General Principles for Yield Optimization of Nucleoside Phosphorylase-Catalyzed Transglycosylations

The biocatalytic synthesis of natural and modified nucleosides with nucleoside phosphorylases offers the protecting-group-free direct glycosylation of free nucleobases in transglycosylation reactions. This contribution presents guiding principles for nucleoside phosphorylase-mediated transglycosylations alongside mathematical tools for straightforward yield optimization. We illustrate how product yields in these reactions can easily be estimated and optimized using the equilibrium constants of phosphorolysis of the nucleosides involved. Furthermore, the varying negative effects of phosphate on transglycosylation yields are demonstrated theoretically and experimentally with several examples. Practical considerations for these reactions from a synthetic perspective are presented, as well as freely available tools that serve to facilitate a reliable choice of reaction conditions to achieve maximum product yields in nucleoside transglycosylation reactions.     

Production,Characterization and Synthetic Application of a Purine Nucleoside Phosphorylase from Aeromonas hydrophila

Purine nucleoside phosphorylase (PNP) from Aeromonas hydrophila encoded by the deoD gene has been over‐expressed in Escherichia coli, purified, characterized about its substrate specificity and used for the preparative synthesis of some 6‐substituted purine‐9‐ribosides. Substrate specificity towards natural nucleosides showed that this PNP catalyzes the phosphorolysis of both 6‐oxo‐ and 6‐aminopurine (deoxy)ribonucleosides. A library of nucleoside analogues was synthesized and then submitted to enzymatic phosphorolysis as well. This assay revealed that 1‐, 2‐, 6‐ and 7‐modified nucleosides are accepted as substrates, whereas 8‐substituted nucleosides are not. A few transglycosylation reactions were carried out using 7‐methylguanosine iodide ( 4 ) as a D ‐ribose donor and 6‐substituted purines as acceptor. In particular, following this approach, 2‐amino‐6‐chloropurine‐9‐riboside ( 2c ), 6‐methoxypurine‐9‐riboside ( 2d ) and 2‐amino‐6‐(methylthio)purine‐9‐riboside ( 2g ) were synthesized in very high yield and purity.     

Enzymatic RNA Production from NTPs Synthesized from Nucleosides and Trimetaphosphate**

A mechanism of nucleoside triphosphorylation would have been critical in an evolving “RNA world” to provide high-energy substrates for reactions such as RNA polymerization. However, synthetic approaches to produce ribonucleoside triphosphates (rNTPs) have suffered from conditions such as high temperatures or high pH that lead to increased RNA degradation, as well as substrate production that cannot sustain replication. Previous reports have demonstrated that cyclic trimetaphosphate (cTmp) can react with nucleosides to form rNTPs under prebiotically-relevant conditions, but their reaction rates were unknown and the influence of reaction conditions not well-characterized. Here we established a sensitive assay that allowed for the determination of second-order rate constants for all four rNTPs, ranging from 1.7×10⁻⁶ to 6.5×10⁻⁶ M⁻¹ s⁻¹. The ATP reaction shows a linear dependence on pH and Mg²⁺, and an enthalpy of activation of 88±4 kJ/mol. At millimolar nucleoside and cTmp concentrations, the rNTP production rate is sufficient to facilitate RNA synthesis by both T7 RNA polymerase and a polymerase ribozyme. We suggest that the optimized reaction of cTmp with nucleosides may provide a viable connection between prebiotic nucleotide synthesis and RNA replication.     

醋酸或醋酸酯加氢制乙醇的热力学计算与分析

对醋酸、醋酸甲酯或醋酸乙酯加氢制乙醇进行了热力学计算和分析。计算了这3个反应的标准摩尔焓变和标准平衡常数,以及温度、压力和反应物配比对平衡转化率的影响。结果表明,3个反应的标准摩尔焓变都小于0,是放热反应;醋酸加氢反应的标准平衡常数较大,而醋酸甲酯加氢反应和醋酸乙酯加氢反应的标准平衡常数都小于0.7;醋酸加氢反应由于标准平衡常数较大,因此其平衡转化率受工艺条件影响较小,而醋酸甲酯加氢和醋酸乙酯加氢反应的平衡转化率受工艺条件的影响较大,醋酸酯加氢制乙醇反应适宜的温度为423~550 K,适宜的压力是2~3 MPa,适宜的氢酯比是10~20。     

Synthesis of tertiary amyl methyl ether (TAME): Equilibrium of the multiple reactions

