1
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Salerno S, Barresi E, Roggia M, Natale B, Marzano S, Hyeraci M, Reina SCR, Baglini E, Amato J, Salvati E, Dalla Via L, Da Settimo F, Cosconati S, Taliani S. Pursuing Polypharmacology: Benzothiopyranoindoles as G-Quadruplex Stabilizers and Topoisomerase I Inhibitors for Effective Anticancer Strategies. ACS Med Chem Lett 2024; 15:1875-1883. [PMID: 39563818 PMCID: PMC11571019 DOI: 10.1021/acsmedchemlett.4c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 09/24/2024] [Accepted: 09/25/2024] [Indexed: 11/21/2024] Open
Abstract
Here, we explored the benzothiopyranoindole scaffold to develop antiproliferative agents with a polypharmacological profile targeting both G-quadruplex (G4)-structures and Topoisomerase (Topo) I enzyme. In a preliminary optimization phase, compound 1 was selected from an in-house collection as a suitable lead for the rational development of a small library of analogs (2-5). When assayed in NIH's NCI-60 Human Cancer Cell Line In Vitro Screen Program, compound 1 and its demethylated analogue 2 showed significant antiproliferative/cytotoxic activity. Furthermore, results suggested for 1 and 2 a dual mechanism of action, effectively binding and stabilizing G4 structures, while inhibiting the relaxation activity of TopoI and II. Notably, these compounds displayed a certain selectivity toward TopoI. The polypharmacological profile of 1 and 2 was validated in a human colon carcinoma cell line, underscoring their potential as lead candidates for developing novel and efficacious anticancer agents.
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Affiliation(s)
- Silvia Salerno
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
- Center for Instrument Sharing of the University of Pisa (CISUP), University of Pisa, Lungarno Pacinotti 43/44, 56126, Pisa, Italy
| | - Elisabetta Barresi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
- Center for Instrument Sharing of the University of Pisa (CISUP), University of Pisa, Lungarno Pacinotti 43/44, 56126, Pisa, Italy
| | - Michele Roggia
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Benito Natale
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Mariafrancesca Hyeraci
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua via F. Marzolo 5, 35131 Padova, Italy
| | - Serena Concetta Rita Reina
- Institute of Molecular Biology and Pathology, National Research Council, Via degli Apuli 4, 00185 Rome, Italy
| | - Emma Baglini
- CNR IFC, Institute of Clinical Physiology, National Research Council of Italy, CNR Research Area, Via G. Moruzzi 1, Pisa 56124, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Erica Salvati
- Institute of Molecular Biology and Pathology, National Research Council, Via degli Apuli 4, 00185 Rome, Italy
| | - Lisa Dalla Via
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua via F. Marzolo 5, 35131 Padova, Italy
| | - Federico Da Settimo
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
- Center for Instrument Sharing of the University of Pisa (CISUP), University of Pisa, Lungarno Pacinotti 43/44, 56126, Pisa, Italy
| | - Sandro Cosconati
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Sabrina Taliani
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
- Center for Instrument Sharing of the University of Pisa (CISUP), University of Pisa, Lungarno Pacinotti 43/44, 56126, Pisa, Italy
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2
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Ryazanova O, Voloshin I, Dubey I, Dubey L, Karachevtsev V. Binding of a Tricationic meso-Substituted Porphyrin to poly(A)⋅poly(U): an Experimental Study. J Fluoresc 2024:10.1007/s10895-024-04000-4. [PMID: 39465484 DOI: 10.1007/s10895-024-04000-4] [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: 06/06/2024] [Accepted: 10/07/2024] [Indexed: 10/29/2024]
Abstract
The porphyrins are macrocyclic compounds widely used as photosensitizers in anticancer photodynamic therapy. The binding of a tricationic meso-tris(N-methylpyridinium)-porphyrin, TMPyP3+, to poly(A)⋅poly(U) polynucleotide has been studied in neutral buffered solution, pH6.9, of low and near-physiological ionic strength in a wide range of molar phosphate-to-dye ratios (P/D). Effective TMPyP3+ binding to the biopolymer was established using absorption spectroscopy, polarized fluorescence, fluorimetric titration and resonance light scattering. We propose a model in which TMPyP3+ binds to the polynucleotide in two competitive binding modes: at low P/D ratios (< 4) external binding of the porphyrin to polynucleotide backbone without self-stacking dominates, and at higher P/D (> 30) the partially stacked porphyrin J-dimers are embedded into the polymer groove. Enhancement of the porphyrin emission was observed upon binding in all P/D range, contrasting the binding of this porphyrin to poly(G)⋅poly(C) with significant quenching of the porphyrin fluorescence at low P/D ratios. This observation indicates that TMPyP3+ can discriminate between poly(A)⋅poly(U) and poly(G)⋅poly(C) polynucleotides at low P/D ratios. Formation of highly scattering extended porphyrin aggregates was observed near the stoichiometric in charge binding ratio, P/D = 3. It was revealed that the efficiency of the porphyrin external binding and aggregation is reduced in the solution of near-physiological ionic strength.
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Affiliation(s)
- Olga Ryazanova
- Department of Molecular Biophysics, B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47 Nauky Ave, Kharkiv, 61103, Ukraine.
| | - Igor Voloshin
- Department of Molecular Biophysics, B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47 Nauky Ave, Kharkiv, 61103, Ukraine
| | - Igor Dubey
- Department of Synthetic Bioregulators, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., Kiev, 03143, Ukraine
| | - Larysa Dubey
- Department of Synthetic Bioregulators, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., Kiev, 03143, Ukraine
| | - Victor Karachevtsev
- Department of Molecular Biophysics, B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47 Nauky Ave, Kharkiv, 61103, Ukraine
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3
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Massalha L, Levin AR, Adiram-Filiba N, Golub E. Selective binding of c-MYC G-quadruplex caged in a dsDNA by a hemopeptide. Chem Commun (Camb) 2024; 60:7769-7772. [PMID: 38973676 DOI: 10.1039/d4cc01389a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
The microperoxidase-11 hemopeptide exhibits configuration-dependent selectivity for guanine-quadruplexes by specifically uncaging c-MYC guanine-quadruplexes from a duplex DNA.
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Affiliation(s)
- Leen Massalha
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Israel.
| | - Adiel Richter Levin
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Israel.
| | - Nurit Adiram-Filiba
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Israel.
| | - Eyal Golub
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Israel.
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4
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Kallingal A, Krzemieniecki R, Maciejewska N, Brankiewicz-Kopcińska W, Baginski M. TRF1 and TRF2: pioneering targets in telomere-based cancer therapy. J Cancer Res Clin Oncol 2024; 150:353. [PMID: 39012375 PMCID: PMC11252209 DOI: 10.1007/s00432-024-05867-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/25/2024] [Indexed: 07/17/2024]
Abstract
This article presents an in-depth exploration of the roles of Telomere Repeat-binding Factors 1 and 2 (TRF1 and TRF2), and the shelterin complex, in the context of cancer biology. It emphasizes their emerging significance as potential biomarkers and targets for therapeutic intervention. Central to the shelterin complex, TRF1 and TRF2 are crucial in maintaining telomere integrity and genomic stability, their dysregulation often being a hallmark of cancerous cells. The article delves into the diagnostic and prognostic capabilities of TRF1 and TRF2 across various cancer types, highlighting their sensitivity and specificity. Furthermore, it reviews current strides in drug discovery targeting the shelterin complex, detailing specific compounds and their modes of action. The review candidly addresses the challenges in developing therapies aimed at the shelterin complex, including drug resistance, off-target effects, and issues in drug delivery. By synthesizing recent research findings, the article sheds light on the intricate relationship between telomere biology and cancer development. It underscores the urgency for continued research to navigate the existing challenges and fully leverage the therapeutic potential of TRF1, TRF2, and the shelterin complex in the realm of cancer treatment.
