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1.
Nature ; 565(7740): 516-520, 2019 01.
Article in English | MEDLINE | ID: mdl-30602789

ABSTRACT

Type A ƎĀ³-aminobutyric acid (GABAA) receptors are pentameric ligand-gated ion channels and the main drivers of fast inhibitory neurotransmission in the vertebrate nervous system1,2. Their dysfunction is implicated in a range of neurological disorders, including depression, epilepsy and schizophrenia3,4. Among the numerous assemblies that are theoretically possible, the most prevalent in the brain are the α1Ɵ2/3ƎĀ³2 GABAA receptors5. The Ɵ3 subunit has an important role in maintaining inhibitory tone, and the expression of this subunit alone is sufficient to rescue inhibitory synaptic transmission in Ɵ1-Ɵ3 triple knockout neurons6. So far, efforts to generate accurate structural models for heteromeric GABAA receptors have been hampered by the use of engineered receptors and the presence of detergents7-9. Notably, some recent cryo-electron microscopy reconstructions have reported 'collapsed' conformations8,9; however, these disagree with the structure of the prototypical pentameric ligand-gated ion channel the Torpedo nicotinic acetylcholine receptor10,11, the large body of structural work on homologous homopentameric receptor variants12 and the logic of an ion-channel architecture. Here we present a high-resolution cryo-electron microscopy structure of the full-length human α1Ɵ3ƎĀ³2L-a major synaptic GABAA receptor isoform-that is functionally reconstituted in lipid nanodiscs. The receptor is bound to a positive allosteric modulator 'megabody' and is in a desensitized conformation. Each GABAA receptor pentamer contains two phosphatidylinositol-4,5-bisphosphate molecules, the head groups of which occupy positively charged pockets in the intracellular juxtamembrane regions of α1 subunits. Beyond this level, the intracellular M3-M4 loops are largely disordered, possibly because interacting post-synaptic proteins are not present. This structure illustrates the molecular principles of heteromeric GABAA receptor organization and provides a reference framework for future mechanistic investigations of GABAergic signalling and pharmacology.


Subject(s)
Cryoelectron Microscopy , Lipid Bilayers/chemistry , Receptors, GABA-A/chemistry , Receptors, GABA-A/ultrastructure , Allosteric Regulation , Amino Acid Sequence , Binding Sites , Electric Conductivity , Humans , Models, Molecular , Molecular Docking Simulation , Nanostructures/chemistry , Nanostructures/ultrastructure , Phosphatidylinositol 4,5-Diphosphate/chemistry , Phosphatidylinositol 4,5-Diphosphate/metabolism , Protein Isoforms/chemistry , Protein Isoforms/metabolism , Protein Isoforms/ultrastructure , Protein Structure, Quaternary , Receptors, GABA-A/metabolism
2.
Bioorg Chem ; 67: 110-5, 2016 08.
Article in English | MEDLINE | ID: mdl-27337226

ABSTRACT

T4 DNA ligase is one of the most commonly used enzymes for in vitro molecular research and a useful model for testing the ligation mechanism of ATP-dependent DNA ligation. To better understand the influence of phosphate group modifications in the ligation process, a series of ATP analogs were tested as cofactors. P-diastereomers of newly developed Ɵ,ƎĀ³-hypo-ATPαS (thio) and Ɵ,ƎĀ³-hypo-ATP (oxo) were synthesized and their activity was compared to ATPαS and their natural precursors. The evaluation of presented ATP analogs revealed the importance of the α-phosphate stereogenic center in ATPαS for the T4 DNA ligase activity and sheds new light on the interaction between ATP-dependent DNA ligases and cofactors.


Subject(s)
Adenosine Triphosphate/metabolism , DNA Ligases/metabolism , Phosphates/metabolism , Sulfhydryl Compounds/metabolism , Adenosine Triphosphate/chemistry , DNA Ligases/chemistry , Molecular Structure , Phosphates/chemical synthesis , Phosphates/chemistry , Sulfhydryl Compounds/chemistry
3.
Biochim Biophys Acta ; 1840(12): 3357-66, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25199874

