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Alshabrmi FM, Aba Alkhayl FF, Rehman A. Novel drug discovery: Advancing Alzheimer's therapy through machine learning and network pharmacology. Eur J Pharmacol 2024; 976:176661. [PMID: 38795753 DOI: 10.1016/j.ejphar.2024.176661] [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: 03/21/2024] [Revised: 04/28/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024]
Abstract
Alzheimer's disease (AD), marked by tau tangles and amyloid-beta plaques, leads to cognitive decline. Despite extensive research, its complex etiology remains elusive, necessitating new treatments. This study utilized machine learning (ML) to analyze compounds with neuroprotective potential. This approach exposed the disease's complexity and identified important proteins, namely MTOR and BCL2, as central to the pathogenic network of AD. MTOR regulates neuronal autophagy and survival, whereas BCL2 regulates apoptosis, both of which are disrupted in AD. The identified compounds, including Armepavine, Oprea1_264702,1-cyclopropyl-7-fluoro-8-methoxy-4-oxoquinoline-3-carboxylic acid,(2S)-4'-Hydroxy-5,7,3'-trimethoxyflavan,Oprea1_130514,Sativanone,5-hydroxy-7,8-dimethoxyflavanone,7,4'-Dihydroxy-8,3'-dimethoxyflavanone,N,1-dicyclopropyl-6,Difluoro-Methoxy-Gatifloxacin,6,8-difluoro-1-(2-fluoroethyl),1-ethyl-6-fluoro-7-(4-methylpiperidin-1-yl),Avicenol C, demonstrated potential modulatory effects on these proteins. The potential for synergistic effects of these drugs in treating AD has been revealed via network pharmacology. By targeting numerous proteins at once, these chemicals may provide a more comprehensive therapeutic approach, addressing many aspects of AD's complex pathophysiology. A Molecular docking, dynamic simulation, and Principle Component Analysis have confirmed these drugs' efficacy by establishing substantial binding affinities and interactions with important proteins such as MTOR and BCL2. This evidence implies that various compounds may interact within the AD pathological framework, providing a sophisticated and multifaceted therapy strategy. In conclusion, our study establishes a solid foundation for the use of these drugs in AD therapy. Thus current study highlights the possibility of multi-targeted, synergistic therapeutic approaches in addressing the complex pathophysiology of AD by integrating machine learning, network pharmacology, and molecular docking simulations. This holistic technique not only advances drug development but also opens up new avenues for developing more effective treatments for this difficult and widespread disease.
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Affiliation(s)
- Fahad M Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, 51452, Saudi Arabia
| | - Faris F Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, 51452, Saudi Arabia
| | - Abdur Rehman
- Center of Bioinformatics, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China.
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2
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Mariana Kustiawan P, Siregar KAAK, Syaifie PH, Zein Muttaqin F, Ibadillah D, Miftah Jauhar M, Djamas N, Mardliyati E, Taufiqu Rochman N. Uncovering the anti-breast cancer activity potential of east Kalimantan propolis by In vitro and bioinformatics analysis. Heliyon 2024; 10:e33636. [PMID: 39071605 PMCID: PMC11283153 DOI: 10.1016/j.heliyon.2024.e33636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/25/2024] [Indexed: 07/30/2024] Open
Abstract
Numerous side effects of breast cancer drugs have prompted researchers to explore more into new therapeutic approaches derived from natural substances. In this context, our study focused on uncovering the potential of East Kalimantan propolis from Trigona apicalis for breast cancer treatment including the underlying mechanisms through bioinformatics approached. We conducted integrated in vitro and bioinformatics analysis of network pharmacology, molecular docking, molecular dynamics and MM-GBSA analysis. Initially, in vitro cytotoxic assay demonstrated the anti-breast cancer activity potential of ethanol extract of East Kalimantan propolis, particularly its ethyl acetate fraction, which exhibited similar activity to doxorubicin, as indicated by their IC50 value. This study revealed eight propolis compounds, consisting of flavonoids and phenolic acids, in East Kalimantan propolis. By integrating microarray datasets (GSE29431, GSE36295, and GSE42568) analysis with potential targets derived from propolis compounds, 39 shared target genes were identified. Subsequently, GO and KEGG pathway, protein-protein interaction (PPI) network, core hub genes and gene expression analysis revealed three major targets, namely, PTGS2, CXCL2, and MMP9. Among them, only MMP9 was highly expressed in breast cancer than normal. Moreover, molecular docking revealed the six of propolis compounds which exhibited pronounced binding affinity towards MMP-9, better than marimastat as control drug. Dynamic simulation confirmed the stability of chrysin and quercetin as best compounds. Additionally, MM-GBSA analysis revealed a relative binding energy for chrysin (-25.6403 kcal/mol) that was comparable to marimastat (-27.3827 kcal/mol). In conclusion, this study reveals how East Kalimantan Propolis affect breast cancer and emphasizes MMP9 as a key target for future therapeutics.