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Affiliation(s)
- Anoop Kallingal
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, 80-233, Poland.
| | - Radosław Krzemieniecki
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, 80-233, Poland
| | - Natalia Maciejewska
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, 80-233, Poland
| | | | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, 80-233, Poland
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5
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Tang J, Yang Y, Yin HY, Ma B, Zhu M, Yang ZS, Peng XX, Jia F, Zhao Y, Wang F, Chen T, Zhang JL. A Platinum-Aluminum Bimetallic Salen Complex for Pro-senescence Cancer Therapy. Chembiochem 2024; 25:e202400105. [PMID: 38639074 DOI: 10.1002/cbic.202400105] [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: 02/01/2024] [Revised: 04/02/2024] [Accepted: 04/17/2024] [Indexed: 04/20/2024]
Abstract
Cell senescence is defined as irreversible cell cycle arrest, which can be triggered by telomere shortening or by various types of genotoxic stress. Induction of senescence is emerging as a new strategy for the treatment of cancer, especially when sequentially combined with a second senolytic drug capable of killing the resulting senescent cells, however severely suffering from the undesired off-target side effects from the senolytic drugs. Here, we prepare a bimetalic platinum-aluminum salen complex (Alumiplatin) for cancer therapy-a combination of pro-senesence chemotherapy with in situ senotherapy to avoid the side effects. The aluminum salen moiety, as a G-quadruplex stabilizer, enhances the salen's ability to induce cancer cell senescence and this phenotype is in turn sensitive to the cytotoxic activity of the monofunctional platinum moiety. It exhibits an excellent capability for inducing senescence, a potent cytotoxic activity against cancer cells both in vitro and in vivo, and an improved safety profile compared to cisplatin. Therefore, Alumiplatin may be a good candidate to be further developed into safe and effective anticancer agents. This novel combination of cell senescence inducers with genotoxic drugs revolutionizes the therapy options of designing multi-targeting anticancer agents to improve the efficacy of anticancer therapies.
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Affiliation(s)
- Juan Tang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Key Laboratory of Medicinal Molecule Science and pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, P. R. China
| | - Yahui Yang
- Department of Chemistry, Jinan University, Guangzhou, 510632, P. R. China
| | - Hao-Yan Yin
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Bin Ma
- Department of Chemistry, Jinan University, Guangzhou, 510632, P. R. China
| | - Mengliang Zhu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Zi-Shu Yang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Xin-Xin Peng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Feifei Jia
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Tianfeng Chen
- Department of Chemistry, Jinan University, Guangzhou, 510632, P. R. China
| | - Jun-Long Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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6
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Gorb L, Voiteshenko I, Hurmach V, Zarudnaya M, Nyporko A, Shyryna T, Platonov M, Roszak S, Rasulev B. From RNA sequence to its three-dimensional structure: geometrical structure, stability and dynamics of selected fragments of SARS-CoV-2 RNA. NAR Genom Bioinform 2024; 6:lqae062. [PMID: 38835951 PMCID: PMC11148665 DOI: 10.1093/nargab/lqae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
In this computational study, we explore the folding of a particular sequence using various computational tools to produce two-dimensional structures, which are then transformed into three-dimensional structures. We then study the geometry, energetics and dynamics of these structures using full electron quantum-chemical and classical molecular dynamics calculations. Our study focuses on the SARS-CoV-2 RNA fragment GGaGGaGGuguugcaGG and its various structures, including a G-quadruplex and five different hairpins. We examine the impact of two types of counterions (K+ and Na+) and flanking nucleotides on their geometrical characteristics, relative stability and dynamic properties. Our results show that the G-quadruplex structure is the most stable among the constructed hairpins. We confirm its topological stability through molecular dynamics simulations. Furthermore, we observe that the nucleotide loop consisting of seven nucleotides is the most flexible part of the RNA fragment. Additionally, we find that RNA networks of intermolecular hydrogen bonds are highly sensitive to the surrounding environment. Our findings reveal the loss of 79 old hydrogen bonds and the formation of 91 new ones in the case when the G-quadruplex containing flanking nucleotides is additionally stabilized by Na+ counterions.
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Affiliation(s)
- Leonid Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Ivan Voiteshenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, Kyiv01033, Ukraine
| | - Vasyl Hurmach
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Margarita Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Alex Nyporko
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, Kyiv01033, Ukraine
| | - Tetiana Shyryna
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Maksym Platonov
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Szczepan Roszak
- Faculty of Chemistry, University of Wrocław, 50-370Wrocław, Poland
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymer Materials, North Dakota State University, NDSU Department 2760, PO Box 6050, Fargo, ND 58108, USA
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7
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Huynh M, Vinck R, Gibert B, Gasser G. Strategies for the Nuclear Delivery of Metal Complexes to Cancer Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2311437. [PMID: 38174785 DOI: 10.1002/adma.202311437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/20/2023] [Indexed: 01/05/2024]
Abstract
The nucleus is an essential organelle for the function of cells. It holds most of the genetic material and plays a crucial role in the regulation of cell growth and proliferation. Since many antitumoral therapies target nucleic acids to induce cell death, tumor-specific nuclear drug delivery could potentiate therapeutic effects and prevent potential off-target side effects on healthy tissue. Due to their great structural variety, good biocompatibility, and unique physico-chemical properties, organometallic complexes and other metal-based compounds have sparked great interest as promising anticancer agents. In this review, strategies for specific nuclear delivery of metal complexes are summarized and discussed to highlight crucial parameters to consider for the design of new metal complexes as anticancer drug candidates. Moreover, the existing opportunities and challenges of tumor-specific, nucleus-targeting metal complexes are emphasized to outline some new perspectives and help in the design of new cancer treatments.
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Affiliation(s)
- Marie Huynh
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry of Life and Health Sciences, Laboratory for Inorganic Chemistry, Paris, F-75005, France
- Gastroenterology and technologies for Health, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS5286, Université Lyon 1, Lyon, 69008, France
| | - Robin Vinck
- Orano, 125 avenue de Paris, Châtillon, 92320, France
| | - Benjamin Gibert
- Gastroenterology and technologies for Health, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS5286, Université Lyon 1, Lyon, 69008, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry of Life and Health Sciences, Laboratory for Inorganic Chemistry, Paris, F-75005, France
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8
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Figueiredo J, Mergny JL, Cruz C. G-quadruplex ligands in cancer therapy: Progress, challenges, and clinical perspectives. Life Sci 2024; 340:122481. [PMID: 38301873 DOI: 10.1016/j.lfs.2024.122481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/20/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
Guanine-rich sequences can form G-quadruplexes (G4) in living cells, making these structures promising anti-cancer targets. Compounds able to recognize these structures have been investigated as potential anticancer drugs; however, no G4 binder has yet been approved in the clinic. Here, we describe G4 ligands structure-activity relationships, in vivo effects as well as clinical trials. Addressing G4 ligand characteristics, targeting challenges, and structure-activity relationships, this review provides insights into the development of potent and selective G4-targeting molecules for therapeutic applications.
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Affiliation(s)
- Joana Figueiredo
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Institut Polytechnique de Paris, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau cedex, France; Institute of Biophysics of the CAS, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Carla Cruz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal; Departamento de Química, Faculdade de Ciências, Universidade da Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal.
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9
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Kumari A, Pandav K, Nath M, Barthwal R, Peddinti RK. Recognition of human telomeric G-quadruplex DNA by 1,5-disubstituted diethyl-amido anthraquinone derivative in different ion environments causing thermal stabilization and apoptosis. J Biomol Struct Dyn 2024:1-17. [PMID: 38174595 DOI: 10.1080/07391102.2023.2298733] [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: 10/09/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
Ligand binding to G-quadruplex (G4) structures at human telomeric DNA ends promotes thermal stabilization, disrupting the interaction of the telomerase enzyme, which is found active in 80-85% of cancers and serves as a molecular marker. Anthraquinone compounds are well-known G-quadruplex (G4) binders that inhibit telomerase and induce apoptosis in cancer cells. Our current investigation is based on 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione, a derivative of anthraquinone and its binding characterization with two different human telomeric DNA structures, wHTel26 and HTel22, in the effect of K+ and Na+ by using an array of biophysical, calorimetry, molecular docking and cell viability assay techniques. Binding constants (Kb) in the range of ∼105-107 M-1 and stoichiometries of 1:1, 2:1 & 4:1 were obtained from the absorbance, fluorescence, and circular dichroism study. Remarkable hypochromism (55, 97%) and ∼17 nm shift in absorbance, fluorescence quenching (95, 97%), the unaltered value of fluorescence lifetime, restoration of Circular Dichroism bands, absence of ICD band, indicated the external groove binding/binding somewhere at loops. This is also evident in molecular docking results, the ligand binds to groove forming base (G4, G5, G24, T25) and in the vicinity to TTA loop (G14, G15, T17) bases of wHTel26 and HTel22, respectively. Thermal stabilization induced by ligand was found greater in Na+ ion (27.5 °C) than (19.1 °C) in K+ ion. Ligand caused cell toxicity in MCF-7 cancer cell lines with an IC50 value of ∼8.4 µM. The above findings suggest the ligand, 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione could be a potent anticancer drug candidate and has great therapeutic implications.Binding of disubstituted amido anthraquinone derivative, 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione to human telomere HTel22 antiparallel conformation induced thermal stabilization.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anjana Kumari
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kumud Pandav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Mala Nath
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Ritu Barthwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Rama Krishna Peddinti
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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10
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Shiekh S, Kodikara SG, Balci H. Structure, Topology, and Stability of Multiple G-quadruplexes in Long Telomeric Overhangs. J Mol Biol 2024; 436:168205. [PMID: 37481156 PMCID: PMC10799177 DOI: 10.1016/j.jmb.2023.168205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Telomeres and their single stranded overhangs gradually shorten with successive cell divisions, as part of the natural aging process, but can be elongated by telomerase, a nucleoprotein complex which is activated in the majority of cancers. This prominent implication in cancer and aging has made the repetitive telomeric sequences (TTAGGG repeats) and the G-quadruplex structures that form in their overhangs the focus of intense research in the past several decades. However, until recently most in vitro efforts to understand the structure, stability, dynamics, and interactions of telomeric overhangs had been focused on short sequences that are not representative of longer sequences encountered in a physiological setting. In this review, we will provide a broad perspective about telomeres and associated factors, and introduce the agents and structural characteristics involved in organizing, maintaining, and protecting telomeric DNA. We will also present a summary of recent research performed on long telomeric sequences, nominally defined as those that can form two or more tandem G-quadruplexes, i.e., which contain eight or more TTAGGG repeats. Results of experimental studies using a broad array of experimental tools, in addition to recent computational efforts will be discussed, particularly in terms of their implications for the stability, folding topology, and compactness of the tandem G-quadruplexes that form in long telomeric overhangs.
