Identification of potential inhibitors for AIRS from de novo purine biosynthesis pathway through molecular modeling studies – a computational approach

In cancer, de novo pathway plays an important role in cell proliferation by supplying huge demand of purine nucleotides. Aminoimidazole ribonucleotide synthetase (AIRS) catalyzes the fifth step of de novo purine biosynthesis facilitating in the conversion of formylglycinamidine ribonucleotide to aminoimidazole ribonucleotide. Hence, inhibiting AIRS is crucial due to its involvement in the regulation of uncontrollable cancer cell proliferation. In this study, the three-dimensional structure of AIRS from P. horikoshii OT3 was constructed based on the crystal structure from E. coli and the modeled protein is verified for stability using molecular dynamics for a time frame of 100 ns. Virtual screening and induced fit docking were performed to identify the best antagonists based on their binding mode and affinity. Through mutational studies, the residues necessary for catalytic activity of AIRS were identified and among which the following residues Lys35, Asp103, Glu137, and Thr138 are important in determination of AIRS function. The mutational studies help to understand the structural and energetic characteristics of the specified residues. In addition to Molecular Dynamics, ADME properties, binding free-energy, and density functional theory calculations of the compounds were carried out to find the best lead molecule. Based on these analyses, the compound from the NCI database, NCI_121957 was adjudged as the best molecule and could be suggested as the suitable inhibitor of AIRS. In future studies, experimental validation of these ligands as AIRS inhibitors will be carried out.     

Octameric structure of the human bifunctional enzyme PAICS in purine biosynthesis

Phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS) is an important bifunctional enzyme in de novo purine biosynthesis in vertebrate with both 5-aminoimidazole ribonucleotide carboxylase (AIRc) and 4-(N-succinylcarboxamide)-5-aminoimidazole ribonucleotide synthetase (SAICARs) activities. It becomes an attractive target for rational anticancer drug design, since rapidly dividing cancer cells rely heavily on the purine de novo pathway for synthesis of adenine and guanine, whereas normal cells favor the salvage pathway. Here, we report the crystal structure of human PAICS, the first in the entire PAICS family, at 2.8 Å resolution. It revealed that eight PAICS subunits, each composed of distinct AIRc and SAICARs domains, assemble a compact homo-octamer with an octameric-carboxylase core and four symmetric periphery dimers formed by synthetase domains. Based on structural comparison and functional complementation analyses, the active sites of SAICARs and AIRc were identified, including a putative substrate CO₂-binding site. Furthermore, four symmetry-related, separate tunnel systems in the PAICS octamer were found that connect the active sites of AIRc and SAICARs. This study illustrated the octameric nature of the bifunctional enzyme. Each carboxylase active site is formed by structural elements from three AIRc domains, demonstrating that the octamer structure is essential for the carboxylation activity. Furthermore, the existence of the tunnel system implies a mechanism of intermediate channeling and suggests that the quaternary structure arrangement is crucial for effectively executing the sequential reactions. In addition, this study provides essential structural information for designing PAICS-specific inhibitors for use in cancer chemotherapy.     

Mapping of the bovine genes of the de novo AMP synthesis pathway

Summary The purine nucleotides adenosine monophosphate (AMP) and guanosine monophosphate (GMP) are critical for energy metabolism, cell signalling and cell reproduction. Despite their essential function, little is known about the regulation and in vivo expression pattern of the genes involved in the de novo purine synthesis pathway. The complete coding region of the bovine phosphoribosylaminoimidazole carboxylase gene (PAICS), which catalyses steps 6 and 7 of the de novo purine biosynthesis pathway, as well as bovine genomic sequences of the six other genes in the pathway producing inosine monophosphate (IMP) and AMP [phosphoribosyl pyrophosphate amidotransferase (PPAT), phosphoribosylglycinamide formyltransferase (GART), phosphoribosylformylglycinamidine synthase (PFAS), adenylosuccinate lyase (ADSL), 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) and adenylosuccinate synthase (ADSS)], were identified. The genes were mapped to segments of six different bovine chromosomes using a radiation hybrid (RH) cell panel. The gene PPAT, coding for the presumed rate-limiting enzyme of the purine de novo pathway was closely linked to PAICS on BTA6. These, and the other bovine locations i.e. GART at BTA1, PFAS at BTA19, ADSL at BTA5, ATIC at BTA2 and ADSS at BTA16, are in agreement with published comparative maps of cattle and man. PAICS and PPAT genes are known to be closely linked in human, rat and chicken. Previously, an expressed sequence fragment of PAICS (Bos taurus corpus luteum, BTCL9) was mapped to BTA13. By isolation and characterization of a BAC clone, we have now identified a PAICS processed pseudogene sequence (psiPAICS) on BTA13. Processed pseudogene sequences of PAICS and other genes of the purine biosynthesis pathway were identified in several mammalian species, indicating that the genes of this pathway have been susceptible to retrotransposition. The seven bovine genes are expressed at a higher level in testicular and ovary tissues compared with skeletal muscle.     

