Computational investigation of ginkgetin and theaflavin as potential inhibitors of heat shock protein 90 (Hsp90)

References

• Banks, J. L., Beard, H. S., Cao, Y., Cho, A. E., Damm, W., Farid, R., Felts, A. K., Halgren, T. A., Mainz, D. T., Maple, J. R., Murphy, R., Philipp, D. M., Repasky, M. P., Zhang, L. Y., Berne, B. J., Friesner, R. A., Gallicchio, E., & Levy, R. M. (2005). Integrated modeling program, applied chemical theory (IMPACT). Journal of Computational Chemistry, 26(16), 1752–1780. https://doi.org/10.1002/jcc.20292
   PubMed Web of Science ®Google Scholar
• Barrott, J. J., & Haystead, T. A. (2013). Hsp90, an unlikely ally in the war on cancer. The FEBS Journal, 280(6), 1381–1396.
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., & Hermans, A. J. (1981). Intermolecular forces (pp. 331–342). John Wiley & Sons.
   Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Bolton, E. E., Wang, Y., Thiessen, P. A., & Bryant, S. H. (2008). PubChem: Integrated platform of small molecules and biological activities. In Annual reports in computational chemistry (Vol. 4, pp. 217–241). Elsevier.
   Google Scholar
• Buchner, J., & Li, J. (2013). Structure, function and regulation of the hsp90 machinery. Biomedical Journal, 36(3), 106–117.
   PubMedGoogle Scholar
• Chatterjee, S., & Burns, T. (2017). Targeting heat shock proteins in cancer: A promising therapeutic approach. International Journal of Molecular Sciences, 18(9), 1978. https://doi.org/10.3390/ijms18091978
   PubMed Web of Science ®Google Scholar
• Condelli, V., Crispo, F., Pietrafesa, M., Lettini, G., Matassa, D. S., Esposito, F., Landriscina, M., & Maddalena, F. (2019). HSP90 molecular chaperones, metabolic rewiring, and epigenetics: Impact on tumor progression and perspective for anticancer therapy. Cells, 8(6), 532. https://doi.org/10.3390/cells8060532
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Dassault Systèmes BIOVIA. (2019). Discovery Studio Visualizer.
   Google Scholar
• De Leo, S. A., Zgajnar, N. R., Mazaira, G. I., Erlejman, A. G., & Galigniana, M. D. (2020). Role of the Hsp90-Immunophilin Heterocomplex in Cancer Biology. Current Cancer Therapy Reviews, 16(1), 19–28. https://doi.org/10.2174/1573394715666190102120801
   Web of Science ®Google Scholar
• Esfahani, K., & Cohen, V. (2016). HSP90 as a novel molecular target in non-small-cell lung cancer. Lung Cancer (Auckland, N.Z.), 7, 11–17. https://doi.org/10.2147/LCTT.S60344
   PubMed Web of Science ®Google Scholar
• Garrido, C., Gurbuxani, S., Ravagnan, L., & Kroemer, G. (2001). Heat shock proteins: Endogenous modulators of apoptotic cell death. Biochemical and Biophysical Research Communications, 286(3), 433–442.
