Elaborate ligand-based modeling reveals new nanomolar heat shock protein 90α inhibitors

Journal of Chemical Information and Modeling

Volumn 50, Issue 9, 2010, Pages 1706-1723

  Al Sha'Er, Mahmoud A ^a   Taha, Mutasem O ^a  

^a UNIVERSITY OF JORDAN   (Jordan)

Author keywords

[No Author keywords available]

Indexed keywords

AGRICULTURAL CHEMICALS; AMINES; BINDING ENERGY; DISEASES; GENETIC ALGORITHMS; HEATING; LIGANDS; LINEAR REGRESSION; PHARMACODYNAMICS; PROTEINS;

BINDING POCKETS; HEAT SHOCK PROTEIN; MULTIPLE LINEAR REGRESSION ANALYSIS; NATIONAL CANCER INSTITUTE; OPTIMAL COMBINATION; PHYSICO-CHEMICAL DESCRIPTORS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS; RECEIVER OPERATING CHARACTERISTIC CURVES;

COMPUTATIONAL CHEMISTRY;

HEAT SHOCK PROTEIN 90; LIGAND;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

HSP90 HEAT-SHOCK PROTEINS; LIGANDS; MODELS, MOLECULAR; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77957221382     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100222k     Document Type: Article

References (70)

1. Prodromou, C.; Pearl, L. H. Structure and Functional Relationships of Hsp90 Curr. Cancer Drug Targets 2003, 3, 301-323 (Pubitemid 37128317)
2. Edwards, C. R. W.; Bouchier, I. A. D., Eds., Oncology. Davidson's Principles and Practice of Medicine, 16th ed.; ELBS publisher: Edinburgh, Churchill Livingstone, 1991; Chapter 7.
3. Solit, D. B.; Rosen, N. Hsp90: A Novel Target for Cancer Therapy Curr. Top. Med. Chem. 2006, 6, 1205-1214 (Pubitemid 44120915)
4. Chiosis, G.; Rodina, A.; Moulick, K. Emerging Hsp90 Inhibitors: From Discovery to Clinic Anti-Cancer Agents Med. Chem. 2006, 6, 1-8 (Pubitemid 43796652)
5. Chiosis, G.; Lucas, B.; Shtil, A.; Huezoa, H.; Rosen, N. Development of a Purine-Scaffold Novel Class of Hsp90 Binders that Inhibit the Proliferation of Cancer Cells and Induce the Degradation of Her2Tyrosine Kinase Bioorg. Med. Chem. 2002, 10, 3555-3564
6. Neckers, L. Using Natural Product Inhibitors to Validate Hsp90 as a Molecular Target in Cancer Curr. Top. Med. Chem. 2006, 6, 1163-1171 (Pubitemid 44110927)
7. Xiao, L.; Lu, X.; Ruden, D. M. Effectiveness of Hsp90 Inhibitors as Anti-Cancer Drugs Mini-Rev. Med. Chem. 2006, 6, 1137-1143 (Pubitemid 44524456)
8. Hideyuki, O.; Masami, K.; Yuichi, T.; Yumiko, U.; Jun, F.; Takayuki, N.; Shiro, S.; Makoto, S.; Shunichi., I.; Yoshinori, Y.; Endang, S. R.; Yutaka, K.; Michio, I. Conformational Significance of EH21A1-A4, Phenolic Derivatives of Geldanamycin, for Hsp90 Inhibitory Activity Bioorg. Med. Chem. Lett. 2008, 18, 1577-1580
9. Kasibhatla, S. R.; Hong, K.; Biamonte, M. A.; Busch, D. J.; Karjian, P. L.; Sensintaffar, J. L.; Kamal, A.; Lough, R. E.; Brekken, J.; Lundgren, K.; Grecko, R.; Timony, G. A.; Ran, Y.; Mansfield, R.; Fritz, L. C.; Ulm, E.; Burrows, F. J.; Boehm, M. F. Rationally Designed High-Affinity 2-Amino-6-halopurine Heat Shock Protein 90 Inhibitors That Exhibit Potent Antitumor Activity J. Med. Chem. 2007, 50, 2767-2778 (Pubitemid 46980848)
10. Hwangseo, P.; Yun-Jung, K.; Ji-Sook, H. A Novel Class of Hsp90 Inhibitors Isolated by Structure-Based Virtual Screening Bioorg. Med. Chem. Lett. 2007, 17, 6345-6349 (Pubitemid 47552807)
