Comparison data sets for benchmarking QSAR methodologies in lead optimization

Journal of Chemical Information and Modeling

Volumn 49, Issue 7, 2009, Pages 1810-1820

  Mittal, Ruchi R ^a   McKinnon, Ross A ^a   Sorich, Michael J ^a  

^a UNIVERSITY OF SOUTH AUSTRALIA   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMISTRY;

3D-QSAR; DIVERSE DATA SETS; LEAD OPTIMIZATION; PREDICTIVE ABILITIES;

CHEMICAL ENGINEERING;

ARTICLE; CHEMICAL STRUCTURE; COMPARATIVE STUDY; DRUG DEVELOPMENT; FACTUAL DATABASE; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

DATABASES, FACTUAL; DRUG DISCOVERY; MOLECULAR STRUCTURE; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 68149101393     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci900117m     Document Type: Article

References (60)

1. Cramer, R. D. Topomer CoMFA: A Design Methodology for Rapid Lead Optimization. J. Med. Chem. 2003, 46, 374-388.
2. Giersiefen, H.; Hilgenfeld, R.; Hillisch, A. Modem Methods of Drug Discovery: An Introduction. In Modern Methods of Drug Discovery; Hilgenfeldl, A. H. R., Ed.; Birkhäuser Verlag: Basel, 2003; pp 1-18.
3. Kim, K. H.; Greco, G.; Novellino, E. A Critical Review of Recent CoMFA Applications. Perspect. Drug Discovery Des. 1998, 12, 257-315.
4. Kubinyi, H. QSAR and 3D QSAR in Drug Design: 1. Methodology. Drug Discovery Today 1997, 2, 457-467.
5. Sutherland, J. J.; O'Brien, L. A.; Weaver, D. F. A Comparison of Methods for Modeling Quantitative Structure-Activity Relationships. J. Med. Chem. 2004, 47, 5541-5554.
6. Akamatsu, M. Current State and Perspectives of 3d-QSAR. Curr. Toy. Med. Chem. 2002, 2, 1381-1394.
7. Yang, G. F.; Huang, X. Development of Quantitative Structure-Activity Relationships and Its Application in Rational Drug Design. Curr. Pharm. Des. 2006, 12, 4601-4611.
8. Cramer, R. D.; Patterson, D. E.; Bunce, J. D. Comparative Molecular Field Analysis (Comfa). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
9. Coats, E. A. The CoMFA Steroids as a Benchmark Dataset for Development of 3D QSAR Methods. Perspect. Drug Discovery Des. 1998, 12, 199-213.
10. Dias, M.; Mittal, R.; McKinnon, R.; Sorich, M. Systematic Statistical Comparison of Comparative Molecular Similarity Indices Analysis Molecular Fields for Computer-Aided Lead Optimization. J. Chem. Inf. Model. 2006, 46, 2015-2021.
11. Mittal, R. R.; Harris, L.; McKinnon, R. A.; Sorich, M. J. Partial Charge Calculation Method Affects CoMFA QSAR Prediction Accuracy. J. Chem. Inf. Model. 2009, 49, 704-709.
12. Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking Sets for Molecular Docking. J. Med. Chem. 2006, 49, 6789-6801.
13. Fukunishi, Y.; Nakamura, H. A New Method for in-Silico Drug Screening and Similarity Search Using Molecular Dynamics Maximum Volume Overlap (Md-Mvo) Method. J. Mol. Graphics 2009, 27, 628-636.
14. Tiikkainen, P.; Poso, A.; Kallioniemi, O. Comparison of Structure Fingerprint and Molecular Interaction Field Based Methods in Explaining Biological Similarity of Small Molecules in Cell-Based Screens. J. Comput.-Aided Mol. Des. 2009, 23, 227-239.
15. Vainio, M. J.; Puranen, J. S.; Johnson, M. S. Shaep: Molecular Overlay Based on Shape and Electrostatic Potential. J. Chem. Inf. Model. 2009, 49, 492-502.
16. von Korff, M.; Freyss, J.; Sander, T. Comparison of Ligand- and Structure-Based Virtual Screening on the Dud Data Set. J. Chem. Inf. Model. 2009, 49, 209-231.
