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Li F, Luo Y, Xi G, Fu J, Tu J. Single-Molecule Analysis of DNA structures using nanopore sensors. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Khanna L, Singhal S, Jain SC, Khanna P. Spiro-Indole-Coumarin Hybrids: Synthesis, ADME, DFT, NBO Studies and In Silico Screening through Molecular Docking on DNA G-Quadruplex. ChemistrySelect 2020; 5:3420-3433. [PMID: 32328514 PMCID: PMC7169502 DOI: 10.1002/slct.201904783] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/09/2020] [Indexed: 01/11/2023]
Abstract
New series of hybrids were synthesized by combination of 4-hydroxycoumarin with spiro[indol-indazole-thiazolidine]-diones and spiro[indol-pyrazole-thiazolidine]-diones, via hitherto unknown Schiff bases. The effects of substituents, such as -F, -Br and -CH3, on the crucial characteristics pertaining to the hybrids were investigated through computational studies. In silico or virtual screening through molecular docking studies on the library of 22 compounds, including reference compounds, precursors, non-hybrid and hybrid derivatives, was performed on DNA G-quadruplex of the human genome. All six freshly synthesized hybrids showed high binding energy as compared to non-hybrids as well as reference compounds. The presence of substituents at 5-position of indole enhanced the binding tendency of the ligand. ADME studies indicated good oral bioavailability and absorption of these compounds. Density Functional Theory (DFT) calculations of hybrids were done at B3LYP/6-311G++(d,p) level of computation. Their HOMO and LUMO energy plots reflected the presence of high charge transfer and chemical potential. Natural bond order (NBO) calculations predicted hyperconjugative interactions. The Molecular Electrostatic Potential (MEP) surface plots showed possible electrophilic and nucleophilic attacking sites of the hybrids. Compound 10 a (5-fluoro-spiro[indol-indazole-thiazolidine]-dione-coumarin hybrid), on the basis of global reactivity descriptors, was filtered to be chemically most reactive with the highest binding energy of -8.23 kcal/mol with DNA G-quadruplex. The synthesized hybrid coumarin derivatives in correlation with theoretical docking studies validate that hybrid derivatives are more reactive compared to their non-hybrid counterparts.
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Affiliation(s)
- Leena Khanna
- Department of ChemistryUniversity of DelhiDelhi110007India
- University School of Basic and Applied SciencesGuru Gobind Singh Indraprastha University, Sector 16-C, DwarkaNew Delhi110078India
| | - Sugandha Singhal
- University School of Basic and Applied SciencesGuru Gobind Singh Indraprastha University, Sector 16-C, DwarkaNew Delhi110078India
| | | | - Pankaj Khanna
- Department of ChemistryUniversity of DelhiDelhi110007India
- Department of ChemistryAcharya Narendra Dev CollegeUniversity of Delhi, KalkajiNew Delhi110019India
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Carvalho J, Santos T, Carrilho R, Sousa F, Salgado GF, Queiroz JA, Cruz C. Ligand screening to pre-miRNA 149 G-quadruplex investigated by molecular dynamics. J Biomol Struct Dyn 2019; 38:2276-2286. [DOI: 10.1080/07391102.2019.1632743] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Josué Carvalho
- CICS-UBI—Centro de Investigacão em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Tiago Santos
- CICS-UBI—Centro de Investigacão em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Rui Carrilho
- CICS-UBI—Centro de Investigacão em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Fani Sousa
- CICS-UBI—Centro de Investigacão em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Gilmar F. Salgado
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, IECB, Université de Bordeaux, Pessac, France
| | - João António Queiroz
- CICS-UBI—Centro de Investigacão em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Carla Cruz
- CICS-UBI—Centro de Investigacão em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
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Novel triazole and morpholine substituted bisnaphthalimide: Synthesis, photophysical and G-quadruplex binding properties. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Sillapapongwarakorn S, Yanarojana S, Pinthong D, Thithapandha A, Ungwitayatorn J, Supavilai P. Molecular docking based screening of triterpenoids as potential G-quadruplex stabilizing ligands with anti-cancer activity. Bioinformation 2017; 13:284-292. [PMID: 29081607 PMCID: PMC5651221 DOI: 10.6026/97320630013284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 08/30/2017] [Accepted: 09/02/2017] [Indexed: 01/13/2023] Open
Abstract
Triterpenoids isolated from Ganoderma lucidum (GLTs) exhibit a broad spectrum of anti-cancer properties, including anti-proliferative, anti-metastatic and anti-angiogenic activities. Current research studies revealed the role by GLTs in inducing apoptosis and suppression of telomerase activity of cancer cells with much lower toxicity to healthy cells. Compounds selectively binding and stabilizing G-quadruplex structures could inhibit the telomerase or downregulate the oncogenes and may act as anti-cancer agents. Targeting human telomeric G-quadruplex DNA could be one of the mechanisms by which these GLTs exert anti-cancer activity. In this study, 208 GLTs were screened for ligands with high binding affinity and selectively to stabilize the pG4DNA by using the docking tool AutoDock4. The results showed that ganoderic acid A and ganoderic acid Df exhibit high binding affinity and selectively bind to the lateral groove of pG4DNA. Based on our findings, we suggest that the triterpenoid represents a new class of G-quadruplex groove binding ligands and thus act as potential anti-cancer agents.
