Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations
Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations
复制标题
DOI：
10.1021/jacs.6b05425
复制
发表时间：
2016-11-02
影响因子：
15
通讯作者：
Gervasio, Francesco L.
中科院分区：
文献类型：
--
作者：
Oleinikovas, Vladimiras;Saladino, Giorgio;Gervasio, Francesco L.
隐藏口袋，即蛋白质靶点上只有在药物结合时才变得明显的位点，为药物开发提供了经典结合位点的有希望的替代方案。在这里，我们研究了四个药理学相关靶点中神秘位点的性质和动力学特性，同时比较了各种基于模拟的方法在发现它们方面的功效。我们发现，所研究的隐蔽网站不对应于本地最小值计算的构象自由能景观的unliganded蛋白质。因此，它们在所有进行的分子动力学模拟中迅速关闭，而不管所使用的力场如何。基于温度的增强采样方法，如平行回火，并没有改善这种情况，因为熵项无助于打开网站。片段探针的使用是有帮助的，因为在长时间的模拟中，它偶尔会导致打开并结合到隐藏位点。我们所观察到的隐蔽位点形成机制暗示了两种经典机制之间的相互作用：诱导适合和构象选择。利用这一洞察力，我们开发了一种新的基于哈密顿量交换的方法“SWISH”（通过标度哈密顿量采样水界面），它与探针相结合，导致了一个有前途的一般方法的神秘网站发现。我们还解决了“假阳性”的问题，并提出了一个简单的方法来区分它们从可药物化的神秘口袋。我们的模拟，其累计采样时间超过200亩s，有助于澄清口袋形成的分子机制，提供了一个坚实的基础，选择一个有效的计算方法。
Cryptic pockets, that is, sites on protein targets that only become apparent when drugs bind, provide a promising alternative to classical binding sites for drug development. Here, we investigate the nature and dynamical properties of cryptic sites in four pharmacologically relevant targets, while comparing the efficacy of various simulation based approaches in discovering them. We find that the studied cryptic sites do not correspond to local minima in the computed conformational free energy landscape of the unliganded proteins. They thus promptly close in all of the molecular dynamics simulations performed, irrespective of the force-field used. Temperature-based enhanced sampling approaches, such as Parallel Tempering, do not improve the situation, as the entropic term does not help in the opening of the sites. The use of fragment probes helps, as in long simulations occasionally it leads to the opening and binding to the cryptic sites. Our observed mechanism of cryptic site formation is suggestive of an interplay between two classical mechanisms: induced-fit and conformational selection. Employing this insight, we developed a novel Hamiltonian Replica Exchange-based method "SWISH" (Sampling Water Interfaces through Scaled Hamiltonians), which combined with probes resulted in a promising general approach for cryptic site discovery. We also addressed the issue of "false-positives" and propose a simple approach to distinguish them from druggable cryptic pockets. Our simulations, whose cumulative sampling time was more than 200 mu s, help in clarifying the molecular mechanism of pocket formation, providing a solid basis for the choice of an efficient computational method.