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Affiliation(s)
- Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA.
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11
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Badalyan M, Vardanyan IV, Haroutiunian SG, Dalyan YB. Structural Transitions in Complementary G-Rich and C-Rich Strands and Their Mixture at Various pH Conditions. ACS OMEGA 2023; 8:47051-47056. [PMID: 38107945 PMCID: PMC10719991 DOI: 10.1021/acsomega.3c06934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/11/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
We used circular dichroism spectroscopy, UV spectrophotometry, and differential scanning calorimetry to investigate pH-dependent structural transitions in an equimolar mixture of complementary G-rich d[5'-A(GGGTTA)3GGG-3'] (TelG) and C-rich d[3'-T(CCCAAT)3CCC-5'] (TelC) human telomeric DNA strands. Our studies were conducted at neutral (pH 7.0) and slightly acidic (pH 5.5 and 6.5) pH. We analyzed the melting thermodynamics of TelG and TelC and their equimolar mixture. Our analysis revealed that the preferred conformation of an equimolar mixture of TelG and TelC is the duplex. At pH 5.5, however, in addition to the duplex state, we observed a significant population of the i-motif state formed by TelC. Our results are consistent with the picture in which an increase in pH from 5.5 to 7.0 has little effect on the melting enthalpy of an isolated G-quadruplex while causing a strong reduction in the melting enthalpy of an isolated i-motif (the latter diminishes to 0 at pH 7.0). These effects summarily lead to a decrease in the contribution of the i-motif to the melting enthalpy of the mixture and, hence, an increase in the apparent melting enthalpy and overall stability of the duplex state.
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Affiliation(s)
- Milena
Kh. Badalyan
- Department of Molecular Physics, Yerevan State University, Yerevan 0025, Armenia
| | - Ishkhan V. Vardanyan
- Department of Molecular Physics, Yerevan State University, Yerevan 0025, Armenia
| | | | - Yeva B. Dalyan
- Department of Molecular Physics, Yerevan State University, Yerevan 0025, Armenia
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12
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Brankiewicz W, Kalathiya U, Padariya M, Węgrzyn K, Prusinowski M, Zebrowska J, Zylicz-Stachula A, Skowron P, Drab M, Szajewski M, Ciesielski M, Gawrońska M, Kallingal A, Makowski M, Bagiński M. Modified Peptide Molecules As Potential Modulators of Shelterin Protein Functions; TRF1. Chemistry 2023; 29:e202300970. [PMID: 37332024 DOI: 10.1002/chem.202300970] [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: 03/28/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
In this work, we present studies on relatively new and still not well-explored potential anticancer targets which are shelterin proteins, in particular the TRF1 protein can be blocked by in silico designed "peptidomimetic" molecules. TRF1 interacts directly with the TIN2 protein, and this protein-protein interaction is crucial for the proper functioning of telomere, which could be blocked by our novel modified peptide molecules. Our chemotherapeutic approach is based on assumption that modulation of TRF1-TIN2 interaction may be more harmful for cancer cells as cancer telomeres are more fragile than in normal cells. We have shown in vitro within SPR experiments that our modified peptide PEP1 molecule interacts with TRF1, presumably at the site originally occupied by the TIN2 protein. Disturbance of the shelterin complex by studied molecule may not in short term lead to cytotoxic effects, however blocking TRF1-TIN2 resulted in cellular senescence in cellular breast cancer lines used as a cancer model. Thus, our compounds appeared useful as starting model compounds for precise blockage of TRF proteins.
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Affiliation(s)
- Wioletta Brankiewicz
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822, Gdańsk, Poland
| | - Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822, Gdańsk, Poland
| | - Katarzyna Węgrzyn
- Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307, Gdansk, Poland
| | - Maciej Prusinowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Joanna Zebrowska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | | | - Piotr Skowron
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Marek Drab
- Unit of Nanostructural Bio-Interactions, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 Weigla-Street, 53-114, Wrocław, Poland
| | - Mariusz Szajewski
- Department of Oncological Surgery, Gdynia Oncology Centre, Gdynia, Poland
- Division of Propaedeutics of Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | - Maciej Ciesielski
- Department of Oncological Surgery, Gdynia Oncology Centre, Gdynia, Poland
- Division of Propaedeutics of Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | - Małgorzata Gawrońska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Anoop Kallingal
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
| | - Mariusz Makowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Maciej Bagiński
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
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13
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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: 2] [Impact Index Per Article: 2.0] [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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14
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Ouyang R, Liu J, Wang S, Zhang W, Feng K, Liu C, Liu B, Miao Y, Zhou S. Virtual Screening-Based Study of Novel Anti-Cancer Drugs Targeting G-Quadruplex. Pharmaceutics 2023; 15:pharmaceutics15051414. [PMID: 37242656 DOI: 10.3390/pharmaceutics15051414] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
In order to develop new anti-cancer drugs more efficiently and reduce side effects based on active drug targets, the virtual drug screening was carried out through the target of G-quadruplexes and 23 hit compounds were, thus, screened out as potential anticancer drugs. Six classical G-quadruplex complexes were introduced as query molecules, and the three-dimensional similarity of molecules was calculated by shape feature similarity (SHAFTS) method so as to reduce the range of potential compounds. Afterwards, the molecular docking technology was utilized to perform the final screening followed by the exploration of the binding between each compound and four different structures of G-quadruplex. In order to verify the anticancer activity of the selected compounds, compounds 1, 6 and 7 were chosen to treat A549 cells in vitro, the lung cancer epithelial cells, for further exploring their anticancer activity. These three compounds were found to be of good characteristics in the treatment of cancer, which revealed the great application prospect of the virtual screening method in developing new drugs.
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Affiliation(s)
- Ruizhuo Ouyang
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Jinyao Liu
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Shen Wang
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Weilun Zhang
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Kai Feng
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Conghao Liu
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Baolin Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yuqing Miao
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Shuang Zhou
- Cancer Institute, Tongji University School of Medicine, Shanghai 200092, China
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15
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Dey A, Anand K, Singh A, Prasad R, Barthwal R. MOSR and NDHA Genes Comprising G-Quadruplex as Promising Therapeutic Targets against Mycobacterium tuberculosis: Molecular Recognition by Mitoxantrone Suppresses Replication and Gene Regulation. Genes (Basel) 2023; 14:978. [PMID: 37239338 PMCID: PMC10217741 DOI: 10.3390/genes14050978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/19/2022] [Accepted: 04/18/2023] [Indexed: 05/28/2023] Open
Abstract
Occurrence of non-canonical G-quadruplex (G4) DNA structures in the genome have been recognized as key factors in gene regulation and several other cellular processes. The mosR and ndhA genes involved in pathways of oxidation sensing regulation and ATP generation, respectively, make Mycobacterium tuberculosis (Mtb) bacteria responsible for oxidative stress inside host macrophage cells. Circular Dichroism spectra demonstrate stable hybrid G4 DNA conformations of mosR/ndhA DNA sequences. Real-time binding of mitoxantrone to G4 DNA with an affinity constant ~105-107 M-1, leads to hypochromism with a red shift of ~18 nm, followed by hyperchromism in the absorption spectra. The corresponding fluorescence is quenched with a red shift ~15 nm followed by an increase in intensity. A change in conformation of the G4 DNA accompanies the formation of multiple stoichiometric complexes with a dual binding mode. The external binding of mitoxantrone with a partial stacking with G-quartets and/or groove binding induces significant thermal stabilization, ~20-29 °C in ndhA/mosR G4 DNA. The interaction leads to a two/four-fold downregulation of transcriptomes of mosR/ndhA genes apart from the suppression of DNA replication by Taq polymerase enzyme, establishing the role of mitoxantrone in targeting G4 DNA, as an alternate strategy for effective anti-tuberculosis action in view of deadly multi-drug resistant tuberculosis disease causing bacterial strains t that arise from existing therapeutic treatments.
