Computational methods for the design of potent aromatase inhibitors

Bibliography

• Siegel R, DeSantis C, Virgo K, Cancer treatment and survivorship statistics, 2012. CA Cancer J Clin 2012;62(4):220-41
   PubMed Web of Science ®Google Scholar
• Amir E, Freedman OC, Seruga B, Assessing women at high risk of breast cancer: a review of risk assessment models. J Natl Cancer Inst 2010;102(10):680-91
   PubMed Web of Science ®Google Scholar
• Vogel VG, Costantino JP, Wickerham DL, Effects of tamoxifen vs raloxifene on the risk of developing invasive breast cancer and other disease outcomes: the NSABP Study of Tamoxifen and Raloxifene (STAR) P-2 trial. JAMA 2006;295(23):2727-41
   PubMed Web of Science ®Google Scholar
• Silverman SL. New selective estrogen receptor modulators (SERMs) in development. Curr Osteoporos Rep 2010;8(3):151-3
   PubMedGoogle Scholar
• Nabholtz JM, Mouret-Reynier MA, Durando X, Comparative review of anastrozole, letrozole and exemestane in the management of early breast cancer. Expert Opin Pharmacother 2009;10(9):1435-47
   PubMed Web of Science ®Google Scholar
• Amir E, Seruga B, Niraula S, Toxicity of adjuvant endocrine therapy in postmenopausal breast cancer patients: a systematic review and meta-analysis. J Natl Cancer Inst 2011;103(17):1299-309
   PubMed Web of Science ®Google Scholar
• Nicolotti O, Giangreco I, Introcaso A, Strategies of multi-objective optimization in drug discovery and development. Expert Opin Drug Discov 2011;6(9):871-84
   PubMed Web of Science ®Google Scholar
• Nicolotti O, Giangreco I, Miscioscia TF, Improving quantitative structure-activity relationships through multiobjective optimization. J Chem Inf Model 2009;49(10):2290-302
   PubMed Web of Science ®Google Scholar
• Recanatini M, Cavalli A, Valenti P. Nonsteroidal aromatase inhibitors: recent advances. Med Res Rev 2002;22(3):282-304
   PubMed Web of Science ®Google Scholar
• Brodie AM, Schwarzel WC, Shaikh AA, The effect of an aromatase inhibitor, 4-hydroxy-4-androstene-3,17-dione, on estrogen-dependent processes in reproduction and breast cancer. Endocrinology 1977;100(6):1684-95
   PubMed Web of Science ®Google Scholar
• Graves PE, Salhanick HA. Stereoselective inhibition of aromatase by enantiomers of aminoglutethimide. Endocrinology 1979;105(1):52-7
   PubMed Web of Science ®Google Scholar
• Mason JI, Murry BA, Olcott M, Imidazole antimycotics: inhibitors of steroid aromatase. Biochem Pharmacol 1985;34(7):1087-92
   PubMed Web of Science ®Google Scholar
• Banting L, Nicholls PJ, Shaw MA, Recent developments in aromatase inhibition as a potential treatment for oestrogen-dependent breast cancer. Prog Med Chem 1989;26:253-98
   PubMedGoogle Scholar
• Cole PA, Robinson CH. Mechanism and inhibition of cytochrome P-450 aromatase. J Med Chem 1990;33(11):2933-42
   PubMed Web of Science ®Google Scholar
• Steele RE, Mellor LB, Sawyer WK, In vitro and in vivo studies demonstrating potent and selective estrogen inhibition with the nonsteroidal aromatase inhibitor CGS 16949A. Steroids 50(1-3):147-61
   PubMedGoogle Scholar
• Bhatnagar AS, Häusler A, Schieweck K, Highly selective inhibition of estrogen biosynthesis by CGS 20267, a new non-steroidal aromatase inhibitor. J Steroid Biochem Mol Biol 1990;37(6):1021-7
   PubMed Web of Science ®Google Scholar
• Dukes M, Edwards PN, Large M, The preclinical pharmacology of "Arimidex" (anastrozole; ZD1033)–a potent, selective aromatase inhibitor. J Steroid Biochem Mol Biol 1996;58(4):439-45
