Synthesis of Oligodeoxynucleoside Phosphoro-Monothioates and Phosphorodithioates by a Phosphotriester Method

Abstract

A phosphotriester method for the synthesis of dithymidine phosphoromonothoates and phosphorodithioates with new S-protecting groups has been investigated. Four of the S-protecting groups possesed catalytic activity, however side reactions occurred during deprotection. The best S-protecting group was 4-chloro-2-nitlobenzyl which could be removed with a minimum of side reactions (0.3 %). The coupling reagent PyFNOP (14) gave protected dithymidine phosphoromonothioate in 96 % yield after 15 min coupling. Furthermore PyFNOP chemoselectively activates oxygen in nucleoside phosphorodithioate monomers 9 and can be used for the synthesis of oligodeoxynucleoside phosphorodithioates with mixed base sequences.     

Solution Phase Synthesis of Dithymidine Phosphorodithioate Using New S-Protecting Groups in Combination with a Chemoselective Coupling Reagent (PyNOP)

Abstract

ABSTRACT

A method for the synthesis of O-thymidin-3′-yl S-alkyl dithiophosphate monomers 1 with different S-protecting groups has been developed. These have been used for solution phase synthesis of dithymidine phosphorodithioate by a new phosphotriester method. Coupling reactions are fast (15 min.) and the products are free from phosphorothioate contaminations.     

Chemoselective Synthesis of Dithymidine Phosphorothioate in Solution Using O-Protected Thiophosphate Monomers

Abstract

Diastereomerically pure O-protected thymine monothioate nucleotide (I) is efficiently coupled to protected thymidine (II) in a chemoselective, but not stereoselective manner, to give dithymidine phosphorothioates (III).     

A New Odorless Procedure for the Synthesis of 2′-Deoxy-6-Thioguanosine and Its Incorporation into Oligodeoxynucleotides

6-S-[2-[(2-ethylhexyl)oxycarbonyl]ethyl)}-3′,5′-O-bis(tert-butyldimethylsilyl)-2′-deoxy-6-thiogua nosine (2) was synthesized in high yield from the corresponding 6-O-mesitylenesulfonyl derivative by the reaction with 2-ethylhexyl 3-mercapto-propionate. The phosphoramidite precursor derived from 2 was successfully applied to an automated DNA synthesizer to produce 2′-deoxy-6-thioguanosine containing ODN. The results showed that 2-ethylhexyl 3-mercaptopropionate is useful as an odor less reagent and also as an S-protecting group of 2′-deoxy-6-thioguanosine.     

Stability Studies in Biological Media of Dimer Phosphotriesters Bearing Glucuronic Acid Residue

Abstract

Hydrolytic stability of dithymidine phosphorothioates and dithioates bearing a glucuronic acid derivative protecting group on the phosphate linkage were studied in various biological media. We found that the enzymatic hydrolysis was accompanied by another reaction resulting in formation of the dithymidine phosphodiesters. We have proposed several possible mechanisms of hydrolysis.     

THE SYNTHESIS OF DITHYMIDINE BORANOPHOSPHATE BY THE OXATHIAPHOSPHOLANE APPROACH

The application of the oxathiaphospholane approach for the synthesis of dithymidine boranphospate was evaluated. It was shown, that although the nucleoside-3′-O-oxathiaphospholane-borane complexes 2 or 6 could not be chromatographically separated into diastereomerically pure species due to their apparent instability to moisture, they can be successfully applied to the non-stereocontrolled formation of internucleotide boranophosphate bond by reaction with 5′-OH-nucleoside in the presence of DBU. Attempts to apply the related dithiaphospholane approach for the preparation of dithymidine boranophosphorothioate were unsuccessful.     

A New Synthesis of the Potent and Selective Anti-Herpesvirus Agent (S)-1-[3-Hydroxy-2-(Phosphonylmethoxy)Propyl]Cytosine

Abstract

A new synthetic approach to (S)-1-[3-hydroxy-2-(phosphonyl-methoxy)propyl]cytosine (3, (S)-HPMPC) is based on coupling of the heterocyclic moiety with a glycerol-derived side chain, followed by introduction of the phosphonylmethyl ether group.     

