3D-QSAR and molecular docking were applied to predict inhibitory activity of 196 compounds towards poly-(ADP-riboso)-polymerase-1 (PARP). Proportion of experimentally active ligands was higher among compounds with good rankings from both methods (57%) compared to compounds scored as inactive by at least one method (40% for docking-active, QSAR-inactive compounds).
A combination of the common quantum mechanics based transition state theory and exhaustive conformational search for the modeling of difficult reactions with hundreds of competing transition states is proposed. This approach is applied to study all transition state conformations of a reaction occurring in the catechol O-methyltransferase (COMT) active site in the absence of a major part of the enzyme, and the results are compared to the recent QM/MM modeling of this reaction within the enzyme. The main points of the method are (i) constraining of forming bonds upon conformer generation and (ii) preliminary constrained optimizations of located conformations to minima using a quantum mechanical method. Importantly, this methodology is applicable to the quantum mechanical part in QM/MM calculations and can reduce demand for large sampling in difficult cases.
A new perfluorinated sulfocationic polymer and a membrane based thereon have been produced using the thermally initiated high-pressure polymerization. The proton conductivity of obtained material is higher than that of commercial Nafion membranes and reaches 57 mS cm−1 at 21 C and 114 mS cm−1 at 79 C.
Although CDK7 inhibitors are considered to be potential anticancer drugs, all inhibitors developed so far have significant disadvantages preventing their further use. We have developed a new CDK7 inhibitor scaffold lacking hepatotoxicity using molecular dynamics (MD) and free energy perturbation (FEP/MD) methods, and were able to double its binding affinity after additional research. The combination of MD and FEP/MD methods was shown to be a valuable instrument for the development of novel and potent CDK7 inhibitors for anticancer therapy.