Abstract
COVID-19, caused by the SARS-CoV-2 virus. This infectious disease significantly targets the upper and lower respiratory tracts of humans and animals. The mechanisms of SARS-CoV-2 infection are crucially mediated by specific viral proteins, such as the spike protein, as well as various enzymes, including proteases and transferases, and host proteins, including the ACE2 receptor. These proteins facilitate viral attachment and viral replication. This study aimed to identify the potential candidate compounds from Andrographis paniculata due to its anti-SARS-CoV-2 property, examined using both in vitro and in silico methodologies. The most effective fractions of the extract provided 15 candidate compounds that were identified based on their binding affinity to papain-like protease (PLpro), 3-chymotrypsin-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), and methyltransferase (MTase). Notably, these compounds showed no satisfactory coupling with the spike protein and the ACE2 receptor. This work revealed a potential mechanism of action that focuses on viral replication rather than initial attachment. Nine candidate compounds of flavonoids (CP14, CP15, CP16, CP26, CP30, CP31, CP32, CP33, and CP39), together with 2-tert-butyl-6-[(3-tert-butyl-2-hydroxy-5-methylphenyl)methyl]-4-methylphenol (CP13), 6-butyryl-5,7-dihydroxy-8-isopentenyl-4-propylcoumarin (CP37), 7-demethyltangeretin (CP38), afromosin (CP43), asperglaucide (CP45), and galanolactone (CP53) have strong binding affinity with the viral proteins, including PLpro, 3CLpro, RdRp, and MTase. The LB-PaCS-MD/FMO framework revealed detailed ligand binding pathways and induced-fit adaptation of CP14 and CP45 within the flexible 3CLpro pocket, providing quantum-level insight into their stabilization mechanisms. This suggests significant potential to disrupt viral replication, and this finding will be the guidance for anti-SARS-CoV-2 products in the future.