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For: Hou JQ, Chen SB, Tan JH, Ou TM, Luo HB, Li D, Xu J, Gu LQ, Huang ZS. New Insights into the Structures of Ligand−Quadruplex Complexes from Molecular Dynamics Simulations. J Phys Chem B 2010;114:15301-10. [DOI: 10.1021/jp106683n] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Number Cited by Other Article(s)
1
Otovat F, Bozorgmehr MR, Mahmoudi A, Morsali A. Porphyrin-based ligand interaction with G-quadruplex: Metal cation effects. J Mol Recognit 2023;36:e3017. [PMID: 37025015 DOI: 10.1002/jmr.3017] [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: 09/19/2022] [Revised: 03/14/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023]
2
Maddah M, Karami L. An atomistic investigation on the interaction of distamycin A and its derivative with the telomeric G-Quadruplex as anticancer agents by molecular dynamics simulation. Arch Biochem Biophys 2021;701:108797. [PMID: 33607110 DOI: 10.1016/j.abb.2021.108797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 10/22/2022]
3
Wang Z, Li G, Tian Z, Lou X, Huang Y, Wang L, Li J, Hou T, Liu JP. Insight Derived from Molecular Dynamics Simulation into the Selectivity Mechanism Targeting c-MYC G-Quadruplex. J Phys Chem B 2020;124:9773-9784. [DOI: 10.1021/acs.jpcb.0c05029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
4
Li F, Guo D, Kang L. Study on the recognition of G-quadruplexes by two stereoisomers of alkaloids. Anal Bioanal Chem 2019;411:5555-5561. [PMID: 31197422 DOI: 10.1007/s00216-019-01937-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/06/2019] [Accepted: 05/21/2019] [Indexed: 11/26/2022]
5
Binding of BRACO19 to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. Molecules 2019;24:molecules24061010. [PMID: 30871220 PMCID: PMC6471034 DOI: 10.3390/molecules24061010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/01/2019] [Accepted: 03/09/2019] [Indexed: 11/30/2022]  Open
6
Sullivan HJ, Readmond C, Radicella C, Persad V, Fasano TJ, Wu C. Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex-Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. ACS OMEGA 2018;3:14788-14806. [PMID: 30555989 PMCID: PMC6289566 DOI: 10.1021/acsomega.8b01574] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 09/11/2018] [Indexed: 06/09/2023]
7
Haider S. Computational Methods to Study G-Quadruplex–Ligand Complexes. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0083-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
8
The estimation of H-bond and metal ion-ligand interaction energies in the G-Quadruplex ⋯ Mn+ complexes. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
9
Mulholland K, Siddiquei F, Wu C. Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent. Phys Chem Chem Phys 2018;19:18685-18694. [PMID: 28696445 DOI: 10.1039/c7cp03313c] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
10
Kurniawan F, Miura Y, Kartasasmita RE, Yoshioka N, Mutalib A, Tjahjono DH. In Silico Study, Synthesis, and Cytotoxic Activities of Porphyrin Derivatives. Pharmaceuticals (Basel) 2018;11:ph11010008. [PMID: 29361701 PMCID: PMC5874704 DOI: 10.3390/ph11010008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/14/2018] [Accepted: 01/19/2018] [Indexed: 01/10/2023]  Open
11
McRae EKS, Booy EP, Padilla-Meier GP, McKenna SA. On Characterizing the Interactions between Proteins and Guanine Quadruplex Structures of Nucleic Acids. J Nucleic Acids 2017;2017:9675348. [PMID: 29250441 PMCID: PMC5700478 DOI: 10.1155/2017/9675348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/08/2017] [Indexed: 01/07/2023]  Open
12
Machireddy B, Kalra G, Jonnalagadda S, Ramanujachary K, Wu C. Probing the Binding Pathway of BRACO19 to a Parallel-Stranded Human Telomeric G-Quadruplex Using Molecular Dynamics Binding Simulation with AMBER DNA OL15 and Ligand GAFF2 Force Fields. J Chem Inf Model 2017;57:2846-2864. [PMID: 29028340 DOI: 10.1021/acs.jcim.7b00287] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
13
Islam B, Stadlbauer P, Gil-Ley A, Pérez-Hernández G, Haider S, Neidle S, Bussi G, Banas P, Otyepka M, Sponer J. Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations. J Chem Theory Comput 2017;13:2458-2480. [PMID: 28475322 PMCID: PMC5514396 DOI: 10.1021/acs.jctc.7b00226] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
14
Effects of the central potassium ions on the G-quadruplex and stabilizer binding. J Mol Graph Model 2017;72:168-177. [PMID: 28092835 DOI: 10.1016/j.jmgm.2017.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/20/2016] [Accepted: 01/04/2017] [Indexed: 12/30/2022]
15
