Potential of Pyridine Amphiphiles as Staphylococcal Nuclease Inhibitor.

The present study explores the potential of pyridine-based synthetic amphiphiles C1 and C2 having 4-carbon and 12-carbon hydrophobic tails, respectively, as staphylococcal nuclease inhibitors. UV-visible titration with calf-thymus DNA (CT-DNA) revealed a hypochromic shift in the absorbance bands of C1 and C2, whereas fluorescence titration indicated a reduction in the emission intensity of the monomer bands of the amphiphiles. Interaction of deoxyribonuclease I (DNase 1) and micrococcal nuclease (MNase) with C1 or C2 led to a decrease in the emission intensity of tryptophan at λ=345 nm along with an increase in the monomer emission intensity of C1 and C2 at λ=375 nm for DNase I and excimer emission intensity at λ=470 nm for both DNase I and MNase. Scatchard's analysis indicated superior interaction of C2 with DNase I. Circular dichroism spectroscopy revealed major changes in the secondary structures of both DNase I and MNase upon interaction with the amphiphiles. A solution-based nuclease assay in conjunction with gel electrophoresis indicated amphiphile-mediated protection against nuclease-directed DNA cleavage. Interestingly, C2 could render inhibition of nuclease present in the culture supernatant of Staphylococcus aureus MTCC 96, which highlights the therapeutic prospect of the amphiphile against S. aureus.

Inhibitors of Streptococcus pneumoniae surface endonuclease EndA discovered by high-throughput screening using a PicoGreen fluorescence assay.

The human commensal pathogen Streptococcus pneumoniae expresses a number of virulence factors that promote serious pneumococcal diseases, resulting in significant morbidity and mortality worldwide. These virulence factors may give S. pneumoniae the capacity to escape immune defenses, resist antimicrobial agents, or a combination of both. Virulence factors also present possible points of therapeutic intervention. The activities of the surface endonuclease, EndA, allow S. pneumoniae to establish invasive pneumococcal infection. EndA's role in DNA uptake during transformation contributes to gene transfer and genetic diversification. Moreover, EndA's nuclease activity degrades the DNA backbone of neutrophil extracellular traps (NETs), allowing pneumococcus to escape host immune responses. Given its potential impact on pneumococcal pathogenicity, EndA is an attractive target for novel antimicrobial therapy. Herein, we describe the development of a high-throughput screening assay for the discovery of nuclease inhibitors. Nuclease-mediated digestion of double-stranded DNA was assessed using fluorescence changes of the DNA dye ligand, PicoGreen. Under optimized conditions, the assay provided robust and reproducible activity data (Z'= 0.87) and was used to screen 4727 small molecules against an imidazole-rescued variant of EndA. In total, six small molecules were confirmed as novel EndA inhibitors, some of which may have utility as research tools for understanding pneumococcal pathogenesis and for drug discovery.

Inhibitor binding increases the mechanical stability of staphylococcal nuclease.

Staphylococcal nuclease (SNase) catalyzes the hydrolysis of DNA and RNA in a calcium-dependent fashion. We used AFM-based single-molecule force spectroscopy to investigate the mechanical stability of SNase alone and in its complex with an SNase inhibitor, deoxythymidine 3',5'-bisphosphate. We found that the enzyme unfolds in an all-or-none fashion at ∼26 pN. Upon binding to the inhibitor, the mechanical unfolding forces of the enzyme-inhibitor complex increase to ∼50 pN. This inhibitor-induced increase in the mechanical stability of the enzyme is consistent with the increased thermodynamical stability of the complex over that of SNase. Because of its strong mechanical response to inhibitor binding, SNase, a model protein folding system, offers a unique opportunity for studying the relationship between enzyme mechanics and catalysis.

Tudor domain proteins in protozoan parasites and characterization of Plasmodium falciparum tudor staphylococcal nuclease.

