QSAR studies on the human sirtuin 2 inhibition by non-covalent 7,5,2-anilinobenzamide derivatives

References

• Alam, S., & Khan, F. (2017). 3D-QSAR studies on Maslinic acid analogs for anticancer activity against breast cancer cell line MCF-7. Scientific Reports, 7(1), 6019. doi:10.1038/s41598-017-06131-0
   PubMedGoogle Scholar
• Andreoli, F., & Del Rio, A. (2015). Computer-aided molecular design of compounds targeting histone modifying enzymes. Computational and Structural Biotechnology Journal, 13, 358–365. doi:10.1016/j.csbj.2015.04.007
   PubMed Web of Science ®Google Scholar
• Bobrowska, A., Donmez, G., Weiss, A., Guarente, L., & Bates, G. (2012). SIRT2 ablation has no effect on tubulin acetylation in brain, cholesterol biosynthesis or the progression of Huntington’s disease phenotypes in vivo. PLoS One, 7(4), e34805. doi:10.1371/journal.pone.0034805
   PubMed Web of Science ®Google Scholar
• Braga, R. C., Alves, V. M., Silva, M. F. B., Muratov, E., Fourches, D., Tropsha, A., & Andrade, C. H. (2014). Tuning HERG out: antitarget QSAR models for drug development. Current Topics in Medicinal Chemistry, 14(11), 1399–1415.
   PubMed Web of Science ®Google Scholar
• Chen, G., Zhou, D., Li, X.-Z., Jiang, Z., Tan, C., Wei, X.-Y., … Li, N. (2017). A natural chalcone induces apoptosis in lung cancer cells: 3D-QSAR, docking and an in vivo/vitro assay. Scientific Reports, 7(1), 10729. doi:10.1038/s41598-017-11369-9
   PubMedGoogle Scholar
• Chirico, N., & Gramatica, P. (2011). Real external predictivity of QSAR models: how to evaluate it? Comparison of different validation criteria and proposal of using the concordance correlation coefficient. Journal of Chemical Information and Modeling, 51(9), 2320–2335. doi:10.1021/ci200211n
   PubMed Web of Science ®Google Scholar
• Choudhary, C., Weinert, B. T., Nishida, Y., Verdin, E., & Mann, M. (2014). The growing landscape of lysine acetylation links metabolism and cell signalling. Nature Reviews Molecular Cell Biology, 15(8), 536–550. doi:10.1038/nrm3841
   PubMed Web of Science ®Google Scholar
• Chuang, Y.-C., Chang, C.-H., Lin, J.-T., & Yang, C.-N. (2015). Molecular modelling studies of sirtuin 2 inhibitors using three-dimensional structure–activity relationship analysis and molecular dynamics simulations. Molecular Biosystems, 11(3), 723–733. doi:10.1039/C4MB00620H
   PubMedGoogle Scholar
• Delano, W. L. (2004). PyMOL reference guide. San Carlos, California, USA: DeLano Scientific LLC.
   Google Scholar
• Feinberg, A. P., & Vogelstein, B. (1983). Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature, 301(5895), 89–92. doi:10.1038/301089a0
   PubMed Web of Science ®Google Scholar
• Feldman, J. L., Baeza, J., & Denu, J. M. (2013). Activation of the protein deacetylase SIRT6 by long-chain fatty acids and widespread deacylation by mammalian sirtuins. Journal of Biological Chemistry, 288(43), 31350–31356. doi:10.1074/jbc.C113.511261
   PubMed Web of Science ®Google Scholar
• Gaudio, A. C., & Zandonade, E. (2001). Proposição, validação e análise dos modelos que correlacionam estrutura química e atividade biológica. Química Nova, 24(5), 658–671. doi:10.1590/S0100-40422001000500013
   Web of Science ®Google Scholar
• Gramatica, P. (2007). Principles of QSAR models validation: internal and external. QSAR & Combinatorial Science, 26(5), 694–701. doi:10.1002/qsar.200610151
   Google Scholar
• Halgren, T. A. (1996). Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. Journal of Computational Chemistry, 17(5–6), 490–519. doi:10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P
   Web of Science ®Google Scholar
• He, B., Hu, J., Zhang, X., & Lin, H. (2014). Thiomyristoyl peptides as cell-permeable Sirt6 inhibitors. Organic & Biomolecular Chemistry, 12(38), 7498–7502. doi:10.1039/C4OB00860J
   PubMed Web of Science ®Google Scholar
• Infometrix. (1985). Pirouette multivariate data analysis software. Bothell, Washington: EUA.
