In Silico Molecular Docking and ADMET Analysis for Drug Development of Phytoestrogens Compound with Its Evaluation of Neurodegenerative Diseases
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Submitted
31 July 2022
31 July 2022
Published
30 November 2022
30 November 2022
Abstract
Neurodegenerative disease is one of the problems faced by postmenopausal women due to estrogen deficiency. Phytoestrogen compounds can be used as an alternative treatment for diseases caused by estrogen deficiency by binding to their receptors through the estrogen receptor (ER) dependent pathway. With in silico studies, this study aims to predict how phytoestrogen compounds will stop neurons from dying by using the dependent ER pathway. Genistein, daidzein, glycitein, formononetin, biochanin A, equol, pinoresinol, 4-methoxypinoresinol, eudesmin, α-amyrin, and β-amyrin compounds were prepared with ChemDraw Ultra 12.0. Then their pharmacokinetic and pharmacodynamic properties were examined using SwissADME. Geometry optimization of the compound was performed using Avogadro 1.0.1, and molecular docking of the compound to the ERα (1A52) and ERβ (5TOA) receptors was performed using AutoDock vina (PyRx 0.8). The interaction visualization stage was carried out with Biovia Discover Studio 2021, while the toxicity values of the compounds were analyzed using pkCSM and ProTox II. The results showed that the equol compound met the pharmacokinetic, pharmacodynamic, toxicity criteria, and had similarities with the native ligand 17β-estradiol. Equol compound inhibits neurodegeneration via an ER-dependent pathway by binding to ERα (1A52) and ERβ (5TOA) receptors.
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2. van Beek JHGM, Kirkwood TBL, Bassingthwaighte JB. Understanding the physiology of the ageing individual: computational modelling of changes in metabolism and endurance. Interface Focus. 2016;6(2):20150079. doi:10.1098/rsfs.2015.0079
3. Liguori I, Russo G, Curcio F, Bulli G, Aran L, Della-Morte D, et al. Oxidative stress, aging, and diseases. Clin Interv Aging. 2018;13:757-72. doi:10.2147/cia.s158513
4. Ferrucci L, Fabbri E. Inflammageing: chronic inflammation in ageing, cardiovascular disease, and frailty. Nat Rev Cardiol. 2018;15(9):505-22. doi:10.1038/s41569-018-0064-2
5. Sehl ME, Ganz PA. Potential Mechanisms of Age Acceleration Caused by Estrogen Deprivation: Do Endocrine Therapies Carry the Same Risks? JNCI Cancer Spectr. 2018;2(3):pky035. doi:10.1093/jncics/pky035
6. McCarthy M, Raval AP. The peri-menopause in a woman’s life: a systemic inflammatory phase that enables later neurodegenerative disease. J Neuroinflammation. 2020;17(1):317. doi:10.1186/s12974-020-01998-9
7. Cheng YJ, Lin CH, Lane HY. From menopause to neurodegeneration-molecular basis and potential therapy. Int J Mol Sci. 2021;22(16):8654. doi:10.3390/ijms22168654
8. Fait T. Menopause hormone therapy: latest developments and clinical practice. Drugs Context. 2019;8:212551. doi:10.7573/dic.212551
9. Mehta J, Kling JM, Manson JE. Risks, Benefits, and Treatment Modalities of Menopausal Hormone Therapy: Current Concepts. Front Endocrinol. 2021;12:564781. doi:10.3389/fendo.2021.564781
