Each ligand was docked independently with the enzyme COMT. and Opicapone have U.S. Food and Drug Administration approval but regular use of these drugs is associated with high risk of side effects. Thus, authors have focused on discovery of phytochemicals and evaluation of their effectiveness against human soluble COMT using virtual screening, molecular docking, drug-like property prediction, generation of pharmacophoric property, and molecular dynamics simulation. Overall, study proposed, nine phytochemicals (withaphysalin D, withaphysalin N, withaferin A, withacnistin, withaphysalin C, withaphysalin O, withanolide B, withasomnine, and withaphysalin F) of plant have strong binding efficiency against human COMT in comparison to both of the drugs i.e., Opicapone and Entacapone, thus may be used as putative bioenhancer in L-DOPA therapy. The present study needs further experimental validation to be used as an adjuvant in PD treatment. studies. Structural geometry optimization and protonation state of these ligands were achieved using Discovery Studio 3.5 suite. Drug-like property prediction Molinspiration (http://www.molinspiration.com/) web server was used to LY2794193 predict the drug-like property of selected phytochemicals. It accepts ligand structure in SMILES (Simplified molecular-input line-entry system) format and predicts its bioactivity and pharmacokinetics properties following Lipinskis rule of five [26]. Screening of ligands Selected natural compounds were screened computationally against complex structure of hCOMT and SAM in order to identify efficient ligand using PyRx0.8 tool (https://pyrx.sourceforge.io/). PyRx 0.8 is an open source tool [27], used to screen libraries of compounds against potential drug target [24,28]. During virtual screening (VS) a grid of 30, 30, 30 ? in x, y, z direction was centred on drug-binding pocket of hCOMT crystal structure using AutoDock Vina [29] and PyRx 0.8 [27]. Molecular docking Molecular docking was performed to validate the efficiency of selected natural compounds obtained from VS and drug-like property prediction. During docking, two FDA-approved anti-Parkinson COMT inhibitor drugs such as opicapone (DB11632), and entacapone (DB00494) were also included to compare their binding affinity with selected natural ligands. Molecular docking was performed using AutoDock 4.2 (http://autodock.scripps.edu/) and Auto-Dock Tools 4 tool [30]. Each ligand was docked independently with the enzyme COMT. During docking and further studies, Mg2+ ion was kept intact in its position. The receptor and ligands were prepared using ADT tool [30]. Kollman charges and polar hydrogen atoms were added to the enzyme structure. Gasteiger partial charge was applied and nonpolar hydrogen atoms were merged within ligand structures. Both receptor and ligands were converted to pdbqt format before docking. A virtual grid box was set around the drug-binding cavity of the target structure with size of 30, 30, 30 ? in x, y, z direction along with spacing of 0.375 ?. Semi-flexible docking was performed by keeping the protein as rigid and allowing ligands to move within the binding cavity. Lamarckian genetic algorithm was employed to perform molecular docking. During the docking process, a maximum of 20 conformers was considered for each docking with 25,000,000 energy evaluation steps. Subsequently, all binding poses of each docking were studied and most energetically as well as geometrically favorable conformation for each independent run was selected for further study. Finally, 2D and 3D view of atomic interaction between best-docked complexes were achieved using Discovery Studio 3.5 and PyMol molecular graphics (http://www.pymol.org) tool, respectively. MD simulation of COMT in the presence of SAM and natural ligands To confirm the stability and efficacy of natural ligands fitted into the active pocket of COMT and in the presence of SAM, MD simulation of protein-ligand complex [24] was performed for 10 suitable phytochemicals. PRODRG [31] web server was used to prepare each ligand topology..Presence of few chemical features such as aromatic ring (AR), hydrogen bond donor (HBD), hydrogen bond acceptor (HBA), hydrophobic property (HY) were predicted for all 10 suitable phytochemicals using ZINC Pharmer (http://zincpharmer.csb.pitt.edu/) web server. Results COMT identified as a significant drug target in PD Possible conversion of exogenous L-DOPA to 3-O-methyldopa in both peripheral and cerebral system occurs due to the metabolic activity of COMT enzyme, is a major concern in PD treatment. exogenous L-DOPA (~80%) that occurs due to metabolic activity of the enzyme catechol-O-methyltransferase (COMT). Although, both Entacapone and Opicapone have U.S. Food and Drug Administration approval but regular use of these drugs is associated with high risk of side effects. Thus, authors have focused on discovery of phytochemicals