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Ciaco S, Aronne R, Fiabane M, Mori M. The Rise of Bacterial G-Quadruplexes in Current Antimicrobial Discovery. ACS OMEGA 2024; 9:24163-24180. [PMID: 38882119 PMCID: PMC11170735 DOI: 10.1021/acsomega.4c01731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024]
Abstract
Antimicrobial resistance (AMR) is a silent critical issue that poses several challenges to health systems. While the discovery of novel antibiotics is currently stalled and prevalently focused on chemical variations of the scaffolds of available drugs, novel targets and innovative strategies are urgently needed to face this global threat. In this context, bacterial G-quadruplexes (G4s) are emerging as timely and profitable targets for the design and development of antimicrobial agents. Indeed, they are expressed in regulatory regions of bacterial genomes, and their modulation has been observed to provide antimicrobial effects with translational perspectives in the context of AMR. In this work, we review the current knowledge of bacterial G4s as well as their modulation by small molecules, including tools and techniques suitable for these investigations. Finally, we critically analyze the needs and future directions in the field, with a focus on the development of small molecules as bacterial G4s modulators endowed with remarkable drug-likeness.
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Affiliation(s)
- Stefano Ciaco
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Rossella Aronne
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Martina Fiabane
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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2
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Banjan B, Koshy AJ, Kalath H, John L, Soman S, Raju R, Revikumar A. Potential protein kinase inhibitors that target G-quadruplex DNA structures in the human telomeric regions. Mol Divers 2024:10.1007/s11030-023-10768-7. [PMID: 38509417 DOI: 10.1007/s11030-023-10768-7] [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: 08/28/2023] [Accepted: 11/10/2023] [Indexed: 03/22/2024]
Abstract
Telomeric regions contain Guanine-rich sequences arranged in a planar manner and connected by Hoogsteen hydrogen bonds that can fold into G-quadruplex (G4) DNA structures, and can be stabilized by monovalent metal cations. The presence of G4 DNA holds significance in cancer-related processes, especially due to their regulatory potential at transcriptional and translational levels of oncogene and tumor suppressor genes. The objective of this current research is to explore the evolving realm of FDA-approved protein kinase inhibitors, with a specific emphasis on their capacity to stabilize the G4 DNA structures formed at the human telomeric regions. This involves investigating the possibility of repurposing FDA-approved protein kinase inhibitors as a novel approach for targeting multiple cancer types. In this context, we have selected 16 telomeric G4 DNA structures as targets and 71 FDA-approved small-molecule protein kinase inhibitors as ligands. To investigate their binding affinities, molecular docking of human telomeric G4 DNA with nuclear protein kinase inhibitors and their corresponding co-crystalized ligands were performed. We found that Ponatinib and Lapatinib interact with all the selected G4 targets, the binding free energy calculations, and molecular dynamic simulations confirm their binding efficacy and stability. Thus, it is hypothesized that Ponatinib and Lapatinib may stabilize human telomeric G4 DNA in addition to their ability to inhibit BCR-ABL and the other members of the EGFR family. As a result, we also hypothesize that the stabilization of G4 DNA might represent an additional underlying mechanism contributing to their efficacy in exerting anti-cancer effects.
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Affiliation(s)
- Bhavya Banjan
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Abel John Koshy
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Haritha Kalath
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Sowmya Soman
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India.
| | - Amjesh Revikumar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India.
- Kerala Genome Data Centre, Kerala Development and Innovation Strategic Council, Vazhuthacaud, Thiruvananthapuram, Kerala, 695014, India.
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3
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Fatma K, Thumpati P, Panda D, Velayutham R, Dash J. Selective Recognition of c-KIT 1 G-Quadruplex by Structural Tuning of Heteroaromatic Scaffolds and Side Chains. ACS Med Chem Lett 2024; 15:388-395. [PMID: 38505840 PMCID: PMC10945540 DOI: 10.1021/acsmedchemlett.3c00537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 03/21/2024] Open
Abstract
In this study, carbazole (MC) and dibenzofuran (MD) derivatives were synthesized to examine their effect on the biomolecular recognition of G-quadruplex (G4) targets. Biophysical studies revealed that MC-4, a carbazole derivative, exhibits a specific affinity and effectively stabilizes the c-KIT 1 G4. Molecular modeling suggests a stable interaction of MC-4 with the terminal G-tetrad of c-KIT 1 G4. Biological studies demonstrate that MC-4 efficiently enters cells, reduces c-KIT gene expression, and induces cell cycle arrest, DNA damage, and apoptosis in cancer cells. These findings demonstrate MC-4 as a selective c-KIT G4 ligand with therapeutic potential, providing insight into the structural basis of its anticancer mechanisms.
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Affiliation(s)
- Khushnood Fatma
- Indian
Association for the Cultivation of Science, 2A & 2B, Raja Subodh Chandra
Mallick Road, Jadavpur, Kolkata-700032, India
| | - Prasanth Thumpati
- Indian
Association for the Cultivation of Science, 2A & 2B, Raja Subodh Chandra
Mallick Road, Jadavpur, Kolkata-700032, India
- National
Institute of Pharmaceutical Education and Research, Chunilal Bhawan, Maniktala, Kolkata-700054, India
| | - Deepanjan Panda
- Indian
Association for the Cultivation of Science, 2A & 2B, Raja Subodh Chandra
Mallick Road, Jadavpur, Kolkata-700032, India
| | - Ravichandiran Velayutham
- National
Institute of Pharmaceutical Education and Research, Chunilal Bhawan, Maniktala, Kolkata-700054, India
| | - Jyotirmayee Dash
- Indian
Association for the Cultivation of Science, 2A & 2B, Raja Subodh Chandra
Mallick Road, Jadavpur, Kolkata-700032, India
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4
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Ahmed AA, Chen S, Roman-Escorza M, Angell R, Oxenford S, McConville M, Barton N, Sunose M, Neidle D, Haider S, Arshad T, Neidle S. Structure-activity relationships for the G-quadruplex-targeting experimental drug QN-302 and two analogues probed with comparative transcriptome profiling and molecular modeling. Sci Rep 2024; 14:3447. [PMID: 38342953 PMCID: PMC10859377 DOI: 10.1038/s41598-024-54080-2] [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: 11/21/2023] [Accepted: 02/08/2024] [Indexed: 02/13/2024] Open
Abstract
The tetrasubstituted naphthalene diimide compound QN-302 binds to G-quadruplex (G4) DNA structures. It shows high potency in pancreatic ductal adenocarcinoma (PDAC) cells and inhibits the transcription of cancer-related genes in these cells and in PDAC animal models. It is currently in Phase 1a clinical evaluation as an anticancer drug. A study of structure-activity relationships of QN-302 and two related analogues (CM03 and SOP1247) is reported here. These have been probed using comparisons of transcriptional profiles from whole-genome RNA-seq analyses, together with molecular modelling and molecular dynamics simulations. Compounds CM03 and SOP1247 differ by the presence of a methoxy substituent in the latter: these two compounds have closely similar transcriptional profiles. Whereas QN-302 (with an additional benzyl-pyrrolidine group), although also showing down-regulatory effects in the same cancer-related pathways, has effects on distinct genes, for example in the hedgehog pathway. This distinctive pattern of genes affected by QN-302 is hypothesized to contribute to its superior potency compared to CM03 and SOP1247. Its enhanced ability to stabilize G4 structures has been attributed to its benzyl-pyrrolidine substituent fitting into and filling most of the space in a G4 groove compared to the hydrogen atom in CM03 or the methoxy group substituent in SOP1247.
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Affiliation(s)
- Ahmed Abdullah Ahmed
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
- Now at Guy's Cancer Centre, Guy's Hospital, London, SE1 9RT, UK
| | - Shuang Chen
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | | | - Richard Angell
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
- Now at Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK
| | - Sally Oxenford
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
- Now at Artios Ltd, Cambridge, CB22 3FH, UK
| | | | | | - Mihiro Sunose
- Sygnature Discovery Ltd, BioCity, Nottingham, NG1 1GR, UK
| | - Dan Neidle
- Tax Policy Associates, London, EC1R 0ET, UK
| | - Shozeb Haider
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Tariq Arshad
- Qualigen Therapeutics Inc, Carlsbad, CA, 92011, USA
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK.
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5
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Gómez-Bra A, Gude L, Arias-Pérez MS. Synthesis, structural study and antitumor activity of novel alditol-based imidazophenanthrolines (aldo-IPs). Bioorg Med Chem 2024; 99:117563. [PMID: 38215623 DOI: 10.1016/j.bmc.2023.117563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024]
Abstract
A series of 1H-imidazo [4,5-f][1,10] phenanthroline derivatives functionalized at 2-position with chiral, and conformationally flexible polyhydroxy alkyl chains derived from carbohydrates (alditol-based imidazophenanthrolines, aldo-IPs) is presented herein. These novel glycomimetics showed relevant and differential cytotoxic activity against several cultured tumor cell lines (PC3, HeLa and HT-29), dependent on the nature and stereochemistry of the polyhydroxy alkyl chain. The mannose-based aldo-IP demonstrated the higher cytotoxicity in the series, substantially better than cisplatin metallo-drug in all cell lines tested, and better than G-quadruplex ligand 360A in HeLa and HT29 cells. Cell cycle experiments and Annexin V-PI assays revealed that aldo-IPs induce apoptosis in HeLa cells. Initial study of DNA interactions by DNA FRET melting assays proved that the aldo-IPs produce only a slight thermal stabilization of DNA secondary structures, more pronounced in the case of quadruplex DNA. Viscosity titrations with CT dsDNA suggest that the compounds behave as DNA groove binders, whereas equilibrium dialysis assays showed that the compounds bind CT with Ka values in the range 104-105 M-1. The aldo-IP derivatives were obtained with synthetically useful yields through a feasible one-pot multistep process, by aerobic oxidative cyclization of 1,10-phenanthroline-5,6-diamine with a selection of unprotected aldoses using (NH4)2SO4 as promoter.
