Virtual screening and selection of drug-like compounds to block noggin interaction with bone morphogenetic proteins.
Noggin is a major natural extracellular antagonist to bone morphogenetic proteins (BMPs) which binds to BMPs and blocks binding of them to BMP-specific receptors and thus negatively regulates BMP-induced osteoblastic differentiation. Bone morphogenetic proteins (BMPs) signal through heteromeric protein complexes composed of type I and type II serine/threonine kinase receptors. Preventing the BMP-2/noggin interaction will preserve free BMP-2 and enhance the efficacy of BMP-2 to induce bone formation. This work is an attempt to use the current understanding of BMP-2, and its interaction with its receptors and antagonist to design an inhibitor of BMP-2/noggin interaction with the goal of lowering the dose of BMP-2 required in clinical applications. The crystal structure of the BMP-7/noggin complex, the BMP-2/BMP receptor IA ectodomain complex and the extracellular domain of BMP receptor II monomer are known. We modeled the BMP-2 based on the structure of its homologue BMP-7 and its binding complex with noggin. We also modeled a complex of BMP-2/BMPRIA/BMPRII by modeling BMPRII and replacing ActRIIB in the BMP-2/BMPRIA/ActRIIB complex. We then identified the binding region of noggin with BMP-2 and the receptors with BMP-2. From the analysis of structures of these complexes and modeling we identified the key amino acids present in the entire interacting surfaces among these proteins that play important physiological role in the regulation of cell differentiation and bone metabolism. By in silico screening we selected and ranked several compounds that have high theoretical scores to bind to noggin to block BMP-noggin interaction.
Laboratory of Bioinformatics and In Silico Drug Design, Biochemistry Department of Graduate Center, Queens College of City University of New York, 65-35 Kissena Blvd, Flushing, NY 11375, USA.
Shaila
S
Ahmed
Raghu Prasad Rao
RP
Metpally
Sreedhara
S
Sangadala
Boojala Vijay B
BV
Reddy
D000595:Amino Acid Sequence; D001665:Binding Sites; D052005:Bone Morphogenetic Protein Receptors, Type I / Q000737:chemistry / Q000378:metabolism; D052006:Bone Morphogenetic Protein Receptors, Type II / Q000737:chemistry / Q000378:metabolism; D019485:Bone Morphogenetic Proteins / Q000737:chemistry / Q000378:metabolism*; D002352:Carrier Proteins / Q000737:chemistry / Q000378:metabolism*; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D004364:Pharmaceutical Preparations / Q000032:analysis*; D011485:Protein Binding / Q000187:drug effects; D025941:Protein Interaction Mapping; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D054852:Small Molecule Libraries / Q000032:analysis / Q000494:pharmacology; D013499:Surface Properties / Q000187:drug effects; D014584:User-Computer Interface; D000099176:Noggin Protein
D052005:Bone Morphogenetic Protein Receptors, Type I; D052006:Bone Morphogenetic Protein Receptors, Type II; D019485:Bone Morphogenetic Proteins; D002352:Carrier Proteins; D004364:Pharmaceutical Preparations; D054852:Small Molecule Libraries; D000099176:Noggin Protein