A quantum chemical study of the catalysis for cytidine deaminase: contribution of the extra water molecule

Cytidine deaminase is known as an important enzyme responsible for the hydrolytic deamination of cytidine, which is applied as a key step to the conversion of the precursor of the cancer drug to an active form in the living body. Cytidine with water is efficiently converted to uridine with ammonia in the cleft of cytidine deaminase. In this work, the catalysis of cytidine deaminase for the hydrolytic deamination was examined using cytosine as a model of cytidine and the model molecules for the active site of cytidine deaminase by means of the quantum chemical method. We especially investigated the contribution of the water molecule from the solvent to the catalysis, because the X-ray diffraction analysis of a crystal structure has revealed the existence of the water molecule in the vicinity of the substrate bound to the active site inside the cleft. Our computations showed that the extra water molecule from the solvent has a possibility to support the catalysis of cytidine deaminase.     

The measurement of nucleoside deaminases by high performance liquid chromatography and their use in clinical chemistry.

The measurement of the nucleoside deaminases--cytidine deaminase, guanosine deaminase and adenosine deaminase--by reversed phase high performance liquid chromatography is reviewed. The clinical value of assaying the enzyme activity is discussed for each of these enzymes. Both cytidine deaminase and adenosine deaminase measurements have proven clinical value, although the use of the assay of cytidine deaminase in the diagnosis of pre-eclampsia is probably not helpful.     

Synthesis of labeled 1-amino-2-methylenecyclopropane-1-carboxylic acid, an inactivator of 1-aminocyclopropane-1-carboxylate deaminase

1-Amino-2-methylenecyclopropane-1-carboxylic acid (2-methylene-ACC) is an irreversible inhibitor for a bacterial enzyme, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which catalyzes the conversion of ACC to alpha-ketobutyrate and ammonia. The inactivation has been proposed to proceed with the ring scission induced by an addition of an enzyme nucleophile, resulting in the formation of a reactive turnover product that then traps an active-site residue. To gain further insight into this unique enzymatic reaction, the tritiated 2-methylene-ACC was prepared and incubated with ACC deaminase to locate and identify the entrapped amino acid residue. The synthesis of this radiolabeled compound and the results of its incubation with ACC deaminase are reported in this paper.     

Analysis of lipoprotein lipase activity using high-performance liquid chromatography

Lipoprotein lipase (LPL) is a key enzyme which regulates the plasma triglyceride concentration by hydrolyzing triglycerides in chylomicrons and very-low-density lipoprotein (VLDL). The activity of LPL was conventionally analyzed using radio-labeled residues or direct sandwich-ELISA. An assay for lipoprotein lipase activity which used a nonradioactive substrate, tri-olein, is described. In this method, LPL activity was detected fluorometrically by reacting 9-anthryldiazomethane (ADAM) with the oleic acid generated from tri-olein by enzyme activity and separated by reversed-phase HPLC. This method has been optimized and the optimum enzyme incubation time and reaction time of the generated oleic acid with ADAM were both at 20 min. The method correlated well with the conventional method.     

Ab initio ONIOM-molecular dynamics (MD) study on the deamination reaction by cytidine deaminase

We applied the ONIOM-molecular dynamics (MD) method to the hydrolytic deamination of cytidine by cytidine deaminase, which is an essential step of the activation process of the anticancer drug inside the human body. The direct MD simulations were performed for the realistic model of cytidine deaminase by calculating the energy and its gradient by the ab initio ONIOM method on the fly. The ONIOM-MD calculations including the thermal motion show that the neighboring amino acid residue is an important factor of the environmental effects and significantly affects not only the geometry and energy of the substrate trapped in the pocket of the active site but also the elementary step of the catalytic reaction. We successfully simulate the second half of the catalytic cycle, which has been considered to involve the rate-determining step, and reveal that the rate-determining step is the release of the NH3 molecule.     

