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首页> 外文期刊>Der Pharma Chemica: journal for medicinal chemistry, pharmaceutical chemistry and computational chemistry >Molecular docking study on Hemagglutinin protein of H1N1 virus with recommended antiviral drugs
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Molecular docking study on Hemagglutinin protein of H1N1 virus with recommended antiviral drugs

机译：推荐抗病毒药物对H1N1病毒血凝素蛋白的分子对接研究

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Molecular docking is routinely used for understanding drug–receptor interaction in modern drug design. The goal of protein docking is to obtain a model for the bound complex from the coordinates of the unbound component molecules. Current docking methods evaluate a vast number of docked conformations by simple functions that measure surface complementarily. Many proteins undergo small side chain or even backbone movements on binding of different ligands into the same protein structure. This is known as induced fit and is potentially problematic for virtual screening of databases against protein targets. In this report we investigate the limits of the flexible protein approximation used by the docking program, AutoDock, through cross-docking using protein structures of influenza hemagglutinin. Here, we describe the suitability of antiviral drugs recommended against influenza for the docking and 3D structure prediction of hemagglutinin protein of the novel influenza A virus H1N1. The 3D structure of the macromolecular complex resulting from the protein-ligand association is a very useful basis to understand its specific functions. Homology model of hemagglutinin protein was constructed using MODELLER 9v6 and the model was energy minimized and validated using Gromacs to obtain a stable structure, which was further used for 3D structure prediction and docking through molecular docking studies using Autodock. The active sites were analyzed by the program Surface Racer.
机译：分子对接通常用于了解现代药物设计中的药物-受体相互作用。蛋白质对接的目的是从未结合的成分分子的坐标中获得结合的复合物的模型。当前的对接方法通过简单的功能来互补地测量表面，从而评估了大量的对接构象。许多蛋白质在不同的配体结合到同一蛋白质结构中时会经历小的侧链甚至主链运动。这被称为诱导拟合，对于针对蛋白质目标的虚拟筛选数据库可能存在问题。在本报告中，我们通过使用流感血凝素的蛋白质结构进行交叉对接，研究了对接程序AutoDock使用的灵活蛋白质近似的极限。在这里，我们描述了针对流感的抗病毒药物对新型A型流感病毒H1N1的血凝素蛋白的对接和3D结构预测的适用性。由蛋白质-配体结合产生的大分子复合物的3D结构是了解其特定功能的非常有用的基础。使用MODELLER 9v6构建血凝素蛋白的同源性模型，并使用Gromacs对模型进行能量最小化和验证，以获得稳定的结构，该结构可进一步用于3D结构预测和通过Autodock的分子对接研究对接。活动程序由Surface Racer程序进行了分析。

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