Purine nucleoside phosphorylase (PNP)

Parte del lavoro per il progetto del mio dottorato DIMET e stato svolto presso L'istituto Neurologico Carlo Besta UO Malattie Cerebrovascolari Laboratorio Neurobiologia Cellulare, direttore Eugenio Agostino Parati, Tutor: Prof Giorgio Battaglia. Parte della tesi e stata pubblicata su: Cristini, S; Navone, S; Canzi, L; Acerbi, F; Ciusani, E; Hladnik, U et al. (2010) Human neural stem cells: a model system for the study of Lesch-Nyhan disease neurological aspects. Human molecular genetics 19 (10) 1939-1950 10.1093/hmg/ddq072.

A set of deazaguanine derivatives 1-3 targeting human purine nucleoside phosphorylase (hPNP) have been designed and synthesized. The new compounds are characterized by the presence of a structurally simplified "azasugar" motif to be more easily accessible by chemical synthesis than previous inhibitors. In the enzymatic assays, some of the new derivatives proved to be able to inhibit hPNP at low nanomolar concentration, thereby showing the same inhibitory potency in vitro as immucillin-H (IMH). Molecular docking experiments revealed a binding mode to hPNP essentially identical to that of IMH. As a result, the lower in vivo activity exhibited by 1d, compared with that exhibited by IMH, might be ascribed to differences in the pharmacokinetic, rather than pharmacodynamic, profile between these compounds. Derivatives 1a, 1d, and 2c emerged as the most active compounds within this new set and may represent interesting leads in the search for novel hPNP inhibitors.

Therapy using erythrocyte-encapsulated enzyme has the advantage of prolonging the half-life of the enzyme and maintaining therapeutic blood levels, reducing the dose and frequency of therapeutic interventions, and preventing the need for expensive chemical modification. The therapeutic index can be strongly improved, especially by reducing immunogenic reactions, which are often observed in enzyme therapy administered by the conventional route. Two products are presented in this paper: erythrocyte-encapsulated L-asparaginase and erythrocyteencapsulated thymidine phosphorylase. For the first, the native enzyme has been the mainstay in the treatment of lymphoblastic leukemia for decades. Improving the therapeutic index by utilizing this new formulation now offers new possibilities in cancer therapy. The second product is proposed for patients diagnosed with mitochondrial neurogastrointestinal encephalomyopathy (MNGIE), an autosomal recessive disorder of nucleotide metabolism caused by mutations in the nuclear TYMP gene (thymidine phosphorylase deficiency). These two approaches illustrate how this new formulation works as an enzyme bioreactor in the treatment of cancer and in enzyme replacement therapy.

Reducing the concentration of thymine in the growth medium of thy-mutants of Eschetihia coli progressively increases the replication time of their chromosomes, without affecting significantly the growth rate of the cultures, down to a concentration that is strain-specific. The replication time of the chromosome of thy-mutants of two unrelated strains of E. coli was estimated to be longer than that in E. coli B/r thy+ even in the presence of saturating concentrations of thymine. The replication time could be further reduced by adding deoxygurtnosine as well as thymine to the growth medium.

A competitive (nonmetabolizable) inhibitor of glucose uptake, a-methylglucoside, was used to limit the growth ofEscherichia coli. Cell division during such a nutritional shift-down was studied in batch cultures and with the "baby-machine" technique. Following a brief delay, the rate of division was maintained for 60 to 70 min in batch cultures and for an extended period in the baby machine. Decreases in cell size were due, in part, to a possible reduction in the mass per chromosome origin at the time of replication initiation and a shorter time interval between initiation and the subsequent division. These unusual findings suggest that this method for abrupt change in growth rate without modifying repression patterns is useful for studying the control of various aspects of the bacterial cell. A bacterial cell divides C + D min after initiation of chromosome replication (10). Initiation capacity builds up during its preceding doubling time, T min. Cell mass at initiation is, to a first approximation, 27-multiple of a mini

Duplication of the bacterial nucleoid is necessary for cell division hence specific arrest of DNA replication inhibits divisions culminating in filamentation, nucleoid dispersion and appearance of a-nucleated cells. It is demonstrated here that during the first 10 min however, Escherichia coli enhanced residual divisions: the proportion of constricted cells doubled (to 40%), nucleoids contracted and cells remodelled dimensions: length decreased and width increased. The preliminary data provides further support to the existence of temporal and spatial couplings between the nucleoid/replisome and the sacculus/divisome, and is consistent with the idea that bacillary bacteria modulate width during the division process exclusively.

It is crucial to the reproducibility of results and their proper interpretation that the conditions under which experiments are carried out be defined with rigour and consistency. In this review we attempt to clarify the differences and interrelationships among steady, balanced and exponential states of culture growth. Basic thermodynamic concepts are used to introduce the idea of steady-state growth in open, biological systems. The classical, sometimes conflicting, definitions of steady-state and balanced growth are presented, and a consistent terminology is proposed. The conditions under which a culture in balanced growth is also in exponential growth and in steady-state growth are indicated. It is pointed out that steady-state growth always implies both balanced and exponential growth, and examples in which the converse does not hold are described. More complex situations are then characterized and the terminology extended accordingly. This leads to the notion of normal growth and growth that can be synchronous or otherwise unbalanced but still reproducible, and to the condition of approximate steady state manifested by growth in batch culture and by asymmetrically dividing cells, which is analysed in some detail.

