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.
The design of novel anti-HIV compounds has now become a crucial area for scientists around the world. In this paper a new set of macromolecular descriptors (that are calculated from the macromolecular graph's nucleotide adjacency matrix) of relevance to nucleic acid QSAR/QSPR studies, nucleic acids' linear indices. A study of the interaction of the antibiotic Paromomycin with the packaging region of the HIV-1 psi-RNA has been performed as example of this approach. A multiple linear regression model predicted the local binding affinity constants [Log K (10(-4) M(-1))] between a specific nucleotide and the aforementioned antibiotic. The linear model explains more than 87% of the variance of the experimental Log K (R = 0.93 and s = 0.102 x 10(-4) M(-1)) and leave-one-out press statistics evidenced its predictive ability (q2 = 0.82 and s(cv) = 0.108 x 10(-4) M(-1)). The comparison with other approaches (macromolecular quadratic indices, Markovian Negentropies and 'stochastic' spectral moments) reveals a good behavior of our method.
Marrero Ponce
Yovani
Y
Department of Pharmacy, Faculty of Chemical-Pharmacy, Chemical Bioactive Center, Central University of Las Villas, Santa Clara 54830, Villa Clara, Cuba. yovanimp@qf.uclv.edu.cu
Castillo Garit
Juan A
JA
Nodarse
Delvin
D
D000900:Anti-Bacterial Agents / Q000737:chemistry*; D020029:Base Pairing; D001483:Base Sequence; D019295:Computational Biology; D018983:DNA Footprinting; D015195:Drug Design; D015497:HIV-1 / Q000737:chemistry*; D006801:Humans; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010303:Paromomycin / Q000737:chemistry*; D011237:Predictive Value of Tests; D021281:Quantitative Structure-Activity Relationship; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012984:Software
D000900:Anti-Bacterial Agents; D012367:RNA, Viral; D010303:Paromomycin