Research Article |
Corresponding author: Iksen Iksen ( ikseniksen08@gmail.com ) Academic editor: Georgi Momekov
© 2023 Aditya Trias Pradana, Ginda Haro, Novarianti Marbun, Sofia Rahmi, Iksen Iksen.
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:
Trias Pradana A, Haro G, Marbun N, Rahmi S, Iksen I (2023) Identification of potential molecular target of hypertension from Allium schoenoprasum by using network pharmacology and molecular docking strategies. Pharmacia 70(3): 699-706. https://doi.org/10.3897/pharmacia.70.e101537
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Hypertension is one of the silent killers in human life which is characterized by uncontrolled blood pressure. Although many therapeutic drugs have demonstrated success in treating hypertension, these treatments have their own drawbacks, most notably in terms of cost and side effects. Hypertension treatment with natural products has lately been proposed. This study focused on the potential of Allium schoenoprasum against hypertension based on network pharmacology and molecular docking strategies. Interested compounds and targets were identified by searching accessible databases. Protein-protein interaction (PPI), Gene ontology (GO), and Kyoto encyclopedia of genes and genomes (KEGG) were conducted to determine the potential targets from Allium schoenoprasum. In this study, 10 potentially active compounds were obtained. PPI results showed SCR, STAT3, PIK3R1, CTNBB1, and ESR1 as the main targets of hypertension. GO and KEGG investigation confirmed the PPI targets are mainly involved in protein binding and catalytic in the membrane and cytoplasm. In the end, by using molecular docking, kaempferol, isorhamnetin, and quercetin showed the most potent compounds in Allium schoenoprasum against hypertension. In summary, Allium schoenoprasum exhibited antihypertensive activity via network pharmacology and molecular docking approaches.
Hypertension, Allium schoenoprasum L., network pharmacology, molecular docking
One of the diseases that is one of the most dangerous to human health and has a high incidence rate all over the world is hypertension. The number of people who have been diagnosed with hypertension continues to rise on an annual basis, and it is anticipated that the number of people who have been diagnosed with hypertension will reach almost 2 billion by the year 2025 (
Improvements in lifestyle and medication both play a role in hypertension treatment. The use of antihypertensive medication, which may also be combined with changes to one’s diet and way of life, has been shown to significantly lower blood pressure and heart rate, which in turn reduces the risk of cardiovascular disease and mortality (
The medicinal plant Allium schoenoprasum, which was used in this study, is a member of the Amaryllidaceae family and may be found growing in large quantities throughout Asia, Europe, and North America (
With so many different pharmacological mechanisms at play, it can be challenging to develop and improve upon solutions that make use of natural resources because these solutions tend to have several targets and pathways (
The information on all possible active compounds of Allium schoenoprasum was obtained by inserting the keyword Allium schoenoprasum from the online database of KNApSAcK Family Databases (http://www.knapsackfamily.com/KNApSAcK/) and our previous report (
Possible targets from the active compounds were obtained from the Swiss Target Prediction database (http://www.swisstargetprediction.ch/) by inserting the SMILE code from each compound into the system. The hypertension-related targets were obtained from the GeneCards database (https://www.genecards.org/). Venny 2.1.0 was used to identify the overlapping targets obtained from the compounds and hypertension-related targets which were then defined as the potential therapeutic targets for Allium schoenoprasum to combat hypertension (https://bioinfogp.cnb.csic.es/tools/venny/).
Firstly, to visualize how is the interaction network between each target protein, we used the STRING database (https://string-db.org/) by inputting the targets we obtained from the Venny diagram before and downloaded the possible PPI network by choosing Homo sapiens as the model with the highest confidence score of 0.9. Then we continue to analyze the PPI network by using Cytoscape 3.9.1 (https://cytoscape.org/). In this program, from all of the PPI networks, we need to analyze which target protein is the most important by seeing several parameters provided by STRING and Cytoscape. Next, by using an additional CytoHubba plug-in, we can visualize the top 5 most important targets by using the color gradients obtained from previous results we obtained from STRING and Cytoscape.
