Molecular Modelling of Resveratrol Derivatives with SIRT1 for the Stimulation of Deacetylase Activity


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Аннотация

Background:Resveratrol is a polyphenol that is found in plants and has been proposed to have a potential therapeutic effect through the activation of SIRT1, which is a crucial member of the mammalian NAD+ -dependent deacetylases. However, how its activity is enhanced toward specific substrates by resveratrol derivatives has not been studied. This study aimed to evaluate the types of interaction of resveratrol and its derivatives with SIRT1 as the target protein, as well as to find out the best ligand with the strangest interaction with SIRT1.

Materials and Methods:In this study, we employed the extensive molecular docking analysis using AutoDock Vina to comparatively evaluate the interactions of resveratrol derivatives (22 molecules from the ZINC database) as ligands with SIRT1 (PDB ID: 5BTR) as a receptor. The ChemDraw and Chem3D tools were used to prepare 3D structures of all ligands and energetically minimize them by the MM2 force field.

Results:The molecular docking and visualizations showed that conformational change in resveratrol derivatives significantly influenced the parameter for docking results. Several types of interactions, including conventional hydrogen bonds, carbon-hydrogen bonds, Pi-donor hydrogen bonds, and Pi-Alkyl, were found via docking analysis of resveratrol derivatives and SIRT1 receptors. The possible activation effect of resveratrol 4'-(6-galloylglucoside) with ZINC ID: ZINC230079516 with higher binding energy score (-46.8608 kJ/mol) to the catalytic domain (CD) of SIRT1 was achieved at the maximum value for SIRT1, as compared to resveratrol and its other derivatives.

Conclusion:Finally, resveratrol 4'-(6-galloylglucoside), as a derivative for resveratrol, has stably interacted with the CD of SIRT1 and might be a potential effective activator for SIRT1.

Об авторах

Mozhdeh Zamani

Autophagy Research Center, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences

Email: info@benthamscience.net

Pooneh Mokarram

Autophagy Research Center, Department of Biochemistry, School of Medicine,, Shiraz University of Medical Sciences

Автор, ответственный за переписку.
Email: info@benthamscience.net

Mehdi Jamshidi

Institute für Chemie, Universität Oldenburg

Email: info@benthamscience.net

Morvarid Siri

Autophagy Research Center, Department of Biochemistry, School of Medicine,, Shiraz University of Medical Sciences,

Email: info@benthamscience.net

Hadi Ghasemi

Autophagy Research Center, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences

