Geranyl Moiety Research Articles

Nitidane: An Irregular Prenylated Diterpene from the Cuticle of the Springtail Heteromurus nitidus.

Collembola are closely related to insects, but our knowledge of their often unique chemistry is limited. Here we report the identification of the epicuticular lipid nitidane, representing a novel class of epicuticular lipids. Nitidane (4) is an irregular terpene consisting of seven isoprene units, made up of a diterpene core that is modified by a geranyl moiety that is itself prenylated. The observed [46+(22+11)1]-terpene structure has not been reported before.

Novel insights into the antibacterial activities of cannabinoid biosynthetic intermediate, olivetolic acid, and its alkyl-chain derivatives.

Investigations of antibacterial activities revealed that the incorporation of longer alkyl chains to the C-6 position in resorcylic acid conferred antibacterial properties against Staphylococcus aureus and Bacillus subtilis. The resultant olivetolic acid (OA) derivatives with n-undecyl and n-tridecyl side-chains, even those lacking the hydrophobic geranyl moiety from their C-3 positions, exhibited strong antibacterial activities against B. subtilis at a MIC value of 2.5μM. Furthermore, the study demonstrated that the n-heptyl alkyl-chain modification at C-6 of cannabigerolic acid (CBGA) effectively enhanced the activity against B. subtilis, demonstrating the importance of the alkyl side-chain in modulating the bioactivity. Overall, the findings in this study provided insight into further evaluations of the antibacterial activities, as well as other various biological activities of OA and CBGA derivatives, especially with optimized hydrophobicities at both the alkyl and prenyl side-chain positions of the core skeleton for the discovery of novel drug seeds.

Catalysts for the Enzymatic Lipidation of Peptides.

Biologically active peptides are a major growing class of drugs, but their therapeutic potential is constrained by several limitations including bioavailability and poor pharmacokinetics. The attachment of functional groups like lipids has proven to be a robust and effective strategy for improving their therapeutic potential. Biochemical and bioactivity-guided screening efforts have identified the cyanobactins as a large class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that are modified with lipids. These lipids are attached by the F superfamily of peptide prenyltransferase enzymes that utilize 5-carbon (prenylation) or 10-carbon (geranylation) donors. The chemical structures of various cyanobactins initially showed isoprenoid attachments on Ser, Thr, or Tyr. Biochemical characterization of the F prenyltransferases from the corresponding clusters shows that the different enzymes have different acceptor residue specificities but are otherwise remarkably sequence tolerant. Hence, these enzymes are well suited for biotechnological applications. The crystal structure of the Tyr O-prenyltransferase PagF reveals that the F enzyme shares a domain architecture reminiscent of a canonical ABBA prenyltransferase fold but lacks secondary structural elements necessary to form an enclosed active site. Binding of either cyclic or linear peptides is sufficient to close the active site to allow for productive catalysis, explaining why these enzymes cannot use isolated amino acids as substrates.Almost all characterized isoprenylated cyanobactins are modified with 5-carbon isoprenoids. However, chemical characterization demonstrates that the piricyclamides are modified with a 10-carbon geranyl moiety, and in vitro reconstitution of the corresponding PirF shows that the enzyme is a geranyltransferase. Structural analysis of PirF shows an active site nearly identical with that of the PagF prenyltransferase but with a single amino acid substitution. Of note, mutation at this residue in PagF or PirF can completely switch the isoprenoid donor specificity of these enzymes. Recent efforts have resulted in significant expansion of the F family with enzymes identified that can carry out C-prenylations of Trp, N-prenylations of Trp, and bis-N-prenylations of Arg. Additional genome-guided efforts based on the sequence of F enzymes identify linear cyanobactins that are α-N-prenylated and α-C-methylated by a bifunctional prenyltransferase/methyltransferase fusion and a bis-α-N- and α-C-prenylated linear peptide. The discovery of these different classes of prenyltransferases with diverse acceptor residue specificities expands the biosynthetic toolkit for enzymatic prenylation of peptide substrates.In this Account, we review the current knowledge scope of the F family of peptide prenyltransferases, focusing on the biochemical, structure-function, and chemical characterization studies that have been carried out in our laboratories. These enzymes are easily amenable for diversity-oriented synthetic efforts as they can accommodate substrate peptides of diverse sequences and are thus attractive catalysts for use in synthetic biology approaches to generate high-value peptidic therapeutics.

