A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design

Cyclic nucleotide phosphodiesterases (PDEs) comprise a large family of enzymes that regulate a variety of cellular processes. We describe a family of potent PDE4 inhibitors discovered using an efficient method for scaffold-based drug design. This method involves an iterative approach starting with low-affinity screening of compounds followed by high-throughput cocrystallography to reveal the molecular basis underlying the activity of the newly identified compounds. Through detailed structural analysis of the interaction of the initially discovered pyrazole carboxylic ester scaffold with PDE4D using X-ray crystallography, we identified three sites of chemical substitution and designed small selective libraries of scaffold derivatives with modifications at these sites. A 4,000-fold increase in the potency of this PDE4 inhibitor was achieved after only two rounds of chemical synthesis and the structural analysis of seven pyrazole derivatives bound to PDE4B or PDE4D, revealing the robustness of this approach for identifying new inhibitors that can be further developed into drug candidates.

Asymmetric interaction between rod cyclic GMP phosphodiesterase gamma subunits and alphabeta subunits

Rod phosphodiesterase (PDE6) is the central effector enzyme in vertebrate visual transduction. Holo-PDE6 consists of two similar catalytic subunits (Palphabeta) and two identical inhibitory subunits (Pgamma). Palphabeta is the only heterodimer in the PDE superfamily, yet its significance for the function of PDE6 is poorly understood. An unequal interaction of Pgamma with Pbeta as compared with Palpha in the PDE6 complex has not been reported. We investigated the interaction interface between full-length Pgamma and Palphabeta, by differentiating Pgamma interaction with each individual Palphabeta subunit through radiolabel transfer from various positions throughout the entire Pgamma molecule. The efficiency of radiolabel transfer indicates that the close vicinity of serine 40 on Pgamma makes a major contribution to the interaction with Palphabeta. In addition, a striking asymmetry of interaction between the Pgamma polycationic region and the Palphabeta subunits was observed when the stoichiometry of Pgamma versus the Palphabeta dimer was below 2. Preferential photolabeling on Pbeta from Pgamma position 40 and on Palpha from position 30 increased while lowering the Pgamma/Palphabeta ratio, but diminished when the Pgamma/Palphabeta ratio was over 2. Our finding leads to the conclusion that two classes of Pgamma binding sites exist on Palphabeta, each composed of GAF domains in both Palpha and Pbeta, differing from the conventional models suggesting that each Pgamma binds only one of the Palphabeta catalytic subunits. This new model leads to insight into how the unique Palphabeta heterodimer contributes to the sophisticated regulation in visual transduction through interaction with Pgamma.

The power of vanadate in crystallographic investigations of phosphoryl transfer enzymes

The formation of transition state mimics of phosphoryl transfer reactions with the metal oxoanion vanadate is a powerful technique in macromolecular crystallography. The tendency of vanadate to form pentacovalent complexes exhibiting trigonal bipyramidal geometry makes this compound a close approximation of the transition state for such reactions. In many cases, vanadate complexes provide the most accurate visualization of the transition state that can be reasonably achieved. A survey of the Protein Data Bank reveals that a relatively small number of structures (39, representing 23 unique proteins) include vanadate, yet these structures represent four of the six E.C. categories of enzymes, and were obtained in crystals with pH values ranging from 5.0 to 7.8. Vanadate has additional advantages over other compounds such as aluminum fluoride, beryllium fluoride and nitrate used for visualization of transition state mimics in that vanadate readily forms covalent bonds with a variety of ligands and has produced a wider variety of transition state mimics. Given the hundreds of crystal structures that have been solved for phosphoryl transfer enzymes, it is surprising that vanadate has not been used more frequently for visualization of transition state analogs. We propose that an opportunity exists for vanadate to become a more commonly utilized component of the macromolecular crystallographer's toolbox.

