In silico study of novel marine alkaloid jolynamine and other marine compounds via molecular docking, MM-GBSA binding energy prediction, ADMET evaluation, and molecular dynamics simulation

In this research article bacterial ( ) and fungal ( and ) enzymes are used for molecular docking of novel marine alkaloid jolynamine ( ) and six marine natural compounds. Till date, no computational studies have been reported. In addition, MM/GBSA analysis is conducted for estimation of binding free...

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Bibliographic Details
Published in:Natural product research 2024-08, Vol.38 (15), p.2715-2721
Main Authors: Gul, Sana, Khan, Abdul Majeed, Ali, Syed Tahir, Rizwan, Samra
Format: Article
Language:English
Subjects:
Alkaloids
Alkaloids - chemistry
Aspergillus niger
Aspergillus niger - drug effects
Binding energy
Biological Products - chemistry
Biological Products - pharmacology
Candida albicans
Candida albicans - drug effects
Chemical compounds
computer simulation
drugs
E coli
energy
Escherichia coli
Escherichia coli - drug effects
Free energy
fungi
Gibbs free energy
Molecular docking
Molecular Docking Simulation
Molecular dynamics
Molecular Dynamics Simulation
Molecular Structure
Natural products
Physicochemical properties
prediction
Pseudomonas aeruginosa
Pseudomonas aeruginosa - drug effects
Stability
Thermodynamics
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Summary:In this research article bacterial ( ) and fungal ( and ) enzymes are used for molecular docking of novel marine alkaloid jolynamine ( ) and six marine natural compounds. Till date, no computational studies have been reported. In addition, MM/GBSA analysis is conducted for estimation of binding free energies. Furthermore, ADMET physicochemical properties were explored to understand the drug likeness property of compounds. results showed that jolynamine ( ) has more negative predicted binding energy among natural products. The ADMET profile of all compounds accepted the Lipinski rule and jolynamine also showed negative MM/GBSA binding free energy. Moreover, MD simulation was subjected to check structure stability. The outcomes of MD simulation of jolynamine ( ) showed structure stability over 50 ns simulation. This study will hopefully facilitate the finding of other natural products and expedite the drug discovery process to screen drug like chemical compounds.
ISSN:1478-6419
1478-6427
1478-6427
DOI:10.1080/14786419.2023.2195177