DOI: 10.12688/f1000research.168214.2 ISSN: 2046-1402

Exploration of Compounds Identified from Amomum cardamomum Seed Extract: LC-MS Profiling, Network Pharmacology, and Computational Analyses for Innovative Multi-Targeted Breast Cancer Therapy

Dessy Arisanty, Salsabila Putri Khairani, Kevin Nathaniel Cuandra, Aldi Tamara Rahman, Christopher Daniel Tristan, Angela Stephanie Yahono, Muhammad Samudra Ilham, Ajib Zaim Alamsyah, Bezalel Tioleyson Sarjono, Daivan Febri Juan Setiya, Phelia Klarissa Huang, Alya Jihan Hafidza, Afiq Triyandi Hakam, Muhammad Farid Hamka, Daffa Zachary Rasendriya, Muhammad Naufal Hibatullah, Kuni Zakiyyah Sumargo
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Background Breast cancer remains one of the leading causes of cancer-related mortality worldwide, and the emergence of drug resistance, systemic toxicity, and limited efficacy of current therapies highlight the need for safer and more effective treatment. Natural products have emerged as promising sources of multi-target anticancer agents. A. cardamomum has demonstrated preliminary anticancer potential, yet the bioactive constituents and their molecular mechanisms in breast cancer remain poorly elucidated. Methods This study integrated in silico approaches to investigate the therapeutic potential of A. cardamomum seed extract against breast cancer. LC–MS analysis identified phytochemical compounds, followed by network pharmacology to determine their potential targets and molecular pathways. Pharmacokinetic and toxicity predictions were assessed through ADMET and Lipinski’s rule of five analyses to evaluate drug-likeness and safety. Molecular docking and molecular dynamics (MD) simulations were conducted to evaluate binding affinity and structural stability of compounds with key oncogenic proteins. Results LC-MS profiling identified 22 distinct compounds in A. cardamomum seeds. ADMET and Lipinski analyses demonstrated that most compounds possessed high gastrointestinal absorption, favorable oral bioavailability, and low toxicity risk. Network pharmacology highlighting SRC, TNF-α, Caspase-3, and EGFR as central nodes in the protein-protein interaction network. Molecular docking identified compounds C17 and C20 as the most promising bioactives, showing strong binding affinities and interactions similar to control ligands. MD simulations confirmed their stable complexes, indicating conformational stability and robust ligand–protein interactions. Conclusion This study highlights the promising multi-target anticancer potential of A. cardamomum seeds. Compounds C17 and C20 were identified as lead candidates with strong and stable interactions with key breast cancer-related proteins and favorable pharmacokinetic properties. These results suggest that A. cardamomum could serve as a potential source for developing new plant-based therapies against breast cancer. Further in vitro and in vivo investigations are warranted to validate their efficacy and safety.

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