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Affiliation(s)
| | - Somchai Yanarojana
- Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand
| | - Darawan Pinthong
- Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand
| | - Amnuay Thithapandha
- Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand
| | - Jiraporn Ungwitayatorn
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayudhaya Road, Bangkok 10400, Thailand
| | - Porntip Supavilai
- Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand
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Ou Z, Xu M, Gao Y, Hu R, Li Q, Cai W, Wang Z, Qian Y, Yang G. Synthesis, G-quadruplex binding properties and cytotoxicity of naphthalimide–thiourea conjugates. NEW J CHEM 2017. [DOI: 10.1039/c7nj02366a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The hydrogen bonding between a thiourea moiety and a G-quadruplex plays a crucial role in the sequence-specific DNA binding of naphthalimide–thiourea conjugates.
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Affiliation(s)
- Zhize Ou
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Moheng Xu
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yunyan Gao
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Rui Hu
- CAS Key laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Qingqing Li
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Wenjiao Cai
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Ziji Wang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yimeng Qian
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Guoqiang Yang
- CAS Key laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
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Targeting human telomeric and c-myc G-quadruplexes with alkynylplatinum(II) terpyridine complexes under molecular crowding conditions. J Inorg Biochem 2016; 166:126-134. [PMID: 27852004 DOI: 10.1016/j.jinorgbio.2016.11.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 11/05/2016] [Accepted: 11/08/2016] [Indexed: 12/27/2022]
Abstract
The interactions between alkynylplatinum(II) terpyridine complexes 1-3 and the G-quadruplex DNA, including c-myc and telomeric quadruplex DNA, are investigated both in dilute solution and under molecular crowding conditions. The UV-vis absorption spectroscopy, circular dichroism and molecular docking studies suggest that 1-3 associate with telomeric and c-myc G-quadruplexes via groove binding, and electrostatic interactions. Experimental studies indicate that under molecular crowding conditions (in the presence of 40wt% PEG 200), 1-2 show weak affinity for c-myc, while 3 still displays high affinity and selectivity for c-myc. On the other hand, 1-3 act as efficient and selective ligand for telomeric quadruplex DNA under molecular crowding conditions. The complex 3 exhibits excellent cytotoxicity against A549, K562 and SGC-7901, with IC50 values that are 35.0-fold, 10.0-fold, and 12.1-fold lower than the values of cisplatin under the same conditions, respectively.
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Ou Z, Qian Y, Gao Y, Wang Y, Yang G, Li Y, Jiang K, Wang X. Photophysical, G-quadruplex DNA binding and cytotoxic properties of terpyridine complexes with a naphthalimide ligand. RSC Adv 2016. [DOI: 10.1039/c6ra01441k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The complex3inhibits A549 cells selectively over non-cancerous NIH3T3 cells, which may correlate with its selective G-quadruplex binding and nuclear location.
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Affiliation(s)
- Zhize Ou
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yimeng Qian
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yunyan Gao
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yunqing Wang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Guoqiang Yang
- CAS Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Yi Li
- Key Laboratory of Photochemical Convesion and Optoelectronic Material
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing
- People's Republic of China
| | - Kaiyue Jiang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Xin Wang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
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Wong WL, Chow CF. Synthesis of Highly Charged C3-Symmetrical Organic Molecule with a Fused Planar Core Structure. SYNTHETIC COMMUN 2015. [DOI: 10.1080/00397911.2015.1017585] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Wing-Leung Wong
- Department of Science and Environmental Studies, Centre for Education in Environmental Sustainability, Hong Kong Institute of Education, Hong Kong, China
| | - Cheuk-Fai Chow
- Department of Science and Environmental Studies, Centre for Education in Environmental Sustainability, Hong Kong Institute of Education, Hong Kong, China
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Chen ZF, Qin QP, Qin JL, Liu YC, Huang KB, Li YL, Meng T, Zhang GH, Peng Y, Luo XJ, Liang H. Stabilization of G-quadruplex DNA, inhibition of telomerase activity, and tumor cell apoptosis by organoplatinum(II) complexes with oxoisoaporphine. J Med Chem 2015; 58:2159-79. [PMID: 25650792 DOI: 10.1021/jm5012484] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Two G-quadruplex ligands [Pt(L(a))(DMSO)Cl] (Pt1) and [Pt(L(b))(DMSO)Cl] (Pt2) have been synthesized and fully characterized. The two complexes are more selective for SK-OV-3/DDP tumor cells versus normal cells (HL-7702). It was found that both Pt1 and Pt2 could be a telomerase inhibitor targeting G-quadruplex DNA. This is the first report demonstrating that telomeric, c-myc, and bcl-2 G-quadruplexes and caspase-3/9 preferred to bind with Pt2 rather than Pt1, which also can induce senescence and apoptosis. The different biological behavior of Pt1 and Pt2 may correlate with the presence of a 6-hydroxyl group in L(b). Importantly, Pt1 and Pt2 exhibited higher safety in vivo and more effective inhibitory effects on tumor growth in the HCT-8 and NCI-H460 xenograft mouse model, compared with cisplatin. Taken together, these mechanistic insights indicate that both Pt1 and Pt2 display low toxicity and could be novel anticancer drug candidates.
