References
- Baird, C. L., Gordon, M. S., Andrenyak, D. M., Marecek, J. F., & Lindsley, J. E. (2001). The ATPase reaction cycle of yeast DNA topoisomerase II. Slow rates of ATP resynthesis and P(i) release. The Journal of Biological Chemistry, 276(30), 27893–27898. https://doi.org/https://doi.org/10.1074/jbc.M102544200
- Bau, J. T., Kang, Z., Austin, C. A., & Kurz, E. U. (2014). Salicylate, a catalytic inhibitor of topoisomerase II, inhibits DNA cleavage and is selective for the α isoform. Molecular Pharmacology, 85(2), 198–207. https://doi.org/https://doi.org/10.1124/mol.113.088963
- Baviskar, A. T., Amrutkar, S. M., Trivedi, N., Chaudhary, V., Nayak, A., Guchhait, S. K., Banerjee, U. C., Bharatam, P. V., & Kundu, C. N. (2015). Switch in site of inhibition: A strategy for structure-based discovery of human topoisomerase IIα catalytic inhibitors. ACS Medicinal Chemistry Letters, 6(4), 481–485. https://doi.org/https://doi.org/10.1021/acsmedchemlett.5b00040
- Baviskar, A. T., Madaan, C., Preet, R., Mohapatra, P., Jain, V., Agarwal, A., Guchhait, S. K., Kundu, C. N., Banerjee, U. C., & Bharatam, P. V. (2011). N-fused imidazoles as novel anticancer agents that inhibit catalytic activity of topoisomerase IIα and induce apoptosis in G1/S phase. Journal of Medicinal Chemistry, 54(14), 5013–5030. https://doi.org/https://doi.org/10.1021/jm200235u
- Bayat Mokhtari, R., Homayouni, T. S., Baluch, N., Morgatskaya, E., Kumar, S., Das, B., & Yeger, H. (2017). Combination therapy in combating cancer. Oncotarget, 8(23), 38022–38043. https://doi.org/https://doi.org/10.18632/oncotarget.16723
- Berendsen, H. J., Postma, J. V., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/https://doi.org/10.1063/1.448118
- Cai, Y.-J., Lu, J.-J., Zhu, H., Xie, H., Huang, M., Lin, L.-P., Zhang, X.-W., & Ding, J. (2008). Salvicine triggers DNA double-strand breaks and apoptosis by GSH-depletion-driven H2O2 generation and topoisomerase II inhibition. Free Radical Biology & Medicine, 45(5), 627–635. https://doi.org/https://doi.org/10.1016/j.freeradbiomed.2008.05.017
- Chen, Y.-T., Collins, T. R. L., Guan, Z., Chen, V. B., & Hsieh, T.-S. (2012). Probing conformational changes in human DNA topoisomerase IIα by pulsed alkylation mass spectrometry. The Journal of Biological Chemistry, 287(30), 25660–25668. https://doi.org/https://doi.org/10.1074/jbc.M112.377606
- Chène, P., Rudloff, J., Schoepfer, J., Furet, P., Meier, P., Qian, Z., Schlaeppi, J.-M., Schmitz, R., & Radimerski, T. (2009). Catalytic inhibition of topoisomerase II by a novel rationally designed ATP-competitive purine analogue. BMC Chemical Biology, 9, 1–1. https://doi.org/https://doi.org/10.1186/1472-6769-9-1
- Classen, S., Olland, S., & Berger, J. M. (2003). Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187. Proceedings of the National Academy of Sciences, 100(19), 10629–10634. https://doi.org/https://doi.org/10.1073/pnas.1832879100
- El-Ezbawy, S. R., & Alshaikh, M. A. (1990 ). Synthesis and antibacterial activity of some new pyridyl diarylsulfide and diarylsulfones. Phosphorus, Sulfur, and Silicon and the Related Elements, 48(1–4), 111–116.
- Frisch, M., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, V., Barone, B., Mennucci, G. A., Petersson, H., Nakatsuji, M., Caricato, X., Li, H. P., Hratchian, A. F., Izmaylov, J., Bloino, G., Zheng, J. L., Sonnenberg, M., Hada, M., … Fox, D. J. (2014). Gaussian∼ 09 Revision D. 01. Gaussian, Inc.
- Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/https://doi.org/10.1517/17460441.2015.1032936
- Gurbani, D., Kukshal, V., Laubenthal, J., Kumar, A., Pandey, A., Tripathi, S., Arora, A., Jain, S. K., Ramachandran, R., Anderson, D., & Dhawan, A. (2012). Mechanism of inhibition of the ATPase domain of human topoisomerase IIα by 1,4-benzoquinone, 1,2-naphthoquinone, 1,4-naphthoquinone, and 9,10-phenanthroquinone. Toxicological Sciences: An Official Journal of the Society of Toxicology, 126(2), 372–390. https://doi.org/https://doi.org/10.1093/toxsci/kfr345
- Hande, K. R. (2008). Topoisomerase II inhibitors. Update on Cancer Therapeutics, 3(1), 13–26. https://doi.org/https://doi.org/10.1016/j.uct.2008.02.001
- Hevener, K., Verstak, T. A., Lutat, K. E., Riggsbee, D. L., & Mooney, J. W. (2018). Recent developments in topoisomerase-targeted cancer chemotherapy. Acta Pharmaceutica Sinica. B, 8(6), 844–861. https://doi.org/https://doi.org/10.1016/j.apsb.2018.07.008
- Hu, C.-X., Zuo, Z.-L., Xiong, B., Ma, J.-G., Geng, M.-Y., Lin, L.-P., Jiang, H.-L., & Ding, J. (2006). Salvicine functions as novel topoisomerase II poison by binding to ATP pocket. Molecular Pharmacology, 70(5), 1593–1601. https://doi.org/https://doi.org/10.1124/mol.106.027714
- Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/https://doi.org/10.1063/1.445869
- Kaiyawet, N., Rungrotmongkol, T., & Hannongbua, S. (2013). Effect of halogen substitutions on dUMP to stability of thymidylate synthase/dUMP/mTHF ternary complex using molecular dynamics simulation. Journal of Chemical Information and Modeling, 53(6), 1315–1323. https://doi.org/https://doi.org/10.1021/ci400131y
- Katrun, P., Chiampanichayakul, S., Korworapan, K., Pohmakotr, M., Reutrakul, V., Jaipetch, T., & Kuhakarn, C. (2010). PhI(OAc)2/KI-mediated reaction of aryl sulfinates with alkenes, alkynes, and α,β-unsaturated carbonyl compounds: Synthesis of vinyl sulfones and β-iodovinyl sulfones. European Journal of Organic Chemistry, 2010(29), 5633–5641. https://doi.org/https://doi.org/10.1002/ejoc.201000641
- Katrun, P., Hlekhlai, S., Meesin, J., Pohmakotr, M., Reutrakul, V., Jaipetch, T., Soorukram, D. ,& Kuhakarn, C. (2015). PhI(OAc)2 mediated decarboxylative sulfonylation of β-aryl-α, β-unsaturated carboxylic acids: A synthesis of (E)-vinyl sulfones. Organic & Biomolecular Chemistry, 13(16), 4785–4794. https://doi.org/https://doi.org/10.1039/C5OB00417A.
- Ke, X., & Shen, L. (2017). Molecular targeted therapy of cancer: The progress and future prospect. Frontiers in Laboratory Medicine, 1(2), 69–75. https://doi.org/https://doi.org/10.1016/j.flm.2017.06.001
- Kesharwani, R. K., & Misra, K. J. C. S. (2011). Prediction of binding site for curcuminoids at human topoisomerase II α protein; an in silico approach. Current Science, 101(8), 1060–1065. https://www.jstor.org/stable/24079286
- Kesharwani, R. K., Singh, D. B., Singh, D. V., & Misra, K. (2018). Computational study of curcumin analogues by targeting DNA topoisomerase II: A structure-based drug designing approach. Network Modeling Analysis in Health Informatics and Bioinformatics, 7(1), 15. https://doi.org/https://doi.org/10.1007/s13721-018-0179-8
- Kollman, P. A., 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, D. A., & Cheatham, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889–897. https://doi.org/https://doi.org/10.1021/ar000033j
- Lee, J. H., Wendorff, T. J., & Berger, J. M. (2017). Resveratrol: A novel type of topoisomerase II inhibitor. The Journal of Biological Chemistry, 292(51), 21011–21022. https://doi.org/https://doi.org/10.1074/jbc.M117.810580
- Liang, H., Wu, X., Yalowich, J. C., & Hasinoff, B. B. (2008). A three-dimensional quantitative structure-activity analysis of a new class of bisphenol topoisomerase IIalpha inhibitors. Molecular Pharmacology, 73(3), 686–696. https://doi.org/https://doi.org/10.1124/mol.107.041624
- Mahalapbutr, P., Chusuth, P., Kungwan, N., Chavasiri, W., Wolschann, P., & Rungrotmongkol, T. (2017). Molecular recognition of naphthoquinone-containing compounds against human DNA topoisomerase IIα ATPase domain: A molecular modeling study. Journal of Molecular Liquids, 247, 374–385. https://doi.org/https://doi.org/10.1016/j.molliq.2017.10.021
- Mahalapbutr, P., Darai, N., Panman, W., Opasmahakul, A., Kungwan, N., Hannongbua, S., & Rungrotmongkol, T. (2019). Atomistic mechanisms underlying the activation of the G protein-coupled sweet receptor heterodimer by sugar alcohol recognition. Scientific Reports, 9(1), 10205. https://doi.org/https://doi.org/10.1038/s41598-019-46668-w
- Mahalapbutr, P., Lee, V. S., Rungrotmongkol, T. J. J. O. A., & Chemistry, F. (2020). Binding hotspot and activation mechanism of maltitol and lactitol toward the human sweet taste receptor. Journal of Agricultural and Food Chemistry, 68(30), 7974–7983. https://doi.org/https://doi.org/10.1021/acs.jafc.0c02580
- Mahalapbutr, P., Sangkhawasi, M., Kammarabutr, J., Chamni, S., & Rungrotmongkol, T (2020, July 29). Rosmarinic acid as a potent influenza neuraminidase inhibitor: In vitro and in silico study. Current Topics in Medicinal Chemistry https://doi.org/https://doi.org/10.2174/1568026619666191118110155. Online ahead of print.
