Dynamics of the α2-chimaerin-Rac1 interface in Duane retraction syndrome and computational design of candidate probes

Authors

Shah, A., Bhargava, Y.

Abstract

Duane retraction syndrome (DRS) is an eye movement disorder caused by gain-of-function mutations in CHN1, which encodes 2-chimaerin. Mutations in CHN1 cause excessive Rac1 suppression during axon guidance, but the dynamics of the 2-chimaerin-Rac1 interaction remain largely uncharacterized. We simulated the CHN1-Rac1 complex with all-atom molecular dynamics to characterize this interface. An Ile420-Arg445 hydrophobic ridge is the persistent core, while the 304-310 patch carrying the catalytic arginine finger scores lower and varies more between replicates. We screened the BioGRID partners of CHN1 with AlphaFold3 and ipSAE; only Rac1, NCK1, and NCK2 gave high-confidence predicted complexes. Rac1 and NCK1 stayed bound in every replicate, and NCK2 in two of three. The MM-GBSA interface {Delta}G for Rac1 was -20 {+/-} 10 kcal/mol. We also explored how the surface could be probed by small molecules and peptides. To identify candidate chemical probes, we sampled natural products from COCONUT, refined top hits through CReM fragment growth, and generated peptides with BoltzGen. Prioritized ligands were evaluated with molecular dynamics and MM-PBSA endpoint free-energy calculations. Across 6 {micro}s of cumulative simulation, the contact network defining the CHN1-Rac1 interface matched ligand and peptide engagement. These results define the key residues of the CHN1-Rac1 interface and identify candidate chemical probes for testing their role experimentally.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 04 Aug 2026.

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