11. Barril, X.; Beswick, M.; Collier, A.; Drysdale, M.; Dymock, B.; Fink, A.; Grant, K.; Howes, R.; Jordan, A.; Massey, A. 4-Amino Derivatives of the Hsp90 Inhibitor CCT018159 Bioorg. Med. Chem. Lett. 2006, 16, 2543-2548
12. Barril, X.; Brough, P.; Drysdale, M.; Hubbard, R. E.; Massey, A.; Surgenor, A.; Wright, L. Structure-Based Discovery of a New Class of Hsp90 Inhibitors Bioorg. Med. Chem. Lett. 2005, 15, 5187-5191 (Pubitemid 41463644)
13. Jeffrey, R. H.; Chang, P.; Andrew, M. P.; Aaron, R. K.; Michael, D. W.; Xilu, W.; Christopher, L. L.; Jamey, C. M.; Kerry, M. S.; Russell, A. J.; Jun, C.; Paul, L. R.; Sha, J.; Stephen, K. T.; Edward, D. M.; Sarah, A. D.; Uri, S. L.; Jean, M. S.; Karl, A. W.; Diane, M. B.; Stephen, W. F.; Steven, W. E.; Philip, J. H. Discovery and Design of Novel HSP90 Inhibitors Using Multiple Fragment-based Design Strategies Chem. Biol. Drug. 2007, 70, 1-12
14. Avila, C.; Hadden, M. K.; Ma, Z.; Kornilayevc, B. A.; Yeb, Q.-Z.; Blagg, B. S. J. High-Throughput Screening for Hsp90 ATPase Inhibitors Bioorg. Med. Chem. Lett. 2006, 16, 3005-3008
15. Sakkiah, S.; Thangapandian, S.; John, S.; Won, Y. J.; Lee, K. W. 3D QSAR Pharmacophore Based Virtual Screening and Molecular Docking for Identification of Potential HSP90 Inhibitors Eur. J. Med. Chem. 2010, 45, 2132-2140
16. Chen, C. Y.-C. Bioinformatics, Chemoinformatics, And Pharmainformatics Analysis of HER2/HSP90 Dual-Targeted Inhibitors J. Taiwan Inst. Chem. E. 2010, 41, 143-149
17. Beeley; Nigel, R. A.; Sage, C. GPCRs: An Update on Structural Approaches to Drug Discovery Targets 2003, 2, 19-25 (Pubitemid 40410995)
18. Klebe, G. Virtual Ligand Screening: Strategies, Perspectives and Limitations Drug Discovery Today 2006, 11, 580-594 (Pubitemid 43912502)
19. Steuber, H.; Zentgraf, M.; Gerlach, C.; Sotriffer, C. A.; Heine, A.; Klebe, G. J. Expect the Unexpected or Caveat for Drug Designers: Multiple Structure Determinations Using Aldose Reductase Crystals Treated under Varying Soaking and Co-crystallisation Conditions Mol. Biol. 2006, 363, 174-187 (Pubitemid 44414846)
20. Stubbs, M. T.; Reyda, S.; Dullweber, F.; Moller, M.; Klebe, G.; Dorsch, D.; Mederski, W.; Wurziger, H. pH-Dependent Binding Modes Observed in Trypsin Crystals: Lessons for Structure-Based Drug Design ChemBioChem 2002, 3, 246-249 (Pubitemid 36004503)
21. DePristo, M. A.; de Bakker, P. I. W.; Blundell, T. L. Heterogeneity and Inaccuracy in Protein Structures Solved by X-ray Crystallography Structure 2004, 12, 831-838 (Pubitemid 38595771)
22. Neckers, L.; Mollapour, M.; Tsutsumi, S. The Complex Dance of the Molecular Chaperone Hsp90 Trends Biochem. Sci. 2009, 34, 223-226
23. Taha, M. O.; Bustanji, Y.; Al-Ghussein, M. A. S.; Mohammad, M.; Zalloum, H.; Al-Masri, I. M.; Atallah, N. Pharmacophore Modeling, Quantitative Structure-Activity Relationship Analysis and In Silico Screening Reveal Potent Glycogen Synthase Kinase-3β Inhibitory Activities for Cimetidine, Hydroxychloroquine and Gemifloxacin J. Med. Chem. 2008, 51, 2062-2077 (Pubitemid 351503262)
24. Taha, M. O.; Atallah, N.; Al-Bakri, A. G.; Paradis-Bleau, C.; Zalloum, H.; Younis, K.; Levesque, R. C. Discovery of New MurF Inhibitors via Pharmacophore Modeling and QSAR Analysis followed by in-silico screening Bioorg. Med. Chem. 2008, 16, 1218-1235 (Pubitemid 351191777)
