AsianScientist (Nov. 4, 2020) – Though antibiotics are known to kill bacteria, they can be harmful towards human cells too. Using a combinatorial approach, scientists from Japan have transformed one of the world’s oldest antibiotics—gramicidin A—into stronger and safer versions. Their findings have been published in Nature Communications.
Alexander Fleming’s 1928 discovery of penicillin may now be scientific legend, but the antibiotic was initially considered a laboratory curiosity with little practical benefit. After being discovered in soil bacteria in 1939, it was gramicidin A that became the world’s first clinically tested antibiotic. While gramicidin A beat penicillin to the clinic, it has since been superseded by the latter over the years.
The reason for gramicidin A’s fall from grace is the side effects it causes. Gramicidin A kills bacteria by creating holes in their cell membranes. These holes, known as ion channels, cause the cell to leak out and the surroundings to leak in. When gramicidin A is taken ingested or injected, it wreaks the same havoc onto human cells. While scientists have developed about 350 analogs of gramicidin A that differ in structure, these analogs are still toxic to humans.
As generating analogs of natural products like gramicidin A is a laborious process, it has proven difficult to pinpoint safer versions of the antibiotic. This has led to a growing need for new strategies to prepare and evaluate large numbers of products like gramicidin A.
By using combinatorial chemistry, researchers from the University of Tokyo designed and analyzed over 4,000 artificial gramicidin A analogs—more than tenfold the number studied in the past 80 years. The team did this by assembling structural combinations of gramicidin A one amino acid at a time on small glass beads. Despite being a fully manual operation, the approach allowed the researchers to quickly construct a bead library of structurally similar, but functionally different gramicidin A analogs.
“Usually, natural product synthesis is a complicated task. There are many steps to make these large molecules and at the end, synthetic yields are very low,” explained Assistant Professor Hiroaki Itoh, one of the study’s authors. “Synthetic approaches like [the one] we used are still uncommon with natural products.”
The researchers then analyzed their new analogs of gramicidin A for activity against Streptococcus bacteria, which are responsible for common diseases like strep throat and pneumonia. The strongest performers were subsequently tested on rabbit blood and mouse leukemia cells to identify versions that may be safe for humans. These analyses revealed about ten gramicidin A variations that show promise as antibacterial drugs.
The team also measured the ion channel-forming ability of the gramicidin A analogs. Despite being less harmful to mammalian cells, the new versions could still form ion channels in bacteria. According to the authors, this means that subtle modifications to gramicidin A’s structure could make its ion channel-forming ability less indiscriminate and more bacteria-specific.
Beyond identifying safer antibiotic analogs, the team’s combinatorial strategy also provides a way for scientists to pinpoint how specific structural changes in protein sequences can affect a molecule’s overall function. Such foundational structure-function information is crucial for a deeper understanding of why and how drugs work.
“It has long been believed [that it is] very difficult to [analyze] species-selective ion channel-forming activity, but our study showed that gramicidin A can have bacteria-selective activity,” concluded Itoh. “This strategy can be used for other types of natural products and other ion-channel forming compounds.”
The article can be found at: Takada et al. (2020) Discovery of Gramicidin A Analogues With Altered Activities by Multidimensional Screening of a One-bead-one-compound Library.
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Source: University of Tokyo; Photo: Shutterstock.
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