Exploring the mechanism of Synechococcus sp. XM-24 in gastric cancer treatment via network pharmacology and molecular docking
We investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed to provide a theoretical basis for developing novel therapeutic drugs for treating GC. The interactions between Synechococcus sp. XM-24 and targeted pro...
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| Published in | PloS one Vol. 20; no. 7; p. e0326664 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
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United States
Public Library of Science
02.07.2025
Public Library of Science (PLoS) |
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| Abstract | We investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed to provide a theoretical basis for developing novel therapeutic drugs for treating GC.
The interactions between Synechococcus sp. XM-24 and targeted proteins in GC were analyzed through network pharmacology and molecular docking. Molecular dynamics (MD) simulation of the protein-small molecule complex obtained from molecular docking were performed using the Gromacs v2022.03 software. Based on the intersecting target genes of Synechococcus sp. XM-24 and GC, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes analyses were performed to obtain the associated biological processes (BP), cellular components (CC), molecular functions (MF), and signal transduction pathways.
In total, 609 intersecting targets were identified between Synechococcus sp. XM-24 and GC, with nine key target genes (AKT1, ALB, IL1B, SRC, STAT3, EGFR, HSP90AA1, ESR1, and BCL2) being identified as active components of Synechococcus sp. XM-24. These key target genes were involved in 1,028 BP, 110 CC, 312 MF, and 200 signaling pathways. The enriched signaling pathways mainly included the cancer pathway, metabolic pathway, phosphatidylinositol 3-kinase-protein kinase B(PI3K-AKT) signaling pathway, and Rat sarcoma signaling pathway. Additionally, molecular docking analysis revealed strong binding activities between 10 active components of Synechococcus sp. XM-24, including methyl vaccenate, allyl methallyl ether, and 11-octadecenoic acid, with key target proteins such as albumin (ALB). MD simulations demonstrated a stable binding of ALB and methyl vaccenate, with a binding free energy of -48.39 kcal/mol.
Overall, the findings of this study reveal the therapeutic potential of Synechococcus sp. XM-24 in the prevention and treatment of GC, along with providing a theoretical basis for further development in GC treatment employing Synechococcus sp. XM-24. |
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| AbstractList | ObjectiveWe investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed to provide a theoretical basis for developing novel therapeutic drugs for treating GC.MethodsThe interactions between Synechococcus sp. XM-24 and targeted proteins in GC were analyzed through network pharmacology and molecular docking. Molecular dynamics (MD) simulation of the protein–small molecule complex obtained from molecular docking were performed using the Gromacs v2022.03 software. Based on the intersecting target genes of Synechococcus sp. XM-24 and GC, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes analyses were performed to obtain the associated biological processes (BP), cellular components (CC), molecular functions (MF), and signal transduction pathways.ResultsIn total, 609 intersecting targets were identified between Synechococcus sp. XM-24 and GC, with nine key target genes (AKT1, ALB, IL1B, SRC, STAT3, EGFR, HSP90AA1, ESR1, and BCL2) being identified as active components of Synechococcus sp. XM-24. These key target genes were involved in 1,028 BP, 110 CC, 312 MF, and 200 signaling pathways. The enriched signaling pathways mainly included the cancer pathway, metabolic pathway, phosphatidylinositol 3-kinase–protein kinase B(PI3K-AKT) signaling pathway, and Rat sarcoma signaling pathway. Additionally, molecular docking analysis revealed strong binding activities between 10 active components of Synechococcus sp. XM-24, including methyl vaccenate, allyl methallyl ether, and 11-octadecenoic acid, with key target proteins such as albumin (ALB). MD simulations demonstrated a stable binding of ALB and methyl vaccenate, with a binding free energy of −48.39 kcal/mol.ConclusionsOverall, the findings of this study reveal the therapeutic potential of Synechococcus sp. XM-24 in the prevention and