Metabolomics combined with network pharmacology to study the mechanism of Shentong Zhuyu decoction in the treatment of rheumatoid arthritis

Exploration of scientific connotation of "Yin-Jing" medical properties of Cyathula officinalis via potentiating therapeutic effect, guidance and targetability

ETHNIC PHARMACOLOGICAL RELEVANCE: "Cyathula officinalis Kuan (COK)" has the effect of "guiding the drug downward" and can enhance the efficacy of formula, e.g., Shentong Zhuyu Decoction (STZYD). However, there is currently no scientific basis on COK to guide drugs to target organs in STZYD.

AIM OF THE STUDY

The main objective of this study was to unclose the scientific connotations of the Yin-Jing medicinal properties of COK using molecular biology and modern chemical methods.

MATERIALS AND METHODS

A rat model of adjuvant arthritis was established. The optimal dose of STZYD was determined by observing a series of indicators, and the therapeutic effects of STZYD and [STZYD - COK] were compared. The water decoction of COK was divided into five fragments (i.e., Fr. A-E) by macroporous adsorption resin and alcohol deposition methods. The Fr. A-E were further characterized by a combination of multiple chromatographic and spectral techniques. The potentiating therapeutic effects, guidance and targetability tests were used to evaluate "Yin-Jing" function by compatible combination of other drugs using pharmacological indicators, pharmacokinetics, high-performance liquid chromatography (HPLC) and small animal live imaging (SALI) techniques.

RESULTS

The optimal dose of STZYD was confirmed to be 1 × dose and COK increased the efficacy of [STZYD - COK]. The results of chemical characterization showed that the main components of Fr. A-E were polysaccharide, fructooligosaccharide and small Mw fructan, saponins and flavonoid glycosides, steroidal ketones, organic acids esters, respectively. Pharmacological experiments showed that Fr. A, Fr. B and Fr. E were attributed to potentiate therapeutic effects. Guidance assays showed that Fr. B enhanced drug distribution and uptake in the kidneys, joints and cells. Targetability assays further confirmed that Fr. B had apparent targetability toward the joints and kidneys rather than other organs and tissues.

CONCLUSIONS

This study for the first time combined potentiating therapeutic effects, guidance and targeting evaluation system, and identified Fr. B as the pharmacodynamic material basis of COK's Yin-Jing medicinal properties.

Regulating Rheumatoid Arthritis From the Perspective of Metabolomics: A Comprehensive Review

Rheumatoid arthritis (RA) is a severe inflammatory autoimmune disease with metabolic changes. RA patients have abnormalities in glycolysis, amino acid metabolism, choline metabolism, and fatty acid synthesis. The differential metabolites in individuals of RA patients and animal models were explored to find the potential biomarkers for the risk prediction, diagnosis, and prognosis of RA in the perspective of metabolism. Moreover, we discussed the changes of related metabolites after treatment with anti-rheumatic drugs, Traditional Chinese Medicine (TCM) and potential metabolites for the treatment of RA to explore promising metabolites. In addition, the immunological mechanism of TCM in the treatment of RA from the perspective of metabolism was also clarified. For the perspectives of research and application of the beneficial metabolites in clinic, relevant technologies and focuses for the future studies in the field have been proposed accordingly.

Amentoflavone Induces Ferroptosis to Alleviate Proliferation, Migration, Invasion and Inflammation in Rheumatoid Arthritis Fibroblast-like Synoviocytes by Inhibiting PIN1

Rheumatoid arthritis (RA) is a systemic autoimmune disease that is prevalent worldwide and seriously threatens human health. RA-fibroblast-like synoviocytes (FLS) play important roles in almost all aspects of RA progression. This study aimed to study the effect of Amentoflavone (AMF), a polyphenol compound derived from extracts of Selaginella tamariscina, on the abnormal biological behaviors of RA-FLS. The immortalized human RA-FLS cell line (MH7A) was treated with AMF or transfected with small interfering RNAs (siRNAs) targeting peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1). Then, cell viability was detected by CCK-8 assay. EDU staining, wound healing and transwell assays were employed to measure the capacities of MH7A cell proliferation, migration and invasion. The levels of inflammatory factors were assessed using ELISA kits. Additionally, ferroptosis was analyzed by detecting Fe2+ content, lipid reactive oxygen species (ROS) level and expression of ferroptosis-related proteins. Pull-down assay was employed to verify the targeted binding of AMF to PIN1. Further, PIN1 overexpression or ferroptosis inhibitor Ferrostatin-1 (Fer-1) addition was conducted to elucidate the regulatory mechanism of AMF on PIN1 and ferroptosis. Results revealed that AMF intervention or PIN1 knockdown inhibited the proliferation, migration, invasion and inflammation in MH7A cells. AMF facilitated lipid peroxidation and ferroptosis in MH7A cells. Moreover, AMF targeted inhibition of PIN1 expression, and PIN1 overexpression restored the promoting effect of AMF on lipid peroxidation and ferroptosis in MH7A cells. Besides, Fer-1 reversed the impacts of AMF on the abnormal biological behaviors of MH7A cells. In summary, AMF induced ferroptosis to inhibit the proliferation, migration, invasion and inflammation in RA-FLS by inhibiting PIN1, providing a promising candidate for RA treatment.

