Electronic databases including PubMed/MEDLINE, Web of Science Core Collection, Embase, and Scopus were searched for publications from January 2000 to June 2024. Additional references were retrieved by manually screening the bibliographies of relevant reviews and primary articles.

A combination of Medical Subject Headings (MeSH) and free-text terms was used to capture three major concepts:

Disease: “liver fibrosis” OR “hepatic fibrosis” OR “hepatic stellate cell*” OR “liver cirrhosis”.

Modification: “post-translational modification” OR “PTM” OR “phosphorylation” OR “acetylation” OR “ubiquitination” OR “SUMOylation” OR “methylation” OR “succinylation” OR “malonylation” OR “glycosylation”.

Natural products: natural product” OR “phytochemical” OR “herbal compound*” OR “traditional medicine” OR names of key classes (“flavonoid” OR “saponin” OR “alkaloid” OR “polyphenol”).

The three groups were combined using AND (e.g., liver fibrosis AND post-translational modification AND natural product). Searches were adapted for the syntax of each database.

Inclusion: i. original experimental or clinical studies evaluating any PTM in the context of liver fibrosis and reporting modulation by a natural product or plant-derived compound; ii. in vitro (e.g., hepatic stellate cell activation), in vivo (animal models), or human clinical studies; iii. Articles in English with full text available.

Exclusion: reviews, editorials, conference abstracts without primary data; studies on liver cancer or metabolic liver disease lacking fibrosis/PTM endpoints; reports of genetic polymorphisms without PTM assessment.

Two independent reviewers screened titles and abstracts for relevance. Full texts of potentially eligible studies were retrieved for detailed assessment. Disagreements were resolved through discussion or consultation with a third reviewer.

For each included study, we extracted: Type of natural product or compound (e.g., flavonoid, saponin, alkaloid); PTM type (phosphorylation, acetylation, ubiquitination, SUMOylation, methylation, succinylation, malonylation, etc.); Target proteins/enzymes (writers, erasers, readers) and signaling pathways.

Protein phosphorylation is a ubiquitous, deeply studied PTM that governs fundamental biological programs—including cell growth, differentiation, apoptosis, gene expression, and signal transduction (Bilbrough et al., 2022). In liver fibrosis, phosphorylation is tightly coupled to disease initiation and progression, largely through effects on ECM deposition and HSCs activation (Okuno et al., 2001). HSCs release and activate transforming growth factor-β1 (TGF-β1) and its intracellular Smad mediators, both of which are pivotal for driving collagen gene transcription (Inagaki et al., 2005; Okuno et al., 2001). TGF-β ligands also promote ECM accumulation and become sequestered within the matrix, thereby amplifying profibrotic signaling (Walton et al., 2017). Following injury, elevated TGF-β in the fibrotic niche activates SMAD2/3 via TGF-β receptors 1/2 (TGFBR1/2) (Budi et al., 2021). The phosphorylated SMAD2/3 complex then translocates to the nucleus to directly induce downstream targets (e.g., COL1A1, COL3A1, COL5A2), initiating ECM gene expression and advancing fibrogenesis (Walton et al., 2017).

Additional upstream cues converge on Smad signaling through canonical kinase cascades. For example, lipopolysaccharide (LPS) induces SMAD2 phosphorylation in HSC-T6 cells via PI3K/AKT and MAPK pathways, promoting ECM production and myofibroblastic transition (Kao et al., 2017). Renin/prorenin signaling increases prorenin receptor (PRR) expression and TGF-β1 production in LX-2 cells; PRR knockdown deactivates HSCs, reduces TGF-β1, and diminishes SMAD3 phosphorylation, thereby alleviating fibrotic responses (Hsieh et al., 2021).

Phosphorylation also regulates hepatocyte fate programs relevant to fibrosis. During hepatocyte apoptosis, caspase activity is modulated by phosphorylation—phospho-caspase-9, for instance, promotes apoptosis—typically accompanied by heightened inflammation and secondary HSC activation (Cardone et al., 1998; Cui et al., 2020; Riedl and Salvesen, 2007). Autophagy, another phosphorylation-tuned process, fuels HSC activation by mobilizing energy from retinoid-rich lipid droplets; its pharmacologic inhibition suppresses HSC activation and mitigates fibrosis in vitro and in vivo (Hernandez-Gea et al., 2012; Thoen et al., 2011). Mechanistically, Sestrin2 may restrain HSC activation by enhancing AMPK phosphorylation and dampening mTOR signaling (Hu Y. J. et al., 2024), whereas the BET inhibitor JQ-1 improves fibrosis by limiting HSC activation and proliferation through reduced JAK2/STAT3 phosphorylation (Song et al., 2023a).

In sum, phosphorylation exerts broad, stage-spanning control over fibrogenesis by modulating key signaling axes (TGF-β/Smad, MAPK, NF-κB, PI3K/AKT) and by shaping HSC activation, proliferation, apoptosis, and autophagy (Dooley and ten Dijke, 2012; Hernandez-Gea and Friedman, 2011). Deeper delineation of these phosphorylation-dependent mechanisms—and their node-specific roles—will aid target identification and inform the rational development of antifibrotic therapies (Figure 2).

