Integrating Chemistry and Evolution to Illuminate Biology and Enable Novel Therapeutics

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Integrating Chemistry and Evolution to Illuminate Biology and Enable Novel Therapeutics Project Summary Our laboratory has led three research programs at the interface of chemistry and evolution. In the first program, we developed DNA-templated synthesis as a novel approach to synthesize and discover bioactive small molecules and polymers that combines biological evolution with organic chemistry. In the second program, we developed prime editing and base editing, two genome editing technologies that collectively enable precise installation of point mutations, insertions, and deletions at targeted sites in mammalian genomes without requiring double-stranded DNA breaks or donor DNA templates. In the third program, we have applied these technologies to rescue animal models of human genetic diseases. This MIRA renewal seeks to advance these three research programs towards novel small-molecule and genome-editing therapeutics. In the first program, we developed DNA-templated synthesis, generated libraries of DNA-templated small molecules containing >250,000 unique macrocycles, and performed in vitro selections on these libraries to discover novel kinase and protease inhibitors, including the first physiological inhibitor of insulin-degrading enzyme (IDE). Recently, we discovered a new class of macrocyclic cyclophilin inhibitors that include CypD- specific variants, and solved X-ray co-crystal structures of several inhibitors bound to CypD. We propose to understand the interactions between these macrocycles and CypD, determine the cellular activity of these compounds, and develop specific inhibitors of other cyclophilins. We will also screen a new DNA-templated library of ~640,000 macrocycles against additional targets of therapeutic interest including DNA repair proteins, tumor suppressors, E3 ubiquitin ligases, interleukin and interleukin receptors, deubiquitinases, and ATPases. In the second program, we developed base editing and prime editing, the two methods that enable precision genome editing in mammalian cells without requiring double-strand DNA breaks or donor DNA templates. Base editing installs transition mutations (C•G→T•A, or A•T→G•C) using programmable DNA-binding proteins fused to natural or laboratory-evolved nucleobase deaminase enzymes, while prime editing enables the installation of all possible types of small substitutions, insertions, deletions, and combinations thereof through the use of Cas9–reverse transcriptase fusions that copy edited DNA information from an engineered prime editing guide RNA directly into targeted sites in mammalian genomes. We propose to advance prime editing by revealing the cell-state and cell-type requirements for efficient prime editing, engineering improved prime editing systems, and developing methods for prime editor delivery into animal models of human genetic disease. In the third program, we have integrated base editing with in vivo delivery methods to directly correct the mutations that cause genetic diseases, achieving phenotypic rescue in animal models of tyrosinemia75, genetic deafnesses53,76, Niemann-Pick syndrome55, and progeria. We propose to apply base editing and prime editing to validate novel in vivo approaches to permanently treat chronic pain and spinal muscular atrophy (SMA).