Prenylated Research Articles

Catalytic mechanism underlying the regiospecificity of coumarin-substrate transmembrane prenyltransferases in Apiaceae.

Plant membrane-bound prenyltransferases (PTs) catalyse the transfer of prenyl groups to acceptor substrates, phenols, using prenyl diphosphates as the donor substrate. The presence of prenyl residues in the reaction products, prenylated phenols, is key to the expression of a variety of physiological activities. Plant PTs generally exhibit high specificities for both substrate recognition and prenylation sites, while the molecular mechanism involved in these enzymatic properties is largely unknown. In this study, we performed a systematic biochemical analysis to elucidate the catalytic mechanism responsible for the reaction specificity of plant PTs. Using two representative PTs, PsPT1 and PsPT2, from parsnip (Pastinaca sativa, Apiaceae), which differ only in the regiospecificity of the prenylation site, we performed domain swapping and site-directed mutagenesis of these PTs, followed by detailed enzymatic analysis combined with three-dimensional modelling. As a result, we discovered the domains that control prenylation site specificity and further defined key amino acid residues responsible for the catalytic mechanism. In addition, we showed that the control mechanism of prenylation specificity revealed here is also highly conserved among coumarin-substrate PTs. These data suggest that the regulatory domain revealed here is commonly involved in prenylation regiospecificity in Apiaceae PTs.

Total synthesis and antibacterial evaluation of lupalbigenin and isolupalbigenin

Lupalbigenin (1) is an antibacterial isoflavone isolated from Maclura cochinchinensis (Lour.) Corner (Moraceae). In this study, we achieved the first gram-scale synthesis of lupalbigenin (1) from commercially available genistein (2), with a yield of 47.7%. The key step was a Claisen rearrangement that simultaneously installed two prenyl groups at the C-6 and C-11 positions of lupalbigenin (1). Antimicrobial activity assays revealed that lupalbigenin (1) exhibited rapid bactericidal activity, inhibited α-hemolysin and biofilm formation, and disrupted bacterial cell membranes. These findings suggest that lupalbigenin (1) is a promising candidate for the development of novel antibiotics to combat bacterial infections.

Three New Polyprenylated Benzophenone Derivatives Isolated from Clusia burle-marxii.

Three new polyprenylated benzophenone derivatives named burlemarxiones G-I (1-3) were isolated from C. burle-marxii trunks (compound 1) and leaves (compounds 2 and 3), along with the known compound burlemarxione F. Burlemarxione G (1) was isolated after methylation with diazomethane and it is the keto-enol tautomeric pair of burlemarxione F. Burlemarxione H (2) derives from burlemarxiones F and G, but it has additional rings due to cyclization of the prenyl group attached to C-5 that establishes new single bonds between C-1 and C-23, as well as, between C-24 and C-29. Burlemarxione I (3) has two additional cyclizations: the first encompasses the cyclization of the former isopentenyl group into an 11,11-dimethyl-six-membered ring, whereas the second produces additional rings due to the cyclization of the prenyl group attached to C-5 that establishes new single bonds between C-1 and C-23, as well as, between C-24 and C-29. All three compounds showed moderate anti-glioma activity. These results show that C. burle-marxii is an important source of sophisticated polyprenylated benzophenone derivatives.

Evolution, structure, and drug-metabolizing activity of mammalian prenylcysteine oxidases

Prenylcysteine oxidases (PCYOXs) metabolize prenylated cysteines produced by protein degradation. They utilize oxygen as a co-substrate to produce free cysteine, an aldehyde, and hydrogen peroxide through the unusual oxidation of a thioether bond. In this study, we explore the evolution, structure, and mechanism of the two mammalian PCYOXs. A gene duplication event in jawed vertebrates originated in these two paralogs. Both enzymes are active on farnesyl- and geranylgeranylcysteine, but inactive on molecules with shorter prenyl groups. Kinetics experiments outline a mechanism where flavin reduction and re-oxidation occur rapidly without any detectable intermediates, with the overall reaction rate limited by product release. The experimentally determined three-dimensional structure of PCYOX1 reveals long and wide tunnels leading from the surface to the flavin. They allow the isoprene substrate to curl up within the protein and position its reactive cysteine group close to the flavin. A hydrophobic patch on the surface mediates membrane association, enabling direct substrate and product exchange with the lipid bilayer. Leveraging established knowledge of flavoenzyme inhibition, we designed sub-micromolar PCYOX inhibitors. Additionally, we discovered that PCYOXs bind and slowly degrade salisirab, an anti-RAS compound. This activity suggests potential and previously unknown roles of PCYOXs in drug metabolism.