17. Filter, version2.0.1; OpenEye Scientific Software Inc.: Santa Fe, NM, USA, 2007.
18. R: A Language and Environment for Statistical Computing, version 2.9.0; R Foundation for Statistical Computing: Vienna, Austria, 2005.
19. Wang, R. X.; Gao, Y.; Liu, L.; Lai, L. H. All-Orientation Search and All-Placement Search in Comparative Molecular Field Analysis. J. Mol. Model. 1998, 4, 276-283.
20. Liang, H.; Wu, X.; Guziec, L. J.; Guziec, F. S.; Larson, K. K.; Lang, J.; Yalowich, J. C.; Hasinoff, B. B. A Structure-Based 3d-QSAR Study of Anthrapyrazole Analogues of the Anticancer Agents Losoxantrone and Piroxantrone. J. Chem. Inf. Model. 2006, 46, 1827-1835.
21. Welch, W.; Ahmad, S.; Airey, J. A.; Gerzon, K.; Humerickhouse, R. A.; Besch, H. R.; Ruest, L.; Deslongchamps, P.; Sutko, J. L. Structural Determinants of High-Affinity Binding of Ryanoids to the Vertebrate Skeletal-Muscle Ryanodine Receptor - a Comparative Molecular-Field Analysis. Biochemistry 1994, 33, 6074-6085.
22. Sybyl, version 8.0; Tripos Inc.: 1699 South Hanley Rd., St. Louis, MO 63144, USA, 2008.
23. Cramer, R. D., III.; Patterson, D. E.; Bunce, J. D. Comparative Molecular Field Analysis (Comfa). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
24. Blackman, B.; Georg, G. L.; Lushington, G. H. CoMSIA/QSAR Models for Vacuolar (H+) Atpase Inhibition by Selected Benzoate and Benzolactone Species. Lett. Drug Des. Discovery 2006, 3, 104-107.
25. Jensen, L. H.; Liang, H.; Shoemaker, R.; Grauslund, M.; Sehested, M.; Hasinoff, B. B. A 3d-QSAR Study of the Inhibition of the Atpase Activity and the Strand Passing Catalytic Activity of Topoisomerase liá by Substituted Purine Analogs. Mol. Pharmacol. 2006, 70, 1503-1513.
26. Martin, Y. C.; Bures, M. G.; Danaher, E. A.; DeLazzer, J.; Lico, I.; Pavlik, P. A. A Fast New Approach to Pharmacophore Mapping and Its Application to Dopaminergic and Benzodiazepine Agonists. J. Comput.-Aided Mol. Des. 1993, 7, 83-102.
27. Belvisi, L.; Bravi, G.; Catalano, G.; Mabilia, M.; Salimbeni, A.; Scolastico, C. A 3D QSAR CoMFA Study of Non-Peptide Angiotensin Ii Receptor Antagonists. J. Comput.-Aided Mol. Des. 1996, 10, 567-582.
28. Bang, S. J.; Cho, S. J. Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Index Analysis (CoMSIA) Study of Mutagen X. Bull. Korean Chem. Soc. 2004, 25, 1525-1530.
29. Srivani, P.; Kiran, K.; Sastry, G. N. Understanding the Structural Requirements of Triarylethane Analogues Towards Pde-Iv Inhibitors: A Molecular Modeling Study. Indian J. Chem., Sect. A: Inorg., Bioinorg., Phys., Theor. Anal. Chem. 2006, 45, 68-76.
30. Guo, J. X.; Wu, J. J. Q.; Wright, J. B.; Lushington, G. H. Mechanistic Insight into Acetylcholinesterase Inhibition and Acute Toxicity of Organophosphorus Compounds: A Molecular Modeling Study. Chem. Res. Toxicol. 2006, 19, 209-216.
31. Salo, O. M. H.; Savinainen, J. R.; Parkkari, T.; Nevalainen, T.; Lahtela-Kakkonen, M.; Gynther, J.; Laitinen, J. T.; Jarvinen, T.; Poso, A. 3d-QSAR Studies on Cannabinoid Cb1 Receptor Agonists: G-Protein Activation as Biological Data. J. Med. Chem. 2006, 49, 554-566.
32. Bostrom, J.; Böhm, M.; Gundertofte, K.; Klebe, G. A 3D QSAR Study on a Set of Dopamine D-4 Receptor Antagonists. J. Chem. Inf. Comput. Sci. 2003, 43, 1020-1027.
33. Melville, J. L.; Hirst, J. D. On the Stability of CoMFA Models. J. Chem. Inf. Comput. Sci. 2004, 44, 1294-1300.
