# Optimization of potential targets for antidepressant Chinese medicines: AI and multi-omics methods

**Authors:** Chaofang Lei, Zhigang Chen, Chongyang Ma, Le Xie, Dahua Wu, Jianbei Chen, Jiaxu Chen

PMC · DOI: 10.1186/s13020-025-01320-w · 2026-02-11

## TL;DR

This paper explores how combining AI and multi-omics methods can improve the discovery of targets for antidepressant Chinese medicines.

## Contribution

The paper proposes integrating AI and multi-omics as a novel approach for optimizing antidepressant Chinese medicine targets.

## Key findings

- Current evaluation methods for Chinese medicine are limited by single, qualitative indicators.
- AI and multi-omics technologies offer a more comprehensive and effective way to evaluate Chinese medicine quality and efficacy.
- The combination of AI and multi-omics is a promising direction for future drug target discovery in TCM.

## Abstract

The complexity of traditional Chinese medicine (TCM), with its numerous components, targets, and varying efficacy, presents challenges for current evaluation methods. Most existing methods rely on single, qualitative indicators, which provide limited insight into the overall quality. These methods fail to fully capture the intrinsic quality, efficacy, and safety of Chinese medicine, highlighting the need for more advanced biological evaluation techniques. Target-based drug discovery has become the primary approach in pharmaceutical research and development, where drug targets play a crucial role in guiding the entire process. As our understanding deepens, integrating artificial intelligence (AI) with multi-omics technologies has opened new possibilities for enhancing treatment precision. AI’s efficiency in identifying drug targets marks a significant leap forward in drug discovery, facilitating the modernization of the drug development process. Meanwhile, omics technologies offer distinct advantages, such as comprehensive controllability, strong correlations with clinical efficacy and safety, and a holistic view of the overall quality of Chinese medicine. These technologies provide an effective and rational approach for evaluating the quality of Chinese medicine and are instrumental in developing quality control systems for TCM. Consequently, combining AI with multi-omics methods is poised to become a key direction for future research into the discovery of targets for antidepressant Chinese medicine.

## Linked entities

- **Diseases:** depression (MONDO:0002050)

