Research on marine algae such as Phaeodactylum tricornutum indicates that fucoxanthin synthesis can be induced by signaling molecules such as methyl jasmonate (MeJA), a known stress-response signal in plants (see Cycloalkenones as MAs), suggesting its role in defense mechanisms [42, 43]. Fucoxanthin is an antioxidant and protects cell components from ROS. Enhanced concentration of ROS has been implicated in many pathological conditions, including cancer. The major machinery in the cells of Animalia that neutralizes excess ROS functions through the activation of the ARE.

Fucoxanthin (3, Figure 2), a major carotenoid in brown algae and diatoms, functions primarily as a light-harvesting pigment and photoprotective agent. In addition, it potentially plays a role as a signaling molecule. Under excess light, fucoxanthin is part of an adaptive, photoprotective signaling system. It plays a role in the xanthophyll cycle, where intermediate pigments like diadinoxanthin are converted to diatoxanthin to dissipate excess energy and prevent ROS-induced damage [44, 45]. The latter controls the activation of many phase II detoxification enzymes. The transcription factor that recognizes the ARE, Nrf2, can be activated by a variety of small molecules, most of which contain an α,β-unsaturated carbonyl system. The MA acceptor functionality enables it to interact with proteins and, in animal models, trigger antioxidant signaling pathways, specifically by activating the Nrf2/ARE system [46–50]. While extensive literature exists on fucoxanthin’s signaling role in animals (e.g., MAPK, NF-κB pathways), in plants and algae, it is primarily defined as a crucial pigment for photosynthetic light-harvesting, structural stabilization of complexes, and light-stress signaling. The importance of fucoxanthin for human health has been extensively reviewed [46–49].

The MA motif has also been found in derivatives of monounsaturated C18 and C16 fatty acids isolated from the green macroalga Ulva lactuca (Figure 3), C18 fatty acid (4a, Figure 3), C16 fatty acid (4b, Figure 3), and an amide derivative (4c, Figure 3) of the C18 acid [51]. These compounds’ activity to ARE is attributed to the presence of the unsaturated keto-moiety between C7 and C9 (Figure 3). The most active compound, the C18 acid 4a (Figure 3) induces the expression of ARE-regulated cytoprotective genes, including NQO1, heme oxygenase 1, thioredoxin reductase 1, both subunits of the glutamate-cysteine ligase (catalytic subunit and modifier subunit), and the cystine/glutamate exchange transporter, in IMR-32 human neuroblastoma cells [51].

In addition to acyclic α,β-unsaturated aldehydes and ketones, another product of oxylipin metabolism is the jasmonic acid (JA) precursor, 12-oxo-phytodienoic acid (12-OPDA), found in algae to higher plants [51–54]. Biologically synthesized 12-OPDA is cis-(+)-12-OPDA, 9, Figure 4, (referred herein as 12-OPDA for the 8-[(1S,5S)-4-oxo-5-[(Z)-pent-2-enyl]cyclopent-2-en-1-yl]octanoic acid, usually found in plants). Allene oxide cyclase is the enzyme responsible for the production of enantiomerically pure cis-(+)-12-OPDA [55, 56]. In Arabidopsis thaliana, bioconjugation of JA, 10, Figure 4 with isoleucine results in the synthesis of the plant hormone (+)-7-iso-Jasmonoyl-L-isoleucine (JA-Ile, 18, Figure 5). JA-Ile regulates growth, reproduction, and defense responses against pathogens and chewing insects by binding to its receptor COI1-JAZ [57–59]. The initiation of the plants’ response to environmental stress via binding of JA-Ile to COI1-JAZ is referred to as the canonical pathway. Several reports have demonstrated that 12-OPDA activates stress responses in A. thaliana, tomato, and maize via a JA-Ile-independent pathway, i.e., a noncanonical pathway (Figure 5) [55, 60].

In the kingdom Plantae, both alkyl α,β-unsaturated enones and 12-OPDA (9, Figure 4) are ubiquitous chemical signaling compounds with overlapping triggers, i.e., environmental stress, including wounding, and pathogenesis [52, 53, 55, 61–64]. Exogenous 12-OPDA affects the expression of approximately 200 genes in A. thaliana. In algae and other representatives of the land plants, the expression of 12-OPDA-specific response genes has been confirmed [53, 54]. The essential compound moiety for this signal appears to be the presence of the α,β-unsaturated carbonyl group [52, 53].

