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Gupta A, Haldhar R, Agarwal V, Rajput DS, Chun KS, Han SB, Raj V, Lee S. Exploring the Potential of Natural Products as FoxO1 Inhibitors: an In Silico Approach. Biomol Ther (Seoul) 2024; 32:390-398. [PMID: 38586882 PMCID: PMC11063485 DOI: 10.4062/biomolther.2023.156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/14/2023] [Accepted: 10/21/2023] [Indexed: 04/09/2024] Open
Abstract
FoxO1, a member of the Forkhead transcription factor family subgroup O (FoxO), is expressed in a range of cell types and is crucial for various pathophysiological processes, such as apoptosis and inflammation. While FoxO1's roles in multiple diseases have been recognized, the target has remained largely unexplored due to the absence of cost-effective and efficient inhibitors. Therefore, there is a need for natural FoxO1 inhibitors with minimal adverse effects. In this study, docking, MMGBSA, and ADMET analyses were performed to identify natural compounds that exhibit strong binding affinity to FoxO1. The top candidates were then subjected to molecular dynamics (MD) simulations. A natural product library was screened for interaction with FoxO1 (PDB ID- 3CO6) using the Glide module of the Schrödinger suite. In silico ADMET profiling was conducted using SwissADME and pkCSM web servers. Binding free energies of the selected compounds were assessed with the Prime-MMGBSA module, while the dynamics of the top hits were analyzed using the Desmond module of the Schrödinger suite. Several natural products demonstrated high docking scores with FoxO1, indicating their potential as FoxO1 inhibitors. Specifically, the docking scores of neochlorogenic acid and fraxin were both below -6.0. These compounds also exhibit favorable drug-like properties, and a 25 ns MD study revealed a stable interaction between fraxin and FoxO1. Our findings highlight the potential of various natural products, particularly fraxin, as effective FoxO1 inhibitors with strong binding affinity, dynamic stability, and suitable ADMET profiles.
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Affiliation(s)
- Anugya Gupta
- Faculty of Medical and Paramedical Sciences, Madhyanchal Professional University, Bhopal 462044, Madhya Pradesh, India
| | - Rajesh Haldhar
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Vipul Agarwal
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, Uttar Pradesh, India
| | - Dharmendra Singh Rajput
- Faculty of Medical and Paramedical Sciences, Madhyanchal Professional University, Bhopal 462044, Madhya Pradesh, India
| | - Kyung-Soo Chun
- College of Pharmacy, Keimyung University, Daegu 42601, Republic of Korea
| | - Sang Beom Han
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Vinit Raj
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sangkil Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
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Alnusaire T, Sabouni IL, Khojah H, Qasim S, Al-Sanea MM, Siddique S, Mokhtar FA, Ahmed SR. Integrating Chemical Profiling, In Vivo Study, and Network Pharmacology to Explore the Anti-inflammatory Effect of Pterocarpus dalbergioides Fruits and Its Correlation with the Major Phytoconstituents. ACS OMEGA 2023; 8:32544-32554. [PMID: 37720803 PMCID: PMC10500659 DOI: 10.1021/acsomega.3c02940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023]
Abstract
The purpose of this study is to explore the anti-inflammatory activity of Pterocarpus dalbergioides fruit extract (PFE) and the underlying mechanism. Chemical profiling using ultraperformance liquid chromatography/mass spectrometry identified 28 compounds in PFE (12 flavonoids, 5 fatty acids, 4 phenolic compounds, 3 alkaloids, 2 sesquiterpenes, and 2 xanthophylls). PFE (2 g/kg) significantly inhibited carrageenan-induced rat paw edema after 4 h of administration (42% inhibition). A network-based strategy and molecular docking studies were utilized to uncover the anti-inflammatory mechanism. Out of the identified compounds, 16 compounds with DL ≥ 0.18 and F ≥ 30% were selected using bioavailability (F) and drug-likeness (DL) metrics. The network analysis revealed that 90 genes are considered key targets for the selected compounds and linked to the anti-inflammatory effect. Among all compounds, linoleic acid was found to be the top-most active constituent as it targets maximum genes. Four targets (TNF, IL6, AKT1, and CCL2) among the top 10 genes were found to be the main target genes that may contribute to the anti-inflammatory potential of PFE. Furthermore, KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis revealed that PFE might regulate inflammation through five pathways: neuroactive ligand-receptor interaction, lipid and atherosclerosis, fluid shear stress and atherosclerosis, TNF signaling pathway, and rheumatoid arthritis. The docking study predicted the significant binding affinity between the top four active constituents (linoleic acid, 9-octadecenoic acid, 11,12,13-trihydroxy-9-octadecenoic acid, and rhamnetin-3-O-rhamnoside) and the selected target proteins (TNF and AKT1). The findings highlight PFE as a promising drug lead for controlling inflammation.
