A Perspective of Modern Methods in Computer-Aided Drugc design. In: Lipkowitz KB, Boyd DB, editors. Reviews in Computational Chemistry. Hoboken: John Wiley & Sons, Inc.; 1994. pp. 337-79. [DOI: 10.1002/9780470125823.ch7]

Novel local (fragment-based) topological molecular descriptors for QSpr/QSAR and molecular design

Novel molecular descriptors based on local spectral moments of the bond matrix are defined. Mathematical expressions relating bond moments to linear combinations of structural fragments are derived. The novel descriptors are used to describe boiling points of alcohols producing a good QSPR model accounting for more than 98% of variance. A quantitative structure-reactivity model is obtained to predict the specific rate constant (log k) of the nucleophilic addition of mercaptoacetic acid to 2-furylethylene derivatives. The model accounts for more than 96% of the variance in log k. Two other models were also obtained by using molecular connectivity indices and total spectral moments of the bond matrix that account for <84% of the variance in this reactivity index. A model based on quantum chemical descriptors accounts for the same variance than that obtained with bond moments. The model based on local moments permitted to compute the contribution of different structural fragments to the reactivity, and a good relationship (r = 0.98) was obtained with these group contributions with Hammett sigma(p) constants for 21 groups.

Discovery of new inhibitors of aldose reductase from molecular docking and database screening

Aldose reductase (ALR2) is a target enzyme for the treatment of diabetic complications. Owing to the limited number of currently available drugs for the treatment of diabetic complications, the discovery of new inhibitors of ALR2 that can potentially be optimized as drugs appears highly desirable. In this study, a molecular docking analysis of the structures of more than 127,000 organic compounds contained in the National Cancer Institute database was performed to find and score molecules that are complementary to ALR2. Besides retrieving several carboxylic acid derivatives, which are known to generally inhibit aldose reductase, docking proposed other families of putative inhibitors such as sulfonic acids, nitro-derivatives, sulfonamides and carbonyl derivatives. Twenty-five compounds, chosen as the highest-scoring representatives of each of these families, were tested as aldose reductase inhibitors. Five of them were found to inhibit aldose reductase in the micromolar range. For these active compounds, selectivity with respect to the closely-related aldehyde reductase was determined by measuring the corresponding inhibitory activities. The structures of the complexes between the new lead inhibitors and aldose reductase, here refined with molecular mechanics and molecular dynamics calculations, suggest that new pharmacophoric groups can bind aldose reductase very efficiently. In the case of the family of the nitro-derivative inhibitors, a class of particularly interesting compounds, a round of optimizations was performed with the synthesis and biological evaluation of a series of derivatives aimed at testing the proposed binding mode and at improving interaction with active site residues. Starting from a hit compound having an IC(50) of 42 microM, the most potent compound synthesized showed a 10-fold increase in inhibitory activity and 10-fold selectivity with respect to ALR1, and structure--activity relationships of the designed compounds were in agreement with the proposed mode of binding at the active site.