title: Active site acidic residues and structural analysis of modelled human aromatase: a potential drug target for breast cancer.
abstract: This study sheds new light on the role of acidic residues present in the active site cavity of human aromatase. Eight acidic residues (E129, D222, E245, E302, D309, E379, D380 and D476) lining the cavity are identified and studied using comparative modeling, docking, molecular dynamics as well as statistical techniques. The structural environment of these acidic residues is studied to assess the stability of the corresponding carboxylate anions. Results indicate that the environment of the residues E245, E302 and D222 is most suitable for carboxylate ion formation in the uncomplexed form. However, the stability of D309, D222 and D476 anions is seen to increase on complexation to steroidal substrates. In particular, the interaction between D309 and T310, which assists proton transfer, is found to be formed following androgen/nor-androgen complexation. The residue D309 is found to be clamped in the presence of substrate which is not observed in the case of the other residues although they exhibit changes in properties following substrate binding. Information entropic analysis indicates that the residues D309, D222 and D476 have more conformational flexibility compared to E302 and E245 prior to substrate binding. Interaction similar to that between D476 and D309, which is expected to assist androgen aromatization, is proposed between E302 and E245. The inhibition of aromatase activity by 4-hydroxy androstenedione (formestane) is attributed to a critical hydrogen bond formation between the hydroxy moiety and T310/D309 as well as the large distance from D476. The results corroborate well with earlier site directed mutagenesis studies.
authors.affiliation: Molecular Modelling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, 500007, Hyderabad, Andhra Pradesh, India.
authors.forename: J Narashima
authors.initials: JN
authors.lastname: Murthy
authors.forename: M
authors.initials: M
authors.lastname: Nagaraju
authors.forename: G Madhavi
authors.initials: GM
authors.lastname: Sastry
authors.forename: A Raghuram
authors.initials: AR
authors.lastname: Rao
authors.forename: G Narahari
authors.initials: GN
authors.lastname: Sastry
mesh_terms: D024342:Amino Acids, Acidic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001141:Aromatase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites / Q000235:genetics; D001943:Breast Neoplasms / Q000188:drug therapy / Q000201:enzymology*; D003198:Computer Simulation; D004795:Enzyme Stability / Q000235:genetics; D005260:Female; D006801:Humans; D008958:Models, Molecular; D013379:Substrate Specificity / Q000235:genetics
chemical_list: D024342:Amino Acids, Acidic; D001141:Aromatase