Abstract Berries from the Vaccinium genus, known for their rich array of bioactive metabolites, are recognized for their antioxidant, anti-inflammatory, and anticancer properties. These compounds, including anthocyanins, flavonoids, and phenolic acids, have attracted significant attention for their potential health benefits, particularly in cancer prevention and treatment. Gastric cancer (GC), a leading cause of cancer-related deaths worldwide, remains challenging to treat, especially in its advanced stages. This study investigates the therapeutic potential of Vaccinium species in GC treatment using computational methods. RNA sequencing revealed upregulated genes associated with GC, while network pharmacology and molecular docking approaches identified strong interactions between cyanidin 3-O-glucoside (C3G), a key bioactive metabolite. Furthermore, molecular dynamics simulations of the HSP90AA1-C3G complex demonstrated stable binding and structural integrity, suggesting that C3G may inhibit HSP90AA1, a protein involved in cancer progression. These findings highlight the therapeutic potential of Vaccinium metabolites, offering a novel approach to GC treatment by targeting key molecular pathways. This research provides valuable insights into the role of berries as natural therapeutics, supporting their integration into future gastric cancer treatment strategies. Keywords: cyanidin 3-O-glucoside, gastric cancer, molecular docking, molecular dynamics, Vaccinium species 1. Introduction Berries are valuable natural resources, representing the intricate connection between ecosystems and biodiversity. Found in diverse environments, these berries are not only integral to plant biodiversity but are also essential for the sustenance of various animal species [[32]1]. Animals consume berries as a source of nutrition, aiding in seed dispersal and fostering ecosystem resilience [[33]2,[34]3,[35]4]. Berries, especially those belonging to the Vaccinium genus, contribute profoundly to health promotion through their abundant antioxidants, diverse flavonoids, and a wide range of other beneficial phytochemicals [[36]5] that benefit not only the animals that consume them but also humans, making them a staple in diets and traditional medicine across cultures. The Vaccinium genus includes around 450 species, with commercially important varieties such as northern highbush blueberry (V. corymbosum L.), rabbiteye blueberry (V. virgatum), lowbush blueberry (V. angustifolium), bilberry (V. myrtillus L.), cranberry (V. macrocarpon), and lingonberry (V. vitis-idaea L.) [[37]6]. Rising consumer demand, driven by scientific interest, has significantly boosted the market for blueberries and cranberries [[38]7]. Wild species also support ecosystem balance as essential food sources for wildlife [[39]8]. The bioactive metabolites in Vaccinium species, particularly in their leaves, stems, and fruits, have been widely used in functional foods and traditional medicine. These compounds exhibit antidiabetic, anti-inflammatory, antioxidant, and anticancer properties, contributing to reduced inflammation, improved digestive and urinary health, and lower risks of cardiovascular disease, obesity, cancer, and type 2 diabetes [[40]5,[41]9,[42]10,[43]11]. Their health benefits are largely attributed to anthocyanins and flavonoids, which have gained attention in crop breeding [[44]6]. Key bioactive compounds include anthocyanins (cyanidin, peonidin, petunidin, delphinidin, and malvidin), proanthocyanidins, flavonols (quercetin, kaempferol, and myricetin), flavanols (epicatechin), phenolic acids (gallic, p-coumaric, caffeic, and chlorogenic), and ursolic acid, many of which exhibit potential anticancer effects [[45]12]. Building on their well-documented bioactive properties, Vaccinium species have demonstrated potential in gastric cancer prevention and treatment. This study explores their underlying mechanisms, highlighting key phytochemicals and their interactions with molecular targets involved in gastric carcinogenesis. Their therapeutic potential aligns with the growing interest in plant-derived compounds as complementary or alternative strategies in cancer therapy. Gastric cancer (GC) is the fifth most common cancer and the fourth leading cause of cancer deaths, with 1.09 million cases and 769,000 deaths in 2020, primarily in Asia, Latin America, and Europe [[46]13,[47]14]. Standard treatments, including surgery, chemotherapy, radiotherapy, immunotherapy, and targeted therapy, are often combined, but survival remains poor, especially in advanced stages [[48]15,[49]16]. Molecular pathologies in GC involve oncogene activation, tumor suppressor gene inactivation, CpG island methylation, and DNA repair defects, influencing diagnosis and treatment. Molecular testing, such as CDH1 gene screening for