Origin of tight binding of a near-perfect transition-state analogue by cytidine deaminase: implications for enzyme catalysis

Cytidine deaminase (CDA) is a zinc metalloenzyme that catalyzes the hydrolytic deamination of cytidine to uridine. Zebularine (ZEB) binds to CDA, and the binding process leads to a near-perfect transition-state analogue (TSA) inhibitor at the active site with an estimated K(i) value of 1.2 x 10(-)(12) M. The interaction of CDA with the TSA inhibitor has become a paradigm for studying the tight TSA binding by enzymes. The formation of the TSA is catalyzed by CDA by a mechanism that is similar to the formation of the tetrahedral intermediate during the CDA-catalyzed reaction (i.e., through the nucleophilic attack of a Zn-hydroxide group on C(4)). It is believed that the TSA formed at the active site is zebularine 3,4-hydrate. In this paper, it is shown from QM/MM molecular dynamics and free energy simulations that zebularine 3,4-hydrate may in fact be unstable in the enzyme and that a proton transfer from the Zn-hydroxide group to Glu-104 during the nucleophilic attack could be responsible for the very high affinity. The nucleophilic attack by the Zn-hydroxide on C(4) is found to be concerted with two proton transfers. Such concerted process allows the TSA, an alkoxide-like inhibitor, to be stabilized through a mechanism that is similar to the transition-state stabilization in the general acid-base catalysis. It is suggested that the proton transfer from the Zn-hydroxide to Glu-104, which is required to generate the general acid for protonating the leaving ammonia, may play an important role in lowering the activation barrier during the catalysis.     

Isocratic high-performance liquid chromatographic method for studying the metabolism of blood plasma pyrimidine nucleosides and bases: concentration and radioactivity measurements

A rapid and efficient isocratic high-performance liquid chromatographic method for studying the metabolism of blood plasma cytosine, uracil, thymine, cytidine, deoxycytidine and uridine has been elaborated. For each compound this method can measure concentrations in the range 0.5-200 microM and determine radioactivity. All the pyrimidine compounds can be eluted in less than 18 min, and the total time elapsed between collection of the blood and completion of the analysis need not exceed 3 h. All measurements can be performed on 0.025-ml blood samples. Blood plasma pyrimidine concentrations were determined for the rat, the rabbit, the guinea pig, the dog and the healthy human. This method could be well applied to experimentation on small animals using radiolabelled pyrimidine derivatives, in order to study the metabolic pathways of nucleotides and nucleic acids. It could also be used to characterize certain illnesses or cases of toxicity created by a chemotherapy affecting the plasma level of pyrimidine bases or nucleosides.     

Quantitation by fast-atom bombardment mass spectrometry: assay of cytidine 3',5'-cyclic monophosphate-responsive protein kinase.

A protein kinase, stimulated by cytidine 3',5'-cyclic monophosphate, is conventionally assayed by monitoring the incorporation of radiolabelled phosphate from adenosine triphosphate into a histone substrate. Here the assay of the protein kinase is carried out by positive-ion fast-atom bombardment mass spectrometric analysis of the enzyme incubation mixture after the reaction has been terminated. The data so obtained show good agreement with data obtained by the conventional radiometric assay: the intrinsic advantage of the mass spectrometric assay is the capacity for multiple component monitoring; the ability of the kinase to bind competing cyclic nucleotides together with integral adenosine triphosphatase (ATPase) and phosphodiesterase activity can also be assessed.     

Superiority of HPLC to Assay for Enzymes Regulating Adenine Nucleotide Pool Intermediates Metabolism: 5'-Nucleotidase,Adenylate Deaminase,Adenosine Deaminase,and Adenylosuccinate Lyase-A Simple and Rapid Determination of Adenosine

Abstract

A new application of HPLC analysis to assay for all the enzymes involved in regulation of adenine nucleotide pool metabolism is described. In vitro, enzymatic reactions were carried out in buffered reaction media containing appropriate concentrations of metal ions, specific substrate, inhibitors and enzymes. Following an incubation period, the enzymatic reactions were terminated and extracted with cold trichloroacetic acid. The soluble acid extracts were neutralized and injected in a HPLC system. Using a C18-Nova Pak reverse phase column, we were able to separate, identify and quantify the substrate, products and their possible catabolites and UV-detectable inhibitors. A complete separation and quantitation of metabolites was accomplished within 16-18 minutes. However, rapid and simple HPLC runs were also developed which can be routinely used to determine adenosine levels within 3-4 minutes, using a single solvent HPLC system. This procedure is extremely reproducible and very reliable as demonstrated in assaying for 5'-nucleotidase, adenylate deaminase, adenosine deaminase and adenylosuccinate lyase activities.     