Following previous studies devoted to trans-Pt(3-af) 2 Cl 2 , in this paper, the molecular structure and intermolecular interactions of the title complex are compared with other cisplatin analogues of which the crystal structures are presented in the Cambridge Structural Database (CSD). Molecular Hirshfeld surface analysis and computational methods were used to examine a possible relationship between the structure and anticancer activity of trans-Pt(3-af) 2 Cl 2. The purpose of the article was also to investigate the effect of hyperthermia on the anticancer activity of cisplatin, cytostatics used in the treatment of patients with ovarian cancer and a new analogue of cisplatin-trans-Pt(3-af) 2 Cl 2. The study was conducted on two cell lines of ovarian cancer sensitive to Caov-3 cytostatics and the OVCAR-3 resistant cisplatin line. The study used the MTT (3-(4,5-dimethylthiazol-2,5-diphenyltetrazolium bromide) cell viability assay, LDH (lactate dehydrogenase), and the quantitative evaluation method for measuring gene expression, i.e., qPCR with TagMan probes. Reduced survivability of OVCAR-3 and Caov-3 cells exposed to cytostatics at elevated temperatures (37 • C, 40 • C, 43 • C) was observed. Hyperthermia may increase the sensitivity of cells to platinum-based antineoplastic drugs and paclitaxel, which may be associated with the reduction of gene expression related to apoptotic processes.

Methylthioadenosine phosphorylase (MTAP) is an important enzyme for the salvage of adenine and methionine and is deficient in a variety of cancers including T-cell acute lymphocytic leukemia (T-ALL). Previously, we reported that the MTAP gene was deleted in over 30% of T-ALL patients at both diagnosis and relapse. We now report that MTAP-primary T-ALL cells are more sensitive to the toxicity of L-alanosine, an inhibitor of de novo AMP synthesis, than are MTAP+ primary T-ALL cells. As measured by [3H]thymidine incorporation, DNA synthesis in all seven MTAP-primary T-ALL cells was inhibited by L-alanosine with a mean IC50 of 4.8+/-5.3 ILM (range, 0.3-11.3 microM). On the other hand, the IC50 for 60% (12 of 20) of MTAP+ primary T-ALL was 19+/-18 microM (range, 1.7-67 microM; P = 0.02), whereas the remaining 40% (8 of 20) had an IC50 of >80 microM4. Furthermore, normal lymphocytes and MTAP+ primary T-ALL cells were rescued from L-alanosine toxicity by the MTAP substrate 5'-deoxya...

Milligram quantities of α-D-ribofuranosyl 1-phosphate (sodium salt) (αR1P) were prepared by the phosphorolysis of inosine, catalyzed by purine nucleoside phosphorylase (PNPase). The αR1P was isolated by chromatography in >95% purity and characterized by 1 H and 13 C NMR spectroscopy. Aqueous solutions of αR1P were stable at pH 6.4 and 4 o C for several months. The isolated αR1P was N-glycosylated with different nitrogen bases (adenine, guanine and uracil) using PNPase or uridine phosphorylase (UPase) to give the corresponding ribonucleosides in high yield based on the glycosyl phosphate. This methodology is attractive for the preparation of stable isotopically labeled ribo-and 2'-deoxyribonucleosides because of the ease of product purification and convenient use and recycling of nitrogen bases. The approach eliminates the need for separate reactions to prepare individual furanose-labeled ribonucleosides, since only one ribonucleoside (inosine) needs to be labeled, if desired, in the furanose ring, the latter achieved by a high-yield chemical N-glycosylation. 2'-Deoxyribonucleosides were prepared from 2'-deoxyinosine using the same methodology with minor modifications.

Purine nucleoside phosphorylase (PNP) is an enzyme involved in biosynthetic pathway of purine nucleosides. Purine nucleoside phosphorylase catalyzes the cleavage of the glycosidic bond of ribo-or deoxyribonucleosides to form the purine base and deoxyribose-or ribose-1-phosphate. The reversible reaction catalyzed by recombinant PNP of E. coli (EcPNP) has been successfully used for the synthesis of nucleoside analogues. The aim of this study was to clone and expression of recombinant PNP in Pichia pastoris. For expression of recombinant EcPNP in Pichia pastoris, a new recombinant plasmid DNA pPICZαA-PNP (4256 bp) containing the deoD gene (720 bp) amplified from E. coli strain RKMUz-221 has been cloned. The substrate specificity of the recombinant EcPNP expressed in yeast cells was studied by hydrolysis of inosine (9-beta-D-ribofuranosylhypoxanthine) to hypoxanthine and 2-deoxy-β-D-ribofuranosyl. The fraction containing the obtained recombinant EcPNP (≈28 kDa, as determined by SDS-PAGE) demonstrates significant hydrolytic activity, resulting in up to a 51% hydrolysis of inosine within a 5 h timeframe. These findings suggest that the recombinant enzyme holds a promise for applications in enzymatic transglycosylation of purine-type nucleosides.

Methylthioadenosine phosphorylase (MTAP) is an important enzyme for the salvage of adenine and methionine and is deficient in a variety of cancers including T-cell acute lymphocytic leukemia (T-ALL). Previously, we reported that the MTAP gene was deleted in over 30% of T-ALL patients at both diagnosis and relapse. We now report that MTAP-primary T-ALL cells are more sensitive to the toxicity of L-alanosine, an inhibitor of de novo AMP synthesis, than are MTAP+ primary T-ALL cells. As measured by [3H]thymidine incorporation, DNA synthesis in all seven MTAP-primary T-ALL cells was inhibited by L-alanosine with a mean IC50 of 4.8+/-5.3 ILM (range, 0.3-11.3 microM). On the other hand, the IC50 for 60% (12 of 20) of MTAP+ primary T-ALL was 19+/-18 microM (range, 1.7-67 microM; P = 0.02), whereas the remaining 40% (8 of 20) had an IC50 of >80 microM4. Furthermore, normal lymphocytes and MTAP+ primary T-ALL cells were rescued from L-alanosine toxicity by the MTAP substrate 5'-deoxyadenosine, but MTAP-T-ALL cells were not. These results indicate that normal cells, which are intrinsically MTAP+, would be protected from L.-alanosine toxicity, whereas MTAP-tumor cells would be killed. Thus, our results support the use of L-alanosine alone or in combination with a salvage agent as a MTAP-selective therapy and therefore lay the foundation for the initiation of clinical trials for the treatment of T-ALL and other MTAP-deficient malignancies with L-alanosine.

