Antibiotics: a trojan horse to overcome the lack of new molecules

Confronted with the bacterial threat, scientists are looking for innovative solutions to overcome bacterial resistance to treatments and the lack of new antibiotics.

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Since their introduction in the 1940s, antibiotics have saved many lives and played a major role in the development of modern medicine. However, bacteria becoming resistant to antibiotics have been observed during the very first treatments during World War II and this resistance has been increasing ever since. After decades of use, the World Health Organization warns that millions of lives could be lost in the fight against bacteria by 2050 if nothing is done 1. Urinary tract infections or surgeries are common occurrences when an infection resistant to antibiotics can lead to death.

Emergence and spreading of antibiotic resistance

Antibiotics (anti: against; bios: life) are molecules synthesized by microorganisms to fight against other rival microorganisms, in a logic of competition.

There are several families of antibiotics, and each family acts through a different mechanism by targeting different processes essential to bacterial life (cell wall formation, DNA replication, protein synthesis, etc.). Since bacteria have always naturally encountered antibiotics in their environment, they also have a genetic arsenal to fight them: this results in antibiotic resistance. This resistance is the ability of bacteria to make an antibiotic ineffective, for example with resistance genes. Some of these genes allow the bacteria to have pumps to send the antibiotic back out of the cell, others produce enzymes that chemically modify the antibiotic to make it ineffective. In addition to these genes present in the genome of the bacteria, another phenomenon participates in the emergence of resistance. Indeed, errors occurring during the copy of the genetic material of the bacteria can happen over generations, inducing the emergence of mutations. For example, a mutation can happen in a pore through which the antibiotic usually enters the cell. If the pore becomes inactive, it will prevent the antibiotic from entering the cell and thus making the bacteria resistant to this molecule.

The conservation and dispersal of these genes in bacterial populations can be explained by natural selection. Imagine being in the middle of a battlefield, with a physical advantage over others. The weaker ones will be eliminated, and as you survive, you will be able to produce offsprings that will inherit your advantage. This is natural selection, and it works the same for bacteria. When we apply a selective pressure (an antibiotic that kills sensitive bacteria and therefore selects resistant individuals able to survive), the resistant bacteria will stand out. They will be able to continue to replicate, generating new cells armed with these resistance genes. In addition, an astonishing feature of bacteria makes the fight against the dissemination of these resistance genes even more complex. Sometimes they have the ability to transfer genes between individuals by mere contact between eachother, this phenomenon is called horizontal gene transfer (in opposition to vertical gene transfer, occurring from parent to offspring). In summary, if a gene with a new function is beneficial to the bacteria when they encounter antibiotics, it will be exchanged, passed on, and preserved over generations.

In humans, animals and in the environment, bacteria are frequently exposed to these molecules. Indeed, antibiotics have been used extensively for decades in human and animal therapies. The promulgation of good practices among physicians, veterinarians, farmers and the general population is now a major goal for health agencies. Excessive uses have resulted in the permanent presence of antibiotics in the environment, generating sufficient selection pressure to maintain and spread resistance in bacterial populations. In some South East Asian countries, the health situation is alarming with the emergence of super bacteria that resist almost all treatments. Antibiotic concentrations in running water are reaching high levels (up to several milligrams per litre). Misuses of these drugs are putting hospitals into a dramatic situation, where even the so-called last resort antibiotics have become ineffective 2.

The antibiotics crisis

After the golden age of antibiotics discovery in the 1950s-1960s, nowadays healthcare professionals are sorely lacking new antibiotics, whereas the resistance to available treatments are on the rise.

Paradoxically, manufacturers are also dissociating themselves from research on antibiotics 3. They most often are low cost treatments over a short period of time, but need years of human and financial investments to obtain a marketing authorization. Thus, long and expensive treatments are favoured for their profitability (diabetes, heart diseases, etc). For instance, the antibiotic Ceftaroline fosamil yielded $130 million to the society that sells it from 2016 to 2018, whereas the 20th best seller among cancer medicines yielded $1.4 billion in 2017 only. This company has now stopped its research on antibiotics, like so many other major pharmaceutical companies. Fortunately, other financial sources have arisen, notably based on patronage and public-private partnerships, encouraging new companies to invest in this domain. Nevertheless, these are insufficient compared to the imminence of the danger.