ABSTRACT

BACKGROUND: One of the activities of histidine triad nucleotide-binding protein 1 (Hint1) under in vitro conditions is the conversion of nucleoside 5'-O-phosphorothioate (NMPS) to its 5'-O-phosphate (NMP), which is accompanied by the release of hydrogen sulfide. METHODS: Non-hydrolyzable derivatives of AMPS and dCMPS, each containing the residue able to form a covalent bond in nucleic acid-protein complexes via photocrosslinking (at 308nm), were applied at the complexing experiments with recombinant and cellular Hint1. The cellular lysates prepared after RNAi-mediated knockdown of Hint1 were incubated with AMPS and the level of desulfuration was measured. RESULTS: Recombinant Hint1 and Hint1 present in the cellular lysate of A549 cells, formed complexes with the used substrate analogs. Computer modeling experiments, in which the ligand was docked at the binding pocket, confirmed that direct interactions between Hint1 and the screened analogs are possible. Using RNAi technology, we demonstrated lowered levels of AMPS substrate desulfuration in reactions that employed the cell lysates with a reduced Hint1 level. CONCLUSIONS: The enzymatic conversion of AMPS to AMP occurred with the participation of cellular Hint1, the protein, which is present in all organisms. GENERAL SIGNIFICANCE: The intracellular Hint1 could be responsible for the in vivo desulfuration of nucleosides-5'-monophosphorothioate, thus it can contribute to the phosphorothioate oligonucleotides metabolism. H2S released during this process may participate in several physiological processes, thus NMPSs can be precursors/donors of H2S in vivo and can be used to study the effects of this gas in biological systems. Moreover, the controlled delivery of (d)NMPSs into cells may be of medicinal utility.

4.
Bioorg Med Chem ; 19(16): 5053-60, 2011 Aug 15.
Article in English | MEDLINE | ID: mdl-21757356

ABSTRACT

Fragile histidine triad (Fhit) protein encoded by tumour suppressor FHIT gene is a proapoptotic protein with diadenosine polyphosphate (Ap(n)A, n=2-6) hydrolase activity. It has been hypothesised that formation of Fhit-substrate complex results in an apoptosis initiation signal while subsequent hydrolysis of Ap(n)A terminates this action. A series of Ap(n)A analogues have been identified in vitro as strong Fhit ligands [Varnum, J. M.; Baraniak, J.; Kaczmarek, R.; Stec, W. J.; Brenner, C. BMC Chem. Biol.2001, 1, 3]. We assumed that in Fhit-positive cells these compounds might preferentially bind to Fhit and inhibit its hydrolytic activity what would prolong the lifetime of apoptosis initiation signalling complex. Therefore, several Fhit inhibitors were tested for their cytotoxicity and ability to induce apoptosis in Fhit-positive HEK293T cells. These experiments have shown that Ap(4)A analogue, containing a glycerol residue instead of the central pyrophosphate and two terminal phosphorothioates [A(PS)-CH(2)CH(OH)CH(2)-(PS)A (1)], is the most cytotoxic among test compounds (IC(50)=17.5Ā±4.2 ĀµM) and triggers caspase-dependent cell apoptosis. The Fhit-negative HEK293T cells (in which Fhit was silenced by RNAi) were not sensitive to compound 1. These results indicate that the Ap(4)A analogue 1 induces Fhit-dependent apoptosis and therefore, it can be considered as a drug candidate for anticancer therapy in Fhit-positive cancer cells and in Fhit-negative cancer cells, in which re-expression of Fhit was accomplished by gene therapy.


Subject(s)
Acid Anhydride Hydrolases/physiology , Antineoplastic Agents/chemical synthesis , Apoptosis/drug effects , Cell Survival/drug effects , Dinucleoside Phosphates/pharmacology , Neoplasm Proteins/physiology , Neoplasms/drug therapy , Acid Anhydride Hydrolases/chemistry , Acid Anhydride Hydrolases/metabolism , Annexin A5/analysis , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Apoptosis/genetics , Caspases/analysis , Caspases/drug effects , Cell Line, Tumor , Cytotoxins , Dinucleoside Phosphates/chemistry , Dinucleoside Phosphates/physiology , Dinucleoside Phosphates/therapeutic use , Dose-Response Relationship, Drug , Drug Screening Assays, Antitumor , Female , Fluorescent Dyes/analysis , Genes, Tumor Suppressor/drug effects , HEK293 Cells , Humans , Neoplasms/genetics , Neoplasms/metabolism , Neoplasms/pathology , RNA, Small Interfering/metabolism
5.
Chirality ; 23(3): 237-44, 2011 Mar.
Article in English | MEDLINE | ID: mdl-20928893

ABSTRACT

A method for stereocontrolled chemical synthesis of P-substituted nucleoside 5'-O-phosphorothioates has been elaborated. Selected 3'-O-acylated deoxyribonucleoside- and 2',3'-O,O-diacylated ribonucleoside-5'-O-(2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane)s were chromatographically separated into P-diastereomers. Their reaction with anions of phosphorus-containing acids was highly stereoselective (≥90%) and furnished corresponding P-chiral α-thiodiphosphates and their phosphonate analogs with satisfactory yield.


