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Stężycka O, Kasperkowiak M, Frańska M, Nowak D, Hoffmann M. Oxygen Atom from Carbonyl Group as an Important Binding Agent to the G-Quadruplex - Study Case of Flavonoids. Chempluschem 2024:e202400186. [PMID: 38713672 DOI: 10.1002/cplu.202400186] [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: 03/10/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024]
Abstract
In the field of anticancer therapy study it is of great interest to find effective G-quadruplex ligands which may be of potential use in medical treatment or cancer prevention. Since among the compounds of natural origin, flavonoids have attracted notable attention because of their unique properties and promising therapeutic applications, an interesting question was to identify the flavonoid structural features that could provide effective binding properties toward G-quadruplex. By using electrospray ionization mass spectrometry, followed by the survival yield method, it has been shown that the flavonoid molecules which contain an available C4=O carbonyl group form more stable adducts with G-tetrads than the other ones. Molecular docking has shown that C4=O carbonyl group can be a source of hydrogen bonds and/or π-stacking interactions. Therefore, the flavonoid molecules which contain an available C4=O carbonyl group can be regarded as good binders of G-quadruplexes.
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Affiliation(s)
- Olga Stężycka
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Małgorzata Kasperkowiak
- Centre for Advanced Technologies, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
| | - Magdalena Frańska
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Damian Nowak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Marcin Hoffmann
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
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Stężycka O, Frańska M. Binding of Quercetin Derivatives toward G-Tetrads as Studied by the Survival Yield Method. ACS OMEGA 2023; 8:39816-39821. [PMID: 37901583 PMCID: PMC10600882 DOI: 10.1021/acsomega.3c06016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/27/2023] [Indexed: 10/31/2023]
Abstract
Recently, much interest has been devoted to finding effective G-quadruplex ligands, both of synthetic or natural origins, which may be of potential use in the field of cancer therapy. Among compounds of natural origin, a common flavonol quercetin has attracted notable attention. Yet, only a modest number of papers have been concerned with a comparison of quercetin conjugates binding to G-quadruplexes. In this study, we applied the survival yield (SY) method in order to compare the stability of G-tetrad complexes with quercetin and its conjugates, namely, 3-O-glycosides and O-methylated conjugates. According to the determined values of Ecomδ50, flavonol glycosides bind most effectively with G-tetrads, whereas, among flavonols, 3-O-methylquercetin makes the most effective bonds. Because the aglycone structure is of crucial importance for biological processes, 3-O-methylquercetin seems to be a suitable candidate for anticancer therapeutics, and the extracts from the plants, which contain high amounts of 3-O-methylquercetin or its glycosides, should be considered as interesting materials for preparation of pharmaceuticals or dietary supplements.
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Affiliation(s)
- Olga Stężycka
- Institute of Chemistry and Technical
Electrochemistry, Poznań University
of Technology, Berdychowo
4, 60-965 Poznań, Poland
| | - Magdalena Frańska
- Institute of Chemistry and Technical
Electrochemistry, Poznań University
of Technology, Berdychowo
4, 60-965 Poznań, Poland
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Taylor CL, Hummert JG, Kang J. Enthalpy-entropy compensation in the binding of quercetin to calf thymus DNA. J Mol Recognit 2023; 36:e2994. [PMID: 36116116 DOI: 10.1002/jmr.2994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Caden L Taylor
- Department of Biology, Valdosta State University, Valdosta, Georgia, USA
| | - Juliana G Hummert
- Department of Biology, Valdosta State University, Valdosta, Georgia, USA
| | - Jonghoon Kang
- Department of Biology, Valdosta State University, Valdosta, Georgia, USA
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Structural insights and shedding light on preferential interactions of dietary flavonoids with G-quadruplex DNA structures: A new horizon. Heliyon 2023; 9:e13959. [PMID: 36879969 PMCID: PMC9984854 DOI: 10.1016/j.heliyon.2023.e13959] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
G-quadruplex, a structurally unique structure in nucleic acids present all throughout the human genome, has sparked great attention in therapeutic investigations. Targeting G-quadruplex structure is a new strategy for the drug development. Flavonoids are found in almost all dietary plant-based beverages and food products; therefore, they are ingested in significant proportions through the human diet. Although synthetically developed drug molecules are used vigorously but they have various adverse effects. While on the other hand, nature supplies chemically unique scaffolds in the form of distinct dietary flavonoids that are easily accessible, less poisonous, and have higher bioavailability. Because of their great pharmacological effectiveness and minimal cytotoxicity, such low molecular weight compounds are feasible alternatives to synthetic therapeutic medicines. Therefore, from a drug-development point of view, investigation on screening the binding capabilities of quadruplex-interactive small natural compounds like dietary flavonoids are expected to be highly effective, with a particular emphasis on the selectivity towards polymorphic G-quadruplex structures. In this respect, quadruplexes have scintillated research into their potential interaction with these dietary flavonoids. The purpose of this review is to offer an up-to-date close-up look at the research on their interaction with structurally varied dietary flavonoids with the goal of providing newer perspectives to construct novel therapeutic agents for next-generation disease managements.
