DEVELOPMENT OF CHEMICAL PROBES TO CBX CHROMODOMAIN USING DNA-ENCODED LIBRARIES AND COVALENT CONJUGATION WITH MANNICH ELECTROPHILES
Creators: name: Wang, Sijie
Publisher: name: Purdue University Graduate School
Year: 2022
Subjects: Medicinal and biomolecular chemistry not elsewhere classified
Cancer cell biology
Organic chemical synthesis

description: Polycomb repressive complex 1 (PRC1) is critical for mediating gene expression during development. Five chromobox (CBX) homolog proteins, CBX2,4,6,7,8, are incorporated into PRC1 complexes, where they mediate targeting to trimethylated lysine 27 of histone H3 (H3K27me3) via the N-terminal chromodomain (ChD). Individual CBX paralogs have been implicated as drug targets in cancer; however, high similarity in sequence and structure among the CBX ChDs provide a major obstacle in developing selective CBX ChD inhibitors. Here a selection of small, focused, DNA-encoded libraries (DELs) against multiple homologous ChDs was reported to identify modifications to a parental ligand that confer both selectivity and potency for the ChD of CBX8. This on-DNA, medicinal chemistry approach enabled the development of SW2_110A, a selective, cell-permeable inhibitor of the CBX8 ChD. SW2_110A binds CBX8 ChD with a Kd of 800 nM, with minimal 5-fold selectivity for CBX8 ChD over all other CBX paralogs in vitro. SW2_110A specifically inhibits the association of CBX8 with chromatin in cells and inhibits the proliferation of THP1 leukemia cells driven by the MLL-AF9 translocation. In THP1 cells, SW2_110A treatment significantly decreases expression of MLL-AF9 target genes, including HOXA9, validating the previously established role for CBX8 in MLL-AF9 transcriptional activation, and defining the ChD as necessary for this function. The success of SW2_110A provides great promise for the development of highly selective and cell permeable probes for the full CBX family. In addition, the approach taken provides a proof-of-principle demonstration of how DELs can be used iteratively for optimization of both ligand potency and selectivity. CBX2 is upregulated in a variety of cancers, particularly in advanced prostate cancers. Using CBX2 inhibitors to understand and target CBX2 in prostate cancer is highly desirable. Here, selections of focused DNA encoded libraries (DELs) were performed for the discovery of a selective CBX2 chromodomain probe, SW2_152F. SW2_152F binds to CBX2 ChD with a Kd of 80 nM and displays 24-1000-fold selectivity for CBX2 ChD over other CBX paralogs <em>in vitro</em>. SW2_152F is cell permeable, selectively inhibits CBX2 chromatin binding in cells, and blocks neuroendocrine differentiation of prostate cancer cell lines in response to androgen deprivation. Targeted covalent inhibitors (TCIs) are rationally designed inhibitors that bind to a target protein and specifically label a non-conserved amino acid on proteins by means of reactive moieties (warheads). TCIs typically function by two steps, in which inhibitors first non-covalently bind to the target protein and then covalent bond formation occurs between the inhibitor- warhead and a proximal nucleophile on protein. Covalent inhibitors or drugs have prolonged target engagement and enhanced pharmacokinetic potency in vivo, compared to non-covalent molecules. Strategies to develop effective warheads of TCIs have been reported for labeling different nucleophilic amino acid residues, of which cysteine and lysine are the most established for covalent labeling. Tyrosine is recently becoming an attractive nucleophile for TCIs as an alternative choice, yet currently developed warheads that label tyrosine do so with modest specificity over other side chains. Here, I report the development of novel Mannich electrophiles and use those electrophiles as covalent warheads on an inhibitor to specifically target tyrosine in protein labeling. To my knowledge, this is first demonstration of the use of Mannich electrophiles in covalent inhibitors. Specifically, I leveraged a previously developed CBX8 chromodomain inhibitor to specifically label a non-conserved tyrosine within CBX8 using cyclic imine derivatives as warheads. This ligand-directed, specific tyrosine conjugation on CBX8 but not on CBX2, significantly improves both the potency and selectivity of inhibition. Biochemical, proteomic, and cellular validation further showed the cyclic imine covalent inhibitors can increase both potency and selectivity to the target protein CBX8 in cells, serving as a robust chemical probe for target function evaluation and modulation. This new type of tyrosine labeling warhead is a useful addition to the toolbox of medicinal chemists for covalent inhibitor development. The following chapters are modified from following publications, with permissions from Sijie Wang, Emily C.Dykhuizen, and Casey J. Krusemark. Wang, S., Denton, K. E., Hobbs, K. F., Weaver, T., McFarlane, J. M., Connelly, K. E., Gignac, M.C., Milosevich, N., Hof, F., Paci, I., Musselman, C. A., Dykhuizen, E.C., Krusemark, C. J. Optimization of Ligands Using Focused DNA-Encoded Libraries To Develop a Selective, Cell-Permeable CBX8 Chromodomain Inhibitor. <em>ACS Chem Biol. </em>2020, 15, 112-131 Wang, S., Alpsoy, A., Sood, S., Ordonez-Rubiano, S. C., Dhiman, A., Sun, Y., Krusemark, C. J., Dykhuizen, E. C. A Potent, Selective CBX2 Chromodomain Ligand and its Cellular Activity During Prostate Cancer Neuroendocrine Differentiation. <em>ChemBioChem.</em> 2021, 22, 2335-2344 Wang, S., Ordonez-Rubiano, S. C., Dhiman, A., Jiao G., Strohmier B. P., Krusemark, C. J., Dykhuizen, E. C. Polycomb Group proteins in cancer: multifaceted functions and strategies for modulation Modulators. <em>NAR Cancer</em>. 2021, 3, zcab039