Subject(s)
Nucleosides/analysis , Nucleosides/chemistry , Nucleotides/analysis , Nucleotides/chemistry , Phosphorothioate Oligonucleotides/chemical synthesis , Ribose/analogs & derivatives , Chromatography, High Pressure Liquid/methods , Deoxyribonucleosides/chemistry , Dinucleoside Phosphates/chemistry , Hydrolysis , Organic Chemistry Phenomena , Ribose/analysis , Ribose/chemistry , Stereoisomerism , Thymidine/chemistry
6.
Org Biomol Chem ; 8(24): 5505-10, 2010 Dec 21.
Article in English | MEDLINE | ID: mdl-20944857

ABSTRACT

A new method for the formation of organohypophosphates containing a P-P bond under mild conditions, based on the DBU-assisted reaction of 2-alkoxy-2-thio-1,3,2-oxathiaphospholanes with O,O-dialkyl H-phosphonates or H-thiophosphonates, has been elaborated. The resulting triesters of P(1)-thio- and P(1),P(2)-dithiohypophosphoric acids, respectively, having O-methyl or O-ethyl groups, can be selectively dealkylated to form the corresponding di- or monoesters. Appropriately protected 2'-deoxyguanosine-3'-O-(2-thio-1,3,2-oxathiaphospholane) was converted into the corresponding P(1)-thio- and P(1),P(2)-dithiohypophosphate esters in a highly stereoselective manner (98%+ and 90%+, respectively).


Subject(s)
Nucleotides/chemistry , Organophosphonates/chemistry , Ribose/analogs & derivatives , Sulfhydryl Compounds/chemistry , Alkylation , Molecular Structure , Ribose/chemistry , Stereoisomerism
7.
Biometals ; 23(6): 1113-21, 2010 Dec.
Article in English | MEDLINE | ID: mdl-20589414

ABSTRACT

The 3'-exonuclease from human plasma is a soluble form of nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) (EC 3.1.4.1/EC 3.6.1.9). Here, the possibility of divalent cation influence for the 3'-exonuclease activity was investigated using the phosphorothioate congener of oligonucleotide containing all phosphorothioate internucleotide linkages of the [R(P)]-configuration ([R(P)-PS]-d[T(12)]) as the substrate for this enzyme. It was found that the 3'-exonuclease is a metalloenzyme, i.e. its phosphodiesterase activity was completely abolished at 0.8 mM concentration EDTA and, in turn, it was restored in the presence of Mg(2+) or Mn(2+) ions. In addition, Mg(2+) can be replaced effectively by Ca(2+), Mn(2+), or Co(2+), but not by Ni(2+) and Cd(2+) during the hydrolysis of the phosphorothioate substrate in human plasma. In addition, the mechanism is postulated, by which a single internucleotide phosphorothioate bond of the S(P)-configuration at the 3'-end of unmodified phosphodiesters (PO-oligos), or their phosporothioate analogs (PS-oligos) protects these compounds against degradation in blood.


Subject(s)
Cations, Divalent/pharmacology , Exonucleases/blood , Catalysis/drug effects , Edetic Acid/pharmacology , Exonucleases/drug effects , Exonucleases/metabolism , Humans , Magnesium/pharmacology , Manganese/pharmacology , Models, Chemical , Phosphates/metabolism , Thionucleotides/metabolism
8.
Org Biomol Chem ; 7(10): 2162-9, 2009 May 21.
Article in English | MEDLINE | ID: mdl-19421455