12-OPDA (9, Figure 4) is structurally similar to the mammalian cyclopentenone PGs (cyPGs, e.g., 15, Figure 4), with the cyclopentenone being the electrophilic (MA) moiety [61]. Both cyPGs and 12-OPDA are important regulators of reproductive systems. For example, while cyPGs play a role in labor contractions, 12-OPDA is involved in regulating seed dormancy, germination, and embryogenesis [65–67]. The covalent binding of 12-OPDA to thiol groups by Michael addition, termed OPDAylation, affects the activity of its target proteins, such as cyclophilin 20-3 (EC:5.2.1.8) and thioredoxins, that are essential for the cellular redox system in plants [55, 68]. Recently, the intricate interplay between the 12-OPDAylation of protein thiols and the binding of 12-OPDA to glutathione (GSH) has been shown to be under kinetic vs. thermodynamic control, respectively. This control of 12-OPDA (9, Figure 4) concentrations permits rapid modification of the target protein due to the higher nucleophilicity of its cysteine as compared to the thiol group of cysteine in GSH. This ensures rapid induction of OPDA signaling followed by detachment from the protein (de-OPDAylation) in response to the increasing levels of GSH [68].

The downstream metabolites of 12-OPDA (9, Figure 4), specifically tetranor-cis-OPDA (tn-cis-OPDA) and 7-iso-4,5-didehydro-JA (4,5-ddh-JA) (17, Figure 5), upregulate the expression of 12-OPDA marker genes, such as ZAT10 and ERF5. Similar to 12-OPDA, its downstream metabolites, tn-cis-OPDA and 4,5-ddh-JA, function independently of the JA-Ile-COI1-JAZ-MYCs canonical jasmonate signaling module, with their electrophilic MA-acceptor functionalities being essential for their bioactivity [69]. This finding suggests that both 12-OPDA (9, Figure 4) and its derivative 4,5-ddh-JA (17, Figure 5), which contains the α,β-unsaturated moiety, function as endogenous chemical signals in A. thaliana. The cyclopentenone functionality embedded in 12-OPDA compounds functions as a chemical response to stress in marine and terrestrial algae as well as vascular plants [69–76]. It has been demonstrated that dn-OPDA is the evolutionary precursor of JA-Ile. It is suggested that the low hydrophilicity of dn-OPDA exerted evolutionary pressure for the formation of the polar JA-Ile hormone, as it permits easier distribution through a plant vasculature [77].

Abscisic acid (ABA, 22, Figure 6) is another MA-containing compound that shares striking similarities with 12-OPDA (9, Figure 4) in both chemical structure and biological function [52, 77–85]. ABA is a 15-carbon sesquiterpenoid (22, Figure 6), synthesized by oxidation from a product of the carotene metabolism, neoxanthin (19, Figure 6), whose structure shares great similarity with that of fucoxanthin (3, Figure 2).

Similarly to 12-OPDA (9, Figure 4), ABA (22, Figure 6) is a chemical signal in the defense responses of plants. In addition, both compounds share the same electrophilic unsaturated moiety, which binds to sulfhydryl groups, such as cysteine in GSH and proteins [77–85]. Furthermore, ABA affects 12-OPDA concentration [86, 87].

ABA (22, Figure 6) has activity across taxonomic kingdoms affecting prokaryotes, fungi, and animals, including humans [88]. The pathway for ABA synthesis in fungi is dissimilar from the oxylipin pathway in plants. In fungi, ABA is synthesized via the mevalonic acid (MVA) pathway, utilizing a unique cyclase (BcStc5) to convert farnesyl diphosphate to α-ionylideneethane [89, 90]. Further oxidative modifications of the cyclized product (α-ionylideneethane) to afford 1ʹ,4ʹ-trans-dihydroxy-α-ionylideneacetic acid, which undergoes alcohol oxidation to furnish ABA. Currently, in many naturopathic products and drug development programs, chiral cyclohexenones, e.g., ABA, are the reactive functionality present [91–98]. Different synthetic approaches have been utilized to achieve regio- and stereoselective C–C and C–X bond formation for cyclohexenone synthesis [98, 99]. Human proteomics research recently showed that there are proteins that specifically bind ABA, some of which may play a role in cancer and diabetes [100]. It has been proposed that ABA (22, Figure 6) synthesis in humans, as in fungi, proceeds via farnesyl pyrophosphate cyclization [100]. It appears that mammals contain a latent, fungal-like ABA synthesis pathway that is inducible under metabolic or xenobiotic stress. If confirmed, this will allow for a rational ABA-based drug design for the treatment of chronic pathologies such as inflammation, diabetes, and cancer. [100].

