Structure and Dynamics of High Mobility Group Box Protein 1 (HMGB1) Complexed With Inhibitors of Its Proinflammatory Activity: A Combined Nuclear Magnetic Resonance and Computational Chemistry Approach

Abstract

High-mobility group box 1 protein (HMGB1) is a nuclear component, but extracellularly it serves as a signaling molecule involved in acute and chronic inflammation, for example in sepsis and arthritis. The identification of HMGB1 inhibitors is therefore of significant experimental and clinical interest. We show that glycyrrhizin, a natural antiinflammatory and antiviral triterpene in clinical use, inhibits HMGB1 chemoattractant and mitogenic activities, and has a weak inhibitory effect on its intranuclear DNA binding function. NMR and fluorescence studies indicate that glycyrrhizin (and its analogue carbenoxolone) binds directly to HMGB1 (Kd ~ 150 μM), interacting with two shallow concave surfaces formed by the two arms of both HMG boxes, altering the internal mobility of proteins (on the millisecond timescale for Box A, on the nanosecond timescale for Box B) without significantly altering their overall diffusive properties. Due to the reduced number of experimentally determined intermolecular contacts, by means of two different computational approaches (QRFF for the Box A - carbenoxolone complex, HADDOCK data driven docking for the glycyrrhizin containing complexes) it was possible to obtain an atomic level model of the protein-ligand interactions. The presented results explain in part the anti-inflammatory properties of glycyrrhizin, and might direct the design of new derivatives with improved HMGB1-binding properties.