   Google Scholar
• Jiang, W., Wang, S., Xiao, M., Lin, Y., Zhou, L., Lei, Q., … Zhao, S. (2011). Acetylation regulates gluconeogenesis by promoting PEPCK1 degradation via recruiting the UBR5 ubiquitin ligase. Molecular Cell, 43(1), 33–44. doi:10.1016/j.molcel.2011.04.028
   PubMed Web of Science ®Google Scholar
• Jing, E., Gesta, S., & Kahn, C. R. (2007). SIRT2 regulates adipocyte differentiation through FoxO1 acetylation/deacetylation. Cell Metabolism, 6(2), 105–114. doi:10.1016/j.cmet.2007.07.003
   PubMed Web of Science ®Google Scholar
• Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997). Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen. Journal of Molecular Biology, 267(3), 727–748. doi:10.1006/jmbi.1996.0897
   PubMed Web of Science ®Google Scholar
• Kim, H.-S., Vassilopoulos, A., Wang, R.-H., Lahusen, T., Xiao, Z., Xu, X., … Deng, C.-X. (2011). SIRT2 maintains genome integrity and suppresses tumorigenesis through regulating APC/C activity. Cancer Cell, 20(4), 487–499. doi:10.1016/j.ccr.2011.09.004
   PubMed Web of Science ®Google Scholar
• Kowalski, B. R. (Ed.). (1977). Chemometrics: Theory and application, vol. 52. Washington, DC: American Chemical Society. doi:10.1021/bk-1977-0052
   Google Scholar
• Kunal, R., Supratik, K., & Das, R. N. (2015). Statistical methods in QSAR/QSPR. In E. Hawkins (Ed.), A primer on QSAR/QSPR modeling – fundamental concepts (pp. 37–59). New York: Springer International Publishing. doi:10.1007/978-3-319-17281-1
   Google Scholar
• Lara, E., Mai, A., Calvanese, V., Altucci, L., Lopez-Nieva, P., Martinez-Chantar, M. L., … Fraga, M. F. (2009). Salermide, a Sirtuin inhibitor with a strong cancer-specific proapoptotic effect. Oncogene, 28(6), 781–791. doi:10.1038/onc.2008.436
   PubMed Web of Science ®Google Scholar
• Lie, M. A., Thomsen, R., Pedersen, C. N. S., Schiøtt, B., & Christensen, M. H. (2011). Molecular docking with ligand attached water molecules. Journal of Chemical Information and Modeling, 51(4), 909–917. doi:10.1021/ci100510m
   PubMed Web of Science ®Google Scholar
• Lin, R., Tao, R., Gao, X., Li, T., Zhou, X., Guan, K.-L., … Lei, Q.-Y. (2013). Acetylation stabilizes ATP-citrate lyase to promote lipid biosynthesis and tumor growth. Molecular Cell, 51(4), 506–518. doi:10.1016/j.molcel.2013.07.002
   PubMed Web of Science ®Google Scholar
• Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. doi:10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Mai, A., Massa, S., Pezzi, R., Valente, S., Loidl, P., & Brosch, G. (2005). Synthesis and biological evaluation of 2-, 3-, and 4-acylaminocinnamyl-N-hydroxyamides as novel synthetic HDAC inhibitors. Medicinal Chemistry (Shariqah (United Arab Emirates)), 1(3), 245–254.
