Structure-Based QSAR Analysis of a Set of 4-Hydroxy-5,6-dihydropyrones as Inhibitors of HIV-1 Protease: An Application of the Receptor-Dependent (RD) 4D-QSAR Formalism

Abstract

Receptor-dependent (RD) 4D-QSAR models were constructed for a set of 39 4-hydroxy-5,6-dihydropyrone analogue HIV-1 protease inhibitors. The receptor model used in this QSAR analysis was derived from the HIV-1 protease (PDB ID ) crystal structure. The bound ligand in the active site of the enzyme, also a 4-hydroxy-5,6-dihydropyrone analogue, was used as the reference ligand for docking the data set compounds. The optimized RD 4D-QSAR models are not only statistically significant (r(2) = 0.86, q(2) = 0.80 for four- and greater-term models) but also possess reasonable predictivity based on test set predictions. The proposed "active" conformations of the docked analogues in the active site of the enzyme are consistent in overall molecular shape with those suggested from crystallographic studies. Moreover, the RD 4D-QSAR models also "capture" the existence of specific induced-fit interactions between the enzyme active site and each specific inhibitor. Hydrophobic interactions, steric shape requirements, and hydrogen bonding of the 4-hydroxy-5,6-dihydropyrone analogues with the HIV-1 protease binding site model dominate the RD 4D-QSAR models in a manner again consistent with experimental conclusions. Some possible hypotheses for the development of new lead HIV-1 protease inhibitors can be inferred from the RD 4D-QSAR models.