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Fadhal E. A Comprehensive Analysis of the PI3K/AKT Pathway: Unveiling Key Proteins and Therapeutic Targets for Cancer Treatment. Cancer Inform 2023; 22:11769351231194273. [PMID: 37649725 PMCID: PMC10462777 DOI: 10.1177/11769351231194273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
Background Cancer development and progression involve a complex network of pathways among which certain pathways play a pivotal role in promoting tumor growth and survival. An important pathway in this context is the PI3K/AKT pathway, which regulates crucial cellular processes including proliferation, viability, and metabolic regulation. Dysregulation of this pathway has been strongly linked to the development of various types of cancers. Consequently, it is imperative to identify the key proteins within this pathway as potential targets for impeding cancer cell proliferation and survival. Results One of the key findings of this study was the identification of signaling proteins that dominate various forms of PI3K/Akt pathway. Furthermore, proteins play critical roles in cancer networks, acting as oncogenes that promote cancer development or as tumor suppressor genes that inhibit tumor growth. This study identified several genes, including KIT, ERBB2, PDGFRA, MET, FGFR2, and FGFR3, which are involved in various types of the PI3K/Akt pathways. Additionally, this study identified 55 proteins that are commonly found in various forms of PI3K/Akt, and these proteins play crucial roles in regulating various biological functions. Conclusions This study highlights the importance of identifying key proteins involved in the PI3K/AKT pathway. In this study, we identified several genes involved in different pathways that play essential roles in the activation, signaling, and regulation of the pathway. Understanding the proteins participating in the PI3K/AKT pathway is vital for the development of targeted therapies, not only for cancer but also for other related diseases. By elucidating their roles and functions, this study contributes to the advancement of knowledge in the field and paves the way for the development of effective treatments targeting this pathway.
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Affiliation(s)
- Emad Fadhal
- Department of Mathematics &Statistics, College of Science, King Faisal University, Al-Ahsa, Saudi Arabia
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Al-Khateeb A, Zureigat H, Abuasbeh K, Fadhal E. Leray–Schauder Alternative for the Existence of Solutions of a Modified Coupled System of Caputo Fractional Differential Equations with Two Point’s Integral Boundary Conditions. Symmetry (Basel) 2023. [DOI: 10.3390/sym15040863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
In this paper, a coupled system of differential equations involving fractional order with integral boundary conditions is discussed. In the problem at hand, three main aspects that are existence, uniqueness, and stability have been investigated. Firstly, the contraction mapping principle is used to discuss the uniqueness of solutions for the proposed fractional system, and secondly, the existence of solutions for the problem is investigated based on Leray–Schauder’s alternative. Thirdly, the stability of the presented coupled system is discussed based on the Hyers–Ulam stability method. Finally, some examples have been given to confirm and illustrate the conclusion. The comparison between the current symmetrical results and the existing literature is deemed satisfactory. It was found that the presented fractional coupled system with two with integral boundary conditions is existent, unique, and stable.
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Affiliation(s)
- Areen Al-Khateeb
- Department of Mathematics, Faculty of Science and Technology, Jadara University, Irbid 21110, Jordan
| | - Hamzeh Zureigat
- Department of Mathematics, Faculty of Science and Technology, Jadara University, Irbid 21110, Jordan
| | - Kinda Abuasbeh
- Department of Mathematics and Statistics, College of Science, King Faisal University, Hafuf 31982, Saudi Arabia
| | - Emad Fadhal
- Department of Mathematics and Statistics, College of Science, King Faisal University, Hafuf 31982, Saudi Arabia
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Abdelli N, Mekawi E, Ebrahim Abdel-Alim M, Salim NS, El-Nagar M, Al-Dalain SY, Adlan Abdalla R, Nagarajan G, Fadhal E, Ibrahim RIH, Afkar E, Morsy MK. QTRAP LC/MS/MS of Garlic Nanoparticles and Improving Sunflower Oil Stabilization during Accelerated Shelf Life Storage. Foods 2022; 11:foods11243962. [PMID: 36553704 PMCID: PMC9778114 DOI: 10.3390/foods11243962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The purpose of this research was to assess and utilize the bioactive compounds of garlic nanoparticles (Ga-NPs) as a natural antioxidant in sunflower oil (SFO) stored at 65 ± 1 °C for 24 days. The garlic nanoparticles (Ga-NPs) from the Balady cultivar were prepared, characterized, and added to SFO at three concentrations: 200, 600, and 1000 ppm (w/v), and they were compared with 600 ppm garlic lyophilized powder extract (Ga-LPE), 200 ppm BHT, 200 ppm α-tocopherol, and SFO without Ga-NPs (control). The QTRAP LC/MS/MS profile of Ga-NPs revealed the presence of four organosulfur compounds. Ga-NPs exhibited the highest capacity for phenolic, flavonoid, and antioxidant compounds. In Ga-NP SFO samples, the values of peroxide, p-anisidine, totox, conjugated dienes, and conjugated trienes were significantly lower than the control. The antioxidant indices of SFO samples containing Ga-NPs were higher than the control. The Ga-NPs enhanced the sensory acceptability of SFO treatments up to day 24 of storage. The shelf life of SFO treated with Ga-NPs was substantially increased (presuming a Q10 amount). The results show that Ga-NPs are a powerful antioxidant that improves SFO stability and extends the shelf life (~384 days at 25 °C).