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Affiliation(s)
| | | | - Hanan Khojah
- Department
of Pharmacognosy, College of Pharmacy, Jouf
University, Sakaka, Aljouf 72341, Saudi Arabia
| | - Sumera Qasim
- Pharmacology
Department, College of Pharmacy, Jouf University, Sakaka, Aljouf 72341, Saudi Arabia
| | - Mohammad M. Al-Sanea
- Pharmaceutical
Chemistry Department, College of Pharmacy, Jouf University, Sakaka, Aljouf 72341, Saudi Arabia
| | - Sadaf Siddique
- Department
of Pharmacognosy, College of Pharmacy, Jouf
University, Sakaka, Aljouf 72341, Saudi Arabia
| | - Fatma Alzahraa Mokhtar
- Department
of Pharmacognosy, Faculty of Pharmacy, El
Saleheya El Gadida University, El Saleheya El Gadida, Sharkia 44813, Egypt
| | - Shaimaa R. Ahmed
- Department
of Pharmacognosy, College of Pharmacy, Jouf
University, Sakaka, Aljouf 72341, Saudi Arabia
- Department
of Pharmacognosy, Faculty of Pharmacy, Cairo
University, Kasr el-Aini
street, Cairo 11562, Egypt
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Huang M, Wu Z, Jia L, Wang Y, Gao S, Liu Y, Zhang Y, Li J. Bioinformatics and network pharmacology identify promotional effects and potential mechanisms of ethanol on esophageal squamous cell carcinoma and experimental validation. Toxicol Appl Pharmacol 2023; 474:116615. [PMID: 37406968 DOI: 10.1016/j.taap.2023.116615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Ethanol is an important risk factor for esophageal squamous cell carcinoma (ESCC); however, the molecular mechanisms behind how ethanol promotes ESCC development remain poorly understood. In this study, ethanol-ESCC-associated target genes were constructed and screened using network pharmacology and subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) and bioinformatics analysis. A mouse ethanol-exposed esophageal cancer model was constructed with 4-nitroquinoline-1-oxide (4-NQO) to assess its survival and tumor lesion status, and the mechanism of ethanol-promoted ESCC lesions was verified by qRT-PCR and Western blotting. The results showed that 126 ethanol-ESCC crossover genes were obtained, which were significantly enriched in the PI3K/AKT signaling pathway. Bioinformatics results showed that the target genes TNF, IL6, IL1β and JUN were highly expressed in esophageal tumor samples and positively correlated with tumor proliferation and apoptosis genes, and the genetic information of these genes was mutated to different degrees. Animal model experiments showed that ethanol decreased the survival rate and aggravated the occurrence of esophageal cancer in mice. qRT-PCR showed that ethanol promoted the expression of TNF, IL6, IL1β and JUN mRNA in mouse esophageal tumor tissues, and Western blotting showed that ethanol promoted p-PI3K and p-AKT protein expression in mouse esophageal tumor tissues. In conclusion, ethanol promotes esophageal carcinogenesis by increasing the expression of TNF, IL6, IL1β and JUN and activating the PI3K/AKT signaling pathway.
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Affiliation(s)
- Ming Huang
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China
| | - Zhongbing Wu
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China
| | - Lei Jia
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China
| | - Yu Wang
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China
| | - Shuang Gao
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China
| | - Ying Liu
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China
| | - Yushuang Zhang
- The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China.
| | - Jing Li
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China; The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China.