25. Taha, M. O.; Bustanji, Y.; Al-Bakri, A. G.; Yousef, M.; Zalloum, W. A.; Al-Masri, I. M.; Atallah, N. Discovery of New Potent Human Protein Tyrosine Phosphatase Inhibitors via Pharmacophore and QSAR Analysis Followed by in Silico Screening J. Mol. Graphics Modell. 2007, 25, 870-884 (Pubitemid 46216122)
26. Al-masri, I. M.; Mohammad, M. K.; Taha, M. O. Discovery of DPP IV Inhibitors by Pharmacophore Modeling and QSAR Analysis Followed by in Silico Screening Chem. Med. Chem. 2008, 3, 1763-1779
27. Taha, M. O.; Dahabiyeh, L. A.; Bustanji, Y.; Zalloum, H.; Saleh, S. Combining Ligand-Based Pharmacophore Modeling, QSAR Analysis and In-Silico Screening for the Discovery of New Potent Hormone Sensitive Lipase Inhibitors J. Med. Chem. 2008, 51, 6478-6494
28. Al-Nadaf, A.; Abu Sheikha, G.; Taha, M. O. Elaborate Ligand-Based Pharmacophore Exploration and QSAR Analysis Guide the Synthesis of Novel Pyridinium-based Potent β-Secretase Inhibitory Leads Bioorg. Med. Chem. 2010, 18, 3088-3115
29. Abu-Hammad, A. M.; Taha, M. O. Pharmacophore Modeling, Quantitative Structure-Activity Relationship Analysis, And Shape-Complemented in Silico Screening Allow Access to Novel Influenza Neuraminidase Inhibitors J. Chem. Inf. Model. 2009, 49, 978-996
30. Abu Khalaf, R.; Abu Sheikha, G.; Bustanji, Y.; Taha, M. O. Discovery of New Cholesteryl Ester Transfer Protein Inhibitors via Ligand-Based Pharmacophore Modeling and QSAR Analysis Followed by Synthetic Exploration Eur. J. Med. Chem. 2010, 45, 1598-1617
31. CATALYST 4.11 Users' Manual; Accelrys Software Inc.: San Diego, CA, 2005.
32. Brough, P. A.; Aherne, W.; Barril, X.; Borgognoni, J.; Boxall, K.; Cansfield, J. E.; Cheung, K.-M. J.; Collins, I.; Davies, N. G. M.; Drysdale, M. J.; Dymock, B.; Eccles, S. A.; Finch, H.; Fink, A.; Hayes, A.; Howes, R.; Hubbard, R. E.; James, K.; Jordan, A. M.; Lockie, A.; Martins, V.; Massey, A.; Matthews, T. P.; McDonald, E.; Northfield, C. J.; Pearl, L. H.; Prodromou, C.; Ray, S.; Raynaud, F. I.; Roughley, S. D.; Sharp, S. Y.; Surgenor, A.; Walmsley, D. L.; Webb, P.; Wood, M.; Workman, P.; Wright, L. 4,5-Diarylisoxazole Hsp90 Chaperone Inhibitors: Potential Therapeutic Agents for the Treatment of Cancer J. Med. Chem. 2008, 51, 196-218
33. McDonald, E.; Jones, K.; Brough, P. A.; Drysdale, M. J.; Workman, P. Discovery and Development of Pyrazole-Scaffold Hsp90 Inhibitors Curr. Top. Med. Chem. 2006, 6, 1193-1203 (Pubitemid 44110930)
34. Gopalsamy, A.; Shi, M.; Golas, J.; Vogan, E.; Jacob, J.; Johnson, M.; Lee, F.; Nilakantan, R.; Petersen, R.; Svenson, K.; Chopra, R.; Tam, M. S.; Wen, Y.; Ellingboe, J.; Arndt, K.; Boschelli, F. Discovery of Benzisoxazoles as Potent Inhibitors of Chaperone Heat Shock Protein 90 J. Med. Chem. 2008, 51, 373-375 (Pubitemid 351252261)
35. Van Drie, J. H. Pharmacophore Discovery- Lessons Learned Curr. Pharm. Des. 2003, 9, 1649-1664
36. Poptodorov, K.; Luu, T.; Langer, T.; Hoffmann, R. In Methods and Principles in Medicinal Chemistry. Pharmacophores and Pharmacophores Searches; Hoffmann, R. D., Ed.; Wiley-VCH: Weinheim, Germany, 2006; Vol. 2, pp 17 - 47.
37. Sheridan, R. P.; Kearsley, S. K. Why Do We Need so Many Chemical Similarity Search Methods Drug Discovery Today 2002, 7, 903-911
38. Li, H.; Sutter, J.; Hoffmann, R. In Pharmacophore Perception, Development, and Use in Drug Design; Güner, O. F., Ed.; International University Line: La Jolla, CA, 2000; pp 173 - 189.