Altered protein glycosylation is a key driver of hepatic fibrogenesis (Eichler, 2019). Glycosylation occurs co- and post-translationally as nascent proteins enter the endoplasmic reticulum, where enzymes install monosaccharides that are subsequently elaborated into oligosaccharide chains in a site-specific manner (Hebert et al., 2005). Two major classes predominate: N-glycosylation on the amide nitrogen of asparagine (Asn) and O-glycosylation on the hydroxyl groups of serine/threonine (Ser/Thr) (Kornfeld, 1998). In liver fibrosis, glycosylation shapes both matrix composition and profibrotic signaling. For example, glycan-dependent Galectin-1/NRP1 interactions potentiate TGF-β and PDGF-like pathways to activate HSCs, while the collagen O-galactosyltransferase GLT25D1 enhances collagen O-glycosylation and stabilizes fibrotic matrix architecture (Wang S. et al., 2023; Wu et al., 2017).

Glycosylation participates directly in ECM deposition by modifying collagens and thereby influencing their stability and susceptibility to degradation. It also regulates HSC activation (Caon et al., 2021; Ogawa and Okajima, 2019; Rockey et al., 2015). A particularly important cytosolic modification is O-GlcNAcylation, which decorates nuclear, cytoplasmic, and mitochondrial proteins. O-GlcNAc transferase (OGT) installs, and O-GlcNAcase (OGA) removes, this modification (Hahne et al., 2013; Ma and Hart, 2014; Ruan et al., 2012). In myofibroblast-like HSCs (MF-HSCs), global O-GlcNAcylation rises in parallel with α-SMA expression; similar increases occur in CCl₄-induced liver injury in mice. Pharmacologic OGT inhibition (e.g., OSMI-1) lowers O-GlcNAcylation and downregulates collagen genes (Col1a1, Col1a2, Col3a1, Col5a2), indicating that O-GlcNAcylation is required for robust expression of fibrosis-related ECM genes and is a determinant of myofibroblast activation (Harvey and Chan, 2018; Housley et al., 2009; Wang et al., 2022).

Glycan-based biomarkers also mirror disease activity. Mac-2 binding protein glycoforms (M2BPGi)—a glycosylated variant of M2BP produced predominantly by HSCs—serve as serum indicators of liver fibrosis. M2BPGi engages Mac-2 on Kupffer cells, which in turn promotes HSC activation and elevates α-SMA expression (Bekki et al., 2017; Gantumur et al., 2021).

Glycosylation intersects with oxidative stress through advanced glycation end products (AGEs), non-enzymatic adducts formed between reducing sugars and proteins, lipids, or nucleic acids. AGE accumulation augments oxidative stress and activates pro-fibrotic, pro-inflammatory signaling via the receptor for AGEs (RAGE) (Hollenbach, 2017; Hyogo and Yamagishi, 2008). In vitro, glyceraldehyde-derived AGEs increase ROS, induce chronic injury signals, and drive HSC activation (Iwamoto et al., 2008). Consistently, RAGE expression is upregulated during HSC transdifferentiation to myofibroblasts, reinforcing profibrotic pathways (Fehrenbach et al., 2001).

Collectively, these findings position glycosylation—enzymatic glycans and non-enzymatic AGEs alike—as a central regulatory layer in hepatic fibrogenesis. Targeting specific glycosylation enzymes, lectin-mediated interactions, or AGE–RAGE signaling may yield promising antifibrotic strategies (Figure 3).

Protein acetylation—installed by acetyltransferases and removed by deacetylases—adds acetyl groups to specific residues, reshaping chromatin architecture, transcription, and signal transduction, and thereby influencing gene expression, protein function, cellular metabolism, and cell-cycle progression (Arnesen, 2011; Verdin and Ott, 2015; Xue et al., 2022). In hepatic fibrosis, epigenetic dysregulation driven by histone modifications is a major determinant of disease progression (Tessarz and Kouzarides, 2014; Tsukamoto et al., 2011). Activation and transdifferentiation of HSCs require broad epigenetic reprogramming that silences adipogenic programs while inducing genes supporting the myofibroblast-like phenotype (Barcena-Varela et al., 2019; Mann and Mann, 2013; Moran-Salvador and Mann, 2017).

A growing body of evidence implicates acetylation in HSC activation and fibrogenesis. Acetylation of C/EBP-α at K298, K302, and K326 enhances its interaction with Beclin-1 and promotes autophagy in activated HSCs (Hou et al., 2021). Pharmacologic inhibition of histone deacetylases with trichostatin A (TSA) alleviates CCl₄-induced fibrosis, in part by increasing C/EBP-α acetylation and blocking its ubiquitin-dependent degradation (Ding et al., 2018). More broadly, hyperacetylation at promoters/enhancers of profibrotic genes associates with elevated TGF-β, collagen, and α-SMA expression. Acetylation also augments NF-κB activity, increasing TNF-α and IL-6 production that further activates HSCs; conversely, HDAC-mediated deacetylation dampens NF-κB signaling and mitigates inflammatory drive and fibrogenesis (Jimenez-Uribe et al., 2021; Joanna et al., 2009; Park et al., 2014). In LX-2 cells, nicotinamide riboside (NR) restrains TGF-β–induced activation by modulating acetylation within the Smad pathway and reduces CCl₄-induced fibrosis in vivo (Jiang et al., 2019).

