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Choudhury SD, Kumar P, Choudhury D. Bioactive nutraceuticals as G4 stabilizers: potential cancer prevention and therapy-a critical review. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:3585-3616. [PMID: 38019298 DOI: 10.1007/s00210-023-02857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023]
Abstract
G-quadruplexes (G4) are non-canonical, four-stranded, nucleic acid secondary structures formed in the guanine-rich sequences, where guanine nucleotides associate with each other via Hoogsteen hydrogen bonding. These structures are widely found near the functional regions of the mammalian genome, such as telomeres, oncogenic promoters, and replication origins, and play crucial regulatory roles in replication and transcription. Destabilization of G4 by various carcinogenic agents allows oncogene overexpression and extension of telomeric ends resulting in dysregulation of cellular growth-promoting oncogenesis. Therefore, targeting and stabilizing these G4 structures with potential ligands could aid cancer prevention and therapy. The field of G-quadruplex targeting is relatively nascent, although many articles have demonstrated the effect of G4 stabilization on oncogenic expressions; however, no previous study has provided a comprehensive analysis about the potency of a wide variety of nutraceuticals and some of their derivatives in targeting G4 and the lattice of oncogenic cell signaling cascade affected by them. In this review, we have discussed bioactive G4-stabilizing nutraceuticals, their sources, mode of action, and their influence on cellular signaling, and we believe our insight would bring new light to the current status of the field and motivate researchers to explore this relatively poorly studied arena.
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Affiliation(s)
- Satabdi Datta Choudhury
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology (IIT), Mandi, Himachal Pradesh, 175005, India
| | - Diptiman Choudhury
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India.
- Centre for Excellence in Emerging Materials, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India.
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2
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Moura NMM, Cavaleiro JAS, Neves MGPMS, Ramos CIV. opp-Dibenzoporphyrin Pyridinium Derivatives as Potential G-Quadruplex DNA Ligands. Molecules 2023; 28:6318. [PMID: 37687146 PMCID: PMC10489911 DOI: 10.3390/molecules28176318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/12/2023] [Accepted: 08/13/2023] [Indexed: 09/10/2023] Open
Abstract
Since the occurrence of tumours is closely associated with the telomerase function and oncogene expression, the structure of such enzymes and genes are being recognized as targets for new anticancer drugs. The efficacy of several ligands in telomerase inhibition and in the regulation of genes expression, by an effective stabilisation of G-quadruplexes (G4) DNA structures, is being considered as a promising strategy in cancer therapies. When evaluating the potential of a ligand for telomerase inhibition, the selectivity towards quadruplex versus duplex DNA is a fundamental attribute due to the large amount of double-stranded DNA in the cellular nucleus. This study reports the evaluated efficacy of three tetracationic opp-dibenzoporphyrins, a free base, and the corresponding zinc(II) and nickel(II) complexes, to stabilise G4 structures, namely the telomeric DNA sequence (AG3(T2AG3)3). In order to evaluate the selectivity of these ligands towards G4 structures, their interaction towards DNA calf thymus, as a double-strand DNA sequence, were also studied. The data obtained by using different spectroscopic techniques, such as ultraviolet-visible, fluorescence, and circular dichroism, suggested good affinity of the free-base porphyrin and of its zinc(II) complex for the considered DNA structures, both showing a pattern of selectivity for the telomeric G4 structure. A pattern of aggregation in aqueous solution was detected for both Zn(II) and Ni(II) metallo dibenzoporphyrins and the ability of DNA sequences to induce ligand disaggregation was observed.
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Affiliation(s)
- Nuno M. M. Moura
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (J.A.S.C.); (M.G.P.M.S.N.)
| | | | | | - Catarina I. V. Ramos
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (J.A.S.C.); (M.G.P.M.S.N.)
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3
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Zegers J, Peters M, Albada B. DNA G-quadruplex-stabilizing metal complexes as anticancer drugs. J Biol Inorg Chem 2023; 28:117-138. [PMID: 36456886 PMCID: PMC9981530 DOI: 10.1007/s00775-022-01973-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022]
Abstract
Guanine quadruplexes (G4s) are important targets for cancer treatments as their stabilization has been associated with a reduction of telomere ends or a lower oncogene expression. Although less abundant than purely organic ligands, metal complexes have shown remarkable abilities to stabilize G4s, and a wide variety of techniques have been used to characterize the interaction between ligands and G4s. However, improper alignment between the large variety of experimental techniques and biological activities can lead to improper identification of top candidates, which hampers progress of this important class of G4 stabilizers. To address this, we first review the different techniques for their strengths and weaknesses to determine the interaction of the complexes with G4s, and provide a checklist to guide future developments towards comparable data. Then, we surveyed 74 metal-based ligands for G4s that have been characterized to the in vitro level. Of these complexes, we assessed which methods were used to characterize their G4-stabilizing capacity, their selectivity for G4s over double-stranded DNA (dsDNA), and how this correlated to bioactivity data. For the biological activity data, we compared activities of the G4-stabilizing metal complexes with that of cisplatin. Lastly, we formulated guidelines for future studies on G4-stabilizing metal complexes to further enable maturation of this field.
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Affiliation(s)
- Jaccoline Zegers
- grid.4818.50000 0001 0791 5666Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Maartje Peters
- grid.4818.50000 0001 0791 5666Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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4
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Qin G, Zhao C, Yang J, Wang Z, Ren J, Qu X. Unlocking G-Quadruplexes as Targets and Tools against COVID-19. CHINESE J CHEM 2022; 41:CJOC202200486. [PMID: 36711116 PMCID: PMC9874442 DOI: 10.1002/cjoc.202200486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 02/01/2023]
Abstract
The applicability of G-quadruplexes (G4s) as antiviral targets, therapeutic agents and diagnostic tools for coronavirus disease 2019 (COVID-19) is currently being evaluated, which has drawn the extensive attention of the scientific community. During the COVID-19 pandemic, research in this field is rapidly accumulating. In this review, we summarize the latest achievements and breakthroughs in the use of G4s as antiviral targets, therapeutic agents and diagnostic tools for COVID-19, particularly using G4 ligands. Finally, strength and weakness regarding G4s in anti-SARS-CoV-2 field are highlighted for prospective future projects.
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Affiliation(s)
- Geng Qin
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Jie Yang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Zhao Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
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Attina G, Mastrangelo S, Ruggiero A. Telomerase and Anticancer Treatment. BIOMEDICAL AND PHARMACOLOGY JOURNAL 2022; 15:1881-1888. [DOI: 10.13005/bpj/2526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Current chemotherapy uses compounds of organometallic nature that act with different mechanisms of action. Many pharmacological studies are directed toward the creation of compounds with more specific and selective activity toward tumor targets, including telomerase. The design and synthesis of such compounds with specific antitelomerase activity must consider the mechanism of action of the enzyme and its structure. The discovery of a close correlation between telomerase activation, cell immortalization and oncogenesis has suggested that telomerase inhibitors could be potent therapeutic agents, capable of selectively killing cancer cells. Inhibition of telomerase is expected to lead toward shortening of telomeres to a critical length, such that replicative senescence and cell death due to irreparable chromosomal damage can result. It has been observed that cancer cells generally have shorter telomeres than the normal replicative cell population, probably because the malignant cells have undergone more divisions. Therefore, the inhibition telomeres of cancer cells after a few cycles of cell division, without the normal cells suffering harmful consequences during therapy. Telomerase is certainly an interesting target on which to continue to study molecules that inhibit its function to obtain a specificity of therapeutic intervention and a reduction of the nonspecific cytotoxicity of chemotherapy.
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Affiliation(s)
- Giorgio Attina
- Pediatric Oncology Unit, Fondazione Policlinico Universitario A.Gemelli IRCCS, Universita’ Cattolica Sacro Cuore, Rome, Italy
| | - Stefano Mastrangelo
- Pediatric Oncology Unit, Fondazione Policlinico Universitario A.Gemelli IRCCS, Universita’ Cattolica Sacro Cuore, Rome, Italy
| | - Antonio Ruggiero
- Pediatric Oncology Unit, Fondazione Policlinico Universitario A.Gemelli IRCCS, Universita’ Cattolica Sacro Cuore, Rome, Italy
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Keane PM, Zehe C, Poynton FE, Bright SA, Estayalo-Adrián S, Devereux SJ, Donaldson PM, Sazanovich IV, Towrie M, Botchway SW, Cardin CJ, Williams DC, Gunnlaugsson T, Long C, Kelly JM, Quinn SJ. Time-resolved infra-red studies of photo-excited porphyrins in the presence of nucleic acids and in HeLa tumour cells: insights into binding site and electron transfer dynamics. Phys Chem Chem Phys 2022; 24:27524-27531. [PMID: 36345709 DOI: 10.1039/d2cp04604k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Cationic porphyrins based on the 5,10,15,20-meso-(tetrakis-4-N-methylpyridyl) core (TMPyP4) have been studied extensively over many years due to their strong interactions with a variety of nucleic acid structures, and their potential use as photodynamic therapeutic agents and telomerase inhibitors. In this paper, the interactions of metal-free TMPyP4 and Pt(II)TMPyP4 with guanine-containing nucleic acids are studied for the first time using time-resolved infrared spectroscopy (TRIR). In D2O solution (where the metal-free form exists as D2TMPyP4) both compounds yielded similar TRIR spectra (between 1450-1750 cm-1) following pulsed laser excitation in their Soret B-absorption bands. Density functional theory calculations reveal that vibrations centred on the methylpyridinium groups are responsible for the dominant feature at ca. 1640 cm-1. TRIR spectra of D2TMPyP4 or PtTMPyP4 in the presence of guanosine 5'-monophosphate (GMP), double-stranded {d(GC)5}2 or {d(CGCAAATTTGCG)}2 contain negative-going signals, 'bleaches', indicative of binding close to guanine. TRIR signals for D2TMPyP4 or PtTMPyP bound to the quadruplex-forming cMYC sequence {d(TAGGGAGGG)}2T indicate that binding occurs on the stacked guanines. For D2TMPyP4 bound to guanine-containing systems, the TRIR signal at ca. 1640 cm-1 decays on the picosecond timescale, consistent with electron transfer from guanine to the singlet excited state of D2TMPyP4, although IR marker bands for the reduced porphyrin/oxidised guanine were not observed. When PtTMPyP is incorporated into HeLa tumour cells, TRIR studies show protein binding with time-dependent ps/ns changes in the amide absorptions demonstrating TRIR's potential for studying light-activated molecular processes not only with nucleic acids in solution but also in biological cells.
