Unnatural Analogues Research Articles

Real-Time Electrochemical Monitoring of the Polymerase Chain Reaction by Mediated Redox Catalysis

We described the proof-of-principle of a nonoptical real-time PCR that uses cyclic voltammetry for indirectly monitoring the amplified DNA product generated in the PCR reaction solution after each PCR cycle. To enable indirect measurement of the amplicon produced throughout PCR, we monitor electrochemically the progressive consumption (i.e., the decrease of concentration) of free electroactive deoxynucleoside triphosphates (dNTPs) used for DNA synthesis. This is accomplished by exploiting the fast catalytic oxidation of native deoxyguanosine triphosphate (dGTP) or its unnatural analogue 7-deaza-dGTP by the one-electron redox catalysts Ru(bpy)(3)(3+) (with bpy = 2,2'-bipyridine) or Os(bpy)(3)(3+) generated at an electrode. To demonstrate the feasibility of the method, a disposable array of eight miniaturized self-contained electrochemical cells (working volume of 50 microL) has been developed and implemented in a classical programmable thermal cycler and then tested with the PCR amplification of two illustrated examples of real-world biological target DNA sequences (i.e., a relatively long 2300-bp sequence from the bacterial genome of multidrug-resistant Achromobacter xylosoxidans and a shorter 283-bp target from the human cytomegalovirus). Although the method works with both mediator/base couples, the catalytic peak current responses recorded with the Ru(bpy)(3)(3+)/dGTP couple under real-time PCR conditions are significantly affected by a continuous current drift and interference with the background solvent discharge, thus leading to poorly reproducible data. Much more reproducible and reliable results are finally obtained with the Os(bpy)(3)(3+)/7-deaza-dGTP, a result that is attributed to the much lower anodic potential at which the catalytic oxidation of 7-deaza-dGTP by Os(bpy)(3)(3+) is detected. Under these conditions, an exponential decrease of the catalytic signal as a function of the number of PCR cycles is obtained, allowing definition of a cycle threshold value (C(t)) that correlates inversely with the initial amount of target DNA. A semilogarithmic plot of C(t) with the initial copy number of target DNA gives a standard linear curve similar to that obtained with fluorescent-based real-time PCR. Although the detection limit (10(3) molecules of target DNA in 50 microL) and sensitivity of the electrochemical method is not as high as conventional optical-based real-time PCR, the methodology described here offers many of the advantages of real-time PCR, such as a high dynamic range (over 8-log(10)) and speed, high amplification efficiency (close to 2), and the elimination of post-PCR processing. The method also has the advantage of being very simple, just requiring the use of low-cost single-use electrodes and the addition of a minute amount of redox catalyst into the PCR mixture. Moreover, compared to the other recently developed electrochemical real-time PCR based on solid-phase amplification, the present approach does not require electrode functionalization by a DNA probe. Finally, on account of the relative insensitivity of electrochemical methods to downscaling, the detection scheme is quite promising for use in miniaturized devices and in the development of point-of-care diagnosis applications.

A chemical-genetic approach for functional analysis of plant protein kinases

Plant genomes encode hundreds of protein kinases, yet only for a small fraction of them precise functions and phosphorylation targets have been identified. Recently, we applied a chemical-genetic approach to sensitize the tomato serine/threonine kinase Pto to analogs of PP1, an ATP-competitive and cell-permeable small-molecule inhibitor. The Pto kinase confers resistance to Pst bacteria by activating immune responses upon specific recognition of bacterial effectors. By using PP1 analogs in combination with the analog-sensitive Pto, we shed new light on the role of Pto kinase activity in effector recognition and signal transduction. Here we broaden the use of this chemical-genetic approach to another defense-related plant protein kinase, the MAP kinase LeMPK3. In addition, we show that analog-sensitive but not wild-type kinases are able to use unnatural N6-modified ATP analogs as phosphodonors that can be exploited for tagging direct phosphorylation targets of the kinase of interest. Thus, sensitization of kinases to analogs of the small-molecule inhibitor PP1 and ATP can be an effective tool for the discovery of cellular functions and phosphorylation substrates of plant protein kinases.

