Evaluation of antiviral potential of Cinchona officinalis derived compounds against COVID-19 and human hepatitis B: An in silico molecular docking and molecular dynamics simulation study

Abstract

COVID-19 has caused 6.95 million deaths with multiple variants. Hepatitis B virus is continuously killing millions of people per year. This study aims to evaluate the anti-COVID-19 and anti-viral Hepatitis B potential of bioactive compounds identified within Cinchona officinalis using in silico methods. Two receptors were targeted per virus: the SARS-CoV-2 main protease (Mpro) and the SARS-CoV-2 RNA-dependent RNA polymerase (Rdrp) for COVID-19, the human hepatitis B virus capsid (HBCAG) and 4-DNA-damage-binding protein 1 (DDB1) HBx. After molecular docking, Cyanidin 3-O-rutinoside, Cinchophyllamine, and Cinchophylline were the three lead hits against COVID-19 and Hepatitis B virus. The molecular dynamics simulations (MDS) between Mpro and Cyanidin 3-O-rutinoside have shown normal fluctuations, stability of the ligand in the binding pocket, multiple contacts between the ligand and receptor residues, and rGyr, MolSA, SASA, and PSA within the recommended range while the MDS between Cinchophylline and HBCAG have shown high fluctuations.