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Affiliation(s)
- Paula Mariana Kustiawan
- Faculty of Pharmacy, Universitas Muhammadiyah Kalimantan Timur, Samarinda, East Kalimantan, 75124, Indonesia
| | - Khalish Arsy Al Khairy Siregar
- Faculty of Pharmacy, Universitas Muhammadiyah Kalimantan Timur, Samarinda, East Kalimantan, 75124, Indonesia
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | - Putri Hawa Syaifie
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | - Fauzan Zein Muttaqin
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Bhakti Kencana, Bandung, Indonesia
| | - Delfritama Ibadillah
- Center of Excellence Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | | | - Nailulkamal Djamas
- Research Center for Horticultural and Estate Crops, National Research and Innovation Agency (BRIN), Bogor, 16915, Indonesia
| | - Etik Mardliyati
- Research Center for Vaccine and Drugs, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Nurul Taufiqu Rochman
- Research Center for Advanced Material, National Research and Innovation Agency (BRIN), PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
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Ez-Zahra Amrati F, Mssillou I, Boukhira S, Djiddi Bichara M, El Abdali Y, Galvão de Azevedo R, Mohamed C, Slighoua M, Conte R, Kiokias S, Soares Pontes G, Bousta D. Phenolic Composition of Crataegus monogyna Jacq. Extract and Its Anti-Inflammatory, Hepatoprotective, and Antileukemia Effects. Pharmaceuticals (Basel) 2024; 17:786. [PMID: 38931453 PMCID: PMC11207108 DOI: 10.3390/ph17060786] [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: 05/02/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Crataegus monogyna (C. monogyna) is a prominent plant used in Moroccan traditional medicine. This study investigated the phenolic composition and the anti-inflammatory, the hepatoprotective, and the anticancer activities of a hydroethanolic extract of C. monogyna leaves and stems. Ultra-high-performance liquid chromatography identified the phenolic profile. The in vitro anticancer activity was evaluated using the MTT assay on HL-60 and K-562 myeloleukemia cells and liver (Huh-7) cell lines. The anti-inflammatory effect was assessed in vivo using carrageenan-induced paw edema in rats. The hepatoprotective effect at 300 and 1000 mg/kg doses against the acetaminophen-induced hepatotoxicity on rats was studied for seven days. Additionally, molecular docking simulations were performed to evaluate the extract's inhibitory potential against key targets: lipoxygenase, cytochrome P450, tyrosine kinase, and TRADD. The extract exhibited significant cytotoxic activity against K-562 and HL-60 cells, but not against lung cancer cells (Huh-7 line). The 1000 mg/kg dose demonstrated the most potent anti-inflammatory effect, inhibiting edema by 99.10% after 6 h. C. monogyna extract displayed promising hepatoprotective properties. Procyanidin (-7.27 kcal/mol), quercetin (-8.102 kcal/mol), and catechin (-9.037 kcal/mol) were identified as the most active molecules against lipoxygenase, cytochrome P450, and tyrosine kinase, respectively. These findings highlight the untapped potential of C. monogyna for further exploration in treating liver damage, inflammation, and leukemia.
