Key issues and essential points in non-clinical pharmacology of traditional Chinese medicine formulas: enhancing the scientization and standardization

Abstract

As the primary form and means of clinical treatment, traditional Chinese medicine formulas (TCM formulas) embody the core of TCM’s syndrome differentiation and treatment approach and serve as a bridge between TCM theory and clinical practice. Exploring the relationship between the chemical constituents of TCM formulas and the body’s vital activities, along with their complex interactive mechanisms, represents one of the key scientific challenges in modern TCM research. However, due to the complexity of TCM chemical constituents and the inherent vast systemic nature of the human body, coupled with the fragmented, experiential, and semi-quantitative nature of TCM formulas pharmacology research, bottlenecks such as complex composition, unclear mechanisms, and insufficient standardization and refinement constrain its in-depth development. Technical guidelines for non-clinical pharmacology research of traditional Chinese medicine formulas systematically review and summarize the research content and relevant advances in non-clinical pharmacology of TCM formulas, integrate multidisciplinary technical approaches, and establish research standards, providing practical standards for systematically elucidating the integrated mechanisms of action between multi-component drugs and the body. This article interprets the core content of the technical guidelines, thereby initiating the following discussion on TCM formulas pharmacology: analyzing critical points, elucidating the complete evidence chain, and describing research content and application scenarios, which aims to enhance the scientization and reliability of TCM formulas pharmacology and to facilitate the research and development of new TCM drugs.

Keywords

Clinical relevance / Evidence chain / Integrative pharmacology / TCM formulas / Technical guidelines

Conflict of interest statement

Junhua Zhang is an editorial board member of this journal. None of the other authors declare any conflicts of interest.

Funding

This study was supported by the National Key R&D Program of China (2023YFC2308200 and 2023YFC3502900).

Author contributions

Hai-Yu Xu and Junhua Zhang conceived and designed this study. Han Li wrote the original draft. Xiao-He Xiao participated in the definition of the relevant concepts. Ping Wang, Wei-Jie Li, Dan Wu, and Yu-Te Zhong participated in the discussion and edited the manuscript. All of the authors have read and approved the published version of the manuscript.

Ethical approval of studies and informed consent

Not applicable.

Data availability

All data generated or analyzed during this study are included in this published article.

References

[1] Li S. Potential Associations Between Traditional Chinese Medicine Syndromes and Molecular Network Regulatory Mechanisms. Scientific and Technological Progress and Socio-Economic Development in the 21st Century (Volume 1). Beijing University of Chinese Medicine; Chinese Association of Chinese Medicine Life Sciences. 1999; 1:519.

[2] Liu CX. Significance of metabonomics in modern research of Chinese materia medica. Chin Tradit Herb Drugs. 2004; 35(6):6-10.

[3] Zhang TJ. From systems biology to biosystems science: a preliminary discussion on approaches to traditional Chinese medicine research. Proceedings of the Eighth National Symposium on Traditional Chinese Medicine and Natural Medicines and the Fifth National Symposium on Medicinal Plants and Phytopharmacy. Tianjin Institute of Pharmaceutical Research. 2005; 1:244-248.

[4] Zhang ZH, Li RR, Chen Y, et al. Integration of traditional, complementary, and alternative medicine with modern biomedicine: the scientization, evidence, and challenges for integration of traditional Chinese medicine. Acupunct Herb Med. 2024; 4(1):68-78.

[5] Hopkins AL. Network pharmacology. Nat Biotechnol. 2007; 25(10):1110-1111.

[6] Zhao J, Jiang P, Zhang W. Molecular networks for the study of TCM pharmacology. Brief Bioinform. 2010; 11(4):417-430.

[7] Hao HP, Zheng CN, Wang GJ. Thoughts and experimental exploration on pharmacokinetic study of herbal medicines with multiple-components and targets. Acta Pharm Sin. 2009; 44(3):270-275.

[8] Wang X, Zhang A, Sun H. Future perspectives of Chinese medical formulae: chinmedomics as an effector. OMICS. 2012; 16(7-8):414-421.

[9] Wang YH, Yang L. Systems pharmacology-based research framework of traditional Chinese medicine. World Chin Med. 2013; 8(7):801-808.

