Semiempirical studies on the interactions of dialkyldi(aquo)tin cations, [R2Sn(H2O)2]2+, with selected nucleotides

Semiempirical calculations have been carried out on the interactions of [R₂Sn(H₂O)₂]²⁺, [R = H(CH₂)_n: n = 1–8], mainly with five nucleotides, 5′‐adenosine monophosphate (5′‐AMP), but also with guanosine 5′‐monophosphate (5′‐GMP), cytidine 5′‐monophosphate (5′‐CMP), uridine‐5′‐monophosphate (5′‐UMP) and inosine 5′‐monophosphate (5′‐IMP). The preferred sites of interaction were calculated to be the ribose O2 and O3 hydroxyl oxygens and/or the phosphate oxygens, with the nitrogen sites in the bases the least attractive to the tin compounds. This is in general agreement with experimental findings. Structures of the 1:1 coordination complexes vary from distorted tetrahedral, to distorted trigonal pyramidal to distorted octahedral geometries. Copyright © 2007 John Wiley & Sons, Ltd.     

Ultra‐fast adenosine 5′‐triphosphate,adenosine 5′‐diphosphate and adenosine 5′‐monophosphate detection by pressure‐assisted capillary electrophoresis UV detection

Herein, we report a new CE method to measure adenine nucleotides adenosine 5′‐triphosphate, adenosine 5′‐diphosphate, and adenosine 5′‐monophosphate in red blood cells. For this purpose, 20 mmol/L sodium acetate buffer at pH 3.80 was used as running electrolyte, and the separation was performed by the simultaneous application of a CE voltage of 25 kV and an overimposed pressure of 0.2 psi from inlet to outlet. A rapid separation of these analytes in less than 1.5 min was obtained with a good reproducibility for intra‐ and inter‐assay (CV<4 and 8%, respectively) and an excellent analytical recovery (from 98.3 to 99%). The applicability of our method was proved by measuring adenine nucleotides in red blood cells.     

An Fe2+‐ and α‐Ketoglutarate‐Dependent Halogenase Acts on Nucleotide Substrates

While halogenated nucleosides are used as common anticancer and antiviral drugs, naturally occurring halogenated nucleosides are rare. Adechlorin (ade) is a 2′‐chloro nucleoside natural product first identified from Actinomadura sp. ATCC 39365. However, the installation of chlorine in the ade biosynthetic pathway remains elusive. Reported herein is a Fe²⁺‐α‐ketoglutarate halogenase AdeV that can install a chlorine atom at the C2′ position of 2′‐deoxyadenosine monophosphate to afford 2′‐chloro‐2′‐deoxyadenosine monophosphate. Furthermore, 2′,3′‐dideoxyadenosine‐5′‐monophosphate and 2′‐deoxyinosine‐5′‐monophosphate can also be converted, albeit 20‐fold and 2‐fold, respectively, less efficiently relative to the conversion of 2′‐deoxyadenosine monophosphate. AdeV represents the first example of a Fe²⁺‐α‐ketoglutarate‐dependent halogenase that converts nucleotides into chlorinated analogues.     

A Facile and Cost‐effective Electroanalytical Strategy for the Quantification of Deoxyguanosine and Deoxyadenosine in Oligonucleotides Using Screen‐printed Graphite Electrodes

The development of electroanalytical methods for the detection and quantification of nucleotides in DNA offers vital implications in assessing the degree of oxidation or epigenetic modification in DNA. Unfortunately, the electrochemical response of oligonucleotides is strongly influenced by the size, composition and nucleic base sequence. In this article, an optimized analytical procedure for the enzymatically breakdown of the oligonucleotides to their corresponding nucleotides for the evaluation of the electrochemical response through the use of square wave voltammetry (SWV) is presented. Enzymatic digestion of oligonucleotides has been optimized in terms of buffer composition, digestion time, strategy for stopping the enzymatic reaction and filtration requirement for enzyme removal, and then compared to an established protocol. Under the optimized protocol SWV response of a number of untreated and enzymatically digested six‐mer oligonucleotides, namely 5′‐GGGGGG‐3′, 5′‐AAAAAA‐3′, 5′‐CGCGCG‐3′ and 5′‐AAACGC‐3′ have been analysed, providing a higher sensitivity for the determination of guanosine and adenosine monophosphate species under digestion conditions with a more facile and cost effective procedure. The novel strategy for the enzymatically treated oligonucleotides in combination with the SWV response provides a proof of principle for feasible applications in the diagnosis of methylated guanosine in DNA as a potential biomarker due to its relation with cancer.     

