Carbapenem Antibiotic Resistance in Enterobacteriaceae: Understanding Interactions of KPC Carbapenemases with Substrates and Inhibitors

肠杆菌科碳青霉烯类抗生素耐药性：了解 KPC 碳青霉烯酶与底物和抑制剂的相互作用

• 批准号: MR/T016035/1
• 负责人: James Spencer
• 金额: $ 86.54万
• 依托单位: University of Bristol
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FT016035%2F1
• 关键词: Carbapenem; Antibiotic; Resistance; Enterobacteriaceae; Understanding

beta-lactams (BLs, penicillin and its relatives) are the most used antibiotics worldwide. Carbapenems are the newest and most potent BLs, and particularly important for treating infections by so-called opportunistic Gram-negative bacteria (GNB). These are organisms, either normally present in the human body or the natural environment (soil, water), that are not considered harmful to healthy individuals but can cause infections, possibly severe and even life-threatening, in patients whose immune defences are compromised. Risk factors for such infections include wounds (surgery, burns, injury), use of medical devices (catheters, ventilators), and conditions (HIV) or treatments (cancer chemotherapy or drugs that prevent transplant rejection) that affect immune defences. Growing numbers of patients fall into these categories. GNB are a particular treatment problem as their cell structure prevents many antibiotics that kill other types of bacteria from reaching their targets; efforts to discover new antibiotics effective against GNB have been largely unsuccessful.Until recently, carbapenems were regarded as "last resort" drugs for infections by GNB unresponsive to other treatments. However, growing resistance to other antibiotics makes carbapenems increasingly a first choice when infection by a GNB is suspected. When carbapenems fail alternatives are limited and often toxic, hence carbapenem resistance is regarded as a major public health challenge. In GNB carbapenem resistance is largely due to proteins called carbapenemases that bind to and degrade carbapenems, removing their ability to kill bacteria. Carbapenemases are part of a larger group of proteins (beta-lactamases) that destroy other types of BL antibiotics, however most beta-lactamases cannot break down carbapenems. beta-lactamases can be countered by a second group of drugs (beta-lactamase inhibitors) that block their activity and enable BL antibiotics to be used to treat bacteria carrying beta-lactamases, but not all beta-lactamases can be blocked by this route and some can mutate or evolve to escape the action of inhibitors.This proposal investigates how one carbapememase from the GNB Klebsiella pneumoniae, KPC (Klebsiella pneumoniae carbapenemase) degrades carbapenems and other BL antibiotics, and interacts with one specific class of inhibitors (diazabicyclooctanes, DBOs) and how these activities are affected by mutations in KPC. Klebsiella pneumoniae is an important cause of infections (urinary and respiratory infections, sepsis) associated with healthcare, and KPC is one of the main causes of carbapenem resistance worldwide.We recently described, for the first time, how KPC binds carbapenems and other BLs (ceftazidime, an antibiotic used for healthcare-associated infections) during a key stage in their breakdown; and how KPC binds DBOs. Based on this information we will use state-of-the-art computational methods to construct detailed models of the reaction of KPC with each of these three classes of molecules, in order to identify the most likely route by which each reaction occurs. The accuracy of these models will be tested by comparing the speed predicted for each reaction with actual values measured in experiments for a range of antibiotics used in patient treatment. We will then investigate how these reactions are affected by specific alterations in KPC, seeking to understand how such changes now identified in bacteria from human patients can improve the ability of KPC to break down antibiotics and reduce the ability of DBOs to block KPC action. Finally we will use this information to design and test, in computer models and experiments, new carbapenems that resist breakdown by KPC and new DBOs that are more effective KPC inhibitors; and that in each case are not affected by KPC mutations. This provides a route by which understanding of KPC can be exploited to design new treatments effective against an important group of antibiotic resistant bacteria.