Acetylation also directly tunes mitochondrial function, influencing cellular energetics and oxidative stress (Anderson and Hirschey, 2012). The mitochondrial deacetylase SIRT3 deacetylates key antioxidant enzymes, attenuating oxidative stress and slowing fibrotic progression (Ning et al., 2024). Additionally, acetylation of apoptosis regulators within the Bcl-2 family can shift cell-death propensity. Some studies suggest that acetylation may increase the activity of pro-apoptotic proteins, promoting the apoptosis of HSCs and limiting the extent of fibrosis (Ma et al., 2022; Zhang et al., 2022). Together, these findings position acetylation—as both a chromatin-level and protein-level switch—as a tractable axis for antifibrotic intervention (Figure 3).

Ubiquitination is a covalent modification in which a small ubiquitin protein is conjugated to target proteins through a cascade of enzymatic reactions (Dikic and Schulman, 2023). This process plays a central role in protein degradation, signal transduction, cell cycle control, DNA repair, immune responses, and other cellular activities (Popovic et al., 2014). It requires the coordinated action of three enzymes: the E1 ubiquitin-activating enzyme, which activates ubiquitin; the E2 ubiquitin-conjugating enzyme, which transfers activated ubiquitin; and the E3 ubiquitin ligase, which attaches ubiquitin to lysine residues of substrate proteins, thereby conferring specificity (Pickart, 2001). Ubiquitination can occur as monoubiquitination (attachment of a single ubiquitin molecule) or polyubiquitination (formation of ubiquitin chains), with the type of linkage determining the fate of the substrate protein (Nakamura, 2018).

Accumulating evidence highlights the pivotal role of ubiquitination in liver fibrosis, regulating signaling pathways, protein turnover, cell activation, and programmed cell death (Filali-Mouncef et al., 2022; Rao et al., 2022; Shu B. et al., 2021; Wu et al., 2023). Ubiquitin has been identified as a biomarker of nonalcoholic liver fibrosis, frequently detected at cell boundaries and within the fibrotic matrix (Lachiondo-Ortega et al., 2019). The deubiquitinating enzyme UCHL1 is markedly upregulated in human HSCs and in livers of patients with alcoholic liver disease. Pharmacologic inhibition of UCHL1 with LDN-57444 mitigates fibrosis progression in CCl₄-induced mouse models (Wilson et al., 2015). Similarly, the E3 ligase FBG1 degrades misfolded A1AT-Z mutants through the ubiquitin–proteasome system and autophagy, preventing their accumulation in the endoplasmic reticulum and attenuating fibrogenic stress (Wen et al., 2015).

Other ubiquitin-related mechanisms also contribute to fibrogenesis. Hepatocyte-specific deletion of the E3 ligase RNF5 exacerbates steatosis, inflammation, and fibrosis in dietary NASH models. Mechanistically, RNF5 binds HRD1 and promotes its K48/K33-linked ubiquitination, leading to proteasomal degradation; HRD1 knockdown reduces lipid accumulation and inflammatory signaling, underscoring the RNF5–HRD1 axis in hepatocyte injury and fibrosis (Yang et al., 2021). In HSCs, TGF-β signaling induces Ndfip1 expression, which recruits the E3 ligase Nedd4-2 to promote ubiquitination and degradation of TrkB. TrkB overexpression suppresses TGF-β/Smad signaling and limits HSC proliferation, suggesting that TrkB ubiquitination contributes to fibrosis progression (Song et al., 2023b). Moreover, Neuropilin-1 (NRP1) enhances HSC activation via TGF-β1, VEGFA, and PDGF-BB, while the deubiquitinase USP9X stabilizes NRP1. Thus, USP9X-mediated deubiquitination amplifies HSC activation, making the USP9X–NRP1 axis a promising therapeutic target (Zhao et al., 2023b).

Ubiquitination also intersects with hepatocyte injury and apoptosis. The transcription factor NRF2, a key antioxidant regulator, is degraded via ubiquitination by the CUL3–KEAP1 E3 ligase complex, a process dependent on neddylation (Zhang et al., 2004). Impaired neddylation disrupts NRF2 stability, induces mitochondrial dysfunction, and exacerbates oxidative stress, thereby promoting hepatocyte death and fibrosis (Xu et al., 2022). In addition, TRAF6 mediates K6-linked ubiquitination of apoptosis signal-regulating kinase 1 (ASK1), facilitating dissociation from thioredoxin and promoting ASK1 dimerization. This event activates the ASK1–JNK1/2–p38 cascade, stimulating pro-inflammatory and pro-fibrotic mediators that drive HSC activation and fibrogenesis (Wang et al., 2020b).

In summary, ubiquitination exerts multifaceted regulatory control over liver fibrosis by modulating HSC activation, ECM metabolism, inflammation, and apoptosis. Elucidating the precise ubiquitin-dependent mechanisms in fibrogenesis may reveal novel molecular targets and foster the development of innovative antifibrotic therapies (Figure 3).

