270
Views
1
CrossRef citations to date
0
Altmetric
Research Articles

In silico screening of small molecule modulators and their binding studies against human sirtuin-6 protein

, , , , , , & ORCID Icon show all
Pages 10033-10044 | Received 09 Feb 2021, Accepted 30 May 2021, Published online: 14 Jun 2021

Reference

  • Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shan, Y., & Shaw, D. E. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters [Paper presentation]. Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, Association for Computing Machinery, New York, NY, USA, 84-es. https://doi.org/10.1145/1188455.1188544
  • Cardinale, A., de Stefano, M. C., Mollinari, C., Racaniello, M., Garaci, E., & Merlo, D. (2015). Biochemical characterization of sirtuin 6 in the brain and its involvement in oxidative stress response. Neurochemical Research, 40(1), 59–69. https://doi.org/10.1007/s11064-014-1465-1
  • Case, D. A., Belfon, K., Ben-Shalom, I. Y., Brozell, S. R., Cerutti, D. S., Cheatham, T. E., III, Cruzeiro, V. W. D., Darden, T. A., Duke, R. E., Giambasu, G., Gilson, M. K., Gohlke, H., Goetz, A. W., Harris, R., Izadi, S., Izmailov, S. A., Kasavajhala, K., Kovalenko, A., Krasny, R., … Kollman, P. A. (2020). AMBER 2020. University of California.
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717. https://doi.org/10.1038/srep42717
  • Dassault Systèmes BIOVIA. (2016). Discovery Studio Visualizer, v 17.2.0.16349. Dassault Systèmes.
  • 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. The Journal of Biological Chemistry, 288(43), 31350–31356. https://doi.org/10.1074/jbc.C113.511261
  • Finnin, M. S., Donigian, J. R., & Pavletich, N. P. (2001). Structure of the histone deacetylase SIRT2. Nature Structural Biology, 8(7), 621–625. https://doi.org/10.1038/89668
  • Fiser, A., & Sali, A. (2003). ModLoop: Automated modeling of loops in protein structures. Bioinformatics, 19(18), 2500–2501. https://doi.org/10.1093/bioinformatics/btg362
  • Fiser, A., Do, R. K. G., & Šali, A. (2000). Modeling of loops in protein structures. Protein Science, 9(9), 1753–1773. https://doi.org/10.1110/ps.9.9.1753
  • 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/10.1517/17460441.2015.1032936
  • Jiang, H., Khan, S., Wang, Y., Charron, G., He, B., Sebastian, C., Du, J., Kim, R., Ge, E., Mostoslavsky, R., Hang, H. C., Hao, Q., & Lin, H. (2013). Sirt6 regulates TNFα secretion via hydrolysis of long chain fatty acyl lysine. Nature, 496(7443), 110–113. https://doi.org/10.1038/nature12038
  • 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/10.1063/1.445869
  • Kaluski, S., Portillo, M., Besnard, A., Stein, D., Einav, M., Zhong, L., Ueberham, U., Arendt, T., Mostoslavsky, R., Sahay, A., & Toiber, D. (2017). Neuroprotective functions for the histone deacetylase SIRT6. Cell Reports, 18(13), 3052–3062. https://doi.org/10.1016/j.celrep.2017.03.008
  • Klein, M. A., & Denu, J. M. (2020). Biological and catalytic functions of sirtuin 6 as targets for small-molecule modulators. The Journal of Biological Chemistry, 295(32), 11021–11041. https://doi.org/10.1074/jbc.REV120.011438
  • 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/10.1021/ar000033j
  • Kugel, S., Feldman, J. L., Klein, M. A., Silberman, D. M., Sebastián, C., Mermel, C., Dobersch, S., Clark, A. R., Getz, G., Denu, J. M., & Mostoslavsky, R. (2015). Identification of and molecular basis for SIRT6 loss-of-function point mutations in cancer. Cell Reports, 13(3), 479–488. https://doi.org/10.1016/j.celrep.2015.09.022
  • Kugel, S., & Mostoslavsky, R. (2014). Chromatin and beyond: The multitasking roles for SIRT6. Trends in Biochemical Sciences, 39(2), 72–81. https://doi.org/10.1016/j.tibs.2013.12.002
  • Lee, S. K., Chang, G. S., Lee, I. H., Chung, J. E., Sung, K. Y., & No, K. T. (2004). The PreADME: Pc-based program for batch prediction of adme properties. EuroQSAR, 9, 5–10.
  • Lee, S. K., Lee, I. H., Kim, H. J., Chang, G. S., Chung, J. E., & No, K. T. (2002). The PreADME approach: Web-based program for rapid prediction of physico-chemical, drug absorption and drug-like properties. EuroQSAR, 1, 418–420.
  • 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/10.1021/acs.jctc.5b00255
  • Mao, Z., Hine, C., Tian, X., Van Meter, M., Au, M., Vaidya, A., Seluanov, A., & Gorbunova, V. (2011). SIRT6 promotes DNA repair under stress by activating PARP1. Science (New York, N.Y.), 332(6036), 1443–1446. https://doi.org/10.1126/science.1202723
  • Massova, I., & Kollman, P. A. (2000). Combined molecular mechanical and continuum solvent approach (MMPBSA/GBSA) to predict ligand binding. Perspectives in Drug Discovery and Design, 18(1), 113–135. https://doi.org/10.1023/A:1008763014207
