Antibiotic resistance circumvented in lab
Strategy suggests ways to prepare for emerging superbugsPablo Tsukayama
As dangerous bacteria grow more savvy at evading antibiotics, researchers are seeking new ways to counterattack. Rather than design new drugs from scratch, some scientists are searching for ways to block the microbes’ evasive maneuvers. If resistance can be shut down, current drugs should remain effective.
That concept is demonstrated in a new study from Washington University School of Medicine in St. Louis. The researchers discovered compounds that block resistance to a major class of antibiotics called tetracyclines. If developed into a drug, such a compound could be given in combination with a tetracycline, should an infection become resistant to tetracycline alone. These types of compounds do not have a direct antimicrobial effect — if given alone, they would not kill bacteria. Instead, they knock down the bacteria’s ability to survive treatment with specific antibiotics.
The research is published May 8 in the journal Nature Chemical Biology. The work is a collaboration of multidisciplinary scientists, including structural biologists in the lab of Niraj H. Tolia, PhD, an associate professor of molecular microbiology; microbial genomicists in the lab of Gautam Dantas, PhD, an associate professor of pathology and immunology; biochemists in the lab of Timothy A. Wencewicz, PhD, an assistant professor of chemistry; and bacteriologists in the lab of Joseph P. Vogel, PhD, an associate professor of molecular microbiology.
“This work identified the first inhibitor that prevents tetracycline resistance in bacteria,” said Tolia, one of the study’s co-senior authors. “The combination of expertise we were able to bring together — all here at Washington University — resulted in the complete picture required for the identification and improvement of tetracycline resistance inhibitors.
“Structural biology drives discovery,” Tolia added. “Seeing the compound bound to the enzyme was one of those ‘Aha!’ moments, and showed that the compound served as a resistance inhibitor — locking the enzyme in an inactive state. This unique method of inhibition was completely unprecedented and is extremely powerful as it inactivates the enzyme while also preventing tetracyclines from binding.”
Tetracyclines are prescribed for a wide variety of bacterial infections, including pneumonia and other infections of the respiratory tract; acne and other skin infections; infections of the genital and urinary systems; and the bacterial infection that causes stomach ulcers. They also are widely used in large farming operations, including the dairy and fish industries.
“These compounds inhibit the ability of tetracycline-resistant bacteria to destroy tetracycline,” said Dantas, a co-senior author. “We’re gunking up the resistance machinery of bacteria capable of destroying tetracycline. If these bugs can’t chew up this antibiotic anymore, they are re-sensitized to the effects of the drug.”
Despite tetracyclines’ widespread use, bacterial infections have not yet demonstrated aggressive resistance to these drugs via destruction mechanisms. Some bacteria are resistant to tetracyclines through other means, such as pumping the drug out of the cell or blocking the drug from reaching its target, but these strategies are not as effective as destroying the drug entirely. The researchers said conditions are favorable for this destructive type of resistance to ramp up.
In past work, researchers in the Dantas lab discovered this type of resistance by conducting genetic surveys of bacteria living in soils from different parts of the country; they were interested in understanding the extent of antibiotic resistance present in bacteria living in the environment. These studies demonstrated that soil bacteria are packed with genes that — if transferred into disease-causing bacteria — would allow that bacteria to survive treatment with many common antibiotics.
According to Dantas, one set of genes stood out because the researchers could not find these sequences listed in any genomic database, and these novel genes allowed bacteria to break down tetracycline antibiotics, a problem that has not yet occurred in the many patients treated with tetracyclines.
The resistance genes enable the bacteria to manufacture proteins the researchers dubbed tetracycline destructases because of their ability to break apart tetracycline. Once the genes were identified, the tetracycline destructases that the genes encoded could be studied in the lab. The structures of the tetracycline destructase proteins and the way tetracyclines interacted with them showed how resistance could be stopped. Now that Tolia and his colleagues have shown this resistance can been blocked in the lab, they will continue developing these inhibitors to combat tetracycline resistant infections in the future.
While the genes are not yet widely present in bacteria that cause infections, researchers in the Dantas lab determined the genes were at high risk of spreading likely because of tetracyclines’ widespread use and the fact that even appropriate antibiotic use favors survival of resistant bacteria. In addition, some of the newly discovered resistance genes were located near sections of the bacterial genome known to be capable of jumping between even distantly related bacteria.
Bacteria carrying tetracycline destructases are not yet at the level of danger posed by superbugs such as carbapenem-resistant Enterobacteriaceae (CREs), but their resistance strategies work in similar ways in terms of the ability to destroy an antibiotic. Last year, a CRE infection resistant to all available antibiotics led to the death of a Nevada woman with a recent history of hospitalizations outside the United States.
Targeting resistance has had success in some bacterial infections that have become resistant to another important class of drugs called beta-lactams, which includes penicillin. Tetracycline destructase inhibitors would serve a similar function to beta-lactamase inhibitors. These inhibitors often have been developed alongside their associated beta-lactam drugs and have helped some beta-lactams regain their effectiveness.
“Staying ahead of antibiotic resistance seems like an obvious approach, but it is not common practice in the field,” said Wencewicz, also a co-senior author. “We are taking a proactive approach by developing destructase inhibitors before resistance becomes a major clinical problem.”
Emphasizing the timeliness of the research, the researchers point out that there is evidence these tetracycline destructase resistance genes are beginning to ramp up the threat to patients with bacterial infections.
“Since we started this work three years ago, one tetracycline destructase now has been found to be present in four of the most deadly pathogens, as defined by the Centers for Disease Control and Prevention,” Dantas said. “This is our motivation for working to find inhibitors of tetracycline destructases.”