Computer-aided screening for suppressor of variegation 4-20 homolog 1 inhibitors and their preliminary activity validation in human osteosarcoma

References

• Adrià, C. M., Laura, G., Cristina, V., Miquel, M., Gerard, P., & Santiago, G. V. (2012). DecoyFinder: An easy-to-use python GUI application for building target-specific decoy sets. Bioinformatics, 28(12), 1661–1662.
   PubMed Web of Science ®Google Scholar
• Andersen, H. C. (1983). Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations. Journal of Computational Physics, 52(1), 24–34. doi:10.1016/0021-9991(83)90014-1
   Web of Science ®Google Scholar
• Balius, T. E., Sudipto, M., & Rizzo, R. C. (2011). Implementation and evaluation of a docking-rescoring method using molecular footprint comparisons. Journal of Computational Chemistry, 32(10), 2273–2289. doi:10.1002/jcc.21814
   PubMed Web of Science ®Google Scholar
• Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., … Zhao, K. (2007). High-resolution profiling of histone methylations in the human genome. Cell, 129(4), 823–837. doi:10.1016/j.cell.2007.05.009
   PubMed Web of Science ®Google Scholar
• Beck, D. B., Oda, H., Shen, S. S., & Reinberg, D. (2012). PR-Set7 and H4K20me1: At the crossroads of genome integrity, cell cycle, chromosome condensation, and transcription. Genes & Development, 26(4), 325–337. doi:10.1101/gad.177444.111
   PubMed Web of Science ®Google Scholar
• Brohm, A., Elsawy, H., Rathert, P., Kudithipudi, S., Schoch, T., Schuhmacher, M. K., … Jeltsch, A. (2019). Somatic cancer mutations in the SUV420H1 protein lysine methyltransferase modulate its catalytic activity. Journal of Molecular Biology, 431(17), 3068–3080. doi:10.1016/j.jmb.2019.06.021
   PubMed Web of Science ®Google Scholar
• Bromberg, K. D., Mitchell, T. R. H., Upadhyay, A. K., Jakob, C. G., Jhala, M. A., Comess, K. M., … Pappano, W. N. (2017). The SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity. Nature Chemical Biology, 13(3), 317–324. doi:10.1038/nchembio.2282
   PubMed Web of Science ®Google Scholar
• Case, D., Anandakrishnan, R., Ayers, K., Betz, R., Bomble, Y., Brown, R., … Zhang, W. (2012). AMBERTOOLS 12. San Francisco: University of California.
   Google Scholar
• Copeland, R. A., Solomon, M. E., & Richon, V. M. (2009). Protein methyltransferases as a target class for drug discovery. Nature Reviews Drug Discovery, 8(9), 724–732. doi:10.1038/nrd2974
   PubMed Web of Science ®Google Scholar
• David, V. D. S., Erik, L., Berk, H., Gerrit, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. doi:10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. doi:10.1063/1.470117
   Web of Science ®Google Scholar
• Farzaneh, K., Thaler, R., Paradise, C. R., Deyle, D. R., Kruijthof-De, J. M., Galindo, M., … van Wijnen, A. J. (2016). Histone H4 methyltransferase Suv420h2 maintains fidelity of osteoblast differentiation. Journal of Cellular Biochemistry, 118(5), 1262–1272.doi:10.1002/jcb.25787
   Web of Science ®Google Scholar
• Faundes, V., Newman, W. G., Bernardini, L., Canham, N., Clayton-Smith, J., Dallapiccola, B., …. Hurles, M. E. (2018). Histone lysine methylases and demethylases in the landscape of human developmental disorders. The American Journal of Human Genetics, 102(1), 175–187. doi:10.1016/j.ajhg.2017.11.013
   PubMed Web of Science ®Google Scholar
• Hawkins, G. D., Cramer, C. J., & Truhlar, D. G. (1996). Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. The Journal of Physical Chemistry, 100(51), 19824–19839. doi:10.1021/jp961710n
   Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Hong, W., Alena, S., Hong, Z., Robert, L., Aiping, D., Xian-Hui, W., … Jinrong, M. (2013). Crystal structures of the human histone H4K20 methyltransferases SUV420H1 and SUV420H2. FEBS Letters, 587(23), 3859–3868.