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Affiliation(s)
- Ana Gómez-Bra
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28805-Alcalá de Henares, Madrid, Spain; Grupo DISCOBAC, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), Spain
| | - Lourdes Gude
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28805-Alcalá de Henares, Madrid, Spain; Grupo DISCOBAC, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), Spain.
| | - María-Selma Arias-Pérez
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28805-Alcalá de Henares, Madrid, Spain.
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6
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Sengupta P, Dutta A, Suseela YV, Roychowdhury T, Banerjee N, Dutta A, Halder S, Jana K, Mukherjee G, Chattopadhyay S, Govindaraju T, Chatterjee S. G-quadruplex structural dynamics at MAPK12 promoter dictates transcriptional switch to determine stemness in breast cancer. Cell Mol Life Sci 2024; 81:33. [PMID: 38214819 PMCID: PMC11073236 DOI: 10.1007/s00018-023-05046-6] [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: 05/11/2023] [Revised: 10/26/2023] [Accepted: 11/09/2023] [Indexed: 01/13/2024]
Abstract
P38γ (MAPK12) is predominantly expressed in triple negative breast cancer cells (TNBC) and induces stem cell (CSC) expansion resulting in decreased survival of the patients due to metastasis. Abundance of G-rich sequences at MAPK12 promoter implied the functional probability to reverse tumorigenesis, though the formation of G-Quadruplex (G4) structures at MAPK12 promoter is elusive. Here, we identified two evolutionary consensus adjacent G4 motifs upstream of the MAPK12 promoter, forming parallel G4 structures. They exist in an equilibria between G4 and duplex, regulated by the binding turnover of Sp1 and Nucleolin that bind to these G4 motifs and regulate MAPK12 transcriptional homeostasis. To underscore the gene-regulatory functions of G4 motifs, we employed CRISPR-Cas9 system to eliminate G4s from TNBC cells and synthesized a naphthalene diimide (NDI) derivative (TGS24) which shows high-affinity binding to MAPK12-G4 and inhibits MAPK12 transcription. Deletion of G4 motifs and NDI compound interfere with the recruitment of the transcription factors, inhibiting MAPK12 expression in cancer cells. The molecular basis of NDI-induced G4 transcriptional regulation was analysed by RNA-seq analyses, which revealed that MAPK12-G4 inhibits oncogenic RAS transformation and trans-activation of NANOG. MAPK12-G4 also reduces CD44High/CD24Low population in TNBC cells and downregulates internal stem cell markers, arresting the stemness properties of cancer cells.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Anindya Dutta
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Y V Suseela
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, Karnataka, 560064, India
| | - Tanaya Roychowdhury
- Department of Cancer Biology and Inflammatory Disorder, IICB, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Ananya Dutta
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Satyajit Halder
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Kuladip Jana
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Gopeswar Mukherjee
- Barasat Cancer Research and Welfare Centre, Barasat, Kolkata, West Bengal, India
| | - Samit Chattopadhyay
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, K. K. Birla Goa Campus, Goa, 403726, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, Karnataka, 560064, India.
| | - Subhrangsu Chatterjee
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India.
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7
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Zareie AR, Dabral P, Verma SC. G-Quadruplexes in the Regulation of Viral Gene Expressions and Their Impacts on Controlling Infection. Pathogens 2024; 13:60. [PMID: 38251367 PMCID: PMC10819198 DOI: 10.3390/pathogens13010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures that play significant roles in regulating various biological processes, including replication, transcription, translation, and recombination. Recent studies have identified G4s in the genomes of several viruses, such as herpes viruses, hepatitis viruses, and human coronaviruses. These structures are implicated in regulating viral transcription, replication, and virion production, influencing viral infectivity and pathogenesis. G4-stabilizing ligands, like TMPyP4, PhenDC3, and BRACO19, show potential antiviral properties by targeting and stabilizing G4 structures, inhibiting essential viral life-cycle processes. This review delves into the existing literature on G4's involvement in viral regulation, emphasizing specific G4-stabilizing ligands. While progress has been made in understanding how these ligands regulate viruses, further research is needed to elucidate the mechanisms through which G4s impact viral processes. More research is necessary to develop G4-stabilizing ligands as novel antiviral agents. The increasing body of literature underscores the importance of G4s in viral biology and the development of innovative therapeutic strategies against viral infections. Despite some ligands' known regulatory effects on viruses, a deeper comprehension of the multifaceted impact of G4s on viral processes is essential. This review advocates for intensified research to unravel the intricate relationship between G4s and viral processes, paving the way for novel antiviral treatments.
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Affiliation(s)
| | | | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, 1664 N Virginia Street, Reno, NV 89557, USA; (A.R.Z.); (P.D.)
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8
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Luo Y, Granzhan A, Marquevielle J, Cucchiarini A, Lacroix L, Amrane S, Verga D, Mergny JL. Guidelines for G-quadruplexes: I. In vitro characterization. Biochimie 2023; 214:5-23. [PMID: 36596406 DOI: 10.1016/j.biochi.2022.12.019] [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: 10/29/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Besides the well-known DNA double-helix, non-canonical nucleic acid structures regulate crucial biological activities. Among these oddities, guanine-rich DNA sequences can form unusual four-stranded secondary structures called G-quadruplexes (G4s). G4-prone sequences have been found in the genomes of most species, and G4s play important roles in essential processes such as transcription, replication, genome integrity and epigenetic regulation. Here, we present a short overview of G-quadruplexes followed by a detailed description of the biophysical and biochemical methods used to characterize G4s in vitro. The principles, experimental details and possible shortcomings of each method are discussed to provide a comprehensive view of the techniques used to study these structures. We aim to provide a set of guidelines for standardizing research on G-quadruplexes; these guidelines are not meant to be a dogmatic set of rules, but should rather provide useful information on the methods currently used to study these fascinating motifs.
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Affiliation(s)
- Yu Luo
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
| | - Julien Marquevielle
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Anne Cucchiarini
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Laurent Lacroix
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Samir Amrane
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France.
| | - Jean-Louis Mergny
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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9
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Clowes SR, Ali Y, Astley OR, Răsădean DM, Pantoş GD. The Influence of Chirality on the β-Amino-Acid Naphthalenediimides/G-Quadruplex DNA Interaction. Molecules 2023; 28:7291. [PMID: 37959711 PMCID: PMC10647805 DOI: 10.3390/molecules28217291] [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: 09/05/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
G-quadruplexes (G4s) have been identified as a potential alternative chemotherapy target. A series of eight β-amino acid derived naphthalenediimides (NDI) were screened against a series of oncogenic G4 sequences: c-KIT1, h-TELO, and TBA. Three sets of enantiomers were investigated to further our understanding of the effect of point chirality on G4 stabilisation. Enantioselective binding behaviour was observed with both c-KIT1 and h-TELO. Docking studies using GNINA and UV-vis titrations were employed to better understand this selective binding behaviour.
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Affiliation(s)
| | | | | | | | - G. Dan Pantoş
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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10
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Serra M, Rubes D, Schinelli S, Paolillo M. Small Molecules against Metastatic Tumors: Concrete Perspectives and Shattered Dreams. Cancers (Basel) 2023; 15:4173. [PMID: 37627201 PMCID: PMC10453213 DOI: 10.3390/cancers15164173] [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: 06/21/2023] [Revised: 07/29/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Metastasis is the main cause of anti-cancer therapy failure, leading to unfavorable prognosis for patients. The true challenge to increase cancer patient life expectancy by making cancer a chronic disease with periodic but manageable relapses relies on the development of efficient therapeutic strategies specifically directed against key targets in the metastatic process. Traditional chemotherapy with classical alkylating agents, microtubule inhibitors, and antimetabolites has demonstrated its limited efficacy against metastatic cells due to their capacity to select chemo-resistant cell populations that undergo epithelial-to-mesenchymal transition (EMT), thus promoting the colonization of distant sites that, in turn, sustain the initial metastatic process. This scenario has prompted efforts aimed at discovering a wide variety of small molecules and biologics as potential anti-metastatic drugs directed against more specific targets known to be involved in the various stages of metastasis. In this short review, we give an overview of the most recent advances related to important families of antimetastatic small molecules: intracellular tyrosine kinase inhibitors, cyclin-dependent kinase inhibitors, KRAS inhibitors, and integrin antagonists. Although the majority of these small molecules are not yet approved and not available in the drug market, any information related to their stage of development could represent a precious and valuable tool to identify new targets in the endless fight against metastasis.
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Affiliation(s)
- Massimo Serra
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (D.R.); (S.S.); (M.P.)