β-内酰胺（BLS，青霉素及其亲戚）是全球最常用的抗生素。碳青霉烯是最新，最有效的BLS，对于通过所谓的机会革兰氏阴性细菌（GNB）治疗感染尤其重要。这些是通常存在于人体中的生物，或者是自然环境（土壤，水），这些生物对健康个体有害，但可能会导致免疫防御能力受到损害的患者，可能引起感染，可能是严重甚至危及生命的。此类感染的危险因素包括伤口（手术，烧伤，受伤），使用医疗设备（导管，呼吸机）和病情（HIV）或治疗（癌症化学疗法或防止移植排斥反应）的治疗方法。越来越多的患者属于这些类别。 GNB是一个特殊的治疗问题，因为它们的细胞结构可防止许多杀死其他类型细菌的抗生素达到靶标。发现针对GNB有效的新抗生素的努力在很大程度上没有成功。最近，碳青霉烯被认为是GNB对其他治疗的反应症的“最后手段”药物。然而，当怀疑GNB感染时，对其他抗生素的耐药性使碳青霉烯越来越成为首选。当碳青霉烯的替代方案有限且经常有毒时，因此碳青霉烯耐药性被视为主要的公共卫生挑战。在GNB中，碳青霉烯耐药性主要是由于蛋白质称为碳青霉酶，它们结合并降解碳青霉烯酶，从而消除了它们杀死细菌的能力。碳酸酶是破坏其他类型的BL抗生素的较大蛋白质（β-内酰胺酶）的一部分，但是大多数β-内酰胺酶不能分解碳纤维烯。可以通过第二组药物（β-内酰胺酶抑制剂）来应对其活性并使BL抗生素可用于治疗携带β-内酰胺酶的细菌，但并非所有β-内酰胺酶都可以通过此途径阻止，但有些途径可以突变或进化以逃避抑制剂的作用。肺炎，KPC（克雷伯氏菌肺炎碳青霉烯酶）降解碳青霉烯和其他BL抗生素，并与一类特定类型的抑制剂（Diazabycyclooctanes，dbos，dbos）相互作用，以及这些活动如何受到KPC突变的影响。 Klebsiella pneumoniae is an important cause of infections (urinary and respiratory infections, sepsis) associated with healthcare, and KPC is one of the main causes of carbapenem resistance worldwide.We recently described, for the first time, how KPC binds carbapenems and other BLs (ceftazidime, an antibiotic used for healthcare-associated infections) during a key stage in他们的崩溃；以及KPC如何结合DBO。基于此信息，我们将使用最先进的计算方法来构建KPC与这三类分子中的每一种的详细模型，以确定每个反应发生的最可能的途径。这些模型的准确性将通过将预测的每种反应的速度与在实验中测量的一系列用于患者治疗的抗生素测量的实际值进行测试。然后，我们将研究这些反应如何受到KPC的特定变化的影响，以寻求了解现在从人类患者细菌中鉴定出的这种变化如何提高KPC分解抗生素的能力并降低DBO阻断KPC作用的能力。最后，我们将使用此信息在计算机模型和实验中设计和测试，这些新的碳青霉烯类抗拒KPC的崩溃和更有效的KPC抑制剂的新DBO；并且在每种情况下都不受KPC突变的影响。这提供了一条途径，可以利用对KPC的理解来设计有效的抗生素耐药细菌的新疗法。

项目成果

A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors.

• DOI: 10.1002/prot.26227
• 发表时间: 2022-03
• 期刊: Proteins
• 影响因子: 2.9
• 作者: Gervasoni S;Spencer J;Hinchliffe P;Pedretti A;Vairoletti F;Mahler G;Mulholland AJ
• 通讯作者: Mulholland AJ

QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A ß-lactamases

QM/MM 模拟揭示了 A 类 - 内酰胺酶中碳青霉烯酶活性的决定因素

• DOI: 10.26434/chemrxiv-2022-4jdc5
• 发表时间: 2022
• 作者: Chudyk E