Research Article |
Corresponding author: Rika Mayasari Alamsyah ( alamsyahrika1981@gmail.com ) Academic editor: Danka Obreshkova
© 2024 Rika Mayasari Alamsyah, Mieke Hemiawati Satari, Sondang Pintauli, Shelly Iskandar.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Alamsyah RM, Satari MH, Pintauli S, Iskandar S (2024) Molecular docking study of ginger (Zingiber officinale) on Immunoglobulin A for smoking cessation. Pharmacia 71: 1-6. https://doi.org/10.3897/pharmacia.71.e116751
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Smoking is a big problem that can cause death throughout the world. The main ingredient in cigarettes, nicotine, is toxic to humans in several ways. Quitting smoking with the help of medication is associated with adverse side effects such as drowsiness, dry mouth, and nausea. The option of quitting smoking with herbal concoctions such as Zingiber officinale is the recommended choice. The active components of ginger are gingerol and shogaol, which are responsible for their pharmacological effects on immunoglobulin A, which can improve the immune system. The method used is molecular docking, which looks at the stability of human secretory immunoglobulin A when interacting with gingerol and bupropion, which are used as comparison compounds. Molecular docking findings of all herbal material samples revealed that almost all bioactive substances had lower binding energies than immunoglobulin A, especially proteins with PDB IDs 6UE7 and 6UEA. However, only a few ginger-derived bioactive compounds interacting with the 6UEA protein show binding energy values smaller than -7 ± 0.5 kcal/mol. The compounds 8-Gingerol, 8-Shogaol, 6-Shogaol, 6-Gingerol, 5-Shogaol, and 4-Shogaol were able to target the immunoglobulin A receptor protein better than the control, although not as good as the native ligand. Gingerol and Bupropion compounds have stable RMSD and RMSF values compared to human secretory immunoglobulin A without the ligand.
Ginger, Immunoglobulin A, smoking cessation, Zingiber officinale
Smoking has become a significant problem in the world that can cause death. The activity of smoking tobacco has spread to all groups of people in the world. Six million fatalities per year are thought to be attributable to tobacco smoking, which an estimated 1.1 billion people use. A further 600,000 fatalities are attributable to secondhand smoking exposure (GBD 2021; Le Foll et al. 2022). However, tobacco smoking is a severe health risk, and according to WHO estimates, almost a billion people worldwide still use tobacco products, including the increasingly common smokeless variants (
Pharmacotherapy, such as nicotine replacement treatment, bupropion, or varenicline, may help people quit smoking. However, these medications include drowsiness, dry mouth, and nausea as adverse effects (
Ginger, commonly known as Zingiber officinale, is often used as a food or beverage component and herbal remedy. Ginger is well-known for its distinctive and essential medicinal properties, including its ability to be chemoprotective and have anticancer, antioxidant, anticoagulant, antibacterial, antiemetic, and antipyretic.
Selected target proteins’ 3D structures were retrieved from the RSCB PDB database at https://www.rcsb.org. In contrast, ChemSketch was used to generate the 3D structures of each ligand using data in the PubChem database (https://www.pubchem.ncbi.nlm.nih.gov). Additionally, the protein was created using the Discovery Studio 2019 program by eliminating water molecules, and Pyrx v.0.9.8 was used to minimize the energy of the ligands. Autodock Vina, included in Pyrx v.09.8, was used for docking (
MMPBSA.py version 16.0 is used to compute free energy (Valdés-Tresanco et al. 2021). At a temperature of 310.15 oK, 500 total frames were examined.
Protein and ligand preparation used GROMACS 2019 (
Redocking cannot be done because the three 3D structures of the IgA receptor protein do not have native ligands/NL, so the binding site is predicted through Prank Web. The findings of molecular docking on all samples of herbal substances revealed that practically all bioactive chemicals, particularly proteins with PDB IDs 6UE7 and 6UEA, had lower energy binding values than IgA. Only a tiny subset of ginger’s bioactive chemicals, Table
IgA receptor target protein binding affinities to drug and control ligands.
6LX3 | 6UE7 | 6UEA | |||||
---|---|---|---|---|---|---|---|
Ligand | Ranking | BA (Kkal/mol | Ranking | BA (Kkal/mol | Ranking | BA (Kkal/mol | Mean ranking |
IgA | 13 | -4.6 | 15 | -4.5 | 15 | -6.2 | 14.33 |
Bupropion | 11 | -5 | 7 | -5.2 | 13 | -6.4 | 10.33 |
8-Shogaol | 10 | -5.1 | 6 | -5.3 | 2 | -7.2 | 6.00 |
8-Gingerol | 2 | -5.3 | 11 | -5 | 6 | -7 | 6.33 |
6-Shogaol | 5 | -5.2 | 3 | -5.7 | 1 | -7.2 | 3.00 |
6-Gingerol | 1 | -5.4 | 9 | -5.2 | 4 | -7.1 | 4.67 |
5-Shogaol | 8 | -5.1 | 2 | -5.7 | 3 | -7.1 | 4.33 |
4-Shogaol | 4 | -5.2 | 1 | -5.7 | 10 | -6.7 | 5.00 |
Furthermore, Table
Interactions of amino acid residues generated in IgA receptor proteins with compounds.