Protein S-nitrosylation is a covalent NO-dependent modification that regulates cell signaling by altering protein–protein interactions, subcellular localization, stability, and reactivity (Zhao et al., 2021). In parallel, protein nitration—most commonly tyrosine nitration mediated by peroxynitrite formed from NO and superoxide—affects transcriptional control, DNA-damage responses, cell growth, differentiation, and apoptosis; dysregulation of these NO-linked processes contributes to diverse diseases (Fernando et al., 2019).

Extensive evidence implicates NO-mediated modifications in hepatic fibrogenesis. Svegliati-Baroni et al. showed that the exogenous NO donor S-nitroso-N-acetylpenicillamine (SNAP) suppresses HSC activation and proliferation by scavenging ROS, thereby limiting the onset of hepatic fibrosis and cirrhosis (Svegliati-Baroni et al., 2001). Within the space of Disse, liver sinusoidal endothelial cells (LSECs) release VEGF, which supports HSC proliferation and angiogenesis; under physiological conditions, VEGF-stimulated eNOS activity in LSECs generates NO that helps revert activated HSCs toward quiescence (Deleve et al., 2008). Consistently, eNOS-derived NO is generally protective, whereas iNOS-derived NO is linked to pathological nitrosative stress and disease progression (Iwakiri and Kim, 2015).

Nitrosative stress is elevated in obesity-related NASH and in models of chronic fructose exposure, as evidenced by increased CYP2E1, iNOS, and protein nitration, changes that associate with fibrotic remodeling (Cho et al., 2021). In HepG2 cells replicating HBV or expressing HBx, mitochondrial superoxide and peroxynitrite rise, leading to mtDNA damage, nitration of respiratory-chain complexes—especially complex I—and bioenergetic impairment; superoxide scavenging (Mito-Tempo) or iNOS inhibition prevents these lesions, implicating mitochondrial nitrosative damage in inflammation and profibrotic signaling (Loureiro et al., 2023). Heat-shock protein 90 (HSP90), highly expressed in hepatocytes, is a nitration target: in aged wild-type mice, HSP90 nitration accompanies oxidative DNA damage, increased mitochondrial nitrosative stress, and alterations in complexes III/IV, culminating in age-dependent steatosis, apoptosis, and fibrosis (Abdelmegeed et al., 2016).

Given the central role of NO-driven S-nitrosylation and nitration in liver fibrosis, therapeutic strategies that rebalance these pathways are promising: enhancing eNOS-derived cytoprotective NO, limiting iNOS-driven nitrosative stress, curbing peroxynitrite formation, and/or strengthening antioxidant defenses may attenuate fibrogenic progression (Figure 3).

Methylation is a major post-translational modification occurring predominantly on lysine and arginine residues of histone and non-histone proteins. By shaping chromatin architecture, gene expression, and intracellular signaling, it exerts wide-ranging control over cellular phenotypes; its dysregulation is closely linked hepatic HSCs activation and liver fibrosis (Mattei et al., 2022; Menezo et al., 2020).

Emerging evidence indicates that the methylation status of fibrotic regulators serves not only as a biomarker but also as a functional driver of disease progression (Yang et al., 2020). For example, PTEN antagonizes PI3K lipid signaling and thereby restrains PI3K/AKT and ERK pathways implicated in HSC activation (Kumar et al., 2018). In TGF-β–stimulated HSCs, the DNA methylation inhibitor 5-Aza sustains PTEN expression, attenuating HSC activation and alleviating fibrosis (Bian et al., 2013). In a CCl₄ model, osteopontin (Spp1) is markedly upregulated; hypomethylation of the Spp1 promoter enhances its transcription, activates PI3K/AKT, promotes profibrogenic mediators (including TGF-β), and increases type I collagen and α-SMA, thereby accelerating HSC activation and matrix remodeling. Persistent activation of this axis has also been implicated in the transition from fibrosis to hepatocarcinogenesis (Song et al., 2019).

DNA methyltransferases (DNMTs) further integrate methylation cues into fibrogenic programs. DNMT1—the maintenance methyltransferase—is elevated in human cirrhotic livers, murine fibrosis, and primary mouse HSCs; in human HSCs, TGF-β1 recruits DNMT1 to chromatin. Genetic DNMT1 knockdown or pharmacologic disruption of the G9a/DNMT1 complex with CM272 suppresses TGF-β1–driven fibrotic responses and mitigates fibrosis (Barcena-Varela et al., 2021). DNMT3b also contributes by repressing SUN2: during CCl₄-induced fibrosis, CpG hypermethylation coincides with low SUN2 expression. AAV9-mediated SUN2 overexpression reduces fibrotic markers in vivo, and SUN2 overexpression in TGF-β1–activated HSC-T6 cells dampens HSC activation (Chen et al., 2018).

Beyond DNA, RNA methylation intersects with fibrogenesis. Coordinated waves of 5-methylcytosine (5 mC, DNA) and N6-methyladenosine (m6A, RNA) modifications align with distinct phases of HSC activation (Luo H. et al., 2023). During initiation, promoter 5 mC hypermethylation at SOCS3 and PPARγ facilitates STAT3-dependent metabolic reprogramming and lipid loss. During maintenance, m6A hypermethylation of collagen transcripts enhances mRNA stability via YTHDF1, driving excessive ECM production (Feng et al., 2023).

