Synthesis pathway for new antibiotics elucidated

Better research and use of odorhabdins thanks to new synthetic biology technology

The antibiotic odilorhabdin is a potential drug for use against resistant bacteria. However, the yield of microbial production is still far too low. Using the new NRPS engineering technique, scientists led by Helge Bode have now identified key steps in the biosynthesis pathway that could enable future optimisation of production. The results contribute to the urgently needed rapid development of effective antibiotics in the face of increasing bacterial resistance.

The peptide antibiotic odilorhabdin, discovered only a few years ago, is effective against many types of bacteria, including those that are resistant to other antibiotics. This makes odilorhabdin a promising candidate for a new class of future medicines. However, the path from potential compound to drug is not easy. Often the bacteria that naturally produce the desired compound only produce it in very small quantities. In the case of odilorhabdin, the yield from microbial production is still far too low, so the way in which the antibiotic is produced is still unknown.

Recently, a team of researchers led by Helge Bode from the Max Planck Institute for Terrestrial Microbiology in Marburg, Germany, in collaboration with the department of Rolf Müller at the Helmholtz Institute for Pharmaceutical Research Saarland, succeeded in fully elucidating the formation of the antibiotic. This technique involves modifying the genetic blueprints for non-ribosomal peptide synthetases (NRPS), large bacterial enzymes in bacteria and fungi that produce some of the most important clinically used antibiotics, such as penicillin and other therapeutic agents. Enzymes with new capabilities are produced, which in turn result in new variants of the antibiotics.

Odilorhabdin, like many other peptide antibiotics, has been difficult in regard to these techniques. Unlike their natural counterparts, which usually have protective mechanisms, odorhabdins are either produced in very small amount or not at all, because it is lethal to the laboratory bacterium E. coli.

Hotspots' in NPRS genes

The researchers took the genetic blueprint of the antibiotic one piece at a time and coupled its parts to known biosynthesis genes in order to analyse the functions of the individual segments. "We recently discovered 'hotspots' in the NPRS genes that allow us to assemble the individual modules of the NRPS biocatalysts into functional hybrids much more effectively," says Leonard Präve, first author of the paper. "We used this to study the biosynthesis of odilorhabdin."

"The advantage of our approach is that we can use this technique to elucidate the biosynthesis without having the whole product in hand," explains Helge Bode. "Therefore, we can still study the relevant parts of the biosynthesis by producing non-toxic derivatives.” Knowing the biosynthesis of the antibiotic opens up the possibility of producing it biotechnologically, which would be cheaper and more environmentally friendly than using purely chemical methods.

The team also showed that odilorhabdin is initially produced as a so-called pro-drug. An inactive precursor is only cleaved into the active antibiotic after it has been transported out of the cell. This means that, in the future, NPRS engineering could be used to produce numerous variants of this new class of antibiotics with a broad spectrum of antimicrobial activity.