[10] Xu HY, Yang HJ. Integrative pharmacology: new paradigm of modernization of Chinese medicine. China J Chin Mater Med. 2014; 39(3):357-362.

[11] Xu H, Zhang Y, Wang P, et al. A comprehensive review of integrative pharmacology-based investigation: a paradigm shift in traditional Chinese medicine. Acta Pharm Sin B. 2021; 11(6):1379-1399.

[12] Yang H, Qi LW, Li HJ, et al. “Bioactive equivalent combinatorial components” as defined labeled amount of active constituents for quality control of traditional Chinese medicines. World Sci Technol Modernization Tradit Chin Med. 2014; 16(3):510-513.

[13] Gan X, Shu Z, Wang X, et al. Network medicine framework reveals generic herb-symptom effectiveness of traditional Chinese medicine. Sci Adv. 2023; 9(43):eadh0215.

[14] Yan Z, Li Y, Xia T, et al. Revitalizing gut health: Liangxue guyuan yishen decoction promotes akkermansia muciniphila -induced intestinal stem cell recovery post-radiation in mice. Phytomedicine. 2024; 132:155888.

[15] Deng S, Li C, Cao J, et al. Organ-on-a-chip meets artificial intelligence in drug evaluation. Theranostics. 2023; 13(13):4526-4558.

[16] Vunjak-Novakovic G, Ronaldson-Bouchard K, Radisic M. Organs-on-a-chip models for biological research. Cell. 2021; 184(18):4597-4611.

[17] Tao Y, Ma Y, Gu L, et al. Single-cell RNA sequencing reveals Shen-Bai-Jie-Du decoction retards colorectal tumorigenesis by regulating the TMEM131-TNF signaling pathway-mediated differentiation of immunosuppressive dendritic cells. Acta Pharm Sin B. 2025; 15(7):3545-3560.

[18] Yin F, Li P, Liu C, et al. Spatially resolved multi-omics reveals the renal cortex-metabolic reprogramming of Shenhua Tablet for intervention on IgA nephropathy. Phytomedicine. 2025; 141:156742.

[19] Li C, Shao X, Zhang S, et al. scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network. Cell Rep Med. 2024; 5(6):101568.

[20] Liu XR, Gong T. Artificial Intelligence and Evidence-Based Research Will Promote the Development of Traditional Medicine. Acupunct Herb Med. 2024; 4(1):134-135.

[21] Yu M, Li W, Yu Y, et al. Deep learning large-scale drug discovery and repurposing. Nat Comput Sci. 2024; 4(8):600-614.

[22] Xiao X, Luo Y, Zhao X, et al. Integrated evidence chain: a new strategy and methodology for effectiveness evaluation of traditional Chinese medicines. China J Chin Mater Med. 2024; 49(19):5113-5124.

[23] Luo Y, Zhao X, Wang R, et al. Integrated evidence chain-based effectiveness evaluation of traditional Chinese medicines (Eff-iEC): a demonstration study. Acta Pharm Sin B. 2025; 15(2):909-918.

[24] Zhang JH, Pang WT, Yang FW, et al. Construction and evaluation of the evidence chain for the efficacy of traditional Chinese medicine. Chin J Evid Med. 2025; 25(4):479-484.

[25] Liu J, Wang Y, Sun Y, et al. Efficacy and safety of Xinfeng capsule in the treatment of osteoarthritis: a multicenter, randomized, double-blinded, controlled trial. J Tradit Chin Med. 2020; 40(2):284-295.

[26] Huang D, Liu J, Cao Y, et al. RNA sequencing for gene expression profiles in peripheral blood mononuclear cells with ankylosing spondylitis RNA. Biomed Res Int. 2020; 2020:5304578.

[27] Gao Y, Wang GQ, Xie YM, et al. Study of integrative evidence chain in clinical trial of Guizhi Fuling Capsules based on “Yibing Tongzhi” in clinical applications. China J Chin Mater Med. 2020; 45(10):2304-2309.

[28] Xu Y, Zhang L, Chen C, et al. Investigation of the efficacy and potential pharmacological mechanism of Yupingfeng in treating chronic obstructive pulmonary disease: a meta-analysis and in silico study. J Ethnopharmacol. 2025; 343:119441.