ABSTRACT

A new type of internucleotide phosphorodithioate linkage is described, wherein one of the sulfur atoms occupies a 5'-bridging position. Representative dinucleotides possessing such a bond were synthesized by S-alkylation of nucleoside-3'-O-phosphorodithioates with 5'-halogeno-5'-deoxy-nucleosides. A fully protected dithymidylate containing internucleotide 5'-S-phosphorodithioate linkage was converted into a 3'-O-phosphoramidite derivative and employed for introduction of a modified dinucleotide into a predetermined position of the oligonucleotide sequence. The 5'-S-phosphorodithioate linkage in dinucleotide analogues was found to be resistant toward nucleolytic degradation with snake venom PDE and nuclease P1. However, P-stereoselective degradation was observed for diastereomers of 5'-S-phosphorodithioate dithymidine analogs under treatment with calf spleen PDE. The new 5'-S-phosphorodithioate linkage was readily degraded by iodine solutions in the presence of water. It was also found that oligothymidylates containing a single 5'-S-phosphorodithioate linkage form much weaker duplexes with their complementary sequences.


Subject(s)
Oligodeoxyribonucleotides/chemical synthesis , Organothiophosphorus Compounds/chemical synthesis , Phosphates/chemistry , Sulfur/chemistry , Dinucleoside Phosphates/chemistry , Nucleic Acid Conformation , Oligonucleotides/chemistry
9.
FEBS Lett ; 582(20): 3152-8, 2008 Sep 03.
Article in English | MEDLINE | ID: mdl-18694747

ABSTRACT

We show here that Fhit proteins, in addition to their function as dinucleoside triphosphate hydrolases, act similarly to adenylylsulfatases and nucleoside phosphoramidases, liberating nucleoside 5'-monophosphates from such natural metabolites as adenosine 5'-phosphosulfate and adenosine 5'-phosphoramidate. Moreover, Fhits recognize synthetic nucleotides, such as adenosine 5'-O-phosphorofluoridate and adenosine 5'-O-(gamma-fluorotriphosphate), and release AMP from them. With respect to the former, Fhits behave like a phosphodiesterase I concomitant with cleavage of the P-F bond. Some kinetic parameters and implications of the novel reactions catalyzed by the human and plant (Arabidopsis thaliana) Fhit proteins are presented.


Subject(s)
Acid Anhydride Hydrolases/metabolism , Arabidopsis Proteins/metabolism , Dinucleoside Phosphates/metabolism , Neoplasm Proteins/metabolism , Phosphoric Diester Hydrolases/metabolism , Acid Anhydride Hydrolases/genetics , Arabidopsis Proteins/genetics , Cloning, Molecular , Humans , Neoplasm Proteins/genetics , Phosphoric Diester Hydrolases/genetics , Substrate Specificity
10.
Mol Biotechnol ; 40(2): 119-26, 2008 Oct.
Article in English | MEDLINE | ID: mdl-18769882

ABSTRACT

Influence of stereochemistry of the 3'-terminal phosphorothioate (PS)-modified primers was studied in a single base extension (SBE) assay to evaluate any improvements in specificity. SBE reactions were catalyzed by members of the high fidelity Pfu family of DNA polymerases with (exo+) or without (exo-) 3' --> 5' exonucleolytic activity. The diastereomerically pure PS-labeled primers used in these studies were obtained either by the stereospecific chemical synthesis invented in our laboratory or by the more conventional ion-exchange chromatographic method for separation of a mixture of diastereomers (R(P) and S(P)). When the SBE reaction was performed in the presence of mispaired 2'-deoxyribonucleoside triphosphates (dNTPs), the "racemic" 3'-phosphorothioate primer mixture resulted in a lower level of 3' --> 5' exonuclease-mediated cleavage products in comparison to the SBE reactions carried out with the corresponding unmodified primer. When the diastereomerically pure RP 3'-phosphorothioate primer was examined, the results were largely the same as for the racemic 3'-phosphorothioate primer mixture. In contrast, a 3'-PS primer of S(P) configuration displayed significantly improved performance in the SBE reaction. This included the lack of 3' --> 5' proofreading products, less mispriming, and improved yield of incorporation of the correct nucleotide.