GelMA@APPA microspheres promote chondrocyte regeneration and alleviate osteoarthritis via Fgfr2 activation

BACKGROUND

In the context of osteoarthritis (OA), a condition marked by joint degeneration, there is a notable absence of efficacious approaches to promote regenerative healing in chondrocytes. Novel therapeutic strategies like nanomicelles-hydrogel microspheres loaded with Astragalus polysaccharide (GelMA@APPA) offer promising avenues for promoting chondrocyte regeneration and mitigating OA progression.

METHODS

Astragalus polysaccharide (APS) has been shown to induce chondrocyte proliferation and promote cartilage matrix secretion, demonstrating biological activity associated with chondrocyte regeneration. However, the clinical efficacy of APS remains uncertain. Therefore, this investigation validated the beneficial impact of APS on reducing knee joint damage severity induced by destabilization of the medial meniscus (DMM) in mice. The application of bioinformatics analysis and in vitro experimentation revealed that fibroblast growth factor receptor 2 (Fgfr2) in chondrocytes is a key target protein for APS in ameliorating OA-induced cartilage injury, as the deletion of chondrocyte Fgfr2 resulted in the complete loss of the therapeutic effect of APS. To enhance the efficacy of APS, we incorporated APS into nanoparticle-laden hydrogel microspheres to further bolster its potential in chondrocyte regeneration therapy. Subsequently, we developed GelMA@APPA, which exhibited no significant cytotoxic effects on normal chondrocytes in vitro and could be efficiently internalized by chondrocytes. Following subsequent in vitro and in vivo experiments, we affirmed the beneficial effects of GelMA@APPA on OA mice and cartilage cells damaged by OA, as well as its enhancement of the therapeutic effects of APS.

RESULTS

APS significantly improved knee joint injuries in OA mice. Bioinformatics and in vitro analyses identified Fgfr2 as a critical target protein for APS's regenerative effects. Disruption of Fgfr2 negated APS's benefits. GelMA@APPA demonstrated good biocompatibility, effective internalization by chondrocytes, and enhanced the therapeutic efficacy of APS in experiments conducted both in vitro and in vivo, improving chondrocyte proliferation and reducing apoptosis.

CONCLUSIONS

This study demonstrates that GelMA@APPA microspheres effectively promote chondrocyte regeneration and OA treatment by activating Fgfr2. These findings suggest a novel therapeutic mechanism for OA and lay the groundwork for future clinical utilization of GelMA@APPA in regenerative medicine.

Investigation into the anti-inflammatory mechanism of Pothos chinensis (Raf.) Merr. By regulating TLR4/MyD88/NF-κB pathway: Integrated network pharmacology, serum pharmacochemistry, and metabolomics

ETHNOPHARMACOLOGICAL RELEVANCE

Inflammation is directly related to disease progression and contributes significantly to the global burden of disease. Pothos chinensis (Raf.) Merr. (PCM) is commonly used in Yao medicine in China to treat tumors, and orthopedic illnesses such as knee osteoarthritis, and rheumatic bone discomfort. PCM was found to have significant anti-inflammatory properties in previous studies.

AIM OF THE STUDY

To explore the active compounds of PCM and their anti-inflammatory pharmacological mechanisms through an integrated strategy of serum pharmacochemistry, network pharmacology, and serum metabolomics.

MATERIALS AND METHODS

The qualitative and quantitative analyses of the chemical components of PCM were performed using UPLC-QTOF-MS/MS and UPLC, respectively, and the prototype components of PCM absorbed into the blood were analyzed. Based on the characterized absorbed into blood components, potential targets and signaling pathways of PCM anti-inflammatory were found using network pharmacology. Furthermore, metabolomics studies using UPLC-QTOF-MS/MS identified biomarkers and metabolic pathways related to the anti-inflammatory effects of PCM. Finally, the hypothesized mechanisms were verified by in vivo and in vitro experiments.

