Receptor-based QSAR study for a series of 3,3-disubstituted-5-aryl oxindoles and 6-aryl benzimidazol-2-ones derivatives as progesterone receptor inhibitors

References

• Mangelsdorf , DJ , Thummel , C , Beato , M , Herrlich , P , Schuetz , G , Umesono , K , Blumberg , B , Kastner , P and Mark , M . 1995 . The nuclear receptor superfamily: The second decade . Cell , 83 : 35 – 839 .
   Web of Science ®Google Scholar
• Rosano , GMC and Fini , M . 2001 . Comparative cardiovascular effects of different progestins in menopause . Int. J. Fertil. Womens Med. , 46 : 248 – 256 .
   PubMed Web of Science ®Google Scholar
• Karas , RH , van Eickels , M , Lydon , J , Roddy , S , Kwoun , M , Aronovitz , M , Baur , WE , Conneely , O , O'Malley , BW and Mendelsohn , ME . 2001 . A complex role for the progesterone receptor in the response to vascular injury . J. Clin. Invest. , 108 : 611 – 618 .
   PubMed Web of Science ®Google Scholar
• Wellington , K and Perry , CM . 2002 . Estradiol valerate/dienogest . Drugs , 62 : 491 – 504 .
   PubMed Web of Science ®Google Scholar
• Brown , A , Cheng , LN , Lin , SQ and Baird , DT . 2002 . Daily low-dose mifepristone has contraceptive potential by suppressing ovulation and menstruation: A double-blind randomized control trial of 2 and 5 mg per day for 120 days . J. Clin. Endocrinol. Metab. , 87 : 63 – 70 .
   PubMed Web of Science ®Google Scholar
• Kettel , LM , Murphy , AA , Morales , AJ , Ulmann , A , Baulieu , EE and Yen , SS . 1996 . Treatment of endometriosis with the antiprogesterone mifepristone (RU486) . Fertil. Steril. , 65 : 23 – 28 .
   PubMed Web of Science ®Google Scholar
• Klijn , JGM , Setyono-Han , B and Foekens , JA . 2000 . Progesterone antagonists and progesterone receptor modulators in the treatment of breast cancer . Steroids , 65 : 825 – 830 .
   PubMed Web of Science ®Google Scholar
• Brogden , RN , Goa , KL and Faulds , D . 1993 . Mifepristone. A review of its pharmacodynamic and pharmacokinetic properties, and therapeutic potential . Drugs , 48 : 384 – 393 .
   Web of Science ®Google Scholar
• Fuhrmann , U , Hess-Stumpp , H , Cleve , AN , Schwede , GW , Hoffmann , J , Fritzemeier , K-H and Chwalisz , K . 2000 . Synthesis and biological activity of a novel, highly potent progesterone receptor antagonist . J. Med. Chem. , 43 : 5010 – 5016 .
   PubMed Web of Science ®Google Scholar
• Kloosterboer , HJ , Deckers , GH , Schoonen , WGEJ , Hanssen , RGJM , Rose , UM , Verbost , PM , Hsiu , JG , Williams , RF and Hodgen , GD . 2000 . Preclinical experience with two selective progesterone receptor modulators on breast and endometrium . Steroids , 65 : 733 – 740 .
   PubMed Web of Science ®Google Scholar
• Tabata , Y , Iizuka , Y , Kashiwa , J , Masuda , NT , Shinei , R , Kurihara , K , Okonogi , T , Hoshiko , S and Kurata , Y . 2001 . Fungal metabolites, PF1092 compounds and their derivatives, are nonsteroidal and selective progesterone receptor modulators . Eur. J. Pharmacol. , 430 : 159 – 165 .
   PubMed Web of Science ®Google Scholar
• Palmer , S , Campen , CA , Allan , GF , Rybczynski , P , Haynes-Johnson , D , Hutchins , A , Kraft , P , Kiddoe , M , Lai , MT , Lombardi , E , Pedersen , P , Hodgen , G and Combs , DW . 2000 . Nonsteroidal progesterone receptor ligands with unprecedented receptor selectivity . J. Steroid. Biochem. , 75 : 33 – 42 .
   Google Scholar
• Hamann , LG , Winn , DT , Pooley , CLF , Tegley , CM , West , SJ , Farmer , LJ , Zhi , L , Edwards , JP , Marschke , KB , Mais , DE , Goldman , ME and Jones , TK . 1998 . Nonsteroidal progesterone receptor antagonists based on a conformationally-restricted subseries of 6-aryl-1,2-dihydro-2,2,4-trimethylquinolines . Bioorg. Med. Chem. Lett. , 8 : 2731 – 2736 .
   PubMed Web of Science ®Google Scholar
• Zhi , L , Tegley , CM , Pio , B , West , SJ , Marschke , KB , Mais , DE and Jones , TK . 2000 . Nonsteroidal progesterone receptor antagonists based on 6-thiophenehydroquinolines . Bioorg. Med. Chem. Lett. , 10 : 415 – 418 .