## Full-text entities

- **Genes:** TRAPPC11 (trafficking protein particle complex subunit 11) [NCBI Gene 60684] {aka C4orf41, FOIGR, GRY, LGMD2S, LGMDR18}, DBNL (drebrin like) [NCBI Gene 28988] {aka ABP1, HIP-55, HIP55, SH3P7}, PRDM1 (PR/SET domain 1) [NCBI Gene 639] {aka BLIMP-1, BLIMP1, PRDI-BF1}, IGFBP1 (insulin like growth factor binding protein 1) [NCBI Gene 3484] {aka AFBP, IBP1, IGF-BP25, PP12, hIGFBP-1}, SERPINH1 (serpin family H member 1) [NCBI Gene 871] {aka AsTP3, CBP1, CBP2, HSP47, OI10, PIG14}, ACHE (acetylcholinesterase (Yt blood group)) [NCBI Gene 43] {aka ACEE, ARACHE, N-ACHE, YT}, STK32C (serine/threonine kinase 32C) [NCBI Gene 282974] {aka PKE, YANK3}, OLFM4 (olfactomedin 4) [NCBI Gene 10562] {aka GC1, GW112, OLM4, OlfD, UNQ362, bA209J19.1}, GPC3 (glypican 3) [NCBI Gene 2719] {aka DGSX, GTR2-2, MXR7, OCI-5, SDYS, SGB}, SLC7A8 (solute carrier family 7 member 8) [NCBI Gene 23428] {aka LAT2, LPI-PC1}, FNDC3B (fibronectin type III domain containing 3B) [NCBI Gene 64778] {aka FAD104, PRO4979, YVTM2421}, PSMB4 (proteasome 20S subunit beta 4) [NCBI Gene 5692] {aka HN3, HsN3, PRAAS3, PROS-26, PROS26}, LHPP (phospholysine phosphohistidine inorganic pyrophosphate phosphatase) [NCBI Gene 64077] {aka HDHD2B}, HSP90AA1 (heat shock protein 90 alpha family class A member 1) [NCBI Gene 3320] {aka EL52, HEL-S-65p, HSP86, HSP89A, HSP90A, HSP90N}, OGDH (oxoglutarate dehydrogenase) [NCBI Gene 4967] {aka AKGDH, E1k, E1o, HsOGDH, KGD1, OGDC}, UBA1 (ubiquitin like modifier activating enzyme 1) [NCBI Gene 7317] {aka A1S9, A1S9T, A1ST, AMCX1, CFAP124, GXP1}, HBA1 (hemoglobin subunit alpha 1) [NCBI Gene 3039] {aka ECYT7, HBA-T3, HBH, METHBA}, CAMK2A (calcium/calmodulin dependent protein kinase II alpha) [NCBI Gene 815] {aka CAMKA, CaMKIINalpha, CaMKIIalpha, MRD53, MRT63}, TSLP (thymic stromal lymphopoietin) [NCBI Gene 85480], Bdnf (brain derived neurotrophic factor) [NCBI Gene 12064], ESR1 (estrogen receptor 1) [NCBI Gene 2099] {aka ER, ESR, ESRA, ESTRR, Era, NR3A1}, MIF (macrophage migration inhibitory factor) [NCBI Gene 4282] {aka GIF, GLIF, MMIF}, SPATA31D1 (SPATA31 subfamily D member 1) [NCBI Gene 389763] {aka FAM75D1}, NTRK3 (neurotrophic receptor tyrosine kinase 3) [NCBI Gene 4916] {aka GP145-TrkC, TRKC, gp145(trkC)}, PROX2 (prospero homeobox 2) [NCBI Gene 283571] {aka PROX-2}, L3MBTL2 (L3MBTL histone methyl-lysine binding protein 2) [NCBI Gene 83746] {aka H-l(3)mbt-l, L3MBT}, COL1A2 (collagen type I alpha 2 chain) [NCBI Gene 1278] {aka EDSARTH2, EDSCV, OI4}, SLIT2 (slit guidance ligand 2) [NCBI Gene 9353] {aka SLIL3, Slit-2}, EGF (epidermal growth factor) [NCBI Gene 1950] {aka HOMG4, URG}, RUNX1 (RUNX family transcription factor 1) [NCBI Gene 861] {aka AML1, AML1-EVI-1, AMLCR1, CBF2alpha, CBFA2, EVI-1}, GPR173 (G protein-coupled receptor 173) [NCBI Gene 54328] {aka SREB3}, MYO16 (myosin XVI) [NCBI Gene 23026] {aka MYAP3, MYR8, Myo16b, NYAP3, PPP1R107}, MYH9 (myosin heavy chain 9) [NCBI Gene 4627] {aka BDPLT6, DFNA17, EPSTS, FTNS, MATINS, MHA}, RNF150 (ring finger protein 150) [NCBI Gene 57484], DNMT1 (DNA methyltransferase 1) [NCBI Gene 1786] {aka ADCADN, AIM, CXXC9, DNMT, HSN1E, MCMT}, SAA1 (serum amyloid A1) [NCBI Gene 6288] {aka PIG4, SAA, TP53I4}, BAG5 (BAG cochaperone 5) [NCBI Gene 9529] {aka BAG-5, CMD2F}, SEMA7A (semaphorin 7A (JohnMiltonHagen blood group)) [NCBI Gene 8482] {aka CD108, CDw108, H-SEMA-K1, H-Sema-L, JMH, PFIC11}, VEGFA (vascular endothelial growth factor A) [NCBI Gene 7422] {aka L-VEGF, MVCD1, VEGF, VPF}, ROBO1 (roundabout guidance receptor 1) [NCBI Gene 6091] {aka CPHD8, DUTT1, NORS, NYS8, SAX3}, GRIA4 (glutamate ionotropic receptor AMPA type subunit 4) [NCBI Gene 2893] {aka GLUR4, GLUR4C, GLURD, GluA4, GluA4-ATD, NEDSGA}, CFB (complement factor B) [NCBI Gene 629] {aka AHUS4, ARMD14, BF, BFD, CFAB, CFBD}, PLSCR1 (phospholipid scramblase 1) [NCBI Gene 5359] {aka MMTRA1B}, P2RX7 (purinergic