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.
Congratulations to Susanna and Andrew on successfully defending their Ph.D. Theses, becoming the 21st and 22nd Mitchell lab students to do so!
Congratulations to Dinh and Shravan on successfully defending their Ph.D. Theses, becoming the 19th and 20th Mitchell lab students to do so!
Andrew, Alex, Dinh, Shravan, and Susanna are presenting their research at the upcoming 2nd Annual RiPPs Conference in Seoul, South Korea!
Congratulations to Guthrie (Milligan Fellowship), Sharon (Janet M. Buhrke and Victor E. Buhrke Fellowship in Physical Chemistry), and Dominic (Walter Burrows Brown Fellowship in Chemical Research) for winning their fellowships!
highlights
Along with collaborators from the Shukla lab and Lassogen, Susanna and former members Tom and Gloria have published a paper in Nature Chemical Biology in which they used a variety of computational and biochemical techniques to identify key interactions between lasso cyclases and their core peptide substrates. Through these findings, they developed a model for binding of the pre-folded intermediate in the cyclase active site and showed that this model is generalizable across cyclases from diverse phyla. They demonstrated the utility of this information for cyclase engineering and lasso peptide diversification by engineering a cyclase to efficiently cyclize previously inaccessible lasso peptide variants that bind with high affinity to cancer-promoting integrin.
Austin and collaborators in the Jiménez-Osés lab have published a paper in JACS in which they investigated the radical SAM enzyme (DarE) responsible for darobactin production. Substrate engineering determined that the enzyme is under substrate control and identified novel darobactins and biosynthetic products. In addition, high-quality quantum mechanical calculations and molecular docking uncovered important principles of DarE catalysis, including the differentiation between ether and C-C crosslink formation and connectivity on the substrate. Through this work, we provide further understanding of rSAM catalysis and darobactin biosynthesis.
Riley and collaborators from the Mitchell and Freeman lab published paper in ACS Chemical Biology where they update the RODEO algorithm to analyze borosins. This enabled a large-scale analysis of borosins, which led to the discovery of two new borosin biosynthetic strategies. These new strategies include a fused borosin with an inverted domain architecture, and a borosin maturing protease that utilizes the N-methylated amino acid installed by the borosin methyltransferase as part of it’s recognition sequence.
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.