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11
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cRGD-Functionalized Silk Fibroin Nanoparticles: A Strategy for Cancer Treatment with a Potent Unselective Naphthalene Diimide Derivative. Cancers (Basel) 2023; 15:cancers15061725. [PMID: 36980611 PMCID: PMC10046852 DOI: 10.3390/cancers15061725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/03/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
Developing drug delivery systems to target cytotoxic drugs directly into tumor cells is still a compelling need with regard to reducing side effects and improving the efficacy of cancer chemotherapy. In this work, silk fibroin nanoparticles (SFNs) have been designed to load a previously described cytotoxic compound (NDI-1) that disrupts the cell cycle by specifically interacting with non-canonical secondary structures of DNA. SFNs were then functionalized on their surface with cyclic pentapeptides incorporating the Arg-Gly-Asp sequence (cRGDs) to provide active targeting toward glioma cell lines that abundantly express ανβ3 and ανβ5 integrin receptors. Cytotoxicity and selective targeting were assessed by in vitro tests on human glioma cell lines U373 (highly-expressing integrin subunits) and D384 cell lines (low-expressing integrin subunits in comparison to U373). SFNs were of nanometric size (d50 less than 100 nm), round shaped with a smooth surface, and with a negative surface charge; overall, these characteristics made them very likely to be taken up by cells. The active NDI-1 was loaded into SFNs with high encapsulation efficiency and was not released before the internalization and degradation by cells. Functionalization with cRGDs provided selectivity in cell uptake and thus cytotoxicity, with a significantly higher cytotoxic effect of NDI-1 delivered by cRGD-SFNs on U373 cells than on D384 cells. This manuscript provides an in vitro proof-of-concept of cRGD-silk fibroin nanoparticles’ active site-specific targeting of tumors, paving the way for further in vivo efficacy tests.
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12
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Tuning between Nuclear Organization and Functionality in Health and Disease. Cells 2023; 12:cells12050706. [PMID: 36899842 PMCID: PMC10000962 DOI: 10.3390/cells12050706] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/08/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
The organization of eukaryotic genome in the nucleus, a double-membraned organelle separated from the cytoplasm, is highly complex and dynamic. The functional architecture of the nucleus is confined by the layers of internal and cytoplasmic elements, including chromatin organization, nuclear envelope associated proteome and transport, nuclear-cytoskeletal contacts, and the mechano-regulatory signaling cascades. The size and morphology of the nucleus could impose a significant impact on nuclear mechanics, chromatin organization, gene expression, cell functionality and disease development. The maintenance of nuclear organization during genetic or physical perturbation is crucial for the viability and lifespan of the cell. Abnormal nuclear envelope morphologies, such as invagination and blebbing, have functional implications in several human disorders, including cancer, accelerated aging, thyroid disorders, and different types of neuro-muscular diseases. Despite the evident interplay between nuclear structure and nuclear function, our knowledge about the underlying molecular mechanisms for regulation of nuclear morphology and cell functionality during health and illness is rather poor. This review highlights the essential nuclear, cellular, and extracellular components that govern the organization of nuclei and functional consequences associated with nuclear morphometric aberrations. Finally, we discuss the recent developments with diagnostic and therapeutic implications targeting nuclear morphology in health and disease.
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13
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Irshad R, Asim S, Mansha A, Arooj Y. Naphthalene and its Derivatives: Efficient Fluorescence Probes for Detecting and Imaging Purposes. J Fluoresc 2023:10.1007/s10895-023-03153-y. [PMID: 36735102 DOI: 10.1007/s10895-023-03153-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/19/2023] [Indexed: 02/04/2023]
Abstract
Naphthalene, white crystalline solid having polycyclic aromatic hydrocarbon with characteristic mothball order is naturally present in crucial oils of various plants. Naphthalene derivatives are extensive drug resources and are use as wetting agents, surfactants and as insecticides. These derivatives exhibit unique photo physical and chemical properties. These characteristics make them the most studied group of organic compounds. Naphthalene dyes have rigid plane and large π-electron conjugation. Therefor they have high quantum yield and excellent photostability. Naphthalene based fluorescence probes due to hydrophobic nature exhibit excellent sensing and selectivity properties towards anions and cations and also used as a part of target biomolecules. In conjugated probe system, introducing naphthalene moiety caused improvement in photo-stability. Therefore among various conjugated framework, naphthalene derivatives are considered excellent candidate for the construction of organic electronic appliances. These derivatives are useful for a variety of applications owing to their strong fluorescence, electroactivity and photostability. This article is based upon investigation of photophysical properties of naphthalene derivatives and fluorescence detecting probe of naphthalene. For photophysical properties the techniques under investigation are UV visible spectroscopy and fluorescence spectroscopy. Concentration dependent spectra and solvatochromic shifts on UV visible spectra are also part of discussion.
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Affiliation(s)
- Ruqaya Irshad
- Department of Physics, Government College Women University, Faisalabad, Pakistan
| | - Sadia Asim
- Department of Chemistry, Government College Women University, Faisalabad, Pakistan.
| | - Asim Mansha
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Yusra Arooj
- Department of Physics, Government College Women University, Faisalabad, Pakistan
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14
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Synergistic effect of naphthalenediimide and squaraine ligand targeting G-quadruplex DNA in cancer cells. Chem Biol Interact 2023; 370:110330. [PMID: 36563735 DOI: 10.1016/j.cbi.2022.110330] [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: 08/11/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
Targeting and stabilizing nonclassical DNA G-quadruplexes (G4s) with a ligand to inhibit cell proliferation is a very promising approach for cancer treatment. Here, we demonstrate that the combination of a naphthalenediimide (NDI) ligand and a squaraine ligand significantly improves the anticancer activity of either ligand alone. The NDI ligand binds the 5'-terminal of hybrid-type G4s and induces the topological conversion from a metastable hybrid to a stable parallel conformation, which allows the end-stacking of the squaraine ligand on the 3'-terminal of the resultant parallel-type G4 structure. Moreover, the NDI ligand promotes the diffusion of the squaraine ligand into the nucleus, and the synergistic effect of the two ligands improves the stability of G4s in cancer cells, blocks the cell cycle in the sub-G1 phase, and induces the DNA damage response. These findings will be helpful in the development of combinational ligands targeting DNA G4s with enhanced bioactivity toward the inhibition of cancer cell proliferation.
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15
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Verma S, Patidar RK, Tiwari K, Tiwari R, Baranwal J, Velayutham R, Ranjan N. Preferential Recognition of Human Telomeric G-Quadruplex DNA by a Red-Emissive Molecular Rotor. J Phys Chem B 2022; 126:7298-7309. [DOI: 10.1021/acs.jpcb.2c04418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Smita Verma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Rajesh K. Patidar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
| | - Khushboo Tiwari
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
| | - Ratnesh Tiwari
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
| | - Jaya Baranwal
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
| | - Ravichandiran Velayutham
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
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16
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Structure-Activity Relationship studies on divalent naphthalene diimide G quadruplex ligands with anticancer and antiparasitic activity. Bioorg Med Chem 2022; 71:116946. [DOI: 10.1016/j.bmc.2022.116946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/18/2022]
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17
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Design, synthesis and anti-tumor activity of novel benzothiophenonaphthalimide derivatives targeting mitochondrial DNA (mtDNA) G-quadruplex. Biochem Pharmacol 2022; 201:115062. [DOI: 10.1016/j.bcp.2022.115062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/19/2022]
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18
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Gurung SK, Kumari S, Dana S, Mandal K, Sen S, Mukhopadhyay P, Mondal N. DNA damage, cell cycle perturbation and cell death by naphthalene diimide derivative in gastric cancer cells. Chem Biol Interact 2022; 358:109881. [DOI: 10.1016/j.cbi.2022.109881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/19/2022] [Accepted: 03/04/2022] [Indexed: 11/25/2022]
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19
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Ahuja M, Saini SK, Chaudhary N, Kumar M, Singh RK, Kumar R. Tuning of energy levels, transport properties and device performance of naphthalenediimide derivatives by introduction of Michael addition reaction. NEW J CHEM 2022. [DOI: 10.1039/d2nj01979e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
NDI derivatives have been synthesized via Michael addition reaction with uplifted HOMO–LUMO energy levels and strong CT interaction in MA products generally not achieved by simple imide-N substitutions.
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Affiliation(s)
- Mehak Ahuja
- Photovoltaic Metrology Group, Advanced Materials and Devices Metrology Division, CSIR-National Physical Laboratory, National Measurement Institute of India, Dr K. S. Krishnan Marg, New Delhi, 110012, India
| | - Saurabh K. Saini
- Photonics Materials Metrology Group, Advanced Materials and Devices Metrology Division, CSIR-National Physical Laboratory, Dr K. S. Krishnan Marg, New Delhi, 110012, India
| | - Neeraj Chaudhary
- Photovoltaic Metrology Group, Advanced Materials and Devices Metrology Division, CSIR-National Physical Laboratory, National Measurement Institute of India, Dr K. S. Krishnan Marg, New Delhi, 110012, India
| | - Mahesh Kumar
- Photonics Materials Metrology Group, Advanced Materials and Devices Metrology Division, CSIR-National Physical Laboratory, Dr K. S. Krishnan Marg, New Delhi, 110012, India
| | - Rajiv K. Singh
- Photovoltaic Metrology Group, Advanced Materials and Devices Metrology Division, CSIR-National Physical Laboratory, National Measurement Institute of India, Dr K. S. Krishnan Marg, New Delhi, 110012, India
| | - Rachana Kumar
- Photovoltaic Metrology Group, Advanced Materials and Devices Metrology Division, CSIR-National Physical Laboratory, National Measurement Institute of India, Dr K. S. Krishnan Marg, New Delhi, 110012, India
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20
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Structured Waters Mediate Small Molecule Binding to G-Quadruplex Nucleic Acids. Pharmaceuticals (Basel) 2021; 15:ph15010007. [PMID: 35056064 PMCID: PMC8781208 DOI: 10.3390/ph15010007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/24/2023] Open
Abstract
The role of G-quadruplexes in human cancers is increasingly well-defined. Accordingly, G-quadruplexes can be suitable drug targets and many small molecules have been identified to date as G-quadruplex binders, some using computer-based design methods and co-crystal structures. The role of bound water molecules in the crystal structures of G-quadruplex-small molecule complexes has been analyzed in this study, focusing on the water arrangements in several G-quadruplex ligand complexes. One is the complex between the tetrasubstituted naphthalene diimide compound MM41 and a human intramolecular telomeric DNA G-quadruplex, and the others are in substituted acridine bimolecular G-quadruplex complexes. Bridging water molecules form most of the hydrogen-bond contacts between ligands and DNA in the parallel G-quadruplex structures examined here. Clusters of structured water molecules play essential roles in mediating between ligand side chain groups/chromophore core and G-quadruplex. These clusters tend to be conserved between complex and native G-quadruplex structures, suggesting that they more generally serve as platforms for ligand binding, and should be taken into account in docking and in silico studies.
