Monitoring ssDNA Binding to the DnaB Helicase from Helicobacter pylori by Solid‐State NMR Spectroscopy

DnaB helicases are bacterial, ATP‐driven enzymes that unwind double‐stranded DNA during DNA replication. Herein, we study the sequential binding of the “non‐hydrolysable” ATP analogue AMP‐PNP and of single‐stranded (ss) DNA to the dodecameric DnaB helicase from Helicobacter pylori using solid‐state NMR. Phosphorus cross‐polarization experiments monitor the binding of AMP‐PNP and DNA to the helicase. ¹³C chemical‐shift perturbations (CSPs) are used to detect conformational changes in the protein upon binding. The helicase switches upon AMP‐PNP addition into a conformation apt for ssDNA binding, and AMP‐PNP is hydrolyzed and released upon binding of ssDNA. Our study sheds light on the conformational changes which are triggered by the interaction with AMP‐PNP and are needed for ssDNA binding of H. pylori DnaB in vitro. They also demonstrate the level of detail solid‐state NMR can provide for the characterization of protein–DNA interactions and the interplay with ATP or its analogues.     

Structural studies on Helicobacter pylori 3‐deoxy‐D‐manno‐2‐octulosonate‐8‐phosphate synthase using electrospray ionization mass spectrometry: a tetrameric complex composed of dimeric dimers

Helicobacter pylori 3‐deoxy‐D ‐manno‐2‐octulosonate‐8‐phosphate (KDO8P) synthase catalyzes the conversion of D ‐arabinose‐5‐phosphate (A5P) and phosphoenolpyruvate (PEP) to produce KDO8P and inorganic phosphate. Since this protein is absent in mammals, it might therefore be an attractive target for the development of new antibiotics. Unlike E. coli KDO8P synthase (class I), the H. pylori counterpart is a class II enzyme, where it requires a divalent transition metal ion for catalysis. Although the metal ions have been shown to be important for catalysis, their role in the structure is not understood. Using electrospray ionization mass spectrometry (ESI‐MS), the role of the metal ions in H. pylori KDO8P synthase has been investigated. This protein is found to be a tetramer in the gas phase but dissociates into the dimer with increasing declustering potential (DP2) suggesting an existence of a ‘structurally specific’ tetramer. An examination of mass spectra revealed that the tetrameric state of the Cd²⁺‐reconstituted enzyme is less stable than those of the Zn²⁺‐, Co²⁺‐ and Cu²⁺‐enzymes. The stoichiometry of metal binding to the protein depends on the nature of the metal ion. Taken together, our data suggest that divalent metal ions play an important role in the quaternary structure of the protein and the tetrameric state may be primarily responsible for catalysis. This study demonstrates the first structural characterization and stoichiometry of metal binding in class II KDO8P synthase using electrospray ionization quadrupole time‐of‐flight mass spectrometry under nondenaturing conditions. Copyright © 2009 John Wiley & Sons, Ltd.     

Heteronuclear 5‐Fluoroisatin Dimers: Design,Synthesis, and Evaluation of Their In Vitro Anti‐mycobacterial Activities

A series of novel heteronuclear 5‐fluoroisatin dimers 4a–j tethered through ethylene were designed, synthesized, and examined for their in vitro anti‐mycobacterial activities against Mycobacterium tuberculosis H37Rv and multi‐drug resistant tuberculosis (MDR‐TB). All hybrids exhibited potential anti‐mycobacterial activities against the tested two strains with minimum inhibitory concentration (MIC) in a range of 25 to 256 μg/mL. In particular, the heteronuclear 5‐fluoroisatin dimer 4a (MIC: 25 and 32 μg/mL) was most active against Mycobacterium tuberculosis H37Rv and MDR‐TB strains, which was twofold and greater than fourfold more potent than rifampicin (MIC: 64 μg/mL) and isoniazid (MIC: >128 μg/mL) against MDR‐TB, warrant further optimization.     