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Affiliation(s)
- Arpita Dey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Kushi Anand
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Amit Singh
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Ritu Barthwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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16
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In Vitro Anticancer Properties of Novel Bis-Triazoles. Curr Issues Mol Biol 2022; 45:175-196. [PMID: 36661500 PMCID: PMC9858002 DOI: 10.3390/cimb45010014] [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: 10/18/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/30/2022] Open
Abstract
Here, we describe the anticancer activity of our novel bis-triazoles MS47 and MS49, developed previously as G-quadruplex stabilizers, focusing specifically upon the human melanoma MDA-MB-435 cell line. At the National Cancer Institute (NCI), USA, bis-triazole MS47 (NCS 778438) was evaluated against a panel of sixty human cancer cell lines, and showed selective, distinct multi-log differential patterns of activity, with GI50 and LC50 values in the sub-micromolar range against human cancer cells. MS47 showed highly selective cytotoxicity towards human melanoma, ovarian, CNS and colon cancer cell lines; in contrast, the leukemia cell lines interestingly showed resistance to MS47 cytotoxic activity. Further studies revealed the potent cell growth inhibiting properties of MS47 and MS49 against the human melanoma MDA-MB-435 cell line, as verified by MTT assays; both ligands were more potent against cancer cells than MRC-5 fetal lung fibroblasts (SI > 9). Melanoma colony formation was significantly suppressed by MS47 and MS49, and time- and dose-dependent apoptosis induction was also observed. Furthermore, MS47 significantly arrested melanoma cells at the G0/G1 cell cycle phase. While the expression levels of Hsp90 protein in melanoma cells were significantly decreased by MS49, corroborating its binding to the G4-DNA promoter of the Hsp90 gene. Both ligands failed to induce senescence in the human melanoma cells after 72 h of treatment, corroborating their weak stabilization of the telomeric G4-DNA.
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17
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Saleh MM, Abuirmeileh AN, Al-Rousan RM, Abudoleh SM, Hassouneh LK, Zihlif MA, Taha MO, Abutayeh RF, Mansour H, Abu-Irmaileh B. Biological Evaluation and Reverse Pharmacophore Mapping of Innovative Bis-Triazoles as Promising Anticancer Agents. THE OPEN MEDICINAL CHEMISTRY JOURNAL 2022; 16. [DOI: 10.2174/18741045-v16-e2207200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/31/2022] [Accepted: 04/28/2022] [Indexed: 07/10/2024]
Abstract
Here, we describe further cytotoxic studies and reverse pharmacophore mapping (pharmacophore profiling) for bis-triazoles MS44-53, which were designed and synthesized previously to stabilize the G-quadruplex nucleic acids capable of being formed at the telomeric region and promoter sequences of genes involved in cellular proliferation and oncogenes. Pharmacophore-based activity profiling screen demonstrated some biological targets that MS44-53 may modulate their biological response, and thus can be considered as potential drugs to treat different kinds of diseases, such as carcinoma, diabetes type II, bacterial infection and cardiovascular diseases. Potent cell growth inhibitory properties were shown by ligands MS47 and MS49 against human melanoma MDA-MB-435, colon cancer HCT-116 and COLO 205, and pancreatic cancer MIA PaCa-2 cell lines, as evidenced by MTT assay. Both ligands were more potent against cancer cells than in skin normal CCD-1064Sk fibroblasts.
Aim:
The aim of this study is to identify the molecular target and mechanism of action of our promising anticancer bis-triazoles MS44-53, focusing specifically on the G-quadruplex stabilizers MS47 and MS49.
Background:
In molecular biology, G-quadruplexes (also known as G4-DNA), one of the higher-order structures of polynucleotides, are four stranded structures formed by nucleic acid sequences which are rich in guanine. They are formed mainly at the single-stranded G-overhang of telomeric DNA and within promoter sequences of genes involved in cellular proliferation and oncogenes such as c-myc, c-kit, and Hsp90. Stabilization of DNA G-quadruplexes is one of the anticancer strategies that has the potential to treat all cancers regardless of the type. A new series of bis-triazoles MS44-53 were developed to stabilize G-quadruplex structures selectively, as G4 ligands and experimental antitumour agents. FRET assay showed that MS47 and MS49 were only the best binders towards the Hsp90 promoter G-guadruplexes. While all bis-triazoles MS44-53 exhibited potent cell growth inhibitory activity against human carcinoma cell lines, suggesting that the ligands perturb molecular targets and mechanisms of action, other than stabilizing G-quadruplexes, contributing to antitumor activity. Therefore, the molecular targets and mechanisms of action of bis-triazoles MS44-53 in different types of human cancer cell lines should be determined by performing further computational studies to MS44-53 and in vitro evaluations for the G-quadruplex stabilizers MS47 and MS49.
Objectives:
1- Determining the exact IC50 for bis-triazoles MS47 & MS49 against four different types of human cancer cell lines; melanoma MDA-MB-435, pancreatic cancer MIA PaCa-2, and colon cancer HCT-116 and COLO 205 cell lines.
2- Predicting the biological targets that bis-triazoles MS44-53 may interact with to trigger or block their biological response.
Methods:
1- MTT assay was used for in vitro evaluation of the antiproliferative activities of MS47 and MS49, and determination of IC50 values.
2- Reverse pharmacophore mapping (pharmacophore profiling) was used for predicting the biological targets of bis-triazoles MS44-53, and determining the % binding probabilities.
Results:
MS49 exhibited more potent proliferation inhibitory activity than MS47 and higher IC50 value against skin normal fibroblasts. Pharmacophore profiling demonstrated FGFR1, PDGFR2, FLT3, mTOR, PPAR-gamma, MUR-F and CETP as biological targets for bis-triazoles MS44-53.
Conclusion:
Bis-triazoles MS47 and MS49 are promising selective innovative compounds with wide spectrum cytotoxic activities against distinct cancer types. Bis-triazoles MS44-53 can be considered as potential drugs to treat different types of carcinoma, in addition to diabetes type II, bacterial infection and cardiovascular diseases.
Other:
Further in vitro evaluations will be performed for bis-triazoles MS44-53 in order to identify their molecular targets and mechanisms of action in different types of human cancer cell lines.
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Panczyk T, Nieszporek K, Wolski P. Stability and Existence of Noncanonical I-motif DNA Structures in Computer Simulations Based on Atomistic and Coarse-Grained Force Fields. Molecules 2022; 27:molecules27154915. [PMID: 35956863 PMCID: PMC9370271 DOI: 10.3390/molecules27154915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/13/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022] Open
Abstract
Cytosine-rich DNA sequences are able to fold into noncanonical structures, in which semi-protonated cytosine pairs develop extra hydrogen bonds, and these bonds are responsible for the overall stability of a structure called the i-motif. The i-motif can be formed in many regions of the genome, but the most representative is the telomeric region in which the CCCTAA sequences are repeated thousands of times. The ability to reverse folding/unfolding in response to pH change makes the above sequence and i-motif very promising components of nanomachines, extended DNA structures, and drug carriers. Molecular dynamics analysis of such structures is highly beneficial due to direct insights into the microscopic structure of the considered systems. We show that Amber force fields for DNA predict the stability of the i-motif over a long timescale; however, these force fields are not able to predict folding of the cytosine-rich sequences into the i-motif. The reason is the kinetic partitioning of the folding process, which makes the transitions between various intermediates too time-consuming in atomistic force field representation. Application of coarse-grained force fields usually highly accelerates complex structural transitions. We, however, found that three of the most popular coarse-grained force fields for DNA (oxDNA, 3SPN, and Martini) were not able to predict the stability of the i-motif structure. Obviously, they were not able to accelerate the folding of unfolded states into an i-motif. This observation must be strongly highlighted, and the need to develop suitable extensions of coarse-grained force fields for DNA is pointed out. However, it will take a great deal of effort to successfully solve these problems.