Автор, ответственный за переписку.
Email: info@benthamscience.net

Список литературы

  1. Ertan-Bolelli, T.; Bolelli, K. In silico design of novel sirtuin 1 enzyme activators for the treatment of age-related diseases and life span. Curr. Computeraided Drug Des., 2021, 17(3), 412-420. doi: 10.2174/1573409916666200422074441 PMID: 32321406
  2. Ng, F.; Tang, B.L. Sirtuins’ modulation of autophagy. J. Cell. Physiol., 2013, 228(12), 2262-2270. doi: 10.1002/jcp.24399 PMID: 23696314
  3. Ou, X.; Lee, M.R.; Huang, X.; Messina-Graham, S.; Broxmeyer, H.E. SIRT1 positively regulates autophagy and mitochondria function in embryonic stem cells under oxidative stress. Stem Cells, 2014, 32(5), 1183-1194. doi: 10.1002/stem.1641 PMID: 24449278
  4. Wu, S.; Wei, Y.; Li, J.; Bai, Y.; Yin, P.; Wang, S. SIRT5 represses neurotrophic pathways and Aβ production in Alzheimer’s disease by targeting autophagy. ACS Chem. Neurosci., 2021, 12(23), 4428-4437. doi: 10.1021/acschemneuro.1c00468 PMID: 34788008
  5. Saha, S.; Panigrahi, D.P.; Patil, S.; Bhutia, S.K. Autophagy in health and disease: A comprehensive review. Biomed. Pharmacother., 2018, 104, 485-495. doi: 10.1016/j.biopha.2018.05.007 PMID: 29800913
  6. Yang, Y.; Klionsky, D.J. Autophagy and disease: Unanswered questions. Cell Death Differ., 2020, 27(3), 858-871. doi: 10.1038/s41418-019-0480-9 PMID: 31900427
  7. Ryter, S.W.; Bhatia, D.; Choi, M.E. Autophagy: A lysosome-dependent process with implications in cellular redox homeostasis and human disease. Antioxid. Redox Signal., 2019, 30(1), 138-159. doi: 10.1089/ars.2018.7518 PMID: 29463101
  8. Hou, X.; Rooklin, D.; Fang, H.; Zhang, Y. Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation. Sci. Rep., 2016, 6(1), 38186. doi: 10.1038/srep38186 PMID: 27901083
  9. Salminen, A.; Kaarniranta, K. SIRT1: Regulation of longevity via autophagy. Cell. Signal., 2009, 21(9), 1356-1360. doi: 10.1016/j.cellsig.2009.02.014 PMID: 19249351
  10. Tıraş, Z.Ş.E.; Okur, H.H.; Günay, Z.; Yıldırım, H.K. Different approaches to enhance resveratrol content in wine. Ciênc. Téc. Vitiviníc., 2022, 37(1), 13-28.
  11. Sun, A.Y.; Wang, Q.; Simonyi, A.; Sun, G.Y. Resveratrol as a therapeutic agent for neurodegenerative diseases. Mol. Neurobiol., 2010, 41(2-3), 375-383. doi: 10.1007/s12035-010-8111-y PMID: 20306310
  12. Morselli, E.; Galluzzi, L.; Kepp, O.; Criollo, A.; Maiuri, M.C.; Tavernarakis, N.; Madeo, F.; Kroemer, G. Autophagy mediates pharmacological lifespan extension by spermidineand resveratrol. Aging (Albany NY), 2009, 1(12), 961-970. doi: 10.18632/aging.100110 PMID: 20157579
  13. Wang, J.; Li, J.; Cao, N.; Li, Z.; Han, J.; Li, L. Resveratrol, an activator of SIRT1, induces protective autophagy in non-small-cell lung cancer via inhibiting Akt/mTOR and activating p38-MAPK. OncoTargets Ther., 2018, 11, 7777-7786. doi: 10.2147/OTT.S159095 PMID: 30464525
  14. Huang, H.; Liao, D.; Zhou, G.; Zhu, Z.; Cui, Y.; Pu, R. Antiviral activities of resveratrol against rotavirus in vitro and in vivo. Phytomedicine, 2020, 77, 153230. doi: 10.1016/j.phymed.2020.153230 PMID: 32682225
  15. Honari, M.; Shafabakhsh, R.; Reiter, R.J.; Mirzaei, H.; Asemi, Z. Resveratrol is a promising agent for colorectal cancer prevention and treatment: focus on molecular mechanisms. Cancer Cell Int., 2019, 19(1), 180. doi: 10.1186/s12935-019-0906-y PMID: 31341423
  16. Singh, S.P.; Hussain, I.; Konwar, B.K.; Deka, R.C.; Singh, C.B. Design of potential IKK-β inhibitors using molecular docking and molecular dynamics techniques for their anti-cancer potential. Curr. Computeraided Drug Des., 2021, 17(1), 83-94. doi: 10.2174/1573409916666200102121505 PMID: 31899679
  17. Wang, N.; Luo, Z.; Jin, M.; Sheng, W.; Wang, H.T.; Long, X.; Wu, Y.; Hu, P.; Xu, H.; Zhang, X. Exploration of age-related mitochondrial dysfunction and the anti-aging effects of resveratrol in zebrafish retina. Aging, 2019, 11(10), 3117-3137. doi: 10.18632/aging.101966 PMID: 31105084
