell. In sharp contrast, the commonly used N-methyl-mesoporphyrin IX G-quadruplex ligand did not affect CEB1 stability. Altogether, these results demonstrate that the Phen-DC bisquinolinium compounds are potent molecular tools for probing the formation of G-quadruplexes in vivo, interfere with their processing and elucidate their biological roles.
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Affiliation(s)
- Aurèle Piazza
- Recombinaison et Instabilité Génétique, Institut Curie Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
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Abstract
A simple thermal melting experiment may be used to demonstrate the stabilization of a given structure by a ligand (usually a small molecule, sometimes a peptide). Preparation of the sample is straightforward, and the experiment itself requires an inexpensive apparatus. Furthermore, reasonably low amounts of sample are required. A qualitative analysis of the data is simple: An increase in the melting temperature (T(m)) indicates preferential binding to the folded form as compared to the unfolded form. However, it is perilous to derive an affinity constant from an increase in T(m) as other factors play a role.
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Affiliation(s)
- Aurore Guédin
- Equipe Santé, Laboratoire Régulation et Dynamique des Génomes, Muséum National d'Histoire Naturelle USM 503, INSERM UR 565, CNRS UMR 5153, Paris, France
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Fernando H, Sewitz S, Darot J, Tavaré S, Huppert JL, Balasubramanian S. Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression. Nucleic Acids Res 2009; 37:6716-22. [PMID: 19745055 PMCID: PMC2777450 DOI: 10.1093/nar/gkp740] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
G-quadruplex nucleic acids have been proposed to play a role in a number of fundamental biological processes that include transcription and translation. We have developed a single-chain antibody that is selective for G-quadruplex DNA over double-stranded DNA, and here show that when it is expressed in human cells, it significantly affects the expression of a wide variety of genes, in a manner that correlates with the presence of predicted G-quadruplexes. We observe cases where gene expression is increased or decreased, and that there are apparent interactions with G-quadruplex motifs at the beginning and end of the genes, and on either strand. The outcomes of this genome-wide study demonstrate that G-quadruplex recognition by the antibody has physiological consequences, and provides insights into some of the complexity associated with G-quadruplex-based regulation.
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Affiliation(s)
- Himesh Fernando
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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Smargiasso N, Gabelica V, Damblon C, Rosu F, De Pauw E, Teulade-Fichou MP, Rowe JA, Claessens A. Putative DNA G-quadruplex formation within the promoters of Plasmodium falciparum var genes. BMC Genomics 2009; 10:362. [PMID: 19660104 PMCID: PMC2736202 DOI: 10.1186/1471-2164-10-362] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 08/06/2009] [Indexed: 11/24/2022] Open
Abstract
Background Guanine-rich nucleic acid sequences are capable of folding into an intramolecular four-stranded structure called a G-quadruplex. When found in gene promoter regions, G-quadruplexes can downregulate gene expression, possibly by blocking the transcriptional machinery. Here we have used a genome-wide bioinformatic approach to identify Putative G-Quadruplex Sequences (PQS) in the Plasmodium falciparum genome, along with biophysical techniques to examine the physiological stability of P. falciparum PQS in vitro. Results We identified 63 PQS in the non-telomeric regions of the P. falciparum clone 3D7. Interestingly, 16 of these PQS occurred in the upstream region of a subset of the P. falciparum var genes (group B var genes). The var gene family encodes PfEMP1, the parasite's major variant antigen and adhesin expressed at the surface of infected erythrocytes, that plays a key role in malaria pathogenesis and immune evasion. The ability of the PQS found in the upstream regions of group B var genes (UpsB-Q) to form stable G-quadruplex structures in vitro was confirmed using 1H NMR, circular dichroism, UV spectroscopy, and thermal denaturation experiments. Moreover, the synthetic compound BOQ1 that shows a higher affinity for DNA forming quadruplex rather than duplex structures was found to bind with high affinity to the UpsB-Q. Conclusion This is the first demonstration of non-telomeric PQS in the genome of P. falciparum that form stable G-quadruplexes under physiological conditions in vitro. These results allow the generation of a novel hypothesis that the G-quadruplex sequences in the upstream regions of var genes have the potential to play a role in the transcriptional control of this major virulence-associated multi-gene family.
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Affiliation(s)
- Nicolas Smargiasso
- Mass Spectrometry Laboratory, GIGA-Research, University of Liege, Liege, Belgium.
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Bertrand H, Bombard S, Monchaud D, Talbot E, Guédin A, Mergny JL, Grünert R, Bednarski PJ, Teulade-Fichou MP. Exclusive platination of loop adenines in the human telomeric G-quadruplex. Org Biomol Chem 2009; 7:2864-71. [PMID: 19582295 DOI: 10.1039/b904599f] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Hélène Bertrand
- Institut Curie, Section Recherche, CNRS UMR176, Centre Universitaire Paris XI, Bât. 110, 91405, Orsay, France
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