1
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Ghosal S, Bag S, Chinnadurai RK, Mukherjee M, Pramanik G, Bhowmik S. Investigating the preferential interaction between imatinib mesylate and VEGF G-quadruplex DNA as therapeutic strategies for cancer treatment: Biophysical and molecular modelling approaches. Comput Biol Med 2024; 177:108683. [PMID: 38838555 DOI: 10.1016/j.compbiomed.2024.108683] [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: 01/04/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
G-Quadruplex DNA (GQ-DNA) is one of the most important non-canonical nucleic acid structures. GQ-DNA forming sequences are present in different crucial genomic regions and are abundant in promoter regions of several oncogenes. Therefore, GQ-DNA is an important target for anticancer drugs and hence binding interactions between GQ-DNA and small molecule ligands are of great importance. Since GQ-DNA is a highly polymorphic structure, it is important to identify ligand molecules which preferentially target a particular quadruplex sequence. In this present study, we have used a FDA approved drug called imatinib mesylate (ligand) which is a selective tyrosine kinase inhibitor, successfully used for the treatment of chronic myelogenous leukaemia, gastrointestinal stromal tumours. Different spectroscopic techniques as well as molecular docking investigations and molecular simulations have been used to explore the interaction between imatinib mesylate with VEGF GQ DNA structures along with duplex DNA, C-Myc, H-Telo GQ DNA. We found that imatinib mesylate shows preferential interaction towards VEGF GQ DNA compared to C-Myc, H-Telo GQ and duplex DNA. Imatinib mesylate seems to be an efficient ligand for VEGF GQ DNA, suggesting that it might be used to regulate the expression of genes in cancerous cells.
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Affiliation(s)
- Souvik Ghosal
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillaiyarkuppam, Pondicherry, 607402, India
| | - Sagar Bag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India
| | - Raj Kumar Chinnadurai
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillaiyarkuppam, Pondicherry, 607402, India
| | - Moupriya Mukherjee
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata, 700 106, India
| | - Goutam Pramanik
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata, 700 106, India
| | - Sudipta Bhowmik
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillaiyarkuppam, Pondicherry, 607402, India; Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India.
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2
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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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3
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Romano F, Di Porzio A, Iaccarino N, Riccardi G, Di Lorenzo R, Laneri S, Pagano B, Amato J, Randazzo A. G-quadruplexes in cancer-related gene promoters: from identification to therapeutic targeting. Expert Opin Ther Pat 2023; 33:745-773. [PMID: 37855085 DOI: 10.1080/13543776.2023.2271168] [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: 06/26/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
INTRODUCTION Guanine-rich DNA sequences can fold into four-stranded noncanonical secondary structures called G-quadruplexes (G4s) which are widely distributed in functional regions of the human genome, such as telomeres and gene promoter regions. Compelling evidence suggests their involvement in key genome functions such as gene expression and genome stability. Notably, the abundance of G4-forming sequences near transcription start sites suggests their potential involvement in regulating oncogenes. AREAS COVERED This review provides an overview of current knowledge on G4s in human oncogene promoters. The most representative G4-binding ligands have also been documented. The objective of this work is to present a comprehensive overview of the most promising targets for the development of novel and highly specific anticancer drugs capable of selectively impacting the expression of individual or a limited number of genes. EXPERT OPINION Modulation of G4 formation by specific ligands has been proposed as a powerful new tool to treat cancer through the control of oncogene expression. Actually, most of G4-binding small molecules seem to simultaneously target a range of gene promoter G4s, potentially influencing several critical driver genes in cancer, thus producing significant therapeutic benefits.
