Developing mass spectrometry to understand molecular mechanisms of antibacterial and antiviral drugs

细菌和病毒利用越来越新颖和巧妙的途径感染它们的人类和动物宿主。他们持续的创造性导致了当今最严重的两个健康威胁：抗药性细菌和卷土重来的病毒流行病，如当前的新冠肺炎大流行。在这两种情况下，我们对药物机制的理解存在差距，这是取得进展的主要障碍。发现新的抗生素是极其缓慢的，设计新的抗生素也很困难，因为我们对大多数现有的抗生素是如何起作用的了解很少。我们也缺乏对细菌如何实现耐药性的详细见解。与此同时，迫切需要更好地理解正在被改变用途以治疗新冠肺炎感染的现有药物。在这项研究中，我们的目标是填补我们在理解抗生素和抗病毒药物方面的关键空白，包括那些对细菌和新冠肺炎都有一定疗效的药物。我们将研究这些药物作用的分子活动--在细菌和病毒周围的膜中。这一领域的一个挑战是膜研究的技术困难，但我们最近开发了使用质谱学的专门技术，使此类研究成为可能。我们的一系列研究将集中在达罗巴汀，一种最近发现的抗生素。我们的目标是了解Darobactin(及其修饰形式)是如何进入细菌细胞的--帮助设计新的抗生素。随着有效抗生素的范围缩小，另一个策略是重新设计我们已经拥有的抗生素。例如，一种新版本的最后手段抗生素万古霉素(将两个万古霉素分子连接在一起)已被证明有效，我们预测其治疗感染的途径不同于传统的万古霉素。发现这种新的作用模式是我们工作的另一个重点，并将为重新设计其他现有抗生素的努力提供参考。我们工作的另一个领域旨在确定新的抗生素靶点。它专注于位于细菌膜中的酶，建立和改造围绕细菌细胞的高度保护的墙。我们将监测细胞壁成分的合成和组装，探索削弱这些细菌防御的干预措施，并可能开发出新的抗生素。我们随后将解决细菌抵抗抗生素治疗的一种方式--通过组装一个外排泵将抗生素冲洗出细胞。一种名为ACEI的泵出口洗必泰，这是一种在低收入国家广泛使用的低成本抗菌剂，阻碍了这种曾是临床卫生高效物质的使用。我们的另一项研究致力于寻找这种泵的抑制剂。我们还致力于发现其他复杂的药物外排泵是如何组装的，以及它们是如何输出药物的。如果成功，这一策略可以继续使用我们现有的许多抗生素。在将我们的方法应用于新冠肺炎的过程中，我们热衷于提高对正被重新用于治疗感染的药物-它们的机制和靶点-以及将它们结合在一起创造“药物鸡尾酒”(如成功用于艾滋病毒)的可能性的了解。我们还将调查病毒组装是如何协调和控制的。随着新冠肺炎疗法的新药物靶点不断涌现，我们将结合驻留在细胞膜上的其他分子来探索它们与药物结合的相互作用。这项研究计划将从多个角度研究细菌和病毒成分之间的相互作用，以及可以防止它们感染我们的药物。通过识别新的药物靶点，设计新的药物，以及对现有药物进行重新设计和重新调整用途，它们共同代表了一种强大的战略，以帮助寻找新的抗生素和应对新冠肺炎。

Bacteria and viruses exploit increasingly novel and ingenious pathways to infect their human and animal hosts. Their continued 'inventiveness' has led to two of today's most serious health threats: drug-resistant bacteria and resurgent viral epidemics such as the current COVID-19 pandemic. In both cases, gaps in our understanding of drug mechanisms pose a major barrier to progress. Discovering new antibiotics is painstakingly slow, and designing new ones is difficult because we have a poor grasp of how most existing antibiotics work. We also lack detailed insight into how bacteria achieve resistance. Meanwhile, there is a critical need to better understand existing drugs that are being repurposed to treat COVID-19 infections. In this research, we aim to fill in the critical gaps in our understanding of both antibiotic and antiviral drugs, including those showing some efficacy against both bacteria and Covid-19. We will study molecular activities taking place where these drugs act - in the membranes that surround bacteria and viruses. A challenge in this area has been the technical difficulty of membrane studies, but we have recently developed specialised techniques, using mass spectrometry, that make such studies possible. One strand of our research will focus on Darobactin, an antibiotic that was discovered recently. We aim to understand how Darobactin (and modified forms of it) enter bacterial cells - aiding the design of new antibiotics. As the range of effective antibiotics dwindles, another strategy is to re-engineer the antibiotics we already have. For example, a new version of the last-resort antibiotic vancomycin (with two vancomycin molecules joined together) has proven effective, and we predict its pathway for treating infection is different to that of traditional vancomycin. Uncovering this new mode of action is another focus of our work, and would inform efforts to re-engineer other existing antibiotics. Another area of our work aims to identify new antibiotic targets. It focuses on enzymes that sit in the membranes of bacteria, building and remodelling the highly protective wall that surrounds bacterial cells. We will monitor the synthesis and assembly of cell wall components, exploring interventions that weaken these bacterial defences and could be developed into new antibiotics. We will subsequently address one of the ways in which bacteria resist antibiotic treatment - by assembling an efflux pump to flush the antibiotic out of the cell. One pump, AceI, exports chlorhexidine, a low cost antimicrobial used widely in low-income countries - hindering use of what had been a highly effective substance for clinical hygiene. A further strand of our research is devoted to finding inhibitors for this pump. We also aim to discover how other complex drug efflux pumps are assembled, and how they export drugs. If successful, this strategy could enable the continued use of many of our existing antibiotics. In applying our approaches to COVID-19, we are keen to improve understanding of drugs that are being repurposed for infection treatment - their mechanisms and targets, and the potential to combine them to create 'drug cocktails' (as successfully employed for HIV). We will also investigate how assembly of the virus is coordinated and controlled. As new drug targets continue to emerge for COVID-19 therapies, we will explore their drug binding interactions in combination with other molecules that reside in the membranes of cells. This research programme will investigate, from multiple perspectives, the interactions between components of bacteria and viruses, and the drugs that can prevent them from infecting us. Together - through identification of new drug targets, design of new drugs and re-engineering and re-purposing of existing drugs - they represent a powerful strategy to help in the search for new antibiotics and to tackle COVID-19.