基于分子对接技术对维生素D₃羟化酶底物谱的筛选及验证

Screening and Validation of Vitamin D₃ Hydroxylase Substrate Profile Based on Molecular Docking Technique

摘要: 维生素D₃羟化酶(Vdh)是生物法合成维生素D₃ (VD₃)活性形式25(OH)VD₃和1α,25(OH)₂VD₃的关键酶之一。然而，至今对Vdh的天然底物了解甚少，限制了其工业上的应用。为了提高Vdh的商业价值，找到Vdh的最佳底物，探究Vdh与底物的作用机制，深入挖掘Vdh的应用潜力。本研究以VD₃与Vdh的结合模型为基础，利用Autodock分子对接技术对ZINC化合物数据库进行筛选，结合打分，性质筛选以及广义伯恩表面积法(MM/GBSA)计算结合自由能，最终从中挑选出4个小分子进行了实验验证。实验结果与筛选结果一致，4个小分子均能与Vdh发生反应，范德华力是Vdh与小分子结合的主要驱动力，推测Vdh是生产类固醇类药物的潜在生物催化剂。我们的研究为生物合成类固醇药物提供了新思路，也为深入了解Vdh提供了理论基础。

Abstract: Vitamin D₃ hydroxylase (Vdh) is one of the vital enzymes in the biosynthesis of 25(OH)VD₃ and 1α,25(OH)₂VD₃. However, little is known about the natural substrates of Vdh so far, which limits its industrial application. Therefore, in order to improve the commercial value of Vdh and to deeply explore the application potential of Vdh, it is necessary to find the best substrate for Vdh and to ex-plore the mechanism of Vdh-substrate interaction. This study is based on the VD₃-Vdh binding model, using molecular docking technology to screen the ZINC compound database, combining scoring, property screening, and generalized Berne surface area method (MM/GBSA) to calculate the binding free energy. Finally, 4 small molecules are selected for the analysis of experimental ver-ification. The experimental results were consistent with the screening results, four compounds from ZINC have the potential to be hydroxylated by Vdh, and van der Waals forces were the main driving force for the binding of Vdh to small molecules. The screening of Vdh substrate spectrum was com-pleted in this study. It was speculated that Vdh was a potential biocatalyst for the production of steroids. Our study provides new ideas for the biosynthesis of steroid drugs and a theoretical basis for a deeper understanding of Vdh.