receptor P2X 7) [NCBI Gene 5027] {aka P2X7}, UCHL1 (ubiquitin C-terminal hydrolase L1) [NCBI Gene 7345] {aka HEL-117, HEL-S-53, NDGOA, PARK5, PGP 9.5, PGP9.5}, SERPINF2 (serpin family F member 2) [NCBI Gene 5345] {aka A2AP, AAP, ALPHA-2-PI, API, PLI, alpha2AP}, ZNF713 (zinc finger protein 713) [NCBI Gene 349075], NECAB2 (N-terminal EF-hand calcium binding protein 2) [NCBI Gene 54550] {aka EFCBP2, stip-2}, APOE (apolipoprotein E) [NCBI Gene 348] {aka AD2, APO-E, ApoE4, LDLCQ5, LPG}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, COX5B (cytochrome c oxidase subunit 5B) [NCBI Gene 1329] {aka COXVB}, FNDC5 (fibronectin type III domain containing 5) [NCBI Gene 252995] {aka FRCP2, irisin}, ADCYAP1 (adenylate cyclase activating polypeptide 1) [NCBI Gene 116] {aka PACAP}, APOC3 (apolipoprotein C3) [NCBI Gene 345] {aka APOCIII, Apo-C3, ApoC-3}, LRG1 (leucine rich alpha-2-glycoprotein 1) [NCBI Gene 116844] {aka HMFT1766, LRG}, BTN3A3 (butyrophilin subfamily 3 member A3) [NCBI Gene 10384] {aka BTF3, BTN3.3}, APOA4 (apolipoprotein A4) [NCBI Gene 337] {aka ADTKD6}, KRT23 (keratin 23) [NCBI Gene 25984] {aka CK23, HAIK1, K23}, C4A (complement C4A (Chido/Rodgers blood group)) [NCBI Gene 720] {aka C4, C4A2, C4A3, C4A4, C4A6, C4AD}, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 2597] {aka G3PD, GAPD, HEL-S-162eP}
- **Diseases:** NMT (OMIM:614922), MDD (MESH:D003865), subcortical cysts (MESH:D003560), CRS (MESH:D003398), GANs (MESH:D004829), RPN (MESH:D020918), CMS (MESH:C536089), megalencephalic leukoencephalopathy (MESH:C536141), disorder (MESH:D009358), XAI (MESH:C538243), cognitive and emotional dysfunctions (MESH:D003072), Depressed mood (MESH:D003866), AI (MESH:C538142), spleen deficiency (MESH:D013160), liver depression (MESH:D017093), VAMP-2 (MESH:D020803), MPC (MESH:C536209), TCM Syndrome (MESH:C562377), tumor (MESH:D009369), COVID-19 (MESH:D000086382), diabetes (MESH:D003920), lung cancer (MESH:D008175), cardiovascular diseases (MESH:D002318), heart attacks (MESH:D009203), anxiety (MESH:D001007), pulmonary nodules (MESH:D055613), neuroinflammation (MESH:D000090862), mental health disorder (OMIM:603663), toxicity (MESH:D064420), CVS (MESH:D003333), CUMS (MESH:D000079225), inflammation (MESH:D007249), LSTM (MESH:D000088562), abnormalities in lipid and amino acid metabolism (MESH:D052439)
- **Chemicals:** NE (MESH:D009356), tryptophan (MESH:D014364), acetic acid (MESH:D019342), resveratrol (MESH:D000077185), luteolin (MESH:D047311), SCFAs (MESH:D005232), glycine (MESH:D005998), flavonoids (MESH:D005419), 5-HT (MESH:D012701), glucose (MESH:D005947), DIA (MESH:C076868), valine (MESH:D014633), kaempferol (MESH:C006552), glutamine (MESH:D005973), butyric acid (MESH:D020148), citrate (MESH:D019343), leucine (MESH:D007930), propionic acid (MESH:C029658), phenolic acids (MESH:C017616), lipids (MESH:D008055), quercetin (MESH:D011794), amino acid (MESH:D000596), choline (MESH:D002794), 20(S)-protopanaxatriol (MESH:C062916), lactic acid (MESH:D019344), CORT (MESH:D003348), alanine (MESH:D000409), phenylalanine (MESH:D010649), corticosterone (MESH:D003345), stearic acids (MESH:D013229), cGMP (MESH:D006152), glycyrrhetinic acid (MESH:D006034), CNTNAP4 (-), trimethylamine oxide (MESH:C005855), acids (MESH:D000143)
- **Species:** gut metagenome (species) [taxon 749906], Bacillota (clostridial firmicutes, phylum) [taxon 1239], Hypericum perforatum (species) [taxon 65561], Mus musculus (house mouse, species) [taxon 10090], Bacteroides (genus) [taxon 816], Prevotella (genus) [taxon 838], Rattus norvegicus (brown rat, species) [taxon 10116], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** rs4656484, Val 66 Met, -308G/A, rs2004237, rs34208798, Leu/Ile

## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12892700/full.md

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Source: https://tomesphere.com/paper/PMC12892700