Formohyperins G-L, polycyclic prenylated benzoylphloroglucinols from the flowers of Hypericum formosanum.

Phytochemical study on the flowers of Hypericum formosanum Maxim. (Hypericaceae) led to the isolation of formohyperins G-L (1-6), whose structures were assigned by detailed spectroscopic analysis. Formohyperins G-L (1-6) are new benzoylphloroglucinols substituted by a C10 unit, a prenyl group, and a methyl group. Formohyperins G-J (1-4) possess a 6/6/6-tricyclic structure, while formohyperins K (5) and L (6) have a unique 6/6/5/4-tetracyclic structure consisting of cyclohexadienone, dihydropyrane, cyclopentane, and cyclobutane rings. The absolute configurations of 1-6 were deduced by analysis of the ECD spectra. Formohyperins G-J (1-4) and L (6) were found to show potent inhibitory activities against IL-1β release from LPS-treated murine microglial cells with EC50 values of 5.0, 10.9, 6.3, 10.8, and 13.7µM, respectively, without cytotoxicity. 6-O-Methylformohyperins G (1a) and I (3a) also exhibited the inhibitory activities with EC50 values of 4.7 and 2.7µM, respectively, although they were cytotoxic against microglial cells.

A review of the ethnomedicinal, phytochemical, and pharmacological properties of the Ferulago genus based on Structure-Activity Relationship (SAR) of coumarins.

The Ferluago W.D.J. Koch genus includes 48 accepted perennial herbs that are distributed in the Mediterranean region, Southeast Europe, Central and Middle East of Asia. These plants are widely used in folk and conventional medicine due to their biological benefits such as anti-microbial, anti-inflammatory, anti-cancer, and immunomodulatory properties. Conducting a comprehensive review based on the structure activity relationships (SARs) of the coumarins, which has not been previously documented, can lead to a better insight into the genus Ferulago and its beneficial therapeutic activities. This review covers literature from 1969 to 2023, were collected from various scientific electronic databases to review phytochemical, pharmacological, and ethnopharmacological data of Ferulago species, as well as latest information on the SAR of reported coumarins from this genus. Phytochemical studies showed that the biological actions of this genus are mediated by the reported specialized metabolites, such as coumarins and flavonoids. Simple coumarins, prenylated coumarins, furanocoumarins, and pyranocoumarins are the largest subclasses of coumarins found in diverse Ferulago species, which have discussed the biological effects of them with a focus on the Structure-Activity Relationship (SAR). For example, prenylated coumarins have shown potential leishmanicidal and anti-neuropsychiatric effects when substituted with a prenyl group at the 7-hydroxy, as well as the C6 and C8 positions in their scaffold. Similarly, furanocoumarins exhibit varied biological activities such as anti-inflammatory, anti-proliferative, and anti-convulsant effects. Modifying substitutions at the C5 and C6 positions in furanocoumarins can enhance these activities. This study conducted a comprehensive review of all available information on the phytochemical and pharmacological characteristics of Ferulago species. Given the high occurrence of coumarins in this genus, which exhibit potential anti-Alzheimer and anti-microbial properties, it presents promising new therapeutic avenues for addressing these common issues. Further investigation is needed to understand the molecular-level mechanisms of action and to explore their clinical applications.

α-Glucosidase Inhibitory Activity of Prenylated Pyranocoumarins from Clausena excavata: Mechanism of Action, ADMET and Molecular Docking.