Another example of a parallel metabolic pathway in mammals and plants is that of the PGs. Until recently, PGs metabolism and functions were mainly associated with mammals. However, recently it has been recognized that PGs are present in plant species, such as onions, poplar trees, and birch (Betula alba L.) pollen [101, 102]. The synthesis of PGs in both macro- and micro-algal marine species occurs when the algae are under stress conditions, but their exact role in mediation of stress responses in marine algae is still under investigation [103]. Recently, studies of the PG biosynthetic pathway during different growth phases of the centric diatom Thalassiosira rotula show that PGs are released primarily during the stationary and senescent growth phases, suggesting a possible signaling function for these compounds [104]. Both PGs and plant hormones are the end result of pathways involving bioactive lipids.

In general, bioactive lipids in both plants and animals have been reported to govern both cellular homeostasis and pathogenic inflammatory processes. The endogenously produced electrophilic α,β-unsaturated ketones and their derivatives (i.e., MA) from hydroxylated PUFAs are chemically reactive signaling mediators that induce tissue-protective events. The mechanism of action of these MAs is post-translational alkylation of nucleophilic cysteines in key transcriptional regulatory proteins and enzymes that govern cellular metabolic and inflammatory homeostasis. The cycloenone motif has been proven by Nature to be a very successful electrophilic warhead that can be produced rapidly to alleviate oxidative stress. Therefore, it is not surprising that MAs evolutionary development for plant cellular homeostasis can be used similarly by mammals.

For OPDA induced growth inhibition in breast cancer cells, 12-OPDA (9, Figure 4) degradation of cyclin D1 protein is a key event [105]. Cancer cells’ treatment with 12-OPDA exhibit a progressive decline in cyclin D1 expression, which is tightly associated with the accumulation of hypophosphorylated form of the retinoblastoma protein (Rb) and G1 arrest. 12-OPDA induces Nrf2-dependent antioxidative response, which in turn may have contributed to the observed decrease in H₂O₂-induced ROS levels in human neuroblastoma SH-SY5Y cells and breast cancer [106–108]. It is interesting to note that in the last several years, the anticancer activity of JA (10, Figure 4) and its derivatives has also been reported [109–111].

The use of MAs as target modulators is currently an active area of drug development. These target modulators bind non-covalently or covalently to their molecular targets. The chronological order of MA-containing compounds in drug development ranges from natural products (irreversible) to current trends (irreversible/reversible) based on nature-inspired warheads. The covalent binding of the enzyme modulators offers significant advantages over non-covalent ones, since the covalent warhead could target a single amino acid residue. However, typically, enzyme modulators rarely act on a single molecular target, and with those being irreversible, the off-target effects can lead to undesired effects, e.g., toxicity. Therefore, strategies to minimize off-target effects both by nature and man include the preparation of compounds with high specificity toward a molecular target and/or those that bind reversibly. The reversible covalent modulation ensures high potency of binding (covalent binding with the molecular target), and the potential for tuning the residence time on target through structural modification around the electrophilic warhead, thus securing the binding through non-covalent interactions in the binding site.

Nature has used plant hormones containing either cyclopentenone or cyclohexenone as electrophilic moieties that are able to bind covalently with sulfhydryl groups, which range from H₂S to those found in proteins. These hormones (12-OPDA and ABA) are not limited to plants but can be found in all living organisms on our planet, including humans. Cyclopentenone and cyclohexenone are present in many of the evolutionarily ancient signaling molecules [76]. The endocyclic double bond of the α,β-unsaturated system of the electrophilic warheads appears to be advantageous in specific binding to target proteins, as compared to open-chain compounds, which in turn should lead to fewer off-target effects. For example, binding of 12-OPDA (9, Figure 4) to proteins containing cysteine, e.g., thioredoxin, is favored over OPDA adduct formation with GSH. This is despite the fact that, under physiological conditions, the concentration of free thiols, for example GSH, exceeds that of 12-OPDA by approximately 10²- to 10³-fold [112]. This rationale from nature has been recently demonstrated to be effective via an increased specificity in using cyclohexenone as the MA functionality in inhibitors of c-Jun kinase, involved in human carcinogenesis [113].

