Department of Drug Science and Technology, University of Turin, Via Giuria 9, 10125, Turin, Italy.
Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, via Vetoio 1, 67100, L'Aquila, Italy.
J Comput Aided Mol Des. 2019 Feb;33(2):295-305. doi: 10.1007/s10822-018-0182-2. Epub 2019 Jan 2.
The worldwide spread of beta-lactamases with hydrolytic activity extended to last resort carbapenems is aggravating the antibiotic resistance problem and endangers the successful antimicrobial treatment of clinically relevant pathogens. As recently highlighted by the World Health Organization, new strategies to contain antimicrobial resistance are urgently needed. Class A carbapenemases include members of the KPC, GES and SFC families. These enzymes have the ability to hydrolyse penicillins, cephalosporins and carbapenems, while also being less susceptible to available beta-lactam inhibitors, such as clavulanic acid. The KPC family is the most prevalent. It is mostly found on plasmids in Klebsiella pneumoniae, meaning that great amounts of attention, in terms of inhibitor design and structural biology, have been dedicated to it, whereas no efforts have yet been dedicated to GES-type enzymes, despite their ability to rapidly and horizontally disseminate. We herein report the first in silico screening against GES-5, which is the most dangerous GES-type beta-lactamase, using a library of 800K commercially available candidates that all share drug-like properties, such as their MW, logP, rotatable bonds and HBA/HBD atoms. The best screening results were filtered to enrich the number of different chemotypes, and then submitted to molecular docking. The 34 most promising candidates were selected for in vitro validation in biochemical assays against recombinant GES-5. Six hits acted as inhibitors, in the high micromolar range, towards GES-5 and led to the identification of the first, novel chemotypes with inhibitory activity against this clinically relevant carbapenemase.
β-内酰胺酶对具有水解活性的β-内酰胺类抗生素的广泛传播，已经扩展到了最后一道防线的碳青霉烯类抗生素，这加剧了抗生素耐药性问题，并危及到对临床相关病原体的成功抗菌治疗。正如世界卫生组织最近所强调的，迫切需要新的策略来遏制抗生素耐药性。A 类碳青霉烯酶包括 KPC、GES 和 SFC 家族的成员。这些酶能够水解青霉素类、头孢菌素类和碳青霉烯类抗生素，同时对现有的β-内酰胺类抑制剂（如克拉维酸）的敏感性较低。KPC 家族是最常见的。它主要存在于肺炎克雷伯菌的质粒上，这意味着在抑制剂设计和结构生物学方面，人们对它给予了极大的关注，而对于 GES 型酶，尽管它们具有快速和水平传播的能力，但尚未进行任何努力。我们在此报告了首次针对 GES-5 的计算机筛选，GES-5 是最危险的 GES 型β-内酰胺酶，使用了 80 万个商业上可获得的候选物的文库，这些候选物都具有类似药物的特性，如分子量（MW）、脂溶性、可旋转键和氢键供体/受体原子。最佳的筛选结果被过滤以富集不同的化学型，然后提交进行分子对接。从 34 种最有前途的候选物中，选择了 6 种作为抑制剂，对重组 GES-5 进行了生化测定的体外验证。这 6 种抑制剂在高微摩尔范围内对 GES-5 具有抑制作用，并确定了具有抑制这种临床相关碳青霉烯酶活性的首个新型化学型。