   PubMedGoogle Scholar
• Mellini, P., Itoh, Y., Tsumoto, H., Li, Y., Suzuki, M., Tokuda, N., … Suzuki, T. (2017). Potent mechanism-based sirtuin-2-selective inhibition by an in situ-generated occupant of the substrate-binding site, “selectivity pocket” and NAD+-binding site. Chemical Science, 8(9), 6400–6408. doi:10.1039/C7SC02738A
   PubMed Web of Science ®Google Scholar
• Menzies, K. J., Zhang, H., Katsyuba, E., & Auwerx, J. (2016). Protein acetylation in metabolism - metabolites and cofactors. Nature Reviews Endocrinology, 12(1), 43–60. doi:10.1038/nrendo.2015.181
   PubMed Web of Science ®Google Scholar
• Napper, A. D., Hixon, J., McDonagh, T., Keavey, K., Pons, J. F., Barker, J.…, Curtis, R. (2005). Discovery of indoles as potent and selective inhibitors of the deacetylase SIRT1. Journal of Medicinal Chemistry, 48(25), 8045–8054. doi:10.1021/JM050522V
   PubMed Web of Science ®Google Scholar
• Puigserver, P., Wu, Z., Park, C. W., Graves, R., Wright, M., & Spiegelman, B. M. (1998). A cold-inducible coactivator of nuclear receptors linked to adaptive thermogenesis. Cell, 92(6), 829–839.(00)81410-5 doi:10.1016/S0092-8674(00)81410-5
   PubMed Web of Science ®Google Scholar
• Ramis, M. R., Esteban, S., Miralles, A., Tan, D. X., & Reiter, R. J. (2015). Caloric restriction, resveratrol and melatonin: Role of SIRT1 and implications for aging and related-diseases. Mech Ageing Dev, 146–148, 28–41. doi:10.1016/j.mad.2015.03.008
   PubMed Web of Science ®Google Scholar
• Rodgers, J. T., Lerin, C., Haas, W., Gygi, S. P., Spiegelman, B. M., & Puigserver, P. (2005). Nutrient control of glucose homeostasis through a complex of PGC-1α and SIRT1. Nature, 434(7029), 113–118. doi:10.1038/nature03354
   PubMed Web of Science ®Google Scholar
• Rodriquez, M., Aquino, M., Bruno, I., De Martino, G., Taddei, M., & Gomez-Paloma, L. (2006). Chemistry and biology of chromatin remodeling agents: state of art and future perspectives of HDAC inhibitors. Current Medicinal Chemistry, 13(10), 1119–1139. doi:10.2174/092986706776360905
   PubMed Web of Science ®Google Scholar
• Rotili, D., Tarantino, D., Nebbioso, A., Paolini, C., Huidobro, C., Lara, E., … Mai, A. (2012). Discovery of salermide-related sirtuin inhibitors: binding mode studies and antiproliferative effects in cancer cells including cancer stem cells. Journal of Medicinal Chemistry, 55(24), 10937–10947. doi:10.1021/jm3011614
   PubMed Web of Science ®Google Scholar
• Roy, K., Das, R. N., Ambure, P., & Aher, R. B. (2016). Be aware of error measures. Further studies on validation of predictive QSAR models. Chemometrics and Intelligent Laboratory Systems, 152, 18–33. doi:10.1016/j.chemolab.2016.01.008
   Web of Science ®Google Scholar
• Rumpf, T., Schiedel, M., Karaman, B., Roessler, C., North, B. J., Lehotzky, A., … Jung, M. (2015). Selective Sirt2 inhibition by ligand-induced rearrangement of the active site. Nature Communications, 6(1), 62–63. doi:10.1038/ncomms7263
   PubMedGoogle Scholar
• Satoh, A., Vudikaria, L. Q., Kurano, N., & Miyachi, S. (2005). Evaluation of the sensitivity of marine microalgal strains to the heavy metals, Cu, As, Sb, Pb and Cd. Environ Int, 31(5), 713–722. doi:10.1016/j.envint.2005.01.001
   PubMed Web of Science ®Google Scholar
• Schiedel, M., Rumpf, T., Karaman, B., Lehotzky, A., Gerhardt, S., Ovádi, J., … Jung, M. (2016). Structure-based development of an affinity probe for Sirtuin 2. Angewandte Chemie International Edition , 55(6), 2252–2256. doi:10.1002/anie.201509843
   PubMed Web of Science ®Google Scholar
• Seel, M., Turner, D. B., & Willett, P. (1999). Effect of parameter variations on the effectiveness of HQSAR analyses. Quantitative Structure-Activity Relationships, 18(3), 245–252.doi:10.1002/(SICI)1521-3838(199907)18:3<245::AID-QSAR245>3.0.CO;2-O