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Affiliation(s)
- Nouara Abdelli
- Department of Basic Sciences, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
- Correspondence: (N.A.); (M.K.M.)
| | - Enas Mekawi
- Department of Agricultural Biochemistry, Faculty of Agriculture, Benha University, Moshtohor, Qaluobia P.O. Box 13736, Egypt
| | - Mohammed Ebrahim Abdel-Alim
- Department of Agricultural Biochemistry, Faculty of Agriculture, Benha University, Moshtohor, Qaluobia P.O. Box 13736, Egypt
| | - Nesreen Saad Salim
- Department of Agricultural Biochemistry, Faculty of Agriculture, Benha University, Moshtohor, Qaluobia P.O. Box 13736, Egypt
| | - Mahran El-Nagar
- Department of Horticulture, Faculty of Agriculture, Benha University, Moshtohor, Qaluobia P.O. Box 13736, Egypt
| | - Sati Y. Al-Dalain
- Department of Medical Support, Al-Karak University College, Al-Balqa Applied University, Salt P.O. Box 19117, Jordan
| | - Ridab Adlan Abdalla
- Department of Basic Sciences, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Ganesan Nagarajan
- Department of Basic Sciences, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Emad Fadhal
- Department of Mathematics & Statistics, College of Science, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Rashid I. H. Ibrahim
- Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
- Department of Botany, Faculty of Science, Khartoum University, P.O. Box 321, Khartoum 11115, Sudan
| | - Eman Afkar
- Department of Basic Sciences, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
- Department of Botany and Microbiology, College of Science, Bani-Suef University, Bani-Suef P.O. Box 52621, Egypt
| | - Mohamed K. Morsy
- Department of Food Technology, Faculty of Agriculture, Benha University, Moshtohor, Qaluobia P.O. Box 13736, Egypt
- Correspondence: (N.A.); (M.K.M.)
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Fadhal E, Gamieldien J, Mwambene EC. Self-similarity of human protein interaction networks: a novel strategy of distinguishing proteins. Sci Rep 2015; 5:7628. [PMID: 25720740 PMCID: PMC4342563 DOI: 10.1038/srep07628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/03/2014] [Indexed: 11/09/2022] Open
Abstract
The successful determination of reliable protein interaction networks (PINs) in several species in the post-genomic era has hitherto facilitated the quest to understanding systems and structural properties of such networks. It is envisaged that a clearer understanding of their intrinsic topological properties would elucidate evolutionary and biological topography of organisms. This, in turn, may inform the understanding of diseases' aetiology. By analysing sub-networks that are induced in various layers identified by zones defined as distance from central proteins, we show that zones of human PINs display self-similarity patterns. What is observed at a global level is repeated at lower levels of inducement. Furthermore, it is observed that these levels of strength point to refinement and specialisations in these layers. This may point to the fact that various levels of representations in the self-similarity phenomenon offer a way of measuring and distinguishing the importance of proteins in the network. To consolidate our findings, we have also considered a gene co-expression network and a class of gene regulatory networks in the same framework. In all cases, the phenomenon is significantly evident. In particular, the truly unbiased regulatory networks show finer level of articulation of self-similarity.