Three naturally occurring prenylated pyranocoumarins, nordentatin (1), dentatin (2), and clausarin (3), isolated from the roots of Clausena excavata (Family Rutaceae), and O-methylclausarin (4) which was obtained by methylation of 3, were investigated for their α-glucosidase inhibitory activity. The mechanism of action and the in silico prediction of their physicochemical and ADMET properties as well as the molecular docking were also studied. Compounds 1-4 exhibited stronger α-glucosidase inhibitory activity than the positive control, acarbose, through a non-competitive mechanism. Among them, 3 exhibited the highest activity, with an IC50 of 8.36 μM, which is significantly stronger than that of acarbose (IC50=430.35 μM). The prenyl group on C-3 and the hydroxyl group on C-5 in 3 may play important roles in enhancing the activity. Calculated physicochemical and ADMET parameters of 1-4 satisfied the Lipinski's and Veber's rules. Molecular simulation analysis indicated they are promising drug candidates with no hepatotoxicity. Compound 3 exhibited potent activity in the experiment and demonstrated good drug properties based on the calculations. A molecular docking study revealed that 3 showed H-bonding and π-π stacking interactions with selective Phe321, as well as interactions with thirteen other amino acid residues of the α-glucosidase.

Insights from degradation studies of alpha mangostin from Garcinia mangostana: key findings

The present study emphasises the necessity of substantiating the stability of plant-derived bioactive compounds for their therapeutic effectiveness in pharmaceutical production. The limelight is on alpha-mangostin (AM), a xanthone from Garcinia mangostana L., renowned for its diverse biological properties. Acid exposure during a forced degradation study on AM resulted in degraded alpha-mangostin (DAM) formation, with structural modifications of the two prenyl groups at C2 and C8 positions as determined by NMR and HRMS analysis. Other conditions (temperature, humidity, photolytic, oxidative, and alkaline) showed a minimal impact on AM. DAM, although showed antibacterial activity at concentration higher than AM (MIC values for AM: 0.39–1.56 µg/mL; DAM: >25 µg/mL), it exhibited potential for binding with Glucosyltransferase-SI from Streptococcus mutans and human Acetylcholinesterase in molecular docking simulations, comparable to AM. This suggests, the importance of prenyl group at C2 and C8 positions for AM’s potent antibacterial activity and the decreased activity of DAM is due to lack of the prenyl groups.

Kinetic and structural characterization of NUDT15 and NUDT18 as catalysts of isoprene pyrophosphate hydrolysis.

Isoprene pyrophosphates play a crucial role in the synthesis of a diverse array of essential nonsterol and sterol biomolecules and serve as substrates for posttranslational isoprenylation of proteins, enabling specific anchoring to cellular membranes. Hydrolysis of isoprene pyrophosphates would be a means to modulate their levels, downstream products, and protein isoprenylation. While NUDIX hydrolases from plants have been described to catalyze the hydrolysis of isoprene pyrophosphates, homologous enzymes with this function in animals have not yet been reported. In this study, we screened an extensive panel of human NUDIX hydrolases for activity in hydrolyzing isoprene pyrophosphates. We found that human nucleotide triphosphate diphosphatase NUDT15 and 8-oxo-dGDP phosphatase NUDT18 efficiently catalyze the hydrolysis of several physiologically relevant isoprene pyrophosphates. Notably, we demonstrate that geranyl pyrophosphate is an excellent substrate for NUDT18, with a catalytic efficiency of 2.1 × 105 m-1·s-1, thus making it the best substrate identified for NUDT18 to date. Similarly, geranyl pyrophosphate proved to be the best isoprene pyrophosphate substrate for NUDT15, with a catalytic efficiency of 4.0 × 104 M-1·s-1. LC-MS analysis of NUDT15 and NUDT18 catalyzed isoprene pyrophosphate hydrolysis revealed the generation of the corresponding monophosphates and inorganic phosphate. Furthermore, we solved the crystal structure of NUDT15 in complex with the hydrolysis product geranyl phosphate at a resolution of 1.70 Å. This structure revealed that the active site nicely accommodates the hydrophobic isoprenoid moiety and helped identify key binding residues. Our findings imply that isoprene pyrophosphates are endogenous substrates of NUDT15 and NUDT18, suggesting they are involved in animal isoprene pyrophosphate metabolism.