A High‐Affinity Fluorescent Sensor for Catecholamine: Application to Monitoring Norepinephrine Exocytosis

A fluorescent sensor for catecholamines, NS510, is presented. The sensor is based on a quinolone fluorophore incorporating a boronic acid recognition element that gives it high affinity for catecholamines and a turn‐on response to norepinephrine. The sensor results in punctate staining of norepinephrine‐enriched chromaffin cells visualized using confocal microscopy indicating that it stains the norepinephrine in secretory vesicles. Amperometry in conjunction with total internal reflection fluorescence (TIRF) microscopy demonstrates that the sensor can be used to observe destaining of individual chromaffin granules upon exocytosis. NS510 is the highest affinity fluorescent norepinephrine sensor currently available and can be used for measuring catecholamines in live‐cell assays.     

Theoretical study of the ring‐closing reaction of 5′‐AMP to cAMP and H2O in the gas phase

The ring‐closing reaction of 5′‐adenosine monophosphate (5′‐AMP) to generate cyclic 3′, 5′‐adenosine monophosphate (cAMP) and H₂O was theoretically investigated at the B3LYP/6‐31G**level. It was found that the ring‐closing reaction of 5′‐AMP may proceed in a synchronous way or in a stepwise way. For the latter, the reaction is a multichannel elimination reaction including inner H transfer. The potential energy surface of Path 3 is lowest in all the ring‐closing reaction paths. In addition, H shuttling reaction with the participation of a water molecule to act as a shuttle were also studied at the same level. The calculations indicate that the participation of a water molecule facilitates hydrogen transfer reaction. Our present calculations rationalized all the possible reaction channels. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Purine 3′:5′‐cyclic nucleotides with the nucleobase in a syn orientation: cAMP,cGMP and cIMP

Purine 3′:5′‐cyclic nucleotides are very well known for their role as the secondary messengers in hormone action and cellular signal transduction. Nonetheless, their solid‐state conformational details still require investigation. Five crystals containing purine 3′:5′‐cyclic nucleotides have been obtained and structurally characterized, namely adenosine 3′:5′‐cyclic phosphate dihydrate, C₁₀H₁₂N₅O₆P·2H₂O or cAMP·2H₂O, (I), adenosine 3′:5′‐cyclic phosphate 0.3‐hydrate, C₁₀H₁₂N₅O₆P·0.3H₂O or cAMP·0.3H₂O, (II), guanosine 3′:5′‐cyclic phosphate pentahydrate, C₁₀H₁₂N₅O₇P·5H₂O or cGMP·5H₂O, (III), sodium guanosine 3′:5′‐cyclic phosphate tetrahydrate, Na⁺·C₁₀H₁₁N₅O₇P⁻·4H₂O or Na(cGMP)·4H₂O, (IV), and sodium inosine 3′:5′‐cyclic phosphate tetrahydrate, Na⁺·C₁₀H₁₀N₄O₇P⁻·4H₂O or Na(cIMP)·4H₂O, (V). Most of the cyclic nucleotide zwitterions/anions [two from four cAMP present in total in (I) and (II), cGMP in (III), cGMP⁻ in (IV) and cIMP⁻ in (V)] are syn conformers about the N‐glycosidic bond, and this nucleobase arrangement is accompanied by C_rib—H…N_pur hydrogen bonds (rib = ribose and pur = purine). The base orientation is tuned by the ribose pucker. An analysis of data obtained from the Cambridge Structural Database made in the context of syn–anti conformational preferences has revealed that among the syn conformers of various purine nucleotides, cyclic nucleotides and dinucleotides predominate significantly. The interactions stabilizing the syn conformation have been indicated. The inter‐nucleotide contacts in (I)–(V) have been systematized in terms of the chemical groups involved. All five structures display three‐dimensional hydrogen‐bonded networks.     