RNA-binding proteins play key roles in post-transcriptional regulation of gene expression. In eukaryotic cells, a multitude of RNA-binding proteins with several RNA-binding domains/motifs have been described. Here, we show the existence of two Tudor domain containing proteins, a survival of motor neuron (SMN)-like protein and a Staphylococcus aureus nuclease homologue referred to as TSN, in Plasmodium and other protozoan parasites. Activity analysis shows that Plasmodium falciparum TSN (PfTSN) possesses nuclease activity and Tudor domain is the RNA-binding domain. A specific inhibitor of micrococcal nucleases, 3',5'-deoxythymidine bisphosphate (pdTp) inhibits the nuclease as well as RNA-binding activities of the protein. PfTSN shows a predominant nuclear localization. Treatment of P. falciparum with pdTp, inhibited in vitro growth of both chloroquine-sensitive and chloroquine-resistant strains of P. falciparum, while a four fold concentration of pdTp did not have any significant effect on the mammalian cell line, Huh-7D12. Altogether, these results suggest that PfTSN is an essential enzyme in the parasite's life cycle.

Effects of Helichrysum italicum extract on growth and enzymatic activity of Staphylococcus aureus.

Helichrysum italicum G. Don (Compositae) is a shrub commonly found in dry, sandy and stony areas of Mediterranean regions. This plant is known for its anti-inflammatory, anti-allergic and antimicrobial activity. The aim of this study was to evaluate the effect of the diethyl ether extract on growth of Staphylococcus aureus (ATCC 6538P, MRSA and MSSA isolates) and the influence of subminimum inhibitory concentrations (subMICs) on some enzymes which are considered virulence factors. The results indicate that the H. italicum extract had an inhibitory effect on S. aureus strains reducing both their growth and some of the enzymes such as coagulase, DNAse, thermonuclease and lipase. Helichrysum italicum extract could be a novel antimicrobial agent, less toxic to human skin and tissues, worthy of further studies.

Inhibition of RNA polymerase III transcription by a ribosome-associated kinase activity.

Ribosomes prepared from somatic tissue of Xenopus laevis inhibit transcription by RNA polymerase III. This observation parallels an earlier report that a high speed fraction from activated egg extract, which is enrichedin ribosomes, inhibits RNA polymerase III activityand destabilizes putative transcription complexes assembled on oocyte 5S rRNA genes. Transcription of somatic- and oocyte-type 5S rRNA genes and a tRNA gene are all repressed in the present experiments. We find that 5S rRNA genes incubated in S150 extract prepared from immature oocytes exhibit an extensive DNase I protection pattern that is nearly identical to that of the ternary complex of TFIIIA and TFIIIC bound to a somatic 5S rRNA gene. The complexes formed in this extract are stable at concentrations of ribosomes that completely repress transcription, indicating that formation of the TFIII(A+C) complex is not the target of inhibition. Ribosomes taken through a high salt treatment no longer repress transcription of class III genes, establishing that the inhibition is due to an associated factor and not the particle itself. The inhibitory activity released from ribosomes is inactivated by treatment with proteinase K, but not micrococcal nuclease. Preincubation of ribosomes with a general protein kinase inhibitor, 6-dimethylaminopurine, eliminates repression of transcription. Western blot analysis demonstrates that p34(cdc2), which is known to mediate repression of transcription by RNA polymerase III, is present in these preparations of ribosomes and can be released from the particles upon extraction with high salt. These results establish that a kinase activity, possibly p34(cdc2), is the actual agent responsible for the observed inhibition of transcription by ribosomes.

Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: nuclease-H124L and its ternary complex with Ca2+ and thymidine-3',5'-bisphosphate.

