Relating structure and function: Discovery of novel inhibitors of myotonic dystrophy
The projects described herein seek to understand the relationship between the function of the drug and the structure of its target, with the aim of discovering novel therapeutics that target nucleic acid secondary structures, selectively. The structure of the expanded DNA and RNA repeats that cause myotonic dystrophy type 1 (DM1) present a unique opportunity to develop sequence-selective small molecule inhibitors that bind to the DNA or RNA and inhibit RNA synthesis or aberrant RNA-protein interactions directly as well as many downstream effects. The motivation behind and progress toward nucleic acid drug targeting is described in Chapter 1 along with the therapeutic approaches applied to DM1. In Chapter 2, a simple computational method was developed to explore the structure of RNA-small molecule complexes, building from the published structures of DM1 RNA. This method was used to not only understand the conformational dynamics of uracil base flipping and how small molecules might interact in this binding mode but also to the development of new ligands through structure-based drug design. The design of base binding ligands was validated by X-ray crystallography. These principles are further investigated in Chapter 3, where the repeated structure of the DNA and RNA targets were used to select their own inhibitors using an in situ click reaction on the target. Hit molecules form the selection assay are multivalent and multitarget inhibitors. In addition, these multivalent ligands bind tighter than their monomeric counterparts and make specific base-binding contacts with their target to act as inhibitors. In Chapter 4, the approaches developed for the template-assisted click reaction were applied to a target-guided screen with DNA and RNA. Many of the hit compounds were able to inhibit the synthesis of RNA bidirectionally at low micromolar concentrations and performed better than their monomeric counterparts. The versatility of the clickable fragment library and the in situ reaction might be applied to other trinucleotide repeat diseases, including Huntington’s disease, ALS, and Fragile X syndrome. Finally, the progress toward finding a cure for DM1 is reflected on, considering kinetic rates of binding in the development of new therapeutics. In Chapter 5, the kinITC protocol is applied to small molecule-nucleic acid complex formation and used to extract thermodynamic and kinetic data from a single experiment. The kinetic rates found are compared to other RNA-small molecule and protein-small molecule interactions. The sum of these works provide new perspective for considering the dynamics and kinetics of drug targeting by understanding how the drug interacts with the target and how the target conformationally responds.
small molecule drug discovery, myotonic dystrophy, RNA-targeted therapeutics
University of Illinois - Urbana-Champaign
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University of Illinois at Urbana-Champaign