Discovery of Prenyltransferase-Guided Hydroxyphenylacetic Acid Derivatives from Marine Fungus Penicillium sp. W21C371.

Traditional isolation methods often lead to the rediscovery of known natural products. In contrast, genome mining strategies are considered effective for the continual discovery of new natural products. In this study, we discovered a unique prenyltransferase (PT) through genome mining, capable of catalyzing the transfer of a prenyl group to an aromatic nucleus to form C-C or C-O bonds. A pair of new hydroxyphenylacetic acid derivative enantiomers with prenyl units, (±)-peniprenydiol A (1), along with 16 known compounds (2-17), were isolated from a marine fungus, Penicillium sp. W21C371. The separation of 1 using chiral HPLC led to the isolation of the enantiomers 1a and 1b. Their structures were established on the basis of extensive spectroscopic analysis, including 1D, 2D NMR and HRESIMS. The absolute configurations of the new compounds were determined by a modified Mosher method. A plausible biosynthetic pathway for 1 was deduced, facilitated by PT catalysis. In the in vitro assay, 2 and 3 showed promising inhibitory activity against Escherichia coli β-glucuronidase (EcGUS), with IC50 values of 44.60 ± 0.84 μM and 21.60 ± 0.76 μM, respectively, compared to the positive control, D-saccharic acid 1,4-lactone hydrate (DSL). This study demonstrates the advantages of genome mining in the rational acquisition of new natural products.

Isolation, derivatization, and anti-microbial evaluation of secondary metabolites from Garcinia dryobalanoides

A detailed study on secondary metabolites from the stem bark of Garcinia dryobalanoides has yielded one triterpenoid and four xanthones. Along with that, five novel rubraxanthone derivatives had been successfully synthesised via Williamson etherification with various alkyl halides. The antibacterial evaluation on crude extract, isolated secondary metabolites (1-5), and synthesised compounds (6-9) against Lactiplantibacillus plantarum, Enterobacter cloacae, Pseudomonas aeruginosa, and Serratia marcescens demonstrated moderate to active activities outlining their bacteriostatic potential. The structure-activity relationship (SAR) study conducted revealed the presence of prenyl and hydroxy groups on the xanthone attributed to good bacterial inhibition. The introduction of the alkyl chain to the hydroxy part eventually decreases the antibacterial activity of the compound which is probably due to the bulkiness that causes steric hindrances, therefore limiting the ability to bind to its target site within the bacterial cell.

Alkene Cross-Metathesis with 2,5-Dimethyl-2,4-Hexadiene Enables Isobutylenyl/Prenyl Functionalizations and Rubber Valorization.

2,5-Dimethyl-2,4-hexadiene is a readily available and easily managable compound, whose symmetric and polymethylated dienic structure should be prone to engage in cross-metathesis reactions with other alkenes, but this has not been apparently exploited so far. Here we show that this reactant enables the easy synthesis of tri- and tetra-susbtituted alkenes (i. e. isobutylenyl and prenyl groups) from simple alkenes under mild reaction conditions, not only with the conventional 2nd generation Grubbs catalyst but also with other Grela-type catalyts such as StickyCat,TM AquaMetTM and GreenCatTM. The use of liquid and low volatile 2,5-dimethyl-2,4-hexadiene avoids the use of gaseous alkene reactants and, besides, showcases the reactivity of polyisoprene (rubber), thus allowing to optimize the reaction conditions for rubber upcycling, after metathesis reaction of the pristine or used polymer with simple alkenes. These results bring low volatile isoprene-type compounds as privileged poly-substituted reactants for alkene cross-metathesis reactions.

Methyl-Jasmonate Functions as a Molecular Switch Promoting Cross-Talk between Pathways for the Biosynthesis of Isoprenoid Backbones Used to Modify Proteins in Plants.

