In silico study on the cytotoxicity against Hela cancer cells of xanthones bioactive compounds from Garcinia cowa: QSAR based on Graph Deep Learning, Network Pharmacology, and Molecular Docking

Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Nighiado, Cau Giay, Hanoi, Vietnam Abstract: Cancer is recognized as a complex group of diseases, contributing to the highest global mortality rates, with increasing prevalence and a trend toward affecting younger populations. It is characterized by uncontrolled proliferation of abnormal cells, invasion of adjacent tissues, and metastasis to distant organs. Garcinia cowa, a traditional medicinal plant widely used in Southeast Asia, including Vietnam, is employed to treat fever, cough, indigestion, as a laxative, and for parasitic diseases. Numerous xanthone compounds isolated from this species exhibit a broad spectrum of biological activities, with some showing promise as anti-cancer and antimalarial agents. Network pharmacology analysis successfully identified key bioactive compounds Rubraxanthone, Garcinone D, Norcowanin, Cowanol, and Cowaxanthone--alongside their primary protein targets (TNF, CTNNB1, SRC, NFKB1, and MTOR), providing critical insights into the molecular mechanisms underlying their anti-cancer effects. The Graph Attention Network algorithm demonstrated superior predictive performance, achieving an R of 0.98 and an RMSE of 0.02 after data augmentation, highlighting its accuracy in predicting pIC50 values for xanthone-based compounds. Additionally, molecular docking revealed MTOR as a potential target for inducing cytotoxicity in HeLa cancer cells from Garcinia cowa. Keywords: Garcinia cowa, Hela, Network pharmacology, Graph neural network, Molecular docking I. Introduction Cancer is a complex group of diseases and one of the leading causes of mortality worldwide, characterized by the uncontrolled proliferation of abnormal cells, the ability to invade adjacent tissues, and metastasis to distant organs in the body [1, 2].