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. doi:10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Jakalian, A., Bush, B. L., Jack, D. B., & Bayly, C. I. (2000). Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method. Journal of Computational Chemistry, 21(2), 132–146. doi:10.1002/(sici)1096-987x(20000130)21:2 < 132::aid-jcc5 > 3.3.co;2-g
   Web of Science ®Google Scholar
• Jie, J., Lin, C., Zhi-Ming, L., & Xue-Song, Z. (2013). miRNA-218 inhibits osteosarcoma cell migration and invasion by down-regulating of TIAM1, MMP2 and MMP9. Asian Pacific Journal of Cancer Prevention: APJCP, 14(6), 3681–3684.
   PubMedGoogle Scholar
• Jorgensen, S., Schotta, G., & Sorensen, C. S. (2013). Histone H4 lysine 20 methylation: Key player in epigenetic regulation of genomic integrity. Nucleic Acids Research, 41(5), 2797–2806. doi:10.1093/nar/gkt012
   PubMed Web of Science ®Google Scholar
• Kitchen, D. B., Hélène, D., Furr, J. R., & Jürgen, B. (2004). Docking and scoring in virtual screening for drug discovery: Methods and applications. Nature Reviews Drug Discovery, 3(11), 935–949. doi:10.1038/nrd1549
   PubMed Web of Science ®Google Scholar
• Konecny, R., Baker, N. A., & McCammon, J. A. (2012). iAPBS: A programming interface to Adaptive Poisson-Boltzmann Solver (APBS). Computational Science & Discovery, 5(1). doi:10.1088/1749-4699/5/1/015005
   PubMedGoogle Scholar
• Kristian, H., & Dashyant, D. (2013). Chromatin proteins and modifications as drug targets. Nature, 502(7472), 480–488.
   PubMed Web of Science ®Google Scholar
• Kuo, A. J., Cheung, P., Chen, K., Zee, B. M., Kioi, M., Lauring, J., … Gozani, O. (2011). NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. Molecular Cell, 44(4), 609–620. doi:10.1016/j.molcel.2011.08.042
   PubMed Web of Science ®Google Scholar
• Lingling, J., & Rizzo, R. C. (2015). Pharmacophore-based similarity scoring for DOCK. The Journal of Physical Chemistry B, 119(3), 1083–1102. doi:10.1021/jp506555w
   PubMed Web of Science ®Google Scholar
• Liu, L., Kimball, S., Liu, H., Holowatyj, A., & Yang, Z. Q. (2015). Genetic alterations of histone lysine methyltransferases and their significance in breast cancer. Oncotarget, 6(4), 2466–2482. doi:10.18632/oncotarget.2967
   PubMed Web of Science ®Google Scholar
• Miyamoto, S., & Kollman, P. A. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13(8), 952–962. doi:10.1002/jcc.540130805
   Web of Science ®Google Scholar
• Morera, L., Lübbert, M., & Jung, M. (2016). Targeting histone methyltransferases and demethylases in clinical trials for cancer therapy. Clinical Epigenetics, 8(1), 57. doi:10.1186/s13148-016-0223-4
   PubMed Web of Science ®Google Scholar
• Nishioka, K., Rice, J. C., Sarma, K., Erdjument-Bromage, H., Werner, J., Wang, Y., … Reinberg, D. (2002). PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Molecular Cell, 9(6), 1201–1213. doi:10.1016/S1097-2765(02)00548-8
   PubMed Web of Science ®Google Scholar
• Nose, S. (1984). A unified formation of the constant temperature molecular dynamics methods. Journal of Chemical Physics, 81(1), 511–519.
   Web of Science ®Google Scholar
• Pedrotti, S., Caccia, R., Neguembor, M. V., Garcia-Manteiga, J. M., Ferri, G., de Palma, C., … Gabellini, D. (2019). The Suv420h histone methyltransferases regulate PPAR-gamma and energy expenditure in response to environmental stimuli. Science Advances, 5(4), eaav1472. doi:10.1126/sciadv.aav1472
   PubMed Web of Science ®Google Scholar
• Pei, H., Zhang, L., Luo, K., Qin, Y., Chesi, M., Fei, F., … Lou, Z. (2011). MMSET regulates histone H4K20 methylation and 53BP1 accumulation at DNA damage sites. Nature, 470(7332), 124–128. doi:10.1038/nature09658
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera–A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. doi:10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Rashmi, K., Rajendra, K., & Andrew, L. (2014). g_mmpbsa–A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information & Modeling, 54(7), 1951–1962.
