Outmanoeuvring multiple defences
Our battle against bad bacteria threatens to end in a defeat. The rise of AMR, where bacteria evolve to resist our attempts to annihilate them, means new drugs are desperately needed. While researchers have no problem coming up with new molecules that can bind to lethal bacterial targets, getting the drugs inside bacterial cells is one of the biggest stumbling blocks in antibiotic drug development. Gram-negative bacteria, uniquely troublesome bugs, are protected by two different membranes; you might find a drug that gets through one of the membranes only to find that it cannot breach the other. Once you find a molecule that can cross both membranes, these bacteria have another weapon up their sleeves in the form of efflux pumps, which literally pump the drug back out of the cell.
Tricking the bacteria with “Trojan horse” antibiotics
TRANSLOCATION discovered many features of the protective cell membranes that control the access and expulsion of compounds from bacteria. For example, several proteins contained in bacterial membranes are used by the organisms to gather food, and the research showed how bacteria might be fooled to allow entry of “Trojan Horse“ antibiotics which are designed to resemble such foods. TRANSLOCATION created new, sensitive methods to detect how much drug ends up inside the cell by means of counting molecules as they pass through single proteins. The team was able to quantify a whole range of membrane proteins at the atomic level and revealed the detailed structures of 40 different proteins involved in drug transport. They also developed new modelling approaches and a scoring function to predict permeability, which represents a loose set of “rules” about a drug’s likelihood to pass through membrane proteins.
The project partners also worked on creating a database, called the InfoCentre, that could link all the data that was generated from the different IMI AMR projects. Securing access to data and putting it together was very difficult, since every project tends to save data according to their own format and standards. This data gathering was part of another key feature of the project’s scope: learning from success and failure. It required a broad knowledge base, varying skill sets and a large body of data from multiple sources.
Legacy: a wealth of protein data, and a new company
Researchers who study molecules that can thwart the evolved protective mechanisms of bacteria will be able to use the work on proteins to help in their search for new antibiotics. The wider antibiotic research community will be able to access data from the results of all projects under the IMI AMR programme including that of TRANSLOCATION.
The experience gained from the development of the InfoCentre will contribute to IMI’s AMR Accelerator programme. Tools from the InfoCentre will form the basis of planned data and knowledge management systems to be used by multiple antibiotic discovery AMR Accelerator projects as they progress through to the clinic.
The Copenhagen-based company, GRIT42 which was founded during the TRANSLOCATION project, will help to support the day-to-day IT needs of AMR Accelerator projects and also aggregate suitable data sets. The data will be used to address complex scientific questions, such as which in-vivo models are best for testing new compounds, or how clinical trial design could be better informed by results from pre-clinical stages.
Such collaboration “impossible” in any other setting
In the area of early drug discovery, TRANSLOCATION solved a number of basic research questions from a much larger perspective compared to smaller nationwide research projects. The combination of skill sets and expertise, especially in bringing together biophysical and theoretical methods with more traditional microbiological approaches, was key to the success of TRANSLOCATION. Such close collaboration between competing pharmaceutical companies would have been impossible in any other setting. The partnership also made it easier to figure out the protocol for the collaborative relationship between the pharma companies and academic partners.
In order to make sure that the expertise generated by the project remains available, the project partners took advantage of the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) to set up a virtual institute. In collaboration with experts from the European Open Screen network (EU-OPENSCREEN), the platform “Translocation-transfer” is now available. It can be used as a portal for the wider scientific community to access key experimental and computational tools established in TRANSLOCATION.
Translocation-transfer will establish a working model for these networks to collaborate and share essential know-how on theoretical and experimental methods for determining compound transport. This can then be integrated into the EU-OPENSCREEN compound profiling workflow for antibiotic programmes. The knowledge transfer process will be carried out through a series of tasks and workshops and facilitated by the New Drugs for Bad Bugs (NDD4B) InfoCentre platform. In the longer term, once these methods have been adopted by EU-OPENSCREEN, the data generated from screening projects specifically related to compound transport quantification will be released via the European Chemical Biology Database and ChEMBL database. The publicly-available data can then be used by the scientific community to improve our understanding of how molecular features mediate compound transport in bacteria, benefiting antibiotic drug discovery overall.
Achievements & News
Scientists from IMI’s Translocation project have uncovered the workings of a ‘molecular vacuum cleaner’ in the outer membrane of certain bacteria. The mechanism, described in a paper in Nature Microbiology, helps to keep the outside of the membrane free of clusters of molecules that could weaken it and the system could prove useful as a target for new antibiotics. ### Gram-negative bacteria like Escherichia coli are enclosed by two membranes which form a significant barrier for many antibiotics, limiting their effectiveness. The outer membrane is asymmentric; while the outside is coated in sugars that ward off many molecules that could be harmful to the bacteria, the inside is lined with phospholipids. Sometimes, phospholipids from the inside of the membrane accumulate on the outside. These clumps of phospholipids represent weak spots in the membrane, rendering it more vulnerable to toxic compounds like antibiotics. In this study, the scientists proposed a functional model of the ‘maintenance of lipid asymmetry’ (Mla) system, which removes phospholipids that have strayed into the outside of the membrane, sucking them back into the inside of the membrane where they belong. ‘Our three-dimensional structures and functional data show that MlaA forms a donut in the inner leaflet of the outer membrane. This binds phospholipids from the outer leaflet and removes these via the central channel, somewhat similar to a vacuum cleaner,’ explains Bert van den Berg of Newcastle University in the UK. ‘Our study illuminates a fundamental and important process in Gram-negative bacteria and is a starting point to determine whether the Mla system of Gram-negative pathogens could be targeted by drugs to decrease bacterial virulence, and to make various antibiotics more effective.’
