重庆理工大学学报(自然科学) ›› 2023, Vol. 37 ›› Issue (2): 357-368.doi: 10.3969/j.issn.1674-8425(z).2023.02.040

• 药学·生物工程 • 上一篇    

结核分枝杆菌1-脱氧-D-木酮糖-5-磷酸还原异构酶抑制剂的3D-QSAR研究及优化设计

谢稳, 谢双龙, 余娜   

  1. 1.重庆理工大学 药学与生物工程学院,重庆 400054; 2.重庆市公共卫生医疗救治中心药学部,重庆 40003
  • 出版日期:2023-03-21 发布日期:2023-03-21
  • 作者简介:谢稳,女,硕士研究生,主要从事药物设计研究,Email:xiewen829@126.com;通讯作者 林治华,男,博士,教授, 主要从事靶向药物设计与活性评价研究,Email:zhlin@cqut.edu.cn。

3D-QSAR study and optimized design of 1-deoxy-D-xylulose-5-phosphate reductoisomerase inhibitors of Mycobacterium tuberculosis

  • Online:2023-03-21 Published:2023-03-21

摘要: 结核分枝杆菌是导致结核病的病原体,1脱氧D木酮糖5磷酸还原异构酶是结核 分枝杆菌代谢的关键限速酶,因此被作为一个有潜力的抗菌靶点。收集了 35个对结核分枝杆 菌 1脱氧D木酮糖5磷酸还原异构酶(mtDXR)有体外抑制活性的膦胺霉素衍生物,运用比较 分子场分析方法和比较分子相似性指数分析方法对它们进行三维定量构效关系研究,建立了相 应模型。结果表明:CoMFA模型的最佳主成分值 n=7,交互检验系数 q2=0.601,相关系数r2= 0.979;CoMSIA模型的最佳主成分值 n=8,交互检验系数 q2=0.609,相关系数 r2=0.983。数据 显示所建模型拥有较为可靠的预测能力。同时,利用分子对接进一步考察膦胺霉素类小分子抑 制剂和靶点活性部位氨基酸残基的非键作用,结合 3DQSAR等势图,明确了该类化合物分子结 构上可供加工和优化的区域,进而设计出 14个全新的膦胺霉素衍生物,并对它们进行活性预 测,得到了拥有更高预测活性的新化合物 27m,为 mtDXR抑制剂的进一步开发提供了理论依据 和重要参考。

关键词: 结核分枝杆菌, 1脱氧D木酮糖5磷酸还原异构酶(DXR), 膦胺霉素衍生物, 3DQSAR, 分子对接

Abstract: Mycobacterium tuberculosis(Mtb) is a pathogen of tuberculosis, and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) is a key rate-limiting enzyme in the metabolism of Mtb, so it is thought to be a potential antibacterial target. This paper collects 35 fosmidomycin derivatives with in vitro inhibitory activity against Mycobacterium tuberculosis1-deoxy-D-xylulose-5-phosphate reductoisomerase (mtDXR), conducts a three dimensional quantitative structure-activity relationship between them by using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), and establishes corresponding models. The results show that, for CoMFA model, the best principal component value n is 7, the cross validation coefficient q2 is 0.601,and the correlation coefficient r2 is 0.979. For CoMSIA model, the best principalcomponent value n is 8, the cross validation coefficient q2 is 0.609, and the correlation coefficient r2 is 0.983. The data show that both CoMFA and CoMSIA models have good predictability. Meanwhile, the molecular docking method is introduced to further investigate the non-bonding interaction between these small molecule inhibitors of fosmidomycin and amino acid residues on target active sites.Combined with contour maps of 3D-QSAR, the modification areas of molecular structure of these compounds are determined which can be processed and optimized.On the basis of these work, this paper designs 14 new fosmidomycin derivatives, predicts their activity, and obtains a new compound 27m with higher predictive activity. The conclusions derived from this paper provide a theoretical basis and important reference for the further development of new mtDXR inhibitors.

中图分类号: 

  • TP21