In silico prediction of aqueous solubility: A multimodel protocol based on chemical similarity

Molecular Pharmaceutics

Volumn 9, Issue 11, 2012, Pages 3127-3135

  Chevillard, Florent ^a,b   Lagorce, David ^a   Reynès, Christelle ^a,c   Villoutreix, Bruno O ^a   Vayer, Philippe ^d   Miteva, Maria A ^a  

^a UNIVERSITÉ PARIS DESCARTES   (France)

^b PHILIPPS UNIVERSITY MARBURG   (Germany)

^c UNIV MONTPELLIER   (France)

^d INSTITUT DE RECHERCHES INTERNATIONALES SERVIER   (France)

Author keywords

dry powder inhalation; macrophage; microspheres; Mycobacterium tuberculosis; nitric oxide donor; poly(lactide co glycolide)

Indexed keywords

DIMETHYL SULFOXIDE;

ALGORITHM; AQUEOUS SOLUBILITY; AQUEOUS SOLUTION; ARTICLE; CLINICAL PROTOCOL; COMPUTER PROGRAM; DRUG SOLUBILITY; DRUG STRUCTURE; PREDICTION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; RANDOM FOREST ALGORITHM; SOLUBILITY;

COMPUTER SIMULATION; MODELS, CHEMICAL; MOLECULAR STRUCTURE; PHARMACEUTICAL PREPARATIONS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SOFTWARE; SOLUBILITY; WATER;

EID: 84868582939     PISSN: 15438384     EISSN: 15438392     Source Type: Journal    
DOI: 10.1021/mp300234q     Document Type: Article

References (47)

