Energy penalties enhance flexible receptor docking in a model cavity
Energy penalties enhance flexible receptor docking in a model cavity
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DOI：
10.1073/pnas.2106195118
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发表时间：
2021-09-07
影响因子：
11.1
通讯作者：
Shoichet, Brian K.
中科院分区：
文献类型：
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作者：
Kamenik, Anna S.;Singh, Isha;Shoichet, Brian K.
蛋白质的灵活性仍然是文库对接中的一个主要挑战，因为用准确的概率采样构象集成是困难的。在这里，我们使用T4溶菌酶L99A的模型空穴位置来测试柔性受体与来自分子动力学(MD)模拟的能量惩罚的对接。较大和较小配体的结晶学表明，该空腔可以采用三种主要构象：开放、中间和闭合。由于较小的配体通常更好地结合到空洞位置，我们预计空洞打开会有能量损失。为了估计它的大小，我们从MD模拟中计算了构象偏好。我们发现，包括惩罚项对于回溯性配体浓缩是必不可少的；否则，高能态主导对接。然后，我们前瞻性地对接了一个包含90多万个化合物的库，以寻找与每个构象状态结合的新分子。在没有惩罚项的情况下，开放构象主导了对接结果；包括这一项导致了针对每个州的配体的平衡采样。用TM升移法和X-射线结晶学对高阶分子进行了实验测试。从33个分子中，我们鉴定了18个配体，确定了13个晶体结构。最有趣的是那些被束缚在开放的空腔上的那些，在那里埋藏的位置向大量的溶剂开放。在这里，预测了这个空腔的极不寻常的配体，包括带有极尾的大配体；这些都得到了结合和结晶学的证实。在对接中，将蛋白质的灵活性与热力学权重结合起来，可能会获得新的配体化学类型。对这些替代国家进行评估并对其进行加权的MD方法可能具有普遍适用性。
Protein flexibility remains a major challenge in library docking because of difficulties in sampling conformational ensembles with accurate probabilities. Here, we use the model cavity site of T4 lysozyme L99A to test flexible receptor docking with energy penalties from molecular dynamics (MD) simulations. Crystallography with larger and smaller ligands indicates that this cavity can adopt three major conformations: open, intermediate, and closed. Since smaller ligands typically bind better to the cavity site, we anticipate an energy penalty for the cavity opening. To estimate its magnitude, we calculate conformational preferences from MD simulations. We find that including a penalty term is essential for retrospective ligand enrichment; otherwise, high-energy states dominate the docking. We then prospectively docked a library of over 900,000 compounds for new molecules binding to each conformational state. Absent a penalty term, the open conformation dominated the docking results; inclusion of this term led to a balanced sampling of ligands against each state. High ranked molecules were experimentally tested by Tm upshift and X-ray crystallography. From 33 selected molecules, we identified 18 ligands and determined 13 crystal structures. Most interesting were those bound to the open cavity, where the buried site opens to bulk solvent. Here, highly unusual ligands for this cavity had been predicted, including large ligands with polar tails; these were confirmed both by binding and by crystallography. In docking, incorporating protein flexibility with thermodynamic weightings may thus access new ligand chemotypes. The MD approach to accessing and, crucially, weighting such alternative states may find general applicability.