RESULTS

Forty chemical components from PCM were identified for the first time, and seven of them were quantitatively analyzed, while five serum migratory prototype components were found. Network pharmacology KEGG enrichment analysis revealed that arachidonic acid metabolism, Tyrosine metabolism, TNF signaling pathway, NF-κB signaling pathway, and phenylalanine metabolism were the main signaling pathways of PCM anti-inflammatory. Pharmacodynamic results showed that PCM ameliorated liver injury and inflammatory cell infiltration and downregulated protein expression of IL-1β, NF-κB p65, and MyD88 in the liver. Metabolomics studies identified 53 different serum metabolites, mainly related to purine and pyrimidine metabolism, phenylalanine metabolism, primary bile acid biosynthesis, and glycerophospholipid metabolism. The comprehensive results demonstrated that the anti-inflammatory modulatory network of PCM was related to 5 metabolites, 3 metabolic pathways, 7 targets, and 4 active components of PCM. In addition, molecular docking identified the binding ability between the active ingredients and the core targets, and the anti-inflammatory efficacy of the active ingredients was verified by in vitro experiments.

CONCLUSION

Our study demonstrated the anti-inflammatory effect of PCM, and these findings provide new insights into the active ingredients and metabolic mechanisms of PCM in anti-inflammation.

Combining untargeted and targeted metabolomics to reveal the mechanisms of herb pair Anemarrhena asphodeloides Bunge and Phellodendron chinense C. K. Schneid on benign prostatic hyperplasia

ETHNOPHARMACOLOGICAL RELEVANCE

Anemarrhena asphodeloides Bunge (Ane) and Phellodendron chinense C. K. Schneid (Phe) is classical herb pair in traditional Chinese medicine, commonly used to ameliorate the symptoms of Benign Prostatic Hyperplasia (BPH). However, the mechanisms underlying this effect are remained indistinct.

AIM OF THE STUDY

This study aimed to clarify potential therapeutic mechanisms of herb pair on BPH from a metabolic perspective.

MATERIALS AND METHODS

Testosterone propionate-induced BPH rat model was established, prostatic parameters, histopathology and the levels of serum dihydrotestosterone (DHT) and testosterone (T) were used to evaluate the pharmacological effect of the herb pair on BPH. Subsequently, untargeted metabolomics of prostate tissues samples was performed by UHPLC-Q-Exactive-Orbitrap-MS, followed by multivariate statistical analysis. Targeted metabolomics by UHPLC-QQQ-MS was further utilized to verify and supplement the results of lipids and amino acids found by untargeted metabolomics, clarifying the relationship between disease, herbal pair and metabolism pathway.

RESULTS

The study found that Ane-Phe could relieve the progression of BPH and regulate metabolic imbalances. The levels of 13 metabolites decreased and 11 increased in prostatic tissues including glycerolphospholipid, arachidonic acid, citric acid and so on, these altered metabolites were primarily associated with TCA cycle, arachidonic acid metabolism, lipid metabolism and amino acid metabolism. Furthermore, targeted metabolomics was fulfilled to further analyze the lipid metabolism disorders, the levels of 5 lipids in serum and 21 in prostatic tissues were changed in the herb pair group compared to the model group, which closely related to glycerophospholipid, sphingolipid and glycerolipid metabolism. Besides, amino acid metabolism may be regulated by activating arginine metabolism pathway.

CONCLUSIONS

In this study, the combination of untargeted metabolomics and targeted metabolomics was applied to explore therapeutic mechanisms of Ane-Phe on BPH. In summary, Ane-Phe could improve the levels of endogenous metabolites by regulating multiple metabolic pathways and plays a role in energy supply, anti-inflammation and oxidative stress in BPH treatment.

Study on analgesic effect of Shentong Zhuyu Decoction in neuropathic pain rats by network pharmacology and RNA-Seq

ETHNOPHARMACOLOGICAL RELEVANCE

Shentong Zhuyu Decoction (STZYD) is a traditional prescription for promoting the flow of Qi and Blood which is often used in the treatment of low back and leg pain clinicall with unclear mechanism. Neuropathic pain (NP) is caused by disease or injury affecting the somatosensory system. LncRNAs may play a key role in NP by regulating the expression of pain-related genes through binding mRNAs or miRNAs sponge mechanisms.

