RT Journal Article
T1 Nucleic acid quadratic indices of the "Macromolecular graph's nucleotides adjacency matrix". Modeling of footprints after the interaction of paromomycin with the HIV-1 Psi-RNA packaging region
A1 Marrero Ponce, Yovani
A1 Nodarse, Delvin
A1 González Díaz, Humberto
A1 Ramos de Armas, Ronald
A1 Romero Zaldívar, Vicente
A1 Torrens, Francisco
A1 Castro, Eduardo A.
K1 Footprinting
K1 Paromomycin
K1 RNA HIV-1
K1 TOMOCOMD-CANAR approach
K1 Nucleic Acid Quadratic Index
K1 QSPR/QSAR
AB This report describes a new set of macromolecular descriptors of relevance tonucleic acid QSAR/QSPR studies, nucleic acids’ quadratic indices. These descriptors arecalculated from the macromolecular graph’s nucleotide adjacency matrix. A study of theinteraction of the antibiotic Paromomycin with the packaging region of the RNA presentin type-1 HIV illustrates this approach. A linear discriminant function gave rise toexcellent 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 classificationof 91.09%. In addition, the model’s overall predictability oscillates from 89.11% until87.13%, when n varies from 2 to 3 in leave-n-out jackknife method. This value stabilizesaround 88.12% when n was > 3. On the other hand, a linear regression model predictedthe local binding affinity constants [log K (10-4M-1)] between a specific nucleotide andthe aforementioned antibiotic. The linear model explains almost 92% of the variance ofthe experimental log K (R = 0.96 and s = 0.07) and LOO press statistics evidenced itspredictive ability (q2 = 0.85 and scv = 0.09). These models also permit the interpretationof the driving forces of the interaction process. In this sense, developed equations involveshort-reaching (k ≤ 3), middle-reaching (4 < k < 9) and far-reaching (k = 10 or greater)nucleotide’s quadratic indices. This situation points to electronic and topologicnucleotide’s backbone interactions control of the stability profile of Paromomycin-RNAcomplexes. Consequently, the present approach represents a novel and rather promisingway to chem & bioinformatics research.
PB MDPI
YR 2004
FD 2004
LK http://hdl.handle.net/10347/22744
UL http://hdl.handle.net/10347/22744
LA eng
NO Ponce, Y.M.; Nodarse, D.; Díaz, H.G.; De Armas, R.R.; Zaldivar, V.R.; Torrens, F.; 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.
NO F. T. acknowledges financial support from the Spanish MCT (Plan Nacional I+D+I, Project No. BQU2001-2935-C02-01).
DS Minerva
RD 4 may 2026