Screening of CTX-M-14-type Ultra-broad-spectrum β-lactamase Inhibitors Based on Pharmacophore Modelling

doi:10.13560/j.cnki.biotech.bull.1985.2023-1228

Abstract

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.

Key words: glycyrrhizic acid, CTX-M-14, pharmacophore modelling, simulation of molecular dynamics, combined bacterial inhibition

WANG Meng-fan, ZHAO Zi-yu, WANG Chun-guang, LIU Ting-yu, CHEN Xi, ZHANG Tie. Screening of CTX-M-14-type Ultra-broad-spectrum β-lactamase Inhibitors Based on Pharmacophore Modelling[J]. Biotechnology Bulletin, 2024, 40(6): 319-329.

Figures/Tables 14

References 31

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ZINC ID	名称Name	拟合值FitValue
ZINC ID	名称Name	SBP	HIPHOP
ZINC901518	茶渍酸Lecanoric acid	2.6156	2.32539
ZINC96015174	甘草酸Glycyrrhizin	2.03995	2.44671
ZINC4164596	富马前冰岛酸Fumarprotocetraric acid	1.25871	2.61666

ZINC ID	名称Name	拟合值FitValue
ZINC ID	名称Name	SBP	HIPHOP
ZINC901518	茶渍酸Lecanoric acid	2.6156	2.32539
ZINC96015174	甘草酸Glycyrrhizin	2.03995	2.44671
ZINC4164596	富马前冰岛酸Fumarprotocetraric acid	1.25871	2.61666

ZINC ID	名称 Name	结合自由能Affinity*/ （kcal·mol^-1）	均方根偏差/RMSD
ZINC ID	名称 Name	结合自由能Affinity*/ （kcal·mol^-1）	最小值l.b.	最大值u.b.
ZINC901518	茶渍酸Lecanoric acid	-8.3	0	0
ZINC96015174	甘草酸Glycyrrhizin	-10.0	0	0
ZINC4164596	富马前冰岛酸Fumarprotocetraric acid	-9.4	0	0

ZINC ID	名称 Name	结合自由能Affinity*/ （kcal·mol^-1）	均方根偏差/RMSD
ZINC ID	名称 Name	结合自由能Affinity*/ （kcal·mol^-1）	最小值l.b.	最大值u.b.
ZINC901518	茶渍酸Lecanoric acid	-8.3	0	0
ZINC96015174	甘草酸Glycyrrhizin	-10.0	0	0
ZINC4164596	富马前冰岛酸Fumarprotocetraric acid	-9.4	0	0

药物Drug/（mg·mL^-1）	E320	蛋白重组阳性菌BL-21 Protein recombinant positive bacterial strain BL-21
甘草酸Glycyrrhizic acid	>25	>25
苯唑西林钠Benzoxacillin sodium	>256（R）	64（R）
氨苄西林钠Ampicillin sodium	>256（R）	64（R）
头孢唑林钠Cefazolin sodium	>256（R）	16（R）
头孢他啶Ceftazidime	>256（R）	8（I）
头孢呋辛Cefuroxime	4（S）	16（I）
头孢曲松钠Ceftriaxone sodium	>256（R）	32（R）
头孢噻肟钠Cefotaxime sodium	1024（R）	>1024（R）