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新型3-脱氢奎尼酸脱水酶(DHQD)抑制剂的抗结核活性鉴定:虚拟筛选、分子对接和动力学模拟的见解

Identification of novel 3-dehydroquinate dehydratase (DHQD) inhibitors for anti-tuberculosis activity: insights from virtual screening, molecular docking, and dynamics simulations.

作者信息

Isa Mustafa Alhaji, Kappo Abidemi Paul

机构信息

Molecular Biophysics and Structural Biology (MBSB) Group, Department of Biochemistry, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, 2006 South Africa.

出版信息

In Silico Pharmacol. 2025 Jan 7;13(1):13. doi: 10.1007/s40203-024-00298-x. eCollection 2025.


DOI:10.1007/s40203-024-00298-x
PMID:39777139
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11704096/
Abstract

Tuberculosis (TB) remains a pressing global health concern, causing substantial mortality and morbidity despite existing drugs and vaccines. The escalating challenge of drug-resistant TB underscores the critical need for novel medications. This study focuses on the enzyme 3-hydroquinate dehydratase (DHQD) in the shikimate pathway of (Mtb), essential for Mtb growth. Using an in silico approach, the crystal structure of DHQD complexed with 1,3,4-trihydroxy-5-(3-phenoxypropyl)-cyclohexane-1-carboxylic acid (CA) was obtained from the Protein Data Bank. After meticulous preparation, a diverse library of 9699 compounds from Zinc and PubChem databases was subjected to virtual screening, complying with Lipinski's rule of five and compounds capable of binding to DHQD with less binding energy. Molecular docking analysis identified eight compounds with highly favorable binding energies, ranging from -8.99 to -8.39 kcal/mol, surpassing CA's -4.93 kcal/mol. To assess their potential as inhibitors, these eight compounds were subjected to scrutiny for pharmacokinetic properties, encompassing Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET). Five compounds (ZINC14981770, ZINC14741224, ZINC14743698, ZINC13165465, and ZINC8442077) demonstrated desirable pharmacokinetic attributes and were selected for further investigation. Subsequent molecular dynamics (MD) simulations and molecular generalized born surface area (MM-GBSA) analyses were conducted. Molecular dynamics (MD) simulations showed that these five compounds formed stable complexes with DHQD over 50 ns, with root mean square deviation (RMSD) values ranging from 1.57 Å to 2.34 Å, indicating high structural stability. In addition, the MM-GBSA binding energy calculations showed that these compounds had favourable binding affinities, with ZINC14981770 exhibiting the lowest free binding energy of -32.70 kcal/mol, followed by ZINC14741224 at -29.67 kcal/mol and ZINC14743698 at -28.79 kcal/mol. These binding energies significantly outperformed the reference compound CA, which had a binding energy of -10.62 kcal/mol. Based on these findings; these five compounds hold promise as potent inhibitors of Mtb DHQD, pending validation through in vitro and in vivo experiments.

摘要

结核病(TB)仍然是一个紧迫的全球健康问题,尽管有现有的药物和疫苗,但仍导致大量的死亡和发病。耐多药结核病不断升级的挑战凸显了对新型药物的迫切需求。本研究聚焦于结核分枝杆菌(Mtb)莽草酸途径中的3-羟基奎尼酸脱水酶(DHQD),该酶对Mtb的生长至关重要。使用计算机模拟方法,从蛋白质数据库中获得了与1,3,4-三羟基-5-(3-苯氧基丙基)-环己烷-1-羧酸(CA)复合的DHQD晶体结构。经过精心准备,对来自锌数据库和PubChem数据库的9699种化合物的多样化文库进行了虚拟筛选,符合Lipinski的五规则且能够以较低结合能与DHQD结合的化合物。分子对接分析确定了八种具有高度有利结合能的化合物,范围从-8.99至-8.39千卡/摩尔,超过了CA的-4.93千卡/摩尔。为了评估它们作为抑制剂的潜力,对这八种化合物进行了药代动力学性质的审查,包括吸收、分布、代谢、排泄和毒性(ADMET)。五种化合物(ZINC14981770、ZINC14741224、ZINC14743698、ZINC13165465和ZINC8442077)表现出理想的药代动力学属性,并被选作进一步研究。随后进行了分子动力学(MD)模拟和分子广义玻恩表面积(MM-GBSA)分析。分子动力学(MD)模拟表明,这五种化合物在50纳秒以上与DHQD形成了稳定的复合物,均方根偏差(RMSD)值范围为1.57埃至2.34埃,表明结构稳定性高。此外,MM-GBSA结合能计算表明这些化合物具有良好的结合亲和力,ZINC14981770表现出最低的自由结合能-32.70千卡/摩尔,其次是ZINC14741224为-29.67千卡/摩尔和ZINC14743698为-28.79千卡/摩尔。这些结合能明显优于参考化合物CA,其结合能为-10.62千卡/摩尔。基于这些发现,这五种化合物有望成为Mtb DHQD的有效抑制剂,有待通过体外和体内实验进行验证。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/2567f54b8b2d/40203_2024_298_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/ea1a14016720/40203_2024_298_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/e2038c89fb1d/40203_2024_298_Fig2a_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/40fb815cc718/40203_2024_298_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/4cf203e96099/40203_2024_298_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/1314c8bdefb7/40203_2024_298_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/2567f54b8b2d/40203_2024_298_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/ea1a14016720/40203_2024_298_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/e2038c89fb1d/40203_2024_298_Fig2a_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/40fb815cc718/40203_2024_298_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/4cf203e96099/40203_2024_298_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/1314c8bdefb7/40203_2024_298_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2bb0/11704096/2567f54b8b2d/40203_2024_298_Fig6_HTML.jpg

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