Accelerate CHNUK AMR discovery: Establishing joint China/UK training and research platforms enabling highthroughput fragment based inhibitor discovery

Lead Research Organisation: University of Warwick
Department Name: School of Life Sciences

Abstract

Antimicrobial drug resistance (AMR) is a growing threat to global public health in China and worldwide. Multidrug resistance in 'ESKAPE' organisms - which includes Pseudomonas aeruginosa, Staphylococcus aureus and Escherichia coli, exacerbates this as these pathogens are responsible for many life- threatening infections in hospitals. Resistance amongst these organisms is widespread in Gram-negative bacteria of particular concern in China causing a high prevalence of carbapenemase-mediated resistance in hospitals, including the recent emergence in E. coli of transmissible resistance to the last line drug, colistin. There is a clear and urgent need for new classes of antibacterials that sidestep resistance. Only two new classes of antibiotics have been developed in the last 20 years this compares unfavourably to the 'golden era' of antibiotic discovery, where. inspired primarily by the early successes of penicillins, 20 new antibiotic classes were developed. In addition to the challenges and complexities of antibacterial drug discovery, contributing factors halting the development of new antibacterials include the difficulty and indeed unpredictability of gaining regulatory approval, the resulting low profit margins and the regulatory restrictions on use as resistance levels continue to rise. These factors have seen the pharmaceutical and biotechnology industry substantially withdraw from investing in antibiotic discovery. The accompanying loss of expertise in the sector has only compounded the threat.

Thus there is a pressing requirement for significant investment in training and discovery to overcome the woeful lack of new antibacterials.

We plan to tackle the lack of specialised AMR training for the next generation of researchers by building a network of activity between outstanding, well funded, AMR research groups in the Uk and China. We will train a cohort of the next generation of researchers in advanced biophysical techniques to accelerate the discovery of new chemical inhibitors. These compounds will prove invaluable tools to probe fundamental aspects of biology and become the chemical start points for the development new antibacterial discovery programs. To achieve this we have exceptional support from industry and have included letters of support from them (for our 5yr UK collaborative SWON alliance science program which provides an important component of the underpinning science for CHNUK). We will arrange joint SWON CHNUK scientific advisory panel meetings to help focus priorities for fragment based discovery.

China and the UK have committed major capital investment in synchrotrons and associated beam lines required for structural biology, and additionally in the UK for fragment based drug discovery. Transfer of automated fragment discovery technology from Harwell to Shanghai (see letters of support) will enable China researchers trained in the UK as part of this program to extend activities available to them to China researchers, further accelerating discovery.

Technical Summary

The synchrotrons at Harwell (UK) and Shanghai (China) and the Drug Discovery unit at Dundee are powerful technology hubs. In particular Diamond Light Source is developing the first synchrotron beamline with an integrated high-throughput fragment based lead discovery (FBLD) platform and Dundee has established expertise in medicinal chemistry and drug discovery. We plan to integrate these hubs with AMR centres of excellence in China and the UK, deliver state of the art training to these researchers (and the wider AMR community) and exploit FBLD capabilities to identify novel chemical probes. These new chemical probes, alongside high throughput structural biology and mechanistic insight, will all importantly, help validate a range of novel AMR targets and provide the structural insight to build new effective inhibitors for these and the panel of well validated targets in cell wall and protein biosynthesis. Specialist workshops in China and the UK will deliver training and outreach to the wider community. To optimise and develop workflows at the interfaces between target production, fragment screening and medicinal chemistry and aid high-throughput characterization of novel targets two posts covering computational chemistry and structural biology are proposed. We will hold workshop(s) in UK, and China to attract new China academic and industry partnership and be guided by medicinal chemistry at Dundee and antibiotic discovery industry experts during the collaboration to prioritise chemical approaches.

Two PDRAs are required, based at Harwell, one to support protein production and crystallography the other in silico modelling and in support of the X-ray crystallography-based FBLD platform. They will be involved in construct designing, cloning, protein production and purification, crystallization, Xchem fragment screening and data processing and analysis chemical docking and design. Moreover, the PDRAs will be involved in Harwell-based workshops and ongoing support.

