MOL2NET, 2017 , 3, doi:10.3390/m 1 10.3390/mol2net-03-xxxx MOL2NET ET, International Conference Series on Multidisc idisciplinary Sciences MDPI http://sciforum.net/conference/mol2net- 2net-03 In silico molecular lar GRIP docking studies of an of antioxidant potenti ntials of black tea compounds ds dari (k.bhandari51@gmail.com) a , Baishak Koushik Bhandar shakhi De (baishakhidey123@gmail.com) b* (ba a School of Medical Sc al Science and Technology, IIT Kharagpur, 721302, haragpur, 721302, India b SSS Indira College ollege of Pharmacy, Vishnupuri, Nanded- 431606, 431606, India . . . Graphical Abstract Abstract. Black tea is a very widel dely accepted and popular beverage that has attracted cted the research limelight and has exhibited multifac ifaceted health effects due to the presence of of wide range of pharmacologically active ve molecules. This paper aims to explore the an antioxidant potentials of black tea catechins by in in silico molecular GRIP docking studies. Basing ng on the result of dock score epicatechin gallate, ate, catechin, epicatechin, epigallocatechin gallate a e all exhibited significant antioxidant potentials s against the targeted enzymes. catechin molecules at me mechanistic level. Rapid Introduction Tea ( Camellia sinensis ) belongi onging to family escalations in drug deve evelopment costs, labor Theaceae is one of the most wide idely consumed intensive screening of innum nnumerable new chemical beverages of the world and have pr ve proven to have entities greatly limits t s the drug development multidimensional health potential ntials due to the process. More protein tar target molecules became actions of several pharmacolog ologically active available with the emer ergence of proteomics, molecules in it (Sen and Bera, 2013 2013). Black tea is genomics, bioinforma matics, NMR and very much preferred in Indian cont ontext due to the crystallography. Comput putational tools like in flavoring contents and astringency cy. Black tea is silico modeling is just suit suitable for the purpose of rich in several pharmacolog ogically active identification and analysis sis of the active sites and molecules the catechins, be benzotropolone potential drug molecules ules binding to such sites compounds the theaflavins, meth ethyl xanthenes (Singla, 2014; Meruva e et al., 2014; Jadhav et viz. caffeine, theobromine, theophy ophylline etc (Sen al.,). Bioinformatic softw software tools offers a fast and Bera, 2013; Bhandari et al., 2015 ., 2015). In silico and frugal screening of of active phytomedicinal molecular GRIP docking studi udies aided in compounds thereby dimini minishing labor, cost and understanding the antioxidant pot potential of tea time (Meruva et al., 2014 2014). The aim of protein-
MOL2NET, 2017 , 3, doi:10.3390/mol2net-03-xxxx 2 ligand docking is to calculate the binding energy minimization was done by using Merck of the protein-ligand reaction complex at given Molecular Force Field (MMFF). MMFF is a atomic co-ordinates. The key parameters for class II force field designed to be a transferable flexible docking include energy functions, force field for pharmaceutical compounds that protein catalytic sites and active residues accurately treats conformational energetics and (Meruva et al., 2014). For rapid, accurate non-bonded interactions. Molecular docking protein-peptide and protein-ligand docking, energy evaluations are usually carried out with GRIP™ by V Life software is a novel the help of scoring function like dock score, PLP methodology available for rigid as well as score, potential mean force (PMF) score, steric flexible docking purposes. It makes use of a set and electrostatic score. PLP score or Piecewise of ligands with its conformers to be docked into Linear Potential scoring function calculates both the receptor cavity. This software helps to search the shape and hydrogen bond complementarity of for the active sites, consists of pre-computation poses to the active site. The PLP score is a pair of grids and tries to maximize favorable wise additive scoring function. The PLP function interaction and minimize unfavorable and is incorporated by the MDS V Life Science repulsive interaction by proving the best possible software in the GRIP docking method which orientation. GRIP scoring function allows for fast calculates the ligand-receptor binding affinity in and precise capturing of ligand-receptor terms of the PLP score. The PLP score is interactions in the active sites of proteins. In designed to enable flexible docking of ligands to GRIP docking, unique conformers of a set of perform a full conformational and positional ligands are considered as input and offers the search within a rigid binding site. These advantages of wide range of parameterizations, molecules were docked into the active site of both ligand guided as well as cavity guided 4B3E (copper-zinc superoxide dismutase), 3KIJ docking options, considers hydrogen bonding, (crystal structure of human peroxidase) and repulsions and dispersion interactions with 1DGB (catalase) that can be obtained as co- manual, automated and batch mode operations crystallized with bicarbonate ion or NADPH or (Jadhav et al.; De et al., 2017). by the use of cavities. The parameters fixed for docking simulation were: number of placements Materials and Methods is 100, rotation angle at 10o, exhaustive method, The Proteins used for GRIP Docking include ligand-wise results-10, scoring function-PLP Copper-zinc superoxide dismutase (4B3E), score. By rotation angle, ligand would be rotated glutathione peroxidase (3KIJ) and erythrocyte inside the receptor cavity to generate different catalase (1DGB) of Homo sapiens were used for poses of ligand inside the receptor cavity. By the current study. Their PDB structures were placements, the method will check all the 100 taken from RCSB. V life MDS 4.3 is very robust possible placements into the active site pocket software with inclusion of all the necessary and will result the best placements out of 100. simulation modules. The 2D-structures of After docking simulation, the best docked catechin (C), epicatechin (EC), epicatechin conformer of test molecules and reference gallate (ECG), epigallo catechin (EGC) and ligands were then checked for their interactions epigallocatechin gallate (EGCG) the major with targeted proteins like hydrogen bonding, catechin available in black tea were drawn in the hydrophobic, pi-staking/aromatic, charge and 2D drawing application (2D Draw app) of MDS van der Waal’s interactions (Singla and Bhat, 4.3, followed by its conversion into 3D form by 2010; Singla et al., 2013; Malleshappa and Patel, using default conversion procedure. Their energy
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