The polyphenol resveratrol (RSV, trans-3,5,4’-trihydroxystilbene) is found in grapes, soybeans, berries, nuts, and pomegranates, among other natural sources (142). In rodent models of IBD, the antioxidant potential of RSV has been investigated. In one trinitrobenzene sulphonic acid (TNBS)-induced colitis study, pretreatment of rats with RSV reduced histologic inflammation and MDA levels but increased GPx activity compared to markers in the TNBS and vehicle groups (91) ( Supplementary Table 1 ).

MPO is responsible for tissue damage in IBD and is inhibited effectively by resveratrol and its derivatives (143). Inhibition of IL-1, IL-6, and TNF-α release from macrophages, iNOS expression and subsequent NO production, prostaglandin production, cyclooxygenase (COX) enzyme activity, apoptosis, and MPO activity are the potential mechanisms by which RSV exerts its anti-inflammatory effect (90, 91) ( Supplementary Table 1 ). The action of resveratrol on ROS generation may involve a direct radical scavenger effect or an effect on the activation of NADPH oxidase (90).

It has been shown that the NF-κB pathway is linked to both colitis and colon cancer development as a consequence of chronic intestinal inflammation (144). Additionally, inflammation in the colon inhibits the activity of the silent information regulator 1 (SIRT-1) gene and increases the activity of NF-κB. By activating SIRT-1 and down-regulating NF-κB activation, RSV plays a vital role in the regulation of inflammation that mediates colitis and colon cancer (145) ( Supplementary Table 1 ).

Curcumin, a polyphenol extracted from Curcuma longa rhizomes, has a wide variety of beneficial antioxidant, anti-inflammatory, immunomodulatory, neuroprotective, hepatoprotective, anti-cancer, antiproliferative, and chemopreventive properties (34, 49, 50, 146–148). Curcumin reduces OS and improves intestinal barrier integrity and mitochondrial functions by inducing Parkin-dependent mitophagy via AMPK (adenosine 5’-monophosphate activated protein kinase) activation and TFEB (transcription factor EB) nuclear translocation (149). As a result of its ability to inhibit the expression of transcription factors and pro-inflammatory cytokines such as TNF-α, IL-1, IL-6, IL-8, IL-12, IL-1β, and monocyte chemoattractant protein-1 (MCP-1), curcumin has demonstrated anti-inflammatory properties ( Supplementary Table 1 ). Curcumin can also compete with LPS for TLR4 receptor activation, thereby inhibiting the TLR4/myeloid differentiation 88 (MyD88)/NF-κB signaling pathways (150, 151). Curcumin can reduce LPS-induced inflammation in vascular smooth muscle cells via TLR4-MAPK/NF-κB pathways by inhibiting ROS generation (93). This effect is mediated through curcumin’s effects on TLR4 as it specifically prevents the LPS-induced generation of MCP-1, TNF-α, and NO (93). Curcumin reduces TNBS-induced colitis in rats by inhibiting the TLR4/NF-κB signaling pathway and pro-inflammatory IL-27 expression (94).

Oral supplementation with curcumin reduces OS generated by hyperthyroidism in rats, as shown by decreased LPx and protein carbonyl (PC) levels and increased SOD and CAT activities in tissues (34, 39, 49). In vitro studies show that curcumin can boost cellular glutathione levels by stimulating the transcription of two Gcl genes (Gclc and Gclm) encoding glutamate cysteine ligase, which is the rate-limiting enzyme in glutathione synthesis (49, 152). It has been reported that curcumin may reduce OS by modulating Nrf2 and KEAP1 function in the rat heart during altered thyroid states (153). Oral delivery of nanoparticles containing curcumin in dextran sulfate sodium (DSS)-induced colitis in Guinea pigs was associated with a substantial drop in tissue LPx and PC levels, leukocyte infiltration, and TNF-α production (95). Antioxidant balance is also regulated by curcumin in rats with UC by lowering both colonic MPO activity and total NO content as well as increasing colonic GST activity and GSH contents when administered prior to the DSS challenge (154). Curcumin has been shown to decrease OS markers MPO and MDA levels and cell apoptosis in different animal models of colitis (155–158) ( Supplementary Table 1 ).

Quercetin (QCT), a member of the flavonols (a subclass of flavonoids), is a polyphenolic molecule found in plants and has demonstrated anti-inflammatory, antioxidant, and antitumoral effects. Several studies have shown that quercetin can suppress the expression of inflammatory mediators and cytokines such as COX-2, NO, NF-kB, prostaglandin E2 (PGE2), iNOS, TNF-α, IL-1β, and IL-6 that are generated through the LPS-TLR4 pathway (159) ( Supplementary Table 1 ). LPS-induced inflammation is suppressed by quercetin-rich Myrsine seguinii ethanolic extract, which inhibits Src- and Syk-mediated phosphoinositide 3-kinase (PI3K) tyrosine phosphorylation and the TLR4/MyD88/PI3K signaling pathways (160). This extract also suppressed iNOS, a high-output Ca⁺⁺-independent NOS stimulated by cytokines (161), and COX-2 gene expression through reduced NF-κB and activator protein (AP-1) stimulation (160).

Modulation of the stress response genes, including the antioxidant enzyme GPX1, was detected after LPS stimulation of the IBD enteroids and colonoids (57). Organoids have more advantages than conventional models and have been employed in fundamental and clinical research, such as for genetic and infectious diseases, regenerative medicine, and accurate and reliable drug screening (162–168). Murine colitis-derived intestinal organoids stimulated by LPS show reduced mRNA expression of inflammatory mediators such as TNF-α and lipocalin-2 (LCN2) when treated with quercetin (96). The anti-inflammatory action of quercetin was also accompanied by a decrease in the expression of C/EBP-β, a transcription factor that induces the expression of several inflammatory mediators, including TNF-α (169). Human apoB promoter analysis shows that a CCAAT enhancer-binding protein (C/EBP)-response element is critical for the action of quercetin. Through its interaction with C/EBPβ, quercetin has the potential to inhibit the recruitment of co-activators. Quercetin also suppresses apolipoprotein B (apoB) expression by inhibiting the transcription of C/EBPβ (169). Several polyphenols, including quercetin, affect the expression of tight junction (TJ) proteins of the intestinal epithelium (88). Using a DSS-colitis murine model, quercetin restored the expression of zonula occludens-1, occludin, junctional adhesion molecule-A, and claudin-3 (88).