Quantitative determination of the cytidine deaminase inhibitor tetrahydrouridine (THU) in mouse plasma by liquid chromatography/electrospray ionization tandem mass spectrometry

A number of anticancer drugs are cytidine analogues that undergo metabolic deactivation catalyzed by cytidine deaminase (CD). 3,4,5,6-Tetrahydrouridine (THU) is a potent inhibitor of CD, by acting as a transition-state analogue of its natural substrate cytidine. However, to date its pharmacokinetic properties have not been fully characterized, which has impaired its optimal preclinical evaluation and clinical use. We report a liquid chromatography/tandem mass spectrometry (LC/MS/MS) assay for the sensitive, accurate and precise quantitation of THU in mouse plasma. Validation was performed according to FDA guidelines. The assay employed deuterated THU as the internal standard and an acetonitrile protein precipitation step. Separation, based on hydrophilic interaction chromatography, was achieved with an amino column and an isocratic mobile phase of 0.1% formic acid in acetonitrile and water followed by a wash. Chromatographic separation was followed by positive-mode electrospray ionization MS/MS detection in the multiple reaction monitoring (MRM) mode. The assay was accurate (92.5-109.9%) and precise (2.1-9.0%) in the concentration range of 0.2-50 microg/mL. Recovery from plasma was near-complete (92.9-119.3%) and ion suppression was negligible (-17.5 to -0.2%). Plasma freeze/thaw stability (93.1-102.1%), stability for 3 months at -80 degrees C (99.5-110.9%), and stability for 4 h at room temperature (92.1-102.4%) were all in order. This assay is currently being used to quantitate THU in ongoing pharmacokinetic studies. In addition, the assay is expected to be a useful tool in any future studies involving co-administration of THU with cytidine analogues.     

Inhibitory activity of hibifolin on adenosine deaminase- experimental and molecular modeling study

Adenosine deaminase (ADA) is an enzyme involved in purine metabolism. ADA converts adenosine to inosine and liberates ammonia. Because of their critical role in the differentiation and maturation of cells, the regulation of ADA activity is considered as a potential therapeutic approach to prevent malignant and inflammatory disorders. In the present study, the inhibitory activity of a plant flavonoid, hibifolin on ADA is investigated using enzyme kinetic assay and isothermal titration calorimetry. The inhibitory constant of hibifolin was found to be 49.92 μM ± 3.98 and the mode of binding was reversible. Isothermal titration calorimetry showed that the compound binds ADA with binding energy of −7.21 Kcal/mol. The in silico modeling and docking studies showed that the bound ligand is stabilized by hydrogen bonds with active site residues of the enzyme. The study reveals that hibifolin can act as a potential inhibitor of ADA.     

Volumetric Properties of Nucleic Acid Bases and Nucleosides in Aqueous Ethanol, 1,2-Ethanediol, 2-Propanol, and 2-Methyl-2-Propanol at 25°C

Partial molar volumes of cytosine, uracil, thymine, cytidine, uridine, thymidine, and adenosine have been measured in different concentrations of aqueous ethanol, 1,2-ethanediol, 2-propanol, and 2-methyl-2-propanol at 25°C using densimetry. These data are utilized in conjunction with the partial molar volumes of these nucleic acid bases and nucleosides in water reported earlier to deduce the partial molar volumes of transfer from water to aqueous alcohol or diol. The results are explained in terms of likely solute–solvent interactions; the role of solvent in these interactions is discussed. The partial molar volume data are also used to calculate the contribution of –CH₂- groups in the nucleic acid base or solvent and of ribose in the nucleoside to the partial molar volume of transfer. The validity of group additivity in these systems is discussed.     

Interaction between N-Phospho-Amino Acids and Nucleoside in Aqueous Medium

Thebiosynthesisofnucleicacid,oneofthemostimportantbio-macromolecules,isahighlyelegantprocess,whichinvolvestheparticipationofmanyenzymesandenergycarriers,suchasATP',whilechemicalsynthesisofoligonucleotidesgenerallyinvolvescomplicatedprotectinganddeprotectingprocesses'.Inthepreviouswork,nucleotidesandoligonucleotidesweredirectlyformedacthereaction,,-ofN-(O,O-diisopropyl)phosphorylthreonineanduridineinanhydrouspyridine'.SoN-(O,O-diisopropyl)phospho-aminoacid(DIPP-aa)wasproposedasamodelcompou…     

Cytidylate cyclase activity: identification of cytidine 3',5'-cyclic monophosphate and four novel cytidine cyclic phosphates as biosynthetic products from cytidine triphosphate