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Affiliation(s)
- Páraic M Keane
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland.
- School of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Clara Zehe
- School of Chemistry, University College Dublin, Dublin 4, Ireland.
| | - Fergus E Poynton
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland.
- Trinity Biomedical Sciences Institute, The University of Dublin, Pearse St., Dublin 2, Ireland
| | - Sandra A Bright
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland.
- Trinity Biomedical Sciences Institute, The University of Dublin, Pearse St., Dublin 2, Ireland
| | - Sandra Estayalo-Adrián
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland.
- Trinity Biomedical Sciences Institute, The University of Dublin, Pearse St., Dublin 2, Ireland
| | | | - Paul M Donaldson
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Igor V Sazanovich
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Stanley W Botchway
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Christine J Cardin
- School of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - D Clive Williams
- Trinity Biomedical Sciences Institute, The University of Dublin, Pearse St., Dublin 2, Ireland
| | - Thorfinnur Gunnlaugsson
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland.
- Trinity Biomedical Sciences Institute, The University of Dublin, Pearse St., Dublin 2, Ireland
| | - Conor Long
- School of Chemical Sciences, Dublin City University, Dublin 9, Ireland.
| | - John M Kelly
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland.
| | - Susan J Quinn
- School of Chemistry, University College Dublin, Dublin 4, Ireland.
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7
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Ruthenium(II) Polypyridyl Complexes and Their Use as Probes and Photoreactive Agents for G-quadruplexes Labelling. Molecules 2022; 27:molecules27051541. [PMID: 35268640 PMCID: PMC8912042 DOI: 10.3390/molecules27051541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/01/2023] Open
Abstract
Due to their optical and electrochemical properties, ruthenium(II) polypyridyl complexes have been used in a wide array of applications. Since the discovery of the light-switch ON effect of [Ru(bpy)2dppz]2+ when interacting with DNA, the design of new Ru(II) complexes as light-up probes for specific regions of DNA has been intensively explored. Amongst them, G-quadruplexes (G4s) are of particular interest. These structures formed by guanine-rich parts of DNA and RNA may be associated with a wide range of biological events. However, locating them and understanding their implications in biological pathways has proven challenging. Elegant approaches to tackle this challenge relies on the use of photoprobes capable of marking, reversibly or irreversibly, these G4s. Indeed, Ru(II) complexes containing ancillary π-deficient TAP ligands can create a covalently linked adduct with G4s after a photoinduced electron transfer from a guanine residue to the excited complex. Through careful design of the ligands, high selectivity of interaction with G4 structures can be achieved. This allows the creation of specific Ru(II) light-up probes and photoreactive agents for G4 labelling, which is at the core of this review composed of an introduction dedicated to a brief description of G-quadruplex structures and two main sections. The first one will provide a general picture of ligands and metal complexes interacting with G4s. The second one will focus on an exhaustive and comprehensive overview of the interactions and (photo)reactions of Ru(II) complexes with G4s.
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I. V. Ramos C, A. S. Almodôvar V, Candeias N, Santos T, Cruz C, Graça P. M. S. Neves M, Tomé AC. Diketopyrrolo[3,4–c]pyrrole derivative as a promising ligand for the stabilization of G-quadruplex DNA structures. Bioorg Chem 2022; 122:105703. [DOI: 10.1016/j.bioorg.2022.105703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 12/11/2022]
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Zhu Z, Tran H, Mathahs MM, Fink BD, Albert JA, Moninger TO, Meier JL, Li M, Schmidt WN. Zinc protoporphyrin binding to telomerase complexes and inhibition of telomerase activity. Pharmacol Res Perspect 2021; 9:e00882. [PMID: 34747573 PMCID: PMC8573827 DOI: 10.1002/prp2.882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/16/2022] Open
Abstract
Zinc protoporphyrin (ZnPP), a naturally occurring metalloprotoporphyrin (MPP), is currently under development as a chemotherapeutic agent although its mechanism is unclear. When tested against other MPPs, ZnPP was the most effective DNA synthesis and cellular proliferation inhibitor while promoting apoptosis in telomerase positive but not telomerase negative cells. Concurrently, ZnPP down-regulated telomerase expression and was the best overall inhibitor of telomerase activity in intact cells and cellular extracts with IC50 and EC50 values of ca 2.5 and 6 µM, respectively. The natural fluorescence properties of ZnPP enabled direct imaging in cellular fractions using non-denaturing agarose gel electrophoresis, western blots, and confocal fluorescence microscopy. ZnPP localized to large cellular complexes (>600 kD) that contained telomerase and dysskerin as confirmed with immunocomplex mobility shift, immunoprecipitation, and immunoblot analyses. Confocal fluorescence studies showed that ZnPP co-localized with telomerase reverse transcriptase (TERT) and telomeres in the nucleus of synchronized S-phase cells. ZnPP also co-localized with TERT in the perinuclear regions of log phase cells but did not co-localize with telomeres on the ends of metaphase chromosomes, a site known to be devoid of telomerase complexes. Overall, these results suggest that ZnPP does not bind to telomeric sequences per se, but alternatively, interacts with other structural components of the telomerase complex to inhibit telomerase activity. In conclusion, ZnPP actively interferes with telomerase activity in neoplastic cells, thus promoting pro-apoptotic and anti-proliferative properties. These data support further development of natural or synthetic protoporphyrins for use as chemotherapeutic agents to augment current treatment protocols for neoplastic disease.
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Affiliation(s)
- Zhaowen Zhu
- Department of Internal Medicine and Research ServiceVeterans Affairs Medical CenterIowa CityIowaUSA
- Department of Internal MedicineRoy G. and Lucille A. Carver College of MedicineUniversity of IowaIowa CityIowaUSA
| | - Huy Tran
- Department of Internal MedicineRoy G. and Lucille A. Carver College of MedicineUniversity of IowaIowa CityIowaUSA
| | - Meleah M. Mathahs
- Department of Internal Medicine and Research ServiceVeterans Affairs Medical CenterIowa CityIowaUSA
| | - Brian D. Fink
- Department of Internal Medicine and Research ServiceVeterans Affairs Medical CenterIowa CityIowaUSA
| | - John A. Albert
- Department of Internal Medicine and Research ServiceVeterans Affairs Medical CenterIowa CityIowaUSA
| | - Thomas O. Moninger
- Central Microscopy Research Facility Roy G. and Lucille A. Carver College of MedicineUniversity of IowaIowa CityIowaUSA
| | - Jeffery L. Meier
- Department of Internal Medicine and Research ServiceVeterans Affairs Medical CenterIowa CityIowaUSA
- Department of Internal MedicineRoy G. and Lucille A. Carver College of MedicineUniversity of IowaIowa CityIowaUSA
| | - Ming Li
- Department of Internal Medicine and Research ServiceVeterans Affairs Medical CenterIowa CityIowaUSA
| | - Warren N. Schmidt
- Department of Internal Medicine and Research ServiceVeterans Affairs Medical CenterIowa CityIowaUSA
- Department of Internal MedicineRoy G. and Lucille A. Carver College of MedicineUniversity of IowaIowa CityIowaUSA
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Jawarkar RD, Bakal RL, Khatale PN, Lewaa I, Jain CM, Manwar JV, Jaiswal MS. QSAR, pharmacophore modeling and molecular docking studies to identify structural alerts for some nitrogen heterocycles as dual inhibitor of telomerase reverse transcriptase and human telomeric G-quadruplex DNA. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021. [DOI: 10.1186/s43094-021-00380-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA are amongst the favorable target for researchers to discover novel and more effective anticancer agents. To understand and elucidate structure activity relationship and mechanism of inhibition of telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA, a QSAR modeling and molecular docking were conducted.
Results
Two robust QSAR model were obtained which consist of full set QSAR model (R2: 0.8174, CCCtr: 0.8995, Q2loo: 0.7881, Q2LMO: 0.7814) and divided set QSAR model (R2: 0.8217, CCCtr: 0.9021, Q2loo: 0.7886, Q2LMO: 0.7783, Q2-F1: 0.7078, Q2-F2: 0.6865, Q2-F3: 0.7346) for envisaging the inhibitory activity of telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA. The analysis reveals that carbon atom exactly at 3 bonds from aromatic carbon atom, nitrogen atom exactly at six bonds from planer nitrogen atom, aromatic carbon atom within 2 A0 from the center of mass of molecule and occurrence of element hydrogen within 2 A0 from donar atom are the key pharmacophoric features important for dual inhibition of TERT and human telomeric G-quadruplex DNA. To validate this analysis, pharmacophore modeling and the molecular docking is performed. Molecular docking analysis support QSAR analysis and revealed that, dual inhibition of TERT and human telomeric DNA is mainly contributed from hydrophobic and hydrogen bonding interactions.