The octane enhancer tertiary amyl methyl ether (TAME) is produced by liquid phase synthesis from methanol and a mixture of isoamylenes, namely 2-methyl-1-butene and 2-methyl-2-butene, using a sulfonic acid ion exchange resin as catalyst. Three reactions take place simultaneously in TAME synthesis: etherification of the two methylbutenes and their isomerisation. In order to study the equilibrium of the multiple reactions in TAME synthesis, the thermodynamic properties of the compounds in the liquid phase and equilibrium constants were calculated using a modified UNIFAC method to describe the nonideality of the system. Four parameters influencing the equilibrium conversion were derived and discussed in detail. Supplemental experiments were performed at three temperatures in the range from 303 to 343 K and at different initial molar ratios of educts. Equilibrium conversions of methanol were determined from these experiments and compared with calculated values. At 298 K the predicted activity based equilibrium constant was 22.9 for TAME synthesis from 2-methyl-1-butene and 1.6 for TAME synthesis from 2-methyl-2-butene; for isomerisation of 2-methyl-1-butene to 2-methyl-2-butene a value of 14.3 was obtained.     

Synthesis of diethyl carbonate from ethanol through different routes: A thermodynamic and comparative analysis

In this study, thermodynamic analysis of various possible synthesis routes of diethyl carbonates (DEC), a benign organic carbonate, was carried out and a comparative analysis was performed. Chemical equilibrium constants at standard conditions were calculated using Gibbs free energy of the system. The Benson group contribution method was used to estimate standard heat of formation and standard entropy change of some raw materials/components like dimethyl carbonate. Variation of heat capacity (C_p) with temperature was estimated for different components from the Rozicka‐Domalski model. Variation of chemical equilibrium constants with temperature and pressure was studied for various routes. Synthesis of DEC from ethylene carbonate (EC) was also found to be better considering equilibrium constants at room temperature. The CO₂ route was found to be the most unfavourable route for DEC synthesis due to stability of CO₂ molecules. Moreover, DEC synthesis through the urea route was found to be best at high temperatures since the equilibrium constants were found to increase exponentially. Experiments were conducted for DEC synthesis using the EC route at two temperatures. Activity coefficients were calculated using the UNIFAC model. Experimentally and theoretically determined chemical equilibrium constant values were found to be similar. PRO/II was also used to minimize Gibbs free energy of the system and estimate the equilibrium constants and the results were comparable with those obtained by the equilibrium constant method and the trend was found to be the same for both the methods.     

Synthesis of biodiesel in supercritical alcohols and supercritical carbon dioxide

Biodiesel was synthesized in supercritical fluids by two routes: non-catalytically in supercritical alcohols and by enzyme catalysis in supercritical carbon dioxide. Two oils, sesame oil and mustard oil, and two alcohols, methanol and ethanol, were used for the synthesis. Complete conversion was observed for synthesis in supercritical alcohols whereas only a maximum of 70% conversion was observed for the enzymatic synthesis in supercritical carbon dioxide. For the synthesis in supercritical alcohols, the activation energies and pseudo-first order rate constants were determined. For the reactions in supercritical carbon dioxide, a mechanism based on ping pong bi-bi was proposed and the kinetic parameters were determined.     

Synthesis of 2,6‐Dihalogenated Purine Nucleosides by Thermostable Nucleoside Phosphorylases

The enzymatic transglycosylation of 2,6‐dichloropurine (26DCP) and 6‐chloro‐2‐fluoropurine (6C2FP) with uridine, thymidine and 1‐(β‐D ‐arabinofuranosyl)‐uracil as the pentofuranose donors and recombinant thermostable nucleoside phosphorylases from G. thermoglucosidasius or T. thermophilus as biocatalysts was studied. Selection of 26DCP and 6C2FP as substrates is determined by their higher solubility in aqueous buffer solutions compared to most natural and modified purines and, furthermore, synthesized nucleosides are valuable precursors for the preparation of a large number of biologically important nucleosides. The substrate activity of 26DCP and 6C2FP in the synthesis of their ribo‐ and 2′‐deoxyribo‐nucleosides was closely similar to that of related 2‐amino‐ (DAP), 2‐chloro‐ and 2‐fluoroadenines; the efficiency of the synthesis of β‐D ‐arabinofuranosides of 26DCP and 6C2FP was lower vs. that of DAP under similar reaction conditions. For a convenient and easier recovery of the biocatalysts, the thermostable enzymes were immobilized on MagReSyn^® epoxide beads and the biocatalyst showed high catalytic efficiency in a number of reactions. As an example, 6‐chloro‐2‐fluoro‐(β‐D ‐ribofuranosyl)‐purine ( 9 ), a precursor of various antiviral and antitumour drugs, was synthesized by the immobilized enzymes at 60 °C under high substrate concentrations (uridine:purine ratio of 2:1, mol). The synthesis was successfully scaled‐up [uridine (2.5 mmol), base (1.25 mmol); reaction mixture 50 mL] to afford 9 in 60% yield. The reaction reveals the great practical potential of this enzymatic method for the efficient production of modified purine nucleosides of pharmaceutical interest.