The interaction of ammonia and xenon with the imidazole glycerol phosphate synthase from Thermotoga maritima as detected by NMR spectroscopy

The imidazole glycerol phosphate (ImGP) synthase from the hyperthermophilic bacterium Thermotoga maritima is a 1:1 complex of the glutaminase subunit HisH and the cyclase subunit HisF. It has been proposed that ammonia generated by HisH is transported through a channel to the active site of HisF, which generates intermediates of histidine (ImGP) and de novo biosynthesis of 5‐aminoimidazole‐4‐carboxamideribotide. Solution NMR spectroscopy of ammonium chloride‐titrated samples was used to study the interaction of NH₃ with amino acids inside this channel. Although numerous residues showed ¹⁵N chemical shift changes, most of these changes were caused by nonspecific ionic strength effects. However, several interactions appeared to be specific. Remarkably, the amino acid residue Thr 78—which is located in the central channel—shows a large chemical shift change upon titration with ammonium chloride. This result and the reduced catalytic activity of the Thr78Met mutant indicate a special role of this residue in ammonia channeling. To detect and further characterize internal cavities in HisF, which might for example contribute to ammonia channeling, the interaction of HisF with the noble gas xenon was analyzed by solution NMR spectroscopy using ¹H‐¹⁵N HSQC experiments. The results indicate that HisF contains three distinct internal cavities, which could be identified by xenon‐induced chemical shift changes of the neighboring amino acid residues. Two of these cavities are located at the active site at opposite ends of the substrate N′‐[(5′‐phosphoribulosyl)formimino]‐5‐aminoimidazole‐4‐carboxamide‐ribonucleotide (PRFAR) binding groove. The third cavity is located in the interior of the central β‐barrel of HisF and overlaps with the putative ammonia transport channel.     

Topoisomerase I‐mediated cleavage at unrepaired ribonucleotides generates DNA double‐strand breaks

Ribonuclease activity of topoisomerase I (Top1) causes DNA nicks bearing 2′,3′‐cyclic phosphates at ribonucleotide sites. Here, we provide genetic and biochemical evidence that DNA double‐strand breaks (DSBs) can be directly generated by Top1 at sites of genomic ribonucleotides. We show that RNase H2‐deficient yeast cells displayed elevated frequency of Rad52 foci, inactivation of RNase H2 and RAD52 led to synthetic lethality, and combined loss of RNase H2 and RAD51 induced slow growth and replication stress. Importantly, these phenotypes were rescued upon additional deletion of TOP1, implicating homologous recombination for the repair of Top1‐induced damage at ribonuclelotide sites. We demonstrate biochemically that irreversible DSBs are generated by subsequent Top1 cleavage on the opposite strand from the Top1‐induced DNA nicks at ribonucleotide sites. Analysis of Top1‐linked DNA from pull‐down experiments revealed that Top1 is covalently linked to the end of DNA in RNase H2‐deficient yeast cells, supporting this model. Taken together, these results define Top1 as a source of DSBs and genome instability when ribonucleotides incorporated by the replicative polymerases are not removed by RNase H2.     