   PubMed Web of Science ®Google Scholar
• Rayasam, G. W. O., Angrand, P. O., Mark, M., Niederreither, K., Song, L. L. T., Hager, G. L., … Losson, R. (2003). NSD1 is essential for early post-implantation development and has a catalytically active SET domain. The EMBO Journal, 22(12), 3153–3163. doi:10.1093/emboj/cdg288
   PubMed Web of Science ®Google Scholar
• Rehman, M. T., AlAjmi, M. F., Hussain, A., Rather, G. M., & Khan, M. A. (2019). High-throughput virtual screening, molecular dynamics simulation, and enzyme kinetics identified ZINC84525623 as a potential inhibitor of NDM-1. International Journal of Molecular Sciences, 20(4), 819. doi:10.3390/ijms20040819
   Web of Science ®Google Scholar
• Robin, X., Turck, N., Hainard, A., Tiberti, N., Lisacek, F., Sanchez, J.-C., & Müller, M. (2011). pROC: An open-source package for R and S + to analyze and compare ROC curves. BMC Bioinformatics, 12(1), 1–8. doi:10.1186/1471-2105-12-77
   PubMed Web of Science ®Google Scholar
• Samudravijaya, K. (2010). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins-Structure Function & Bioinformatics, 65(3), 712–725.
   Google Scholar
• Sander, P., Szilárd, P., Roland, S., Per, L., Pär, B., Rossen, A., … David, V. D. S. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7), 845–854.
   PubMed Web of Science ®Google Scholar
• Sanders, S. L., Portoso, M., Mata, J., Bahler, J., Allshire, R. C., & Kouzarides, T. (2004). Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage. Cell, 119(5), 603–614. doi:10.1016/j.cell.2004.11.009
   PubMed Web of Science ®Google Scholar
• Schotta, G., Lachner, M., Sarma, K., Ebert, A., Sengupta, R., Reuter, G., … Jenuwein, T. (2004). A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes & Development, 18(11), 1251–1262. doi:10.1101/gad.300704
   PubMed Web of Science ®Google Scholar
• Silva, A. W. S. D., & Vranken, W. F. (2012). ACPYPE - AnteChamber PYthon Parser interfacE. BMC Research Notes, 5(1), 367. doi:10.1186/1756-0500-5-367
   PubMedGoogle Scholar
• Song, Y., Wu, F., & Wu, J. (2016). Targeting histone methylation for cancer therapy: Enzymes, inhibitors, biological activity and perspectives. Journal of Hematology & Oncology, 9(1), 49. doi:10.1186/s13045-016-0279-9
   PubMed Web of Science ®Google Scholar
• Team, C. R. (2010). Team RDC.R: A language and environment for statistical computing. R Foundation for Statistical Computing: Vienna, Austria. Computing, 14, 12–21.
   Google Scholar
• Tony, K. (2007). Chromatin modifications and their function. Cell, 128(4), 693–705.
   PubMed Web of Science ®Google Scholar
• Vougiouklakis, T., Sone, K., Saloura, V., Cho, H.-S., Suzuki, T., Dohmae, N., … Hamamoto, R. (2015). SUV420H1 enhances the phosphorylation and transcription of ERK1 in cancer cells. Oncotarget, 6(41), 43162–43171. doi:10.18632/oncotarget.6351
   PubMedGoogle Scholar
• Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2007). Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling, 25(2), 247–260. doi:10.1016/j.jmgm.2005.12.005
   Web of Science ®Google Scholar
• Xu, H. L., Wang, Z. J., Liang, X. M., Li, X., Shi, Z., Zhou, N., & Bao, J. K. (2014). In silico identification of novel kinase inhibitors targeting wild-type and T315I mutant ABL1 from FDA-approved drugs. Molecular Biosystems, 10(6), 1524–1537. doi:10.1039/c3mb70577c
   PubMedGoogle Scholar
• Zacchi, P., Gostissa, M., Uchida, T., Salvagno, C., Avolio, F., Volinia, S., … Sal, G. D. (2002). The prolyl isomerase Pin1 reveals a mechanism to control p53 functions after genotoxic insults. Nature, 419(6909), 853–857. doi:10.1038/nature01120
   PubMed Web of Science ®Google Scholar