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Affiliation(s)
- Francesca Romano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Anna Di Porzio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | | | | | - Sonia Laneri
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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4
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Han ZQ, Wen LN. Application of G-quadruplex targets in gastrointestinal cancers: Advancements, challenges and prospects. World J Gastrointest Oncol 2023; 15:1149-1173. [PMID: 37546556 PMCID: PMC10401460 DOI: 10.4251/wjgo.v15.i7.1149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/11/2023] [Accepted: 05/08/2023] [Indexed: 07/12/2023] Open
Abstract
Genomic instability and inflammation are considered to be two enabling characteristics that support cancer development and progression. G-quadruplex structure is a key element that contributes to genomic instability and inflammation. G-quadruplexes were once regarded as simply an obstacle that can block the transcription of oncogenes. A ligand targeting G-quadruplexes was found to have anticancer activity, making G-quadruplexes potential anticancer targets. However, further investigation has revealed that G-quadruplexes are widely distributed throughout the human genome and have many functions, such as regulating DNA replication, DNA repair, transcription, translation, epigenetics, and inflammatory response. G-quadruplexes play double regulatory roles in transcription and translation. In this review, we focus on G-quadruplexes as novel targets for the treatment of gastrointestinal cancers. We summarize the application basis of G-quadruplexes in gastrointestinal cancers, including their distribution sites, structural characteristics, and physiological functions. We describe the current status of applications for the treatment of esophageal cancer, pancreatic cancer, hepatocellular carcinoma, gastric cancer, colorectal cancer, and gastrointestinal stromal tumors, as well as the associated challenges. Finally, we review the prospective clinical applications of G-quadruplex targets, providing references for targeted treatment strategies in gastrointestinal cancers.
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Affiliation(s)
- Zong-Qiang Han
- Department of Laboratory Medicine, Beijing Xiaotangshan Hospital, Beijing 102211, China
| | - Li-Na Wen
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
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5
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Synthesis and evaluation of 2,9-disubstituted-1,10-phenanthroline derivatives as G-quadruplex binders. Bioorg Med Chem 2022; 73:116971. [DOI: 10.1016/j.bmc.2022.116971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/14/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022]
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6
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Bachurin SS, Kletskii ME, Burov ON, Bibov MY, Dobaeva NM, Berezovskiy DP. Oligonucleotides-transformers for molecular biology and nanoengineering. Gene X 2022; 820:146277. [PMID: 35149154 DOI: 10.1016/j.gene.2022.146277] [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: 08/02/2021] [Revised: 01/14/2022] [Accepted: 02/03/2022] [Indexed: 11/04/2022] Open
Abstract
In the present review, numerous experimental and theoretical data describing the properties of non-canonical DNA structures (NSs) are analyzed. NSs (G-quadruplex, i-motif, hairpin, and triplex) play an important role in epigenetic processes (including the genetic variability of viruses), are prone to energetically low-cost conformational transformations and can very effectively be used in the design of nanoscale devices. Numerous experimental data have been analyzed in connection with the so-called oligonucleotides-transformers (nucleotide sequences that able to fold not only into one, but also into several NSs). These sequences were recently predicted by our calculations using automata and graph theories ("Dafna" algorithm). Possible applications of the oligonucleotides-transformers in nanoengineering and genetic editing of organisms are considered.
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Affiliation(s)
- Stanislav S Bachurin
- Rostov State Medical University, 29 Nakhichevanskiy Lane, Rostov-on-Don 344022, Russian Federation.
| | - Mikhail E Kletskii
- Chemical Department of Southern Federal University, 7 Zorge Str, Rostov-on-Don 344090, Russian Federation
| | - Oleg N Burov
- Chemical Department of Southern Federal University, 7 Zorge Str, Rostov-on-Don 344090, Russian Federation
| | - Mikhail Yu Bibov
- Rostov State Medical University, 29 Nakhichevanskiy Lane, Rostov-on-Don 344022, Russian Federation
| | - Natalya M Dobaeva
- Rostov State Medical University, 29 Nakhichevanskiy Lane, Rostov-on-Don 344022, Russian Federation
| | - Dmitriy P Berezovskiy
- I.M. Sechenov First Moscow State Medical University (Sechenov University), build. 4, 2 Bolshaya Pirogovskaya Str, Moscow 119435, Russian Federation
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7
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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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8
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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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9
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Sanchez-Martin V, Soriano M, Garcia-Salcedo JA. Quadruplex Ligands in Cancer Therapy. Cancers (Basel) 2021; 13:3156. [PMID: 34202648 PMCID: PMC8267697 DOI: 10.3390/cancers13133156] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/18/2021] [Accepted: 06/20/2021] [Indexed: 02/07/2023] Open
Abstract
Nucleic acids can adopt alternative secondary conformations including four-stranded structures known as quadruplexes. To date, quadruplexes have been demonstrated to exist both in human chromatin DNA and RNA. In particular, quadruplexes are found in guanine-rich sequences constituting G-quadruplexes, and in cytosine-rich sequences forming i-Motifs as a counterpart. Quadruplexes are associated with key biological processes ranging from transcription and translation of several oncogenes and tumor suppressors to telomeres maintenance and genome instability. In this context, quadruplexes have prompted investigations on their possible role in cancer biology and the evaluation of small-molecule ligands as potential therapeutic agents. This review aims to provide an updated close-up view of the literature on quadruplex ligands in cancer therapy, by grouping together ligands for DNA and RNA G-quadruplexes and DNA i-Motifs.