AIM OF THE STUDY

To investigate the effect and potential mechanism of STZYD on neuropathic pain.

METHODS

Chronic constriction injury (CCI) rats, a commonly used animal model, were used in this study. The target of STZYD in NP was analyzed by network pharmacology, and the analgesic effect of STZYD in different doses (H-STZYD, M-STZYD, L-STZYD) on CCI rats was evaluated by Mechanical withdrawal thresholds (MWT) and thermal withdrawal latency (TWL). Meanwhile, RNA-seq assay was used to detect the changed mRNAs and lncRNAs in CCI rats after STZYD intervention. GO analysis, KEGG pathway analysis, and IPA analysis were used to find key target genes and pathways, verified by qPCR and Western Blot. The regulatory effect of lncRNAs on target genes was predicted by co-expression analysis and ceRNA network construction.

RESULTS

We found that STZYD can improve hyperalgesia in CCI rats, and H-STZYD has the best analgesic effect. The results of network pharmacological analysis showed that STZYD could play an analgesic role in CCI rats through the MAPK/ERK/c-FOS pathway. By mRNA-seq and lncRNA-seq, we found that STZYD could regulate the expression of Cnr1, Cacng5, Gucy1a3, Kitlg, Npy2r, and Grm8, and inhibited the phosphorylation level of ERK in the spinal cord of CCI rats. A total of 27 lncRNAs were associated with the target genes and 30 lncRNAs, 83 miRNAs and 5 mRNAs participated in the ceRNA network.

CONCLUSION

STZYD has the effect of improving hyperalgesia in CCI rats through the MAPK/ERK/c-FOS pathway, which is related to the regulation of lncRNAs to Cnr1 and other key targets.

Network pharmacology combined with affinity ultrafiltration to elucidate the potential compounds of Shaoyao Gancao Fuzi Decoction for the treatment of rheumatoid arthritis

ETHNOPHARMACOLOGICAL RELEVANCE

Shaoyao Gancao Fuzi Decoction (SGFD), has been employed for thousands of years in the treatment of rheumatoid arthritis (RA) with remarkable clinical efficacy. However, the material basis underlying the effectiveness of SGFD still remains unclear.

AIM OF THE REVIEW

This study aims to elucidate the material basis of SGFD through the application of network pharmacology and biological affinity ultrafiltration.

RESULTS

UPLC-Q-TOF-MS/MS was employed to characterize the components in SGFD, the identified 145 chemical components were mainly categorized into alkaloids, flavonoids, triterpenoids, and monoterpenoids according to the structures. Network pharmacology method was utilized to identify potential targets and signaling pathways of SGFD in the RA treatment, and the anti-inflammatory and anti-RA effects of SGFD were validated through in vivo and in vitro experiments. Moreover, as the significant node in the pharmacology network, TNF-α, a classical therapeutic target in RA, was subsequent employed to screen the interacting compounds in SGFD via affinity ultrafiltration screening method, 6 active molecules (i.e.,glycyrrhizic acid, paeoniflorin, formononetin, isoliquiritigenin, benzoyl mesaconitine, and glycyrrhetinic acid) were exhibited significant interactions. Finally, the significant anti-inflammatory and anti-TNF-α effects of these compounds were validated at the cellular level.

CONCLUSIONS

In conclusion, this study comprehensively elucidates the pharmacodynamic material basis of SGFD, offering a practical reference model for the systematic investigation of traditional Chinese medicine formulas.

Active metabolites combination therapies: towards the next paradigm for more efficient and more scientific Chinese medicine

Traditional Chinese medicine (TCM) formulae have been studied extensively in various human diseases and have proven to be effective due to their multi-component, multi-target advantage. However, its active metabolites are not clear and the specific mechanisms are not well established, which limits its scientific application. Recently, combination therapies are attracting increasing attention from the scientific community in the past few years and are considered as the next paradigm in drug discovery. Here, we tried to define a new concept of "active metabolites combination therapies (AMCT)" rules to elucidate how the bioactive metabolites from TCMs to produce their synergistic effects in this review. The AMCT rules integrate multidisciplinary technologies like molecular biology, biochemistry, pharmacology, analytical chemistry and pharmacodynamics, etc. Meanwhile, emerging technologies such as multi-omics combined analysis, network analysis, artificial intelligence conduce to better elucidate the mechanisms of these combination therapies in disease treatment, which provides new insights for the development of novel active metabolites combination drugs. AMCT rules will hopefully further guide the development of novel combination drugs that will promote the modernization and international needs of TCM.

