Virtual screening studies of Chinese medicine Coptidis Rhizoma as alpha7 nicotinic acetylcholine receptor agonists for treatment of Alzheimer’s disease

Insight into the IgE-binding sites of allergenic peptides of tropomyosin in shrimp (Penaeus chinensis) induced by cold plasma active particles

Tropomyosin (TM) is a major allergen in crustaceans, and its allergenicity mainly depends on epitopes. In this study, the locations of IgE-binding sites between plasma active particles and allergenic peptides of TM in shrimp (Penaeus chinensis) during cold plasma (CP) treatment were explored. Results showed that the IgE-binding ability of two critical peptides (P1 and P2) increased and then decreased by 9.97 % and 19.50 % after 15 min of CP treatment. It was the first time to show that the contribution rate of target active particles was •O > e_(aq)^- > •OH for reducing IgE-binding ability by 23.51 %-45.40 %, and the contribution rates of other long-lived particles including NO₃^- and NO₂^- was about 54.60 %-76.49 %. In addition, Glu131 and Arg133 in P1 and Arg255 in P2 were certified as the IgE sites. These results were helpful for accurately controlling TM allergenicity, shedding more light on allergenicity mitigation during food processing.

Screening of potential inhibitors targeting the main protease structure of SARS-CoV-2 via molecular docking

The novel coronavirus disease (COVID-19) caused by SARS-CoV-2 virus spreads rapidly to become a global pandemic. Researchers have been working to develop specific drugs to treat COVID-19. The main protease (M^pro) of SARS-CoV-2 virus plays a pivotal role in mediating viral replication and transcription, which makes it a potential therapeutic drug target against COVID-19. In this study, a virtual drug screening method based on the M^pro structure (Protein Data Bank ID: 6LU7) was proposed, and 8,820 compounds collected from the DrugBank database were used for molecular docking and virtual screening. A data set containing 1,545 drug molecules, derived from compounds with a low binding free energy score in the docking experiment, was established. N-1H-Indazol-5-yl-2-(6-methylpyridin-2-yl)quinazolin-4-amine, ergotamine, antrafenine, dihydroergotamine, and phthalocyanine outperformed the other compounds in binding conformation and binding free energy over the N3 inhibitor in the crystal structure. The bioactivity and ADMET properties of these five compounds were further investigated. These experimental results for five compounds suggested that they were potential therapeutics to be developed for clinical trials. To further verify the results of molecular docking, we also carried out molecular dynamics (MD) simulations on the complexes formed by the five compounds and M^pro. The five complexes showed stable affinity in terms of root mean square distance (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and hydrogen bond. It was further confirmed that the five compounds had potential inhibitory effects on SARS-CoV-2 M^pro.

Hetero-Tricyclic Lead Scaffold as Novel PDE5A Inhibitor for Antihypertensive Activity: In Silico Docking Studies

Objective:

To screen the phytochemicals for phosphodiesterase 5A (PDE5A) inhibitory potential and identify lead scaffolds of antihypertensive phytochemicals using in silico docking studies.

Methods:

In this perspective, reported 269 antihypertensive phytochemicals were selected. Sildenafil, a PDE5A inhibitor was used as the standard. In silico docking study was carried out to screen and identify the inhibiting potential of the selected phytochemicals against PDE5A enzyme using vLife MDS 4.4 software.

Results:

Based on docking score, π-stacking, H-bond and ionic interactions, 237 out of 269 molecules were selected which have shown one or more interactions. Protein residue Gln817A was involved in H-boding whereas Val782A, Phe820A and Leu804A were involved in π-stacking interaction with ligand. The selected 237 phytochemicals were structurally diverse, therefore 82 out of 237 molecules with one or more tricycles were filtered out for further analysis. Amongst tricyclic molecules, 14 molecules containing nitrogen heteroatom were selected for lead scaffold identification which finally resulted in three different basic chemical backbones like pyridoindole, tetrahydro-pyridonaphthyridine and dihydro-pyridoquinazoline as lead scaffolds.

Conclusion:

In silico docking studies revealed that nitrogen-containing tetrahydro-pyridonaphthyridine and dihydro-pyridoquinazoline tricyclic lead scaffolds have emerged as novel PDE5A inhibitors for antihypertensive activity. The identified lead scaffolds may provide antihypertensive lead molecules after its optimization.