One of the most featured techniques to analyze the physical movement of molecules is Molecular Dynamics (MD) simulations. Among the different programs used to perform them, GROMACS is one of the most widely used open-source packages. We present ASGARD, a software to perform analysis of MD protein or protein-ligand complex simulations and to generate the corresponding report via an automated MD workflow. This tool automatically generates a set of analyses after completing the simulation, including reports about overall system stability and system flexibility analysis with RMSD Fluctuation and Distribution calculations. Finally, a dynamic analysis with SASA and DSSP method graphs, and different interaction analyses are performed. In conclusion, ASGARD allows the user to run MD simulation analysis with a single command line instead of using the GROMACS programs individually. Following this, it automatically creates an analysis report which helps to understand the molecular interactions and structural changes.

Antcins obtained from the fruiting bodies of Taiwanofungus camphoratus, have been traditionally used to treat infections, whereas their role in the SARS-CoV-2 3-chymotrypsin-like protease (3CLPro) remains unclear. We employed both in vitro and in silico approaches to understand the underlying chemical mechanism comprehensively. Our finding revealed that various antcins (A, B, C, H, I, and M) and non-antcins (citronellol and limonene) exhibited lower toxicity to cells than GC376, along with favorable drug-likeness based MTT assay and ADMET prediction. Molecular docking analysis predicted that antcin-B possessed the lowest binding affinity energy and interacts with key residues such as Glu169, Gln189, His41, Leu141, Asn142, Glu16, and His165 employing hydrophobic interaction, hydrogen bonding, and salt bridge. These interactions were further confirmed by molecular dynamics (MD) simulation, which demonstrated the formation of hydrogen bonds with Asn142 and Gly143 and bridge with Glu166 for approximately 40% and 70% of the simulation time, respectively. Indeed, in vitro, 3CLPro activity analysis supports the above notion that antcin-B significantly (96.39%) inhibits 3CLPro activity, which is highly comparable with a known antiviral drug GC367 (96.72%). Consequently, antcin-B could be considered for developing a potential drug candidate for inhibiting 3CLPro activity, thereby impeding reducing the severity of COVID-19 in patients.