New insights toward the discovery of antibacterial agents: Multi-tasking QSBER model for the simultaneous prediction of anti-tuberculosis activity and toxicological profiles of drugs

European Journal of Pharmaceutical Sciences

Volumn 48, Issue 4-5, 2013, Pages 812-818

  Speck Planche, Alejandro ^a   Kleandrova, Valeria V ^a,b   Cordeiro, M Natália D S ^a  

^a UNIVERSITY OF PORTO   (Portugal)

^b MOSCOW STATE UNIVERSITY OF FOOD PRODUCTION   (Russian Federation)

Author keywords

In silico selection; Inhibitors; Linear discriminant analysis; mtk QSBER; Mycobacterium tuberculosis; Spectral moments

Indexed keywords

TUBERCULOSTATIC AGENT;

ANTIBACTERIAL ACTIVITY; ARTICLE; DISCRIMINANT ANALYSIS; HUMAN; NONBIOLOGICAL MODEL; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; QUANTITATIVE STRUCTURE BIOLOGICAL EFFECT RELATIONSHIP; RELATIVE BIOLOGIC EFFECTIVENESS; TOXICOLOGY;

ANIMALS; ANTITUBERCULAR AGENTS; COMPUTER-AIDED DESIGN; DRUG DISCOVERY; DRUG TOXICITY; MICE; MODELS, BIOLOGICAL; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RATS;

EID: 84874161667     PISSN: 09280987     EISSN: 18790720     Source Type: Journal    
DOI: 10.1016/j.ejps.2013.01.011     Document Type: Article

References (59)

