Scientists have revealed how bacteria naturally produce multiple versions of a powerful anti-cancer drug, solving a mystery that has puzzled researchers for decades. The discovery could help accelerate the development of new treatments for cancers that remain difficult to treat.
For years, scientists have hoped to harness bacterial enzymes to create new drug variants through a process known as combinatorial biosynthesis. However, progress has been limited because researchers have not fully understood how enzymes regulate their actions.
Published in nature communicationsnew research has revealed how bacterial enzymes communicate with each other to assemble a family of closely related anti-cancer compounds. That family includes romidepsin (Istdax), an FDA-approved treatment for certain blood cancers. By uncovering this natural “combinatorial” system and recreating its underlying principles in the laboratory, researchers have established a new strategy for designing future cancer treatments.
“We’ve known for decades that bacteria can naturally produce multiple versions of powerful cancer drugs, but we didn’t know how they achieved this,” said lead author Dr Munro Passmore, a research fellow in the University of Warwick’s Department of Chemistry. “This study has finally cracked that code. We have determined how the various enzymes communicate and work together to produce these drug variants. This system has such great economics that researchers never discovered this. This is the breakthrough we need to actually engineer these drugs ourselves.”
Small molecular connectors reveal nature’s drug discovery strategy
The researchers discovered that small molecular regions known as “docking domains” act as connectors between the core drug-building machinery and the enzymes responsible for adding various components. These docking domains share conserved connection points that allow them to interact with multiple enzyme partners.
This flexible design explains how bacteria can produce a variety of related drug molecules while maintaining the precision necessary to maintain the compound’s effectiveness.
The study also sheds light on how these natural drug production systems evolved. Researchers say the newly identified compounds most likely arose from related drug production pathways through gene duplication and recombination over time.
Professor Greg Challis, Monash Warwick Alliance Professor of Sustainable Chemistry at the University of Warwick and Monash University, concludes: “This research gives us a blueprint to do what nature does, better and faster. By reverse-engineering nature’s evolutionary logic, we can create products optimized for clinical use, including superior efficacy, improved selectivity, and fewer side effects.” Our immediate goal is to build an expanded anticancer drug library for a variety of cancers where new treatments are urgently needed. This discovery moves us from understanding how systems work to building new treatments. ”
How this discovery could improve cancer drug development
This research focuses on a class of anti-cancer drugs known as HDAC inhibitors. These drugs block histone deacetylases, enzymes that help regulate which genes are turned on and off in cells. Romidepsin (Istodax) is an FDA-approved HDAC inhibitor used to treat T-cell lymphoma.
A chemically related compound called FR-901375 has been known for decades, but scientists had never identified the biological pathway bacteria use to produce it. This research finally fills that missing piece.
Like other HDAC inhibitors in its family, FR-901375 belongs to a group of complex cyclic molecules called depsipeptides. These compounds are assembled from amino acid building blocks with a conserved hydroxy acid pharmacophore, all linked by a combination of peptide and ester bonds.
Inside the bacterium, these molecules are assembled by large protein complexes called PKS-NRPS hybrids, which combine the activities of polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS). New research shows that the key to this assembly process is the docking domain. Docking domains act like molecular connectors that allow one part of a production line to recognize and pass its product to the next part. This mechanism enables combinatorial biosynthesis, allowing bacteria to naturally produce multiple drug variants.
How did researchers solve the mystery?
To uncover how this system works, the team combined structural biology, biochemistry, genetics, and computational modeling.
Their work includes:
- FR-901375 Bioinformatics search of public databases identifying biosynthetic gene clusters Pseudomonas chlororaphis subspecies fisha finding confirmed by mass spectrometry of extracted metabolites.
- In vitro reconstitution experiments using purified protein domains demonstrated productive enzyme-enzyme interactions, which were verified by intact protein mass spectrometry.
- AlphaFold computational modeling predicts protein complex structures, followed by experimental mapping of interaction sites by carbene footprinting mass spectrometry.
- Site-directed mutagenesis experiments confirmed the importance of the predicted binding residues.
- Studies of gene deletions in bacterial strains have shown that the docking domain is essential for the system to function in vivo.
- Comparative analysis of biosynthetic gene clusters in multiple HDAC inhibitor-producing bacteria reveals evolutionarily conserved features shared by these natural drug manufacturing systems.