IMI’s antimicrobial resistance (AMR) programme New Drugs for Bad Bugs (ND4BB) is the focus of a recent comment piece in Nature Reviews Microbiology by John Rex of AstraZeneca, who is involved in ND4BB.### The article explains how IMI and other projects around the world are tackling the biggest challenges in antibiotic research and development. For example, TRANSLOCATION is investigating how to transport antibiotics into bacteria, while COMBACTE focuses on the design and implementation of more efficient clinical trials. ENABLE, IMI’s newest AMR project, is creating a drug discovery platform to fast-track the development of promising molecules. The article also highlights IMI project RAPP-ID, which is working on point-of-care tests, as well as a number of US-based initiatives. Looking to the future, the article notes that IMI has a project in development which will investigate new business models and economic strategies to incentivise the development of new antibiotics.
The article concludes: ‘Although the [AMR] crisis is far from resolved, the leadership of the European Commission are to be commended for their far-sighted approach to creating ND4BB and its projects, all of which provide hope that the global community will have access to an adequate pipeline of novel antimicrobial agents with which to address the challenge of AMR.’
IMI’s TRANSLOCATION project is featured in an editorial in top science journal Science Translational Medicine. The editorial by Robert Stavenger of GSK and Mathias Winterhalter of Jacobs University Bremen### is entitled How to get good drugs into bad bugs and looks more closely at the project’s aims and objectives. As one of several projects involved in IMI’s ND4BB platform, TRANSLOCATION is focused on addressing drug penetration into Gram-negative bacteria.
IMI’s first antimicrobial resistance projects, COMBACTE and TRANSLOCATION, have signed a Memorandum of Understanding (MoU) to facilitate their collaboration. The projects are part of the New Drugs for Bad Bugs (ND4BB) programme.### As such, there was always an understanding that the projects would work together – this MoU simply formalises and sets out the framework for collaboration. Specifically, the MoU covers issues such as data sharing (and confidentiality), communication and coordination, as well as the creation of a shared Ethics Committee. One of the tasks of the TRANSLOCATION project is the creation of an Info Centre that would gather data from all ND4BB projects. With this in mind, the MoU also contains a section devoted to data standards and analysis. Looking to the future, the new ND4BB projects that will be set up in the coming months will also be invited to join the MoU.
ParticipantsShow participants on map
- Astrazeneca AB, Södertälje, Sweden
- Basilea Pharmaceutica International AG, Basel, Switzerland
- Glaxosmithkline Research And Development LTD., Brentford, Middlesex, United Kingdom
- Janssen Pharmaceutica Nv, Beerse, Belgium
- Sanofi-Aventis Recherche & Developpement, Chilly Mazarin, France
Universities, research organisations, public bodies, non-profit groups
- Assistance Publique Hopitaux De Paris, Paris, France
- Centre National De La Recherche Scientifique Cnrs, Paris, France
- Fraunhofer Gesellschaft Zur Forderung Der Angewandten Forschung Ev, München, Germany
- Fundacion Privada Instituto De Salud Global Barcelona, Barcelona, Spain
- Jacobs University Bremen Ggmbh, Bremen, Germany
- Johann Wolfgang Goethe-Universitaet Frankfurt Am Main, Frankfurt am Main, Germany
- Synchrotron Soleil Societe Civile, GIF-sur-YVETTE CEDEX, France
- The University Court Of The University Of St Andrews, St Andrews, Fife, United Kingdom
- Universita Degli Studi Di Cagliari, Cagliari, Italy
- Universitaetsklinikum Freiburg, Freiburg, Germany
- Universitat Basel, Basel, Switzerland
- Universite D'Aix Marseille, Marseille, France
- Universite De Geneve, Genève 4, Switzerland
- University College Dublin, National University Of Ireland, Dublin, Dublin, Ireland
- University Of Newcastle Upon Tyne, Newcastle upon Tyne, United Kingdom
Small and medium-sized enterprises (SMEs)
- Gritsystems As, Dragør, Denmark
- Ionovation GmbH, Osnabrück, Germany
- Nanion Technologies GMBH, München, Germany
- The Hyve BV, Utrecht, Netherlands
- Yelen, Ensues La Redonne, France
Non EFPIA companies
- Bruker Daltonik GMBH, Bremen, Germany
|Name||IHI funding in €|
|Assistance Publique Hopitaux De Paris||103 931|
|Centre National De La Recherche Scientifique Cnrs||540 600|
|European Screeningport GMBH (left the project)||232 618|
|Fraunhofer Gesellschaft Zur Forderung Der Angewandten Forschung Ev||672 679|
|Fundacion Privada Instituto De Salud Global Barcelona||203 639|
|Gritsystems As||349 875|
|Ionovation GmbH||450 400|
|Jacobs University Bremen Ggmbh||4 178 960|
|Johann Wolfgang Goethe-Universitaet Frankfurt Am Main||499 000|
|Nanion Technologies GMBH||293 200|
|Nanospot GmbH (left the project)||57 284|
|Synchrotron Soleil Societe Civile||304 000|
|The Hyve BV||326 064|
|The University Court Of The University Of St Andrews||886 152|
|Universita Degli Studi Di Cagliari||1 678 960|
|Universitaetsklinikum Freiburg||299 351|
|Universitat Basel||1 221 131|
|Universite D'Aix Marseille||1 653 621|
|Universite De Geneve||937 537|
|University College Dublin, National University Of Ireland, Dublin||90 313|
|University Of Newcastle Upon Tyne||894 625|
|Total Cost||15 984 203|