Subject(s)
DNA Primers/chemistry , DNA Primers/metabolism , DNA-Directed DNA Polymerase/metabolism , Phosphorothioate Oligonucleotides/chemistry , Phosphorothioate Oligonucleotides/metabolism , Polymerase Chain Reaction/methods , Chromatography, High Pressure Liquid , DNA Primers/genetics , Molecular Structure , Phosphorothioate Oligonucleotides/genetics , Stereoisomerism
11.
PLoS One ; 13(1): e0191583, 2018.
Article in English | MEDLINE | ID: mdl-29352320

ABSTRACT

The inhibitory ƎĀ³-aminobutyric acid type A receptors are implicated in numerous physiological processes, including cognition and inhibition of neurotransmission, rendering them important molecular targets for many classes of drugs. Functionally, the entire GABAAR family of receptors can be subdivided into phasic, fast acting synaptic receptors, composed of α-, Ɵ- and ƎĀ³-subunits, and tonic extrasynaptic receptors, many of which contain the ƎĀ“-subunit in addition to α- and Ɵ-subunits. Whereas the subunit arrangement of the former group is agreed upon, that of the αƟƎĀ“ GABAARs remains unresolved by electrophysiological and pharmacological research. To resolve such issues will require biophysical techniques that demand quantities of receptor that have been previously unavailable. Therefore, we have engineered a stable cell line with tetracycline inducible expression of human α4-, Ɵ3- and N-terminally Flag-tagged ƎĀ“-subunits. This cell line achieved a specific activity between 15 and 20 pmol [3H]muscimol sites/mg of membrane protein, making it possible to obtain 1 nmole of purified α4Ɵ3ƎĀ“ GABAAR from sixty 15-cm culture dishes. When induced, these cells exhibited agonist-induced currents with characteristics comparable to those previously reported for this receptor and a pharmacology that included strong modulation by etomidate and the ƎĀ“-subunit-specific ligand, DS2. Immunoaffinity purification and reconstitution in CHAPS/asolectin micelles resulted in the retention of equilibrium allosteric interactions between the separate agonist, anesthetic and DS2 sites. Moreover, all three subunits retained glycosylation. The establishment of this well-characterized cell line will allow molecular level studies of tonic receptors to be undertaken.


Subject(s)
Receptors, GABA-A/biosynthesis , Electrophysiological Phenomena , HEK293 Cells , Humans , Kinetics , Protein Engineering , Protein Subunits , Radioligand Assay , Receptors, GABA-A/genetics , Receptors, GABA-A/isolation & purification , Recombinant Fusion Proteins/biosynthesis , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/isolation & purification , Transfection , gamma-Aminobutyric Acid/metabolism
12.
FEBS J ; 274(4): 1062-72, 2007 Feb.
Article in English | MEDLINE | ID: mdl-17250742

ABSTRACT

The RNA phosphodiester bond cleavage activity of a series of 16 thio-deoxyribozymes 10-23, containing a P-stereorandom single phosphorothioate linkage in predetermined positions of the catalytic core from P1 to P16, was evaluated under single-turnover conditions in the presence of either 3 mM Mg(2+) or 3 mM Mn(2+). A metal-specificity switch approach permitted the identification of nonbridging phosphate oxygens (proR(P) or proS(P)) located at seven positions of the core (P2, P4 and P9-13) involved in direct coordination with a divalent metal ion(s). By contrast, phosphorothioates at positions P3, P6, P7 and P14-16 displayed no functional relevance in the deoxyribozyme-mediated catalysis. Interestingly, phosphorothioate modifications at positions P1 or P8 enhanced the catalytic efficiency of the enzyme. Among the tested deoxyribozymes, thio-substitution at position P5 had the largest deleterious effect on the catalytic rate in the presence of Mg(2+), and this was reversed in the presence of Mn(2+). Further experiments with thio-deoxyribozymes of stereodefined P-chirality suggested direct involvement of both oxygens of the P5 phosphate and the proR(P) oxygen at P9 in the metal ion coordination. In addition, it was found that the oxygen atom at C6 of G(6) contributes to metal ion binding and that this interaction is essential for 10-23 deoxyribozyme catalytic activity.