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Affiliation(s)
- Victoria Sanchez-Martin
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Microbiology Unit, Biosanitary Research Institute IBS, University Hospital Virgen de las Nieves, 18014 Granada, Spain
- Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, 18016 Granada, Spain
| | - Miguel Soriano
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Centre for Intensive Mediterranean Agrosystems and Agri-Food Biotechnology (CIAMBITAL), University of Almeria, 04001 Almeria, Spain
| | - Jose Antonio Garcia-Salcedo
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Microbiology Unit, Biosanitary Research Institute IBS, University Hospital Virgen de las Nieves, 18014 Granada, Spain
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10
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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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11
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Gong YP, Yang J, Fang JW, Li Q, Yu ZY, Guan A, Gong HY. A DNA small molecular probe with increasing K + concentration promoted selectivity. RSC Adv 2021; 11:15030-15035. [PMID: 35424063 PMCID: PMC8697834 DOI: 10.1039/d0ra06274j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 03/28/2021] [Indexed: 11/21/2022] Open
Abstract
DNA small molecular probe study was considered as a promising approach to achieve DNA related disease diagnosis. Most related reports were performed under specific salinity. Herein, 4-imino-3-(pyridin-2-yl)-4H-quinolizine-1-carbonitrile (IPQC) was generated via a facile procedure with high yield (85%). It is found that IPQC could act as a universal probe for most tested ssDNA, dsDNA and G4 DNA in low [K+] concentration (less than 20 mM). However, IPQC showed highly selective G4 DNA binding via UV-vis and fluorescence response in increasing [K+] (e.g., 150 mM) conditions. The ion atmosphere effects are instructive for DNA probe exploration. This provides guidance for the design, selection and optimization of the probes for target DNA sensing. DNA small molecular probe study was considered as a promising approach to achieve DNA related disease diagnosis.![]()
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Affiliation(s)
- Ya-Ping Gong
- Department of Chemistry
- Renmin University of China
- Beijing
- P. R. China
- Institute of Chemistry
| | - Jian Yang
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
| | - Ji-Wang Fang
- Department of Chemistry
- Renmin University of China
- Beijing
- P. R. China
- College of Chemistry
| | - Qian Li
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Zhi-Yong Yu
- Department of Chemistry
- Renmin University of China
- Beijing
- P. R. China
| | - Aijiao Guan
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Han-Yuan Gong
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
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12
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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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13
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Ahmed AA, Marchetti C, Ohnmacht SA, Neidle S. A G-quadruplex-binding compound shows potent activity in human gemcitabine-resistant pancreatic cancer cells. Sci Rep 2020; 10:12192. [PMID: 32699225 PMCID: PMC7376204 DOI: 10.1038/s41598-020-68944-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Gemcitabine is a drug of choice in the treatment of human pancreatic cancer. Chemo-resistance to this drug is common and has been attributed to a variety of distinct mechanisms, involving > 100 genes. A recently developed small-molecule G-quadruplex ligand, the trisubstituted naphthalene diimide compound CM03, has previously been shown to have equivalent potency to gemcitabine in the pancreatic cancer cell line MIA PaCa-2. We report here on cell lines of increased resistance to gemcitabine that have been generated from this line, with the most resistant having 1,000-fold reduced sensitivity to gemcitabine. These resistant lines retain nM sensitivity to CM03. The molecular basis for the retention of potency by this G-quadruplex ligand has been examined using whole transcriptome data analysis with RNA-seq. This has revealed that the pattern of pathways down regulated by CM03 in the parental MIA PaCa-2 cell line is largely unaffected in the gemcitabine-resistant line. The analysis has also shown that the expression patterns of numerous genes involved in gemcitabine sensitivity are down regulated in the resistant line upon CM03 treatment. These results are supportive of the concept that G-quadruplex small molecules such as CM03 have potential for clinical use in the treatment of gemcitabine-resistant human pancreatic cancer.