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Poddar NK, Agarwal D, Agrawal Y, Wijayasinghe YS, Mukherjee A, Khan S. Deciphering the enigmatic crosstalk between prostate cancer and Alzheimer's disease: A current update on molecular mechanisms and combination therapy. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166524. [PMID: 35985445 DOI: 10.1016/j.bbadis.2022.166524] [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: 06/02/2022] [Revised: 08/05/2022] [Accepted: 08/11/2022] [Indexed: 11/26/2022]
Abstract
Alzheimer's disease (AD) and prostate cancer (PCa) are considered the leading causes of death in elderly people worldwide. Although both these diseases have striking differences in their pathologies, a few underlying mechanisms are similar when cell survival is considered. In the current study, we employed an in-silico approach to decipher the possible role of bacterial proteins in the initiation and progression of AD and PCa. We further analyzed the molecular connections between these two life-threatening diseases. The androgen deprivation therapy used against PCa has been shown to promote castrate resistant PCa as well as AD. In addition, cell signaling pathways, such as Akt, IGF, and Wnt contribute to the progression of both AD and PCa. Besides, various proteins and genes are also common in disease progression. One such similarity is mTOR signaling. mTOR is the common downstream target for many signaling pathways and plays a vital role in both PCa and AD. Targeting mTOR can be a favorable line of treatment for both AD and PCa. However, drug resistance is one of the challenges in effective drug therapy. A few drugs that target mTOR have now become ineffective due to the development of resistance. In that regard, phytochemicals can be a rich source of novel drug candidates as they can act via multiple mechanisms. This review also presents mTOR targeting phytochemicals with promising anti-PCa, anti-AD activities, and approaches to overcome the issues associated with phytochemical-based therapies in clinical trials.
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Affiliation(s)
- Nitesh Kumar Poddar
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India.
| | - Disha Agarwal
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India
| | - Yamini Agrawal
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India
| | | | - Arunima Mukherjee
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India
| | - Shahanavaj Khan
- Department of Health Sciences, Novel Global Community Educational Foundation, NSW, Australia; Department of Pharmaceutics, College of Pharmacy, PO Box 2457, King Saud University, Riyadh 11451, Saudi Arabia; Department of Medical Lab Technology, Indian Institute of health and Technology (IIHT), Deoband, 247554 Saharanpur, UP, India.
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Biver T. Discriminating between Parallel, Anti-Parallel and Hybrid G-Quadruplexes: Mechanistic Details on Their Binding to Small Molecules. Molecules 2022; 27:molecules27134165. [PMID: 35807410 PMCID: PMC9268745 DOI: 10.3390/molecules27134165] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
G-quadruplexes (G4) are now extensively recognised as a peculiar non-canonical DNA geometry that plays a prime importance role in processes of biological relevance whose number is increasing continuously. The same is true for the less-studied RNA G4 counterpart. G4s are stable structures; however, their geometrical parameters may be finely tuned not only by the presence of particular sequences of nucleotides but also by the salt content of the medium or by a small molecule that may act as a peculiar topology inducer. As far as the interest in G4s increases and our knowledge of these species deepens, researchers do not only verify the G4s binding by small molecules and the subsequent G4 stabilisation. The most innovative studies now aim to elucidate the mechanistic details of the interaction and the ability of a target species (drug) to bind only to a peculiar G4 geometry. In this focused review, we survey the advances in the studies of the binding of small molecules of medical interest to G4s, with particular attention to the ability of these species to bind differently (intercalation, lateral binding or sitting atop) to different G4 topologies (parallel, anti-parallel or hybrid structures). Some species, given the very high affinity with some peculiar G4 topology, can first bind to a less favourable geometry and then induce its conversion. This aspect is also considered.
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Affiliation(s)
- Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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Evaluating Molecular Docking Software for Small Molecule Binding to G-Quadruplex DNA. Int J Mol Sci 2021; 22:ijms221910801. [PMID: 34639142 PMCID: PMC8509811 DOI: 10.3390/ijms221910801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 01/08/2023] Open
Abstract
G-quadruplexes are four-stranded nucleic acid secondary structures of biological significance and have emerged as an attractive drug target. The G4 formed in the MYC promoter (MycG4) is one of the most studied small-molecule targets, and a model system for parallel structures that are prevalent in promoter DNA G4s and RNA G4s. Molecular docking has become an essential tool in structure-based drug discovery for protein targets, and is also increasingly applied to G4 DNA. However, DNA, and in particular G4, binding sites differ significantly from protein targets. Here we perform the first systematic evaluation of four commonly used docking programs (AutoDock Vina, DOCK 6, Glide, and RxDock) for G4 DNA-ligand binding pose prediction using four small molecules whose complex structures with the MycG4 have been experimentally determined in solution. The results indicate that there are considerable differences in the performance of the docking programs and that DOCK 6 with GB/SA rescoring performs better than the other programs. We found that docking accuracy is mainly limited by the scoring functions. The study shows that current docking programs should be used with caution to predict G4 DNA-small molecule binding modes.
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Ribaudo G, Oselladore E, Ongaro A, Zagotto G, Memo M, Gianoncelli A. Enhanced G-quadruplex selectivity of flavonoid glycoside rutin over quercetin. Nat Prod Res 2020; 36:3469-3473. [PMID: 33307807 DOI: 10.1080/14786419.2020.1859505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In drug discovery, ligand-mediated stabilization of G-quadruplexes is pursued for regulating gene expression and key cellular processes. Electrospray ionization mass spectrometry (ESI-MS) has been optimized for screening putative DNA-binding small molecules of natural and synthetic origin. Several flavonoids were reported to interact with G-quadruplex, and quercetin is among them. In this contribution, the interaction with G-quadruplex DNA of rutin, a glycoside of quercetin extracted from flower buds of Styphnolobium japonicum (L.) Schott, was investigated by means of ESI-MS and molecular docking. While rutin and quercetin showed similar G-quadruplex binding affinity values, rutin was characterized by enhanced selectivity for G-quadruplex over double stranded DNA. Moreover, collision-induced dissociation (CID) assays demonstrated that rutin stabilizes the G-quadruplex arrangement more efficiently, and molecular docking predicted stacking as the preferential interaction pattern.
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Affiliation(s)
- Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Erika Oselladore
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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