Identification of novel influenza polymerase PB2 inhibitors using virtual screening approach and molecular dynamics simulation analysis of active compounds.

Hierarchical virtual screening combined with ADME prediction and cluster analysis methods were used to identify influenza virus PB2 inhibitors with high activity, good druggability properties, and diverse structures. The 200,000 molecules in the ChemDiv core library were narrowed down to a final set of 97 molecules, of which six compounds were found to rescue cells from both H1N1 and H3N2 virus-induced CPE with EC50 values ranging from 5.81 µM to 42.77 µM, and could bind to the PB2 CBD of H1N1, with Kd values of 0.11 µM to 6.4 µM. The six compounds have novel structures and low molecular weight and are, thus, suitable serve as lead compounds for development as PB2 inhibitors. A receptor-based pharmacophore model was successfully constructed using key amino acid residues for the binding of inhibitors to PB2, provided by the MD simulations. This pharmacophore model suggested that to improve the activity of our active compounds, we should mainly focus on optimizing their existing structures with the aim of increasing their adaptability to the binding site, rather than adding chemical fragments to increase their binding to adjacent sites. This pharmacophore construction method facilitates the creation of a reasonable pharmacophore model without the need to fully understand the structure-activity relationships, and our descriptions provide a useful reference for similar research.

Virtual Screening and Molecular Dynamics Simulation Study of Influenza Polymerase PB2 Inhibitors.

Influenza A virus is the main cause of worldwide epidemics and annual influenza outbreaks in humans. In this study, a virtual screen was performed to identify compounds that interact with the PB2 cap-binding domain (CBD) of influenza A polymerase. A virtual screening workflow based on Glide docking was used to screen an internal database containing 8417 molecules, and then the output compounds were selected based on solubility, absorbance, and structural fingerprints. Of the 16 compounds selected for biological evaluation, six compounds were identified that rescued cells from H1N1 virus-mediated death at non-cytotoxic concentrations, with EC50 values ranging from 2.5-55.43 µM, and that could bind to the PB2 CBD of H1N1, with Kd values ranging from 0.081-1.53 µM. Molecular dynamics (MD) simulations of the docking complexes of our active compounds revealed that each compound had its own binding characteristics that differed from those of VX-787. Our active compounds have novel structures and unique binding modes with PB2 proteins, and are suitable to serve as lead compounds for the development of PB2 inhibitors. An analysis of the MD simulation also helped us to identify the dominant amino acid residues that play a key role in binding the ligand to PB2, suggesting that we should focus on increasing and enhancing the interaction between inhibitors and these major amino acids during lead compound optimization to obtain more active PB2 inhibitors.

Studies on the synthesis and biological evaluation of the metabolite of clausenamide CM2 and its stereoisomers.

The synthesis and biological evaluation of 5-hydroxy clausenamide (CM2), one of the major metabolites of clausenamide, and its stereoisomers have been carried out. The absolute configurations of (-)- and (+)-CM2 were assigned as 3S,4S,5S,6S and 3R,4R,5R,6R respectively based on (1)H NMR spectroscopic investigation and their chemical correlation to (-)- and (+)-clausenamidone (3). Electrophysiological assay showed that compound (+)-CM2 and its C6 epimer (+)-8a had significant effects on synaptic transmission and thus induced the long-term potentiation of the dentate gyrus.

Synthesis and activity in enhancing long-term potentiation (LTP) of clausenamide stereoisomers.

Clausenamide, isolated from aqueous extract of dry leaves of Clausena lansium, a Chinese folk medicine, was found to have potent activity in enhancing LTP and show nootropic activity in animal tests. In order to discovery more potent stereoisomers and to analyze the relationship of structure-activity, the synthesis of 16 (8 pairs) optically pure stereoisomers of clausenamide with four chiral centers was achieved. The results of LTP assay showed that the nootropic activity of the stereoisomers of clausenamide is closely related to the configuration of stereoisomers.