   PubMed Web of Science ®Google Scholar
• Vanden Bossche HV, Moereels H, Koymans LM. Aromatase inhibitors–mechanisms for non-steroidal inhibitors. Breast Cancer Res Treat 1994;30(1):43-55
   PubMed Web of Science ®Google Scholar
• Lamb HM, Adkins JC. Letrozole. A review of its use in postmenopausal women with advanced breast cancer. Drugs 1998;56(6):1125-40
   PubMed Web of Science ®Google Scholar
• Smith IE, Norton A. Fadrozole and letrozole in advanced breast cancer: clinical and biochemical effects. Breast Cancer Res Treat 1998;49(Suppl 1):S67-71; discussion S73-7
   PubMedGoogle Scholar
• Wiseman LR, Adkins JC. Anastrozole. A review of its use in the management of postmenopausal women with advanced breast cancer. Drugs Aging 1998;13(4):321-32
   PubMed Web of Science ®Google Scholar
• Lønning PE, Geisler J, Dowsett M. Pharmacological and clinical profile of anastrozole. Breast Cancer Res Treat 1998;49(Suppl 1):S53-7; discussion S73-7
   PubMedGoogle Scholar
• Wiseman LR, Spencer CM. Vorozole. Drugs Aging 1997;11(3):245-50; discussion 51-2
   PubMed Web of Science ®Google Scholar
• Graham-Lorence S, Amarneh B, White RE, A three-dimensional model of aromatase cytochrome P450. Protein Sci 1995;4(6):1065-80
   PubMed Web of Science ®Google Scholar
• Kao YC, Korzekwa KR, Laughton CA, Evaluation of the mechanism of aromatase cytochrome P450. A site-directed mutagenesis study. Eur J Biochem 2001;268(2):243-51
   PubMedGoogle Scholar
• Lang M, Batzl C, Furet P, Structure-activity relationships and binding model of novel aromatase inhibitors. J Steroid Biochem Mol Biol 1993;44(4-6):421-8
   PubMed Web of Science ®Google Scholar
• Furet P, Batzl C, Bhatnagar A, Aromatase inhibitors: synthesis, biological activity, and binding mode of azole-type compounds. J Med Chem 1993;36(10):1393-400
   PubMed Web of Science ®Google Scholar
• Recanatini M. Comparative molecular field analysis of non-steroidal aromatase inhibitors related to fadrozole. J Comput Aided Mol Des 1996;10(1):74-82
   PubMed Web of Science ®Google Scholar
• Recanatini M, Cavalli A. Comparative molecular field analysis of non-steroidal aromatase inhibitors: an extended model for two different structural classes. Bioorg Med Chem 1998;6(4):377-88
   PubMed Web of Science ®Google Scholar
• Recanatini M, Bisi A, Cavalli A, A new class of nonsteroidal aromatase inhibitors: design and synthesis of chromone and xanthone derivatives and inhibition of the P450 enzymes aromatase and 17 alpha-hydroxylase/C17,20-lyase. J Med Chem 2001;44(5):672-80
   PubMed Web of Science ®Google Scholar
• Koymans LM, Moereels H, Vanden Bossche H. A molecular model for the interaction between vorozole and other non-steroidal inhibitors and human cytochrome P450 19 (P450 aromatase). J Steroid Biochem Mol Biol 1995;53(1-6):191-7
   PubMed Web of Science ®Google Scholar
• Kao YC, Zhou C, Sherman M, Molecular basis of the inhibition of human aromatase (estrogen synthetase) by flavone and isoflavone phytoestrogens: a site-directed mutagenesis study. Environ Health Perspect 1998;106(2):85-92
   PubMed Web of Science ®Google Scholar
• Chen S, Kao YC, Laughton CA. Binding characteristics of aromatase inhibitors and phytoestrogens to human aromatase. J Steroid Biochem Mol Biol 1997;61(3-6):107-15
   PubMed Web of Science ®Google Scholar
• Cavalli A, Greco G, Novellino E, Linking CoMFA and protein homology models of enzyme-inhibitor interactions: an application to non-steroidal aromatase inhibitors. Bioorg Med Chem 2000;8(12):2771-80