There have been several studies on animal models of UC that provide evidence for the use of quercetin to treat IBD (92, 170). Oral quercetin (doses ranging from 25 to 100 mg/kg for 11 days) was associated with decreases in loss of body weight loss, rectal bleeding, and macroscopic and biochemical intestinal damage. It is possible that the antioxidant activity of QCT reduces LPx and OS by regulating nitrites and nitrates, increasing glutathione (GSH), and decreasing MPO activity in the colonic mucosa (92, 170) ( Supplementary Table 1 ). Additional research using animal models demonstrates that QCT activity is mediated through the inhibition of TNF-α expression. By regulating the anti-inflammatory effects and bactericidal activity of macrophages through heme oxygenase-1 (HO-1)-dependent pathway, QCT may reduce the severity of experimental colitis (170, 171). Dietary delivery of QCT to restore intestinal homeostasis and intestinal normobiosis is a potentially promising treatment for IBD (171). Quercetin inhibits the apical efflux of N-acetyl 5-aminosalicylic acid (Ac-5-ASA) from Caco-2 cells, which was mediated by multidrug resistance-associated protein 2. This suggests that using QCT as an additional therapy may contribute to reduced dosages of sulfasalazine required for therapeutic action while reducing adverse drug effects (172). In another murine colitis model study (173), quercetin-loaded microcapsule-treated mice showed significantly more 2,2’-Azino-bis (3-ethylbenzothiazole-6-sulfonic acid) (ABTS) radical cation scavenging and ferric reducing activity as compared to colitis control mice. Results indicated that the QCT-treated mice had significant reduction in neutrophil influx (MPO activity), edema, and colonic macroscopic and histologic inflammation. Finally, this treatment reduced the levels of the pro-inflammatory cytokines IL-1β and IL-33 while maintaining anti-inflammatory cytokine IL-10 levels, and maintained the levels of endogenous antioxidants in the colons of colitic mice (173)( Supplementary Table 1 ).

Currently, there is no established tolerable upper limit for flavonoids in the Dietary Reference Intake framework (174). However, the consumption of flavonoids in quantities naturally present in foods does not pose any toxicity concerns (175). A high consumption of flavonoids may increase the likelihood of iron deficiency in populations with suboptimal iron levels (e.g., the elderly). Nonetheless, in Western societies where sufficient intake of heme iron and ascorbic acid occurs, the likelihood of developing anemia is minimal (175). The bioavailability of flavonoids is limited, as only a small fraction (i.e., less than 10% of the ingested quantity) can attain peak concentrations in the bloodstream within a few hours The bioavailability of flavonoids may be subject to various factors, such as ingestion of dietary fiber, macro and micronutrients, the duration of GI transit times, and composition of the gut microbiota (176, 177).

Flavonoids in green tea have been shown to regulate the expression of pro-inflammatory genes that target TLRs and inhibit downstream MyD88- and Toll/IL-1R domain-containing adaptor-inducing IFN-β (TRIF)-dependent signaling pathways (89). Epigallocatechin-3-gallate (EGCG), a flavonoid present in green tea, reduces TNF-α and also gene expression and the effects of nitric oxide synthase (NOS) and COX in murine RAW 264.7 macrophages (97). Treatment with EGCG-docosapentaenoic acid (DPA) esters has been shown to reduce the production of the pro-inflammatory mediators like nitric oxide (NO) and PGE2 via down-regulation of iNOS and COX-2 gene expression. Other EGCG ester derivatives (stearic acid, eicosapentaenoic acid, and docosahexaenoic acids) also have anti-inflammatory activity in murine RAW 264.7 macrophages (97). The mechanism of action is believed to be the inhibition of downstream TLR signaling affecting the MyD88- and/or TRIF-dependent pathways with activation of NF-κB. A study also demonstrated that EGCG blocks both the MyD88-dependent and TRIF-dependent signaling pathways of TLRs in RAW264.7 cells (89). In TRIF-dependent signaling pathways of TLR3 and TLR4, the molecular target of EGCG is TANK-binding kinase1 (TBK1), resulting in the decrease of interferon regulatory factor 3 (IRF3) activation, as TBK1 is the downstream kinase of TRIF and phosphorylates IRF3 resulting in its activation (89).

The combination of EGCG and piperine (piperine for enhancing the bioavailability of EGCG) significantly decreased weight loss, improved the clinical course, and increased overall survival in the DSS-murine model of colitis (87). Reduced severity of the colitis was linked to improved histology scores and reduced colonic MDA and MPO activity ( Supplementary Table 1 ). The combination of EGCG and piperine improved SOD and GPx expression and suppressed the generation of proinflammatory cytokines in vitro. It appears that the powerful antioxidative potential of EGCG is responsible for its anti-inflammatory effects in the DSS-murine model of colitis. Lipid peroxidation occurs during IBD inflammation when ROS are not neutralized, altering the permeability and selectivity of the cell membrane and the activity of transmembrane transporters, receptors, and enzymes (87). DSS-colitis mice that had been administered EGCG and piperine had increased levels of AOEs (SOD and GPx), indicating that the antioxidant capacity had improved (87) ( Supplementary Table 1 ).

The anti-inflammatory, anti-cancer, and antioxidant effects of caffeic acid phenethyl ester (CAPE) have been studied extensively (98, 99, 178–181). Caffeic acid phenethyl ester inhibits LPS-induced IL-12 production and NF-κB activation in monocyte-derived dendritic cells (178). Caffeic acid phenethyl ester prevents the activation of TLR4 by interfering with the interaction between the TLR4/MD2 complex (180). In LPS-induced breast cancer cells, CAPE can down-regulate the expression of TLR4, NF-kB p65, TRIF, MyD88, and IRAK4 while stimulating cell apoptosis and autophagy (181). In gingival fibroblasts, CAPE suppresses LPS-induced production of IL-6, IL-8, iNOS, COX-2, TLR4/MyD88 mediated NF-κB, and phosphorylation of PI3K and protein kinase B (PKB, or Akt) (179).

