Combinatorial biocatalysis: taking the lead from nature

Combinatorial biocatalysis is an emerging technology in the field of drug discovery. The biocatalytic approach to combinatorial chemistry uses enzymatic, chemoenzymatic, and microbial transformations to generate libraries from lead compounds. Important recent advances in combinatorial biocatalysis include iterative derivatization of small molecules and complex natural products, regioselectively controlled libraries, novel one-pot library syntheses, process automation, and biocatalyst enhancements.     

Annelated pyrrolo-pyrimidines from amino-cyanopyrroles and BMMAs as leads for new DNA-interactive ring systems

The efficient one-pot synthesis of several new tricyclic systems of type 1 and 2, obtained from the reaction of substituted 2-amino-3-cyanopyrroles and 3-amino-4-cyanopyrroles with BMMAs, is reported. The duration and yields of the reaction strongly depend on the reactivity of the starting pyrrole and on the size of the ring to be formed. Mechanist features of the reaction were investigated and proposed by studying also the reactivity of a 3-aminopyrrole-2,4-dicyano substituted. The method reported represents the first example of the use of BMMA reagents in combination with pyrrole derivatives and allows an easy and versatile entry to a large number of hitherto unknown pyrrolo-pyrimidines further annelated with nitrogen heterocycles of different sizes. These new polycondensed heterocycles possess the requisite to interact with DNA.     

Discovery of potent antiviral (HSV-1) quinazolinones and initial structure-activity relationship studies

The discovery of antiviral activity of 2,3-disubstituted quinazolinones, prepared by a one-pot, three-component condensation of isatoic anhydride with amines and aldehydes, against Herpes Simplex Virus (HSV)-1 is reported. Sequential iterative synthesis/antiviral assessment allowed structure-activity relationship (SAR) generation revealing synergistic structural features required for potent anti-HSV-1 activity. The most potent derivatives show greater efficacy than acyclovir against acute HSV-1 infections in neurons and minimal toxicity to the host.     

A facile approach to diosgenin and furostan type saponins bearing a 3beta-chacotriose moiety

Combination of a one-pot coupling technique and the use of benzyl ethers as permanent protecting groups offered a short and simple route to dioscin-type saponins. This strategy in combination with a mild reductive opening procedure of the spiroketal function in diosgenin also offered a convenient approach to bidesmosidic furostan type saponins. Me(3)N.BH(3)/AlCl(3) promoted acetal opening of 3-O-TBDMS-protected diosgenin gave the 26-OH acceptor 9 into which a benzylated beta-glucose moiety was introduced by a S(N)2-type imidate coupling. After cleavage of the silyl ether, the 3beta-O-glucose and the 4-O-linked rhamnose of the chacotriose unit were introduced by a NIS/AgOTf-promoted one-pot coupling sequence utilising thioglycoside donors and their different reactivity in different solvents. After removal of a benzoyl group, the same coupling conditions were also used for the coupling of the second 2-O-linked rhamnose unit. The target substance was obtained after cleavage of the protecting benzyl ethers under Birch-type conditions, which did not affect the double bond in the steroid skeleton.     

Synthesis of trifluoroborate functionalised imidazolium salts as precursors to weakly coordinating bidentate NHC ligands

A new class of trifluoroborate functionalised N-heterocyclic carbene precursors have been synthesised, isolated and characterised structurally. The ligands were obtained via a serendipitous one-pot reaction in which deprotection, cyclisation and fluorination of boryl-functionalised diarylethylenediamine derivatives occur concurrently. Deprotonation of the imidazolium salts was found to yield the free carbene, though 18-crown-6 was found necessary to prevent further reactivity of the resulting aryl potassium trifluoroborate salts; in the absence of 18-crown-6, elimination of KF resulted in a cyclic carbene-BF₂ arene adduct. Complexation to rhodium was facile, and yielded four-coordinate complexes in which the Rh-BF₃ interaction was determined by ¹⁹F NMR spectroscopy to be weak.     

