3′-5′ tRNA guanylyltransferase in bacteria

The identity of the histidine specific transfer RNA (tRNA^His) is largely determined by a unique guanosine residue at position −1. In eukaryotes and archaea, the tRNA^His guanylyltransferase (Thg1) catalyzes 3′-5′ addition of G to the 5′-terminus of tRNA^His. Here, we show that Thg1 also occurs in bacteria. We demonstrate in vitro Thg1 activity for recombinant enzymes from the two bacteria Bacillus thuringiensis and Myxococcus xanthus and provide a closer investigation of several archaeal Thg1. The reaction mechanism of prokaryotic Thg1 differs from eukaryotic enzymes, as it does not require ATP. Complementation of a yeast thg1 knockout strain with bacterial Thg1 verified in vivo activity and suggests a relaxed recognition of the discriminator base in bacteria.     

Structural and functional interaction of (±)-2-(N-tert-butylamino)-3′-iodo-4′-azidopropiophenone,a photoreactive bupropion derivative,with nicotinic acetylcholine receptors

The pharmacological properties of (±)-2-(N-tert-butylamino)-3′-iodo-4′-azidopropiophenone [(±)-SADU-3-72], a photoreactive analog of bupropion (BP), were characterized at different muscle nicotinic acetylcholine receptors (AChRs) by functional and structural approaches. Ca²⁺ influx results indicate that (±)-SADU-3-72 is 17- and 6-fold more potent than BP in inhibiting human (h) embryonic (hα1β1γδ) and adult (hα1β1εδ) muscle AChRs, respectively. (±)-SADU-3-72 binds with high affinity to the [³H]TCP site within the resting or desensitized Torpedo AChR ion channel, whereas BP has higher affinity for desensitized AChRs. Molecular docking results indicate that both SADU-3-72 enantiomers interact with the valine (position 13′) and serine (position 6′) rings. However, an additional domain, between the outer (position 20′) and valine rings, is observed in Torpedo AChR ion channels. Our results indicate that the azido group of (±)-SADU-3-72 may enhance its interaction with polar groups and the formation of hydrogen bonds at AChRs, thus supporting the observed higher potency and affinity of (±)-SADU-3-72 compared to BP. Collectively our results are consistent with a model where BP/SADU-3-72 and TCP bind to overlapping sites within the lumen of muscle AChR ion channels. Based on these results, we believe that (±)-SADU-3-72 is a promising photoprobe for mapping the BP binding site, especially within the resting AChR ion channel.     

Platinum(II) triammine antitumour complexes: structure-activity relationship with guanosine 5′-monophosphate (5′-GMP)

The multinuclear (¹H, ¹⁵N, ³¹P and ¹⁹⁵Pt) NMR spectroscopies, ES-MS and HPLC have been employed to investigate the structure-activity relationship for the reactions between guanosine 5′-monophosphate (5′-GMP) and the platinum(II)-triamine complexes of the general formulation cis-[Pt(NH₃)₂(Am)Cl]NO₃ (where Am represents a substituted pyridine). The order of reaction rate of the reactions was found to be: 3-phpy > 4-phpy > py > 4-mepy > 3-mepy > 2-mepy. The two basic factors, steric and electronic, were attributed to the order of the binding rate constants. A possible mechanism of the reaction of cis-[Pt(NH₃)₂(Am)Cl]⁺ with 5′-GMP suggested that the reactions proceed via direct nucleophilic attack and no loss of ammonia. cis-[Pt(NH₃)₂(Am)Cl]⁺ binds to the N7 nitrogen of the guanine residue of 5′-GMP to form a coordinate bond with the Pt metal centre. This mechanism is apparently different from that of cisplatin. The pK_a value of cis-[Pt(NH₃)₂(4-mepy)(H₂O)](NO₃)₂ (5.63) has been determined at 298 K by the use of distortionless enhancement by polarization transfer (DEPT) ¹⁵N NMR spectroscopy and compared to the pK_a value of cis-[PtCl(H₂O)(NH₃)₂]⁺.     