Conclusion
The findings of molecular docking, pharmacophore modelling, and QSAR are all consistent and in strong agreement. The validated QSAR analyses can detect structural alerts, pharmacophore modelling can classify a molecule's consensus pharmacophore involving hydrophobic and acceptor regions, whereas docking analysis can reveal the mechanism of dual inhibition of telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA. The combination of QSAR, pharmacophore modeling and molecular docking may be useful for the future drug design of dual inhibitors to combat the devastating issue of resistance.
Graphical abstract
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11
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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Ramos CIV, Monteiro AR, Moura NMM, Faustino MAF, Trindade T, Neves MGPMS. The Interactions of H 2TMPyP, Analogues and Its Metal Complexes with DNA G-Quadruplexes-An Overview. Biomolecules 2021; 11:biom11101404. [PMID: 34680037 PMCID: PMC8533071 DOI: 10.3390/biom11101404] [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: 08/28/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 12/26/2022] Open
Abstract
The evidence that telomerase is overexpressed in almost 90% of human cancers justifies the proposal of this enzyme as a potential target for anticancer drug design. The inhibition of telomerase by quadruplex stabilizing ligands is being considered a useful approach in anticancer drug design proposals. Several aromatic ligands, including porphyrins, were exploited for telomerase inhibition by adduct formation with G-Quadruplex (GQ). 5,10,15,20-Tetrakis(N-methyl-4-pyridinium)porphyrin (H2TMPyP) is one of the most studied porphyrins in this field, and although reported as presenting high affinity to GQ, its poor selectivity for GQ over duplex structures is recognized. To increase the desired selectivity, porphyrin modifications either at the peripheral positions or at the inner core through the coordination with different metals have been handled. Herein, studies involving the interactions of TMPyP and analogs with different DNA sequences able to form GQ and duplex structures using different experimental conditions and approaches are reviewed. Some considerations concerning the structural diversity and recognition modes of G-quadruplexes will be presented first to facilitate the comprehension of the studies reviewed. Additionally, considering the diversity of experimental conditions reported, we decided to complement this review with a screening where the behavior of H2TMPyP and of some of the reviewed metal complexes were evaluated under the same experimental conditions and using the same DNA sequences. In this comparison under unified conditions, we also evaluated, for the first time, the behavior of the AgII complex of H2TMPyP. In general, all derivatives showed good affinity for GQ DNA structures with binding constants in the range of 106–107 M−1 and ligand-GQ stoichiometric ratios of 3:1 and 4:1. A promising pattern of selectivity was also identified for the new AgII derivative.
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Affiliation(s)
- Catarina I. V. Ramos
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.M.); (N.M.M.M.); (M.A.F.F.); (M.G.P.M.S.N.)
- Correspondence: ; Tel.: +351-234-370-692
| | - Ana R. Monteiro
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.M.); (N.M.M.M.); (M.A.F.F.); (M.G.P.M.S.N.)
- CICECO-Aveiro, Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Nuno M. M. Moura
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.M.); (N.M.M.M.); (M.A.F.F.); (M.G.P.M.S.N.)
| | - Maria Amparo F. Faustino
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.M.); (N.M.M.M.); (M.A.F.F.); (M.G.P.M.S.N.)
| | - Tito Trindade
- CICECO-Aveiro, Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Maria Graça P. M. S. Neves
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.M.); (N.M.M.M.); (M.A.F.F.); (M.G.P.M.S.N.)
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Gold(III) porphyrins: Synthesis and interaction with G-quadruplex DNA. J Inorg Biochem 2021; 223:111551. [PMID: 34340058 DOI: 10.1016/j.jinorgbio.2021.111551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/09/2021] [Accepted: 07/15/2021] [Indexed: 12/25/2022]
Abstract
G-quadruplex nucleic acids (G4s) are RNA and DNA secondary structures involved in the regulation of multiple key biological processes. They can be found in telomeres, oncogene promoters, RNAs, but also in viral genomes. Due to their unique structural features, very distinct from the canonical duplexes or single-strands, G4s represent promising pharmacological targets for small molecules, namely G4-ligands. Gold(III) penta-cationic porphyrins, as specific G4 ligands, are able to inhibit HIV-1 infectivity and their antiviral activity correlates with their affinity for G4s. Up to now, one of the best antiviral compounds is meso-5,10,15,20-tetrakis[4-(N-methyl-pyridinium-2-yl)phenyl]porphyrinato gold(III) (1). Starting from this compound, we report a structure/affinity relationship study of gold(III) cationic porphyrins to find out the best porphyrin candidate for functionalization, in order to study the antiviral mechanism of action of these gold(III) porphyrins.
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Lauria A, La Monica G, Terenzi A, Mannino G, Bonsignore R, Bono A, Almerico AM, Barone G, Gentile C, Martorana A. Antiproliferative Properties and G-Quadruplex-Binding of Symmetrical Naphtho[1,2-b:8,7-b']dithiophene Derivatives. Molecules 2021; 26:molecules26144309. [PMID: 34299583 PMCID: PMC8303715 DOI: 10.3390/molecules26144309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 12/04/2022] Open
Abstract
Background: G-quadruplex (G4) forming sequences are recurrent in telomeres and promoter regions of several protooncogenes. In normal cells, the transient arrangements of DNA in G-tetrads may regulate replication, transcription, and translation processes. Tumors are characterized by uncontrolled cell growth and tissue invasiveness and some of them are possibly mediated by gene expression involving G-quadruplexes. The stabilization of G-quadruplex sequences with small molecules is considered a promising strategy in anticancer targeted therapy. Methods: Molecular virtual screening allowed us identifying novel symmetric bifunctionalized naphtho[1,2-b:8,7-b’]dithiophene ligands as interesting candidates targeting h-Telo and c-MYC G-quadruplexes. A set of unexplored naphtho-dithiophene derivatives has been synthesized and biologically tested through in vitro antiproliferative assays and spectroscopic experiments in solution. Results: The analysis of biological and spectroscopic data highlighted noteworthy cytotoxic effects on HeLa cancer cell line (GI50 in the low μM range), but weak interactions with G-quadruplex c-MYC promoter. Conclusions: The new series of naphtho[1,2-b:8,7-b’]dithiophene derivatives, bearing the pharmacophoric assumptions necessary to stabilize G-quadruplexes, have been designed and successfully synthesized. The interesting antiproliferative results supported by computer aided rational approaches suggest that these studies are a significant starting point for a lead optimization process and the isolation of a more efficacious set of G-quadruplexes stabilizers.
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Affiliation(s)
- Antonino Lauria
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Gabriele La Monica
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Alessio Terenzi
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Giuseppe Mannino
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Via Quarello 15/A, 10135 Turin, Italy;
| | - Riccardo Bonsignore
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany;
| | - Alessia Bono
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Carla Gentile
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Annamaria Martorana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
- Correspondence: ; Tel.: +39-091-2389-6821
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Otsuki J, Okumura T, Sugawa K, Kawano SI, Tanaka K, Hirao T, Haino T, Lee YJ, Kang S, Kim D. A Light-Harvesting/Charge-Separation Model with Energy Gradient Made of Assemblies of meta-Pyridyl Zinc Porphyrins. Chemistry 2021; 27:4053-4063. [PMID: 33124114 DOI: 10.1002/chem.202003327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/07/2020] [Indexed: 11/08/2022]
Abstract
Self-assembly of porphyrins is a fascinating topic, not only for mimicking chlorophyll assemblies in photosynthetic organisms, but also for the potential of creating molecular-level devices. Herein, zinc porphyrin derivatives bearing a meta-pyridyl group at the meso position were prepared and their assemblies studied in chloroform. Among the porphyrins studied, one with a carbamoylpyridyl moiety gave a distinct 1 H NMR spectrum in CDCl3 , which allowed the supramolecular structure in solution to be probed in detail. Ring-current-induced chemical-shift changes in the 1 H NMR spectrum, together with vapor-pressure osmometry and diffusion-ordered NMR spectroscopy, among other evidence, suggested that the porphyrin molecules form a trimer with a triangular cone structure. Incorporation of a directly linked porphyrin-ferrocene dyad with the same assembling properties in the assemblies led to a rare example of a light-harvesting/charge-separation system in which an energy gradient is incorporated and reductive quenching occurs.
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Affiliation(s)
- Joe Otsuki
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda Surugadai, Chiyoda-ku, Tokyo, 101-8308, Japan
| | - Takumi Okumura
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda Surugadai, Chiyoda-ku, Tokyo, 101-8308, Japan
| | - Kosuke Sugawa
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda Surugadai, Chiyoda-ku, Tokyo, 101-8308, Japan
| | - Shin-Ichiro Kawano
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Kentaro Tanaka
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Takehiro Hirao
- Department of Chemistry, Graduate School of Advanced, Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Takeharu Haino
- Department of Chemistry, Graduate School of Advanced, Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Yu Jin Lee
- Spectroscopy Laboratory for Functional π-Electronic Systems, and Department of Chemistry, Yonsei University, Seoul, 03722, South Korea
| | - Seongsoo Kang
- Spectroscopy Laboratory for Functional π-Electronic Systems, and Department of Chemistry, Yonsei University, Seoul, 03722, South Korea
| | - Dongho Kim
- Spectroscopy Laboratory for Functional π-Electronic Systems, and Department of Chemistry, Yonsei University, Seoul, 03722, South Korea
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16
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Le Guern F, Ouk TS, Yerzhan I, Nurlykyz Y, Arnoux P, Frochot C, Leroy-Lhez S, Sol V. Photophysical and Bactericidal Properties of Pyridinium and Imidazolium Porphyrins for Photodynamic Antimicrobial Chemotherapy. Molecules 2021; 26:molecules26041122. [PMID: 33672630 PMCID: PMC7924203 DOI: 10.3390/molecules26041122] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 01/21/2023] Open
Abstract
Despite advances achieved over the last decade, infections caused by multi-drug-resistant bacterial strains are increasingly becoming important societal issues that need to be addressed. New approaches have already been developed in order to overcome this problem. Photodynamic antimicrobial chemotherapy (PACT) could provide an alternative to fight infectious bacteria. Many studies have highlighted the value of cationic photosensitizers in order to improve this approach. This study reports the synthesis and the characterization of cationic porphyrins derived from methylimidazolium and phenylimidazolium porphyrins, along with a comparison of their photophysical properties with the well-known N-methylpyridyl (pyridinium) porphyrin family. PACT tests conducted with the tetracationic porphyrins of these three families showed that these new photosensitizers may offer a good alternative to the classical pyridinium porphyrins, especially against S.aureus and E.coli. In addition, they pave the way to new cationic photosensitizers by the means of derivatization through amide bond formation.