1. Y.L. Chen, S.T. Huang, F.M. Sun, Y.L. Chiang, C.J. Chiang, C.M. Tsai, and C.J. Weng Transformation of cinnamic acid from trans- to cis-form raises a notable bactericidal and synergistic activity against multiple-drug resistant mycobacterium tuberculosis Eur. J. Pharm. Sci. 43 2011 188 194
2. R. Concu, M.A. Dea-Ayuela, L.G. Perez-Montoto, F.J. Prado-Prado, E. Uriarte, F. Bolas-Fernandez, G. Podda, A. Pazos, C.R. Munteanu, F.M. Ubeira, and H. Gonzalez-Diaz 3D entropy and moments prediction of enzyme classes and experimental-theoretic study of peptide fingerprints in Leishmania parasites Biochim. Biophys. Acta 1794 2009 1784 1794
3. S. Croes, A.H. Koop, S.A. van Gils, and C. Neef Efficacy, nephrotoxicity and ototoxicity of aminoglycosides, mathematically modelled for modelling-supported therapeutic drug monitoring Eur. J. Pharm. Sci. 45 2012 90 100
4. J.V. de Assis, M.G. Teixeira, C.G. Soares, J.F. Lopes, G.S. Carvalho, M.C. Lourenco, M.V. de Almeida, W.B. de Almeida, and S.A. Fernandes Experimental and theoretical NMR determination of isoniazid and sodium p-sulfonatocalix[n] arenes inclusion complexes Eur. J. Pharm. Sci. 47 2012 539 548
5. EBI-Team. 2010. ChEMBL Database. < http://www.ebi.ac.uk/chembldb/ >.
6. E. Estrada Spectral moments of the edge adjacency matrix in molecular graphs. 1. Definition and applications for the prediction of physical properties of alkanes J. Chem. Inf. Comput. Sci. 36 1996 844 849
7. E. Estrada Spectral moments of the edge adjacency matrix in molecular graphs. 2. Molecules containing heteroatoms and QSAR applications J. Chem. Inf. Comput. Sci. 37 1997 320 328
8. E. Estrada Spectral moments of the edge adjacency matrix in molecular graphs. 3. Molecules containing cycles J. Chem. Inf. Comput. Sci. 38 1998 23 27
9. E. Estrada, and H. Gonzalez What are the limits of applicability for graph theoretic descriptors in QSPR/QSAR? Modeling dipole moments of aromatic compounds with TOPS-MODE descriptors J. Chem. Inf. Comput. Sci. 43 2003 75 84
10. Estrada, E., Gutiérrez, Y., 2002-2004. MODESLAB, v1.5. Santiago de Compostela.
11. E. Estrada, and E. Molina Automatic extraction of structural alerts for predicting chromosome aberrations of organic compounds J. Mol. Graph. Model. 25 2006 275 288
12. E. Estrada, and A. Peña In silico studies for the rational discovery of anticonvulsant compounds Bioorg. Med. Chem. 8 2000 2755 2770
13. E. Estrada, A. Pena, and R. Garcia-Domenech Designing sedative/hypnotic compounds from a novel substructural graph-theoretical approach J. Comput. Aided Mol. Des. 12 1998 583 595
14. E. Estrada, Y. Gutierrez, and H. Gonzalez Modeling diamagnetic and magnetooptic properties of organic compounds with the TOSS-MODE approach J. Chem. Inf. Comput. Sci. 40 2000 1386 1399
15. E. Estrada, E. Uriarte, A. Montero, M. Teijeira, L. Santana, and E. De Clercq A novel approach for the virtual screening and rational design of anticancer compounds J. Med. Chem. 43 2000 1975 1985
16. E. Estrada, E. Molina, and E. Uriarte Quantitative structure-toxicity relationships using TOPS-MODE. 2. Neurotoxicity of a non-congeneric series of solvents SAR QSAR Environ. Res. 12 2001 445 459
17. E. Estrada, E. Uriarte, Y. Gutierrez, and H. Gonzalez Quantitative structure-toxicity relationships using TOPS-MODE. 3. Structural factors influencing the permeability of commercial solvents through living human skin SAR QSAR Environ. Res. 14 2003 145 163
18. E. Estrada, G.A. Diaz, and E.J. Delgado Predicting infinite dilution activity coefficients of organic compounds in water by quantum-connectivity descriptors J. Comput. Aided Mol. Des. 20 2006 539 548
19. S. Feuerriegel, B. Oberhauser, A.G. George, F. Dafae, E. Richter, S. Rusch-Gerdes, and S. Niemann Sequence analysis for detection of first-line drug resistance in Mycobacterium tuberculosis strains from a high-incidence setting BMC Microbiol. 12 2012 90
20. I. Garcia, Y. Fall, G. Gomez, and H. Gonzalez-Diaz First computational chemistry multi-target model for anti-Alzheimer, anti-parasitic, anti-fungi, and anti-bacterial activity of GSK-3 inhibitors in vitro, in vivo, and in different cellular lines Mol. Divers. 15 2011 561 567
21. H. González-Díaz, A. Pérez-Bello, M. Cruz-Monteagudo, Y. González-Díaz, L. Santana, and E. Uriarte Chemometrics for QSAR with low sequence homology: mycobacterial promoter sequences recognition with 2D-RNA entropies Chemometr. Intell. Lab. Syst. 85 2007 20 26