Integrated network pharmacology and metabolomics reveal the mechanisms of Jasminum elongatum in anti-ulcerative colitis

Jasminum elongatum (JE), an ethnic Chinese medicine, is widely used in the Lingnan region of China, because of its analgesic and antidiarrheal action, as well as its anti-inflammatory effects in gastrointestinal diseases. However, whether JE could against ulcerative colitis (UC) remains unclear. This research aims to reveal JE in treating UC and clarify the underlying mechanism. We used the 2.5% dextran sulfate sodium (DSS)-induced UC mice (C57BL/6J) to evaluate the therapeutic effects of JE. Metabolomics of serum and network pharmacology were combined to draw target-metabolite pathways. Apart from that, the targets of associated pathways were confirmed, and the mechanism of action was made clear, using immunohistochemistry. The pharmacodynamic results, including disease activity index (DAI), histological evaluation, and inflammatory cytokines in colon tissues, demonstrated that JE significantly relieved the physiological and pathological symptoms of UC. Network pharmacology analysis indicated 25 core targets, such as TNF, IL-6, PTGS2 and RELA, and four key pathways, including the NF-κB signaling pathway and arachidonic acid metabolism pathway, which were the key connections between JE and UC. Metabolomics analysis identified 45 endogenous differential metabolites and 9 metabolic pathways by enrichment, with the arachidonic acid metabolism pathway being the main metabolism pathway, consistent with the prediction of network pharmacology. IκB, p65 and COX-2 were identified as key targets and this study demonstrated for the first time that JE reverses 2.5% DSS-induced UC in mice via the IκB/p65/COX-2/arachidonic acid pathway. This study reveals the complex mechanisms underlying the therapeutic effects of JE on UC and provides a new approach to identifying the underlying mechanisms of the pharmacological action of Chinese natural medicines such as JE.

Exploring the effect of the Uyghur medicine Munziq Balgam on a collagen-induced arthritis rat model by UPLC-MS/MS-based metabolomics approach

ETHNOPHARMACOLOGICAL RELEVANCE

Munziq Balgam (MBm) is a classic preparation of a traditional Uyghur medicine used for many years to treat abnormal body fluid diseases. The formula, as an in-hospital preparation, has already been used in the Hospital of Xinjiang Traditional Uyghur Medicine to treat rheumatoid arthritis (RA) with significant clinical effects.

AIM OF THE STUDY

This study intends to reveal the intervention effect of MBm on collagen-induced arthritis (CIA) rats, discover the potential biomarkers with efficacy, and explore the mechanisms of metabolic regulation by using metabolomics method.

MATERIAL AND METHODS

Sprague Dawley (SD) rats were randomly divided into five groups: blank group, CIA model group, Munziq Balgam nomal-dosage, Munziq Balgam high-dosage group and control group. Body weight, paw swelling, arthritis index, immune indices and histopathological experiments were carried out. Plasma from rats were detected by UPLC-MS/MS. Metabolomics of plasma was performed to analyze metabolic profiles, potential biomarkers, and metabolic pathways of MBm for CIA rats. The main metabolic result of Uyghur medicine MBm was compared with that of Zhuang medicine Longzuantongbi granules (LZTBG) to explore the characteristics of two ethnic medicines from different regions for RA.

RESULTS

MBm could significantly alleviate symptoms of CIA rats by relieving arthritis symptoms on paw redness and swelling, inflammatory cell infiltration, synovial hyperplasia, pannus, cartilage and bone tissue destruction, as well as inhibiting the expression of IL-1β, IL-6, TNF-α, UA and ALP. Linoleic acid, alpha-linolenic acid, pantothenate and CoA biosynthesis, achidonic acid, gycerophospholipid, sphingolipid metabolism, primary bile acid biosynthesis, porphyrin and chlorophyll metabolism and fatty acid degradation served as the main nine pathways of the interventional effect of MBm on CIA rats. Twenty-three different metabolites were screened out and strongly associated with the indicator makes of RA. Eight potential efficacy-related biomarkers were finally discovered in metabolic pathway network (phosphatidylcholine, bilirubin, sphinganine 1-phosphate, phytosphingosine, SM (d18:1/16:0), pantothenic acid, l-palmitoylcarnitine, chenodeoxycholate). Three metabolites (chenodeoxycholate, hyodeoxycholic acid and O-palmitoleoylcarnitine) were changed in both the metabolic study of MBm and LZTBG intervention effects on CIA rats. Additionally, MBm and LZTBG shared the same 6 metabolic pathways including linoleic acid, alpha-linolenic acid, pantothenate and CoA biosynthesis, achidonic acid, gycerophospholipid, and primary bile acid biosynthesis.

