QSAR and classification study of 1,4-dihydropyridine calcium channel antagonists based on least squares support vector machines.

The least squares support vector machine (LSSVM), as a novel machine learning algorithm, was used to develop quantitative and classification models as a potential screening mechanism for a novel series of 1,4-dihydropyridine calcium channel antagonists for the first time. Each compound was represented by calculated structural descriptors that encode constitutional, topological, geometrical, electrostatic, quantum-chemical features. The heuristic method was then used to search the descriptor space and select the descriptors responsible for activity. Quantitative modeling results in a nonlinear, seven-descriptor model based on LSSVM with mean-square errors 0.2593, a predicted correlation coefficient (R(2)) 0.8696, and a cross-validated correlation coefficient (R(cv)(2)) 0.8167. The best classification results are found using LSSVM: the percentage (%) of correct prediction based on leave one out cross-validation was 91.1%. This paper provides a new and effective method for drug design and screening.

CISOC-PSCT: a predictive system for carcinogenic toxicity.

A SAR based carcinogenic toxicity prediction system, CISOC-PSCT, was developed. It consisted of two principal phases: the construction of relationships between structural descriptors and carcinogenic toxicity indices, and prediction of the toxicity from the SAR model. The training set included 2738 carcinogenic and 4130 non-carcinogenic compounds. Three predefined topological types of substructures termed Star, Path and Ring were used to generate the descriptors for each structure in the training set. In this system, the defined carcinogenic toxicity index (CTI) was obtained from the probability of a structural descriptor to either belong to the carcinogenic or non-carcinogenic compounds. Based on these structural descriptors and their CTI, a SAR model was derived. Then the carcinogenic possibility (CP) and the carcinogenic impossibility (CIP) of compounds were predicted. The model was tested from a testing set of 304 carcinogenic compounds (MDL toxicity database), 460 non-carcinogenic compounds (CMC database) and 94 compounds extracted from two traditional Chinese medicine herbs.

Virtual screening and rational drug design method using structure generation system based on 3D-QSAR and docking.

An efficient virtual and rational drug design method is presented. It combines virtual bioactive compound generation with 3D-QSAR model and docking. Using this method, it is possible to generate a lot of highly diverse molecules and find virtual active lead compounds. The method was validated by the study of a set of anti-tumor drugs. With the constraints of pharmacophore obtained by DISCO implemented in SYBYL 6.8, 97 virtual bioactive compounds were generated, and their anti-tumor activities were predicted by CoMFA. Eight structures with high activity were selected and screened by the 3D-QSAR model. The most active generated structure was further investigated by modifying its structure in order to increase the activity. A comparative docking study with telomeric receptor was carried out, and the results showed that the generated structures could form more stable complexes with receptor than the reference compound selected from experimental data. This investigation showed that the proposed method was a feasible way for rational drug design with high screening efficiency.

Theoretical study of fast repair of DNA damage by cistanoside C and analogs: mechanism and docking.

Experiments show that the natural substances phenylpropanoid glycosides (PPGs) extracted from pelicularis spicata are capable of repairing DNA damaged by oxygen radicals. Based on kinetic measurements and experiments on tumor cells, a theoretical study of the interaction between PPG molecules and isolated DNA bases, as well as a DNA fragment has been performed. An interaction mechanism reported early has been refined. The docking calculations performed using junction minimization of nucleic acids (JUMNA) software showed that the PPG molecules can be docked into the minor groove of DNA and form complexes with the geometry suitable for an electron transfer between guanine radical and the ligand. Such complexes can be formed without major distortions of DNA structure and are further stabilized by the interaction with the rhamnosyl side-groups.

Docking study of cistanoside C to telomeric DNA fragment.

Experiments show that the natural products phenyl propanoid glycosides (PPGs) extracted from the plant Pedicularis spicata are capable of repairing DNA damaged by oxygen radicals. Based on kinetic measurements and experiments on tumor cells, a theoretical study of the interaction between PPG molecule Cistanoside C and telomeric DNA fragment has been carried out. The docking calculations performed using JUMNA software showed that the Cistanoside C could be docked into the minor groove of telomeric DNA and form complexes with the geometry suitable for an electron transfer between guanine radical and the ligand. Such complexes can be formed without major distortions of DNA structure and are further stabilized by the interaction with the saccharide side-groups.