第五型磷酸二酯酵素 (PDE5) 在細胞中扮演著調控cGMP濃度的重要角色，與男性陽痿有直接的相關性。Tadalafil，也稱為犀力士 (Cialis®)，是一個β-carbolin衍生物能夠專一的抑制第五型磷酸二酯酵素的活性。對於52個β-carbolin衍生物，利用三維定量構效關係 (3D-QSAR) 的方法來分析描述此類藥物的活性與結構之間的定量關係。利用Catalyst及CoMFA這兩套軟體來分析31個位於訓練組的化合物以建立兩個三維定量構效關係的電腦模型；另一方面，則利用21個位於測試組中的化合物以確定此電腦模型的可信度。經由比較生物體外實驗與電腦模型預測的結果分析得知，Catalyst及CoMFA所得到的電腦模型皆具有相當高的預測性。Catalyst方面，相關係數高達0.816，藥效基團模型包括一個氫鍵的提供者、兩個氫鍵的接受者以及一個疏水性作用區；CoMFA所建立的分子力場模型則具有4個要素並且得到相關係數為0.945，在測試組也得到0.810的高相關性。經過比對兩個電腦模型的結果得知一個氫鍵提供者以及另外有兩個氫鍵接受者，對於此類化合物在第五型磷酸二酯酵素的抑制作用上，扮演一個相當重要的角色。進一步地，利用LigBuilder程式來建立一個以犀利士為先導藥物的虛擬化合物資料庫，總共產生了200個新生藥物。我們便利用先前所建立的兩個電腦模型來重新評分這200新生的化合藥物，除此之外，我們再利用SCORE及AutoDock這兩個評分函數來加以評分，我們從中得到 11個候選藥物位於三個評分函數的前50名，因此可做為新一代藥物開發的研究目標。我們建立了一個PDE5-DDDB線上資料庫。此資料庫提供了所有與虛擬化合物資料庫相關的資訊。而此資料庫提供了一個相當方便的平台讓研究PDE5和抑制物交互關係的研究者或是藥物發展的研發者更加容易取得此虛擬資料庫的相關訊息。

Phosphodiesterase type 5 (PDE5) is an important enzyme for controlling the levels of the intracellular cGMP which significantly corresponds to male erection dysfunction. Tadalafil, also known as Cialis, is a β-carboline derivative which inhibits PDE5 specifically. Three-dimensional quantitative structure-activity relationship (3D-QSAR) approach was used to construct pharmacophore models for a series of β-carboline derivative inhibitors of PDE5. The models generated using Catalyst and CoMFA packages with a training set of 31 molecules were confirmed by the test set of 21 molecules. The high r2 value (0.816) between the predicted and observed activity showed that the Catalyst pharmacophore hypothesis was predictive. This hypothesis contained four features, including a hydrogen bond donor, two hydrogen bond acceptors and a hydrophobic feature. The CoMFA model consisted of four components with an r2 of 0.945 and produced good predictions for test set (r2 = 0.810). Comparison between these two models, two hydrogen bond acceptors and one hydrogen bond donor were found to contribute significantly to the inhibition activities of β-carboline derivatives. LigBuilder package was used to establish a new drug library. Totally 200 compounds were generated and rescored by using 3D-QSAR models and two scoring functions, SCORE and AutoDock. Eleven drugs were selected and thought as candidates for further analysis because of ranked among top fifty for at least three rescoring functions. PDE5-Drug Development Database (PDE5-DDDB) has been built up as a friendly platform for study of PDE5-inhibitor interactions, which archives information of new drugs.

