Yang Yanan, Guo Yan, Zhou Yonglin, Gao Yawen, Wang Xiyan, Wang Jianfeng, Niu Xiaodi
College of Food Science and Engineering, Jilin University, Changchun, China.
Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China.
Front Pharmacol. 2020 Oct 2;11:581001. doi: 10.3389/fphar.2020.581001. eCollection 2020.
At present, the resistance of New Delhi metallo-β-lactamase-1 (NDM-1) to carbapenems and cephalosporins, one of the mechanisms of bacterial resistance against β-lactam antibiotics, poses a threat to human health. In this work, based on the virtual ligand screen method, we found that carnosic acid (CA), a natural compound, exhibited a significant inhibitory effect against NDM-1 (IC = 27.07 μM). Although carnosic acid did not display direct antibacterial activity, the combination of carnosic acid and meropenem still showed bactericidal activity after the loss of bactericidal effect of meropenem. The experimental results showed that carnosic acid can enhance the antibacterial activity of meropenem against ZC-YN3. To explore the inhibitory mechanism of carnosic acid against NDM-1, we performed the molecular dynamics simulation and binding energy calculation for the NDM-1-CA complex system. Notably, the 3D structure of the complex obtained from molecular modeling indicates that the binding region of carnosic acid with NDM-1 was not situated in the active region of protein. Due to binding to the allosteric pocket of carnosic acid, the active region conformation of NDM-1 was observed to have been altered. The distance from the active center of the NDM-1-CA complex was larger than that of the free protein, leading to loss of activity. Then, the mutation experiments showed that carnosic acid had lower inhibitory activity against mutated protein than wild-type proteins. Fluorescence experiments verified the results reported above. Thus, our data indicate that carnosic acid is a potential NDM-1 inhibitor and is a promising drug for the treatment of NDM-1 producing pathogens.
目前，作为细菌对β-内酰胺类抗生素耐药机制之一的新德里金属β-内酰胺酶-1（NDM-1）对碳青霉烯类和头孢菌素类的耐药性对人类健康构成威胁。在这项工作中，基于虚拟配体筛选方法，我们发现天然化合物肌醇六磷酸（CA）对NDM-1表现出显著的抑制作用（IC = 27.07 μM）。尽管肌醇六磷酸没有显示出直接的抗菌活性，但在美罗培南失去杀菌效果后，肌醇六磷酸与美罗培南的组合仍显示出杀菌活性。实验结果表明，肌醇六磷酸可以增强美罗培南对ZC-YN3的抗菌活性。为了探索肌醇六磷酸对NDM-1的抑制机制，我们对NDM-1-CA复合体系进行了分子动力学模拟和结合能计算。值得注意的是，从分子建模获得的复合物的三维结构表明，肌醇六磷酸与NDM-1的结合区域不在蛋白质的活性区域。由于与肌醇六磷酸的变构口袋结合，观察到NDM-1的活性区域构象发生了改变。NDM-1-CA复合物的活性中心距离比游离蛋白的活性中心距离大，导致活性丧失。然后，突变实验表明，肌醇六磷酸对突变蛋白的抑制活性低于野生型蛋白。荧光实验验证了上述结果。因此，我们的数据表明肌醇六磷酸是一种潜在的NDM-1抑制剂，是治疗产生NDM-1的病原体的有前景的药物。