Crystal structure of the catalytic fragment of human brain 2',3'-cyclic-nucleotide 3'-phosphodiesterase

2',3'-Cyclic-nucleotide 3'-phosphodiesterase (CNP), a member of the 2H phosphoesterase superfamily, is firmly bound to brain white matter and found mainly in the central nervous system of vertebrates, and it catalyzes the hydrolysis of 2',3'-cyclic nucleotide to produce 2'-nucleotide. Recent studies on CNP-knockout mice have revealed that the absence of CNP causes axonal swelling and neuronal degeneration. Here, the crystal structure of the catalytic fragment (CF) of human CNP (hCNP-CF) is solved at 1.8A resolution. It is an alpha+beta type structure consisting of three alpha-helices and nine beta-strands. The structural core of the molecule is comprised of two topologically equivalent three-stranded antiparallel beta-sheets that are related by a pseudo 2-fold symmetry. Each beta-sheet contains an H-X-T-X motif, which is strictly conserved among members of the 2H phosphoesterase superfamily. The phosphate ion is bound to the side-chains of His and Thr from each of the two motifs. Structural comparison of hCNP-CF with plant 1'',2''-cyclic nucleotide phosphodiesterase (CPDase) and bacterial 2'-5' RNA ligase reveals that the H-X-T-X motifs are structurally conserved among these enzymes, but the surface properties of the active site are quite different among the enzymes, reflecting the differences in their substrates. On the basis of the present crystal structure of the hCNP-CF/phosphate complex, the available structure of the CPDase/cyclic-nucleotide analogue complex, and the recent functional studies of rat CNP-CF, we propose a possible substrate-binding mode and catalytic mechanism of CNP, which employs the nucleophilic water molecule activated by His310. The proposed mechanism is basically equivalent to the second step of the well-accepted reaction mechanism of RNase A. Since the overall structure of hCNP-CF differs considerably from that of RNase A, it is likely that the similar active sites with two catalytic histidine residues in these enzymes arose through convergent evolution.

Structural chemoproteomics and drug discovery

Our laboratories have developed several technologies to accelerate drug discovery process on the basis of structural chemoproteomics. They include SPS technology for the efficient determination of protein structures, SCP technology for the rapid lead generation and SDF technology for the productive lead optimization. Using these technologies, we could determine many 3D structures of target proteins bound with biologically active chemicals including the structure of phosphodiesterase 5/Viagra complex and obtain highly potent compounds in animal models of obesity, diabetes, cancer and inflammation. In this paper, we will discuss concepts and applications of structural chemoproteomics for drug discovery.

Effects of BAY 41-2272, a soluble guanylate cyclase activator, on pulmonary vascular reactivity in the ovine fetus

Nitric oxide (NO)-cGMP signaling plays a critical role during the transition of the pulmonary circulation at birth. BAY 41-2272 is a novel NO-independent direct stimulator of soluble guanylate cyclase that causes vasodilation in systemic and local circulations. However, the hemodynamic effects of BAY 41-2272 have not been studied in the perinatal pulmonary circulation. We hypothesized that BAY 41-2272 causes potent and sustained fetal pulmonary vasodilation. We performed surgery on 14 fetal lambs (125-130 days gestation; term = 147 days) and placed catheters in the main pulmonary artery, aorta, and left atrium to measure pressures. An ultrasonic flow transducer was placed on the left pulmonary artery (LPA) to measure blood flow, and a catheter was placed in the LPA for drug infusion. Pulmonary vascular resistance (PVR) was calculated as pulmonary artery pressure minus left atrial pressure divided by LPA blood flow. BAY 41-2272 caused dose-related increases in pulmonary blood flow up to threefold above baseline and reduced PVR by 75% (P < 0.01). Prolonged infusion of BAY 41-2272 caused sustained pulmonary vasodilation throughout the 120-min infusion period. The pulmonary vasodilator effect of BAY 41-2272 was not attenuated by N(omega)-nitro-l-arginine, a NO synthase inhibitor. In addition, compared with sildenafil, a phosphodiesterase 5 inhibitor, the pulmonary vasodilator response to BAY 41-2272 was more prolonged. We conclude that BAY 41-2272 causes potent and sustained fetal pulmonary vasodilation independent of NO release. We speculate that BAY 41-2272 may have therapeutic potential for pulmonary hypertension associated with failure to circulatory adaptation at birth, especially in the setting of impaired NO production.