Syntheses of Amorfrutins and Derivatives via Tandem Diels-Alder and Anionic Cascade Approaches.

We describe two complementary approaches based on a convergent [4+2] logic toward the synthesis of amorfrutins, cannabinoids, and related plant metabolites. An anionic cascade cyclization employing β-methoxycrotonates and β-chloro-α,β-unsaturated esters yielded amorfrutins in four linear steps and demonstrated utility of β-alkoxycrotonate-derived nucleophiles as functional equivalents of β-ketoester-derived dianions. Analogously, tandem Diels-Alder/retro-Diels-Alder cycloaddition of dimedone-derived bis(trimethylsiloxy)-dienes and α,β-alkynyl ester dienophiles provided facile access to resorcinol precursors of amorfrutins and cannabinoids, avoiding late-stage installation of prenyl or geranyl moieties as in previous approaches.

Complete Decoration of the Indolyl Residue in cyclo-l-Trp-l-Trp with Geranyl Moieties by Using Engineered Dimethylallyl Transferases.

Mutation of the gatekeeping residues for prenyl donor selectivity in six dimethylallyl transferases significantly increased their activities toward geranyl diphosphate. Forty-two geranylated derivatives were obtained from 15 cyclic dipeptides by using the engineered enzymes. Taking cyclo-l-Trp-l-Trp as an example, the geranyl moiety can be attached to all seven possible positions of the indole nucleus. This study demonstrates a convenient way to increase the structural diversity of geranylated products by structure-based engineering of the available dimethylallyl transferases.

Unprecedented Cyclization Catalyzed by a Cytochrome P450 in Benzastatin Biosynthesis.

Benzastatins have unique structures probably derived from geranylated p-aminobenzoic acids. The indoline and tetrahydroquinoline scaffolds are presumably formed by cyclization of the geranyl moiety, but the cyclization mechanism was unknown. We studied the benzastatin biosynthetic gene cluster of Streptomyces sp. RI18; functions of the six enzymes encoded by it were analyzed by gene disruption in a heterologous host and in vitro enzyme assays. We propose the biosynthetic pathway for benzastatins in which a cytochrome P450 (BezE) is responsible for the cyclization of geranylated p-acetoxyaminobenzoic acids; BezE catalyzes elimination of acetic acid to form an iron nitrenoid, nitrene transfer to form an aziridine ring, and nucleophilic addition of hydroxide ion to C-10 and chloride ion to C-9 to generate the indoline and tetrahydroquinoline scaffolds, respectively. Discovery of this enzyme, which should be termed cytochrome P450 nitrene transferase, provides an important insight into the functional diversity of cytochrome P450.

New Naphthoquinone Terpenoids from Marine Actinobacterium, Streptomyces sp. CNQ-509.

A member of the marine streptomycete clade MAR4, Streptomyces sp. CNQ-509, has genetic potential for the biosynthesis of hybrid isoprenoids and produces several meroterpenoids such as naphterpin, nitropyrrolin and marinophenazine. Our research on the strain CNQ-509 led to the isolation of two new naphterpin derivatives (1 and 2) comprised of naphthoquinone and geranyl moieties along with the known terpenoid, debromomarinone. The two-dimensional structure of these compounds was determined through spectral data analysis using data from NMR, MS and UV spectroscopy. Furthermore, the full structures of 1 and 2 including absolute configurations were unequivocally established by a combination of NMR experiments and chemical modifications.

Antifungal toxicity of linear geranylphenol. Influence of oxigenate substituents

Twenty four linear geranylphenols were evaluated for their antifungal properties against ATCC and clinical isolates of Candida albicans and Cryptococcus neoformans. For the analysis of their antifungal behavior the compounds were grouped into two series: (i) compounds with only one geranyl substituent on the benzene ring and (ii) compounds with two geranyl moieties on the benzene ring. Results showed that compounds of series (i) present better antifungal activities than those of series (ii). In addition, within group (i) all compounds showed better activities against C. neoformans than against C. albicans which can be easily verified by comparing MIC100 or MIC50 of each compound against both fungi. Di- (10 and 11) and tri-hydroxy (3 and 4) compounds showed significant anti-cryptoccocal activity, being 3, 10 and 11 highly active with MIC100 or MIC50 = 3.9 μg/mL similar to the standard drug amphotericin B. Moreover, when evaluating the toxicity of compounds 6, 10 and 11 on the HDF cell line (human dermal fibroblasts), results were obtained with IC50 values > 100 μM, considered as non-toxic for the cell. This indicates that the toxicity of the analyzed compounds is selective towards fungi, which makes them a very attractive family for the development of future drugs.

