Analysis of hydrophobic interactions of antagonists with the beta2-adrenergic receptor

References

• Fredriksson , R and Schiöth , HB . 2005 . The repertoire of G-protein-coupled receptors in fully sequenced genomes . Mol. Pharmacol. , 67 : 1414 – 1425 .
   PubMed Web of Science ®Google Scholar
• Wishart , DS , Knox , C , Guo , AC , Cheng , D , Shrivastava , S , Tzur , D , Gautam , B and Hassanali , M . 2008 . DrugBank: A knowledge base for drugs drug actions and drug targets . Nucleic Acids Res. , 36 : D901 – 906 .
   PubMed Web of Science ®Google Scholar
• Cherezov , V , Rosenbaum , DM , Hanson , MA , Rasmussen , SG , Thian , FS , Kobilka , TS , Choi , HJ , Kuhn , P , Weis , WI , Kobilka , BK and Stevens , RC . 2007 . High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor . Science , 318 : 1258 – 1265 .
   PubMed Web of Science ®Google Scholar
• Rasmussen , SG , Choi , HJ , Rosenbaum , DM , Kobilka , TS , Thian , FS , Edwards , PC , Burghammer , M , Ratnala , VR , Sanishvili , R , Fischetti , RF , Schertler , GF , Weis , WI and Kobilka , BK . 2007 . Crystal structure of the human beta2 adrenergic G-protein-coupled receptor . Nature , 450 : 383 – 387 .
   PubMed Web of Science ®Google Scholar
• Hanson , MA , Cherezov , V , Griffith , MT , Roth , CB , Jaakola , VP , Chien , EY , Velasquez , J , Kuhn , P and Stevens , RC . 2008 . A specific cholesterol binding site is established by the 2.8 A structure of the human beta2-adrenergic receptor . Structure , 16 : 897 – 905 .
   PubMed Web of Science ®Google Scholar
• Lands , AM , Arnold , A , MacAuliff , JP and Brown , TG . 1967 . Differentiation of receptor systems activated by sympathomimetic amines . Nature , 214 : 597 – 598 .
   PubMed Web of Science ®Google Scholar
• Weiland , GA , Minneman , KP and Molinoff , PB . 1979 . Fundamental difference between the molecular interactions of agonists and antagonists with the beta-adrenergic receptor . Nature , 281 : 114 – 117 .
   PubMed Web of Science ®Google Scholar
• Bree , F , el Tayar , N , Van de Waterbeemd , H , Testa , B and Tillement , JP . 1986 . The binding of agonists and antagonists to rat lung beta-adrenergic receptors as investigated by thermodynamics and structure-activity relationships . J. Recept. Res. , 6 : 381 – 409 .
   PubMed Web of Science ®Google Scholar
• Contreras , ML , Wolfe , BB and Molinoff , PB . 1986 . Thermodynamic properties of agonist interactions with the beta-adrenergic receptor-coupled adenylate cyclase system. I. High- and low-affinity states of agonist binding to membrane-bound beta-adrenergic receptors . J. Pharmacol. Exp. Ther. , 237 : 154 – 164 .
   PubMedGoogle Scholar
• Contreras , ML , Wolfe , BB and Molinoff , PB . 1986 . Thermodynamic properties of agonist interactions with the beta-adrenergic receptor-coupled adenylate cyclase system. II. Agonist binding to soluble beta-adrenergic receptors . J. Pharmacol. Exp. Ther. , 237 : 165 – 172 .
   PubMed Web of Science ®Google Scholar
• van de Waterbeemd , H , Smith , DA and Jones , BC . 2001 . Lipophilicity in PK design: Methyl, ethyl, futile . J. Comput.-Aided Mol. Des. , 15 : 273 – 286 .
   PubMed Web of Science ®Google Scholar
• Mannhold , R . 2005 . The impact of lipophilicity in drug research: A case report on beta-blockers . Mini Rev. Med. Chem. , 5 : 197 – 205 .
   PubMed Web of Science ®Google Scholar
• Rivail , L , Giner , M , Gastineau , M , Berthouze , M , Soulier , JL , Fischmeister , R , Lezoualc'h , F , Maigret , B , Sicsic , S and Berque-Bestel , I . 2004 . New insights into the human 5-HT4 receptor binding site: Exploration of a hydrophobic pocket . Br. J. Pharmacol. , 143 : 361 – 370 .
   Google Scholar
• Varady , J , Wu , X , Fang , X , Min , J , Hu , Z , Levant , B and Wang , S . 2003 . Molecular modeling of the three-dimensional structure of dopamine 3 (D3) subtype receptor: Discovery of novel and potent D3 ligands through a hybrid pharmacophore- and structure-based database searching approach . J. Med. Chem. , 46 : 4377 – 4392 .