Real-space protein-model completion: an inverse-kinematics approach

Rapid protein-structure determination relies greatly on software that can automatically build a protein model into an experimental electron-density map. In favorable circumstances, various software systems are capable of building over 90% of the final model. However, completeness falls off rapidly with the resolution of the diffraction data. Manual completion of these partial models is usually feasible, but is time-consuming and prone to subjective interpretation. Except for the N- and C-termini of the chain, the end points of each missing fragment are known from the initial model. Hence, fitting fragments reduces to an inverse-kinematics problem. A method has been developed that combines fast inverse-kinematics algorithms with a real-space torsion-angle refinement procedure in a two-stage approach to fit missing main-chain fragments into the electron density between two anchor points. The first stage samples a large number of closing conformations, guided by the electron density. These candidates are ranked according to density fit. In a subsequent refinement stage, optimization steps are projected onto a carefully chosen subspace of conformation space to preserve rigid geometry and closure. Experimental results show that fitted fragments are in excellent agreement with the final refined structure for lengths of up to 12-15 residues in areas of weak or ambiguous electron density, even at medium to low resolution.

Characteristics of photoreceptor PDE (PDE6): similarities and differences to PDE5

Phosphodiesterase 6 (PDE6) is highly concentrated in the retina. It is most abundant in the internal membranes of retinal photoreceptors, where it reduces cytoplasmic levels of cyclic guanosine monophosphate (cGMP) in rod and cone outer segments in response to light. The rod PDE6 holoenzyme comprises alpha and beta catalytic subunits and two identical inhibitory gamma subunits. Each catalytic subunit contains three distinct globular domains corresponding to the catalytic domain and two GAF domains (responsible for allosteric cGMP binding). The PDE6 catalytic subunits resemble PDE5 in amino-acid sequence as well as in three-dimensional structure of the catalytic dimer; preference for cGMP over cyclic adenosine monophosphate (cAMP) as a substrate; and the ability to bind cGMP at the regulatory GAF domains. Most PDE5 inhibitors inhibit PDE6 with similar potency, and electroretinogram studies show modest effects of PDE5 inhibitors on visual function-an observation potentially important in designing PDE5-specific therapeutic agents.

Brown spiders and loxoscelism

Accidents caused by brown spiders (Loxosceles genus) are classically associated with dermonecrotic lesions and systemic manifestations including intravascular haemolysis, disseminated intravascular coagulation and acute renal failure. Systemic reactions occur in a minority of cases, but may be severe in some patients and occasionally fatal. The mechanisms by which Loxosceles venom exerts these noxious effects are currently under investigation. The venom contains several toxins, some of which have been well-characterised biochemically and biologically. The purpose of the present review is to describe some insights into loxoscelism obtained over the last ten years. The biology and epidemiology of the brown spider, the histopathology of envenomation and the immunogenicity of Loxosceles venom are reviewed, as are the clinical features, diagnosis and therapy of brown spider bites. The identification and characterisation of some toxins and the mechanism of induction of local and systemic lesions caused by brown spider venom are also discussed. Finally, the biotechnological application of some venom toxins are covered.

