Analyzing bacterial enzymes in pikromycin synthesis

Macrolides are an important class of antibiotics that includes drugs such as azithromycin and erythromycin, which are widely used to treat a range of infections, including pneumonia and skin infections.

A defining feature of their biochemistry is a large ring of atoms called a macrolactone ring, which includes a chemical group called a lactone. The composition and structure of the macrolactone ring play an important role in the drug's biological activity, but it can be challenging to modify and control that structure in the biosynthesis of macrolides.

A team of researchers led by Professor Takayuki Doi from the Graduate School of Pharmaceutical Sciences at Tohoku University in Sendai and Professor Shunji Takahashi at RIKEN Center for Sustainable Resource Science has published a study in Chemical Science analysing the bacterial enzymes involved in the synthesis of the macrolide antibiotic pikromycin.

They studied the biosynthesis process in the bacteria Streptomyces, which produces pikromycin, and investigated what effect modifying the biosynthetic enzymes has on the resulting biochemistry of pikromycin.

In particular, they focused on an enzyme called Module 5 of pikromycin biosynthesis (PikAIII-M5), which is one of the most well-characterized enzymes in the process. PikAIII-M5 includes a domain called beta-ketoreductase, and the research group wanted to engineer a version of the enzyme in which that beta-ketoreductase was swapped out for a different domain.

Exchanging the ketoreductase-domain type within module enzymes could be a central strategy for controlling the stereochemistry of macrolide chains. This strategic engineering is a process analogous to swapping interchangeable parts in a machine."

Takayuki Doi, Professor, Graduate School of Pharmaceutical Science, Tohoku University

The researchers successfully replaced the beta-ketoreductase domain in PikAIII-M5, creating a new chimeric version of the enzyme. This not only advances our understanding of the chemical structure of this particular domain of PikAIII-M5 but also sheds light on how changes to that chemical structure can affect the output of the enzyme and, ultimately, the function of the macrolide antibiotic it generates.

"The application of the chimeric enzyme and synthetic substrate evaluation system established in this research is expected to accelerate combinatorial biosynthesis, enabling the creation of new macrolide antibiotics with structures not found in nature," Professor Takahashi said.

The finding also paves the way for more accurate predictions of the chemical structure of naturally occurring macrolide antibiotics based on analysis of genomic data, which in turn can enable the creation of non-natural drug molecules.

This research has never been more important, as the threat of antibiotic resistance rises and the pipeline of new antibiotics shrinks. "This approach provides design guidelines for the biosynthesis of novel macrolide antibiotics in the future," Professor Doi said.