   Google Scholar
• Serrano, L., Martínez-Redondo, P., Marazuela-Duque, A., Vazquez, B. N., Dooley, S. J., Voigt, P., … Vaquero, A. (2013). The tumor suppressor SirT2 regulates cell cycle progression and genome stability by modulating the mitotic deposition of H4K20 methylation. Genes & Development, 27(6), 639–653. doi:10.1101/gad.211342.112
   PubMed Web of Science ®Google Scholar
• Siligardi, G., Hussain, R., Patching, S. G., & Phillips-Jones, M. K. (2014). Ligand-and drug-binding studies of membrane proteins revealed through circular dichroism spectroscopy. Biochimica Biophysics Acta, 1838, 34–42. doi:10.1016/j.bbamem.2013.06.019
   PubMed Web of Science ®Google Scholar
• Suzuki, T., Imai, K., Imai, E., Iida, S., Ueda, R., Tsumoto, H., … Miyata, N. (2009). Design, synthesis, enzyme inhibition, and tumor cell growth inhibition of 2-anilinobenzamide derivatives as SIRT1 inhibitors. Bioorganic & Medicinal Chemistry, 17(16), 5900–5905. doi:10.1016/j.bmc.2009.07.001
   PubMed Web of Science ®Google Scholar
• Suzuki, T., Khan, M. N. A., Sawada, H., Imai, E., Itoh, Y., Yamatsuta, K., … Miyata, N. (2012). Design, synthesis, and biological activity of a novel series of human Sirtuin-2-selective inhibitors. Journal of Medicinal Chemistry, 55(12), 5760–5773. doi:10.1021/jm3002108
   PubMed Web of Science ®Google Scholar
• Teng, Y.-B., Jing, H., Aramsangtienchai, P., He, B., Khan, S., Hu, J., … Hao, Q. (2015). Efficient demyristoylase activity of SIRT2 revealed by kinetic and structural studies. Scientific Reports, 5(1), 8529. doi:10.1038/srep08529
   PubMedGoogle Scholar
• Tripos, Inc. (2011). SYBYL ® expert molecular modeling environment.
   Google Scholar
• van de Ven, R. A. H., Santos, D., & Haigis, M. C. (2017). Mitochondrial Sirtuins and molecular mechanisms of aging. Trends in Molecular Medicine, 23(4), 320–331. doi:10.1016/j.molmed.2017.02.005
   PubMed Web of Science ®Google Scholar
• Verdonk, M. L., Chessari, G., Cole, J. C., Hartshorn, M. J., Murray, C. W., Nissink, J. W., …., Taylor, R. (2005). Modeling water molecules in protein − ligand docking using GOLD. Journal of Medicinal Chemistry, 48(20), 6504–6515. doi: 10.1021/JM050543P
   Google Scholar
• Verdonk, M. L., Cole, J. C., Hartshorn, M. J., Murray, C. W., & Taylor, R. D. (2003). Improved protein-ligand docking using GOLD. Proteins: Structure, Function, and Bioinformatics, 52(4), 609–623. doi:10.1002/prot.10465
   PubMed Web of Science ®Google Scholar
• Wilkes, J. G., Stoyanova-Slavova, I. B., & Buzatu, D. A. (2016). Alignment-independent technique for 3D QSAR analysis. Journal of Computer-Aided Molecular Design, 30(4), 331–345. doi:10.1007/s10822-016-9909-0
   Google Scholar
• Yang, M. H., Laurent, G., Bause, A. S., Spang, R., German, N., Haigis, M. C., & Haigis, K. M. (2013). HDAC6 and SIRT2 regulate the acetylation state and oncogenic activity of mutant K-RAS. Molecular Cancer Research, 11(9), 1072–1077. doi:10.1158/1541-7786.MCR-13-0040-T
   PubMed Web of Science ®Google Scholar
• Yap, C. W. (2011). PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints. Journal of Computational Chemistry, 32(7), 1466–1474. doi:10.1002/jcc.21707
   PubMed Web of Science ®Google Scholar
• Yoon, J. C., Puigserver, P., Chen, G., Donovan, J., Wu, Z., Rhee, J., … Spiegelman, B. M. (2001). Control of hepatic gluconeogenesis through the transcriptional coactivator PGC-1. Nature, 413(6852), 131–138. doi:10.1038/35093050
   PubMed Web of Science ®Google Scholar
• Zhao, M., Wang, L., Zheng, L., Zhang, M., Qiu, C., Zhang, Y., … Niu, B. (2017). 2D-QSAR and 3D-QSAR analyses for EGFR inhibitors. BioMed Research International, 2017, 4649191. doi:10.1155/2017/4649191
   PubMed Web of Science ®Google Scholar