and evaluation of their effectiveness against human soluble COMT using virtual screening, molecular docking, drug-like property prediction, generation of pharmacophoric property, and molecular dynamics simulation. Overall, study proposed, nine phytochemicals (withaphysalin D, withaphysalin N, withaferin A, withacnistin, withaphysalin C, withaphysalin O, withanolide B, withasomnine, and withaphysalin F) of plant have strong binding efficiency against human COMT in comparison to both of the drugs i.e., Opicapone and Entacapone, thus may be used as putative bioenhancer in L-DOPA therapy. The present study needs further experimental validation to be used as an adjuvant in PD treatment. studies. Structural geometry optimization and protonation state of these ligands were achieved using Discovery Studio 3.5 suite. Drug-like property prediction Molinspiration (http://www.molinspiration.com/) web server was used to predict the drug-like property of selected phytochemicals. It accepts ligand structure in SMILES (Simplified molecular-input line-entry system) format and predicts its bioactivity and pharmacokinetics properties following Lipinskis LY2794193 rule of five [26]. Screening of ligands Selected natural compounds were screened computationally against complex structure of hCOMT and SAM in order to identify efficient ligand using PyRx0.8 tool (https://pyrx.sourceforge.io/). PyRx 0.8 is an open source tool [27], used to screen libraries of compounds against potential drug target [24,28]. During virtual screening (VS) a grid of 30, 30, 30 ? in x, y, z direction was centred on drug-binding pocket of hCOMT crystal structure using AutoDock Vina [29] and PyRx 0.8 [27]. Molecular docking Molecular docking was performed to validate the efficiency of selected natural compounds obtained from VS and drug-like property prediction. During docking, two FDA-approved anti-Parkinson COMT inhibitor drugs such as opicapone (DB11632), and entacapone (DB00494) were also included to compare their binding affinity with selected natural ligands. Molecular docking was performed using AutoDock 4.2 (http://autodock.scripps.edu/) and Auto-Dock Tools 4 tool [30]. Each ligand was docked independently with the enzyme COMT. During docking and further studies, Mg2+ ion was kept intact in its position. The receptor and ligands were prepared using ADT tool [30]. Kollman charges and polar hydrogen atoms were added to the enzyme structure. Gasteiger partial charge was applied and non-polar hydrogen atoms had been merged within ligand constructions. Both receptor and ligands had been changed into pdbqt format before docking. A digital grid package was set across the drug-binding cavity of the prospective framework with size of 30, 30, 30 ? in x, con, z path along with spacing of 0.375 ?. Semi-flexible docking was performed by keeping the proteins as rigid and permitting ligands to go inside the binding cavity. Lamarckian hereditary TIAM1 algorithm was used to execute molecular docking. Through the docking procedure, no more than 20 conformers was regarded as for every docking with 25,000,000 energy evaluation measures. Subsequently, all binding poses of every docking were researched & most energetically aswell as geometrically beneficial conformation for every independent operate was selected for even more research. Finally, 2D and 3D look at of atomic discussion between best-docked complexes had been achieved using Finding Studio room 3.5 and PyMol molecular graphics (http://www.pymol.org) device, respectively. MD simulation of COMT in the current presence of SAM and organic ligands To verify the balance and effectiveness of organic ligands fitted in to the energetic pocket of COMT and in the current presence of SAM, MD simulation of protein-ligand complicated [24] was performed for 10 appropriate phytochemicals. PRODRG [31] internet server was utilized to get ready each ligand topology. Remaining protocol was identical to referred to above. Ten 3rd party MD run had been performed for 50 ns time frame. Trajectories of most 10 simulations had been preserved in 10 fs period. Microsoft Excel was utilized to storyline graphs through the produced outcomes. Prediction of pharmacophoric features Understanding on different pharmacophoric properties of the lead molecule includes a essential role in pc aided drug style (CADD). Existence of few chemical substance features such as for example aromatic band (AR), hydrogen relationship donor (HBD), hydrogen relationship acceptor (HBA), hydrophobic home (HY) were expected for many 10 appropriate LY2794193 phytochemicals using ZINC Pharmer (http://zincpharmer.csb.pitt.edu/) internet server. Outcomes COMT defined as a significant medication focus on in PD Feasible transformation of exogenous L-DOPA to 3-O-methyldopa in both peripheral and cerebral program occurs because of the.
Each ligand was docked independently with the enzyme COMT