treatment of GC, along with providing a theoretical basis for further development in GC treatment employing Synechococcus sp. XM-24. We investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed to provide a theoretical basis for developing novel therapeutic drugs for treating GC. The interactions between Synechococcus sp. XM-24 and targeted proteins in GC were analyzed through network pharmacology and molecular docking. Molecular dynamics (MD) simulation of the protein-small molecule complex obtained from molecular docking were performed using the Gromacs v2022.03 software. Based on the intersecting target genes of Synechococcus sp. XM-24 and GC, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes analyses were performed to obtain the associated biological processes (BP), cellular components (CC), molecular functions (MF), and signal transduction pathways. In total, 609 intersecting targets were identified between Synechococcus sp. XM-24 and GC, with nine key target genes (AKT1, ALB, IL1B, SRC, STAT3, EGFR, HSP90AA1, ESR1, and BCL2) being identified as active components of Synechococcus sp. XM-24. These key target genes were involved in 1,028 BP, 110 CC, 312 MF, and 200 signaling pathways. The enriched signaling pathways mainly included the cancer pathway, metabolic pathway, phosphatidylinositol 3-kinase-protein kinase B(PI3K-AKT) signaling pathway, and Rat sarcoma signaling pathway. Additionally, molecular docking analysis revealed strong binding activities between 10 active components of Synechococcus sp. XM-24, including methyl vaccenate, allyl methallyl ether, and 11-octadecenoic acid, with key target proteins such as albumin (ALB). MD simulations demonstrated a stable binding of ALB and methyl vaccenate, with a binding free energy of -48.39 kcal/mol. Overall, the findings of this study reveal the therapeutic potential of Synechococcus sp. XM-24 in the prevention and treatment of GC, along with providing a theoretical basis for further development in GC treatment employing Synechococcus sp. XM-24. Objective We investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed to provide a theoretical basis for developing novel therapeutic drugs for treating GC. Methods The interactions between Synechococcus sp. XM-24 and targeted proteins in GC were analyzed through network pharmacology and molecular docking. Molecular dynamics (MD) simulation of the protein–small molecule complex obtained from molecular docking were performed using the Gromacs v2022.03 software. Based on the intersecting target genes of Synechococcus sp. XM-24 and GC, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes analyses were performed to obtain the associated biological processes (BP), cellular components (CC), molecular functions (MF), and signal transduction pathways. Results In total, 609 intersecting targets were identified between Synechococcus sp. XM-24 and GC, with nine key target genes ( AKT1 , ALB , IL1B , SRC , STAT3 , EGFR , HSP90AA1 , ESR1 , and BCL2 ) being identified as active components of Synechococcus sp. XM-24. These key target genes were involved in 1,028 BP, 110 CC, 312 MF, and 200 signaling pathways. The enriched signaling pathways mainly included the cancer pathway, metabolic pathway, phosphatidylinositol 3-kinase–protein kinase B(PI3K-AKT) signaling pathway, and Rat sarcoma signaling pathway. Additionally, molecular docking analysis revealed strong binding activities between 10 active components of Synechococcus sp. XM-24, including methyl vaccenate, allyl methallyl ether, and 11-octadecenoic acid, with key target proteins such as albumin (ALB). MD simulations demonstrated a stable binding of ALB and methyl vaccenate, with a binding free energy of −48.39 kcal/mol. Conclusions Overall, the findings of this study reveal the therapeutic potential of Synechococcus sp. XM-24 in the prevention and treatment of GC, along with providing a theoretical basis for further development in GC treatment employing Synechococcus sp. XM-24. We investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed to provide a theoretical basis for developing novel therapeutic drugs for treating GC.OBJECTIVEWe investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed to provide a theoretical basis for developing novel therapeutic drugs for treating GC.The interactions between Synechococcus sp. XM-24 and targeted proteins in GC were analyzed through network pharmacology and molecular docking. Molecular dynamics (MD) simulation of the