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Affiliation(s)
- Emad Fadhal
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Junaid Gamieldien
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Eric C Mwambene
- Department of Mathematics and Applied Mathematics, University of the Western Cape, P/Bag X17, Bellville, South Africa
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Fadhal E, Mwambene EC, Gamieldien J. Modelling human protein interaction networks as metric spaces has potential in disease research and drug target discovery. BMC Syst Biol 2014; 8:68. [PMID: 24929653 PMCID: PMC4088370 DOI: 10.1186/1752-0509-8-68] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/04/2014] [Indexed: 01/06/2023]
Abstract
Background We have recently shown by formally modelling human protein interaction networks (PINs) as metric spaces and classified proteins into zones based on their distance from the topological centre that hub proteins are primarily centrally located. We also showed that zones closest to the network centre are enriched for critically important proteins and are also functionally very specialised for specific ‘house keeping’ functions. We proposed that proteins closest to the network centre may present good therapeutic targets. Here, we present multiple pieces of novel functional evidence that provides strong support for this hypothesis. Results We found that the human PINs has a highly connected signalling core, with the majority of proteins involved in signalling located in the two zones closest to the topological centre. The majority of essential, disease related, tumour suppressor, oncogenic and approved drug target proteins were found to be centrally located. Similarly, the majority of proteins consistently expressed in 13 types of cancer are also predominantly located in zones closest to the centre. Proteins from zones 1 and 2 were also found to comprise the majority of proteins in key KEGG pathways such as MAPK-signalling, the cell cycle, apoptosis and also pathways in cancer, with very similar patterns seen in pathways that lead to cancers such as melanoma and glioma, and non-neoplastic diseases such as measles, inflammatory bowel disease and Alzheimer’s disease. Conclusions Based on the diversity of evidence uncovered, we propose that when considered holistically, proteins located centrally in the human PINs that also have similar functions to existing drug targets are good candidate targets for novel therapeutics. Similarly, since disease pathways are dominated by centrally located proteins, candidates shortlisted in genome scale disease studies can be further prioritized and contextualised based on whether they occupy central positions in the human PINs.
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Affiliation(s)
| | | | - Junaid Gamieldien
- South African National Bioinformatics Institute/ MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Bellville 7530, South Africa.
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Fadhal E, Gamieldien J, Mwambene EC. Protein interaction networks as metric spaces: a novel perspective on distribution of hubs. BMC Syst Biol 2014; 8:6. [PMID: 24438364 PMCID: PMC3902029 DOI: 10.1186/1752-0509-8-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 01/07/2014] [Indexed: 02/02/2023]
Abstract
Background In the post-genomic era, a central and overarching question in the analysis of protein-protein interaction networks continues to be whether biological characteristics and functions of proteins such as lethality, physiological malfunctions and malignancy are intimately linked to the topological role proteins play in the network as a mathematical structure. One of the key features that have implicitly been presumed is the existence of hubs, highly connected proteins considered to play a crucial role in biological networks. We explore the structure of protein interaction networks of a number of organisms as metric spaces and show that hubs are non randomly positioned and, from a distance point of view, centrally located. Results By analysing how the human functional protein interaction network, the human signalling network, Saccharomyces cerevisiae, Arabidopsis thaliana and Escherichia coli protein-protein interaction networks from various databases are distributed as metric spaces, we found that proteins interact radially through a central node, high degree proteins coagulate in the centre of the network, and those far away from the centre have low degree. We further found that the distribution of proteins from the centre is in some hierarchy of importance and has biological significance. Conclusions We conclude that structurally, protein interaction networks are mathematical entities that share properties between organisms but not necessarily with other networks that follow power-law. We therefore conclude that (i) if there are hubs defined by degree, they are not distributed randomly; (ii) zones closest to the centre of the network are enriched for critically important proteins and are also functionally very specialised for specific 'house keeping’ functions; (iii) proteins closest to the network centre are functionally less dispensable and may present good targets for therapy development; and (iv) network biology requires its own network theory modelled on actual biological evidence and that simply adopting theories from the social sciences may be misleading.
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Affiliation(s)
| | | | - Eric C Mwambene
- Department of Mathematics and Applied Mathematics, University of the Western Cape, P/Bag X17, Bellville, South Africa.
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