   PubMed Web of Science ®Google Scholar
• Pooley , CLF , Edwards , JP , Goldman , ME , Wang , MW , Marschke , KB , Crombie , DL and Jones , TK . 1998 . Discovery and preliminary SAR studies of a novel, nonsteroidal progesterone receptor antagonist pharmacophore . J. Med. Chem. , 41 : 3461 – 3466 .
   PubMed Web of Science ®Google Scholar
• Zhang , P , Terefenko , EA , Wrobel , J , Zhang , Z , Zhu , Y , Cohen , J , Marschke , KB and Mais , D . 2001 . Synthesis and progesterone receptor antagonist activities of 6-aryl benzimidazolones and benzothiazolones . Bioorg. Med. Chem. Lett. , 11 : 2747 – 2750 .
   PubMed Web of Science ®Google Scholar
• Zhang , P , Terefenko , EA , Fensome , A , Zhang , Z , Zhu , Y , Cohen , J , Winneker , R , Wrobel , J and Yardley , J . 2002 . Potent nonsteroidal progesterone receptor agonists: Synthesis and SAR study of 6-aryl benzoxazines . Bioorg. Med. Chem. Lett. , 12 : 787 – 790 .
   PubMed Web of Science ®Google Scholar
• Zhi , L , Tegley , CM , Pio , B , Edwards , JP , Motamedi , M , Jones , TK , Marschke , KB , Mais , DE , Risek , B and Schrader , WT . 2003 . 5-Benzylidene-1,2-dihydrochromeno[3,4-f]quinolines as selective progesterone receptor modulators . J. Med. Chem. , 46 : 4104 – 4112 .
   PubMed Web of Science ®Google Scholar
• Jain , N , Allan , G , Linton , O , Tannenbaum , P , Chen , X , Xu , J , Zhu , PF , Gunnet , J , Demarest , K , Lundeen , S , Murray , W and Sui , ZH . 2009 . Synthesis and SAR study of novel pseudo-steroids as potent and selective progesterone receptor antagonists . Bioorg. Med. Chem. Lett. , 19 : 3977 – 3980 .
   PubMed Web of Science ®Google Scholar
• Kern , JC , Terefenko , E , Trybulski , E , Berrodin , TJ , Cohen , J , Winneker , RC , Yudt , MR , Zhang , ZM , Zhu , YA and Zhang , PW . 2010 . 1-Methyl-1H-pyrrole-2-carbonitrile containing tetrahydronaphthalene derivatives as non-steroidal progesterone receptor antagonists . Bioorg. Med. Chem. Lett. , 20 : 4816 – 4818 .
   PubMed Web of Science ®Google Scholar
• Fensome , A , Bender , R , Cohen , J , Collins , MA , Mackner , VA , Miller , LL , Ullrich , JW , Winneker , R , Wrobel , J , Zhang , PW , Zhang , ZM and Zhu , Y . 2002 . New progesterone receptor antagonists: 3,3-disubstituted-5-aryloxindoles . Bioorg. Med. Chem. Lett. , 12 : 3487 – 3490 .
   PubMed Web of Science ®Google Scholar
• Fensome , A , Koko , M , Wrobel , J , Zhang , PW , Zhang , ZM , Cohen , J , Lundeen , S , Rudnick , K , Zhu , YA and Winneker , R . 2003 . Novel 5-aryl-1,3-dihydro-indole-2-thiones: Potent, orally active progesterone receptor agonists . Bioorg. Med. Chem. Lett. , 13 : 1317 – 1320 .
   PubMed Web of Science ®Google Scholar
• Terefenko , EA , Kern , J , Fensome , A , Wrobel , J , Zhu , Y , Cohen , J , Winneker , R , Zhang , ZM and Zhang , PW . 2005 . SAR studies of 6-aryl-1,3-dihydrobenzimidazol-2-ones as progesterone receptor antagonists . Bioorg. Med. Chem. Lett. , 15 : 3600 – 3603 .
   PubMed Web of Science ®Google Scholar
• Kern , JC , Terefenko , E , Trybulski , E , Berrodin , TJ , Cohen , J , Winneker , RC , Yudt , MR , Zhang , ZM , Zhu , Y and Zhang , PW . 2009 . 5-Aryl indanones and derivatives as non-steroidal progesterone receptor modulators . Bioorg. Med. Chem. Lett. , 19 : 6666 – 6669 .
   PubMed Web of Science ®Google Scholar
• Collins , MA , Hudak , V , Bender , R , Fensome , A , Zhang , PW , Miller , L , Winneker , RC , Zhang , ZM , Zhu , Y , Cohen , J , Unwalla , RJ and Wrobel , J . 2004 . Novel pyrrole-containing progesterone receptor modulators . Bioorg. Med. Chem. Lett. , 14 : 2185 – 2189 .
