Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear transcription factors. They are involved in mediating numerous physiological effects in humans, including glucose and lipid metabolism. PPAR alpha ligands effectively treat dyslipidemia and have significant antiinflammatory and anti-atherosclerotic activities. These effects and their ligand-dependent activity make nuclear receptors obvious targets for drug design. Here, we present the structure of the human PPAR alpha in complex with WY14643, a member of fibrate class of drug, and a widely used PPAR activator. The crystal structure of this complex suggests that WY14643 induces activation of PPAR alpha in an unusual bipartite mechanism involving conventional direct helix 12 stabilization and an alternative mode that involves a second ligand in the pocket. We present structural observations, molecular dynamics and activity assays that support the importance of the second site in WY14643 action. The unique binding mode of WY14643 reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering clues for improving the binding affinity and selectivity of ligand. We show that binding of WY14643 to PPAR alpha was associated with antiinflammatory disease in a human corneal cell model, suggesting possible applications for PPAR alpha ligands. (C) 2013 Elsevier Ltd. All rights reserved.4251628782893Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)National Institutes of Health [DK41482]Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)National Institutes of Health [DK41482]