The dynamic—and reversible—nature of methylation makes it an attractive therapeutic axis. Modulating methyltransferases/demethylases can reset profibrotic programs: DNA demethylating agents or histone demethylase inhibitors have been shown to restore more physiological methylation states at key loci (e.g., TGF-β1), reduce overexpression of profibrotic genes, and ameliorate fibrosis in animal models. Collectively, these findings position protein/DNA/RNA methylation as a convergent regulatory layer in hepatic fibrogenesis and a promising target space for antifibrotic drug development (Figure 3).

Flavonoids are widely distributed plant-derived compounds with multiple pharmacological properties, such as anti-inflammatory, antioxidant, anti-apoptotic, and lipid-regulating effects (Li et al., 2016; Pourcel et al., 2007; Serafini et al., 2010). They have been shown to ameliorate liver diseases, including acute liver injury and fatty liver (Blankson et al., 2000; Luo S. et al., 2023).

Recent studies demonstrate that flavonoids exert antifibrotic effects primarily through the regulation of PTMs, especially phosphorylation. For example, total flavonoids from Scabiosa comosa (TF-SC) selectively inhibit TGF-β1–induced Smad3 phosphorylation by blocking the TβRI–Smad3 interaction, thereby attenuating CCl₄-induced liver fibrosis and identifying TF-SC as a potential TGF-β1/Smad3 pathway inhibitor (Ma et al., 2018). Similarly, luteolin promotes HSC apoptosis by activating caspase-3 and upregulating p53, while downregulating bcl-2, cyclin E, and p-Cdk2. In vivo, luteolin alleviates fibrotic injury by suppressing PDGF- and TGF-β1-mediated AKT and Smad phosphorylation (Li et al., 2015). Naringin inhibits PI3K/AKT signaling, decreases fibronectin and TGF-β1 expression, and induces caspase-3–dependent apoptosis to mitigate fibrosis (El-Mihi et al., 2017). Myricetin suppresses TGF-β1–induced phosphorylation of Smad2, p38 MAPK, ERK, and AKT, and dose-dependently inhibits PDGF-BB–induced ERK/AKT activation. In CCl₄ models, myricetin reduces α-SMA expression and collagen deposition, indicating multitarget regulation of PTMs (Geng et al., 2017). Quercetin attenuates HSC activation by downregulating p38 MAPK phosphorylation and modulating the NF-κB/IκBα axis (Wang et al., 2017).

Other flavonoids demonstrate similar PTM-mediated mechanisms. Limonin blocks TGF-β–induced Smad2/3 phosphorylation and nuclear translocation, while enhancing Smad7 expression to suppress epithelial–mesenchymal transition (EMT) and HSC activation (Shu et al., 2022). Isoliquiritigenin inhibits STAT3 phosphorylation by targeting ANXA2 and the SPHK/S1P/IL-17 pathway, reversing HSC activation (Liu et al., 2023). Catechin-7-O-β-d-apiofuranoside (C7A) represses TGF-β1–induced STAT3 phosphorylation and downstream ECM gene expression, reducing fibrosis (Park et al., 2019). In addition, luteolin-7-diglucuronide (L7DG) has been identified as an inhibitor of protein tyrosine phosphatase 1B (PTP1B), which promotes AMPK phosphorylation and suppresses cell activation in TGF-β1–stimulated HSCs (Tang et al., 2024).

Beyond phosphorylation, other PTMs also play important roles in the anti-fibrotic mechanisms of flavonoids. Ampelopsin (Amp) has been shown to exert regulatory effects largely through deacetylation. Specifically, Amp downregulates collagen I, α-SMA, TIMP1, TGF-β1, and p-Smad3 expression, while promoting the upregulation of MMP9 and SIRT1, thereby inhibiting the sustained activation of HSCs. Importantly, SIRT1 activation is central to this process, as its inhibition reverses the protective effects of Amp. Moreover, Amp induces autophagy by upregulating LC3-II and Beclin-1, whereas the autophagy inhibitor 3-MA partially abrogates its anti-fibrotic effects (Ma et al., 2019). Physalin B enhances the acetylation of the transcription factor GLI1, preventing its interaction with the LAP2α/HDAC1 complex, leading to its inactivation, downregulation of α-SMA and COL1A1 expression, and ultimately exerting anti-fibrotic activity (Zhu X. et al., 2021).

In summary, flavonoids and related bioactive compounds exert anti-fibrotic effects not only through classical signaling pathways such as TGF-β/Smad, PI3K/AKT, MAPK, STAT3, and NF-κB, but more importantly through the regulation of diverse PTMs. Phosphorylation is central to blocking the Smad, AKT, and MAPK axes; deacetylation and acetylation regulate HSC fate via SIRT1 activation and GLI1 inactivation, respectively; and autophagy induction contributes to the suppression of fibrosis progression. These findings highlight PTMs as critical therapeutic targets of natural compounds, underscoring their multi-target and multi-pathway advantages and providing a solid theoretical foundation for the development of novel PTM-oriented anti-fibrotic drugs.

