Virtual screening of flavonoids from <i>Chamaecrista</i> genus: ADME and pharmacokinetic properties, interactions of flavonoid–DNA complex by molecular docking and molecular dynamics

This research aimed to conduct an <i>in silico</i> study of compounds, mainly flavonoids, that are found in several plants, including the species of the <i>Chamaecrista</i> genus. The ADME properties, the drug-likeness score and properties of Lipinski and Veber rules of the molecules were determined using online databases. Based on the predicted properties, four flavonoids, apigenin, fisetin, luteolin and ononin were selected for molecular docking and dynamic simulations to study their interactions with DNA (PDB ID: 1BNA). The molecular docking showed that ononin has a high affinity for B-DNA, exhibiting a ΔG value of −9.3 kcal mol⁻¹, compared with the other flavonoids. The molecular dynamic simulations of the flavonoid–DNA complexes showed that the flavonoids interacted with DNA by hydrogen bonding, hydrophobic interaction and <i>π</i>-stacking. The flavonoid ononin showed the best interaction energy value of −291.3490 kJ mol⁻¹, compared with the other flavonoids. Communicated by Ramaswamy H. Sarma本研究旨在针对多种植物中提取的化合物（主要为黄酮类）开展计算机（in silico）模拟研究，所涉植物包括山扁豆属（Chamaecrista）物种。研究人员通过在线数据库测定了这些分子的ADME（吸收、分布、代谢、排泄）性质、类药性评分，以及符合Lipinski规则与Veber规则的相关参数。基于上述预测性质，研究人员筛选出4种黄酮类化合物：芹菜素（apigenin）、漆黄素（fisetin）、木犀草素（luteolin）与芒柄花苷（ononin），开展分子对接与动力学模拟实验，以探究其与DNA（PDB编号：1BNA）的相互作用机制。分子对接结果显示，相较于其余黄酮类化合物，芒柄花苷与B型DNA（B-DNA）具有更高的结合亲和力，其吉布斯自由能变化量（ΔG）为-9.3 kcal·mol⁻¹。黄酮-DNA复合物的分子动力学模拟结果表明，此类黄酮类化合物可通过氢键作用、疏水相互作用与π堆积效应与DNA结合。相较于其余黄酮类化合物，芒柄花苷展现出最优的结合相互作用能，其数值为-291.3490 kJ·mol⁻¹。本文由Ramaswamy H. Sarma转交。

搜集汇总

背景与挑战

背景概述

该数据集聚焦于Chamaecrista属植物中黄酮类化合物的虚拟筛选研究，通过计算机模拟方法评估了化合物的ADME和药代动力学性质，并利用分子对接与分子动力学模拟深入分析了四种选定黄酮类化合物（芹菜素、非瑟酮、木犀草素和芒柄花素）与DNA的相互作用机制。研究结果显示芒柄花素在黄酮类中表现出最高的DNA亲和力和最优的相互作用能量值，为相关药物开发提供了关键数据支持。数据集包含原始研究文档，覆盖生物物理学、生物化学等多个学科领域，适用于药物发现和分子生物学研究。