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Interaction Models of a Series of Oxadiazole-Substituted α-Isopropoxy Phenylpropanoic Acids Against PPARα and PPARγ: Molecular Modeling and Comparative Molecular Similarity Indices Analysis Studies

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Molecular recognition of a series of oxadiazole-substituted α-isopropoxy phenylpropanoic acids by PPARα and PPARγ was investigated by using molecular modeling and 3D-QSAR analyses. The binding models of these compounds were determined by hydrophobic property analyses and molecular docking procedure FlexX. It was found that the hydrophilic heads of these compounds form four specific conserved hydrogen bonds with the ligand binding pockets of PPARα and PPARγ, which results in fixed head conformations. On the contrary, their hydrophobic tails adopt different configurations to make contacts with hydrophobic region. The oxadiazole-ring-related hydrogen bond interactions well elucidate the structural features governing the different binding behavior of these agonists against PPARα and PPARγ. Based on these active conformations, highly predictive comparative molecular similarity indices analysis (CoMSIA) models were derived, which not only is consistent with the experimental results but also could be mapped back to the receptor topology and the ligand-receptor interaction models. The simulation results reveal the structure-activity relationship of these compounds at the molecular level and provide new insights for the design of novel potent PPARα and PPARγ dual agonists.

Keywords: 3D-QSAR analyses; Molecular Modeling; PPARα; PPARγ; ligand-receptor; oxadiazole; structure-activity relationship

Document Type: Research Article


Publication date: February 1, 2009

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.

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