     

Synthesis and Antiviral Evaluation of TriPPPro‐AbacavirTP,TriPPPro‐CarbovirTP,and Their 1′,2′‐cis‐Disubstituted Analogues

Herein we describe the synthesis of lipophilic triphosphate prodrugs of abacavir, carbovir, and their 1′,2′‐cis‐substituted carbocyclic analogues. The 1′,2′‐cis‐carbocyclic nucleosides were prepared by starting from enantiomerically pure (1R,2S)‐2‐((benzyloxy)methyl)cyclopent‐3‐en‐1‐ol by a microwave‐assisted Mitsunobu‐type reaction with 2‐amino‐6‐chloropurine. All four nucleoside analogues were prepared from their 2‐amino‐6‐chloropurine precursors. The nucleosides were converted into their corresponding nucleoside triphosphate prodrugs (TriPPPro approach) by application of the H‐phosphonate route. The TriPPPro compounds were hydrolyzed in different media, in which the formation of nucleoside triphosphates was proven. While the TriPPPro compounds of abacavir and carbovir showed increased antiviral activity over their parent nucleoside, the TriPPPro compounds of the 1′,2′‐cis‐substituted analogues as well as their parent nucleosides proved to be inactive against HIV.     

Influence of sugar ring conformation on the transportability of nucleosides by human nucleoside transporters

The conformational preference of human nucleoside transporters (hNTs) with respect to sugar ring was examined using conformationally fixed purine and pyrimidine nucleosides built on a bicyclo[3.1.0]hexane template. These fixed-conformation nucleosides, methanocarba-deoxyadenosine or methanocarba-deoxycytidine in North (C3'-endo, N-MCdA and N-MCdC) or South (C2'-endo, S-MCdA and S-MCdC) conformations, were used to study inhibition of equilibrative (hENT1-4) and concentrative (hCNT1-3) nucleoside transport by individual recombinant hNTs produced in Saccharomyces cerevisiae cells or Xenopus laevis oocytes. Our results indicated that nucleosides in the North conformation were potent inhibitors of transport mediated by hCNTs whereas South nucleosides were inhibitors of hENTs, thus showing differences in the interaction with the hNTs. In summary, hCNTs exhibited strong preferences for North nucleosides whereas hENTs exhibited slight preferences for South nucleosides, demonstrating for the first time different conformational preferences among members of the two families of hNTs.     

Incorporation of 2'-deoxy-2'-isonucleoside 5'-triphosphates (iNTPs) into DNA by A- and B-family DNA polymerases with different recognition mechanisms

Recently, α-L-threofuranosyl nucleoside 3'-triphosphates (tNTPs) have been reported to be incorporated into DNA by DNA polymerases. Isonucleosides especially the 2'-deoxy-2'-isonucleosides, would be considered regioisomers of α-L-threofuranosyl nucleosides. Therefore, we investigated the synthesis of 2'-deoxy-2'-isonucleoside 5'-triphosphates (iNTPs) having the four natural nucleobases and their incorporation into primer-template duplexes consisting of oligonucleotides containing natural 2'-deoxyribonucleosides and 2'-deoxy-2'-isonucleosides by using primer-extension reactions. We found that Klenow fragment (exo-; an A-family DNA polymerase) has strict recognition of the shape of nucleoside 5'-triphosphates and Therminator (a B-family DNA polymerase) has strict recognition of the shape of primer-template complexes, especially two base pairs upstream of the primer 3' terminus.     