Ligand | 6LX3 | 6UE7 | 6UEA |
---|---|---|---|
IgA | A:PHE279 | F:TRP281 F:ALA289 | E:SER306, E:CYS323, E:ALA325, E:THR282, E:PRO283, E:CYS266 |
Bupropion | A:VAL304, A:PHE279, A:THR278, A:LEU268, A:ALA325 | F:PHE279, F:TRP281, F:ALA289 | E:VAL304, E:LEU268, E:LEU271, E:ALA277, E:LEU246, E:CYS266, E:ALA325, E:PHE279, E:HIS327 |
8-Shogaol | A:THR278, A:VAL304, A:PHE279, A:TYR302, A:ALA325 | F:TRP281, F:PRO283, F:ALA289, F:PHE279 | E:VAL304, E:ALA325, E:LEU271, E:ALA277, E:TRP281, E:THR280, E:SER306, E:HIS327, E:CYS266, E:LEU268 |
8-Gingerol | A:LEU268, A:ALA325, A:THR278, A:VAL304, A:PHE279 | F:PHE279, F:PRO283, F:TRP281, F:LEU308, F:ALA289 | E:THR280, E:SER306, E:LEU268, E:ALA326, E:HIS327, E:CYS266, E:CYS323, E:ALA325, E:LEU271, E:ALA277, E:LEU246, E:LEU248, E:VAL304 |
6-Shogaol | A:PHE279, A:TYR302, A:LEU268, A:VAL304 | F:TRP281, F:PRO283, F:LEU308, F:ALA289, F:PHE279 | E:VAL304, E:ALA325, E:CYS266, E:CYS323, E:LEU268, E:LEU271, E:ALA277, E:HIS327 |
6-Gingerol | A:LEU268, A:THR278, A:VAL304, A:TYR302 | F:PHE279, F:PRO283, F:TRP281, F:LEU308, F:ALA289 | E:THR280, E:HIS327, E:THR324, E:LEU268, E:LEU271, E:LEU246, E:LEU248, E:CYS266, E:CYS323, E:ALA277, E:VAL304 |
5-Shogaol | A:TYR302, A:VAL304, A:PHE279 | F:PRO283, F:LEU308, F:ALA289, F:TRP281 | E:VAL304, E:ALA325, E:TRP281, E:HIS327, E:SER306, E:LEU268, E:LEU271, E:CYS266 |
4-Shogaol | A:TYR302, A:VAL304, A:PHE279 | F:TRP281, F:PRO283, F:LEU308, F:ALA289, F:PHE279 | E:VAL304, E:THR280 E:ALA325 |
The 3D visualization of the corresponding complexes of the IgA receptor protein with compound and control ligands is shown in Fig.
The herbal component ginger has a more significant interaction potential than the control but is not as excellent as the native ligand, according to molecular docking studies. It is projected that 8Gingerol, 8-Shogaol, 6-Shogaol, 6-Gingerol, 5-Shogaol, and 4-Shogaol may target IgA receptor proteins.
The free energy value of bupropion is more harmful, according to the mmPBSA findings of a molecular dynamics simulation between human secretory immunoglobulin A and Gingerol and bupropion. Human secretory immunoglobulin A and bupropion have a free energy difference of -3.42 kcal/mol. The Bupropion chemical interacts more favorably with human secretory immunoglobulin A, as shown by free energy calculations using mmPBSA. The results match those of the molecular dynamics simulation.
RMSD is a crucial indication for assessing the structural stability of a protein since it quantifies the typical departure of a protein structure from its initial shape at a particular period. To determine the stability of human secretory immunoglobulin A in its interactions with the test substances gingerol and bupropion, a molecular dynamics simulation has been run for 50,000 ps. The Native protein (human secretory immunoglobulin A) has an RMSD of around 0.8 nm, according to MD findings. Human secretory immunoglobulin A’s interaction with the Bupropion test substance slightly reduced the RMSD value, which was 0.7 nm. On interaction with Gingerol, it slightly increased by 0.9 nm (Fig.
We also examined immunoglobulin A’s adaptability and interactions with the test substances (Fig.
The protein surface area that solvents may reach is determined by SASA analysis. As SASA values rise, relative growth may be seen (
Based on MD results for 50 ns, the Buprion compound has RMSD and RMSF values which are more stable compared to human secretory immunoglobulin A without the ligand. Thus, Bupropion may have the ability to bind to human secretory immunoglobulin A stably. To validate these in silico results, it is necessary to carry out in vitro and in vivo validation tests.
Energy | Average (kcal/mol) | |
---|---|---|
Component | Gingerol | Bupropion |
ΔBOND | 0 | 0 |
ΔANGLE | 0 | 0 |
ΔDIHED | 0 | 0 |
ΔVDWAALS | -12.71 | -14.96 |
ΔEEL | -6.31 | -71.54 |
Δ1-4 VDW | 0 | 0 |
Δ1-4 EEL | 0 | 0 |
ΔEPB | 11.99 | 75.05 |
ΔENPOLAR | -10.74 | -11.9 |
ΔEDISPER | 17.16 | 19.93 |
ΔGGAS | -19.02 | -86.5 |
ΔGSOLV | 18.41 | 83.08 |
ΔTOTAL | -0.61 | -3.42 |
Molecular docking findings on all herbal material samples show that almost all bioactive compounds have lower binding energies than immunoglobulin A, especially for proteins with PDB IDs 6UE7 and 6UEA. However, only a few ginger-derived bioactive compounds interacting with the 6UEA protein show binding energy values smaller than -7 ± 0.5 kcal/mol. Herbal compounds derived from ginger have better interaction potential than controls. 8-Gingerol, 8-Shogaol, 6-Shogaol, 6-Gingerol, 5-Shogaol, and 4Shogaol can potentially interact with the immunoglobulin A receptor protein. Gingerol and Bupropion have more stable RMSD and RMSF values when human secretory immunoglobulin A is compared without ligand. Bupropion may have the ability to bind human secretory immunoglobulin A stably. However, Gingerol can bind to human secretory immunoglobulin A. In vitro and in vivo tests need to be carried out to validate the in silico results.
The authors are grateful to Indonesian Endowment Fund for Education/Lembaga Pengelola Dana Pendidikan (LPDP) from the Ministry of Finance Republic Indonesia for funding this research.