Methyl reader proteins recognize and bind to post-translationally methylated residues and have functional roles in diverse cellular processes including gene regulation, development and oncogenesis. The CBX polycomb paralog family of methyllysine readers recognize trimethyllysine lysine residues on histone tail 3 and repress transcription by compacting chromatin. The polycomb paralogs form multi-protein complexes that silence the expression of tumour suppressor genes, and play important roles in regulating cell cycle and differentiation. Each paralog is structurally similar, yet has distinct functions, of which many are unknown. My work has focused on the design and synthesis of CBX inhibitors and on the development of new methodologies for the discovery of inhibitors targeting methyllysine readers. In this work, I report on a series of potent peptidic inhibitors that selectively target the CBX polycombs, as well as the first selective inhibitor for the family member CBX6, and dual-active inhibitors that target CBX6/CBX8. The results demonstrate the potential to achieve selectivity through interactions outside of the methyllysine binding domain. Structural determinants in the binding pocket of each protein that differ within the family and give rise to selectivity were discovered. I will also report on a series of peptidomimetic CBX inhibitors that are active in cells. Cellular active inhibitors are critical for understanding the biological role of each CBX protein and their potential as therapeutic targets. New high-throughput approaches are needed to efficiently target methyllysine readers by chemical inhibition. I describe in this work a strategy for creating massive libraries of phage-displayed peptidic inhibitors containing methyllysine mimics. Synthetic optimization on cysteine-containing peptide phage constructs allowed for the successful installation of Kme3 mimics. This is the first report of a post-translational methylated peptide phage library. The methodology I developed can be used in a synthetic chemistry-driven adaptation of traditional phage display for the screening of millions of peptide-based compounds. Strategies that allow for diversity and high throughput screening will aid in future efforts in targeting the highly similar CBX proteins. / Graduate / 2021-06-01

Epigenetic control of gene expression by histone post-translational modifications (PTMs) is a complex process regulated by proteins that can 'read', 'write' or 'erase' these PTMs. The histone lysine demethylase (KDM) family of epigenetic enzymes remove methyl modifications from lysines on histone tails. The Jumonji C domain (JmjC) family is the largest family of KDMs. Investigating the scope and mechanisms of the JmjC KDMs is of interest for understanding the diverse functions of the JmjC KDMs in vivo, as well as for the application of the basic science to medicinal chemistry design. The work described in this thesis aimed to biochemically investigate the inhibitor and substrate diversity of the JmjC KDMs, it led to the identification of new inhibitors and substrates and revealed a potential combinatorial dependence between adjacent histone PTMs. Structure-activity relationship studies gave rise to an n-octyl ester form of IOX1 with improved cellular potency and selectivity towards the KDM4 subfamily. This compound should find utility as a basis for the development of JmjC inhibitors and as a tool compound for biological studies. The rest of this thesis focused on the biochemical investigations of potential substrates and inhibitors for KDM3A, a JmjC demethylase with varied physiological functions. Kinetic characterisation of reported KDM3A substrates was used as the basis for evaluations of novel substrates and inhibitors. Further studies found TCA cycle intermediates to be moderate co-substrate competitive inhibitors of KDM3A. Biochemical investigations were carried out to study potential protein-protein interactions of KDM3A with intraflagellar transport proteins (IFTs), non-histone proteins involved in the formation of sperm flagellum. Work then addressed the exploration of novel in vitro substrates for KDM3 (KDM3A and JMJD1C) mediated catalysis, including: methylated arginines, lysine analogues, acetylated and formylated lysines. KDM3A, and other JmjC KDMs, were found to catalyse novel arginine demethylation reaction in vitro. Knowledge gained from studies with unnatural lysine analogues was utilised to search for additional novel PTM substrates for KDM3A. These results constitute the first evidence of JmjC KDM catalysed hydroxylation of an Nε-acetyllysine residue. The H3 K4me3 position seems to be required for acetyllysine substrate recognition, implying a combinatorial effect between PTMs. Preliminary results provide evidence that JMJD1C, a KDM3 protein previously reported to be inactive, may catalyse deacetylation in vitro. An additional novel reaction, observed with both KDM3A and JMJD1C, is deformylation of N^ε-formyllysine residues on histone H3 fragment peptides. Interestingly, H3 K4 methylation was also observed to enhance the apparent deformylation of both KDM3A and JMJD1C catalysed reactions. Overall, findings in this thesis suggest that the catalytic activity of JmjC KDMs extends beyond lysine demethylation. In a cellular context, members of the KDM3 subfamily might provide a regulatory link between methylation and acylation marks. Such a link will further highlight the complex relationships between histone PTMs and the epigenetic enzymes that regulate them. The observed dependency of H3 K9 catalysis on H3 K4 methylation adds another layer of complexity to the epigenetic regulation by histone PTMs.

Writer, eraser, and reader proteins are three classes of proteins/enzymes that add, remove, and recognize post-translational modifications (PTMs) on histone tails, respectively. The orchestrated action of these protein classes controls dynamic state of chromatin and influences gene expression. Dysregulation of these proteins are often associated with disease conditions. All three classes are targeted with small molecule inhibitors for various disease conditions. This is a promising area of research to develop therapeutics for various clinical conditions. I worked on a methyllysine reader protein Cbx7, which belong to polycomb group of proteins. Cbx7 is a chromodomain containing protein and it uses its chromodomain to recognize methyllysine partners such as H3K27me3. Aberrant expression of Cbx7 is observed in several cancers including prostate, breast, colon, thyroid, etc. Hence targeting Cbx7 with potent and selective inhibitors would be beneficial for therapeutic intervention for Cbx7 associated diseases. Here I report my work on design, synthesis, and evaluation of Cbx7 inhibitors. In my work, we identified several potent and selective inhibitors for Cbx7 and we published first-in-class antagonists for Cbx7. Few of these inhibitors were tested on cancer stem cell models. Further, I propose future work for targeting Cbx7 and other chromodomain containing proteins. / Graduate / 2018-09-04