Design and Synthesis of Inhibitors Targeting DCN1/3 and Inhibitors Targeting MLL1 Methyltransferase
Year: 2019
Type: dissertation
Abstract: The goal of my work presented in this dissertation was to fill the unmet need for compounds that can be used to interrogate the biology of the Cullin-RING ubiquitin ligases (CRLs) and the MLL1 methyltransferase. We conducted structure-based design, organic synthesis, and biochemical/biophysical assays to discover potent inhibitors targeting DCN1, DCN3 and, MLL1 methyltransferase. In DCN1 project, we describe the design, synthesis, and evaluation of peptidomimetics targeting the DCN1-UBC12 protein-protein interaction. Starting from a 12-residue UBC12 peptide, we successfully obtained a series of peptidomimetic compounds that bind to DCN1 protein with KD values of < 10 nM. Determination of a co-crystal structure of a potent peptidomimetic inhibitor complexed with DCN1 provided the structural basis for their high-affinity interaction. Cellular investigation of one potent DCN1 inhibitor, compound DI-404, reveals that it effectively and selectively inhibits the neddylation of cullin 3 over other cullin members. Further optimization of DI-404 may yield a new class of therapeutics for the treatment of human diseases in which cullin 3 CRL plays a key role. In DCN3 Project, we report the discovery of first-in-class, small-molecule inhibitors targeting the DCN3-UBE2F interaction, hereafter called DCN3 inhibitors. Our efforts have yielded potent and highly selective small-molecule DCN3 inhibitors, exemplified by TC-6304 which binds to DCN3 with a Ki value of 35 nM and fails to bind to DCN1 at concentrations as high as 30 µM. Cellular thermal shift assays showed that TC-6304 engages DCN3 in cells in a dose-dependent manner but does not affect the neddylation of any of the cullins that were examined, indicating the different roles of DCN3 when compared to DCN1. This study provides first-in-class, potent and selective small-molecule inhibitors of DCN3. In MLL project, we describe the design, synthesis and evaluation of a chemical library focused on S-adenosylmethionine-based compounds which led to the discovery of first-in-class, potent small-molecule inhibitors directly targeting the MLL1 SET domain. These are exemplified by compound TC-5115 with an IC50 value of 15 nM against MLL1 methyltransferase, which is 48 times more potent than the pan-HMT inhibitor, SAH. Determination of co-crystal structures for a number of these MLL1 inhibitors reveals that they adopt a unique binding mode that interacts with SET-I domain of MLL1 methyltransferase.
Author: Ting‐Rong Chern
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W3003207675