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Journal of Medicinal Chemistry

Journal of Medicinal Chemistry

IF: 6.8
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ComplexDnet: A Network-Based Strategy to Discover Critical Targets and Screen Active Compounds for Complex Diseases

Published:4 September 2025 DOI: 10.1021/acs.jmedchem.5c01682
Fei Pan, , , Zhao-min Xu, , , Ze-hui Liu, , , Cai-yue Chen, , , Jing-wei Yu, , , Zeng-rui Wu, , , Ze Wang, , , Long Chen, , , Cheng-yuan Yue, , , Wei-hua Li, , , Gui-xia Liu, , , Jin Huang*, , and , Yun Tang*, 

Abstract

The etiology of complex diseases such as metabolic-associated steatohepatitis (MASH) presents significant challenges for therapeutic discovery. Here, we developed ComplexDnet, a transcriptome- and network-integrated framework to prioritize disease-relevant targets. Applied across eight cancer types, ComplexDnet achieved an average recall of 77.63%, outperforming four advanced methods by 10–40%. Then, we applied ComplexDnet in MASH and revealed retinoid-related orphan receptor γt (RORγt) as a central regulator of MASH-associated inflammatory and fibrotic cascades. Network-based virtual screening revealed panaxatriol (PXT) as a potent RORγt inverse agonist (IC50 = 0.01 μM), confirmed via X-ray crystallography (2.8 ?). PXT was further shown to significantly attenuate fibrosis in murine models. These findings demonstrated the utility of ComplexDnet in discovering functionally and structurally relevant targets and accelerating drug discovery. Finally, we integrated this pipeline into an open-source software (https://github.com/sirpan/ComplexDnet), which would benefit the drug discovery community for complex diseases.

Substances (126)

Materials
Procduct Name CAS Molecular Formula Supplier Price
18β-Glycyrrhetinic Acid 471-53-4 C30H46O4 695 suppliers $12.00-$3176.25
18β-Glycyrrhetinic Acid 471-53-4 C30H46O4 695 suppliers $12.00-$3176.25
18β-Glycyrrhetinic Acid 471-53-4 C30H46O4 695 suppliers $12.00-$3176.25
18β-Glycyrrhetinic Acid 471-53-4 C30H46O4 695 suppliers $12.00-$3176.25
PROTOPANAXDIOL 30636-90-9 C30H52O3 312 suppliers $35.00-$2273.00
PROTOPANAXDIOL 30636-90-9 C30H52O3 312 suppliers $35.00-$2273.00
PROTOPANAXDIOL 30636-90-9 C30H52O3 312 suppliers $35.00-$2273.00
PROTOPANAXDIOL 30636-90-9 C30H52O3 312 suppliers $35.00-$2273.00
Panaxatriol 32791-84-7 C30H52O4 262 suppliers $39.00-$1497.00
Panaxatriol 32791-84-7 C30H52O4 262 suppliers $39.00-$1497.00

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