   PubMed Web of Science ®Google Scholar
• Testa , B , Carrupt , PA , Gaillard , P , Billois , F and Weber , P . 1996 . Lipophilicity in molecular modeling . Pharm. Res. , 13 : 335 – 343 .
   PubMedGoogle Scholar
• Berman , HM , Westbrook , J , Feng , Z , Gilliland , G , Bhat , TN , Weissig , H , Shindyalov , IN and Bourne , PE . 2000 . The protein data bank . Nucleic Acid Res. , 28 : 235 – 242 .
   PubMed Web of Science ®Google Scholar
• Jones , G , Willett , P , Glen , RC , Leach , AR and Taylor , RD . 1997 . Development and validation of a genetic algorithm for flexible docking . J. Mol. Biol. , 267 : 727 – 748 .
   PubMed Web of Science ®Google Scholar
• MacroModel, version 9.5. Schrödinger, LLC, New York, NY, 2007; software available at http://www.schrodinger.com
   Google Scholar
• Strader , CD , Sigal , IS , Candelore , MR , Rands , E , Hill , WS and Dixon , RA . 1988 . Conserved aspartic acid residues 79 and 113 of the beta-adrenergic receptor have different roles in receptor function . J. Biol. Chem. , 263 : 10267 – 10271 .
   PubMed Web of Science ®Google Scholar
• Zuurmond , HM , Hessling , J , Blüml , K , Lohse , M and Ijzerman , AP . 1999 . Study of interaction between agonists and asn293 in helix VI of human beta(2)-adrenergic receptor . Mol. Pharmacol. , 56 : 909 – 916 .
   Google Scholar
• Kobilka , BK . 2007 . G protein coupled receptor structure and activation . Biochim. Biophys. Acta. , 1768 : 794 – 807 .
   PubMed Web of Science ®Google Scholar
• Eldridge , MD , Murray , CW , Auton , TR , Paolini , GV and Mee , RP . 1997 . Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes . J. Comp.-Aided Molec. Des. , 11 : 425 – 445 .
   PubMed Web of Science ®Google Scholar
• Glide, version 4.5. Schrödinger, LLC, New York, NY, 2007; software available at http://www.schrodinger.com
   Google Scholar
• Gaillard , P , Carrupt , PA , Testa , B and Boudon , A . 1994 . Molecular lipophilicity potential, a tool in 3D QSAR: Method and applications . J. Comput.-Aided Mol. Des. , 8 : 83 – 96 .
   PubMed Web of Science ®Google Scholar
• Efremov , RG , Chugunov , AO , Pyrkov , TV , Priestle , JP , Arseniev , AS and Jacoby , E . 2007 . Molecular lipophilicity in protein modeling and drug design . Curr. Med. Chem. , 14 : 393 – 415 .
   PubMed Web of Science ®Google Scholar
• Ghose , AK , Viswanadhan , VN and Wendoloski , JJ . 1998 . Prediction of hydrophobic (lipophilic) properties of small organic molecules using fragmental methods: An analysis of ALOGP and CLOGP methods . J. Phys. Chem. , 102 : 3762 – 3772 .
   Web of Science ®Google Scholar
• Connolly , ML . 1983 . Solvent-accessible surfaces of proteins and nucleic acids . Science , 221 : 709 – 713 .
   PubMed Web of Science ®Google Scholar
• Pyrkov , TV , Chugunov , AO , Krylov , NA , Nolde , DE and Efremov , RG . 2009 . PLATINUM: A web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes . Bioinformatics , 25 : 1201 – 1202 .
   PubMed Web of Science ®Google Scholar
• Pyrkov , TV and Efremov , RG . 2007 . A fragment-based scoring function to re-rank ATP docking results . Int. J. Mol. Sci. , 8 : 1083 – 1094 .
   Google Scholar
• Brown , EM , Fedak , SA , Woodard , CJ and Aurbach , GD . 1976 . Beta-Adrenergic receptor interactions. Direct comparison of receptor interaction and biological activity . J. Biol. Chem. , 251 : 1239 – 1246 .
   PubMed Web of Science ®Google Scholar
• Manalan , AS , Besch , HR Jr and Watanabe , AM . 1981 . Characterization of [3H](+/−) carazolol binding to beta-adrenergic receptors . Circ. Res. , 49 : 326 – 336 .
   PubMed Web of Science ®Google Scholar
• Ijzerman , AP , Aué , GH , Bultsma , T , Linschoten , MR and Timmerman , H . 1985 . Quantitative evaluation of the beta 2-adrenoceptor affinity of phenoxypropanolamines and phenylethanolamines . J. Med. Chem. , 28 : 1328 – 1334 .