Safer one-pot synthesis of the ‘SHAPE’ reagent 1-methyl-7-nitroisatoic anhydride (1m7)

Estimating the reactivity of 2′-hydroxyl groups along an RNA chain of interest aids in the modeling of the folded RNA structure; flexible loops tend to be reactive, whereas duplex regions are generally not. Among the most useful reagents for probing 2′-hydroxyl reactivity is 1-methyl-7-nitroisatoic anhydride (1m7), but the absence of a reliable, inexpensive source has prevented widespread adoption. An existing protocol for the conversion of an inexpensive precursor 4-nitroisatoic anhydride (4NIA) recommends the use of NaH in dimethylformamide (DMF), a reagent combination that most molecular biology labs are not equipped to handle, and that does not scale safely in any case. Here we describe a safer, one-pot method for bulk conversion of 4NIA to 1m7 that reduces costs and bypasses the use of NaH. We show that 1m7 produced by this method is free of side products and can be used to probe RNA structure in vitro.     

Radioactive phosphorylation of alcohols to monitor biocatalytic Diels-Alder reactions

Nature has efficiently adopted phosphorylation for numerous biological key processes, spanning from cell signaling to energy storage and transmission. For the bioorganic chemist the number of possible ways to attach a single phosphate for radioactive labeling is surprisingly small. Here we describe a very simple and fast one-pot synthesis to phosphorylate an alcohol with phosphoric acid using trichloroacetonitrile as activating agent. Using this procedure, we efficiently attached the radioactive phosphorus isotope (32)P to an anthracene diene, which is a substrate for the Diels-Alderase ribozyme-an RNA sequence that catalyzes the eponymous reaction. We used the (32)P-substrate for the measurement of RNA-catalyzed reaction kinetics of several dye-labeled ribozyme variants for which precise optical activity determination (UV/vis, fluorescence) failed due to interference of the attached dyes. The reaction kinetics were analyzed by thin-layer chromatographic separation of the (32)P-labeled reaction components and densitometric analysis of the substrate and product radioactivities, thereby allowing iterative optimization of the dye positions for future single-molecule studies. The phosphorylation strategy with trichloroacetonitrile may be applicable for labeling numerous other compounds that contain alcoholic hydroxyl groups.     

Rapid Differentiation of Soybean Mosaic Virus Isolates by Antigenic Signature Analysis

Antigenic differences among 14 soybean mosaic virus (SMV) isolates were shown by signature analysis employing a panel of nine well-characterized monoclonal antibodies. Sets of binding curves were generated by reacting aliquots of serial dilutions of leaf extracts from soybean plants infected with each strain of SMV simultaneously with each antibody in the panel. An iterative alignment procedure allowed comparison of binding profiles from different assays in which the starting concentrations of SMV antigen were unknown. Desiccation of infected soybean leaf tissue altered antigenic signatures by inducing changes in reactivity of epitopes recognized by certain antibodies. The method was useful for the elucidation of subtle antigenic differences amongSMV strains. The procedure requires a minimum amount of tissue processing, the analysis is rapid and sensitive, and it requires neither purification nor knowledge of concentration of virus in ground leaf tissue from infected plants.     

One-pot bioethanol production from cellulose by co-culture of Acremonium cellulolyticus and Saccharomyces cerevisiae