Cyanoacrylamide is often the electrophilic warhead of the currently used reversible synthetic covalent enzyme modulators, such as, but not limited to, those used as kinase inhibitors, including the recently FDA-approved rilzabrutinib (23, Figure 7, formerly known as PRN1008, in 2025) [114].

Cyanoacrylamide moiety is attacked by one reachable nucleophile in the enzyme binding site (most often, but not limited to, a non-catalytic cysteine). However, the potential for binding of the reversible acyclic warheads (i.e., cyanoacrylamide) to other molecular targets, including those in the redox system in cells (e.g., GSH), still exists. Introducing a cyclic MA acceptor moiety in compound (24, Figure 8) to reduce the aforementioned potential interactions with off-target cysteines due to its less accessible 3D shape (found in naturally occurring MAs) has hindered its binding to GSH [113, 115]. This strategy, utilizing cyclohexenone-based MA (25, Figure 8), led to the preparation of inhibitors of c-Jun Terminal Kinase, where, in addition to the cyclic moiety, the chirality of the γ-carbon in 1aR-IN-8 (25, Figure 8) plays a significant role in guiding the inhibitor to the “correct” nucleophile and secures binding specificity equivalent to that of its irreversible counterpart JNK-IN-8 [113, 115].

The placement of the cyano group at the α-position of the α,β-conjugated system leads to highly reactive cyanoenone functionality, which preferentially binds covalently to cysteines in proteins [116–118]. An example of this is the replacement of the original secondary alcohol of the glycyrrhetinic acid scaffold with a 2-cyano-substituted cyclohexenone ring (Figure 9), resulting in a pentacyclic triterpenoid derivative equipped with a potentially reversible MA [116].

Orally active omaveloxolone (29, Figure 10) binds primarily to Cys151, of the cysteine-based sensor protein Keap1, which leads to the accumulation of transcription factor Nrf2. In Friedreich’s ataxia, an autosomal recessive degenerative disease of the nervous system, the nuclear factor Nrf2 pathway is suppressed, causing oxidative stress and mitochondrial dysfunction. This stress leads to central and peripheral neuron cell damage. The Nrf2 pathway may be activated by omaveloxolone as it blocks the ubiquitination and degradation of Nrf2, which in turn inhibits transcription of proinflammatory genes. An additive effect of omaveloxolone may be its binding to cysteines in proteins involved in inflammatory cascades (e.g., IKKβ), resulting in inhibition of inflammation [117, 118].

The cyclohexenone motif has been used in other small molecules biosynthesized by plants. Zeylenone (30, Figure 11), a naturally occurring cyclohexene oxide, was first isolated from the extract of Uvaria grandiflora. This naturally occurring compound has demonstrated activity against cervical carcinoma, gastric cancer, and prostate cancer, with limited cytotoxicity against normal cell lines [119–121]. While a detailed mechanism of action/role in plants of zeylenone is currently lacking in the literature, it is predicted to act as a defense compound against different stressors due to its MA moiety, and having cytotoxic activity suggests a role in defending the plant against external threats.

Studies in vivo show that zeylenone (30, Figure 11) is susceptible to esterase hydrolysis with accompanying loss of biological activity. Thus, structural modifications to address hydrolytic instability and resultant activity of the prepared zeylenone derivatives have been carried out using glioblastoma (GBM) cancer lines as the target cell [122]. (+)-Zeylenone derivative CA (33, Figure 11, (1R, 2R, 3S)-3-p-fluorobenzoyl-zeylenone) demonstrated the lowest IC₅₀ value in GBM cells. IC₅₀ values of CA were notably low in GBM cell lines, particularly in U251 (5.161 µM) and A172 (6.440 µM). The molecular mechanism by which CA exerts its anticancer activity is by attenuating the downregulation of cyclin-dependent kinase inhibitors p27 and p16 by the polycomb repressive complex 2 (PRC2). This has been confirmed by in vivo studies. Furthermore, compound CA has the potential to synergistically potentiate the anti-tumor effects of EZH2 inhibitors.