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Affiliation(s)
- Florent Le Guern
- Institut Lavoisier de Versailles, Université Paris-Saclay, UVSQ, CNRS, 78035 Versailles, France;
- Laboratoire PEIRENE, Université de Limoges, EA 7500, 123 Avenue Albert Thomas, 87060 Limoges CEDEX, France; (T.-S.O.); (S.L.-L.)
| | - Tan-Sothéa Ouk
- Laboratoire PEIRENE, Université de Limoges, EA 7500, 123 Avenue Albert Thomas, 87060 Limoges CEDEX, France; (T.-S.O.); (S.L.-L.)
| | - Issabayev Yerzhan
- Laboratoire Réactions et Génie des Procédés (LRGP), Université de Lorraine, UMR 7274 CNRS, ENSIC, 1 rue Grandville, 54000 Nancy, France; (I.Y.); (Y.N.); (P.A.); (C.F.)
| | - Yesmurzayeva Nurlykyz
- Laboratoire Réactions et Génie des Procédés (LRGP), Université de Lorraine, UMR 7274 CNRS, ENSIC, 1 rue Grandville, 54000 Nancy, France; (I.Y.); (Y.N.); (P.A.); (C.F.)
| | - Philippe Arnoux
- Laboratoire Réactions et Génie des Procédés (LRGP), Université de Lorraine, UMR 7274 CNRS, ENSIC, 1 rue Grandville, 54000 Nancy, France; (I.Y.); (Y.N.); (P.A.); (C.F.)
| | - Céline Frochot
- Laboratoire Réactions et Génie des Procédés (LRGP), Université de Lorraine, UMR 7274 CNRS, ENSIC, 1 rue Grandville, 54000 Nancy, France; (I.Y.); (Y.N.); (P.A.); (C.F.)
| | - Stéphanie Leroy-Lhez
- Laboratoire PEIRENE, Université de Limoges, EA 7500, 123 Avenue Albert Thomas, 87060 Limoges CEDEX, France; (T.-S.O.); (S.L.-L.)
| | - Vincent Sol
- Laboratoire PEIRENE, Université de Limoges, EA 7500, 123 Avenue Albert Thomas, 87060 Limoges CEDEX, France; (T.-S.O.); (S.L.-L.)
- Correspondence:
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17
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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: 85] [Impact Index Per Article: 21.3] [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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18
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Caporaletti F, Rubio-Magnieto J, Lo M, Longevial JF, Rose C, Clément S, van der Lee A, Surin M, Richeter S. Design of metalloporphyrins fused to imidazolium rings for binding DNA G-quadruplexes. J PORPHYR PHTHALOCYA 2020. [DOI: 10.1142/s1088424619501128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Synthesis and characterization of nickel(II) meso-tetraarylporphyrins fused to imidazolium rings across [Formula: see text],[Formula: see text]-pyrrolic positions and X-ray structure of the porphyrin where two opposed pyrrole units are fused to an imidazolium ring are presented. The interactions between these mono-, bis-, tris- and tetrakis(imidazolium) porphyrins with human telomeric DNA G-quadruplexes (G4) were investigated using UV-vis absorption spectroscopy, Circular Dichroism (CD) spectroscopy and Fluorescence Resonance Energy Transfer (FRET) melting assay. Possible binding modes between cationic porphyrins and a selected G4 sequence (d[AG3(T2AG[Formula: see text]]), and relative stabilities of porphyrin/G4 complexes are discussed. Excepting porphyrins fused to one imidazolium ring, the other derivatives interact with G4 structures and their stabilization strongly depends on the porphyrin structure (number and localization of the imidazolium rings).
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Affiliation(s)
- Francesca Caporaletti
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons-UMONS, Place du Parc 20, 7000 Mons, Belgium
| | - Jenifer Rubio-Magnieto
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons-UMONS, Place du Parc 20, 7000 Mons, Belgium
| | - Mamadou Lo
- Institut Charles Gerhardt Montpellier, ICGM, UMR 5253, CNRS, Université de Montpellier, ENSCM, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Jean-François Longevial
- Institut Charles Gerhardt Montpellier, ICGM, UMR 5253, CNRS, Université de Montpellier, ENSCM, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Clémence Rose
- Institut Charles Gerhardt Montpellier, ICGM, UMR 5253, CNRS, Université de Montpellier, ENSCM, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Sébastien Clément
- Institut Charles Gerhardt Montpellier, ICGM, UMR 5253, CNRS, Université de Montpellier, ENSCM, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Arie van der Lee
- Institut Européen des Membranes, IEM, UMR 5635, CNRS, Université de Montpellier, ENSCM, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons-UMONS, Place du Parc 20, 7000 Mons, Belgium
| | - Sébastien Richeter
- Institut Charles Gerhardt Montpellier, ICGM, UMR 5253, CNRS, Université de Montpellier, ENSCM, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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19
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Laurencin D, Yot PG, Gervais C, Guari Y, Clément S, Elkaim E, Paillet M, Cot D, Richeter S. Synthesis, characterization and modeling of self-assembled porphyrin nanorods. J PORPHYR PHTHALOCYA 2020. [DOI: 10.1142/s1088424619501451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Porphyrin nanorods were prepared by ion-association between free-base meso 5,10,15,20-tetrakis-(4-[Formula: see text]-methylpyridinium)porphyrin cations and tetraphenylborate anions. The nanorods have variable lengths (up to a few micrometers long) and diameters ([Formula: see text]50–500 nm). Their structure at the molecular level was elucidated by combining multinuclear solid state NMR spectroscopy, synchrotron X-ray powder diffraction and DFT calculations.
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Affiliation(s)
- Danielle Laurencin
- Institut Charles Gerhardt de Montpellier, ICGM, UMR 5253, CNRS UM ENSCM, 34095 Montpellier, France
| | - Pascal G. Yot
- Institut Charles Gerhardt de Montpellier, ICGM, UMR 5253, CNRS UM ENSCM, 34095 Montpellier, France
| | - Christel Gervais
- Laboratoire de Chimie de la Matière Condensée de Paris, LCMCP, UMR 7574, Sorbonne Université, Collège de France, 75005 Paris, France
| | - Yannick Guari
- Institut Charles Gerhardt de Montpellier, ICGM, UMR 5253, CNRS UM ENSCM, 34095 Montpellier, France
| | - Sébastien Clément
- Institut Charles Gerhardt de Montpellier, ICGM, UMR 5253, CNRS UM ENSCM, 34095 Montpellier, France
| | - Erik Elkaim
- Synchrotron SOLEIL, L’Orme des Merisiers Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Matthieu Paillet
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France
| | - Didier Cot
- Institut Européen des Membranes, IEM, UMR 5635, Université Montpellier, ENSCM, CNRS, 34095 Montpellier, France
| | - Sébastien Richeter
- Institut Charles Gerhardt de Montpellier, ICGM, UMR 5253, CNRS UM ENSCM, 34095 Montpellier, France
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21
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Kench T, Vilar R. Metal complexes as G-quadruplex binders. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2020. [DOI: 10.1016/bs.armc.2020.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Ramos CIV, Almeida SP, Lourenço LMO, Pereira PMR, Fernandes R, Faustino MAF, Tomé JPC, Carvalho J, Cruz C, Neves MGPMS. Multicharged Phthalocyanines as Selective Ligands for G-Quadruplex DNA Structures. Molecules 2019; 24:E733. [PMID: 30781675 PMCID: PMC6412362 DOI: 10.3390/molecules24040733] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 01/21/2023] Open
Abstract
The stabilization of G-Quadruplex DNA structures by ligands is a promising strategy for telomerase inhibition in cancer therapy since this enzyme is responsible for the unlimited proliferation of cancer cells. To assess the potential of a compound as a telomerase inhibitor, selectivity for quadruplex over duplex DNA is a fundamental attribute, as the drug must be able to recognize quadruplex DNA in the presence of a large amount of duplex DNA, in the cellular nucleus. By using different spectroscopic techniques, such as ultraviolet-visible, fluorescence and circular dichroism, this work evaluates the potential of a series of multicharged phthalocyanines, bearing four or eight positive charges, as G-Quadruplex stabilizing ligands. This work led us to conclude that the existence of a balance between the number and position of the positive charges in the phthalocyanine structure is a fundamental attribute for its selectivity for G-Quadruplex structures over duplex DNA structures. Two of the studied phthalocyanines, one with four peripheral positive charges (ZnPc1) and the other with less exposed eight positive charges (ZnPc4) showed high selectivity and affinity for G-Quadruplex over duplex DNA structures and were able to accumulate in the nucleus of UM-UC-3 bladder cancer cells.