10. Cagnacci A, Venier M. The Controversial History of Hormone Replacement Therapy. Medicina. 2019;55(9):602. doi:10.3390/medicina55090602
11. Desmawati D, Sulastri D. Phytoestrogens and Their Health Effect. Open Acdess Maced J Med Sci. 2019;7(3):495-9. doi:10.3889/oamjms.2019.044
12. Lecomte S, Demay F, Ferrière F, Pakdel F. Phytochemicals Targeting Estrogen Receptors: Beneficial Rather Than Adverse Effects? Int J Mol Sci. 2017;18(7):1381. doi:10.3390/ijms18071381
13. Ma'arif B, Suryanto S, Muslikh FA, Suryadinata A, Fauziyah, B. Systematic Review: Anti-Osteoporosis Potential Activities Of Phytoestrogen Compounds In Chrysophyllum cainito L., Elaeis guineensis Jacq., Lannea acida Rich., Marsilea crenata Presl., and Medicago sativa L. J Farmasi Sains Komunitas JFSK. 2022;19(1):41-52. doi:10.24071/jpsc.003166
14. Křížová L, Dadáková K, Kašparovská J, Kašparovský T. Isoflavones. Molecules. 2019;24(6):1076. doi:10.3390/molecules24061076
15. Zhou J, Chen Y, Wang Y, Gao X, Qu D, Liu C. A comparative study on the metabolism of Epimedium koreanum Nakai-prenylated flavonoids in rats by an intestinal enzyme (lactase phlorizin hydrolase) and intestinal flora. Molecules. 2013;19(1):177-203. doi:10.3390/molecules19010177
16. Rusnaidi, Shalahuddin, Rahuddin. Peran Fitoestrogen sebagai Terapi Alternatif pada Menopause. JKS J Kedokteran Syiah Kuala. 2022;22(3):187-97. doi:10.24815/jks.v22i3.24285
17. Wang X, Ha D, Yoshitake R, Chan YS, Sadava D, Chen S. Exploring the Biological Activity and Mechanism of Xenoestrogens and Phytoestrogens in Cancers: Emerging Methods and Concepts. Int J Mol Sci. 2021;22(16):8798. doi:10.3390/ijms22168798
18. Ma'arif B, Aminullah M, Saidah NL, Muslikh FA, Rahmawati A, Indrawijaya YYA, et al. Prediction of antiosteoporosis activity of thirty-nine phytoestrogen compounds in estrogen receptor-dependent manner through in silico approach. Trop J Nat Prod Res. 2021;5(10):1727-34. doi:10.26538/tjnpr/v5i10.6
19. Fuentes N, Silveyra P. Estrogen receptor signaling mechanisms. Adv Protein Chem Struct Biol. 2019;116:135-70. doi:10.1016/bs.apcsb.2019.01.001
20. Tang ZR, Zhang R, Lian ZX, Deng SL, Yu K. Estrogen-receptor expression and function in female reproductive disease. Cells. 2019;8(10):1123. doi:10.3390/cells8101123
21. Pinto CL, Bloom RA, Laurenson JP. An Approach for Using In Vitro and In Silico Data to Identify Pharmaceuticals with Potential (Anti-)Estrogenic Activity in Aquatic Vertebrates at Environmentally Relevant Concentrations. Environ Toxicol Chem. 2019;38(10):2154-68. doi:10.1002/etc.4533
22. Defitiana W, Sanjaya IGM. Studi Komputatif Jalur Sintesis Asam Elagat dari Asam Galat. UNESA J Chem. 2020;9(1):83–90. doi:10.26740/ujc.v9n1.p83-90
23. Sliwoski G, Kothiwale S, Meiler J, Lowe EW. Computational Methods in Drug Discovery. Pharmacol Rev. 2014;66(1):334-95. doi:10.1124/pr.112.007336
24. Hevener KE, Zhao W, Ball DM, Babaoglu K, Qi J, White SW, et al. Validation of molecular docking programs for virtual screening against dihydropteroate synthase. J Chem Inf Model. 2009;49(2):444-60. doi:10.1021/ci800293n