22. H. Gonzalez-Diaz, L. Muino, A.M. Anadon, F. Romaris, F.J. Prado-Prado, C.R. Munteanu, J. Dorado, A.P. Sierra, M. Mezo, M. Gonzalez-Warleta, T. Garate, and F.M. Ubeira MISS-Prot: web server for self/non-self discrimination of protein residue networks in parasites; theory and experiments in Fasciola peptides and Anisakis allergens Mol. BioSyst. 7 2011 1938 1955
23. H. Gonzalez-Diaz, F. Prado-Prado, E. Sobarzo-Sanchez, M. Haddad, S. Maurel Chevalley, A. Valentin, J. Quetin-Leclercq, M.A. Dea-Ayuela, M. Teresa Gomez-Munos, C.R. Munteanu, J. Jose Torres-Labandeira, X. Garcia-Mera, R.A. Tapia, and F.M. Ubeira NL MIND-BEST: a web server for ligands and proteins discovery-Theoretic-experimental study of proteins of Giardia lamblia and new compounds active against Plasmodium falciparum J. Theor. Biol. 276 2011 229 249
24. H. Gonzalez-Diaz, C.R. Munteanu, L. Postelnicu, F. Prado-Prado, M. Gestal, and A. Pazos LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria Mol. BioSyst. 8 2012 851 862
25. B. Hanczar, J. Hua, C. Sima, J. Weinstein, M. Bittner, and E.R. Dougherty Small-sample precision of ROC-related estimates Bioinformatics 26 2010 822 830
26. J. Hau, and S.J. Schapiro Handbook of Laboratory Animal Science: Essential Principles and Practices 2011 CRC Press, Taylor & Francis Group, LLC Boca Raton, FL
27. T. Hill, and P. Lewicki Statistics Methods and Applications: A Comprehensive Reference for Science Industry and Data Mining 2006 Statsoft Tulsa
28. C.J. Huberty, and S. Olejnik Applied MANOVA and Discriminant Analysis second ed. 2006 John Wiley & Sons, Inc. Hoboken, New Jersey
29. H. Kubinyi QSAR: Hansch Analysis and Related Approaches 1993 VCH Publishers Weinheim, New York, Basel, Cambridge, Tokyo
30. C. Lienhardt, P. Glaziou, M. Uplekar, K. Lonnroth, H. Getahun, and M. Raviglione Global tuberculosis control: lessons learnt and future prospects Nat. Rev. Microbiol. 10 2012 407 416
31. G. Marzaro, A. Chilin, A. Guiotto, E. Uriarte, P. Brun, I. Castagliuolo, F. Tonus, and H. Gonzalez-Diaz Using the TOPS-MODE approach to fit multi-target QSAR models for tyrosine kinases inhibitors Eur. J. Med. Chem. 46 2011 2185 2192
32. E. Molina, E. Sobarzo-Sánchez, A. Speck-Planche, M.J. Matos, E. Uriarte, L. Santana, M. Yáñez, and F. Orallo Monoamino Oxidase A: An Interesting Pharmacological Target for the Development of Multi-Target QSAR Mini Rev. Med. Chem. 12 2012 947 958
33. T. Oprea Chemoinformatics in Drug Discovery 2005 WILEY-VCH Verlag GmbH & Co., KGaA Weinheim
34. D.S. Pope, R.E. Chaisson, and G.W. Comstock Tuberculosis P.S. Brachman, E. Abrutyn, Bacterial Infections of Humans: Epidemiology and Control 2012 Springer Science+Business Media, LLC New York, NY
35. F.J. Prado-Prado, F. Borges, L.G. Perez-Montoto, and H. Gonzalez-Diaz Multi-target spectral moment: QSAR for antifungal drugs vs. different fungi species Eur. J. Med. Chem. 44 2009 4051 4056
36. F.J. Prado-Prado, O. Martinez de la Vega, E. Uriarte, F.M. Ubeira, K.C. Chou, and H. Gonzalez-Diaz Unified QSAR approach to antimicrobials. 4. Multi-target QSAR modeling and comparative multi-distance study of the giant components of antiviral drug-drug complex networks Bioorg. Med. Chem. 17 2009 569 575
37. F.J. Prado-Prado, F.M. Ubeira, F. Borges, and H. Gonzalez-Diaz Unified QSAR & network-based computational chemistry approach to antimicrobials. II. Multiple distance and triadic census analysis of antiparasitic drugs complex networks J. Comput. Chem. 31 2009 164 173
38. F.J. Prado-Prado, E. Uriarte, F. Borges, and H. Gonzalez-Diaz Multi-target spectral moments for QSAR and complex networks study of antibacterial drugs Eur. J. Med. Chem. 44 2009 4516 4521
39. F.J. Prado-Prado, X. Garcia-Mera, and H. Gonzalez-Diaz Multi-target spectral moment QSAR versus ANN for antiparasitic drugs against different parasite species Bioorg. Med. Chem. 18 2010 2225 2231
40. F. Prado-Prado, X. Garcia-Mera, P. Abeijon, N. Alonso, O. Caamano, M. Yanez, T. Garate, M. Mezo, M. Gonzalez-Warleta, L. Muino, F.M. Ubeira, and H. Gonzalez-Diaz Using entropy of drug and protein graphs to predict FDA drug-target network: theoretic-experimental study of MAO inhibitors and hemoglobin peptides from Fasciola hepatica Eur. J. Med. Chem. 46 2011 1074 1094