[29] Sun JY, Du LJ, Shi XR, et al. An IL-6/STAT3/MR/FGF21 axis mediates heart-liver cross-talk after myocardial infarction. Sci Adv. 2023; 9(14):eade4110.

[30] Tian X, Wang P, Li T, et al. Self-assembled natural phytochemicals for synergistically antibacterial application from the enlightenment of traditional Chinese medicine combination. Acta Pharm Sin B. 2020; 10(9):1784-1795.

[31] Xiao Y, Xin L, Li L, et al. Quercetin and kaempferol increase the intestinal absorption of isorhamnetin coexisting in Elaeagnus rhamnoides (L.) A. Nelson (Elaeagnaceae) extracts via regulating multidrug resistance-associated protein 2. Phytomedicine. 2019; 53:154-162.

[32] Huang LP, Liu SJ, Yao YQ, et al. Research methods of pharmacokinetic-pharmacodynamics (PK-PD) model and its advantages and application in traditional Chinese medicines. Chin Tradit Herb Drugs. 2023; 54(2):367-374.

[33] Tan LF, Chen C, Fan XL, et al. Study on pharmacodynamic material basis of Naomaitong to protect neuronal cells based on PK-PD model. China J Chin Mater Med. 2019; 44(12):2588-2593.

[34] Zhang F, Zhang Y, Li X, et al. Research on Q-markers of Qiliqiangxin capsule for chronic heart failure treatment based on pharmacokinetics and pharmacodynamics association. Phytomedicine. 2018; 44:220-230.

[35] Wu EH, Zhang JH, Chen WJ, et al. Pharmacodynamics study and establishment of a PK-PD model for Epimedii Folium-Chuanxiong Rhizoma in treating osteoarthritis in rats. China J Chin Mater Med. 2025; 50(5):1377-1384.

[36] Li X, Mao X, Jiang H, et al. Shirebi granules ameliorate acute gouty arthritis by inhibiting NETs-induced imbalance between immunity and inflammation. Chin Med. 2024; 19(1):105.

[37] Wu D, Su J, Wang, et al. Exploration on pharmacological mechanisms of YZP against neuropathic pain via inhibiting spinal inflammation and the rationality of its compatibility. J Ethnopharmacol. 2024; 331:118316.

[38] Zhang Y, Li X, Shi Y, et al. ETCM v2.0: An update with comprehensive resource and rich annotations for traditional Chinese medicine. Acta Pharm Sin B. 2023; 13(6):2559-2571.

[39] Xu H, Li S, Liu J, et al. Bioactive compounds from Huashi Baidu decoction possess both antiviral and anti-inflammatory effects against COVID-19. Proc Natl Acad Sci U S A. 2023; 120(18):e2301775120.

[40] Zhao F, Jiang H, Zhang T, et al. Mechanism repositioning based on integrative pharmacology: anti-inflammatory effect of safflower in myocardial ischemia-reperfusion injury. Int J Mol Sci. 2023; 24(6):5313.

[41] Zhang Y, Wang N, Du X, et al. SoFDA: an integrated web platform from syndrome ontology to network-based evaluation of disease-syndrome-formula associations for precision medicine. Sci Bull (Beijing). 2022; 67(11):1097-1101.

[42] Li WJ, Zhang YQ, Zhou SF, et al. Clinical advantage staging and underlying mechanisms of Wangbi Tablets against knee osteoarthritis based on “disease-formula” interaction network. China J Chin Mater Med. 2024; 49(14):3924-3935.

[43] Chen WJ, Li T, Xu MZ, et al. Exploring biological connotation of blood stasis syndrome of rheumatoid arthritis and establishment of improved animal models based on syndrome-symptom mapping. Acta Pharm Sin. 2023; 58(8):2434-2441.

[44] Zhang Y, Xu H, Chen X, et al. Simultaneous quantification of 17 constituents from Yuanhu Zhitong tablet using rapid resolution liquid chromatography coupled with a triple quadrupole electrospray tandem mass spectrometry. J Pharm Biomed Anal. 2011; 56(3):497-504.

