Researchers have successfully replaced a section of the antibiotic-synthesizing enzyme PikAIII-M5, advancing our understanding of its structure and function and moving us closer to the creation of synthetic antibiotics.
Illustration Credit: ©Tohoku University
Scientific Frontline: "At a Glance" Summary
- Main Discovery: Researchers successfully engineered a chimeric version of the enzyme PikAIII-M5, a key component in pikromycin biosynthesis, by swapping its beta-ketoreductase domain to control the stereochemistry of macrolide chains.
- Methodology: The team utilized a synthetic substrate evaluation system to physically replace the beta-ketoreductase domain within the PikAIII-M5 enzyme with an alternative domain, subsequently analyzing how these structural modifications altered the enzyme's biochemical output.
- Key Data: The study validated that the beta-ketoreductase domain acts as an interchangeable module; its successful replacement demonstrated that specific domain swapping can predictably dictate the structural composition of the resulting macrolactone ring.
- Significance: This research establishes a verified "design guideline" for combinatorial biosynthesis, enabling more accurate predictions of chemical structures from genomic data and facilitating the engineering of complex, non-natural drug molecules.
- Future Application: The findings will be applied to create novel macrolide antibiotics with structures not found in nature, directly addressing the global crisis of antibiotic resistance and the shrinking pipeline of effective antimicrobial drugs.
- Branch of Science: Synthetic Biology, Biochemistry, and Pharmaceutical Sciences.
- Additional Detail: The researchers describe the strategic engineering process as analogous to "swapping interchangeable parts in a machine," emphasizing the high potential for modular manipulation in antibiotic development.
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 analyzing 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.
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," said Professor Doi. "This strategic engineering is a process analogous to swapping interchangeable parts in a machine."
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.
Published in journal: Chemical Science
Title: Characterization of the ketoreductase domain of pikromycin module 2
Authors: Eiji Okamura, Kosuke Ohsawa, Hidetoshi Ban, Yoshiyuki Sugiyama, Junko Hashimoto, Kei Kudo, Masahito Yoshida, Kazuo Shin-ya, Haruo Ikeda, Shunji Takahashi, and Takayuki Doi
Source/Credit: Tohoku University
Reference Number: phar012126_01
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