   PubMed Web of Science ®Google Scholar
• Sippl , W . 2000 . Receptor-based 3D QSAR analysis of estrogen receptor ligands - merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods . J. Comput.-Aided Mol. Des. , 14 : 559 – 572 .
   PubMed Web of Science ®Google Scholar
• Sippl , W and Holtje , HD . 2000 . Structure-based 3D-QSAR - merging the accuracy of structure-based alignments with the computational efficiency of ligand-based methods . J. Mol. Struct.: THEOCHEM. , 503 : 31 – 50 .
   Web of Science ®Google Scholar
• Costanzi , S , Tikhonova , IG , Harden , TK and Jacobson , KA . 2009 . Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands . J. Comput.-Aided Mol. Des. , 23 : 747 – 754 .
   PubMed Web of Science ®Google Scholar
• Furuhama , A , Toida , T , Nishikawa , N , Aoki , Y , Yoshioka , Y and Shiraishi , H . 2010 . Development of an ecotoxicity QSAR model for the KAshinhou Tool for Ecotoxicity (KATE) system, March 2009 version . SAR QSAR Environ. Res. , 21 : 403 – 413 .
   PubMed Web of Science ®Google Scholar
• Basak abd , SC and Mills , D . 2010 . Quantitative structure-activity relationships for cycloguanil analogs as PfDHFR inhibitors using mathematical molecular descriptors . SAR QSAR Environ. Res. , 21 : 215 – 229 .
   PubMed Web of Science ®Google Scholar
• Wang , JH , Tang , K , Hou , QQ , Cheng , XL , Dong , LH , Liu , YJ and Liu , CB . 2010 . 3D-QSAR studies on C24-monoalkylated Vitamin D3 26,23-lactones and their C2α-modified derivatives with inhibitory activity to Vitamin D receptor . Mol. Inf. , 29 : 621 – 632 .
   PubMed Web of Science ®Google Scholar
• Cramer , R.D. III , Patterson , DE and Bunce , JD . 1988 . Comparative molecular field analysis (CoMFA).1.Effect of shape on binding of steroids to carrier proteins . J. Am. Chem. Soc. , 110 : 5959 – 5967 .
   PubMed Web of Science ®Google Scholar
• Klebe , G , Abraham , U and Mietzner , T . 1994 . Molecular similarity in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity . J. Med. Chem. , 37 : 4130 – 4146 .
   PubMed Web of Science ®Google Scholar
• Leo , A , Hansch , C and Elkins , D . 1971 . Partition coefficients and their uses . Chem. Rev. , 71 : 525 – 616 .
   Web of Science ®Google Scholar
• Cho , DH , Lee , SK , Kim , BT and No , KT . 2001 . Quantitative structure–activity relationship (QSAR) study of new fluorovinyloxyacetamides . Bull. Korean Chem. Soc. , 22 : 388 – 394 .
   Web of Science ®Google Scholar
• T. A. S. H. R. SYBYL6.91 (2003), Suite 303, St Louis, MO, USA
   Google Scholar
• Trott , O and Olson , AJ . 2010 . Software news and update AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading . J. Comput. Chem. , 31 : 455 – 461 .
   PubMed Web of Science ®Google Scholar
• Morris , GM , Goodsell , DS , Halliday , RS , Huey , R , Hart , WE , Belew , RK and Olson , AJ . 1998 . Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function . J. Comput. Chem. , 19 : 1639 – 1662 .
   Web of Science ®Google Scholar
• Madauss , KP , Grygielko , ET , Deng , SJ , Sulpizio , AC , Stanley , TB , Wu , C , Short , SA , Thompson , SK , Stewart , EL , Laping , NJ , Williams , SP and Bray , JD . 2007 . A structural and in vitro characterization of asoprisnil: A selective progesterone receptor modulator . Mol. Endocrinol. , 21 : 1066 – 1081 .
   PubMed Web of Science ®Google Scholar
• Lemmen , C and Lengauer , T . 2000 . Computational methods for the structural alignment of molecules . J. Comput.-Aided Mol. Des. , 14 : 215 – 232 .
   PubMed Web of Science ®Google Scholar
• Tetko , IV , Tanchuk , VY and Villa , AEP . 2001 . Prediction of n-octanol/water partition coefficients from PHYSPROP database using artificial neural networks and E-state indices . J. Chem. Inf. Comput. Sci. , 41 : 1407 – 1421 .
   PubMedGoogle Scholar
• Richmond , NJ , Abrams , CA , Wolohan , PRN , Abrahamian , E , Willett , P and Clark , RD . 2006 . GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D . J. Comput.-Aided Mol. Des. , 20 : 567 – 587 .