Application of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry for the study of Helicobacter pylori

The characteristics of matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry based investigation of extremely variable bacteria such as Helicobacter pylori were studied. H. pylori possesses a very high natural variability. Accurate tools for species identification and epidemiological characterization could help the scientific community to better understand the transmission pathways and virulence mechanisms of these bacteria. Seventeen clinical as well as two laboratory strains of H. pylori were analyzed by the MALDI Biotyper method for rapid species identification. Mass spectra collected were found containing 7–13 significant peaks per sample, and only six protein signals were identical for more than half of the strains. Four of them could be assigned to ribosomal proteins RL32, RL33, RL34, and RL36. The reproducible peak with m/z 6948 was identified as a histidine‐rich metal‐binding polypeptide by tandem mass spectrometry (MS/MS). In spite of the evident protein heterogeneity of H. pylori the mass spectra collected for a particular strain under several cultivations were highly reproducible. Moreover, all clinical strains were perfectly identified as H. pylori species through comparative analysis using the MALDI Biotyper software (Bruker Daltonics, Germany) by pattern matching against a database containing mass spectra from different microbial strains (n = 3287) including H. pylori 26695 and J99. The results of this study allow the conclusion that the MALDI‐TOF direct bacterial profiling is suited for H. pylori identification and could be supported by mass spectra fragmentation of the observed polypeptide if necessary. Copyright © 2010 John Wiley & Sons, Ltd.     

Design and Synthesis of High‐Affinity Dimeric Inhibitors Targeting the Interactions between Gephyrin and Inhibitory Neurotransmitter Receptors

Gephyrin is the central scaffolding protein for inhibitory neurotransmitter receptors in the brain. Here we describe the development of dimeric peptides that inhibit the interaction between gephyrin and these receptors, a process which is fundamental to numerous synaptic functions and diseases of the brain. We first identified receptor‐derived minimal gephyrin‐binding peptides that displayed exclusive binding towards native gephyrin from brain lysates. We then designed and synthesized a series of dimeric ligands, which led to a remarkable 1220‐fold enhancement of the gephyrin affinity (K_D=6.8 nM ). In X‐ray crystal structures we visualized the simultaneous dimer‐to‐dimer binding in atomic detail, revealing compound‐specific binding modes. Thus, we defined the molecular basis of the affinity‐enhancing effect of multivalent gephyrin inhibitors and provide conceptually novel compounds with therapeutic potential, which will allow further elucidation of the gephyrin–receptor interplay.     

Crystal structure of the flagellin protein FlaG from Helicobacter pylori

Flagella, comprising flagellin proteins, are essential virulence factors for Helicobacter pylori to colonize human stomach mucosa. The flagellin‐associated flaG operon of H. pylori consists of the flaG, fliD, and fliS genes under the control of a σ²⁸‐dependent promoter. The flaG gene is involved in chemotaxis and motility. We cloned, expressed, and purified the H. pylori flaG gene encoding the flagellin protein HpFlaG. Sequence alignment revealed that HpFlaG exhibits low sequence identity with other FlaG proteins. Overall, N‐terminal sequences of FlaG proteins are mostly divergent, and C‐terminal regions might be important for dimer interactions between protein subunits. Here, we report the crystal structure of the N‐terminal truncated protein (NT‐HpFlaG), as determined by multiwavelength anomalous dispersion at a resolution of 2.7 å. The overall structure of NT‐HpFlaG consists of two helices and three strands, folded into a palm‐like conformation. Two monomers strongly interact as a dimer by hydrophobic coiled‐coil interactions. Based on our structure, we suggest that the functional state of HpFlaG is as a dimer.     