34. Li, W.; Tang, Y.; Zheng, Y. L.; Qiu, Z. B. Molecular Modeling and 3d-QSAR Studies of Indolomorphinan Derivatives as Kappa Opioid Antagonists. Bioorg. Med. Chem. 2006, 14, 601-610.
35. Hu, X.; Stebbins, C. E. Molecular Docking and 3d-QSAR Studies of Yersinia Protein Tyrosine Phosphatase Yoph Inhibitors. Bioorg. Med. Chem. 2005, 13, 1101-1109.
36. Melville, J. L.; Lovelock, K. R. J.; Wilson, C.; Allbutt, B.; Burke, E. K.; Lygo, B.; Hirst, J. D. Exploring Phase-Transfer Catalysis with Molecular Dynamics and 3d/4d Quantitative Structure-Selectivity Relationships. J. Chem Inf. Model. 2005, 45, 971-981.
37. Chern, J. H.; Lee, C. C.; Chang, C. S.; Lee, Y. C.; Tai, C. L.; Lin, Y. T.; Shia, K. S.; Lee, C. Y.; Shih, S. R. Synthesis and Antienteroviral Activity of a Series of Novel, Oxime Ether-Containing Pyridyl Imidazolidinones. Bioorg. Med. Chem. Lett. 2004, 14, 5051-5056.
38. Ke, Y. Y.; Lin, T. H. Modeling the Ligand-Receptor Interaction for a Series of Inhibitors of the Capsid Protein of Enterovirus 71 Using Several Three-Dimensional Quantitative Structure-Activity Relationship Techniques. J. Med. Chem. 2006, 49, 4517-4525.
39. Shia, K. S.; Li, W. T.; Chang, C. M.; Hsu, M. C.; Chern, J. H.; Leong, M. K.; Tseng, S. N.; Lee, C. C.; Lee, Y. C.; Chen, S. J.; Peng, K. C.; Tseng, H. Y.; Chang, Y. L.; Tai, C. L.; Shih, S. R. Design, Synthesis, and Structure-Activity Relationship of Pyridyl Imidazolidinones: A Novel Class of Potent and Selective Human Enterovirus 71 Inhibitors. J. Med. Chem. 2002, 45, 1644-1655.
40. Yuan, H. B.; Kozikowski, A. P.; Petukhov, P. A. CoMFA Study of Piperidine Analogues of Cocaine at the Dopamine Transporter: Exploring the Binding Mode of the 3 Alpha-Substituent of the Piperidine Ring Using Pharmacophore-Based Flexible Alignment. J. Med. Chem. 2004, 47, 6137-6143.
41. Wong, G.; Koehler, K. F.; Skolnick, P.; Gu, Z. Q.; Ananthan, S.; Schonholzer, P.; Hunkeler, W.; Zhang, W. J.; Cook, J. M. Synthetic and Computer-Assisted Analysis of the Structural Requirements for Selective, High-Affinity Ligand-Binding to Diazepam-Insensitive Benzodiazepine Receptors. J. Med. Chem. 1993, 36, 1820-1830.
42. Zhang, N.; Jiang, Y. J.; Zou, J. W.; Zhang, B.; Jin, H. X.; Wang, Y. H.; Yu, Q. S. 3D QSAR for Gsk-3 Beta Inhibition by Indirubin Analogues. Eur. J. Med. Chem. 2006, 41, 373-378.
43. Hudock, M. P.; Sanz-Rodriguez, C. E.; Song, Y. C.; Chan, J. M. W.; Zhang, Y. H.; Odeh, S.; Kosztowski, T.; Leon-Rossell, A.; Concepcion, J. L.; Yardley, V.; Croft, S. L.; Urbina, J. A.; Oldfield, E. Inhibition of Trypanosoma Cruzi Hexokinase by Bisphosphonates. J. Med. Chem. 2006, 49, 215-223.
44. Nakagawa, Y.; Takahashi, K.; Kishikawa, H.; Ogura, T.; Minakuchi, C.; Miyagawa, H. Classical and Three-Dimensional QSAR for the Inhibition of H-3 Ponasterone a Binding by Diacylhydrazine-Type Ecdysone Agonists to Insect Sf-9 Cells. Bioorg. Med. Chem. 2005, 13, 1333-1340.
45. Rivara, S.; Mor, M.; Silva, C.; Zuliani, V.; Vacondio, F.; Spadoni, G.; Bedini, A.; Tarzia, G.; Lucini, V.; Pannacci, M.; Fraschini, F.; Plazzi, P. V. Three-Dimensional Quantitative Structure-Activity Relationship Studies on Selected Mt1 and Mt2 Melatonin Receptor Ligands: Requirements for Subtype Selectivity and Intrinsic Activity Modulation. J. Med. Chem. 2003, 46, 1429-1439.
46. Gohlke, H.; Klebe, G. Drugscore Meets CoMFA: Adaptation of Fields for Molecular Comparison (Afmoc) or How to Tailor Knowledge-Based Pair-Potentials to a Particular Protein. J. Med. Chem. 2002, 45, 4153-4170.
