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The outbreak of SARS-CoV-2 and deaths caused by it all over the world have imposed great concern on the scientific community to develop potential drugs to combat Coronavirus disease-19 (COVID-19). In this regard, lichen metabolites may offer a vast reservoir for the discovery of antiviral drug candidates. Therefore, to find novel compounds against COVID-19, we created a library of 412 lichen compounds and subjected to virtual screening against the SARS-CoV-2 Main protease (Mpro). All the ligands were virtually screened, and 27 compounds were found to have high affinity with Mpro. These compounds were assessed for drug-likeness analysis where two compounds were found to fit well for redocking studies. Molecular docking, drug-likeness, X-Score, and toxicity analysis resulting in two lichen compounds, Calycin and Rhizocarpic acid with Mpro-inhibiting activity. These compounds were finally subjected to molecular dynamics simulation to compare the dynamics behavior and stability of the Mpro after ligand binding. The binding energy was calculated by MM-PBSA method to determine the intermolecular protein-ligand interactions. Our results showed that two compounds; Calycin and Rhizocarpic acid had the binding free energy of − 42.42 kJ mol/1 and − 57.85 kJ mol/1 respectively as compared to reference X77 (− 91.78 kJ mol/1). We concluded that Calycin and Rhizocarpic acid show considerable structural and pharmacological properties and they can be used as hit compounds to develop potential antiviral agents against SARS-CoV-2. These lichen compounds may be a suitable candidate for further experimental analysis.

COVID-19 caused by the SARS-CoV-2 is a current global challenge and urgent discovery of potential drugs to combat this pandemic is a need of the hour. 3-chymotrypsin-like cysteine protease (3CLpro) enzyme is the vital molecular target against the SARS-CoV-2. Therefore, in the present study, 1528 anti-HIV1compounds were screened by sequence alignment between 3CLpro of SARS-CoV-2 and avian infectious bronchitis virus (avian coronavirus) followed by machine learning predictive model, drug-likeness screening and molecular docking, which resulted in 41 screened compounds. These 41 compounds were re-screened by deep learning model constructed considering the IC50 values of known inhibitors which resulted in 22 hit compounds. Further, screening was done by structural activity relationship mapping which resulted in two structural clefts. Thereafter, functional group analysis was also done, where cluster 2 showed the presence of several essential functional groups having pharmacological importance. In the final stage, Cluster 2 compounds were re-docked with four different PDB structures of 3CLpro, and their depth interaction profile was analyzed followed by molecular dynamics simulation at 100 ns. Conclusively, 2 out of 1528 compounds were screened as potential hits against 3CLpro which could be further treated as an excellent drug against SARS-CoV-2.

The whole world is facing a great challenging time due to Coronavirus disease (COVID-19) caused by SARS-CoV-2. Globally, more than 14.6 M people have been diagnosed and more than 595 K deaths are reported. Currently, no effective vaccine or drugs are available to combat COVID-19. Therefore, the whole world is looking for new drug candidates that can treat the COVID-19. In this study, we conducted a virtual screening of natural compounds using a deep-learning method. A deep-learning algorithm was used for the predictive modeling of a CHEMBL3927 dataset of inhibitors of Main protease (Mpro). Several predictive models were developed and evaluated based on R 2 , MAE MSE, RMSE, and Loss. The best model with R 2 ¼0.83, MAE ¼ 1.06, MSE ¼ 1.5, RMSE ¼ 1.2, and loss ¼ 1.5 was deployed on the Selleck database containing 1611 natural compounds for virtual screening. The model predicted 500 hits showing the value score between 6.9 and 3.8. The screened compounds were further enriched by molecular docking resulting in 39 compounds based on comparison with the reference (X77). Out of them, only four compounds were found to be drug-like and three were non-toxic. The complexes of compounds and Mpro were finally subjected to Molecular dynamic (MD) simulation for 100 ns. The MMPBSA result showed that two compounds Palmatine and Sauchinone formed very stable complex with Mpro and had free energy of À71.47 kJ mol À1 and À71.68 kJ mol À1 respectively as compared to X77 (À69.58 kJ mol À1). From this study, we can suggest that the identified natural compounds may be considered for therapeutic development against the SARS-CoV-2.

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