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

被引:52
作者
Nath, Ashutosh [1 ]
Kumer, Ajoy [1 ]
Zaben, Fahmida [1 ]
Khan, Md. Wahab [1 ]
机构
[1] Bangladesh Univ Engn & Technol, Dept Chem, Organ Res Lab, Dhaka 1000, Bangladesh
关键词
2,3-Dihydrobenzofuran; Molecular docking; Molecular dynamic simulation; Binding affinity; AUTOMATED DOCKING; DRUG; DISCOVERY; DESIGN;
D O I
10.1186/s43088-021-00117-8
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Background: 2,3-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 (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. Results: From 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. Conclusion: Finding 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.
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页数:13
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