In Silico Evaluation of Molecular Interactions for Parkinson’s Disease Drug Discovery
DOI:
https://doi.org/10.22399/ijcesen.5202Keywords:
Parkinson, Enzyme, Passiflora incarnata, Flavonoids, Molecular dockingAbstract
Monoamine oxidase B (MAO-B) and Catechol-O-methyltransferase (COMT) inhibitors are crucial for the treatment of Parkinson’s disease (PD). Inhibition of these enzymes involves both natural and synthetic compounds. Passiflora incarnata serves as a significant source of natural bioactive molecules, primarily flavonoids (including Apigenin, Luteolin, Myricetin, Orientin, Quercetin, Kaempferol, Vitexin, Isovitexin, and Isoorientin) and alkaloids (such as Harman, Harmine, Harmol, Harmaline, Harmalol, 8-hydroxy Harmine, and Harmine N-oxide). Synthetic options include inhibitors such as Rasagiline, Selegiline, and Safinamide (targeting MAO-B), as well as Entacapone, Tolcapone, and Opicapone (targeting COMT).In this study, molecular docking was employed to identify ligands with optimal interaction energies for each enzyme and to characterize binding affinities, thereby aiding the potential design of new inhibitors. The docking analysis of natural compounds revealed that flavonoids exhibited the strongest affinities and consistent interaction patterns; notably, Myricetin demonstrated the most effective binding to both MAO-B and COMT. Among the synthetic compounds, Safinamide displayed the highest affinity for MAO-B, while Opicapone showed the highest affinity for COMT. These findings highlight the potential of both natural and synthetic inhibitors in reducing enzyme activity associated with PD, providing valuable insights for the development of more effective therapeutic agents.
References
1 L.M. Bekris, I.F. Mata & C.P. Zabetian, The genetics of Parkinson disease, J. Geriatr. Psychiatry Neurol., 23, 2010, 228–242. DOI: https://doi.org/10.1177/0891988710383572
2 M.B.H. Youdim, Why do we need multifunctional neuroprotective and neurorestorative drugs, RMMJ, 1, 2010, 1–18. DOI: https://doi.org/10.5607/en.2010.19.1.1
3 N. Singh, V. Pillay & Y.E. Choonara, Advances in the treatment of Parkinson’s disease, Prog. Neurobiol., 81, 2007, 29–44. DOI: https://doi.org/10.1016/j.pneurobio.2006.11.009
4 C.W. Olanow, M.B. Stern & K. Sethi, The scientific and clinical basis for the treatment of Parkinson disease, Neurology, 72(21 Suppl. 4), 2009, S1–S136. DOI: https://doi.org/10.1212/WNL.0b013e3181a1d44c
5 R. Pahwa, K.E. Lyons, S. Fahn et al., Pharmacological treatment of Parkinson disease, J. Neurol., 311(4), 2014, 442–449. DOI: https://doi.org/10.1097/WCO.0000000000000113
6 S. Fahn, D. Oakes, I. Shoulson et al., Levodopa and the progression of Parkinson’s disease, N. Engl. J. Med., 351(24), 2004, 2498–2508. DOI: https://doi.org/10.1056/NEJMoa033447
7 J. Knoll, The possible mechanisms of action of (-)deprenyl in Parkinson’s disease, J. Neural Transm., 43(3–4), 1978, 177–198. https://doi.org/10.1007/BF01246955. DOI: https://doi.org/10.1007/BF01246955
8 P. Riederer, M.B. Youdim, W.D. Rausch, W. Birkmayer, K. Jellinger & D. Seemann, On the mode of action of l-deprenyl in the human central nervous system, J. Neural Transm., 43, 1978, 217–226. https://doi.org/10.1007/BF01246958. DOI: https://doi.org/10.1007/BF01246958
9 T. Tábi, L. Vécsei, M.B. Youdim, R. Riederer & E. Szökő, Selegiline: a molecule with innovative potential, J. Neural Transm., 127, 2020, 831–842. https://doi.org/10.1007/s00702-019-02082-0. DOI: https://doi.org/10.1007/s00702-019-02082-0
10 H.C. Guldberg & C.A. Marsden, Catechol-O-methyl transferase: pharmacological aspects and physiological role, Pharmacol. Rev., 27, 1975, 135–206. DOI: https://doi.org/10.1016/S0031-6997(25)06681-5
11 V.S. Kostić, COMT inhibition in the treatment of Parkinson’s disease: neuroprotection and future perspectives, Adv. Exp. Med. Biol., 541, 2004, 75–90. DOI: https://doi.org/10.1007/978-1-4419-8969-7_5
12 A. Sazci, E. Ergul, I. Kucukali, G. Kilic, G. Kaya & I. Kara, Catechol-O-methyltransferase gene Val108/158Met polymorphism and susceptibility to schizophrenia: association is more significant in women, Brain Res. Mol. Brain Res., 132(1), 2004, 51–56. DOI: https://doi.org/10.1016/j.molbrainres.2004.09.005