hereditary diffuse gastric carcinoma (HDGC) and HER2 expression analysis, is now standard in clinical practice [[50]17]. Plant-derived compounds have gained increasing attention in cancer therapy due to their bioactive properties, lower toxicity, and potential to complement conventional treatments. Medicinal herbs and their phytocompounds not only enhance survival and quality of life in cancer patients but also modulate immune function, which plays a critical role in cancer progression and treatment outcomes [[51]18]. Notably, over half of cancer prescription drugs are derived from natural plant sources, emphasizing their essential role in drug development. These compounds can act as standalone therapeutic agents or be integrated with existing treatments to improve efficacy and reduce adverse effects [[52]19]. Studies have demonstrated that phytochemicals can mitigate chemotherapy-induced toxicity, enhance immune responses, and potentially lower the risk of recurrence and metastasis [[53]20,[54]21,[55]22]. Furthermore, plant-derived bioactive compounds—such as phytochemicals, minerals, and vitamins—have been shown to inhibit cancer cell proliferation and promote apoptotic cell death in various malignancies [[56]23,[57]24]. Given their diverse mechanisms of action, natural products continue to be a valuable resource for providing safer and more effective cancer therapies. This study explores the therapeutic potential of Vaccinium species in the context of gastric cancer. Conducted entirely in silico, it integrates natural compounds with advanced computational methods such as RNA sequencing, network pharmacology, molecular docking, and molecular dynamics to identify how these bioactive metabolites target cancer-related pathways. Ultimately, this study advances the therapeutic potential of natural plant metabolites while promoting eco-friendly approaches in cancer treatment. It underscores the role of berries in health promotion and offers valuable insights into their potential as functional foods and natural therapeutics. 2. Materials and Methods 2.1. Collection, Screening, and ADMET-Based Filtering of Metabolites in the Vaccinium Genus The National Center for Biotechnology Information (NCBI) PubChem Database ([58]https://pubchem.ncbi.nlm.nih.gov, accessed on 11 June 2024) [[59]25]; KNApSAcK: A Comprehensive Species-Metabolite Relationship Database ([60]http://www.knapsackfamily.com/KNApSAcK/, accessed on 12 September 2024) [[61]26]; and HMDB: The Human Metabolome Database ([62]https://hmdb.ca/, accessed on 12 September 2024) [[63]27] were utilized to identify metabolites present in the Vaccinium genus. These open-access chemistry databases enabled the retrieval of metabolites and their canonical SMILES. The SMILES were subsequently entered into ADMETLab 3.0 ([64]https://admetmesh.scbdd.com/, accessed on 18 September 2024) [[65]28] to filter the metabolites based on Lipinski’s rule and cell permeability (Caco-2). 2.2. Target Gene Prediction for the Vaccinium Genus The potential target proteins of the bioactive metabolites were screened using SuperPred (SuperPred: update on drug classification and target prediction ([66]https://prediction.charite.de/, accessed on 18 September 2024)) [[67]29]. The canonical SMILES of the metabolites were entered into SuperPred to predict target proteins for Vaccinium genus, their probability scores where the structure binds with the specific target, and their target–gene interaction. 2.3. Collection of RNA Sequence Data Associated with Gastric Cancer The RNA-Seq counts used in this study were retrieved and preprocessed using the R library recount3 version 1.16.0. The use of recount3 enabled the integration of multiple studies, as the data were processed in a uniform and annotation-agnostic manner [[68]30]. Three RNA-seq studies were included in this analysis. They were queried through recount3 using the project IDs ERP010795, ERP010889, and STAD. When combined, the data provide a comprehensive view of the Correa Human Model of Gastric Carcinogenesis. Specifically, the data from project ERP010889, retrieved by recount3 from the European Nucleotide Archive, consist of RNA-seq from stomach tissue biopsies suffering from gastritis, atrophy, extensive atrophy, and intestinal metaplasia. Project ERP010795, also retrieved from the European Nucleotide Archive, includes data on low- and high-grade dysplasia, as well as early gastric cancer. Lastly, the project STAD was retrieved from The Cancer Genome Atlas (TCGA) Program. After retrieving and cleaning the count files and metadata, DESeq2 was used to identify upregulated genes for each condition. To further minimize batch effects and protocol variations, the normal samples available for each experiment were used as references for their corresponding diseased states. The standard