   PubMed Web of Science ®Google Scholar
• Cavalli A, Recanatini M. Looking for selectivity among cytochrome P450s inhibitors. J Med Chem 2002;45(2):251-4
   PubMed Web of Science ®Google Scholar
• Cavalli A, Bisi A, Bertucci C, Enantioselective nonsteroidal aromatase inhibitors identified through a multidisciplinary medicinal chemistry approach. J Med Chem 2005;48(23):7282-9
   PubMed Web of Science ®Google Scholar
• Gobbi S, Cavalli A, Rampa A, Lead optimization providing a series of flavone derivatives as potent nonsteroidal inhibitors of the cytochrome P450 aromatase enzyme. J Med Chem 2006;49(15):4777-80
   PubMed Web of Science ®Google Scholar
• Gobbi S, Cavalli A, Negri M, Imidazolylmethylbenzophenones as highly potent aromatase inhibitors. J Med Chem 2007;50(15):3420-2
   PubMed Web of Science ®Google Scholar
• Leonetti F, Favia A, Rao A, Design, synthesis, and 3D QSAR of novel potent and selective aromatase inhibitors. J Med Chem 2004;47(27):6792-803
   PubMed Web of Science ®Google Scholar
• Neves MA, Dinis TC, Colombo G, Combining computational and biochemical studies for a rationale on the anti-aromatase activity of natural polyphenols. ChemMedChem 2007;2(12):1750-62
   PubMed Web of Science ®Google Scholar
• Goodford PJ. A computational-procedure for determining energetically favorable binding-sites on biologically important macromolecules. J Med Chem 1985;28(7):849-57
   PubMed Web of Science ®Google Scholar
• Neves MA, Dinis TC, Colombo G, Biochemical and computational insights into the anti-aromatase activity of natural catechol estrogens. J Steroid Biochem Mol Biol 2008;110(1-2):10-17
   PubMed Web of Science ®Google Scholar
• Schuster D, Laggner C, Steindl TM, Pharmacophore modeling and in silico screening for new P450 19 (aromatase) inhibitors. J Chem Inf Model 46(3):1301-11
   PubMed Web of Science ®Google Scholar
• Bak A, Polanski J. Modeling robust QSAR 3: SOM-4D-QSAR with iterative variable elimination IVE-PLS: application to steroid, azo dye, and benzoic acid series. J Chem Inf Model 47(4):1469-80
   PubMed Web of Science ®Google Scholar
• Su B, Tian R, Darby MV, Novel sulfonanilide analogs decrease aromatase activity in breast cancer cells: synthesis, biological evaluation, and ligand-based pharmacophore identification. J Med Chem 2008;51(5):1126-35
   PubMed Web of Science ®Google Scholar
• Oprea TI, García AE. Three-dimensional quantitative structure-activity relationships of steroid aromatase inhibitors. J Comput Aided Mol Des 1996;10(3):186-200
   PubMed Web of Science ®Google Scholar
• Neves MA, Dinis TC, Colombo G, Fast three dimensional pharmacophore virtual screening of new potent non-steroid aromatase inhibitors. J Med Chem 2009;52(1):143-50
   PubMed Web of Science ®Google Scholar
• Neves MA, Totrov M, Abagyan R. Docking and scoring with ICM: the benchmarking results and strategies for improvement. J Comput Aided Mol Des 2012;26(6):675-86
   PubMed Web of Science ®Google Scholar
• Clement OO, Freeman CM, Hartmann RW, Three dimensional pharmacophore modeling of human CYP17 inhibitors. Potential agents for prostate cancer therapy. J Med Chem 2003;46(12):2345-51
   PubMed Web of Science ®Google Scholar
• Jacobs C, Frotscher M, Dannhardt G, 1-imidazolyl(alkyl)-substituted di- and tetrahydroquinolines and analogues: syntheses and evaluation of dual inhibitors of thromboxane A(2) synthase and aromatase. J Med Chem 2000;43(9):1841-51
