Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 1. Prediction of intestinal absorption

Journal of Pharmaceutical Sciences

Volumn 88, Issue 8, 1999, Pages 807-814

  Clark, David E ^a  

^a SANOFI   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CALCULATION; CHEMICAL STRUCTURE; CONTROLLED STUDY; INTESTINE ABSORPTION; SCREENING TEST; STRUCTURE ANALYSIS; SURFACE PROPERTY; SYNTHESIS; TRANSPORT KINETICS;

EID: 0032795192     PISSN: 00223549     EISSN: None     Source Type: Journal    
DOI: 10.1021/js9804011     Document Type: Article

References (57)

1. Lloyd, A. W. Can We Relieve the Drug Development Bottleneck? Pharm. Sci. Technol. Today 1998, 1, 45-46.
2. Rodrigues, A. D. Preclinical Drug Metabolism in the Age of High-Throughput Screening: An Industrial Perspective. Pharm. Res. 1997, 14, 1504-1510.
3. Lin, J. H.; Lu, A. Y. H. Role of Pharmacokinetics and Metabolism in Drug Discovery and Development. Pharmacol. Rev. 1997, 49, 403-449.
4. Smith, D. A.; Jones, B. C.; Walker, D. K. Design of Drugs Involving the Concepts and Theories of Drug Metabolism and Pharmacokinetics. Med. Res. Rev. 1996, 16, 243-266.
5. Tarbit, M. H.; Berman, J. High-throughput Approaches for Evaluating Absorption, Distribution, Metabolism and Excretion Properties of Lead Compounds. Curr. Opin. Chem. Biol. 1998, 2, 411-416.
6. Artursson, P.; Palm, K.; Luthman, K. Caco-2 Monolayers in Experimental and Theoretical Predictions of Drug Transport. Adv. Drug Deliv. Rev. 1996, 22, 67-84.
7. Artursson, P.; Borchardt, R. Intestinal Drug Absorption and Metabolism in Cell Cultures: Caco-2 and Beyond. Pharm. Res. 1997, 14, 1655-1658.
8. Ito, K.; Iwatsubo, T.; Kanamitsu, S.; Nakajima, Y.; Sugiyama, Y. Quantitative Prediction of In Vivo Drug Clearance and Drug Interactions from In Vitro Data on Metabolism, together with Binding and Transport. Annu. Rev. Pharmacol. Toxicol. 1998, 38, 461-499.
9. Kansy, M.; Senner, F.; Gubernator, K. Physicochemical High Throughput Screening: Parallel Artificial Membrane Permeation Assay in the Description of Passive Absorption Processes. J. Med. Chem. 1998, 41, 1007-1010.
10. Berman, J.; Halm, K.; Adkison, K.; Shaffer, J. Simultaneous Pharmacokinetic Screening of a Mixture of Compounds in the Dog using API LC/MSMS Analysis for Increased Throughput. J. Med. Chem. 1997, 40, 827-829.
11. Gillet, V. J.; Willett, P.; Bradshaw, J. Identification of Biological Activity Profiles Using Substructural Analysis and Genetic Algorithms. J. Chem. Inf. Comput. Sci. 1998, 38, 165-179.
12. Ajay; Walters, W. P.; Murcko, M. A. Can We Learn to Distinguish Between Drug-like and Non-Drug-Like Molecules? J. Med. Chem. 1998, 41, 3314-3324.
13. Sadowski, J.; Kubinyi, H. A Scoring Scheme for Discriminating between Drugs and Nondrugs. J. Med. Chem. 1998, 41, 3325-3329.
14. Navia, M. A.; Chaturvedi, P. R. Design Principles for Orally Bioavailable Drugs. Drug Discov. Today 1996, 1, 179-189.
15. Chan, O. H.; Stewart, B. H. Physicochemical and Drug-Delivery Considerations for Oral Drug Bioavailability. Drug Discov. Today 1996, 1, 461-473.
16. 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 Deliv. Rev. 1997, 23, 3-25.
17. Clog P. Daylight Chemical Information Software, version 4.51. Daylight Chemical Information Inc.: 27401 Los Altos, Suite #370, Mission Viejo, CA 92691.
18. Moriguchi, I.; Hirono, S.; Liu, Q.; Nakagome, I.; Matsushita, Y. Simple Method of Calculating Octanol/Water Partition Coefficient. Chem. Pharm. Bull. 1992, 40, 127-130.
19. Wessel, M. D.; Jurs, P. C.; Tolan, J. W.; Muskal, S. M. Prediction of Human Intestinal Absorption of Drug Compounds From Molecular Structure. J. Chem. Inf. Comput. Sci. 1998, 38, 726-735.