47. Depriest, S. A.; Mayer, D.; Naylor, C. B.; Marshall, G. R. 3d-QSAR of Angiotensin-Converting Enzyme and Thermolysin Inhibitors - a Comparison of Comfa Models Based on Deduced and Experimentally Determined Active-Site Geometries. J. Am. Chem. Soc. 1993, 115, 5372-5384.
48. Sulea, T.; Oprea, T. I.; Muresan, S.; Chan, S. L. A Different Method for Steric Field Evaluation in CoMFA Improves Model Robustness. J. Chem. Inf. Comput. Sci. 1997, 37, 1162-1170.
49. Bohm, M.; Sturzebecher, J.; Klebe, G. Three-Dimensional Quantitative Structure-Activity Relationship Analyses Using Comparative Molecular Field Analysis and Comparative Molecular Similarity Indices Analysis to Elucidate Selectivity Differences of Inhibitors Binding to Trypsin, Thrombin, and Factor Xa. J. Med. Chem. 1999, 42, 458-477.
50. Tervo, A. J.; Nyronen, T. H.; Ronkko, T.; Poso, A. A Structure-Activity Relationship Study of Catechol-O-Methyltransferase Inhibitors Combining Molecular Docking and 3D QSAR Methods. J. Comput.-Aided Mol. Des. 2003, 17, 797-810.
51. Nayyar, A.; Malde, A.; Jain, R.; Coutinho, E. 3d-QSAR Study of Ring-Substituted Quinoline Class of Anti-Tuberculosis Agents. Bioorg. Med. Chem. 2006, 14, 847-856.
52. Luco, J. M.; Feretti, F. H. QSAR Based on Multiple Linear Regression and Pls Methods for the Anti-Hiv Activity of a Large Group of Hept Derivatives. J. Chem. Inf. Comput. Sci. 1997, 37, 392-401.
53. Hannongbua, S.; Lawtrakul, L.; Sotriffer, C. A.; Rode, B. M. Comparative Molecular Field Analysis of Hiv-1 Reverse Transcriptase Inhibitors in the Class of 1 (2-Hydroxyethoxy)-Methyl-6(Phenylthio)Thymine. Quant. Struct.-Act. Rel. 1996, 15, 389-394.
54. Tervo, A. J.; Nyronen, T. H.; Ronkko, T.; Poso, A. Comparing the Quality and Predictiveness between 3D QSAR Models Obtained from Manual and Automated Alignment. J. Chem. Inf. Comput. Sci. 2004, 44, 807-816.
55. Marini, F.; Roncaglioni, A.; Novic, M. Variable Selection and Interpretation in Structure-Affinity Correlation Modeling of Estrogen Receptor Binders. J. Chem. Inf. Model. 2005, 45, 1507-1519.
56. Blair, R. M.; Fang, H.; Branham, W. S.; Hass, B. S.; Dial, S. L.; Moland, C. L.; Tong, W.; Shi, L.; Perkins, R.; Sheehan, D. M. The Estrogen Receptor Relative Binding Affinities of 188 Natural and Xenochemicals: Structural Diversity of Ligands. Toxicol. Sci. 2000, 54, 138-153.
57. Hou, T. J.; McLaughlin, W.; Lu, B.; Chen, K.; Wang, W. Prediction of Binding Affinities between the Human Amphiphysin-1 Sh3 Domain and Its Peptide Ligands Using Homology Modeling, Molecular Dynamics and Molecular Field Analysis. J. Proteome Res. 2006, 5, 32-43.
58. Landgraf, C.; Panni, S.; Montecchi-Palazzi, L.; Castagnoli, L.; Schneider-Mergener, J.; Volkmer-Engert, R.; Cesareni, G. Protein Interaction Networks by Proteome Peptide Scanning. PLoS Biol. 2004, 2, 94-103.
59. Taha, M. O.; AlDamen, M. A. Effects of Variable Docking Conditions and Scoring Functions on Corresponding Protein-Aligned Comparative Molecular Field Analysis Models Constructed from Diverse Human Protein Tyrosine Phosphatase 1b Inhibitors. J. Med. Chem. 2005, 48, 8016-8034.
60. Haefely, W.; Kyburz, E.; Gerecke, M.; Mohler, H. Recent Advances in the Molecular Pharmacology of Benzodiazepine Receptors and in the Structure Activity Relationships of Their Agonists and Antagonists. Adv. Drug Res. 1985, 14, 165-322.