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Affiliation(s)
- Catarina I V Ramos
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Susana P Almeida
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Leandro M O Lourenço
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Patrícia M R Pereira
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal.
- CNC.IBILI Consortium, University of Coimbra, 3000-548 Coimbra, Portugal.
| | - Rosa Fernandes
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal.
- CNC.IBILI Consortium, University of Coimbra, 3000-548 Coimbra, Portugal.
| | - M Amparo F Faustino
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - João P C Tomé
- CQE & Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, n1, 1049-001 Lisboa, Portugal.
| | - Josué Carvalho
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal.
| | - Carla Cruz
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal.
| | - M Graça P M S Neves
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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23
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Pipier A, De Rache A, Modeste C, Amrane S, Mothes-Martin E, Stigliani JL, Calsou P, Mergny JL, Pratviel G, Gomez D. G-Quadruplex binding optimization by gold(iii) insertion into the center of a porphyrin. Dalton Trans 2019; 48:6091-6099. [PMID: 30860519 DOI: 10.1039/c8dt04703k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Porphyrins represent a valuable class of ligands for G-quadruplex nucleic acids. Herein, we evaluate the binding of cationic porphyrins metallated with gold(iii) to G-quadruplex DNA and we compare it with other porphyrin derivatives. The G-quadruplex stabilization capacity and the selectivity of the various porphyrins were evaluated by biophysical and biochemical assays. The porphyrins were also tested as inhibitors of telomerase. It clearly appeared that the insertion of gold(iii) ion in the center of the porphyrin increases the binding affinity of the porphyrin for the G-quadruplex target. Together with modelling studies, it is possible to propose that the insertion of the square planar gold(iii) ion adds an extra positive charge on the complex and decreases the electron density in the porphyrin aromatic macrocycle, both properties being in favour of stronger electrostatic and π-staking interactions.
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Affiliation(s)
- Angélique Pipier
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
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24
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Interactions Between Spermine-Derivatized Tentacle Porphyrins and The Human Telomeric DNA G-Quadruplex. Int J Mol Sci 2018; 19:ijms19113686. [PMID: 30469358 PMCID: PMC6274827 DOI: 10.3390/ijms19113686] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/14/2018] [Accepted: 11/17/2018] [Indexed: 01/31/2023] Open
Abstract
G-rich DNA sequences have the potential to fold into non-canonical G-Quadruplex (GQ) structures implicated in aging and human diseases, notably cancers. Because stabilization of GQs at telomeres and oncogene promoters may prevent cancer, there is an interest in developing small molecules that selectively target GQs. Herein, we investigate the interactions of meso-tetrakis-(4-carboxysperminephenyl)porphyrin (TCPPSpm4) and its Zn(II) derivative (ZnTCPPSpm4) with human telomeric DNA (Tel22) via UV-Vis, circular dichroism (CD), and fluorescence spectroscopies, resonance light scattering (RLS), and fluorescence resonance energy transfer (FRET) assays. UV-Vis titrations reveal binding constants of 4.7 × 106 and 1.4 × 107 M−1 and binding stoichiometry of 2–4:1 and 10–12:1 for TCPPSpm4 and ZnTCPPSpm4, respectively. High stoichiometry is supported by the Job plot data, CD titrations, and RLS data. FRET melting indicates that TCPPSpm4 stabilizes Tel22 by 36 ± 2 °C at 7.5 eq., and that ZnTCPPSpm4 stabilizes Tel22 by 33 ± 2 °C at ~20 eq.; at least 8 eq. of ZnTCPPSpm4 are required to achieve significant stabilization of Tel22, in agreement with its high binding stoichiometry. FRET competition studies show that both porphyrins are mildly selective for human telomeric GQ vs duplex DNA. Spectroscopic studies, combined, point to end-stacking and porphyrin self-association as major binding modes. This work advances our understanding of ligand interactions with GQ DNA.
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25
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Kim J, Jang D, Park H, Jung S, Kim DH, Kim WJ. Functional-DNA-Driven Dynamic Nanoconstructs for Biomolecule Capture and Drug Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1707351. [PMID: 30062803 DOI: 10.1002/adma.201707351] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/13/2018] [Indexed: 06/08/2023]
Abstract
The discovery of sequence-specific hybridization has allowed the development of DNA nanotechnology, which is divided into two categories: 1) structural DNA nanotechnology, which utilizes DNA as a biopolymer; and 2) dynamic DNA nanotechnology, which focuses on the catalytic reactions or displacement of DNA structures. Recently, numerous attempts have been made to combine DNA nanotechnologies with functional DNAs such as aptamers, DNAzymes, amplified DNA, polymer-conjugated DNA, and DNA loaded on functional nanoparticles for various applications; thus, the new interdisciplinary research field of "functional DNA nanotechnology" is initiated. In particular, a fine-tuned nanostructure composed of functional DNAs has shown immense potential as a programmable nanomachine by controlling DNA dynamics triggered by specific environments. Moreover, the programmability and predictability of functional DNA have enabled the use of DNA nanostructures as nanomedicines for various biomedical applications, such as cargo delivery and molecular drugs via stimuli-mediated dynamic structural changes of functional DNAs. Here, the concepts and recent case studies of functional DNA nanotechnology and nanostructures in nanomedicine are reviewed, and future prospects of functional DNA for nanomedicine are indicated.
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Affiliation(s)
- Jinhwan Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Korea
| | - Donghyun Jang
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Hyeongmok Park
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Sungjin Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Dae Heon Kim
- Department of Biology, Sunchon National University, Sunchon, 57922, Korea
| | - Won Jong Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
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26
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Monsen RC, Trent JO. G-quadruplex virtual drug screening: A review. Biochimie 2018; 152:134-148. [PMID: 29966734 PMCID: PMC6134840 DOI: 10.1016/j.biochi.2018.06.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 06/28/2018] [Indexed: 12/18/2022]
Abstract
Over the past two decades biologists and bioinformaticians have unearthed substantial evidence supporting a role for G-quadruplexes as important mediators of biological processes. This includes telomere damage signaling, transcriptional activity, and splicing. Both their structural heterogeneity and their abundance in oncogene promoters makes them ideal targets for drug discovery. Currently, there are hundreds of deposited DNA and RNA quadruplex atomic structures which have allowed researchers to begin using in silico drug screening approaches to develop novel stabilizing ligands. Here we provide a review of the past decade of G-quadruplex virtual drug discovery approaches and campaigns. With this we introduce relevant virtual screening platforms followed by a discussion of best practices to assist future G4 VS campaigns.
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Affiliation(s)
- Robert C Monsen
- Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, KY, 40206, USA
| | - John O Trent
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, 40206, USA; Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, KY, 40206, USA; Department of Medicine, University of Louisville, Louisville, KY, 40206, USA.
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27
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Halder D, Purkayastha P. A flavonol that acts as a potential DNA minor groove binder as also an efficient G-quadruplex loop binder. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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28
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Heo ME, Lee YA, Hirakawa K, Okazaki S, Kim SK, Cho DW. Sequence selective photoinduced electron transfer of a pyrene-porphyrin dyad to DNA. Phys Chem Chem Phys 2018; 20:16386-16392. [PMID: 29873346 DOI: 10.1039/c8cp01870g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding modes of a pyrene-porphyrin dyad, (1-pyrenyl)-tris(N-methyl-p-pyridino)porphyrin (PyTMpyP), to various DNAs (calf thymus DNA (Ct-DNA), poly[d(G-C)2], and poly[d(A-T)2]) have been investigated using circular dichroism and linear dichroism measurements. Based on the polarization spectroscopic results, it can be shown that the pyrenyl and porphryin planes are skewed to a large extent for PyTMPyP in an aqueous environment and in the binding site of poly[d(G-C)2]. In this complex, a photoinduced electron transfer (PET) process between the pyrenyl and porphyrin moieties occurs. On the other hand, PET was not observed in the PyTMPyP-poly[d(A-T)2] complex, whereas the fluorescence intensity of TMPyP was enhanced. The molecular planes of the pyrene and porphyrin moieties are almost parallel in the poly[d(A-T)2] and Ct-DNA adducts. Moreover, the generation of 1O2 species occurs only for the PyTMPyP-Ct-DNA and PyTMPyP-poly[d(A-T)2] complexes. We discuss the photophysical properties of PyTMPyP which are attributed to the binding patterns and the sequence of DNA bases.
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Affiliation(s)
- Myeong Eun Heo
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea.
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29
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Lebedeva NS, Yurina ES, Gubarev YA, Syrbu SA. Interactions of tetracationic porphyrins with DNA and their effects on DNA cleavage. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 199:235-241. [PMID: 29625380 DOI: 10.1016/j.saa.2018.03.066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 03/19/2018] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
The interaction of tetracationic porphyrins with DNA was studied using UV-Vis absorption, fluorescence spectroscopy and viscometry, and the particle sizes were determined. Аs cationic porphyrins, two isomer porphyrins, 3,3',3″,3‴-(5,10,15,20-Porphyrintetrayl)tetrakis(1-methylpyridinium) (TMPyP3) and 4,4',4″,4‴-(5,10,15,20-Porphyrintetrayl)tetrakis(1-methylpyridinium) (TMPyP4), were studied. They differ in the position of NCH3+ group in phenyl ring of the porphyrins and hence, in degree of freedom of rotation of the phenyl rings about the central macrocycle. It was found that intercalated complexes are formed at DNA/porphyrin molar ratios (R) of 2.2 and 3.9 for TMPyP3 и TMPyP4, respectively. Decreasing R up to 0.4 and 0.8 for TMPyP3 и TMPyP4, respectively, leads mainly to formation of outside complexes due to π-π stacking between the porphyrin chromophores interacting electrostatically with phosphate framework of DNA. Each type of the obtained complexes was characterized using Scatchard approach. It was ascertained that the affinity of TMPyP4 to DNA is stronger than TMPyP3, meanwhile the wedge effect of the latter is higher. The differences between the porphyrin isomers become more evident at irradiation of their complexes with DNA. It was established that irradiation of the intercalated complexes results in DNA fragmentation. In the case of TMPyP4, DNA fragments of different size are formed. The irradiation of the outside DNA/porphyrin complexes leads to cleavage of DNA (TMPyP3 and TMPyP4) and partial destruction of the complex due to photolysis of the porphyrin (TMPyP3).