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Affiliation(s)
- Zhen-Feng Chen
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University , Yucai Road 15, Guilin 541004, P. R. China
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Mortier J, Rakers C, Bermudez M, Murgueitio MS, Riniker S, Wolber G. The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes. Drug Discov Today 2015; 20:686-702. [PMID: 25615716 DOI: 10.1016/j.drudis.2015.01.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 12/08/2014] [Accepted: 01/08/2015] [Indexed: 10/24/2022]
Abstract
Among all tools available to design new drugs, molecular dynamics (MD) simulations have become an essential technique. Initially developed to investigate molecular models with a limited number of atoms, computers now enable investigations of large macromolecular systems with a simulation time reaching the microsecond range. The reviewed articles cover four years of research to give an overview on the actual impact of MD on the current medicinal chemistry landscape with a particular emphasis on studies of ligand-protein interactions. With a special focus on studies combining computational approaches with data gained from other techniques, this review shows how deeply embedded MD simulations are in drug design strategies and articulates what the future of this technique could be.
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Affiliation(s)
- Jérémie Mortier
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany.
| | - Christin Rakers
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
| | - Marcel Bermudez
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
| | - Manuela S Murgueitio
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany.
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Maji B, Bhattacharya S. Advances in the molecular design of potential anticancer agents via targeting of human telomeric DNA. Chem Commun (Camb) 2014; 50:6422-38. [DOI: 10.1039/c4cc00611a] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Telomerase is an attractive drug target to develop new generation drugs against cancer.
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Affiliation(s)
- Basudeb Maji
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
- Chemical Biology Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
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Shan C, Tan JH, Ou TM, Huang ZS. Natural products and their derivatives as G-quadruplex binding ligands. Sci China Chem 2013. [DOI: 10.1007/s11426-013-4920-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Akbay N, Mahdavi F, Lakowicz JR, Ray K. Metal-enhanced intrinsic fluorescence of nucleic acids using platinum nanostructured substrates. Chem Phys Lett 2012; 548:45-50. [PMID: 23002289 PMCID: PMC3446211 DOI: 10.1016/j.cplett.2012.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated the feasibility of using platinum nanostructures to accomplish the metal-enhanced fluorescence (MEF) in the UV spectral region. We examine the possibility for detection of the intrinsic fluorescence from nucleotides and G-quadruplex DNA on platinum nanoparticles. Guanosine monophosphate (GMP) showed significant increases (~20-fold) in fluorescence intensities in the presence of platinum nanostructures when compared to quartz controls. G-quadruplex DNA demonstrated ~5-fold increase in fluorescence intensity and higher photostability in the presence of Pt nanostructures. We performed finite element method simulations to explore how Pt nanoparticles interact with plane waves and conformed that the Pt nanostructures are promising for enhancing the fluorescence emission in the UV region.
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Affiliation(s)
- Nuriye Akbay
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD, 21201, USA
| | - Farhad Mahdavi
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD, 21201, USA
| | - Joseph R. Lakowicz
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD, 21201, USA
| | - Krishanu Ray
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD, 21201, USA
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šponer J, Cang X, Cheatham TE. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods 2012; 57:25-39. [PMID: 22525788 PMCID: PMC3775459 DOI: 10.1016/j.ymeth.2012.04.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 04/04/2012] [Accepted: 04/06/2012] [Indexed: 11/29/2022] Open
Abstract
The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.
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Affiliation(s)
- Jiří šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Xiaohui Cang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, 2000 East 30 South, University of Utah, Salt Lake City, UT 84112, United States
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