   PubMed Web of Science ®Google Scholar
• Kim YW, Hackett JC, Brueggemeier RW. Synthesis and aromatase inhibitory activity of novel pyridine-containing isoflavones. J Med Chem 2004;47(16):4032-40
   PubMed Web of Science ®Google Scholar
• Hackett JC, Kim YW, Su B, Brueggemeier RW. Synthesis and characterization of azole isoflavone inhibitors of aromatase. Bioorg Med Chem 2005;13(12):4063-70
   PubMed Web of Science ®Google Scholar
• Lipinski CA, Lombardo F, Dominy BW, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 2001;46(1-3):3-26
   PubMed Web of Science ®Google Scholar
• Neves MA, Dinis TC, Colombo G, An efficient steroid pharmacophore-based strategy to identify new aromatase inhibitors. Eur J Med Chem 2009;44(10):4121-7
   PubMed Web of Science ®Google Scholar
• Stauffer F, Furet P, Floersheimer A, New aromatase inhibitors from the 3-pyridyl arylether and 1-aryl pyrrolo[2,3-c]pyridine series. Bioorg Med Chem Lett 2012;22(5):1860-3
   PubMed Web of Science ®Google Scholar
• Balunas MJ, Kinghorn AD. Natural compounds with aromatase inhibitory activity: an update. Planta Med 2010;76(11):1087-93
   PubMed Web of Science ®Google Scholar
• Le Bail JC, Pouget C, Fagnere C, Chalcones are potent inhibitors of aromatase and 17beta-hydroxysteroid dehydrogenase activities. Life Sci 2001;68:751-61
   PubMed Web of Science ®Google Scholar
• Blanco JG, Gil RR, Bocco JL, Aromatase inhibition by an 11,13-dihydroderivative of a sesquiterpene lactone. J Pharmacol Exp Ther 2001;297:1099-105
   PubMed Web of Science ®Google Scholar
• Ghosh D, Griswold J, Erman M, Structural basis for androgen specificity and oestrogen synthesis in human aromatase. Nature 2009;457(7226):219-23
   PubMed Web of Science ®Google Scholar
• Favia AD, Cavalli A, Masetti M, Three-dimensional model of the human aromatase enzyme and density functional parameterization of the iron-containing protoporphyrin IX for a molecular dynamics study of heme-cysteinato cytochromes. Proteins 2006;62(4):1074-87
   PubMed Web of Science ®Google Scholar
• Hong Y, Yu B, Sherman M, Molecular basis for the aromatization reaction and exemestane-mediated irreversible inhibition of human aromatase. Mol Endocrinol 2007;21(2):401-14
   PubMed Web of Science ®Google Scholar
• Karkola S, Höltje HD, Wähälä K. A three-dimensional model of CYP19 aromatase for structure-based drug design. J Steroid Biochem Mol Biol 105(1-5):63-70
   PubMed Web of Science ®Google Scholar
• Ludwig M, Beck A, Wickert L, Female pseudohermaphroditism associated with a novel homozygous G-to-A (V370-to-M) substitution in the P-450 aromatase gene. J Pediatr Endocrinol Metab 1998;11(5):657-64
   PubMed Web of Science ®Google Scholar
• Woo LW, Bubert C, Sutcliffe OB, Dual aromatase-steroid sulfatase inhibitors. J Med Chem 2007;50(15):3540-60
   PubMed Web of Science ®Google Scholar
• Jackson T, Woo LW, Trusselle MN, Non-steroidal aromatase inhibitors based on a biphenyl scaffold: synthesis, in vitro SAR, and molecular modelling. ChemMedChem 2008;3(4):603-18
   PubMed Web of Science ®Google Scholar
• Graham-Lorence S, Peterson JA. P450s: structural similarities and functional differences. FASEB J 1996;10(2):206-14
   PubMed Web of Science ®Google Scholar
• Numazawa M, Kamiyama T, Tachibana M, Synthesis and structure-activity relationships of 6-substituted androst-4-ene analogs as aromatase inhibitors. J Med Chem 1996;39(11):2245-52
   PubMed Web of Science ®Google Scholar
