Assessing the inhibition of glycation of ζ-crystallin by thymoquinone: A mechanistic approach using experimental and computational methods

Abstract

The taxon-specific protein, ζ-crystallin is abundantly present in the eye lens of several ecologically divergent species like the camelids, Japanese tree frog and few hystricomorphic rodents, and also in comparatively in lesser amount in humans. The glycation of eye lens proteins is a prime cause of cataract. Here, for the first time, the inhibition of glycation of ζ-crystallin by thymoquinone (TQ) has been revealed using biochemical, biophysical and computational methods, to unravel the plausible anti-glycating mechanism of TQ. Significant inhibition in the formation of early and advanced glycation end products (AGEs), and notable recoveries in the biochemical and free amino group modifications were observed in presence of TQ. Computational studies were employed to decipher the specificity of methylglyoxal (MGO) binding with the free amino group residues. Furthermore, molecular docking was performed to explore the protective binding of TQ with ζ-crystallin which was found to be spontaneous and energetically favorable. Molecular dynamics (MD) simulation showed stable binding nature of ζ-crystallin-TQ complex. The binding energies for the ζ-crystallin-TQ complex were evaluated using molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) calculations which were significantly contributed by van der Waals forces and moderately with electrostatic and solvent accessible surface area (SASA) energy. All these findings clearly demonstrate TQ as an anti-glycating agent, facilitating its emergence as a therapeutic agent against glycation of ζ-crystallin.