Crystal structure and enantioselectivity of terpene cyclization in SAM-dependent methyltransferase TleD.

TleD is a SAM (S-adenosyl-l-methionine)-dependent methyltransferase and acts as one of the key enzymes in the teleocidin B biosynthesis pathway. Besides methyl transferring, TleD also rearranges the geranyl and indole moieties of the precursor to form a six-membered ring. Moreover, it does not show homologies with any known terpenoid cyclases. In order to elucidate how such a remarkable reaction could be achieved, we determined the complex crystal structures of TleD and the cofactor analogue S-adenosyl-l-homocysteine with or without the substrate teleocidin A1. A domain-swapped pattern via an additional N-terminal α-helix is observed in TleD hexamers. Structural comparison and alignment shows that this additional N-terminal α-helix is the common feature of SAM methyltransferase-like cyclases TleD and SpnF. The residue Tyr21 anchors the additional N-terminal α-helix to a 'core SAM-MT fold' and is a key residue for catalytic activity. Molecular dynamics simulation results suggest that the dihedral angle C23-C24-C25-C26 of teleocidin A1 is preferred to 60-90° in the TleD and substrate complex structure, which tend to adopt a Re-face stereocenter at C25 position after reaction and is according to in vitro enzyme reaction experiments. Our results also demonstrate that methyl transfer can be a new chemical strategy for carbocation formation in the terpene cyclization, which is the key initial step.

Total Synthesis of (±)-Isoperbergins and Correction of the Chemical Structure of Perbergin.

On the basis of its reported chemical structure, perbergin, a Rhodococcus fascians virulence quencher from the bark of Dalbergia pervillei, and its isomer were synthesized in nine steps with a 13.5% yield. However, the NMR spectra of the synthetic products were inconsistent with those reported in the literature. Re-evaluation of the 1D and 2D NMR spectra of the natural product perbergin revealed that the geranyl moiety of this compound is located at C-6 and has an E-configuration, instead of the reported C-8 geranylation with a Z-configuration. Interestingly, the synthetic isoperbergins demonstrated good antibacterial activity against R. fascians, Mycobacterium smegmatis, and Staphylococcus aureus, but not against the Gram-negative bacteria Pseudomonas aeruginosa and Escherichia coli.

A Membrane‐Bound Prenyltransferase Catalyzes the O‐Prenylation of 1,6‐Dihydroxyphenazine in the Marine Bacterium Streptomyces sp. CNQ‐509

Streptomyces sp. CNQ-509 produces the rare O-prenylated phenazines marinophenazines A and B. To identify the enzyme catalyzing the O-prenyl transfer in marinophenazine biosynthesis, we sequenced the genome of S. sp. CNQ-509. This led to the identification of two genomic loci harboring putative phenazine biosynthesis genes. The first locus contains orthologues for all seven genes involved in phenazine-1-carboxylic acid biosynthesis in pseudomonads. The second locus contains two known phenazine biosynthesis genes and a putative prenyltransferase gene termed cnqPT1. cnqPT1 codes for a membrane protein with sequence similarity to the prenyltransferase UbiA of ubiquinone biosynthesis. The enzyme CnqPT1 was identified as a 1,6-dihydroxyphenazine geranyltransferase, which catalyzes the C-O bond formation between C-1 of the geranyl moiety and O-6 of the phenazine scaffold. CnqPT1 is the first example of a prenyltransferase catalyzing O-prenyl transfer to a phenazine.

A methyltransferase initiates terpene cyclization in teleocidin B biosynthesis.