39. Sutter, J.; Güner, O.; Hoffmann, R.; Li, H.; Waldman, M. In Pharmacophore Perception, Development, and Use in Drug Design; Güner, O. F., Ed.; International University Line: La Jolla, CA, 2000; pp 501 - 511.
40. Kurogi, Y.; Güner, O. F. Pharmacophore Modeling and Three Dimensional Database Searching for Drug Design Using Catalyst Curr. Med. Chem. 2001, 8, 1035-1055 (Pubitemid 32633658)
41. Bersuker, I. B.; Bahçeci, S.; Boggs, J. E. In Pharmacophore Perception, Development, and Use in Drug Design; Güner, O. F., Ed.; International University Line: La Jolla, CA, 2000, pp 457 - 473.
42. Fischer, R. The Principle of Experimentation Illustrated by a Psycho-Physical, 8th ed.; ExpeHafner Publishing Co., Hafner Publishing: New York, 1966; Chapter II.
43. CERIUS2, QSAR Users' Manual, version 4.10; Accelrys Inc.: San Diego, CA, 2005; pp 43 - 88, 221 - 235, 237 - 250.
44. Ramsey, L. F.; Schafer, W. D. The Statistical Sleuth, 1st ed.; Wadsworth Publishing Company: Belmont, CA, 1997.
45. Clement, O. O.; Mehl, A. T. Pharmacophore Perception, Development, and Use in Drug Design. In IUL Biotechnology Series; Guner, O. F., Ed.; International University Line: La Jolla, CA, 2000; pp 71 - 84.
46. Verdonk, M. L.; Marcel, L.; Berdini, V.; Hartshorn, M. J.; Mooij, W.T. M.; Murray, C. W.; Taylor, R. D.; Watson, P. Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment J. Chem. Inf. Comput. Sci. 2004, 44, 793-806
47. Kirchmair, J.; Markt, P.; Distinto, S.; Wolber, G.; Langer, T. Evaluation of the Performance of 3D Virtual Screening Protocols: RMSD Comparisons, Enrichment Assessments, and Decoy Selection-What Can We Learn from Earlier Mistakes J. Comput.-Aided. Mol. Des. 2008, 22, 213-228 (Pubitemid 351447959)
48. Irwin, J. J.; Shoichet, B. K. ZINC-A Free Database of Commercially Available Compounds for Virtual Screening J. Chem. Inf. Comput. Sci. 2005, 45, 177-182
49. Triballeau, N.; Acher, F.; Brabet, I.; Pin, J.-P.; Bertrand, H.-O. Virtual Screening Workflow Development Guided by the "Receiver Operating Characteristic" Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4 J. Med. Chem. 2005, 48, 2534-2547 (Pubitemid 40520517)
50. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings Adv. Drug Delivery Rev. 2001, 46, 3-26 (Pubitemid 33653411)
51. Veber, D. F.; Johnson, S. R.; Cheng, H. Y.; Smith, B. R.; Ward, K. W.; Kopple, K. D. Molecular Properties That Influence the Oral Bioavailability of Drug Candidates J. Med. Chem. 2002, 45, 2615-2623
52. Ganesh, T.; Thepchatri, P.; Li, L.; Du, Y.; Fu, H.; Snyder, J. P.; Sun, A. Synthesis and SAR Study of N -[4-Hydroxy-3-(2-hydroxynaphthalene-1-yl)phenyl] -arylsulfonamides: Heat Shock Protein 90 (Hsp90) Inhibitors with Submicromolar Activity in an in Vitro Assay Bioorg. Med. Chem. Lett. 2008, 18, 4982-4987
53. Matsuda, M. M.; Moynet, D.; Molimard, M.; Dumazet, H. F.; Marit, G.; Reiffers, J.; Mossalayi, M. D. Long-Acting beta2-Adrenergic Formoterol and Salmeterol Induce the Apoptosis of B-Chronic Lymphocytic Leukaemia Cells Br. J. Hamaetol. 2004, 124, 141-150 (Pubitemid 38122185)
54. Krovat, E. M.; Langer, T. Non-Peptide Angiotensin II Receptor Antagonists: Chemical Feature Based Pharmacophore Identification J. Med. Chem. 2003, 46, 716-726 (Pubitemid 36258863)
