Waking up to a new era in antibiotics? Bacteria can effectively hibernate during antibiotic treatment through a mechanism called persistence, and when they ‘wake up’ they can be as infectious as they were beforehand. Researchers in the PP-MAGIC project are investigating how bacteria become persisters, which could lead to the development of more effective antibiotics, as Professor Henning Jessen explains. Many of the antibiotics currently in use target an active metabolism in bacteria, such as protein or DNA synthesis. However dormant bacteria, which don’t have an active metabolism and are essentially asleep, are generally not targeted by antibiotics and so can represent an ongoing threat to health. “If these bacteria ‘wake up’ again they can be as infectious as they were before,” explains Professor Henning Jessen, Chair of Bioorganic Chemistry at the University of Freiburg. Bacteria can essentially hibernate through antibiotic treatment, then wake up in more or less the same form, a mechanism called persistence. “Basically all bacteria can do this, it’s just a ramping down of metabolism,” continues Professor Jessen. “One idea about how they become persister bacteria is through the stringent response. They encounter stress – such as heat, PH changes, or limited nutrition – then go into this metabolic shutdown and become persisters. It’s actually quite easy to generate persister bacteria, because it’s a very general evasion mechanism.”
PP-MAGIC project As the Principal Investigator of the ERCfunded PP-MAGIC project, Professor Jessen is now investigating a number of questions around the stringent response, including how bacteria become persisters. Molecules called magic spot nucleotides (MSNs) are known to play an important role in this respect. “This is not the only molecule regulating the stringent response, but it’s certainly very important,” says Professor Jessen. Researchers in the project have generated derivatives of these MSNs, and Professor Jessen and his colleagues are investigating whether they can be used to modulate the stringent response. “Some analogues that we generate in the lab should be inactive in a so-called ‘caged’ form. Once they are irradiated, they would be transformed into the real MSNs, a process called ‘uncaging’; then we can study how
they affect cell growth, antibiotic resistance, and so forth,” he outlines. “There is also the possibility of not only turning them on, but also potentially reversibly switching the structures, providing the ability to turn them ‘on’ and ‘off’ repeatedly.” These MSNs are fairly well conserved in bacteria and the system is not present in humans, so in principle they represent a promising target for drug development. However, different enzymes are used to make these MSNs in different bacteria, and Professor Jessen says generating derivatives of them is a complex task. “The issue is that currently there are not many crystal structures available of these enzymes, where you could really do structure-guided design of inhibitors,” he explains. Researchers do however have the crystal structure of Staphylococcus aureus, a clinically relevant bacterium resistant to many drugs. “We already have the compounds and the enzymes, and we’re now starting the in vitro tests. The hope is that it would work on several different pathogenic bacteria, but this
is not yet clear,” says Professor Jessen. “We’re making small libraries of hopefully active compounds, and if they show promise then we could approach industry in future.” The idea will be to activate or de-activate these molecules with light. This approach would essentially enable researchers to look into the structures of different types of MSN, a topic about which little is currently known. “The way these different MSNs operate is not well understood,” acknowledges Professor Jessen. There is also an applied dimension to the project, with Professor Jessen and his colleagues aiming to ultimately translate their findings into improved antibiotics. “The idea would be to develop entirely new compounds, which - for example - prohibit bacteria from entering the stringent response. The compound itself wouldn’t be an antibiotic, but it would suppress this evasion mechanism,” he outlines. “In principle, bacteria in the presence of such compounds would not shut down their metabolism and would not stop dividing. An aggressive bacterium that continues to divide might not sound desirable, yet these more visible bacteria would then make better targets for traditional antibiotics or the immune system.”
One idea about how bacteria become persisters is through the stringent response. They encounter stress – such as heat, pH changes, or limited nutrition – then go into metabolic shutdown and become persisters. Antibiotic resistance This research is being conducted against a backdrop of growing concern about antibiotic resistance and the prospect of a post antibiotic era, where treatments against common infections are no longer effective. This so-called ‘silent pandemic’ of increased antibiotic resistance is a major public health concern, and is a correspondingly urgent research priority. “Bacteria can acquire resistance through several mechanisms. In this project, we’re studying one of the mechanisms by which bacteria can evade antibiotic treatments,” says Professor Jessen. The presence of these persister bacteria is one of the reasons why some antibiotics are typically prescribed for quite long periods. “There will always be a sub-population of bacteria that is dormant and then wakes up. If there’s no antibiotic present at that point
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then they will grow again, but if it is present they will die,” explains Professor Jessen. “This is why antibiotics should be taken for an extended period of time, even if you don’t have any symptoms any more.” A lot of antibiotics still work effectively, and are commonly prescribed to treat different conditions. The question is for how long that will continue, and many companies have halted their development programmes. “Cheap antibiotics are still available so they cannot make a lot of money from this, and development is very expensive,” explains Professor Jessen. The project’s research holds wider relevance in this context, as a deeper understanding of the mechanisms behind the stringent response could aid the development of effective new antibiotics. However, at this stage Professor Jessen is focused more on synthesising the MSNs rather than moving towards pharmaceutical development. “We now have very good methods of making these molecules. We have also developed the analytical abilities to measure and quantify these molecules, for example by incorporation of stable heavy isotope labels such as 18O for quantitative mass spectrometry,” he says. Researchers in the project have started to make inhibitors and switchable molecules,
while issues around the delivery of them into bacteria are also being investigated, and the early data looks promising. The next step would be to analyse these molecules and assess their effect on bacteria. “How do bacteria behave in the presence of the molecules we have made? Can we track this and somehow connect it to the stringent response?” outlines Professor Jessen. The hope is to measure the effect of these molecules on the growth rate of bacteria. “Do we get increased or inhibited growth rates? We also plan to measure the activity of known antibiotics in the presence of the molecules that we have made - hopefully we will see an increase,” says Professor Jessen. “We’re in quite a good position at this stage of the project. The synthesis and the analytics are both in place, and we now start to look into how bacteria respond to our novel compounds.”
PP-MAGIC (Photo-)Control of Persisters: Targeting the Magic Spot Project Objectives
Resistance of bacteria to antibiotics is an emerging threat to our societies. New antibiotics are required that rely on unexplored mechanisms. The project PPMAGIC aims to understand the bacterial stringent response to stress mediated by so called magic spot nucleotides. Inhibiting this central stress adaptation mechanism appears as a promising strategy to develop new antibiotics.
Project Funding
This project has received funding from the European Research Council Consolidator Grant (CoG). The Jessen lab is funded by the European Research Council Consolidator Grant (CoG)., the Deutsche Forschungsgemeinschaft (DFG), the Volkswagen Foundation and the University of Freiburg.
Project Partners
• Urs Jenal, University of Basel
Contact Details
Project Coordinator, Prof. Dr. Henning Jacob Jessen Chair of Bioorganic Chemistry Institute of Organic Chemistry Albert-Ludwigs-University, Freiburg Albertstr. 21 79104 Freiburg i. B., Germany E: henning.jessen@oc.uni-freiburg.de W: http://www.jessen-lab.uni-freiburg.de
Professor Henning Jessen
Henning Jessen was born in Hamburg, Germany. He received his doctorate in Chemistry in 2008. He then moved for a postdoctoral stay to the Ecole Polytechnique Federale de Lausanne, Switzerland. In 2011 he moved to the University of Zuerich, Switzerland, to start his Habilitation. He was promoted to SNF assistant professor early 2015. Since October 2015 he holds a chair of Bioorganic Chemistry at the University of Freiburg.
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