Phenolic compounds are naturally occurring substances abundant in fruits, vegetables, grains, legumes, chocolate, and beverages such as tea and wine (Spencer et al., 2008). They display diverse pharmacological properties, including anti-inflammatory, antioxidant, anti-proliferative, lipid-regulating, and anti-aging activities (Toma et al., 2020; Urso and Clarkson, 2003; Van Hung, 2016). Clinically, phenolics have been applied in the management of hypertension, metabolic disorders, infections, and neurodegenerative diseases (Lin et al., 2016; Rahman et al., 2021). Increasing evidence supports their therapeutic role in HF through the regulation of PTMs and epigenetic processes.

Capsaicin (CPS) has been shown to upregulate Smad7 expression through the activation of PPAR-γ, thereby suppressing DMN-induced TGF-β1 production. In HSCs, CPS effectively reduced TGF-β1–mediated α-SMA and collagen I expression via this pathway, suggesting that it ameliorates fibrosis by negatively regulating the TGF-β1/Smad signaling axis through the PPAR-γ/Smad7 pathway (Choi et al., 2017). Similarly, ferulic acid (FA) markedly inhibits the phosphorylation of Smad2/3 and the downstream signal transduction of Smad4, thereby attenuating TGF-β1–induced HSC activation and contributing to the reversal of fibrosis progression (Mu et al., 2018). Honokiol exhibits broader multi-pathway regulatory effects. In HSCs, honokiol reduces the expression of α-SMA, TGF-β1, p-Smad3, p-AKT, Cyclin D1, c-Myc, and Wnt3a/β-catenin, while inhibiting the phosphorylation of GSK3β, which leads to GSK3β activation, blockade of Wnt3a/β-catenin signaling, and apoptosis induction (Lee et al., 2021). Further studies revealed that honokiol also suppresses non-canonical TGF-β1 pathways (AKT, ERK, and p38) while promoting GSK3β/JNK phosphorylation, which enhances E-cadherin expression and inhibits EMT progression. In vivo, honokiol has been shown to attenuate CCl₄-induced hepatic fibrosis and necrosis (Seo et al., 2023).

Tea polyphenols also confer hepatoprotection. Green tea catechins [epigallocatechin (EGC), epicatechin-3-O-gallate (ECG), and epigallocatechin-3-O-gallate (EGCG)] significantly reduce desmin, α-SMA, and TGF-β expression, while inhibiting the phosphorylation of ERK1/2 and Smad1/2, thereby ameliorating fibrosis (Wang et al., 2019). Sugarcane polyphenol extract (SPE) has also been shown to inhibit the phosphorylation of p38 and JNK1/2 and downregulate α-SMA expression in TGF-β1–induced HSCs (Wang L. et al., 2018). In addition, the compound extract of Astragalus and Salvia miltiorrhiza (CASE) suppresses linker-region phosphorylation of Smad2/3 and the nuclear import of Smad4 and Imp7/8, thereby reducing the transcriptional activity of PAI-1, a key target gene of TGF-β signaling. This effect is accompanied by inhibition of the MAPK pathway (pERK, pJNK), ultimately suppressing the fibrotic response of HSCs (Boye et al., 2015).

Among active compounds from S. miltiorrhiza, Danshensu (DSS) is identified as an inhibitor of indoleamine 2,3-dioxygenase 1 (IDO1). DSS downregulates JAK2/STAT3 signaling by reducing JAK2/STAT3 phosphorylation and STAT3 nuclear localization, thereby inhibiting ECM deposition and liver injury. Overexpression of IDO1 reverses these effects, confirming its role in fibrosis (Cao et al., 2019). Salvianolic acid B (Sal B) suppresses fibrosis via the MAPK/Smad axis and Hedgehog pathway, significantly reducing p-ERK1/2, p-JNK1/2, p-p38, p-Smad2/3, and PAI-1 levels (Wu et al., 2019). In addition, Sal B attenuates HSC activation by regulating miR-152/DNMT1-mediated DNA methylation, thereby suppressing the hypermethylation of PTCH1 and restoring its expression (Yu et al., 2015). Oroxylin A further demonstrates epigenetic action by inhibiting DNMT3A-mediated methylation of the cGAS promoter. This activates the cGAS–STING pathway and induces cellular senescence, while DNMT3A overexpression reverses these effects (Zhao et al., 2023).

In summary, phenolic compounds—including alkaloids, phenolic acids, polyphenols, and herbal extracts—exert potent antifibrotic effects by targeting both canonical and noncanonical pathways (TGF-β/Smad, MAPK, PI3K/AKT, Wnt/β-catenin, and JAK/STAT), as well as by modulating DNA methylation and other epigenetic processes. Their ability to act at multiple levels of regulation underscores PTMs and epigenetic remodeling as promising therapeutic intervention points, providing a strong foundation for the development of novel antifibrotic strategies.

Terpenoids are a large and structurally diverse class of bioactive natural compounds found in plants, animals, marine organisms, and microorganisms. They exhibit a wide spectrum of pharmacological properties, including antitumor cytotoxicity, neuroprotection, anti-inflammatory activity, regulation of lipid metabolism, as well as hepatoprotective and hypoglycemic effects (Cassiano et al., 2014; El Omari et al., 2021; Hua et al., 2022; Yao and Liu, 2022).

