作者
Riccardo Capelli, Anna Bochicchio, GiovanniMaria Piccini, Rodrigo Casasnovas, Paolo Carloni, Michele Parrinello
发表日期
2019/3/26
期刊
Journal of chemical theory and computation
卷号
15
期号
5
页码范围
3354-3361
出版商
American Chemical Society
简介
Predicting the complete free energy landscape associated with protein–ligand unbinding may greatly help designing drugs with highly optimized pharmacokinetics. Here we investigate the unbinding of the iperoxo agonist to its target human neuroreceptor M2, embedded in a neuronal membrane. By feeding out-of-equilibrium molecular simulations data in a classification analysis, we identify the few essential reaction coordinates of the process. The full landscape is then reconstructed using an exact enhanced sampling method, well-tempered metadynamics in its funnel variant. The calculations reproduce well the measured affinity, provide a rationale for mutagenesis data, and show that the ligand can escape via two different routes. The allosteric modulator LY2119620 turns out to hamper both escapes routes, thus slowing down the unbinding process, as experimentally observed. This computationally affordable …
引用总数
20192020202120222023202431291296
学术搜索中的文章
R Capelli, A Bochicchio, GM Piccini, R Casasnovas… - Journal of chemical theory and computation, 2019