FA-97 (caffeic acid phenethyl ester 4-O-glucoside) is a new synthetic CAPE derivative shown to attenuate body weight loss, colon length shortening, increased colonic inflammatory cell infiltration, and pro-inflammatory cytokine production (99). While FA-97 increased overall antioxidant capacity in DSS-treated mice and LPS-treated BMDMs and RAW 264.7 cells, it also decreased ROS and MDA production. The mechanism of action of FA-97 is believed to be the activation of the Nrf2/HO-1 pathway in both in vivo and in vitro models. FA-97 activates Nrf2 and promotes its nuclear translocation to increase expression of its downstream target proteins HO-1 and NAD(P)H:quinone oxidoreductase (NQO-1), which reduces ROS. It also inhibits the NF-κB and AP-1 signaling to suppress the expression of pro-inflammatory cytokines IL-1, IL-6, TNF-α, and IL-12 ( Supplementary Table 1 ). In addition to ameliorating DSS-induced colitis, FA-97 promotes normal epithelial barrier function (98, 99).

The flavonoid compound luteolin, found in various plant extracts, has been shown to have anti-inflammatory, antioxidant, anti-metastasis, and apoptosis-inducing properties. Luteolin has been reported to reduce LPS-stimulated expression of NF-κB, TNF-α, and ICAM-1 and TBK1-kinase activity via the MyD88-independent signaling pathway (182). Luteolin inhibited the expression of target genes IL-6, IL-12, IL-27, TNF-α, IP-10, IFNβ, CXCL9 (C-X-C motif chemokine ligand 9) in macrophages by inhibiting IRF3 and NF-κB activation ( Supplementary Table 1 ). Luteolin was able to suppress the ligand-independent activation of IRF3 or NF-κB triggered by TLR4, TRIF, or TBK1. Luteolin also reduces the amount of TBK1-dependent gene expression by inhibiting TBK1-kinase activity, and IRF3 dimerization and phosphorylation. Moreover, luteolin structural analogs, such as quercetin, chrysin, and eriodictyol, also inhibit TBK1-kinase activity and TBK1-target gene expression. These findings indicate that TBK1 is a unique target of anti-inflammatory flavonoids resulting in the inhibition of the TRIF-dependent signaling pathway (182).

LPS-induced inflammatory responses are controlled at the transcriptional level through the MAPK and NF-κB pathways (100, 183, 184). Toll-like receptors trigger NF-κB and MAPK cascades responses to LPS stimulation, causing the production of ROS, increased MPO expression, and expression of pro-inflammatory molecules and chemokines. In mice with LPS-induced acute lung injury (ALI), luteolin reduced the activation of ERK, p38MAPK, and JNK in lung tissue. The protective action of luteolin is due to its ability to block MAPK pathways, which prevents the activation of NF-κB and the degradation of IκB. Upon administration of LPS, luteolin pretreatment prevents these inflammatory processes from developing (100). In addition, the results in mice indicate that the activities of SOD and CAT increased following pretreatment with luteolin versus LPS treatment alone. MPO levels are reduced in LPS-induced acute lung injury (ALI) when pretreated with luteolin. This mechanism of action is believed to be due to luteolin suppression of LPS-induced ALI-related MDA generation in the lungs (100) ( Supplementary Table 1 ).

Xanthohumol (XN), a compound derived from hop plants, is a prenylated chalcone with, antioxidant, anti-cancer, and anti-inflammatory activities via inhibition of TLR4/MD-2 complex (185). Downstream, XN suppresses macrophage iNOS expression and NO, and interferon-gamma (IFN-γ) production (186, 187). Pretreatment with XN in DSS-treated mice decreased the severity of diarrhea, hematochezia, rectal bleeding, and reduced colon length. Moreover, XN protected against epithelial cell injury, cellular infiltration, pro-inflammatory cytokines, and crypt changes following the DSS challenge (101). Pre-treatment with XN prior to DSS exposure resulted in decreased MDA levels and COX-2 expression suggesting a protective effect against experimental colitis (101) ( Supplementary Table 1 ). Moreover, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IκBα) phosphorylation, nuclear translocation of p65, p50, and p105 NF-κB subunits, and NF-κB DNA-binding transcriptional activity were suppressed by XN treatment of DSS-treated mice and H₂O₂- or LPS-treated IEC-6 cells (101).

XN protects mice from DSS-induced colitis and H₂O₂- or LPS-treated IEC-6 injury, possibly by the interaction between the α, β-unsaturated carbonyl moiety of XN and Cys99 in IKKβ, and thus by its ability to inhibit the IKKβ/NF-κB signaling pathway. Additionally, XN inhibited the activation of the canonical NF-κB pathway, as evidenced by the downregulation of NF-κB target genes, like A1a, A20, Bcl-xL, and c-myc (101) ( Supplementary Table 1 ). These collective results indicate that XN may be a promising therapeutic agent for the prevention or treatment of colitis (188).

A soy isoflavone, genistein, is a powerful antioxidant and anti-inflammatory agent (102–105, 189). Following treatment with genistein, reduced levels of IL-6, TNF-α, and NF-κB activation have been observed in in vitro and in vivo studies (104, 189). Genistein also inhibited BV2 microglia LPS-induced NO production, prostaglandin E2 release and expression of inflammatory cytokines (IL-1β, TNF-α), TLR4, and MyD88 expression (102). Expression of interferon beta (IFN-β), IL-1α, IL-1β, IL-6, IL-10, TNF-α, colony-stimulating factor 2 (CSF-2), colony-stimulating factor 3 (CSF-3), chemokines CCL2 (chemokine ligand 2), and CXCL10 (C-X-C motif chemokine ligand 10), transcription factor NF-κB, IκBα, and COX-2 are all decreased in genistein-pretreated LPS-induced RAW264.7 macrophages (103) ( Supplementary Table 1 ). In humans, six months of daily oral administration of genistein has been shown to decrease TNF-α levels decreased in obese postmenopausal women (106). Dietary supplementation with genistein lowered the expression of vascular adhesion molecule-1 (VCAM-1), a major cell adhesion molecule involved in inflammation (190), and F4/80 positive macrophages in the aorta of TNF-α-treated C57BL/6 mice (104). Human umbilical vein endothelial cells (HUVECs) in culture showed significant increases in the activities of GR, GPx, GST, NQO-1, SOD, and CAT when treated with 50 µM genistein (104) ( Supplementary Table 1 ). Due to its ability to stimulate IL-1β secretion, the NLRP3 inflammasome has been linked to IBD in experimental models as well as human studies (191). In the DSS murine colitis model, treatment with genistein significantly slowed weight loss and reduced colon shortening, infiltration of inflammatory cells as well as the production of pro-inflammatory mediators in both serum and colon (105). Genistein’s protective properties may stem from the ubiquitination of NLRP3 caused by the interaction of cAMP with the protein. It has been shown that genistein can inhibit the NLRP3 inflammasome via TGR5-cAMP signaling in human macrophages (105).