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Alnusaire TS, Qasim S, Al-Sanea MM, Hendawy O, Uttra AM, Ahmed SR. Revealing the Underlying Mechanism of Acacia Nilotica against Asthma from a Systematic Perspective: A Network Pharmacology and Molecular Docking Study. Life (Basel) 2023; 13:life13020411. [PMID: 36836768 PMCID: PMC9966740 DOI: 10.3390/life13020411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/13/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Acacia Nilotica (AN) has long been used as a folk cure for asthma, but little is known about how AN could possibly modulate this disease. Thus, an in-silico molecular mechanism for AN's anti-asthmatic action was elucidated utilizing network pharmacology and molecular docking techniques. DPED, PubChem, Binding DB, DisGeNET, DAVID, and STRING were a few databases used to collect network data. MOE 2015.10 software was used for molecular docking. Out of 51 searched compounds of AN, eighteen compounds interacted with human target genes, a total of 189 compounds-related genes, and 2096 asthma-related genes were found in public databases, with 80 overlapping genes between them. AKT1, EGFR, VEGFA, and HSP90AB were the hub genes, whereas quercetin and apigenin were the most active components. p13AKT and MAPK signaling pathways were found to be the primary target of AN. Outcomes of network pharmacology and molecular docking predicted that AN might exert its anti-asthmatic effect probably by altering the p13AKT and MAPK signaling pathway.
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Affiliation(s)
| | - Sumera Qasim
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
- Correspondence:
| | - Mohammad M. Al-Sanea
- Pharmaceutical Chemistry Department, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
| | - Omnia Hendawy
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
- Department of Clinical Pharmacology, Faculty of Medicine, Beni-Suef University, Beni-Suef 11562, Egypt
| | - Ambreen Malik Uttra
- Department of Pharmacology, College of Pharmacy, University of Sargodha, Sargodha 40100, Pakistan
| | - Shaimaa R. Ahmed
- Department of Pharmacognosy, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt
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Zhang J, Wang R, Qin Y, Feng C. Defining the Potential Targets for Biological Activity of Isoegomaketone Based on Network Pharmacology and Molecular Docking Methods. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122115. [PMID: 36556480 PMCID: PMC9788221 DOI: 10.3390/life12122115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/01/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Isoegomaketone is a water-soluble natural ketone compound that is commonly present in Rabdosia angustifolia and Perilla frutescens. At present, it is known that isoegomaketone has a wide range of pharmacological activity, but there has been no thorough investigation of its potential targets. As a result, we examined the potential targets of isoegomaketone using the network pharmacology approach. In our study, the TCM Database@Taiwan was utilized to search for the chemical formula. The pharmacological characteristics of isoegomaketone were then evaluated in silico using the Swiss Absorption, Distribution, Metabolism, and Excretion (Swiss ADME) and Deep Learning-Acute Oral Toxicity (DL-AOT) methods, and the potential isoegomaketone target genes were identified using a literature study. Additionally, using the clusterProfiler R package 3.8.1, the Gene Ontology (GO) enrichment analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of target genes were performed. In order to obtain the protein interaction network, we simultaneously submitted the targets to the STRING database. After this, we performed molecular docking with respect to targets and isoegomaketone. Finally, we created visual networks of protein-protein interactions (PPI) and examined these networks. Our results showed that isoegomaketone had good drug-likeness, bioavailability, medicinal chemistry friendliness, and acceptable toxicity. Subsequently, through the literature analysis, 48 target genes were selected. The bioinformatics analysis and network analysis found that these target genes were closely related to the biological processes of isoegomaketone, such as atherosclerotic formation, inflammation, tumor formation, cytotoxicity, bacterial infection, virus infection, and parasite infection. These findings show that isoegomaketone may interact with a wide range of proteins and biochemical processes to form a systematic pharmacological network, which has good value for the creation and use of drugs.
