環狀單磷鳥糞核糖苷(cyclic guanosine monophosphate, cGMP)-特定的磷酸雙水解酶第五型(phosphodiesterase type 5, PDE5)的蛋白質結構及抑制劑已被廣泛研究及發表。
一個藥物上市需花費大量的時間與金錢，為了縮短和節省藥物研發的時間與金錢，電腦輔助藥物設計的方法便由此因運而生。本實驗利用直接藥物設計及間接藥物設計的方法，提供資訊找出新的有潛力之PDE5抑制劑。
第一部分實驗以犀利士和PDE5的抑制為基礎利用分子對接軟體GOLD中Goldscore及Chemscore兩種不同評分函數虛擬篩選Maybridge資料庫找出Fitness值前一千五百名化合物後，再以Pscore 及更精確的參數設定找出共90個候選的化合物；第二部分是利用33個犀利士衍生物產生一疏水作用力、一芬香環作用力、一氫鍵提供者、一氫鍵接受者四個藥效集團以預測候選化合物的活性，提供了cis-form及trans-form衍生物不同抑制機制的線索；而此實驗所產生的藥效集團，也可用來當做化學資料庫虛擬篩選的工具。

Protein structures and inhibitors of cGMP-specific phosphodiesterase 5 (PDE 5) have been widely studied.
A new drug takes a lot time and money from lab to market. With the methodology of computer-aided drug design, it is able to save and decrease time and money in R&D. Using the way of protein-based and ligand-based design to provide information of finding new possible PDE5 inhibitors of high selectivity.
First part of the experiment is based on mechanism of inhibition of tadalafil, and 1500 compounds are found out with two different scoring functions (Goldscore and Chemscore) in GOLD software. Then we get 90 compounds through the filter of Pscore , Druglike and more precise parameter settings. Secondly, one hydrophobic, one ring aromatic, one hydrogen bond donor, and one hydrogen bond acceptor based pharmacophore models which are developed by a series of Tadalafil derivatives is able to estimate the inhibition activity of compounds, provide the clue of different inhibition mechanism between cis- form and trans-form derivatives, and virtually screen the chemical database.

1. Johannes CB , Araujo AB , Feldman HA , Derby CA , Kleinman KP , McKinlay JB . Incidence of erectile dysfunction in men 40 to 69 years old : longitudinal results from the Massachusetts male aging study . J Urol . 2000 Feb ; 163 ( 2 ) : 460-3.

2. The process of care model for evaluation and treatment of erectile dysfunction . The Process of Care Consensus Panel . Int J Impot Res . 1999 Apr ; 11 ( 2 ) : 59-70 ; discussion 70-4 . Review .

3. Corbin JD , Francis SH . Cyclic GMP phosphodiesterase-5 : target of sildenafil .
J Biol Chem . 1999 May 14 ; 274 ( 20 ) : 13729-32.Review .

4. Rotella DP . Phosphodiesterase 5 inhibitors : current status and potential applications .
Nat Rev Drug Discov . 2002 Sep ; 1 ( 9 ) : 674-82.Review .

5. Gresser U , Gleiter CH . Erectile dysfunction : comparison of efficacy and side effects of the PDE-5 inhibitors sildenafil , vardenafil and tadalafil --review of the literature . Eur J Med Res . 2002 Oct 29 ; 7 ( 10 ) : 435-46.Review .

6. Manganiello VC , Degerman E. Cyclic nucleotide phosphodiesterases ( PDEs ) : diverse regulators of cyclic nucleotide signals and inviting molecular targets for novel therapeutic agents . Thromb Haemost . 1999 Aug ; 82 ( 2 ) : 407-11.Review .

7. Manallack DT , Hughes RA , Thompson PE . The next generation of phosphor- diesterase inhibitors : structural clues to ligand and substrate selectivity of phosphodiesterases . J Med Chem . 2005 May 19 ; 48 ( 10 ) : 3449-62.Review .

8. Pfizer Inc . http://www.pfizer.com/

9. Bayer Pharmaceuticals http://www.bayerpharma-na.com/

10. Lilly ICOS LLC http://www.lillyicos.com/

11.Sung BJ , Hwang KY , Jeon YH , Lee JI , Heo YS , Kim JH , Moon J , Yoon JM , Hyun YL , Kim E , Eum SJ , Park SY , Lee JO , Lee TG , Ro S , Cho JM . Structure of the catalytic domain of human phosphodiesterase 5 with bound drug molecules . Nature . 2003 Sep 4 ; 425 ( 6953 ) : 98-102.