AMP/GMP Analogs as Affinity ESIPT Probes for Highly Selective Sensing of Alkaline Phosphatase Activity in Living Systems

Current probes for alkaline phosphatase (ALP) detection had been developed mainly by adding a phosphate group to a dye, which would lead to indistinct performance when implemented in a living system as several phosphatases exist together. In this study, the nucleotides adenosine monophosphate (AMP) and guanosine monophosphate (GMP) were introduced into 2′‐(2′‐hydroxyphenyl)‐benzothiazole‐based probes, and highly fluorescent turn‐on probes with good selectivity towards ALP over several phosphatases, as well as high affinity and low toxicity were obtained. In the presence of l ‐phenylalanine, an ALP inhibitor, a strong decrease in fluorescence recovery was observed. These probes allowed for real‐time imaging of endogenous ALP activity in living cells as well as in a zebrafish model.     

Enzymatic Conversion of Cypridina Luciferyl Sulfate to Cypridina Luciferin with Coenzyme A as a Sulfate Acceptor in Cypridina (Vargula) hilgendorfii

In the luminous ostracod Cypridina (presently Vargula) hilgendorfii, Cypridina luciferyl sulfate (3‐enol sulfate of Cypridina luciferin) is converted to Cypridina luciferin by a sulfotransferase with 3′‐phosphoadenosine‐5′‐phosphate (PAP) as a sulfate acceptor. The resultant Cypridina luciferin is used for the luciferase–luciferin reaction of Cypridina to emit blue light. The luminescence stimulation with major organic cofactors was examined using the crude extracts of Cypridina specimens, and we found that the addition of coenzyme A (CoA) to the crude extracts significantly stimulated luminescence intensity. Further, the light‐emitting source in the crude extracts stimulated with CoA was identified as Cypridina luciferyl sulfate, and we demonstrated that CoA could act as a sulfate acceptor from Cypridina luciferyl sulfate. In addition, the sulfate group of Cypridina luciferyl sulfate was also transferred to adenosine 5′‐monophosphate (5′‐AMP) and adenosine 3′‐monophosphate (3′‐AMP) by a sulfotransferase. The sulfated products corresponding to CoA, 5′‐AMP and 3′‐AMP were identified using mass spectrometry. This is the first report that CoA can act as a sulfate acceptor in a sulfotransferase reaction.     

An Fe2+- and α-Ketoglutarate-Dependent Halogenase Acts on Nucleotide Substrates

While halogenated nucleosides are used as common anticancer and antiviral drugs, naturally occurring halogenated nucleosides are rare. Adechlorin (ade) is a 2′-chloro nucleoside natural product first identified from Actinomadura sp. ATCC 39365. However, the installation of chlorine in the ade biosynthetic pathway remains elusive. Reported herein is a Fe²⁺-α-ketoglutarate halogenase AdeV that can install a chlorine atom at the C2′ position of 2′-deoxyadenosine monophosphate to afford 2′-chloro-2′-deoxyadenosine monophosphate. Furthermore, 2′,3′-dideoxyadenosine-5′-monophosphate and 2′-deoxyinosine-5′-monophosphate can also be converted, albeit 20-fold and 2-fold, respectively, less efficiently relative to the conversion of 2′-deoxyadenosine monophosphate. AdeV represents the first example of a Fe²⁺-α-ketoglutarate-dependent halogenase that converts nucleotides into chlorinated analogues.     

