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bioRxiv · 10.64898/2026.06.05.730337

Discovery of ILT3 (LILRB4) Small Molecule Inhibitors by Affinity Se-lection-Mass Spectrometry Reveals Druggability of a Neuroimmune Checkpoint in Alzheimers Disease

Abdel-Rahman, S.·Murugan, N.·Gabr, M.
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Abstract

Leukocyte immunoglobulin-like receptor B4 (LILRB4/ILT3) is an emerging neuroimmune checkpoint that restricts microglial activation and amyloid clearance in Alzheimers disease (AD) through ApoE-dependent signaling. Here, we establish ILT3 as a tractable small molecule target using affinity selection-mass spectrometry (AS-MS) to identify direct binders. Biophysical validation confirmed high-affinity engagement, with LT12 exhibiting nanomolar binding by MST and SPR. Computational modeling and mutagenesis defined a discrete ILT3 binding pocket, revealing a distributed interaction network critical for ligand engagement. Targeting ILT3 disrupted the ILT3-ApoE interaction, with LT12 showing potent inhibition in orthogonal biochemical assays. In human iPSC-derived microglia, ILT3 modulation attenuated SHP1/2 signaling, suppressed NF-{kappa}B activation, reduced IL-1{beta} secretion, and restored A{beta} uptake. In vivo, pharmacological targeting of ILT3 improved cognition, reduced amyloid burden, and attenuated neuroinflammation in 5xFAD mice. Together, these findings validate ILT3 as a druggable neuroimmune checkpoint and support its therapeutic targeting in AD.

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Abdel-Rahman, S., Murugan, N., Gabr, M.. 2026-06-09. Discovery of ILT3 (LILRB4) Small Molecule Inhibitors by Affinity Se-lection-Mass Spectrometry Reveals Druggability of a Neuroimmune Checkpoint in Alzheimers Disease. https://doi.org/10.64898/2026.06.05.730337

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