基于药效团模型筛选CTX-M-14型超广谱β-内酰胺酶抑制剂
Screening of CTX-M-14-type Ultra-broad-spectrum β-lactamase Inhibitors Based on Pharmacophore Modelling
王梦帆 1赵子玉 1王春光 1刘廷玉 2陈曦 1张铁1
作者信息
- 1. 河北农业大学动物医学院,保定 071000
- 2. 河北省畜牧良种工作总站,石家庄 050049
- 折叠
摘要
[目的]开发针对头孢噻肟-水解酶-14(CTX-M-14)型超广谱β-内酰胺酶(extended-spectrum β-lactamase,ESBLs)的抑制剂,用以缓解细菌耐药带来的严重危害.[方法]使用DiscoveryStudio Visualizer(DS Visualizer)构建基于受体结构的药效团模型(structure-based pharmacophore,SBP)和基于配体共同特征的定性药效团模型(common feature pharmacophore generation,HIPHOP),并将验证后的模型作为查询条件对ZINC数据库进行以CTX-M-14 蛋白为靶标的虚拟筛选,得到拟合分数良好的中药单体成分甘草酸(glycyrrhizic acid,GL),对其进行相关作用力分析、分子动力学模拟和结合自由能计算,分析甘草酸与CTX-M-14 蛋白的结合模式、结合能力及稳定性;最后通过联合抑菌试验及酶动力学试验考察甘草酸的抗菌增敏活性、抑酶作用及抑酶方式.[结果]中药单体成分甘草酸主要与CTX-M-14 蛋白活性中心多个氨基酸残基形成氢键和范德华作用力,两者的对接分数与结合自由能分别为-10 kcal/mol及-22.06 kcal/mol;甘草酸与头孢噻肟钠联用呈协同作用(FICI≤0.5);甘草酸可竞争性抑制β-内酰胺酶对底物抗生素的水解作用,对头孢噻肟钠的抑酶保护率可达 58.53%,与克拉维酸接近(60.98%).[结论]中药单体甘草酸可与CTX-M-14 蛋白稳定结合,通过竞争性抑制β-内酰胺酶对底物抗生素的水解作用,提高多重耐药大肠杆菌E320 和重组蛋白阳性菌BL-21 对头孢噻肟钠的敏感性,实现抗生素的减量增效.
Abstract
[Objective]Development of inhibitors against cefotaxime-hydrolase-14(CTX-M-14)-type ultra-broad-spectrum β-lactamases(ESBLs)to mitigate the serious harm caused by bacterial drug resistance.[Method]DiscoveryStudio Visualizer(DS Visualizer)was used to construct a receptor structure-based pharmacophore(SBP)and a ligand common feature-based qualitative pharmacophore model(HIPHOP),and the validated models were used as query conditions for virtual screening of the ZINC database targeting CTX-M-14 protein,and glycyrrhizic acid(GL),a monomer component of traditional Chinese medicine(TCM)with good fitting scores,was obtained.The related force analysis,molecular dynamics simulation and binding free energy calculation were carried out to analyse the binding mode,binding capacity and stability of glycyrrhizic acid and CTX-M-14 protein.Finally,the antibacterial sensitizing activity,enzyme inhibition and enzyme inhibition of glycyrrhizic acid were investigated by the combined bacterial inhibition assay and enzyme kinetic assay.[Result]Glycyrrhizic acid,a single component of traditional Chinese medicine,mainly formed hydrogen bonds and van der Waals forces with multiple amino acid residues in the active centre of CTX-M-14 protein,and the docking fraction and binding free energy of the two were-10 kcal/mol and-22.06 kcal/mol,respectively.Glycyrrhizic acid synergistically interacted with cefotaxime sodium(FICI≤0.5);glycyrrhizic acid competitively inhibited the hydrolysis of the substrate antibiotic by β-lactamase,and the enzyme inhibition and protection rate of cefotaxime sodium reached 58.53%,which was close to that of clavulanic acid(60.98%).[Conclusion]The Chinese medicine monomer glycyrrhizic acid can bind stably to CTX-M-14 protein and increase the sensitivity of multi-drug-resistant Escherichia coli E320 and recombinant protein-positive bacterium BL-21 to cefotaxime sodium by competitively inhibiting the hydrolysis of the substrate antibiotic by β-lactamase,so as to achieve a reduction in the quantity and increase in the effectiveness of the antibiotic.
关键词
甘草酸/CTX-M-14/药效团模型/分子动力学模拟/联合抑菌Key words
glycyrrhizic acid/CTX-M-14/pharmacophore modelling/simulation of molecular dynamics/combined bacterial inhibition引用本文复制引用
基金项目
河北省省级科技计划(21326617D)
河北省现代农业产业技术体系建设专项(HBCT2024240207)
河北省现代农业产业技术体系建设专项(HBCT2024250206)
出版年
2024
国家科技期刊平台
NSTL
万方数据