25. Torres PHM, Sodero ACR, Jofily P, Silva-Jr FP. Key Topics in Molecular Docking for Drug Design. Int J Mol Sci. 2019;20(18):4574. doi:10.3390/ijms20184574
26. Pratama MRF, Praditapuspa EN, Kesuma D, Poerwono H, Widiandani T, Siswodihardjo S. Boesenbergia Pandurata as an Anti-Breast Cancer Agent: Molecular Docking and ADMET Study. Lett Drug Des Discov. 2022;19(7):606-26. doi:10.2174/1570180819666211220111245
27. Nursamsiar N, Mangande MM, Awaluddin A, Nur S, Asnawi A. In Silico Study of Aglycon Curculigoside A and Its Derivatives as α-Amilase Inhibitors. Indones J Pharm Sci Technol. 2020;7(1):29-37. doi:10.24198/ijpst.v7i1.23062
28. Ma’arif B, Muslikh FA, Fihuda DAP, Syarifuddin S, Fauziyah B. Prediction of Compounds from 96% Ethanol Extract of Marsilea crenata Presl. Leaves in Increasing Estrogen Receptor-α Activation. Proceed Int Pharm Ulul Albab Conf Sem PLANAR. 2021;1:67-76. doi:10.18860/planar.v1i0.1461
29. Ma’arif B, Muslikh FA, Najib LA, Atmaja RRD, Dianti MR. In Silico Antiosteoporosis Activity of 96% Ethanol Extract of Chrysophyllum cainito L. Leaves. Proceed Int Pharm Ulul Albab Conf Sem PLANAR. 2021;1:61-6. doi:10.18860/planar.v1i0.1460
30. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings. Adv Drug Deliv Rev. 2012;64(Supplement):4-17. doi:10.1016/j.addr.2012.09.019
31. Martin YC. A Bioavailability Score. J Med Chem. 2005;48(9):3164–70. doi:10.1021/jm0492002
32. Villa A, Vegeto E, Poletti A, Maggi A. Estrogens, Neuroinflammation, and Neurodegeneration. Endocr Rev. 2016;37(4):372-402. doi:10.1210/er.2016-1007
33. Pinto VS, Araújo JSC, Silva RC, Costa GV, Cruz JN, Neto MFDA, et al. In silico study to identify new antituberculosis molecules from natural sources by hierarchical virtual screening and molecular dynamics simulations. Pharmaceuticals. 2019;12(1):36. doi:10.3390/ph12010036
34. Miyagawa M. [Globally harmonized system of classification and labelling of chemicals (GHS) and its implementation in Japan]. Nihon Eiseigaku Zasshi. 2010;65(1):5-13. doi:10.1265/jjh.65.5
35. Supandi, Yeni, Merdekawati F. In Silico Study of Pyrazolylaminoquinazoline Toxicity by Lazar, Protox and Admet Predictor. J Appl Pharma Sci. 2018;8(9):119-29. doi:10.7324/JAPS.2018.8918
36. Cheng A. In silico Prediction of Hepatotoxicity. Curr Comput Aid Drug Des. 2009;5(2):122-7. doi:10.2174/157340909788451883
37. Verheyen GR, Braeken E, Deun KV, Miert SV. Evaluation of in silico tools to predict the skin sensitization potential of chemicals. SAR QSAR Environ Res. 2012;28(1):59-73. doi:10.1080/1062936x.2017.1278617
38. Vijay U, Gupta S, Mathur P, Suravajhala P, Bhatnagar P. Microbial Mutagenicity Assay: Ames Test. Bio Protoc. 2018;8(6):e2763. doi:10.21769/bioprotoc.2763
39. Del Rio D, Rodriguez-Mateos A, Spencer JP, Tognolini M, Borges G, Crozier A. Dietary (poly) phenolics in human health: structures, bioavailability, and evidence of protective effects against chronic diseases. Antioxid Redox Signal. 2013;18(14):1818-92. doi:10.1089/ars.2012.4581
40. Mayo B, Vázquez L, Flórez AB. Equol: a bacterial metabolite from the daidzein isoflavone and its presumed beneficial health effects. Nutrients. 2019;11(9):2231. doi:10.3390/nu11092231