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Affiliation(s)
- Fatima Ez-Zahra Amrati
- Laboratory of Cell Biology and Molecular Genetics (LBCGM), Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir 8106, Morocco
| | - Ibrahim Mssillou
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health & Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez 30000, Morocco;
| | - Smahane Boukhira
- Higher Institute of Nursing Professions and Health Techniques, Ministry of Health and Social Protection, Guelmim 81000, Morocco;
| | - Mehdi Djiddi Bichara
- Laboratory of Biotechnology, Health, Agrofood and Environment (LBEAS), Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez 30000, Morocco; (M.D.B.); (Y.E.A.)
| | - Youness El Abdali
- Laboratory of Biotechnology, Health, Agrofood and Environment (LBEAS), Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez 30000, Morocco; (M.D.B.); (Y.E.A.)
| | - Renata Galvão de Azevedo
- Laboratory of Virology, National Institute of Amazonian Research (INPA), Manaus 69067-375, Brazil; (R.G.d.A.)
- Post-Graduate Program in Basic and Applied Immunology, Institute of Biological Science, Federal University of Amazonas, Manaus 69077-000, Brazil
| | - Chebaibi Mohamed
- Higher Institute of Nursing Professions and Health Techniques, Ministry of Health and Social Protection, Fez 30050, Morocco
- Biomedical and Translational Research Laboratory, Faculty of Medicine and Pharmacy of the Fez, Sidi Mohamed Ben Abdellah University, Fez 30000, Morocco
| | - Meryem Slighoua
- Laboratory of Biotechnology, Health, Agrofood and Environment (LBEAS), Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez 30000, Morocco; (M.D.B.); (Y.E.A.)
| | - Raffaele Conte
- Research Institute on Terrestrial Ecosystems (IRET), National Research Council, 05010 Naples, Italy;
| | - Sotirios Kiokias
- European Research Executive Agency (REA), 1210 Brussels, Belgium;
| | - Gemilson Soares Pontes
- Laboratory of Virology, National Institute of Amazonian Research (INPA), Manaus 69067-375, Brazil; (R.G.d.A.)
- Post-Graduate Program in Basic and Applied Immunology, Institute of Biological Science, Federal University of Amazonas, Manaus 69077-000, Brazil
| | - Dalila Bousta
- National Agency of Medicinal and Aromatic Plants, Taounate 34000, Morocco
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Zhou Z, Nan Y, Li X, Ma P, Du Y, Chen G, Ning N, Huang S, Gu Q, Li W, Yuan L. Hawthorn with "homology of medicine and food": a review of anticancer effects and mechanisms. Front Pharmacol 2024; 15:1384189. [PMID: 38915462 PMCID: PMC11194443 DOI: 10.3389/fphar.2024.1384189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/29/2024] [Indexed: 06/26/2024] Open
Abstract
Over the past few years, there has been a gradual increase in the incidence of cancer, affecting individuals at younger ages. With its refractory nature and substantial fatality rate, cancer presents a notable peril to human existence and wellbeing. Hawthorn, a medicinal food homology plant belonging to the Crataegus genus in the Rosaceae family, holds great value in various applications. Due to its long history of medicinal use, notable effects, and high safety profile, hawthorn has garnered considerable attention and plays a crucial role in cancer treatment. Through the integration of modern network pharmacology technology and traditional Chinese medicine (TCM), a range of anticancer active ingredients in hawthorn have been predicted, identified, and analyzed. Studies have shown that ingredients such as vitexin, isoorientin, ursolic acid, and maslinic acid, along with hawthorn extracts, can effectively modulate cancer-related signaling pathways and manifest anticancer properties via diverse mechanisms. This review employs network pharmacology to excavate the potential anticancer properties of hawthorn. By systematically integrating literature across databases such as PubMed and CNKI, the review explores the bioactive ingredients with anticancer effects, underlying mechanisms and pathways, the synergistic effects of drug combinations, advancements in novel drug delivery systems, and ongoing clinical trials concerning hawthorn's anticancer properties. Furthermore, the review highlights the preventive health benefits of hawthorn in cancer prevention, offering valuable insights for clinical cancer treatment and the development of TCM with anticancer properties that can be used for both medicinal and edible purposes.