Scaglioni L, Mondelli R, Artali R, Sirtori FR, Mazzini S. Nemorubicin and doxorubicin bind the G-quadruplex sequences of the human telomeres and of the c-MYC promoter element Pu22. Biochim Biophys Acta Gen Subj 2016;1860:1129-38. [PMID: 26922833 DOI: 10.1016/j.bbagen.2016.02.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/12/2016] [Accepted: 02/21/2016] [Indexed: 12/22/2022]
16
Islam B, Stadlbauer P, Krepl M, Koca J, Neidle S, Haider S, Sponer J. Extended molecular dynamics of a c-kit promoter quadruplex. Nucleic Acids Res 2015;43:8673-93. [PMID: 26245347 PMCID: PMC4605300 DOI: 10.1093/nar/gkv785] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/21/2015] [Indexed: 01/29/2023]  Open
17
Model of complex chiral drug metabolic systems and numerical simulation of the remaining chirality toward analysis of dynamical pharmacological activity. J Theor Biol 2015;373:117-31. [PMID: 25791284 DOI: 10.1016/j.jtbi.2015.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 03/06/2015] [Accepted: 03/07/2015] [Indexed: 11/22/2022]
18
Arba M, Kartasasmita RE, Tjahjono DH. Molecular docking and dynamics simulations on the interaction of cationic porphyrin-anthraquinone hybrids with DNA G-quadruplexes. J Biomol Struct Dyn 2015;34:427-38. [PMID: 25808513 DOI: 10.1080/07391102.2015.1033015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
19
Verdian Doghaei A, Housaindokht M, Bozorgmehr M. Molecular crowding effects on conformation and stability of G-quadruplex DNA structure: Insights from molecular dynamics simulation. J Theor Biol 2015;364:103-12. [DOI: 10.1016/j.jtbi.2014.09.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 07/14/2014] [Accepted: 09/10/2014] [Indexed: 11/25/2022]
20
Bagherzadeh K, Shirgahi Talari F, Sharifi A, Ganjali MR, Saboury AA, Amanlou M. A new insight into mushroom tyrosinase inhibitors: docking, pharmacophore-based virtual screening, and molecular modeling studies. J Biomol Struct Dyn 2014;33:487-501. [PMID: 24601849 DOI: 10.1080/07391102.2014.893203] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
21
Arba M, Tjahjono DH. The binding modes of cationic porphyrin-anthraquinone hybrids to DNA duplexes: in silico study. J Biomol Struct Dyn 2014;33:657-65. [PMID: 24580066 DOI: 10.1080/07391102.2014.887480] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
22
Gkionis K, Kruse H, Platts JA, Mládek A, Koča J, Šponer J. Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations. J Chem Theory Comput 2014;10:1326-40. [DOI: 10.1021/ct4009969] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
23
Jissy AK, Datta A. Design and Applications of Noncanonical DNA Base Pairs. J Phys Chem Lett 2014;5:154-166. [PMID: 26276196 DOI: 10.1021/jz402352d] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
24
Chen SB, Shi QX, Peng D, Huang SY, Ou TM, Li D, Tan JH, Gu LQ, Huang ZS. The role of positive charges on G-quadruplex binding small molecules: learning from bisaryldiketene derivatives. Biochim Biophys Acta Gen Subj 2013;1830:5006-13. [PMID: 23880070 DOI: 10.1016/j.bbagen.2013.07.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/10/2013] [Accepted: 07/15/2013] [Indexed: 10/26/2022]
25
New insights from molecular dynamic simulation studies of the multiple binding modes of a ligand with G-quadruplex DNA. J Comput Aided Mol Des 2012;26:1355-68. [PMID: 23239169 DOI: 10.1007/s10822-012-9619-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 11/27/2012] [Indexed: 01/06/2023]
26
Jissy AK, Datta A. Effect of External Electric Field on H-Bonding and π-Stacking Interactions in Guanine Aggregates. Chemphyschem 2012;13:4163-72. [DOI: 10.1002/cphc.201200690] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 09/07/2012] [Indexed: 01/19/2023]
27
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
28
JISSY AK, RAMANA JHV, DATTA AYAN. π-Stacking interactions between G-quartets and circulenes: A computational study. J CHEM SCI 2011. [DOI: 10.1007/s12039-011-0155-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
29
Murat P, Singh Y, Defrancq E. Methods for investigating G-quadruplex DNA/ligand interactions. Chem Soc Rev 2011;40:5293-307. [PMID: 21720638 DOI: 10.1039/c1cs15117g] [Citation(s) in RCA: 192] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
30
Nakayama S, Kelsey I, Wang J, Sintim HO. c-di-GMP can form remarkably stable G-quadruplexes at physiological conditions in the presence of some planar intercalators. Chem Commun (Camb) 2011;47:4766-8. [PMID: 21399808 DOI: 10.1039/c0cc05432a] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
31
Hou JQ, Tan JH, Wang XX, Chen SB, Huang SY, Yan JW, Chen SH, Ou TM, Luo HB, Li D, Gu LQ, Huang ZS. Impact of planarity of unfused aromatic molecules on G-quadruplex binding: Learning from isaindigotone derivatives. Org Biomol Chem 2011;9:6422-36. [DOI: 10.1039/c1ob05884c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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