   PubMed Web of Science ®Google Scholar
• Shepphird , JK and Clark , RD . 2006 . A marriage made in torsional space: Using GALAHAD models to drive pharmacophore multiplet searches . J. Comput.-Aided Mol. Des. , 20 : 763 – 771 .
   PubMed Web of Science ®Google Scholar
• Andrade , CH , Salum , LD , Pasqualoto , KFM , Ferreira , EI and Andricopulo , AD . 2008 . Three-dimensional quantitative structure-activity relationships for a large series of potent antitubercular agents . Lett. Drug Des. Discov. , 5 : 377 – 387 .
   Web of Science ®Google Scholar
• v. Desmond Molecular Dynamics System, D.E. Shaw Research, New York, 2009
   Google Scholar
• v. Maestro-Desmond Interoperability Tools, Schr-dinger, New York, 2009
   Google Scholar
• K.J. Bowers, E. Chow, H. Xu, R.O. Dror, M.P. Eastwood, B.A. Gregerson, J.L. Klepeis, I. Kolossvary, M.A. Moraes, F.D. Sacerdoti, J.K. Salmon, Y. Shan, and D.E. Shaw, Scalable algorithms for molecular dynamics simulations on commodity clusters, in Proceedings of theACM/IEEE Conference on Supercomputing(SC06), Tampa, Florida, 2006, pp. 11–17
   Google Scholar
• Essmann , U , Perera , L , Berkowitz , M , Darden , T , Lee , H and Pedersen , L . 1995 . Differential diagnosis of atypically located single or double hot spots in whole bone scanning . J. Chem. Phys. , 103 : 8577 – 8593 .
   Web of Science ®Google Scholar
• Brooks , BR , Bruccoleri , RE , Olafson , BD , States , DJ , Swaminathan , S and Karplus , M . 1983 . CHARMM: A program for macromolecular energy, minimization, and dynamics calculations . J. Comput. Chem. , 4 : 187 – 217 .
   Web of Science ®Google Scholar
• MacKerell , ADJ , Bashford , D , Bellot , M , Dunbrack , R.L. Jr , Evanseck , JD , Field , MJ , Fischer , S , Gao , J , Guo , H , Ha , S , Joseph-McCarthy , D , Kuchnir , L , Kuczera , K , Lau , FTK , Mattos , C , Michnick , S , Ngo , T , Nguyen , DT , Prodhom , B , Reiher , WE , Roux , B , Schlenkrich , M , Smith , JC , Stote , R , Straub , J , Watanabe , M , Wiórkiewicz-Kuczera , D , Yin , D and Karplus , M . 1998 . All-atom empirical potential for molecular modeling and dynamics studies of proteins . J. Phys. Chem. B , 102 : 3586 – 3616 .
   PubMed Web of Science ®Google Scholar
• Bakowies , D and Thiel , W . 1996 . Hybrid models for combined quantum mechanical and molecular mechanical approaches . J. Phys. Chem. , 100 : 10580 – 10594 .
   Web of Science ®Google Scholar
• Sherwood , P , de Vries , AH , Collins , SJ , Greatbanks , SP , Burton , NA , Vincent , MA and Hillier , IH . 1997 . Computer simulation of zeolite structure and reactivity using embedded cluster methods . Faraday Discuss. , 106 : 79 – 92 .
   Web of Science ®Google Scholar
• de Vries , AH , Sherwood , P , Collins , SJ , Rigby , AM , Rigutto , M and Kramer , GJ . 1999 . Zeolite structure and reactivity by combined quantum-chemical-classical calculations . J. Phys. Chem. B , 103 : 6133 – 6141 .
   Web of Science ®Google Scholar
• Sherwood , P , de Vries , AH , Guest , MF , Schreckenbach , G , Catlow , CRA , French , SA , Sokol , AA , Bromley , ST , Thiel , W , Turner , AJ , Billeter , S , Terstegen , F , Thiel , S , Kendrick , J Rogers , SC . 2003 . QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis . J. Mol. Struct.: THEOCHEM. , 632 : 1 – 28 .
   Web of Science ®Google Scholar
• Ahlrichs , R , Bar , M , Haser , M , Horn , H and Kolmel , C . 1989 . Electronic structure calculations on workstation computers: The program system TURBOMOLE . Chem. Phys. Lett. , 162 : 165 – 169 .
   Web of Science ®Google Scholar
• Smith , W and Forester , TR . 1996 . DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package . J. Mol. Graphics Modell. , 14 : 136 – 141 .
   PubMedGoogle Scholar
• Bringmann , G and Rummey , C . 2003 . 3D QSAR investigations on antimalarial naphthylisoquinoline alkaloids by comparative molecular similarity indices analysis (CoMSIA), based on different alignment approaches . J. Chem. Inf. Comput. Sci. , 43 : 304 – 316 .
   PubMedGoogle Scholar