Synthesis and luminescence properties of [Pt{4′-(Np1)-trpy}(CCPh)]SbF6 and [Pt{4′-(Np1)-trpy}{CC(CH2)2CH3}]SbF6 [4′-(Np1)-trpy = 4′-(1-naphthyl)-2,2′:6′,2″-terpyridine]

The synthesis and characterisation of [Pt{4′-(Np1)-trpy}(CCPh)]SbF₆ (1) and [Pt{4′-(Np1)-trpy}{CC(CH₂)₂CH₃}]SbF₆ (2) [4′-(Np1)-trpy = 4′-(1-naphthyl)-2,2:6′,2′-terpyridine] are described. Complexes 1 and 2 exhibit unimolecular ³MLCT (MLCT = metal-to-ligand charge transfer) emission in acetonitrile and in a low concentration 77 K glass solution in butyronitrile. The high concentration glass emission as well as the emission in the solid state is from a ³MMLCT (MMLCT, metal-metal-to-ligand charge transfer) excited state, reflecting the presence of interactions in these media.     

Crystal structure of the novel neutral octahedral complex [(4′-(4-tbutylphenyl)-2,2′:6′,2″-terpyridine)Rh(Br)(acetonyl)2]

The synthesis and the crystal and molecular structure of a unique Rh(III) complex, [Rh^III(Br)(acetonyl)₂(4′-(4-tbutylphenyl)-2,2′:6′,2″-terpyridine)] (1) are described. The yellow crystals separate from the acetone solution of the starting complex [Rh(Br)(COD)]₂ and the ligand 4′-(4-tbutylphenyl)-2,2′:6′,2″-terpyridine after standing at room temperature for a prolonged period of time. The crystals are almost insoluble in all common organic solvents. The single-crystal X-ray structure determination shows that compound 1 is the first Rh-complex with a terdentate nitrogen ligand and two axially oriented, σ-bound acetonyl groups. DFT-calculations on a model complex without the substituent on the terpyridine ligand were carried out and agree very well with the X-ray results, confirming the constitution and geometry of the molecule.     

Repair efficiency of (5′S)-8,5′-cyclo-2′-deoxyguanosine and (5′S)-8,5′-cyclo-2′-deoxyadenosine depends on the complementary base

5′-R and 5′-S diastereoisomers of 8,5′-cyclo-2′-deoxyadenosine (cdA) and 8,5′-cyclo-2′-deoxyguanosine (cdG) containing a base-sugar covalent bond are formed by hydroxyl radicals. R-cdA and S-cdA are repaired by nucleotide excision repair (NER) in mammalian cellular extracts. Here, we have examined seven purified base excision repair enzymes for their ability to repair S-cdG or S-cdA. We could not detect either excision or binding of these enzymes on duplex oligonucleotide substrates containing these lesions. However, both lesions were repaired by HeLa cell extracts. Dual incisions by human NER on a 136-mer duplex generated 24–32 bp fragments. The time course of dual incisions were measured in comparison to cis-anti-B[a]P-N²-dG, an excellent substrate for human NER, which showed that cis-anti-B[a]P-N²-dG was repaired more efficiently than S-cdG, which, in turn, was repaired more efficiently than S-cdA. When NER efficiency of S-cdG with different complementary bases was investigated, the wobble pair S-cdG·dT was excised more efficiently than the S-cdG·dC pair that maintains nearly normal Watson-Crick base pairing. But S-cdG·dA mispair with no hydrogen bonds was excised less efficiently than the S-cdG·dC pair. Similar pattern was noted for S-cdA. The S-cdA·dC mispair was excised much more efficiently than the S-cdA·dT pair, whereas the S-cdA·dA pair was excised less efficiently. This result adds to complexity of human NER, which discriminates the damaged base pairs on the basis of multiple criteria.     

Enzymatic characteristics of two novel Myxococcus xanthus enzymes, PdeA and PdeB, displaying 3′,5′- and 2′,3′-cAMP phosphodiesterase, and phosphatase activities

Myxococcus xanthus PdeA and PdeB, enzymes homologous to class III 3′,5′-cyclic nucleotide phosphodiesterases, hydrolyzed 3′,5′- and 2′,3′-cyclic AMP (cAMP) to adenosine, and also demonstrated phosphatase activity toward nucleoside 5′-tri-, 5′-di-, 5′- and 3′-monophosphates with highest activities for nucleoside 5′-monophosphates. The substrate specificities of PdeA and PdeB show no similarity to that of any known cNMP phosphodiesterase, nucleotidase, or phosphatase. The enzyme activities of PdeA and PdeB were stimulated by 50 μM Mn²⁺ or Co²⁺. The K_m values of PdeA and PdeB for 3′,5′-cAMP, 2′,3′-cAMP, 5′-ATP, and 5′-AMP were in the low micromolar range (1.4-12.5  μM).     

