Conformational preferences of plumbagin with phenyl-1-thioglucoside conjugates in solution and bound to MshB determined by aromatic association

Here we show that a series of inhibitors, constructed from plumbagin conjugated to a phenyl thioglucoside via an alkyl chain of variable length, are bound in solution-favoured ligand conformations to a mycothiol biosynthetic enzyme MshB, a GlcNAc-Ins deacetylase. The kinetic studies of this ligand series show that MshB is more strongly inhibited as a function of increasing alkyl chain length. While docking studies yielded highest ranked conformations in which the ligands extended along the catalytic site, these conformations produced free energy values prone to large errors and which were inconsistent with experimental kinetic measurements. Solution-favoured conformations of the inhibitors feature a preference for intramolecular aromatic association that results in curled conformations. Free energy perturbation calculations of MshB bound to the inhibitors in the preconfigured solution-favoured curled conformations gave the same binding pattern observed in the kinetic experiments. On investigation of these conformations lodged in the catalytic domain, we found that the selective feature determining their relative binding strength was the result of an optimisation of the dispersion interactions between the ligand aromatic groups phenyl and plumbagin, and the enzyme aromatic groups His144 and Tyr142 respectively. These results show that rather than deform the preferred folded ligand solution conformation, such that the hydrophobic C-2 acyl chain is linearly projected into a buried hydrophobic rich binding cavity adjacent to the active site, MshB binds preconfigured solution inhibitor curled conformations with a preference for aromatic association.

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► Pharmacophore shows 95% inhibition of the mycothiol biosynthesis enzyme MshB.
► Docking calculations are inconsistent with experimental binding pattern.
► Free energy of the preferred solution conformations correspond with experiment.
► Preferred in solution ligand conformations are preserved upon binding to the enzyme.
► This in the context of Fischer’s ‘lock-and key’ and Koshland’s induced-fit model.