Department of Nursing, College of Applied Medical Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia.
College of Applied Medical Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia.
Molecules. 2022 Feb 14;27(4):1283. doi: 10.3390/molecules27041283.
Bacteria expressing New Delhi metallo-β-lactamase-1 (NDM-1) can hydrolyze β-lactam antibiotics (penicillins, cephalosporins, and carbapenems) and, thus, mediate multidrug resistance. The worldwide dissemination of NDM-1 poses a serious threat to public health, imposing a huge economic burden in the development of new antibiotics. Thus, there is an urgent need for the identification of novel NDM-1 inhibitors from a pool of already-known drug molecules. Here, we screened a library of FDA-approved drugs to identify novel non-β-lactam ring-containing inhibitors of NDM-1 by applying computational as well as in vitro experimental approaches. Different steps of high-throughput virtual screening, molecular docking, molecular dynamics simulation, and enzyme kinetics were performed to identify risedronate and methotrexate as the inhibitors with the most potential. The molecular mechanics/generalized Born surface area (MM/GBSA) and molecular dynamics (MD) simulations showed that both of the compounds (risedronate and methotrexate) formed a stable complex with NDM-1. Furthermore, analyses of the binding pose revealed that risedronate formed two hydrogen bonds and three electrostatic interactions with the catalytic residues of NDM-1. Similarly, methotrexate formed four hydrogen bonds and one electrostatic interaction with NDM-1's active site residues. The docking scores of risedronate and methotrexate for NDM-1 were -10.543 kcal mol and -10.189 kcal mol, respectively. Steady-state enzyme kinetics in the presence of risedronate and methotrexate showed a decreased catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics, owing to poor catalytic proficiency and affinity. The results were further validated by determining the MICs of imipenem and meropenem in the presence of risedronate and methotrexate. The IC values of the identified inhibitors were in the micromolar range. The findings of this study should be helpful in further characterizing the potential of risedronate and methotrexate to treat bacterial infections.
表达新德里金属β-内酰胺酶-1（NDM-1）的细菌可以水解β-内酰胺抗生素（青霉素、头孢菌素和碳青霉烯类），从而介导多药耐药性。NDM-1 的全球传播对公共健康构成严重威胁，给新抗生素的开发带来了巨大的经济负担。因此，迫切需要从已有的药物分子库中寻找新型 NDM-1 抑制剂。在这里，我们通过应用计算和体外实验方法，从 FDA 批准的药物库中筛选出新型非β-内酰胺环含有的 NDM-1 抑制剂。进行了不同步骤的高通量虚拟筛选、分子对接、分子动力学模拟和酶动力学实验，以鉴定出利塞膦酸钠和甲氨蝶呤为最有潜力的抑制剂。分子力学/广义 Born 表面积（MM/GBSA）和分子动力学（MD）模拟表明，这两种化合物（利塞膦酸钠和甲氨蝶呤）都与 NDM-1 形成了稳定的复合物。此外，结合构象分析表明，利塞膦酸钠与 NDM-1 的催化残基形成了两个氢键和三个静电相互作用。同样，甲氨蝶呤与 NDM-1 的活性位点残基形成了四个氢键和一个静电相互作用。利塞膦酸钠和甲氨蝶呤对 NDM-1 的对接得分分别为-10.543 kcal/mol 和-10.189 kcal/mol。在利塞膦酸钠和甲氨蝶呤存在的情况下进行稳态酶动力学实验表明，NDM-1 对各种抗生素的催化效率（即 kcat/Km）降低，这是由于催化效率和亲和力较差所致。这些结果通过测定利塞膦酸钠和甲氨蝶呤存在时亚胺培南和美罗培南的 MIC 值进一步得到验证。鉴定出的抑制剂的 IC 值在微摩尔范围内。本研究的结果有助于进一步研究利塞膦酸钠和甲氨蝶呤治疗细菌感染的潜力。