Trypanosome cyclic nucleotide phosphodiesterase 2B binds cAMP through its GAF-A domain

Trypanosoma brucei, the causative agent of sleeping sickness in humans and livestock, expresses at least three cAMP-specific class I phosphodiesterases (PDEs), all of which are essential for survival of the parasite. These PDEs have either one or two N-terminal GAF domains, which in other proteins function as signaling domains. However, neither the functional roles nor ligands for these domains in trypanosome PDEs are known. The present study shows that TbPDE2B, which contains two tandem GAF domains, binds cAMP with high affinity through its GAF-A domain. A purified recombinant N terminus + GAF-A domain binds cAMP with an affinity (Ki) of approximately 16 nM. It also binds cGMP but with a 15-fold lower affinity of approximately 275 nM. The TbPDE2B holoenzyme has a somewhat lower affinity (approximately 55 nM) for cAMP but a greatly lower affinity (approximately 10 microM) for cGMP. This suggests that both the selectivity and affinity for a ligand can be determined not only by the nature of the binding domain but also by the adjacent domains. Additionally, binding of cAMP to the holoenzyme showed positive cooperativity, with a Hill coefficient value of 1.75. However, binding of cGMP to the holoenzyme did not show any cooperativity, suggesting differences in the conformational changes caused by binding of these two cyclic nucleotides with the protein. Point mutation of a key predicted binding site residue (T317A) resulted in a complete loss of high affinity cAMP binding. This mutation increased the apparent Km of the mutant enzyme for substrate without altering the Vmax. A truncated catalytic domain construct of TbPDE2B also exhibited an increased Km, strongly suggesting that cAMP binding to the GAF-A domain can regulate TbPDE2B by allowing the full activity of the enzyme to be expressed. These properties of the GAF-A domain of TbPDE2B thus suggest that it could be a new target for anti-trypanosomal drugs.

Substrate-specifying determinants of the nucleotide pyrophosphatases/phosphodiesterases NPP1 and NPP2

The nucleotide pyrophosphatases/phosphodiesterases NPP1 and NPP2/autotaxin are structurally related eukaryotic ecto-enzymes, but display a very different substrate specificity. NPP1 releases nucleoside 5'-monophosphates from various nucleotides, whereas NPP2 mainly functions as a lysophospholipase D. We have used a domain-swapping approach to map substrate-specifying determinants of NPP1 and NPP2. The catalytic domain of NPP1 fused to the N- and C-terminal domains of NPP2 was hyperactive as a nucleotide phosphodiesterase, but did not show any lysophospholipase D activity. In contrast, chimaeras of the catalytic domain of NPP2 and the N- and/or C-terminal domains of NPP1 were completely inactive. These data indicate that the catalytic domain as well as both extremities of NPP2 contain lysophospholipid-specifying sequences. Within the catalytic domain of NPP1 and NPP2, we have mapped residues close to the catalytic site that determine the activities towards nucleotides and lysophospholipids. We also show that the conserved Gly/Phe-Xaa-Gly-Xaa-Xaa-Gly (G/FXGXXG) motif near the catalytic site is required for metal binding, but is not involved in substrate-specification. Our data suggest that the distinct activities of NPP1 and NPP2 stem from multiple differences throughout the polypeptide chain.

GGDEF and EAL domains inversely regulate cyclic di-GMP levels and transition from sessility to motility

Cyclic nucleotides represent second messenger molecules in all kingdoms of life. In bacteria, mass sequencing of genomes detected the highly abundant protein domains GGDEF and EAL. We show here that the GGDEF and EAL domains are involved in the turnover of cyclic-di-GMP (c-di-GMP) in vivo whereby the GGDEF domain stimulates c-di-GMP production and the EAL domain c-di-GMP degradation. Thus, most probably, GGDEF domains function as c-di-GMP cyclase and EAL domains as phosphdiesterase. We further show that, in the pathogenic organism Salmonella enterica serovar Typhimurium, the nosocomial pathogen Pseudomonas aeruginosa and the commensal species Escherichia coli, GGDEF and EAL domains mediate similar phenotypic changes related to the transition between sessility and motility. Thus, the data suggest that c-di-GMP is a novel global second messenger in bacteria the metabolism of which is controlled by GGDEF and EAL domain proteins.

