Key words: Natural products medicinal chemistry, combinatorial synthesis and biosynthesis, structure-based drug design and mode of action.
Overview. New targets need new molecules. In recent years, we have seen new generations of molecular medicines push the boundaries of size and complexity. The BH3-mimetic, Venetoclax (Venclexta, Abbvie, FW: 868.45), underlines the molecular features required to face the sheer surfaces of protein-protein interfaces, among other challenging targets. Similarly, new molecular degraders or glues continue to be pressed into higher molecular weight regimes by the need for bivalency. Meanwhile, natural products (NPs) have gotten considerable traction out of macrocyclic peptides against similar target spaces. Macrocyclization can augment peptide affinity by helping to pre-adopt a lower energy binding conformation and typically makes peptides more resistant to proteolysis and more cell permeable. The broad goal of our research is to translate insights from natural products into advances in macrocycles as molecular therapeutics for challenging targets. To this end, we seek to address two major challenges within the field: 1) the ability to rapidly synthesize and test natural product-like macrocycle inhibitors as a means to 2) increase knowledge about the molecular mechanisms of this powerful class of inhibitors against challenging therapeutic targets.
mRNA display. Our lab uses mRNA display as our main discovery platform for new peptide macrocycles. mRNA display is particularly powerful, because it tightly integrates rapid synthesis and testing of some of the largest libraries (up to 1013 molecules) of peptide-based macrocycles, in high fidelity, and with relatively minimal effort. Biosynthesis is the key to this power. In contrast to DNA-encoded libraries (DELs) and other small molecule libraries, mRNA display libraries are synthesized directly from their genetic barcodes, allowing for multiple, iterative rounds of screening to be easily performed for the enrichment of high affinity ligands. We are working to expand the diversity of mRNA display macrocycles to access new target space. We are working to develop an mRNA display compatible cell-free toolkit for rapidly building and testing new macrocyclic libraries. This approach, based on a combination of enzymes and biocompatible chemistry will open the door to natural product chemical space, decrease the time and investment required to access these chemical libraries, and speed the development of new macrocycle therapeutics.
Biocatalysis. We believe that robust and efficient new biocatalysts can empower mRNA display and speed the development of new peptide therapeutics. As part of our research program, we work on characterizing and adapting enzymes from the biosynthesis of ribosomally synthesized and post-translationally modified peptide (or RiPP) natural products for use with mRNA display. RiPP enzymes exploit substrate recruitment domains (SRDs), to bind short epitopes on their substrates and direct the rest of the peptide into the catalytic center. This effective separation of affinity and catalysis makes RiPP enzymes exceptionally promiscuous biocatalysts and powerful tools for library generation. In recent work, we have demonstrated compatibility of mRNA display with RiPP enzymes and established new technology for measuring efficient library modification in display. By combining RiPP enzymes with mRNA display, we are pushing mRNA display libraries towards smaller, yet more complex, more hydrophobic and overall more drug-like macrocycle libraries.
Challenging targets. We test and hone our new mRNA display libraries against high value, emergent therapeutic targets. Target selection is based primarily on: 1) therapeutic relevance, 2) known structural challenges in small molecule targeting, and 3) available structural and biological collaborators. These efforts establish the viability of mRNA display selections against these targets in our hands and also elucidate key aspects of the biology of these targets. We have funded projects and extant collaborations with several labs at UNC, including: Cyrus Vaziri (MAGE-A4 and other cancer testes antigens), Chad Pecot (EGFR, B7-H3, and other checkpoint receptors), Bryan Roth (G-protein coupled receptors), and Nick Brown (ubiquitin proteasome pathway).