ArticleJournal of cheminformatics2026
Hold on tight: the kinetic profiling of opioid receptor ligands using the CORAL-MD.
Article in Journal of cheminformatics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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4 authors.
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Abstract
Opioid receptors, particularly the μ-opioid receptor, are central targets in pain management, yet opioid therapeutics remain limited by adverse effects. Recent work indicates that ligand residence time may contribute to signaling bias (a potential avenue to dissociate therapeutic effects from deleterious side effects) by stabilizing distinct receptor conformations. Here, we investigated molecular determinants underlying prolonged residence time of μ-opioid receptor ligands. Seven compounds with experimentally measured residence times and diverse signaling profiles were studied using conventional MD, random accelerated MD, and metadynamics to characterize their unbinding behavior and contact patterns with the receptor.To enable the systematic extraction and qualitative exploration of interaction features associated with residence time, we developed CORAL-MD (Correlational Analysis of Ligand-Protein Interactions)-an automated platform that analyzes MD-derived interaction profiles in relation to compound kinetics and other experimental outcomes (activity/properties). Application of CORAL-MD revealed specific interaction motifs associated with extended ligand retention, offering valuable guidance for designing safer, more selective opioid therapeutics. The tool is freely accessible at http://coralmd.if-pan.krakow.pl and it facilitates biological interpretation of MD simulations without requiring any programming expertise.Scientific contributionWe identified key ligand-receptor interaction patterns and structural determinants that contribute to prolonged complex stability, including persistent interactions with Asp147
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