• Berman H, Henrick K, Nakamura H. Announcing the worldwide Protein Data Bank. Nat Struct Biol 2003;10(12):980
   PubMedGoogle Scholar
• Loge C, Le Borgne M, Marchand P, Three-dimensional model of cytochrome P450 human aromatase. J Enzyme Inhib Med Chem 2005;20(6):581-5
   PubMed Web of Science ®Google Scholar
• Thompson EA, Siiteri PK. Utilization of oxygen and reduced nicotinamide adenine dinucleotide phosphate by human placental microsomes during aromatization of androstenedione. J Biol Chem 1974;249(17):5364-72
   PubMed Web of Science ®Google Scholar
• Simpson ER, Mahendroo MS, Means GD, Aromatase cytochrome P450, the enzyme responsible for estrogen biosynthesis. Endocr Rev 1994;15(3):342-55
   PubMed Web of Science ®Google Scholar
• Ghosh D, Lo J, Morton D, Novel aromatase inhibitors by structure-guided design. J Med Chem 2012;55(19):8464-76
   PubMed Web of Science ®Google Scholar
• Zhao Y, White MA, Muralidhara BK, Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction. J Biol Chem 2006;281(9):5973-81
   PubMed Web of Science ®Google Scholar
• Friesner RA, Banks JL, Murphy RB, Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004;47(7):1739-49
   PubMed Web of Science ®Google Scholar
• Halgren TA, Murphy RB, Friesner RA, Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 2004;47(7):1750-9
   PubMed Web of Science ®Google Scholar
• Cosconati S, Forli S, Perryman AL, Virtual screening with autodock: theory and practice. Expert Opin Drug Discov 2010;5(6):597-607
   PubMed Web of Science ®Google Scholar
• Sherman W, Day T, Jacobson MP, Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 2006;49(2):534-53
   PubMed Web of Science ®Google Scholar
• Varela C, Tavares da Silva EJ, Amaral C, New structure-activity relationships of A- and D-ring modified steroidal aromatase inhibitors: design, synthesis, and biochemical evaluation. J Med Chem 2012;55(8):3992-4002
   PubMed Web of Science ®Google Scholar
• Stefanachi A, Favia AD, Nicolotti O, Design, synthesis, and biological evaluation of imidazolyl derivatives of 4,7-disubstituted coumarins as aromatase inhibitors selective over 17-α-hydroxylase/C17-20 lyase. J Med Chem 2011;54(6):1613-25
   PubMed Web of Science ®Google Scholar
• Caporuscio F, Rastelli G, Imbriano C, Structure-based design of potent aromatase inhibitors by high-throughput docking. J Med Chem 2011;54(12):4006-17
   PubMed Web of Science ®Google Scholar
• Bottegoni G, Kufareva I, Totrov M, Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem 2009;52(2):397-406
   PubMed Web of Science ®Google Scholar
• Bottegoni G, Rocchia W, Rueda M, Systematic exploitation of multiple receptor conformations for virtual ligand screening. PLoS One 2011;6(5):e18845
   PubMed Web of Science ®Google Scholar
• Rueda M, Bottegoni G, Abagyan R. Recipes for the selection of experimental protein conformations for virtual screening. J Chem Inf Model 2010;50(1):186-93
   PubMed Web of Science ®Google Scholar
• Galeazzi R, Massaccesi L. Insight into the binding interactions of CYP450 aromatase inhibitors with their target enzyme: a combined molecular docking and molecular dynamics study. J Mol Model 2012;18(3):1153-66
   PubMed Web of Science ®Google Scholar
• Shahrokh K, Orendt A, Yost GS, Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle. J Comput Chem 2012;33(2):119-33
   PubMed Web of Science ®Google Scholar
• Röhrig UF, Grosdidier A, Zoete V, Docking to heme proteins. J Comput Chem 2009;30(14):2305-15
   PubMed Web of Science ®Google Scholar
