In silico identification of a druggable α-genu allosteric site for small-molecule activation of α3β1 integrin: a candidate therapeutic strategy for ILNEB syndrome

Integrin α3β1, encoded in part by ITGA3 , is a laminin-binding receptor essential for epithelial adhesion in the lung, kidney, and skin. Biallelic loss-of-function mutations in ITGA3 cause interstitial lung disease, nephrotic syndrome, and epidermolysis bullosa (ILNEB), a disorder that, unlike most integrin-related diseases, would require receptor function restoration rather than inhibition. However, no small-molecule activator of α3β1 has been reported, and almost all integrin-directed small molecules are antagonists. Here, using an integrated in silico approach combining homology modeling, molecular docking, and all-atom molecular dynamics simulation (OpenMM), we sought a druggable allosteric site capable of supporting conformational activation of α3β1. We identified a candidate pocket at the α3 genu, the thigh–calf-1 hinge governing the bent-to-extended transition, and characterized the binding and conformational effects of the candidate compound pyrintegrin at this site. Across replicate 100 ns simulations of the Thr658Arg variant, pyrintegrin remained stably bound, bridging the α3 and β1 subunits through anchoring contacts to α3 Gln610 and Asp669, and β1 Arg539, in both replicates and reorganized long-range coupling to the hinge, with the ensemble showing a trend toward extension. This trend was not consistent across the two replicates; we present it as a hypothesis for enhanced sampling and experimental testing. Nonetheless, this work provides the first proof of concept for small-molecule allosteric activation of ITGA3, establishing a structural and computational foundation and motivating enhanced sampling and experimental validation for a new therapeutic strategy in ILNEB syndrome.