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Merging innovations in chemical biology with academic drug discovery
Although previously regarded as a simple intermediate between genes and proteins, the completion of the human genome project surprisingly revealed that the vast majority of our genome, over 98%, encodes for non-coding RNAs such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). This has subsequently led to an RNA renaissance in biology and medicine, uncovering the fundamental roles that RNAs, and RNA biology more generally, play in the maintenance of human health and connection to disease. Aberrant regulation of non-coding RNAs has now been linked to nearly all human pathologies from neurodegenerative diseases to cancer and metabolic disorders. Targeting of coding messenger RNAs (mRNAs), rather than the proteins in which they encode, has also emerged as a new therapeutic strategy for affecting the biology of as-yet undruggable protein targets. In addition to human RNAs, RNAs from other organisms, including bacterial RNAs and RNA viruses, are regarded as leading drug targets for the discovery of new infectious disease agents. Combined, the search for and development of RNA-targeted therapeutics has never been more pressing!
Research in the Garner Laboratory is focused on tackling this last frontier in drug discovery. To do so, we engage in interdisciplinary research efforts bridging chemistry and biology. Projects in the lab range from the development of new high-throughput screening technologies for RNAs and RNA-protein interactions to rational drug design, structural biology and chemical biology. Through these diverse research enterprises, we hope to elucidate the druggability of RNA and RNA-binding proteins, ultimately leading to the development of next-generation medicines for the betterment of human health.
Select Project 1: An Integrated Pipeline for the Discovery of RNA-Protein Interaction Inhibitors
Using Garner lab high-throughput screening technologies, RNA-interaction with Protein-mediated Complementation Assay (RiPCA) and catalytic enzyme-linked click chemistry assay (cat-ELCCA), we have designed an integrated drug discovery pipeline for targeting RNA-protein interactions. We are currently developing and carrying out screening campaigns against cancer-relevant RNA-protein interactions, including pre-let-7/Lin28 and Dicer processing of pre-miR-21.
Select publications: “cat-ELCCA: Catalyzing Drug Discovery Through Click Chemistry.” Chem. Commun. 2018, 54, 6531; “Development and Implementation of an HTS-Compatible Assay for the Discovery of Selective Small Molecule Ligands for pre-microRNAs.” SLAS Discovery 2018, 23, 47; “Expansion of cat-ELCCA for the Discovery of Small Molecule Inhibitors of the Pre-let-7-Lin28 RNA-Protein Interaction.” ACS Med. Chem. Lett. 2018, 9, 517; “A Live-Cell Assay for the Detection of pre-microRNA-Protein Interactions.” RSC Chem. Biol. 2021, 2, 241
Select Project 2: Small Molecule and Peptide Inhibitors of eIF4E
Eukaryotic translation initiation factor 4E (eIF4E) is an RNA-binding protein that binds to the m7GpppX-cap at the 5’ terminus of coding mRNAs to initiate cap-dependent translation. While all cells require cap-dependent translation, cancer cells become addicted to enhanced translational capacity, driving the production of oncogenic proteins involved in proliferation, evasion of apoptosis, metastasis, and angiogenesis among other cancerous phenotypes. Although many mechanisms lead to dysregulation of cap-dependent translation, the predominant paths are through hyperactivation of the PI3K-AKT-mTORC1, RAS-RAF-MAPK and MYC signaling pathways, all of which converge on eIF4E and cap-dependent mRNA translation initiation. Indeed, eIF4E is the rate-limiting translation factor and its activation, through enhanced expression, phosphorylation and/or aberration of its regulatory protein-protein interactions (PPI), has been shown to drive cancer initiation, progression, metastasis, and drug resistance, thereby establishing eIF4E as a translational oncogene and promising, albeit challenging, anti-cancer therapeutic target. The Garner lab is taking a multi-faceted approach for targeting eIF4E through the discovery, design and development of mechanistically distinct inhibitors of eIF4E and cap-dependent translation, including stapled peptide inhibitors of eIF4E PPIs, natural product inhibitors of eIF4E PPIs and small molecule inhibitors of eIF4E-cap binding.
Select publications: “High-Throughput Chemical Probing of Full-Length Protein-Protein Interactions.” ACS Comb. Sci. 2017, 19, 763; “Synthesis of 7-Benzylguanosine Cap Analogue Conjugates for eIF4E Targeted Degradation.” Eur. J. Med. Chem. 2019, 166, 339; “Consideration of Binding Kinetics in the Design of Stapled Peptide Mimics of the Disordered Proteins Eukaryotic Translation Initiation Factor 4E-Binding Protein 1 and Eukaryotic Translation Initiation Factor 4G.” J. Med. Chem. 2019, 62, 4967; “A Cell-Penetrant Lactam Stapled Peptide for Targeting eIF4E Protein-Protein Interactions.” Eur. J. Med. Chem. 2020, 205, 112655
Select Project 3: Chemoproteomic Profiling of Site-Selective Kinase-Substrate Interactions
As part of our efforts to investigate eIF4E and the regulation of cap-dependent translation in cancer drug discovery, we developed a chemoproteomic profiling technology for the discovery of site-selective kinase-substrate interactions, Phosphosite-Accurate Kinase-Substrate X-Linking Assay (PhAXA). Using this technology, we revealed, for the first time, the ability of CDK4/cyclin D to phosphorylate 4E-BP1, the endogenous inhibitor of eIF4E, and regulate cap-dependent translation. We are currently applying this technology to discover additional 4E-BP1 kinases that can be explored as potential combination therapies with mTOR and other eIF4E-targeted inhibitors.
Select publications: “Chemoproteomic Profiling Uncovers CDK4-Mediated Phosphorylation of the Translational Suppressor 4E-BP1.” Cell Chem. Biol. 2019, 26, 980; “Cyclin-Dependent Kinase 4 Inhibits the Translational Repressor 4E-BP1 to Promote Cap-Dependent Translation During Mitosis-G1 Transition.” FEBS Lett. 2020, 594, 1307
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