In silico investigation of phytochemicals from Glycosmis parviflora for potential TNF-α inhibition

Ngũ Thị Trà Giang; Đoàn Lê Bình; Trần Phương Thảo; Võ Hương Giang; Nguyễn Trâm Anh; Đoàn Thị Minh Khai; Thuy Phan Thi

doi:10.62239/jca.2026.020

Authors

Ngu Thị Tra Giang Vinh University
Doan Le Binh Vinh University
Tran Phuong Thao Vinh University
Vo Huong Giang Vinh University
Nguyen Tram Anh Vinh University
Doan Thi Minh Khai Vinh University
Phan Thi Thuy Vinh University

DOI:

https://doi.org/10.62239/jca.2026.020

Keywords:

TNF-α inhibitors, Glycosmis parviflora, triterpenoids, molecular docking

Abstract

This study investigates the TNF-α inhibitory potential of natural compounds using molecular docking with AutoDock Vina. The docking protocol was validated by re-docking the co-crystallized ligand into the active site of TNF-α (PDB ID: 2AZ5), yielding an RMSD of 1,02 Å, indicating reliable accuracy. Several compounds showed strong binding affinities, with Isoarborinol (−10,47 kcal/mol), Flavacitropone A (−9,97 kcal/mol), Friedelin (−9,83 kcal/mol), and Arborinol (−9,82 kcal/mol) identified as the most promising candidates. These compounds mainly belong to triterpenoid and citropones classes. Interaction analysis revealed that they formed stable hydrophobic and π–π interactions with key residues, including Tyr119, Tyr59, Leu57, and Leu55 within the binding site. The results provide insight into the binding behavior of these compounds and support their potential as TNF-α inhibitors, which may be further evaluated through experimental studies.

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References

T. Pacher, M. Bacher, O. Hofer, H. Greger, Phytochemistry, 58 (2001) 129-135. https://doi.org/10.1016/S0031-9422(01)00228-5

D.Z.T.G. Hartley, Flora of China, 11 (2008) 80-83.

M. Yasir, M.K. Tripathi, P. Singh, R. Shrivastava, Nat. Prod. J., 9 (2019) 98-124. https://doi.org/10.2174/2210315508666180622121212

P.H. Ho, An Illustrated Flora of Vietnam, Tre Publishing House, Ho Chi Minh City (2003).

O. Hofer, H. Greger, Prog. Chem. Org. Nat. Prod., Springer, Vienna (2000).

A. Monks, D. Scudiero, P. Skehan, R. Shoemaker, K. Paull, D. Vistica, C. Hose, J. Langley, P. Cronise, A. Vaigro-Wolff, M. Gray-Goodrich, H. Campbell, J. Mayo, M. Boyd, J. Natl. Cancer Inst., 83 (1991) 757-766. https://doi.org/10.1093/jnci/83.11.757

J.L. Ren, P.L. Liu, H.Y. Yang, Z.L. Zhou, Z.M. Chen, S.Y. Wu, Nat. Prod. Res., 40 (2026) 854-859. https://doi.org/10.1080/14786419.2024.2426210

C. Ito, T. Matsui, K. Mamiya, T.S. Wu, M. Itoigawa, Nat. Prod. Res., 40 (2024) 466-472. https://doi.org/10.1080/14786419.2024.2412844

J.R. Bradley, J. Pathol., 214 (2008) 149-160. https://doi.org/10.1002/path.2287

D. Tracey, L. Klareskog, E.H. Sasso, J.G. Salfeld, P.P. Tak, Pharmacol. Ther., 117 (2008) 244-279. https://doi.org/10.1016/j.pharmthera.2007.10.001

G.M. Morris, R. Huey, A.J. Olson, Curr. Protoc. Bioinformatics, (2008). https://doi.org/10.1002/0471250953.bi0814s24

D.B. Kitchen, H. Decornez, J.R. Furr, J. Bajorath, Nat. Rev. Drug Discov., 3 (2004) 935-949. https://doi.org/10.1038/nrd1549

M.M. He, A.S. Smith, J.D. Oslob, W.M. Flanagan, A.C. Braisted, A. Whitty, M.T. Cancilla, J. Wang, A.A. Lugovskoy, J.C. Yoburn, A.D. Fung, G. Farrington, J.K. Eldredge, E.S. Day, L.A. Cruz, T.G. Cachero, S.K. Miller, J.E. Friedman, I.C. Choong, B.C. Cunningham, Science, 310 (2005) 1022-1025. https://doi.org/10.1126/science.1116304

P.Q.D. Nguyen, H.T. Nguyen, L.T.K. Nguyen, H.Q. Vo, A.T. Le, T.T. Do, D.V. Ho, Trop. J. Nat. Prod. Res., 4 (2020) 703-707. https://doi.org/10.26538/tjnpr/v4i10.8

J. Eberhardt, D. Santos-Martins, A.F. Tillack, S. Forli, J. Chem. Inf. Model., 61 (2021) 3891-3898. https://doi.org/10.1021/acs.jcim.1c00203

O. Trott, A.J. Olson, J. Comput. Chem., 31 (2010) 455-461. https://doi.org/10.1002/jcc.21334

H.T.T. Trang, N.X. Ha, C.L. Hong, T.T.T. Nhung, D.T.T. Giang, N.T.D. Hang, P.T. Thuy, J. Chem. Res., 48 (2024). https://doi.org/10.1177/17475198241263837

D.L. Ma, D.S.-H. Chan, C.-H. Leung, Chem. Sci., 2 (2011) 1656-1665. https://doi.org/10.1039/C1SC00152C

C.H.M. Chau, N.T.T. Giang, N.T.T. Tram, L.T.M. Chau, N.X. Ha, P.T. Thuy, J. Chem. Res., 48 (2024). https://doi.org/10.1177/17475198241305879

C.H. Le, B.T. Thuc, N.X. Ha, T.T.T. Nhung, N.V. Hue, D.M. Linh, N.T.T. Giang, P.T. Thuy, Vietnam J. Chem., 1 (2025). https://doi.org/10.1002/vjch.70047

N.X. Ha, C.H. Le, Vietnam J. Chem., 62 (2024) 387-393. https://doi.org/10.1002/vjch.202300187

N.T.T. Giang, N.X. Ha, H.T. Oanh, N.T.T. Tram, C.H.M. Chau, T.T.N. Mai, P.T. Thuy, Vietnam J. Chem., 63 (2025) 723-729. https://doi.org/10.1002/vjch.70004

M. Sandhu, H.M. Irfan, L. Arshad, A. Ullah, S.A. Shah, H. Ali, Neurotoxicology, 99 (2023) 274-281. https://doi.org/10.1016/j.neuro.2023.11.002