[45] Huang B, Chen XM, Zhang YC, et al. Effect of intestinal absorption solution of Yuanhu Zhitong Preparation on the tension of rat thoracic aortic ring. Chin J Exp Tradit Med Form. 2012; 18(5):117-120.

[46] Tao Y, Xu H, Wang S, et al. Identification of the absorbed constituents after oral administration of Yuanhu Zhitong prescription extract and its pharmacokinetic study by rapid resolution liquid chromatography/quadrupole time-of-flight. J Chromatogr B Analyt Technol Biomed Life Sci. 2013; 935:1-9.

[47] Wang P, Zhang TL, Yu GH, et al. Poly-pharmacokinetic strategy-delineated metabolic fate of bioactive compounds in a traditional Chinese medicine formula, Yuanhu Zhitong tablets, using parallel reaction monitoring mode. Phytomedicine. 2019; 53:53-61.

[48] Li K, Li J, Su J, et al. Identification of quality markers of Yuanhu Zhitong tablets based on integrative pharmacology and data mining. Phytomedicine. 2018; 44:212-219.

[49] Wu D, Zhang Y, Zhao C, et al. Disruption of C/EBPβ-Clec7a axis exacerbates neuroinflammatory injury via NLRP3 inflammasome-mediated pyroptosis in experimental neuropathic pain. J Transl Med. 2022; 20(1):583.

[50] Chen KK. A study of ephedrine. Br Med J. 1927; 2(3482):593.

[51] Maeda S, Sudo K, Aburada M, et al. Pharmacological studies on Schizandra fruit. I. General pharmacological effects of gomisin A and schizandrin (author’s transl). Yakugaku Zasshi. 1981; 101(11):1030-1041.

[52] Ma N, Zhang Z, Liao F, et al. The birth of artemisinin. Pharmacol Ther. 2020; 216:107658.

[53] Wani MC, Taylor HL, Wall ME, et al. Plant antitumor agents. VI. The isolation and structure of taxol, a novel antileukemic and antitumor agent from Taxus brevifolia. J Am Chem Soc. 1971; 93(9):2325-2327.

[54] Yin FT, Zhou XH, Kang SY, et al. Prediction of the mechanism of Dachengqi Decoction treating colorectal cancer based on the analysis method of “ into serum components -action target-key pathway.” J Ethnopharmacol. 2022; 293:115286.

[55] Kong L, Sun Y, Sun H, et al. Chinmedomics strategy for elucidating the pharmacological effects and discovering bioactive compounds from Keluoxin against diabetic retinopathy. Front Pharmacol. 2022; 13:728256.

[56] Wang Y, Yang L, Zhang X, et al. Quality marker discovery of Danggui Jianzhong decoction for treating primary dysmenorrhoea based on chinmedomics strategy. Phytomedicine. 2023; 115:154724.

[57] Mao X, Liu Y, Li W, et al. A promising drug combination of mangiferin and glycyrrhizic acid ameliorates disease severity of rheumatoid arthritis by reversing the disturbance of thermogenesis and energy metabolism. Phytomedicine. 2022; 104:154216.

[58] Hou J, Zhou X, Wang P, et al. An integrative pharmacology-based approach for evaluating the potential effects of purslane seed in diabetes mellitus treatment using UHPLC-LTQ-Orbitrap and TCMIP V2.0. Front Pharmacol. 2020; 11:593693.

[59] Fu S, Yi X, Li Y, et al. Berberine and chlorogenic acid-assembled nanoparticles for highly efficient inhibition of multidrug-resistant Staphylococcus aureus. J Hazard Mater. 2024; 473:134680.

[60] Zhu X, Gao Q, Zhao G, et al. Comparison study of bone defect healing effect of raw and processed pyritum in rats. Biol Trace Elem Res. 2018; 184(1):136-147.

[61] Liu Y, Zhang L, Cai H, et al. Biomass-derived carbon dots with pharmacological activity for biomedicine: recent advances and future perspectives. Sci Bull (Beijing). 2024; 69(19):3127-3149.

