Predicting antimicrobial drugs and targets with the MARCH-INSIDE approach

Current Topics in Medicinal Chemistry

Volumn 8, Issue 18, 2008, Pages 1676-1690

  González Díaz, Humberto ^a   Prado Prado, Francisco ^a   Ubeira, Florencio M ^a  

^a UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

Author keywords

And complex networks; Anti protozooal agents; Anti viral drugs; Antibacterial compounds; Antimicrobial agents; Graph theory; HIV RNA secondary structure; Human rhinoviruses; Markov chains; QSAR; Topographic indices; Topological indices; Viral surface proteins

Indexed keywords

ANTIINFECTIVE AGENT; ANTIPARASITIC AGENT; ANTIVIRUS AGENT; COCCIDIOSTATIC AGENT; LACTOFERRICIN; ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; LACTOFERRICIN B; LACTOFERRIN; VIRUS RNA;

ACCURACY; ANTIFUNGAL ACTIVITY; ANTIVIRAL ACTIVITY; BIOLOGICAL ACTIVITY; CHIRALITY; COMPUTER AIDED DESIGN; COMPUTER PREDICTION; COMPUTER PROGRAM; DRUG BINDING; DRUG CLASSIFICATION; DRUG DESIGN; DRUG DETERMINATION; DRUG RIBONUCLEIC ACID BINDING; DRUG STRUCTURE; DRUG TARGETING; FASCIOLIASIS; MATHEMATICAL COMPUTING; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REVIEW; STATISTICAL MODEL; STRUCTURE ANALYSIS; VALIDITY; ARTIFICIAL NEURAL NETWORK; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ANTI-HIV AGENTS; ANTI-INFECTIVE AGENTS; BASE SEQUENCE; CHEMISTRY, PHARMACEUTICAL; LACTOFERRIN; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NEURAL NETWORKS (COMPUTER); NUCLEIC ACID CONFORMATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RNA, VIRAL;

EID: 59149084486     PISSN: 15680266     EISSN: None     Source Type: Journal    
DOI: 10.2174/156802608786786543     Document Type: Review

References (59)