1. Chen, K. K., Chiang, H. S., Jiann, B. P., Lin, J. S., Liu, W. J., Wu, C. J., Hsieh, J. T., Wang, C. J., Hwang, T. I. and Lee, S. S. (2004) Prevalence of erectile dysfunction and impacts on sexual activity and self-reported intercourse satisfaction in men older than 40 years in Taiwan. Int J Impot Res. 16, 249-255
2. Nicolosi, A., Glasser, D. B., Kim, S. C., Marumo, K. and Laumann, E. O. (2005) Sexual behaviour and dysfunction and help-seeking patterns in adults aged 40-80 years in the urban population of Asian countries. BJU Int. 95, 609-614
3. Fazio, L. and Brock, G. (2004) Erectile dysfunction: management update. Cmaj. 170, 1429-1437
4. Beavo, J. A. (1995) Cyclic nucleotide phosphodiesterases: functional implications of multiple isoforms. Physiol Rev. 75, 725-748
5. Soderling, S. H. and Beavo, J. A. (2000) Regulation of cAMP and cGMP signaling: new phosphodiesterases and new functions. Curr Opin Cell Biol. 12, 174-179
6. Hetman, J. M., Robas, N., Baxendale, R., Fidock, M., Phillips, S. C., Soderling, S. H. and Beavo, J. A. (2000) Cloning and characterization of two splice variants of human phosphodiesterase 11A. Proc Natl Acad Sci U S A. 97, 12891-12895
7. Manganiello, V. C., Murata, T., Taira, M., Belfrage, P. and Degerman, E. (1995) Diversity in cyclic nucleotide phosphodiesterase isoenzyme families. Arch Biochem Biophys. 322, 1-13
8. Uckert, S., Kuthe, A., Stief, C. G. and Jonas, U. (2001) Phosphodiesterase isoenzymes as pharmacological targets in the treatment of male erectile dysfunction. World J Urol. 19, 14-22
9. Wallis, R. M., Corbin, J. D., Francis, S. H. and Ellis, P. (1999) Tissue distribution of phosphodiesterase families and the effects of sildenafil on tissue cyclic nucleotides, platelet function, and the contractile responses of trabeculae carneae and aortic rings in vitro. Am J Cardiol. 83, 3C-12C
10. Boolell, M., Allen, M. J., Ballard, S. A., Gepi-Attee, S., Muirhead, G. J., Naylor, A. M., Osterloh, I. H. and Gingell, C. (1996) Sildenafil: an orally active type 5 cyclic GMP-specific phosphodiesterase inhibitor for the treatment of penile erectile dysfunction. Int J Impot Res. 8, 47-52
11. Rosen, R. C. and Kostis, J. B. (2003) Overview of phosphodiesterase 5 inhibition in erectile dysfunction. Am J Cardiol. 92, 9M-18M
12. Rybalkin, S. D., Yan, C., Bornfeldt, K. E. and Beavo, J. A. (2003) Cyclic GMP phosphodiesterases and regulation of smooth muscle function. Circ Res. 93, 280-291
13. Lue, T. F. (2000) Erectile dysfunction. N Engl J Med. 342, 1802-1813
14. Sung, B. J., Hwang, K. Y., Jeon, Y. H., Lee, J. I., Heo, Y. S., Kim, J. H., Moon, J., Yoon, J. M., Hyun, Y. L., Kim, E., Eum, S. J., Park, S. Y., Lee, J. O., Lee, T. G., Ro, S. and Cho, J. M. (2003) Structure of the catalytic domain of human phosphodiesterase 5 with bound drug molecules. Nature. 425, 98-102
15. Daugan, A., Grondin, P., Ruault, C., Le Monnier de Gouville, A. C., Coste, H., Kirilovsky, J., Hyafil, F. and Labaudiniere, R. (2003) The discovery of tadalafil: a novel and highly selective PDE5 inhibitor. 1: 5,6,11,11a-tetrahydro-1H-imidazo[1',5':1,6]pyrido[3,4-b]indole-1,3(2H)-dio ne analogues. J Med Chem. 46, 4525-4532
16. Daugan, A., Grondin, P., Ruault, C., Le Monnier de Gouville, A. C., Coste, H., Linget, J. M., Kirilovsky, J., Hyafil, F. and Labaudiniere, R. (2003) The discovery of tadalafil: a novel and highly selective PDE5 inhibitor. 2: 2,3,6,7,12,12a-hexahydropyrazino[1',2':1,6]pyrido[3,4-b]indole-1,4-dione analogues. J Med Chem. 46, 4533-4542
17. Maw, G. N., Allerton, C. M., Gbekor, E. and Million, W. A. (2003) Design, synthesis and biological activity of beta-carboline-based type-5 phosphodiesterase inhibitors. Bioorg Med Chem Lett. 13, 1425-1428