Increased ribonucleotide reductase activity in hydroxyurea-resistant mosquito cells

Hydroxyurea-resistant Aedes albopictus mosquito cells were selected by incremental exposure of unmutagenized cells to hydroxyurea concentrations ranging from 0.1 to 8 mM. Clonal populations that had become 40-fold more resistant to hydroxyurea than wild-type cells varied in morphology, and their growth rate decreased to a ∼45 h doubling time, relative to an 18 h doubling time in unselected cells. At this level of resistance, the cells remained diploid, with a modal chromosome number of 6. When labelled with ³⁵S[methionine/cysteine], clone HU1062, which grew in the presence of 8 mM hydroxyurea, overproduced a labeled protein with the approximate size of the 45,000 dalton M2 subunit of ribonucleotide reductase. Consistent with this observation, ribonucleotide reductase activity in HU-1062 cells was approximately 10-fold higher than in wild-type control cells. This is the first example of an hydroxyurea-resistant insect cell line. © 1997 Wiley-Liss, Inc.     

Response of ad-2 mutants of Saccharomyces cerevisiae to carbon dioxide

Summary Confirmation that the ad-2 locus of yeast controls the carboxylation of aminoimidazole ribonucleotide (AIR) to 5-amino-4-imidazole carboxylate ribonucleotide (CAIR) is provided by the observation that 21 out of a sample of 113 ad-2 mutants were affected by CO₂. 19 of the mutants were stimulated by CO₂ and 2 were inhibited. The majority of the CO₂-stimulated mutants were confined to one section of the complementation map of the ad-2 locus.     

Melatonin synthesis in the optic lobes and midbrain of the grasshopper Oedipoda caerulescens

The pathways of insect melatonin (MEL) biosynthesis apparently follow the same routes as those identified in vertebrates but information on MEL synthesis variations related with serotonin (5‐HT), 5‐hydroxy‐indole acetic acid (5HIAA), and N‐acetylserotonin (NAS) levels, as well as 5‐HT N‐acetyltransferase (NAT) activity throughout the day, is very limited in the insect nervous system. In the present study, the levels of MEL, metabolites (5‐HT, NAS, and 5‐HIAA) and enzyme NAT were determined in the optic lobes and the midbrain of the grasshopper Oedipoda caerulescens, in conditions of light and darkness. In both tissues, a different pattern of MEL synthesis was observed over the light/dark cycle. Variations in the levels of 5‐HT, NAS and NAT activity related to the synthesis of cerebral MEL follow a pattern very similar to that observed in the pineal of mammals, with a peak of synthesis in the first half of the scotophase. Also, we observed differences in the metabolism of 5‐HT between the optic lobes and the midbrain light/dark‐dependent.     

Novel nonclassical inhibitors of glycinamide ribonucleotide formyltransferase: 10-Formyl and 10-hydroxymethyl derivatives of 5,8,10-trideazapteroic acid

Several new 10-formyl and 10-hydroxymethyl derivatives of 5,8,10-trideazapteroic acid have been synthesized by a novel and convenient enamine alkylation procedure. Two of these compounds (10a and 10b) were shown to be very powerful inhibitors of L. casei (10a, IC₅₀ = 8 × 10⁻⁶ M ; 10b, IC₅₀ = 7 × 10⁻⁶ M ) and recombinant mouse (10a, IC₅₀ = 3.4 × 10⁻⁵ M ; 10b, IC₅₀ = 2.8 × 10⁻⁵ M ) glycinamide ribonucleotide formyltransferase (GARFT). These IC₅₀ values are comparable to the classical GARFT inhibitor (6R)-DDATHF (IC₅₀, L. casei 2.3 × 10⁻⁶M ; recombinant mouse 2.3 × 10⁻⁵ M ) under identical assay conditions. For both compounds, the inhibition of L. casei GARFT increased with time of incubation, but not markedly with the recombinant mouse enzyme. Due to their potential ability to interfere with purine biosynthesis and to penetrate microbial cells the new nonclassical GARFT inhibitors reported here may be useful for the treatment of infections caused by microorganisms that are sensitive and resistant to conventional antimicrobial agents.     