EZH2, a histone methyltransferase enzyme, is the catalytic subunit of the PRC2. PRC2 primarily targets developmental genes, particularly transcription factors, to keep them in a repressed state in specific cell types (e.g., HoX gene family) by methylating histone H3 on lysine 27. It plays a crucial role in cell differentiation, development, and, when mutated or overexpressed, promotes cancer progression, making it a key therapeutic target [122].

Structures found in natural and synthetic sesquiterpene lactones (STLs), e.g., cyclopentenone, have also been explored as potential enzyme inhibitors in the treatment of cancers [123, 124]. Cyclopentenone has been established as a structural motif in anticancer drug development that, when present in compounds, increases the likelihood of specific binding [124]. The simplest representative, 2-cyclopenten-1-one, inhibits the activity of cyclin A promoters in breast cancer cells and cyclin D1, which, when overexpressed, acts as a proto-oncogene in cancers like breast, lung, and lymphoma [123]. Pentacyclic lactones with an exocyclic double bond (α-exo-methylene-γ-butyrolactones) found in terpenes such as andrographolide are also among the highly explored MA-containing compounds as anti-inflammatory agents and as potential treatments for neurological disease, e.g., Alzheimer’s disease [125–127].

The cyclopentenone-based PGs and their cyclopentenone-based synthetic mimics have been demonstrated to be potent inhibitors of NF-κB activation by inflammatory cytokines, mitogens, and viral infection [128]. In addition, these compounds inhibit NF-κB-dependent anticancer activity by directly binding and modifying the β subunit of the IκB kinase complex (IKK) [128]. Specifically, the natural cyclopentenone 15-deoxy-Δ^12,14PG J₂ (15-dPGJ₂) (15, Figure 4) is a potent inhibitor of constitutive IκB kinase and NF-κB activities in chemotherapy-resistant ER-negative breast cancer cells [128]. Development of various approaches to modify the cyclopentenone ring to explore its potential in drug development followed [129, 130]. Illustrative examples of strategies using masked MA functionality by utilizing the presence of suitable substituents at either α- or β-position of the α,β-unsaturated systems are discussed below [131, 132].

Conversely, highly reactive MAs are of concern since their promiscuity can lead to high toxicity [133–135]. Since exocyclic enones, such as parthenin 1 (34, Figure 12), are highly reactive MAs, different approaches to lower their toxicity have been employed, such as blocking the exocyclic MA acceptor group, which lowers their MA reactivity.

STLs are 15-carbon secondary metabolites, primarily found in the Asteraceae family, that act as crucial chemical defenses against other plants, insects, and microbes. They commonly contain a cyclopentenone moiety as the electrophilic center. Their different roles in benefiting the plant producer vary depending on the plant and the compound type, being able to function against both environmental stress and pathogens [136, 137]. STLs are currently under investigation by numerous research groups due to their ability to bind to targets relevant to the treatment of cancer, inflammation, and infectious diseases [138].

The STL, parthenin 1 (34, Figure 12), is the main allelopathic compound in the invasive Parthenium hysterophorus (famine weed). It serves as a natural defensive mechanism, suppressing the germination and growth of competing plants. It enables P. hysterophorus to dominate ecosystems by hindering the growth of the surrounding flora. Spiro derivatives of parthenin 1 (35, Figure 12) reduce the natural product’s active MAs functionalities from two to one. After determining that the cyclopentenone functionality is essential for the bioactivity, derivatives were synthesized and then tested against three cancer cell lines as inhibitors of NF-κB. [131]. The in vivo screening showed improved activity with low mammalian toxicity of the spiro parthenin 1 derivatives (35, Figure 12) as compared to parthenin 1 [131]. For additional modification of this double MA, the reader is directed to the recent review [139].

The cyclopentenone derivatives shown below (Figure 13) with different substituents on the α-carbon of the conjugated system have been prepared. These derivatives have activity against cancer lines and low cytotoxicity to normal human cells [132]. From the derivative series, the most active compound was compound HCP33 (Figure 13), of the α-hydroxy-substituted cyclopentenones (37, Figure 13) having a p-chloro-substituted phenylthio group at C4 of the cyclopentenone. Derivative HCP33 is nontoxic to healthy cell lines, while showing significant activity in the breast cancer cell lines [132].