The solution structures of staphylococcal nuclease (nuclease) H124L and its ternary complex, (nuclease-H124L).pdTp.Ca2+, were determined by ab initio dynamic simulated annealing using 1925 NOE, 119 phi, 20 chi 1 and 112 hydrogen bond constraints for the free protein, and 2003 NOE, 118 phi, 20 chi 1 and 114 hydrogen bond constraints for the ternary complex. In both cases, the final structures display only small deviations from idealized covalent geometry. In structured regions, the overall root-mean-square deviations from mean atomic coordinates are 0.46 (+/- 0.05) A and 0.41 (+/- 0.05) A for the backbone heavy atoms of nuclease and its ternary complex, respectively. The backbone conformations of residues in the loop formed by Arg81-Gly86, which is adjacent to the active site, are more precisely defined in the ternary complex than in unligated nuclease. Also, the protein side chains that show NOEs and evidence for hydrogen bonds to pdTp (Arg35, Lys84, Tyr85, Arg87, Tyr113, and Tyr115) are better defined in the ternary complex. As has been observed previously in the X-ray structures of nuclease-WT, the binding of pdTp causes the backbone of Tyr113 to change from an extended to a left-handed alpha-helical conformation. The NMR structures reported here were compared with available X-ray structures: nuclease-H124L [Truckses et al. (1996) Protein Sci., 5, 1907-1916] and the ternary complex of wild-type staphylococcal nuclease [Loll and Lattman (1989) Proteins Struct. Funct. Genet., 5, 183-201]. Overall, the solution structures of nuclease-H124L are consistent with these crystal structures, but small differences were observed between the structures in the solution and crystal environments. These included differences in the conformations of certain side chains, a reduction in the extent of helix 1 in solution, and many fewer hydrogen bonds involving side chains in solution.

Inhibition of NAD(H)/NADP(H)--requiring enzymes by aurintricarboxylic acid.

Aurintricarboxylic acid (ATA), an inhibitor of Ca(2+)-dependent endonuclease activity, is often used to implicate a role for increased intracellular calcium in mechanistic toxicology studies. We report here on the ability of ATA to inhibit the activity of several NAD(H)/NADP(H)-requiring enzymes (purified or cellular homogenates), including lactic dehydrogenase, alcohol dehydrogenase, cytochrome c reductase, ethoxycoumarin o-dealkylase, isocitric dehydrogenase, glutathione reductase and glucose-6-phosphate dehydrogenase. These results were compared with the ability of ATA to inhibit micrococcal nuclease and rat liver Ca(2+)-dependent endonuclease activity in similar incubations. With the exception of alcohol dehydrogenase, ATA was a potent inhibitor of each of the purified enzymes, with IC50s ranging from 0.5 to 82 microM. In cell homogenates, however, ATA was from 10 to 100-fold less potent at inhibiting these enzymes. When exogenous protein was added to purified enzyme incubations, the effect of ATA was similarly diminished. Our results demonstrate that ATA inhibits a wide range of NAD(H)/NADP(H)-requiring enzymes in in vitro incubations using purified enzymes, but that the inhibitory effects are markedly reduced in incubations which more closely resemble a cellular milieu.

X-ray crystal structures of staphylococcal nuclease complexed with the competitive inhibitor cobalt(II) and nucleotide.

Two crystal structures of ternary complexes of staphylococcal nuclease, cobalt(II), and the mononucleotide pdTp are reported. The first has been refined at 1.7 A to a crystallographic R value of 0.198; the second, determined from a crystal soaked for 9 months in a slightly different mother liquor than the first crystal, has been refined at 1.85 A to an R value of 0.174. In the first structure, the cobalt ion is displaced 1.94 A from the normal calcium position, and the active site is dominated by a salt bridge between Asp-21 and Lys-70 from a symmetry-related molecule in the crystal lattice. The Co2+ ion appears unable to displace this lysine; consequently, the metal is bound in a vestibular site adjacent to the calcium site. The metal-binding pocket in the second structure adopts a configuration similar to that of the calcium complex, with the cobalt ion binding only 0.36 A from the calcium position. However, an inner sphere water seen in the calcium structure is missing from this structure. The cobalt ion in the second structure appears to be loosely or transiently coordinated within the calcium binding pocket, as evidenced by the high value of its refined thermal factor. Loss of catalytic activity for cobalt(II)-substituted nuclease is perhaps due to its inability to bind this inner sphere water.

