Topological charge-transfer indices: From small molecules to proteins

Current Proteomics

Volumn 6, Issue 4, 2009, Pages 204-213

  Torrens, Francisco ^a   Castellano, Gloria ^b  

^a UNIVERSITY OF VALENCIA   (Spain)

^b UNIVERSIDAD CATÓLICA DE VALENCIA SAN VICENTE MÁRTIR   (Spain)

Author keywords

Amino acid; Charge distribution; Dipole moment; Isoelectric point; Lysozyme; Protein; Valence isoelectronic series; Valence topological charge transfer index

Indexed keywords

EID: 72449155238     PISSN: 15701646     EISSN: None     Source Type: Journal    
DOI: 10.2174/157016409789973770     Document Type: Article

References (74)

1. Pogliani, L. From molecular connectivity indices to semiempirical connectivity terms: recent trends in graph theoretical descriptors. Chem. Rev., 2000, 100, 3827-3858.
2. Pogliani, L. Implementing molecular connectivity theory, a basic tool in modeling drugs. J. Pharm. Sci., 2007, 96, 1856-1871.
3. Garcia-Domenech, R.; Galvez, J.; de Julian-Ortiz, J.V. and Pogliani, L. Some new trends in chemical graph theory. Chem. Rev., 2008, 108, 1127-1169.
4. Estrada, E. and Uriarte, E. Recent advances on the role of topological indices in drug discovery research. Curr. Med. Chem., 2001, 8, 1573-1588.
5. Vilar, S.; Cozza, G. and Moro, S. Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery. Curr. Top Med. Chem., 2008, 8, 1555-1572.
6. Gonzalez-Diaz, H.; Prado-Prado, F. and Ubeira, F.M. Predicting antimicrobial drugs and targets with the MARCH-INSIDE approach. Curr. Top. Med. Chem., 2008, 8, 1676-1690.
7. González-Díaz, H.; Vilar, S.; Santana, L. and Uriarte, E. Medicinal chemistry and bioinformatics - current trends in drugs discovery with networks topological indices. Curr. Top Med. Chem., 2007, 7, 1025-1039.
8. Estrada, E.; Uriarte, E.; Molina, E.; Simon-Manso, Y. and Milne, G.W. An integrated in silico analysis of drug-binding to human serum albumin. J. Chem. Inf. Model., 2006, 46, 2709-2724.
9. Garcia, I.; Munteanu, C.R.; Fall, Y.; Gomez, G.; Uriarte, E. and Gonzalez-Diaz, H. QSAR and complex network study of the chiral HMGR inhibitor structural diversity. Bioorg. Med. Chem., 2009, 17, 165-175.
10. Vina, D.; Uriarte, E.; Orallo, F. and Gonzalez-Diaz, H. Alignmentfree prediction of a drug-target complex network based on parameters of drug connectivity and protein sequence of receptors. Mol. Pharm., 2009, 6, 825-835.
11. Prado-Prado, F.J.; Ubeira, F.M.; Borges, F. and Gonzalez-Diaz, H. Unified QSAR & network-based computational chemistry approach to antimicrobials. II. Multiple distance and triadic census analysis of antiparasitic drugs complex networks. J. Comput. Chem., 2009, [Epub ahead of print].
12. Prado-Prado, F.J.; de la Vega, O.M.; Uriarte, E.; Ubeira, F.M.; Chou, K.C. and Gonzalez-Diaz, H. 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., 2009, 17, 569-575.
13. Prado-Prado, F.; Borges, F.; Uriarte, E. and González-Díaz, H. Multi-target spectral moments for QSAR & complex networks study of antibacterial drugs. Eur. J. Med. Chem., 2009; 44(11), 4516-4521.
14. Munteanu, C.R.; Dorado, J.; Pazos-Sierra, A.; Prado-Prado, F.; Perez-Montoto, L.G.; Vilar, S.; Ubeira, F.M.; Sanchez-Gonzalez, A.; Cruz-Monteagudo, M.; Arrasate, S.; Sotomayor, N.; Lete, E.; Duardo-Sanchez, A.; Diaz-Lopez, A.; Patlewicz, G. and Gonzalez-Diaz, H. In Towards an information theory of Complex Networks: Statistical Methods and Applications. Emmert-Streib F.; Dehmer, M. and Mehler, A. Eds. Birkhäuser/Springer Publisher: Germany, 2009.
15. Aguero-Chapin, G.; Varona-Santos, J.; de la Riva, G.A.; Antunes, A.; Gonzalez-Villa, T.; Uriarte, E. and Gonzalez-Diaz, H. Alignment-free prediction of polygalacturonases with pseudofolding topological indices: experimental isolation from coffea arabica and prediction of a new sequence. J. Proteome Res., 2009, 8, 2122-2128.