Co-administration of total astragalosides (AST) and glycyrrhizic acid (GA) markedly inhibits HSC activation, lowers α-SMA and COL1A1 expression, and suppresses transcription and phosphorylation of TGF-β1 and Smad2/3, thereby reversing dimethylnitrosamine (DMN)– or bile duct ligation (BDL)–induced hepatic fibrosis (Zhou et al., 2016). Similarly, corosolic acid (CA) mitigates fibrosis by blocking TGF-β1/Smad2 phosphorylation and concomitantly regulating the AMPK and NF-κB pathways, which decreases ECM deposition and inflammation (Liu et al., 2021). Ginsenoside Rg1 restores Smad7 expression through promoter demethylation, blocking TGF-β/Smad signaling and suppressing epithelial–mesenchymal transition (EMT); consistent with this mechanism, the DNMT inhibitor 5-Aza also enhances Smad7 demethylation and expression (Zhang et al., 2023).

Several terpenoids act through STAT3 modulation. Cryptotanshinone (CTS), a derivative of tanshinone IIA, inhibits STAT3 nuclear translocation, reduces CPT1A-dependent fatty acid oxidation, and promotes an adipocyte-like phenotype in HSCs, collectively producing antifibrotic effects. In CCl4-induced fibrosis, p-STAT3 co-localizes with the HSC activation marker α-SMA; CTS reduces p-STAT3 and favors HSC adipogenic reprogramming, thereby attenuating fibrosis (Li et al., 2024). Similarly, Asiatic acid (AA) further suppresses JAK1/STAT3 phosphorylation, preventing persistent pathway activation and ameliorating fibrosis (Fan et al., 2018). Sclareol (SCL) suppresses SENP1 expression, augments VEGFR2 SUMOylation, and disrupts the VEGFR2–STAT3 interaction, thereby inhibiting downstream STAT3 phosphorylation and providing new evidence that SUMOylation contributes to antifibrotic effects (Ge et al., 2023).

Other terpenoids target cytoskeletal and metabolic signaling. Demethylzeylasteral (T-96), from Tripterygium wilfordii, selectively inhibits FAK and AKT phosphorylation and disrupts the AGAP2–FAK interaction, suppressing HSC proliferation and migration (Chen et al., 2022). Triptolide acts as an AMPK agonist, increases AMPK Thr172 phosphorylation and phosphorylation of its downstream substrate ACC1, thereby attenuating fibrosis (Huang et al., 2021). Similarly, celastrol mitigates hepatic fibrosis by activating the AMPK–SIRT3 axis, improving mitochondrial homeostasis and anti-inflammatory defenses (Wang et al., 2020a). Likewise, the ginsenoside metabolite 20(S)-protopanaxadiol (20S-PPD) activates LKB1-dependent AMPK Thr172 phosphorylation, downregulates the mTOR/S6K pathway, and promotes HSC apptosis (Park et al., 2017).

Other mechanisms have also been reported. The saponin extract of Panax japonicus rhizomes (SEPJ) augments phosphorylation of AKT and GSK-3β to activate NRF2 signaling, upregulates NRF2 and its downstream antioxidant genes, thereby inhibiting EMT and HSC activation, and demonstrates antifibrotic efficacy in vitro and in vivo (Dai et al., 2021). Carnosol (CS) activates SIRT1 to reduce EZH2 acetylation and stability, limiting myofibroblast differentiation and ECM accumulation (Zhao et al., 2018). Ginsenoside Rg3 augments ferroptosis through ACSL4 demethylation to restrain HSC activation; this effect is mediated via the miR-6945-3p/DNMT3B axis, unveiling a ferroptosis-based mechanism underlying Rg3’s antifibrotic activity (Hu Y. et al., 2024).

Alkaloids are nitrogen-containing basic compounds with broad pharmacological activity. More than 18,000 alkaloids have been identified across >300 plant families as well as from microorganisms, marine invertebrates, insects, and other sources (Elissawy et al., 2021; Nair and van Staden, 2019). Research has demonstrated that various alkaloids possess pharmacological effects such as antihypertensive, anti-inflammatory, anticancer, and anti-fibrotic properties (Bhambhani et al., 2021; Feng et al., 2016; Halim et al., 2019).

Mechanistically, representative alkaloids modulate key PTM-linked signaling nodes to restrain HSC activation and ECM accumulation. The matrine derivative MD-1 engages EGFR on HSC-T6 cells to suppress EGFR/AKT phosphorylation, downregulate cyclin D1, and block persistent HSC activation; in DMN–induced rat fibrosis, MD-1 attenuates disease progression, improves liver function, and preserves hepatocyte integrity (Feng et al., 2016). Berberine (BBR) exerts antifibrotic activity predominantly via AMPK activation with concomitant repression of NOX4/AKT expression, thereby reducing oxidative stress and ECM deposition (Li et al., 2014). Neferine (NEF) protects against NASH-associated fibrosis by inhibiting TGF-β/Smad2/3 signaling, preventing HSC activation and downregulating profibrotic genes (Wang M. Y. et al., 2023). In AML-12 hepatocytes and LX-2 HSCs, piperine (PIP) drives NRF2 nuclear translocation and antioxidant gene transcription to limit TGF-β1–elicited ROS; concurrently it increases SMAD7 while restraining SMAD2/3 phosphorylation/nuclear entry, an effect blunted by NRF2 knockdown, implicating NRF2 as a key mediator (Shu G. et al., 2021).

