Molecular modeling of the Toxoplasma gondii adenosine kinase inhibitors

Medicinal Chemistry Research

Volumn 21, Issue 5, 2012, Pages 590-600

  Da Cunha, Elaine F F ^a   Mancini, Daiana Teixeira ^a   Ramalho, Teodorico C ^a  

^a FEDERAL UNIVERSITY OF LAVRAS   (Brazil)

Author keywords

Adenosine kinase; Molecular modeling; Toxoplasma gondii

Indexed keywords

2 CHLORO 6 FLUORO 6 BENZYLTHIOINOSINE; 2,4 DICHLORO 6 BENZYLTHIOINOSINE; 2,4,6 TRIMETHYL 6 BENZYLTHIOINOSINE; 3,4 DICHLORO 6 BENZYLTHIOINOSINE; 6 BENZYLTHIOINOSINE; ADENOSINE KINASE INHIBITOR; M FLUORO N 6 BENZYLADENOSINE; M METHYL 6 BENZYLTHIOINOSINE; M METHYL N 6 BENZYLADENOSINE; M NITRO 6 BENZYLTHIOINOSINE; M TRIFLUOROMETHYL 6 BENZYLTHIOINOSINE; O CHLORO 6 BENZYLTHIOINOSINE; O FLUORO 6 BENZYLTHIOINOSINE; O METHYL 6 BENZYLTHIOINOSINE; ORTHO CHLORO N 6 BENZYLADENOSINE; ORTHO FLUORO N 6 BENZYLADENOSINE; ORTHO NITRO N 6 BENZYLADENOSINE; PARA ACETOXY 6 BENZYLTHIOINOSINE; PARA BROMO 6 BENZYLTHIOINOSINE; PARA CHLORO 6 BENZYLTHIOINOSINE; PARA CHLORO N 6 BENZYLADENOSINE; PARA CYANO 6 BENZYLTHIOINOSINE; PARA FLUORO 6 BENZYLTHIOINOSINE; PARA FLUORO N 6 BENZYLADENOSINE; PARA METHOXY 6 BENZYLTHIOINOSINE; PARA METHYL 6 BENZYLTHIOINOSINE; PARA NITRO 6 BENZYLTHIOINOSINE; PARA TERT BUTHYL 6 BENZYLTHIOINOSINE; PARA TRIFLUOROMETHOXY 6 BENZYLTHIOINOSINE; UNCLASSIFIED DRUG; UNINDEXED DRUG;

ARTICLE; DRUG STRUCTURE; GENETIC ALGORITHM; IC 50; MOLECULAR DOCKING; QUANTITATIVE STRUCTURE ACTIVITY RELATION; TOXOPLASMA GONDII;

EID: 84861850756     PISSN: 10542523     EISSN: 15548120     Source Type: Journal    
DOI: 10.1007/s00044-011-9554-z     Document Type: Article

References (41)