Background: Both histopathological image features and genomics data were associated with survival outcome of cancer patients. However, integrating features of histopathological images, genomics and other omics for improving prognosis prediction has not been reported in head and neck squamous cell carcinoma (HNSCC). Methods: A dataset of 216 HNSCC patients was derived from the Cancer Genome Atlas (TCGA) with information of clinical characteristics, genetic mutation, RNA sequencing, protein expression and histopathological images. Patients were randomly assigned into training (n = 108) or validation (n = 108) sets. We extracted 593 quantitative image features, and used random forest algorithm with 10-fold cross-validation to build prognostic models for overall survival (OS) in training set, then compared the area under the time-dependent receiver operating characteristic curve (AUC) in validation set. Results: In validation set, histopathological image features had significant predictive value for OS (5-year AUC = 0.784). The histopathology + omics models showed better predictive performance than genomics, transcriptomics or proteomics alone. Moreover, the multi-omics model incorporating image features, genomics, transcriptomics and proteomics reached the maximal 1-, 3-, and 5-year AUC of 0.871, 0.908, and 0.929, with most significant survival difference (HR = 10.66, 95%CI: 5.06-26.8, p < 0.001). Decision curve analysis also revealed a better net benefit of multi-omics model. Conclusion: The histopathological images could provide complementary features to improve prognostic performance for HNSCC patients. The integrative model of histopathological image features and omics data might serve as an effective tool for survival prediction and risk stratification in clinical practice.

HPV infection is associated with high p16 expression and good prognosis in head and neck squamous cell carcinomas (HNSCCs). Analysis of CDKN2A, the gene encoding p16, may further elucidate the association between p16 expression and prognosis. We sought to determine whether CDKN2A copy number loss was associated with poor survival in HPV-negative HNSCCs. The Cancer Genome Atlas HNSCC clinical and genomic data were obtained and integrated. Patients &lt;80 years old with a primary tumor in the oral cavity, oropharynx, hypopharynx, or larynx were included. Stratifying by copy number loss status, CDKN2A mRNA and p16 protein expression levels were examined and overall survival (OS) and disease-free survival (DFS) were evaluated. 401 patients with HPV-negative HNSCC were identified. 146 patients demonstrated CDKN2A copy number loss. The CDKN2A copy number loss group expressed significantly lower levels of CDKN2A mRNA and p16 protein than did the non-copy number loss group. Median OS for pa...

Loss of the 3p chromosome arm has previously been reported to be a biomarker of poorer outcome in both human papillomavirus (HPV)-positive and HPV-negative head and neck cancer. However, the precise operational measurement of 3p arm loss is unclear and the mutational profile associated with the event has not been thoroughly characterized. We downloaded the clinical, single nucleotide variation (SNV), copy number aberration (CNA), RNA sequencing, and reverse phase protein assay (RPPA) data from The Cancer Genome Atlas (TCGA) and The Cancer Proteome Atlas HNSCC cohorts. Survival data and hypoxia scores were downloaded from published studies. In addition, we report the inclusion of an independent Memorial Sloan Kettering cohort. We assessed the frequency of loci deletions across the 3p arm separately in HPV-positive and -negative disease. We found that deletions on chromosome 3p were almost exclusively an all or none event in the HPV-negative cohort; patients either had &lt;1% or &gt;9...

IFNα-2b as a protein is a cytokine used to treat more than 14 diseases all around the world, the recombinant human IFN-2b was synthesized and a genetic engineering method or recombinant DNA technology. IFNα-2b as a protein with broad biological action, including antiviral and anticancer properties, might be a useful therapeutic protein for a variety of diseases, including hepatitis C and cancer. IFN-α2b sequence was taken from the National Center for Biotechnology Information (NCBI) gene database and optimized before being cloned and produced in the pET28a+ vector. Escherichia coli was considered as a prokaryotic expression system. IFN-α2b expression was carried out in E. coli strains BL21 (DE3) and BL21(DE3) pLysS and E. coli DH5α strain used for cloning. isopropyl-d-thiogalactoside (IPTG) induced protein production in bacteria cells bearing the pET28a+ IFN-α2b construct, followed by sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) separation of total proteins. ...

Even being a bacterial purine nucleoside phosphorylase (PNP), which normally shows hexameric folding, the Mycobacterium tuberculosis PNP (MtPNP) resembles the mammalian trimeric structure. The crystal structure of the MtPNP apoenzyme was solved at 1.9 Å resolution. The present work describes the first structure of MtPNP in complex with phosphate. In order to develop new insights into the rational drug design, conformational changes were profoundly analyzed and discussed. Comparisons over the binding sites were specially studied to improve the discussion about the selectivity of potential new drugs.

Purine salvage pathways are predicted to be present from the genome sequence of Mycobacterium tuberculosis. The M. tuberculosis deoD gene encodes a presumptive purine nucleoside phosphorylase (PNP). The gene was cloned, expressed, purified, and found to exhibit PNP activity. Purified M. tuberculosis PNP is trimeric, similar to mammalian PNP's but unlike the hexameric Escherichia coli enzyme. Immucillin-H is a rationally designed analogue of the transition state that has been shown to be a potent inhibitor of mammalian PNP's. This inhibitor also exhibits slow-onset inhibition of M. tuberculosis PNP with a rapid, reversible inhibitor binding (K i of 2.2 nM) followed by an overall dissociation constant (K i *) of 28 pM, yielding a K m /K i * value of 10 6. Time-dependent tight binding of the inhibitor occurs with a rate of 0.1 s-1 , while relaxation of the complex is slower at 1.4 × 10-3 s-1. The pH dependence of the K i value of immucillin-H to the M. tuberculosis PNP suggests that the inhibitor binds as the neutral, unprotonated form that is subsequently protonated to generate the tight-binding species. The M. tuberculosis enzyme demonstrates independent and equivalent binding of immucilin-H at each of the three catalytic sites, unlike mammalian PNP. Analysis of the components of immucillin-H confirms that the inhibition gains most of its binding energy from the 9-deazahypoxanthine group (K is of 0.39 µM) while the 1,4dideoxy-1,4-iminoribitol binds weakly (K is of 2.9 mM). Double-inhibition studies demonstrate antagonistic binding of 9-deazahypoxanthine and iminoribitol () 13). However, the covalent attachment of these two components in immucillin-H increases equilibrium binding affinity by a factor of >14 000 (28 pM vs 0.39 µM) compared to 9-deazahypoxanthine alone, and by a factor of >10 8 compared to iminoribitol alone (28 pM vs 2.9 mM), from initial velocity measurements. The structural basis for M. tuberculosis PNP inhibition by immucillin-H and by its component parts is reported in the following paper [