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Affiliation(s)
- Natalya Sh Lebedeva
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya, 1, 153045 Ivanovo, Russia
| | - Elena S Yurina
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya, 1, 153045 Ivanovo, Russia
| | - Yury A Gubarev
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya, 1, 153045 Ivanovo, Russia.
| | - Sergey A Syrbu
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya, 1, 153045 Ivanovo, Russia
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30
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Saftić D, Ban Ž, Matić J, Tumirv LM, Piantanida I. Conjugates of Classical DNA/RNA Binder with Nucleobase: Chemical, Biochemical and Biomedical Applications. Curr Med Chem 2018; 26:5609-5624. [PMID: 29737251 DOI: 10.2174/0929867325666180508090640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/27/2018] [Accepted: 04/10/2018] [Indexed: 11/22/2022]
Abstract
Among the most intensively studied classes of small molecules (molecular weight < 650) in biomedical research are small molecules that non-covalently bind to DNA/RNA, and another intensively studied class is nucleobase derivatives. Both classes have been intensively elaborated in many books and reviews. However, conjugates consisting of DNA/RNA binder covalently linked to nucleobase are much less studied and have not been reviewed in the last two decades. Therefore, this review summarized reports on the design of classical DNA/RNA binder - nucleobase conjugates, as well as data about their interactions with various DNA or RNA targets, and even in some cases protein targets are involved. According to these data, the most important structural aspects of selective or even specific recognition between small molecule and target are proposed, and where possible related biochemical and biomedical aspects were discussed. The general conclusion is that this, rather new class of molecules showed an amazing set of recognition tools for numerous DNA or RNA targets in the last two decades, as well as few intriguing in vitro and in vivo selectivities. Several lead research lines show promising advancements toward either novel, highly selective markers or bioactive, potentially druggable molecules.
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Affiliation(s)
- Dijana Saftić
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Željka Ban
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Josipa Matić
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Lidija-Marija Tumirv
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
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31
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Tang S, Xu Y, Su G, Bao J, Zhang A. Photoelectric and flexible poly(styrene-b-ethylene/butylene-b-styrene)-zinc porphyrin–graphene hybrid composite: synthesis, performance, and mechanism. RSC Adv 2018; 8:35429-35436. [PMID: 35547892 PMCID: PMC9087907 DOI: 10.1039/c8ra07003b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/01/2018] [Indexed: 01/17/2023] Open
Abstract
Stretchable and flexible photoelectric materials are highly desirable for the development of artificial intelligence products.
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Affiliation(s)
- Shumei Tang
- State Key Laboratory of Polymer Materials Engineering of China
- Polymer Research Institute of Sichuan University
- Chengdu 610065
- China
| | - Yu Xu
- State Key Laboratory of Polymer Materials Engineering of China
- Polymer Research Institute of Sichuan University
- Chengdu 610065
- China
| | - Gehong Su
- State Key Laboratory of Polymer Materials Engineering of China
- Polymer Research Institute of Sichuan University
- Chengdu 610065
- China
| | - Jianjun Bao
- State Key Laboratory of Polymer Materials Engineering of China
- Polymer Research Institute of Sichuan University
- Chengdu 610065
- China
| | - Aimin Zhang
- State Key Laboratory of Polymer Materials Engineering of China
- Polymer Research Institute of Sichuan University
- Chengdu 610065
- China
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32
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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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33
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Kudrev AG. The Evidence of Cooperative Binding of a Ligand to G4 DNA. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2017; 2017:6780521. [PMID: 29181223 PMCID: PMC5664379 DOI: 10.1155/2017/6780521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/24/2017] [Indexed: 06/07/2023]
Abstract
Intrinsic constants of the ligand binding with G4 DNA (guanine-rich DNA sequence) using quantitative standards can be convenient providing the assessment for elucidating the possibility of such structures participation in biochemical processes. In the present communication, the hard + soft modelling approach to calculate intrinsic constants of a ligand binding with short DNA molecule, particularly such as G4 DNA, has been proposed. The suggested approach has focused upon the quantitative evaluating of a mutual influence between sites and between bound ligands. The cross-validation between a new hard + soft modelling and conventional stepwise complex formation algorithm has been conducted. A number of simulated examples will illustrate the methodology. The experimental mole-ratio titration of TMPyP4 by G4 DNA [(CG3)2CGC(AG3)2G] has been reexamined. The [(CG3)2CGC(AG3)2G] that folds from a G-rich sequence found in the promoter region of c-kit oncogene can be considered as a molecule with two equivalent mutually influence binding sites.
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Affiliation(s)
- A. G. Kudrev
- Saint Petersburg State University, 7/9 Universitetskaya Nab., St. Petersburg 199034, Russia
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34
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Wang X, Goodrich KJ, Gooding AR, Naeem H, Archer S, Paucek RD, Youmans DT, Cech TR, Davidovich C. Targeting of Polycomb Repressive Complex 2 to RNA by Short Repeats of Consecutive Guanines. Mol Cell 2017; 65:1056-1067.e5. [PMID: 28306504 DOI: 10.1016/j.molcel.2017.02.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 12/20/2016] [Accepted: 02/01/2017] [Indexed: 11/18/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that trimethylates H3K27, a mark of repressed chromatin. Mammalian PRC2 binds RNA promiscuously, with thousands of target transcripts in vivo. But what does PRC2 recognize in these RNAs? Here we show that purified human PRC2 recognizes G > C,U ≫ A in single-stranded RNA and has a high affinity for folded guanine quadruplex (G4) structures but little binding to duplex RNAs. Importantly, G-tract motifs are significantly enriched among PRC2-binding transcripts in vivo. DNA sequences coding for PRC2-binding RNA motifs are enriched at PRC2-binding sites on chromatin and H3K27me3-modified nucleosomes. Collectively, the abundance of PRC2-binding RNA motifs rationalizes the promiscuous RNA binding of PRC2, and their enrichment at Polycomb target genes provides a means for RNA-mediated regulation.
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Affiliation(s)
- Xueyin Wang
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Karen J Goodrich
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Anne R Gooding
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Haroon Naeem
- Monash Bioinformatics Platform, Monash University, Clayton, VIC 3800, Australia; Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Stuart Archer
- Monash Bioinformatics Platform, Monash University, Clayton, VIC 3800, Australia; Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Richard D Paucek
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Daniel T Youmans
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA; University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Thomas R Cech
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA.
| | - Chen Davidovich
- Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; EMBL-Australia and the ARC Centre of Excellence in Advanced Molecular Imaging, Clayton, VIC 3800, Australia.