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Affiliation(s)
- Ziying Zhou
- Department of Pharmacy, General Hospital of Ningxia Medical University, Yinchuan, China
- College of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Yi Nan
- Key Laboratory of Ningxia Minority Medicine Modernization Ministry of Education, Ningxia Medical University, Yinchuan, China
| | - Xiangyang Li
- College of Traditional Chinese Medicine, Ningxia Medical University, Yinchuan, China
| | - Ping Ma
- Department of Pharmacy, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Yuhua Du
- College of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Guoqing Chen
- College of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Na Ning
- College of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Shicong Huang
- College of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Qian Gu
- College of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Weiqiang Li
- Department of Chinese Medical Gastrointestinal, The Affiliated TCM Hospital of Ningxia Medical University, Wuzhong, China
| | - Ling Yuan
- College of Pharmacy, Ningxia Medical University, Yinchuan, China
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Razola-Díaz MDC, Aznar-Ramos MJ, Benítez G, Gómez-Caravaca AM, Verardo V. Exploring the potential of phenolic and antioxidant compounds in new Rosaceae fruits. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:3705-3718. [PMID: 38160248 DOI: 10.1002/jsfa.13255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Rosaceae fruits have been used in traditional medicine for the prevention and treatment of diseases. However, these fruits have not extensively been studied regarding their phenolic composition. Thus, this research focuses on the determination of phenolic compounds by high-performance liquid chromatography electrospray ionization time-of-flight mass spectrometry, flavan-3-ols by high-performance liquid chromatography with fluorescence detection, and the antioxidant activity by 2,2-diphenyl-1-picrylhydrazyl, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), and ferric reducing antioxidant power of the fruits of five species of genera Crataegus and Sorbus (Rosaceae). RESULTS We found a total of 71 phenolic compounds from which 30 were identified in these berries for the first time. Crataegus monogyna and Crataegus laciniata revealed higher total phenolic and flavan-3-ol contents than the other species and the highest antioxidant activities. CONCLUSIONS Therefore, the fruits evaluated have demonstrated to be important sources of bioactive compounds with huge potential for being used in nutraceutical or food scopes. Additional studies could be needed to evaluate the influence of the different production areas on the phenolic content. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
| | | | - Guillermo Benítez
- Department of Botany, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Ana María Gómez-Caravaca
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Granada, Spain
- Institute of Nutrition and Food Technology 'José Mataix', Biomedical Research Centre, University of Granada, Granada, Spain
| | - Vito Verardo
- Department of Nutrition and Food Science, University of Granada, Granada, Spain
- Institute of Nutrition and Food Technology 'José Mataix', Biomedical Research Centre, University of Granada, Granada, Spain
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Alamri MA, Tahir ul Qamar M. Network pharmacology based virtual screening of Flavonoids from Dodonea angustifolia and the molecular mechanism against inflammation. Saudi Pharm J 2023; 31:101802. [PMID: 37822694 PMCID: PMC10563060 DOI: 10.1016/j.jsps.2023.101802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023] Open
Abstract