20. Hirono, S.; Nakagome, I.; Hirano, H.; Matsushita, Y.; Yoshii, F.; Moriguchi, I. Noncongeneric Structure-Pharmacokinetic Property Correlation Studies Using Fuzzy Adaptive Least-Squares: Oral Bioavailability. Biol. Pharm. Bull. 1994, 17, 306-309.
21. Hermann, R. B. Theory of Hydrophobic Bonding. II. Correlation of Hydrocarbon Solubility in Water with Solvent Cavity Surface Area. J. Phys. Chem. 1972, 76, 2754-2759.
22. Pearlman, R. S. Molecular Surface Areas and Volumes and their Use in Structure-Activity Relationships. In Physical Chemical Properties of Drugs; Medicinal Research Series Vol. 10; Yalkowsky, S. H., Sinkula, A. A., Valvani, S. C., Eds.; Marcel Dekker: New York, 1980; pp 321-347.
23. van de Waterbeemd, H.; Camenisch, G.; Folkers, G.; Raevsky, O. A. Estimation of Caco-2 Cell Permeability using Calculated Molecular Descriptors. Quant. Struct.-Act. Relat. 1996, 15, 480-490.
24. Palm, K.; Luthman, K.; Ungell, A.-L.; Strandlund, G.; Artursson, P. Correlation of Drug Absorption with Molecular Surface Properties. J. Pharm. Sci. 1996, 85, 32-39.
25. Lipkowitz, K. B.; Baker, B.; Larter, R. Dynamic Molecular Surface Areas. J. Am. Chem. Soc. 1989, 111, 7750-7753.
26. Palm, K.; Stenberg, P.; Luthman, K.; Artursson, P. Polar Molecular Surface Properties Predict the Intestinal Absorption of Drugs in Humans. Pharm. Res. 1997, 14, 568-571.
27. Krarup, L. H.; Christensen, I. T.; Hovgaard, L.; Frokjaer, S. Predicting Drug Absorption from Molecular Surface Properties Based on Molecular Dynamics Simulations. Pharm. Res. 1998, 15, 972-978.
28. Palm, K.; Luthman, K.; Ungell, A.-L.; Strandlund, G.; Beigi, F.; Lundahl, P.; Artursson, P. Evaluation of Dynamic Polar Molecular Surface Area as Predictor of Drug Absorption: Comparison with Other Computational and Experimental Predictors. J. Med. Chem. 1998, 41, 5382-5392.
29. Weininger, D. SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Comput. Sci. 1988, 28, 31-36.
30. Pearlman, R. S. Rapid Generation of High Quality Approximate 3D Molecular Structures. Chem. Des. Auto. News 1987, 2, 1-7.
31. CONCORD v4.02. Balducci, R.; McGarity, C. M.; Rusinko, A., III; Skell, J.; Smith, K.; Pearlman, R. S (University of Texas at Austin). Distributed by Tripos, Inc., 1699 S. Hanley Rd., Suite 303, St. Louis, MO 63144-2913.
32. SYBYL 6.4.2. Tripos, Inc., 1699 S. Hanley Rd., Suite 303, St. Louis, MO 63144-2913.
33. Dodd, L. R.; Theodorou, D. N. Analytical Treatment of the Volume and Surface Area of Molecules Formed by an Arbitrary Collection of Unequal Spheres Intersected by Planes. Mol. Phys. 1991, 72, 1313-1345.
34. 50 is the PSA value at which %FA = 50. Bottom and top refer to the minimum and maximum values of %FA, respectively.
35. Chungi, V. S.; Bourne, D. W. A.; Dittert, L. W. Competitive Inhibition between Folic Acid and Methotrexate for Transport Carrier in the Rat Small Intestine. J. Pharm. Sci. 1979, 68, 1552-1553.
36. Dudeja, P. K.; Torania, S. A.; Said, H. M. Evidence for the Existence of Carrier-Mediated Folate Uptake Mechanism in Human Colonic Luminal Membranes. Am. J. Physiol. 1997, 272, G1408-G1415.
37. Yao, S. Y.; Cass, C. E.; Young, J. D. Transport of the Antiviral Nucleoside Analogues 3′-azido-3′-deoxythymine and 2′,3′-dideoxycytidine by a Recombinant Nucleoside Transporter (rCNT) Expressed in Xenopus Laevis Oocytes. Mol. Pharmacol. 1996, 50, 388-393.
38. Westphal, J. F.; Deslandes, A.; Brogard, J. M.; Carbon, C. Reappraisal of Amoxycillin Absorption Kinetics. J. Antimicrob. Chemother. 1991, 27, 647-654.
39. Reigner, B. G.; Couet, W.; Guedes, J. P.; Fourtillan, J. B.; Tozer, T. N. Saturable Rate of Cefatrizine Absorption after Oral Administration in Humans. J. Pharmacokinet. Biopharm. 1990, 18, 17-34.
40. Ruiz-Balaguer, N.; Nacher, A.; Casabo, V. G.; Merino, M. Nonlinear Intestinal Absorption Kinetics of Cefuroxime Axetil in Rats. Antimicrob. Agents Chemother. 1997, 41, 445-448.