Subject(s)
DNA, Catalytic/chemistry , DNA, Single-Stranded/chemistry , Organophosphates/chemistry , Binding Sites , Catalysis , Catalytic Domain , Cations, Divalent/chemistry , Cations, Divalent/metabolism , DNA, Catalytic/metabolism , DNA, Single-Stranded/metabolism , Magnesium/chemistry , Magnesium/metabolism , Manganese/chemistry , Manganese/metabolism , Organophosphates/metabolism , Oxygen/chemistry , Oxygen/metabolism , Stereoisomerism , Structure-Activity Relationship , Time Factors
13.
Oligonucleotides ; 17(1): 134-45, 2007.
Article in English | MEDLINE | ID: mdl-17461770

ABSTRACT

The rapid degradation of unmodified phosphodiester oligodeoxynucleotides (PO-oligos) by exo -and endonucleases limits their application as antisense constructs and requires the synthesis and use of modified oligonucleotides. Phosphorothioate analogs of oligonucleotides (PS-oligos) are much more stable against nucleolytic degradation than their unmodified counterparts, and this is one of the reasons for which they are a promising class of antisense oligonucleotides. However, PS-oligos also undergo slow hydrolysis by enzymes present in plasma. The oligonucleotide degradation proceeds mainly from the 3' -end, resulting in the formation of a typical ladder of shorter products and the release of the mononucleoside 5' -phosphorothioates. So far, little has been known concerning the molecular identity of the enzymes involved in the degradation of PS-oligos. We now identify the human plasma 3' -exonuclease responsible for their degradation as a soluble form of nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) (EC 3.1.4.1/EC 3.6.1.9), also known as the plasma cell differentiation antigen PC-1. We also show that adenosine or deoxyadenosine (alpha-thio)triphosphates can act as potent inhibitors of NPPs.


Subject(s)
Oligonucleotides, Antisense/chemistry , Phosphoric Diester Hydrolases/chemistry , Pyrophosphatases/chemistry , Thionucleotides/chemistry , Enzyme Inhibitors/pharmacology , Exonucleases/antagonists & inhibitors , Exonucleases/metabolism , Humans , Immunoprecipitation , Phosphoric Diester Hydrolases/blood , Pyrophosphatases/antagonists & inhibitors , Pyrophosphatases/blood , Substrate Specificity
15.
J Cancer ; 8(1): 146-151, 2017.
Article in English | MEDLINE | ID: mdl-28123609

ABSTRACT

Background: The presence as well as the potential role of EGFRvIII in tumors other than glioblastoma still remains a controversial subject with many contradictory data published. Previous analyses, however, did not consider the level of EGFRvIII mRNA expression in different tumor types. Methods: Appropriately designed protocol for Real-time quantitative reverse-transcription PCR (Real-time qRT-PCR) was applied to analyze EGFRvIII and EGFRWT mRNA expression in 155 tumor specimens. Additionally, Western Blot (WB) analysis was performed for selected samples. Stable cell lines showing EGFRvIII expression (CAS-1 and DK-MG) were analyzed by means of WB, immunocytochemistry (ICC) and fluorescence in situ hybridization (FISH). Results: Our analyses revealed EGFRvIII expression in 27.59% of glioblastomas (8/29), 8.11% of colorectal cancers (3/37), 6.52% of prostate cancers (3/46) and none of breast cancers (0/43). Despite the average relative expression of EGFRvIII varying greatly among tumors of different tissues (approximately 800-fold) or even within the same tissue group (up to 8000-fold for GB), even the marginal expression of EGFRvIII mRNA can be detrimental to cancer progression, as determined by the analysis of stable cell lines endogenously expressing the oncogene. Conclusion: EGFRvIII plays an unquestionable role in glioblastomas with high expression of this oncogene. Our data suggests that EGFRvIII importance should not be underestimated even in tumors with relatively low expression of this oncogene.

16.
Oligonucleotides ; 16(1): 68-82, 2006.
Article in English | MEDLINE | ID: mdl-16584296

ABSTRACT

S(C) and R(C) diastereomers of 5'-C-(O,O-diethyl)-phosphonylthymidine ((R)T and (S)T) were used for the synthesis of the dimers T(R)T and T(S)T, respectively. These dimers were incorporated at selected sites in oligonucleotide constructs. Melting temperature (Tm) experiments demonstrated that relative to the unmodified oligodeoxyribonucleotide, the presence of the (R)T moiety reduced the thermal stability of the duplexes by approximately 5.0 degrees C per modification, whereas their (S)T counterparts only slightly destabilized the duplex structure (deltaTm < or = 1 degree C/modification). The stability of the triple-helical complexes containing one, two, or three modified thymidines is slightly higher than that of the parent complex. Nuclease resistance studies performed with snake venom phosphodiesterase, calf spleen phosphodiesterase, and 3'-exonuclease from human plasma showed that cleavage of the oligonucleotides at the site of the modification was completely suppressed regardless of the stereochemistry of the 5'-C-chiral center. The influence of the (R)T and (S)T modification in the recognition sequence of HindIII, EcoRI, and HpaI restriction endonucleases was also investigated. Although the catalytic activity of HindIII was not affected by the presence of the 5'-C-ethoxyphosphonyl modification, the activities of the two remaining restriction enzymes were partially suppressed depending on the site of modification or the stereochemistry of the modification or both ((R)T vs. (S)T).


