title: Lead discovery for Alzheimer's disease related target protein RbAp48 from traditional Chinese medicine.
abstract: Deficiency or loss of function of Retinoblastoma-associated proteins (RbAp48) is related with Alzheimer's disease (AD), and AD disease is associated with age-related memory loss. During normal function, RbAp48 forms a complex with the peptide FOG-1 (friend of GATA-1) and has a role in gene transcription, but an unstable complex may affect the function of RbAp48. This study utilizes the world's largest traditional Chinese medicine (TCM) database and virtual screening to provide potential compounds for RbAp48 binding. A molecular dynamics (MD) simulation was employed to understand the variations after protein-ligand interaction. FOG1 was found to exhibit low stability after RbAp48 binding; the peptide displayed significant movement from the initial docking position, a phenomenon which matched the docking results. The protein structure of the other TCM candidates was not variable during MD simulation and had a greater stable affinity for RbAp48 binding than FOG1. Our results reveal that the protein structure does not affect ligand binding, and the top three TCM candidates Bittersweet alkaloid II, Eicosandioic acid, and Perivine might resolve the instability of the RbAp48-FOG1 complex and thus be used in AD therapy.
authors.affiliation: Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, College of Pharmacy, China Medical University, Taichung 40402, Taiwan.
authors.forename: Hung-Jin
authors.initials: HJ
authors.lastname: Huang
authors.affiliation: School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan.
authors.forename: Cheng-Chun
authors.initials: CC
authors.lastname: Lee
authors.affiliation: School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan ; Department of Biomedical Informatics, Asia University, Taichung 41354, Taiwan.
authors.forename: Calvin Yu-Chian
authors.identifier: 0000-0003-3306-250X
authors.initials: CY
authors.lastname: Chen
mesh_terms: D000544:Alzheimer Disease / Q000188:drug therapy* / Q000378:metabolism* / Q000473:pathology; D001665:Binding Sites; D006801:Humans; D008024:Ligands; D008516:Medicine, Chinese Traditional; D008569:Memory Disorders / Q000188:drug therapy / Q000378:metabolism / Q000473:pathology; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D046912:Multiprotein Complexes / Q000187:drug effects; D009687:Nuclear Proteins / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D056505:Retinoblastoma-Binding Protein 4 / Q000737:chemistry* / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism
chemical_list: D008024:Ligands; D046912:Multiprotein Complexes; D009687:Nuclear Proteins; C082637:RBBP4 protein, human; D056505:Retinoblastoma-Binding Protein 4; D014157:Transcription Factors; C498432:ZFPM1 protein, human