  18. Ahmad, M.; Gani, A. Development of novel functional snacks containing nano-encapsulated resveratrol with anti-diabetic, anti-obesity and antioxidant properties. Food Chem., 2021, 352, 129323. doi: 10.1016/j.foodchem.2021.129323 PMID: 33691210
  19. Banez, M.J.; Geluz, M.I.; Chandra, A.; Hamdan, T.; Biswas, O.S.; Bryan, N.S.; Von Schwarz, E.R. A systemic review on the antioxidant and anti-inflammatory effects of resveratrol, curcumin, and dietary nitric oxide supplementation on human cardiovascular health. Nutr. Res., 2020, 78, 11-26. doi: 10.1016/j.nutres.2020.03.002 PMID: 32428778
  20. Jia, R.; Li, Y.; Cao, L.; Du, J.; Zheng, T.; Qian, H.; Gu, Z.; Jeney, G.; Xu, P.; Yin, G. Antioxidative, anti-inflammatory and hepatoprotective effects of resveratrol on oxidative stress-induced liver damage in tilapia (Oreochromis niloticus). Comp. Biochem. Physiol. C Toxicol. Pharmacol., 2019, 215, 56-66. doi: 10.1016/j.cbpc.2018.10.002 PMID: 30336289
  21. Ho, Y.; Wu, C.Y.; Chin, Y.T.; Li, Z.L.; Pan, Y.; Huang, T.Y.; Su, P.Y.; Lee, S.Y.; Crawford, D.R.; Su, K.W.; Chiu, H.C.; Shih, Y.J.; Changou, C.A.; Yang, Y.C.S.H.; Whang-Peng, J.; Chen, Y.R.; Lin, H.Y.; Mousa, S.A.; Davis, P.J.; Wang, K. NDAT suppresses pro-inflammatory gene expression to enhance resveratrol-induced anti-proliferation in oral cancer cells. Food Chem. Toxicol., 2020, 136, 111092. doi: 10.1016/j.fct.2019.111092 PMID: 31883986
  22. Gomes, B.A.Q.; Silva, J.P.B.; Romeiro, C.F.R.; Dos Santos, S.M.; Rodrigues, C.A.; Gonçalves, P.R.; Sakai, J.T.; Mendes, P.F.S.; Varela, E.L.P.; Monteiro, M.C. Neuroprotective mechanisms of resveratrol in Alzheimer’s disease: Role of SIRT1. Oxid. Med. Cell. Longev., 2018, 2018, 8152373. doi: 10.1155/2018/8152373
  23. Griñán-Ferré, C.; Bellver-Sanchis, A.; Izquierdo, V.; Corpas, R.; Roig-Soriano, J.; Chillón, M.; Andres-Lacueva, C.; Somogyvári, M.; Sőti, C.; Sanfeliu, C.; Pallàs, M. The pleiotropic neuroprotective effects of resveratrol in cognitive decline and Alzheimer’s disease pathology: From antioxidant to epigenetic therapy. Ageing Res. Rev., 2021, 67, 101271. doi: 10.1016/j.arr.2021.101271 PMID: 33571701
  24. Cao, W.; Dou, Y.; Li, A. Resveratrol boosts cognitive function by targeting SIRT1. Neurochem. Res., 2018, 43(9), 1705-1713. doi: 10.1007/s11064-018-2586-8 PMID: 29943083
  25. Cao, D.; Wang, M.; Qiu, X.; Liu, D.; Jiang, H.; Yang, N.; Xu, R.M. Structural basis for allosteric, substrate-dependent stimulation of SIRT1 activity by resveratrol. Genes Dev., 2015, 29(12), 1316-1325. doi: 10.1101/gad.265462.115 PMID: 26109052
  26. Knutson, M.D.; Leeuwenburgh, C. Resveratrol and novel potent activators of SIRT1: Effects on aging and age-related diseases. Nutr. Rev., 2008, 66(10), 591-596. doi: 10.1111/j.1753-4887.2008.00109.x PMID: 18826454
  27. Borra, M.T.; Smith, B.C.; Denu, J.M. Mechanism of human SIRT1 activation by resveratrol. J. Biol. Chem., 2005, 280(17), 17187-17195. doi: 10.1074/jbc.M501250200 PMID: 15749705
  28. Dalal, V.; Kumari, R. Screening and identification of natural product‐like compounds as potential antibacterial agents targeting femc of staphylococcus aureus: An in‐Silico Approach. ChemistrySelect, 2022, 7(42), e202201728. doi: 10.1002/slct.202201728
  29. Kumari, R.; Dhankhar, P.; Dalal, V. Structure-based mimicking of hydroxylated biphenyl congeners (OHPCBs) for human transthyretin, an important enzyme of thyroid hormone system. J. Mol. Graph. Model., 2021, 105, 107870. doi: 10.1016/j.jmgm.2021.107870 PMID: 33647754
  30. Kumari, R.; Rathi, R.; Pathak, S.R.; Dalal, V. Structural-based virtual screening and identification of novel potent antimicrobial compounds against YsxC of Staphylococcus aureus. J. Mol. Struct., 2022, 1255, 132476. doi: 10.1016/j.molstruc.2022.132476
  31. Singh, V.; Dhankhar, P.; Dalal, V.; Tomar, S.; Kumar, P. In-silico functional and structural annotation of hypothetical protein from Klebsiella pneumonia: A potential drug target. J. Mol. Graph. Model., 2022, 116, 108262. doi: 10.1016/j.jmgm.2022.108262 PMID: 35839717