Alpinetin, a naturally occurring dihydroflavone (192), ameliorates clinical severity (disease activity index; DAI), colonic shortening, histological scores, and MPO activity in DSS-treated mice (108). The expression of occludin and zonula occludens-1 and SOD activity were increased, while the MDA amount was decreased by alpinetin in DSS-treated mice. Also, Nrf2/HO-1 signaling pathways were activated by alpinetin in DSS-treated mice (108). Alpinetin exhibits its anti-inflammatory activities by suppressing TLR4/IκBα/NF-κB signaling (107). In that study, alpinetin decreased the expression levels of IL-1β, IL-6 and TNF-α ( Supplementary Table 1 ) in LPS-treated RAW 264.7 macrophages in vitro and in the in vivo LPS-induced acute lung injury murine model (107) by disrupting ERK/p38MAPK signaling (193).

Grape seed proanthocyanidin extract (GSPE) is composed of approximately 90% proanthocyanidins, including oligomers (74.8%), dimers (6.6%), trimers (5.0%) and tetramers (2.9%) (194). Inhibiting the expression of NF-κB-targeted genes is a primary mechanism by which GSPs exert their antioxidant and anticarcinogenic actions (109, 195, 196). It is proposed that GSPs inhibit NF-κB activation by inhibiting the activation of IκK (inhibitor of κB kinase) to prevent phosphorylation-induced degradation of IκBα (196). The effect of GSPs on enhancing antioxidant enzymatic defense was confirmed by their ability to boost colonic SOD activity (109, 195).

Nutritional and pharmacological dosages of proanthocyanidins protect against endotoxin (LPS)-induced intestinal inflammation, OS, and intestinal permeability in colitic rats (197). Notably, area-specific LPS-induced inflammation in the intestine has been identified, and a unique gene signature may be useful to determine the affected intestinal region (57). Treatment with GSPE reduces MPO and COX-2 activity, modifies the gene expression of ileal inflammatory and permeability proteins, and reduces ROS, MDA, and NO levels, and iNOS activities ( Supplementary Table 1 ) in the large intestine (109, 197). Also, GSPE treatment enhances SOD, GPx activity, and glutathione levels in colon tissues and serum of TNBS-induced colitis in rats (109) ( Supplementary Table 1 ).

The antioxidant properties of anthocyanins, as well as their ability to influence gut microbiota and to down-regulate the immune response, have significant implications for reducing intestinal inflammation (198, 199). In human monocytic THP-1 cells, treatment with bilberry extract (BE), rich in anthocyanins, inhibited IFN-γ activation of STAT1 and STAT3 and lowered mRNA expression and/or secretion of MCP-1, TNF-α, IL-6, and ICAM-1 (110). The effects of genetically engineered tomato extracts (enriched in anthocyanins) (200) showed that the extract reduced the activation of epithelial cells SAPK/JNK (stress-activated protein kinase/c-Jun NH (2)-terminal kinase) and p38MAPK signaling pathways. Furthermore, pro-inflammatory cytokines and chemokines, including TNF-α and IL-10, were inhibited by anthocyanin-rich tomato extracts (200). It has been shown that anthocyanin-rich fractions from red raspberries (112) and purple carrots (111) decrease the production of iNOS, COX-2, IL-1β, and IL-6 in LPS/IFN-γ activated macrophages in vitro. In murine colitis, anthocyanins extracted from the Chinese plant Dioscorea alata L (201). decreased DAI (body weight loss, fecal occult blood, and fecal consistency), increased the gene expression of tight junction proteins and reduced OS markers (MPO and iNOS) along with IFN-γ and TNF-α levels. Red raspberry berry (RB) powder (202) can attenuate the effects of DSS treatment by preventing weight loss, neutrophil infiltration, colon shortening by inhibiting IL-1, IL-6, IL-17, and TNF- α and COX-2 levels in inflamed tissues ( Supplementary Table 1 ). Supplementation with RB restored CAT levels to normal, decreased xanthine oxidase (XO) levels and expression of MCP-1, and thus reduced neutrophil infiltration and ROS formation (202). Similarly, when an extract of blueberry anthocyanins (BBA) (203) was used, disease activity, MPO and MDA levels were reduced in murine colitis. In addition to decreasing serum prostaglandin E2 levels, BBA reduces OS marked by increased SOD and CAT levels. Moreover, mRNA expression of NF-κB, IFN-γ, COX-2, IL-1β, and iNOS was reduced, indicating that blueberry’s protective effect is at least partially mediated by the inhibition of inflammatory mediators (203). Similarly, it has been shown that colitis symptoms (colon shortening, DAI, loss of appetite, and weight gain), decreased SOD, and increased MPO can be mitigated and that GPx and GR activities ( Supplementary Table 1 ) can be increased by administering grape pomace extract (GPE) (86). Anti-inflammatory effects of GPE were observed in DSS-treated mice as evidenced by reduced IL-1β, IL-1α, IL-6, and IFN-γ and also TNF-α activities. Gene expression for the p65 subunit of NF-κB, TNF-α, and COX-2 was reduced, which down-regulates the production of pro-inflammatory cytokines by GPE (86). Similarly, cocoa (anthocyanidins/anthocyanins) supplementation (204) decreased MDA, increased SOD, CAT, GPx, and GRx, and reduced iNOS and COX-2 gene expression in murine colitis. Moreover, cocoa is able to stimulate Nrf-2 transcription factor-activated expression of NQO1 and UDP-GT to reduce OS. Cocoa supplementation can also lower CD68⁺ neutrophils, MPO, TNF-α, IL-1β and IL-17 and suppress STAT-3 activation in colitic tissues (204) ( Supplementary Table 1 ).

One randomized, placebo-controlled trial involving healthy humans found that eating anthocyanins-rich, purple-fleshed potatoes for six weeks reduced the levels of inflammatory markers like IL-6 and C-reactive protein (CRP) and the oxidative DNA-damage marker 8-hydroxydeoxyguanosine (8-HdG) (205). In another study, patients with mild to moderate UC were given an anthocyanin-rich bilberry preparation for six weeks and showed improvements in endoscopic Mayo score, histologic Riley index, and fecal calprotectin levels for intestinal inflammation (206).