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Affiliation(s)
- Ahmed Abdullah Ahmed
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Chiara Marchetti
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Stephan A Ohnmacht
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
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14
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Zhirov AM, Kovalev DA, Ulshina DV, Pisarenko SV, Demidov OP, Borovlev IV. Diazapyrenes: interaction with nucleic acids and biological activity. Chem Heterocycl Compd (N Y) 2020; 56:674-693. [PMID: 32836316 PMCID: PMC7366485 DOI: 10.1007/s10593-020-02717-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
Abstract
The review summarizes data on the practical aspects of the interaction of nucleic acids with diazapyrene derivatives. The information on biological activity is given and the probable mechanisms underlying the action of diazapyrenes are analyzed. It contains 119 references.
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Affiliation(s)
- Andrey M. Zhirov
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Dmitry A. Kovalev
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Diana V. Ulshina
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Sergey V. Pisarenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Oleg P. Demidov
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
| | - Ivan V. Borovlev
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
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15
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D’Aguanno S, Del Bufalo D. Inhibition of Anti-Apoptotic Bcl-2 Proteins in Preclinical and Clinical Studies: Current Overview in Cancer. Cells 2020; 9:cells9051287. [PMID: 32455818 PMCID: PMC7291206 DOI: 10.3390/cells9051287] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/30/2022] Open
Abstract
The dynamic interplay between pro-death and pro-survival Bcl-2 family proteins is responsible for a cell’s fate. Due to the recognized relevance of this family in cancer progression and response to therapy, different efforts have made in recent years in order to develop small molecules able to target anti-apoptotic proteins such as Bcl-2, Bcl-xL and Mcl-1. The limitations of the first Bcl-2 family targeted drugs, regarding on-target and off-target toxicities, have been overcome with the development of venetoclax (ABT-199), the first BH3 mimetic inhibitor approved by the FDA. The purpose of this review is to discuss the state-of-the-art in the development of drugs targeting Bcl-2 anti-apoptotic proteins and to highlight the potential of their application as single agents or in combination for improving anti-cancer therapy, focusing in particular on solid tumors.
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16
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Guo P, Farahat AA, Paul A, Kumar A, Boykin DW, Wilson WD. Extending the σ-Hole Motif for Sequence-Specific Recognition of the DNA Minor Groove. Biochemistry 2020; 59:1756-1768. [PMID: 32293884 DOI: 10.1021/acs.biochem.0c00090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The majority of current drugs against diseases, such as cancer, can bind to one or more sites in a protein and inhibit its activity. There are, however, well-known limits on the number of druggable proteins, and complementary current drugs with compounds that could selectively target DNA or RNA would greatly enhance the availability of cellular probes and therapeutic progress. We are focusing on the design of sequence-specific DNA minor groove binders that, for example, target the promoter sites of transcription factors involved in a disease. We have started with AT-specific minor groove binders that are known to enter human cells and have entered clinical trials. To broaden the sequence-specific recognition of these compounds, several modules that have H-bond acceptors that strongly and specifically recognize G·C base pairs were identified. A lead module is a thiophene-N-alkyl-benzimidazole σ-hole-based system with terminal phenyl-amidines that have excellent affinity and selectivity for a G·C base pair in the minor groove. Efforts are now focused on optimizing this module. In this work, we are evaluating modifications to the compound aromatic system with the goal of improving GC selectivity and affinity. The lead compounds retain the thiophene-N-alkyl-BI module but have halogen substituents adjacent to an amidine group on the terminal phenyl-amidine. The optimum compounds must have strong affinity and specificity with a residence time of at least 100 s.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States.,Master of Pharmaceutical Sciences Program, California Northstate University, 9700 West Taron Drive, Elk Grove, California 95757, United States
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
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17
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Duan J, Wang X, Kizer ME. Biotechnological and Therapeutic Applications of Natural Nucleic Acid Structural Motifs. Top Curr Chem (Cham) 2020; 378:26. [PMID: 32067108 DOI: 10.1007/s41061-020-0290-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/11/2020] [Indexed: 11/28/2022]
Abstract
Genetic information and the blueprint of life are stored in the form of nucleic acids. The primary sequence of DNA, read from the canonical double helix, provides the code for RNA and protein synthesis. Yet these already-information-rich molecules have higher-order structures which play critical roles in transcription and translation. Uncovering the sequences, parameters, and conditions which govern the formation of these structural motifs has allowed researchers to study them and to utilize them in biotechnological and therapeutic applications in vitro and in vivo. This review covers both DNA and RNA structural motifs found naturally in biological systems including catalytic nucleic acids, non-coding RNA, aptamers, G-quadruplexes, i-motifs, and Holliday junctions. For each category, an overview of the structural characteristics, biological prevalence, and function will be discussed. The biotechnological and therapeutic applications of these structural motifs are highlighted. Future perspectives focus on the addition of proteins and unnatural modifications to enhance structural stability for greater applicability.
