Scientists Discover How a Widely Used Cancer Drug Is Made in Nature

For six decades, one of medicine’s most important anticancer drugs has kept a remarkable secret. 5-Azacytidine, a nucleoside analogue used to treat myelodysplastic syndrome, a group of blood cancers, was first synthesized in a laboratory in the 1960s and only later recognized as a natural product made by soil bacteria. Yet despite its clinical prominence, no one knew how a living organism actually builds the molecule. A new study published in Nature Catalysis has now cracked the mystery, identifying the biosynthetic gene cluster responsible and exposing a series of extraordinary enzymatic reactions, including a rare skeletal-editing process that remodels a pyrimidine ring into a triazine, a transformation chemists would consider formidable even with synthetic tools.

The story begins with the molecule itself. 5-Azacytidine is a mimic of cytidine, one of the four canonical letters of RNA, but with a crucial difference: the carbon at position 5 of the pyrimidine ring is replaced by nitrogen, converting the base into 5-azacytosine, a member of the 1,3,5-triazine family. This single atom swap is what gives the drug its therapeutic power. Once incorporated into RNA, the analogue disrupts RNA metabolism and traps methyltransferase enzymes, ultimately reactivating tumor suppressor genes that cancer cells had silenced. Approved by the FDA in 2004 under the brand name Vidaza, the compound has become a mainstay of treatment for patients with myelodysplastic syndromes.

Because the drug was first made synthetically by Czech chemists in 1964 and only isolated from microbial cultures two years later, most researchers assumed its biosynthesis would never be found, or simply never thought to look. The prevailing view treated 5-azacytidine as a synthetic analogue that happened to also occur in nature, rather than as the product of an evolved metabolic pathway. That assumption, the new work shows, hid one of the most unusual enzymatic cascades yet discovered in natural product chemistry.

A team led by Yasushi Ogasawara and Tohru Dairi of Hokkaido University, together with Hiroyuki Morita of the University of Toyama and collaborators across Japan and Taiwan, set out to find the gene cluster. Through comparative genomics and biochemical screening of the producing organism, they pinpointed a set of genes designated azc that is both necessary and sufficient for assembling the triazine nucleobase. The identification immediately posed a puzzle: how does a cell convert ordinary purine and pyrimidine building blocks into a ring system with an extra nitrogen in an arrangement that is otherwise essentially unknown among natural nucleosides?

The answer begins with AzcE, an enzyme the researchers identify as a guanosine triphosphate cyclohydrolase. GTP cyclohydrolases are best known for opening the purine ring of GTP during the biosynthesis of folate and riboflavin, but AzcE repurposes this chemistry to generate 2,5,6-triaminopyrimidin-4(1H)-one, a pyrimidine intermediate carrying three amino groups. Structural analysis of AzcE, determined in complex with zinc and its product, revealed how the enzyme positions the substrate for ring opening, providing the first stepping stone on the path from a standard nucleotide precursor toward the triazine scaffold of the drug.

The centerpiece of the pathway, and of the study, is AzcA, a cupin domain-containing enzyme that performs what the authors describe as a skeletal editing reaction. Rather than building the triazine ring from scratch, AzcA takes the pyrimidine delivered by AzcE and surgically reworks it: the enzyme selectively cleaves the carbon-nitrogen framework of the heterocycle and reassembles it into 6-amino-4-oxo-1,4-dihydro-1,3,5-triazine-2-carboxylic acid. In effect, the protein performs molecular surgery on a ring, cutting specific bonds and stitching the fragments back together with an additional nitrogen inserted into the skeleton. X-ray crystal structures of AzcA bound to manganese and to reaction intermediates, combined with biochemical assays and density functional theory calculations, allowed the team to trace the mechanism in atomic detail, showing how the metal center and active-site residues orchestrate bond cleavage and reformation with remarkable selectivity.

The final step is equally unconventional. The carboxylic acid that AzcA installs must be removed to yield 5-azacytosine, and the enzyme pair AzcB/C accomplishes this through a thiamine pyrophosphate-dependent decarboxylation acting on the alpha-imino carboxylic acid moiety of the AzcA product. Thiamine-dependent enzymes typically handle alpha-keto acids, so acting on an imino acid represents an atypical use of this cofactor class. Cryo-electron microscopy structures of AzcB/C captured with thiamine pyrophosphate and substrate analogues revealed the active-site architecture that stabilizes the reactive intermediates, completing the mechanistic picture of how the triazine base is finished and presumably glycosylated to give the mature nucleoside antibiotic.

What makes the discovery resonate beyond one molecule is the concept of enzymatic skeletal editing itself. Synthetic chemists have in recent years celebrated skeletal editing, the late-stage insertion, deletion, or transmutation of single atoms within a molecular framework, as a frontier strategy for drug discovery. The demonstration that a cupin enzyme performs precisely this kind of single-atom logic on a heterocyclic ring during natural biosynthesis shows that nature arrived at the same idea long ago, and suggests that related enzymes scattered across bacterial genomes may perform similar transformations on other scaffolds. Genome mining guided by the azc gene cluster could therefore uncover new triazine and related azine natural products, or inspire engineered enzymes for late-stage functionalization of existing drugs.

There are also practical implications for the drug itself. Current industrial production of 5-azacytidine relies on multi-step chemical synthesis, and a biosynthetic route defined by just a handful of enzymes offers a potential platform for biocatalytic or fermentative manufacturing, possibly enabling access to analogues that are difficult to make chemically. The work also resolves a long-standing oddity in natural product history: a molecule used daily in oncology wards worldwide turns out to be a genuine bacterial metabolite, forged by enzymes that edit the very skeletons of nucleobases. For a drug whose clinical value stems from impersonating DNA’s own letters, it is fitting that its maker turns out to be a master of rewriting them.

Subject of Research: Enzymatic biosynthesis of the anticancer nucleoside analogue 5-azacytidine

Article Title: Enzymatic skeletal editing reaction forming the 1,3,5-triazine core during biosynthesis of the anticancer nucleoside analogue 5-azacytidine

Article References: Enzymatic skeletal editing reaction forming the 1,3,5-triazine core during biosynthesis of the anticancer nucleoside analogue 5-azacytidine. (n.d.). https://doi.org/10.1038/s41929-026-01611-x

Image Credits: AI Generated

DOI: 10.1038/s41929-026-01611-x

Keywords: 5-azacytidine, biosynthesis, natural products, enzymes, skeletal editing, 1,3,5-triazine, anticancer drugs, myelodysplastic syndrome, GTP cyclohydrolase, cupin enzyme, thiamine pyrophosphate, enzyme mechanisms