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Volume 26
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10.3390/ijms262311629
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Integrative Discovery Through Network Pharmacology and Molecular Docking Approaches of Phenolic Compounds Isolated from Torreya nucifera to Treat Rheumatoid Arthritis

by
Duc Dat Le
1,2,
Thinhulinh Dang
1,
Vinhquang Truong
1,
Soojung Yu
2,
Seung-Hwa Yang
3,
Moon-Hee Choi
3 and
Mina Lee
1,2,*
1
College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, 255 Jungangno, Suncheon, Jeonnam 57922, Republic of Korea
2
Department of Natural Cosmetics Science and Smart Beautytech Research Institute, Sunchon National University, 255 Jungangno, Suncheon, Jeonnam 57922, Republic of Korea
3
SUMSUMBIO Co. Ltd., Nano Bio Research Center, Jeonnam Bioindustry Foundation, 123 Nanosandan-ro, Jangseong, Jeonnam 57248, Republic of Korea
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2025, 26(23), 11629; https://doi.org/10.3390/ijms262311629
Submission received: 5 November 2025 / Revised: 24 November 2025 / Accepted: 27 November 2025 / Published: 30 November 2025
(This article belongs to the Special Issue Natural Product as Therapeutic Agent: From Molecular Targets to Cellular and Functional Modulation)
Versions Notes

Abstract

Torreya nucifera, a consumable botanical species native to the southern regions of Korea, has a history of ethnopharmacological application to treat inflammatory conditions. This study employed feature-based molecular networking and integrated with the GNPS database to separate and identify ten phenolic compounds from T. nucifera. We further investigated the therapeutic potential of these isolated compounds and their structural features in the context of rheumatoid arthritis. Protein–protein interaction networks, constructed using compound–target and disease-associated target data, identified NFKB1, RELA, and TNFRSF1A as key hub genes. Gene Ontology (GO) enrichment analysis revealed inflammatory response as the most significantly modulated biological process. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the NF–kB signaling pathway is the most critical of the regulatory cascades influencing the pathogenesis of rheumatoid arthritis. Molecular docking studies verified strong binding affinities between the identified compounds and key target proteins. Furthermore, Western blot results validate that T. nucifera extract suppressed the LPS-activated NF–kB signaling pathways by inhibiting p65 and IκBα phosphorylation. The results underscore the significance of T. nucifera and its anti-inflammatory properties in relation to rheumatoid arthritis, establishing a scientific basis to formulate plant-based products within functional foods, nutraceuticals, and therapeutic interventions targeting rheumatoid arthritis.
Keywords: Torreya nucifera; phenolics; rheumatoid arthritis; network pharmacology; NFκB pathway Torreya nucifera; phenolics; rheumatoid arthritis; network pharmacology; NFκB pathway

Share and Cite

MDPI and ACS Style

Le, D.D.; Dang, T.; Truong, V.; Yu, S.; Yang, S.-H.; Choi, M.-H.; Lee, M. Integrative Discovery Through Network Pharmacology and Molecular Docking Approaches of Phenolic Compounds Isolated from Torreya nucifera to Treat Rheumatoid Arthritis. Int. J. Mol. Sci. 2025, 26, 11629. https://doi.org/10.3390/ijms262311629

AMA Style

Le DD, Dang T, Truong V, Yu S, Yang S-H, Choi M-H, Lee M. Integrative Discovery Through Network Pharmacology and Molecular Docking Approaches of Phenolic Compounds Isolated from Torreya nucifera to Treat Rheumatoid Arthritis. International Journal of Molecular Sciences. 2025; 26(23):11629. https://doi.org/10.3390/ijms262311629

Chicago/Turabian Style

Le, Duc Dat, Thinhulinh Dang, Vinhquang Truong, Soojung Yu, Seung-Hwa Yang, Moon-Hee Choi, and Mina Lee. 2025. "Integrative Discovery Through Network Pharmacology and Molecular Docking Approaches of Phenolic Compounds Isolated from Torreya nucifera to Treat Rheumatoid Arthritis" International Journal of Molecular Sciences 26, no. 23: 11629. https://doi.org/10.3390/ijms262311629

APA Style

Le, D. D., Dang, T., Truong, V., Yu, S., Yang, S.-H., Choi, M.-H., & Lee, M. (2025). Integrative Discovery Through Network Pharmacology and Molecular Docking Approaches of Phenolic Compounds Isolated from Torreya nucifera to Treat Rheumatoid Arthritis. International Journal of Molecular Sciences, 26(23), 11629. https://doi.org/10.3390/ijms262311629

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