Affinity Crosslinking of Y1036 to Nerve Growth Factor Identifies Pharmacological Targeting Domain for Small Molecule Neurotrophin Antagonists

Classically, small molecule antagonists have targeted membrane bound receptors and intracellular enzyme targets. While this drug discovery strategy is extremely successful, the number of new chemical entities in the pharmaceutical pipeline is diminishing and complementary strategies are in need. A particularly attractive therapeutic strategy is to neutralize soluble signalling proteins using small molecules. Small molecule-based technologies have the potential to sufficiently alter the molecular topology of a given ligand and inhibit ligand/receptor interactions—effectively neutralizing the ligand’s signalling capacity. Recent technical advances in the field of structural biology have enabled the elucidation of ligand/receptor complexes at atomic resolution enabling a detailed appreciation of the molecular interactions governing ligand-mediated receptor activation. Exploiting molecular modeling techniques to study these signalling complexes allows for a paradigm shift from “receptorcentric” to “ligandcentric” screening strategies. Nerve growth factor (NGF) is a prototypical protein signalling ligand, which binds two receptors, TrkA and p75NTR. We first explore the molecular landscape governing the ligand/receptor interactions of NGF/TrkA and NGF/p75 structures. Next, we use the recently reported NGF neutralizing small-molecule, Y1036, as an affinity probe to determine residues in proximity to the pharmacological targeting domain of NGF and perform theoretical docking experiments to predict the residues which comprise distinct pharmacological targeting domains on the surface of NGF. Exploiting such strategies may facilitate “ligandcentric” drug discovery and could further the development of a trophic-factor-selective compound such as a BDNF-selective antagonist.