Fourteen immunomodulatory alkaloids and two prenylated phenylpropanoids with dual therapeutic approach for COVID-19: molecular docking and dynamics studies

Screening Asian Medicinal Plants for SARS-CoV-2 Inhibitors: A Computational Approach

This work aimed to evaluate the antiviral potential of compounds from Asian medicinal plants against SARS-CoV-2's main protease and spike glycoprotein, identifying dual inhibitors from these plants that target both proteins through advanced virtual screening, molecular dynamics simulations, and pharmacophore analysis. An in-house library of 335 antiviral natural products was prepared from the selected medicinal plants. Following the virtual screening of this library against the main protease and spike glycoprotein, top compounds were subjected to downstream analysis for evaluating druggability potential and toxicity analysis. Molecular dynamic simulations were performed to confirm the stability of interactions between the ligands and target proteins. Our analysis demonstrated 67 compounds as dual inhibitors. The six top dual inhibitors, namely trans-delta-viniferin, trans-E-viniferin, 3,4-DHPEA-EDA, oleuropein aglycone, lactucopicrin, and 11β,13-dihydrolactucopicrin, exhibited superior docking scores and met drug-likeness criteria, including Lipinski's rule, bioavailability, and favorable ADME and toxicity profiles. Trans-delta-viniferin and trans-E-viniferin, featuring a stilbene scaffold, emerged as the most promising candidates due to their stable interactions, minimal fluctuations, and consistent hydrogen bonding across SARS-CoV-2's Mpro and S-protein in MD simulations, while 3,4-DHPEA-EDA displayed comparatively less stability. All compounds demonstrated key pharmacophoric features and lacked mutagenicity or PAINS alerts, although lactucopicrin and 11β,13-dihydrolactucopicrin showed risks for hepatotoxicity. Overall, the critical bonding and drug-like features, biological activity spectra, and favorable medicinal characteristics predict their biological behavior in laboratory testing. Although additional experimental validations are necessary, our findings indicate that the three lead compounds-namely, trans-delta-viniferin, trans-E-viniferin, and 3,4-DHPEA-EDA, isolated from traditional medicinal plants-are promising novel dual inhibitors of two critical SARS-CoV-2 proteins.

Identifying plant-derived antiviral alkaloids as dual inhibitors of SARS-CoV-2 main protease and spike glycoprotein through computational screening

COVID-19 is currently considered the ninth-deadliest pandemic, spreading through direct or indirect contact with infected individuals. It has imposed a consistent strain on both the financial and healthcare resources of many countries. To address this challenge, there is a pressing need for the development of new potential therapeutic agents for the treatment of this disease. To identify potential antiviral agents as novel dual inhibitors of SARS-CoV-2, we retrieved 404 alkaloids from 12 selected medicinal antiviral plants and virtually screened them against the renowned catalytic sites and favorable interacting residues of two essential proteins of SARS-CoV-2, namely, the main protease and spike glycoprotein. Based on docking scores, 12 metabolites with dual inhibitory potential were subjected to drug-likeness, bioactivity scores, and drug-like ability analyses. These analyses included the ligand-receptor stability and interactions at the potential active sites of target proteins, which were analyzed and confirmed through molecular dynamic simulations of the three lead metabolites. We also conducted a detailed binding free energy analysis of pivotal SARS-CoV-2 protein inhibitors using molecular mechanics techniques to reveal their interaction dynamics and stability. Overall, our results demonstrated that 12 alkaloids, namely, adouetine Y, evodiamide C, ergosine, hayatinine, (+)-homoaromoline, isatithioetherin C, N,alpha-L-rhamnopyranosyl vincosamide, pelosine, reserpine, toddalidimerine, toddayanis, and zanthocadinanine, are shortlisted as metabolites based on their interactions with target proteins. All 12 lead metabolites exhibited a higher unbound fraction and therefore greater distribution compared with the standards. Particularly, adouetine Y demonstrated high docking scores but exhibited a nonspontaneous binding profile. In contrast, ergosine and evodiamide C showed favorable binding interactions and superior stability in molecular dynamics simulations. Ergosine demonstrated exceptional performance in several key pharmaceutical metrics. Pharmacokinetic evaluations revealed that ergosine exhibited pronounced bioactivity, good absorption, and optimal bioavailability. Additionally, it was predicted not to cause skin sensitivity and was found to be non-hepatotoxic. Importantly, ergosine and evodiamide C emerged as superior drug candidates for dual inhibition of SARS-CoV-2 due to their strong binding affinity and drug-like ability, comparable to known inhibitors like N3 and molnupiravir. This study is limited by its in silico nature and demands the need for future in vitro and in vivo studies to confirm these findings.

Bioassay-Guided Fractionation of Pittosporum angustifolium and Terminalia ferdinandiana with Liquid Chromatography Mass Spectroscopy and Gas Chromatography Mass Spectroscopy Exploratory Study

Bioprospecting native Australian plants offers the potential discovery of latent and novel bioactive compounds. The promising cytotoxic and antibacterial activity of methanolic extracts of Pittosporum angustifolium and Terminalia ferdinandiana led to further fractionation and isolation using our laboratory's bioassay-guided fractionation protocol. Hence, the aim of this study was to further evaluate the bioactivity of the fractions and subfractions and characterize bioactive compounds using liquid chromatography mass spectroscopy (LC-MS/MS) and gas chromatography MS (GC-MS). Compounds tentatively identified in P. angustifolium Fraction 1 using LC-ESI-QTOF-MS/MS were chlorogenic acid and/or neochlorogenic acid, bergapten, berberine, 8'-epitanegool and rosmarinic acid. GC-MS analysis data showed the presence of around 100 compounds, mainly comprising carboxylic acids, sugars, sugar alcohols, amino acids and monoalkylglycerols. Furthermore, the fractions obtained from T. ferdinandiana flesh extracts showed no cytotoxicity, except against HT29 cell lines, and only Fraction 2 exhibited some antibacterial activity. The reduced bioactivity observed in the T. ferdinandiana fractions could be attributed to the potential loss of synergy as compounds become separated within the fractions. As a result, the further fractionation and separation of compounds in these samples was not pursued. However, additional dose-dependent studies are warranted to validate the bioactivity of T. ferdinandiana flesh fractions, particularly since this is an understudied species. Moreover, LC-MS/GC-MS studies confirm the presence of bioactive compounds in P. angustifolium Fraction 1/subfractions, which helps to explain the significant acute anticancer activity of this plant. The screening process designed in this study has the potential to pave the way for developing scientifically validated phytochemical/bioactivity information on ethnomedicinal plants, thereby facilitating further bioprospecting efforts and supporting the discovery of novel drugs in modern medicine.