1. 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. 1997, 23, 3-25
2. Di, L.; Kerns, E. H. Biological assay challenges from compound solubility: strategies for bioassay optimization Drug Discovery Today 2006, 11, 446-451
3. Alelyunas, Y. W.; Empfield, J. R.; McCarthy, D.; Spreen, R. C.; Bui, K.; Pelosi-Kilby, L.; Shen, C. Experimental solubility profiling of marketed CNS drugs, exploring solubility limit of CNS discovery candidate Bioorg. Med. Chem. Lett. 2010, 20, 7312-7316
4. Ishikawa, M.; Hashimoto, Y. Improvement in Aqueous Solubility in Small Molecule Drug Discovery Programs by Disruption of Molecular Planarity and Symmetry J. Med. Chem. 2011, 54, 1539-1554
5. Wang, J.; Hou, T. Recent Advances on Aqueous Solubility Prediction Comb. Chem. High Throughput Screening 2011, 14, 328-338
6. van de Waterbeemd, H. Improving Compound Quality through in vitro and in silico Physicochemical Profiling Chem. Biodiversity 2009, 6, 1760-1766
7. Wang, J.; Krudy, G.; Hou, T.; Zhang, W.; Holland, G.; Xu, X. Development of Reliable Aqueous Solubility Models and Their Application in Druglike Analysis J. Chem. Inf. Model. 2007, 47, 1395-1404
8. Hopfinger, A. J.; Esposito, E. X.; Llinas, A.; Glen, R. C.; Goodman, J. M. Findings of the Challenge To Predict Aqueous Solubility J. Chem. Inf. Model. 2008, 49, 1-5
9. Llinas, A.; Glen, R. C.; Goodman, J. M. Solubility Challenge: Can You Predict Solubilities of 32 Molecules Using a Database of 100 Reliable Measurements? J. Chem. Inf. Model. 2008, 48, 1289-1303
10. Hewitt, M.; Cronin, M. T. D.; Enoch, S. J.; Madden, J. C.; Roberts, D. W.; Dearden, J. C. In Silico Prediction of Aqueous Solubility: The Solubility Challenge J. Chem. Inf. Model. 2009, 49, 2572-2587
11. Kuhne, R.; Ebert, R.-U.; Schormann, G. Model Selection Based on Structural Similarity: Method Description and Application to Water Solubility Prediction J. Chem. Inf. Model. 2006, 46, 636-641
12. Delaney, J. S. Predicting aqueous solubility from structure Drug Discovery Today 2005, 10, 289-295
13. Ran, Y.; Yalkowsky, S. H. Prediction of Drug Solubility by the General Solubility Equation (GSE) J. Chem. Inf. Comput. Sci. 2001, 41, 354-357
14. Yalkowsky, S. H.; Valvani, S. C. Solubility and partitioning I: Solubility of nonelectrolytes in water J. Pharm. Sci. 1980, 69, 912-922
15. Jain, N.; Yalkowsky, S. H. Estimation of the aqueous solubility I: Application to organic nonelectrolytes J. Pharm. Sci. 2001, 90, 234-252
16. Sanghvi, T.; Jain, N.; Yang, G.; Yalkowsky, S. H. Estimation of Aqueous Solubility By The General Solubility Equation (GSE) The Easy Way QSAR Comb. Sci. 2003, 22, 258-262
17. Wassvik, C. M.; Holmen, A. G.; Draheim, R.; Artursson, P.; Bergstrom, C. A. Molecular characteristics for solid-state limited solubility J. Med. Chem. 2008, 51, 3035-3039
18. Ali, J.; Camilleri, P.; Brown, M. B.; Hutt, A. J.; Kirton, S. B. Revisiting the General Solubility Equation: In Silico Prediction of Aqueous Solubility Incorporating the Effect of Topographical Polar Surface Area J. Chem. Inf. Model. 2012, 52, 420-428
19. McElroy, N. R.; Jurs, P. C. Prediction of Aqueous Solubility of Heteroatom-Containing Organic Compounds from Molecular Structure J. Chem. Inf. Comput. Sci. 2001, 41, 1237-1247
20. McFarland, J. W.; Avdeef, A.; Berger, C. M.; Raevsky, O. A. Estimating the Water Solubilities of Crystalline Compounds from Their Chemical Structures Alone J. Chem. Inf. Comput. Sci. 2001, 41, 1355-1359
21. Butina, D.; Gola, J. M. R. Modeling Aqueous Solubility J. Chem. Inf. Comput. Sci. 2003, 43, 837-841
22. Hou, T.; Wang, J. Structure-ADME relationship: still a long way to go? Expert Opin. Drug Metab. Toxicol. 2008, 4, 759-770
23. Tropsha, A.; Gramatica, P.; Gombar, V. K. The Importance of Being Earnest: Validation is the Absolute Essential for Successful Application and Interpretation of QSPR Models QSAR Comb. Sci. 2003, 22, 69-77
24. Jorgensen, W. L.; Duffy, E. M. Prediction of drug solubility from structure Adv. Drug Delivery Rev. 2002, 54, 355-366
25. Lagorce, D.; Maupetit, J.; Baell, J.; Sperandio, O.; Tuffery, P.; Miteva, M. A.; Galona, H.; Villoutreix, B. O. The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections Bioinformatics 2011, 27, 2018-2020
26. Cheng, A.; Merz, K. M. Prediction of Aqueous Solubility of a Diverse Set of Compounds Using Quantitative Structure Property Relationships J. Med. Chem. 2003, 46, 3572-3580
27. Stuart, M.; Box, K. Chasing Equilibrium: Measuring the Intrinsic Solubility of Weak Acids and Bases Anal. Chem. 2005, 77, 983-990
28. PhysProp. http://www.syrres.com/, 2012.
29. Huuskonen, J.; Salo, M.; Taskinen, J. Aqueous Solubility Prediction of Drugs Based on Molecular Topology and Neural Network Modeling J. Chem. Inf. Comput. Sci. 1998, 38, 450-456
30. Tetko, I. V.; Tanchuk, V. Y.; Kasheva, T. N.; Villa, A. E. P. Estimation of Aqueous Solubility of Chemical Compounds Using E-State Indices J. Chem. Inf. Comput. Sci. 2001, 41, 1488-1493
31. Hou, T. ADME evaluation in drug discovery. 4. Prediction of aqueous solubility based on atom contribution approach J. Chem. Inf. Comput. Sci. 2004, 44, 266-275
32. Breiman, L. Random Forests Mach. Learn. 2001, 45, 5-32
33. R Development Core Team. R Foundation for Statistical Computing. R: A language and environment for statistical computing. http://www.R-project.org, 2005.
34. McGregor, M. J.; Pallai, P. V. Clustering of Large Databases of Compounds: Using the MDL Keys as Structural Descriptors J. Chem. Inf. Comput. Sci. 1997, 37, 443-448
35. Delaney, J. S. ESOL: Estimating Aqueous Solubility Directly from Molecular Structure J. Chem. Inf. Comput. Sci. 2004, 44, 1000-1005
36. Klopman, G.; Wang, S.; Balthasar, D. M. Estimation of aqueous solubility of organic molecules by the group contribution approach. Application to the study of biodegradation J. Chem. Inf. Comput. Sci. 1992, 32, 474-482
37. Klopman, G.; Zhu, H. Estimation of the Aqueous Solubility of Organic Molecules by the Group Contribution Approach J. Chem. Inf. Comput. Sci. 2001, 41, 439-445
38. MOE. Chemical Computing Group, Inc., (2010).
39. ACD/Labs. http://www.acdlabs.com/products/pc-admet/physchem/ physchemsuite/, 2012.
40. Schrodinger. http://www.schrodinger.com/products/14/17/, 2009.
41. Simulation-Plus. http://www.simulations-plus.com/Products.aspx?grpID= 1&cID=11&pID=13, 2012.
42. Cruciani, G.; Pastor, M.; Guba, W. VolSurf: a new tool for the pharmacokinetic optimization of lead compounds Eur. J. Pharm. Sci. 2000) 11 (Suppl. 2) S29-S39
43. Volsurf. http://www.moldiscovery.com, 2011.
44. Tetko, I. V.; Tanchuk, V. Y. Application of Associative Neural Networks for Prediction of Lipophilicity in ALOGPS 2.1 Program J. Chem. Inf. Comput. Sci. 2002, 42, 1136-1145
45. Infochimie, L. ISIDA. www.infochim.u-strasbg.fr, 2012.
46. Zhang, H.; Ando, H. Y.; Chen, L.; Lee, P. H. On-the-fly selection of a training set for aqueous solubility prediction Mol. Pharmaceutics 2007, 4, 489-497
47. Palmer, D. S.; OBoyle, N. M.; Glen, R. C.; Mitchell, J. B. O. Random Forest Models To Predict Aqueous Solubility J. Chem. Inf. Model. 2006, 47, 150-158