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Saleem M, Mazhar Fareed M, Salman Akbar Saani M, Shityakov S. Network pharmacology and multitarget analysis of Nigella sativa in the management of diabetes and obesity: a computational study. J Biomol Struct Dyn 2024; 42:4800-4816. [PMID: 37350443 DOI: 10.1080/07391102.2023.2222837] [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: 02/02/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
Obesity and diabetes are commonly associated with one another and represent a significant global health issue, with a recent surge in disease incidence. Nigella sativa, also known as black cumin, is believed to possess several health benefits, including anti-diabetic, anticancer, antioxidant, antimicrobial, and anti-obesity properties. In this study, we aimed to identify the active compounds derived from N. sativa, which can potentially inhibit key protein targets and signaling pathways associated with diabesity treatment. We employed an exhaustive in silico search, which led to the identification of 22 potential compounds. Out of these, only five hits were found to be non-toxic, including Arabic and ascorbic acids, dihydrocodeine, catechin, and kaempferol. Our analysis revealed that these hits were associated with genes such as AKT1, IL6, SRC, and EGFR. Finally, we conducted molecular docking and molecular dynamics simulations, which identified kaempferol as the best binder for AKT1 in comparison to the reference molecule. Overall, our in silico integrated pipeline provides a useful approach to identify non-toxic phytocompounds as promising drug candidates to treat diabetes and obesity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muntaha Saleem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Mazhar Fareed
- Department of Computer Science, School of Science and Engineering, Università degli studi di Verona, Verona, Italy
- Department of Biotechnology, Applied Bioinformatics Group, Università degli studi di Verona, Verona, Italy
| | | | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russian Federation
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Asghar A, Qasim M, Noor F, Ashfaq UA, Tahir Ul Qamar M, Masoud MS, Bhatti R, Almatroudi A, Alrumaihi F, Allemailem KS. Systematic elucidation of the multi-target pharmacological mechanism of Terminalia arjuna against congestive cardiac failure via network pharmacology and molecular modelling approaches. Nat Prod Res 2023; 37:3733-3740. [PMID: 37665010 DOI: 10.1080/14786419.2023.2252565] [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: 04/15/2023] [Revised: 08/12/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023]
Abstract
Congestive cardiac failure (CCF) is a pathophysiologic state when the heart is not able to maintain its cardiac output to meet the demand of metabolising tissues. CCF is responsible for approximately 2.9 million deaths worldwide. The heterogeneous nature of CCF draws the attention of researchers to find more enthralling and promising diagnostic and treatment options. Terminalia arjuna (Arjuna) is an evergreen, deciduous tree exhibited various astringent, anti-bacterial, and anti-microbial properties. T. arjuna is being used in various regions for anginal pain, hypertension, congestive heart failure, and dyslipidemia. Although previous in vitro studies have demonstrated the therapeutic potential of T. arjuna, the exact molecular mechanism underlying its protective effect on the heart remains unclear. In this study, a network pharmacology technique was used to explore the active ingredients, potential targets in T. arjuna for the treatment of CCF. In the framework of this study, we explored the active ingredient-target-pathway network and figured out that oleanolic acid, arjunolic acid, luteolin, kaempferol, cholesterol, ellagic acid 4-O-xylopyranoside 3,3'-dimethyl ether, and cyclohexyl (2,4-dimethyl phenyl) methanone contributed significantly to the development of CCF by affecting AKT1, MAPK14, TNF, IL6, ESR1, and HSP90AA1 genes. Molecular docking analysis further validated the activities of these compounds against potential targets. To sum up, integrated network pharmacology and docking analysis revealed that T. arjuna exerts its cardioprotective effect by acting on various signalling pathways, including the thyroid hormone, VEGF signalling pathway, AGE-RAGE signalling pathway in diabetic complications, HIF signalling pathway, sphingolipid signalling pathway, and oestrogen signalling pathways. Overall, this study provides valuable insights into the molecular mechanism of T. arjuna in CCF and highlights its potential as a promising preventive treatment for this condition.