16. Shen, H.B. and Chou, K.C. PseAAC: A flexible web server for generating various kinds of protein pseudo amino acid composition. Anal. Biochem., 2008, 373, 386-388.
17. Chou, K.C. and Shen, H.B. Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms. Nat. Protoc., 2008, 3, 153-162.
18. Marrero-Ponce, Y.; Castillo, G.J.A. and Nodarse, D. Linear indices of the 'macromolecular graph's nucleotides adjacency matrix' as a promising approach for bioinformatics studies. Part 1: prediction of paromomycin's affinity constant with HIV-1 psi-RNA packaging region. Bioorg. Med. Chem., 2005, 13, 3397-3404.
19. Marrero-Ponce, Y.; Nodarse, D.; González-Díaz, H.; Ramos de Armas, R.; Romero-Zaldivar, V.; Torrens, F. and Castro, E.A. Nucleic acid quadratic indices of the "Macromolecular Graph's Nucleotides Adjacency Matrix". Modeling of footprints after the interaction of paromomycin with the HIV-1 Ψ-RNA packaging region. Int. J. Mol. Sci., 2004, 5, 276-293.
20. Marrero-Ponce, Y.; Ortega-Broche, S.E.; Diaz, Y.E.; Alvarado, Y.J.; Cubillan, N.; Cardoso, G.C.; Torrens, F. and Perez-Gimenez, F. Nucleotide's bilinear indices: novel bio-macromolecular descriptors for bioinformatics studies of nucleic acids. I. Prediction of paromomycin's affinity constant with HIV-1 Psi-RNA packaging region. J. Theor. Biol., 2009, 259, 229-241.
21. Marrero-Ponce, Y.; Medina-Marrero, R.; Castillo-Garit, J.A.; Romero-Zaldivar, V.; Torrens, F. and Castro, E.A. Protein linear indices of the 'macromolecular pseudograph alpha-carbon atom adjacency matrix' in bioinformatics. Part 1: prediction of protein stability effects of a complete set of alanine substitutions in Arc repressor. Bioorg. Med. Chem., 2005, 13, 3003-3015.
22. Marrero-Ponce, Y.; Medina-Marrero, R.; Castro, A.E.; Ramos de Armas, R.; González-Díaz, H.; Romero-Zaldivar, V. and Torrens, F. Protein quadratic indices of the "Macromolecular Pseudograph's α-Carbon Atom Adjacency Matrix". 1. Prediction of Arc repressor alanine-mutant's stability. Molecules, 2004, 9, 1124-1147.
23. González-Díaz, H.; Saiz-Urra, L.; Molina, R.; Santana, L. and Uriarte, E. A model for the recognition of protein kinases based on the entropy of 3D van der waals interactions. J. Proteome Res., 2007, 6, 904-908.
24. Concu, R.; Podda, G.; Uriarte, E. and Gonzalez-Diaz, H. Computational chemistry study of 3D-structure-function relationships for enzymes based on Markov models for protein electrostatic, HINT, and van der Waals potentials. J. Comput. Chem., 2009, 30, 1510-1520.
25. Concu, R.; Dea-Ayuela, M.A.; Perez-Montoto, L.G.; Bolas-Fernandez, F.; Prado-Prado, F.J.; Podda, G.; Uriarte, E.; Ubeira, F.M. and Gonzalez-Diaz, H. Prediction of enzyme classes from 3D structure: a general model and examples of experimental-theoretic scoring of peptide mass fingerprints of leishmania proteins. J. Proteome Res., 2009, 8, 4372-4382.
26. González-Díaz, H. and Uriarte, E. Biopolymer stochastic moments. I. Modeling human rhinovirus cellular recognition with protein surface electrostatic moments. Biopolymers, 2005, 77, 296-303.
27. Estrada, E. and Rodriguez-Velazquez, J.A. Subgraph centrality in complex networks. Phys. Rev. E., 2005, 71, 056103.
28. Ferino, G.; Gonzalez-Diaz, H.; Delogu, G.; Podda, G. and Uriarte, E. Using spectral moments of spiral networks based on PSA/mass spectra outcomes to derive quantitative proteome-disease relationships (QPDRs) and predicting prostate cancer. Biochem. Biophys. Res. Commun., 2008, 372, 320-325.
29. González-Díaz, H.; González-Díaz, Y.; Santana, L.; Ubeira, F.M. and Uriarte, E. Proteomics, networks and connectivity indices. Proteomics, 2008, 8, 750-778.
