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

This report describes a new set of macromolecular descriptors of relevance to nucleic acid QSAR/QSPR studies, nucleic acids' quadratic indices. These descriptors are calculated from the macromolecular graph's nucleotide adjacency matrix. A study of the interaction of the antibiotic Paromom...

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Autores principales: Marrero Ponce, Yovani, Nodarse, Delvin, González Díaz, Humberto, Armas, Ronal Ramos de, Zaldívar, Vicente Romero, Torrens, Francisco, Castro, Eduardo A.
Formato: Articulo
Lenguaje:Inglés
Publicado: 2004
Materias:
Ciencias Médicas
binding affinity
footprinting
DNA footprinting
nucleic acid quadratic index
paromomycin
Human Immunodeficiency Virus
QSPR/QSAR
RNA HIV-1
TOMOCOMD-CANAR approach
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/37463
http://www.mdpi.com/1422-0067/5/11/276
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-37463
record_format dspace
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Ciencias Médicas
binding affinity
footprinting
DNA footprinting
nucleic acid quadratic index
paromomycin
Human Immunodeficiency Virus
QSPR/QSAR
RNA HIV-1
TOMOCOMD-CANAR approach
spellingShingle Ciencias Médicas
binding affinity
footprinting
DNA footprinting
nucleic acid quadratic index
paromomycin
Human Immunodeficiency Virus
QSPR/QSAR
RNA HIV-1
TOMOCOMD-CANAR approach
Marrero Ponce, Yovani
Nodarse, Delvin
González Díaz, Humberto
Armas, Ronal Ramos de
Zaldívar, Vicente Romero
Torrens, Francisco
Castro, Eduardo 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
topic_facet Ciencias Médicas
binding affinity
footprinting
DNA footprinting
nucleic acid quadratic index
paromomycin
Human Immunodeficiency Virus
QSPR/QSAR
RNA HIV-1
TOMOCOMD-CANAR approach
description This report describes a new set of macromolecular descriptors of relevance to nucleic acid QSAR/QSPR studies, nucleic acids' quadratic indices. These descriptors are calculated from the macromolecular graph's nucleotide adjacency matrix. A study of the interaction of the antibiotic Paromomycin with the packaging region of the RNA present in type-1 HIV illustrates this approach. A linear discriminant function gave rise to excellent discrimination between 90.10% (91/101) and 81.82% (9/11) of interacting/noninteracting sites of nucleotides in training and test set, respectively. The LOO crossvalidation procedure was used to assess the stability and predictability of the model. Using this approach, the classification model has shown a LOO global good classification of 91.09%. In addition, the model's overall predictability oscillates from 89.11% until 87.13%, when <i>n</i> varies from 2 to 3 in leave-<i>n</i>-out jackknife method. This value stabilizes around 88.12% when <i>n</i> was > 3. On the other hand, a linear regression model predicted the local binding affinity constants [log <i>K</i> (10<SUP>-4</SUP>M<SUP>-1</SUP>)] between a specific nucleotide and the aforementioned antibiotic. The linear model explains almost 92% of the variance of the experimental log <i>K</i> (R = 0.96 and s = 0.07) and LOO press statistics evidenced its predictive ability (q<SUP>2</SUP> = 0.85 and s<SUB>cv</SUB> = 0.09). These models also permit the interpretation of the driving forces of the interaction process. In this sense, developed equations involve short-reaching (<i>k</i> ≤ 3), middle-reaching (4 < <i>k</i> < 9) and far-reaching (<i>k</i> = 10 or greater) nucleotide's quadratic indices. This situation points to electronic and topologic nucleotide's backbone interactions control of the stability profile of Paromomycin-RNA complexes. Consequently, the present approach represents a novel and rather promising way to chem & bioinformatics research.
format Articulo
Articulo
author Marrero Ponce, Yovani
Nodarse, Delvin
González Díaz, Humberto
Armas, Ronal Ramos de
Zaldívar, Vicente Romero
Torrens, Francisco
Castro, Eduardo A.
author_facet Marrero Ponce, Yovani
Nodarse, Delvin
González Díaz, Humberto
Armas, Ronal Ramos de
Zaldívar, Vicente Romero
Torrens, Francisco
Castro, Eduardo A.
author_sort Marrero Ponce, Yovani
title 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
title_short 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
title_full 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
title_fullStr 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
title_full_unstemmed 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
title_sort 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
publishDate 2004
url http://sedici.unlp.edu.ar/handle/10915/37463
http://www.mdpi.com/1422-0067/5/11/276
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