Even being a bacterial purine nucleoside phosphorylase (PNP), which normally shows hexameric folding, the Mycobacterium tuberculosis PNP (MtPNP) resembles the mammalian trimeric structure. The crystal structure of the MtPNP apoenzyme was solved at 1.9 Å resolution. The present work describes the first structure of MtPNP in complex with phosphate. In order to develop new insights into the rational drug design, conformational changes were profoundly analyzed and discussed. Comparisons over the binding sites were specially studied to improve the discussion about the selectivity of potential new drugs.

A modificação experimental para a síntese do MESG (2-amino-6-mercapto-7-metilpurina ribonucleosídeo) 1 foi realizada com sucesso e sua caracterização total apresentada. ESI(+)-MSMS em alta resolução foram realizados indicando que a clivagem nucleosídica como principal e um possível mecanismo S N 1. Cálculos ab initio baseados em estados de transição blueprint corroboram com a proposta de um mecanismo S N 1 e descartam a possibilidade de um mecanismo S N 2. Ensaios com a enzima purina nucleosídica fosforilase (PNP, tanto humana como de M. tuberculosis) indicam a eficiência do substrato na reação de fosforilação do MESG e permitem a determinação de fosfato inorgânico em tempo real em ensaios biológicos. A modified experimental procedure for the synthesis of MESG (2-amino-6-mercapto-7methylpurine ribonucleoside) 1 has been successfully performed and its full characterization is presented. High resolution ESI(+)-MSMS indicates both the nucleoside bond cleavage as the main fragmentation in the gas phase and a possible S N 1 mechanism. Ab initio transition state calculations based on the blue print transition state support this mechanistic rationale and discard an alternative S N 2 mechanism. Assays using purine nucleoside phosphorylase (PNP) enzyme (human and M. tuberculosis sources) indicate its efficiency in the phosphorolysis of MESG and allow the quantitative determination of inorganic phosphate in real time assay.

A competitive (nonmetabolizable) inhibitor of glucose uptake, alpha-methylglucoside, was used to limit the growth of Escherichia coli. Cell division during such a nutritional shift-down was studied in batch cultures and with the &quot;baby-machine&quot; technique. Following a brief delay, the rate of division was maintained for 60 to 70 min in batch cultures and for an extended period in the baby machine. Decreases in cell size were due, in part, to a possible reduction in the mass per chromosome origin at the time of replication initiation and a shorter time interval between initiation and the subsequent division. These unusual findings suggest that this method for abrupt change in growth rate without modifying repression patterns is useful for studying the control of various aspects of the bacterial cell.

One of the major limitations to the application of high-resolution biophysical techniques such as X-crystallography and spectroscopic analyses to structure-function studies of Saccharomyces cerevisiae Hop1 protein has been the non-availability of sufficient quantities of functionally active pure protein. This has, indeed, been the case of many proteins, including yeast synaptonemal complex proteins. In this study, we have performed expression screening in Escherichia coli host strains, capable of high-level expression of soluble S. cerevisiae Hop1 protein. A new protocol has been developed for expression and purification of S. cerevisiae Hop1 protein, based on the presence of hexa-histidine tag and doublestranded DNA-Cellulose chromatography. Recombinant S. cerevisiae Hop1 protein was >98% pure and exhibited DNA-binding activity with high-affinity to the Holliday junction. The availability of the recombinant HOP1 expression vector and active Hop1 protein would facilitate structure-function investigations as well as the generation of appropriate truncated and site-directed mutant proteins, respectively.

Over the past two decades, several research groups have focused on the functioning of microRNAs (miRNAs), because many of them function as positive or negative endogenous regulators of processes that alter during the development of cancer. Prostate cancer is the second most commonly occurring cancer in men. New biomarkers are needed to support the diagnosis of prostate cancer. Although it is necessary to deepen the research on this molecule to explore its potential utility in the diagnosis, follow-up, and prognosis of cancer, our results support a role of miR-107 in the signaling cascades that allow cancer progression, and as shown here, in the progression of Prostate Cancer (PCa). These findings strongly suggest that miR-107 may be a potential circulating biomarker for the diagnosis and prognosis of prostate cancer.

