Alkhatabi Heba Ahmed, Alatyb Hisham N
Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
Hematology Research Unit (HRU), King Fahd Medical Research Center (KFMRC), Jeddah 80200, Saudi Arabia.
Pharmaceuticals (Basel). 2024 Sep 9;17(9):1183. doi: 10.3390/ph17091183.
In the ongoing battle against antibiotic-resistant bacteria, New Delhi metallo-β-lactamase-1 (NDM-1) has emerged as a significant therapeutic challenge due to its ability to confer resistance to a broad range of β-lactam antibiotics. This study presents a pharmacophore-based virtual screening, docking, and molecular dynamics simulation approach for the identification of potential inhibitors targeting NDM-1, a critical enzyme associated with antibiotic resistance. Through the generation of a pharmacophore model and subsequent virtual screening of compound libraries, candidate molecules (ZINC29142850 (Z1), ZINC78607001 (Z2), and ZINC94303138 (Z3)) were prioritized based on their similarity to known NDM-1 binder (hydrolyzed oxacillin (0WO)). Molecular docking studies further elucidated the binding modes and affinities of the selected compounds towards the active site of NDM-1. These compounds demonstrated superior binding affinities to the enzyme compared to a control compound (-7.30 kcal/mol), with binding scores of -7.13, -7.92, and -8.10 kcal/mol, respectively. Binding interactions within NDM-1's active site showed significant interactions with critical residues such as His250, Asn220, and Trp93 for these compounds. Subsequent molecular dynamics simulations were conducted to assess the stability of the ligand-enzyme complexes, showing low root mean square deviation (RMSD) values between 0.5 and 0.7 nm for Z1, Z2, which indicate high stability. Z2's compactness in principal component analysis (PCA) suggests that it can stabilize particular protein conformations more efficiently. Z2 displays a very cohesive landscape with a notable deep basin, suggesting a very persistent conformational state induced by the ligand, indicating robust binding and perhaps efficient inhibition. Z2 demonstrates the highest binding affinity among the examined compounds with a binding free energy of -25.68 kcal/mol, suggesting that it could offer effective inhibition of NDM-1. This study highlights the efficacy of computational tools in identifying novel antimicrobial agents against resistant bacteria, accelerating drug discovery processes.
在对抗耐抗生素细菌的持续斗争中，新德里金属β-内酰胺酶-1（NDM-1）因其能使细菌对多种β-内酰胺抗生素产生耐药性而成为一个重大的治疗挑战。本研究提出了一种基于药效团的虚拟筛选、对接和分子动力学模拟方法，用于识别靶向NDM-1的潜在抑制剂，NDM-1是一种与抗生素耐药性相关的关键酶。通过生成药效团模型并随后对化合物库进行虚拟筛选，根据候选分子（ZINC29142850（Z1）、ZINC78607001（Z2）和ZINC94303138（Z3））与已知NDM-1结合剂（水解苯唑西林（0WO））的相似性对其进行了优先级排序。分子对接研究进一步阐明了所选化合物与NDM-1活性位点的结合模式和亲和力。与对照化合物（-7.30千卡/摩尔）相比，这些化合物对该酶表现出更高的结合亲和力，结合分数分别为-7.13、-7.92和-8.10千卡/摩尔。NDM-1活性位点内的结合相互作用显示，这些化合物与关键残基如His250、Asn220和Trp93有显著相互作用。随后进行分子动力学模拟以评估配体-酶复合物的稳定性，Z1、Z2的均方根偏差（RMSD）值在0.5至0.7纳米之间，表明稳定性较高。Z2在主成分分析（PCA）中的紧凑性表明它可以更有效地稳定特定的蛋白质构象。Z2显示出非常紧密的态势，有一个明显的深谷，表明由配体诱导的构象状态非常持久，表明结合牢固且可能抑制有效。Z2在所研究的化合物中表现出最高的结合亲和力，结合自由能为-25.68千卡/摩尔，表明它可以有效抑制NDM-1。本研究突出了计算工具在识别针对耐药细菌的新型抗菌剂、加速药物发现过程方面的功效。