Inflammation is a nonspecific immune response against injury caused by a harmful agent that strives to restore tissue function and homeostasis. Dodonaea angustifolia L.f. (Sapindaceae) is a medium-sized shrub used to treat a variety of diseases in traditional medicine. In the current study, integrated network-pharmacology and molecular docking approaches were used to identify the active constituents, their possible targets, signaling pathways, and anti-inflammatory effects of flavonoids from D.angustifolia. D. angustifolia active ingredients were acquired from the Indian Medicinal Plants, Phytochemistry and Therapeutics (IMPPAT), and Traditional Chinese Medicine System Pharmacology (TCMSP) databases. The screening included the ten most prevalent D. angustifolia components, and the SwissTargetPrediction database was utilized to anticipate the targets of these compounds. Anti-inflammatory genes were found using the GeneCards database. The 175 overlapping genes were discovered as prospective D. angustifolia anti-inflammatory targets. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the overlapped targets were closely related to the major pathogenic processes linked to inflammation, such as response to organonitrogen compound, protein kinase activity, phosphotransferase activity, pI3k-Akt signaling pathway, metabolic pathways, and chemical carcinogenesis. Compound-target-pathway, and protein-protein interaction networks revealed 6-Methoxykaempferol and 5-Hydroxy-7,8 dimethoxyflavone as key compounds, and AKT1, VEGFA, and EGFR as key targets. Furthermore, molecular docking followed by molecular dynamic (MD) simulation of D. angustifolia active ingredients with core proteins fully complemented the binding affinity of these compounds and indicated stable complexes at the docked site. These findings reveal D. angustifolia 's multi-target, multi-compound, and multi-pathway strategies against inflammation. Our study paved the way for further research into the mechanism for developing D. angustifolia -based natural products as alternative therapies for inflammation.
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Affiliation(s)
- Mubarak A. Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Muhammad Tahir ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
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Islam MM, Sreeharsha N, Alshabrmi FM, Asif AH, Aldhubiab B, Anwer MK, Krishnasamy R, Rehman A. From seeds to survival rates: investigating Linum usitatissimum's potential against ovarian cancer through network pharmacology. Front Pharmacol 2023; 14:1285258. [PMID: 37964873 PMCID: PMC10642394 DOI: 10.3389/fphar.2023.1285258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023] Open
Abstract
Ovarian cancer is a malignant tumor that primarily forms in the ovaries. It often goes undetected until it has spread to the pelvis and abdomen, making it more challenging to treat and often fatal. Historically, natural products and their structural analogues have played a pivotal role in pharmacotherapy, especially for cancer. Numerous studies have demonstrated the therapeutic potential of Linum usitatissimum against ovarian cancer, but the specific molecular mechanisms remain elusive. This study combines data mining, network pharmacology, and molecular docking analysis to pioneer an innovative approach for ovarian cancer treatment by identifying potent phytochemicals. Findings of current study revealed that Apigenin, Vitamin E, Palmitic acid, Riboflavin, Isolariciresinol, 5-Dehydro-avenasterol, Cholesterol, Pantothenic acid, Nicotinic acid, Campesterol, Beta-Sitosterol, Stigmasterol, Daucosterol, and Vitexin suppress tumor growth by influencing AKT1, JUN, EGFR, and VEGFA. Kaplan-Meier survival analysis spotlighted AKT1, JUN, EGFR, and VEGFA as potential diagnostic and prognostic biomarkers for ovarian cancer. However, it is imperative to conduct in vivo and in vitro examinations to ascertain the pharmacokinetics and biosafety profiles, bolstering the candidacy of L. usitatissimum in ovarian cancer therapeutics.