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Affiliation(s)
- Tomasz Panczyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30239 Cracow, Poland;
- Correspondence:
| | - Krzysztof Nieszporek
- Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University in Lublin pl. Maria Curie-Sklodowska 3, 20031 Lublin, Poland;
| | - Pawel Wolski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30239 Cracow, Poland;
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Jiang J, Teunens T, Tisaun J, Denuit L, Moucheron C. Ruthenium(II) Polypyridyl Complexes and Their Use as Probes and Photoreactive Agents for G-quadruplexes Labelling. Molecules 2022; 27:1541. [PMID: 35268640 PMCID: PMC8912042 DOI: 10.3390/molecules27051541] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Affiliation(s)
- Julie Jiang
- Laboratoire de Chimie Organique et Photochimie, Service de Chimie et PhysicoChimie Organiques, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50-CP 160/08, 1050 Brussels, Belgium; (J.J.); (T.T.); (J.T.); (L.D.)
| | - Titouan Teunens
- Laboratoire de Chimie Organique et Photochimie, Service de Chimie et PhysicoChimie Organiques, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50-CP 160/08, 1050 Brussels, Belgium; (J.J.); (T.T.); (J.T.); (L.D.)
- Laboratoire de Chimie des Matériaux Nouveaux, Université de Mons, Place du Parc 20, 7000 Mons, Belgium
| | - Jérôme Tisaun
- Laboratoire de Chimie Organique et Photochimie, Service de Chimie et PhysicoChimie Organiques, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50-CP 160/08, 1050 Brussels, Belgium; (J.J.); (T.T.); (J.T.); (L.D.)
| | - Laura Denuit
- Laboratoire de Chimie Organique et Photochimie, Service de Chimie et PhysicoChimie Organiques, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50-CP 160/08, 1050 Brussels, Belgium; (J.J.); (T.T.); (J.T.); (L.D.)
| | - Cécile Moucheron
- Laboratoire de Chimie Organique et Photochimie, Service de Chimie et PhysicoChimie Organiques, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50-CP 160/08, 1050 Brussels, Belgium; (J.J.); (T.T.); (J.T.); (L.D.)
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20
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Debbarma S, Acharya PC. Targeting G-Quadruplex Dna For Cancer Chemotherapy. Curr Drug Discov Technol 2022; 19:e140222201110. [PMID: 35156574 DOI: 10.2174/1570163819666220214115408] [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: 08/23/2021] [Revised: 09/24/2021] [Accepted: 12/03/2021] [Indexed: 11/22/2022]
Abstract
The self-association of DNA formed by Hoogsteen hydrogen bonding comprises several layers of four guanine or G-tetrads or G4s. The distinct feature of G4s, such as the G-tetrads and loops, qualify structure-selective recognition by small molecules and various ligands and can act as potential anticancer therapeutic molecules. The G4 selective-ligands, can influence gene expression by targeting a nucleic acid structure rather than sequence. Telomere G4 can be targeted for cancer treatment by small molecules inhibiting the telomerase activity whereas c-MYC is capable of controlling transcription, can be targeted to influence transcription. The k-RAS is one of the most frequently encountered oncogenic driver mutations in pancreatic, colorectal, and lung cancers. The k-RAS oncogene plays important role in acquiring and increasing the drug resistance and can also be directly targeted by small molecules to combat k-RAS mutant tumors. Modular G4 ligands with different functional groups, side chains and rotatable bonds as well as conformation affect the binding affinity/selectivity in cancer chemotherapeutic interventions. These modular G4 ligands act by targeting the diversity of G4 loops and groves and assists to develop more drug-like compounds with selectivity. In this review, we present the recent research on synthetic G4 DNA-interacting ligands as an approach toward the discovery of target specific anticancer chemotherapeutic agents.
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Affiliation(s)
- Sumanta Debbarma
- Department of Pharmacy, Tripura University, Suryamaninagar-799022, India
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21
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22
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Beals N, Farhath MM, Kharel P, Croos B, Mahendran T, Johnson J, Basu S. Rationally designed DNA therapeutics can modulate human TH expression by controlling specific GQ formation in its promoter. Mol Ther 2022; 30:831-844. [PMID: 33992806 PMCID: PMC8822133 DOI: 10.1016/j.ymthe.2021.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 02/04/2023] Open
Abstract
Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the catecholamine (CA) biosynthesis pathway, making TH a molecular target for controlling CA production, specifically dopamine. Dysregulation of dopamine is correlated with neurological diseases such as Parkinson's disease (PD) and post-traumatic stress disorder (PTSD), among others. Previously, we showed that a 49-nucleotide guanine (G)-rich sequence within the human TH promoter adopts two different sets of G-quadruplex (GQ) structures (5'GQ and 3'GQ), where the 5'GQ uses G-stretches I, II, IV, and VI in TH49, which enhances TH transcription, while the 3'GQ utilizes G-stretches II, IV, VI, and VII, which represses transcription. Herein, we demonstrated targeted switching of these GQs to their active state using rationally designed DNA GQ Clips (5'GQ and 3'GQ Clips) to modulate endogenous TH gene expression and dopamine production. As a translational approach, we synthesized a targeted nanoparticle delivery system to effectively deliver the 5'GQ Clip in vivo. We believe this strategy could potentially be an improved approach for controlling dopamine production in a multitude of neurological disorders, including PD.
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Affiliation(s)
- Nathan Beals
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Mohamed M. Farhath
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA,Department of Chemical Sciences, Faculty of Applied Sciences, South Eastern University of Sri Lanka, Oluvil, Sri Lanka
| | - Prakash Kharel
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA,Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Brintha Croos
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Thulasi Mahendran
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - John Johnson
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA,Corresponding author: Soumitra Basu, Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA.
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23
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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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24
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Ongaro A, Desiderati G, Oselladore E, Auricchio D, Memo M, Ribaudo G, Sissi C, Gianoncelli A. Amino-Acid-Anthraquinone Click Chemistry Conjugates Selectively Target Human Telomeric G-Quadruplexes. ChemMedChem 2021; 17:e202100665. [PMID: 34882992 DOI: 10.1002/cmdc.202100665] [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: 10/14/2021] [Revised: 12/07/2021] [Indexed: 11/06/2022]
Abstract
Guanine-rich sequences are known to fold into G-quadruplex (G4) arrangements, which are present in oncogenes and in the telomeric regions of chromosomes. In particular, G4s represent an obstacle to functioning of telomerase, an enzyme overexpressed in cancer cells causing their immortalization. Therefore, G4 stabilization using small molecules represents an appealing strategy for the medicinal chemist. Ligands based on an anthraquinone scaffold, to which peptidic side chains were attached by an amide bond, were previously reported. We envisioned improving this ligand concept leveraging the click chemistry approach, which, besides representing a flexible, high yielding synthetic strategy, allows an elongation of the side chains and an increase of π-π stacking and H-bond interactions with the nucleobases through the triazole ring. Compounds were tested for their ability to interact with G4 DNA with a multiple analytical approach, demonstrating an elevated aptitude to stabilize the G4 and high selectivity over double stranded DNA.
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Affiliation(s)
- Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Giovanni Desiderati
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Erika Oselladore
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Davide Auricchio
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
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25
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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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26
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Liu YC, Yang DY, Sheu SY. Insights into the free energy landscape and salt-controlled mechanism of the conformational conversions between human telomeric G-quadruplex structures. Int J Biol Macromol 2021; 191:230-242. [PMID: 34536474 DOI: 10.1016/j.ijbiomac.2021.09.057] [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: 06/29/2021] [Revised: 08/23/2021] [Accepted: 09/10/2021] [Indexed: 12/16/2022]
Abstract
G-quadruplexes have become attractive drug targets in cancer therapy. However, due to the polymorphism of G-quadruplex structures, it is difficult to experimentally verify the relevant structures of multiple intermediates and transition states in dynamic equilibrium. Hence, understanding the mechanism by which structural conversions of G-quadruplexes occur is still challenging. We conducted targeted molecular dynamics simulation with umbrella sampling to investigate how salt affects the conformational conversion of human telomeric G-quadruplex. Our results explore a unique view into the structures and energy barrier of the intermediates and transition states in the interconversion process. The pathway of G-quadruplex conformational interconversion was mapped out by a free energy landscape, consisting of branched parallel pathways with multiple energy basins. We propose a salt-controlled mechanism that as the salt concentration increases, the conformational conversion mechanism switches from multi-pathway folding to sequential folding pathways. The hybrid-I and hybrid-II structures are intermediates in the basket-propeller transformation. In high-salt solutions, the conformational conversion upon K+ binding is more feasible than upon Na+ binding. The free energy barrier for conformational conversions ranges from 1.6 to 4.6 kcal/mol. Our work will be beneficial in developing anticancer agents.
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Affiliation(s)
- Yu-Cheng Liu
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan.
| | - Sheh-Yi Sheu
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
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27
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Oshchepkov AS, Reznichenko O, Xu D, Morozov BS, Granzhan A, Kataev EA. Dye-functionalized phosphate-binding macrocycles: from nucleotide to G-quadruplex recognition and "turn-on" fluorescence sensing. Chem Commun (Camb) 2021; 57:10632-10635. [PMID: 34581337 DOI: 10.1039/d1cc04096k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel strategy to design "turn-on" fluorescent receptors for G-quadruplexes of DNA is presented, which relies on the connection of phosphate binding macrocycles (PBM) with naphthalimide dyes. A new PBM-dye family was synthesized and evaluated in terms of binding and detection of nucleotides and DNA G-quadruplexes of different topologies.
