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Telomere DNA assumes a high-order G-quadruplex (G4) structure, stabilization of which prevents telomere lengthening by telomerase in cancer. Through applying combined molecular simulation methods, an investigation on the selective binding mechanism of anionic phthalocyanine 3,4ʹ,4ʹʹ,4ʹʹʹ-tetrasulfonic acid (APC) and human hybrid (3 + 1) G4s was firstly performed at the atomic level. Compared to the groove binding mode of APC and the hybrid type I (hybrid-I) telomere G4, APC preferred to bind to the hybrid type II (hybrid-II) telomere G4 via end-stacking interactions, which showed much more favorable binding free energies. Analyses of the non-covalent interaction and binding free energy decomposition revealed a decisive role of van der Waals interaction in the binding of APC and telomere hybrid G4s. And the binding of APC and hybrid-II G4 that showed the highest binding affinity adopted the end-stacking binding mode to form the most extensive van der Waals interactions. These findings add new knowledge to the design of selective stabilizers targeting telomere G4 in cancer.
Amadei A, Linssen A, Berendsen H (1993) Essential dynamics of proteins. Proteins 17(4): 412−25
Attila A, Chen D, Dai J, Tiffanie B, Jones RA, Yang D (2006) Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acids Res 34(9): 2723−2735
Balasubramanian S, Hurley LH, Neidle S (2011) Targeting G-quadruplexes in gene promoters: a novel anticancer strategy. Nat Rev Drug Discov 10(4): 261−275
Bochman ML, Paeschke KK, Zakian VA (2012) DNA secondary structures: Stability and function of G-quadruplex structures. Nat Rev Genet 13(11): 770−780
Case DA, Iii T, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ (2010) The Amber biomolecular simulation programs. J Comput Chem 26(16): 1668−1688
Christiansen J, Kofod M, Nielsen FC (1994) A guanosine quadruplex and two stable hairpins flank a major cleavage site in insulin-like growth factor II mRNA. Nucleic Acids Res 22(25): 5709−5716
Collie GW, Haider SM, Neidle S, Parkinson GN (2010) A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex. Nucleic Acids Res 38(16): 5569−5580
Contreras-García J, Johnson ER, Keinan S, Chaudret R, Piquemal JP, Beratan DN, Yang W (2011) NCIPLOT: a program for plotting noncovalent interaction regions. J Chem Theory Comput 7(3): 625−632
Dai J, Megan C, Chandanamali P, Jones RA, Yang D (2007) Structure of the Hybrid-2 type intramolecular human telomeric G-quadruplex in K+ solution: insights into structure polymorphism of the human telomeric sequence. Nucleic Acids Res 35(15): 4927−4940
Dalia DGG, Rodrigo GM, Cortes-Guzman F (2017) The role of DNA-backbone in minor groove ligand binding. ChemPhysChem 18(14): 1909−1915
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1): 33−38
Huppert JL, Balasubramanian S (2005) Prevalence of quadruplexes in the human genome. Nucleic Acids Res 33(9): 2908−2916
Islam B, Stadlbauer P, Neidle S, Haider S, Sponer J (2016) Can we execute reliable MM-PBSA free energy computations of relative stabilities of different guanine quadruplex folds. J Phys Chem B 120(11): 2899−2912
Joung IS, Cheatham III TE (2008) Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B 112(30): 9020−9041
Kim MY, Vankayalapati H, Shin-Ya K, Wierzba K, Hurley LH (2002) Telomestatin, a potent telomerase inhibitor that interacts quite specifically with the human telomeric intramolecular g-quadruplex. J Am Chem Soc 124(10): 2098−2099
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc Chem Res 33(12): 889−897
Lim KW, Amrane S, Bouaziz S, Xu W, Mu Y, Patel DJ, Luu KN, Phan AT (2009) Structure of the human telomere in K+ solution: a stable basket-type G-quadruplex with only two G-tetrad layers. J Am Chem Soc 131(12): 4301−4309
Machireddy B, Kalra G, Jonnalagadda SC, Ramanujachary KV, Wu C (2017) 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 57(11): 2846−2864
Machireddy B, Sullivan H-J, Wu C (2019) Binding of BRACO19 to a telomeric G-quadruplex DNA probed by all-atom molecular dynamics simulations with explicit solvent. Molecules 24(6): 1010. https://doi.org/10.3390/molecules24061010
Martino L, Pagano B, Fotti Cc Hia I, Neidle S, Giancola C (2009) Shedding light on the interaction between TMPyP4 and human telomeric quadruplexes. J Phys Chem B 113(44): 14779−14786