ABSTRACT: BACKGROUND: While the ethanol production from biomass by consolidated bioprocess (CBP) is considered to be the most ideal process, simultaneous saccharification and fermentation (SSF) is the most appropriate strategy in practice. In this study, one-pot bioethanol production, including cellulase production, saccharification of cellulose, and ethanol production, was investigated for the conversion of biomass to biofuel by co-culture of two different microorganisms such as a hyper cellulase producer, Acremonium cellulolyticus C-1 and an ethanol producer Saccharomyces cerevisiae. Furthermore, the operational conditions of the one-pot process were evaluated for maximizing ethanol concentration from cellulose in a single reactor. RESULTS: Ethanol production from cellulose was carried out in one-pot bioethanol production process. A. cellulolyticus C-1 and S. cerevisiae were co-cultured in a single reactor. Cellulase producing-medium supplemented with 2.5 g/l of yeast extract was used for productions of both cellulase and ethanol. Cellulase production was achieved by A. cellulolyticus C-1 using Solka-Floc (SF) as a cellulase-inducing substrate. Subsequently, ethanol was produced with addition of both 10%(v/v) of S. cerevisiae inoculum and SF at the culture time of 60 h. Dissolved oxygen levels were adjusted at higher than 20% during cellulase producing phase and at lower than 10% during ethanol producing phase. Cellulase activity remained 8--12 FPU/ml throughout the one-pot process. When 50--300 g SF/l was used in 500 ml Erlenmeyer flask scale, the ethanol concentration and yield based on initial SF were as 8.7--46.3 g/l and 0.15--0.18 (g ethanol/g SF), respectively. In 3-l fermentor with 50--300 g SF/l, the ethanol concentration and yield were 9.5--35.1 g/l with their yields of 0.12--0.19 (g/g) respectively, demonstrating that the one-pot bioethanol production is a reproducible process in a scale-up bioconversion of cellulose to ethanol. CONCLUSION: A. cellulolyticus cells produce cellulase using SF. Subsequently, the produced cellulase saccharifies the SF, and then liberated reducing sugars are converted to ethanol by S. cerevisiae. These reactions were carried out in the one-pot process with two different microorganisms in a single reactor, which does require neither an addition of extraneous cellulase nor any pretreatment of cellulose. Collectively, the one-pot bioethanol production process with two different microorganisms could be an alternative strategy for a practical bioethanol production using biomass.     

Autoimmune epitopes in messenger RNA

Patients with systemic autoimmune disorders produce autoantibodies against sequence-specific conformational RNA epitopes on U1 snRNA, 28S rRNA, and transfer RNAs. The molecular basis for immunological reactivity with these highly abundant and stable RNAs is not understood. Here, we report the existence of discrete RNA epitopes in messenger RNAs that are generally less abundant and less stable than snRNAs and tRNAs. An iterative selection and amplification procedure using pooled autoimmune patient sera identified immunoreactive mRNA species. Following deconvolution of the pools to identify the reactive sera, several mRNAs recognized by these autoantibodies were cloned and sequenced. Detailed analysis using one particular serum indicated reactivity against the messages encoding alternative splicing factor (ASF/SF2) and calmodulin. Deletion and site-directed mutagenesis determined that an epitope recognized by this serum is located in a 17-base stem-loop structure common to both messages. This serum was then used to immunoprecipitate native mRNAs encoding ASF/SF2 and calmodulin from total HeLa cell RNA. Our results demonstrate that despite its low abundance and instability, messenger RNA is capable of reacting with autoantibodies generated during an autoimmune response. These data are consistent with direct presentation as a model to explain the generation of RNA conformation-specific autoantibodies.     

One-pot alpha-glycosylation pathway via the generation in situ of alpha-glycopyranosyl imidates in N,N-dimethylformamide

Divergent pathways are disclosed in the activation of 2-O-benzyl-1-hydroxy sugars by a reagent combination of CBr4 and Ph3P, all of which afford one-pot alpha-glycosylation methods. When this reagent is used in CH2Cl2, the 1-hydroxy sugar is converted to the alpha-glycosyl bromide in a conventional way and leads to the one-pot alpha-glycosylation method based on a halide ion-catalytic mechanism. In either DMF or a mixture of DMF and CHCl3, however, alternative alpha-glycosyl species are generated. From the 1H and 13C NMR study of the products, as well as the reactions using Vilsmeier reagents [(CH3)2N+=CHX]X- (X=Br and Cl), these were identified as cationic alpha-glycopyranosyl imidates having either Br- or Cl- counter ion. The cationic alpha-glycosyl imidate (Br-), derived specifically in the presence of DMF, is more reactive than the alpha-glycosyl bromide and thus is responsible for the accelerated one-pot alpha-glycosylation. The one-pot alpha-glycosylation methodology performed in DMF was assessed also with different types of acceptor substrates including tertiary alcohols and an anomeric mixture of 1-OH sugars.     