12. Joseph A. DiMasi , Ronald W. Hansen , Henry G. Grabowski The price of innovation: new estimates of drug development costs. Journal of Health Economics 2003 22;151–185

13. Cohen, N. C.; Blaney, J. M.; Humblet, C.; Gund, P.; Barry, D. C. Molecular Modeling Software and Methods for Medicinal Chemistry. J. Med. Chem. 1990;33, 883-894.

14. Liu HL, Hsu JP. Recent developments in structural proteomics for protein structure determination. Proteomics. 2005 May;5(8):2056-68.

15. Schneider G, Bohm HJ. Virtual screening and fast automated docking methods.
Drug Discov Today. 2002 Jan 1;7(1):64-70. Review.

16. Abagyan R, Totrov M.High-throughput docking for lead generation.Curr Opin Chem Biol. 2001 Aug;5(4):375-82. Review.

17. Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov. 2004 Nov;3(11):935-49. Review.
,
18. E. M. Krovat, T. Steindl and T. Langer. Recent Advances in Docking and Scoring Current Computer-Aided Drug Design, (2005), 1, 93-102

19. GOLD, version 2.2; The Cambridge Crystallographic Data Centre 12 Union Road, Cambridge, CB2 1EZ, UK, http://www.ccdc.cam.ac.uk/

20. CATALYST, version 4.10 (software package); Accelrys, Inc. (previously known as Molecular Simulations, Inc.): San Diego, 2004. http://www.accelrys.com/

21. Sybyl, version7.0 Tripos Associates: St. Louis, MO. http://www.tripos.com/

22. IDEA Breadth technology Inc. http://www.breadth.com.tw/

23. Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol. 1997 Apr 4;267(3):727-48.

24. Wang R, Lai L, Wang S.Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput Aided Mol Des. 2002 Jan;16(1):11-26.

25. Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des. 1997 Sep; 11(5): 425-45.

26. Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD. Improved protein- ligand docking using GOLD. Proteins. 2003 Sep 1;52(4):609-23.

27. Debnath AK.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. 2003 Oct 9;46(21):4501-15. Erratum in: J Med Chem. 2004 Jan 29;47(3):768

28. Parenti MD, Pacchioni S, Ferrari AM, Rastelli G. Three-dimensional quantitative structure- activity relationship analysis of a set of Plasmodium falciparum dihydrofolate reductase inhibitors using a pharmacophore generation approach. J Med Chem. 2004 Aug 12;47(17):4258-67.

29. Huai Q, Liu Y, Francis SH, Corbin JD, Ke H. Crystal structures of phosphor- diesterases 4 and 5 in complex with inhibitor 3-isobutyl-1-methylxanthine suggest a conformation determinant of inhibitor selectivity. J Biol Chem. 2004 Mar 26;279(13):13095-101. Epub 2003 Dec 10.

30. Zhang KY, Card GL, Suzuki Y, Artis DR, Fong D, Gillette S, Hsieh D, Neiman J, West BL, Zhang C, Milburn MV, Kim SH, Schlessinger J, Bollag G.A glutamine switch mechanism for nucleotide selectivity by phosphodiesterases. Mol Cell. 2004 Jul 23;15(2):279-86. Erratum in: Mol Cell. 2004 Aug 27;15(4):659.

31. Card GL, England BP, Suzuki Y, Fong D, Powell B, Lee B, Luu C, Tabrizizad M, Gillette S, Ibrahim PN, Artis DR, Bollag G, Milburn MV, Kim SH, Schlessinger J, Zhang KY. Structural basis for the activity of drugs that inhibit phosphodiesterases. Structure (Camb). 2004 Dec;12(12):2233-47.

32. Daugan A, Grondin P, Ruault C, Le Monnier de Gouville AC, Coste H, Kirilovsky J, Hyafil F, Labaudiniere R. 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)-dione analogues. J Med Chem. 2003 Oct 9;46(21):4525-32.

33. Daugan A, Grondin P, Ruault C, Le Monnier de Gouville AC, Coste H, Linget JM, Kirilovsky J, Hyafil F, Labaudiniere R.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. 2003 Oct 9;46(21):4533-42.

34. Zoraghi R, Bessay EP, Corbin JD, Francis SH.Structural and functional features in human PDE5A1 regulatory domain that provide for allosteric cGMP binding, dimerization, and regulation. J Biol Chem. 2005 Mar 25;280(12):12051-63. Epub 2005 Jan 27. Roya Zoraghi, Emmanuel P. Bessay, et al.