title: Homology model of human retinoic acid metabolising enzyme cytochrome P450 26A1 (CYP26A1): active site architecture and ligand binding.
abstract: Homology models of cytochrome P450 RA1 (CYP26A1) were constructed using three human P450 structures, CYP2C8, CYP2C9 and CYP3A4 as templates for the model building. Using MOE software the lowest energy CYP26A1 model was then assessed for stereochemical quality and side chain environment. Further active site optimisation of the CYP26A1 model built using the CYP3A4 template was performed by molecular dynamics to generate a final CYP26A1 model. The natural substrate, all-trans-retinoic acid (atRA), and inhibitor R 15866, were docked into the model allowing further validation of the active site architecture. Using the docking studies structurally and functionally important residues were identified with subsequent characterisation of secondary structure. Multiple hydrophobic interactions, including the side chains of TRP112, PHE299, PHE222, PHE84, PHE374 and PRO371, are important for binding of atRA and R115866. Additional hydrogen bonding interactions were noted as follows: atRA-- C==O of the atRA carboxylate group and ARG86; R115866--benzothiazole nitrogen and the backbone NH of SER115.
authors.affiliation: Medicinal Chemistry, Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff CF10 3XF, UK.
authors.forename: Mohamed Sayed
authors.initials: MS
authors.lastname: Gomaa
authors.forename: Sook Wah
authors.initials: SW
authors.lastname: Yee
authors.forename: Ceri Elizabeth
authors.initials: CE
authors.lastname: Milbourne
authors.forename: Maria Chiara
authors.initials: MC
authors.lastname: Barbera
authors.forename: Claire
authors.initials: C
authors.lastname: Simons
authors.forename: Andrea
authors.initials: A
authors.lastname: Brancale
mesh_terms: D000426:Alcohol Dehydrogenase / Q000737:chemistry; D000465:Algorithms; D000595:Amino Acid Sequence; D052160:Benzothiazoles / Q000494:pharmacology; D001665:Binding Sites; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D000072516:Retinoic Acid 4-Hydroxylase; D017386:Sequence Homology, Amino Acid; D014212:Tretinoin / Q000378:metabolism*; D014230:Triazoles / Q000494:pharmacology
chemical_list: D052160:Benzothiazoles; D008024:Ligands; D014230:Triazoles; D014212:Tretinoin; D003577:Cytochrome P-450 Enzyme System; D000426:Alcohol Dehydrogenase; D000072516:Retinoic Acid 4-Hydroxylase; C406527:R 115866