An insilico approach to high altitude pulmonary edema - Molecular modeling of human beta2 adrenergic receptor and its interaction with Salmeterol & Nifedipine.
Knowledge of the three-dimensional structures of protein targets from genomic data has the potential to accelerate researches pertaining to drug discovery. Human beta(2) adrenergic receptor is a G-protein-coupled receptor with seven transmembrane helices, and is important in pharmaceutical targeting on pulmonary and cardiovascular diseases. The human beta(2) adrenergic receptor has been found to play a very important role in the pathogenesis of high altitude pulmonary edema (HAPE). In the present study, a high quality of protein 3D structure has been predicted for the human beta(2) adrenergic receptor sequence with primary accession number P07550. Homologous template protein sequence with known 3D structure was identified and the template-query protein sequence validation was done by multiple sequence alignment method. The homology model was performed through Modeller and depended on the quality of the sequence alignment by BLAST, template structure and the consolidated result performed by Gene silico meta-server. The statistical verification of the generated model was evaluated by PROCHECK which revealed that the structure modeled through Modeller to be of good quality with 84.1% of residues in the most favored region. Docking studies were carried out after modeling with two well known ligands namely Salmeterol and Nifedipine, and the fitness score revealed that Salmeterol has a higher fitness score than Nifedipine. Estimation of binding affinity by X-Score revealed that Salmeterol had -10.40 binding affinity while Nifedipine showed -9.62 binding affinity. From the present study, it can be concluded that the generated model of human beta(2) adrenergic receptor can be used for further studies related to this receptor and Salmeterol was found to have a high binding affinity with human beta(2) adrenergic receptor.
Chandramoorthi
Gayathri Devi
GD
Department of Bioinformatics, Bharathiar University, Coimbatore, 641 046 Tamilnadu, India.
Piramanayagam
Shanmughavel
S
Marimuthu
Parthiban
P
D058666:Adrenergic beta-2 Receptor Agonists; D000420:Albuterol / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D000532:Altitude Sickness; D000595:Amino Acid Sequence; D001665:Binding Sites; D001993:Bronchodilator Agents / Q000737:chemistry / Q000378:metabolism; D003198:Computer Simulation; D006801:Humans; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D015394:Molecular Structure; D008970:Molecular Weight; D009543:Nifedipine / Q000737:chemistry / Q000378:metabolism* / Q000627:therapeutic use; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011654:Pulmonary Edema / Q000209:etiology*; D018343:Receptors, Adrenergic, beta-2 / Q000737:chemistry* / Q000378:metabolism*; D015203:Reproducibility of Results; D000068299:Salmeterol Xinafoate; D017386:Sequence Homology, Amino Acid; D013059:Spectrum Analysis, Raman; D014665:Vasodilator Agents / Q000737:chemistry / Q000378:metabolism
D058666:Adrenergic beta-2 Receptor Agonists; D001993:Bronchodilator Agents; D008024:Ligands; D018343:Receptors, Adrenergic, beta-2; D014665:Vasodilator Agents; D000068299:Salmeterol Xinafoate; D009543:Nifedipine; D000420:Albuterol