O desenvolvimento de métodos rápidos e eficazes para a identificação de novas moléculas bioativas é fundamental para o processo de descoberta e planejamento de fármacos. A integração de um sistema de cromatografia liquida de alta eficiência (CLAE), com biorreatores como fase estacionária (IMER) é uma estratégia atrativa e versátil para a triagem de coleções de compostos visando à identificação de novos agentes terapêuticos. Os parâmetros cinéticos da enzima imobilizada gliceraldeído-3-fosfato desidrogenase (GAPDH) de Trypanosoma cruzi e humana foram determinados (T. cruzi: K M G3P = 0.50 mmol L-1 ; K M NAD+ = 0.67 mmol L-1 ; humana: K M G3P = 3.7 mmol L-1 ; K M NAD+ = 0.75 mmol L-1) e comparados com aqueles observados em solução (T. cruzi: K M G3P = 0.42 mmol L-1 ; K M NAD+ = 0.26 mmol L-1 ; humana: K M G3P = 0.16 mmol L-1 ; K M NAD+ = 0.18 mmol L-1). Os resultados indicaram uma diminuição na afinidade das enzimas imobilizadas, entretanto, os elementos estruturais necessários para o processo de reconhecimento molecular e atividade biológica permaneceram inalterados, aumentando a estabilidade das enzimas. Além disso, a análise estrutural forneceu dados moleculares importantes envolvidos nos efeitos da imobilização sobre as interações entre ligante e receptor e, consequentemente, sobre a atividade enzimática e parâmetros cinéticos. The development of fast and reliable methods for the identification of new bioactive compounds is of utmost importance to boost the process of drug discovery and development. Immobilized enzyme reactors (IMERs), integrated with high performance liquid chromatography (HPLC), are attractive and versatile tools for screening collections consisting of natural products and synthetic small molecules. Standard kinetic parameters of the immobilized enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from both Trypanosoma cruzi de and human have been determined (T. cruzi: K M G3P = 0.50 mmol L-1 ; K M NAD+ = 0.67 mmol L-1 ; humana: K M G3P = 3.7 mmol L-1 ; K M NAD+ = 0.75 mmol L-1), and comparisons of these values with those of the parasite and human free enzymes indicate a decrease in the affinity for the immobilized system (T. cruzi: K M G3P = 0.42 mmol L-1 ; K M NAD+ = 0.26 mmol L-1 ; humana: K M G3P = 0.16 mmol L-1 ; K M NAD+ = 0.18 mmol L-1). Interestingly, despite the kinetic differences between the two systems, the immobilized GAPDHs retained the required structural requirements for molecular recognition and biological activity, increasing the stability the enzyme. In the present work, we described an integrated structural analysis which has provided important insights into the molecular basis underlying the effects of immobilization on the ligand-receptor interactions and consequent enzymatic activity and kinetics parameters.

Background: Human papillomavirus (HPV)-driven oropharyngeal cancer (OPC) patients are characterised by a better prognosis than their HPV-negative counterparts. However, this significant survival advantage is not homogeneous and among HPV-positive patients those with a smoking history have a significantly increased risk of oncologic failure. The reason why tobacco consumption impacts negatively the prognosis is still elusive. Tobacco might induce additional genetic alterations leading to a more aggressive phenotype. The purpose of this study was to characterise the mutational profile of HPV-positive OPCs by smoking status. We hypothesise a higher frequency of mutations affecting smokers. Methods: Targeted next-generation sequencing of 39 genes that are recurrently mutated in head and neck cancers (HNCs) caused by tobacco/alcohol consumption was performed in 62 HPV-driven OPC cases including smokers and non-smokers. Results: The study population included 37 (60%) non-smokers and 25 (40%) smokers. Twenty (32%) patients had no mutation, 14 (23%) had 1 mutation and 28 (45%) had 2 or more mutations. The most commonly mutated genes regardless of tobacco consumption were PIK3CA (19%), MLL2 (19%), TP53 (8%), FAT 1 (15%), FBXW7 (16%), NOTCH1 (10%) and FGFR3 (10%). Mutation rate was not significantly different in smokers compared with non-smokers

The levels of adenosine deaminase (ADA), purine nucleoside phosphorylase (PNP), lactic dehydrogenase (LDH), and LDH isoenzyme patterns (LD1 to LD5) have been measured in lymphocyte extract from 28 patients with 8-chronic iyrnphocytic leukemia (8-CLL). The activities of ADA, PNP, and LDH have been correlated with two morphological groups of 8-CLL classified according to the percentage of large, nongranuiar, atypical lymphocytes (AL) in peripheral blood: "typical" BCLL (less than 10% of AL, 21 cases) and "atypical" B-CLL (10-25% of AL, seven cases). Patients with atypical BCLL had significantly (P c 0.001) higher activities of ADA (0.46 f 0.17 UllO' cells), PNP (1.74 f 1.0 UllO' cells), and LDH (48.3 f 9.7 U/109 cells) than patients with typical B-CLL (ADA, 0.29 f 0.1 UHO' cells; PNP, 0.58 f 0.23 UllO' cells; and LDH, 29 f 10 U/lOo cells). in addition, the "treatment-free perlod" was also signficantly (P c 0.025) shorter In the group of atypical 8-CLL compared with the typical BCLL group. No clear-cut statistical differences in lymphocyte surface markers or In several other prognostic factors between the two subgroups of B-CLL were found. The present study supports the idea that in 8-CLL the simultaneous determination of ADA, PNP, and LDH might be helpful in better understanding the pathophyslology, prognosis, and natural history of the disease.

Deletions on the short arm of chromosome 9 (9~21 region) have been reported in a number of hematopoietic and solid tumors. These aberrations on 9p have been previously associated with the loss of the interferon gene cluster and the gene for methylthioadenosine phosphorylase (MTAP), localized to the 9~21-22 region. Recently, two putative tumor suppressor gene(s) CDKN2 and MTS2 have been mapped to the 9~21 region, and shown to be deleted in a large number of fumars including leukemias, melanomas, bladder cancers and brain tumors. We have previously reported a similar 9~21 abnormality and deletions of the CDKN2 and MTS2 genes in a myxoid chondrosarcoma cell line and its subclones. In this study we report consistent abnormalities of chromosome 9 in additional chondrosarcomas examined by a detailed cytogenetic and molecular analysis. Seven chondrosarcoma cell lines, one primary chondrosarcoma, and a benign chondroma were examined. Four of the seven tumor cell lines examined showed grossly visible aberrations of chromosome 9. Molecular analysis of these chondrosarcoma cell lines revealed hemizygous deletions of the interferon genes, and the absence of the MTAP gene, protein or activity. In addition, four of the seven chondrosarcoma cell lines also showed deletions of the CDKN2 and/or MTS2 putative tumor suppressor genes, or the absence of the CDKN2 protein product. No such chromosome 9 related aberrations were dctected in the benign chondroma. These data suggest that chromosome 9~21 abnormality, and deletions of the CD&V2 and MTS2 tumor suppressor genes may be a significant event in the development of chondrosarcomas.

