from genes to molecules

We are a chemical biology group that focuses on the study of natural products. Natural products are highly evolved and functionally privileged compounds that often display complex chemical structures. These molecules have inspired generations of synthetic organic chemists, unveiled numerous fundamental biological processes as chemical probes, and served as the most significant source of chemical matter for drug discovery.

As the field of genomics has expanded, it has revealed a vast untapped wealth of natural products encoded in the DNA of sequenced organisms, particularly bacteria. Our lab has developed new tools to expedite the discovery of natural products from genomic information, including molecules from bacteria that cannot be cultivated in a lab. In particular, our lab focuses on Ribosomally synthesized and Post-translationally modified Peptides (RiPPs) which have genetically encoded substrates and an incredible diversity of post-translational modifications. Using a genes-to-molecule approach, we have uncovered numerous structurally unique RiPP molecules and revealed the unprecedented mechanistic enzymology through which they form. We can then leverage this knowledge to produce new-to-nature compounds with improved properties or novel activity with the long-term goal of unleashing the full synthetic potential of Nature to reshape the diagnosis and treatment of human disease.

outsmarting bacteria since 2009»

Plantazolicin, a genetically-encoded molecule

recent news

Dinh and collaborators from the UIUC NMR lab, Materials Research lab, X-ray lab and van der Donk lab have published a paper in ACS Central Science where they utilize bioinformatics to discover a novel RiPP class biosynthesized by distinct metalloenzyme families.

Shravan, Mayuresh and collaborators in the Zhao lab, have published a paper in Nature Chemistry where they discover a new fatty acid/RiPP hybrid compound: lipoavitide.

Hamada and former lab members Lonnie, Kyle and Xiaorui, have published a paper in Biochemistry in which they used a bioinformatic strategy to discover two lasso peptides with new modifications to tryptophan; Chlorolassin and Wygwalassin A1.

Dinh published a review in ACS catalysis that details the advances made in mining genomes and new chemical transformations.

Sangeetha has left to start her postdoctoral position with Pamela Ronald. We wish her continued success!


Dinh and collaborators in the UIUC NMR lab, Materials Research lab, X-ray lab and van der Donk lab published a paper in ACS Central Science where they uncovered a new compound class involving modifications installed by a cytochrome P450, a multinuclear iron-dependent non-heme oxidative enzyme, B12-rSAM, and a methyltransferase. Structural characterization demonstrated that the P450 enzyme catalyzed the formation of a biaryl C–C cross-link between two Tyr residues with the B12-rSAM generating β-methyltyrosine. The MNIO transformed a C-terminal Asp residue into aminopyruvic acid, while the methyltransferase acted on the β-carbon of this α-keto acid. The MNIO featured in this pathway is the first to modify a residue other than Cys. This study underscores the utility of genome mining to isolate new macrocyclic RiPPs biosynthesized via previously undiscovered enzyme chemistry.

In collaboration with the Zhao lab, Shravan and Mayuresh have published a paper in Nature Chemistry discovering a new compound, “lipoavitide.” The Zhao lab was able to identify and produce the fatty acid/RiPP hybrid compound, and after bioactivity testing, lipoavitide was found to be a hemolysin. Shravan and Mayuresh assisted in structural characterization of lipoavitide. The compound was found to contain a unique fatty acid, 4-hydroxy-2,4-dimethylpentanoate, and a new glycosylation, 2-O-methyl-β-6-deoxygulose. After heterologous expression and in vitro reconstitution, a putative biosynthetic pathway was suggested for production of the fatty acid and its attachment to the peptide. Substrate scope studies suggest the biosynthetic machinery may be engineered to produce new lipopeptides.

Hamada, along with former lab members Lonnie, Kyle and Xiaorui, have published a paper in Biochemistry in which a bioinformatic strategy was developed to discover lasso peptides with new modifications to tryptophan. This effort resulted in uncovering many Trp-rich biosynthetic gene clusters (BGCs) associated with several modifying enzymes. As a proof of concept, two groups of lasso peptide BGCs chemical characterizatized yielding a lasso peptide with two 5-Cl-Trp modifications, Chlorolassin and another bearing 5-dimethylallyl-Trp and 2,3-didehydro-Tyr modifications, Wygwalassin A1. We anticipate such a substrate-centric strategy to be of use in the functional prediction of enzymes that act on specific amino acids for other RiPP classes.

Hamada and his former colleagues from the Gross Lab along with Dinh from the Mitchell Lab have published a paper in Chemical Science reporting two new scaffolds of (C-N) biaryl-tailored lasso peptides. Using genome mining, a pair of lasso peptide biosynthetic gene clusters associated with cytochrome P450 genes were discovered. The usage of mass spectrometry, stable isotope incorporation, and extensive 2D-NMR spectroscopy assisted in characterizing their cognate products, nocapeptin A and longipeptin A. Moreover, longipeptin A is decorated with a rare trivalent sulfonium moiety as an unprecedented RiPP modification catalyzed by a co-occurring new Met S-methyltransferase, This work proves the value of genome mining in the targeted discovery of new PTMs.

Shravan and collaborators from the Zhao and Sarlah labs published a paper in Nature Communications discovering the new “daptide” RiPP class. Using the RiPP Recognition Element (RRE) as a genomic handle, Shravan and co-workers built a class-independent genome mining workflow to identify biosynthetic gene clusters (BGCs) in new classes. After heterologous expression and chemical characterization of two predicted BGCs, it was found that the daptides’ C-terminus had been replaced by an amine and that daptides can disrupt cell membranes. A combination of pathway refactoring, substrate scope analysis, and protein structure prediction also determined the role for each enzyme in the biosynthetic gene cluster. This work showcases the utility of genome mining and synthetic biology in discovering new PTMs and RiPP classes.