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2000
Volume 20, Issue 8
  • ISSN: 1573-4129
  • E-ISSN: 1875-676X

Abstract

Background and Objective

Lipopolysaccharide (LPS) is an essential constituent of the outer membrane of gram-negative bacteria, such as , and it plays a crucial role by inducing disease in the host. Penicillin-binding protein 1B (LpoB) is a key enzyme in the production of peptidoglycans, making it a potential target for the development of new antimicrobials. Flavonoids are naturally occurring plant-derived chemicals with a wide range of pharmacological properties, including antibacterial capabilities. The goal of this study was to identify the potential flavonoid that inhibits the protein LpoB using computational approaches and compare it with the standard antibiotic ciprofloxacin.

Methods

The study was carried out by selecting fifty flavonoids based on Lipinski’s rule of five. Molecular docking was carried out for selected flavonoids and ciprofloxacin against the LpoB protein using AutoDock 4. A 100 nanosecond molecular dynamic simulation was performed for apoprotein, LpoB-fisetin, and LpoB-ciprofloxacin complexes, followed by free energy calculation by Molecular Mechanics Generalized Born Surface Area (MMGBSA) solvation analysis.

Results

The docking results revealed that fisetin displayed five hydrogen bonds with a binding affinity of -4.67 kcal/mol, and ciprofloxacin exhibited a binding affinity of -4.36 kcal/mol with two hydrogen bonds. The apoprotein and fisetin complex remained stable throughout the 100 ns molecular dynamic simulation, while the ciprofloxacin complex lost its stability. The MMGBSA analysis with fisetin showed better binding free energy compared to ciprofloxacin.

Conclusion

The present study has emphasized the potential of flavonoids as probable candidates that can inhibit the protein LpoB. The integration of molecular docking, dynamic simulations, and MMGBSA analysis has provided significant insight into the thermodynamics and binding interactions of the LpoB- fisetin complex, and it has enabled further experimental validations.

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  • Article Type:
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Keyword(s): dynamic simulation; Flavonoids; LpoB; MMGBSA; molecular docking; Salmonella typhimurium
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