1. Mukhopadhyay, A.; Peterson, R.T. Curr. Opin. Chem. Biol., 2006, 10 (4), 327-333.
2. Balaban, A.T.; Basak, S.C.; Beteringhe, A.; Mills, D.; Supuran, C.T. Mol. Divers., 2004, 8 (4), 401-412.
3. Abraham, M.H.; Kumarsingh, R.; Cometto-Muniz, J.E.; Cain, W.S. Ann. N. Y. Acad. Sci., 1998, 855, 652-656.
4. Agrawal, V.K.; Bano, S.; Khadikar, P.V. Bioorg. Med. Chem., 2003, 11 (18), 4039-4047.
5. Barratt, M.D. Toxicol. Lett., 1998, 102-103, 617-621.
6. Benigni, R.; Andreoli, C.; Giuliani, A. Environ. Mol. Mutagen., 1994, 24 (3), 208-219.
7. Garcia-Garcia, A.; Galvez, J.; de Julian-Ortiz, J.V.; Garcia-Domenech, R.; Munoz, C.; Guna, R.; Borras, R. J. Biomol. Screen., 2005, 10 (3), 206-214.
8. Katritzky, A.R.; Gordeeva, E.V. J. Chem. Inf. Comput. Sci., 1993, 33 (6), 835-857.
9. González-Díaz, H.; González-Díaz, Y.; Santana, L.; Ubeira, F.M.; Uriarte, E. Proteomics, 2008, 8, 750-778.
10. González-Díaz, H.; Vilar, S.; Santana, L.; Uriarte, E. Curr. Top. Med. Chem., 2007, 7 (10), 1025-1039.
11. Mas-Coma, S.; Bargues, M.D.; Valero, M.A. Int. J. Parasitol., 2005, 35 (11-12), 1255-1278.
12. Mas-Coma, M.S.; Esteban, J.G.; Bargues, M.D. Bull. World Health Organ, 1999, 77 (4), 340-346.
13. González-Díaz, H.; Olazabal, E.; Castanedo, N.; Sanchez, I.H.; Morales, A.; Serrano, H.S.; Gonzalez, J.; de Armas, R.R. J. Mol. Model., 2002, 8 (8), 237-245.
14. González-Díaz, H.; Cruz-Monteagudo, M.; Vina, D.; Santana, L.; Uriarte, E.; De Clercq, E. Bioorg. Med. Chem. Lett., 2005, 15 (6), 1651-1657.
15. Golbraikh, A.; Bonchev, D.; Tropsha, A. J. Chem. Inf. Comput. Sci., 2002, 42 (4) 769-787.
16. Randic, M. Acta Chim. Slov., 1998, 45 (3), 239-252.
17. de Julián-Ortiz, J.V.; de Gregorio Alapont, C.; Ríos-Santamarina, I.; García-Doménech, R.; Gálvez, J. J. Mol. Graph. Model., 1998, 16 (1), 14-18
18. Golbraikh, A.; Tropsha, A. J. Chem. Inf. Comput. Sci., 2003, 43 (1), 144-154.
19. Marrero-Ponce, Y.; Diaz, H.G.; Zaldivar, V.R.; Torrens, F.; Castro, E.A. Bioorg. Med. Chem., 2004, 12 (20), 5331-5342.
20. Castillo-Garit, J.A.; Marrero-Ponce, Y.; Torrens, F. Bioorg. Med. Chem., 2006, 14, 2398-2408.
21. Marrero-Ponce, Y.; Castillo-Garit, J.A. J. Comput. Aided Mol. Des., 2005, 19 (6), 369-383.
22. González-Díaz, H.; Sanchez, I.H.; Uriarte, E.; Santana, L. Comput. Biol. Chem., 2003, 27 (3), 217-227.
23. González-Díaz, H.; Torres-Gomez, L.A.; Guevara, Y.; Almeida, M.S.; Molina, R.; Castanedo, N.; Santana, L.; Uriarte, E. J. Mol. Model., 2005, 11 (2), 116-123.
24. González-Díaz, H.; Bastida, I.; Castanedo, N.; Nasco, O.; Olazabal, E.; Morales, A.; Serrano, H.S.; de Armas, R.R. Bull. Math. Biol., 2004, 66 (5), 1285-1311.
25. Allen, P.C.; Fetterer, R.H. Clin. Microbiol. Rev., 2002, 15 (1), 58-65.
26. Cruz-Monteagudo, M.; González-Díaz, H.; Agüero-Chapin, G.; Santana, L.; Borges, F.; Domínguez, R.E.; Podda, G.; Uriarte, E. J. Comput. Chem., 2007, 28, 1909-1922.
27. González-Díaz, H.; Prado-Prado, F.J.; Santana, L.; Uriarte, E. Bioorg. Med. Chem., 2006, 14 5973-5980.
28. González-Díaz, H.; Prado-Prado, F. J. Comput. Chem., 2008, 29, 656-657.
29. Prado-Prado, F.; González-Díaz, H.; Santana, L.; Uriarte, E. Bioorg. Med. Chem., 2007, 15, 897-902.