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21
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Cebrián R, Belmonte-Reche E, Pirota V, de Jong A, Morales JC, Freccero M, Doria F, Kuipers OP. G-Quadruplex DNA as a Target in Pathogenic Bacteria: Efficacy of an Extended Naphthalene Diimide Ligand and Its Mode of Action. J Med Chem 2021; 65:4752-4766. [PMID: 34928608 PMCID: PMC8958502 DOI: 10.1021/acs.jmedchem.1c01905] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Guanidine DNA quadruplex
(G4-DNA) structures convey a distinctive
layer of epigenetic information that is critical for regulating key
biological activities and processes as transcription, replication,
and repair in living cells. The information regarding their role and
use as therapeutic drug targets in bacteria is still scarce. Here,
we tested the biological activity of a G4-DNA ligand library, based
on the naphthalene diimide (NDI) pharmacophore, against both Gram-positive
and Gram-negative bacteria. For the best compound identified, NDI-10, a different action mechanism was described for Gram-positive
or negative bacteria. This asymmetric activity profile could be related
to the different prevalence of putative G4-DNA structures in each
group, the influence that they can exert on gene expression, and the
different roles of the G4 structures in these bacteria, which seem
to promote transcription in Gram-positive bacteria and repress transcription
in Gram-negatives.
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Affiliation(s)
- Rubén Cebrián
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Efres Belmonte-Reche
- Advanced (magnetic) Theranostic Nanostructures Lab, International Iberian Nanotechnology Laboratory, Nanomedicine unit, Avenida Mestre José Veiga, s/n 4715-310 Braga, Portugal
| | - Valentina Pirota
- Department of Chemistry, University of Pavia, via Taramelli 10, I-27100 Pavia (PV), Italy
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, via Taramelli 10, I-27100 Pavia (PV), Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, via Taramelli 10, I-27100 Pavia (PV), Italy
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
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22
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Scalabrin M, Nadai M, Tassinari M, Lago S, Doria F, Frasson I, Freccero M, Richter SN. Selective Recognition of a Single HIV-1 G-Quadruplex by Ultrafast Small-Molecule Screening. Anal Chem 2021; 93:15243-15252. [PMID: 34762806 PMCID: PMC8613737 DOI: 10.1021/acs.analchem.0c04106] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/18/2021] [Indexed: 12/05/2022]
Abstract
G-quadruplexes (G4s) are implicated in pathological processes such as cancer and infective diseases. Their targeting with G4-ligands has shown therapeutic capacity. Most of the current G4-ligands are planar molecules, do not discriminate among G4s, and have poor druglike properties. The available methods to identify compounds selective for one single G4 are often time-consuming. Here, we describe the development, validation, and application of an affinity-selection mass spectrometry method that employs unlabeled G4 oligonucleotides as targets and allows testing of up to 320 unmodified small molecules in a single tube. As a proof of concept, this method was applied to screen a library of 40 000 druglike molecules against two G4s, transcriptional regulators of the HIV-1 LTR promoter. We identified nonplanar pyrazolopyrimidines that selectively recognize and stabilize the major HIV-1 LTR G4 possibly by fitting and binding through H-bonding in its unique binding pocket. The compounds inhibit LTR promoter activity and HIV-1 replication. We propose this method to prompt the fast development of new G4-based therapeutics.
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Affiliation(s)
- Matteo Scalabrin
- Department
of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Matteo Nadai
- Department
of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Martina Tassinari
- Department
of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Sara Lago
- Department
of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Filippo Doria
- Department
of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Ilaria Frasson
- Department
of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Mauro Freccero
- Department
of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Sara N. Richter
- Department
of Molecular Medicine, University of Padua, 35121 Padua, Italy
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23
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Sanchez-Martin V, Schneider DA, Ortiz-Gonzalez M, Soriano-Lerma A, Linde-Rodriguez A, Perez-Carrasco V, Gutierrez-Fernandez J, Cuadros M, González C, Soriano M, Garcia-Salcedo JA. Targeting ribosomal G-quadruplexes with naphthalene-diimides as RNA polymerase I inhibitors for colorectal cancer treatment. Cell Chem Biol 2021; 28:1590-1601.e4. [PMID: 34166611 DOI: 10.1016/j.chembiol.2021.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/05/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022]
Abstract
Guanine quadruplexes (G4s) are non-canonical nucleic acid structures commonly found in regulatory genomic regions. G4 targeting has emerged as a therapeutic approach in cancer. We have screened naphthalene-diimides (NDIs), a class of G4 ligands, in a cellular model of colorectal cancer (CRC). Here, we identify the leading compound T5 with a potent and selective inhibition of cell growth by high-affinity binding to G4s in ribosomal DNA, impairing RNA polymerase I (Pol I) elongation. Consequently, T5 induces a rapid inhibition of Pol I transcription, nucleolus disruption, proteasome-dependent Pol I catalytic subunit A degradation and autophagy. Moreover, we attribute the higher selectivity of carbohydrate-conjugated T5 for tumoral cells to its preferential uptake through the overexpressed glucose transporter 1. Finally, we succinctly demonstrate that T5 could be explored as a therapeutic agent in a patient cohort with CRC. Therefore, we report a mode of action for these NDIs involving ribosomal G4 targeting.
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Affiliation(s)
- Victoria Sanchez-Martin
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain; Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, Granada 18016, Spain
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Matilde Ortiz-Gonzalez
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Centre for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, Almeria 04001, Spain
| | - Ana Soriano-Lerma
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Department of Physiology, University of Granada, Granada 18011, Spain
| | - Angel Linde-Rodriguez
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain
| | - Virginia Perez-Carrasco
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain
| | - Jose Gutierrez-Fernandez
- Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain; Department of Microbiology, University of Granada, Granada 18011, Spain
| | - Marta Cuadros
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, Granada 18016, Spain
| | - Carlos González
- Instituto de Química Física "Rocasolano", CSIC, Madrid 28006, Spain
| | - Miguel Soriano
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Centre for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, Almeria 04001, Spain
| | - Jose A Garcia-Salcedo
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain.
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24
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Ruggiero E, Zanin I, Terreri M, Richter SN. G-Quadruplex Targeting in the Fight against Viruses: An Update. Int J Mol Sci 2021; 22:ijms222010984. [PMID: 34681641 PMCID: PMC8538215 DOI: 10.3390/ijms222010984] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/16/2022] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of key cellular processes, such as transcription and replication. Since their discovery, G4s have been mainly investigated for their role in cancer and as targets in anticancer therapy. More recently, exploration of the presence and role of G4s in viral genomes has led to the discovery of G4-regulated key viral pathways. In this context, employment of selective G4 ligands has helped to understand the complexity of G4-mediated mechanisms in the viral life cycle, and highlighted the possibility to target viral G4s as an emerging antiviral approach. Research in this field is growing at a fast pace, providing increasing evidence of the antiviral activity of old and new G4 ligands. This review aims to provide a punctual update on the literature on G4 ligands exploited in virology. Different classes of G4 binders are described, with emphasis on possible antiviral applications in emerging diseases, such as the current COVID-19 pandemic. Strengths and weaknesses of G4 targeting in viruses are discussed.
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25
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Selective Binding and Redox-Activity on Parallel G-Quadruplexes by Pegylated Naphthalene Diimide-Copper Complexes. Molecules 2021; 26:molecules26165025. [PMID: 34443620 PMCID: PMC8397950 DOI: 10.3390/molecules26165025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/06/2021] [Accepted: 08/16/2021] [Indexed: 11/17/2022] Open
Abstract
G-quadruplexes (G4s) are higher-order supramolecular structures, biologically important in the regulation of many key processes. Among all, the recent discoveries relating to RNA-G4s, including their potential involvement as antiviral targets against COVID-19, have triggered the ever-increasing need to develop selective molecules able to interact with parallel G4s. Naphthalene diimides (NDIs) are widely exploited as G4 ligands, being able to induce and strongly stabilize these structures. Sometimes, a reversible NDI-G4 interaction is also associated with an irreversible one, due to the cleavage and/or modification of G4s by functional-NDIs. This is the case of NDI-Cu-DETA, a copper(II) complex able to cleave G4s in the closest proximity to the target binding site. Herein, we present two original Cu(II)-NDI complexes, inspired by NDI-Cu-DETA, differently functionalized with 2-(2-aminoethoxy)ethanol side-chains, to selectively drive redox-catalyzed activity towards parallel G4s. The selective interaction toward parallel G4 topology, controlled by the presence of 2-(2-aminoethoxy)ethanol side chains, was already firmly demonstrated by us using core-extended NDIs. In the present study, the presence of protonable moieties and the copper(II) cavity, increases the binding affinity and specificity of these two NDIs for a telomeric RNA-G4. Once defined the copper coordination relationship and binding constants by competition titrations, ability in G4 stabilization, and ROS-induced cleavage were analyzed. The propensity in the stabilization of parallel topology was highlighted for both of the new compounds HP2Cu and PE2Cu. The results obtained are particularly promising, paving the way for the development of new selective functional ligands for binding and destructuring parallel G4s.
