PhD Research
Arora Lab
PI: Paramjit S. Arora, PhD
New York University
Department of Chemistry
Doctoral thesis: Peptidomimetic-based strategies for targeting oncogenic Ras
Covalent Targeting of Oncogenic KRas G12C
The activation of the small GTPase Ras, catalyzed by the guanine nucleotide exchange factor (GEF) Son of Sevenless (Sos), involves GDP release and GTP binding. Aberrant Ras activation can result from mutations in genes encoding GEFs, GAPs, RTKs, and Ras itself, with the G12C mutation present in 10-20% of Ras-driven cancers. Protein–protein interactions (PPIs) are crucial for biological processes, and competitive inhibition requires compounds that access large, shallow surfaces. Covalent targeting can enhance specificity but risks nonselective binding. Sos catalyzes nucleotide exchange by binding Ras at its Switch I/II surface, and mimics of this interaction can inhibit its GEF activity. Iterative design led to a proteolytically stable α3β chimeric helix mimic that covalently targets oncogenic Ras G12C, optimizing preferential alkylation with Cys12 on Ras. This peptide modulates nucleotide exchange, inhibits Ras signaling, and is selectively toxic to Ras G12C mutant cancer cells. The prevalence of cysteine mutations in cancer suggests covalent peptides may offer a promising therapeutic approach for targeting aberrant protein interactions.
Publication reference: Yoo, D.Y. et al., ACS Chem Bio, 2020, 15(6), 1604-1612.
Coiled Coil Mimics as Pan-Ras Inhibitors
Oncogenic Ras isoforms are challenging to target due to their “undruggable” nature. Recent successes in covalent targeting illustrate possible design avenues, but many mutant Ras forms lack suitable nucleophiles, necessitating strategies for noncovalent engagement. We designed a conformationally defined proteomimetic that mimics a key binding surface of Sos, a crucial Ras effector. This proteomimetic binds both wild-type and various mutant Ras forms, modulating downstream signaling. Our compound demonstrates enhanced internalization and selective toxicity toward cancer cells with upregulated macropinocytosis. These findings, incorporating rational design principles and computational modeling, suggest new therapeutic approaches for engaging mutant Ras. The optimized proteomimetic binds Ras with high affinity, modulates nucleotide exchange, inhibits Ras-mediated signaling, and shows selective toxicity to cancer cells with oncogenic Ras mutations, offering a promising new modality for targeting these challenging proteins.
Publication reference: Hong, S.H.*, Yoo, D.Y.* et al., Proc Natl Acad Sci, 2021, 118(18), 1-11.
Macropinocytosis as a Therapeutic Route for Larger Peptidomimetics
Small molecules are attractive for targeting intracellular receptors due to favorable cellular transport properties but often lack specificity for nonenzymatic or large protein interfaces. Therapeutic peptides and proteins have emerged as effective inhibitors of protein complex formation, particularly for extracellular receptors, but their intracellular application is limited due to low proteolytic stability and poor permeation. Peptides and peptidomimetics occupy a middle space between small molecules and large proteins, combining small size and synthetic accessibility with high binding specificity. Enhancing peptide uptake can involve positively charged patches, pro-drug strategies, amide bond surrogates, and macrocyclization. Our research focuses on conformationally defined peptides that mimic protein epitopes to inhibit native complex formation. We observed that peptide uptake is cell line-dependent, with better uptake in cancer cells exhibiting high macropinocytic activity. We tested linear peptides, peptide macrocycles, stabilized helices, β-hairpin peptides, and cross-linked helix dimers across 11 cell lines and found that uptake efficiency correlated with macropinocytic activity, particularly in cells with specific signaling pathway mutations. Constrained peptides, like proteins, follow the same uptake mechanism in macropinocytic cells but are designed to resist denaturation and proteolytic degradation. Our findings suggest that cancer cells with certain mutations are suitable for studying biological pathways using peptide leads and expand the understanding of cellular uptake in cancer cells by designed peptidomimetics.
Publication reference: Yoo, D.Y., et al., J Am Chem Soc, 2020, 143(34), 11461-14471.