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

开发质谱分析法来了解抗菌和抗病毒药物的分子机制

• 批准号: MR/V028839/1
• 负责人: Carol Robinson
• 金额: $ 229.2万
• 依托单位: University of Oxford
• 依托单位国家: 英国
• 项目类别: Research Grant
• 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=MR%2FV028839%2F1
• 关键词: Developing; mass; spectrometry; understand; molecular

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.

细菌和病毒利用了越来越新颖而巧妙的途径来感染其人类和动物宿主。他们持续的“创造力”导致了当今最严重的健康威胁：耐药细菌和复兴的病毒流行病，例如当前的COVID-19大流行。在这两种情况下，我们对药物机制的理解差距都构成了进步的主要障碍。发现新的抗生素非常缓慢，而且设计新抗生素很困难，因为我们对大多数现有抗生素的工作原理的掌握不佳。我们还缺乏对细菌如何获得抗性的详细见解。同时，迫切需要更好地理解正在重新使用以治疗Covid-19感染的现有药物。在这项研究中，我们旨在填补对抗生素和抗病毒药物的理解，包括对细菌和COVID-19的疗效的差异。我们将研究这些药物作用的分子活动 - 在围绕细菌和病毒的膜上。该领域的挑战是膜研究的技术困难，但是我们最近使用质谱法开发了专业技术，从而使这些研究成为可能。我们研究的一组将集中在Darobactin上，Darobactin是最近发现的一种抗生素。我们旨在了解darobactin（和修饰的形式）如何进入细菌细胞 - 帮助新抗生素的设计。随着有效抗生素的各种范围，另一种策略是重新设计我们已经拥有的抗生素。例如，一种新版本的上一式抗生素万古霉素（有两个Vansomycin分子加在一起）已被证明有效，我们预测其治疗感染的途径与传统的万古霉素不同。揭示这种新的行动方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帮助。我们工作的另一个领域旨在确定新的抗生素靶标。它的重点是位于细菌膜中的酶，建造和重塑围绕细菌细胞的高度保护壁。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，并可以发展为新的抗生素。随后，我们将通过组装出外排泵将抗生素从细胞中冲洗出来，以抗生素治疗的一种方法之一。一个泵，ACEI出口洗涤胺，一种低成本的抗菌剂，在低收入国家中广泛使用 - 阻碍使用临床卫生的高效物质。我们的研究进一步致力于寻找该泵的抑制剂。我们还旨在发现其他复杂的药物外排泵如何组装，以及它们如何出口药物。如果成功，该策略可以继续使用我们现有的许多抗生素。在运用Covid -19的方法时，我们渴望提高人们对被重新用于感染治疗的药物的理解 - 它们的机制和靶标，并有可能将它们结合起来创建“药物鸡尾酒”（如HIV成功使用）。我们还将研究病毒的组装如何协调和控制。随着新药物靶标继续用于COVID-19疗法，我们将与其他存在于细胞膜中的分子结合使用它们的药物结合相互作用。该研究计划将从多个角度研究细菌与病毒组成部分之间的相互作用，以及可以阻止它们感染我们的药物。通过确定新药物的识别，新药的设计以及重新设计和重新定位现有药物 - 它们代表了一种有力的策略，可以帮助寻找新的抗生素并解决Covid-19。

项目成果

An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition.

• DOI: 10.1038/s41467-023-37035-5
• 发表时间: 2023-03-20
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Noske, Gabriela Dias;Song, Yun;Fernandes, Rafaela Sachetto;Chalk, Rod;Elmassoudi, Haitem;Koekemoer, Lizbe;Owen, C. David J.;El-Baba, Tarick V.;Robinson, Carol;Oliva, Glaucius;Godoy, Andre Schutzer
• 通讯作者: Godoy, Andre Schutzer

Ion currents through Kir potassium channels are gated by anionic lipids

通过 Kir 钾通道的离子电流由阴离子脂质门控

• DOI: 10.1101/2021.09.21.461288
• 发表时间: 2021
• 作者: Jin R

ProSight Native: Defining Protein Complex Composition from Native Top-Down Mass Spectrometry Data.

• DOI: 10.1021/acs.jproteome.3c00171
• 发表时间: 2023-08-04
• 期刊: JOURNAL OF PROTEOME RESEARCH
• 影响因子: 4.4
• 作者: Durbin, Kenneth R. R.;Robey, Matthew T. T.;Voong, Lilien N. N.;Fellers, Ryan T. T.;Lutomski, Corinne A. A.;El-Baba, Tarick J. J.;Robinson, Carol V. V.;Kelleher, Neil L. L.
• 通讯作者: Kelleher, Neil L. L.

Mass spectrometry enables the discovery of inhibitors of an LPS transport assembly via disruption of protein-protein interactions.

• DOI: 10.1039/d1cc04186j
• 发表时间: 2021-10-14
• 期刊: Chemical communications (Cambridge, England)
• 作者: Fiorentino F;Rotili D;Mai A;Bolla JR;Robinson CV
• 通讯作者: Robinson CV

Peptidoglycan biosynthesis is driven by lipid transfer along enzyme-substrate affinity gradients.

• DOI: 10.1038/s41467-022-29836-x
• 发表时间: 2022-04-27
• 期刊: Nature communications
• 影响因子: 16.6