Antibiotics 2.0

In the 1980s, some of the worst scourges of humanity seemed to have been vanquished: patients suffering from tuberculosis, diphtheria, urinary tract diseases or meningitis, cholera, syphilis, typhoid – all of them bacterial infections – could be helped with antibiotics. When Alexander Fleming produced penicillin, a bactericidal extract from molds, in 1928, and, above all, after it healed soldiers with infected wounds in World War II, the triumphal march of antibiotics began.

In the second half of the 20th century, hundreds of substances that rendered bacteria harmless with few harmful side effects were produced, initially from soil bacteria and fungi and, later, increasingly by chemical synthesis. Doctors could use them singly and in combination and, in case the treatment didn’t work, there were medicines in reserve as a second or third line of defense for use in emergencies. The job seemed to be over. More and more pharmaceutical companies withdrew from the cost-intensive development of antibiotics and left the playing field to manufacturers of generics, located primarily in India and China, where the majority of today’s antibiotic drugs are produced. Every year sees the use of more than 90 billion packs of drugs for the treatment of infections. [1]

Numerous experts are issuing warnings about the curse of success. Antibiotics resistance is growing at an alarming rate – some bacteria are now already multidrug resistant, meaning that they fail to respond to several different active agents. A survey in the EU revealed that 25,000 people died from infections with resistant pathogens in 2007. In 2015, there were already almost 700,000 infections and 33,000 deaths, around 2,400 of which were in Germany [3]. The US public health authority CDC estimates there are 2.8 million antibiotic-resistant infections and 35,000 deaths in the USA each year [4] and, according to the Access to Medicine Foundation, the global death toll could be as high as 500,000, including 200,000 infants [1].

The primary cause of this is the careless handling of antibiotics during their production and use. For instance, in 2018, scientists examining bodies of water near factories in India found concentrations of antibiotics that were sometimes 100 times higher than permitted threshold values – ideal breeding grounds for resistant bacteria [5]. In India, the resistance levels for many bacteria is already over 70 percent [1]. Similarly, dangerous is the excessive use of antibiotics in intensive livestock farming; only resistant pathogens survive, and these can be passed on to humans. In the USA it is estimated that at least as many antibiotics are administered to poultry, pigs, cattle, and other animals as to people [6].  

In addition, doctors in many countries often prescribe antibiotics without checking whether their use is necessary. And we also see a large variation in antibiotic consumption by country: for instance, consumption of antibiotics in Italy and Greece is around two or three times higher than in Germany [3]. If patients then stop taking the medicine too soon, the low concentration of the active agent in the body fails to kill off all bacteria and lets those bacteria that have developed resistance to thrive. The consequence: in relation to the population, the number of deaths due to antibiotic-resistant bacteria in Italy and Greece is five to six times higher than in Germany [3] – and, in Germany, still twice as high as in the Netherlands, where microbiological laboratory tests before elective surgery are often used to identify whether patients are bringing multidrug-resistant germs into the hospital. If this is the case, these are treated beforehand. 

What makes  this situation particularly problematic is that hardly any new classes of antibiotics are under development. In 2017, a report by the World Health Organization (WHO) rated nine bacteria families that show dangerous levels of resistance for which new  antibiotics are urgently needed as severe or critical threats – whereas practically all drugs currently being trialed in Europe are only gradual improvements of existing medicines[2]. 

Stephan Sieber, professor of organic chemistry at the Technical University of Munich (Germany), reports, “Only two classes of antibiotics with new mechanisms of action have appeared on the market since 2000.” Practically all conventional antibiotics attack one of three targets in bacteria: they either inhibit cell-wall synthesis – like penicillin or vancomycin – or, like tetracycline, inhibit protein synthesis, or, in the case of quinolones, block two essential enzymes required for the replication of bacterial DNA. For bacteria, a single mutation can be enough to develop antibiotic resistance. For example, this could be a mutation that leads to a change in the targeted protein which in turn prevents the drug from binding. “Another possibility is that the bacterial cell simply ejects the antibiotic or selectively destroys it,” says Sieber. 

In the light of this, Stephan Sieber already set his research group the target of identifying new points of attack in bacteria more than ten years ago: they discovered, for example, that so-called beta-lactones are able to inhibit bacterial virulence factors – in a sense, disarming the bacteria without killing them [7]. At least as promising is the scientists’ latest discovery, an antibiotic by the name of PK150 that employs two new attack strategies [8]. It targets one of the most feared germs: multi-resistant Staphylococcus aureus (MRSA), a spherical bacteria that is often found on the skin or in the nasal mucous membranes and is responsible for thousands of fatalities around the world – for example, if it finds its way into surgical wounds.  

Stephan Sieber was awarded the Future Insight Prize for his new antibiotics approaches on July 13, 2020. Awarded annually by Merck KGaA, Darmstadt, Germany since 2019, the prize value of up to one million euros is higher than that of the Nobel Prize. “This prize is about future visions for ambitious, currently unrealized, dream products,” explains Ulrich Betz, the initiator of innovation competitions and the Future Insight Prize. “The category Multi-Drug Resistance Breaker, for which this year’s prize was awarded, focuses on solving the problem of bacterial resistance to multiple antibiotics in the battle against infections.”