A MLCT-switched photochromic copper(II) coordination polymer with 1,2-bis(2′-methyl-5′-(4″-pyridyl)-3′-thienyl)perfluorocyclopentene in crystalline phase

A novel Cu(II) coordination polymer with photochromic 1,2-bis(2′-methyl-5′-(4″-pyridyl)-3′-thienyl)perfluorocyclopentene (BM-4-PTP) was prepared and crystallographically characterized. Its photochromic behavior as well as magnetic property was investigated in crystalline phase. In complex [Cu(BM-4-PTP)Br₂(DMF)₂] (1), each copper atom is bridged by two N atoms of BM-4-PTP, two Br atoms from anions and two O atoms of DMF in an slightly distorted octahedral geometry. The basal planar center is in turn linked by bidentate ligand forming a 1-D polymeric chain. Free ligand showed typical spectral changes upon appropriate optical excitation, indicating the reversible photochromism in crystalline phase. Complex 1 occurred reversible photoisomerization not only through the π-π^∗ transition but also the MLCT transition in crystalline phase. On the other hand, the magnetic property of complex 1 has been investigated by means of ESR. The spectra slightly and reversibly changed in response to UV and visible light supporting the normal photoreactivity in crystalline phase.     

Reversible photochromism of novel silver(I) coordination complexes with 1,2-bis(2′-methyl-5′-(2″-pyridyl)-3′-thienyl)perfluorocyclopentene in crystalline phase

Three novel silver(I) complexes with 1,2-bis(2-methyl-5′-(2″-pyridyl)-3′-thienyl)perfluorocyclopentene (BM-2-PTP) were synthesized by the reaction of Ag(CF₃SO₃) or Ag(CF₃COO) with BM-2-PTP in benzene at different temperatures. The structures of these metal complexes were revealed by X-ray crystallographic analyses and the correlation between crystal structures and photochromic performance was discussed. In complexes 1 and 2, silver(I) is three-coordinated to two nitrogens from distinct ligand molecules as well as one oxygen from anions to form a 1-D polymeric structure. On the other hand, complex 3 contains two crystallographic independent Ag(I) with different coordination environments, and the adjacent BM-2-PTP molecules are connected by Ag-CF₃CO₂-Ag chains to afford a 1-D double chain structure. The difference in structures of three complexes shows the interesting anionic effect on coordination and the subtleness of crystal engineering. It is noted that complex 3 underwent reversible photochromic reaction in crystalline state despite the unfavorable framework to the rotation of thiophene groups.     

Synthesis and characterization of Os(II)(dpop′) (dpop′ = dipyrido(2,3-a;3′,2′-j)phenazine) complexes with 2,2′-bipyridine(bpy); 2,2′-bipyrimidine(bpm) and 2,3-bis(2-pyridyl)pyrazine(dpp)