Subject(s)
DNA/chemistry , Oligodeoxyribonucleotides/chemistry , DNA/chemical synthesis , Deoxyribonuclease EcoRI/chemistry , Deoxyribonuclease HindIII/chemistry , Dimerization , Nucleic Acid Hybridization , Oligodeoxyribonucleotides/chemical synthesis , Organophosphorus Compounds , Thymidine/analogs & derivatives
17.
Structure ; 12(10): 1775-88, 2004 Oct.
Article in English | MEDLINE | ID: mdl-15458627

ABSTRACT

Proteins that bind to specific sites on DNA often do so in order to carry out catalysis or specific protein-protein interaction while bound to the recognition site. Functional specificity is enhanced if this second function is coupled to correct DNA site recognition. To analyze the structural and energetic basis of coupling between recognition and catalysis in EcoRI endonuclease, we have studied stereospecific phosphorothioate (PS) or methylphosphonate (PMe) substitutions at the scissile phosphate GpAATTC or at the adjacent phosphate GApATTC in combination with molecular-dynamics simulations of the catalytic center with bound Mg2+. The results show the roles in catalysis of individual phosphoryl oxygens and of DNA distortion and suggest that a "crosstalk ring" in the complex couples recognition to catalysis and couples the two catalytic sites to each other.


Subject(s)
DNA/chemistry , Deoxyribonuclease EcoRI/chemistry , Adenine Nucleotides/chemistry , Base Sequence , Binding Sites , Catalysis , Catalytic Domain , DNA/metabolism , Deoxyribonuclease EcoRI/metabolism , Magnesium/chemistry , Models, Molecular , Nucleic Acid Conformation , Organophosphorus Compounds/chemistry , Oxygen/chemistry , Phosphates/chemistry , Substrate Specificity
18.
PLoS One ; 11(5): e0154726, 2016.
Article in English | MEDLINE | ID: mdl-27145078

ABSTRACT

BACKGROUND: The high frequency of mutations in the isocitrate dehydrogenase 1 (IDH1) gene in diffuse gliomas indicates its importance in the process of gliomagenesis. These mutations result in loss of the normal function and acquisition of the neomorphic activity converting α-ketoglutarate to 2-hydroxyglutarate. This potential oncometabolite may induce the epigenetic changes, resulting in the deregulated expression of numerous genes, including those related to the differentiation process or cell survivability. METHODS: Neural stem cells were derived from human induced pluripotent stem cells following embryoid body formation. Neural stem cells transduced with mutant IDH1R132H, empty vector, non-transduced and overexpressing IDH1WT controls were differentiated into astrocytes and neurons in culture. The neuronal and astrocytic differentiation was determined by morphology and expression of lineage specific markers (MAP2, Synapsin I and GFAP) as determined by real-time PCR and immunocytochemical staining. Apoptosis was evaluated by real-time observation of Caspase-3 activation and measurement of PARP cleavage by Western Blot. RESULTS: Compared with control groups, cells expressing IDH1R132H retained an undifferentiated state and lacked morphological changes following stimulated differentiation. The significant inhibitory effect of IDH1R132H on neuronal and astrocytic differentiation was confirmed by immunocytochemical staining for markers of neural stem cells. Additionally, real-time PCR indicated suppressed expression of lineage markers. High percentage of apoptotic cells was detected within IDH1R132H-positive neural stem cells population and their derivatives, if compared to normal neural stem cells and their derivatives. The analysis of PARP and Caspase-3 activity confirmed apoptosis sensitivity in mutant protein-expressing neural cells. CONCLUSIONS: Our study demonstrates that expression of IDH1R132H increases apoptosis susceptibility of neural stem cells and their derivatives. Robust apoptosis causes differentiation deficiency of IDH1R132H-expressing cells.