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Affiliation(s)
- Aleksandr S Oshchepkov
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany. .,Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Oksana Reznichenko
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, Bât. 110, Centre Universitaire Paris Sud, F-91405 Orsay, France
| | - Dan Xu
- Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Boris S Morozov
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany. .,Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, Bât. 110, Centre Universitaire Paris Sud, F-91405 Orsay, France
| | - Evgeny A Kataev
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany. .,CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, Bât. 110, Centre Universitaire Paris Sud, F-91405 Orsay, France
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28
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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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29
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Ribaudo G, Ongaro A, Oselladore E, Memo M, Gianoncelli A. Combining Electrospray Mass Spectrometry (ESI-MS) and Computational Techniques in the Assessment of G-Quadruplex Ligands: A Hybrid Approach to Optimize Hit Discovery. J Med Chem 2021; 64:13174-13190. [PMID: 34510895 PMCID: PMC8474113 DOI: 10.1021/acs.jmedchem.1c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
Guanine-rich sequences
forming G-quadruplexes (GQs) are present
in several genomes, ranging from viral to human. Given their peculiar
localization, the induction of GQ formation or GQ stabilization with
small molecules represents a strategy for interfering with crucial
biological functions. Investigating the recognition event at the molecular
level, with the aim of fully understanding the triggered pharmacological
effects, is challenging. Native electrospray ionization mass spectrometry
(ESI-MS) is being optimized to study these noncovalent assemblies.
Quantitative parameters retrieved from ESI-MS studies, such as binding
affinity, the equilibrium binding constant, and sequence selectivity,
will be overviewed. Computational experiments supporting the ESI-MS
investigation and boosting its efficiency in the search for GQ ligands
will also be discussed with practical examples. The combination of
ESI-MS and in silico techniques in a hybrid high-throughput-screening
workflow represents a valuable tool for the medicinal chemist, providing
data on the quantitative and structural aspects of ligand–GQ
interactions.
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Affiliation(s)
- Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Erika Oselladore
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
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30
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Bağda E, Bağda E, Kocak A, Durmuş M. Investigation of Binding behaviour of a water-soluble gallium (III) phthalocyanine with double-stranded and G-quadruplex DNA via experimental and computational methods. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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Libera V, Andreeva EA, Martel A, Thureau A, Longo M, Petrillo C, Paciaroni A, Schirò G, Comez L. Porphyrin Binding and Irradiation Promote G-Quadruplex DNA Dimeric Structure. J Phys Chem Lett 2021; 12:8096-8102. [PMID: 34406777 DOI: 10.1021/acs.jpclett.1c01840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nucleic acid sequences rich in guanines can organize into noncanonical DNA G-quadruplexes (G4s) of variable size. The design of small molecules stabilizing the structure of G4s is a rapidly growing area for the development of novel anticancer therapeutic strategies and bottom-up nanotechnologies. Among a multitude of binders, porphyrins are very attractive due to their light activation that can make them valuable conformational regulators of G4s. Here, a structure-based strategy, integrating complementary probes, is employed to study the interaction between TMPyP4 porphyrin and a 22-base human telomeric sequence (Tel22) before and after irradiation with blue light. Porphyrin binding is discovered to promote Tel22 dimerization, while light irradiation of the Tel22-TMPyP4 complex controls dimer fraction. Such a change in quaternary structure is found to be strictly correlated with modifications at the secondary structure level, thus providing an unprecedented link between the degree of dimerization and the underlying conformational changes in G4s.
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Affiliation(s)
- Valeria Libera
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
- CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - Elena A Andreeva
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Aurelien Thureau
- Swing Beamline, Synchrotron SOLEIL, 91192 Gif sur Yvette, France
| | - Marialucia Longo
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Lucia Comez
- CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
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32
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Peterková K, Durník I, Marek R, Plavec J, Podbevšek P. c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry. Nucleic Acids Res 2021; 49:8947-8960. [PMID: 34365512 PMCID: PMC8421218 DOI: 10.1093/nar/gkab659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022] Open
Abstract
Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (Upy) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with Upy and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π–π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.
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Affiliation(s)
- Kateřina Peterková
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Ivo Durník
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Radek Marek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Peter Podbevšek
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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33
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Honisch C, Ragazzi E, Hussain R, Brazier J, Siligardi G, Ruzza P. Interaction of a Short Peptide with G-Quadruplex-Forming Sequences: An SRCD and CD Study. Pharmaceutics 2021; 13:1104. [PMID: 34452065 PMCID: PMC8401852 DOI: 10.3390/pharmaceutics13081104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/11/2022] Open
Abstract
G-quadruplex (G4) forming DNA sequences were recently found to play a crucial role in the regulation of genomic processes such as replication, transcription and translation, also related to serious diseases. Therefore, systems capable of controlling DNA and RNA G-quadruplex structures would be useful for the modulation of various cellular events. In particular, peptides represent good candidates for targeting G-quadruplex structures, since they are easily tailored to enhance their functionality. In this work, we analyzed, by circular dichroism and synchrotron radiation circular dichroism spectroscopies, the interaction of a 25-residue peptide deriving from RHAU helicases (Rhau25) with three G-quadruplex-forming oligonucleotide sequences, in both sodium- and potassium-containing buffers, the most relevant monovalent cations in physiological conditions. The peptide displayed greater affinity for the G4 sequences adopting a parallel structure. However, it showed the ability to also interact with antiparallel or hybrid G-quadruplex structures, inducing a conformation conversion to the parallel structure. The stability of the oligonucleotide structure alone or in presence of the Rhau25 peptide was studied by temperature melting and UV denaturation experiments, and the data showed that the interaction with the peptide stabilized the conformation of oligonucleotide sequences when subjected to stress conditions.
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Affiliation(s)
- Claudia Honisch
- Institute of Biomolecular Chemistry of CNR, Via F. Marzolo, 1, 35131 Padova, Italy;
- Department of Chemical Sciences, University of Padua, Via F. Marzolo, 1, 35131 Padova, Italy
| | - Eugenio Ragazzi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Largo Meneghetti, 2, 35131 Padova, Italy;
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (R.H.); (G.S.)
| | - John Brazier
- School of Pharmacy, University of Reading, Reading RG6 6DX, UK;
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (R.H.); (G.S.)
| | - Paolo Ruzza
- Institute of Biomolecular Chemistry of CNR, Via F. Marzolo, 1, 35131 Padova, Italy;
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Singh U, Morya V, Datta B, Ghoroi C, Bhatia D. Stimuli Responsive, Programmable DNA Nanodevices for Biomedical Applications. Front Chem 2021; 9:704234. [PMID: 34277571 PMCID: PMC8278982 DOI: 10.3389/fchem.2021.704234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
Of the multiple areas of applications of DNA nanotechnology, stimuli-responsive nanodevices have emerged as an elite branch of research owing to the advantages of molecular programmability of DNA structures and stimuli-responsiveness of motifs and DNA itself. These classes of devices present multiples areas to explore for basic and applied science using dynamic DNA nanotechnology. Herein, we take the stake in the recent progress of this fast-growing sub-area of DNA nanotechnology. We discuss different stimuli, motifs, scaffolds, and mechanisms of stimuli-responsive behaviours of DNA nanodevices with appropriate examples. Similarly, we present a multitude of biological applications that have been explored using DNA nanodevices, such as biosensing, in vivo pH-mapping, drug delivery, and therapy. We conclude by discussing the challenges and opportunities as well as future prospects of this emerging research area within DNA nanotechnology.