Pyrido[1,2‐a]pyrimidin‐4‐ones: Ligand‐based Design,Synthesis, and Evaluation as an Anti‐inflammatory Agent

In the present study, a series of novel pyrido[1,2‐a]pyrimidin‐4‐one derivatives ( 1 – 45 ) were synthesized, characterized, and evaluated for their anti‐inflammatory activity. The structures of all newly synthesized compounds were confirmed by ¹H NMR, ¹³C NMR, mass spectroscopy, and C, H, and N analyses. Preliminary these newly synthesized compounds were evaluated for their in vitro cyclooxygenase (COX)‐2/COX‐1 inhibitory activity. The celecoxib, a COX‐2 inhibitor, was used as a reference standard drug. In this inhibitory study, compounds 42 , 43 , 44 , and 45 were found to have significant in vitro inhibitory profile as compared with the reference drug. These compounds were then subjected to their in vivo anti‐inflammatory assay by using carrageenan‐induced rat paw edema method in next level of screening. Later, these same compounds were tested for their ulcerogenic property. Based on these activity data, the compound 43 (in vitro COX‐2 activity—IC₅₀ = 0.4 μM, SI = 400, in vivo anti‐inflammatory activity—72% inhibition after 3 h, and 0.38%—Ulcer index) was emerged as most promising anti‐inflammatory agent with very low ulcerogenic action.     

Design,Synthesis, and in vitro Anti‐mycobacterial Activities of Propylene‐tethered Heteronuclear Bis‐isatin Derivatives

A series of novel propylene‐tethered heteronuclear bis‐isatin derivatives were designed, synthesized, and assessed for their in vitro and anti‐mycobacterial activities. All hybrids exhibited considerable antibacterial and anti‐mycobacterial activities against Mycobacterium tuberculosis H37Rv and multi‐drug‐resistant tuberculosis (MDR‐TB) with minimum inhibitory concentration (MIC) ranging from 16 to 256 μg/mL. In particular, the heteronuclear bis‐isatin 4i (MIC: 25 and 16 μg/mL) was most active against M. tuberculosis H₃₇Rv and MDR‐TB strains, which was fourfold and greater than eightfold more potent than the first‐line anti‐tubercular agents rifampicin (MIC: 64 μg/mL) and isoniazid (MIC: >128 μg/mL) against MDR‐TB, could act as a lead for further optimization.     

Synthesis and characterization of water‐soluble copper(II), cobalt(II) and zinc(II) complexes derived from 8‐hydroxyquinoline‐5‐sulphonic acid: DNA binding and cleavage studies

Three water‐soluble complexes, [Cu₂L₂Cl₂] ( 1 ), [CoL₂(im)₂] ( 2 ) and [ZnLClH₂O] ( 3 ) (HL = 8‐hydroxyquinoline‐5‐sulphonic acid; im = N ‐methylimidazole), were prepared and characterized using various spectral techniques. The DNA binding behaviour of complexes 1 – 3 was studied using UV–visible and circular dichroism (CD) spectra and cyclic voltammetry. All three complexes exhibit hypochromism but complexes 1 and 3 alone give a red shift of 4 nm with a significant binding constant of K _b = 2.1 × 10⁴ and 1.0 × 10⁴ M⁻¹, respectively, but complex 2 shows no red shift with lower K _b of 4.1 × 10³ M⁻¹. The voltammetric E _1/2 of complex 1 on interaction with herring sperm DNA shifts to a more positive potential, as expected, than complex 2 due to higher DNA affinity. Additionally, analysis of electrochemical data yields a value of K ₊/K ₂₊ greater than one suggesting that complex 1 binds to DNA through intercalation in the M(I) state. Evidently in CD spectral analysis, complex 1 exhibits a decrease in molar ellipticity with a red shift of 10 nm and a significant decrease in intensity compared to complexes 2 and 3 . This clearly indicates that complex 1 induces the B → A transition to a greater extent than 2 and 3 . Oxidative cleavage using circular plasmid pUC18 DNA with complex 1 was investigated using gel electrophoresis. Interestingly, complex 1 displays a strong DNA binding affinity and is efficient in cleaving DNA in the presence of H₂O₂ at pH = 8.0 at 37 °C.     