Planned Impact

Antibiotics have been a mainstay of human healthcare for over 70 years. However, the inexorable spread of antibiotic resistance limits their ability to prevent and to cure life-threatening diseases. Enduring targets for antibiotics included components of bacterial cell wall biosynthesis, in particular the targets of penicillin (e.g. penicillin binding proteins or PBPs that synthesise peptidoglycan) and protein biosynthesis (e.g. RNA polymerase). We will focus upon these as well validated targets that new mechanistic and structural insight can be used to develop novel inhibitors alongside new approaches to identify inhibitors that may simultaneously knock of penicillin resistance (penicillin destroying enzymes, beta-lactameses) and inhibit PBPs. This search for new non-lactam antibiotics that target PBPs that also target beta-lactamases, if successful, would side-step decades of beta-lactamase evolution in one leap.

In addition we will identify chemical probes to help validate novel cell wall and novel anti-virulence targets. This process of validation is crucial for the global AMR research community to best understand where research priorities should be. This information is also vitally important to help inform global pharma.
This proposal brings together a globally unique group of recognised world leaders in complementary aspects of bacterial biochemistry, chemistry, genetics, physics and physiology in the area of peptidoglycan metabolism, structure and architecture. Our aim is to build from this proposal a nationally integrated, multi-centre, multidisciplinary programme of research to address the critical and unresolved understanding of PBPs in relevant Gram negative and Gram positive pathogens that is essential for future antibiotic discovery.

This will extend key competencies and capabilities of academia to support and engage effectively with the global biotechnology and pharmaceutical sector. As such the project will have diverse impacts within the UK and internationally. Some of the expected impacts will be relatively short-term (i.e. within the life-time of the grant itself) while we expect others to be medium- to long-term in nature. The PI and industry advisory panel, populated with world leading industry consultants, with recognised track records in antibiotic discovery, and senior representatives from current pharma partners, will ensure that impact activities are considered and acted upon throughout the project. This will provide exceptional opportunities to engage with industry and through workshops to expand this across the wider academic community.

Extension of a unique multidisciplinary multi-institutional training environment in cell wall biosynthesis to a wide cohort of students will be another important impact, including the development of training across the antibiotic discovery pipeline with a clear industry focus and specialist input from our industry consultants. The results will be of widespread academic and pharmaceutical interest, because of almost all efforts to date on PBP inhibition have focused on beta-lactams.

We have unprecedented support from global pharma, from PhD support to running screens and providing access to probe compounds, and engaging as members of our exceptional scientific advisory panel. All have a strong interest in using the pre-competitive information that will be generated. To help achieve this engagement we have well defined objectives and routes for further exploitation.

Publications


10 25 50
 
Description Dundee Drug Discovery Unit 
Organisation College of Life Sciences
Department Drug Discovery Unit
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Dundee Drug Discovery Unit
Collaborator Contribution Future chemistry and NMR screening support
Impact International collaboration is the future of antibiotic discovery - this was embedded within the recent Radio 4 AMR drama 'Resistance' http://www.bbc.co.uk/programmes/b08hylsn
Start Year 2016
 
Description SME collaboration 
Organisation Argenta Discovery Ltd
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution Collaboration with Antimicrobial Discovery Solutions not Argenta Discovery
Collaborator Contribution Knowledge transfer
Impact Multidisciplinary microbiology, biochemistry structural biology chemistry
Start Year 2017
 
Description Vernalis 
Organisation Vernalis
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution Knowledge transfer bidirectional
Collaborator Contribution Access to a fragment based discovery training course for students and post docs
Impact Training
Start Year 2016
 
Description Radio 4 3 part drama production 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Radio drama highlighting factors driving antibiotic resistance and global consequences - raising public awareness at the National level
Year(s) Of Engagement Activity 2017
URL http://www.bbc.co.uk/programmes/b08g7y1l
 
Description United Nations General Assembley 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Invited to attended AMR working group presentations
Year(s) Of Engagement Activity 2016
URL http://www.un.org/pga/71/event-latest/high-level-meeting-on-antimicrobial-resistance/