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Investigating the binding affinity, molecular dynamics, and ADMET properties of 2,3-dihydrobenzofuran derivatives as an inhibitor of fungi, bacteria, and virus protein

Authors
  • Nath, Ashutosh1
  • Kumer, Ajoy1
  • Zaben, Fahmida1
  • Khan, Md. Wahab1
  • 1 Bangladesh University of Engineering and Technology(BUET), Dhaka, 1000, Bangladesh , Dhaka (Bangladesh)
Type
Published Article
Journal
Beni-Suef University Journal of Basic and Applied Sciences
Publisher
Springer Berlin Heidelberg
Publication Date
Jun 02, 2021
Volume
10
Issue
1
Identifiers
DOI: 10.1186/s43088-021-00117-8
Source
Springer Nature
Keywords
License
Green

Abstract

Background2,3-Dihydrobenzofurans (DHB) have proposed as advantages structures, and used as chemical entresol to design small compound libraries. The present study illustrates to explore 2,3-dihydrobenzofurans(DHB) in comparison to selected some derivatives drugs by using molecular docking and molecular dynamics, as well as ADMET studies. The online database “Molinspiration online server” was used to detect the physicochemical pharmacokinetics and drug likeness score of DHB drugs. For estimation of molecular docking, six pathogens, such as Aspergillus niger (PDB id: 1kum), Candida albicans (3dra), Escherichia coli (6og7), Salmonella typhi (4k6l), Influenza (1ru7), and Hepatitis C (4tyd), were chosen due to close biological studies.ResultsFrom Molinspiration online server has showed that DHB did not violate the “Lipinski five rule” as drugs, leading compound for molecular docking exhibited the potential interaction to the active residue. The binding affinity of DHB2 (−7.00 kcal/mol) against 3dra was higher than DHB8 (−6.40 kcal/mol) and DHB (5.70 kcal/mol) for compounds. The results of molecular docking show that the compounds mentioned in this study are not equally effective against pathogens, such as fungi, viruses, and bacteria. However, DHB2, DHB3, and DHB 8 compounds can work against almost given pathogens which results are derived from auto dock vina in terms of binding affinity around 6.00 kcal/mol, and Fire Dock has values from about 38.0 to 42.0 kcal/mol. To explore the dynamic nature of the interaction, 50 ns molecular dynamics (MD) simulation was performed on the selected protein-DHB complexes. Thus, DHB 8 has greater potential to interact for further for fungi.ConclusionFinding from this study can play an effective role as a drug in any biological system. This study as well recommends to researchers to synthesize these DHBs for evaluation of its biological activity.Graphical abstract

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