13 H.Y. Handoko, D.R. Nyholt, N.K. Hayward et al., Separate and interacting effects within the catechol-O-methyltransferase (COMT) are associated with schizophrenia, Mol. Psychiatry, 10, 2005, 589–597. DOI: https://doi.org/10.1038/sj.mp.4001606
14 M. Fava, J.F. Rosenbaum, A.R. Kolsky et al., Open study of the catechol-O-methyltransferase inhibitor tolcapone in major depressive disorder, J. Clin. Psychopharmacol., 19, 1999, 329–335. DOI: https://doi.org/10.1097/00004714-199908000-00008
15 P.T. Männistö & S. Kaakkola, Catechol-O-methyltransferase (COMT): Biochemistry, molecular biology, pharmacology, and clinical efficacy of the new selective COMT inhibitors, Pharmacol. Rev., 51, 1999, 593–628. DOI: https://doi.org/10.1016/S0031-6997(24)01423-6
16 P.T. Männistö, I. Ulmanen, K. Lundström, J. Taskinen, J. Tenhunen, C. Tilgmann & S. Kaakkola, Characteristics of catechol O-methyl-transferase (COMT) and properties of selective COMT inhibitors, Prog. Drug Res., 39, 1992, 291–350. DOI: https://doi.org/10.1007/978-3-0348-7144-0_9
17 V. Bonifati & G. Meco, New, selective catechol-O-methyltransferase inhibitors as therapeutic agents in Parkinson’s disease, Pharmacol. Ther., 81, 1999, 1–36. DOI: https://doi.org/10.1016/S0163-7258(98)00032-1
18 A. Antonini, E. Moro, C. Godeiro & H. Reichmann, Medical and surgical management of advanced Parkinson’s disease, Mov. Disord., 33(6), 2018, 900–908. DOI: https://doi.org/10.1002/mds.27340
19 A. Annus & L. Vécsei, Spotlight on opicapone as an adjunct to levodopa in Parkinson’s disease: Design, development and potential place in therapy, Drug Des. Devel. Ther., 11, 2017, 143–151. DOI: https://doi.org/10.2147/DDDT.S104227
20 G.M. Keating & K.A. Lyseng-Williamson, Tolcapone – A review of its use in the management of Parkinson’s disease, CNS Drugs, 29, 2005, 165–184. DOI: https://doi.org/10.2165/00023210-200519020-00006
21 A.J. Lees, Evidence-based efficacy comparison of tolcapone and entacapone as adjunctive therapy in Parkinson’s disease, CNS Neurosci. Ther., 14(1), 2008, 83–93. https://doi.org/10.1111/j.1527-3458.2007.00035. DOI: https://doi.org/10.1111/j.1755-5949.2007.00035.x
22 S. Parashos, C. Wielinski & J.A. Kern, Frequency, reasons, and risk factors of entacapone discontinuation in Parkinson disease, Clin. Neuropharmacol., 27, 2004, 119–123. https://doi.org/10.1097/00002826-200405000-00006. DOI: https://doi.org/10.1097/00002826-200405000-00006
23 A.S. Awaad & N.A. Al-Jaber, Antioxidant Natural Plant, RPMP Ethnomed. Source Mech., 27, 2010, 1–35.
24 H. Dok-Go, K.H. Lee, H.J. Kim et al., Neuroprotective effects of antioxidative flavonoids, quercetin, (+)-dihydroquercetin and quercetin 3-methyl ether, isolated from Opuntia ficus-indica var. Saboten, Brain Res., 965(1–2), 2003, 130–136. DOI: https://doi.org/10.1016/S0006-8993(02)04150-1
25 D. Vauzour, K. Vafeiadou, A. Rodriguez-Mateos, C. Rendeiro & J.P. Spencer, The neuroprotective potential of flavonoids: A multiplicity of effects, Genes Nutr., 3, 2008, 115–126. DOI: https://doi.org/10.1007/s12263-008-0091-4
26 E. Abbasi, M. Nassiri-Asl, M. Shafeei & M. Sheikhi, Neuroprotective effects of vitexin, a flavonoid, on pentylenetetrazole-induced seizure in rats, Chem. Biol. Drug Des., 80, 2012, 274–278. DOI: https://doi.org/10.1111/j.1747-0285.2012.01400.x
27 Mesli, Fouzia, et al. "In silico comparison of synthetic and natural molecules bindings with acetylcholinesterase enzyme using molecular docking." J. Adv. Mol. Biol 2 (2018): 17-26. DOI: https://doi.org/10.22606/jamb.2018.23001
28 Theoretical Investigation of Some Donepezil-based Derivatives as Dual Inhibitors for beta-Amyloid-and Cholinesterase Enzymes A Meziane, A Ghomri, S Bouchentouf, M El-Shazly Journal of Biochemical Technology 12 (2-2021), 48-61 1 2021. DOI: https://doi.org/10.51847/xEKyD9bMjR
29 Identification Of Natural Compounds and Selective Inhibitors Targeting Ptps, PTP1B And ABCG2 Using Molecular Docking and Screening Tools Against Breast Cancer H Bendriss, A Ghomri, M Hammoudi, D Amour, K Otmanine, A Benomier Azerbaijan Pharmaceutical and Pharmacotherapy Journal 24 (2), 10-19 2025.