A enzima purina nucleosídeo fosforilase do parasita Schistosoma mansoni (SmPNP) é um alvo molecular atrativo para o desenvolvimento de candidatos a novos fármacos para o tratamento da esquistossomose, doença tropical negligenciada que afeta mais de 200 milhões de pessoas em todo mundo. No presente trabalho, estudos de cinética enzimática foram conduzidos para a determinação da potência e do mecanismo de inibição de uma série de inibidores da enzima SmPNP. Além das investigações bioquímicas, estudos cristalográficos e de modelagem molecular revelaram importantes bases moleculares para a afinidade de ligação frente à enzima alvo, levando ao desenvolvimento de relações entre a estrutura e atividade (SAR). The enzyme purine nucleoside phosphorylase from Schistosoma mansoni (SmPNP) is an attractive molecular target for the development of novel drugs against schistosomiasis, a neglected tropical disease that affects about 200 million people worldwide. In the present work, enzyme kinetic studies were carried out in order to determine the potency and mechanism of inhibition of a series of SmPNP inhibitors. In addition to the biochemical investigations, crystallographic and molecular modeling studies revealed important molecular features for binding affinity towards the target enzyme, leading to the development of structure-activity relationships (SAR).

A set of deazaguanine derivatives 1-3 targeting human purine nucleoside phosphorylase (hPNP) have been designed and synthesized. The new compounds are characterized by the presence of a structurally simplified "azasugar" motif to be more easily accessible by chemical synthesis than previous inhibitors. In the enzymatic assays, some of the new derivatives proved to be able to inhibit hPNP at low nanomolar concentration, thereby showing the same inhibitory potency in vitro as immucillin-H (IMH). Molecular docking experiments revealed a binding mode to hPNP essentially identical to that of IMH. As a result, the lower in vivo activity exhibited by 1d, compared with that exhibited by IMH, might be ascribed to differences in the pharmacokinetic, rather than pharmacodynamic, profile between these compounds. Derivatives 1a, 1d, and 2c emerged as the most active compounds within this new set and may represent interesting leads in the search for novel hPNP inhibitors.

Deoxycytidine kinase (dCK) is an enzyme with broad substrate specificity which can phosphorylate pyrimidine and purine deoxynucleosides, including important antiviral and cytostatic agents. In this study, stopped-flow experiments were used to monitor intrinsic fluorescence changes induced upon binding of various phosphate donors (ATP, UTP, and the nonhydrolyzable analogue AMP-PNP) and the acceptor dCyd to recombinant dCK. Monophasic kinetics were observed throughout. The nucleotides as well as dCyd bound to the enzyme by a two-step mechanism, involving a rapid initial equilibrium step, followed by a protein conformational change that is responsible for the fluorescence change. The bimolecular association rate constants for nucleotide binding [(4-10) × 10 3 M-1 s-1 ] were 2-3 orders of magnitude lower than those for dCyd binding [(1.3-1.5 × 10 6 M-1 s-1 ]. This difference most likely is due predominantly to the large difference in the forward rate constants of the conformational changes (0.04-0.26 s-1 vs 560-710 s-1). Whereas the kinetics of the binding of ATP, UTP, and AMP-PNP to dCK showed some differences, UTP exhibiting the tightest binding, no significant differences were observed for the binding of dCyd to dCK in the presence or absence of phosphate donors. However, the binding of dCyd to dCK in the presence of ATP or UTP was accompanied by a 1.5-or 3-fold higher quenching amplitude as compared with dCyd alone or in the presence of AMP-PNP. We conclude that ATP and UTP induce a conformational change in the enzyme, thereby enabling efficient phosphoryl transfer.

A new series of flexible 5′-norcarbocyclic aza/deaza-purine nucleoside analogs were synthesized from 6-oxybicyclo[3.1.0.]hex-2-ene and pyrazole-containing fleximer analogs of heterocyclic bases using the Trost procedure. The compounds were evaluated as potential inhibitors of E. coli purine nucleoside phosphorylase. Analog 1-3 were found to be noncompetitive inhibitors with inhibition constants of 14-24 mM. From the data obtained, it can be assumed that the new 5′-norcarbocyclic nucleoside analogs interact with the active site of the PNP like natural heterocyclic bases. But at the same time the presence of a cyclopentyl moiety with 2′ and 3′ hydroxyls is necessary for the inhibitory properties, since compounds 8-10, without those groups did not exhibit an inhibitory effect under the experimental conditions.

The enzymatic synthesis of nucleoside analogues has been shown to be a sustainable and efficient alternative to chemical synthesis routes. In this study, dihalogenated nucleoside analogues were produced by thermostable nucleoside phosphorylases in transglycosylation reactions using uridine or thymidine as sugar donors. Prior to the enzymatic process, ideal maximum product yields were calculated after the determination of equilibrium constants through monitoring the equilibrium conversion in analytical-scale reactions. Equilibrium constants for dihalogenated nucleosides were comparable to known purine nucleosides, ranging between 0.071 and 0.081. To achieve 90% product yield in the enzymatic process, an approximately five-fold excess of sugar donor was needed. Nucleoside analogues were purified by semi-preparative HPLC, and yields of purified product were approximately 50% for all target compounds. To evaluate the impact of halogen atoms in positions 2 and 6 on the antiproliferative ...

Widely used as anticancer and immunosuppressive agents, thiopurines have narrow therapeutic indices owing to frequent toxicities, partly explained by TPMT genetic polymorphisms. Recent studies identified germline NUDT15 variation as another critical determinant of thiopurine intolerance, but the underlying molecular mechanisms and the clinical implications of this pharmacogenetic association remain unknown. In 270 children enrolled in clinical trials for acute lymphoblastic leukemia in Guatemala, Singapore and Japan, we identified four NUDT15 coding variants (p.Arg139Cys, p.Arg139His, p.Val18Ile and p.Val18_Val19insGlyVal) that resulted in 74.4-100% loss of nucleotide diphosphatase activity. Loss-of-function NUDT15 diplotypes were consistently associated with thiopurine intolerance across the three cohorts (P = 0.021, 2.1 × 10(-5) and 0.0054, respectively; meta-analysis P = 4.45 × 10(-8), allelic effect size = -11.5). Mechanistically, NUDT15 inactivated thiopurine metabolites and de...