[62] Guo Q, Gao Z, Zhao L, et al. Multiomics analyses with stool-type stratification in patient cohorts and blautia identification as a potential bacterial modulator in type 2 diabetes mellitus. Diabetes. 2024; 73(3):511-527.

[63] Li Q, Yan X, Zhang Y, et al. Risk compounds, potential mechanisms and biomarkers of traditional Chinese medicine-induced reproductive toxicity. J Appl Toxicol. 2022; 42(11):1734-1756.

[64] Wang XY, Zhang Y, Chen WJ, et al. Exploration on “Efficacy-toxicity” association mechanisms of tripterygium wilfordii polyglycoside tablets against rheumatoid arthritis based on multi-omics integrated regulatory network. Chin J Exp Tradit Med Formulae. 2023; 29(5):49-57.

[65] Chen J, Li M, Chen R, et al. Gegen Qinlian standard decoction alleviated irinotecan-induced diarrhea via PI3K/AKT/NF-κB axis by network pharmacology prediction and experimental validation combination. Chin Med. 2023; 18(1):46.

[66] Liu XT, Chen WJ, Liu W, et al. Mechanism of Tianhe Zhuifeng Ointment in treating rheumatoid arthritis with syndrome of internal obstruction and cold-dampness and compatibility principles based on “disease-syndrome-formula” association network. China J Chin Mater Med. 2022; 47(18):4978-4986.

[67] Sun R, Liang Y, Zhu S, et al. Homotherapy-for-heteropathy of Bupleurum Chinense DC.-Scutellaria baicalensis Georgi in treating depression and colorectal cancer: a network pharmacology and animal model approach. J Ethnopharmacol. 2024; 328:118038.

[68] Tawulie D, Jin L, Shang X, et al. Jiang-Tang-San-Huang pill alleviates type 2 diabetes mellitus through modulating the gut microbiota and bile acids metabolism. Phytomedicine. 2023; 113:154733.

[69] Pan L, Li Z, Wang Y, et al. Network pharmacology and metabolomics study on the intervention of traditional Chinese medicine Huanglian Decoction in rats with type 2 diabetes mellitus. J Ethnopharmacol. 2020; 258:112842.

[70] Wang JB, Xu HY, Yang HJ, et al. Cross-organ effects of drug intervention: indirect pharmacology. China J Chin Mater Med. 2025; 50(13):3549-3555.

[71] Xu HY, Hou WB, Li K, et al. Discovery and application of quality marker of traditional Chinese medicine based on integrative pharmacology. Chin J Exp Tradit Med Formulae. 2019; 25(6):1-8.

[72] Liu CX. Quality marker(Q-marker) of Chinese materia medica: Improving quality standard and quality control theory of CMM and promoting scientific development of CMM industry. Chin Tradit Herb Drugs. 2019; 50(19):4517-4518.

[73] Gao X, Du X, An L, et al. Wilforine, the Q-marker and PK-maker of tripterygium glycosides tablet: based on preparation quantitative analysis and PK-PD study. Phytomedicine. 2019; 54:357-364.

[74] Li S, Wang P, Yang W, et al. Characterization of the components and pharmacological effects of mountain-cultivated ginseng and garden ginseng based on the integrative pharmacology strategy. Front Pharmacol. 2021; 12:659954.

[75] Dong XT, Ke JT, Gan PR, et al. To explore the quality markers of Huangqin Qingre Chubi capsule in the treatment of rheumatoid arthritis based on network pharmacology combined with pharmacokinetics and target verification. Acta Pharm Sin. 2023; 58(6):1422-1429.

[76] Xu Q, Li Z, Wan MX, et al. Research progress on screening technology of active ingredients in traditional Chinese medicine. Drug Eval Res. 2021; 44(7):1541-1547.

[77] Chen X, Wang Y, Ma N, et al. Target identification of natural medicine with chemical proteomics approach: probe synthesis, target fishing and protein identification. Signal Transduct Target Ther. 2020; 5(1):72.

[78] Wang C, Shi J, Rao Q, et al. Obtain substance of anti-glioblastoma from Erigeron breviscapus through Fragment-based Target Research (FBTR): an efficient strategy for pharmacology investigation and optimization of natural products. J Pharm Anal. 2025; 15(11):101366.