Peptides and small-molecules targeting signaling proteins and protein-protein interfaces

Cell-surface receptors and intracellular regulatory proteins are preeminent mediators of cellular signaling. These proteins are involved in a host of interactions and pathways, so various stages of their signaling cycles provide opportunities for unique therapeutic intervention. However, the conventional approaches of directly targeting their active sites or protein-protein interfaces via peptides and small-molecules have met with significant challenges due to the need to compete with the native ligands, lack of well-defined binding pockets in relatively featureless interfaces, or the inability to overcome the binding energy of proteins with small- molecules. Motivated by these challenges, the overarching theme of this long-term MIRA research program is to study a novel conceptual paradigm of targeting allosteric sites in selected proteins to achieve greater compound selectivity and target specificity. Specifically, we will study three classes of proteins: (1) receptor proteins from the hormonal and visual signaling pathways; (2) regulatory signaling proteins of the G-protein family; and (3) protease enzymes from SARS-CoV-2, where allosteric modulation via peptides, non-covalent and covalent small-molecules, and novel nanobodies is emerging. The discovery of these allosteric molecules has opened the avenues for designing novel therapeutic agents for treatment of metabolic and mitogenic diseases, cancers, and viral infections. In this project, we will conduct computational studies for characterizing the binding modes and mechanisms of newly discovered insulin-like peptides from viruses and venomous cone-snails as well as allosteric small molecules targeting extracellular and intracellular domains of hormonal/growth-factor receptors, allosteric modulators of the catalytic domains of photoreceptor phosphodiesterase, covalent allosteric small molecules targeting cysteine residues in regulatory signaling proteins and viral proteases, and small allosteric nanobodies targeting viral proteases. We will develop and employ a broad spectrum of computational methods spanning structural modeling, protein folding, molecular docking, interface residue mapping, mutational energetics characterization, and enhanced sampling and will integrate them with available experimental data. Overall, the research program will provide a strong basis for establishing novel therapeutic approaches for initiating, inhibiting, activating, or modulating cellular signaling outcomes.