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Abstract：
In silico studies are attracting considerable interest due to their ability to understand protein-ligand interactions at the atomic level. The main principal tools of this in silico analyses are molecular docking and molecular dynamic (MD) simulation. This paper examines how can natural compounds that are derived from Salviae miltiorrhizae to block Neisseria adhesion A Regulatory protein (NadR). In molecular docking analysis, only four compounds were found in higher binding affinity with NadR among 10 candidates (tanshinol B, tanshinol A, lithospermic acid and tournefolal were -7.61, -7.56, -8.22 and -7.81 kcal/mol, respectively, compared to -7.23 kcal/mol of native ligand). Absorption, distribution, metabolism, excretion (ADME) and toxicity properties, medicinal chemistry profile, and physicochemical features were displayed that tournefolal contains good properties to work as a safe and good anti-adhesive drug. Therefore, the complexes of these four ligands with NadR protein were subjected to 100 ns of MD simulation. RMSD, RMSF, RG and hydrogen bonding exhibited that tournefolal showed stable binding affinity and molecular interaction with NadR protein. In light of these results, there is now a need to conduct much more in vitro and in vivo studies about the efficacy of tournefolal.Communicated by Ramaswamy H. Sarma.
摘要：
由于能够在原子水平上理解蛋白质-配体相互作用，因此计算机研究吸引了相当大的兴趣。这种计算机模拟分析的主要主要工具是分子对接和分子动力学（MD）模拟。本文研究了如何从丹参中提取的天然化合物来阻断奈瑟菌粘附A调节蛋白（NadR）。在分子对接分析中，在10个候选物中，只有4个化合物与NadR具有较高的结合亲和力(TanshinolB，TanshinolA,紫精酸和Tournefolal分别为-7.61，-7.56，-8.22和-7.81kcal/mol，分别,与-7.23kcal/mol的天然配体相比)。吸收,分布，新陈代谢，排泄(ADME)和毒性特性，药物化学简介，和物理化学特征显示，tournefolal具有良好的性能，可以作为安全和良好的抗粘连药物。因此,对这四种配体与NadR蛋白的复合物进行了100ns的MD模拟。RMSD,RMSF,RG和氢键显示出Tournefolal与NadR蛋白具有稳定的结合亲和力和分子相互作用。鉴于这些结果,现在有必要进行更多的体外和体内研究，关于tournefolal的疗效。由RamaswamyH.Sarma沟通。