In plants, the plastidial mevalonate (MVA)-independent pathway is required for the modification with geranylgeranyl groups of CaaL-motif proteins, which are substrates of protein geranylgeranyltransferase type-I (PGGT-I). As a consequence, fosmidomycin, a specific inhibitor of 1-deoxy-d-xylulose (DX)-5 phosphate reductoisomerase/DXR, the second enzyme in this so-called methylerythritol phosphate (MEP) pathway, also acts as an effective inhibitor of protein prenylation. This can be visualized in plant cells by confocal microscopy by expressing GFP-CaM-CVIL, a prenylation sensor protein. After treatment with fosmidomycin, the plasma membrane localization of this GFP-based sensor is altered, and a nuclear distribution of fluorescence is observed instead. In tobacco cells, a visual screen of conditions allowing membrane localization in the presence of fosmidomycin identified jasmonic acid methyl esther (MeJA) as a chemical capable of gradually overcoming inhibition. Using Arabidopsis protein prenyltransferase loss-of-function mutant lines expressing GFP-CaM-CVIL proteins, we demonstrated that in the presence of MeJA, protein farnesyltransferase (PFT) can modify the GFP-CaM-CVIL sensor, a substrate the enzyme does not recognize under standard conditions. Similar to MeJA, farnesol and MVA also alter the protein substrate specificity of PFT, whereas DX and geranylgeraniol have limited or no effect. Our data suggest that MeJA adjusts the protein substrate specificity of PFT by promoting a metabolic cross-talk directing the origin of the prenyl group used to modify the protein. MVA, or an MVA-derived metabolite, appears to be a key metabolic intermediate for this change in substrate specificity.

In vitro Evaluation of the Antileishmanial and Antischistosomal Activities of p-Coumaric Acid Prenylated Derivatives.

We have evaluated eight p-coumaric acid prenylated derivatives in vitro for their antileishmanial activity against Leishmania amazonensis promastigotes and their antischistosomal activity against Schistosoma mansoni adult worms. Compound 7 ((E)-3,4-diprenyl-4-isoprenyloxycinnamic alcohol) was the most active against L. amazonensis (IC50=45.92 μM) and S. mansoni (IC50=64.25 μM). Data indicated that the number of prenyl groups, the presence of hydroxyl at C9, and a single bond between C7 and C8 are important structural features for the antileishmanial activity of p-coumaric acid prenylated derivatives.

Bioorthogonal labeling and profiling of N6-isopentenyladenosine (i6A) modified RNA.

Chemical modifications in RNAs play crucial roles in diversifying their structures and regulating numerous biochemical processes. Since the 1990s, several hydrophobic prenyl-modifications have been discovered in various RNAs. Prenyl groups serve as precursors for terpenes and many other biological molecules. The processes of prenylation in different macromolecules have been extensively studied. We introduce here a novel chemical biology toolkit that not only labels i6A, a prenyl-modified RNA residue, by leveraging the unique reactivity of the prenyl group, but also provides a general strategy to incorporate fluorescence functionalities into RNAs for molecular tracking purposes. Our findings revealed that iodine-mediated cyclization reactions of the prenyl group occur rapidly, transforming i6A from a hydrogen-bond acceptor to a donor. Based on this reactivity, we developed an Iodine-Mediated Cyclization and Reverse Transcription (IMCRT) tRNA-seq method, which can profile all nine endogenous tRNAs containing i6A residues in Saccharomyces cerevisiae with single-base resolution. Furthermore, under stress conditions, we observed a decline in i6A levels in budding yeast, accompanied by significant decrease of mutation rate at A37 position. Thus, the IMCRT tRNA-seq method not only permits semi-quantification of i6A levels in tRNAs but also holds potential for transcriptome-wide detection and analysis of various RNA species containing i6A modifications.

Akedanones A-C, In Vitro and In Vivo Antiplasmodial 2,3-Dihydronaphthoquinones Produced by Streptomyces sp. K20-0187.