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26
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Substituent effects of cyclic naphthalene diimide on G-quadruplex binding and the inhibition of cancer cell growth. Bioorg Med Chem Lett 2021; 50:128323. [PMID: 34400300 DOI: 10.1016/j.bmcl.2021.128323] [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: 02/23/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 11/21/2022]
Abstract
Interaction of cyclic naphthalene diimide derivatives (cNDIs), 1-4, with TA-core and c-myc as G-quartet (G4) DNA was studied under dilute or molecular crowding condition. Binding study for TA-core based on an isothermal titration calorimetry showed that 1-4 has 106 M-1 order of binding affinity with the following order: 1 > 4 > 2 > 3 under both conditions. Meting temperature (Tm) of TA-core obtained from the temperature dependence of circular dichroism spectra shows that TA-core was most stabilized by 4, which is in agreement with the result of PCR stop assay and the stabilization effect for 1-3 was correlated with their binding affinity under dilute condition. 3 showed specific growth inhibition of cancer cell line Ca9-22 at <0.03 μM of IC50, with no inhibitory effect against normal bone marrow cells. 3, which has highest value of ΔH/ΔG, shows the highest inhibition ability for Ca9-22, carrying a highest expression level of telomerase mRNA.
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27
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Manoli F, Doria F, Colombo G, Zambelli B, Freccero M, Manet I. The Binding Pocket at the Interface of Multimeric Telomere G-quadruplexes: Myth or Reality? Chemistry 2021; 27:11707-11720. [PMID: 34152657 PMCID: PMC8456957 DOI: 10.1002/chem.202101486] [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: 04/26/2021] [Indexed: 01/23/2023]
Abstract
Human telomeric DNA with hundreds of repeats of the 5'-TTAGGG-3' motif plays a crucial role in several biological processes. It folds into G-quadruplex (G4) structures and features a pocket at the interface of two contiguous G4 blocks. Up to now no structural NMR and crystallographic data are available for ligands interacting with contiguous G4s. Naphthalene diimide monomers and dyads were investigated as ligands of a dimeric G4 of human telomeric DNA comparing the results with those of the model monomeric G4. Time-resolved fluorescence, circular dichroism, isothermal titration calorimetry and molecular modeling were used to elucidate binding features. Ligand fluorescence lifetime and induced circular dichroism unveiled occupancy of the binding site at the interface. Thermodynamic parameters confirmed the hypothesis as they remarkably change for the dyad complexes of the monomeric and dimeric telomeric G4. The bi-functional ligand structure of the dyads is a fundamental requisite for binding at the G4 interface as only the dyads engage in complexes with 1 : 1 stoichiometry, lodging in the pocket at the interface and establishing multiple interactions with the DNA skeleton. In the absence of NMR and crystallographic data, our study affords important proofs of binding at the interface pocket and clues on the role played by the ligand structure.
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Affiliation(s)
- Francesco Manoli
- Institute for Organic Synthesis and Photoreactivity (ISOF)National Research Council (CNR)Via P. Gobetti 10140129BolognaItaly
| | - Filippo Doria
- Department of ChemistryUniversity of PaviaV. le Taramelli 1027100PaviaItaly
| | - Giorgio Colombo
- Department of ChemistryUniversity of PaviaV. le Taramelli 1027100PaviaItaly
| | - Barbara Zambelli
- Department of Pharmacy and BiotechnologyUniversity of BolognaV. le Fanin 4040127BolognaItaly
| | - Mauro Freccero
- Department of ChemistryUniversity of PaviaV. le Taramelli 1027100PaviaItaly
| | - Ilse Manet
- Institute for Organic Synthesis and Photoreactivity (ISOF)National Research Council (CNR)Via P. Gobetti 10140129BolognaItaly
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28
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Bhosale SV, Al Kobaisi M, Jadhav RW, Morajkar PP, Jones LA, George S. Naphthalene diimides: perspectives and promise. Chem Soc Rev 2021; 50:9845-9998. [PMID: 34308940 DOI: 10.1039/d0cs00239a] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this review, we describe the developments in the field of naphthalene diimides (NDIs) from 2016 to the presentday. NDIs are shown to be an increasingly interesting class of molecules due to their electronic properties, large electron deficient aromatic cores and tendency to self-assemble into functional structures. Almost all NDIs possess high electron affinity, good charge carrier mobility, and excellent thermal and oxidative stability, making them promising candidates for applications in organic electronics, photovoltaic devices, and flexible displays. NDIs have also been extensively studied due to their potential real-world uses across a wide variety of applications including supramolecular chemistry, sensing, host-guest complexes for molecular switching devices, such as catenanes and rotaxanes, ion-channels, catalysis, and medicine and as non-fullerene accepters in solar cells. In recent years, NDI research with respect to supramolecular assemblies and mechanoluminescent properties has also gained considerable traction. Thus, this review will assist a wide range of readers and researchers including chemists, physicists, biologists, medicinal chemists and materials scientists in understanding the scope for development and applicability of NDI dyes in their respective fields through a discussion of the main properties of NDI derivatives and of the status of emerging applications.
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Affiliation(s)
- Sheshanath V Bhosale
- School of Chemical Sciences, Goa University, Taleigao Plateau, Goa-403 206, India.
| | - Mohammad Al Kobaisi
- Centre for Advanced Materials and Industrial Chemistry (CAMIC), School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Ratan W Jadhav
- School of Chemical Sciences, Goa University, Taleigao Plateau, Goa-403 206, India.
| | - Pranay P Morajkar
- School of Chemical Sciences, Goa University, Taleigao Plateau, Goa-403 206, India.
| | - Lathe A Jones
- Centre for Advanced Materials and Industrial Chemistry (CAMIC), School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Subi George
- New Chemistry Unit (NCU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur PO, Bangalore-560064, India
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29
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Yang M, Carter S, Parmar S, Bume DD, Calabrese DR, Liang X, Yazdani K, Xu M, Liu Z, Thiele CJ, Schneekloth JS. Targeting a noncanonical, hairpin-containing G-quadruplex structure from the MYCN gene. Nucleic Acids Res 2021; 49:7856-7869. [PMID: 34289065 DOI: 10.1093/nar/gkab594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/10/2021] [Accepted: 07/20/2021] [Indexed: 11/12/2022] Open
Abstract
The MYCN gene encodes the transcription factor N-Myc, a driver of neuroblastoma (NB). Targeting G-quadruplexes (G4s) with small molecules is attractive strategy to control the expression of undruggable proteins such as N-Myc. However, selective binders to G4s are challenging to identify due to the structural similarity of many G4s. Here, we report the discovery of a small molecule ligand (4) that targets the noncanonical, hairpin containing G4 structure found in the MYCN gene using small molecule microarrays (SMMs). Unlike many G4 binders, the compound was found to bind to a pocket at the base of the hairpin region of the MYCN G4. This compound stabilizes the G4 and has affinity of 3.5 ± 1.6 μM. Moreover, an improved analog, MY-8, suppressed levels of both MYCN and MYCNOS (a lncRNA embedded within the MYCN gene) in NBEB neuroblastoma cells. This work indicates that the approach of targeting complex, hybrid G4 structures that exist throughout the human genome may be an applicable strategy to achieve selectivity for targeting disease-relevant genes including protein coding (MYCN) as well as non-coding (MYCNOS) gene products.
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Affiliation(s)
- Mo Yang
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Sakereh Carter
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - Shaifaly Parmar
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Desta D Bume
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - David R Calabrese
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Xiao Liang
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Kamyar Yazdani
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Man Xu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - Zhihui Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - Carol J Thiele
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
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30
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Zhu Y, Li Z, Wang P, Qiu QM, Ma H, Li H. The Research of G-Motif Construction and Chirality in Deoxyguanosine Monophosphate Nucleotide Complexes. Front Chem 2021; 9:709777. [PMID: 34277575 PMCID: PMC8278404 DOI: 10.3389/fchem.2021.709777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
A detailed understanding of the mismatched base-pairing interactions in DNA will help reveal genetic diseases and provide a theoretical basis for the development of targeted drugs. Here, we utilized mononucleotide fragment to simulate mismatch DNA interactions in a local hydrophobic microenvironment. The bipyridyl-type bridging ligands were employed as a mild stabilizer to stabilize the GG mismatch containing complexes, allowing mismatch to be visualized based on X-ray crystallography. Five single crystals of 2′-deoxyguanosine–5′–monophosphate (dGMP) metal complexes were designed and obtained via the process of self-assembly. Crystallographic studies clearly reveal the details of the supramolecular interaction between mononucleotides and guest intercalators. A novel guanine–guanine base mismatch pattern with unusual (high anti)–(high anti) type of arrangement around the glycosidic angle conformations was successfully constructed. The solution state 1H–NMR, ESI–MS spectrum studies, and UV titration experiments emphasize the robustness of this g–motif in solution. Additionally, we combined the methods of single-crystal and solution-, solid-state CD spectrum together to discuss the chirality of the complexes. The complexes containing the g–motif structure, which reduces the energy of the system, following the solid-state CD signals, generally move in the long-wave direction. These results provided a new mismatched base pairing, that is g–motif. The interaction mode and full characterizations of g–motif will contribute to the study of the mismatched DNA interaction.
