Network pharmacology integrated molecular docking of fucoidan against oral cancer and <i>in vitro</i> evaluation- A study using GEO datasets

Oral cancer is a widespread health concern in rural India due to a lack of awareness, delayed diagnosis and limited access to affordable treatment options. The current chemotherapy has notable side effects, underscoring the need for new drug candidates with improved bioavailability and specificity. In this current research, fucoidan, a sulphated polysaccharide, was extracted from the brown algae <i>Spatoglossum asperum,</i> and shown to be cytotoxic <i>in vitro</i> against oral cancer cells (KB cell line) at an IC₅₀ of 107.76 µg/ml, suggesting its potential as a drug candidate. This study further aimed to explore the potential therapeutic implications of fucoidan in managing oral cancer using network pharmacology. PharmMapper, Comparative Toxicogenomics Database and SuperPred were initially used to identify fucoidan protein targets. The identified targets were further screened against Gene Expression Omnibus (GSE23558, GSE25099 and GSE146483), OMIM, TCGA and GeneCards datasets to identify oral cancer-specific protein targets. The interactions between the selected proteins were visualised using STRING and Cytoscape. Subsequently, <b>D</b>atabase for <b>A</b>nnotation, <b>V</b>isualization and <b>I</b>ntegrated <b>D</b>iscovery was used for gene ontology and <b>K</b>yoto <b>E</b>ncyclopedia of <b>G</b>enes and <b>G</b>enomes pathway enrichment analysis of candidate targets. The cancer-related network was assessed using CancerGeneNet, while life expectancy based on the expression of the top 10 CytoHubba ranked hub genes was evaluated using Kaplan-Meier plots. Finally, EGFR, AKT1, HSP90AA1 and SRC were selected for docking and molecular dynamics simulation with fucoidan, using Maestro and GROMACS, respectively.

口腔癌在印度农村地区是广泛存在的健康问题，其成因包括公众健康认知匮乏、诊断延迟以及可负担治疗方案的可及性不足。当前临床使用的化疗方案存在显著不良反应，这凸显了开发生物利用度更高、特异性更强的新型抗癌候选药物的必要性。本研究从褐藻<italic>Spatoglossum asperum</italic>中提取了岩藻聚糖（fucoidan）——一种硫酸化多糖，体外（in vitro）实验证实其对口腔癌细胞KB细胞系的半数抑制浓度（IC₅₀）为107.76 µg/ml，表明其具备开发为抗癌候选药物的潜力。本研究进一步旨在通过网络药理学（network pharmacology）探究岩藻聚糖在口腔癌治疗中的潜在应用价值：首先采用PharmMapper、比较毒理基因组学数据库（Comparative Toxicogenomics Database）与SuperPred预测岩藻聚糖的蛋白靶点；随后将所识别的靶点与基因表达综合数据库（Gene Expression Omnibus，包含数据集GSE23558、GSE25099与GSE146483）、在线人类孟德尔遗传数据库（OMIM，Online Mendelian Inheritance in Man）、癌症基因组图谱（TCGA，The Cancer Genome Atlas）以及GeneCards数据集进行比对筛选，以获取口腔癌特异性蛋白靶点。利用STRING数据库与Cytoscape软件对筛选得到的蛋白间相互作用进行可视化分析；随后采用注释、可视化与整合发现数据库（Database for Annotation, Visualization and Integrated Discovery，DAVID）对候选靶点开展基因本体（Gene Ontology，GO）功能富集分析与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）通路富集分析。借助CancerGeneNet评估癌症相关调控网络，并通过Kaplan-Meier生存曲线分析排名前10的CytoHubba核心基因的表达水平与患者生存期的关联。最后，分别采用Maestro与GROMACS软件，针对EGFR、AKT1、HSP90AA1及SRC四个靶点，开展岩藻聚糖的分子对接与分子动力学模拟实验。