Acid?Base Properties of Adenosine 5′‐Monophosphate,Guanosine 5′‐Monophosphate,and Inosine 5′‐Monophosphate in Aqueous Solutions of Methanol

The protonation constants of adenosine 5′‐monophosphate, guanosine 5′‐monophosphate, and inosine 5′‐monophosphate were determined in binary mixtures of H₂O containing 0, 10, 15, 20, 25, 30, 35, 40, 45, and 50% MeOH, using a combination of potentiometric and spectrophotometric methods at a constant temperature (25°) and constant ionic strength (0.1 mol?dm^?3 NaClO₄). The protonation constants were analyzed using the normalized polarity parameter (E ), and Kamlet, Abboud, and Taft (KAT) parameters. A linear correlation of log K vs. the normalized polarity parameter was obtained. Dual‐parameter correlation of log K vs. π* (dipolarity/polarizability) and α (H‐bond‐donor acidity), as well as π* and β (H‐bond‐acceptor basicity) also gives good results in various aqueous organic solvent mixtures. Finally, the results are discussed in terms of the effect of solvent on the protonation equilibria.     

Fast,efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method

The AM1‐BCC method quickly and efficiently generates high‐quality atomic charges for use in condensed‐phase simulations. The underlying features of the electron distribution including formal charge and delocalization are first captured by AM1 atomic charges for the individual molecule. Bond charge corrections (BCCs), which have been parameterized against the HF/6‐31G* electrostatic potential (ESP) of a training set of compounds containing relevant functional groups, are then added using a formalism identical to the consensus BCI (bond charge increment) approach. As a proof of the concept, we fit BCCs simultaneously to 45 compounds including O‐, N‐, and S‐containing functionalities, aromatics, and heteroaromatics, using only 41 BCC parameters. AM1‐BCC yields charge sets of comparable quality to HF/6‐31G* ESP‐derived charges in a fraction of the time while reducing instabilities in the atomic charges compared to direct ESP‐fit methods. We then apply the BCC parameters to a small “test set” consisting of aspirin, d ‐glucose, and eryodictyol; the AM1‐BCC model again provides atomic charges of quality comparable with HF/6‐31G* RESP charges, as judged by an increase of only 0.01 to 0.02 atomic units in the root‐mean‐square (RMS) error in ESP. Based on these encouraging results, we intend to parameterize the AM1‐BCC model to provide a consistent charge model for any organic or biological molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 132–146, 2000     

Ultraviolet Radiation‐Induced Downregulation of SERCA2 Mediates Activation of NLRP3 Inflammasome in Basal Cell Carcinoma

Basal cell carcinomas (BCCs) account for majority of skin malignancies in the United States. The incidence of BCCs is strongly associated with exposure of ultraviolet (UV) radiation. Nucleotide‐binding domain, leucine‐rich‐repeat‐containing family, pyrin domain‐containing 3 (NLRP3) inflammasome plays an important role in innate immune responses. Different stimuli such as toxins, microorganisms and particles released from injured cells activate the NLRP3 inflammasome. Activated NLRP3 results in activation of caspase‐1, which cleaves pro‐IL‐1β to active IL‐1β. In this study, we have shown that NLRP3 is expressed in human basal cell carcinomas. The proximal steps in activation of NLRP3 inflammasome are not well understood. Here, we have attempted to elucidate a critical role for Ca²⁺ mobilization in activation of the NLRP3 inflammasome by UVB exposure using HaCaT keratinocytes. We have demonstrated that UVB exposure blocks Ca²⁺ mobilization by downregulating the expression of sarco/endoplasmic reticulum Ca²⁺‐ATPase (SERCA2), a component of store‐operated Ca²⁺ entry that leads to activation of the NLRP3 inflammasome.     