Collectively, these alkaloids converge on receptor signaling (EGFR), metabolic/oxidative pathways (AMPK/NOX4), and canonical profibrotic axes (TGF-β/Smad) with NRF2 crosstalk, highlighting PTM-centered mechanisms as tractable targets for antifibrotic intervention.

Accumulating evidence indicates that natural products of varied origin mitigate hepatic fibrosis by tuning PTMs across key signaling nodes. Ganoderma lucidum polysaccharide (GLP) lowers hepatic TGF-β and SMAD2/3 phosphorylation in CCl4-injured mice while restoring SMAD7, thereby preventing activation of HSC-T6 cells (Chen C. et al., 2023). Likewise, Suaeda glauca extract (SGE) suppresses TGF-β1–evoked SMAD2/3 phosphorylation and nuclear translocation and reduces SBE-dependent transcriptional activity—without affecting JNK or ERK—implicating selective blockade of the TGF-β/SMAD axis (Hong et al., 2023). Moreover, amygdalin diminishes TGF-β/SMAD2/3 phosphorylation and downregulates profibrotic gene expression, thereby curbing HSC activation and ECM deposition and mitigating CCl4-induced hepatic injury (Wang et al., 2021).

Several agents act through coordinated pathway inhibition. In HSCs, emodin reduces TGF-β1, TβRI/TβRII, and SMAD4 expression and markedly suppresses SMAD-responsive luciferase activity and p38 MAPK activation. Notably, single inhibition of SMAD4 or p38 only partially attenuates emodin’s effect, whereas combined inhibition abolishes it, indicating that emodin represses collagen gene transcription via cooperative blockade of SMAD and p38 MAPK signaling (Wang X. et al., 2018). Chrysophanol 8-O-glucoside (C8G) selectively inhibits p38 phosphorylation and blocks STAT3 activation/nuclear import, reducing MMP2 expression and ECM accumulation (Park et al., 2020). In NASH, cordycepin augments AMPK phosphorylation to restrain NF-κB activation and, via ACC phosphorylation, corrects lipid dysregulation, yielding anti-inflammatory and antifibrotic benefits; AMPK inhibition abrogates these effects, underscoring AMPK dependence (Lan et al., 2021). Plumbagin (PL) lowers IκB phosphorylation in CCl4-injured rat liver and IL-1β–stimulated HSCs, preventing NF-κB nuclear entry/transactivation and thus mitigating inflammation and ECM build-up (Chen et al., 2019). The Kampo formula Inchin-ko-to (TJ-135) decreases collagen deposition and α-SMA in fibrotic rats and represses COL1A1, COL3A1, and fibronectin transcription in HSCs by inhibiting PDGFRβ phosphorylation and downstream signaling (Imanishi et al., 2004).

Epigenetic targeting is also prominent. Emodin suppresses ERK/Nur77 signaling, drives Nur77 nuclear translocation and DNMT3b binding, increases GLS1 promoter methylation, inhibits glutaminolysis, triggers energetic stress and HSC senescence, and thereby exerts antifibrotic activity (Chen L. et al., 2023). Sennoside A (SA) upregulates SOCS1 in a DNMT1-dependent manner and suppresses macrophage pro-inflammatory cytokines, indirectly limiting HSC proliferation and ECM deposition; SOCS1 blockade diminishes efficacy, highlighting a pivotal epigenetic component in SA’s antifibrotic action (Zhu H. et al., 2021).

These natural products—polysaccharides, halophyte extracts, anthraquinones, nucleosides, naphthoquinones, and multi-component formulas—converge on PTM-regulated nodes (e.g., SMAD, p38, STAT3, AMPK/ACC, NF-κB, PDGFRβ) and epigenetic machinery (DNMT1/DNMT3b, promoter methylation) to suppress HSC activation, inflammation, and ECM deposition. Their multi-target profiles reinforce PTMs and epigenetic remodeling as tractable intervention points for antifibrotic drug development.

To overcome these limitations and correct the PTM imbalance, priority areas include: i. expanding research from single-PTM (phosphorylation) analysis to multi-PTM network interrogation using integrated phosphoproteomics, acetylomics, ubiquitinomics, and emerging succinyl/malonyl modifications; ii. systematically evaluating PTM “writers,” “erasers,” and “readers” (e.g., deacetylases, ubiquitin ligases, SUMO E3 ligases, methyltransferases) as potential therapeutic targets; iii. validating candidate PTM changes not only in animal and cell models but also in human liver tissues and circulating biomarkers; iv. advancing compounds with defined pharmacokinetics, acceptable safety, and concordant in vitro/in vivo mechanisms into standardized Phase I/II trials (dose finding, PK/PD, interaction studies), followed by multicenter randomized trials with long-term antifibrotic endpoints; and v. implementing rigorous standards for extraction, chemical characterization, and reporting of PTM data to reduce selective reporting and publication bias. Only by broadening the PTM perspective beyond phosphorylation, integrating high-throughput epigenomics and systems biology, and coupling mechanistic insight with early pharmacokinetic/toxicological evaluation can natural-product discoveries be efficiently translated into clinically useful antifibrotic therapeutics.