Mobley David L, Graves Alan P, Chodera John D, McReynolds Andrea C, Shoichet Brian K, Dill Ken A
Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143-2518, USA.
J Mol Biol. 2007 Aug 24;371(4):1118-34. doi: 10.1016/j.jmb.2007.06.002. Epub 2007 Jun 8.
A central challenge in structure-based ligand design is the accurate prediction of binding free energies. Here we apply alchemical free energy calculations in explicit solvent to predict ligand binding in a model cavity in T4 lysozyme. Even in this simple site, there are challenges. We made systematic improvements, beginning with single poses from docking, then including multiple poses, additional protein conformational changes, and using an improved charge model. Computed absolute binding free energies had an RMS error of 1.9 kcal/mol relative to previously determined experimental values. In blind prospective tests, the methods correctly discriminated between several true ligands and decoys in a set of putative binders identified by docking. In these prospective tests, the RMS error in predicted binding free energies relative to those subsequently determined experimentally was only 0.6 kcal/mol. X-ray crystal structures of the new ligands bound in the cavity corresponded closely to predictions from the free energy calculations, but sometimes differed from those predicted by docking. Finally, we examined the impact of holding the protein rigid, as in docking, with a view to learning how approximations made in docking affect accuracy and how they may be improved.
基于结构的配体设计中的一个核心挑战是准确预测结合自由能。在此，我们在显式溶剂中应用炼金术自由能计算来预测T4溶菌酶模型腔中的配体结合。即使在这个简单的位点，也存在挑战。我们进行了系统的改进，从对接的单个构象开始，然后包括多个构象、额外的蛋白质构象变化，并使用改进的电荷模型。相对于先前确定的实验值，计算得到的绝对结合自由能的均方根误差为1.9千卡/摩尔。在盲法前瞻性测试中，这些方法正确地区分了对接鉴定出的一组假定结合物中的几种真实配体和诱饵。在这些前瞻性测试中，相对于随后通过实验确定的结合自由能，预测结合自由能的均方根误差仅为0.6千卡/摩尔。在腔中结合的新配体的X射线晶体结构与自由能计算的预测结果非常吻合，但有时与对接预测的结果不同。最后，我们研究了像对接中那样保持蛋白质刚性的影响，目的是了解对接中所做的近似如何影响准确性以及如何改进它们。