A ~35 kDa polypeptide from insect cells binds to yeast ACS like elements in the presence of ATP

Background  

The S. cerevisiae origin recognition complex binds to the ARS consensus sequence in an ATP dependent fashion. Recently, the yeast Cdc6 has been reported to have DNA binding activity. Conservation of replication proteins among different species strongly supports their functional similarity. Here we report the results of an investigation into the DNA binding activity of human Cdc6 protein. Cdc6 was expressed and purified from baculovirus infected Sf9 (Spodoptera frugiperda) insect cells as GST fusion protein (GST-Cdc6) and its DNA binding activity was tested.     

Synthesis,structure and in vitro anticancer,DNA binding and cleavage activity of palladium (II) complexes based on isatin thiosemicarbazone derivatives

Six novel palladium(II) complexes of a thiosemicarbazone Schiff base with isatin moiety (PdL1 to PdL6) were synthesized by the reaction of palladium(II) with the following: (Z )‐2‐(2‐oxoindolin‐3‐ylidene)‐N ‐phenylhydrazinecarbothioamide (L1H), (Z )‐2‐(5‐methyl‐2‐oxoindolin‐3‐ylidene)‐N ‐phenylhydrazinecarbothioamide (L2H), (Z )‐2‐(5‐fluoro‐2‐oxoindolin‐3‐ylidene)‐N ‐phenylhydrazinecarbothioamide (L3H), (Z )‐N ‐methyl‐2‐(5‐nitro‐2‐oxoindolin‐3‐ylidene)hydrazinecarbothioamide (L4H), (Z )‐N ‐methyl‐2‐(5‐methyl‐2‐oxoindolin‐3‐ylidene)hydrazinecarbothioamide (L5H) and (Z )‐N ‐ethyl‐2‐(5‐methyl‐2‐oxoindolin‐3‐ylidene)hydrazinecarbothioamide (L6H). The structures of these complexes were characterized using elemental analysis and infrared, UV–visible, ¹H NMR and mass spectroscopies. The structure of PdL5 was further characterized using single‐crystal X‐ray diffraction. The interaction of these complexes with calf thymus DNA was characterized with a high intrinsic binding constant (K _b = 5.78 × 10⁴ to 1.79 × 10⁶ M⁻¹), which reflected the intercalative activity of these complexes towards calf thymus DNA. This result was also confirmed from viscosity data. Electrophoresis studies revealed that complexes PdL1 to PdL6 could cleave DNA via an oxidative pathway in the presence of an external agent. Data obtained from an in vitro anti‐proliferative study clearly established the anticancer potency of these compounds against the human colorectal carcinoma cell line HCT 116.     

Crystal Structures of β‐Cyclodextrin Inclusion Complexes with 7‐Hydroxycoumarin and 4‐Hydroxycoumarin and Substituent Effects on Inclusion Geometry

Two inclusion complexes of β‐cyclodextrin‐7‐hydroxycoumarin ( 1 ) and β‐cyclodextrin‐4‐hydroxycoumarin ( 2 ) were prepared and their crystal structures were investigated by single crystal X‐ray crystallography under cryogenic condition. Both structures consist of stacks of face‐to‐face cyclodextrin dimers arranged in brickwork‐like pattern along the crystallographic a‐axis. For complex 1 , each of the two dimeric β‐cyclodextrins includes one 7‐hydroxycoumarin molecule that penetrates deeply into the cyclodextrin dimer and locates its lactonering at the center of the dimer cavity. For complex 2 , each cyclodextrin dimer accommodates three 4‐hydroxycoumarin molecules. One of them is sandwiched between two units of the cyclodextrin dimer, the other two are shallowly included in the cavities of the dimeric cyclodextrins respectively and protrude their lactone rings from the primary end of the cyclodextrin. The substituent effects of guest molecules on inclusion geometry of various coumarin molecules in β‐cyclodextrin were examined.     