41. Friedman, D. I.; Amidon, G. L. Intestinal Absorption Mechanism of Dipeptide Angiotensin Converting Enzyme Inhibitors of the Lysyl-Prolyl Type: Lisinopril and SQ 29, 852. J. Pharm. Sci. 1989, 78, 995-998.
42. Burgio, D. E.; Gosl, M. P.; McNamara, P. J. Effects of P-glycoprotein Modulators on Etoposide Elimination and Central Nervous System Distribution. J. Pharmacol. Exp. Ther. 1998, 287, 911-917.
43. Shah, J. C.; Chen, J. R.; Chow, D. Preformulation Study of Etoposide: Identification of Physicochemical Characteristics Responsible for the Low and Erratic Oral Bioavailability of Etoposide. Pharm. Res. 1989, 6, 408-412.
44. Joel, S. P.; Clark, P. I.; Heap, L.; Webster, L.; Robbins, S.; Craft, H.; Slevin, M. L. Pharmacological Attempts to Improve the Bioavailability of Oral Etoposide. Cancer Chemother. Pharmacol. 1995, 37, 125-133.
45. Good, A. C.; Lewis, R. A. New Methodology for Profiling Combinatorial Libraries and Screening Sets: Cleaning Up the Design Process with HARPick. J. Med. Chem. 1997, 40, 3926-3936.
46. Doring, F.; Will, J.; Amasheh, S.; Clauss, W.; Ahlbrecht, H.; Daniel, H. Minimal Molecular Determinants of Substrates for Recognition by the Intestinal Peptide Transporter. J. Biol. Chem. 1998, 273, 23211-23218.
47. Conradi, R. A.; Burton, P. S.; Borchardt, R. T. Physicochemical and Biological Factors that Influence a Drug's Cellular Permeability by Passive Diffusion. In Lipophilicity in Drug Action and Toxicology; Pliška, V., Testa, B., van de Waterbeemd, H., Eds.; VCH: Weinheim, 1996; pp 233-252.
48. Carrupt, P.-A.; Testa, B.; Gaillard, P. Computational Approaches to Lipophilicity: Methods and Applications. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; Wiley-VCH: New York, 1997; Vol. 11, pp 241-315.
49. Luthman, K. Private communication, 1998.
50. 1D Receptor Agonists: Fluorinated 3-[3-(Piperidin-1-yl)propyl]indoles. J. Med. Chem. 1998, 41, 2667-2670.
51. Wils, P.; Warnery, A.; Phung-Ba, V.; Legrain, S.; Scherman, D. High Lipophilicity Decreases Drug Transport Across Intestinal Epithelial Cells. J. Pharmacol. Exp. Ther. 1994, 269, 654-658.
52. Winiwarter, S.; Bonham, N. M.; Ax, F.; Hallberg, A.; Lennernäs, H.; Karlén, A. Correlation of Human Jejunal Permeability (in Vivo) of Drugs with Experimentally and Theoretically Derived Parameters. A Multivariate Data Analysis Approach. J. Med. Chem. 1998, 41, 4939-4949.
53. Stenberg, P.; Luthman, K.; Artursson, P. Prediction of Membrane Permeability to Peptides from Calculated Dynamic Molecular Surface Properties. Pharm. Res. 1999, 16, 205-212.
54. Böhm, H.-J.; Brode, S.; Hesse, U.; Klebe, G. Oxygen and Nitrogen in Competitive Situations: Which is the Hydrogen-Bond Acceptor? Chem. Eur. J. 1996, 2, 1509-1513.
55. Bruno, I. J.; Cole, J. C.; Lommerse, J. P. M.; Rowland, R. S.; Taylor, R.; Verdonk, M. L. Isostar: A Library of Information about Nonbonded Interactions. J. Comput.-Aided Mol. Des. 1997, 11, 525-537.
56. Rablen, P. R.; Lockman, J. W.; Jorgensen, W. L. Ab Initio Study of Hydrogen-Bonded Complexes of Small Organic Molecules with Water. J. Phys. Chem. A 1998, 102, 3782-3797.
57. During the revision of this paper, van de Waterbeemd et al. published a paper describing the use of single conformation PSA values in the classification of drug compounds as CNS active or CNS inactive: van de Waterbeemd, H.; Camenisch, G.; Folkers, G.; Chretien, J. R.; Raevsky, O. A. Estimation of Blood-Brain Barrier Crossing of Drugs Using Molecular Size and Shape, and H-bonding Descriptors. J. Drug Target. 1998, 6, 151-165. In their experience, the conformational effect in low molecular weight molecules represents a variation of about ±10% in the polar surface area which they do not consider as critical when making first estimates of BBB uptake.