30. Prado-Prado, F.J.; González-Díaz, H.; Martinez de la Vega, O.; Ubeira, F.M.; Chou, K.C. Bioorg. Med. Chem., 2008, 16, 5871-5880.
31. Lejon, T.; Stiberg, T.; Strom, M.B.; Svendsen, J.S. J. Pept. Sci., 2004, 10 (6), 329-335.
32. Lejon, T.; Strom, M.B.; Svendsen, J.S. J. Pept. Sci., 2001, 7 (2), 74-81.
33. Strom, M.B.; Haug, B.E.; Rekdal, O.; Skar, M.L.; Stensen, W.; Svendsen, J.S. Biochem. Cell Biol., 2002, 80 (1), 65-74.
34. Ramos de Armas, R.; González-Díaz, H.; Molina, R.; Uriarte, E. Proteins, 2004, 56 (4), 715-723.
35. Ramos de Armas, R.; González-Díaz, H.; Molina, R.; Perez Gonzalez, M.; Uriarte, E. Bioorg. Med. Chem., 2004, 12 (18), 4815-4822.
36. Ramos de Armas, R.; González-Díaz, H.; Molina, R.; Uriarte, E. Biopolymers, 2005, 77 (5), 247-256.
37. González-Díaz, H.; Agüero-Chapin, G.; Varona, J.; Molina, R.; Delogu, G.; Santana, L.; Uriarte, E.; Gianni, P. J. Comput. Chem., 2007, 28, 1049-1056.
38. Zuker, M. Nucleic Acids Res., 2003, 31 (13), 3406-3415.
39. Wiese, K.C.; Hendriks, A. Bioinformatics, 2006, 22 (8), 934-942.
40. Kalate, R.N.; Tambe, S.S.; Kulkarni, B.D., Comput. Biol. Chem., 2003, 27 (6), 555-564.
41. González-Díaz, H.; Aguero-Chapin, G.; Varona-Santos, J.; Molina, R.; de la Riva, G.; Uriarte, E. Bioorg. Med. Chem. Lett., 2005, 15 (11), 2932-2937.
42. González-Díaz, H.; Pérez-Bello, A.; Uriarte, E. Polymer, 2005, 46 6461-6473.
43. González-Díaz, H.; Perez-Bello, A.; Uriarte, E.; Gonzalez-Diaz, Y. Bioorg. Med. Chem. Lett., 2006, 16 (3), 547-553.
44. González-Díaz, H.; Pérez-Bello, A.; Cruz-Monteagudo, M.; González-Díaz, Y.; Santana, L.; Uriarte, E. Chemom. Intell. Lab. Systs., 2007, 85, 20-26.
45. Varani, L.; Spillantini, M.G.; Goedert, M.; Varani, G. Nucleic Acids Res., 2000, 28 (3), 710-719.
46. Patel, D.J.; Suri, A.K. J. Biotechnol., 2000, 74 (1), 39-60.
47. Leclerc, F.; Cedergren, R. J. Med. Chem., 1998, 41 (2), 175-182.
48. Gonzalez-Diaz, H.; de Armas, R.R.; Molina, R. Bioinformatics, 2003, 19 (16), 2079-2087.
49. Gonzalez-Diaz, H.; de Armas, R.R.; Molina, R. Bull Math Biol., 2003, 65 (6), 991-1002.
50. Marrero Ponce, Y.; Castillo Garit, J.A.; Nodarse, D. Bioorg. Med. Chem., 2005, 13 (10), 3397-3404.
51. Marrero-Ponce, Y.; Nodarse, D.; González-Díaz, H.; Ramos de Armas, R.; Romero-Zaldivar, V.; Torrens, F.; Castro, E.A. Int. J. Mol. Sci., 2004, 5, 276-293.
52. Vlasak, M.; Roivainen, M.; Reithmayer, M.; Goesler, I.; Laine, P.; Snyers, L.; Hovi, T.; Blaas, D. J. Virol., 2005, 79 (12), 7389-7395.
53. Vlasak, M.; Blomqvist, S.; Hovi, T.; Hewat, E.; Blaas, D. J. Virol., 2003, 77 (12), 6923-6930.
54. Rossmann, M.G. Protein Sci., 1994, 3 (10), 1712-1725.
55. Suzuki, T.; Yamaya, M.; Kamanaka, M.; Jia, Y.X.; Nakayama, K.; Hosoda, M.; Yamada, N.; Nishimura, H.; Sekizawa, K.; Sasaki, H. Am. J. Physiol. Lung Cell Mol. Physiol., 2001, 280 (3), L409-420.
56. Xing, L.; Casasnovas, J.M.; Cheng, R.H. J. Virol., 2003, 77 (11), 6101-6107.
57. Chapman, M.S. Prot. Sci., 1993, 2 (3), 459-469.
58. Chapman, M.S.; Rossmann, M.G. Virology, 1993, 195 (2), 745-756.
59. Rosssmann, M.G.; Palmenberg, A.C. Virology, 1988, 164, 373-382.