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Affiliation(s)
- Mohammed Monirul Islam
- Department of Biomedical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
- Department of Pharmaceutics, Vidya Siri College of Pharmacy, Bangalore, India
| | - Fahad M. Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Afzal Haq Asif
- Department of Pharmacy Practice, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Bandar Aldhubiab
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Md Khalid Anwer
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | | | - Abdur Rehman
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, China
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Aloufi B, Alshabrmi FM, Sreeharsha N, Rehman A. Exploring therapeutic targets and drug candidates for obesity: a combined network pharmacology, bioinformatics approach. J Biomol Struct Dyn 2023:1-22. [PMID: 37811763 DOI: 10.1080/07391102.2023.2265491] [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: 08/24/2023] [Accepted: 09/24/2023] [Indexed: 10/10/2023]
Abstract
The remarkably high prevalence of obesity in Saudi Arabia reflects a global epidemic demanding urgent attention due to its associated health risks. The integration of traditional medicine, a vital cultural aspect, involves the use of medicinal plants to address various diseases, including obesity. This research merges network pharmacology (NP) and bioinformatics to innovate obesity treatment by identifying effective phytochemicals from native plants in the Taif valley. Focusing on six indigenous plants-Senna alexandrina, Capsicum annuum, Zingiber officinale, Curcuma longa, Trigonella foenum-graecum, and Foeniculum vulgare-we conducted preliminary screenings for potential bioactive compounds. We systematically compiled compound data from public databases and reviewed literature, revealing active compounds like apigenin, kaempferol, moupinamide, cyclocurcumin, chrysoeriol, isorhamnetin, rheinanthrone, cyclocurcumin, and riboflavin.Constructing a compound-target genes-obesity network unveiled their significant impact on metabolic regulation and fat accumulation, interacting notably with key proteins AKT1 and PTGS2. Molecular docking and 100 ns Molecular Dynamic (MD) simulations demonstrated robust binding affinity and stability at the docking site. Employing adipocytes as a cellular model, we gauged their viability and response to obesity-related stressors post-treatment with these native plant compounds.In conclusion, Saudi Arabia's indigenous plants hold promise as natural solutions for obesity treatment. This research opens new avenues in the battle against this pervasive health crisis by incorporating the potential of native botanicals.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bandar Aloufi
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Fahad M Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
- Department of Pharmaceutics, Vidya Siri College of Pharmacy, Bangalore, India
| | - Abdur Rehman
- Department of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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Krishnamoorthy HR, Karuppasamy R. A multitier virtual screening of antagonists targeting PD-1/PD-L1 interface for the management of triple-negative breast cancer. Med Oncol 2023; 40:312. [PMID: 37777635 DOI: 10.1007/s12032-023-02183-7] [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: 07/21/2023] [Accepted: 09/04/2023] [Indexed: 10/02/2023]
Abstract
Immunotherapies are promising therapeutic options for the management of triple-negative breast cancer because of its high mutation rate and genomic instability. Of note, the blockade of the immune checkpoint protein PD-1 and its ligand PD-L1 has been proven to be an efficient and potent strategy to combat triple-negative breast cancer. To date, various anti-PD-1/anti-PD-L1 antibodies have been approved. However, the intrinsic constraints of these therapeutic antibodies significantly limit their application, making small molecules a potentially significant option for PD-1/PD-L1 inhibition. In light of this, the current study aims to use a high-throughput virtual screening technique to identify potential repurposed candidates as PD-L1 inhibitors. Thus, the present study explored binding efficiency of 2509 FDA-approved compounds retrieved from the drug bank database against PD-L1 protein. The binding affinity of the compounds was determined using the glide XP docking programme. Furthermore, prime-MM/GBSA, DFT calculations, and RF score were used to precisely re-score the binding free energy of the docked complexes. In addition, the ADME and toxicity profiles for the lead compounds were also examined to address PK/PD characteristics. Altogether, the screening process identified three molecules, namely DB01238, DB06016 and DB01167 as potential therapeutics for the PD-L1 protein. To conclude, a molecular dynamic simulation of 100 ns was run to characterise the stability and inhibitory action of the three lead compounds. The results from the simulation study confirm the robust structural and thermodynamic stability of DB01238 than other investigated molecules. Thus, our findings hypothesize that DB01238 could serve as potential PD-L1 inhibitor in the near future for triple-negative breast cancer patients.
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Affiliation(s)
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
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