NMR docking of the competitive inhibitor thymidine 3',5'-diphosphate into the X-ray structure of staphylococcal nuclease.

In the X-ray structure of the ternary staphylococcal nuclease-Ca(2+)-3',5'-pdTp complex, the conformation of the bound inhibitor 3',5'-pdTp is distorted by Lys-70* and Lys-71* from an adjacent molecule of the enzyme in the crystal lattice (Loll, P. J. and Lattman, E. E. Proteins 5:183-201, 1989; Serpersu, E. H., Hibler, D. W., Gerlt, J. A., and Mildvan, A. S. Biochemistry 28:1539-1548, 1989). Since this interaction does not occur in solution, the NMR docking procedure has been used to correct this problem. Based on 8 Co(2+)-nucleus distances measured by paramagnetic effects on T1, and 9 measured and 45 lower limit interproton distances determined by 1D and 2D NOE studies of the ternary Ca2+ complex, the conformation of enzyme-bound 3',5'-pdTp is high-anti (chi = 58 +/- 10 degrees) with a C2' endo/O1' endo sugar pucker (delta = 143 +/- 2 degrees), (-) synclinal about the C3'-O3' bond (epsilon = 273 +/- 4 degrees), trans, gauche about the C4'-C5' bond (gamma = 301 +/- 29 degrees) and either (-) or (+) clinal about the C5'-O5' bond (beta = 92 +/- 8 degrees or 274 +/- 3 degrees). The structure of 3',5'-pdTp in the crystalline complex differs due to rotations about the C4'-C5' bond (gamma = 186 +/- 12 degrees, gauche, trans) and the C5'-O5' bond [beta = 136 +/- 10 degrees, (+) anticlinal]. The undistorted conformation of enzyme-bound metal-3',5'-pdTp determined by NMR was docked into the X-ray structure of the enzyme, using 19 intermolecular NOEs from ring proton resonances of Tyr-85, Tyr-113, and Tyr-115 to proton resonances of the inhibitor. van der Waals overlaps were then removed by energy minimization. Subsequent molecular dynamics and energy minimization produced no significant changes, indicating the structure to be in a global rather than in a local minimum. While the metal-coordinated 5'-phosphate of the NMR-docked structure of 3',5'-pdTp overlaps with that in the X-ray structure, and similarly receives bifunctional hydrogen bonds from both Arg-35 and Arg-87, the thymine, deoxyribose, and 3'-phosphate are significantly displaced from their positions in the X-ray structure, with the 3'-phosphate receiving hydrogen bonds from Lys-49 rather than from Lys-84 and Tyr-85. The repositioned thymine ring permits hydrogen bonding to the phenolic hydroxyl of Tyr-115.(ABSTRACT TRUNCATED AT 400 WORDS)

Introduction of a metal-dependent regulatory switch into an enzyme.

A cysteine has been introduced into the hydrophobic binding pocket of staphylococcal nuclease via oligonucleotide-directed mutagenesis. The L89C mutation does not significantly alter the catalytic activity or specificity of the nuclease yet provides a metal-dependent switch for regulating enzymatic activity. The L89C mutant can be inactivated by addition of mercuric or cupric salts and subsequently reactivated by addition of chelating agents. This work may provide a general strategy for regulating the catalytic activity of other enzymes or the binding affinity of proteins to DNA or other proteins.

The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A.

