Pan Yue, Qi Renrui, Li Minghao, Wang Bingda, Huang Honglan, Han Weiwei
Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University 2699 Qianjin Street Changchun 130012 China
Department of Pathobiology, College of Basic Medical Sciences, Jilin University Changchun China
RSC Adv. 2020 Dec 11;10(72):43994-44002. doi: 10.1039/d0ra07796h. eCollection 2020 Dec 9.
Adenosine deaminase (ADA) is an important enzyme related to purine nucleoside metabolism in human serum and various tissues. Abnormal ADA levels are related to a wide variety of diseases such as rheumatoid arthritis, AIDS, anemia, lymphoma, and leukemia and ADA is considered as a useful target for various diseases. Currently, ADA can be divided into open conformation and closed conformation according to the inhibitors of binding. As a consequence, we chose two inhibitors, namely, 6-hydroxy-1,6-dihydro purine nucleoside (PRH) and -[4,5-bis(4-hydroxyphenyl)-1,3-thiazol-2-yl]hexanamide (FRK) to bind to ADA in the closed conformation or open conformation respectively. In this study, we performed the random acceleration molecular dynamics (RAMD) method, steered molecular dynamics (SMD) simulations and adaptive basing force (ABF) simulation to explore the unbinding tunnels and tunnel characteristics of the two inhibitors in ADA. Our results showed that PRH and FRK escaped from ADA using three main tunnels (namely, T1, T2, and T3). Inhibitors (PRH and FRK) escape through T3 more frequently and more easily. The results from ABF simulations confirm that the free energy barrier in T1 or T2 is larger than that in T3 when inhibitors dissociate from the ADA and have potential mean of force (PMF) depth. Moreover, in the complexes (ADA-PRH, ADA-FRK), we also found that the most active residue that remarkably contributed to the binding affinity is W117 in T3, and the residue played an important role in the unbinding tunnel for inhibitor leaving. Our theoretical study provided insight into the ADA inhibitor passway mechanism and may be a clue for potent ADA inhibitor design.
腺苷脱氨酶（ADA）是人体血清和各种组织中与嘌呤核苷代谢相关的一种重要酶。ADA水平异常与多种疾病有关，如类风湿性关节炎、艾滋病、贫血、淋巴瘤和白血病，ADA被认为是多种疾病的一个有用靶点。目前，根据结合抑制剂的不同，ADA可分为开放构象和封闭构象。因此，我们选择了两种抑制剂，即6-羟基-1,6-二氢嘌呤核苷（PRH）和-[4,5-双（4-羟基苯基）-1,3-噻唑-2-基]己酰胺（FRK），分别与处于封闭构象或开放构象的ADA结合。在本研究中，我们采用随机加速分子动力学（RAMD）方法、引导分子动力学（SMD）模拟和自适应基力（ABF）模拟，来探索这两种抑制剂在ADA中的解离通道及通道特征。我们的结果表明，PRH和FRK通过三条主要通道（即T1、T2和T3）从ADA中逃逸。抑制剂（PRH和FRK）通过T3逃逸的频率更高且更容易。ABF模拟结果证实，当抑制剂从ADA解离时，T1或T2中的自由能垒大于T3中的自由能垒，且具有潜在平均力（PMF）深度。此外，在复合物（ADA-PRH、ADA-FRK）中，我们还发现对结合亲和力有显著贡献的最活跃残基是T3中的W117，该残基在抑制剂离开的解离通道中起重要作用。我们的理论研究为ADA抑制剂的通道机制提供了见解，可能为设计有效的ADA抑制剂提供线索。