An Expedient Synthesis of Flexible Nucleosides through Enzymatic Glycosylation of Proximal and Distal Fleximer Bases

The structurally unique “fleximer” nucleosides were originally designed to investigate how flexibility in a nucleobase could potentially affect receptor–ligand recognition and function. Recently they have been shown to have low-to-sub-micromolar levels of activity against a number of viruses, including coronaviruses, filoviruses, and flaviviruses. However, the synthesis of distal fleximers in particular has thus far been quite tedious and low yielding. As a potential solution to this issue, a series of proximal fleximer bases (flex-bases) has been successfully coupled to both ribose and 2′-deoxyribose sugars by using the N-deoxyribosyltransferase II of Lactobacillus leichmannii (LlNDT) and Escherichia coli purine nucleoside phosphorylase (PNP). To explore the range of this facile approach, transglycosylation experiments on a thieno-expanded tricyclic heterocyclic base, as well as several distal and proximal flex-bases were performed to determine whether the corresponding fleximer nucleosides could be obtained in this fashion, thus potentially significantly shortening the route to these biologically significant compounds. The results of those studies are reported herein.     

二甲醚与合成气反应制乙醇的热力学计算与分析

采用Benson基团贡献法估算得到二甲醚（DME）和乙酸甲酯（MA）的标准生成焓和标准生成吉布斯自由能,在298～1000K时计算了DME与合成气制乙醇（DME羰基化反应、MA加氢反应以及二者组成的总反应）过程中的反应焓变、反应熵变、反应吉布斯自由能变和化学反应的平衡常数。在此基础上,分析了反应压力、反应温度和原料比对DME转化率的影响。在413K、1×105Pa、CO∶DME=1条件下考察了不同H2浓度情况下合成乙醇反应中两个反应的协同效应。分析结果表明,在低于493K、3MPa、n(CO)∶n(DME)=1的条件下有利于合成反应的进行,由于两反应的协同效应,使MA加氢反应的平衡转化率有大幅度提高。     

Application of Galactose Oxidase in Chemoenzymatic One-Pot Cascade Reactions Without Intermediate Recovery Steps

Various cascade routes starting from D-galactose derivatives—via 6-CH₂OH oxidation catalyzed by galactose oxidase—are reported as one-pot procedures. The approach consists of combined bio- and chemocatalytic reactions as well as “spontaneous” chemical conversions. Workup is avoided by using compatible aqueous reaction conditions for all the consecutive reactions involved. A great benefit of this method is that D-galactose containing di-, tri- and oligosaccharides can be modified without the use of protecting groups and without any isolation and/or purification of intermediate products in these syntheses. The one-pot cascades, consisting of up to five consecutive transformations, gave rapid access to more than 40 uronic acid, amino sugar and deoxy sugar derivatives through enzymatic, homogeneous and heterogeneous catalytic conversions in water under mild conditions.     

Microwave Accelerated Transglycosylation of Rutin by Cyclodextrin Glucanotransferase from Bacillus sp. SK13.002

Rutin was subjected to intermolecular transglycosylation assisted with microwave irradiation using cyclodextrin glucanotransferase (CGTase) produced from Bacillus sp. SK13.002. Compared with the conventional enzymatic method for rutin transglycosylation (without microwave irradiation), microwave-assisted reaction (MAR) was much faster and thus more efficient. While the conventional reaction took dozens of hours to reach the highest conversion rate of rutin and yield of transglycosylated rutin, MAR of rutin transglycosylation completed within only 6 min providing almost the same conversion rate of rutin and yield of products consisting of mono-, di-, tri-, tetra-, penta-glucosylated rutins. The optimum transglycosylation conditions for microwave irradiation were 40 °C and 60 W with the reaction system consisting mainly of the mixture of 0.3 g rutin (0.49 mmol) pre-dissolved in 15 mL methanol, 1.8 g maltodextrin in 15 mL of 0.2 M sodium acetate buffer (pH 5.5) and CGTase (900 U). Results from this study indicated that MAR could be a potentially useful and economical technique for a faster and more efficient transglycosylation of rutin.     

