Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas , Universidade Estadual Paulista Júlio de Mesquita Filho , Rua Cristóvão Colombo, 2265, Jardim Nazareth, São José do Rio Preto , São Paulo , CEP 15054-000 , Brazil.
Laboratório de Dinâmica e Modelagem Molecular, Instituto de Biofísica Carlos Chagas Filho , Universidade Federal do Rio de Janeiro , Ave. Carlos Chagas Filho, 373, CCS-Bloco D sala 30, Cidade Universitária Ilha de Fundão, Rio de Janeiro , CEP 21941-902 , Brazil.
J Phys Chem B. 2019 Aug 29;123(34):7327-7342. doi: 10.1021/acs.jpcb.9b05021. Epub 2019 Aug 15.
Falcipain-2 (FP-2) is a cysteine protease that has been extensively targeted to identify novel antimalarials. Remarkably, previous reports have shown that FP-2 can be allosterically modulated and, for a particular noncompetitive chalcone inhibitor, the existing lines of experimental evidence can guide the prediction of its unknown binding mode to the enzyme in a reliable fashion. In this work, we propose a structure of FP-2 in complex with the aforementioned compound that fulfills all of the experimental data, by employing a combination of molecular modeling tools, such as pocket volume measurements, docking, molecular dynamics (MD) simulations, and free energy calculations. Our results show that the studied inhibitor binds a transient pocket occluded in all of the available FP-2 crystal structures and lying in a region previously characterized as a potential allosteric site in related cysteine proteases. In addition, we detected the occurrence of significant community reorganization in FP-2, increased signal transmission between the allosteric pocket and the active site, and change in loop motions and residue p values upon the compound binding, thus providing insight into the uncharacterized allosteric mechanism. Overall, this study yields valuable predictions for the design of novel allosteric inhibitors against FP-2 and other cysteine proteases.
疟原虫半胱氨酸蛋白酶 2（FP-2）是一种半胱氨酸蛋白酶，已被广泛用于鉴定新型抗疟药物。值得注意的是，先前的报告表明 FP-2 可以被别构调节，对于特定的非竞争性查尔酮抑制剂，现有的实验证据可以可靠地指导预测其与酶的未知结合模式。在这项工作中，我们通过使用分子建模工具（如口袋体积测量、对接、分子动力学（MD）模拟和自由能计算），提出了一个与上述化合物结合的 FP-2 结构，该结构满足所有实验数据。我们的结果表明，研究中的抑制剂结合了一个在所有可用的 FP-2 晶体结构中都被封闭的瞬态口袋，位于先前在相关半胱氨酸蛋白酶中被表征为潜在别构位点的区域。此外，我们检测到 FP-2 中发生了显著的社区重组，别构口袋和活性位点之间的信号传递增加，以及化合物结合时环运动和残基 p 值的变化，从而深入了解了未表征的别构机制。总的来说，这项研究为设计针对 FP-2 和其他半胱氨酸蛋白酶的新型别构抑制剂提供了有价值的预测。