Catalytic alkynone generation by Sonogashira reaction and its application in three-component pyrimidine synthesis

The Sonogashira alkynylation of acid chlorides can be efficiently conducted in less than an hour by performing the reaction in tetrahydrofuran as a solvent and in the presence of one stoichiometrically necessary equivalent of triethylamine as a base. This approach also opens new avenues for consecutive one-pot multicomponent reactions. As an example, the one-pot three-component pyrimidine synthesis illustrates the versatility of this modified Sonogashira protocol as an entry to diversity-oriented heterocycle synthesis in a one-pot fashion. The protocol can be completed within a few hours.     

One-pot, two-step enzymatic synthesis of amoxicillin by complexing with Zn2+

A one-pot, two-step enzymatic synthesis of amoxicillin from penicillin G, using penicillin acylase, is presented. Immobilized penicillin acylase from Kluyvera citrophila was selected as the biocatalyst for its good pH stability and selectivity. Hydrolysis of penicillin G and synthesis of amoxicillin from the 6-aminopenicillanic acid formed and d-p-hydroxyphenylglycine methyl ester were catalyzed in situ by a single enzyme. Zinc ions can react with amoxicillin to form complexes, and the yield of 76.5% was obtained after optimization. In the combined one-pot synthesis process, zinc sulfate was added to remove produced amoxicillin as complex for shifting the equilibrium to the product in the second step. By controlling the conditions in two separated steps, the conversion of the first and second step was 93.8% and 76.2%, respectively. With one-pot continuous procedure, a 71.5% amoxicillin yield using penicillin G was obtained.     

One-pot synthesis of tetrazole-1,2,5,6-tetrahydronicotinonitriles and cholinesterase inhibition: Probing the plausible reaction mechanism via computational studies

In the present study, one-pot synthesis of 1H-tetrazole linked 1,2,5,6-tetrahydronicotinonitriles under solvent-free conditions have been carried out in the presence of tetra-n-butyl ammonium fluoride trihydrated (TBAF) as catalyst and solvent. Computational studies have been conducted to elaborate two plausible mechanistic pathways of this one-pot reaction. Moreover, the synthesized compounds were screened for cholinesterases (acetylcholinesterase and butyrylcholinesterase) inhibition which are consider to be major malefactors of Alzheimer’s disease (AD) to find lead compounds for further research in AD therapy.     

Bouquet-type dendrimerlike poly(ethylene oxide)s with a focal aldehyde and peripheral hydroxyls

Doubly functionalized dendrimerlike poly(ethylene oxide)s (PEOs) carrying 16 hydroxyl groups at their periphery and one aldehyde group at their focal point were synthesized up to the fourth generation through an iterative divergent approach. First, a protected aldehyde dihydroxyl compound, namely, 3,3-diethoxy-1,2-propanediol, was used as initiator for the anionic ring-opening polymerization (AROP) of ethylene oxide after partial deprotonation (30%) in dimethyl sulfoxide. The two hydroxyls carried by the PEO chain ends of the first generation were subsequently derivatized so as to generate four hydroxyls via a two-step reaction (allylation and osmylation). The next generations of such dendrimerlike PEOs were grown upon repeating the same cycle of AROP and chain-end modification. At the completion of these reactions, the acetal group present at the core was deprotected under acidic conditions to afford the targeted dendrimerlike PEO of fourth generation with a central aldehyde group. The reactivity and accessibility of the latter function was demonstrated upon its conjugation with aniline used as a model compound.     

A new, efficient, and simple method for the one-pot synthesis of alpha-acetoxyphosphonates from aldehydes under solvent-free conditions

A simple, efficient, and new method has been developed for the synthesis of alpha-acetoxyphosphonates from aldehydes through a one-pot reaction of aldehydes with diethylphosphite in the presence of acetic anhydride under solvent-free conditions using magnesium oxide. This method is easy, rapid, and high yielding for the one-pot synthesis of alpha-acetoxyphosphonates from aldehydes.     