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Affiliation(s)
- Aqsa Asghar
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Tahir Ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Rashid Bhatti
- National Centre of Excellence in Molecular Biology, The University of Punjab, Lahore, Pakistan
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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Retraction: Integrative bioinformatics approaches to map key biological markers and therapeutic drugs in Extramammary Paget’s disease of the scrotum. PLoS One 2022; 17:e0273532. [PMID: 36044437 PMCID: PMC9432758 DOI: 10.1371/journal.pone.0273532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Noor F, Ahmad S, Saleem M, Alshaya H, Qasim M, Rehman A, Ehsan H, Talib N, Saleem H, Bin Jardan YA, Aslam S. Designing a multi-epitope vaccine against Chlamydia pneumoniae by integrating the core proteomics, subtractive proteomics and reverse vaccinology-based immunoinformatics approaches. Comput Biol Med 2022; 145:105507. [DOI: 10.1016/j.compbiomed.2022.105507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/03/2022] [Accepted: 04/05/2022] [Indexed: 12/26/2022]
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Noor F, Saleem MH, Javed MR, Chen JT, Ashfaq UA, Okla MK, Abdel-Maksoud MA, Alwasel YA, Al-Qahtani WH, Alshaya H, Yasin G, Aslam S. Comprehensive computational analysis reveals H5N1 influenza virus-encoded miRNAs and host-specific targets associated with antiviral immune responses and protein binding. PLoS One 2022; 17:e0263901. [PMID: 35533150 PMCID: PMC9084522 DOI: 10.1371/journal.pone.0263901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/30/2022] [Indexed: 02/06/2023] Open
Abstract
H5N1 virus (H5N1V) is highly contagious among birds and it was first detected in humans in 1997 during a poultry outbreak in Hong Kong. As the mechanism of its pathogenesis inside the host is still lacking, in this in-silico study we hypothesized that H5N1V might create miRNAs, which could target the genes associated with host cellular regulatory pathways, thus provide persistent refuge to the virus. Using bioinformatics approaches, several H5N1V produced putative miRNAs as well as the host genes targeted by these miRNAs were found. Functional enrichment analysis of targeted genes revealed their involvement in many biological pathways that facilitate their host pathogenesis. Eventually, the microarray dataset (GSE28166) was analyzed to validate the altered expression level of target genes and found the genes involved in protein binding and adaptive immune responses. This study presents novel miRNAs and their targeted genes, which upon experimental validation could facilitate in developing new therapeutics against H5N1V infection.
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Affiliation(s)
- Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | | | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Mohammad K. Okla
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mostafa A. Abdel-Maksoud
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Yasmeen A. Alwasel
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Wahidah H. Al-Qahtani
- Department of food sciences & nutrition, College of food & Agriculture sciences, King Saud University, Riyadh, Saudi Arabia
| | - Huda Alshaya
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
| | - Ghulam Yasin
- Department of Botany, Bahauddin Zakariya University, Multan, Pakistan
| | - Sidra Aslam
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
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Noor F, Saleem MH, Chen JT, Javed MR, Al-Megrin WA, Aslam S. Correction: Integrative bioinformatics approaches to map key biological markers and therapeutic drugs in Extramammary Paget's disease of the scrotum. PLoS One 2021; 16:e0259408. [PMID: 34705874 PMCID: PMC8550377 DOI: 10.1371/journal.pone.0259408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches. BIOLOGY 2021; 10:biology10100997. [PMID: 34681096 PMCID: PMC8533590 DOI: 10.3390/biology10100997] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022]
Abstract
Chlamydia trachomatis, a Gram-negative bacterium that infects the rectum, urethra, congenital sites, and columnar epithelium of the cervix. It is a major cause of preventable blindness, ectopic pregnancy, and bacterial sexually transmitted infections worldwide. There is currently no licensed multi-epitope vaccination available for this pathogen. This study used core proteomics, immuno-informatics, and subtractive proteomics approaches to identify the best antigenic candidates for the development of a multi-epitope-based vaccine (MEBV). These approaches resulted in six vaccine candidates: Type III secretion system translocon subunit CopD2, SctW family type III secretion system gatekeeper subunit CopN, SycD/LcrH family type III secretion system chaperone Scc2, CT847 family type III secretion system effector, hypothetical protein CTDEC_0668, and CHLPN 76kDa-like protein. A variety of immuno-informatics tools were used to predict B and T cell epitopes from vaccine candidate proteins. An in silico vaccine was developed using carefully selected epitopes (11 CTL, 2 HTL & 10 LBL) and then docked with the MHC molecules (MHC I & MHC II) and human TLR4. The vaccine was coupled with Cholera toxin subunit B (CTB) adjuvant to boost the immune response. Molecular dynamics (MD) simulations, molecular docking, and MMGBSA analysis were carried out to analyze the molecular interactions and binding affinity of MEBV with TLR4 and MHC molecules. To achieve the highest level of vaccine protein expression, the MEBV was cloned and reverse-translated in Escherichia coli. The highest level of expression was achieved, and a CAI score of 0.97 was reported. Further experimental validation of the MEBV is required to prove its efficacy. The vaccine developed will be useful in preventing infections caused by C. trachomatis.
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