Preparation,Hydrolysis and Intramolecular Transesterification of 3′-Deoxy-3′-thioinosine 3′-S-Dimethylphosphorothiolate

Abstract

The hydrolytic reactions of the dimethyl ester of 3′-deoxy-3′-thioinosine 3′-S-phosphorothiolate have been followed over a wide aciditty range by HPLC. At pH > 3, only hydroxide ion catalyzed isomerization to the 2′-dimethylphosphate takes place, whereas under more acidic conditions hydrolysis to the 2′-monomethylphosphate and 3′-S-monomethylphosphorothiolate competes. The latter is the only product accumulating in very acidic solutions (1 M hydrochloric acid). Mechanisms of the reactions are discussed.     

Highly enantioselective bioreduction of prochiral ketones by stem and germinated plant of Brassica oleracea variety italica

Abstract

An eco-friendly and environmentally benign asymmetric reduction of a broad range of prochiral ketones employing Brassica oleracea variety italica (stems and germinated plant) as a novel biocatalyst was developed. It was found that B. oleracea variety italica could be used effectively for enantioselective bioreduction in aqueous medium with moderate to excellent chemical yield and enantiomeric excess (ee). This process is more efficient and generates less waste than conventional chemical reagents or microorganisms. Both R- and S-configurations were obtained by these asymmetric reactions. The best ee were achieved for pyridine derivatives (92–99%). The ee in germinated plant reactions were significantly higher than those of stem reactions. The low cost and the easy availability of these biocatalysts suggest their possible use for large scale preparations of important chiral alcohols.     

The headspace-GC/MS: Alternative methodology employed in the bioreduction of (4S)-(+)-carvone mediated by human skin fungus

Abstract

The development of more efficient and environmentally friendly analytical methods represents a current focus for the fine chemical industry. In particular, microscale methodologies that are free of solvents/reagents. The headspace-GC/MS (HS-GC) methodology was employed in this study as a tool for monitoring a biocatalysed reaction of (4S)-(+)-carvone using Phoma sp., a filamentous fungus from human skin. Biocatalysis provides some advantages, such as high efficiency, high degrees of regioselectivity, chemoselectivity, and enantioselectivity. In order to optimize the small scale biocatalytic reaction of the (4S)-(+)-carvone by the filamentous fungus Phoma sp. was used headspace GC/MS methodology, factorial design of experiments and the response surface methodology (RSM) was performed using the biomass of the fungus, substrate mass and pH as parameters. It was observed that for all reactions conditions tested, forming the products (1?R,4S)-dihydrocarvone and (1S,4S)-dihydrocarvone. The most influential factor was pH, with the highest conversion rate (>95%) and diastereomeric excess (d.e.) (>80%) obtained at pH 5.0. Thus, it was demonstrated that human skin Phoma sp. fungus showed significant bioreduction activity and that headspace GC/MS is an efficient approach for real-time monitoring the biocatalysed reactions.     

Simultaneous synthesis of enantiomerically pure (S)-amino acids and (R)-amines using α/ω-aminotransferase coupling reactions with two-liquid phase reaction system

An efficient simultaneous synthesis of enantiopure (S)-amino acids and chiral (R)-amines was achieved using α/ω-aminotransferase (α/ω-AT) coupling reaction with two-liquid phase system. As, among the enzyme components in the α/ω-AT coupling reaction systems, only ω-AT is severely hampered by product inhibition by ketone product, the coupled reaction cannot be carried out above 60 mM substrates. To overcome this problem, a two-liquid phase reaction was chosen, where dioctylphthalate was selected as the solvent based upon biocompatibility, partition coefficient and effect on enzyme activity. Using 100 mM of substrates, the AroAT/ω-AT and the AlaAT/ω-AT coupling reactions asymmetrically synthesized (S)-phenylalanine and (S)-2-aminobutyrate with 93% (>99% ee^S) and 95% (>99% ee^S) of conversion yield, and resolved the racemic α-methylbenzylamine with 56% (95% ee^R) and 54% (96% ee^R) of conversion yield, respectively. Moreover, using 300 mM of 2-oxobutyrate and 300 mM of racemic α-methylbenzylamine as substrates, the coupling reactions yielded 276 mM of (S)-2-aminobutyrate (>99% ee) and 144 mM of (R)-α-methylbenzylamine (>96% ee) in 9 h. Here, most of the reactions take place in the aqueous phase, and acetophenone mainly moved to the organic phase according to its partition coefficient.     