New Os(II) complexes including [Os(dpop′)₂](PF₆)₂ (dpop′= dipyrido(2,3-a;3′,2′-j)phenazine) and a series of mixed ligand [Os(dpop′)(N-N)Cl]PF₆ (N-N = 2,2′-bipyridine(bpy); 2,2′-bipyrimidine(bpm) and 2,3-bis(2-pyridyl)pyrazine(dpp)) were synthesized. The Os dπ → dpop′ π^∗ MLCT transitions for [Os(dpop′)₂]²⁺ are observed at lower energy than for Os dπ → tpy π^∗ (tpy = 2,2′:6′,2″-terpyridine) and Os dπ → tppz π^∗ (tppz = 2,3,5,6-tetrakis(2-pyridyl)pyrazine) (The ligand abbreviations tpd, tpp and tpypz have also appeared in the literature for 2,3,5,6- tetrakis(2-pyridyl)pyrazine in addition to tppz.) MLCT transitions in the comparative [Os(tpy)₂]²⁺ and [Os(tppz)₂]²⁺ complexes. The Os dπ → dpop′ π^∗ MLCT transitions are observed at lower energy in mixed bidentate ligand N-N systems compared with [Os(dpop′)₂]²⁺. Cyclic voltammetry shows more positive osmium oxidation, and less negative ligand reduction potentials for [Os(dpop′)₂]²⁺ as compared to [Os(tpy)₂]²⁺ and [Os(tppz)₂]²⁺ complexes. The osmium oxidation potentials in mixed ligand [Os(dpop′)(N-N)Cl]⁺ complexes are at less positive potential than for the [Os(dpop′)₂]²⁺ ion. NMR results show different chemical shifts for ring protons either trans or cis to dpop′ in mixed ligand systems, and also show two geometrical isomers for the [Os(dpop′)(dpp)Cl]⁺ complex. The [Os(dpop′)(dpp)Cl]⁺ geometric isomer with the pyrazine ring of dpp trans to dpop′ is found more predominate by 1.0/0.7 over the isomer with the pyrazine ring of dpp cis to dpop′ and that inter-conversion of geometric isomers does not occur in room temperature solution on the NMR timescale.     

Synthesis and characterisation of bis(2,2′-bipyridine)(4-carboxy-4′-(pyrid-2-ylmethylamido)-2,2′-bipyridine)ruthenium(II) di(hexafluorophosphate): Comparison of spectroelectrochemical properties with related complexes

The new complex, [Ru^II(bpy)₂(4-HCOO-4′-pyCH₂ NHCO-bpy)](PF₆)₂ · 3H₂O (1), where 4-HCOO-4′-pyCH₂NHCO-bpy is 4-(carboxylic acid)-4′-pyrid-2-ylmethylamido-2,2′-bipyridine, has been synthesised from [Ru(bpy)₂(H₂dcbpy)](PF₆)₂ (H₂dcbpy is 4,4′-(dicarboxylic acid)-2,2′-bipyridine) and characterised by elemental analysis and spectroscopic methods. An X-ray crystal structure determination of the trihydrate of the [Ru(bpy)₂(H₂dcbpy)](PF₆)₂ precursor is reported, since it represented a different solvate to an existing structure. The structure shows a distorted octahedral arrangement of the ligands around the ruthenium(II) centre and is consistent with the carboxyl groups being protonated. A comparative study of the electrochemical and photophysical properties of [Ru^II(bpy)₂(4-HCOO-4′-pyCH₂NHCO-bpy)]²⁺ (1), [Ru(bpy)₂(H₂dcbpy)]²⁺ (2), [Ru(bpy)₃]²⁺ (3), [Ru(bpy)₂Cl₂] (4) and [Ru(bpy)₂Cl₂]⁺ (5) was then undertaken to determine their variation upon changing the ligands occupying two of the six ruthenium(II) coordination sites. The ruthenium(II) complexes exhibit intense ligand centred (LC) transition bands in the UV region, and broad MLCT bands in the visible region. The ruthenium(III) complex, 5, displayed overlapping LC bands in the UV region and a LMCT band in the visible. 1, 2 and 3 were found, via cyclic voltammetry at a glassy carbon electrode, to exhibit very positive reversible formal potentials of 996, 992 and 893 mV (versus Fc/Fc⁺) respectively for the Ru(III)/Ru(II) half-cell reaction. As expected the reversible potential derived from oxidation of 4 (−77 mV (versus Fc/Fc⁺)) was in excellent agreement with that found via reduction of 5 (−84 mV (versus Fc/Fc⁺)). Spectroelectrochemical experiments in an optically transparent thin-layer electrochemical cell configuration allowed UV-Vis spectra of the Ru(III) redox state to be obtained for 1, 2, 3 and 4 and also confirmed that 5 was the product of oxidative bulk electrolysis of 4. These spectrochemical measurements also confirmed that the oxidation of all Ru(II) complexes and reduction of the corresponding Ru(III) complex are fully reversible in both the chemical and electrochemical senses.     