Development of a practical mass spectrometry based assay for determining enantiomeric excess. A fast and convenient method for the optimization of PLE-catalyzed hydrolysis of prochiral disubstituted malonates

A practical mass spectrometry-based enantioselectivity assay is presented which makes use of enantiomerically enriched, but not enantiomerically pure, probe molecules readily obtained from esterase hydrolysis of prochiral malonates. The technique presented here allows us to recycle materials obtained from esterase hydrolysis which give substantial, but synthetically insufficient, enantiomeric excess as probe molecules in an enantioselectivity assay. The enantiomerically enriched products are esterified using deuterium-labelled alcohol. The enantiomeric excess is measured using mass spectrometry (LC–MS and LDI) by measuring the D 5/H 5 ratio in the resulting products obtained from an enzymatic hydrolysis. The D 5/H 5 ratio is corrected to account for the enantiomeric purity of the probe. Herein we report the results obtained from Pig Liver Esterase hydrolyses of prochiral malonate esters and outline the strengths and limitations of this approach to enantioselectivity determinations. This assay strategy was able to identify reaction conditions that led to an improvement in ee from 70% ee to >97% ee in the PLE-catalyzed hydrolysis of a prochiral malonate used to prepare unnatural serine analogues.

A Quantitative Comparison of Wild‐Type and Gatekeeper Mutant Cdk2 for Chemical Genetic Studies with ATP Analogues

Chemical genetic studies with enlarged ATP binding sites and unnatural ATP analogues have been applied to protein kinases for characterisation and substrate identification. Although this system is becoming widely used, there are limited data available about the kinetic profile of the modified system. Here we describe a detailed comparison of the wild-type cdk2 and the mutant gatekeeper kinase to assess the relative efficiencies of these kinases with ATP and unnatural ATP analogues. Our data demonstrate that mutation of the kinase alters neither the substrate specificity nor the phosphorylation site specificity. We find comparable K(M)/V(max) values for mutant cdk2 and wild-type kinase. Furthermore, F80G cdk2 is efficiently able to compensate for a defective cdk in a biological setting.

Unnatural nucleosides with unusual base pairing properties.

Synthetic modified nucleosides designed to pair in unusual ways with natural nucleobases have many potential applications in biology and biotechnology. This overview lays the foundation for future protocol units on synthesis and application of unnatural bases, with particular emphasis on unnatural base analogs that mimic natural bases in size, shape, and biochemical processing. Topics covered include base pairs with alternative H-bonding schemes, dimensionally expanded base pairs, hydrophobic base pairs, metal-ligated bases, degenerate bases, universal nucleosides, and triplex constituents.

A novel class of H 3 antagonists derived from the natural product guided synthesis of unnatural analogs of the marine bromopyrrole alkaloid dispyrin

This Letter describes the natural product guided synthesis of unnatural analogs of the marine bromopyrrole alkaloid dispyrin, and the resulting SAR of H 3 antagonism. Multiple rounds of iterative parallel synthesis improved human H 3 IC 50 ∼33-fold, and afforded a new class of H 3 antagonists based on the novel bromotyramine core of dispyrin.

Semisynthesis and Biological Activity of Stemofoline Alkaloids

The semisynthesis of the Stemona alkaloids (3'R)-stemofolenol (1), (3'S)-stemofolenol (2), methylstemofoline (3), and (3'S)-hydroxystemofoline (5) and the unnatural analogues (11E)-methylstemofoline (15) and 3'R-hydroxystemofoline (11) has been achieved starting from (11Z)-1',2'-didehydrostemofoline (4). This synthesis allowed, for the first time, access to diastereomerically enriched samples of 1 and 2 and the assignment of their absolute configurations at C-3'. These compounds were obtained in sufficient quantities to allow for their biological testing. In a quantitative assay as AChE inhibitors, (11Z)-1',2'-didehydrostemofoline (4) and (3'S)-hydroxystemofoline (5) were found to be the most active.