41. Hod R, Maniam S, Nor NHM. A systematic review of the effects of equol (soy metabolite) on breast cancer. Molecules. 2021;26(4):1105. doi:10.3390/molecules26041105
42. Setchell KDR, Clerici C. Equol: history, chemistry, and formation. J Nutr. 2010;140(7):1355S-62S. doi:10.3945/jn.109.119776
43. Zárate S, Stevnsner T, Gredilla R. Role of estrogen and other sex hormones in brain aging. Neuroprotection and DNA repair. Front Aging Neurosci. 2017;9:430. doi:10.3389/fnagi.2017.00430
44. Warfvinge K, Krause DN, Maddahi A, Edvinsson JC, Edvinsson L, Haanes KA. Estrogen receptors α, β and GPER in the CNS and trigeminal system-molecular and functional aspects. J Headache Pain. 2020;21(1):131. doi:10.1186/s10194-020-01197-0
45. Fathi M, Vakili K, Yaghoobpoor S, Qadirifard MS, Kosari M, Naghsh N, et al. Pre-clinical Studies Identifying Molecular Pathways of Neuroinflammation in Parkinson’s Disease: A Systematic Review. Front Aging Neurosci. 2022;14:855776. doi:10.3389/fnagi.2022.855776
46. Luis JP, Simoes CJV, Brito RMM. The Theraupetic Prospects of Targeting IL-1R1 for the Modulation of Neuroinflammation in Central Nervous System Disorders. Int J Mol Sci. 2022;23(3):1731. doi:10.3390/ijms23031731
47. Kip E, Parr-Brownlie LC. Reducing Neuroinflammation Via Therapeutic Compounds and Lifestyle to Prevent or Delay Progression of Parkinson’s Disease. Ageing Res Rev. 2022;78:101618. doi:10.1016/j.arr.2022.101618
48. Fricker M, Tolkovsky AM, Borutaite V, Coleman M Brown GC. Neuronal Cell Death. Physiol Rev. 2018;2(98):813-80. doi:10.1152/physrev.00011.2017
49. Ma'arif B, Muslikh FA, Anggraini W, Taek MM, Laswati H, Agil M. In vitro anti-neuroinflammatory effect of genistein (4',5,7-trihydroxyisoflavone) on microglia HMC3 cell line, and in silico evaluation of its interaction with estrogen receptor-β. Int J Appl Pharm. 2021;13(4):183-7. doi:10.22159/ijap.2021.v13s4.43855
50. Badanjak K, Fixemer S, Smaji´c S, Skupin A, Grünewald A. The Contribution of Microglia to Neuroinflammation in Parkinson’s Disease. Int J Mol Sci. 2021;22(9):4676. doi:10.3390/ijms22094676
51. Zhao W, Hou Y, Song X, Wang L, Zhang F, Zhang H, et al. Estrogen Deficiency Induces Mitochondrial Damage Prior to Emergence of Cognitive Deficits in a Postmenopausal Mouse Model. Front Aging Neurosci. 2021;13:713819. doi:10.3389/fnagi.2021.713819
52. Shao F, Wang X, Wu H, Wu Q, Zhang J. Microglia and Neuroinflammation: Crucial Pathological Mechanisms in Traumatic Brain Injury-Induced Neurodegeneration. Front Aging Neurosci. 2022;14:825086. doi:10.3389/fnagi.2022.825086
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Authors
1.
Muslikh FA, Samudra RR, Ma’arif B, Ulhaq ZS, Hardjono S, Agil M. In Silico Molecular Docking and ADMET Analysis for Drug Development of Phytoestrogens Compound with Its Evaluation of Neurodegenerative Diseases. Borneo J Pharm [Internet]. 2022Nov.30 [cited 2025Apr.3];5(4):357-66. Available from: https://ojs.umpr.ac.id/bjop/article/view/3801
Copyright (c) 2022 Faisal Akhmal Muslikh, Reyhan Rahma Samudra, Burhan Ma’arif, Zulvikar Syambani Ulhaq, Suko Hardjono, Mangestuti Agil
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