Syntheses and characterization of nano-scale of the Mn complex with 4′-(4-pyridyl)-2,2′:6′,2″-terpyridine (pyterpy): The influence of the nano-structure upon catalytic properties

Nano-scale and single crystals of a new Mn^II complex, {[Mn(pyterpy)(H₂O)(NCS)_1.88Cl_0.12] · DMF} (1) [pyterpy = 4′-(4-pyridyl)-2,2′:6′,2″-terpyridine] have been synthesized by the reaction of pyterpy and mixtures of manganese(II) acetate and potassium thiocyanate as well as potassium chloride using sonochemical and heat gradient methods, respectively. The nano-structure was characterized by IR spectroscopy and scanning electron microscopy (SEM), and the structure of compound 1 was determined by single-crystal X-ray diffraction. Thermal stability and catalytic properties of nanoparticles and single crystalline samples of compound 1 were studied and are compared with each other.     

4,4′-Bis(tert-butyl)-2,2′-bipyridinedichlorometal(II) - Synthesis, structure and EPR spectroscopy

Due to the better solubility of the 4,4′-substituted bipyridine ligand a series of 4,4′-bis(tert-butyl)-2,2′-bipyridinedichlorometal(II) complexes, [M(tbbpy)Cl₂], with M = Cu, Ni, Zn, Pd, Pt was synthesised and characterised. The blue copper complex 4,4′-bis(tert-butyl)-2,2′-bipyridinedichlorocopper(II) was isolated in two different polymorphic forms, as prisms 1 with a solvent inclusion and solvent-free as needles 2. Both structures were determined by X-ray structure analysis. They crystallise in the monoclinic space group P2₁/c with four molecules in the unit cell, but with different unit cells and packing motifs. Whereas in the prisms 1, with the unit cell parameters a = 12.1613(12), b = 10.6363(7), c = 16.3074(15) Å, β = 94.446(8)°, the packing is dominated by intra- and intermolecular hydrogen bonds, in the needles 2, with a = 7.738(1), b = 18. 333(2), c = 13.291(3) Å, β = 97.512(15)°, only intramolecular hydrogen bonds appear and the complex molecules are arranged in columns which are stabilised by π-π-stacking interactions. In both complexes the copper has a tetrahedrally distorted coordination sphere. These copper complexes were also studied by EPR spectroscopy in solution, as frozen glass and diamagnetically diluted powder with the analogue [Pd(tbbpy)Cl₂] as host lattice.     

Regioselective synthesis of novel 3-alkoxy (phenyl) thiophosphorylamido-2-(per-O-acetylglycosyl-1′-imino)thiazolidine-4-one derivatives from O-alkyl N-glycosyl(thiosemicarbazido)phosphonothioates

A series of 3-alkoxy(phenyl)thiophosphorylamido-2-(per-O-acetylglycosyl-1′-imino)thiazolidine-4-one derivatives were prepared by the reaction of 1-alkoxy(phenyl)thiophosphoryl-4-(per-O-acetylglycosyl) thiosemicarbazides with ethyl bromoacetate. ¹H/¹³C HMBC measurements corroborated by X-ray crystallographic results revealed the exclusive regioselectivity of these ring closures toward the N-2 position of the thiosemicarbazide moiety. The bioactivity data of 3a-k suggest that the thiazolidine-4-one ring is critical for the herbicidal and fungicidal activities.     

The Henry reaction of (1R)-(1,4:3,6-dianhydro-d-mannitol-2-yl)-1,4:3,6-dianhydro-d-fructose 5,5′-dinitrate. Different reactive features of nitromethane to nitroethane

Henry reactions of a novel higher sugar derivative, (1R)-(1,4:3,6-dianhydro-d-mannitol-2-yl)-1,4:3,6-dianhydro-d-fructose 5,5′-dinitrate (Alternate nomenclature: (1R)-(isomannid-2-yl)-1,4:3,6-dianhydro-d-fructose 5,5′-dinitrate), with nitromethane and nitroethane were studied. The kinetic and thermodynamic reactions with nitromethane under different conditions were carried out to afford (2S)- and (2R)-β-nitroalcohols, respectively. But when using nitroethane the reaction gave a (2S)-β-nitroalcohol with an inverted configuration at vicinal carbon C-1. Two stereogenic centers were generated, and one was altered in the reaction.     