30 K. Dhawan, S. Kumar & A. Sharma, Anti-anxiety studies on extracts of Passiflora incarnata Linneaus, J. Ethnopharmacol., 78, 2001, 165–170. DOI: https://doi.org/10.1016/S0378-8741(01)00339-7
31 T. Brasseur & L. Angenot, Contribution à l’étude pharmacognostique de la passiflore, J. Pharmacol. Belg., 39(1), 1984, 15–22.
32 R. Soulimani, C. Younos, S. Jarmouni, D. Bousta, R. Misslin & F. Mortier, Behavioural effects of Passiflora incarnata L. and its indole alkaloid and flavonoid derivatives and maltol in the mouse, J. Ethnopharmacol., 57, 1997, 11–20. DOI: https://doi.org/10.1016/S0378-8741(97)00042-1
33 M. Miroddi, G. Calapai, M. Navarra, P.L. Minciullo & S. Gangemi, Passiflora incarnata L.: Ethnomethodology, clinical application, safety and evaluation of clinical trials, J. Ethnopharmacol., 150(3), 2013, 791–804. DOI: https://doi.org/10.1016/j.jep.2013.09.047
34 H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shipchandler & P.E. Bourne, The Protein Data Bank, Nucleic Acids Res., 28, 2000, 235–242. DOI: https://doi.org/10.1093/nar/28.1.235
35 M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman et al., Gaussian 03, Revision D.01, Gaussian Inc., Wallingford, Vol. 3, 2004, 1–28.
36 C.A. Lipinski, F. Lombardo, B.W. Dominy & P.J. Feeney, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Adv. Drug Deliv. Rev., 46(1–3), 2001, 3–26.
37 A.H. Thomas, Merck Molecular Force Field. I. Basis, form, scope, parameterization, and performance of MMFF94, J. Comput. Chem., 17, 1996, 490–519. DOI: https://doi.org/10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P
38 M.J.S. Dewar, E.G. Zoebisch, E.F. Healy & J.J.P. Stewart, Journal of the American Chemical Society, 107(13), 1985, 3902–3909. doi:10.1021/ja00299a02 DOI: https://doi.org/10.1021/ja00299a024
39 Ghomri, A., and S. M. Mekelleche. "Reactivity and regioselectivity of five-membered heterocycles in electrophilic aromatic substitution: A theoretical investigation." Journal of Molecular Structure: THEOCHEM 941.1-3 (2010): 36-40. DOI: https://doi.org/10.1016/j.theochem.2009.10.035
40 Ghomri, Amina, and Sidi Mohamed Mekelleche. "Prediction of the chemo-and regioselectivity of Diels–Alder reactions of o-benzoquinone derivatives with thiophenes by means of DFT-based reactivity indices." Molecular Physics 112.5-6 (2014): 566-574. DOI: https://doi.org/10.1080/00268976.2013.831141
41 Bassou, Djilali, Amina Ghomri, and Abdelkrim Atmani. "Reactivity of β-substituted phosphoenol pyruvates towards alkoxides: a theoretical and experimental study." Progress in Reaction Kinetics and Mechanism 43.3-4 (2018): 211-218. DOI: https://doi.org/10.3184/146867818X15161889114466
42 A.M. Clark, P. Labute, M. Santavy & J. Chem. Inf. Model., 46, 2006, 1107–1123. DOI: https://doi.org/10.1021/ci050550m
43 A.M. Clark & P. Labute, Detection and assignment of common scaffolds in project databases of lead molecules, J. Med. Chem., 52, 2008, 469–483. DOI: https://doi.org/10.1021/jm801098a
44 D. Ritchie, Macromolecular Docking Using Spherical Polar Fourier Correlations, University of Aberdeen, 1996–2005.
45 H. Yamaguchi, K. Kamiie, Y. Kidachi, T. Noshita, H. Umetsu, Y. Fuke & K. Ryoyama, Bioorg. Med. Chem., 22(1), 2014, 440–446. DOI: https://doi.org/10.1016/j.bmc.2013.11.008
46 C.A. Lipinski, Lead- and drug-like compounds: The rule-of-five revolution, Drug Discov. Today Technol., 1(4), 2004, 337–341. DOI: https://doi.org/10.1016/j.ddtec.2004.11.007
47 C.A. Lipinski, F. Lombardo, B.W. Dominy & P.J. Feeney, Adv. Drug Deliv. Rev., 23, 1997, 3–25. DOI: https://doi.org/10.1016/S0169-409X(96)00423-1
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2026 International Journal of Computational and Experimental Science and Engineering

This work is licensed under a Creative Commons Attribution 4.0 International License.