CONCLUSION

The study suggested that MBm may effectively alleviate RA by regulating inflammation, immunity-related pathways and multiple targets. Metabolomics analysis showed that MBm (Xinjiang, the north of China) and LZTBG (Guangxi, the south of China), two ethnic medicines from different regions in China, share common metabolites and pathways but also have distinct differences in their interventions for RA.

Panlongqi tablet suppresses adjuvant-induced rheumatoid arthritis by inhibiting the inflammatory reponse in vivo and in vitro

ETHNOPHARMACOLOGICAL RELEVANCE

Panlongqi Tablet is prepared with the ancestral secret recipe provided by Mr. Wang Jiacheng, a famous specialist in orthopedics and traumatology of China. The efficacy and safety of PLQT have been supported by years of clinical practice in the treatment of joint-related conditions. Has remarkable effect for treating rheumatoid arthritis (RA) clinically. However, its mechanism is not entirely clear.

AIM OF THE STUDY

We aim to evaluate the anti-inflammatory activity of PLQT and explore its mechanism in adjuvant-induced arthritis (AA) mice and LPS-induced Human fibroblast-like synovial (HFLS) cells.

MATERIALS AND METHODS

To this end, we analyzed the active ingredients in PLQT by HPLC-MS/MS. Furthermore, the anti-RA effect of PLQT was studied through proliferation, apoptosis, foot swelling, cytokine levels, immune organ index, histopathology and related signal pathways in LPS-induced HFLS cells and AA-treated mice.

RESULTS

HPLC-MS/MS results showed that PLQT contained a variety of active compounds, such as epicatechin, imperatorin, hydroxysafflor yellow A and so on. PLQT significantly inhibited the abnormal proliferation of HFLS cells induced by LPS, promoted cell apoptosis. In AA-treated mice, PLQT alleviated RA symptoms by alleviating paw swelling, synovial hyperplasia, pannus formation, inflammatory cell infiltration, and inhibiting abnormal immune responses. The results showed that PLQT significantly decreased the expression of inflammatory mediators (IL-1β, IL-6, IL-17) in vivo and in vitro, which may be related to the regulation of PI3K/Akt, MAPK and JAK/STAT signaling pathways.

CONCLUSION

Based on serum pharmacology and in vivo pharmacology studies, PLQT may regulate RA symptoms by regulating inflammatory and immune response-related pathways, which is an effective method for the treatment of RA.

Traditional Tibetan Medicine Twenty-Five Wei'er Tea Pills Ameliorate Rheumatoid Arthritis Based on Chemical Crosstalk Between Gut Microbiota and the Host

Twenty-Five Wei'er Tea Pills (TFP), a traditional Tibetan medicine, has shown to have a promising therapeutic effect in patients with Rheumatoid arthritis (RA), as well as being safe. Nonetheless, there have been limited pharmacological studies that have explored this therapeutic option. As gut microbiota has been proven to have a critical role in the pathogenesis of RA, this study aims to explore and reveal relevant ways by which TFP interacts with the chemical crosstalk between the gut microbiome and its host. 16S rRNA sequencing, combined with un-targeted metabolomics, were conducted on collagen-induced arthritis (CIA) rats. CIA model rats treated with TFP showed significant improvement in weight gain, pathological phenomena in joints, as well as decreased serum levels of TNF-α, IL-6 and increased level of IL-4 and IL-10. Significant dysfunction in the gut microbiome and alteration in serum metabolites were observed in CIA model rats, which were restored by TFP treatment. Coherence analysis indicated that TFP modulated the pathways of histidine metabolism, phenylalanine metabolism, alanine, aspartate, glutamate metabolism, amino sugar and nucleotide sugar metabolism owing to the abundances of Lactobacillus, Bacteroides, Prevotellaceae_UCG-001 and Christensenellaceae_R-7_group in the gut microflora. The corresponding metabolites involved L-histidine, histamine, phenylethylamine, asparagine, L-aspartic acid, D-fructose 1-phosphate, D-Mannose 6-phosphate, D-Glucose 6-phosphate, and Glucose 1-phosphate. In conclusion, this study reveals the ameliorative effects of TFP on RA through the chemical crosstalk that exists between the gut microbiota and its host, and also further enriches our understandings of the pathogenesis of RA.