Brenk Ruth, Vetter Stefan W, Boyce Sarah E, Goodin David B, Shoichet Brian K
University of California San Francisco, QB3 Building, Department of Pharmaceutical Chemistry, 1700 4th Street, San Francisco, CA 94143-2550, USA.
J Mol Biol. 2006 Apr 14;357(5):1449-70. doi: 10.1016/j.jmb.2006.01.034. Epub 2006 Feb 2.
A model binding site was used to investigate charge-charge interactions in molecular docking. This simple site, a small (180A(3)) engineered cavity in cyctochrome c peroxidase (CCP), is negatively charged and completely buried from solvent, allowing us to explore the balance between electrostatic energy and ligand desolvation energy in a system where many of the common approximations in docking do not apply. A database with about 5300 molecules was docked into this cavity. Retrospective testing with known ligands and decoys showed that overall the balance between electrostatic interaction and desolvation energy was captured. More interesting were prospective docking scre"ens that looked for novel ligands, especially those that might reveal problems with the docking and energy methods. Based on screens of the 5300 compound database, both high-scoring and low-scoring molecules were acquired and tested for binding. Out of 16 new, high-scoring compounds tested, 15 were observed to bind. All of these were small heterocyclic cations. Binding constants were measured for a few of these, they ranged between 20microM and 60microM. Crystal structures were determined for ten of these ligands in complex with the protein. The observed ligand geometry corresponded closely to that predicted by docking. Several low-scoring alkyl amino cations were also tested and found to bind. The low docking score of these molecules owed to the relatively high charge density of the charged amino group and the corresponding high desolvation penalty. When the complex structures of those ligands were determined, a bound water molecule was observed interacting with the amino group and a backbone carbonyl group of the cavity. This water molecule mitigates the desolvation penalty and improves the interaction energy relative to that of the "naked" site used in the docking screen. Finally, six low-scoring neutral molecules were also tested, with a view to looking for false negative predictions. Whereas most of these did not bind, two did (phenol and 3-fluorocatechol). Crystal structures for these two ligands in complex with the cavity site suggest reasons for their binding. That these neutral molecules do, in fact bind, contradicts previous results in this site and, along with the alkyl amines, provides instructive false negatives that help identify weaknesses in our scoring functions. Several improvements of these are considered.
一个模型结合位点被用于研究分子对接中的电荷-电荷相互作用。这个简单的位点是细胞色素c过氧化物酶（CCP）中一个小的（180ų）工程化空腔，带负电荷且完全被溶剂掩埋，这使我们能够在一个对接中许多常见近似方法不适用的系统中探索静电能和配体去溶剂化能之间的平衡。一个包含约5300个分子的数据库被对接至这个空腔。用已知配体和诱饵进行的回顾性测试表明，总体上静电相互作用和去溶剂化能之间的平衡被捕捉到了。更有趣的是寻找新配体的前瞻性对接筛选，尤其是那些可能揭示对接和能量方法问题的配体。基于对5300个化合物数据库的筛选，获取了高分和低分分子并测试其结合情况。在测试的16种新的高分化合物中，有15种被观察到能结合。所有这些都是小的杂环阳离子。测定了其中几种的结合常数，范围在20μM至60μM之间。确定了其中10种配体与蛋白质复合物的晶体结构。观察到的配体几何结构与对接预测的结构非常接近。还测试了几种低分的烷基氨基阳离子，发现它们能结合。这些分子对接分数低是由于带电氨基的相对高电荷密度以及相应的高去溶剂化惩罚。当确定那些配体的复合物结构时，观察到一个结合的水分子与空腔的氨基和一个主链羰基相互作用。相对于对接筛选中使用的“裸露”位点，这个水分子减轻了去溶剂化惩罚并提高了相互作用能。最后，还测试了6种低分中性分子，以寻找假阴性预测。虽然这些分子大多不结合，但有两种结合了（苯酚和3-氟儿茶酚）。这两种配体与空腔位点复合物的晶体结构表明了它们结合的原因。事实上这些中性分子能结合，这与该位点之前的结果相矛盾，并且与烷基胺一起提供了有指导意义的假阴性结果，有助于识别我们评分函数中的弱点。考虑了对这些的几种改进。
