From DNA-encoded library (DEL) screening to in vivo validation: LILRB4 (ILT3)-targeted small molecules reprograms...

Alzheimer's disease (AD) remains a major unmet clinical challenge, with limited therapeutic strategies capable of effectively modulating neuroimmune dysfunction. Leukocyte immunoglobulin-like receptor B4 (LILRB4/ILT3) has recently emerged as an inhibitory microglial immune checkpoint implicated in ApoE-mediated suppression of amyloid-β (Aβ) clearance and inflammatory signaling, supporting its potential as a therapeutic target in AD. Here, we applied DNA-encoded library (DEL) screening of approximately 3.6 billion compounds to identify small molecule binders of LILRB4. Biophysical validation identified APX1 as a direct LILRB4 ligand with submicromolar affinity, which was further confirmed by cellular thermal shift assay (CETSA). Docking-guided mutagenesis studies defined a discrete ligand-binding interface involving key hotspot residues required for stable target engagement. Functionally, APX1 disrupted the LILRB4-ApoE interaction in orthogonal ELISA and biolayer interferometry assays. In human iPSC-derived microglia, APX1 suppressed SHP1/2 phosphorylation, attenuated NF-κB activation and IL-1β secretion, and restored Aβ42 uptake under ApoE-driven inflammatory conditions. APX1 further demonstrated favorable in vitro developability, metabolic stability, and CNS exposure properties. In the 5xFAD mouse model of AD, oral administration of APX1 improved cognitive performance, reduced cortical and hippocampal Aβ42 burden, suppressed neuroinflammatory cytokines, and decreased activated microglial populations. Collectively, these findings establish APX1 as a promising small molecule modulator of the LILRB4-ApoE signaling axis and support pharmacological targeting of neuroimmune checkpoints as a therapeutic strategy for AD.