30. Torrens, F. Structural, chemical topological, electrotopological and electronic structure hypotheses. Comb. Chem. High Throughput Screen, 2003, 6, 801-809.
31. Torrens, F.; Sanchez-Marin, J. and Nebot-Gil, I. Torsional effects on the molecular polarizabilities of the benzothiazole (A)-benzobisthiazole (B) oligomer A-B13-A. J. Mol. Graph., 1996, 14, 245-259, 277.
32. Torrens, F.; Sánchez-Marín, J. and Nebot-Gil, I. Polarization by the effect of a small torsional change in the benzothiazole (A)-benzobisthiazole (B) oligomer A-B13-A. Molecules, 1999, 4.
33. Torrens, F.; Sánchez-Marín, J. and Nebot-Gil, I. Interacting induced dipoles polarization model for molecular polarizabilities. Reference molecules, amino acids and model peptides. J. Mol. Struct., (THEOCHEM), 1999, 463, 27-39.
34. Torrens, F. A new topological index to elucidate apolar hydrocarbons. J. Comput. Aided Mol. Des., 2001, 15, 709-719.
35. Gálvez, J.; García, R.; Salabert, M.T. and Soler, R. Charge indexes. New topological descriptors. J. Chem. Inf. Comput. Sci., 1994, 34, 520-525.
36. Torrens, F. Valence topological charge-transfer indices for dipole moments. J. Mol. Struct. (THEOCHEM), 2003 621, 37-42.
37. Torrens, F. Valence topological charge-transfer indices for dipole moments. Mol. Divers, 2004, 8, 365-370.
38. Torrens, F. Valence topological charge-transfer indices for reflecting polarity: correction for heteromolecules. Molecules, 2005, 10, 334-345.
39. Torrens, F. Valence topological charge-transfer indices for dipole moments. Molecules, 2003, 8, 169-185.
40. Torrens, F. Valence topological charge-transfer indices for dipole moments: Percutaneous enhancers. Molecules, 2004, 9, 1222-1235.
41. Torrens, F. Fractal dimension of transdermal-delivery drug models. Lab. Sci. J., 2004, 5, 61-70.
42. Torrens, F. and Castellano, G. Fractal dimension of transdermaldelivery drug models: 4-Alkylanilines. J. Liq. Chromatogr. Relat. Technol., 2008, 31, 2337-2347.
43. Torrens, F. A new chemical index inspired by biological plastic evolution. Indian J. Chem., Sect. A., 2003, 42, 1258-1263.
44. Torrens, F. A chemical index inspired by biological plastic evolution: valence-isoelectronic series of aromatics. J. Chem. Inf. Comput. Sci., 2004, 44, 575-581.
45. Torrens, F. and Castellano, G. In QSPR-QSAR Studies on Desired Properties for Drug Design, E.A. Castro, ed.; Research Signpost: Trivandrum (India), 2009, in press.
46. Torrens, F. and Castellano, G. In Synthetic Organic Chemistry, Seijas, J.A. and Vázquez-Tato, M.P. Eds. MDPI: Basel (Switzerland), 2007, Vol. 11, pp. 1-16.
47. Torrens, F. and Castellano, G. Improvement of charge-transfer indices for multifunctional amino acids: application to lysozyme. SAR QSAR Environ. Res., 2008, 19, 643-654.
48. Randic, M. On characterization of molecular branching. J. Am. Chem. Soc., 1975, 97, 6609-6615.
49. Hosoya, H. A newly proposed quantity characterizing the topological nature of structural isomers of saturated hydrocarbons. Bull. Chem. Soc. Jpn., 1971, 44, 2332-2339.
50. Gálvez, J. On a topological interpretation of electronic and vibrational molecular energies. J. Mol. Struct. (THEOCHEM), 1998, 429, 255-264.
51. Gálvez, J.; García-Domenech, R.; de Julián-Ortiz, J.V. and Soler, R. Topological approach to drug design. J. Chem. Inf. Comput. Sci., 1995, 35, 272-284.
52. Kier, L.B. and Hall, L.H. Molecular connectivity VII: Specific treatment to heteroatoms. J. Pharm. Sci., 1976, 65, 1806-1809.
53. Pauling, L. Influence of valence, electronegativity, atomic radii, and crest-trough interaction with phonons on the high-temperature copper oxide superconductors. Phys. Rev. Lett., 1987, 59, 225-227.