Identification of cytidine 3',5'-cyclic monophosphate (cyclic CMP) as one of the products resulting from the incubation of dialysed cell-free preparations from rat brain, liver and kidney with cytidine 5'-triphosphate (CTP) is described. The non-acidic precipitable products after incubation of the tissue preparations with unlabelled, with 14C-single labelled, and with 14C- and 32P-dual labelled CTP were examined by thin-layer chromatography and high-pressure liquid chromatography, isotopic ratio determination, UV absorbance spectrophotometry, selective hydrolysis with nucleotidase, phosphodiesterase and acid, and by fast atom bombardment mass spectrometry with mass-analysed ion kinetic energy spectrum scanning. In addition to cyclic CMP and unchanged CTP, the products of the reaction were found to include cytidine monophosphate (CMP) and cytidine diphosphate (CDP) together with four novel cytidine compounds identified as cytidine 3',5'-cyclic pyrophosphate, cytidine 2'-monophosphate 3',5'-cyclic monophosphate, cytidine 2'-O-aspartyl-3',5'-cyclic monophosphate and cytidine 2'-O-glutamyl-3',5'-cyclic monophosphate. The evidence presented constitutes conclusive proof of the natural occurrence of cytidylate cyclase activity; the four novel cytidine cyclic phosphates described provide a feasible explanation of the discrepancies in previous reports which have led to the controversy which exists concerning the existence of cytidylate cyclase activity.     

Preparation of a mixture of nucleoside triphosphates suitable for use in synthesis of nucleotide phosphate sugars from ribonucleic acid using nuclease P1, a mixture of nucleoside monophosphokinases and acetate kinase

This paper (1) describes the enzymatic synthesis of a mixture of adenosine, guanosine, cytidine, and uridine triphosphates (ATP, GTP, CTP, and UTP) from ribonucleic acid (RNA). RNA was hydrolyzed by nuclease P1 to a mixture of 5'-nucleoside monophosphates. This mixture was converted to the nucleoside triphosphates using a mixture of nucleoside monophosphate kinases and acetate kinase, with acetyl phosphate as the ultimate phosphoryl donor. The nucleoside monophosphokinases were extracted from brewer's yeast in a four-step procedure. The specific activity of the yeast enzyme preparation after gel permeation chromatography was sufficiently high that the yeast kinases could be immobilized in volumes that were practical for laboratory scale syntheses. Conversions from NMP to NTP in a mixture containing 0.34 mol of total nucleoside phosphates were: ATP, 90%; GTP, 90%; CTP, 60%; and UTP, 40%.     

A rapid assay to screen adenosine deaminase inhibitors from Ligustri Lucidi Fructus against metabolism of cordycepin utilizing ultra-high-performance liquid chromatography–tandem mass spectrometry

Cordycepin has recently received increased attention owing to its extensive pharmacological activity. Adenosine deaminase (ADA) is widely distributed in mammalian blood and tissues; as a result, cordycepin is quickly metabolized upon entering into the body and converted into the inactive metabolite 3′-deoxyinosine, thus limiting its activity when administered alone. We herein present a novel ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS) method for screening ADA inhibitors against the metabolism of cordycepin. Cordycepin and 3′-deoxyinosine were chosen as substrate and product, respectively. A proper separation was achieved for all analytes within 3 min. 3′-Deoxyinosine was quantified in the presence or absence of potential ADA inhibitors to evaluate ADA activity. The assay can simultaneously determine substrate and product, with the endogenous substance and ADA inhibitors added not interfering in its activity. After optimizing the enzymatic incubation and UHPLC–MS/MS conditions, K_m and V_max values for ADA deamination of cordycepin were 95.18 ± 7.85 μm and 363.90 ± 12.16 μmol/min/unit, respectively. Oleanolic acid and ursolic acid from Ligustri Lucidi Fructus were chosen as ADA inhibitors with half maximal inhibitory concentration values of 21.82 ± 0.39 and 18.41 ± 0.14 μm , respectively. A non-competitive inhibition model was constructed and this assay can be used to screen other potential ADA inhibitors quickly and accurately.     

Synthesis of Sugar and Nucleoside Analogs and Evaluation of Their Anticancer and Analgesic Potentials

Chemical modification of sugars and nucleosides has a long history of producing compounds with improved selectivity and efficacy. In this study, several modified sugars (2–3) and ribonucleoside analogs (4–8) have been synthesized from α-d-glucose in a total of 21 steps. The compounds were tested for peripheral anti-nociceptive characteristics in the acetic acid-induced writhing assay in mice, where compounds 2, 7, and 8 showed a significant reduction in the number of writhes by 56%, 62%, and 63%, respectively. The compounds were also tested for their cytotoxic potential against human HeLa cell line via trypan blue dye exclusion test followed by cell counting kit-8 (CCK-8) assay. Compound 6 demonstrated significant cytotoxic activity with an IC₅₀ value of 54 µg/mL. Molecular docking simulations revealed that compounds 2, 7, and 8 had a comparable binding affinity to cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2) enzymes. Additionally, the bridged nucleoside analogs 7 and 8 potently inhibited adenosine kinase enzyme as well, which indicates an alternate mechanistic pathway behind their anti-nociceptive action. Cytotoxic compound 6 demonstrated strong docking with cancer drug targets human cytidine deaminase, proto-oncogene tyrosine-protein kinase Src, human thymidine kinase 1, human thymidylate synthase, and human adenosine deaminase 2. This is the first ever reporting of the synthesis and analgesic property of compound 8 and the cytotoxic potential of compound 6.     

