Byun Jung Ah, VanSchouwen Bryan, Akimoto Madoka, Melacini Giuseppe
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada.
Comput Struct Biotechnol J. 2020 Nov 11;18:3803-3818. doi: 10.1016/j.csbj.2020.10.026. eCollection 2020.
Allosteric modulation provides an effective avenue for selective and potent enzyme inhibition. Here, we summarize and critically discuss recent advances on the mechanisms of allosteric partial agonists for three representative signalling enzymes activated by cyclic nucleotides: the cAMP-dependent protein kinase (PKA), the cGMP-dependent protein kinase (PKG), and the exchange protein activated by cAMP (EPAC). The comparative analysis of partial agonism in PKA, PKG and EPAC reveals a common emerging theme, the sampling of distinct "mixed" conformational states, either within a single domain or between distinct domains. Here, we show how such "mixed" states play a crucial role in explaining the observed functional response, partial agonism and allosteric pluripotency, as well as in maximizing inhibition while minimizing potency losses. In addition, by combining Nuclear Magnetic Resonance (NMR), Molecular Dynamics (MD) simulations and Ensemble Allosteric Modeling (EAM), we also show how to map the free-energy landscape of conformational ensembles containing "mixed" states. By discussing selected case studies, we illustrate how MD simulations and EAM complement NMR to quantitatively relate protein dynamics to function. The resulting NMR- and MD-based EAMs are anticipated to inform not only the design of new generations of highly selective allosteric inhibitors, but also the choice of multidrug combinations.
变构调节为选择性和强效酶抑制提供了一条有效途径。在此，我们总结并批判性地讨论了环核苷酸激活的三种代表性信号酶变构部分激动剂机制的最新进展：环磷酸腺苷（cAMP）依赖性蛋白激酶（PKA）、环磷酸鸟苷（cGMP）依赖性蛋白激酶（PKG）以及cAMP激活的交换蛋白（EPAC）。对PKA、PKG和EPAC中部分激动作用的比较分析揭示了一个共同的新主题，即在单个结构域内或不同结构域之间对不同的“混合”构象状态进行抽样。在此，我们展示了这种“混合”状态如何在解释观察到的功能反应、部分激动作用和变构多能性方面发挥关键作用，以及如何在使效力损失最小化的同时实现最大抑制。此外，通过结合核磁共振（NMR）、分子动力学（MD）模拟和整体变构建模（EAM），我们还展示了如何绘制包含“混合”状态的构象集合的自由能景观。通过讨论选定的案例研究，我们说明了MD模拟和EAM如何补充NMR，以将蛋白质动力学与功能定量关联起来。基于NMR和MD的所得EAMs不仅有望为新一代高选择性变构抑制剂的设计提供信息，也有助于多药组合的选择。
