RESEARCH
PROTACs and small molecule inhibitors
Our lab is dedicated to advancing therapeutic strategies by developing and investigating both (a) selective small molecule inhibitors and (b) PROTACs (Proteolysis Targeting Chimeras) aimed at targeting epigenetic regulators in the fight against cancer.
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Developing selective inhibitors for epigenetic regulators is particularly challenging due to the highly conserved nature of these protein families. To address this, we have implemented a comprehensive approach through the following key steps:
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Utilizing High-Throughput Screening (HTS) to discover potential compounds.
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Employing Structure-Activity Relationship (SAR) exploration to refine and improve the activity, selectivity, and potency of the identified hits.
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Validation of lead with higher potency, fewer off-target effects, improved pharmacokinetic properties and in vivo efficacy.
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PROTACs represent a groundbreaking approach in drug discovery, leveraging the cell’s natural degradation pathways to target disease-causing proteins for elimination. These bifunctional molecules work by linking the target protein to an E3 ubiquitin ligase, leading to the protein’s ubiquitination and subsequent degradation by the proteasome. This revolutionary technology offers the ability to “remove” proteins from the cell, rather than merely inhibiting them. Our research is focused on designing and optimizing novel PROTACs based on our selective inhibitors to enhance therapeutic efficacy, improve selectivity, and reduce resistance in cancer treatment.
Immunotherapy
Chimeric Antigen Receptor (CAR) T-cell therapy is a revolutionary approach in cancer immunotherapy, harnessing a patient’s own immune cells to more effectively target and eliminate cancer. By genetically engineering T-cells to express CARs—receptors designed to recognize specific antigens on tumor cells. This therapy offers efficient tumor remission in cancer treatment, especially in hematologic malignancies like acute myeloid leukemia and B-cell lymphomas. CAR T-cell therapy has shown remarkable success, particularly in cases where traditional treatments have failed.
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However, despite its efficacy, CAR T-cell therapy is not without limitations and risks. One of the most significant challenges is the uncontrollable activation of CAR T-cells, which can lead to severe side effects, such as Cytokine Release Syndrome (CRS), a potentially life-threatening condition caused by an overwhelming immune response. To mitigate these risks, we developed a novel chemo-genetic CAR T-cell system that incorporates an HCV NS3 protease switch to regulate CAR T-cell activity. This innovative design equips CAR T-cells with a "switch", allowing the receptor to be deactivated when necessary. In the absence of NS3 inhibitors, the NS3 protease cleaves the CAR’s single-chain variable fragment (ScFv) binding domain, inactivating the CAR T-cells. When an NS3 inhibitor is present, the protease is blocked, allowing full CAR expression on the T-cell surface and maintaining its functionality.
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This controlled activation allows for the management of CAR T-cell activity, reducing the risk of adverse events like CRS. By regulating the binding of CARs to tumor-associated antigens (TAAs), we can control cytokine release, offering a safer and more effective treatment option. This approach enhances the safety profile of CAR T-cell therapy while maintaining its potent anti-tumor efficacy.
Phage Display
Phage display has revolutionized the discovery of novel ligands for diverse biological targets and facilitated the exploration of protein-protein and protein-DNA interactions, tumor antigens, in vitro protein evolution, and the development of vaccines and immunotherapies. Its remarkable efficiency in identifying peptides from vast polypeptide libraries has made it a powerful tool for therapeutic interventions. By advancing phage display methodologies, we can target critical molecular pathways and components across a wide spectrum of diseases, including cancer, AIDS, cardiovascular conditions, and autoimmune disorders. However, traditional phage display peptide libraries are inherently limited in their structural motifs and functional groups, as they are restricted to the 20 natural amino acids. To overcome these limitations, we have developed an innovative approach that significantly broadens the chemical diversity of these libraries. By utilizing the phagemid system, we incorporate multiple noncanonical amino acids and apply targeted chemical modifications, dramatically enhancing the functional diversity of the library. This expanded unnatural phage display library enables us to screen against therapeutic targets with greater precision and efficacy. Notably, we are focusing on epigenetic readers such as bromodomain and chromodomain proteins, as well as key signaling molecules like c-Abl tyrosine kinase. The ultimate goal of this screening process is to identify highly potent and selective inhibitors that hold promise as novel therapeutic agents. Our approach represents a groundbreaking strategy for generating diverse polypeptide libraries enriched with noncanonical amino acids, unlocking new avenues for drug discovery and therapeutic innovation.
Proteomics
Ubiquitin is a small, highly conserved regulatory protein present in nearly all eukaryotic organisms. It plays a key role in numerous cellular processes by attaching to other proteins, thereby altering their function, location, or lifespan in a process called ubiquitination. This involves the covalent attachment of ubiquitin molecules to a substrate protein, leading to various cellular outcomes. One of the most significant outcomes is marking proteins for degradation by the proteasome, a process central to the ubiquitin-proteasome system. This system is essential for regulating protein levels and function, and its disruption has been linked to diseases such as cancer, neurodegenerative disorders, and inflammatory conditions, making it a valuable target for therapeutic interventions.
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In the ubiquitination/deubiquitination cascade, there are four groups of enzymes. E1 and E2 enzymes are primarily cysteine-based, as are a small subset of E3 enzymes, while most deubiquitinating enzymes (DUBs) are cysteine proteases. All cysteine enzymes in this pathway form a covalent complex with ubiquitin, which can be either stable or transient during catalysis. Due to their catalytic nature and the high nucleophilicity of the cysteine residue, we develop a variety of ubiquitin-based covalent probes have been developed to target these enzymes and map them by activity-based protein profiling (ABPP).
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One valuable use of covalent ubiquitin probes is in ABPP of cysteine enzymes in the ubiquitination/deubiquitination cascade. ABPP, a technique allows researchers to study the activity of enzymes within complex biological systems. It is particularly effective for identifying active enzymes in a sample, understanding their roles in various biological pathways, and assessing their response to stimuli or treatments. When combined with covalent ubiquitin probes, ABPP has been instrumental in identifying functionally active cysteine enzymes, especially deubiquitinating enzymes (DUBs), in the ubiquitin cascade in both tissues and disease cells.