Inhibition of chlamydial class Ic ribonucleotide reductase by C‐terminal peptides from protein R2

Chlamydia trachomatis ribonucleotide reductase (RNR) is a class Ic RNR. It has two homodimeric subunits: proteins R1 and R2. Class Ic protein R2 in its most active form has a manganese–iron metal cofactor, which functions in catalysis like the tyrosyl radical in classical class Ia and Ib RNRs. Oligopeptides with the same sequence as the C‐terminus of C. trachomatis protein R2 inhibit the catalytic activity of C. trachomatis RNR, showing that the class Ic enzyme shares a similar highly specific inhibition mechanism with the previously studied radical‐containing class Ia and Ib RNRs. The results indicate that the catalytic mechanism of this class of RNRs with a manganese–iron cofactor is similar to that of the tyrosyl‐radical‐containing RNRs, involving reversible long‐range radical transfer between proteins R1 and R2. The competitive binding of the inhibitory R2‐derived oligopeptide blocks the transfer pathway. We have constructed three‐dimensional structure models of C. trachomatis protein R1, based on homologous R1 crystal structures, and used them to discuss possible binding modes of the peptide to protein R1. Typical half maximal inhibitory concentration values for C. trachomatis RNR are about 200 µ m for a 20‐mer peptide, indicating a less efficient inhibition compared with those for an equally long peptide in the Escherichia coli class Ia RNR. A possible explanation is that the C. trachomatis R1/R2 complex has other important interactions, in addition to the binding mediated by the R1 interaction with the C‐terminus of protein R2. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

CARBOCYCLIC SUBSTRATES AND INHIBITORS FOR THE BIFUNCTIONAL LYASE OF PURINE NUCLEOTIDE BIOSYNTHESIS

Abstract

The carbocyclic analogs of succinoaminoimidazole carboxamide ribonucleotide (SAICAR) and adenylosuccinate (SAMP) are substrates for the bifunctional lyase of purine biosynthesis, which catalyzes the elimination of fumarate from both SAICAR and SAMP to generate aminoimidazole carboxamide ribonucleotide (AICAR) and AMP, respectively. The glutamate analogs of both ribo- and carbo-SAICAR are inhibitors.     

Metformin prevents the effects of Pseudomonas aeruginosa on airway epithelial tight junctions and restricts hyperglycaemia‐induced bacterial growth

Lung disease and elevation of blood glucose are associated with increased glucose concentration in the airway surface liquid (ASL). Raised ASL glucose is associated with increased susceptibility to infection by respiratory pathogens including Staphylococcus aureus and Pseudomonas aeruginosa. We have previously shown that the anti‐diabetes drug, metformin, reduces glucose‐induced S. aureus growth across in vitro airway epithelial cultures. The aim of this study was to investigate whether metformin has the potential to reduce glucose‐induced P. aeruginosa infections across airway epithelial (Calu‐3) cultures by limiting glucose permeability. We also explored the effect of P. aeruginosa and metformin on airway epithelial barrier function by investigating changes in tight junction protein abundance. Apical P. aeruginosa growth increased with basolateral glucose concentration, reduced transepithelial electrical resistance (TEER) and increased paracellular glucose flux. Metformin pre‐treatment of the epithelium inhibited the glucose‐induced growth of P. aeruginosa, increased TEER and decreased glucose flux. Similar effects on bacterial growth and TEER were observed with the AMP activated protein kinase agonist, 5‐aminoimidazole‐4‐carboxamide ribonucleotide. Interestingly, metformin was able to prevent the P. aeruginosa‐induced reduction in the abundance of tight junction proteins, claudin‐1 and occludin. Our study highlights the potential of metformin to reduce hyperglycaemia‐induced P. aeruginosa growth through airway epithelial tight junction modulation, and that claudin‐1 and occludin could be important targets to regulate glucose permeability across airway epithelia and supress bacterial growth. Further investigation into the mechanisms regulating metformin and P. aeruginosa action on airway epithelial tight junctions could yield new therapeutic targets to prevent/suppress hyperglycaemia‐induced respiratory infections, avoiding the use of antibiotics.     

