Structure-Based Virtual Screening Identifies TREM2-Targeted Small Molecules that Enhance Microglial Phagocytosis.

Triggering receptor expressed on myeloid cells 2 (TREM2) is a microglia-specific receptor whose activation promotes phagocytosis and neuroprotection in Alzheimer's disease (AD) and related neurodegenerative disorders. While therapeutic efforts have largely focused on antibodies, small-molecule TREM2 modulators remain limited. Here, we applied a structure-based virtual screening workflow targeting a putative allosteric site on TREM2, guided by PyRod-derived pharmacophores from molecular dynamics simulations. Screening of the Enamine Collection (ESC) yielded 20 candidate compounds, three of which demonstrated binding in TRIC assays. The top hit, EN020, exhibited a K_D of 14.2 µM (MST) and 35.9 µM (SPR), and significantly enhanced microglial phagocytosis in BV2 cells, outperforming the known TREM2 agonist VG-3927. A preliminary structure-activity relationship (SAR) study, including synthetic and catalog-derived analogs, highlighted a narrow tolerance for scaffold modifications, with only T2V002 retaining partial TREM2 binding affinity. This work identifies EN020 as a novel small-molecule TREM2 modulator with functional activity, providing a framework for rational optimization toward potential AD therapeutics.