The main protease of SARS-CoV-2 is one of the important targets to design and develop antiviral drugs. In this study, we have selected 40 antiviral phytochemicals to find out the best candidates which can act as potent inhibitors against the main protease. Molecular docking is performed using AutoDock Vina and GOLD suite to determine the binding affinities and interactions between the phytochemicals and the main protease. The selected candidates strongly interact with the key Cys145 and His41 residues. To validate the docking interactions, 100 ns molecular dynamics (MD) simulations on the five top-ranked inhibitors including hypericin, cyanidin 3-glucoside, baicalin, glabridin, and α-ketoamide-11r were performed. Principal component analysis (PCA) of potential energy components of MD discloses that baicalin, cyanidin 3-glucoside, and α-ketoamide-11r have structural similarity with the apo-form of the main protease. These findings are also strongly supported by root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), and solvent accessible surface area (SASA) investigations. PCA is also used to find out the quantitative structure-activity relationship (QSAR) for pattern recognition of the best ligands. Multiple linear regression (MLR) of QSAR reveals the R2 value of 0.842 for the training set and 0.753 for the test set. Our proposed MLR model can predict the favorable binding energy compared with the binding energy detected from molecular docking. ADMET analysis demonstrates that these candidates appear to be safer inhibitors. Our comprehensive computational and statistical analysis show that these selected phytochemicals can be used as potential inhibitors against the SARS-CoV-2. Graphical Abstract
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1 June 2020 in Current Research in Green and Sustainable Chemistry
Due to the increased and excessive consumption of fossil fuels, sustainable alternative energy sources are badly needed to replace fossil fuels. The conversion of biomass into energy and value-added chemicals is one of the most promising potential pathways to solve this problem. Millions of tons of lignin, one of the major components of biomass, are produced annually as a byproduct of various industries, where it is treated as a low-value material. However, since it has an aromatic polymer nature, lignin is a proven source for different value-added products. Studies suggest that the selective cleavage of a specific bond of the complex lignin structure is one of the major challenges of converting lignin to a targeted product. In this study, eight different lignin depolymerization methods, both traditional and green, are reviewed. Acid and base catalytic depolymerization methods are straightforward, but due to their low selectivity and comparatively severe reaction conditions, they are expensive and not eco-friendly. Pyrolysis-based depolymerization comes with similar problems but has a higher conversion. In contrast, greener approaches, such as oxidative, microwave-assisted, super/sub-critical fluids (SCF), ionic liquid (IL), and deep eutectic solvent (DES)-based depolymerization techniques, have shown higher efficiency in terms of converting the lignin into phenolic compounds even under milder reaction conditions. SCF, IL, and DES-based approaches will likely become more popular in the future for their greener nature. Overall, depolymerization of lignin with greener technologies could make this process more economically viable and sustainable.
12 May 2020 in The Journal of Physical Chemistry A