protein-small molecule complex obtained from molecular docking were performed using the Gromacs v2022.03 software. Based on the intersecting target genes of Synechococcus sp. XM-24 and GC, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes analyses were performed to obtain the associated biological processes (BP), cellular components (CC), molecular functions (MF), and signal transduction pathways.METHODSThe interactions between Synechococcus sp. XM-24 and targeted proteins in GC were analyzed through network pharmacology and molecular docking. Molecular dynamics (MD) simulation of the protein-small molecule complex obtained from molecular docking were performed using the Gromacs v2022.03 software. Based on the intersecting target genes of Synechococcus sp. XM-24 and GC, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes analyses were performed to obtain the associated biological processes (BP), cellular components (CC), molecular functions (MF), and signal transduction pathways.In total, 609 intersecting targets were identified between Synechococcus sp. XM-24 and GC, with nine key target genes (AKT1, ALB, IL1B, SRC, STAT3, EGFR, HSP90AA1, ESR1, and BCL2) being identified as active components of Synechococcus sp. XM-24. These key target genes were involved in 1,028 BP, 110 CC, 312 MF, and 200 signaling pathways. The enriched signaling pathways mainly included the cancer pathway, metabolic pathway, phosphatidylinositol 3-kinase-protein kinase B(PI3K-AKT) signaling pathway, and Rat sarcoma signaling pathway. Additionally, molecular docking analysis revealed strong binding activities between 10 active components of Synechococcus sp. XM-24, including methyl vaccenate, allyl methallyl ether, and 11-octadecenoic acid, with key target proteins such as albumin (ALB). MD simulations demonstrated a stable binding of ALB and methyl vaccenate, with a binding free energy of -48.39 kcal/mol.RESULTSIn total, 609 intersecting targets were identified between Synechococcus sp. XM-24 and GC, with nine key target genes (AKT1, ALB, IL1B, SRC, STAT3, EGFR, HSP90AA1, ESR1, and BCL2) being identified as active components of Synechococcus sp. XM-24. These key target genes were involved in 1,028 BP, 110 CC, 312 MF, and 200 signaling pathways. The enriched signaling pathways mainly included the cancer pathway, metabolic pathway, phosphatidylinositol 3-kinase-protein kinase B(PI3K-AKT) signaling pathway, and Rat sarcoma signaling pathway. Additionally, molecular docking analysis revealed strong binding activities between 10 active components of Synechococcus sp. XM-24, including methyl vaccenate, allyl methallyl ether, and 11-octadecenoic acid, with key target proteins such as albumin (ALB). MD simulations demonstrated a stable binding of ALB and methyl vaccenate, with a binding free energy of -48.39 kcal/mol.Overall, the findings of this study reveal the therapeutic potential of Synechococcus sp. XM-24 in the prevention and treatment of GC, along with providing a theoretical basis for further development in GC treatment employing Synechococcus sp. XM-24.CONCLUSIONSOverall, the findings of this study reveal the therapeutic potential of Synechococcus sp. XM-24 in the prevention and treatment of GC, along with providing a theoretical basis for further development in GC treatment employing Synechococcus sp. XM-24. Objective We investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed to provide a theoretical basis for developing novel therapeutic drugs for treating GC. Methods The interactions between Synechococcus sp. XM-24 and targeted proteins in GC were analyzed through network pharmacology and molecular docking. Molecular dynamics (MD) simulation of the protein-small molecule complex obtained from molecular docking were performed using the Gromacs v2022.03 software. Based on the intersecting target genes of Synechococcus sp. XM-24 and GC, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes analyses were performed to obtain the associated biological processes (BP), cellular components (CC), molecular functions (MF), and signal transduction pathways. Results In total, 609 intersecting targets were identified between Synechococcus sp. XM-24 and GC, with nine key target genes (AKT1, ALB, IL1B, SRC, STAT3, EGFR, HSP90AA1, ESR1, and BCL2) being identified as active components of Synechococcus sp. XM-24. These key target genes were involved in 1,028 BP, 110 CC, 312 MF, and 200 signaling pathways. The enriched signaling pathways mainly included