Silymarin (SM), an extract from milk thistle (Silybum marianum), has been shown to have anti-inflammatory and antioxidant properties. Silymarin decreases inflammation by inhibiting NF-κB pathways and by optimizing the redox balance in the cell through activating AOEs and non-enzymatic antioxidants via Nrf2 activation (207). Studies show that SM increases the total antioxidant capacity of colonic tissue to reduce LPx levels, neutrophilic infiltration and pro-inflammatory cytokine production in TNBS-induced colitic rats. Also, treatment with SM in TNBS-colitic rodents dramatically decreased colonic NF-κB activity, levels of IL-1β, TNF-α, TBARS and MPO activity (113) ( Supplementary Table 1 ). In one randomized, double-blind, placebo-controlled clinical trial, 35/38 UC patients administered SM for 6 months achieved remission. Moreover, remission was accompanied by improved patient biochemical parameters such as decreased erythrocyte sedimentation rates, increased hemoglobin levels, and decreased DAI scores (208). However, the bioavailability of oral SM appears to vary widely between species and is impacted by preparation methods (209–211). Thus, care should be taken when designing experimental trials and extrapolating results between species and preparations.

Essential oils from Thymus, Origanum, and Lippia species are rich in thymol (2-isopropyl-5-methylphenol), a monoterpene phenol derivative of cymene (212). Thymol has demonstrated a wide range of biological and pharmacological activities, such as anti-inflammatory, antioxidant, anti-tumor, and antimicrobial effects (213). Thymol exhibits gastroprotective effects on both acute and chronic ulcer models by modulating the enhancement of mucus production, prostaglandin synthesis, and activation of ATP-sensitive K(+) channels (212). Thymol mitigates the reduction of trans-epithelial electrical resistance (TEER) in a porcine IPEC-J2 monolayer cell model stimulated with LPS by increasing ZO-1 and actin expression (118). In the DSS-induced murine colitis model, thymol mitigates intestinal damage induced by DSS by up-regulating the expression of tight junction protein claudin-3 (119). Similarly, thymol enhances the tight junction integrity and induces up-regulation of cyclooxygenase-1 (COX1) activity in Caco-2 cells (115).

Along with improving barrier function, thymol can decrease the production of ROS and the expression of pro-inflammatory cytokines following stimulation with LPS (118). Thymol exhibits the ability to attenuate increased MPO and MDA levels induced by LPS, as well as the expression of NF-κB, in a murine model of acute lung injury (214) and in colonic homogenates in murine colitis (215). Thymol exhibits inhibitory effects on the expression of TLR4 and the activation of NF-κB signaling in mice treated with acetic acid to induce colitis (117, 120). Thymol has been found to exhibit inhibitory effects on p38 phosphorylation, and it disrupts the activation of the MAPK signaling pathway, thereby contributing to the maintenance of immune homeostasis (216). Moreover, thymol exhibits inhibitory effects on the activation of p-p38, p-JNK, and p-ERK induced by LPS in RAW264.7 cells (116). Consequently, thymol effectively suppresses the production of various inflammatory cytokines such as NO, IL-6, TNF-α and COX-2 (116), thus exhibiting the ability to attenuate the inflammatory response through the inhibition of MAPK signaling pathway. Similarly, thymol had the potential to mitigate inflammatory responses by regulating the expression of JNK, AP-1, STAT-3, and nuclear factors of activated T-cells (NFATs) in LPS-stimulated J774.1 mouse macrophages (117).

Berberine, an isoquinoline alkaloid from Berberis aristata, has been used for decades to treat intestinal parasites and enteropathogenic diarrhea due to its bactericidal activity, its ability to inhibit protozoan growth, and also to inhibit enterotoxin-induced intestinal electrolyte secretion (217–219). Several in vivo studies confirm its anti-inflammatory role in decreasing the expression of IL-1β, TNF-α, iNOS, ICAM-1, IL-6, and NF-κB activation (220) ( Supplementary Table 1 ). Berberine reduces damage, inflammation scores, MPO activity, and colon shortening caused by oral DSS ingestion. Moreover, berberine has been shown to decrease levels of the pro-inflammatory cytokines IFN-γ, TNF-α, KC (keratinocyte chemoattractant or CXCL1), and IL-17 and to maintain colon epithelial barrier function in DSS-treated mice. Additionally, berberine enhanced apoptosis of colonic macrophages and decreased proinflammatory cytokine production in colonic macrophages and epithelial cells of DSS-treated mice. Berberine suppresses Src activation and TLR4-mediated cell motility in LPS-stimulated macrophages (121). Berberine also inhibits the activation of MAPK and NF-κB signaling pathways that stimulate proinflammatory cytokine production in both colonic macrophages and epithelial cells from DSS-treated mice (122). Multiple cellular kinases and signaling pathways, including AMPK, MAPKs, and Nrf2 and NF-κB pathways, are involved in berberine’s antioxidant and anti-inflammatory activities (221). By suppressing the expression of NADPH oxidase, a key enzyme in the generation of ROS in cells, berberine can mitigate OS (222). Superoxide anion production in LPS-stimulated macrophages was suppressed, while SOD activity normally was restored following berberine treatment. Since it can suppress gp91phox (a plasma membrane subunit of NADPH oxidase) expression and boost SOD activity, berberine is able to restore cellular redox activity (222) ( Supplementary Table 1 ). In this instance, it is possible that berberine enhances SOD expression through the silent mating type information regulation 2 homolog 1 (SIRT1)/Forkhead Box Class O (FOXO) pathway (221). In other experiments, berberine has been shown to directly bind to PLA2G4A and inhibit the MAPK/JNK signaling pathway to suppress PLA2G4A activity in murine colitis (223). A double-blind placebo-controlled phase I trial (123) demonstrated that berberine reduced colonic tissue inflammation (Geboes score) (224) in mesalamine-treated UC patients. However, it had no effect on inflammatory biomarkers in other tissues or blood (123).

Tamarind xyloglucan (TXG), a nanofiber extracted from tamarind, is a novel antioxidant that prevents DSS-induced colitis in mice (124, 125). TXG protects the colon by reducing the total inflammatory index, infiltration of inflammatory cells, submucosal edema, goblet cell loss, epithelial erosion, granulation tissue, epithelial hyperplasia, and crypt irregularity, abscesses and loss (124, 125). While TXG reduces inflammation by reducing TNF-α and increasing anti-inflammatory IL-10, it reduces OS by lowering levels of MDA, superoxide anion production, and the expression of iNOS, NOX, COX-2, and p47 (125) ( Supplementary Table 1 ).