• Maurelli S, Chiesa M, Giamello E, Direct spectroscopic evidence for binding of anastrozole to the iron heme of human aromatase. Peering into the mechanism of aromatase inhibition. Chem Commun (Camb) 2011;47(38):10737-9
   PubMed Web of Science ®Google Scholar
• Poulos TL, Howard AJ. Crystal structures of metyrapone- and phenylimidazole-inhibited complexes of cytochrome P-450cam. Biochemistry 1987;26(25):8165-74
   PubMed Web of Science ®Google Scholar
• Favia AD, Masetti M, Recanatini M, Substrate binding process and mechanistic functioning of type 1 11β-hydroxysteroid dehydrogenase from enhanced sampling methods. PLoS One 2011;6(9):e25375
   PubMed Web of Science ®Google Scholar
• Bussi G, Laio A, Parrinello M. Equilibrium free energies from nonequilibrium metadynamics. Phys Rev Lett 2006;96(9):090601
   Google Scholar
• Laio A, Parrinello M. Escaping free-energy minima. Proc Natl Acad Sci USA 2002;99(20):12562-6
   PubMed Web of Science ®Google Scholar
• Kumar S, Bouzida D, Swendsen RH, The weighted histogram analysis method for free-energy calculations on biomolecules. 1. the method. J Comput Chem 1992;13(8):1011-21
   Web of Science ®Google Scholar
• Park S, Schulten K. Calculating potentials of mean force from steered molecular dynamics simulations. J Chem Phys 2004;120(13):5946-61
   PubMed Web of Science ®Google Scholar
• Tribello GA, Ceriotti M, Parrinello M. A self-learning algorithm for biased molecular dynamics. Proc Natl Acad Sci USA 2010;107(41):17509-14
   PubMed Web of Science ®Google Scholar
• Favia AD. Theoretical and computational approaches to ligand-based drug discovery. Front Biosci 2011;16:1276-90
   Web of Science ®Google Scholar
• Sgrignani J, Magistrato A. Influence of the membrane lipophilic environment on the structure and on the substrate access/egress routes of the human aromatase enzyme. A computational study. J Chem Inf Model 2012;52(6):1595-606
   PubMed Web of Science ®Google Scholar
• Colizzi F, Perozzo R, Scapozza L, Single-molecule pulling simulations can discern active from inactive enzyme inhibitors. J Am Chem Soc 2010;132(21):7361-71
   PubMed Web of Science ®Google Scholar
• Conejo-García A, Pisani L, Núñez Mdel C, Homodimeric bis-quaternary heterocyclic ammonium salts as potent acetyl- and butyrylcholinesterase inhibitors: a systematic investigation of the influence of linker and cationic heads over affinity and selectivity. J Med Chem 2011;54(8):2627-45
   PubMed Web of Science ®Google Scholar
• Nicolotti O, Carotti A. QSAR and QSPR studies of a highly structured physicochemical domain. J Chem Inf Model 46(1):264-76
   PubMed Web of Science ®Google Scholar
• Nicolotti O, Miscioscia TF, Carotti A, An integrated approach to ligand- and structure-based drug design: development and application to a series of serine protease inhibitors. J Chem Inf Model 2008;48(6):1211-26
   PubMed Web of Science ®Google Scholar
• Harvey MJ, De Fabritiis G. High-throughput molecular dynamics: the powerful new tool for drug discovery. Drug Discov Today 2012;17(19-20):1059-62
   PubMed Web of Science ®Google Scholar
• Sen K, Hackett JC. Coupled electron transfer and proton hopping in the final step of cyp19-catalyzed androgen aromatization. Biochemistry 2012;51(14):3039-49
   PubMed Web of Science ®Google Scholar
• Hong YY, Hongzhi L, Jingjing Y, Epitope characterization of an aromatase monoclonal antibody suitable for the assessment of intratumoral aromatase activity. PLoS One 2009;4(11):e8050
   PubMedGoogle Scholar