Mengual Gomez DL, Armando RG, Cerrudo CS, Ghiringhelli PD, Gomez DE (2016) Telomerase as a cancer target. Development of new molecules. Curr Top Med Chem 16(22): 2432−2440
Mongan J (2004) Interactive essential dynamics. J Comput-Aided Mol Des 18(6): 433−436
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16): 2785−2791
Onel B, Lin C, Yang D (2014) DNA G-quadruplex and its potential as anticancer drug target. Sci China Chem 57(12): 1605−1614
Parkinson GN, Lee M, Neidle S (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417(6891): 876−880
Phan AT (2010) Human telomeric G-quadruplex: structures of DNA and RNA sequences. FEBS J 277(5): 1107−1117
Phan AT, Kuryavyi V, Luu KN, Patel DJ (2007) Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution. Nucleic Acids Res 35(19): 6517−6525
Phan AT, Luu KN, Patel DJ (2006) Different loop arrangements of intramolecular human telomeric (3 + 1) G-quadruplexes in K+ solution. Nucleic Acids Res 34(19): 5715−5719
Phan AT, Patel DJ (2003) Two-repeat human telomeric d(TAGGGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution: distinct topologies, thermodynamic properties, and folding/unfolding kinetics. J Am Chem Soc 125(49): 15021−15027
Ruan TL, Davis SJ, Powell BM, Harbeck CP, Habdas J, Habdas P, Yatsunyk LA (2016) Lowering the overall charge on TMPyP4 improves its selectivity for G-quadruplex DNA. Biochimie 132: 121−130
Salomon-Ferrer R, Case DA, Walker RC (2013) An overview of the Amber biomolecular simulation package. WIREs Comput Mol Sci 3(2): 198−210
Seenisamy J, Rezler EM, Powell TJ, Tye D, Gokhale V, Joshi CS, Siddiqui-Jain A, Hurley LH (2004) The dynamic character of the G-quadruplex element in the c-MYC promoter and modification by TMPyP4. J Am Chem Soc 126(28): 8702−8709
Siddiqui-Jain A, Grand CL, Bearss DJ, Hurley LH (2002) Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc Natl Acad Sci USA 99(18): 11593−11598
Sumi M, Tauchi T, Sashida G, Nakajima A, Ohyashiki K (2004) A G-quadruplex-interactive agent, telomestatin (SOT-095), induces telomere shortening with apoptosis and enhances chemosensitivity in acute myeloid leukemia. Int J Oncol 24(6): 1481−1487
Sun H, Duan L, Chen F, Liu H, Wang Z, Pan P, Zhu F, Zhang JZH, Hou T (2018) Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches. Phys Chem Chem Phys 20(21): 14450−14460
Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T (2019) End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design. Chem Rev 119(16): 9478−9508
Wang E, Weng G, Sun H, Du H, Zhu F, Chen F, Wang Z, Hou T (2019) Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein–protein interactions. Phys Chem Chem Phys 21(35): 18958−18969
Wang Y, Li G, Meng T, Qi L, Yan H, Wang Z (2022) Molecular insights into the selective binding mechanism targeting parallel human telomeric G-quadruplex. J Mol Graph Model 110: 108058. https://doi.org/10.1016/j.jmgm.2021.108058
Wang Z, Li J, Liu JP (2018) Effects of cation charges on the binding of stabilizers with human telomere and TERRA G-quadruplexes. J Biomol Struct Dyn 37(7): 1908−1921
Wang Z, Liu JP (2017) Effects of the central potassium ions on the G-quadruplex and stabilizer binding. J Mol Graph Model 72: 168−177
Weiser J, Shenkin PS, Still WC (1999) Approximate solvent-accessible surface areas from tetrahedrally directed neighbor densities. Biopolymers 50(4): 373−380
Weng G, Wang E, Wang Z, Liu H, Zhu F, Li D, Hou T (2019) HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA. Nucleic Acids Res 47(W1): W322−W330
Wu Y, Brosh RM (2010) G-quadruplex nucleic acids and human disease. FEBS J 277(17): 3470−3488
Yaku H, Fujimoto T, Murashima T, Miyoshi D, Sugimoto N (2012) Phthalocyanines: a new class of G-quadruplex-ligands with many potential applications. Chem Commun 48(50): 6203−6216
Yaku H, Murashima T, Miyoshi D, Sugimoto N (2010) Anionic phthalocyanines targeting G-quadruplexes and inhibiting telomerase activity in the presence of excessive DNA duplexes. Chem Commun 46(31): 5740−5742
Yan Y, Tan J, Ou T, Huang Z, Gu L (2013) DNA G-quadruplex binders: a patent review. Expert Opin Ther Pat 23(11): 1495−1509
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