The structure of a complex of staphylococcal nuclease with Ca2+ and deoxythymidine 3',5'-bisphosphate (pdTp) has been refined by stereochemically restrained least-squares minimization to a crystallographic R value of 0.161 at 1.65 A resolution. The estimated root-mean-square (rms) error in the coordinates is 0.16 A. The final model comprises 1082 protein atoms, one calcium ion, the pdTp molecule, and 82 solvent water molecules; it displays an rms deviation from ideality of 0.017 A for bond distances and 1.8 degrees for bond angles. The mean distance between corresponding alpha carbons in the refined and unrefined structures is 0.6 A; we observe small but significant differences between the refined and unrefined models in the turn between residues 27 and 30, the loop between residues 44 and 50, the first helix, and the extended strand between residues 112 and 117 which forms part of the active site binding pocket. The details of the calcium liganding and solvent structure in the active site are clearly shown in the final electron density map. The structure of the catalytic site is consistent with the mechanism that has been proposed for this enzyme. However, we note that two lysines from a symmetry-related molecule in the crystal lattice may play an important role in determining the geometry of inhibitor binding, and that only one of the two required calcium ions is observed in the crystal structure; thus, caution is advised in extrapolating from the structure of the complex of enzyme and inhibitor to that of enzyme and substrate.

ATP as an alternative inhibitor of bacterial and endogenous nucleases and its effect on native chromatin compaction.

The studies reported here demonstrate that ATP may be used in lieu of EDTA to inhibit nuclease digestion of DNA and chromatin. Because ATP is a milder chelator than EDTA and is a biochemical common to the cellular microenvironment in vivo, critical studies of cellular processes that require native structure to be maintained are more feasible without the presence of strong chelators. During the digestion of chromatin into its components by nuclease treatment, ATP assures the retention of nucleoprotein compaction, particularly for large to intermediate-sized oligosomes (2400bp-1000bp in length). ATP used at a concentration of 3.3 mM appears to be somewhat better than EDTA, 1.0 mM, for minimizing degradation of nuclease-treated chromatin. However, termination of nuclease digestion of chromatin and minimization of further degradation by the addition of ATP to a concentration of 1.0 mM was almost equivalent to the addition of EDTA to a concentration of 1.0 mM. Slightly more degradation was observed for the latter condition. In addition, ATP can be used to inhibit endogenous nuclease activity when specific restriction enzymes are needed. Standard low ionic strength DNP, deoxyribonucleoprotein, and DNA electrophoresis of proteinized and deproteinized chromatin oligomers, respectively, indicated that ATP effectively inhibits staphylococcal nuclease. Low ionic strength nucleoprotein electrophoresis to resolve staphylococcal nuclease-digested chromatin indicates that as little as 10(-4) M EDTA can promote structural unfolding resulting in changes in apparent mobilities for chromatin oligomers 250 and 600 bp in length. Comparative digestion of chromatin with staphylococcal nuclease followed by reaction termination by ATP or EDTA showed that this observation was not merely the result of degradation due to inefficiency of ATP enzyme inhibition.

Effect of ionic strength on chain elongation in ADP-ribosylation of various nucleases.

With the use of a reconstituted poly(ADP-ribosyl)ating enzyme system and three purified nucleases, micrococcal nuclease (MN), bull seminal RNase (BS RNase) and Ca2+, Mg2+-dependent endonuclease (BS DNase), as model acceptor proteins for ADP-ribose, the effect of ionic strength on the modification reaction was examined in detail. When these three nucleases were extensively poly(ADP-ribosyl)ated in this system at a low ionic strength (5 mM Tris), they were all inhibited by about 80% and the chain length of the polymer covalently bound to the nucleases was 13 to 23 ADP-ribose units. The observed inhibition was markedly prevented by increasing the ionic strength in the reaction mixture with a concomitant decrease in the polymer size bound to the nucleases. The NaCl concentrations required for decreasing the extent of the inhibition to half of the maximum were calculated to be 20, 50, and 100 mM for MN, BS RNase, and BS DNase, respectively. These values are similar to the NaCl concentrations required for decreasing the average chain lengths of the polymer to half, suggesting that the length of polymer is closely correlated to the extent of inhibition of these nucleases. DNA-binding affinities of these nucleases, expressed in terms of the NaCl concentrations required for eluting the enzymes from DNA-cellulose, were 140, 280, and 340 mM for MN, BS RNase, and BS DNase, respectively. Considering that maintainance of a ternary complex of poly(ADP-ribose) synthetase, acceptor and DNA may be essential for the modification reaction, the relatively strong salt effect observed in the modification of MN may be explained by its low DNA-binding affinity.

