Abstract：
BACKGROUND: Diabetes mellitus (DM) is a metabolic disorder disease that causes hyperglycemia conditions and associated with various chronic complications leading to mortality. Due to high toxicity of conventional diabetic drugs, the exploration of natural compounds as alternative diabetes treatments has been widely carried out. Previous in silico studies have highlighted berberine, a natural compound, as a promising alternative in antidiabetic therapy, potentially acting through various pathways, including the inhibition of the FOXO1 transcription factor in the gluconeogenesis pathway. However, the specific mechanism by which berberine interacts with FOXO1 remains unclear, and research in this area is relatively limited. Therefore, this study aims to determine the stability of berberine structure with FOXO1 based on RMSD, RMSF, binding energy, and trajectory analysis to determine the potential of berberine to inhibit the gluconeogenesis pathway. This research was conducted by in silico method with molecular docking using AutoDock4.2 and molecular dynamics study using Amber20, then visualized by VMD.
METHODS: Docking between ligand and FOXO1 receptor was carried out with Autodock4.2. For molecular dynamics simulations, the force fields of DNA.OL15, protein.ff14SB, gaff2, and tip3p were used.
METHODS: Docking between ligand and FOXO1 receptor was carried out with Autodock4.2. For molecular dynamics simulations, the force fields of DNA.OL15, protein.ff14SB, gaff2, and tip3p were used.
摘要：
背景：糖尿病（DM）是一种代谢紊乱疾病，可引起高血糖症，并与导致死亡的各种慢性并发症有关。由于常规糖尿病药物的高毒性，天然化合物作为替代糖尿病治疗的探索已经广泛进行。以前的计算机研究强调了黄连素，一种天然化合物,作为抗糖尿病治疗的一种有希望的替代方案，可能通过各种途径起作用，包括对糖异生途径中FOXO1转录因子的抑制。然而,小檗碱与FOXO1相互作用的具体机制尚不清楚，这方面的研究相对有限。因此,本研究旨在基于RMSD确定黄连素与FOXO1结构的稳定性，RMSF,结合能,和轨迹分析确定小檗碱抑制糖异生途径的潜力。这项研究是通过计算机模拟方法进行的，使用AutoDock4.2进行分子对接，使用Amber20进行分子动力学研究，然后通过VMD进行可视化。
方法：配体和FOXO1受体之间的对接用Autodock4.2进行。对于分子动力学模拟，DNA的力场。OL15，蛋白质。ff14SB,使用gaff2和tip3p。
方法：配体和FOXO1受体之间的对接用Autodock4.2进行。对于分子动力学模拟，DNA的力场。OL15，蛋白质。ff14SB,使用gaff2和tip3p。
