Binding affinity prediction of non-peptide inhibitors of HIV-1 protease using COMBINE model introduced from peptide inhibitors.
Comparative binding energy (COMBINE) analysis method is one of the QSAR techniques for the prediction of biological activities of inhibitors based on interaction energies between ligands and proteins decomposed into each amino acid residue. We supposed that the predictive ability of the COMBINE method does not depend essentially on the molecular frameworks of ligands. To verify this idea, we performed the COMBINE analysis of non-peptide inhibitors of HIV-1 protease (HIVp), where the prediction model was constructed using inhibitors with a peptide scaffold as a training set. The predictive performance of the AMBER and CHARMm force fields was very high and at the same level (q(2)=0.75, 0.67, SDEP(cv)=0.76, 0.89, and SDEP(ex)=0.92, 0.66, respectively). The high predictive ability of the COMBINE method for the distinct scaffold compounds is due to the informative description of the interaction energies for compounds that are located at the binding site. This result suggests that COMBINE analysis may be applied not only to the lead optimization stage but also to the lead evolution stages.
Nakamura
Shinya
S
Department of Theoretical Drug Design, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
Nakanishi
Isao
I
Kitaura
Kazuo
K
D000596:Amino Acids; D001665:Binding Sites; D015195:Drug Design; D016333:HIV Protease / Q000378:metabolism*; D017320:HIV Protease Inhibitors / Q000494:pharmacology* / Q000627:therapeutic use; D006801:Humans; D008954:Models, Biological; D008958:Models, Molecular; D010455:Peptides / Q000494:pharmacology* / Q000627:therapeutic use; D021281:Quantitative Structure-Activity Relationship
D000596:Amino Acids; D017320:HIV Protease Inhibitors; D010455:Peptides; D016333:HIV Protease