Teleocidin B is an indole terpenoid isolated from Streptomyces. Due to its unique chemical structure and ability to activate protein kinase C, it has attracted interest in the areas of organic chemistry and cell biology. Here, we report the identification of genes encoding enzymes for teleocidin B biosynthesis, including nonribosomal peptide synthetase (tleA), P-450 monooxygenase (tleB), prenyltransferase (tleC), and methyltransferase (tleD). The tleD gene, which is located outside of the tleABC cluster on the chromosome, was identified by transcriptional analysis and heterologous expression. Remarkably, TleD not only installs a methyl group on the geranyl moiety of the precursor but also facilitates the nucleophilic attack from the electron-rich indole to the resultant cation, to form the indole-fused six-membered ring. This is the first demonstration of a cation, generated from methylation, triggering successive terpenoid ring closure.

A Cytochrome P450 Serves as an Unexpected Terpene Cyclase during Fungal Meroterpenoid Biosynthesis

Viridicatumtoxin (1) is a tetracycline-like fungal meroterpenoid with a unique, fused spirobicyclic ring system. Puzzlingly, no dedicated terpene cyclase is found in the gene cluster identified in Penicillium aethiopicum. Cytochrome P450 enzymes VrtE and VrtK in the vrt gene cluster were shown to catalyze C5-hydroxylation and spirobicyclic ring formation, respectively. Feeding acyclic previridicatumtoxin to Saccharomyces cerevisiae expressing VrtK confirmed that VrtK is the sole enzyme required for cyclizing the geranyl moiety. Thus, VrtK is the first example of a P450 that can catalyze terpene cyclization, most likely via initial oxidation of C17 to an allylic carbocation. Quantum chemical modeling revealed a possible new tertiary carbocation intermediate E that forms after allylic carbocation formation. Intermediate E can readily undergo concerted 1,2-alkyl shift/1,3-hydride shift, either spontaneously or further aided by VrtK, followed by C7 Friedel-Crafts alkylation to afford 1. The most likely stereochemical course of the reaction was proposed on the basis of the results of our computations.

Synthesis of isoprenoid chain-contained chemical probes for an investigation of molecular interactions by using quartz crystal microbalance

Five probes including four that contained isoprenoid chain were synthesized. These probes were assembled onto the gold-coated quartz crystal chips for analysis of their interactions with four yeast proteins by using the quartz crystal microbalance technology. Results showed that 3-phosphoglycerate phosphokinase and triosephosphate isomerase had clear interactions with certain probes, while glutathione reductase and phosphoglucose isomerase gave much lower interaction signals. It also suggested that 3-phosphoglycerate phosphokinase had two sites interacting with the probe attached with a geranyl moiety. Further molecule simulation experiments provided supportive information on these intermolecular interactions. Together, our data suggested that there are hydrophobic interactions, with relatively good selectivity, between isoprenoid chain and proteins.

Geranylation of Cyclic Dipeptides by the Dimethylallyl Transferase AnaPT Resulting in a Shift of Prenylation Position on the Indole Ring

The dimethylallyl transferase AnaPT from Neosartorya fischeri is involved in the biosynthesis of acetylaszonalenin and catalyses the regioselective and stereospecific C3α-prenylation of (R)-benzodiazepinedione in the presence of dimethylallyl diphosphate. This enzyme also converts several tryptophan-containing cyclic dipeptides to C3α-prenylated indolines. In this study, we demonstrate the geranylation of (R)-benzodiazepinedione and five other cyclic dipeptides by AnaPT in the presence of geranyl diphosphate (GPP). Interestingly, structure elucidation by NMR and MS analyses revealed that, with GPP, the geranyl moiety is attached to C-6 or C-7 rather than C-3 of the indole ring of the enzyme products. For (R)-benzodiazepinedione, one dominant C6-geranylated derivative was obtained, whereas the other five substrates yielded both C6- and C7-geranylated products. Neither acceptance of GPP by a dimethylallyl transferase from the dimethylallyltryptophan synthase superfamily, nor the alkylation shift from C-3 to the benzene ring of the indole nucleus has been reported previously.

Bioactive Dimeric Carbazole Alkaloids fromMurraya koenigii

Phytochemical studies on the CHCl3 extract of the fruit pulp of Murraya koenigii afforded three new dimeric carbazole alkaloids, bisgerayafolines A-C (1-3). Bisgerayafolines A-C (1-3) are structurally unique dimeric carbazole alkaloids comprising geranyl moieties incorporated in their structures. Compounds 1-3 exhibited various levels of antioxidant, anti-α-glucosidase, DNA binding, and cytotoxic activities and protein interactions.