Sulforaphane, found in cruciferous vegetables, contains a wide range of antibacterial, antioxidant, anti-inflammatory, and immunomodulatory properties (225, 226). Treatment of rats with colitis using sulforaphane reduces NO and MDA levels, accompanied by increased GPx and reduced glutathione levels, demonstrating its therapeutic antioxidant properties (8). Treatment with sulforaphane increases the levels of Nrf2 and HO-1 (8) ( Supplementary Table 1 ). It has been observed that HO-1, an antioxidant defense protein downstream of Nrf-2, prevents oxidative damage to colonic tissue (99). Sulforaphane possesses anti-inflammatory characteristics by decreasing TNF-α and IL-6 levels, inhibiting COX-2 expression, TLR4 oligomerization, TLR4/MyD88 pathway and blocking the degradation of IL-1R-associated kinase-1, NF-κB, and IFN regulatory factor 3 activation (227, 228).

Flaxseed oil is an herbal product with a high α-linolenic acid content, and it has been shown to reduce colonic damage in DSS-induced colitis by modulating inflammatory factors, oxidative state, and the cecal microbiota imbalances. DSS-colitic rat colon showed low SOD activity and GSH levels, increased MPO activity and MDA levels, and flaxseed oil dose-dependently alleviated this condition. Compared to the DSS-treated group, flaxseed oil treatment for six weeks raised SOD activity and GSH levels while decreasing MDA levels and MPO activity (127) ( Supplementary Table 1 ). A metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid (HYA), inhibits TNF-α expression and DSS-induced alterations in the expression of TJs such as occludin, zonula occludens-1, and myosin light chain kinase. The metabolite HYA partially restores the integrity of the intestinal epithelial barrier via the GPR40-MEK-ERK pathway, as reported in human Caco-2 cells and the murine DSS-colitis model (126).

Ginger rhizomes, a rich source of many active compounds, including gingerols, shogaols, gingediols, zingerone, dehydrozingerone, gingerinone, and diarylheptanoids, have a wide range of anti-inflammatory, analgesic, antioxidant, and anti-cancer effects (129, 151, 229). S-[6]-gingerol inhibits the expression of the inflammatory mediators IL-6, IL-8, and serum amyloid A1 (SAA1) in cytokine-stimulated human HuH7 hepatocyte cells by inhibiting the NF-κB/COX-2 pathway to reduce OS (129). Concentration-dependent inhibition of LPS-induced IL-1β, IL-6, TNF-α and PGE2 levels was demonstrated with 6-shogaol, the most bioactive component of ginger (230). 6-Shogaol also reduces the phosphorylation and nuclear translocation of NF-κB p65, thus preventing LPS-induced NF-κB activation. In LPS-induced murine RAW 264.7 macrophages, 6-shogaol was reported to inhibit protein and mRNA expression of iNOS and COX-2 (128). By inhibiting the phosphorylation of inhibitor κB (IκB)α and p65 and the subsequent degradation of IκBα, 6-shogaol decreased the LPS-induced activity of NF-κB. PI3K/Akt and extracellular signal-regulated kinase 1/2 activation by LPS is also blocked by 6-shogaol, although the p38MAPK activation is not (128). Since TLR4 dimerization mediated by LPS is necessary for the activation of downstream signaling pathways, including NF-κB, 6-shogaol blocks this process and prevents NF-κB activation (231). Also, 6-shogaol can block TLR-mediated signaling pathways directly at the receptor (231). In LPS-induced macrophages, 6-shogaol suppresses the MyD88-dependent signaling pathway by inhibiting IκB kinase activity and TRIF-dependent signaling pathways that target TBK1 (232). Compounds extracted from ginger were tested for their ability to stimulate phagocytosis and suppress nitric oxide generation in the RAW 264.7 cell line induced by LPS (229). Significant reductions in both LPS-induced nitric oxide production and inducible nitric oxide synthase expression were observed when 6-shogaol, 1-dehydro-10-gingerdione, and 10-gingerdione were applied (229). Macrophages are essential components of the immune system as they are responsible for the elimination of necrotic cells. This function is critical as it prevents the release of harmful contents from these cells, thereby minimizing a proinflammatory response (233). RAW 264.7 cells treated with 1-dehydro-10-gingerdione (1D10G) showed increased phagocytic activity similar to stimulation by LPS. Also, RAW 264.7 cells treated with 6-gingerol, 8-gingerol, 10-gingerol, 6-paradol, 10-gingerdione, 1,7-bis-(4’ hydroxyl-3’ methoxyphenyl)-5-methoxyhepthan-3-one, and methoxy-10-gingerol exhibited increases in phagocytic activity (229). 1D10G directly decreased the catalytic activity of cell-free IκB kinase β (IKKβ) in RAW 264.7 macrophages activated with the TLR4 agonist LPS. In LPS-activated macrophages, 1D10G inhibited TLR4-mediated expression of TNF-α, NF-κB, IL-1β, IRF3, IFN-β and IP-10 (234). Furthermore, in macrophages triggered by the TLR agonists LPS or TNF-α, D10G irreversibly blocks cytoplasmic IKKβ-catalysed IκBα phosphorylation and IKKβ vector elicited NF-κB transcriptional activity to minimize inflammatory signals (235). Substitution of Cys (179) with Ala in the activation loop of IKKβ abrogates these effects suggesting a direct interaction site of D10G. Lastly, D10G reduced NF-κB activation in LPS-stimulated macrophages and decreased the expression of iNOS, COX-2, and IL-6 (235).

In mice with DSS-induced colitis, ginger alleviates the pathological lesions and reduces the expression of IL-6 and iNOS (131). This study also showed that ginger has an anti-inflammatory effect like that of the anti-inflammatory medication sulfasalazine (SASP), reducing DAI and preventing further weight loss (131). Ginger reduces IBD activity by targeting IL-17, IFN-γ, and TNF-α, while increasing the anti-inflammatory cytokines IL-10, IL-22, and TGF-β (236) ( Supplementary Table 1 ).

