Countering antimicrobial resistance: investigating activity of beta-lactamase inhibitors using atomistic simulation and experiment

对抗抗菌素耐药性：使用原子模拟和实验研究 β-内酰胺酶抑制剂的活性

• 批准号: 2625332
• 金额: --
• 依托单位: University of Bristol
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2021
• 资助国家: 英国
• 起止时间: 2021 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2625332
• 关键词: Countering; antimicrobial; resistance; investigating; activity

Rising antibiotic resistance is a major problem for human health. Resistance to beta-lactams, the single most important antibiotic class, often arises through their breakdown by beta-lactamases (BLs). Many BL producing bacteria are multi-drug resistant and may cause untreatable infections. A clinically important class of BL inhibitors to combat this resistance are diazabicyclooctanes (DBOs), used together with beta-lactams (e.g. avibactam-ceftazidime, relebactam-imipenem) to treat complicated secondary care infections. Interestingly, new DBOs in development (e.g. Nacubactam, Zidebactam) show inhibition of penicillin binding proteins (PBPs, the cellular targets of the -lactams) as well as BLs, leading to a so-called "enhancer" effect upon beta-lactam action and possible use as 'dual mode' antibiotics. To inhibit BLs and PBPs, DBO inhibitors form stable covalent acyl-enzyme complexes. Using multi-scale computer simulations, we have calculated the efficiency of -lactam acyl-enzyme formation and breakdown for a number of BLs, thereby predicting whether individual enzymes can confer resistance to specific beta-lactams (Chem Comm 2014, 50, 14736; J Chem Inf Model 2019, 59, 3365; ACS Catal 2020, 10, 6188) and their susceptibility to BL inhibitors (Biochemistry 2018, 57, 3560). Crystal structures of complexes of key BLs and PBPs with multiple inhibitors are now available and experimental data provide evidence that in some cases these complexes can slowly degrade to regenerate active enzyme, potentially providing a route to inhibitor resistance.This multidisciplinary project aims to address why certain DBOs inhibit both BLs and PBPs, whereas others inhibit BLs only. Computational assays based on multi-scale simulations will be used to assess formation and breakdown of the acyl-enzymes formed by a range of DBOs with clinically relevant serine BLs (e.g. KPC-2, OXA-48 and variants) as well as PBPs from target bacteria. This is challenging, as different reaction mechanisms will need to be explored. The accuracy of these assays will be validated by experimental determination of DBO inhibition of specific BLs and PBPs, using a range of kinetic methods (co-supervisor Spencer). The BL test set will include new variants identified in regions with endemic resistance.The project will provide training in cutting-edge techniques using state-of-the-art facilities in the context of a collaborative multi-disciplinary environment (e.g. www.bristol.ac.uk/amr/). Insights obtained into DBO inhibition will inform development of new DBOs with desirable characteristics, which may contribute to new, effective treatment of bacterial infections.

抗生素耐药性的上升是人类健康的一个主要问题。对 β-内酰胺（最重要的单一抗生素类别）的耐药性通常是通过 β-内酰胺酶 (BL) 的分解而产生的。许多产生 BL 的细菌具有多重耐药性，可能会导致无法治疗的感染。临床上对抗这种耐药性的一类重要的 BL 抑制剂是二氮杂双环辛烷 (DBO)，与 β-内酰胺类药物（例如阿维巴坦-头孢他啶、瑞巴坦-亚胺培南）一起使用来治疗复杂的二级护理感染。有趣的是，正在开发的新 DBO（例如 Nacubactam、Zidebactam）显示出对青霉素结合蛋白（PBP，β-内酰胺的细胞靶标）和 BL 的抑制作用，从而对 β-内酰胺作用产生所谓的“增强”效应，并可能用作“双模式”抗生素。为了抑制 BL 和 PBP，DBO 抑制剂形成稳定的共价酰基酶复合物。使用多尺度计算机模拟，我们计算了许多 BL 的 β-内酰胺酰基酶形成和分解的效率，从而预测单个酶是否可以赋予特定 β-内酰胺抗性 (Chem Comm 2014, 50, 14736; J Chem Inf Model 2019, 59, 3365; ACS Catal 2020, 10, 6188) 及其对 BL 抑制剂的敏感性 （生物化学 2018, 57, 3560）。关键 BL 和 PBP 与多种抑制剂的复合物的晶体结构现已可用，实验数据提供的证据表明，在某些情况下，这些复合物可以缓慢降解以再生活性酶，可能提供抑制剂抗性的途径。这个多学科项目旨在解决为什么某些 DBO 同时抑制 BL 和 PBP，而其他 DBO 只抑制 BL。基于多尺度模拟的计算测定将用于评估一系列 DBO 与临床相关丝氨酸 BL（例如 KPC-2、OXA-48 和变体）以及来自目标细菌的 PBP 形成的酰基酶的形成和分解。这是具有挑战性的，因为需要探索不同的反应机制。这些测定的准确性将通过使用一系列动力学方法（共同主管 Spencer）对特定 BL 和 PBP 的 DBO 抑制进行实验测定来验证。 BL 测试集将包括在具有地方性耐药性的地区发现的新变种。该项目将在协作的多学科环境中使用最先进的设施提供尖端技术的培训（例如 www.bristol.ac.uk/amr/）。对 DBO 抑制的深入了解将为开发具有理想特性的新 DBO 提供信息，这可能有助于新的、有效的细菌感染治疗。