Minor C-geranylated flavanones from Paulownia tomentosa fruits with MRSA antibacterial activity

Exhaustive chromatographic separation of the chloroform portion of the ethanolic extract obtained from Paulownia tomentosa (Thunb). Steud. (Paulowniaceae) fruits has led to isolation of ten C-6 geranylated flavanones tomentodiplacone C-I and mimulone C-E, featured by 3'-methoxy and 4'-hydroxy or 4'-hydroxy substitution of the B-ring of the flavonoid, respectively. The structures of these compounds were determined by using mass spectrometry (including HRMS) and 1D and 2D NMR spectroscopy. The absolute configurations of the compounds at C-2 were determined using circular dichroism. The obtained compounds showed the presence of a geranyl moiety functionalized by a carbonyl, hydroxyl or methoxyl group, or by formation of tetrahydrofuran or fused-pyrane ring, respectively. All of the flavanones described were isolated for the first time from a natural source. The antibacterial activities of selected compounds isolated along with the previously isolated geranylated flavanones were evaluated against a common panel of microbes and MRSA strains. The selected isolated compounds were tested for their ability to affect eukaryotic translation initiation via dual-luciferase reporter assay (firefly and renilla).

Nucleoterpenes of Thymidine and 2′‐Deoxyinosine: Synthons for a Biomimetic Lipophilization of Oligonucleotides

2'-Deoxyinosine (1) and thymidine (7) were N-alkylated with geranyl and farnesyl moieties. These hydrophobic derivatives, 3a and 3b, and 9a and 9b, respectively, represent the first synthetic biomimetic nucleoterpenes and were subsequently 5'-protected and converted into the corresponding 3'-O-phosphoramidites, 5a and 5b and 11a and 11b, respectively. The latter were used to prepare a series of lipophilized oligonucleotide dodecamers, a part of which were additionally labelled with indocarbocyanine fluorescent dyes (Cy3 or Cy5), 18-23. The insertion of the lipooligonucleotides into, as well as duplex formation at artificial lipid bilayers was studied by single-molecule fluorescence spectroscopy and fluorescence microscopy.

First synthesis of acrovestone, desmethylacrovestone and derivatives

Acrovestone 1 and desmethylacrovestone 2 are natural products belonging to the family of bis-acetophenone. They were isolated from the leaves and fruits of Acronychia penduculata L. (Miq.). New derivatives1 have been recently discovered and showed a substantial cytotoxic activity on A2058 melanoma cells. However, some structural features remain to be elucidated. To conclude on their structures we realized the first synthesis of acrovestone 1 and its natural and non-natural derivatives. This three steps synthesis involved the key dimerization between two acetoxyphloroglucinol monomers using a Friedel and Craft reaction. This dimer was then functionalized by e.g. prenyl, geranyl or furane moieties. The cytotoxic activities of the new compounds have been evaluated and are reported.

Bioactive C-geranylated metabolites from Piper crassinervium: biological and biosynthetic studies

Piperaceae family comprises 4 genera and more than 4000 species being the Piper genus the most abundant with approximately 2000 species [1]. Piper crassinervium accumulates antifungal, trypanocidal and antioxidant geranylated metabolites derived from p-hydroquinone and benzoic acid [2,3]. Aromatic geranyltransferases are a group of geranyltransferases that catalyze the C-geranylation step on aromatic substrates; they are membrane-bound enzymes and have showed strict substrate specificity for geranyldiphosphate (GPP) as the prenyl donor, although accept a variety of substrates as acceptors of GPP moieties [4,5]. Here we report the in vivo and in vitro biosynthetic studies carried out to elucidate the biosynthetic origin of geranyl moiety in compounds 1 and 2. The pattern of incorporation of [1-13C]-D-glucose determined by quantitative 13C NMR spectroscopy indicated that geranyl moiety come from mevalonate and triose/piruvate pathways in compound 1, but only the triose/piruvate pathway appear involved in compound 2. In addition, in vitro enzymatic studies of proteic extracts from leaves of P. crassinervium with 4-hydroxy and 3,4-dihydroxy benzoic acids as substrates, showed that O-geranylated products were biosynthesized instead of the C-geranylated ones. Purification and characterization processes of geranyltransferase activity, involving 1D, 2D SDS PAGE and MS studies of microsomal fractions are also discussed.