MTAP (5′-methylthioadenosine phosphorylase) catalyses the reversible phosphorolytic cleavage of methylthioadenosine leading to the production of methylthioribose-1-phosphate and adenine. Deficient MTAP activity has been correlated with human diseases including cirrhosis and hepatocellular carcinoma. In the present study we have investigated the regulation of MTAP by ROS (reactive oxygen species). The results of the present study support the inactivation of MTAP in the liver of bacterial LPS (lipopolysaccharide)-challenged mice as well as in HepG2 cells after exposure to t-butyl hydroperoxide. Reversible inactivation of purified MTAP by hydrogen peroxide results from a reduction of Vmax and involves the specific oxidation of Cys136 and Cys223 thiols to sulfenic acid that may be further stabilized to sulfenyl amide intermediates. Additionally, we found that Cys145 and Cys211 were disulfide bonded upon hydrogen peroxide exposure. However, this modification is not relevant to the mediat...

It is crucial to the reproducibility of results and their proper interpretation that the conditions under which experiments are carried out be defined with rigour and consistency. In this review we attempt to clarify the differences and interrelationships among steady, balanced and exponential states of culture growth. Basic thermodynamic concepts are used to introduce the idea of steady-state growth in open, biological systems. The classical, sometimes conflicting, definitions of steady-state and balanced growth are presented, and a consistent terminology is proposed. The conditions under which a culture in balanced growth is also in exponential growth and in steady-state growth are indicated. It is pointed out that steady-state growth always implies both balanced and exponential growth, and examples in which the converse does not hold are described. More complex situations are then characterized and the terminology extended accordingly. This leads to the notion of normal growth and growth that can be synchronous or otherwise unbalanced but still reproducible, and to the condition of approximate steady state manifested by growth in batch culture and by asymmetrically dividing cells, which is analysed in some detail.

Objective: Small non-coding RNA molecules are dysregulated in prostate cancer (PCa). In our previous study, downregulation of miR-1266 and miR-185 was demonstrated in PCa tissues and cell lines. The aim of the present study was to investigate whether miR-1266 and miR-185 are involved in the regulation of B-cell lymphoma (BCL) 2 and BCL2L1, respectively, and whether transfection of PCa cell lines with miR-1266 and miR-185 mimics can alter tumorigenic phenotypes. Methods: In order to investigate the regulation of BCL2 and BCL2L1 mRNA levels by miR-1266 and miR-185, respectively, a luciferase reporter assay was used. Real-time PCR was also used to analyze changes in the levels of BCL2 and BCL2L1 mRNAs in PCa cell lines following transfection with synthetic miR-1266 and miR-185. Cell apoptosis was determined by Annexin V protein expression analysis via flow cytometry. In addition to the MTT assay, a cell proliferation assay was performed. Result: A luciferase assay confirmed that the BC...

HPV infection is associated with high p16 expression and good prognosis in head and neck squamous cell carcinomas (HNSCCs). Analysis of CDKN2A, the gene encoding p16, may further elucidate the association between p16 expression and prognosis. We sought to determine whether CDKN2A copy number loss was associated with poor survival in HPV-negative HNSCCs. The Cancer Genome Atlas HNSCC clinical and genomic data were obtained and integrated. Patients &lt;80 years old with a primary tumor in the oral cavity, oropharynx, hypopharynx, or larynx were included. Stratifying by copy number loss status, CDKN2A mRNA and p16 protein expression levels were examined and overall survival (OS) and disease-free survival (DFS) were evaluated. 401 patients with HPV-negative HNSCC were identified. 146 patients demonstrated CDKN2A copy number loss. The CDKN2A copy number loss group expressed significantly lower levels of CDKN2A mRNA and p16 protein than did the non-copy number loss group. Median OS for pa...

Methylthioadenosine (MTA) is released as a by-product of S-adenosylmethionine (AdoMet)-dependent reactions central to ethylene, polyamine, or phytosiderophore biosynthesis. MTA is hydrolysed by methylthioadenosine nucleosidase (MTN; EC 3.2.2.16) into adenine and methylthioribose which is processed through the methionine (Met) cycle to produce a new molecule of AdoMet. In deepwater rice, submergence enhances ethylene biosynthesis, and ethylene in turn influences the methionine cycle through positive feedback regulation of the acireductone dioxygenase gene OsARD1. In rice, MTN is encoded by a single gene designated OsMTN. Recombinant OsMTN enzyme had a K M for MTA of 2.1 mM and accepted a wide array of 5# substitutions of the substrate. OsMTN also metabolized S-adenosylhomocysteine (AdoHcy) with 15.9% the rate of MTA. OsMTN transcripts and OsMTN-specific activity increased slowly and in parallel upon submergence, indicating that regulation occurred mainly at the transcriptional level. Neither ethylene, MTA, nor Met regulated OsMTN expression. Analysis of steadystate metabolite levels showed that MTN activity was sufficiently high to prevent Met and AdoMet depletion during long-term ethylene biosynthesis.