Ginger extract exhibited the antioxidant effects in IL-1β-mediated OS in human C28I2 chondrocyte cells by stimulating the expression of several AOEs, decreasing IL-1β-induced ROS production, LPx, and by reducing apoptosis (Bax/Bcl-2 ratio, and caspase-3 activity) (130) ( Supplementary Table 1 ). Patients with active mild to moderate UC who ingested 2000 mg/day of dried ginger powder in a randomized, placebo-controlled clinical trial had lowered MDA without affecting serum total antioxidant capacity (132).

Estrogens have been shown to increase AOEs by upregulating their expression (34, 147, 245). The antioxidant impact of estrogen is thought to be the principal method by which this hormone protects various tissues from oxidative damage (246–248). It has been postulated that sex hormones such as estrogen, progesterone, and androgen contribute to the pathophysiology of sexual dimorphism in human IBD (249). These control the behavior of many different types of immune cells, including lymphocytes, macrophages, granulocytes, and mast cells. Multiple clinical features of the disease, including intestinal barrier disintegration and mucosal immune activation, may be modulated by sex hormones, as shown in both clinical and experimental models (249). There is growing interest in the potential regulation of the intestinal microbiota by sex hormones. Estrogens have an effect on the microbicidal activity that is carried out by MPO in polymorphonuclear leukocytes (250). In CD, the G protein-coupled estrogen receptor (GPER) appears to be a powerful therapeutic target in maintaining remission because it promotes anti-inflammatory effects. Reducing mortality, improving macroscopic and microscopic scores, and lowering CRP levels were all achieved with GPER activation in a TNBS-induced CD murine model (251). Immunohistochemistry verified that estrogen signaling inhibits intestinal inflammation. Genes involved in signal transduction and immunological response, as well as the expression of certain miRNAs (miR-145, miR-148-5p, and miR-592), were shown to be altered in tandem with GPER activation, as was the extracellular-signal-regulated kinase (ERK) signaling pathway (251).

Increased expression of tight junction proteins was a mechanism by which progesterone and estrogen facilitated wound healing and epithelial barrier function in intestinal epithelial cells, as reported using 2D cell lines and IBD patient-derived inflammatory organoid models (252). These sex hormones also inhibited the generation of pro-inflammatory cytokines in intestinal epithelial models and greatly decreased endoplasmic reticulum (ER)-stress. Pregnancy hormones like estrogen and progesterone have been shown to have beneficial effects on disease activity by positively modulating the intestinal epithelial lining (252).

Glucagon decreased iNOS expression and plasma levels of nitrite/nitrate in LPS-treated rats (253). Glucagon is responsible for inducing the antioxidant response by increasing GSH levels and reducing both protein carbonyl and 3-nitrotyrosine (254) or by upregulating AOEs as indicated by high levels of CAT expression in the α cells of diabetic vs. non-diabetic murine models (255).

Glucagon-like peptide-1 (GLP-1) and GLP-2 are important enterohormones that mediate local and systemic effects (gut-brain-periphery axis), contribute to glucose homeostasis, and modulate GI functions such as the intestinal absorption of lipids and antioxidant defense (256). The effects of these molecules critically depend upon nitric oxide synthase (NOS) in the enteric nervous system (ENS) and the intestinal microbiome (257).

Activation of the GLP-1 receptor has anti-inflammatory, antioxidant, and anti-apoptotic effects, which include a reduction of the pro-inflammatory actions of advanced glycation end products (258) and of the accumulation of intracellular ROS, the release of NO, and GPx and SOD production (259). Moreover, it has been proposed that GLP-1 plays a critical role in the production of NO (260), and intestinal GLP-1 production can be increased by the ingestion of grape-seed procyanidin extract (GSPE), resveratrol, and curcumin (261–264). GSPE also increases intestinal peptide YY (PYY) and varied cholecystokinin (CCK) secretion, which modulates food intake (261, 265, 266).

The enterotrophic peptide hormone glucagon-like peptide 2 (GLP-2) was shown to abrogate OS and improve intestinal antioxidant capacity by reducing LPS-induced increases in intestinal IL-1β and oxidized glutathione levels (267) and increasing intestinal SOD activity and reduced-glutathione levels (268, 269) ( Supplementary Table 1 ). Additionally, GLP-2 has a protective effect on the function of the intestinal barrier (270), intestinal IgA production (270), NO-regulated intestinal perfusion (271), and stabilizes the expression and function of intestinal xenobiotic transporters (267). Because intestinal barrier function is critically impaired in IBD and CIE, complex neutraceuticals that provide antioxidants and can enhance intestinal GLP-2 secretion, and thus support enterocyte tight junctions and intestinal barrier integrity (e.g., berberine, soy flavonoids, pre-/probiotics, soluble fiber, glutamine), may be useful to restore and maintain intestinal health (272).

Given the effects of GLP-1 and GLP-2 in maintaining intestinal homeostasis, including cross-talk with the immune and central nervous systems (273, 274), they appear to present potentially beneficial treatment targets in IBD and CIE.

Reduced levels of serum motilin and gastrin, together with lower pro-inflammatory cytokines and reduced tissue NF-κB and COX-2 levels, and increased serum somatostatin, vasoactive intestinal peptide, and tissue SOD, NO, and MDA levels were associated with genistein- and daidzein-rich fermented soy (shuidouchi) in an experimental animal model (275). Similar antioxidative, anti-inflammatory, and enterohormone signature-modulating effects have been demonstrated in experimental mice receiving unsaturated fatty acid-rich silkworm pupa oil (276).

The presence of glucocorticoid receptors in endothelial and inflammatory cells (240–243), as well as increased concentrations of circulating glucocorticoids at the onset of inflammation downregulating inflammatory responses, is proof that glucocorticoids are modulators of inflammatory responses (243, 277). Adrenalectomized animals also showed greater microvascular responses to inflammatory mediators and cell migration to inflamed regions (243, 278). Glucocorticoids have powerful anti-inflammatory and immunosuppressive effects, such as lowering cytokine production or activity, reducing microvascular responses to inflammatory mediators, preventing leukocyte accumulation at inflamed sites, impeding phagocytic functions and microbicidal capacity of polymorphonuclear leukocytes, preventing the recruitment of mononuclear phagocytes to injured areas, and interfering with immune function (243, 278–280).