Sieber’s team achieved precisely this in the case of MRSA. Bacteria have several thousand proteins, 300 to 400 of which are essential for their survival. In view of such large numbers, says Sieber, it is quite possible to identify points of attack that differ significantly from those already known. “We began by examining substances that we knew addressed the important class of human proteins, kinases – and sorafenib, a cancer medication, actually did show an antimicrobial effect.”

This is where the chemists stepped in: they systematically chemically modified atomic groups of this molecule, synthesized 70 new chemical bonds, and studied their effects on MRSA. When they finally substituted a pyridine ring with an acetal group, the breakthrough was there. As an antibiotic, the new drug, PK150, was ten times more effective than the original substance – it was now at least as powerful as the mighty antibiotic vancomycin. There was more: no antibiotic resistance was observed after weeks of testing – even under the influence of substances that promote genetic mutation. And, in contrast to vancomycin, the new drug also actively combated persisters and biofilms, namely non-replicating bacteria that, for example, lie dormant behind sugar layers until they break out again at some future time and become dangerously active.

What is the secret of PK150? Sieber emphasizes, “Our ambition is not only the development of new drugs; we also want to find out precisely where they attack the bacteria.” To do this, his researchers attached tiny markers to the antibiotic that enabled the identification of the bacterial proteins to which the drug binds. The surprise: there were two, and they no longer had anything to do with kinases. On the one hand, PK150 inhibits menaquinone production and clearly disrupts the bacterial energy metabolism. On the other hand, it enhances the activity of a signal peptidase. “This was particularly astonishing here, because no enzyme inhibition takes place and, in fact, its activity actually increased,” says Sieber. “Ultimately, this leads to too many proteins being released from the cell. The bacteria burst and are destroyed.”

In a collaboration with the Helmholtz Centre for Infection Research in Brunswick, Germany, precisely this was observed: in scanning electron micrographs, the researchers saw that the addition of PK150 literally dissolved the spherical MRSA bacteria. In Sieber’s opinion, the two entirely different points of attack could also explain why no resistance to PK150 was observed: “For a bacterial cell, it’s naturally much more difficult to develop a strategy against an attacker that’s shooting at two weak points at once than against conventional antibiotics that attack only one protein.”  

So, what comes next? Sieber is convinced: “The prize money will open up many new opportunities for us.” The optimization of PK150 is one target. In the context of the aBACTER project, his team has already synthesized 300 further variants, for instance to increase the drug level in the body or to ensure that it does not bind to any essential human proteins. It is already known that the drug can be administered in tablet form. First testing has already confirmed its efficacy, so the next step is now the clinical development phase. At the same time, the scientists discovered that the active agent is also effective against tuberculosis – “now we would like to modify it in a way that allows us to use it against gram-negative bacteria with their double cell membranes,” explains Sieber. And he’s thinking even further ahead: he wants to initiate collaborations with companies and is also looking for a new team member who will focus on machine learning methods. Initial approaches are already in place: for instance, a research team in the USA recently performed computer-aided testing of millions of molecular structures for antibacterial effects – and found them in some unexpected substances. In short: the renaissance of antibiotics development has clearly begun.

• _{https://www.emdgroup.com/en/news/future-insight-prize-2020-13-07-2020.html} 
• _{http://futureinsightprize.emdgroup.com}
• _{https://www.professoren.tum.de/en/sieber-stephan Professor Stephan A. Sieber, TU Munich}
• _{https://www.department.ch.tum.de/oc2/home/ Sieber Research Group}
• _{https://www.tum.de/nc/en/about-tum/news/press-releases/details/35823/ From cancer medication to antibiotic, TU Munich (12/16/2019)}

_{[1] https://accesstomedicinefoundation.org/amr-benchmark/the-fragile-antibiotic-market-has-reached-a-tipping-point or Report 2020 Antimicrobial Resistance Benchmark https://accesstomedicinefoundation.org/publications/2020-antimicrobial-resistance-benchmark
[2] https://www.who.int/news-room/detail/27-02-2017-who-publishes-list-of-bacteria-for-which-new-antibiotics-are-urgently-needed
[3] https://www.tagesschau.de/inland/antibiotika-keime-resistent-101.html and original source Lancet Study 2019: https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(18)30605-4/fulltext
[4] https://www.cdc.gov/drugresistance/biggest-threats.html
[5] https://www.tagesschau.de/ausland/antibiotika-113.html (10/22/2019) and
https://www.tagesschau.de/ausland/antibiotika-indien-107.html (3/2/2020)
[6] https://en.wikipedia.org/wiki/Antibiotic
[7] https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cbic.200800743
[8] https://www.nature.com/articles/s41557-019-0378-7, Nat. Chem. 12, 145–158 (2020)
[9] https://www.ifpma.org/resource-centre/new-amr-action-fund-steps-in-to-save-collapsing-antibiotic-pipeline/}