the cancer pathway, metabolic pathway, phosphatidylinositol 3-kinase-protein kinase B(PI3K-AKT) signaling pathway, and Rat sarcoma signaling pathway. Additionally, molecular docking analysis revealed strong binding activities between 10 active components of Synechococcus sp. XM-24, including methyl vaccenate, allyl methallyl ether, and 11-octadecenoic acid, with key target proteins such as albumin (ALB). MD simulations demonstrated a stable binding of ALB and methyl vaccenate, with a binding free energy of -48.39 kcal/mol. Conclusions Overall, the findings of this study reveal the therapeutic potential of Synechococcus sp. XM-24 in the prevention and treatment of GC, along with providing a theoretical basis for further development in GC treatment employing Synechococcus sp. XM-24. We investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed to provide a theoretical basis for developing novel therapeutic drugs for treating GC. The interactions between Synechococcus sp. XM-24 and targeted proteins in GC were analyzed through network pharmacology and molecular docking. Molecular dynamics (MD) simulation of the protein-small molecule complex obtained from molecular docking were performed using the Gromacs v2022.03 software. Based on the intersecting target genes of Synechococcus sp. XM-24 and GC, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes analyses were performed to obtain the associated biological processes (BP), cellular components (CC), molecular functions (MF), and signal transduction pathways. In total, 609 intersecting targets were identified between Synechococcus sp. XM-24 and GC, with nine key target genes (AKT1, ALB, IL1B, SRC, STAT3, EGFR, HSP90AA1, ESR1, and BCL2) being identified as active components of Synechococcus sp. XM-24. These key target genes were involved in 1,028 BP, 110 CC, 312 MF, and 200 signaling pathways. The enriched signaling pathways mainly included the cancer pathway, metabolic pathway, phosphatidylinositol 3-kinase-protein kinase B(PI3K-AKT) signaling pathway, and Rat sarcoma signaling pathway. Additionally, molecular docking analysis revealed strong binding activities between 10 active components of Synechococcus sp. XM-24, including methyl vaccenate, allyl methallyl ether, and 11-octadecenoic acid, with key target proteins such as albumin (ALB). MD simulations demonstrated a stable binding of ALB and methyl vaccenate, with a binding free energy of -48.39 kcal/mol. Overall, the findings of this study reveal the therapeutic potential of Synechococcus sp. XM-24 in the prevention and treatment of GC, along with providing a theoretical basis for further development in GC treatment employing Synechococcus sp. XM-24. ObjectiveWe investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed to provide a theoretical basis for developing novel therapeutic drugs for treating GC.MethodsThe interactions between Synechococcus sp. XM-24 and targeted proteins in GC were analyzed through network pharmacology and molecular docking. Molecular dynamics (MD) simulation of the protein-small molecule complex obtained from molecular docking were performed using the Gromacs v2022.03 software. Based on the intersecting target genes of Synechococcus sp. XM-24 and GC, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes analyses were performed to obtain the associated biological processes (BP), cellular components (CC), molecular functions (MF), and signal transduction pathways.ResultsIn total, 609 intersecting targets were identified between Synechococcus sp. XM-24 and GC, with nine key target genes (AKT1, ALB, IL1B, SRC, STAT3, EGFR, HSP90AA1, ESR1, and BCL2) being identified as active components of Synechococcus sp. XM-24. These key target genes were involved in 1,028 BP, 110 CC, 312 MF, and 200 signaling pathways. The enriched signaling pathways mainly included the cancer pathway, metabolic pathway, phosphatidylinositol 3-kinase-protein kinase B(PI3K-AKT) signaling pathway, and Rat sarcoma signaling pathway. Additionally, molecular docking analysis revealed strong binding activities between 10 active components of Synechococcus sp. XM-24, including methyl vaccenate, allyl methallyl ether, and 11-octadecenoic acid, with key target proteins such as albumin (ALB). MD simulations demonstrated a stable binding of ALB and methyl vaccenate, with a binding free energy of -48.39 kcal/mol.ConclusionsOverall, the findings of this study reveal the therapeutic potential of Synechococcus sp. XM-24 in the prevention and treatment of GC, along with providing a theoretical basis for further development in GC treatment employing Synechococcus sp. XM-24. |