Subject(s)
Apoptosis/physiology , Cell Differentiation/physiology , Isocitrate Dehydrogenase/metabolism , Neural Stem Cells/metabolism , Astrocytes/metabolism , Biomarkers/metabolism , Caspase 3/metabolism , Cell Lineage/physiology , Cells, Cultured , Embryoid Bodies/metabolism , Glioma/metabolism , Humans , Induced Pluripotent Stem Cells/metabolism , Neurogenesis/physiology , Neurons/metabolism
19.
Oncotarget ; 7(22): 31907-25, 2016 May 31.
Article in English | MEDLINE | ID: mdl-27004406

ABSTRACT

Glioblastoma is the most common and malignant brain tumor, characterized by high cellular heterogeneity. About 50% of glioblastomas are positive for EGFR amplification, half of which express accompanying EGFR mutation, encoding truncated and constitutively active receptor termed EGFRvIII. Currently, no cell models suitable for development of EGFRvIII-targeting drugs exist, while the available ones lack the intratumoral heterogeneity or extrachromosomal nature of EGFRvIII.The reports regarding the biology of EGFRvIII expressed in the stable cell lines are often contradictory in observations and conclusions. In the present study, we use DK-MG cell line carrying endogenous non-modified EGFRvIII amplicons and derive a sub-line that is near depleted of amplicons, whilst remaining identical on the chromosomal level. By direct comparison of the two lines, we demonstrate positive effects of EGFRvIII on cell invasiveness and populational growth as a result of elevated cell survival but not proliferation rate. Investigation of the PI3K/Akt indicated no differences between the lines, whilst NFκB pathway was over-active in the line strongly expressing EGFRvIII, finding further supported by the effects of NFκB pathway specific inhibitors. Taken together, these results confirm the important role of EGFRvIII in intrinsic and extrinsic regulation of tumor behavior. Moreover, the proposed models are stable, making them suitable for research purposes as well as drug development process utilizing high throughput approach.


Subject(s)
Brain Neoplasms/enzymology , Drug Discovery/methods , ErbB Receptors/metabolism , Glioblastoma/enzymology , Antineoplastic Agents/pharmacology , Brain Neoplasms/drug therapy , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Cell Line, Tumor , Cell Movement , Cell Proliferation , Dose-Response Relationship, Drug , ErbB Receptors/antagonists & inhibitors , ErbB Receptors/genetics , Gene Expression Regulation, Enzymologic , Gene Expression Regulation, Neoplastic , Glioblastoma/drug therapy , Glioblastoma/genetics , Glioblastoma/pathology , High-Throughput Screening Assays , Humans , Neoplasm Invasiveness , Phenotype , Protein Kinase Inhibitors/pharmacology , Signal Transduction , Time Factors , Transfection , Tumor Cells, Cultured
20.
J Med Chem ; 48(17): 5504-8, 2005 Aug 25.
Article in English | MEDLINE | ID: mdl-16107149

ABSTRACT

The pyrimidine nucleoside beta-d-2'-deoxy-2'-fluoro-2'-C-methylcytidine (1) was designed as a hepatitis C virus RNA-dependent RNA polymerase (HCV RdRp) inhibitor. The title compound was obtained by a DAST fluorination of N(4)-benzoyl-1-(2-methyl-3,5-di-O-benzoyl-beta-d-arabinofuranosyl]cytosine to provide N(4)-benzoyl-1-[2-fluoro-2-methyl-3,5-di-O-benzoyl-beta-d-ribofuranosyl]cytosine. The protected 2'-C-methylcytidine was obtained as a byproduct from the DAST fluorination and allowed for the preparation of two biologically active compounds from a common precursor. Compound 1 and 2'-C-methylcytidine were assayed in a subgenomic HCV replicon assay system and found to be potent and selective inhibitors of HCV replication. Compound 1 shows increased inhibitory activity in the HCV replicon assay compared to 2'-C-methylcytidine and low cellular toxicity.


Subject(s)
Antiviral Agents/chemical synthesis , Deoxycytidine/analogs & derivatives , Hepacivirus/drug effects , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Crystallography, X-Ray , Deoxycytidine/chemical synthesis , Deoxycytidine/chemistry , Deoxycytidine/pharmacology , Drug Design , Hepacivirus/physiology , Molecular Structure , Structure-Activity Relationship , Virus Replication/drug effects
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