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35
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Xi SF, Bao LY, Xu ZL, Wang YX, Ding ZD, Gu ZG. Enhanced Stabilization of G-Quadruplex DNA by [Ni4
L6
]8+
Cages with Large Rigid Aromatic Ligands. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sai-Fei Xi
- The Key Laboratory of Synthetic and Biological Colloids; Ministry of Education; School of Chemical and Material Engineering; Jiangnan University; 214122 Wuxi China
| | - Ling-Yu Bao
- The Key Laboratory of Synthetic and Biological Colloids; Ministry of Education; School of Chemical and Material Engineering; Jiangnan University; 214122 Wuxi China
| | - Zong-Li Xu
- The Key Laboratory of Synthetic and Biological Colloids; Ministry of Education; School of Chemical and Material Engineering; Jiangnan University; 214122 Wuxi China
| | - Yu-Xia Wang
- The Key Laboratory of Synthetic and Biological Colloids; Ministry of Education; School of Chemical and Material Engineering; Jiangnan University; 214122 Wuxi China
| | - Zheng-Dong Ding
- The Key Laboratory of Synthetic and Biological Colloids; Ministry of Education; School of Chemical and Material Engineering; Jiangnan University; 214122 Wuxi China
| | - Zhi-Guo Gu
- The Key Laboratory of Synthetic and Biological Colloids; Ministry of Education; School of Chemical and Material Engineering; Jiangnan University; 214122 Wuxi China
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36
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Fang Y, Zhu J, Cui Y, Zeng L, Naitana ML, Chang Y, Desbois N, Gros CP, Kadish KM. Protonation and Electrochemical Properties of Pyridyl- and Sulfonatophenyl-Substituted Porphyrins in Nonaqueous Media. ChemElectroChem 2017. [DOI: 10.1002/celc.201700199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yuanyuan Fang
- School of Chemistry and Chemical Engineering; Jiangsu University; 301 Xuefu Road Zhenjiang, Jiangsu P. R. China
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77204-5003 USA
| | - Jialiang Zhu
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77204-5003 USA
| | - Yan Cui
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77204-5003 USA
| | - Lihan Zeng
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77204-5003 USA
| | - Mario L. Naitana
- ICMUB (UMR CNRS 6302); Université de Bourgogne Franche-Comté; Dijon France
| | - Yi Chang
- ICMUB (UMR CNRS 6302); Université de Bourgogne Franche-Comté; Dijon France
| | - Nicolas Desbois
- ICMUB (UMR CNRS 6302); Université de Bourgogne Franche-Comté; Dijon France
| | - Claude P. Gros
- ICMUB (UMR CNRS 6302); Université de Bourgogne Franche-Comté; Dijon France
| | - Karl M. Kadish
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77204-5003 USA
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37
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Huo YF, Zhu LN, Liu KK, Zhang LN, Zhang R, Kong DM. Water-Soluble Cationic Metalloporphyrins: Specific G-Quadruplex-Stabilizing Ability and Reversible Chirality of Aggregates Induced by AT-Rich DNA. Inorg Chem 2017; 56:6330-6342. [DOI: 10.1021/acs.inorgchem.7b00426] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yan-Fang Huo
- Department of Chemistry, Tianjin University, Tianjin 300072, People’s Republic of China
- State Key
Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of
Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, People’s Republic of China
| | - Li-Na Zhu
- Department of Chemistry, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, People’s Republic of China
| | - Ke-Ke Liu
- Department of Chemistry, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Li-Na Zhang
- Department of Chemistry, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Ran Zhang
- Department of Chemistry, Tianjin University, Tianjin 300072, People’s Republic of China
| | - De-Ming Kong
- State Key
Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of
Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, People’s Republic of China
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38
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Squarcina A, Sorarù A, Rigodanza F, Carraro M, Brancatelli G, Carofiglio T, Geremia S, Larosa V, Morosinotto T, Bonchio M. Merged Heme and Non-Heme Manganese Cofactors for a Dual Antioxidant Surveillance in Photosynthetic Organisms. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Andrea Squarcina
- ITM-CNR
and Department of Chemical Sciences, University of Padova, Via Marzolo
1, 35131 Padova, Italy
| | - Antonio Sorarù
- ITM-CNR
and Department of Chemical Sciences, University of Padova, Via Marzolo
1, 35131 Padova, Italy
| | - Francesco Rigodanza
- Department
of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Mauro Carraro
- ITM-CNR
and Department of Chemical Sciences, University of Padova, Via Marzolo
1, 35131 Padova, Italy
| | - Giovanna Brancatelli
- Department
of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Tommaso Carofiglio
- ITM-CNR
and Department of Chemical Sciences, University of Padova, Via Marzolo
1, 35131 Padova, Italy
| | - Silvano Geremia
- Department
of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Véronique Larosa
- Department
of Biology, University of Padova, via Bassi 58b, 35131 Padova, Italy
| | - Tomas Morosinotto
- Department
of Biology, University of Padova, via Bassi 58b, 35131 Padova, Italy
| | - Marcella Bonchio
- ITM-CNR
and Department of Chemical Sciences, University of Padova, Via Marzolo
1, 35131 Padova, Italy
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39
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Perrier A, Mothes E, Bonduelle C, Pratviel G. Synthesis of asymmetric guanidiniumphenyl-aminophenyl porphyrins. J PORPHYR PHTHALOCYA 2017. [DOI: 10.1142/s1088424616501170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The symmetric meso-tetrakis(4-aminophenyl)porphyrin was reacted with nonstoichiometric amount of [Formula: see text],[Formula: see text]-bis(tert-butoxycarbonyl)-[Formula: see text]-methylisothiourea with respect to the amine functions of the porphyrin to afford (after deprotection of the Boc residues) the asymmetric guanidiniumphenyl-aminophenyl porphyrins carrying two or three guanidiniumphenyl substituents at the meso-position. The adjacent and opposite isomers of the bis(guanidiniumphenyl) modified porphyrins were isolated separately.
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Affiliation(s)
- Arnaud Perrier
- Centre National de la Recherche Scientifique, Laboratoire de Chimie de Coordination, 205 Route de Narbonne, 31077 Toulouse, France
- Université de Toulouse, 31077 Toulouse, France
| | - Emmanuelle Mothes
- Centre National de la Recherche Scientifique, Laboratoire de Chimie de Coordination, 205 Route de Narbonne, 31077 Toulouse, France
- Université de Toulouse, 31077 Toulouse, France
| | - Colin Bonduelle
- Centre National de la Recherche Scientifique, Laboratoire de Chimie de Coordination, 205 Route de Narbonne, 31077 Toulouse, France
- Université de Toulouse, 31077 Toulouse, France
| | - Geneviève Pratviel
- Centre National de la Recherche Scientifique, Laboratoire de Chimie de Coordination, 205 Route de Narbonne, 31077 Toulouse, France
- Université de Toulouse, 31077 Toulouse, France
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40
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Kanti Si M, Sen A, Ganguly B. Exploiting hydrogen bonding interactions to probe smaller linear and cyclic diamines binding to G-quadruplexes: a DFT and molecular dynamics study. Phys Chem Chem Phys 2017; 19:11474-11484. [DOI: 10.1039/c7cp00472a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This report reveals that hydrogen bonding interactions between the ligand and G-quadruplex can initiate an alternative binding motif to typical π-stacking interactions.
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Affiliation(s)
- Mrinal Kanti Si
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR-Central Salt & Marine Chemicals Research Institute
- Bhavnagar
- India
- Academy of Scientific and Innovative Research
| | - Anik Sen
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR-Central Salt & Marine Chemicals Research Institute
- Bhavnagar
- India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR-Central Salt & Marine Chemicals Research Institute
- Bhavnagar
- India
- Academy of Scientific and Innovative Research
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41
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Ruan TL, Davis SJ, Powell BM, Harbeck CP, Habdas J, Habdas P, Yatsunyk LA. Lowering the overall charge on TMPyP4 improves its selectivity for G-quadruplex DNA. Biochimie 2017; 132:121-130. [DOI: 10.1016/j.biochi.2016.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/07/2016] [Indexed: 12/24/2022]
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42
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Cao Q, Li Y, Freisinger E, Qin PZ, Sigel RKO, Mao ZW. G-quadruplex DNA targeted metal complexes acting as potential anticancer drugs. Inorg Chem Front 2017. [DOI: 10.1039/c6qi00300a] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review summarizes the recent development of G4 DNA targeted metal complexes and discusses their potential as anticancer drugs.
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Affiliation(s)
- Qian Cao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Yi Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Eva Freisinger
- University of Zurich
- Department of Chemistry
- CH-8057 Zurich
- Switzerland
| | - Peter Z. Qin
- Department of Chemistry
- University of Southern California
- Los Angeles
- USA
| | | | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
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43
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Naganagowda G, Mahlaka TJ, Meijboom R. Crystal structure of methyl-2-methyl-4-(2-oxo-2-phenylethyl)-5-phenyl-1 H-pyrrole-3-carboxylate, C 21H 19NO 3. Z KRIST-NEW CRYST ST 2017. [DOI: 10.1515/ncrs-2016-0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C21H19NO3, monoclinic, P21/n (no. 14), a = 10.137(2) Å, b = 12.3205(18) Å, c = 14.700(3) Å, β = 106.432(1)°, V = 1760.9(6) Å3, Z = 4, R
gt(F) = 0.0511, wR
ref(F
2) = 0.1808, T = 293 K.
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Affiliation(s)
- Gadada Naganagowda
- Research Centre for Synthesis and Catalysis, Department of Chemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
| | - Thabo Joel Mahlaka
- Research Centre for Synthesis and Catalysis, Department of Chemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
| | - Reinout Meijboom
- Research Centre for Synthesis and Catalysis, Department of Chemistry, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
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44
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Boschi E, Davis S, Taylor S, Butterworth A, Chirayath LA, Purohit V, Siegel LK, Buenaventura J, Sheriff AH, Jin R, Sheardy R, Yatsunyk LA, Azam M. Interaction of a Cationic Porphyrin and Its Metal Derivatives with G-Quadruplex DNA. J Phys Chem B 2016; 120:12807-12819. [PMID: 27936741 DOI: 10.1021/acs.jpcb.6b09827] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
G-quadruplex (GQ) structures formed from guanine-rich sequences are found throughout the genome and are overrepresented in the promoter regions of some oncogenes, at the telomeric ends of eukaryotic chromosomes, and at the 5'-untranslated regions of mRNA. Interaction of small molecule ligands with GQ DNA is an area of great research interest to develop novel anticancer therapeutics and GQ sensors. In this paper we examine the interactions of TMPyP4, its isomer TMPyP2 (containing N-methyl-2-pyridyl substituents, N-Me-2Py) as well as two metal derivatives ZnTMPyP4 and CuTMPyP4 with GQs formed by dT4G4 and dT4G4T in 100 mM K+ or Na+ conditions. The DNA sequences were chosen to elucidate the effect of the 3'-T on the stabilization effect of porphyrins, binding modes, affinities, and stoichiometries determined via circular dichroism melting studies, UV-vis titrations, continuous variation analysis, and fluorescence studies. Our findings demonstrate that the stabilizing abilities of porphyrins are stronger toward (dT4G4)4 as compared to (dT4G4T)4 (ΔTm is 4.4 vs -6.4 for TMPyP4; 12.7 vs 5.7 for TMPyP2; 16.4 vs 12.1 for ZnTMPyP4; and 1.9 vs -8.4 °C for CuTMPyP4) suggesting that the 3'G-tetrad presents at least one of the binding sites. The binding affinity was determined to be moderate (Ka ∼ 106-107 μM-1) with a typical binding stoichiometry of 1:1 or 2:1 porphyrin-to-GQ. In all studies, ZnTMPyP4 emerged as a ligand superior to TMPyP4. Overall, our work contributes to clearer understanding of interactions between porphyrins and GQ DNA.