Convenient Synthesis of 4-C-Branched Lactones and 3′-C-Branched 2′,3′-Dideoxynucleosides

Abstract

The regio- and stereoselective photocatalysed addition of 2-propanol and cyclopentanol to (5S)-hydroxymethylfuran-2(5H)-one (1) gave 4-C-branched lactones 2 and 3 after selective silylations. The lactones 2 and 3 were radically deoxygenated affording lactones 4 and 5, respectively. As an example, compound 2 was transformed without purification of the intermediates into an anomeric mixtures of deprotected 3′-C-branched 2′, 3′-dideoxynucleosides 6 by the following reaction sequence: silylation, reduction, acetylation, coupling with silylated thymine and desilylation.     

Preparation of an Octadeoxyribonucleoside Heptaphosphorothioate by the Phosphotriester Approach in Solution†

Abstract

The synthesis of the octadeoxyribonucleoside heptaphosphorothioate, d[Tp(s)Tp(s)Gp(s)Gp(s)Gp(s)Gp(s)Tp(s)T] by the phosphotriester approach in solution is described. The phosphorothioate internucleotide linkages are protected by the S-(2-cyanoethyl) group and 1-(mesitylene-2-sulfonyl)-3-nitro-1,2,4-1H-triazole (MSNT) is used as the coupling agent. A block synthesis strategy (2 + 2 → 4 and 4 + 4 → 8) is followed.

     

A toolbox approach for the rapid evaluation of multi-step enzymatic syntheses comprising a ‘mix and match’ E. coli expression system with microscale experimentation

Abstract

This work describes an experimental ‘toolbox’ for the rapid evaluation and optimisation of multi-step enzymatic syntheses comprising a ‘mix and match’ E. coli-based expression system and automated microwell scale experimentation. The approach is illustrated with a de novo designed pathway for the synthesis of optically pure amino alcohols using the enzymes transketolase (TK) and transaminase (TAm) to catalyze asymmetric carbon-carbon bond formation and selective chiral amine group addition respectively. The E. coli expression system, based on two compatible plasmids, enables pairs of enzymes from previously engineered and cloned TK and TAm libraries to be evaluated for the sequential conversion of different initial substrates. This is complemented by the microwell experimentation which enables efficient investigation of different biocatalyst forms, use of different amine donors and substrate feeding strategies. Using this experimental ‘toolbox’, one-pot syntheses of the diastereoisomers (2S,3S)-2-aminopentane-1,3-diol (APD) and (2S,3R)-2-amino-1,3,4-butanetriol (ABT) were designed and performed, which gave final product yields of 90% mol/mol for APD and 87% mol/mol for ABT (relative to the initial TK substrates) within 25 hours. For the synthesis of APD, the E coli TK mutant D469E was paired with the TAm from Chromobacterium violaceum 2025 while for ABT synthesis the wild-type E. coli TK exhibited the highest specific activity and ee( enantiomeric excess) of >95%. For both reactions, whole-cell forms of the TK-TAm biocatalyst performed better than cell lysates while isopropylamine (IPA) was a preferable amine donor than methylbenzylamine (MBA) since side reactions with the initial TK substrates were avoided. The available libraries of TK and TAm enzymes and scalable nature of the microwell data suggest this ‘toolbox’ provides an efficient approach to early stage bioconversion process design in the chemical and pharmaceutical sectors.     