  • Mautone, N., Zwergel, C., Mai, A., & Rotili, D. (2020). Sirtuin modulators: Where are we now? A review of patents from 2015 to 2019. Expert Opinion on Therapeutic Patents, 30(6), 389–407. https://doi.org/10.1080/13543776.2020.1749264
  • Mendelsohn, L. D. (2004). ChemDraw 8 Ultra, Windows and Macintosh versions. Journal of Chemical Information and Computer Sciences, 44(6), 2225–2226. https://doi.org/10.1021/ci040123t
  • Michan, S., & Sinclair, D. (2007). Sirtuins in mammals: Insights into their biological function. The Biochemical Journal, 404(1), 1–13. https://doi.org/10.1042/BJ20070140
  • Michishita, E., McCord, R. A., Berber, E., Kioi, M., Padilla-Nash, H., Damian, M., Cheung, P., Kusumoto, R., Kawahara, T. L. A., Barrett, J. C., Chang, H. Y., Bohr, V. A., Ried, T., Gozani, O., & Chua, K. F. (2008). SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin. Nature, 452(7186), 492–496. https://doi.org/10.1038/nature06736
  • Michishita, E., McCord, R. A., Boxer, L. D., Barber, M. F., Hong, T., Gozani, O., & Chua, K. F. (2009). Cell cycle-dependent deacetylation of telomeric histone H3 lysine K56 by human SIRT6. Cell Cycle (Georgetown, Tex.), 8(16), 2664–2666. https://doi.org/10.4161/cc.8.16.9367
  • Min, J., Landry, J., Sternglanz, R., & Xu, R. M. (2001). Crystal structure of a SIR2 homolog-NAD complex. Cell, 105(2), 269–279. https://doi.org/10.1016/S0092-8674(01)00317-8
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Mostoslavsky, R., Chua, K. F., Lombard, D. B., Pang, W. W., Fischer, M. R., Gellon, L., Liu, P., Mostoslavsky, G., Franco, S., Murphy, M. M., Mills, K. D., Patel, P., Hsu, J. T., Hong, A. L., Ford, E., Cheng, H.-L., Kennedy, C., Nunez, N., Bronson, R., … Alt, F. W. (2006). Genomic instability and aging-like phenotype in the absence of mammalian SIRT6. Cell, 124(2), 315–329. https://doi.org/10.1016/j.cell.2005.11.044
  • Nissink, J. W. M. (2009). Simple size-independent measure of ligand efficiency. Journal of Chemical Information and Modeling, 49(6), 1617–1622. https://doi.org/10.1021/ci900094m
  • O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/10.1186/1758-2946-3-33
  • Pan, P. W., Feldman, J. L., Devries, M. K., Dong, A., Edwards, A. M., & Denu, J. M. (2011). Structure and biochemical functions of SIRT6. The Journal of Biological Chemistry, 286(16), 14575–14587. https://doi.org/10.1074/jbc.M111.218990
  • Sacconnay, L., Carrupt, P.-A., & Nurisso, A. (2016). Human sirtuins: Structures and flexibility. Journal of Structural Biology, 196(3), 534–542. https://doi.org/10.1016/j.jsb.2016.10.008
  • Sanders, B. D., Jackson, B., & Marmorstein, R. (2010). Structural basis for sirtuin function: What we know and what we don’t. Biochimica et Biophysica Acta, 1804(8), 1604–1616. https://doi.org/10.1016/j.bbapap.2009.09.009
  • Sauve, A. A., Wolberger, C., Schramm, V. L., & Boeke, J. D. (2006). The biochemistry of sirtuins. Annual Review of Biochemistry, 75, 435–465. https://doi.org/10.1146/annurev.biochem.74.082803.133500
  • Schrödinger, L. (2017). The PyMol molecular graphics system, version 2.0. Schrödinger.
  • Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J., & Sherman, W. (2010). Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. Journal of Chemical Theory and Computation, 6(5), 1509–1519. https://doi.org/10.1021/ct900587b
  • 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. https://doi.org/10.1002/jcc.21334
  • Yang, B., Zwaans, B. M. M., Eckersdorff, M., & Lombard, D. B. (2009). The sirtuin SIRT6 deacetylates H3 K56Ac in vivo to promote genomic stability. Cell Cycle (Georgetown, Tex.), 8(16), 2662–2663. https://doi.org/10.4161/cc.8.16.9329
  • You, W., Rotili, D., Li, T.-M., Kambach, C., Meleshin, M., Schutkowski, M., Chua, K. F., Mai, A., & Steegborn, C. (2017). Structural basis of sirtuin 6 activation by synthetic small molecules. Angewandte Chemie (International Ed. in English), 56(4), 1007–1011. https://doi.org/10.1002/anie.201610082
  • You, W., Zheng, W., Weiss, S., Chua, K. F., & Steegborn, C. (2019). Structural basis for the activation and inhibition of Sirtuin 6 by quercetin and its derivatives. Scientific Reports, 9(1), 19176. https://doi.org/10.1038/s41598-019-55654-1
  • Zhang, X., Khan, S., Jiang, H., Antonyak, M. A., Chen, X., Spiegelman, N. A., Shrimp, J. H., Cerione, R. A., & Lin, H. (2016). Identifying the functional contribution of the defatty-acylase activity of SIRT6. Nature Chemical Biology, 12(8), 614–620. https://doi.org/10.1038/nchembio.2106

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.