Protein Study Could Help in Battle Against Antibiotic Resistance

Researchers in Japan report new insights into the structure of a particular bacterial protein that is involved in antibiotic resistance. Known as efflux pumps, the team at Institute of Scientific and Industrial Research at Osaka University (SANKEN) were able to describe the relationship between the position of “bulky” amino acids on the proteins and the ability of the bacteria to resist antibiotics. The work could inform the rational design of drugs that target efflux pumps, helping us to eliminate drug-resistant bacteria in the future.

Increasing bacterial antibiotic resistance threatens the ability to treat infection and to carry out life-saving procedures, like coronary bypasses and organ transplants, where infection is a risk. The number of new antimicrobials is also being developed is declining each year. In short, the medical community is losing an arms race, and better understanding of how bacteria develop resistance could help turn the tide.

Many conventional antibiotics, such as penicillin or erythromycin, work by making their way into a bacterial cell. Once there, the antibiotic prevents the cell from working properly by interfering with its molecular machinery. From a bacterium’s perspective, this is where the efflux pump comes in handy; by pumping any compounds that are harmful to it (like antibiotics) out of the cell using an efflux pump, the bacterium can protect itself from them. Bacteria that have mutated to become particularly resistant to antibiotics often have many of these efflux pumps on their surface.

To counter this, the SANKEN team produced a class of drugs that stop efflux pumps from working. These drugs, called efflux pump inhibitors, are effective at preventing the activity of some but not all types of efflux pump. Understanding how these drugs bind to efflux pumps is essential for understanding how they work, and so to producing new drugs.

 “We discovered the spatial characteristics of the inhibitor binding site in a bacterial efflux pump,” says lead author Seiji Yamasaki. “We have succeeded in this analysis by examining the protein structure and by generating and analyzing a series of mutant pumps.”

By using genetic manipulation to change the position of a “bulky” amino acid called tryptophan, the researchers were able to show which positions were important for the ability of a specific inhibitor called ABI-PP to bind to, and prevent the action of, a specific efflux pump called MexB. Specifically, they found that bulky mutations to the top and the middle of the binding site were particularly effective at preventing ABI-PP binding.

 “Our results highlight that the overall spatial characteristics of the inhibitor binding site are more relevant to prevention of inhibition than single mutations,” says senior author Kunihiko Nishino.  “We hope that this work will inform the rational design of drugs that target efflux pumps, helping us to eliminate drug-resistant bacteria in the future.”

The paper, entitled “Spatial Characteristics of the Efflux Pump MexB Determine Inhibitor Binding,” was published recently in the journal Antimicrobial Agents and Chemotherapy.