L'effet du molybdène sur l'oxydation partielle du méthane par l'oxygène-pur

An investigation was carried out to establish the influence of molybdenum powder on the partial oxidation of methane with pure oxygen and to find the reaction conditions that lead to its complete conversion to synthesis gas without excess oxygen nor formation of carbon dioxide, water vapor and carbon deposits. Carbidization of molybdenum by methane and its decarbidization by oxygen lead one to suggest steps that explain the observed products. Thermodynamic feasibility of the steps suggested was established from equilibrium constants. Gas compositions at equilibrium were calculated for various reaction conditions. Sixty experiments were carried out to verify the calculated compositions. The temperature was varied from 1200 to 1900°K; the weight of molybdenum, from 0 to 5 grams; the methane to oxygen ratio, from 1.6 to 2.2 and the hourly space velocity, from 50 to 250. Above 1600°K, 2 to 1 ratio stoichiometric mixtures of methane and oxygen in the presence of molybdenum, generally yield pure synthesis gas (no carbon deposits, water vapor or carbon dioxide). X-ray diffraction analysis of the solids in the reactor confirmed the presence of large amounts of molybdenum carbide (but no oxide). This is strong evidence in support of the role assigned to molybdenum in eliminating carbon deposits.     

Prebiotic Pathway from Ribose to RNA Formation

At the focus of abiotic chemical reactions is the synthesis of ribose. No satisfactory explanation was provided as to the missing link between the prebiotic synthesis of ribose and prebiotic RNA (preRNA). Hydrogen cyanide (HCN) is assumed to have been the principal precursor in the prebiotic formation of aldopentoses in the formose reaction and in the synthesis of ribose. Ribose as the best fitting aldopentose became the exclusive sugar component of RNA. The elevated yield of ribose synthesis at higher temperatures and its protection from decomposition could have driven the polymerization of the ribose-phosphate backbone and the coupling of nucleobases to the backbone. RNA could have come into being without the involvement of nucleotide precursors. The first nucleoside monophosphate is likely to have appeared upon the hydrolysis of preRNA contributed by the presence of reactive 2′-OH moieties in the preRNA chain. As a result of phosphorylation, nucleoside monophosphates became nucleoside triphosphates, substrates for the selective synthesis of genRNA.     

生物质气催化合成甲醇的热力学分析

由生物质气合成甲醇是一复杂反应系统,本文计算了其中各个反应的反应热和平衡常数与温度的关系.并以CO 21.5%、CO₂ 22.8%、H₂ 52.5%、N₂ 3.2%的气体模拟生物质气,用平衡常数法计算了在473.15～553.15 K、3～6 MPa下的平衡组成、碳的平衡转化率和所得甲醇的浓度.计算结果表明,这一体系中,主要是CO+H₂生成甲醇.低温和高压有利于提高碳的平衡转化率和甲醇的浓度.并用工业C306催化剂验证了上述规律的正确性.由于反应既受热力学控制,又受动力学控制,在3 MPa时碳的转化率在533.15 K时达到最大,接近平衡转化率.随压力升高,甲醇产率及液相产物中的浓度逐渐升高.     

苯酚与异丙醇烷基化合成异丙基苯酚的热力学和动力学

基于Benson基团贡献法研究苯酚与异丙醇烷基化反应过程,确定了主、副反应的反应热、平衡常数及平衡转化率,得到反映热力学性质的反应方程式并建立反应的网络结构,为该体系的工艺设计提供热力学依据。在苯酚与异丙醇物质的量比为0.5~2.0、温度(513.15~573.15)K、空速8 h-1和催化剂颗粒(40~60)目[相当于粒径(0.45~0.30)mm]条件下进行本征动力学实验。选用幂数型动力学模型,对参数进行估值。用Runge-Kutta法进行数值积分,Simplex法对参数进行优化,F统计法对模型进行检验,最终得到能较好描述反应的本征动力学模型。     

Prodrugs of Nucleoside Triphosphates as a Sound and Challenging Approach: A Pioneering Work That Opens a New Era in the Direct Intracellular Delivery of Nucleoside Triphosphates

Synthetic nucleosides, designed to mimic naturally occurring nucleosides, are important antiviral and anticancer chemotherapeutic agents. However, nucleosides are not active as such and need to be metabolized, step by step, to their corresponding active nucleoside triphosphates (NTPs). This is mediated by phosphorylating enzymes, mainly host cellular kinases with strong specificity for their substrates; in many cases, this specificity prevents efficient conversion into the NTPs. To circumvent this metabolic handicap, successful nucleo(s/t)ide prodrugs have been developed as a valuable concept in the design of effective drugs. The unique concept of the TriPPPro approach, developed by Chris Meier and colleagues, is a powerful tool for the intracellular delivery of active NTPs, bypassing all the phosphorylation steps required by nucleosides to yield the active NTP metabolites. This concept is illustrated herein with general examples.