   Google Scholar
• Del Carmine , R , Ambrosio , C , Sbraccia , M , Cotecchia , S , Ijzerman , AP and Costa , T . 2002 . Mutations inducing divergent shifts of constitutive activity reveal different modes of binding among catecholamine analogues to the beta(2)-adrenergic receptor . Br. J. Pharmacol. , 135 : 1715 – 1722 .
   Google Scholar
• Baker , JG . 2005 . The selectivity of beta-adrenoceptor antagonists at the human beta1, beta2 and beta3 adrenoceptors . Br. J. Pharmacol. , 144 : 317 – 322 .
   PubMed Web of Science ®Google Scholar
• Kolb , P , Rosenbaum , DM , Irwin , JJ , Fung , JJ , Kobilka , BK and Shoichet , BK . 2009 . Structure-based discovery of beta2-adrenergic receptor ligands . Proc. Natl. Acad. Sci. USA , 106 : 6843 – 6848 .
   PubMed Web of Science ®Google Scholar
• Katritch , V , Reynolds , KA , Cherezov , V , Hanson , MA , Roth , CB , Yeager , M and Abagyan , R . 2009 . Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes . J. Mol. Recognit. , 22 : 307 – 318 .
   PubMed Web of Science ®Google Scholar
• Suryanarayana , S and Kobilka , BK . 1993 . Amino acid substitutions at position 312 in the seventh hydrophobic segment of the beta 2-adrenergic receptor modify ligand-binding specificity . Mol. Pharmacol. , 44 : 111 – 114 .
   Google Scholar
• Bhattacharya , S , Hal , SE , Li , H and Vaidehi , N . 2008 . Ligand-stabilized conformational states of human beta(2) adrenergic receptor: Insight into G-protein-coupled receptor activation . Biophys. J. , 94 : 2027 – 2042 .
   PubMed Web of Science ®Google Scholar
• Strader , CD , Sigal , IS and Dixon , RA . 1989 . Structural basis of beta-adrenergic receptor function . FASEB J. , 3 : 1825 – 1832 .
   PubMed Web of Science ®Google Scholar
• Maestro, version 8.0. Schrödinger, LLC, New York, NY, 2007; software available at http://www.schrodinger.com
   Google Scholar
• Reynolds , KA , Katritch , V and Abagyan , R . 2009 . Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators . J. Comput.-Aided Mol. Des. , 23 : 273 – 288 .
   PubMed Web of Science ®Google Scholar
• Jones , G , Willett , P and Glen , RC . 1995 . Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation . J. Mol. Biol. , 245 : 43 – 53 .
   PubMed Web of Science ®Google Scholar
• Eldridge , MD , Murray , CW , Auton , TR , Paolin , GV and Mee , RP . 1997 . Empirical scoring functions: Part 1, the development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes . J. Comput.-Aided Mol. Des. , 11 : 425 – 445 .
   PubMed Web of Science ®Google Scholar
• Banks , JL , Beard , HS , Cao , Y , Cho , AE , Damm , W , Farid , R , Felts , AK , Halgren , TA , Mainz , DT , Maple , JR , Murphy , R , Philipp , DM , Repasky , MP , Zhang , LY , Berne , BJ , Friesner , RA , Gallicchio , E and Levy , RM . 2005 . Integrated modeling program, applied chemical theory (IMPACT) . J. Comput. Chem. , 26 : 1752 – 1780 .
   PubMed Web of Science ®Google Scholar
• CombiGlide, version 1.5. Schrödinger, LLC, New York, NY, 2007; software available at http://www.schrodinger.com
   Google Scholar
• Warne , T , Serrano-Vega , MJ , Baker , JG , Moukhametzianov , R , Edwards , PC , Henderson , R , Leslie , AG , Tate , CG and Schertler , GF . 2003 . Structure of a beta1-adrenergic G-protein-coupled receptor . Nature , 454 : 486 – 491 .
   Google Scholar
• Louis , SN , Rezmann-Vitti , LA , Nero , TL , Iakovidis , D , Jackman , GP and Louis , WJ . 2002 . CoMFA analysis of the human beta(1)-adrenoceptor binding affinity of a series of phenoxypropanolamines . Eur. J. Med. Chem. , 37 : 111 – 125 .
   Google Scholar
• el Tayar , N , Testa , B , van de Waterbeemd , H , Carrupt , PA and Kaumann , AJ . 1988 . Influence of lipophilicity and chirality on the selectivity of ligands for beta 1- and beta 2-adrenoceptors . J. Pharm. Pharmacol. , 40 : 609 – 612 .
   Google Scholar