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Affiliation(s)
- Udisha Singh
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
| | - Vinod Morya
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
| | - Bhaskar Datta
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, India
| | - Chinmay Ghoroi
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, India
- Chemical Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, India
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Xu J, Jiang R, He H, Ma C, Tang Z. Recent advances on G-quadruplex for biosensing, bioimaging and cancer therapy. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116257] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Wang S, Yang Y, Yang Y, Li H, Chen DDY. Quantitative characterization of human oncogene promoter G-quadruplex DNA-ligand interactions using a combination of mass spectrometry and capillary electrophoresis. Electrophoresis 2021; 42:1450-1460. [PMID: 33990994 DOI: 10.1002/elps.202100077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 11/08/2022]
Abstract
Human c-KIT oncogene is known to regulate cell growth and proliferation, and thus, acts as a probable target in the treatment of gastrointestinal tumors (GIST). To identify small molecule ligands which can specifically bind with the G-quadruplex (G4) in the c-KIT promoter region as potential antitumor agents, we propose the combination of electrospray ionization-mass spectrometry (ESI-MS), capillary electrophoresis frontal analysis (CE-FA), and Taylor dispersion analysis (TDA) to accurately investigate the G4/ligands binding properties. First, ESI-MS was used for initial screening of natural products (NPs). CE-FA was then used to calculate specific binding constants and the stoichiometry of the native state binding pair in solution. Next, TDA, a micro-capillary flow technique was used to examine the effect of the ligand binding on the diffusivity and particle size of the c-KIT G4. Two of the screened NPs, scopolamine butylbromide (L1) and isorhamnetin-3-O-neohesperidoside (L3), were found to specifically bind to the c-KIT G4 with binding constants of around 104 M-1 and 1:1 stoichiometry in a free solution. TDA data showed that ligand binding (both L1 and L3) induced the c-KIT strands to fold into a tightly structured G4 with a decreased hydrodynamic radius. These ligands have the potential to be drug candidates for the regulation of c-KIT gene transcription by stabilizing the G4 structure. This methodology not only increased the speed of analysis but also improved its accuracy and specificity compared with the conventional binding approaches.
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Affiliation(s)
- Shuangshuang Wang
- National and local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Changzhou Institute of Innovation and Development, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, P. R. China
| | - Yang Yang
- National and local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Changzhou Institute of Innovation and Development, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, P. R. China
| | - Yunhe Yang
- National and local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Changzhou Institute of Innovation and Development, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, P. R. China
| | - Huihui Li
- National and local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Changzhou Institute of Innovation and Development, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, P. R. China
| | - David D Y Chen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
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Carloni LE, Wechselberger R, De Vijlder T. Characterization of In Vitro G-Quadruplex Formation of Imetelstat Telomerase Inhibitor. Nucleic Acid Ther 2021; 31:341-350. [PMID: 34018844 DOI: 10.1089/nat.2020.0918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Imetelstat (GRN163L) is a potent and specific telomerase inhibitor currently in clinical development for the treatment of hematological malignancies such as myelofibrosis and myelodysplastic syndrome. It is a 13-mer N3'-P5' thio-phosphoramidate oligonucleotide covalently functionalized at the 5'-end with a palmitoyl lipid moiety through an aminoglycerol linker. As a competitive inhibitor of human telomerase, imetelstat directly binds to the telomerase RNA component sequence (hTR) in the catalytic site of the enzyme and acts as a direct competitor of human telomere binding. Administration of imetelstat causes progressive shortening of the telomeres, thereby inhibiting malignant cells' proliferation. We report here the ability of imetelstat to form stable, parallel, intermolecular G-quadruplex structures in vitro. The impact of the ionic environment on the formation and stability of imetelstat higher-order structure was investigated through circular dichroism spectroscopy, thermal denaturation analysis, and size-exclusion chromatography. We demonstrated that different structural elements, such as the 5'-palmitoyl linker and the thio-phosphoramidate backbone, critically contribute to G-quadruplex stability. Experiments further showed that G-quadruplex formation does not hamper binding to the hTR oligonucleotide sequence in vitro.
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Affiliation(s)
- Laure-Elie Carloni
- Small Molecule Pharmaceutical Development, Janssen Research & Development, Beerse, Belgium
| | - Rainer Wechselberger
- Small Molecule Pharmaceutical Development, Janssen Research & Development, Beerse, Belgium
| | - Thomas De Vijlder
- Small Molecule Pharmaceutical Development, Janssen Research & Development, Beerse, Belgium
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Unraveling the binding characteristics of small ligands to telomeric DNA by pressure modulation. Sci Rep 2021; 11:9714. [PMID: 33958702 PMCID: PMC8102477 DOI: 10.1038/s41598-021-89215-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
Recently, non-canonical DNA structures, such as G-quadruplexes (GQs), were found to be highly pressure sensitive, suggesting that pressure modulation studies can provide additional mechanistic details of such biomolecular systems. Using FRET and CD spectroscopy as well as binding equilibrium measurements, we investigated the effect of pressure on the binding reaction of the ligand ThT to the quadruplex 22AG in solutions containing different ionic species and a crowding agent mimicking the intracellular milieu. Pressure modulation helped us to identify the different conformational substates adopted by the quadruplex at the different solution conditions and to determine the volumetric changes during complex formation and the conformational transitions involved. The magnitudes of the binding volumes are a hallmark of packing defects and hydrational changes upon ligand binding. The conformational substates of the GQ as well as the binding strength and the stoichiometry of complex formation depend strongly on the solution conditions as well as on pressure. High hydrostatic pressure can also impact GQs inside living cells and thus affect expression of genetic information in deep sea organisms. We show that sub-kbar pressures do not only affect the conformational dynamics and structures of GQs, but also their ligand binding reactions.
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Müller D, Bessi I, Richter C, Schwalbe H. The Folding Landscapes of Human Telomeric RNA and DNA G-Quadruplexes are Markedly Different. Angew Chem Int Ed Engl 2021; 60:10895-10901. [PMID: 33539622 PMCID: PMC8252441 DOI: 10.1002/anie.202100280] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/04/2021] [Indexed: 01/23/2023]
Abstract
We investigated the folding kinetics of G-quadruplex (G4) structures by comparing the K+ -induced folding of an RNA G4 derived from the human telomeric repeat-containing RNA (TERRA25) with a sequence homologous DNA G4 (wtTel25) using CD spectroscopy and real-time NMR spectroscopy. While DNA G4 folding is biphasic, reveals kinetic partitioning and involves kinetically favoured off-pathway intermediates, RNA G4 folding is faster and monophasic. The differences in kinetics are correlated to the differences in the folded conformations of RNA vs. DNA G4s, in particular with regard to the conformation around the glycosidic torsion angle χ that uniformly adopts anti conformations for RNA G4s and both, syn and anti conformation for DNA G4s. Modified DNA G4s with 19 F bound to C2' in arabino configuration adopt exclusively anti conformations for χ. These fluoro-modified DNA (antiTel25) reveal faster folding kinetics and monomorphic conformations similar to RNA G4s, suggesting the correlation between folding kinetics and pathways with differences in χ angle preferences in DNA and RNA, respectively.
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Affiliation(s)
- Diana Müller
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Irene Bessi
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
- Present address: Julius-Maximilians-University Würzburg, Institute of Organic Chemistry, Am Hubland 16, 97074, Würzburg, Germany
| | - Christian Richter
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
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40
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Panczyk T, Camp PJ. Lorentz forces induced by a static magnetic field have negligible effects on results from classical molecular dynamics simulations of aqueous solutions. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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41
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The Folding Landscapes of Human Telomeric RNA and DNA G‐Quadruplexes are Markedly Different. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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42
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Moharana P, Ghosh D, Paira P. Drive to organoruthenium and organoiridium complexes from organoplatinum: Next-generation anticancer metallotherapeutics. INORG CHEM COMMUN 2021. [DOI: 10.1016/j.inoche.2020.108364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Zell J, Rota Sperti F, Britton S, Monchaud D. DNA folds threaten genetic stability and can be leveraged for chemotherapy. RSC Chem Biol 2021; 2:47-76. [PMID: 35340894 PMCID: PMC8885165 DOI: 10.1039/d0cb00151a] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/20/2020] [Indexed: 12/22/2022] Open
Abstract
Damaging DNA is a current and efficient strategy to fight against cancer cell proliferation. Numerous mechanisms exist to counteract DNA damage, collectively referred to as the DNA damage response (DDR) and which are commonly dysregulated in cancer cells. Precise knowledge of these mechanisms is necessary to optimise chemotherapeutic DNA targeting. New research on DDR has uncovered a series of promising therapeutic targets, proteins and nucleic acids, with application notably via an approach referred to as combination therapy or combinatorial synthetic lethality. In this review, we summarise the cornerstone discoveries which gave way to the DNA being considered as an anticancer target, and the manipulation of DDR pathways as a valuable anticancer strategy. We describe in detail the DDR signalling and repair pathways activated in response to DNA damage. We then summarise the current understanding of non-B DNA folds, such as G-quadruplexes and DNA junctions, when they are formed and why they can offer a more specific therapeutic target compared to that of canonical B-DNA. Finally, we merge these subjects to depict the new and highly promising chemotherapeutic strategy which combines enhanced-specificity DNA damaging and DDR targeting agents. This review thus highlights how chemical biology has given rise to significant scientific advances thanks to resolutely multidisciplinary research efforts combining molecular and cell biology, chemistry and biophysics. We aim to provide the non-specialist reader a gateway into this exciting field and the specialist reader with a new perspective on the latest results achieved and strategies devised.
