基于生物信息学及分子动力学探讨牛膝影响铁死亡治疗骨质疏松机制

The Mechanism of Achyranthes bidentata’s Influence on Ferroptosis in the Treatment of Osteoporosis Based on Bioinformatics and Molecular Dynamics

通过生物信息学分析、分子对接及分子动力学来研究牛膝通过影响铁死亡治疗骨质疏松(Osteoporosis,OP)的潜在作用机制。在GEO数据库获取GSE56116、GSE2208和GSE7158共3个数据集,采用R软件进行差异分析得出OP潜在的发病基因。利用中药系统药理学技术平台(TCMSP)检索牛膝的成分和作用靶点,再通过FerrDb数据库获取铁死亡相关靶点与分析3个数据集所得的差异基因取交集得到关键治疗靶点。通过蛋白质印迹试验验证关键治疗靶点在对照组与OP患者血液中的差异表达情况,再对关键治疗靶点与牛膝的活性成分黄芩素进行分子对接及分子动力学模拟。本研究共筛选出关键靶基因1个(花生四烯酸-12-脂加氧酶,ALOX12)。蛋白质印迹试验结果显示ALOX12在OP中表达显著升高(P<0.05)。分子对接及分子动力学结果显示黄芩素能够与ALOX12紧密对接,通过氢键及疏水键形成稳定结构而发挥作用。牛膝可能通过作用于ALOX12影响铁死亡从而起到治疗OP作用。

The aim of this study was to to dentify the potential mechanism of Achyranthes bidentata in the treatment of Osteoporosis(OP)by affecting Ferroptosis based on the bioinformatic analysis,molecular docking and molecular dynamics.GSE56116、GSE2208 and GSE7158 datasets were obtained through the GEO database,and the potential pathogenic genes of OP were derived by the differential analysis using R software.The components and targets of Achyranthes bidentata were retrieved through the Technology of Chinese Medicine Systemic Pharmacology Platform(TCMSP).The targets of ferroptosis were obtained through the FerrDb database,and the differential genes obtained from the analysis of 3 datasets were intersected to obtain the key therapeutic targets.The differential expression of key therapeutic targets in control group and OP patients was verified by the western blot.The key therapeutic target and the baicalein were used for molecular docking and molecular dynamics simulation.There was 1 related targets identified overall(Arachidonate 12-Lipoxygenase,ALOX12).The result of WB showed that the expression of ALOX12 was significantly increased in OP(Normal group:0.63±0.17,OP group:0.99±0.34,P<0.05).The molecular docking and molecular dynamics results showed that baicalin could dock closely with ALOX12 and play a role by forming a stable structure through hydrogen and hydrophobic bonds.This study showed that the effective ingredients of Achyranthes bidentata may affect the ferroptosis in OP by acting on the target genes of ALOX12.