VEGETOS: An International Journal of Plant Research & Biotechnology
(Society For Plant Research)

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Print ISSN : 0970-4078.
Online ISSN : 2229-4473.
Website:www.vegetosindia.org
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Doi: 10.1007/s42535-021-00263-5
Doi Link: https://doi.org/10.1007/s42535-021-00263-5
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Published: 16 July, 2021

Exploring novel natural compound inhibitors for Parkinsonian receptor (DJ1) by homology modeling, molecular docking and MD simulations


Abstract:

The present study has been done with the aim of applying computational tools for the analysis of bioactive constituents that are active against neurodegenerative disorders. Chemo-informatics and bio-informatic tools have proven helpful for the identification of complementary leads on the targets. The in silico studies were performed using Schrodinger suite packages like prime application, sitemap generation, grid and glide SP that are available in version 10.2 Maestro. The therapeutic effects of phyto-compounds obtained through medicinal plants were evaluated. The target of DJ 1 was rescued from Uniport to retrieve medicinal plant based bioactive compounds (ligands) from the chemical database. Homology modeling, molecular docking and molecular dynamic (MD) simulations were performed as potential tools for computational studies in these proteins. Results revealed that the biomolecule, Punigluconin had a better binding affinity compared to other molecules. Hence, in the present study it was accomplished that the Punigluconin molecule would serve as a better drug candidate for Parkinson disease, subjected to further research exploration.

Vegetos

Keywords:


Parkinson disease, 1UCF, Homology modeling, Molecular modeling, MD simulation, Punigluconin


References:


Barlowa DJ, Buriani A, Ehrmana T, Bosisio E, Eberini I, Hylands PJ (2012) In-silico studies in Chinese herbal medicines’ research: evaluation of in-silico methodologies and phytochemical data sources, and a review of research to date. J Ethnopharma 140:526–534


Beitz JM (2014) Parkinson’s disease: a review. Front Biosci 6:65–74


Berman HM, Westbrook J, Feng Z (2000) The protein data bank. Nucleic Acids Res 28:235–242


Bhatt H (2010) In Silico Analysis of Parkinson’s Diseases. Mehsana Urban Bank Institute of Biosciences (MUBIOB), Ganpat University Kherva, Thesis


Choi JG, Kim HG, Kim MC, Yang WM, Huh Y, Kim SY, Oh MS (2011) Polygalae radix inhibits toxin-induced neuronal death in the Parkinson’s disease models. J Ethnopharm 134:414–421


Desmond user manual Copyright 2012. Schrodinger, LLC, New York


Essa MM, Vijayan RK, Castellano-Gonazalez G, Memon MA, Braidy N, Guillemin GJ (2012) Neuroprotective effect of natural products against Alzheimer disease. Neuro Chem Res 37:1829–1842


Garrido DM, Corbett DF, Dwornik KA, Goetz AS, Littleton TR, Mckeown SC, Mills WY, Smalley TL, Briscoe CP, Peat AJ (2006) Synthesis and activity of small molecule GPR40 agonist. Bioorg Med Chem Lett 16:1840–1845


Giasson BI, Ischiropoulos H, Lee VM, Trojanowski JQ (2002) The relationship between oxidative/nitrative stress and pathological inclusions in Alzheimer’s and Parkinson’s diseases. Free Radical Biol Med 32:1264–1275


Grundy WN (1998) Homology detection via family pairwise search. J Comput Biol 3:479–491


Honbou K, Suzuki NN, Horiuchi M (2003) The crystal structure of DJ-1, a protein related to male fertility and Parkinson’s disease. J Biolog Chem 33:31380–31384


Horvath MM, Grishin NV (2001) The C-terminal domain of HPII catalase is a member of the type I glutamine amidotransferase superfamily. Proteins 42:230–236


Jeyam M, Raj Karthika GR, Poornima V (2012) Molecular understanding and Insilico valsidation of traditional medicines for Parkinson’s disease. Asia J Pharm Clin Res 5:125–128


Lig Prep, Version 2.5, Schrödinger, LLC, New York, 2011


Maestro 10.2 version. Schrodinger, LLC, New York, 2005


Mckeown SC, Corbett DF, Goetz AS (2007) Solid phase synthesis and SAR of small molecule agonist for the GPR40 receptor. Bioorg Med Chem Lett 17:1584–1589


Merlino A, Vieites M, Gambino D, Cruzi T (2014) Homology modelling of and L. major NADH dependent fumarate reductases: ligand docking, molecular dynamic validation, and insights on their binding modes. J Mol Graph Model 48:57–59


Mitsumoto A, Nakagawa Y (2001) DJ-1 is an indicator for endogenous reactive oxygen species elicited by endotoxin. Free Radical Res 35:885–893


Perry G, Cash AD, Nunomura A, Zhu X, Zentino-Savin T, Drew KL, Shimohama S, Avila J, Castellani RJ, Smith MA (2002) Alzimer disease and oxidative stress. J Biomed Biotechnol 2120–23


Prime version 10.2 Schrodinger, LLC, New York, 2005


Prime, adaptation 10.2 Schrodinger, LLC, New York, 2015


Salameh BA, Cumpstey I, Sundin A, Leffler H, Nilsson UJ (2010) 1H–1, 2,3-triazol-1-yl thiodigalactoside derivatives as high affinity galectin-3 inhibitors. Bioorg Med Chem 18:5367–5378


Schrodinger, LLC, New York, 2015


Shahlei M, Sobhani AM, Mahnam K, Fassihi A, Saghaie L, Mansourian M (2011) Homology modelling of human CCR5 and analysis of its binding properties through molecular docking and molecular dynamics simulation. Biochi Etio Biophy Act 1808:802–817


Subhani S, Jayaraman A, Jamil K (2015) Homology modelling and molecular docking of MDR1 with chemotherapeutic agents in non-small cell lung cancer. Biomed Pharmacother 71:37–45


Surronen OT, Kolehmainen P, Salminen A (2000) Protective effect of L-deprenyl against apoptosis induced by okadaic acid in cultured neuronal cells. Biochem Pharmacol 59:1589–1595


Venable RM, Brooks BR, Pastor RW (2000) Molecular dynamic simulations of gel (L-beta I) phase lipid bi layers in constant pressure and constant surface area ensembles. J Chem Phys 112:4822–4832


Vijayakumar S, Prabhu S, Rajalakhsmi S, Manogar P (2016) Review on potential phytocompounds in drug development for Parkinson disease: a pharmacoinformatic approach. Inf Med Unlocked 5:15–25


Winters RA, Zukowski J, Ercal N, Matthews RH, Spitz DR (1995) Analysis of glutathione, glutathione disulfide, cysteine, homocysteine, and other biological thiols by high- performance liquid chromatography following derivatization by n-(1-pyrenyl) maleimide. Anal Biochem 227:14–21




 


Acknowledgements :



The authors are grateful to the DST-SERB (SB/YS/LS-109/2014) for providing financial assistance in this project. We sincerely express our thanks to the management of A.V.V.M. Sri Pushpam College (Autonomous), Poondi, for providing us the necessary facilities and support to carry out this work.


Author Information:



S. Vijayakumar
Computational Phytochemistry Lab, P.G. and Research Department of Botany, A.V.V.M. Sri Pushpam College (Autonomous), (Affiliated to Bharathidasan University), Poondi, India
svijaya_kumar2579@rediff.com




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