Crystallization and preliminary X-ray crystallographic studies of human 2′,3′-cyclic nucleotide 3′-phosphodiesterase

The catalytic fragment of human 2',3'-cyclic nucleotide 3'-phosphodiesterase (hCNP-CF) has been crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 300 as the precipitating agent. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 44.39, b = 55.35, c = 78.76 A. There is one molecule per asymmetric unit. The crystals diffract to at least 1.8 A resolution using synchrotron radiation and are suitable for X-ray structure analysis at high resolution.

Characterization of an Escherichia coli elaC deletion mutant

The elaC gene of Escherichia coli encodes a binuclear zinc phosphodiesterase (ZiPD). ZiPD homologs from various species act as3' tRNA processing endoribonucleases, and although the homologous gene in Bacillus subtilis is essential for viability [EMBO J. 22(2003) 4534], the physiological function of E. coli ZiPD has remained enigmatic. In order to investigate the function of E. coli ZiPDwe generated and characterized an E. coli elaC deletion mutant. Surprisingly, the E. coli elaC deletion mutant was viable and had wild-type like growth properties. Microarray-based transcriptional analysis indicated expression of the E. coli elaC gene at basal levels during aerobic growth. The elaC gene deletion had no effect on the expression of genes coding for RNases or amino-acyl tRNA synthetases or any other gene among a total of > 1300 genes probed. 2D-PAGE analysis showed that the elaC mutation, like-wise, had no effect on the proteome. These results strengthen doubts about the involvement of E. coli ZiPD in tRNA maturation and suggest functional diversity within the ZiPD/ElaC1 protein family. In addition to these unexpected features of the E. coli elaC deletion mutant, a sequence comparison of ZiPD (ElaC1) proteins revealed specific regions for either enterobacterial or mammalian ZiPD (ElaC1) proteins.

Site-directed mutagenesis of human soluble calcium-activated nucleotidase 1 (hSCAN-1): identification of residues essential for enzyme activity and the Ca(2+)-induced conformational change

Human soluble calcium-activated nucleotidase 1 (hSCAN-1) is the human homologue of soluble apyrases found in blood-sucking insects. This family of nucleotidases is unrelated in sequence to more well-studied nucleotidases, and very little is known about the enzymatic mechanism. By multiple sequence alignment, eight regions that are highly conserved in the hSCAN-1 family were identified and named. To identify amino acids important for catalytic activity and enzyme specificity, seven point mutations were constructed, expressed in bacteria, refolded, purified, and characterized. Substitution of glutamic acid 130 with tyrosine resulted in dramatically increased nucleotidase activities, while mutagenesis of aspartic acid 151 to alanine and aspartic acid 84 to alanine completely abolished activity. Mutagenesis of arginine 133 and arginine 271 resulted in enzymes with very little nucleotidase activity. Mutagenesis of aspartic acid 175 to alanine and glycine 122 to glutamic acid had smaller negative effects on enzyme activities. Previously, our laboratory showed that calcium triggers a conformational change in hSCAN-1 necessary for nucleotidase activity. Here we show that several mutants (D84A, R133A, and D151A) that lost most of their activity were unable to undergo the conformational change induced by Ca(2+), as shown by Cibacron blue binding, limited proteolysis, and tryptophan fluorescence. We conclude that aspartic acid residues 84 and 151, as well as arginine residue 133, are essential for the Ca(2+)-induced conformational change that is necessary for enzyme activity. Aspartic acid 175 and glutamic acid 130 are important for determining substrate specificity. In addition, we show that Sr(2+), unlike Mg(2+) and other divalent cations, can substitute for Ca(2+) to induce the conformational change necessary for enzyme activity. However, Sr(2+) cannot substitute for Ca(2+) to support nucleotide hydrolysis, presumably because Sr(2+) cannot substitute for Ca(2+) in its second role as a nucleotide cosubstrate. The ramifications of our results on the interpretation of a recently published crystal structure are discussed. This information will facilitate future engineering of this enzyme designed to enhance its ability to hydrolyze ADP and thus increase its potential for therapeutic use in the treatment of pathological ischemic events triggered via activation of platelets by ADP.