Sensitive and validated LC‐MS/MS methods to evaluate mycophenolic acid pharmacokinetics and pharmacodynamics in hematopoietic stem cell transplant patients

Monitoring of pharmacodynamics in addition to pharmacokinetics is one of strategies to individualize mycophenolate mofetil therapy. The purpose of this study was to develop sensitive liquid chromatography–tandem mass spectrometry (LC‐MS/MS) methods for evaluation of the pharmacokinetics and pharmacodynamics of mycophenolic acid (MPA). Concentrations of mycophenolic acid glucuronide (MPAG), mycophenolic acid acyl‐glucuronide, as well as unbound MPA and MPAG, were determined, and inosine‐5′‐monophosphate dehydrogenase activity was calculated by measuring concentrations of produced xanthosine‐5′‐monophosphate (XMP) and intracellular adenosine‐5′‐monophosphate after incubation of peripheral blood mononuclear cell (PBMC) lysates. A metal‐free Mastro^TM column and two gradient patterns were used to improve the quantification limit of XMP to 0.1 μm . In the clinical MPA concentration range, the linearity of the calibration curve, inter‐ and intra‐day precision and accuracy satisfied the relevant US Food and Drug Administration guidelines. The MPA concentrations in hematopoietic stem cell transplant (HSCT) patients determined by the enzyme assay and the present LC‐MS/MS method showed a good correlation (r² = 0.95, p < 0.001). In this study, we report sensitive and validated LC‐MS/MS methods to evaluate the pharmacokinetics and pharmacodynamics of MPA, which are sufficiently sensitive to assess small quantities of PBMC lysates collected shortly after HSCT. Copyright © 2015 John Wiley & Sons, Ltd.     

碳链长度对芳香异羟肟酸二烃基锡配合物与5’-AMP或DNA相互作用的影响

选择体外筛选活性强的Bu₂Sn(4-FC₆H₄C(O)NHO)₂和活性弱的有机锡化合物Me₂Sn(4-FC₆H₄C(O)NHO)₂为模型,利用高分辨¹H NMR和³¹P NMR 技术比较研究这两个有代表性的有机锡化合物与DNA的基本组成单元5’-AMP在不同时间、不同条件下的作用模式并用紫外法进一步研究其与DNA的相互作用。结果显示,具有不同碳链的有机锡化合物与5’-AMP相互作用明显不同,含较长碳链的Bu₂Sn(4-FC₆H₄C(O)NHO)₂与5’-AMP的作用明显强于Me₂Sn(4-FC₆H₄C(O)NHO)₂,Me₂Sn(4-FC₆H₄C(O)NHO)₂分子可能只与5’-AMP的磷酸骨架静电结合,与整个分子作用较弱,而含丁基的Bu₂Sn(4-FC₆H₄C(O)NHO)₂可能除了与磷酸骨架静电结合,也与疏水碱基具有超分子相互作用而更有利于与5’-AMP稳定结合。Bu₂Sn(4-FC₆H₄C(O)NHO)₂的长链有机配体在与DNA的作用模式上发挥了重要作用。     

Molecular Recognition of Nucleotides in Water by Scorpiand‐Type Receptors Based on Nucleobase Discrimination

The detection of nucleotides is of crucial importance because they are the basic building blocks of nucleic acids. Scorpiand‐based polyamine receptors functionalized with pyridine or anthracene units are able to form stable complexes with nucleotides in water, based on coulombic, π–π stacking, and hydrogen‐bonding interactions. This behavior has been rationalized by means of an exploration with NMR spectroscopy and DFT calculations. Binding constants were determined by potentiometry. Fluorescence spectroscopy studies have revealed the potential of these receptors as sensors to effectively and selectively distinguish guanosine‐5′‐triphosphate (GTP) from adenosine‐5′‐triphosphate (ATP).     