1. Al Safarjalani ON, Naguib FNM, El Kouni MH (2003) Uptake of nitrobenzylthioinosine and purine â-l-nucleosides by intracellular Toxoplasma gondii. Antimicrob Agents Chemother 47: 3247-3251 (Pubitemid 37229585)
2. Al Safarjalania ON, Raisa RH, Ah Kimb Y, Chub CK, Naguib FNM, El Kouni MH (2007) 7-Deaza-6-benzylthioinosine analogues as subversive substrate of Toxoplasma gondii adenosine kinase: activities and selective toxicities. Biochem Pharmacol 73: 1558-1572
3. Besler BH, Merz KM, Kollman PA (1990) Atomic charges derived form semiempirical methods. J Comput Chem 11:431-436
4. 4D-QSAR (1997) User's Manual v.1.00. The Chem21 Group Inc., 1780 Wilson Dr., Lake forest, IL, 60045
5. da Cunha EFF, Martins RCA, Alencastro RB, Albuquerque MG (2004) LIV-3D-QSAR model for estrogen receptor ligands. J Mol Model 10:297-304 (Pubitemid 39236652)
6. da Cunha EFF, Alencastro RB, Albuquerque MG, Antunes OAC (2005) 4D-QSAR models of HOE/BAY-793 analogues as HIV-1 protease inhihitors. QSAR Comb Sci 24:240-253
7. da Cunha EFF, Ramalho TC, Taft CA (2006) Computer-assisted analysis of the interactions of macrocyclic inhibitors with wild type and mutant D168A hepatitis C virus NS3 serine protease. Lett Drug Des Discov 3:17-28
8. da Cunha EFF, Ramalho TC, Reynolds RC (2008) Binding mode analysis of 2,4-diamino-5-methyl-5-deaza-6-substituted pteridines with Mycobacterium tuberculosis and human dihydrofolate reductases. J Biomol Struct Dyn 25:377-385
9. da Cunha EFF, Alencastro RB, Albuquerque MG, Antunes OAC (2009) 3D-QSAR CoMFA/CoMSIA models based on theoretical active conformers of HOE/BAY-793 analogs derived from HIV-1 protease-inhibitor complexes. Eur J Med Chem 44:4344-4352
10. da Cunha EFF, Ramalho TC, Mancini DT, Fonseca BEM, Oliveira AA (2010) New approaches to the development of antiprotozoan drug candidates: a review of patents. J Braz Chem Soc 21:1787-1806
11. Designed by MakoLab (C) (1985-2007) Hypercube, Inc. All Rights Reserved
12. El Kouni MH (2003) Potential chemotherapeutic targets in the purine metabolism of parasites. Pharmacol Ther 99:283-309 (Pubitemid 37311196)
13. El Kouni MH, Guarcello V, Al Safarjalani ON, Naguib FNM (1999) Metabolism and selective toxicity of 6-nitrobenzylthioinosine in Toxoplasma gondii. Antimicrob Agents Chemother 43: 2437-2443 (Pubitemid 29471224)
14. Friesner RA, Banks JL, Murphy RB, Halgren TA (2004) Glide: a new approach for rapid accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739-1749 (Pubitemid 38380917)
15. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Salvador P, Dannenberg JJ, Malick DK., Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, Pople JA (1998) Gaussian, Inc., Pittsburgh PA
16. Gustin DJ, Mattei P, Kast P, Wiest O, Lee L, Cleland WW, Hilvert D (1999) Heavy atom isotope effects reveal a highly polarized transition state for chorismate mutase. J Am Chem Soc 121:1756-1765
17. Hopfinger AJ, Wang S, Tokarski JS, Jin B, Albuquerque M, Madhav PJ, Duraiswami CJ (2007) Construction of 3D-QSAR models using the 4D-QSAR analysis formalism. J Am Chem Soc 119:10509-10524
18. Jain AN (2003) Surflex: fully automatic molecular docking using a molecular similarity-based search engine. J Med Chem 46:499-511 (Pubitemid 36182752)
19. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748 (Pubitemid 27170693)
20. Jorgensen WL (1991) Rusting of the lock and key model for proteinligand binding. Science 254:954-963
21. Josa D, da Cunha EFF, Ramalho TC (2008) Homology modeling of wild-type, D516V, and H526L Mycobacterium tuberculosis RNA polymerase and their molecular docking study with inhibitors. J Biomol Struct Dyn 25:373-376
22. Martins JP, Barbosa EG, Pasqualoto KFM, Ferreira MM (2009) LQTA-QSAR: A new 4D-QSAR methodology. J Chem Inform Model 49:1428-1436
23. MOLSIM (1997) User's Guide v.3.0. Doherty DC & The Chem21Group Inc., 1780 Wilson Dr., Lake Forest, IL 60045, 1997
24. Ngo HM, Ngo EO, Bzik DJ, Joiner KA (2000) Toxoplasma gondii: Are host cell adenosine nucleotides a direct source for purine salvage? Exp Parasitol 95:148-153 (Pubitemid 30618690)
25. Nissink JWM, Murray C, Hartshorn M, Verdonk ML, Cole JC, Taylor R (2002) A new test set for validating predictions of proteinligand interaction. Proteins 49:457-471 (Pubitemid 35388132)
26. Oliveira AA, da Cunha EFF, Ramalho TC (2009) QSAR study of androstenedione analogs as aromatase inhibitors. Lett Drug Des Discov 6:554-562
27. Petersen E (2007) Prevention and treatment of congenital toxoplasmosis. Expert Rev Anti-Infect Ther 5:285-293 (Pubitemid 46690956)
28. Rais HR, Al Safarjalani ON, Yadav V, Guarcello V, Kirk M, Chu CK, Naguib FNM, El Kouni MH (2005) 6-Benzylthioinosine analogues as subversive substrate of Toxoplasma gondii adenosine kinase: activities and selective toxicities. Biochem Pharmacol 69:1409-1419 (Pubitemid 40602441)
29. Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-489 (Pubitemid 26335901)
30. Reddy MCM, Palaninathan SK, Shetty ND, Owen JL, Watson MD, Sacchettini JC (2007) High resolution crystal structures of Mycobacterium tuberculosis adenosine kinase. J Biol Chem 282:27334-27342
31. Rogers D, Hopfinger AJ (1994) Application of genetic function approximation to QSAR and QSPR. J Chem Inf Comput Sci 34:854-866
32. Rutkowska-Zbik D, Witko M (2006) Following nature-theoretical studies on factors modulating catalytic activity of porphyrins. J Mol Catal A Chem 258:376-380 (Pubitemid 44354266)
33. Senese CL, Hopfinger AJ (2003) A simple clustering technique to improve QSAR model selection and predictivity: application to a receptor independent 4D-QSAR analysis of cyclic urea derived inhibitors of HIV-1 protease. J Chem Inf Comput Sci 43:2180-2193
34. Silveira NJF (2005) Bioinformática Estrutural Aplicada ao Estudo de Proteínas Alvo do Genoma do Mycobacterium tuberculosis. 117f. (Tese de Doutorado) Universidade Estadual Paulista, UNESP, Brazil
35. Singh UC, Kollman PA (1984) An approach to computing electrostatic charges for molecules. J Comput Chem 5:129-134
36. Souza TCS, Josa D, Ramalho TC, da Cunha EFF (2008) Molecular modelling of Mycobacterium tuberculosis acetolactate synthase catalytic subunit and its molecular docking study with inhibitors. Mol Simul 34:707-713
37. Thomsen R, Christensen MH (2006) MolDock: a new technique for high-accuracy molecular docking. J Med Chem 49:3315-3332
38. Vieth M, Hirst JD, Brooks CL (1998) Do active site conformations of small ligands correspond to low free-energy solution structures? J Comput Aided Mol Des 12:563-572 (Pubitemid 128512192)
39. Wang P, Zhang YL, Streitwieser A (1991) The effects of the first- and second-row substituents on the structures and energies of PH4X phosphoranes. An ab initio study. J Am Chem Soc 113:55-64
40. Weiner SJ, Kollman PA, Nguyen DT (1986) An All atom force-field for simulations of proteins and nucleic-acids. J Comput Chem 7:230-252
41. Yadav V, Chu CK, Rais RH, Al Safarjalani ON, Guarcello V, Naguib FNM, El Kouni MH (2004) Synthesis, biological activity and molecular modeling of 6-benzylthioinosine analogues as subversive substrates of Toxoplasma gondii adenosine kinase. J Med Chem 47:1987-1996 (Pubitemid 38453917)