One-pot synthesis of chitosan-g-(PEO-PLLA-PEO) via "click" chemistry and "SET-NRC" reaction

For the development of biocompatible and degradable biomaterials, a kind of well-defined graft copolymer consisting of chitosan back-bone and amphiphilic PEO-PLLA-PEO branch chains was synthesized by Cu(0) catalyzed one-pot strategy combining "click" chemistry and single electron transfer-nitroxide radical coupling (SET-NRC) reaction. First, the precursors of 6-azide-N-phthaloyl-chitosan, TEMPO-PEO-alkyne and mPEO-PLLA-Br were designed and produced. Then, the one-pot coupling reactions between these precursors were performed in the presence of nanosized Cu and PMDETA. The efficiencies of the coupling reactions were greater than 90% determined by the FTIR and ESR spectra. The structure of graft copolymer with 43% of the grafting ratio was confirmed by the spectral analysis. This work provided a route to prepare chitosan graft copolymer.     

Reaction modelling and simulation to assess the integrated use of transketolase and ω-transaminase for the synthesis of an aminotriol

The most attractive, as well as challenging, multistep organic syntheses would preferably be carried out in a single reactor, as a one-pot synthesis. For biocatalytic syntheses, multistep reactions in one-pot mode bring a number of advantages, while at the same time raising unique challenges such as the compatibility of different biocatalysts. In this paper, we have developed a transketolase–transaminase (TK-TAm) two-step one-pot aminotriol synthesis reaction model, which integrates reaction kinetic models with process characterization (consisting of component degradation as a function of pH and concentration, aldehyde toxicity towards the enzyme, and ketol donor and acceptor side-reactions with TAm). Based on the analysis of the effect of the TAm/TK activity ratio on product yield, simulations provided guidance for further process and biocatalyst development.     

A one-pot analysis approach to simplify measurements of protein stability and folding kinetics

To achieve a good understanding of the characteristics of a protein, it is important to study its stability and folding kinetics. Investigations of protein stability have been recently applied to drug-target identification, drug screening, and proteomic studies. The efficiency of the experiments performed to study protein stability and folding kinetics is now a crucial factor that needs to be optimized for these potential applications. However, the standard procedures used to carry out these experiments are usually complicated and time consuming. Large number of measurements is the bottleneck that limits the application of protein folding to large-scale experiments. To overcome this limitation, we developed a method denoted as “one-pot analysis” which is based on taking a single measurement from a mixture of samples rather than from every sample. We combined one-pot analysis with pulse proteolysis to determine the effects of the binding of maltose to maltose-binding protein on the protein folding properties. After carrying out a simple optimization, we demonstrated that protein stability or unfolding kinetics could be measured accurately with just one detection measurement. We then further applied the optimized conditions to cellular thermal shift assay (CETSA). Combining one-pot analysis with CETSA led to a successful determination of the effects of the binding of methotrexate to dihydrofolate reductase in HCT116 cancer cells. Our results demonstrated the applicability of one-pot analysis to energetics-based methods for studying protein folding. We expect the combination of one-pot analysis and energetics-based methods to significantly benefit studies such as drug-target identification, proteomic investigations, and drug screening.     

Reaction modelling and simulation to assess the integrated use of transketolase and ω-transaminase for the synthesis of an aminotriol

The most attractive, as well as challenging, multistep organic syntheses would preferably be carried out in a single reactor, as a one-pot synthesis. For biocatalytic syntheses, multistep reactions in one-pot mode bring a number of advantages, while at the same time raising unique challenges such as the compatibility of different biocatalysts. In this paper, we have developed a transketolase-transaminase (TK-TAm) two-step one-pot aminotriol synthesis reaction model, which integrates reaction kinetic models with process characterization (consisting of component degradation as a function of pH and concentration, aldehyde toxicity towards the enzyme, and ketol donor and acceptor side-reactions with TAm). Based on the analysis of the effect of the TAm/TK activity ratio on product yield, simulations provided guidance for further process and biocatalyst development.