   PubMed Web of Science ®Google Scholar
• Jakubík, J., Randáková, A., & Doležal, V. (2013). On homology modeling of the M 2 muscarinic acetylcholine receptor subtype. Journal of Computer-Aided Molecular Design, 27(6), 525–538. https://doi.org/10.1007/s10822-013-9660-8
   PubMed Web of Science ®Google Scholar
• Krieger, E., Darden, T., Nabuurs, S. B., Finkelstein, A., & Vriend, G. (2004). Making optimal use of empirical energy functions: Force‐field parameterization in crystal space. Proteins: Structure, Function, and Bioinformatics, 57(4), 678–683. https://doi.org/10.1002/prot.20251
   PubMed Web of Science ®Google Scholar
• Krieger, E., Joo, K., Lee, J., Lee, J., Raman, S., Thompson, J., Tyka, M., Baker, D., & Karplus, K. (2009). Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins: Structure, Function, and Bioinformatics, 77(S9), 114–122. https://doi.org/10.1002/prot.22570
   PubMed Web of Science ®Google Scholar
• Kumar, S. P., Patel, C. N., Rawal, R. M., & Pandya, H. A. (2020). Energetic contributions of amino acid residues and its cross‐talk to delineate ligand‐binding mechanism. Proteins: Structure, Function, and Bioinformatics, 88(9), 1207–1225. https://doi.org/10.1002/prot.25894
   PubMed Web of Science ®Google Scholar
• Li, J., Abel, R., Zhu, K., Cao, Y., Zhao, S., & Friesner, R. A. (2011). The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling. Proteins, 79(10), 2794–2812. https://doi.org/10.1002/prot.23106
   PubMed Web of Science ®Google Scholar
• Maestro-Desmond Interoperability Tools. (2021). Schrödinger.
   Google Scholar
• Martyna, G. J., Klein, M. L., & Tuckerman, M. (1992). Nosé–Hoover chains: The canonical ensemble via continuous dynamics. The Journal of Chemical Physics, 97(4), 2635–2643. https://doi.org/10.1063/1.463940
   Web of Science ®Google Scholar
• Martyna, G. J., Tobias, D. J., & Klein, M. L. (1994). Constant pressure molecular dynamics algorithms. The Journal of Chemical Physics, 101(5), 4177–4189. https://doi.org/10.1063/1.467468
   Web of Science ®Google Scholar
• Marvin Sketch v16.6.27. (2016). ChemAxon LLC.
   Google Scholar
• Mayo, S. L., Olafson, B. D., & Goddard, W. A. (1990). DREIDING: A generic force field for molecular simulations. The Journal of Physical Chemistry, 94(26), 8897–8909. https://doi.org/10.1021/j100389a010
   Web of Science ®Google Scholar
• Rong, B., & Rong, B. (2018). Molecular mechanism and targeted therapy of Hsp90 involved in lung cancer: New discoveries and developments (Review). International Journal of Oncology, 52(2), 321–336. https://doi.org/10.3892/ijo.2017.4214
   PubMed Web of Science ®Google Scholar
• Schrödinger Release 2021-3: Desmond Molecular Dynamics System. (2021). D. E. Shaw Research.
   Google Scholar
• Soo, E. T., Yip, G. W., Lwin, Z. M., Kumar, S. D., & Bay, B. H. (2008). Heat shock proteins as novel therapeutic targets in cancer. In Vivo (Athens, Greece), 22(3), 311–315.
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461.
   PubMed Web of Science ®Google Scholar
• Tuckerman, M. B. B. J. M., Berne, B. J., & Martyna, G. J. (1992). Reversible multiple time scale molecular dynamics. The Journal of Chemical Physics, 97(3), 1990–2001. https://doi.org/10.1063/1.463137
   Web of Science ®Google Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, Design and Selection, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
   Web of Science ®Google Scholar
• Woodhead, A. J., Angove, H., Carr, M. G., Chessari, G., Congreve, M., Coyle, J. E., Cosme, J., Graham, B., Day, P. J., Downham, R., Fazal, L., Feltell, R., Figueroa, E., Frederickson, M., Lewis, J., McMenamin, R., Murray, C. W., O'Brien, M. A., Parra, L., … Woolford, A. J.-A. (2010). Discovery of (2, 4-dihydroxy-5-isopropylphenyl)-[5-(4-methylpiperazin-1-ylmethyl)-1, 3-dihydroisoindol-2-yl] methanone (AT13387), a novel inhibitor of the molecular chaperone Hsp90 by fragment based drug design. Journal of Medicinal Chemistry, 53(16), 5956–5969. https://doi.org/10.1021/jm100060b
   PubMed Web of Science ®Google Scholar