Molecular docking study of natural compounds from red betel (Piper crocatum Ruiz & Pav) as inhibitor of secreted aspartic proteinase 5 (Sap 5) in Candida albicans

Candida albicans can cause adverse infections in humans. The targeting of Sap 5 is due to its virulence factor in C. albicans. The method used is molecular docking using YASARA structure and BIOVIA Discovery Studio. The purpose of this study was to investigate the molecular interaction between red betel and Sap 5 as a potential inhibitor of C. albicans in infecting humans. The results showed that CHEMBL216163 (9,644 kcal/mol) and MLS000557666 (9,525 kcal/mol) have Binding energy above Pepstatin (9,484 kcal/mol) and affect the active site of Sap 5 so that the two test ligands could be further analyzed

Molecular docking: Bioactive compounds of Mimosa pudica as an inhibitor of Candida albicans Sap 3

Candida albicans (C. albicans) is a commensal microbiota that resides in humans. However, in certain cases, C. albicans can infect and cause several diseases to humans. This study aimed to investigate the interaction between Mimosa pudica bioactive compounds and C. albicans Sap 3. Molecular docking analysis was carried out using YASARA structure. The procedures involved preparation of ligands and target receptor, molecular docking, data analysis and visualization. All 3D ligands were downloaded from PubChem NCBI, while target receptor was downloaded from RCSB PDB. The interaction between Mimosa pudica bioactive compounds against Sap 3 resulted in a binding energies ranges from 5,168 – 7,480 kcal/mol and most of the interactions formed were relatively strong. Furthermore, the test ligands had contact with the catalytic residues and substrate binding site pockets S1/S2/S3/S4 on the target receptor. Bioactive compounds of Mimosa pudica have relatively good interactions in inhibiting C. albicans Sap

Molecular Docking Study of Nigella sativa Alkaloid Compounds as the Inhibitor of Papain-Like Protease SARS-CoV-2

SARS-CoV-2 causes about 66% of China’s Wuhan market workers to experience fever, dry cough, and fatigue. Black cumin (Nigella sativa) is a plant with many benefits to cure many illnesses like hypertension, headache, infection, and inflammation. This study aimed to investigate the inhibition by compounds belonging to the Alkaloid group from Black Cumin Seed to inhibit PLpro activity as a target for SARS-CoV-2. The study used five alkaloid compounds ((2E,4E)-Decadienal, (2E,4Z)-Decadienal, Nigellicine, Nigellidine, and Nigellimine) from the Black cumin seed and a PLpro SARS-CoV-2 receptor (PDB ID: 6WX4). The methods used are ligand and receptor preparation, grid box validation, molecular docking, 2D and 3D visualisation, and data analysis using Gibbs free energy, type of interaction, and contact of amino acid residues data. This study used YASARA structure and BIOVIA Discovery Studio. The results showed that Nigellidine has the highest Gibbs free energy with a -2.67 kcal/mol score, higher than VIR251. PLpro has a catalytic triad at Cys111, His272, and Asp286 residues, the compound that binds to the active site is Nigellicine found at amino acid Cys111 with Pi-Sulfur