54. Kubinyi, H. In Pharmacokinetic Optimization in Drug Research, H. van de Waterbeemd Testa, B.; Folkers G.; and Guy, R.; Eds. Helvetia Chimica Acta: Zurich, 2001, pp. 513-524.
55. Pogliani, L. The hydrogen perturbation in molecular connectivity computations. J. Comput. Chem., 2006, 27, 868-882.
56. Pogliani, L. Model of the physical properties of halides with complete graph-based indices. Int. J. Quantum. Chem., 2005, 102, 38-52.
57. Pogliani, L. Topics in molecular modeling: Dual indices, quality of modeling and missing information, truncation. J. Mol. Struct. (THEOCHEM), 2002, 581, 87-109.
58. Walsh, L.L. Navigating the Brookhaven Protein Data Bank. Comput. Appl. Biosci., 1994, 10, 551-557.
59. Bernstein, F.C.; Koetzle, T.F.; Williams, G.J.; Meyer, E.F.Jr.; Brice, M.D.; Rodgers, J.R.; Kennard, O.; Shimanouchi, T. and Tasumi, M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 1977, 112, 535-542.
60. Torrens, F. and Castellano, G. In Foundation on Computational Intelligence, A. E. Hassanien and A. Abraham, ed.; Springer: Berlin, 2009, vol. 5, pp. 243-315.
61. Torrens, F. and Castellano, G. In Biomedical Data and Applications, Sidhu, A.S.; Dillon, T.S. and Chang E. Eds. Springer: Berlin, 2009, in press.
62. Torrens, F. and Castellano, G. In Organic Chemistry Vayssilov, G.; and Nikolova, R. Ed.: Heron, Sofia, 2009; Vol. 2, pp. in press.
63. Torrens, F. and Castellano, G. Comparative analysis of the electrostatics of the binding of cationic proteins to vesicles: Asymmetric location of anionic phospholipids. Anal. Chim. Acta, 2009, submitted for publication.
64. Torrens, F.; Castellano, G.; Campos, A. and Abad, C. Negatively cooperative binding of melittin to neutral phospholipid vesicles. J. Mol. Struct., 2007, 834-836, 216-228.
65. Torrens, F.; Campos, A. and Abad, C. Binding of vinyl polymers to anionic model membranes. Cell Mol Biol (Noisy-le-grand), 2003, 49, 991-998.
66. Torrens, F.; Abad, C.; Codoñer, A.; García-Lopera, R. and Campos, A. Interaction of polyelectrolytes with oppositely charged micelles studied by fluorescence and liquid chromatography. Eur. Polym. J., 2005, 41, 1439-1452.
67. Sánchez-Muñoz, O.L.; Capote-Peña, O.; Ledgeer, E.D.; Llovera-González, J.J. and Kenndler, E. Affinity electrophoresis in capillary format: zeta potential of staphylococcal protein A (Z-domain) and determination of complex constant with immunoglobulin Fc fragments. J. Capill. Electrophor. Microchip Technol., 2001, 7, 31-36.
68. Sánchez-Muñoz, O.L.; Nordström, E.G. and Pérez-Hernández, E. Electrophoretic and thermodynamic properties for biomaterial particles with Bovine Serum Albumin adsorption. Biomed. Mater. Eng., 2003, 13, 147-158.
69. Rosado, E.; Caroll, H.; Sánchez, O. and Peniche, C. Passive adsorption of human antirrabic immunoglobulin onto a polystyrene surface. J. Biomater. Sci., 2005, 16, 435-448.
70. Kinnari, T.J.; Esteban, J.; Martin-de-Hijas, N.Z.; Sánchez- Muñoz, O.; Sánchez-Salcedo, S.; Colilla, M.; Vallet-Regí, M. and Gomez-Barrena, E. Influence of surface porosity and pH on bacterial adherence to hydroxyapatite and biphasic calcium phosphate bioceramics. J. Med. Microbiol., 2009, 58, 132-137.
71. McClellan, A.L. Tables of experimental dipole moments, Freeman: San Francisco 1963.
72. Tasi, G. and Mizukami, F. Scaled effective one-electron method based on G2 theory: Results for aliphatic alkane molecules. J. Chem. Inf. Comput. Sci., 1998, 38, 632-638.
73. Molina, V.; Smith, B.R. and Merchán, M. A theoretical study of the electronic spectrum of styrene. Chem. Phys. Lett., 1999, 309, 486-494. (Pubitemid 129592662)
74. Molina, V. and Merchán, M. Theoretical analysis of the electronic spectra of benzaldehyde. J. Phys. Chem. A., 2001, 105, 3745-3751.