55. Jacobsson, M.; Liden, P.; Stjernschantz, E.; Bostroem, H.; Norinder, U. Improving Structure-Based Virtual Screening by Multivariate Analysis of Scoring Data J. Med. Chem. 2003, 46, 5781-5789 (Pubitemid 37543328)
56. Gao, H.; Williams, C.; Labute, P.; Bajorath, J. Binary Quantitative Structure Activity Relationship (QSAR) Analysis of Estrogen Receptor Ligands J. Chem. Inf. Comput. Sci. 1999, 39, 164-168 (Pubitemid 129676572)
57. Lanzetta, P. A.; Alvarez, L. J.; Reinach, P. S.; Candia, O. A. An Improved Assay for Nanomole Amounts of Inorganic Phosphate Anal. Biochem. 1979, 100, 95-97 (Pubitemid 10157636)
58. Christopher, A.; Boris, A. K.; Brian, S. J. Development and Optimization of a Useful Assay for Determining Hsp90-s Inherent ATPase Activity Bioorg. Med. Chem. 2006, 14, 1134-1142
59. Ganesh, T.; Min, J.; Thepchatri, P.; Dua, Y.; Li, L.; Lewis, I.; Wilson, L.; Fu, H.; Chiosis, G.; Dingledine, R.; Liotta, D.; Snyder, J. P.; Sun, A. Discovery of Aminoquinolines As a New Class of Potent Inhibitors of Heat Shock Protein 90 (Hsp90): Synthesis, Biology, and Molecular Modeling Bioorg. Med. Chem. 2008, 16, 6903-6910
60. CERIUS2 4.10 LigandFit User Manual; Accelrys Inc.: San Diego, CA, 2000.
61. Venkatachalam, C. M.; Jiang, X.; Oldfield, T.; Waldman, M. LigandFit: A Novel Method for the Shape-Directed Rapid Docking of Ligands to Protein Active Sites J. Mol. Graphics Modell. 2003, 21, 289-307 (Pubitemid 35441326)
62. Howes, R.; Barril, X.; Dymock, B. W.; Grant, K.; NorthWeld, C. J.; Robertson, A. G. S.; Surgenor, A.; Wayne, J.; Wright, L.; James, K.; Matthews, T.; Cheung, K.-M.; McDonald, E.; Workman, P.; Drysdale, M. J. A Xuorescence Polarization Assay for Inhibitors of Hsp90 Anal. Biochem. 2006, 350, 202-213 (Pubitemid 43332820)
63. Obermann, W. M. J.; Sondermann, H.; Russo, A. A.; Pavletich, N. P.; Hart, F. U. In Vivo Function of Hsp90 Is Dependent on ATP Binding and ATP Hydrolysis J. Cell Biol. 1998, 143, 4901-910 (Pubitemid 28547391)
64. Richter, K.; Moser, S.; Hagn, F.; Friedrich, R.; Hainz, O.; Heller, M.; Schlee, S.; Kessler, H.; Reinstein, J.; Buchner, J. Intrinsic Inhibition of the Hsp90 ATPase Activity J. Biol. Chem. 2006, 281, 11301-11311 (Pubitemid 43855555)
65. Rowlands, M. G.; Newbatt, Y. M.; Prodromou, C.; Pearl, L. H.; Workman, P.; Aherne, W. High-Throughput Screening Assay for Inhibitors of Heat-Shock Protein 90 ATPase Activity Anal. Biochem. 2004, 327, 176-183 (Pubitemid 38402186)
66. Bemis, G. W.; Murcko, M. A. The Properties of Known Drugs. 1. Molecular Frameworks J. Med. Chem. 1996, 39, 2887-2893
67. Discovery Studio 2.5.5 User Guide, Accelrys Inc.: San Diego, CA, 2010.
68. Wang, M.; Shen, G.; Blagg, B. S. J. Radanamycin, a Macrocyclic Chimera of Radicicol and Geldanamycin Bioorg. Med. Chem. Lett. 2006, 16, 2459-2462
69. Chiosis, G.; Lucas, B.; Shtil, A.; Huezoa, H.; Rosen, N. Development of a Purine-Scaffold Novel Class of Hsp90 Binders that Inhibit the Proliferation of Cancer Cells and Induce the Degradation of Her2Tyrosine Kinase Bioorg. Med. Chem. 2002, 10, 3555-3564
70. Llauger, L.; He, H.; Kim, J.; Aguirre, J.; Rosen, N.; Peters, U.; Davies, P.; Chiosis, G. Evaluation of 8-Arylsulfanyl, 8-Arylsulfoxyl, and 8-Arylsulfonyl Adenine Derivatives as Inhibitors of the Heat Shock Protein 90 J. Med. Chem. 2005, 48, 2892-2905 (Pubitemid 40548103)