Evaluation of acid‐labile S‐protecting groups to prevent Cys racemization in Fmoc solid‐phase peptide synthesis

Phosphonium and uronium salt‐based reagents enable efficient and effective coupling reactions and are indispensable in peptide chemistry, especially in machine‐assisted SPPS. However, after the activating and coupling steps with these reagents in the presence of tertiary amines, Fmoc derivatives of Cys are known to be considerably racemized during their incorporation. To avoid this side reaction, a coupling method mediated by phosphonium/uronium reagents with a weaker base, such as 2,4,6‐trimethylpyridine, than the ordinarily used DIEA or that by carbodiimide has been recommended. However, these methods are appreciably inferior to the standard protocol applied for SPPS, that is, a 1 min preactivation procedure of coupling with phosphonium or uronium reagents/DIEA in DMF, in terms of coupling efficiency, and also the former method cannot reduce racemization of Cys(Trt) to an acceptable level (<1.0%) even when the preactivation procedure is omitted. Here, the 4,4′‐dimethoxydiphenylmethyl and 4‐methoxybenzyloxymethyl groups were demonstrated to be acid‐labile S‐protecting groups that can suppress racemization of Cys to an acceptable level (<1.0%) when the respective Fmoc derivatives are incorporated via the standard SPPS protocol of phosphonium or uronium reagents with the aid of DIEA in DMF. Furthermore, these protecting groups significantly reduced the rate of racemization compared to the Trt group even in the case of microwave‐assisted SPPS performed at a high temperature. © 2013 The Authors. European Peptide Society published by John Wiley & Sons, Ltd.     

Synthesis of Oligonucleotide Building Blocks of 2′-Deoxyguanosine Bearing a C8-Arylamine Modification

Abstract

C8-Arylamine-dG adducts were synthesized by palladium-catalyzed cross- coupling reactions. The corresponding 5′-O-DMTr-3′-O-phosphoramidite-C8-arylamine-dG adducts were synthesized as potential building blocks for the automated synthesis of site-specifically modified oligonucleotides.     

Biocatalytic potential of laccase-like multicopper oxidases from Aspergillus niger

Background

The integration of biotechnology into chemical manufacturing has been recognized as a key technology to build a sustainable society. However, the practical applications of biocatalytic chemical conversions are often restricted due to their complexities involving the unpredictability of product yield and the troublesome controls in fermentation processes. One of the possible strategies to overcome these limitations is to eliminate the use of living microorganisms and to use only enzymes involved in the metabolic pathway. Use of recombinant mesophiles producing thermophilic enzymes at high temperature results in denaturation of indigenous proteins and elimination of undesired side reactions; consequently, highly selective and stable biocatalytic modules can be readily prepared. By rationally combining those modules together, artificial synthetic pathways specialized for chemical manufacturing could be designed and constructed.

Results

A chimeric Embden-Meyerhof (EM) pathway with balanced consumption and regeneration of ATP and ADP was constructed by using nine recombinant E. coli strains overproducing either one of the seven glycolytic enzymes of Thermus thermophilus, the cofactor-independent phosphoglycerate mutase of Pyrococcus horikoshii, or the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase of Thermococcus kodakarensis. By coupling this pathway with the Thermus malate/lactate dehydrogenase, a stoichiometric amount of lactate was produced from glucose with an overall ATP turnover number of 31.

Conclusions

In this study, a novel and simple technology for flexible design of a bespoke metabolic pathway was developed. The concept has been testified via a non-ATP-forming chimeric EM pathway. We designated this technology as “synthetic metabolic engineering”. Our technology is, in principle, applicable to all thermophilic enzymes as long as they can be functionally expressed in the host, and thus would be potentially applicable to the biocatalytic manufacture of any chemicals or materials on demand.

     

Synthesis of 1′,2′-Seco-nucleoside Analogues of AZT

Abstract

1′,2′-Seco-AZT (3) and its 3′R,4′S diastereomer (19) were prepared and evaluated as antiviral agents. The chiral, acyclic side chains of these thymine acyclonuleosides were derived from D-isoascorbic acid. The two AZT analogues, 3 and 19, were screened against HIV, other RNA viruses, and two DNA viruses and they were found to be inactive.     

The Synthesis of Carbocyclic 5′-Nor Thymidine and an Isomer as Oligonucleotide Monomers

Abstract

The chiral synthesis of (1S,3S,4S)-1-(3,4-dihydroxycyclopent-1-yl)-1H?thymine (carbocyclic 5′-nor thymidine, 4) has been achieved in 5 steps from (+)-(lR,4S)-4-hydroxy-2-cyclopenten-1-yl acetate (5) and N³?benzoylthymine. Compound 4 is viewed as a monomeric building block for poly-T-like oligomers.