Biochemical and clinical studies on human pancreatic deoxyribonuclease I inhibitor.

Human pancreatic Deoxyribonuclease I (DNase I), inhibitor was partially purified from duodenal juice of healthy subjects collected in the Pancreozymin-Secretin test, by a procedure which included ammonium sulfate fractionation, DEAE cellulose fractionation, Sepharose 4B affinity chromatography, and gel filtration. The final preparation inhibited DNase I only, and had no inhibitory activity on pancreatic RNase, and trypsin. The inhibitor had a molecular weight of approximately 40,000, as determined by gel filtration, and showed the same mobility as skeletal muscle actin on SDS gel electrophoresis. Then clinical studies were made on the DNase I inhibitor in duodenal juice obtained after administration of Pancreozymin and Secretin to patients with various pancreatic diseases. In patients with suspected chronic pancreatitis with whom the ordinary test, containing the assay of the total volume, amylase output and maximum bicarbonate concentration of duodenal juice had produced normal results, the DNase I inhibitor output was observed to be higher than that in control subjects. While it was lower in patients with confirmed chronic pancreatitis than in control subjects. There results imply that DNase I inhibitor output may be an indicator of the pancreatic inflammation state and be useful for the early detection of pancreatic diseases.

[Analysis of the activity of Micrococcus luteus endonucleases with respect to gamma-irradiated DNA]. / Analiz aktivnosti éndonukleaz kletok Micrococcus luteus po otnosheniiu K gamma-obluchennoi DNK.

Endonucleases from Micrococcus luteus that induce single-strand breaks in gamma-irradiated DNA have been separated chromatographycally into two groups. The first group involves two different enzymes: AP-endonuclease II (mol. weight 30 000) and AP, UV-endonuclease I (mol. weight 15 000) that recognize alkali-labile lesions in gamma-irradiated DNA and apurinic sites in DNA heated at 70 degrees C, pH 6.08 AP-endonuclease II in cooperation with DNA polymerase from M. luteus and T4 phage-induced polynucleotide ligase is capable of carrying out in vitro complete excision repair of alkali-labile lesins in gamma-irradiated DNA. The second group involves gamma-endonucleases X and Y that act on alkalistable gamma-ray lesions. gamma-endonucleases X and Y can be separated by chromatography on DEAE-cellulose but possess similar properties. Activity of gamma-endonucleases toward gamma-irradiated DNA is inhibited by only heavily UV-irradiated DNA (15 000 ergs/mm2). The data are consistent with the hypothesis that gamma-endonucleases are specific for thymine glycols (t' and tUV) in UV- and gamma-irradiated DNA.

Specificity of the antiviral agent calcium elenolate.

Calcium elenolate, an antiviral agent which inhibits reverse transcriptases, inhibits the growth of chicken embryo fibroblast cells, as well as Echerichia coli and Bacillus subtilis strains. The drug in vitro inhibits E. coli deoxyribonucleic acid (DNA) polymerase II and DNA polymerase III holoenzyme, as well as several unrelated enzymes. The usual DNA polymerase assay components, with the exception of spermidine, have no effect on the observed inhibition. Inhibition of DNA polymerase II by the drug appears to be due to a direct and irreversible effect on the enzyme. However, DNA synthesis in E. coli is no more susceptible to the drug than is the increase in cell mass. These results suggest that calcium elenolate is an inhibitor of rather low specificity.