Analysis of gene ontology was conducted the in the aspect of biological process, molecular function, and cellular components. Kyoto Encyclopedia of Genes and Genomes (https://www.genome.jp/kegg/) pathway enrichment analysis was conducted to obtain the possible pathway related to the treatment of Allium schoenoprasum in hypertension disease. All the data were analyzed by using RStudio with a ggplot2 plug-in as the bubble plot (
The possible interaction between active compounds from Allium schoenoprasum and the top 5 targets was conducted by using PyRx 0.8 Virtual Screening (https://pyrx.sourceforge.io/). Each protein target was obtained from the Protein Data Bank (https://www.rcsb.org/pages/policies) with the PDB ID 3F3V, 6NJS, 2IUG, 1JDH, 7UJO respectively for Proto-oncogene c-Src (SRC), Signal transducer and activator of transcription 3 (STAT3), Phosphoinositide-3-Kinase Regulatory Subunit 1 (PIK3R1), Catenin beta-1 (CTNBB1), and Estrogen receptor 1 (ESR1). All proteins were prepared by using PyMol 2.5 (https://pymol.org/2/) in the format of PDB by removing the water molecules and specific ligands (
The potential active compounds from Allium schoenoprasum were obtained from our previous report (
The main compounds information from Allium schoenoprasum and Lipinski’s rule.
Molecule | MW | Rotatable bonds | H-bond acceptors | H-bond donors | Molar refractivity | TPSA | Log P | Lipinski violations | Bioavailability score |
---|---|---|---|---|---|---|---|---|---|
Diallyl disulfide | 146.27 | 5 | 0 | 0 | 45.19 | 50.6 | 2.49 | 0 | 0.55 |
2-Methyl-2-pentenal | 98.14 | 2 | 1 | 0 | 30.68 | 17.07 | 1.71 | 0 | 0.55 |
Methyl propyl disulfide | 122.25 | 3 | 0 | 0 | 36.52 | 50.6 | 2.19 | 0 | 0.55 |
Methyl pentyl disulfide | 150.31 | 5 | 0 | 0 | 46.14 | 50.6 | 2.66 | 0 | 0.55 |
1-Pentanesulfenothioic acid | 136.28 | 4 | 0 | 0 | 41.67 | 64.1 | 2.37 | 0 | 0.55 |
Tiglaldehyde | 84.12 | 1 | 1 | 0 | 25.87 | 17.07 | 1.47 | 0 | 0.55 |
Gallic acid | 170.12 | 1 | 5 | 4 | 39.47 | 97.99 | 0.21 | 0 | 0.56 |
p-Coumaric acid | 164.16 | 2 | 3 | 2 | 45.13 | 57.53 | 0.95 | 0 | 0.85 |
Ferulic acid | 194.18 | 3 | 4 | 2 | 51.63 | 66.76 | 1.62 | 0 | 0.85 |
Sinapic acid | 224.21 | 4 | 5 | 2 | 58.12 | 75.99 | 1.63 | 0 | 0.56 |
Kaempferol | 286.24 | 1 | 6 | 4 | 76.01 | 111.13 | 1.7 | 0 | 0.55 |
Isorhamnetin | 316.26 | 2 | 7 | 4 | 82.5 | 120.36 | 2.35 | 0 | 0.55 |
Quercetin | 302.24 | 1 | 7 | 5 | 78.03 | 131.36 | 1.63 | 0 | 0.55 |
The number of potential targets for each compound from Allium schoenoprasum against hypertension. A. Each compound consists of at least 3 potential targets against hypertension obtained from the Swiss target prediction database; B. Venny diagram showing 168 intercepting targets between main compounds from Allium schoenoprasum against hypertension. The yellow color represents hypertensive-related targets, and the blue represents targets from Allium schoenoprasum.
To visualize the interaction network between the potential targets from Allium schoenoprasum and the majority compound, we construct the compound-target network (Fig.
Interactions between proteins are a common mechanism by which proteins exert control of physiological processes. We used STRING 11.5 to construct a protein-protein interaction network (Fig.
Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were carried out with the assistance of RStudio in order to further assess and acquire a better understanding of the molecular mechanism that the compounds-targets have on hypertension. These possible target genes were subjected to three different kinds of gene ontology functional annotation assessments. These analyses comprised the biological process (Fig.
The protein-protein interaction analysis showed that the targets SRC, STAT3, PIK3R1, CTNNB1, and ESR1 were the most important target hub in the network. We conducted further analysis by using PDB ID 3F3V, 6NJS, 2IUG, 1JDH, and 7UJO respectively for SRC, STAT3, PIK3R1, CTNNB1, and ESR1 obtained from the protein data bank and performed the molecular docking analysis to confirm the possibility of interaction between the compounds and target protein. The outcome of the docking affinity is reported in Table
Binding energy (kcal/mol) of active compounds in Allium schoenoprasum and main targets.