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Affiliation(s)
- Yanhong Zhu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Zhongkui Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Pengfei Wang
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Qi-Ming Qiu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Hongwei Ma
- Analytical and Testing Centre, Beijing Institute of Technology, Beijing, China
| | - Hui Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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31
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On the Road to Fight Cancer: The Potential of G-quadruplex Ligands as Novel Therapeutic Agents. Int J Mol Sci 2021; 22:ijms22115947. [PMID: 34073075 PMCID: PMC8198608 DOI: 10.3390/ijms22115947] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/14/2022] Open
Abstract
Nucleic acid sequences able to adopt a G-quadruplex conformation are overrepresented within the human genome. This evidence strongly suggests that these genomic regions have been evolutionary selected to play a pivotal role in several aspects of cell biology. In the present review article, we provide an overview on the biological impact of targeting G-quadruplexes in cancer. A variety of small molecules showing good G-quadruplex stabilizing properties has been reported to exert an antitumor activity in several preclinical models of human cancers. Moreover, promiscuous binders and multiple targeting G-quadruplex ligands, cancer cell defense responses and synthetic lethal interactions of G-quadruplex targeting have been also highlighted. Overall, evidence gathered thus far indicates that targeting G-quadruplex may represent an innovative and fascinating therapeutic approach for cancer. The continued methodological improvements, the development of specific tools and a careful consideration of the experimental settings in living systems will be useful to deepen our knowledge of G-quadruplex biology in cancer, to better define their role as therapeutic targets and to help design and develop novel and reliable G-quadruplex-based anticancer strategies.
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32
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Tikhomirov AS, Abdelhamid MAS, Nadysev GY, Zatonsky GV, Bykov EE, Chueh PJ, Waller ZAE, Shchekotikhin AE. Water-Soluble Heliomycin Derivatives to Target i-Motif DNA. JOURNAL OF NATURAL PRODUCTS 2021; 84:1617-1625. [PMID: 33974416 DOI: 10.1021/acs.jnatprod.1c00162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Heliomycin (also known as resistomycin) is an antibiotic with a broad spectrum of biological activities. However, low aqueous solubility and poor knowledge of its chemical properties have limited the development of this natural product. Here, we present an original scheme for the introduction of aminoalkylamine residues at positions 3, 5, and 7 of heliomycin and, using this, have prepared a series of novel water-soluble derivatives. The addition of side chains to the heliomycin scaffold significantly improves their interaction with different DNA secondary structures. One derivative, 7-deoxy-7-(2-aminoethyl)amino-10-O-methylheliomycin (8e), demonstrated affinity, stabilization potential, and good selectivity toward i-motif-forming DNA sequences over the duplex and G-quadruplex. Heliomycin derivatives therefore represent promising molecular scaffolds for further development as DNA-i-motif interacting ligands and potential chemotherapeutic agents.
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Affiliation(s)
- Alexander S Tikhomirov
- Laboratory of Chemical Transformation of Antibiotics, Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow 119021, Russia
| | | | - Georgy Y Nadysev
- Laboratory of Chemical Transformation of Antibiotics, Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow 119021, Russia
| | - George V Zatonsky
- Laboratory of Chemical Transformation of Antibiotics, Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow 119021, Russia
| | - Eugene E Bykov
- Laboratory of Chemical Transformation of Antibiotics, Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow 119021, Russia
| | - Pin Ju Chueh
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Zoë A E Waller
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Andrey E Shchekotikhin
- Laboratory of Chemical Transformation of Antibiotics, Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow 119021, Russia
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33
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Street STG, Peñalver P, O'Hagan MP, Hollingworth GJ, Morales JC, Galan MC. Imide Condensation as a Strategy for the Synthesis of Core-Diversified G-Quadruplex Ligands with Anticancer and Antiparasitic Activity*. Chemistry 2021; 27:7712-7721. [PMID: 33780044 PMCID: PMC8251916 DOI: 10.1002/chem.202100040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Indexed: 11/22/2022]
Abstract
A facile imide coupling strategy for the one-step preparation of G-quadruplex ligands with varied core chemistries is described. The G-quadruplex stabilization of a library of nine compounds was examined using FRET melting experiments, and CD, UV-Vis, fluorescence and NMR titrations, identifying several compounds that were capable of stabilizing G-quadruplex DNA with interesting selectivity profiles. The best G4 ligand was identified as compound 3, which was based on a perylene scaffold and exhibited 40-fold selectivity for a telomeric G-quadruplex over duplex DNA. Surprisingly, a tetra-substituted flexible core, compound 11, also exhibited selective stabilization of G4 DNA over duplex DNA. The anticancer and antiparasitic activity of the library was also examined, with the lead compound 3 exhibiting nanomolar inhibition of Trypanosoma brucei with 78-fold selectivity over MRC5 cells. The cellular localization of this compound was also studied via fluorescence microscopy. We found that uptake was time dependant, with localization outside the nucleus and kinetoplast that could be due to strong fluorescence quenching in the presence of small amounts of DNA.
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Affiliation(s)
- Steven T. G. Street
- School of ChemistryUniversity of BristolCantocks CloseBristolBS8 1TSUK
- Department of ChemistryUniversity of VictoriaDr. S. T. G. StreetVictoriaBC V8P 5C2Canada
| | - Pablo Peñalver
- Instituto de Parasitología y Biomedicina López NeyraCSIC, PTS GranadaAvenida del Conocimiento, 1718016Armilla, GranadaSpain
| | | | | | - Juan C. Morales
- Instituto de Parasitología y Biomedicina López NeyraCSIC, PTS GranadaAvenida del Conocimiento, 1718016Armilla, GranadaSpain
| | - M. Carmen Galan
- School of ChemistryUniversity of BristolCantocks CloseBristolBS8 1TSUK
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34
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Platella C, Napolitano E, Riccardi C, Musumeci D, Montesarchio D. Disentangling the Structure-Activity Relationships of Naphthalene Diimides as Anticancer G-Quadruplex-Targeting Drugs. J Med Chem 2021; 64:3578-3603. [PMID: 33751881 PMCID: PMC8041303 DOI: 10.1021/acs.jmedchem.1c00125] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
In the context of
developing efficient anticancer therapies aimed
at eradicating any sort of tumors, G-quadruplexes represent excellent
targets. Small molecules able to interact with G-quadruplexes can
interfere with cell pathways specific of tumors and common to all
cancers. Naphthalene diimides
(NDIs) are among the most promising, putative anticancer G-quadruplex-targeting
drugs, due to their ability to simultaneously target multiple G-quadruplexes
and their strong, selective in vitro and in vivo anticancer activity.
Here, all the available biophysical, biological, and structural data
concerning NDIs targeting G-quadruplexes were systematically analyzed.
Structure–activity correlations were obtained by analyzing
biophysical data of their interactions with G-quadruplex targets and
control duplex structures, in parallel to biological data concerning
the antiproliferative activity of NDIs on cancer and normal cells.
In addition, NDI binding modes to G-quadruplexes were discussed in
consideration of the structures and properties of NDIs by in-depth
analysis of the available structural models of G-quadruplex/NDI complexes.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.,Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
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35
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Malik MS, Farooq Adil S, Moussa Z, Altass HM, Althagafi II, Morad M, Ansari MA, Sajid Jamal QM, Obaid RJ, Al-Warthan AA, Shaik TB, Ahmed SA. Rational Design and Synthesis of Naphthalene Diimide Linked Bis-Naphthalimides as DNA Interactive Agents. Front Chem 2021; 9:630357. [PMID: 33777897 PMCID: PMC7988716 DOI: 10.3389/fchem.2021.630357] [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: 11/17/2020] [Accepted: 01/07/2021] [Indexed: 01/23/2023] Open
Abstract
A molecular modeling assisted rational design and synthesis of naphthalene diimide linked bis-naphthalimides as potential DNA interactive agents is described. Chemical templates incorporating naphthalene diimide as a linker in bis-naphthalimide motif were subjected to molecular docking analysis at specific intercalation and telomeric DNA G-quadruplex sites. Excellent results were obtained, which were better than the standards. A short and convenient synthetic route was employed to access these hybrids experimentally, followed by evaluation of their ability to cause thermal denaturation of DNA and cytotoxic properties along with ADME predictions. The obtained results provided useful insights and two potential molecules were identified for further development.
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Affiliation(s)
- M Shaheer Malik
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Syed Farooq Adil
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ziad Moussa
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Hatem M Altass
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ismail I Althagafi
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Moataz Morad
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research & Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
| | - Rami J Obaid
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Thokhir B Shaik
- Research on Advanced BioMedical Solutions Pvt Ltd, KPHB, Hyderabad, 500071, India
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia.,Department of Chemistry, Faculty of Science, Assiut University, 71516, Assiut, Egypt.,Research Laboratories Unit, Faculty of Applied Science, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
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36
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Abstract
G-quardruplex (G4) DNA forms through the gathering together of G-quartet planes formed with four guanine (G) bases. G4 DNA stabilizes with potassium ions (K+) by coordination with the G-quartet center. Fluorometric G4 DNA carrying the fluorescence resonance energy transfer (FRET) chromophore pair at both termini has been applied for the fluorometric sensing or imaging of K+ under a homogeneous aqueous medium. This system has realized non-conventional K+ selectivity over the sodium ion (Na+). The selectivity of the fluorescence G4 was converted to Na+ from K+ with a modification of its sequence. On the other hand, G4 DNA detection has been achieved in terms of cancer diagnosis because of a strong relationship of G4 DNA and cancer development. Ligands interacting with G4 are expected to have anti-cancer potential. In addition, fluorometric G4 ligands have been developed and tested as tools for the dynamic monitoring of G4 in living cells. Moreover, fluorometric G4 DNA has been utilized to evaluate the G4 ligand performance.