Three new antiplasmodial compounds, named akedanones A (1), B (2), and C (3), were discovered from the cultured material of Streptomyces sp. K20-0187 isolated from a soil sample collected at Takeda, Kofu, Yamanashi prefecture in Japan. The structures of compounds 1-3 were elucidated as new 2,3-dihydronaphthoquinones having prenyl and reverse prenyl groups by mass spectrometry and nuclear magnetic resonance analyses. Compound 1 and the known furanonaphthoquinone I (4) showed potent in vitro antiplasmodial activity against chloroquine-sensitive and chloroquine-resistant Plasmodium falciparum strains, with half-maximal inhibitory concentration values ranging from 0.06 to 0.3 μM. Compounds 1 and 4 also displayed potent in vivo antiplasmodial activity against drug-sensitive rodent malaria Plasmodium berghei N strain, with inhibition rates of 47.6 and 43.1%, respectively, on intraperitoneal administration at a dose of 5 mg kg-1 day-1 for 4 days.

Effect of peanut stilbenoids, arachidin-1 and arachidin-3, on Streptococcus mutans growth and acid production

In this study we evaluated the effect of prenylated peanut stilbenoids on the growth, biofilm accumulation and acid production of the dental caries pathogen Streptococcus mutans. Prior research with the non-prenylated stilbenes, resveratrol and piceatannol, has shown that these molecules are active against S. mutans. Here we sought to determine if the addition of a prenyl group to the stilbene backbone increased anti-S. mutans activities. Two prenylated stilbenes, arachidin-1 and arachidin-3, were produced using a peanut hairy root production system. Compared to resveratrol and piceatannol, both arachidin-1 and arachidin-3 led to greater inhibition of S. mutans planktonic growth. This effect also led to reduced biofilm formation, by inhibiting growth, instead of a specific action against biofilm cells. Lastly, sub-MIC concentrations of arachidin-3 reduced the acid production of S. mutans above the ‘critical pH’ that leads to tooth enamel erosion. In summary, stilbenoids have anti-S. mutans activity, and prenylation enhances this activity.

Copper catalyzed benzylic sp3 C-H alkenylation.

The prenyl group is present in numerous biologically active small molecule drugs and natural products. We introduce benzylic C-H alkenylation of substrates Ar-CH3 with alkenylboronic esters (CH2)3O2B-CH[double bond, length as m-dash]CMe2 as a pathway to form prenyl functionalized arenes Ar-CH2CH[double bond, length as m-dash]CMe2. Mechanistic studies of this radical relay catalytic protocol reveal diverse reactivity pathways exhibited by the copper(ii) alkenyl intermediate [CuII]-CH[double bond, length as m-dash]CMe2 that involve radical capture, bimolecular C-C bond formation, and hydrogen atom transfer (HAT).

Potential protein tyrosine phosphatase 1B and α-glucosidase inhibitory flavonoids from Erythrina variegata: Experimental and computational results

Erythrina variegata L., a member of the Fabaceae family, is a valuable medicinal plant with a rich history of traditional medicinal uses. However, its potential as an antidiabetic agent has remained largely unexplored. In this study, three isoflavonoid compounds, namely eryvarin M (1), eryvarin H (2), and neobavaisoflavone (3), were isolated from E. variegata. These compounds displayed significant inhibitory effects on both protein tyrosine phosphatase 1B and α-glucosidase enzymes. The specific attachment position of the prenyl group to the isoflavonoid skeleton plays a pivotal role in determining the variation in their activity. Moreover, the results obtained from docking simulations corroborate the experimental findings, confirming the robust binding affinities of these metabolites toward the target proteins. The docking analysis further highlights that these compounds exhibit highly negative values of binding-free energies against proteins, indicative of their favorable binding affinities. In addition, the formation of hydrogen bonds in the binding region contributes to their binding interactions. These findings significantly enhance our understanding of the therapeutic potential of both E. variegata and its isoflavonoids as potential inhibitors for diabetes and related metabolic disorders, shedding light on their promising role in the field of diabetes research.

5,6-dihydroxypyranoflavone, a New Flavonoid with an Oxidized Prenyl Group from Dietary Plant Citrus hystrix

5,6-dihydroxypyranoflavone, a New Flavonoid with an Oxidized Prenyl Group from Dietary Plant Citrus hystrix