In the quest for the next miracle drug, several obstacles cumulate in addition to the financial barrier:

• Most of the newer molecules have a mechanism of action close to already used antibiotics, for which bacteria have already developed resistance.

• Truly novel molecules should come from novel sources. We estimate that 99% of microorganisms cannot be cultivated in a laboratory. In other words they exist and can develop in their natural habitat, but it is very challenging for scientists to isolate them and, therefore, to identify the production of new efficient compounds produced by these organisms.

• A new antibiotic does not necessarily mean that it can be used in human medicine. Some molecules are actually less effective for humans than in the animal models used to test them, others hide toxic side effects, are complex to synthesize or prone to quickly arising resistance. Furthermore, a marketing authorization will only be granted if the new molecule is at least as effective as the antibiotics that are already available, even if its activity is attested.

• Some molecules are theoretically effective, but do not cross the bacterial membranes, which act as filters. This is an issue that can be worked around, for instance we use the principle of vectorization in our laboratory of Bacterial Genome Plasticity.

Vectorization: an alternative solution to counter the lack of new molecules

To face the lack of new molecules, scientists have developed alternative solutions. If it is not possible to find new molecules anymore, one of these new approaches is to modify antibiotics in order to counteract already existing resistance.

Vectorization consists in chemically linking an active antibacterial molecule with another molecule capable of entering the cell (the vector). This allows it to drive the active substance to its target. Just like a Trojan horse, a molecule considered inactive because it is blocked outside the bacteria can now enter and accumulate inside it, then act upon its target and kill the bacteria!

This principle was recently shown to work with Cefiderocol 4, a molecule that possesses 1) antibiotic moiety that need to cross the outer membrane of bacteria to reach its target, and 2) a moiety that can capture the iron present in the environment (called a siderophore). Thus, this molecule enters the cell by using the iron-siderophore transporters of the bacteria (see Figure). Cefiderocol is the first marketed antibiotic that uses a vector.

Figure: Simplified model of Cefiderocol entry in bacteria (adapted from 4): Iron is essential for bacterial growth. In order to capture the iron available in the environment for their growth, bacteria excrete molecules called siderophores which link it. By grafting a siderophore on the antibiotic, this new hybrid molecule is now recognized by the transporters of the complex iron-siderophore, and hijacks them to enter the cell, like a trojan horse! Thus, once the membrane has been crossed, the antibiotic will be able to reach its target: the protein responsible for the synthesis of the cell wall, the external skeleton of the bacterium, which will prevent it from doing its job, and interrupt the growth of the bacteria.

In our laboratory, we seek to apply this principle of vectorization in order to deliver antibiotics across the membrane by using different transporter families. Thus, we hope to create molecules that are effective against the most menacing bacterial pathogens encountered in nosocomial infections, and overcome their high level of resistance to antibiotics by helping these molecules to penetrate the bacteria.

References

1. Antibiotic resistance (2020) World Health Organisation https://www.who.int/news-room/fact-sheets/detail/antibiotic-resistance

2. Lise Barnéoud (2020) L’état sanitaire de l’Inde menacé par la résistance aux antibiotiques. Le Monde https://www.lemonde.fr/sciences/article/2020/01/27/en-inde-la-resistance-aux-antibiotiques-devient-un-probleme-sanitaire-tres-serieux_6027416_1650684.html

3. Maryn McKenna (2020) The antibiotic paradox: why companies can’t afford to create life-saving drugs. Nature https://www.nature.com/articles/d41586-020-02418-x

4. Zhanel, GG. et al (2019) Cefiderocol: A Siderophore Cephalosporin with Activity Against Carbapenem-Resistant and Multidrug-Resistant Gram-Negative Bacilli. Drugs. https://doi.org/10.1007/s40265-019-1055-2

This article was specialist edited by Dr Philippe Glaser, copy edited by Dr Marie Juzans and translated by Emile Auria.