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Affiliation(s)
- Shigeori Takenaka
- Department of Applied Chemistry, Kyushu Institute of Technology, Kitakyushu, 804-8550, Japan
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37
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Andreeva DV, Tikhomirov AS, Shchekotikhin AE. Ligands of G-quadruplex nucleic acids. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4968] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Platella C, Trajkovski M, Doria F, Freccero M, Plavec J, Montesarchio D. On the interaction of an anticancer trisubstituted naphthalene diimide with G-quadruplexes of different topologies: a structural insight. Nucleic Acids Res 2020; 48:12380-12393. [PMID: 33170272 PMCID: PMC7708068 DOI: 10.1093/nar/gkaa1001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/29/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Naphthalene diimides showed significant anticancer activity in animal models, with therapeutic potential related to their ability to strongly interact with G-quadruplexes. Recently, a trifunctionalized naphthalene diimide, named NDI-5, was identified as the best analogue of a mini-library of novel naphthalene diimides for its high G-quadruplex binding affinity along with marked, selective anticancer activity, emerging as promising candidate drug for in vivo studies. Here we used NMR, dynamic light scattering, circular dichroism and fluorescence analyses to investigate the interactions of NDI-5 with G-quadruplexes featuring either parallel or hybrid topology. Interplay of different binding modes of NDI-5 to G-quadruplexes was observed for both parallel and hybrid topologies, with end-stacking always operative as the predominant binding event. While NDI-5 primarily targets the 5'-end quartet of the hybrid G-quadruplex model (m-tel24), the binding to a parallel G-quadruplex model (M2) occurs seemingly simultaneously at the 5'- and 3'-end quartets. With parallel G-quadruplex M2, NDI-5 formed stable complexes with 1:3 DNA:ligand binding stoichiometry. Conversely, when interacting with hybrid G-quadruplex m-tel24, NDI-5 showed multiple binding poses on a single G-quadruplex unit and/or formed different complexes comprising two or more G-quadruplex units. NDI-5 produced stabilizing effects on both G-quadruplexes, forming complexes with dissociation constants in the nM range.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Filippo Doria
- Department of Chemistry, University of Pavia, Viale Taramelli 10, I-27100 Pavia, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, Viale Taramelli 10, I-27100 Pavia, Italy
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
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39
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Ahmed AA, Neidle S. A G-Quadruplex-Binding Small Molecule and the HDAC Inhibitor SAHA (Vorinostat) Act Synergistically in Gemcitabine-Sensitive and Resistant Pancreatic Cancer Cells. Molecules 2020; 25:molecules25225407. [PMID: 33227941 PMCID: PMC7699281 DOI: 10.3390/molecules25225407] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
The stabilisation of G-quadruplexes (G4s) by small-molecule compounds is an effective approach for causing cell growth arrest, followed by cell death. Some of these compounds are currently being developed for the treatment of human cancers. We have previously developed a substituted naphthalene diimide G4-binding molecule (CM03) with selective potency for pancreatic cancer cells, including gemcitabine-resistant cells. We report here that CM03 and the histone deacetylase (HDAC) inhibitor SAHA (suberanilohydroxamic acid) have synergistic effects at concentrations close to and below their individual GI50 values, in both gemcitabine-sensitive and resistant pancreatic cancer cell lines. Immunoblot analysis showed elevated levels of γ-H2AX and cleaved PARP proteins upon drug combination treatment, indicating increased levels of DNA damage (double-strand break events: DSBs) and apoptosis induction, respectively. We propose that the mechanism of synergy involves SAHA relaxing condensed chromatin, resulting in higher levels of G4 formation. In turn, CM03 can stabilise a greater number of G4s, leading to the downregulation of more G4-containing genes as well as a higher incidence of DSBs due to torsional strain on DNA and chromatin structure.
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40
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Hao X, Wang C, Wang Y, Li C, Hou J, Zhang F, Kang C, Gao L. Topological conversion of human telomeric G-quadruplexes from hybrid to parallel form induced by naphthalene diimide ligands. Int J Biol Macromol 2020; 167:1048-1058. [PMID: 33188810 DOI: 10.1016/j.ijbiomac.2020.11.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 12/17/2022]
Abstract
G-quadruplexes (GQs) have become promising anti-cancer therapeutic targets, which are formed by the folding of a guanine-rich repeat DNA/RNA sequence at human telomeres or oncogene promoters. Polymorphism has been observed for the folding topologies of intramolecular GQs. Here we report the topological conversion of human telomeric GQ induced by naphthalene diimide (NDI) ligands in K+ solution. The ligands selectively induce metastable hybrid-type GQs to highly stable parallel-type GQ at physiological temperature (37 °C) in dilute aqueous solutions and under crowding conditions that mimic cellular bioenvironment. According to spectroscopic analyses, the topological conversion is speculated to undergo stepwise unfolding of hybrid-type GQ through intermediate states to parallel-type GQ. The results will prompt further studies on the designs of ligands with GQ conformation regulation functions and nanotechnological systems based on nucleic acids with dynamic regulation of GQ conformation.
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Affiliation(s)
- Xueyu Hao
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; University of Science and Technology of China, Hefei 230026, China
| | - Chunyu Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Yu Wang
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; University of Science and Technology of China, Hefei 230026, China
| | - Chunjie Li
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jingwei Hou
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Feng Zhang
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Chuanqing Kang
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; University of Science and Technology of China, Hefei 230026, China.
| | - Lianxun Gao
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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Pirota V, Platella C, Musumeci D, Benassi A, Amato J, Pagano B, Colombo G, Freccero M, Doria F, Montesarchio D. On the binding of naphthalene diimides to a human telomeric G-quadruplex multimer model. Int J Biol Macromol 2020; 166:1320-1334. [PMID: 33166559 DOI: 10.1016/j.ijbiomac.2020.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023]
Abstract
To selectively target telomeric G-quadruplex (G4) DNA, monomeric and dimeric naphthalene diimides (NDIs) were investigated as binders of multimeric G4 structures able to discriminate duplex DNA. These NDIs were analysed by the affinity chromatography-based screening G4-CPG (G-quadruplex on Controlled Pore Glass), using the sequence d[AGGG(TTAGGG)7] (tel46), folding into two consecutive G4s, as model of the human telomeric G4 multimer. In parallel, a telomeric G4 monomer (tel26) and a duplex structure (ds27) were used as controls. According to G4-CPG screening, NDI-5 proved to be the best ligand in terms of dimeric G4 vs. duplex DNA selectivity and was analysed by circular dichroism (CD), gel electrophoresis, isothermal titration calorimetry (ITC) and fluorescence spectroscopy in its interactions with tel46. NDI-5 strongly binds and stabilizes tel46 G4, favouring a hybrid folding in K+-containing buffer. Under these conditions, the binding process comprises a first event involving three molecules of NDI-5 and a second one in which other six molecules bind to the DNA. In a metal cation-free system, NDI-5 induces tel46 G4 folding, as indicated by CD and PAGE, favouring an antiparallel structuring. Docking simulations showed that NDI-5 can effectively bind to the pocket between two G4 units, representing a promising ligand for multimeric G4s.
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Affiliation(s)
- Valentina Pirota
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | | | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy.
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43
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Tassinari M, Zuffo M, Nadai M, Pirota V, Sevilla Montalvo AC, Doria F, Freccero M, Richter SN. Selective targeting of mutually exclusive DNA G-quadruplexes: HIV-1 LTR as paradigmatic model. Nucleic Acids Res 2020; 48:4627-4642. [PMID: 32282912 PMCID: PMC7229848 DOI: 10.1093/nar/gkaa186] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 02/28/2020] [Accepted: 03/11/2020] [Indexed: 02/06/2023] Open
Abstract
Targeting of G-quadruplexes, non-canonical conformations that form in G-rich regions of nucleic acids, has been proposed as a novel therapeutic strategy toward several diseases, including cancer and infections. The unavailability of highly selective molecules targeting a G-quadruplex of choice has hampered relevant applications. Herein, we describe a novel approach, based on naphthalene diimide (NDI)-peptide nucleic acid (PNA) conjugates, taking advantage of the cooperative interaction of the NDI with the G-quadruplex structure and hybridization of the PNA with the flanking region upstream or downstream the targeted G-quadruplex. By biophysical and biomolecular assays, we show that the NDI-PNA conjugates are able to specifically recognize the G-quadruplex of choice within the HIV-1 LTR region, consisting of overlapping and therefore mutually exclusive G-quadruplexes. Additionally, the conjugates can induce and stabilize the least populated G-quadruplex at the expenses of the more stable ones. The general and straightforward design and synthesis, which readily apply to any G4 target of choice, together with both the red-fluorescent emission and the possibility to introduce cellular localization signals, make the novel conjugates available to selectively control G-quadruplex folding over a wide range of applications.