Enantioseparation of β-substituted tryptophan analogues with modified cyclodextrins by capillary zone electrophoresis

Direct capillary zone electrophoretic methods were developed for the separation of the enantiomers of unnatural β-substituted tryptophan analogues such as erythro- and threo-β-methyl-, β-2-propyl-, β-3-pentyl-, β-phenyl- and β-2,5-dimethoxyphenyltryptophan. Cyclodextrins (CDs) were chosen as chiral selectors because of their favorable properties (stability, commercial availability, low cost, UV transparency, inertness, etc.). Capillary zone electrophoresis was carried out using sulfopropylated-α-CD (SP2-α-CD), sulfopropylated-β-CD (SP2-β-CD) both with a degree of substitution of 2 moles/mole cyclodextrin, and sulfopropylated-β-CD (SP4-β-CD) with a degree of substitution of 4 moles/mole β-cyclodextrin. With this technique all compounds investigated are baseline resolved using different background electrolytes and chiral additives. The elution sequence was determined in all cases.

Chemical Transformations of Parthenin, a Natural Bioactive Sesquiterpenoid [1

Chemical modifications of parthenin, a naturally occurring bioactive sesquiterpenoid, were carried out in regio- and stereoselective manners using various inexpensive reagents to form different natural and unnatural analogues. Reactions including dehydration, reduction, alkylation, addition and hydroxylation have been studied. In some of the analogues, the alpha-methylene-gamma-lactone moiety, which plays a vital role for bioactivity ofparthenin, remained intact.

Structural studies of C-ring substituted unnatural analogues of prodigiosin

The structure of both the free base and the hydrochloride of an unnatural analogue of prodigiosin, 4-methoxy-5-((4,5-dimethyl -2H-pyrrol-2-ylidene)methyl)- 2,2′-bi-1H-pyrrole, are reported. The free base crystallizes from methylene chloride as a hydrogen bonded dimer. The structure of the hemihydrate hydrochloride of the related 4-methoxy-5-((1-methyl -2H-pyrrol-2-ylidene)methyl)- 2,2′-bi-1H-pyrrole is also reported.

An Overview of Syntheses of Apogalanthamine Analogues and 7‐Aza Derivatives of Steganacin and Steganone (Eur. J. Org. Chem. 35/2008)

AbstractThe cover picture shows flowers belonging to the crinum family, a member of the well‐known amaryllidaceae family, in the background. A number of naturally occurring alkaloids with very intriguing biological potential have been isolated from the amaryllidaceae family of flowers. The structures shown in the foreground of the cover picture are some representative examples of amaryllidaceae alkaloids, such as narciclassine, hippadine, lycorine etc., as well as a few unnatural analogues bearing close structural similarity to some of the amaryllidaceae alkaloids. Details of some of the structures and the recent advances in the synthesis of some of the unnatural and yet structurally similar alkaloid analogues are presented in the Microreview by P. Appukkuttan and E. Van der Eycken on p. 5867ff.

Macrolactamization versus Macrolactonization: Total Synthesis of FK228, the Depsipeptide Histone Deacetylase Inhibitor

The cyclic depsipeptide FK228 is the only natural product histone deacetylase (HDAC) inhibitor that has advanced to clinical trials as an anticancer agent. While currently obtained by fermentation, total synthesis is an attractive alternative that will facilitate the preparation of unnatural analogues. The previous total syntheses of FK228 featured macrocylization by ester bond formation from a seco-hydroxy acid. Such routes are operationally jeopardized by the steric hindrance of the carboxylic acid and the sensitivity of the allylic alcohol toward elimination. We report a strategically different approach whereby the ester bond is formed intermolecularly at an early stage and macrocyclization is efficiently achieved by amide bond formation.

Total synthesis of Ciliatamides A-C: stereochemical revision and the natural product-guided synthesis of unnatural analogs.

The first total synthesis of Ciliatamides A-C was completed, leading to a revision of the reported stereochemistry from (S,S) to the (R,R) enantiomers. Due to the expedited route, a library of over 50 unnatural ciliatamide analogs was also prepared.

Diastereoselective Synthesis of α,β′-Disubstituted Aminomethyl(2-carboxyethyl)phosphinates as Phosphinyl Dipeptide Isosteres

A new and efficient method has been developed for the diastereoselective synthesis of unnatural dipeptide analogues containing the metabolically stable phosphinic moiety, NH 2XaaPsi[P(O)OHCH 2]XaaOH, which mimics the transition state of tetrahedral geometry of a scissile peptide bond in hydrolysis by protease. The method is based upon stereospecific Michael addition of stereodefined alpha-aminoalkyl- H-phosphinates to acrylates and subsequent diastereoselective alkylation at the beta'-position of the resulting Michael adducts.