X-ray crystallography, molecular modeling, and site-directed mutagenesis were used to delineate the catalytic mechanism of purine nucleoside phosphorylase (PNP). PNP catalyzes the reversible phosphorolysis of purine nucleosides to the corresponding purine base and ribose 1-phosphate using a substrate-assisted catalytic mechanism. The proposed transition state (TS) features an oxocarbenium ion that is stabilized by the cosubstrate phosphate dianion which itself functions as part of a catalytic triad (Glu89-His86-PO 4 d). Participation of phosphate in the TS accounts for the poor hydrolytic activity of PNP and is likely to be the mechanistic feature that differentiates phosphorylases from glycosidases. The proposed PNP TS also entails a hydrogen bond between N7 and a highly conserved Asn. Hydrogen bond donation to N7 in the TS stabilizes the negative charge that accumulates on the purine ring during glycosidic bond cleavage. Kinetic studies using N7-modified analogs provided additional support for the hydrogen bond. Crystallographic studies of 13 human PNP-ligand complexes indicated that PNP uses a ligand-induced conformational change to position Asn243 and other key residues in the active site for catalysis. These studies also indicated that purine nucleosides bind to PNP with a nonstandard glycosidic torsion angle (+anticlinal) and an uncommon sugar pucker (C4′-endo). Single point energy calculations predicted the binding conformation to enhance phosphorolysis through ligand strain. Structural data also suggested that purine binding precedes ribose 1-phosphate binding in the synthetic direction whereas the order of substrate binding was less clear for phosphorolysis. Conservation of the catalytically important residues across nucleoside phosphorylases with specificity for 6-oxopurine nucleosides provided further support for the proposed catalytic mechanism.

The production of uric acid in murine white adipose tissue (mWAT), and that such production was augmented in obese mice, was recently reported. However, little is known about the secretion of metabolites associated with purine catabolism in human WAT (hWAT). The present study analyzed this in hWAT. Freshly isolated hWAT and mWAT were cultured. The secretion of metabolites associated with purine catabolism was measured. Tissue distribution profiles of genes associated with purine metabolism and metabolite profiling of adipocytes in hypoxia were analyzed. Secretion of hypoxanthine from hWAT was higher than those of xanthine and uric acid. On the other hand, secretion of uric acid was relatively higher than xanthine and hypoxanthine in mWAT. Xanthine oxidoreductase (XOR) mRNA expression levels in hWAT were markedly lower than that in the human liver. In murine tissues, XOR mRNA expression levels in mWAT were comparable with those in the liver. Cultured human adipocytes secreted hypoxan...

Head and neck cancer (HNC) is among the ten leading malignancies worldwide, with India solely contributing one-third of global oral cancer cases. The current focus of all cutting-edge strategies against this global malignancy are directed towards the heterogeneous tumor microenvironment that obstructs most treatment blueprints. Subsequent to the portrayal of established information, the review details the application of single cell technology, organoids and spheroid technology in relevance to head and neck cancer and the tumor microenvironment acknowledging the resistance pattern of the heterogeneous cell population in HNC. Bioinformatic tools are used for study of differentially expressed genes and further omics data analysis. However, these tools have several challenges and limitations when analyzing single-cell gene expression data that are discussed briefly. The review further examines the omics of HNC, through comprehensive analyses of genomics, transcriptomics, proteomics, met...

Biocatalysis reproduce nature&#39;s synthetic strategies in order to synthesize different organic compounds. Natural metabolic pathways usually involve complex networks to support cellular growth and survival. In this regard, multi-enzymatic systems are valuable tools for the production of a wide variety of organic compounds. Methods: The production of different purine nucleosides and nucleoside-5-monophosphates has been performed for first time, catalyzed by the sequential action of 2-deoxyribosyltransferase from Lactobacillus delbrueckii (LdNDT) and hypoxanthine-guanine-xanthine phosphoribosyltransferase from Thermus themophilus HB8 (TtHGXPRT). Results: The biochemical characterization of LdNDT reveals that the enzyme is active and stable in a broad range of pH, temperature, and ionic strength. Substrate specificity studies showed a high promiscuity in the recognition of purine analogues. Finally, the enzymatic production of different purine derivatives was performed to evaluate t...

We have investigated the regulation of the Escherichia coli deoCp2 promoter by the CytR repressor and the cyclic AMP (cAMP) receptor protein (CRP) complexed to cAMP. Promoter regions controlled by these two proteins characteristically contain tandem cAMP-CRP binding sites. Here we show that (i) CytR selectively regulated cAMP-CRP-dependent initiations, although transcription started from the same site in deoCp2 in the absence or presence of cAMP-CRP; (ii) deletion of the uppermost cAMP-CRP target (CRP-2) resulted in loss of CytR regulation, but had only a minor effect on positive control by the cAMP-CRP complex; (iii) introduction of point mutations in either CRP target resulted in loss of CytR regulation; and (iv) regulation by CytR of deletion mutants lacking CRP-2 could be specifically reestablished by increasing the intracellular concentration of CytR. These findings indicate that both CRP targets are required for efficient CytR repression of deoCp2. Models for the action of Cyt...

Drug resistance is one of the primary obstacles in cancer chemotherapy. The causes of drug resistances are varied. The primary resistance attributed to genomic instability while alteration in membrane permeability of drug and inability to reach the target sites, drug inactivation by enzymes, mutation and altered expression of target proteins there by affecting drug target interactions are some of the mechanism of acquired drug resistance. In addition to genetic changes there are epigenetic changes or non mutational mechanisms which occur quickly in response to environmental changes. Normal tissues never develop resistance to chemotherapy, because they possess intact genetic machinery. Drug resistance in addition to reducing clinical effectiveness, result in early termination of treatment, reduced relapse free interval and survival. There are various methods for overcoming these major disadvantages of cancer chemotherapy. Combination chemotherapy with clear understanding of the bioch...

MTAP (5′-methylthioadenosine phosphorylase) catalyses the reversible phosphorolytic cleavage of methylthioadenosine leading to the production of methylthioribose-1-phosphate and adenine. Deficient MTAP activity has been correlated with human diseases including cirrhosis and hepatocellular carcinoma. In the present study we have investigated the regulation of MTAP by ROS (reactive oxygen species). The results of the present study support the inactivation of MTAP in the liver of bacterial LPS (lipopolysaccharide)-challenged mice as well as in HepG2 cells after exposure to t-butyl hydroperoxide. Reversible inactivation of purified MTAP by hydrogen peroxide results from a reduction of Vmax and involves the specific oxidation of Cys136 and Cys223 thiols to sulfenic acid that may be further stabilized to sulfenyl amide intermediates. Additionally, we found that Cys145 and Cys211 were disulfide bonded upon hydrogen peroxide exposure. However, this modification is not relevant to the mediat...