Molecular Dynamics, Prediction of Toxicity, and Interaction of the Active Compound Caesalpinia sappan on Essential Lipids Klebsiella pneumoniae

Abstract

Pneumonia is the highest cause of death in the world. The presence of COVID-19 can worsen the patient's condition. One of the causes of pneumonia is Klebsiella pneumoniae. These bacteria can be resistant to antibiotics. In this case, an alternative treatment is needed. Caesalpinia sappan, based on pre-clinical trials, has an activity to be used as an antimicrobial. The activity predictions, molecular docking, and molecular dynamics simulations were performed using computational methods. The log P values were found in the range of 0.86-2.26. The molecular weights were in the range of 272.25-344.36 g/mol. All active compounds qualify with the Lipinski rule of 5. The lowest binding affinity value is -9.8 (kcal/mol), suggesting it can bind more strongly to the lipid from Klebsiella pneumoniae. Structure alert was obtained, namely catechol and aldehyde. The results of molecular dynamics of compound 7 in Klebsiella pneumonia protein got an eigenvalue of 5.186e-05. The active compound from Caesalpinia sappan is predicted to develop as a lipid inhibitor from Klebsiella pneumoniae. It has interaction such as Compound 7 has one hydrogen bond in the amino acid Trp46, one π-cation in Arg80, and one π-Sulfur bond in Met156.

In Silico and In Vitro Study of The Ethanol Extract of The White Garland Lily (Hedychium coronarium J. Koenig) as a Tyrosinase Inhibitor

“…Molecular docking is a computational method to see the interactions and binding between ligands and receptors. 29,22 Triparanol molecules have the best binding affinity in the molecular docking simulation data, with a value of -8.00 kcal/mol compared to the native ligand mimosine, with a docking score of -5.86 kcal/mol. It was an interaction of a hydrogen bond with an amino acid in TYR362 and ARG321 when engaged with 3-hydroxysuberic acid.…”