Human Tudor staphylococcal nuclease (Tudor-SN) protein modulates the kinetics of AGTR1-3′UTR granule formation

Human Tudor staphylococcal nuclease (Tudor-SN) interacts with the G3BP protein and is recruited into stress granules (SGs), the main type of discrete RNA-containing cytoplasmic foci structure that is formed under stress conditions. Here, we further demonstrate that Tudor-SN binds and co-localizes with AGTR1-3′UTR (3′-untranslated region of angiotensin II receptor, type 1 mRNA) into SG. Tudor-SN plays an important role in the assembly of AGTR1-3′UTR granules. Moreover, endogenous Tudor-SN knockdown can decrease the recovery kinetics of AGTR1-3′UTR granules. Collectively, our data indicate that Tudor-SN modulates the kinetics of AGTR1-3′UTR granule formation, which provides an additional biological role of Tudor-SN in RNA metabolism during stress.     

Identification and quantification of (5′R)- and (5′S)-8,5′-cyclo-2′-deoxyadenosines in human urine as putative biomarkers of oxidatively induced damage to DNA

Biomarkers of oxidatively induced DNA damage are of great interest and can potentially be used for the early detection of disease, monitoring the progression of disease and determining the efficacy of therapy. The present work deals with the measurement in human urine of (5′R)-8,5′-cyclo-2′-deoxyadenosine (R-cdA) and (5′S)-8,5′-cyclo-2′-deoxyadenosine (S-cdA). These modified nucleosides had hitherto not been considered or investigated to be present in urine as possible biomarkers of oxidatively induced DNA damage. Urine samples were collected from volunteers, purified and analyzed by LC-MS/MS with isotope-dilution. R-cdA and S-cdA were detected in urine and quantified. Creatinine levels were also measured. In addition, we measured 8-hydroxy-2′-deoxyguanosine that is commonly used as a biomarker. This study shows, for the first time, that R-cdA and S-cdA exist in human urine and can be identified and quantified by LC-MS/MS. We propose that R-cdA and S-cdA may be well-suited biomarkers for disease processes such as carcinogenesis.     

Coordination properties of 3′,5′-cyclic adenosine monophosphate towards copper(II) ions

The metal binding ability of 3′,5′-cyclic adenosine monophosphate (3′,5′-cAMP) molecule using copper(II) ion, as an example of biologically available divalent metal ion, was investigated by potentiometry, EPR and differential spectroscopy (UV-Vis, CD). One complex with stoichiometry Cu(3′,5′-cAMP)⁺ was found, where Cu(II) ion is bound by N-7 nitrogen of adenine moiety.     

Non-covalent interactions between cations in the crystal structure of [Pt{4′-(p-tolyl)trpy}Cl]SbF6, where trpy is 2,2′:6′,2″-terpyridine, underpin the salt’s complex solid-state luminescence spectrum

The synthesis and characterization of [Pt{4′-(p-tolyl)trpy}Cl]SbF₆ is described where trpy is 2,2′:6′,2″-terpyridine. A single crystal X-ray structure determination at 100 K shows that the cations are stacked in columns that comprise cations arranged in a staircase motif. Successive cations within a column are linked by π(trpy)-π(phenyl) stabilizing interactions; and each cation in one column is linked to a cation in an adjacent column by a weakly stabilizing Pt···Pt interaction. The Pt···Pt distance is 3.434(1) Å. The metrics governing non-covalent interactions between [Pt{4′-(aryl)trpy}Cl]⁺ cations have been analyzed for the present structure and related structures in the CSD (Cambridge Structural Database). Cation dimers cluster into three distinct groups based on their lateral shifts and, to a lesser extent, the angular parameters governing their relative displacements; the dominant grouping exhibits Pt···Pt and π(trpy)-π(trpy) stabilizing interactions. An emission spectrum recorded at 77 K on a solid sample of the compound is best interpreted as arising from the decay of three photoexcited states: a ³MLCT (MLCT = metal-to-ligand charge transfer) state; a ³MMLCT (MMLCT = metal-metal-to-ligand charge transfer) state, and an excimeric ³π-π^∗ state.