Identification and characterization of plant glycerophosphodiester phosphodiesterase

GPX-PDE (glycerophosphodiester phosphodiesterase; EC 3.1.4.46) is a relatively poorly characterized enzyme that catalyses the hydrolysis of various glycerophosphodiesters (glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol, glycerophosphoserine and bis-glycerophosphoglycerol), releasing sn-glycerol 3-phosphate and the corresponding alcohol. In a previous study, we demonstrated the existence of a novel GPX-PDE in the cell walls and vacuoles of plant cells. Since no GPX-PDE had been identified in any plant organism, the purification of GPX-PDE from carrot cell walls was attempted. After extraction of cell wall proteins from carrot cell suspension cultures with CaCl2, GPX-PDE was purified up to 2700-fold using, successively, ammonium sulphate precipitation, gel filtration and concanavalin A-Sepharose. Internal sequence analysis of a 55 kDa protein identified in the extract following 2700-fold purification revealed strong similarity to the primary sequence of GLPQ, a bacterial GPX-PDE. To confirm the identity of plant GPX-PDE, an Arabidopsis thaliana cDNA similar to that encoding the bacterial GPX-PDE was cloned and overexpressed in a bacterial expression system, and was used to raise antibodies against the putative Arabidopsis thaliana GPX-PDE. Immunochemical assays performed on carrot cell wall proteins extracted by CaCl2 treatment showed a strong correlation between GPX-PDE activity and detection of the 55 kDa protein, validating the identity of the plant GPX-PDE. Finally, various properties of the purified enzyme were investigated. GPX-PDE is a multimeric enzyme, specific for glycerophosphodiesters, exhibiting a K(m) of 36 microM for glycerophosphocholine and active within a wide pH range (from 4 to 10). Since these properties are similar to those of GLPQ, the bacterial GPX-PDE, the similarities between plant and bacterial enzymes are also discussed.

Critical roles of Asp40 at the haem proximal side of haem-regulated phosphodiesterase from Escherichia coli in redox potential, auto-oxidation and catalytic control

In haem-regulated phosphodiesterase (PDE) from Escherichia coli (Ec DOS), haem is bound to the PAS domain, and the redox state of the haem iron regulates catalysis by the PDE domain. We generated mutants of Asp40, which forms a hydrogen bond with His77 (a proximal haem axial ligand) via two water molecules, and a salt bridge with Arg85 at the protein surface. The redox potential of haem was markedly increased from 67 mV vs. the standard hydrogen electrode in the wild-type enzyme to 95 mV and 114 mV in the Ala and Asn mutants, respectively. Additionally, the auto-oxidation rate of Ec DOS PAS was significantly increased from 0.0053 to 0.051 and 0.033 min(-1), respectively. Interestingly, the catalytic activities of the Asp40 mutants were abolished completely. Thus, Asp40 appears to play a critical role in the electronic structure of the haem iron and redox-dependent catalytic control of the PDE domain. In this report, we discuss the mechanism of catalytic control of Ec DOS, based on the physico-chemical characteristics of the Asp40 mutants.