A New Catalytic Cu(II)/Sparteine Oxidant System for β,β-Phenolic Couplings of Styrenyl Phenols: Synthesis of Carpanone and Unnatural Analogs

A new catalytic Cu(II)/sparteine system has been developed to promote beta,beta-phenolic couplings of styrenyl phenols en route to carpanone and related unnatural congeners in yields exceeding 85%.

Total Synthesis of the Immunosuppressants Myriocin and 2-epi-Myriocin

Total syntheses of the natural immunosuppressant myriocin (1) and the equipotent unnatural analogue 2-epi-myriocin (in protected form) have been achieved through a common strategy. The key transformations are the efficient synthesis of a quaternary (E)-vinylglycine by asymmetric deconjugative alkylation of a dehydroamino acid and an unusually highly diastereoselective dihydroxylation of the vinylglycine alkene.

Explorations of Stemona Alkaloid-Inspired Analogues: Skeletal Modification and Functional Group Diversification

A tandem Diels-Alder/Schmidt reaction provided an efficient route for the exploration of unnatural Stemona alkaloid analogues. Thus, a series of tricyclic scaffolds were efficiently prepared and then elaborated into seven sets of functionalized analogues. These derivatives incorporated appended heterocycles, such as indoles and quinolines, or other diversity-incorporating moieties such as carbamates and amines. Both the scaffold-generation sequence and the diversification steps could be manipulated to provide regio- and diastereochemically pure products.

Asymmetric Synthesis of (-)-6-epi-Centrolobine

A stereoselective total synthesis of (-)-6-epi-centrolobine, an unnatural analogue of (-)-centrolobine, starting from readily available tri-O-acetyl-D-glucal has been described for the first time. The key steps involved in this synthetic approach are stereoselective C-glycosidation, dehydroxylation and Wittig reaction. The target molecule was achieved in nine steps with 49% overall yield.

Synthesis and bioorthogonal coupling chemistry of a novel cyclopentenone-containing unnatural tyrosine analogue

Herein we report the synthesis of a novel amino acid with orthogonal functionality to the natural amino acid side chains. Tyrosine was O-alkylated with a cyclic 5-membered α,β-unsaturated ketone ring ( 5). We have established that this amino acid analogue can undergo cycloaddition reactions in aqueous media with in situ generated nitrones. Nitrone formation occurred by micellar catalysis can undergo aqueous 1,3-dipolar cycloaddition reactions with the unnatural Tyr. We also performed a linear free energy analysis of the one pot bioconjugation reaction in water using cyclopentenone as a model for the Tyr analogue and seven different aryl nitrones. We found that the Hammett ρ value was −0.94, suggesting that the reaction occurs in a concerted fashion with a slight positive charge buildup in the transition state. The Hammett ρ value also suggests that the bioconjugation reaction is tolerant of different substituents and thus may be useful for introducing novel functionality into peptides and proteins containing the Tyr analogue 5. The aqueous 1,3-dipolar cycloaddition reactions, that use nitrones to trap the O-alkylated Tyr 5, establish a novel strategy for rapid, water compatible bioconjugation reactions.

Expanding the Substrate Tolerance of Biotin Ligase through Exploration of Enzymes from Diverse Species

Technologies that enable the site-specific conjugation of chemical probes onto proteins are extremely useful for applications in cell biology and proteomics. We cloned, expressed, and purified biotin ligases from nine different species and screened them for the ability to ligate unnatural analogues of biotin onto the human p67 biotin acceptor domain. We discovered that the biotin ligases of Saccharomyces cerevisiae (yeast) and Pyrococcus horikoshii could accept alkyne and azide derivatives of biotin, respectively. HPLC, gel-shift, and mass spectrometry assays confirmed that these ligation reactions were ATP- and enzyme-dependent, as well as site-specific. We used the P. horikoshii-catalyzed azide ligation reaction to site-specifically introduce a phosphine probe onto p67 using the Staudinger ligation. These new ligation reactions demonstrate the differential substrate specificities of biotin ligases from different organisms and open the door to novel protein labeling applications.