甲氧氯普胺作为多巴胺D2受体小分子的计算机研究:量子力学(QM)分子对接处理

IF 3.5 Q2 CHEMISTRY, MULTIDISCIPLINARY
M. Nabati, Hossein Mohammadnejad-Mehrabani, Abdolnaser Tavakkoli, M. Mazidi, E. Lohrasbi, Afshar Gravand, Hamideh Sabahnoo
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引用次数: 6

摘要

目前的研究探索将包括研究标题分子的分子结构、键性质、稳定性、反应性和电子性质。采用6-31G(d,p)基理论集,采用B3LYP (Becke,三参数,Lee-Yang-Parr)交换相关泛函,采用密度泛函理论(DFT)方法进行分子优化和所有理论计算。所研究分子的分子结构几何的量子力学(QM)计算是用尺度量子力学计算的。能隙(Eg)、电离势(IP)、电子亲和力(EA)、化学硬度(η)、化学柔软度(S)、电负性(χ)、电子化学势(µ)和亲电性指数(ω)等全局反应性描述符可由前沿分子轨道(HOMO和LUMO)的能量得到。计算的整体反应性指数表明,甲氧氯普胺是一种稳定的小分子,可以与多巴胺D2受体(D2R)残基结合。分子对接研究表明,该配体与蛋白结合位点上的氨基酸残基Phe 198、Phe 382、Ala 122、Thr 119、Ser 197、Trp 386、Phe 390、Val 115、Cys 118和Asp 114的空间相互作用是该配体与受体的主要结合方式。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
In Silico Study of Metoclopramide as A Small Molecule of Dopamine D2 Receptor: a Quantum-Mechanical (QM) Based Molecular Docking Treatment
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.
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来源期刊
Chemical Methodologies
Chemical Methodologies CHEMISTRY, MULTIDISCIPLINARY-
CiteScore
3.10
自引率
1.80%
发文量
8
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