Identification of a novel aβ-overlapping binding site on the TREM2 Ectodomain engaged by the small-molecule agonist VG-3927.

Triggering receptor expressed on myeloid cells 2 (TREM2) is a microglial immune receptor genetically and functionally linked to Alzheimer's disease (AD). VG-3927, the first small-molecule TREM2 agonist to enter clinical development, has been proposed to act as a transmembrane molecular glue and positive allosteric modulator (PAM), but whether it also engages the TREM2 ectodomain has not been systematically explored. Here, we used DiffDock-L, a deep learning-based blind docking algorithm, to map potential VG-3927 binding sites across the TREM2 structure and identified a binding site within the ectodomain hydrophobic groove, a ligand-recognition surface previously implicated in Aβ and apoE binding. Microscale thermophoresis (MST) confirmed VG-3927 interaction with TREM2 under optimized polyethylene glycol 400 (PEG-400) buffer conditions and showed that Aβ1-42 binds directly to TREM2. In the presence of Aβ, the VG-3927 MST signal was reduced, supporting interference at an overlapping ectodomain binding surface. Consistently, Aβ induced a rightward shift in the VG-3927 dose-response curve in a Jurkat TREM2-DAP12 Nuclear Factor of Activated T Cells (NFAT) reporter assay and attenuated VG-3927-induced phospho-spleen tyrosine kinase (p-SYK) signaling. Together, these findings support the presence of a previously unrecognized ectodomain interaction mode for VG-3927 and suggest that amyloid-associated ligand occupancy may modulate TREM2 agonist activity in the AD microenvironment.