Logo-jhp
J Herbmed Pharmacol. 2023;12(4): 453-458.
doi: 10.34172/jhp.2023.42334

Scopus ID: 85173786555
  Abstract View: 1080
  PDF Download: 720

Original Article

Evaluation of berberine inhibitory effects on influenza neuraminidase enzyme: A molecular dynamics study

Majid Asadi-Samani 1 ORCID logo, Dhiya Altememy 2 ORCID logo, Aziz H. Jasim 3 ORCID logo, Javad Saffari-Chaleshtori 4* ORCID logo, Mohammad-Taghi Moradi 5* ORCID logo

1 Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
2 Department of Pharmaceutics, College of Pharmacy, Al-Zahraa University for Women, Karbala, Iraq
3 Department of Laboratory Sciences, College of Pharmacy, Al-Zahraa University for Women, Karbala, Iraq
4 Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
5 Medical Plant Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
*Corresponding Authors: Javad Safari-Chaleshtori, Email: j_saffari@yahoo.com; Mohammad-Taghi Moradi, Email: mtmoradi65@gmail.com

Abstract

Introduction: Due to the high prevalence and drug resistance reported for the influenza virus in recent years, much research is being conducted on the discovery and introduction of more effective drugs against the virus. In this regard, the present bioinformatics study examined the inhibitory effects of berberine, a plant-based alkaloid, on influenza virus neuraminidase using docking and molecular dynamics studies.

Methods: To conduct this study, the three-dimensional structure and PDB file of influenza virus neuraminidase were prepared from the protein and molecular information database, and the structure file of the berberine and oseltamivir (as positive control) molecules were prepared from the PubChem database. Using GROMACS software, simulation and molecular dynamics calculations were performed in the absence of an inhibitor. Molecular docking studies were performed using AutoDock software, and re-simulation of the protein-ligand complex was performed using GROMACS software.

Results: Berberine was bound to the neuraminidase molecule with three hydrogen bonds and eleven hydrophobic bonds at the binding site. The amount of binding energy (BE) of berberine and oseltamivir was equal to -7.93 and -6.27 kcal/mol with the estimated inhibition constant (EIC) of 1.5 and 25.2 μM, respectively. Over simulation time, the radius of gyration (Rg) of the enzyme at berberine binding increased, but there was no significant difference in system energy changes (TE).

Conclusion: Due to berberine binding, structural changes occur in the secondary and tertiary structures of influenza virus neuraminidase. The large number of created bonds, the low level of binding energy, and the low concentration of the EIC indicate the high tendency of berberine to bind to the binding site of neuraminidase.


Implication for health policy/practice/research/medical education:

The results of this study can be used for the appropriate understanding of the drug’s effect mechanism on the virus neuraminidase from the perspective of molecular dynamics and assist researchers in the design and production of anti-influenza drugs.

Please cite this paper as: Asadi-Samani M, Altememy D, Jasim AZ, Saffari-Chaleshtori J, Moradi MT. Evaluation of berberine inhibitory effects on influenza neuraminidase enzyme: A molecular dynamics study. J Herbmed Pharmacol. 2023;12(4):453-458. doi: 10.34172/jhp.2023.42334.

First Name
 
Last Name
 
Email Address
 
Comments
 
Security code


Abstract View: 1081

Your browser does not support the canvas element.


PDF Download: 720

Your browser does not support the canvas element.

Submitted: 26 Feb 2023
Revision: 30 May 2023
Accepted: 16 Jun 2023
ePublished: 10 Aug 2023
EndNote EndNote

(Enw Format - Win & Mac)

BibTeX BibTeX

(Bib Format - Win & Mac)

Bookends Bookends

(Ris Format - Mac only)

EasyBib EasyBib

(Ris Format - Win & Mac)

Medlars Medlars

(Txt Format - Win & Mac)

Mendeley Web Mendeley Web
Mendeley Mendeley

(Ris Format - Win & Mac)

Papers Papers

(Ris Format - Win & Mac)

ProCite ProCite

(Ris Format - Win & Mac)

Reference Manager Reference Manager

(Ris Format - Win only)

Refworks Refworks

(Refworks Format - Win & Mac)

Zotero Zotero

(Ris Format - Firefox Plugin)