- Mahalapbutr, P., Thitinanthavet, K., Kedkham, T., Nguyen, H., Theu, L. t h., Dokmaisrijan, S., Huynh, L., Kungwan, N., & Rungrotmongkol, T. (2019). A theoretical study on the molecular encapsulation of luteolin and pinocembrin with various derivatized beta-cyclodextrins. Journal of Molecular Structure, 1180, 480–490. https://doi.org/https://doi.org/10.1016/j.molstruc.2018.12.025
- Mahalapbutr, P., Wonganan, P., Chavasiri, W., & Rungrotmongkol, T. (2019). Butoxy Mansonone G inhibits STAT3 and Akt signaling pathways in non-small cell lung cancers: Combined experimental and theoretical investigations. Cancers, 11(4), 437. https://doi.org/https://doi.org/10.3390/cancers11040437
- Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/https://doi.org/10.1021/acs.jctc.5b00255
- Masoud, V., & Pagès, G. (2017). Targeted therapies in breast cancer: New challenges to fight against resistance. World Journal of Clinical Oncology, 8(2), 120–134. https://doi.org/https://doi.org/10.5306/wjco.v8.i2.120
- Meesin, J., Katrun, P., Pareseecharoen, C., Pohmakotr, M., Reutrakul, V., Soorukram, D., & Kuhakarn, C. (2016). Iodine-catalyzed sulfonylation of arylacetylenic acids and arylacetylenes with sodium sulfinates: Synthesis of arylacetylenic sulfones. The Journal of Organic Chemistry, 81(7), 2744–2752. https://doi.org/https://doi.org/10.1021/acs.joc.5b02810
- Meesin, J., Katrun, P., Reutrakul, V., Pohmakotr, M., Soorukram, D., & Kuhakarn, C. (2016). Decarboxylative sulfonylation of arylpropiolic acids with sulfinic acids: Synthesis of (E)-vinyl sulfones. Tetrahedron, 72(11), 1440–1446. https://doi.org/https://doi.org/10.1016/j.tet.2016.01.042
- Meng, L-H., Zhang, J-S., & Ding, J. (2001). Salvicine, a novel DNA topoisomerase II inhibitor, exerting its effects by trapping enzyme-DNA cleavage complexes. Biochemical Pharmacology, 62(6), 733–741. https://doi.org/https://doi.org/10.1016/s0006-2952(01)00732-8.
- Morris, K. F., Geoghegan, R. M., Palmer, E. E., George, M., & Fang, Y. (2020). Molecular dynamics simulation study of AG10 and tafamidis binding to the Val122Ile transthyretin variant. Biochemistry and Biophysics Reports, 21, 100721. https://doi.org/https://doi.org/10.1016/j.bbrep.2019.100721
- Nitiss, J. L. (2009). Targeting DNA topoisomerase II in cancer chemotherapy. Nature Reviews Cancer, 9(5), 338–350. https://doi.org/https://doi.org/10.1038/nrc2607
- Olsson, M. H., Søndergaard, C. R., Rostkowski, M., & Jensen, J. H. (2011). PROPKA3: Consistent treatment of internal and surface residues in empirical p K a predictions. Journal of Chemical Theory and Computation, 7(2), 525–537. https://doi.org/https://doi.org/10.1021/ct100578z
- Pandey, A. K., Gurbani, D., Bajpayee, M., Parmar, D., Ajmani, S., & Dhawan, A. (2009). In silico studies with human DNA topoisomerase-II alpha to unravel the mechanism of in vitro genotoxicity of benzene and its metabolites. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 661(1–2), 57–70. https://doi.org/https://doi.org/10.1016/j.mrfmmm.2008.11.006
- Paquet, E., & Viktor, H. L. J. B. R. I. (2015). Molecular dynamics, Monte Carlo simulations, and langevin dynamics: A computational review. BioMed Research International, 2015, 183918.
