Author: Dr Ken Yokoyama, Ph.D.

In this work, we combined cryo-EM, enzymology, and antifungal assays to investigate how an experimental antifungal, diynyl arylamine (DA), inhibits Candida albicans chitin synthase (CaChs1). Our structures reveal that DA binds within the chitin translocation channel, blocking the passage of the growing polymer. We also found strong synergy with nikkomycin Z against both C. albicans and C. auris, supporting a strategy that targets complementary chitin synthase classes. Find out more here.

Our new paper, published in PNAS, resolves a decades-long question about how MoaC constructs the core of molybdenum cofactor (Moco), a small molecule required for essential metabolic enzymes. By combining biochemical experiments, mass spectrometry, and X-ray crystallography, we captured short-lived reaction intermediates and discovered that MoaC temporarily forms a covalent bond with its substrate. This bond acts as a molecular tether, carrying and positioning a carbon atom during a complex molecular rearrangement. We term this previously unrecognized strategy “guiding covalent catalysis.” The findings reveal a new way enzymes can control complex chemistry and suggest that related mechanisms may operate in the biosynthesis of other essential cofactors.

Our work on fungal β-1,3-glucan synthase, in close collaboration with Seok-Yong Lee’s lab, has been published in Nature. Using cryo-EM, we reveal how the clinically important antifungal caspofungin inhibits β-1,3-glucan synthase, how resistance mutations arise, and how enzyme activity is regulated. Unexpectedly, caspofungin binds the enzyme through the nascent polysaccharide product, overturning the prevailing model of direct enzyme binding. Together, these results provide a structural framework for future antifungal drug design.

Bach’s new paper on the mechanism of the radical SAM oxygenase DarE, in collaboration with the Dave Britt lab (UC Davis) and the Alex Smirnov lab (NC State University), is now published in JACS. DarE catalyzes ether cross-link formation between two tryptophan residues during darobactin antibiotic RiPP biosynthesis. In this study, we trapped and characterized a key tryptophan Cβ-centered radical, illuminating a mechanism for enzyme-catalyzed de novo ether formation via a radical-mediated O₂ addition reaction. Congratulations, Bach!!

We are excited to share that Yanan’s recent Nature Chemistry paper on azetidine amino acid biosynthesis by two non-heme iron enzymes has been highlighted in Nature Chemical Biology: link. In this work, we uncovered how these enzymes construct a highly strained azetidine ring — a key building block in many bioactive small molecules — through an unprecedented radical mechanism. Our findings expand understanding of enzymatic chemistry and open new avenues for bioengineering novel molecules. Congratulations to the entire team for this achievement!

The study reveals how the radical SAM enzyme MoaA controls essential yet potentially dangerous radical chemistry by using its flexible C-terminal tail to sense the correct substrate and safely trigger radical formation. Disruption of this mechanism in humans leads to a fatal disease. This discovery also provides a testable model for radical initiation across the radical SAM enzyme superfamily. Read “How an Enzyme Controls Essential Radical Chemistry — and Its Links to Human Disease” on the PNAS Showcase.

In this study, we characterized the mechanism of oxidative C-C bond cleavage reaction catalyzed by Fe and 2-oxoglutarate-dependent oxidase, PolD. This enzyme diverges the biosynthetic pathways between C6 and C7-sugar nucleoside antifungals, and therefore, its mechanistic and structural understanding is important for the future genome-mining discovery of novel antifungals. The results suggested that the reaction is initiated by an unexpected O-H bond homolysis. Aliphatic O-H bonds have very high bond dissociation energy (~105 kcal/mol), and this report represents, to our knowledge, the very first example of radical initiation by O-H activation in Fe and 2-OG enzymes.

Bach received a poster award during the Biochemistry Department’s annual retreat. He presented his discovery of a novel mechanism of the radical SAM enzyme DynA in catalyzing post-translational crosslinking in dynobactin biosynthesis. Congratulations, Bach!

We moved to a new space within the Nanaline Duke building.  More unified and less compartmentalized space.  It was quite a bit of effort but well worth it. Well done, everyone!

A graduate student, Bach Nguyen, is awarded the prestigious predoctoral fellowship from the American Heart Association (AHA). His proposed project aims to study the functions and mechanisms of enzymes responsible for the biosynthesis of peptide antibiotics that selectively kill Gram-negative pathogens, whose infections could lead to severe complications and devastating consequences on the cardiovascular system. Congratulations, Bach!