Determination of five nucleosides by LC‐MS/MS and the application of the method to quantify N6‐methyladenosine level in liver messenger ribonucleic acid of an acetaminophen‐induced hepatotoxicity mouse model

Ribonucleic acid N⁶‐methyladenosine methylation plays an important role in a variety of biological processes and diseases. Acetaminophen‐induced hepatotoxicity is one of the major challenges faced by clinicians. To date, the link between N⁶‐methyladenosine and acetaminophen‐induced hepatotoxicity has not been studied. In this study, a simple ultra high performance liquid chromatography with tandem mass spectrometry method was developed for the simultaneous determination of five nucleosides (adenosine, uridine, cytidine, guanosine, and N⁶‐methyladenosine) in messenger ribonucleic acid. After enzymatic digestion of messenger ribonucleic acid, the nucleosides sample was separated on an Acquity UPLC column with gradient elution using methanol and 0.02% formic acid water, and detected by a Qtrap 4500 mass spectrometer with an electrospray ionization mode. The method was validated over the concentration ranges of 4–800 ng/mL for adenosine, uridine, cytidine, and guanosine and 0.1–20 ng/mL for N⁶‐methyladenosine. It was successfully applied to the determination of N⁶‐methyladenosine levels in liver messenger ribonucleic acid in an acetaminophen‐induced hepatotoxicity mouse model and a control group. This study offers a method for the determination of nucleoside contents in epigenetic studies and constitutes the first step toward the investigation of ribonucleic acid methylation in acetaminophen‐induced hepatotoxicity, which will facilitate the elucidation of its mechanism.     

In silico structural and functional analysis of Mesorhizobium ACC deaminase

Nodulation is one of the very important processes of legume plants as it is the initiating event of fixing nitrogen. Although ethylene has essential role in normal plant metabolism but it has also negative impact on plants particularly in nodule formation in legume plants. It is also produced due to a variety of biotic or abiotic stresses. 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase is a rhizobial enzyme which cleaves ACC (immediate precursor of ethylene) into α-ketobutyrate and ammonia. As a result, the level of ethylene from the plant cells is decreased and the negative impact of ethylene on nodule formation is reduced. ACC deaminase is widely studied in several plant growth promoting rhizobacterial (PGPR) strains including many legume nodulating bacteria like Mesorhizobium sp. It is an important symbiotic nitrogen fixer belonging to the class – alphaproteobacteria under the order Rhizobiales. ACC deaminase has positive role in Legume-rhizobium symbiosis. Rhizobial ACC deaminase has the potentiality to reduce the adverse effects of ethylene, thereby triggering the nodulation process. The present study describes an in silico comparative structural (secondary structure prediction, homology modeling) and functional analysis of ACC deaminase from Mesorhizobium spp. to explore physico-chemical properties using a number of bio-computational tools. M. loti was selected as a representative species of Mesorhizobium genera for 3D modelling of ACC deaminase protein. Correlation by the phylogenetic relatedness on the basis of both ACC deaminase enzymes and respective acdS genes of different strains of Mesorhizobium has also studied.     

Biochemical and computational insights of adenosine deaminase inhibition by Epigallocatechin gallate

Epigallocatechin gallate, a flavonoid from Camellia sinensis possess various pharmacological activities such as anticancer, antimicrobial and antioxidant etc. Adenosine deaminase, (ADA), is a key enzyme involved in the purine metabolism, the inhibitors of which is being considered as highly promising candidate for the development of anti-proliferative and anti-inflammatory drugs. In this work we studied adenosine deaminase inhibitory activity of epigallocatechin gallate by using biophysical and computational methods. The enzyme inhibition study result indicated that epigallocatechin gallate possess strong inhibitory activity on ADA. ITC study revealed the energetics of binding. Also the binding is confirmed by using fluorescence spectroscopy. The structural details of binding are obtained from molecular docking and MD simulation studies.