Molecular simulations of fluconazole-mediated inhibition of sterol biosynthesis.

Invasive opportunistic fungal infections and antifungal drug resistance prompt the investigation of the underlying molecular mechanisms of the inhibition of the triazole drugs. The target of triazoles is the product of the ERG11 gene, the cytochrome P450 sterol 14α-demethylase (CYP51), which is part of the ergosterol biosynthetic pathway. In this study, molecular dynamics (MD) simulations were performed to reveal the mechanisms of fluconazole inhibitory activities in orthologs of CYP51 present in humans (Hs), and in Mycobacterium tuberculosis (Mt), Candida albicans (Ca) and Candida glabrata (Cg). The conformational diversity of the BC loop in the CYP51-Hs and CYP51-Mt structures alter the catalytic site of these enzymes when compared to the fungal CYPs, resulting in greater conformational variability of the inhibitor. Overall interaction energies are consistent with the observed affinities, but are the result of the competitive interactions of the ligand with the protein residues, the HEME group and water molecules. Specifically, protein–fluconazole interactions are more effective in CYP51-Mt due to polar interactions with the Arg96 residue. These interactions are, however, substituted in fungal enzymes by ligand–HEME interactions, which compensate for the loss of the polar bond and result in a more energetically favored binding. Therefore, the development of ligand with increased specificity to fungal enzymes should focus on the strengthening polar ligand–HEME interactions, while larger hydrophobic ligands are probably best suited to target mycobacterial and human enzymes. These differences and other ligand-binding site-specific interactions are presented and can inspire the design of new inhibitors with greater ortholog specificity.