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Affiliation(s)
- Jinwei Duan
- Department of Chemistry and Materials Science, College of Sciences, Chang'an University, Xi'an, 710064, Shaanxi, People's Republic of China.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Xing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Megan E Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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18
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Naphthalene Diimides as Multimodal G-Quadruplex-Selective Ligands. Molecules 2019; 24:molecules24030426. [PMID: 30682828 PMCID: PMC6384834 DOI: 10.3390/molecules24030426] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 02/03/2023] Open
Abstract
G-quadruplexes are four-stranded nucleic acids structures that can form in guanine-rich sequences. Following the observation that G-quadruplexes are particularly abundant in genomic regions related to cancer, such as telomeres and oncogenes promoters, several G-quadruplex-binding molecules have been developed for therapeutic purposes. Among them, naphthalene diimide derivatives have reported versatility, consistent selectivity and high affinity toward the G-quadruplex structures. In this review, we present the chemical features, synthesis and peculiar optoelectronic properties (absorption, emission, redox) that make naphtalene diimides so versatile for biomedical applications. We present the latest developments on naphthalene diimides as G-quadruplex ligands, focusing on their ability to bind G-quadruplexes at telomeres and oncogene promoters with consequent anticancer activity. Their different binding modes (reversible versus irreversible/covalent) towards G-quadruplexes and their additional use as antimicrobial agents are also presented and discussed.
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19
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Lin C, Dickerhoff J, Yang D. NMR Studies of G-Quadruplex Structures and G-Quadruplex-Interactive Compounds. Methods Mol Biol 2019; 2035:157-176. [PMID: 31444749 PMCID: PMC7263470 DOI: 10.1007/978-1-4939-9666-7_9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
G-quadruplexes are noncanonical, four-stranded nucleic acid secondary structures formed in sequences containing consecutive runs of guanines. These G-quadruplex structures have been found to form in nucleic acid regions of biological significance, including human telomeres, gene promoters, and untranslated regions of mRNA. Thus, they are considered attractive therapeutic targets. Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for understanding the structures of G-quadruplexes and their interactions with small molecules under physiologically relevant conditions. Here, we present the NMR methodology used in our research group for the study of DNA G-quadruplex structures in physiologically relevant solution and their ligand interactions.
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Affiliation(s)
- Clement Lin
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Jonathan Dickerhoff
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA.
- Purdue Center for Cancer Research, West Lafayette, IN, USA.
- Purdue Institute for Drug Discovery, West Lafayette, IN, USA.
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20
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Nadai M, Doria F, Scalabrin M, Pirota V, Grande V, Bergamaschi G, Amendola V, Winnerdy FR, Phan AT, Richter SN, Freccero M. A Catalytic and Selective Scissoring Molecular Tool for Quadruplex Nucleic Acids. J Am Chem Soc 2018; 140:14528-14532. [PMID: 30351011 PMCID: PMC6242190 DOI: 10.1021/jacs.8b05337] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A copper complex embedded in the structure of a water-soluble naphthalene diimide has been designed to bind and cleave G-quadruplex DNA. We describe the properties of this ligand, including its catalytic activity in the generation of ROS. FRET melting, CD, NMR, gel sequencing, and mass spectrometry experiments highlight a unique and unexpected selectivity in cleaving G-quadruplex sequences. This selectivity relies both on the binding affinity and structural features of the targeted G-quadruplexes.
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Affiliation(s)
- Matteo Nadai
- Department of Molecular Medicine , University of Padua , via Gabelli 63 , 35121 Padua , Italy
| | - Filippo Doria
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine , University of Padua , via Gabelli 63 , 35121 Padua , Italy
| | - Valentina Pirota
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Vincenzo Grande
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Greta Bergamaschi
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Valeria Amendola
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Sara N Richter
- Department of Molecular Medicine , University of Padua , via Gabelli 63 , 35121 Padua , Italy
| | - Mauro Freccero
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
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