Compounds | Binding energy (kcal/mol) | ||||
---|---|---|---|---|---|
SRC | STAT3 | PIK3R1 | CTNNB1 | ESR1 | |
Diallyl disulfide | -3.9 | -3.2 | -3.3 | -3.4 | -3.8 |
2-Methyl-2-pentenal | -4.1 | -4.1 | -4.3 | -3.8 | -4.5 |
Tiglaldehyde | -3.8 | -3.8 | -3.9 | -3.6 | -4 |
Gallic acid | -5.6 | -5.2 | -5.1 | -5.4 | -6.4 |
p-Coumaric acid | -6.2 | -5.5 | -5.3 | -5.6 | -6.1 |
Ferulic acid | -6.4 | -5.8 | -5.1 | -5.5 | -6.2 |
Sinapic acid | -6.3 | -6 | -4.8 | -5.3 | -6.2 |
Kaempferol | -9.2 | -7.2 | -5.8 | -7.5 | -7.7 |
Isorhamnetin | -9.5 | -7.3 | -5.8 | -6.5 | -7.6 |
Quercetin | -9.4 | -7.5 | -5.9 | -7.8 | -7.5 |
Dasatinib (SRC inhibitor) | -8.4 | - | - | - | - |
Napabucasin (STAT3 inhibitor) | - | -6.6 | - | - | - |
LY294002 (PI3K inhibitor) | - | - | -6.4 | - | - |
MSAB (Beta catenin inhibitor) | - | - | - | -6.5 | - |
Elacestrant (ESR inhibitor) | - | - | - | - | -6.1 |
Hypertension is a condition that occurs when a person’s systolic blood pressure increases by more than 140 mmHg and the diastolic blood pressure increases by more than 90 mmHg. This condition is one of the silent killers (
It is indisputable that traditional medicine can be applied to prevent or cure a diverse range of complex illnesses, and it also provides a feasible source for the identification of further candidate drugs for managing hypertension (
Using data mining, we first identified 13 compounds from Allium schoenoprasum that might be useful in treating hypertension in this investigation. We also integrated hypertension-related targets from the GeneCards database into the screening process, narrowing the pool of candidate targets down to only 10, from a total of 168. The investigation of protein-protein interactions provides an in-depth understanding of the network of interactions between drugs and their targets. According to the findings of network pharmacology and PPI analysis, there are five primary targets in Allium schoenoprasum that are effective against hypertension. These targets include SRC, STAT3, PIK3R1, CTNNB1, and ESR1. Inhibition of SRC has been shown in previous research to result in a reduction in blood pressure as well as improvements in cardiac and vascular function (
A comprehensive Gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analysis revealed that these targets are mostly involved in protein binding in the membrane and cytoplasm. The findings from the KEGG pathway enrichment study provide further credence to this interpretation. To confirm the results obtained from the network pharmacology, we conducted molecular docking against the top 5 targets from hypertension. Molecular docking analysis results corroborated the preceding findings, showing that the target proteins and the active ingredients in Allium schoenoprasum interact closely, providing proof of the binding between the active ingredients and the target protein. The results of the molecular docking study showed that the active components of Allium schoenoprasum had a strong ability to bind with these essential targets. This finding suggests that the active components of Allium schoenoprasum function regulate numerous targets at the same time, rather than a single target agent. However, our works have some limitations, especially in data mining. Additional study is required to determine the precise antihypertensive mechanisms that are at work when Allium schoenoprasum is administered. In the future, we intend to carry out additional research utilizing an in vivo model while making use of extract from Allium schoenoprasum.
Network pharmacology and molecular docking were used to investigate the hypertension-treating mechanism of Allium schoenoprasum. According to the protein-protein interaction network study, Allium schoenoprasum’s active components may target SCR, STAT3, PIK3R1, CTNNB1, and ESR1 to treat hypertension. Gene ontology functional enrichment analysis and KEGG pathway enrichment analysis showed that the target largely bound and catalyzed proteins in the cell’s membrane and cytoplasm. Kaempferol, isorhamnetin, and quercetin are the most potential antihypertensive components from Allium schoenoprasum, according to molecular docking.
The authors wish to express their thanks for the full support from the Faculty of Pharmacy University of Surabaya, Faculty of Pharmacy Universitas Sumatera Utara, and Sekolah Tinggi Ilmu Kesehatan Senior Medan. We also expressed our gratitude to Prof. Ginda Haro, Ph.D. for the guidance and resources for data mining.