Thyroid hormones are associated with the oxidative and antioxidative status of an organism because of their role in regulating oxidative metabolism and in the formation of ROS (34, 39, 50–55, 281). Rats with thyroid dysfunction, produced by hormone injection or thyroidectomy, were evaluated for their ability to respond to noxious stimuli in an effort to determine the processes through which thyroid gland activity can influence the development of inflammatory reactions (243, 282, 283). Rats with hypothyroidism exhibit typical inflammatory responses, whereas animals with a sustained excess of circulating thyroid hormones exhibit consistently suppressed inflammatory responses (282, 283).

A study was conducted to investigate the impact of administering Corticotropin releasing hormone (CRH) to induce psychosocial stress in DSS-treated colitic mice, specifically by examining the potential enhancement of autophagy in intestinal macrophages. The inflammatory challenges associated with IBD led to increased autophagy in both intestinal macrophages and murine bone marrow-derived macrophages, and these effects were further increased by CRH (284).

IBD is distinguished by symptoms such as reduced appetite, inadequate nutrition, changes in body composition, and the enlargement of mesenteric white adipose tissue (mWAT) (285, 286). Adipokines, namely leptin, adiponectin, and resistin, play a significant role in anorexia, malnutrition, changes in body composition, and hypertrophy of mWAT (285, 286). Studies have demonstrated that there is an increased expression of leptin, adiponectin, and resistin in mWAT in individuals diagnosed with CD.

Previous research conducted on animals has indicated that the presence of peroxisome proliferator-activated receptor γ (PPAR γ) in the intestinal epithelial cells, macrophages, and T cells of mice with experimental IBD demonstrates immunoregulatory effects and potentially plays a role in the prevention of intestinal inflammation (303, 304). The administration of the gamma subtype of peroxisome proliferator-activated receptors (PPARγ) ligands has been demonstrated to reduce the production of inflammatory cytokines, such as IL-1β and TNF-α, as well as inhibit the proliferation of inflammatory cells and the expression of specific adhesion molecules (305). The thiazolidinedione (TZD) antidiabetic medications for the treatment of type 2 diabetes function as ligands for the gamma subtype of PPARs. Several trials with TZD in the context of IBD have yielded intriguing outcomes (237, 306, 307). In a multicenter randomized, double-blind, placebo-controlled clinical trial, the effectiveness of rosiglitazone in managing UC with mild to moderate activity has been demonstrated (306). Here, 17% of patients who received treatment with rosiglitazone were able to achieve remission. Significant clinical improvement was observed in as short as 4 weeks, with enhanced quality of life by the 8th week (306). In another study, it was determined that TZD does not confer any discernible benefits in comparison to alternative oral antidiabetic drugs with regard to the prevention of UC-related flares. Nevertheless, the utilization of TZD may diminish the probability of experiencing more severe disease flares that necessitate oral steroid treatment (307).

Melatonin (N-acetyl-5-methoxytryptamine) has several unique scavenging effects making it an exceptionally potent direct free radical scavenger and multifunctional antioxidant (34, 308, 309). Melatonin is an electron-rich molecule that can react with free radicals to produce stable compounds that are excreted in the urine (310). Melatonin is frequently referred to as a suicidal or terminal antioxidant because it eliminates free electrons from the system throughout its chemical rearrangement, and each of the rearrangement products is again a potent antioxidant. Melatonin acts as an indirect antioxidant, increasing AOEs, including SOD, CAT, GPx, GR (311, 312), and glucose-6-phosphate dehydrogenase (G6PD) (313). Increased intracellular levels of the antioxidant GSH are generated as a consequence of melatonin stimulating γ-glutamyl cysteine synthetase (the rate-limiting enzyme in GSH formation) and GR (the enzyme converting GSSG to GSH) (314, 315). Melatonin also potentiates the function of the mitochondrial electron transport chain, which reduces free radical generation and electron leakage (316). Melatonin inhibits the production of free radicals by acting as a negative modulator of several pro-oxidant enzymes including 5-lipoxygenase, 12-lipoxygenase, and NO synthase (309). It also prevents mitochondrial damage and reduces NF-κB signaling, suggesting a repair mechanism for intestinal injury caused by OS (317). Decreased levels of hydroxyl radical (HO•), peroxynitrite (ONOO^-), RO₂ ^•, and singlet oxygen, and decreased expression of COX-2 and iNOS and NF-kB activation are all antioxidant effects of melatonin (318, 319), pointing to the possibility that melatonin is beneficial in UC by lowering inflammation and regulating OS. Pineal-derived melatonin and de novo synthesis in the GI tract both produce melatonin which helps regulate gut immunity and intestinal barrier integrity. Due to its antiapoptotic action and ability to decrease bacterial translocation across epithelia, melatonin can limit mucosal damage (73). Animal studies have demonstrated that melatonin treatment reduces inflammation by blocking the production of IL-10, IFN-γ, TNF-α, IL-6, and NO^• (320) ( Supplementary Table 1 ). In murine colitis, melatonin reduces the generation of ROS and reactive nitrogen species (RNS), characterized by lowering colonic MDA levels and MPO activity and improved antioxidant defenses with increased GSH and SOD levels in the colon (134).

By modulating autophagy and Nrf2 signaling pathways, melatonin slows the progression of colitis-associated colon cancer in mice. In this colon cancer model, melatonin decreased the levels of inflammatory markers IL-6, IL-17, TNF-α, NF-κB, COX-2 and STAT3, as well as reduced DNA damage and OS indicated by reduced TBARS and increased GSH levels ( Supplementary Table 1 ). The decrease in the expression of Beclin-1 and the LC3-II/LC3-I ratio, along with an increased expression of p62, indicate melatonin-inhibited cancer-associated autophagy. These results are like those showing upregulation of Nrf2 and AOEs NQO-1 and HO-1 in melatonin-treated mice with colon cancer (321). Another study investigated the role of oral melatonin therapy on OS in dogs before and after ovariohysterectomy (OHE) (135). The levels of SOD, GPx, and CAT were increased, and MDA decreased in ovariohysterectomized dogs ( Supplementary Table 1 ) that received melatonin compared to those of the control group. These preliminary findings suggest that melatonin administration may reduce OS induced by OHE in dogs. Adjuvant melatonin treatment may aid in maintaining remission in patients with UC (136). In this clinical trial, patients receiving melatonin adjuvant treatment-maintained remission (e.g., lower disease activity scores and inflammatory biomarkers such as CRP levels with increased hemoglobin concentrations) over 12 months of observation (136).