New anticancer zinc(II) complexes comprising thiosemicarbazones of saturated ring: structure,DNA/protein binding,DNA cleavage,topoisomerase‐1 inhibition and anti‐proliferation studies

The reaction of the thiosemicarbazones (CH₂)₄C?NN(H)C(?S)NHR (R = H, Me) with zinc(II) acetate in methanolic solution proceeds readily under mild conditions to form stable mononuclear complexes Zn[(CH₂)₄C?NN?C(S)NHR]₂. DNA interaction studies show that the zinc(II) complexes bind to DNA via groove mode and exhibit efficient DNA cleavage activity in the presence of hydrogen peroxide. Also, the complexes display a binding affinity to bovine serum albumin protein with K_BSA values of ca 10⁵ M^?1. Topoisomerase catalytic inhibition studies suggest that both complexes are efficient topoisomerase‐I impeders. Furthermore, the anti‐proliferative effects of the two complexes on five human tumor cell lines (Caki‐2, MCF‐7, CaSki, NCI‐H322M and Co‐115) indicate that both complexes have the potential to act as effective anticancer drugs. Copyright © 2016 John Wiley & Sons, Ltd.     

DNA interaction,antimicrobial and molecular docking studies of biologically interesting Schiff base complexes incorporating 4‐formyl‐N,N‐dimethylaniline and propylenediamine

Four new transition metal complexes incorporating a Schiff base ligand derived from propylenediamine and 4‐formyl‐N ,N ‐dimethylaniline have been synthesized using transition metal salts. The characterization of the newly formed complexes was done from physicochemical parameters and using various techniques like ¹H NMR, ¹³C NMR, IR, UV, electron paramagnetic resonance and mass spectroscopies, powder X‐ray diffraction and magnetic susceptibility. All the complexes were found to be monomeric in nature with square planar geometry. X‐ray powder diffraction illustrates that the complexes have a crystalline nature. The interaction of metal complexes with calf thymus DNA was investigated using UV–visible absorption, viscosity measurements, cyclic voltammetry, emission spectroscopy and docking analysis. The results indicate that the Cu(II), Co(II), Ni(II) and Zn(II) complexes interact with DNA by intercalative binding mode with optimum intrinsic binding constants of 4.3 × 10⁴, 3.9 × 10⁴, 4.7 × 10⁴ and 3.7 × 10⁴ M⁻¹, respectively. These DNA binding results were rationalized using molecular docking in which the docked structures indicate that the metal complexes fit well into the A‐T rich region of target DNA through intercalation. The metal complexes exhibit an effective cleavage with pUC19 DNA by an oxidative cleavage mechanism. The synthesized ligand and the complexes were tested for their in vitro antimicrobial activity. The complexes show enhanced antifungal and antibacterial activities compared to the free ligand.     

Tetraethylene Glycol Tethered Heteronuclear Bis‐isatin Derivatives: Design,Synthesis, and In Vitro Anti‐mycobacterial Activities

A series of novel tetraethylene glycol tethered heteronuclear bis‐isatin derivatives 7a – l were designed, synthesized, and evaluated for their in vitro anti‐mycobacterial activities against Mycobacterium tuberculosis (MTB) H37Rv and multidrug‐resistant TB (MDR‐TB) as well as cytotoxicity in VERO cell line. All hybrids exhibited potential anti‐mycobacterial activities against MTB H37Rv and MDR‐TB, and acceptable cytotoxicity. Among them, the heteronuclear bis‐isatin 7l [minimum inhibitory concentration (MIC): 16 and 16 μg/mL] was found to be most active against MTB H37Rv and MDR‐TB strains, which was 2‐fold and >8‐fold, respectively, more potent than were the first‐line anti‐tubercular agents rifampicin (MIC: 32 μg/mL) and isoniazid (MIC: >128 μg/mL) against MDR‐TB, also demonstrated acceptable cytotoxicity profile (CC₅₀: 62.5 μg/mL), could act as a starting point for further optimization.     

Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout

By using (S)‐2‐amino‐1,3‐propanediol as a linker, thiazole orange (TO) was incorporated in a dimeric form into DNA. The green fluorescence (λ=530 nm) of the intrastrand TO dimer is quenched, whereas the interstrand TO dimer shows a characteristic redshifted orange emission (λ=585 nm). Steady‐state optical spectroscopic methods reveal that the TO dimer fluorescence is independent of the sequential base contexts. Time‐resolved pump–probe measurements and excitation spectra reveal the coexistence of conformations, including mainly stacked TO dimers and partially unstacked ones, which yield exciton and excimer contributions to the fluorescence, respectively. The helicity of the DNA framework distorts the excitonic coupling. In particular, the interstrand TO dimer could be regarded as an excitonically interacting base pair with fluorescence readout for DNA hybridization. Finally, the use of this fluorescent readout was representatively demonstrated in molecular beacons.     