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Affiliation(s)
- Joanna Zell
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS Toulouse France
- Équipe Labellisée la Ligue Contre le Cancer 2018 Toulouse France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
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Fundamental insights into the interaction between telomerase/TERT and intracellular signaling pathways. Biochimie 2020; 181:12-24. [PMID: 33232793 DOI: 10.1016/j.biochi.2020.11.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 11/07/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022]
Abstract
Telomerase activity is critical for cancer cells to provide unrestricted proliferation and cellular immortality through maintaining telomeres. Telomerase enzymatic activity is regulatable at the level of DNA, mRNA, post translational modifications, cellular transport and enzyme assembly. More recent studies confirm the interaction of the telomerase with various intracellular signaling pathways including PI3K/AKT/mTOR, NF-κB and Wnt/β-catenin which mainly participating in inflammation, epithelial to mesenchymal transition (EMT) and tumor cell invasion and metastasis. Furthermore, hTERT protein has been detected in non-nuclear sites such as the mitochondria and cytoplasm in cells. Mitochondrial TERT indicates various non-telomere-related functions such as decreasing reactive oxygen species (ROS) generation, boosting the respiration rate, protecting mtDNA by direct binding, interacting with mitochondrial tRNAs and increasing mitochondrial membrane potential which can lead to higher chemoresistance rate in cancer cells during therapies. Understanding the molecular mechanisms of the TERT function and depended interactions in tumor cells can suggest novel therapeutic approaches. Hence, in this review we will explain the telomerase activity regulation in translational and post translational levels besides the established correlations with various cell signaling pathways with possible pathways for therapeutic targeting.
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Obi I, Rentoft M, Singh V, Jamroskovic J, Chand K, Chorell E, Westerlund F, Sabouri N. Stabilization of G-quadruplex DNA structures in Schizosaccharomyces pombe causes single-strand DNA lesions and impedes DNA replication. Nucleic Acids Res 2020; 48:10998-11015. [PMID: 33045725 PMCID: PMC7641769 DOI: 10.1093/nar/gkaa820] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 12/30/2022] Open
Abstract
G-quadruplex (G4) structures are stable non-canonical DNA structures that are implicated in the regulation of many cellular pathways. We show here that the G4-stabilizing compound PhenDC3 causes growth defects in Schizosaccharomyces pombe cells, especially during S-phase in synchronized cultures. By visualizing individual DNA molecules, we observed shorter DNA fragments of newly replicated DNA in the PhenDC3-treated cells, suggesting that PhenDC3 impedes replication fork progression. Furthermore, a novel single DNA molecule damage assay revealed increased single-strand DNA lesions in the PhenDC3-treated cells. Moreover, chromatin immunoprecipitation showed enrichment of the leading-strand DNA polymerase at sites of predicted G4 structures, suggesting that these structures impede DNA replication. We tested a subset of these sites and showed that they form G4 structures, that they stall DNA synthesis in vitro and that they can be resolved by the breast cancer-associated Pif1 family helicases. Our results thus suggest that G4 structures occur in S. pombe and that stabilized/unresolved G4 structures are obstacles for the replication machinery. The increased levels of DNA damage might further highlight the association of the human Pif1 helicase with familial breast cancer and the onset of other human diseases connected to unresolved G4 structures.
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Affiliation(s)
- Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Matilda Rentoft
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Vandana Singh
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Karam Chand
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
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Macii F, Perez-Arnaiz C, Arrico L, Busto N, Garcia B, Biver T. Alcian blue pyridine variant interaction with DNA and RNA polynucleotides and G-quadruplexes: changes in the binding features for different biosubstrates. J Inorg Biochem 2020; 212:111199. [DOI: 10.1016/j.jinorgbio.2020.111199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022]
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47
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Gillard M, Weynand J, Bonnet H, Loiseau F, Decottignies A, Dejeu J, Defrancq E, Elias B. Flexible Ru
II
Schiff Base Complexes: G‐Quadruplex DNA Binding and Photo‐Induced Cancer Cell Death. Chemistry 2020; 26:13849-13860. [DOI: 10.1002/chem.202001409] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/28/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Martin Gillard
- Institut de la Matière Condensée et des Nanosciences (IMCN) Molecular Chemistry, Materials and Catalysis (MOST) Université catholique de Louvain (UCLouvain) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
| | - Justin Weynand
- Institut de la Matière Condensée et des Nanosciences (IMCN) Molecular Chemistry, Materials and Catalysis (MOST) Université catholique de Louvain (UCLouvain) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Hugues Bonnet
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Frédérique Loiseau
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Anabelle Decottignies
- Université catholique de Louvain (UCLouvain) de Duve Institute Avenue Hippocrate 75 1200 Brussels Belgium
| | - Jérôme Dejeu
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Eric Defrancq
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Benjamin Elias
- Institut de la Matière Condensée et des Nanosciences (IMCN) Molecular Chemistry, Materials and Catalysis (MOST) Université catholique de Louvain (UCLouvain) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
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Barthwal R, Raje S, Pandav K. Structural basis for stabilization of human telomeric G-quadruplex [d-(TTAGGGT)] 4 by anticancer drug epirubicin. Bioorg Med Chem 2020; 28:115761. [PMID: 32992248 DOI: 10.1016/j.bmc.2020.115761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/25/2020] [Accepted: 09/06/2020] [Indexed: 02/07/2023]
Abstract
Anthracycline anticancer drugs show multiple strategies of action on gene functioning by regulation of telomerase enzyme by apoptotic factors, e.g. ceramide level, p53 activity, bcl-2 protein levels, besides inhibiting DNA/RNA synthesis and topoisomerase-II action. We report binding of epirubicin with G-quadruplex (G4) DNA, [d-(TTAGGGT)]4, comprising human telomeric DNA sequence TTAGGG, using 1H and 31P NMR spectroscopy. Diffusion ordered spectroscopy, sequence selective changes in chemical shift (~0.33 ppm) and line broadening in DNA signals suggest formation of a well-defined complex. Presence of sequential nuclear Overhauser enhancements at all base quartet steps and absence of large downfield shifts in 31P resonances preclude intercalative mode of interaction. Restrained molecular dynamics simulations using AMBER force field incorporating intermolecular drug to DNA interproton distances, involving ring D protons of epirubicin depict external binding close to T1-T2-A3 and G6pT7 sites. Binding induced thermal stabilization of G4 DNA (~36 °C), obtained from imino protons and differential scanning calorimetry, is likely to come in the way of telomerase association with telomeres. The findings pave the way for drug-designing with modifications at ring D and daunosamine sugar.
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Affiliation(s)
- Ritu Barthwal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India.
| | - Shailja Raje
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Kumud Pandav
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India
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Chalikian TV, Liu L, Macgregor RB. Duplex-tetraplex equilibria in guanine- and cytosine-rich DNA. Biophys Chem 2020; 267:106473. [PMID: 33031980 DOI: 10.1016/j.bpc.2020.106473] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Noncanonical four-stranded DNA structures, including G-quadruplexes and i-motifs, have been discovered in the cell and are implicated in a variety of genomic regulatory functions. The tendency of a specific guanine- and cytosine-rich region of genomic DNA to adopt a four-stranded conformation depends on its ability to overcome the constraints of duplex base-pairing by undergoing consecutive duplex-to-coil and coil-to-tetraplex transitions. The latter ability is determined by the balance between the free energies of participating ordered and disordered structures. In this review, we present an overview of the literature on the stability of G-quadruplex and i-motif structures and discuss the extent of duplex-tetraplex competition as a function of the sequence context of the DNA and environmental conditions including temperature, pH, salt, molecular crowding, and the presence of G-quadruplex-binding ligands. We outline how the results of in vitro studies can be expanded to understanding duplex-tetraplex equilibria in vivo.
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Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
| | - Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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Nao SC, Wu KJ, Wang W, Leung CH, Ma DL. Recent Progress and Development of G-Quadruplex-Based Luminescent Assays for Ochratoxin A Detection. Front Chem 2020; 8:767. [PMID: 33088800 PMCID: PMC7490745 DOI: 10.3389/fchem.2020.00767] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
Ochratoxin A (OTA) is a mycotoxin that is widespread throughout the world. It contaminates foods such as vegetables, fruits, and rice. It harms human health and has potential carcinogenic effects. The G-quadruplex (G4) is a tetraplexed DNA structure generated from guanine-rich DNA that has found emerging use in aptamer-based sensing systems. This review outlines the status of OTA contamination and conventional detection methods for OTA. Various G4-based methods to detect OTA developed in recent years are summarized along with their advantages and disadvantages compared to existing approaches.
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Affiliation(s)
- Sang-Cuo Nao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, China
| | - Ke-Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, China
| | - Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, China
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