Unraveling the Degradation Mechanism of Purine Nucleotides Photosensitized by Pterins: The Role of Charge‐Transfer Steps

Photosensitized reactions contribute to the development of skin cancer and are used in many applications. Photosensitizers can act through different mechanisms. It is currently accepted that if the photosensitizer generates singlet molecular oxygen (¹O₂) upon irradiation, the target molecule can undergo oxidation by this reactive oxygen species and the reaction needs dissolved O₂ to proceed, therefore the reaction is classified as ¹O₂‐mediated oxidation (type II mechanism). However, this assumption is not always correct, and as an example, a study on the degradation of 2′‐deoxyguanosine 5′‐monophosphate photosensitized by pterin is presented. A general mechanism is proposed to explain how the degradation of biological targets, such as nucleotides, photosensitized by pterins, naturally occurring ¹O₂ photosensitizers, takes place through an electron‐transfer‐initiated process (type I mechanism), whereas the contribution of the ¹O₂‐mediated oxidation is almost negligible.     

A novel and facile reaction to N6‐alkylated adenosine via benzotriazole as a synthetic auxiliary

The reaction of benzotriazole with aliphatic, aromatic or heteroaromatic aldehyde and adenosine leads to a benzotriazole adduct which is reduced with sodium borohydride to the corresponding N⁶‐alkylated adenosine derivatives. This procedure is also utilized in a new route to N⁶‐(3‐iodobenzyl)adenosine‐5′‐N‐methyluronamide (IB‐MECA) which is considered an important adenosine agonist at A₃ adenosine receptors.     

Crystal structure and sequential dehydration transitions of disodium guanosine 5′‐monophosphate tetrahydrate

Disodium guanosine 5′‐monophosphate was reported previously to crystallize as both the tetrahydrate and the heptahydrate. We herein report a determination of the molecular and crystal structures of the title tetrahydrated salt, 2Na⁺·C₁₀H₁₂N₅O₈P²⁻·4H₂O. It was found that the structure differs markedly from that of the heptahydrate, but greatly resembles that of disodium deoxyguanosine 5′‐monophosphate tetrahydrate. The C2′—O2′H moiety of ribose is surrounded by hydrophilic moieties and is disordered over two sites. The sugar puckering mode is O4′‐endo‐C1′‐exo at both sites and the conformation around the C4′—C5′ bond is gauche–trans. Powder X‐ray diffraction and thermal analyses revealed that the temperature‐controlled transition from the tetrahydrate to the anhydride proceeded through three intermediate phases between 40 and 60 °C at 0% relative humidity. Large induction periods were observed.     

Properties of the Magnesium(II) and Calcium(II) Complexes of 5‐ and 6‐Uracilmethylphosphonate (5 Umpa2– and 6 Umpa2–) in Aqueous Solution

The stability constants of the 1 : 1 complexes formed between Mg²⁺ or Ca²⁺ and 5 Umpa^2– or 6 Umpa^2– were determined by potentiometric pH titrations in aqueous solution (25 °C; I = 0.1 M, NaNO₃). Based on previously established log K^M_M(R‐PO3) versus pK^H_H(R‐PO3) straight‐line plots (M²⁺ = Mg²⁺ or Ca²⁺; R‐PO₃^2– = simple phosphate monoester or phosphonate ligands where R is a non‐interacting residue), it is shown that the Mg(5 Umpa), Ca(5 Umpa), Mg(6 Umpa) and Ca(6 Umpa) complexes have the stability expected on the basis of the basicity of the phosphonate group in 5 Umpa^2– and 6 Umpa^2–. This means, these ligands may be considered as simple analogues of nucleotides, e. g. of uridine 5′‐monophosphate. In the higher pH range deprotonation of the uracil residue in the M(5 Umpa) and M(6 Umpa) complexes occurs and this leads to the negatively charged M(5 Umpa–H)^– and M(6 Umpa–H)^– species. Based on the comparison of various acidity constants it is shown that the M(5 Umpa) complexes are especially acidic; or to say it differently, the M(5 Umpa–H)^– species are especially stable. This increased stability is attributed to the formation of a seven‐membered chelate involving next to the phosphonate group also the carbonyl oxygen atom at C4 (after deprotonation of the (N3)H site). The formation degree of this chelated isomer reaches about 45% for the Mg(5 Umpa–H)^– and Ca(5 Umpa–H)^– species. No indication for chelate formation was observed for the M(6 Umpa–H)^– complexes.