Design,synthesis, pharmacological evaluation and DNA interaction studies of binuclear Pt(II) complexes with pyrazolo[1,5‐a]pyrimidine scaffold

Substituted pyrazolo[1,5‐a]pyrimidine ligands were synthesized by cyclization, using 3‐(thiophen‐2‐yl)‐1H‐pyrazol‐5‐amine with substituted enones (3‐phenyl‐1‐(pyridin‐2‐yl)prop‐2‐en‐1‐one) in presence of KOH and DMF as solvent to form cyclic aromatic compounds. The substituted pyrazolo[1,5‐a] pyrimidine based binuclear Pt^II complexes containing neutral tetradentated ligands have general formula [Pt₂(5a–5f)Cl₄], (where, (5a ‐5f) = pyrazolo[1,5‐a] pyrimidine ligand). This compounds were characterized by physicochemical and spectroscopic method like elemental analyses, UV‐Visible, FT‐IR, EDX, TGA, molar conductivity, magnetic susceptibility measurements, mass spectroscopy, ¹H and ¹³C NMR method. The square planar geometry was predicted by electronic spectral study. All Pt^II compounds were evaluated by antimicrobial assay, in vitro brine shrimp assay, in vivo cellular level bioassay using S. Pombe cells and anti‐tuberculosis study. LC₅₀ (50% lethal concentration) values of compounds are observed between 6.450 ‐ 102.07 μg/mL. UV‐vis absorption titration, competitive displacement assay, molecular docking and viscosity measurement were carried out to examine the binding type and binding strength of complexes. The binding studies suggest partial intercalative binding mode of the complexes and the observed binding constant (K_b) values are found in the order of 6d > 6b > 6c > 6a > 6e > 6 f. The anti‐proliferative cytotoxicity of the synthesized Pt^II complexes (6a‐6f) were tested against the HCT‐116 (Human Colorectal Carcinoma) cancer cell line.     

DNA interaction,cytotoxicity and molecular structure of cobalt complex of 4‐amino‐N‐(6‐chloropyridazin‐3‐yl)benzene sulfonamide in the presence of secondary ligand pyridine

Novel cobalt complex of 4‐amino‐N‐(6‐chloropyridazin‐3‐yl)benzene sulfonamide (sulfachloropyridazine) has been synthesized and characterized by elemental analysis, FT‐IR spectroscopy and magnetic susceptibility (VSM). Cobalt complex of Sulfachloropyridazine (Co‐SCP) crystallized in monoclinic space group P2₁/n with Z = 4. The structure is solved by direct method and refined to R = 0.099 for 4720 reflections with I ?4σ(I). The results of FT‐IR spectra suggest the binding of cobalt atom to the sulfonamide ligand which is in agreement with the crystal structure determination. In crystal structure, molecule is linked via, C‐H … π, C‐Cl … π and π … π intermolecular interactions. The computational studies like the optimization energy and root means square deviation compare with single crystal structure, frontier molecular orbital (Homo‐Lumo energy) and binding energy of the Co‐SCP has been carried out using DFT/B3LYP level of theory in gaseous phase. Hirshfeld surfaces and the 2D‐fingerprint analysis are performed to study the nature of interactions and their measurable contributions towards crystal packing. The interaction of the complex with DNA is investigated using viscosity measurement and absorption titration studies. The result shows the complex bind to DNA with intercalative mode with high DNA‐binding constant (K_b). Also, in vivo and in vitro cytotoxic studies are performed using S. pombe cells and brine shrimp lethality bioassay. DNA‐cleavage study shows better cleaving ability of the complex.