Heinzelmann Germano, Henriksen Niel M, Gilson Michael K
Departamento de Fı́sica, Universidade Federal de Santa Catarina , Florianópolis, Santa Catarina 88040-900, Brazil.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States.
J Chem Theory Comput. 2017 Jul 11;13(7):3260-3275. doi: 10.1021/acs.jctc.7b00275. Epub 2017 Jun 13.
Bromodomains, protein domains involved in epigenetic regulation, are able to bind small molecules with high affinity. In the present study, we report free energy calculations for the binding of seven ligands to the first BRD4 bromodomain, using the attach-pull-release (APR) method to compute the reversible work of removing the ligands from the binding site and then allowing the protein to relax conformationally. We test three different water models, TIP3P, TIP4PEw, and SPC/E, as well as the GAFF and GAFF2 parameter sets for the ligands. Our simulations show that the apo crystal structure of BRD4 is only metastable, with a structural transition happening in the absence of the ligand typically after 20 ns of simulation. We compute the free energy change for this transition with a separate APR calculation on the free protein and include its contribution to the ligand binding free energies, which generally causes an underestimation of the affinities. By testing different water models and ligand parameters, we are also able to assess their influence in our results and determine which one produces the best agreement with the experimental data. Both free energies associated with the conformational change and ligand binding are affected by the choice of water model, with the two sets of ligand parameters affecting their binding free energies to a lesser degree. Across all six combinations of water model and ligand potential function, the Pearson correlation coefficients between calculated and experimental binding free energies range from 0.55 to 0.83, and the root-mean-square errors range from 1.4-3.2 kcal/mol. The current protocol also yields encouraging preliminary results when used to assess the relative stability of ligand poses generated by docking or other methods, as illustrated for two different ligands. Our method takes advantage of the high performance provided by graphics processing units and can readily be applied to other ligands as well as other protein systems.
溴结构域是参与表观遗传调控的蛋白质结构域，能够与小分子高亲和力结合。在本研究中，我们报告了使用附着-拉动-释放（APR）方法计算七种配体与第一个BRD4溴结构域结合的自由能，该方法用于计算将配体从结合位点移除并使蛋白质构象松弛的可逆功。我们测试了三种不同的水模型，即TIP3P、TIP4PEw和SPC/E，以及配体的GAFF和GAFF2参数集。我们的模拟表明，BRD4的无配体晶体结构只是亚稳态的，在没有配体的情况下，通常在模拟20 ns后会发生结构转变。我们通过对游离蛋白质进行单独的APR计算来计算这种转变的自由能变化，并将其对配体结合自由能的贡献包括在内，这通常会导致亲和力的低估。通过测试不同的水模型和配体参数，我们还能够评估它们对我们结果的影响，并确定哪一个与实验数据的一致性最好。与构象变化和配体结合相关的自由能都受到水模型选择的影响，两组配体参数对它们结合自由能的影响较小。在水模型和配体势函数的所有六种组合中，计算得到的和实验测得的结合自由能之间的皮尔逊相关系数范围为0.55至0.83，均方根误差范围为1.4 - 3.2 kcal/mol。当用于评估通过对接或其他方法生成的配体构象的相对稳定性时，当前方案也产生了令人鼓舞的初步结果，如针对两种不同配体所示。我们的方法利用了图形处理单元提供的高性能，并且可以很容易地应用于其他配体以及其他蛋白质系统。
