Affinity and energy docking results.

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.

研究目的：本研究探讨聚球藻属（Synechococcus sp.）XM-24影响胃癌（gastric cancer, GC）发生发展的潜在分子机制，并为研发新型胃癌治疗药物提供理论基础。
研究方法：本研究通过网络药理学与分子对接技术，分析聚球藻属XM-24与胃癌靶蛋白之间的相互作用。利用Gromacs v2022.03软件，对分子对接得到的蛋白质-小分子复合物开展分子动力学（MD）模拟。基于聚球藻属XM-24与胃癌的交集靶基因，进行基因本体（Gene Ontology, GO）功能注释与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）富集分析，以获取相关的生物过程（BP）、细胞组分（CC）、分子功能（MF）及信号转导通路。
研究结果：本研究共鉴定出聚球藻属XM-24与胃癌之间的609个交集靶标，其中9个关键靶基因（AKT1、ALB、IL1B、SRC、STAT3、EGFR、HSP90AA1、ESR1及BCL2）被确定为聚球藻属XM-24活性成分相关的作用靶点。上述关键靶基因共参与1028个生物过程、110个细胞组分、312个分子功能及200条信号通路。富集得到的信号通路主要包括癌症通路、代谢通路、磷脂酰肌醇3-激酶-蛋白激酶B（PI3K-AKT）信号通路以及大鼠肉瘤信号通路。此外，分子对接分析显示，聚球藻属XM-24的10种活性成分（包括11-十八碳烯酸甲酯、烯丙基甲基烯丙基醚及11-十八碳烯酸）与白蛋白（ALB）等关键靶蛋白之间具有较强的结合活性。分子动力学模拟结果证实，ALB与11-十八碳烯酸甲酯结合稳定，结合自由能为-48.39 kcal/mol。
研究结论：综上，本研究结果揭示了聚球藻属XM-24在胃癌预防与治疗中的潜在治疗潜力，同时为基于聚球藻属XM-24的胃癌治疗药物的进一步研发提供了理论依据。