18. Ekins, S., Durst, G. L., Stratford, R. E., Thorner, D. A., Lewis, R., Loncharich, R. J. and Wikel, J. H. (2001) Three-dimensional quantitative structure-permeability relationship analysis for a series of inhibitors of rhinovirus replication. J Chem Inf Comput Sci. 41, 1578-1586
19. Bureau, R., Daveu, C., Baglin, I., Sopkova-De Oliveira Santos, J., Lancelot, J. C. and Rault, S. (2001) Association of two 3D QSAR analyses. application to the study of partial agonist serotonin-3 ligands. J Chem Inf Comput Sci. 41, 815-823
20. Tsai, K. C. and Lin, T. H. (2004) A ligand-based molecular modeling study on some matrix metalloproteinase-1 inhibitors using several 3D QSAR techniques. J Chem Inf Comput Sci. 44, 1857-1871
21. Cramer III, R. D., Patterson, D. E. and Bunce, J. D. (1988) Comparative Molecular Field Analysis (CoMFA) 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 110, 5959-5967
22. Wang, R., Gao, Y. and Lai, L. (2000) LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design. J Mol Model. 6, 498-516
23. Wang, R., Liu, L., Lai, L. and Tang, Y. (1998) SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex. J Mol Model. 4, 379-394
24. Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K. and J., O. A. (1998) Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function. J. Comp. Chem. 19, 1639-1662
25. Debnath, A. K. (2003) Generation of predictive pharmacophore models for CCR5 antagonists: study with piperidine- and piperazine-based compounds as a new class of HIV-1 entry inhibitors. J Med Chem. 46, 4501-4515
26. Sybyl version 6.92. Tripos, Inc., 1669 Hanley Road, St. Louis.
27. Catalyst. Catalyst software package, Vers. 4.7; Accelrys Software Inc.: San Diego, CA.
28. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. and Karplus, M. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem. 4, 187-217
29. Smellie, A., Kahn, S. D. and Teig, S. L. (1995) Analysis of Conformational Space. 2. Application of Conformational Models. J Chem Inf Comput Sci. 35, 295-304
30. Smellie, A., Kahn, S. D. and Teig, S. L. (1995) Analysis of Conformational Coverage. 1. Validation and Estimation of Coverage. J Chem Inf Comput Sci. 35, 285-294
31. Smellie, A. (1995) Poling: Promoting Conformational Variation. J. Comp. Chem. 16, 171-187
32. Clark, M., Cramer, R. D., III and Van Opdenbosch, N. (1989) Validation of the general purpose tripos 5.2 force field. J Comput Chem. 10, 982-1012
33. Lipinski, C. A., Lombardo, F., Dominy, B. W. and Feeney, P. J. (1997) Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings. Adv. Drug Del. Rev. 23, 3-25
34. Charifson, P. S., Corkery, J. J., Murcko, M. A. and Walters, W. P. (1999) Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem. 42, 5100-5109
35. Wesson, L. and Eisenberg, D. (1992) Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1, 227-235
36. Elgoyhen, B., Lorenzo, P. S., Tellez-Inon, M. T. and Adler-Graschinsky, E. (1992) Relaxant effects of beta-carbolines on rat aortic rings. J Pharmacol Exp Ther. 261, 534-539
37. Hou, T. J., Wang, J. M., Liao, N. and Xu, X. J. (1999) Applications of genetic algorithms on the structure-activity relationship analysis of some cinnamamides. J Chem Inf Comput Sci. 39, 775-781
38. So, S. S. and Karplus, M. (1996) Genetic neural networks for quantitative structure-activity relationships: improvements and application of benzodiazepine affinity for benzodiazepine/GABAA receptors. J Med Chem. 39, 5246-5256
39. So, S. S. and Karplus, M. (1999) A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors. J Comput Aided Mol Des. 13, 243-258
40. Wang, R., Gao, Y. and Lai, L. (2000) Calculating partition coefficient by atom-additive method. Perspectives in Drug Discovery & Design. 19, 47-66
41. Wallace, A. C., Laskowski, R. A. and Thornton, J. M. (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8, 127-134