Integrative computational protocol for the discovery of inhibitors of the Helicobacter pylori nickel response regulator (NikR)

Pyrazole-promoted synthesis of pyrrolo[3,4-c] quinoline-1,3-diones in a novel diketene-based reaction

We describe the first classic example of green synthesis of pyrrolo[3,4-c]quinolones scaffolds by catalyst-free unusual reaction of diketene, isatin, and primary amines in ethanol in the presence of pyrazole as a promoter for 4 h. The whole structure of the new product was confirmed by X-ray analysis. The overall transformation involves the cleavage and generation of multiple carbon-nitrogen and carbon-carbon bonds. This report represents a simple and straightforward approach for the synthesis of pyrrolo[3,4-c]quinoline-1,3-diones, which has significant advantages like readily available precursors, non-use of toxic solvent, operational simplicity, mild conditions, good atom economy, and excellent yields; therefore it provides a green and sustainable strategy for access to a range of interesting N-containing heterocyclic compounds in medicinal and organic chemistry.

Contact-based ligand-clustering approach for the identification of active compounds in virtual screening

Evaluation of docking results is one of the most important problems for virtual screening and in silico drug design. Modern approaches for the identification of active compounds in a large data set of docked molecules use energy scoring functions. One of the general and most significant limitations of these methods relates to inaccurate binding energy estimation, which results in false scoring of docked compounds. Automatic analysis of poses using self-organizing maps (AuPosSOM) represents an alternative approach for the evaluation of docking results based on the clustering of compounds by the similarity of their contacts with the receptor. A scoring function was developed for the identification of the active compounds in the AuPosSOM clustered dataset. In addition, the AuPosSOM efficiency for the clustering of compounds and the identification of key contacts considered as important for its activity, were also improved. Benchmark tests for several targets revealed that together with the developed scoring function, AuPosSOM represents a good alternative to the energy-based scoring functions for the evaluation of docking results.