Enantiospecific Synthesis of Carbocyclic Aminoimidazole Carboxamide Ribonucleotide (C-AICAR), Succinoaminoimidazole Carboxamide Ribonucleotide (C-SAICAR), and a New Intermediate for SAICAR Analogs

Abstract

The (-)-enantiomer of the carbocyclic analogs of aminoimidazole carboxamide ribonucleotide (C-AICAR¹, 7), and succinoaminoimidazole carboxamide ribonucleotide (C-SAICAR, 14) have been prepared. En route, a new intermediate (19) for the preparation of SAICAR analogs was developed.     

Engineering Escherichia coli for renewable production of the 5‐carbon polyamide building‐blocks 5‐aminovalerate and glutarate

Through metabolic pathway engineering, novel microbial biocatalysts can be engineered to convert renewable resources into useful chemicals, including monomer building‐blocks for bioplastics production. Here we describe the systematic engineering of Escherichia coli to produce, as individual products, two 5‐carbon polyamide building blocks, namely 5‐aminovalerate (AMV) and glutarate. The modular pathways were derived using “parts” from the natural lysine degradation pathway of Pseudomonas putida KT2440. Endogenous over‐production of the required precursor, lysine, was first achieved through metabolic deregulation of its biosynthesis pathway by introducing feedback resistant mutants of aspartate kinase III and dihydrodipicolinate synthase. Further disruption of native lysine decarboxylase activity (by deleting cadA and ldcC) limited cadaverine by‐product formation, enabling lysine production to 2.25 g/L at a glucose yield of 138 mmol/mol (18% of theoretical). Co‐expression of lysine monooxygenase and 5‐aminovaleramide amidohydrolase (encoded by davBA) then resulted in the production of 0.86 g/L AMV in 48 h. Finally, the additional co‐expression of glutaric semialdehyde dehydrogenase and 5‐aminovalerate aminotransferase (encoded by davDT) led to the production of 0.82 g/L glutarate under the same conditions. At this output, yields on glucose were 71 and 68 mmol/mol for AMV and glutarate (9.5 and 9.1% of theoretical), respectively. These findings further expand the number and diversity of polyamide monomers that can be derived directly from renewable resources. Biotechnol. Bioeng. 2013; 110: 1726–1734. © 2013 Wiley Periodicals, Inc.     

Hydroxyurea-resistant mouse L cells with elevated levels of drug-resistant ribonucleotide reductase activity

We describe the isolation and partial characterization of a mouse L-cell line which is resistant to normally highly cytotoxic concentrations of hydroxyurea. A detailed analysis of the target enzyme ribonucleotide reductase in both wild-type and hydroxyurea-resistant enzyme preparations suggests that the drug-resistant cells form a ribonucleotide reductase enzyme which contains a structural alteration, rendering it less sensitive to inhibition by hydroxyurea. K₁ values for hydroxyurea inhibition of ribonucleotide reduction in enzyme preparations from hydroxyurea-resistant cells were significantly higher than corresponding values from preparations from wild-type cells. The K_m for CDP reduction in enzyme preparations of drug-resistant cells was approximately threefold higher than the corresponding parental wild-type value. In addition, in vivo enzyme assays detected a major difference between the temperature profiles of ribonucleotide reduction in nucleotide-permeable drug-resistant and wild-type cells. When levels of ribonucleotide reductase activity were measured in vivo, it was found that the drug-resistant cells contained approximately 3 times the wild-type level of CDP reductase activity and twice wild-type level of GDP reductase activity. This combination of enhanced enzyme levels plus an altered sensitivity to drug inhibition can easily account for the drug-resistance phenotype. The properties of these hydroxyurea-resistant cells indicate that they will be useful for genetic and biochemical studies.This work was supported by the N.S.E.R.C. of Canada and the Muscular Dystrophy Association of Canada through research funds (J. A. W.) and by the N.R.C. of Canada through a graduate scholarship (B. A. K.).     

