Abstract：
We present in this article a case study on the thermodynamics of binding to human carbonic anhydrase II (HCA II) by three well-known inhibitors, viz. (a) acetazolamide (AZM) that directly binds to the catalytic Zn(II) ion at the active site, (b) non-zinc binding 6-hydroxy-2-thioxocoumarin (FC5) (c) 2-[(S)-benzylsulfinyl]benzoic acid (3G1). In each case, the crystal structure or its analogue of inhibitor-bound HCA II has been used to perform classical molecular dynamics (MD) simulation in water till 1 μ s ${1\\hskip0.33em\\mu s}$ . AZM and FC5 are found to undergo repeated binding and unbinding with markedly different dynamics from the partially buried, substrate-binding hydrophobic pocket near the active site. 3G1, on the other hand, is found to remain mostly at its crystallographic binding site occluded from the active site of HCA II. The associated binding free energies ( Δ G b i n d , s o l v ${{\\rm \\Delta }{G}_{bind,solv}}$ ) have been computed using the known MM/GBSA method and compared to the available experimental data. Our results show that Δ G b i n d , s o l v ${{\\rm \\Delta }{G}_{bind,solv}}$ encounters several issues including limited sampling of multiple binding sites and incorrect prediction of the affinity of the chosen ligands. Possible use of the simulation results in further construction of Markov state models is also discussed.
摘要：
我们在本文中介绍了三种众所周知的抑制剂与人碳酸酐酶II（HCAII）结合的热力学的案例研究，viz.（a）乙酰唑胺（AZM），在活性位点直接与催化Zn（II）离子结合，(b)非锌结合性6-羟基-2-硫代香豆素(FC5)(c)2-[(S)-苄基亚磺酰基]苯甲酸(3G1)。在每种情况下，抑制剂结合的HCAII的晶体结构或其类似物已用于在水中进行经典分子动力学（MD）模拟，直到1μs${1\\hskip0.33em\\mus}$。发现AZM和FC5经历重复的结合和解结合，其动力学与部分掩埋的动力学明显不同，活性位点附近的底物结合疏水口袋。3G1，另一方面，发现大部分保留在其从HCAII的活性位点闭塞的晶体学结合位点。相关的束缚自由能(ΔGbind，solv${\\rm\\Delta}{G}_{绑定,solv}}$)已使用已知的MM/GBSA方法进行了计算，并与可用的实验数据进行了比较。我们的结果表明，ΔGbind，solv${\\rm\\Delta}{G}_{绑定,solv}}$遇到了几个问题，包括多个结合位点的有限采样和对所选配体的亲和力的错误预测。还讨论了仿真结果在进一步构建马尔可夫状态模型中的可能用途。