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Affiliation(s)
- Eric Boschi
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Supriya Davis
- Department of Chemistry and Biochemistry, Swarthmore College , 500 College Avenue, Swarthmore, Pennsylvania 19081, United States
| | - Scott Taylor
- Department of Chemistry and Biochemistry, Swarthmore College , 500 College Avenue, Swarthmore, Pennsylvania 19081, United States
| | - Andrew Butterworth
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Lilyan A Chirayath
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Vaishali Purohit
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Laura K Siegel
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Janesha Buenaventura
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Alexandra H Sheriff
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Rowen Jin
- Department of Chemistry and Biochemistry, Swarthmore College , 500 College Avenue, Swarthmore, Pennsylvania 19081, United States
| | - Richard Sheardy
- Department of Chemistry & Biochemistry, Texas Woman's University , 324 Ann Stuart Science Center, P.O. Box 425859, Denton, Texas 76204-5859, United States
| | - Liliya A Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College , 500 College Avenue, Swarthmore, Pennsylvania 19081, United States
| | - Mahrukh Azam
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
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45
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Abstract
Corroles are exceptionally promising platforms for the development of agents for simultaneous cancer-targeting imaging and therapy. Depending on the element chelated by the corrole, these theranostic agents may be tuned primarily for diagnostic or therapeutic function. Versatile synthetic methodologies allow for the preparation of amphipolar derivatives, which form stable noncovalent conjugates with targeting biomolecules. These conjugates can be engineered for imaging and targeting as well as therapeutic function within one theranostic assembly. In this review, we begin with a brief outline of corrole chemistry that has been uniquely useful in designing corrole-based anticancer agents. Then we turn attention to the early literature regarding corrole anticancer activity, which commenced one year after the first scalable synthesis was reported (1999-2000). In 2001, a major advance was made with the introduction of negatively charged corroles, as these molecules, being amphipolar, form stable conjugates with many proteins. More recently, both cellular uptake and intracellular trafficking of metallocorroles have been documented in experimental investigations employing advanced optical spectroscopic as well as magnetic resonance imaging techniques. Key results from work on both cellular and animal models are reviewed, with emphasis on those that have shed new light on the mechanisms associated with anticancer activity. In closing, we predict a very bright future for corrole anticancer research, as it is experiencing exponential growth, taking full advantage of recently developed imaging and therapeutic modalities.
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Affiliation(s)
- Ruijie D Teo
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Jae Youn Hwang
- Department of Information and Communication Engineering, Daegu Gyeongbuk Institute of Science & Technology , Daegu, Republic of Korea
| | - John Termini
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope , 1500 East Duarte Road, Duarte, California 91010, United States
| | - Zeev Gross
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , Haifa 32000, Israel
| | - Harry B Gray
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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46
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Ghimire S, Bork MA, Zhang H, Fanwick PE, Zeller M, Choi JH, McMillin DR. DNA binding of Pd(TC3), a conformable cationic porphyrin with a long-lived triplet state. Dalton Trans 2016; 45:14277-84. [PMID: 27534907 DOI: 10.1039/c6dt01918h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The goal of this work has been to synthesize and investigate Pd(TC3), an intercalating porphyrin that has conformable substituents capable of groove binding to B-form DNA. (TC3 denotes the doubly deprotonated form of 5,10,15,20-tetra[3-(3'-methylimidazolium-1'-yl)prop-1-yl]porphyrin.) Palladium(ii) is an apt choice for the central metal ion because it remains strictly four-coordinate and provides for a luminescent triplet excited state with a long lifetime. The DNA hosts are hairpin-forming sequences programmed to differ in base composition. Luminescence, absorbance, and circular dichroism results are consistent with the idea that congruent structural reorganization takes place at the host and ligand during uptake. Photoexcitation of DNA-bound Pd(TC3) generates a comparatively modest steady state concentration of singlet oxygen, due to a relatively slow reaction with molecular oxygen in solution. The sheer size of the substituent groups disfavors quenching, but groove-binding interactions compound the problem by inhibiting mobility. The results show how ligand design affects adduct structure as well as function.
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Affiliation(s)
- Srijana Ghimire
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA.
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47
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Katsuda Y, Sato SI, Asano L, Morimura Y, Furuta T, Sugiyama H, Hagihara M, Uesugi M. A Small Molecule That Represses Translation of G-Quadruplex-Containing mRNA. J Am Chem Soc 2016; 138:9037-40. [DOI: 10.1021/jacs.6b04506] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | | | - Masaki Hagihara
- Graduate
School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
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48
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Durec M, Zaccaria F, Fonseca Guerra C, Marek R. Modified Guanines as Constituents of Smart Ligands for Nucleic Acid Quadruplexes. Chemistry 2016; 22:10912-22. [PMID: 27385491 DOI: 10.1002/chem.201601608] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 01/25/2023]
Abstract
Repetitive guanine-rich nucleic acid sequences play a crucial role in maintaining genome stability and the cell life cycle and represent potential targets for regulatory drugs. Recently, it has been demonstrated that guanine-based ligands with a porphyrin core can be used as markers of G-quadruplex assemblies in cell tissues. Herein, model systems of guanine-based ligands are explored by DFT methods. The energies of formation of modified guanine tetrads and those of modified tetrads stacked on the top of natural guanine tetrads have been calculated. The interaction energy has been decomposed into contributions from hydrogen bonding, stacking, and ion coordination and a twist-rise potential energy scan has been performed to find the individual local minima. Energy decomposition analysis reveals the impact of various substituents (F, Cl, Br, I, Me, NMe2 ) on individual energy terms. In addition, cooperative reinforcement in forming the modified and stacked tetrads, as well as the frontier orbitals participating in the hydrogen-bonding framework involving the HOMO-LUMO gap between the occupied σHOMO on the proton-accepting C=O and =N- groups and unoccupied σLUMO on the N-H groups, has been studied. The investigated systems are demonstrated to have a potential in ligand development, mainly due to stacking enhancement compared with natural guanine, which is used as a reference.
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Affiliation(s)
- Matúš Durec
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5A4, 62500, Brno, Czech Republic.,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5A4, 62500, Brno, Czech Republic
| | - Francesco Zaccaria
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.
| | - Radek Marek
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5A4, 62500, Brno, Czech Republic. .,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5A4, 62500, Brno, Czech Republic.
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49
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Keane PM, Kelly JM. Ground and excited state interactions of metalloporphyrin PtTMPyP4 with polynucleotides [poly(dG-dC)]2 and [poly(dA-dT)]2. Photochem Photobiol Sci 2016; 15:980-7. [PMID: 27377608 DOI: 10.1039/c6pp00105j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ground- and excited-state interactions of Pt(ii) meso-tetrakis(4-N-methylpyridyl)porphyrin (PtTMPyP4) with polynucleotides [poly(dG-dC)]2 and [poly(dA-dT)]2 have been investigated using UV/visible, circular dichroism, and steady-state and time-resolved emission spectroscopy. PtTMPyP4 intercalates into [poly(dG-dC)]2 with K∼ 10(6) M(-1). When bound to [poly(dG-dC)]2 in aerated solution there is a six-fold emission enhancement with 18 nm red-shift in emission maximum. Emission lifetimes are biexponential. In the presence of [poly(dA-dT)]2 at least two distinct groove-binding modes are observed, depending on the binding ratio. In [poly(dA-dT)]2 the emission intensity increases by a maximum factor of 17 with no shift in the emission spectrum. Three exponentials were required for lifetime fitting. The lower extent of emission enhancement in the presence of [poly(dG-dC)]2 suggests that a slow electron transfer may take place to guanine, which is significantly less efficient than that previously observed for PtTMPyP4 in the presence of guanosine 5'-monophosphate (GMP). The results are compared to those previously recorded with free base H2TMPyP4.
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Affiliation(s)
- Páraic M Keane
- School of Chemistry, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
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50
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Marchand A, Strzelecka D, Gabelica V. Selective and Cooperative Ligand Binding to Antiparallel Human Telomeric DNA G-Quadruplexes. Chemistry 2016; 22:9551-5. [PMID: 27168452 DOI: 10.1002/chem.201601937] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Indexed: 01/16/2023]
Abstract
The quest for ligands that specifically bind to particular G-quadruplex nucleic acid structures is particularly important to conceive molecules with specific effects on gene expression or telomere maintenance, or conceive structure-specific molecular probes. Using electrospray mass spectrometry in native conditions, we reveal a highly cooperative and selective 2:1 binding of Cu(II) -tolylterpyridine complexes to human telomeric G-quadruplexes. Circular dichroism and comparisons of affinities for different sequences reveal a marked preference for antiparallel structures with diagonal loops and/or wide-medium-narrow-medium groove-width order. The cooperativity is attributed to conformational changes in the polymorphic telomeric G-quadruplex sequences, which convert preferably into an antiparallel three-quartet topology upon binding of two ligands.
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Affiliation(s)
- Adrien Marchand
- Université de Bordeaux, IECB, ARNA Laboratory, 33600, Pessac, France.,Inserm, U1212, ARNA Laboratory, 33000, Bordeaux, France.,CNRS, UMR 5320, ARNA Laboratory, 33400, Talence, France
| | - Dominika Strzelecka
- Université de Bordeaux, IECB, ARNA Laboratory, 33600, Pessac, France.,Inserm, U1212, ARNA Laboratory, 33000, Bordeaux, France.,Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
| | - Valerie Gabelica
- Université de Bordeaux, IECB, ARNA Laboratory, 33600, Pessac, France. .,Inserm, U1212, ARNA Laboratory, 33000, Bordeaux, France. .,CNRS, UMR 5320, ARNA Laboratory, 33400, Talence, France.
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