Yildiz Ibrahim, Yildiz Banu Sizirici
Chemistry Department, Khalifa University, PO Box 127788, Abu Dhabi 00000, UAE.
CIVE Department, Khalifa University, PO Box 127788, Abu Dhabi 00000, UAE.
ACS Omega. 2022 Apr 7;7(15):13333-13342. doi: 10.1021/acsomega.2c01044. eCollection 2022 Apr 19.
Notum is a member of serine hydrolyses that cleaves the palmitoleate moiety from Wingless-related integration site (Wnt) ligands. This enzyme plays crucial functions through modulating the Wnt signaling pathway. Inhibition of Notum carries therapeutic effects against a number of maladies including osteoporosis, cancer, and Alzheimer's disease. Recently, a class of irreversible inhibitors based on esters of 4-(indolin-1-yl)-4-oxobutanoic acid have been reported. Using the crystal structures of enzyme-4-(indolin-1-yl)-4-oxobutanoate adduct and 4-(indolin-1-yl)-4-oxobutanoic acid-enzyme complex, we studied computationally the proposed inhibition mechanism using model systems based on the own n-layered integrated molecular orbital and molecular mechanics (ONIOM) method. In the first place, model systems were formulated to investigate the transesterification between the catalytic serine residue, Ser-232, and the methyl ester of 4-(indolin-1-yl)-4-oxobutanoate. In the second place, the hydrolysis mechanism of the resultant enzyme-inhibitor adduct was studied. The energetics of these steps were analyzed using a density functional theory functional in the ONIOM method. In addition, the roles of active-site residues during these steps were highlighted. It was found that the hydrolysis of the covalent adduct is highly endergonic corroborating the irreversible inhibition mechanism. These results will shed light not only on the inhibition mechanism but also on the catalytic mechanism.
Notum是丝氨酸水解酶家族的一员，可从无翅相关整合位点（Wnt）配体上切割棕榈油酸部分。该酶通过调节Wnt信号通路发挥关键作用。抑制Notum对包括骨质疏松症、癌症和阿尔茨海默病在内的多种疾病具有治疗作用。最近，已经报道了一类基于4-（吲哚啉-1-基）-4-氧代丁酸酯的不可逆抑制剂。利用酶-4-（吲哚啉-1-基）-4-氧代丁酸酯加合物和4-（吲哚啉-1-基）-4-氧代丁酸-酶复合物的晶体结构，我们使用基于自身n层集成分子轨道和分子力学（ONIOM）方法的模型系统对提出的抑制机制进行了计算研究。首先，构建模型系统以研究催化丝氨酸残基Ser-232与4-（吲哚啉-1-基）-4-氧代丁酸甲酯之间的酯交换反应。其次，研究了所得酶-抑制剂加合物的水解机制。使用ONIOM方法中的密度泛函理论泛函分析了这些步骤的能量学。此外，还强调了活性位点残基在这些步骤中的作用。发现共价加合物的水解是高度吸热的，这证实了不可逆抑制机制。这些结果不仅将阐明抑制机制，还将阐明催化机制。