41. F. Prado-Prado, X. Garcia-Mera, M. Escobar, E. Sobarzo-Sanchez, M. Yanez, P. Riera-Fernandez, and H. Gonzalez-Diaz 2D MI-DRAGON: a new predictor for protein-ligands interactions and theoretic-experimental studies of US FDA drug-target network, oxoisoaporphine inhibitors for MAO-A and human parasite proteins Eur. J. Med. Chem. 46 2011 5838 5851
42. P. Riera-Fernandez, C.R. Munteanu, M. Escobar, F. Prado-Prado, R. Martin-Romalde, D. Pereira, K. Villalba, A. Duardo-Sanchez, and H. Gonzalez-Diaz New Markov-Shannon entropy models to assess connectivity quality in complex networks: from molecular to cellular pathway, parasite-host, neural, industry, and legal-social networks J. Theor. Biol. 293 2012 174 188
43. K.J. Ryan, and C.G. Ray Sherris Medical Microbiology: An Introduction to Infectious Diseases fourth ed. 2004 McGraw Hill, Medical Publishing Division New York, Chicago, San Francisco, Lisbon, London, Madrid, Mexico City, Milan, New Delhi, San Juan, Seoul, Singapore, Sydney, Toronto
44. M.F. Simoes, E. Valente, M.J. Gomez, E. Anes, and L. Constantino Lipophilic pyrazinoic acid amide and ester prodrugs stability, activation and activity against M. tuberculosis Eur. J. Pharm. Sci. 37 2009 257 263
45. A. Speck-Planche, and M.N.D.S. Cordeiro Application of bioinformatics for the search of novel anti-viral therapies: rational design of anti-herpes agents Curr. Bioinform. 6 2011 81 93
46. A. Speck-Planche, and V.V. Kleandrova In silico design of multi-target inhibitors for C-C chemokine receptors using substructural descriptors Mol. Divers. 16 2012 183 191
47. A. Speck-Planche, V.V. Kleandrova, F. Luan, and M.N.D.S. Cordeiro Fragment-based QSAR model toward the selection of versatile anti-sarcoma leads Eur. J. Med. Chem. 46 2011 5910 5916
48. A. Speck-Planche, V.V. Kleandrova, and J.A. Rojas-Vargas QSAR model toward the rational design of new agrochemical fungicides with a defined resistance risk using substructural descriptors Mol. Divers. 15 2011 901 909
49. A. Speck-Planche, V.V. Kleandrova, F. Luan, and M.N.D.S. Cordeiro In silico discovery and virtual screening of multi-target inhibitors for proteins in Mycobacterium tuberculosis Comb. Chem. High Throughput Screen. 15 2012 666 673
50. A. Speck-Planche, V.V. Kleandrova, F. Luan, and M.N.D.S. Cordeiro Chemoinformatics in multi-target drug discovery for anti-cancer therapy: in silico design of potent and versatile anti-brain tumor agents Anticancer Agents Med. Chem. 12 2012 678 685
51. A. Speck-Planche, V.V. Kleandrova, F. Luan, and M.N.D.S. Cordeiro A ligand-based approach for the in silico discovery of multi-target inhibitors for proteins associated with HIV infection Mol. BioSyst. 8 2012 2188 2196
52. A. Speck-Planche, V.V. Kleandrova, F. Luan, and M.N.D.S. Cordeiro Predicting multiple ecotoxicological profiles in agrochemical fungicides: a multi-species chemoinformatic approach Ecotoxicol. Environ. Saf. 80 2012 308 313
53. A. Speck-Planche, V.V. Kleandrova, F. Luan, and M.N.D.S. Cordeiro Rational drug design for anti-cancer chemotherapy: multi-target QSAR models for the in silico discovery of anti-colorectal cancer agents Bioorg. Med. Chem. 20 2012 4848 4855
54. A. Speck-Planche, F. Luan, and M.N.D.S. Cordeiro Role of ligand-based drug design methodologies toward the discovery of new anti- alzheimer agents: futures perspectives in fragment-based ligand design Curr. Med. Chem. 19 2012 1635 1645
55. StatSoft, 2001. STATISTICA: Data Analysis Software System v6.0. Tulsa.
56. E. Tenorio-Borroto, C.G. Peñuelas Rivas, J.C. Vásquez Chagoyán, N. Castañedo, F.J. Prado-Prado, G. García-Mera, and H. González-Díaz ANN multiplexing model of drugs effect on macrophages; theoretical and flow cytometry study on the cytotoxicity of the anti-microbial drug G1 in spleen Bioorg. Med. Chem. 20 2012 6181 6194
57. R. Todeschini, and V. Consonni Handbook of Molecular Descriptors 2000 WILEY-VCH Verlag GmbH Weinheim, New York, Chichester, Brisbane, Singapore, Toronto
58. R. Todeschini, and V. Consonni Molecular Descriptors for Chemoinformatics 2009 WILEY-VCH Verlag GmbH & Co. KGaA Weinheim
59. D. Vina, E. Uriarte, F. Orallo, and H. Gonzalez-Diaz Alignment-free prediction of a drug-target complex network based on parameters of drug connectivity and protein sequence of receptors Mol. Pharm. 6 2009 825 835