In Silico Study of Metoclopramide as A Small Molecule of Dopamine D2 Receptor: a Quantum-Mechanical (QM) Based Molecular Docking Treatment
Journal Title: Chemical Methodologies - Year 2020, Vol 4, Issue 1
Abstract
The present research exploration will contain studying the molecular structure, bonds nature, stability, reactivity and electronic properties of the title molecule.The molecular optimization and all theoretical computations were carried out by density functional theory (DFT) method using the hybrid B3LYP (Becke, three-parameter, Lee-Yang-Parr) exchange-correlation functional employing the 6-31G(d,p) basis set of theory. Quantum-mechanical (QM) computations of the molecular structure geometry of the molecule under study were calculated with scaled quantum mechanics. The global reactivity descriptors like energy gap (Eg), ionization potential (IP), electron affinity (EA), chemical hardness (η), chemical softness (S), electronegativity (χ), electronic chemical potential (µ) and electrophilicity index (ω) can be obtained from the energies of the frontier molecular orbitals (HOMO and LUMO). The calculated global reactivity indices indicated that metoclopramide which was a stable small molecule can bind with the residues of the dopamine D2 receptor (D2R). Molecular docking studies showed that the steric interactions of the ligand with the residues Phe 198, Phe 382, Ala 122, Thr 119, Ser 197, Trp 386, Phe 390, Val 115, Cys 118 and Asp 114 from the protein binding site are the main binding modes between the ligand and the receptor.
Authors and Affiliations
Mehdi Nabati, Elaheh Lohrasbi, Hamideh Sabahnoo, Vida Bodaghi-Namileh, Mohammad Mazidi, Hossein Mohammadnejad-Mehrabani, Abdolnaser Tavakkoli, Afshar Gervand
Keywords
Related Articles
- EP ID EP617340
- DOI 10.33945/SAMI/CHEMM.2020.1.2
- Views 91
- Downloads 0
Metal-Organic Frameworks (MOFs): Recent Advances in Synthetic Methodologies and Some Applications
The pursuit of rapid development in the area of catalysis, solar energy, environmental remediation, wastewater treatment and other aspects of ecological and sustainable chemistry has prompted substantial research by mate...
Computational NQR−NBO Parameters and DFT Calculations of Ampicillin and Zwitterion (Monomer and Dimer Structures)
Density functional theory (DFT) was used to analyze the structure and Nuclear quadrupole coupling constants (NQCC), χ, and asymmetry parameters, η, of 14N nuclei have been calculated for the antimicrobialampicillin in mo...
Design and Synthesis of a Diaza-bicyclo-naphthalen-oxiranyl-methanone Derivative. Theoretical Analysis of Their Interaction with Cytochrome P450-17A1
Several agents have been used for the treatment of prostate cancer such as flutamide, galeterone, abiraterone and others; however, some of these drugs can produce some secondary effects. The aim of this study was to synt...
Studies on Mechanical and Thermal Properties of PP with Natural Carbon Powder
The work has to develop polypropylene (PP) mixed for the purpose of compatible into the Prosopis juliflora bark powder (PB), Wheat husk carbon powder (WC) and Banyan carbon powder (BBC) using renewable bio resources. PB,...
Green Synthesis of ZnO Nanoparticles via Sol-gel Method and Investigation of Its Application in Solvent-free Synthesis of 12-Aryl-tetrahydrobenzo[α]xanthene-11-one Derivatives Under Microwave Irradiation
In this work, zinc oxide (ZnO) nanoparticles were fabricated using Arabic gum as a reducing and stabilizing agent by the novel sol-gel method without adding any surfactants. The synthesized nanoparticles were characteriz...