- Phanich, J., Rungrotmongkol, T., Sindhikara, D., Phongphanphanee, S., Yoshida, N., Hirata, F., Kungwan, N., & Hannongbua, S. (2016). A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase. Protein Science: A Publication of the Protein Society, 25(1), 147–158. https://doi.org/https://doi.org/10.1002/pro.2718
- Piazza, G. A., Rahm, A. L., Krutzsch, M., Sperl, G., Paranka, N. S., Gross, P. H., Brendel, K., Burt, R. W., Alberts, D. S., & Pamukcu, R. (1995). Antineoplastic drugs sulindac sulfide and sulfone inhibit cell growth by inducing apoptosis. Cancer Research, 55(14), 3110–3116.
- Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/https://doi.org/10.1016/0021-9991(77)90098-5
- Sangpheak, K., Mueller, M., Darai, N., Wolschann, P., Suwattanasophon, C., Ruga, R., Chavasiri, W., Seetaha, S., Choowongkomon, K., Kungwan, N., Rungnim, C., & Rungrotmongkol, T. (2019). Computational screening of chalcones acting against topoisomerase IIα and their cytotoxicity towards cancer cell lines. Journal of Enzyme Inhibition and Medicinal Chemistry, 34(1), 134–143. https://doi.org/https://doi.org/10.1080/14756366.2018.1507029
- Sarkar, B., Ullah, M. A., & Islam, S. S. (2020). In silico analysis of some phytochemicals as potential anti-cancer agents targeting cyclin dependent kinase-2, human topoisomerase IIa and vascular endothelial growth factor receptor-2. bioRxiv.Journal of Receptors and Signal Transduction.https://doi.org/https://doi.org/10.1080/10799893.2020.1805628
- Schrank, Z., Chhabra, G., Lin, L., Iderzorig, T., Osude, C., Khan, N., Kuckovic, A., Singh, S., Miller, R., & Puri, N. (2018). Current molecular-targeted therapies in NSCLC and their mechanism of resistance. Cancers, 10(7), 224. https://doi.org/https://doi.org/10.3390/cancers10070224
- Tripathi, N., Guchhait, S. K., & Bharatam, P. V. (2019). Pharmacoinformatics analysis of merbarone binding site in human topoisomerase IIα. Journal of Molecular Graphics & Modelling, 86, 1–18. https://doi.org/https://doi.org/10.1016/j.jmgm.2018.09.013
- Tripathi, N., Shaikh, N., Bharatam, P. V., & Garg, P. (2019). HToPred: A tool for human topoisomerase II inhibitor prediction. Molecular Informatics, 380, 1800046. https://doi.org/https://doi.org/10.1002/minf.201800046
- Vedula, M. S., Pulipaka, A. B., Venna, C., Chintakunta, V. K., Jinnapally, S., Kattuboina, V. A., Vallakati, R. K., Basetti, V., Akella, V., Rajgopal, S., Reka, A. K., Teepireddy, S. K., Mamnoor, P. K., Rajagopalan, R., Bulusu, G., Khandelwal, A., Upreti, V. V., & Mamidi, S. R. (2003). New styryl sulfones as anticancer agents. European Journal of Medicinal Chemistry, 38(9), 811–824. https://doi.org/https://doi.org/10.1016/S0223-5234(03)00144-2
- Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/https://doi.org/10.1002/jcc.20035
- Wei, H., Ruthenburg, A. J., Bechis, S. K., & Verdine, G. L. (2005). Nucleotide-dependent domain movement in the ATPase domain of a human type IIA DNA topoisomerase. The Journal of Biological Chemistry, 280(44), 37041–37047. https://doi.org/https://doi.org/10.1074/jbc.M506520200
- Wu, T., Wang, Y., & Yuan, Y. (2014). Antiviral activity of topoisomerase II catalytic inhibitors against Epstein-Barr virus. Antiviral Research, 107, 95–101. https://doi.org/https://doi.org/10.1016/j.antiviral.2014.05.003
- York, D. M., Darden, T. A., & Pedersen, L. G. (1993). The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods. The Journal of Chemical Physics, 99(10), 8345–8348. https://doi.org/https://doi.org/10.1063/1.465608
- Zhang, C., Lovering, F., Behnke, M., Zask, A., Sandanayaka, V., Sun, L., Zhu, Y., Xu, W., Zhang, Y., & Levin, J. I. (2009). Synthesis and activity of quinolinylmethyl P1' alpha-sulfone piperidine hydroxamate inhibitors of TACE . Bioorganic & Medicinal Chemistry Letters, 19(13), 3445–3448. https://doi.org/https://doi.org/10.1016/j.bmcl.2009.05.020