Application of NMR spectroscopy for assignment of the absolute configuration of 8‐tert‐butyl‐2‐hydroxy‐7‐methoxy‐8‐methyl‐9‐oxa‐6‐azaspiro[4.5]dec‐6‐en‐10‐one

In order to assign the absolute configurations of 8‐tert‐butyl‐2‐hydroxy‐7‐methoxy‐8‐methyl‐9‐oxa‐6‐azaspiro[4.5]dec‐6‐en‐10‐one ( 2a , 2b ), their esters ( 5a , 5b , 5c , 5d ) with (R)‐ or (S)‐2‐methoxyphenylacetic acid ( 4a , 4b ) have been synthesized. The absolute configurations of these compounds have been determined on the basis of NOESY correlations between the protons of the tert‐butyl group and the cyclopentane fragment of the molecules. The crucial part of this analysis was assignment of the absolute configuration at C‐5. Additionally, by calculation of the chemical shift anisotropy, δ^RS, for the relevant protons, it was also possible to confirm the absolute configurations at the C‐2 centres of compounds 2a , 2b and 5a , 5b , 5c , 5d . Chirality, 25:422–426, 2013.© 2013 Wiley Periodicals, Inc.     

Synthesis of some novel quinone diimine derivatives of benzo‐15‐crown‐5 for application in Hg2+ recognition

A series of novel fluoroionophore bearing derivatives of benzo‐15‐crown‐5 were synthesized by the amination of benzo‐15‐crown‐5 followed by condensation with different quinones in the presence of titanium tetrachloride (TiCl₄) and 1,4‐diazabicyclo‐[2.2.2]octane. The compounds were characterized by infrared, ¹H and ¹³C nuclear magnetic resonance, mass spectroscopy and elemental analysis. Absorption and fluorescence spectral characteristics of these compounds were studied. It was observed that the anthraquinone derivative was acting as an Hg²⁺ ion sensor. Copyright © 2013 John Wiley & Sons, Ltd.     

Effect of head‐to‐tail cyclization on conformation of histatin‐5

Histatin‐5 (Hst‐5, DSHAKRHHGYKRKFHEKHHSHRGY) is a member of a histidine‐rich peptide family secreted by major salivary glands, exhibiting high fungicidal activity against Candida albicans. In the present work, we demonstrate the 3D structure of the head‐to‐tail cyclic variant of Hst‐5 in TFE solution determined using NMR spectroscopy and molecular dynamics simulations. The cyclic histatin‐5 reveals a helix‐loop‐helix motif with α‐helices at positions Ala⁴‐His⁷ and Lys¹¹‐Ser²⁰. Both helical segments are arranged relative to each other at an angle of ca. 142°. The head‐to‐tail cyclization increases amphipathicity of the peptide, this, however, does not affect its antimicrobial potency. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

Spodoptera frugiperda FKBP‐46 is a consensus p53 motif binding protein

p53 protein, the central molecule of the apoptosis pathway, is mutated in 50% of the human cancers. Of late, p53 homologues have been identified from different invertebrates including Drosophila melanogaster, Caenorhabditis elegans, Squid, and Clams. We report the identification of a p53‐like protein in Spodoptera frugiperda (Sf9) insect cells, which is activated during oxidative stress, caused by exposure to UV‐B or H₂O₂, and binds to p53 consensus DNA binding motifs as well as other p53 cognate motifs. Sf9 p53 motif‐binding protein is similar to murine and Drosophila p53 in terms of molecular size, which is around 50–60 kDa, as evident from UV cross‐linking, and displays DNA binding characteristics similar to both insect and vertebrate p53 as seen from electrophoretic mobility shift assays. The N‐terminal sequencing of the purified Sf9 p53 motif‐binding protein reveals extensive homology to the pro‐apoptotic FK‐506 binding protein (FKBP‐46), earlier identified in Sf9 cells as a factor which interacts with murine casein kinase. FKBP, an evolutionarily conserved protein of mammalian origin functions as a pro‐apoptotic factor. Identification of FKBP‐46 as a novel p53 motif‐binding protein in insect cells adds a new facet to our understanding of the mechanisms of apoptosis under oxidative stress in the absence of a typical p53 homologue. J. Cell. Biochem. 114: 899–907, 2013. © 2012 Wiley Periodicals, Inc.