| Audience | Academic |
| Author | Liu, Junhong Ma, Yamei Li, Lin Li, Jiayi Guo, Longzhi |
| AuthorAffiliation | 1 Department of Geriatric Medicine, The Henan Rongjun Hospital, Xinxiang, Henan, China 4 Department of Endocrinology, Central Hospital of Haining, Jiaxing, Zhejiang, China King Abdulaziz University, SAUDI ARABIA 3 Department of Gastroenterology, The Fuyang Affiliated Hospital of Anhui Medical University, Fuyang, Anhui, China 2 Department of Electrocardiography and Cardiac Function, The Fuyang Affiliated Hospital of Anhui Medical University, Fuyang, Anhui, China |
| AuthorAffiliation_xml | – name: 2 Department of Electrocardiography and Cardiac Function, The Fuyang Affiliated Hospital of Anhui Medical University, Fuyang, Anhui, China – name: 3 Department of Gastroenterology, The Fuyang Affiliated Hospital of Anhui Medical University, Fuyang, Anhui, China – name: 1 Department of Geriatric Medicine, The Henan Rongjun Hospital, Xinxiang, Henan, China – name: King Abdulaziz University, SAUDI ARABIA – name: 4 Department of Endocrinology, Central Hospital of Haining, Jiaxing, Zhejiang, China |
| Author_xml | – sequence: 1 givenname: Jiayi surname: Li fullname: Li, Jiayi – sequence: 2 givenname: Yamei surname: Ma fullname: Ma, Yamei – sequence: 3 givenname: Longzhi surname: Guo fullname: Guo, Longzhi – sequence: 4 givenname: Junhong surname: Liu fullname: Liu, Junhong – sequence: 5 givenname: Lin orcidid: 0009-0005-1088-5425 surname: Li fullname: Li, Lin |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/40601671$$D View this record in MEDLINE/PubMed |
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| Copyright | Copyright: © 2025 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. COPYRIGHT 2025 Public Library of Science 2025 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2025 Li et al 2025 Li et al 2025 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
| Copyright_xml | – notice: Copyright: © 2025 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. – notice: COPYRIGHT 2025 Public Library of Science – notice: 2025 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. – notice: 2025 Li et al 2025 Li et al – notice: 2025 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
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| DOI | 10.1371/journal.pone.0326664 |
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| Snippet | We investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed to provide... Objective We investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed... ObjectiveWe investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed to... Objective We investigated the potential molecular mechanisms of Synechococcus sp. XM-24 affect gastric cancer (GC) development. Furthermore, this study aimed... |
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| SubjectTerms | 1-Phosphatidylinositol 3-kinase AKT protein AKT1 protein Algae Apoptosis Bcl-2 protein Binding Bioinformatics Biological activity Biology and Life Sciences Cancer Cancer therapies Care and treatment Cyanobacteria Diagnosis Disease Drug development ESR1 protein Free energy Gastric cancer Genes Health aspects Humans Ingredients Kinases Ligands Medical prognosis Medicine and Health Sciences Metabolic pathways Metabolites Molecular docking Molecular Docking Simulation Molecular dynamics Molecular Dynamics Simulation Molecular modelling Mortality Natural products Network Pharmacology Oxidative stress Pharmacology Phosphatidylinositol Physical Sciences Prevention Proteins Sarcoma Signal Transduction Software Solvents Stat3 protein Stomach cancer Stomach Neoplasms - drug therapy Stomach Neoplasms - metabolism Stomach Neoplasms - microbiology Stomach Neoplasms - therapy Synechococcus Synechococcus - chemistry Synechococcus - metabolism Testing |
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| Title | Exploring the mechanism of Synechococcus sp. XM-24 in gastric cancer treatment via network pharmacology and molecular docking |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/40601671 https://www.proquest.com/docview/3226650404 https://www.proquest.com/docview/3226713117 https://pubmed.ncbi.nlm.nih.gov/PMC12221042 https://doaj.org/article/bede5ef6afa14ed4847065c3fcc22e8e http://dx.doi.org/10.1371/journal.pone.0326664 |
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