New Modeling Techniques Could Be Key To Developing Antibiotics To Combat Superbugs

A new project by researchers at Newcastle University could help in the fight against drug-resistant strains of bacteria. By using a new form of neutron imaging, the team was able to create an extremely accurate model of the interaction between the outer membrane of Gram-negative bacteria and Polymyxin B, a powerful antibiotic.

This model provides a valuable way for researchers to test and describe in great detail the way that antibiotics interact with the outer membrane of bacteria. Such data could help to develop new antibiotic treatments to combat bacteria, especially recently emerging strains of drug-resistant bacteria.

Since their discovery in 1928 by Alexander Fleming, antibiotics have been the go-to treatment for most sicknesses, their introduction having drastically reduced the mortality rate from illness and injury. However, the proliferation of antibiotics has been a double-edged sword. The overprescription, overuse and general ignorance of antibiotics in a number of modern countries have caused strains of bacteria to develop resistances to commonly prescribed drugs such as penicillin or methicillin.

By extrapolating from available bacterial genome sequences, it is predicted that there are over 20,000 potential resistance genes (r genes) in over 400 different types of bacteria. Fortunately, the actual number of bacteria that have developed resistances is smaller but still enough to cause concern. The looming threat of so-called superbugs has caused many clinicians to focus their research efforts on developing new drugs and finding effective alternative treatments to drug-resistant strains of bacteria.

Mechanism of Antibiotics

Unlike cells found in most mammals, Gram-negative bacterial cells have an extremely selective asymmetrical membrane, which can make the delivery of treatments to the interior of the cell difficult. Most prescribed antibiotics, such as penicillin, function by targeting selective protein channels that occupy the outer membrane of bacteria. Typically, these protein channels serve to pump nutrients inside of the bacteria. Antibiotics use the protein channels to enter the cell wall and then stymie the bacteria’s functioning from the inside. In many strains of drug-resistant bacteria, the protein channels have mutated to no longer allow the antibiotics through. What has been needed are other viable ways to interact with the outer membrane of bacterial cells.

This is easier said than done though. While the chemical composition of the outer membrane of Gram-negative bacteria has long been known, less understood is its actual structure and dynamic arrangement. It is difficult to study the actual dynamics and fine-grained structure of bacterial cells in vitro. Without a detailed knowledge of the mechanistic interactions between the membrane and antibiotics, it can be hard to determine how exactly the antibiotic is functioning on the target cell.

Modeling the Membrane

To investigate the structure of the outer membrane, researchers used a technique known as neutron reflectometry. Similar to X-ray imaging, neutron reflectometry takes advantage of the unique properties of neutrons to take very detailed pictures of small regions. Neutrons are fired into the structure and reflect back into a receiver. The information reflected back to the receiver is then compiled to create an image of the area. Neutrons are very small and are a form of non-ionizing radiation, so they are ideal for probing minute and delicate organic structures like the membrane of bacteria. By using this technique, researchers were able to construct an extremely accurate model of the chemical structure of the outer membrane and its interaction with the drug Pylomyxin B.

Using this model, the researchers primarily determined that the effectiveness of Polymyxin B as an antibiotic is dependent upon the specific temperature of the cell’s outer membrane. At approximately room temperature, the lipopolysaccharide layer of the outer membrane undergoes a phase transition from a gel-like state to a liquid crystalline state, causing the membrane to slightly expand. This expansion allows the Polymyxin B to bond easier to negatively charged sites in the lipopolysaccharide layer which de-stabilizes the outer membrane.

While it was known previously that Pylomyxin B works by binding with the outer membrane, the model developed by the team gives an extremely precise description of the actual molecular dynamics during the phase shift and the interaction of the drug with the membrane. “Targeting the outer membrane offers alternative ways to kill pathogens and our new data shows us why bacteria are vulnerable to this type of attack,” said Professor Jeremy Lakey, one of the lead researchers on the team. “They need to keep their outer membrane flexible to grow but that provides the weakness exploited by the Polymyxin.” It is thought that neutron imaging techniques can be further used to probe the structure of the outer membrane and provide mechanistic explanations for a wide class of membrane affecting drugs.

Future Developments

Of course, this research raises the question: if bacteria have been developing resistances to antibiotics, won’t they just develop resistances against any new drugs? The answer is yes, but this research changes the game a bit. Now, instead of playing catch up with evolving bacteria, we have techniques for probing molecular details of the adaptations bacteria may develop. This knowledge would allow us to investigate the development of bacterial drug resistance in real time and show us how to exploit the molecular structure of bacterial cells to circumvent those resistances. If the precise molecular dynamics are known, it is easier to test and develop new types of antibiotics.

Developing new drugs is not the only way to combat the evolution of drug-resistant bacteria. A study conducted in 2014 determined that out of 568 practices in the UK, over 54% of adults 18-59 diagnosed with respiratory tract infections are prescribed antibiotics. A separate study indicated that over 40% of patients in the UK think that antibiotics are effective against viruses and almost a fifth disagreed with the statement “antibiotics can kill bacteria.” Such studies indicate that resources directed towards public education on the proper use of antibiotics could go lengths to reducing rates of drug-resistant strains.