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Noor S, Mohammad T, Rub MA, Raza A, Azum N, Yadav DK, Hassan MI, Asiri AM. Biomedical features and therapeutic potential of rosmarinic acid. Arch Pharm Res 2022; 45:205-228. [PMID: 35391712 PMCID: PMC8989115 DOI: 10.1007/s12272-022-01378-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/18/2022] [Indexed: 12/17/2022]
Abstract
For decades, the use of secondary metabolites of various herbs has been an attractive strategy in combating human diseases. Rosmarinic acid (RA) is a bioactive phenolic compound commonly found in plants of Lamiaceae and Boraginaceae families. RA is biosynthesized using amino acids tyrosine and phenylalanine via enzyme-catalyzed reactions. However, the chemical synthesis of RA involves an esterification reaction between caffeic acid and 3,4-dihydroxy phenyl lactic acid contributing two phenolic rings to the structure of RA. Several studies have ascertained multiple therapeutic benefits of RA in various diseases, including cancer, diabetes, inflammatory disorders, neurodegenerative disorders, and liver diseases. Many previous scientific papers indicate that RA can be used as an anti-plasmodic, anti-viral and anti-bacterial drug. In addition, due to its high anti-oxidant capacity, this natural polyphenol has recently gained attention for its possible application as a nutraceutical compound in the food industry. Here we provide state-of-the-art, flexible therapeutic potential and biomedical features of RA, its implications and multiple uses. Along with various valuable applications in safeguarding human health, this review further summarizes the therapeutic advantages of RA in various human diseases, including cancer, diabetes, neurodegenerative diseases. Furthermore, the challenges associated with the clinical applicability of RA have also been discussed.
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Affiliation(s)
- Saba Noor
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Malik Abdul Rub
- Center of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Ali Raza
- Department of Medical Biochemistry, Jawahar Lal Nehru Medical College, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh, India
| | - Naved Azum
- Center of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Dharmendra Kumar Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro, Yeonsugu, Incheon, 21924, Korea.
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
| | - Abdullah M Asiri
- Center of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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Dong R, Huang R, Shi X, Xu Z, Mang J. Exploration of the mechanism of luteolin against ischemic stroke based on network pharmacology, molecular docking and experimental verification. Bioengineered 2021; 12:12274-12293. [PMID: 34898370 PMCID: PMC8810201 DOI: 10.1080/21655979.2021.2006966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Stroke is a leading cause of morbidity and mortality worldwide. As the most common type of stroke cases, treatment effectiveness is still limited despite intensive research. Recently, traditional Chinese medicine has attracted attention because of potential benefits for stroke treatment. Among these, luteolin, a natural plant flavonoid compound, offers neuroprotection following against ischemic stroke, although the specific mechanisms are unknown. Here we used network pharmacology, molecular docking, and experimental verification to explore the mechanisms whereby luteolin can benefit stroke recovery. The pharmacological and molecular properties of luteolin were obtained from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. The potential targets of luteolin and ischemic stroke were collected from interrogating public databases. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed by Funrich and Database for Annotation, Visualization and Integrated Discovery respectively, a luteolin-target-pathway network constructed using Cytoscape, Autodock vina was used for molecular docking simulation with Discovery Studio was used to visualize and analyze the docked conformations. Lastly, we employed an in vitro model of stroke injury to evaluate the effects of luteolin on cell survival and expression of the putative targets. From 95 candidate luteolin target genes, our analysis identified six core targets . KEGG analysis of the candidate targets identified that luteolin provides therapeutic effects on stroke through TNF signaling and other pathways. Our experimental analyses confirmed the conclusions analyzed above. In summary, the molecular and pharmacological mechanisms of luteolin against stroke are indicated in our study from a systematic perspective.
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Affiliation(s)
- Rui Dong
- Department of Neurology, China-Japan Union Hospital of Jilin University
| | - Renxuan Huang
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University
| | - Xiaohua Shi
- Department of Neurology, China-Japan Union Hospital of Jilin University
| | - Zhongxin Xu
- Department of Neurology, China-Japan Union Hospital of Jilin University
| | - Jing Mang
- Department of Neurology, China-Japan Union Hospital of Jilin University
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İSTİFLİ ES, ŞIHOĞLU TEPE A, SARIKÜRKCÜ C, TEPE B. Molecular interactions of some phenolics with 2019-nCoV and related pathway elements. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2021. [DOI: 10.21448/ijsm.958597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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