BioInfoBank Institute, Poznań, Poland.
J Chem Inf Model. 2011 Feb 28;51(2):455-62. doi: 10.1021/ci100403b. Epub 2011 Jan 13.
Squalene epoxidase (SE) is a key flavin adenine dinucleotide (FAD)-dependent enzyme of ergosterol and cholesterol biosynthetic pathways and an attractive potential target for drugs used to inhibit the growth of pathogenic fungi or to lower cholesterol level. Although many studies on allylamine drugs activity have been published during the last 30 years, up until now no detailed mechanism of the squalene epoxidase inhibition has been presented. Our study brings such a model at atomic resolution in the case of yeast Saccharomyces cerevisiae . Presented data resulting from modeling studies are in excellent agreement with experimental findings. A fully atomic three-dimensional (3D) model of squalene epoxidase (EC 1.14.99.7) from S. cerevisiae was built with the help of 3D-Jury approach and further screened based on data known from mutation experiments leading to terbinafine resistance. Docking studies followed by molecular dynamics simulations and quantum interaction energy calculations [MP2/6-31G(d)] resulted in the identification of the terbinafine-squalene epoxidase mode of interaction. In the energetically most likely orientation of terbinafine its interaction energy with the protein is ca. 120 kJ/mol. In the favorable position the terbinafine lipophilic moiety is located vertically inside the squalene epoxidase binding pocket with the tert-butyl group oriented toward its center. Such a position results in the SE conformational changes and prevents the natural substrate from being able to bind to the enzyme's active site. That would explain the noncompetitive manner of SE inhibition. We found that the strongest interaction between terbinafine and SE stems from hydrogen bonding between hydrogen-bond donors, hydroxyl group of Tyr90 and amine nitrogen atom of terbinafine. Moreover, strong attractive interactions were recorded for amino acids whose mutations resulted in terbinafine resistance. Our results, elucidating at a molecular level the mode of terbinafine inhibitory activity, can be utilized in designing more potent or selective antifungal drugs or even medicines lowering cholesterol in humans.
角鲨烯环氧化酶（SE）是甾醇和胆固醇生物合成途径中关键的黄素腺嘌呤二核苷酸（FAD）依赖性酶，也是用于抑制致病真菌生长或降低胆固醇水平的药物的有吸引力的潜在靶标。尽管在过去的 30 年中已经发表了许多关于烯丙胺类药物活性的研究，但直到现在，还没有提出角鲨烯环氧化酶抑制作用的详细机制。我们的研究在酵母酿酒酵母中以原子分辨率提供了这样的模型。基于建模研究得到的数据与实验结果非常吻合。在 3D-Jury 方法的帮助下构建了酿酒酵母角鲨烯环氧化酶（EC 1.14.99.7）的全原子三维（3D）模型，然后根据导致特比萘芬耐药的突变实验数据进一步筛选。对接研究随后进行分子动力学模拟和量子相互作用能计算[MP2/6-31G（d）]，确定了特比萘芬与角鲨烯环氧化酶的相互作用模式。在特比萘芬与蛋白质相互作用的最可能的能量取向中，其相互作用能约为 120 kJ/mol。在有利的位置，特比萘芬的亲脂部分垂直位于角鲨烯环氧化酶结合口袋内，叔丁基基团朝向其中心。这种位置导致 SE 构象变化，并阻止天然底物能够结合到酶的活性位点。这可以解释 SE 抑制的非竞争性方式。我们发现，特比萘芬与 SE 之间的最强相互作用源于供氢体，即 Tyr90 的羟基和特比萘芬的胺氮原子之间的氢键。此外，记录了与氨基酸的强吸引相互作用，这些氨基酸的突变导致特比萘芬耐药。我们的结果从分子水平阐明了特比萘芬抑制活性的模式，可用于设计更有效或选择性的抗真菌药物，甚至是降低人类胆固醇的药物。