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Affiliation(s)
- Martina Tassinari
- Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy
| | - Michela Zuffo
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100, Pavia, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy
| | - Valentina Pirota
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100, Pavia, Italy
| | | | - Filippo Doria
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100, Pavia, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100, Pavia, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy
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Ahmed A, Angell R, Oxenford S, Worthington J, Williams N, Barton N, Fowler TG, O’Flynn DE, Sunose M, McConville M, Vo T, Wilson WD, Karim SA, Morton JP, Neidle S. Asymmetrically Substituted Quadruplex-Binding Naphthalene Diimide Showing Potent Activity in Pancreatic Cancer Models. ACS Med Chem Lett 2020; 11:1634-1644. [PMID: 32832034 PMCID: PMC7429975 DOI: 10.1021/acsmedchemlett.0c00317] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
Targeting of genomic quadruplexes is an approach to treating complex human cancers. We describe a series of tetra-substituted naphthalene diimide (ND) derivatives with a phenyl substituent directly attached to the ND core. The lead compound (SOP1812) has 10 times superior cellular and in vivo activity compared with previous ND compounds and nanomolar binding to human quadruplexes. The pharmacological properties of SOP1812 indicate good bioavailability, which is consistent with the in vivo activity in xenograft and genetic models for pancreatic cancer. Transcriptome analysis shows that it down-regulates several cancer gene pathways, including Wnt/β-catenin signaling.
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Affiliation(s)
- Ahmed
A. Ahmed
- School
of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Richard Angell
- School
of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Sally Oxenford
- School
of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Jenny Worthington
- Axis
Bio Discovery Services, Ltd., Coleraine, Northern Ireland BT51 3RP, United Kingdom
| | - Nicole Williams
- Axis
Bio Discovery Services, Ltd., Coleraine, Northern Ireland BT51 3RP, United Kingdom
| | - Naomi Barton
- Sygnature
Discovery Limited, Nottingham NG1 1GR, United Kingdom
| | | | | | - Mihiro Sunose
- Sygnature
Discovery Limited, Nottingham NG1 1GR, United Kingdom
| | | | - Tam Vo
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - W. David Wilson
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Saadia A. Karim
- Cancer
Research UK Beatson Institute, Glasgow G61 1BD, United
Kingdom
| | - Jennifer P. Morton
- Cancer
Research UK Beatson Institute, Glasgow G61 1BD, United
Kingdom
- Institute
of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Stephen Neidle
- School
of Pharmacy, University College London, London WC1N 1AX, United Kingdom
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45
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Heterocyclic analogs of 5,12-naphthacenequinone 16*. Synthesis and properties of new DNA ligands based on 4,11-diaminoanthra[2,3-b]thiophene-5,10-dione. Chem Heterocycl Compd (N Y) 2020. [DOI: 10.1007/s10593-020-02723-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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46
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Vo T, Oxenford S, Angell R, Marchetti C, Ohnmacht SA, Wilson WD, Neidle S. Substituted Naphthalenediimide Compounds Bind Selectively to Two Human Quadruplex Structures with Parallel Topology. ACS Med Chem Lett 2020; 11:991-999. [PMID: 32435416 PMCID: PMC7236248 DOI: 10.1021/acsmedchemlett.0c00041] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/30/2020] [Indexed: 11/28/2022] Open
Abstract
Interactions are reported of three representative naphthalenediimide derivatives with three quadruplex targets, from the promoter region of the telomerase (hTERT) gene, a human telomeric DNA quadruplex, and a telomeric RNA quadruplex (TERRA). Thermal melting studies showed that these compounds strongly stabilize the quadruplexes, with weak stabilization of a duplex DNA. Binding studies by surface plasmon resonance and fluorescence spectroscopy found that the compounds bind to the quadruplexes with nanomolar equilibrium dissociation constants. Plausible topologies for the quadruplex complexes were deduced from CD spectra, which together with the surface plasmon resonance data indicate that the quadruplexes with parallel quadruplex folds are preferred by two compounds, which was confirmed by qualitative molecular modeling.
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Affiliation(s)
- Tam Vo
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Sally Oxenford
- UCL
School of Pharmacy, University College London, London WC1N 1AX, U.K.
| | - Richard Angell
- UCL
School of Pharmacy, University College London, London WC1N 1AX, U.K.
| | - Chiara Marchetti
- UCL
School of Pharmacy, University College London, London WC1N 1AX, U.K.
| | | | - W. David Wilson
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- Center
for Diagnostics and Therapeutics, Georgia
State University, Atlanta, Georgia 30303, United States
| | - Stephen Neidle
- UCL
School of Pharmacy, University College London, London WC1N 1AX, U.K.
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47
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Trifunctionalized Naphthalene Diimides and Dimeric Analogues as G-Quadruplex-Targeting Anticancer Agents Selected by Affinity Chromatography. Int J Mol Sci 2020; 21:ijms21061964. [PMID: 32183038 PMCID: PMC7139804 DOI: 10.3390/ijms21061964] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/14/2022] Open
Abstract
A focused library of newly designed monomeric and dimeric naphthalene diimides (NDIs) was analyzed in its ability to recognize specific G-quadruplex (G4) structures discriminating duplex DNA. The best G4 ligands—according to an affinity chromatography-based screening method named G4-CPG—were tested on human cancer and healthy cells, inducing DNA damage at telomeres, and in parallel, showing selective antiproliferative activity on HeLa cancer cells with IC50 values in the low nanomolar range. CD and fluorescence spectroscopy studies allowed detailed investigation of the interaction in solution with different G4 and duplex DNA models of the most promising NDI of the series, as determined by combining the biophysical and biological assays’ data.
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48
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49
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Kaneyoshi S, Zou T, Ozaki S, Takeuchi R, Udou A, Nakahara T, Fujimoto K, Fujii S, Sato S, Takenaka S. Cyclic Naphthalene Diimide with a Ferrocene Moiety as a Redox-Active Tetraplex-DNA Ligand. Chemistry 2019; 26:139-142. [PMID: 31680317 DOI: 10.1002/chem.201903883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/27/2019] [Indexed: 12/31/2022]
Abstract
Cyclic naphthalene diimides (cNDIs), with a ferrocene moiety (cFNDs) and different linker lengths between the ferrocene and cNDI moieties, were designed and synthesized as redox-active, tetraplex-DNA ligands. Intramolecular stacking was observed between ferrocene and the NDI planes, which could affect the binding properties for G-quadruplexes. Interestingly, the circular dichroism spectrum of one of these compounds clearly shows new Cotton effects around 320-380 and 240 nm, which can be considered a direct evidence of intramolecular stacking of ferrocene and the NDI. Regarding recognition of hybrid G-quadruplexes, the less rigid structures (longer linkers) show higher binding affinity (106 m-1 order of magnitude). All new compounds show higher selectivity for G4 during electrochemical detection than noncyclic FND derivatives, which further identifies the redox-active potentiality of the cFNDs. Two of the three compounds tested even show preferential inhibition of cell growth in cancer cells over normal cells in a low concentration range, highlighting the potential for bioapplications of these cFNDs.
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Affiliation(s)
- Shuma Kaneyoshi
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| | - Tingting Zou
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan.,Research Center for Bio-microsensing Technology, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| | - Shunsuke Ozaki
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| | - Ryusuke Takeuchi
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| | - Ayano Udou
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| | - Takumi Nakahara
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| | - Kazuhisa Fujimoto
- Department of Applied Chemistry and Biochemistry, Kyushu Sangyo University, Fukuoka, 813-8503, Japan
| | - Satoshi Fujii
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, 820-8502, Japan
| | - Shinobu Sato
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan.,Research Center for Bio-microsensing Technology, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| | - Shigeori Takenaka
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan.,Research Center for Bio-microsensing Technology, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
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50
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Recagni M, Tassinari M, Doria F, Cimino-Reale G, Zaffaroni N, Freccero M, Folini M, Richter SN. The Oncogenic Signaling Pathways in BRAF-Mutant Melanoma Cells are Modulated by Naphthalene Diimide-Like G-Quadruplex Ligands. Cells 2019; 8:cells8101274. [PMID: 31635389 PMCID: PMC6830342 DOI: 10.3390/cells8101274] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/27/2019] [Accepted: 10/16/2019] [Indexed: 01/12/2023] Open
Abstract
Melanoma is the most aggressive and deadly type of skin cancer. Despite the advent of targeted therapies directed against specific oncogene mutations, melanoma remains a tumor that is very difficult to treat, and ultimately remains incurable. In the past two decades, stabilization of the non-canonical nucleic acid G-quadruplex structures within oncogene promoters has stood out as a promising approach to interfere with oncogenic signaling pathways in cancer cells, paving the way toward the development of G-quadruplex ligands as antitumor drugs. Here, we present the synthesis and screening of a library of differently functionalized core-extended naphthalene diimides for their activity against the BRAFV600E-mutant melanoma cell line. The most promising compound was able to stabilize G-quadruplexes that formed in the promoter regions of two target genes relevant to melanoma, KIT and BCL-2. This activity led to the suppression of protein expression and thus to interference with oncogenic signaling pathways involved in BRAF-mutant melanoma cell survival, apoptosis, and resistance to drugs. This G-quadruplex ligand thus represents a suitable candidate for the development of melanoma treatment options based on a new mechanism of action and could reveal particular significance in the context of resistance to targeted therapies of BRAF-mutant melanoma cells.
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Affiliation(s)
- Marta Recagni
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy.
| | - Martina Tassinari
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy.
| | - Filippo Doria
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100 Pavia, Italy.
| | - Graziella Cimino-Reale
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy.
| | - Nadia Zaffaroni
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy.
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100 Pavia, Italy.
| | - Marco Folini
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy.
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy.
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