  32. Kumari, R.; Dalal, V. Identification of potential inhibitors for LLM of Staphylococcus aureus: Structure-based pharmacophore modeling, molecular dynamics, and binding free energy studies. J. Biomol. Struct. Dyn., 2022, 40(20), 9833-9847. doi: 10.1080/07391102.2021.1936179 PMID: 34096457
  33. Kumari, R.; Kumar, V.; Dhankhar, P.; Dalal, V. Promising antivirals for PLpro of SARS-CoV-2 using virtual screening, molecular docking, dynamics, and MMPBSA. J. Biomol. Struct. Dyn., 2023, 41(10), 4650-4666. doi: 10.1080/07391102.2022.2071340 PMID: 35510600
  34. Hubbard, B.P.; Sinclair, D.A. Small molecule SIRT1 activators for the treatment of aging and age-related diseases. Trends Pharmacol. Sci., 2014, 35(3), 146-154. doi: 10.1016/j.tips.2013.12.004 PMID: 24439680
  35. Kuningas, M.; Putters, M.; Westendorp, R.G.J.; Slagboom, P.E.; van Heemst, D. SIRT1 gene, age-related diseases, and mortality: The Leiden 85-plus study. J. Gerontol. A Biol. Sci. Med. Sci., 2007, 62(9), 960-965. doi: 10.1093/gerona/62.9.960 PMID: 17895433
  36. Grau, L.; Soucek, R.; Pujol, M.D. Resveratrol derivatives: Synthesis and their biological activities. Eur. J. Med. Chem., 2023, 246, 114962. doi: 10.1016/j.ejmech.2022.114962 PMID: 36463729
  37. Arbo, B.D.; André-Miral, C.; Nasre-Nasser, R.G.; Schimith, L.E.; Santos, M.G.; Costa-Silva, D.; Muccillo-Baisch, A.L.; Hort, M.A. Resveratrol derivatives as potential treatments for Alzheimer’s and Parkinson’s disease. Front. Aging Neurosci., 2020, 12, 103. doi: 10.3389/fnagi.2020.00103 PMID: 32362821
  38. Ranjbar, A.; Jamshidi, M.; Torabi, S. Molecular modelling of the antiviral action of Resveratrol derivatives against the activity of two novel SARS CoV-2 and 2019-nCoV receptors. Eur. Rev. Med. Pharmacol. Sci., 2020, 24(14), 7834-7844. PMID: 32744711
  39. Zhou, S.; Yang, R.; Teng, Z.; Zhang, B.; Hu, Y.; Yang, Z.; Huan, M.; Zhang, X.; Mei, Q. Dose-dependent absorption and metabolism of trans-polydatin in rats. J. Agric. Food Chem., 2009, 57(11), 4572-4579. doi: 10.1021/jf803948g PMID: 19397265
  40. Feng, X.; Liang, N.; Zhu, D.; Gao, Q.; Peng, L.; Dong, H.; Yue, Q.; Liu, H.; Bao, L.; Zhang, J.; Hao, J.; Gao, Y.; Yu, X.; Sun, J. Resveratrol inhibits β-amyloid-induced neuronal apoptosis through regulation of SIRT1-ROCK1 signaling pathway. PLoS One, 2013, 8(3), e59888. doi: 10.1371/journal.pone.0059888 PMID: 23555824
  41. Lange, K.W.; Li, S. Resveratrol, pterostilbene, and dementia. Biofactors, 2018, 44(1), 83-90. doi: 10.1002/biof.1396 PMID: 29168580
  42. Vergoten, G.; Bailly, C. Molecular modeling of alkaloids bouchardatine and orirenierine binding to sirtuin-1 (SIRT1). Digital Chinese Medicine, 2022, 5(3), 276-285. doi: 10.1016/j.dcmed.2022.10.004
  43. Liu, J.; Zhao, H.; He, L.; Yu, R.; Kang, C. Discovery and design of dual inhibitors targeting Sphk1 and Sirt1. J. Mol. Model., 2023, 29(5), 141. doi: 10.1007/s00894-023-05551-2 PMID: 37059848
  44. Sandak, B.; Wolfson, H.J.; Nussinov, R. Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers. Proteins, 1998, 32(2), 159-174. doi: 10.1002/(SICI)1097-0134(19980801)32:23.0.CO;2-G PMID: 9714156
  45. Davenport, A.M.; Huber, F.M.; Hoelz, A. Structural and functional analysis of human SIRT1. J. Mol. Biol., 2014, 426(3), 526-541. doi: 10.1016/j.jmb.2013.10.009 PMID: 24120939
  46. Zhao, X.; Allison, D.; Condon, B.; Zhang, F.; Gheyi, T.; Zhang, A.; Ashok, S.; Russell, M.; MacEwan, I.; Qian, Y.; Jamison, J.A.; Luz, J.G. The 2.5 Å crystal structure of the SIRT1 catalytic domain bound to nicotinamide adenine dinucleotide (NAD+) and an indole (EX527 analogue) reveals a novel mechanism of histone deacetylase inhibition. J. Med. Chem., 2013, 56(3), 963-969. doi: 10.1021/jm301431y PMID: 23311358
  47. Bakhtiari, N.; Mirzaie, S.; Hemmati, R.; Moslemee-jalalvand, E.; Noori, A.R.; Kazemi, J. Mounting evidence validates Ursolic Acid directly activates SIRT1: A powerful STAC which mimic endogenous activator of SIRT1. Arch. Biochem. Biophys., 2018, 650, 39-48. doi: 10.1016/j.abb.2018.05.012 PMID: 29758202

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