Identification of Metal Binding Residues for the Binuclear Zinc Phosphodiesterase Reveals Identical Coordination as Glyoxalase II

Zinc phosphodiesterase (ZiPD) is a member of the metallo-beta-lactamase family with a binuclear zinc binding site. As an experimental attempt to identify the metal ligands of Escherichia coli ZiPD and to investigate their function in catalysis, we mutationally exchanged candidate metal coordinating residues and performed kinetic and X-ray absorption spectroscopic analysis of the mutant proteins. All mutants (H66E, H69A, H141A, D212A, D212C, H231A, H248A, and H270A) show significantly lower catalytic rates toward the substrate bis(p-nitrophenyl)phosphate. Substrate binding, represented by the kinetic value K', remains unchanged for six mutants, whereas it is increased 3-4-fold for H231A and H270A. Accordingly, these two residues are supposed to be involved in substrate binding, whereas the others are more important for catalytic turnover and thus are assumed to be involved in zinc ligation. Structural insight into the metal binding of D212 was gained by zinc K-edge extended X-ray absorption fine structure (EXAFS). The sulfur coordination number of the cysteine mutant was found to be 1, demonstrating binding to both zinc metals in a bridging mode. Taken together with two residues from a strictly conserved sequence region within the metallo-beta-lactamase family, the metal site of ZiPD is proposed with H64, H66, and H141 coordinating ZnA, D68, H69, and H248 coordinating ZnB, and D212 bridging both metals. Surprisingly, the same coordination sphere is found in glyoxalase II. This is further substantiated by comparable EXAFS spectra of both native enzymes. This is the first example of the same metal site in two members of the metallo-beta-lactamase domain proteins catalyzing different reactions. The kinetic analysis of mutants provides unexpected insights into the reaction mechanism of ZiPD.

Structural and Functional Characterization of a Novel Phosphodiesterase from Methanococcus jannaschii

Methanococcus jannaschii MJ0936 is a hypothetical protein of unknown function with over 50 homologs found in many bacteria and Archaea. To help define the molecular (biochemical and biophysical) function of MJ0936, we determined its crystal structure at 2.4-A resolution and performed a series of biochemical screens for catalytic activity. The overall fold of this single domain protein consists of a four-layered structure formed by two beta-sheets flanked by alpha-helices on both sides. The crystal structure suggested its biochemical function to be a nuclease, phosphatase, or nucleotidase, with a requirement for some metal ions. Crystallization in the presence of Ni(2+) or Mn(2+) produced a protein containing a binuclear metal center in the putative active site formed by a cluster of conserved residues. Analysis of MJ0936 against a panel of general enzymatic assays revealed catalytic activity toward bis-p-nitrophenyl phosphate, an indicator substrate for phosphodiesterases and nucleases. Significant activity was also found with two other phosphodiesterase substrates, thymidine 5'-monophosphate p-nitrophenyl ester and p-nitrophenylphosphorylcholine, but no activity was found for cAMP or cGMP. Phosphodiesterase activity of MJ0936 had an absolute requirement for divalent metal ions with Ni(2+) and Mn(2+) being most effective. Thus, our structural and enzymatic studies have identified the biochemical function of MJ0936 as that of a novel phosphodiesterase.

Sensing DNA damage by PARP-like fingers

PARP-like zinc fingers are protein modules, initially described as nick-sensors of poly(ADP-ribosyl)-polymerases (PARPs), which are found at the N-terminus of different DNA repair enzymes. I chose to study the role of PARP-like fingers in AtZDP, a 3' DNA phosphoesterase, which is the only known enzyme provided with three such finger domains. Here I show that PARP-like fingers can maintain AtZDP onto damaged DNA sites without interfering with its DNA end repair functions. Damage recognition by AtZDP fingers, in fact, relies on the presence of flexible joints within double-strand DNA and does not entail DNA ends. A single AtZDP finger is already capable of specific recognition. Two fingers strengthen the binding and extend the contacts on the bound DNA. A third finger further enhances the specific binding to damaged DNA sites. Unexpectedly, gaps but not nicks are bound by AtZDP fingers, suggesting that nicks on a naked DNA template do not provide enough flexibility for the recognition. Altogether these results indicate that AtZDP PARP-like fingers, might have a role in positioning the enzyme at sites of enhanced helical flexibility, where single-strand DNA breaks are present or are prone to occur.

Correlation of Structure and Function in Oligonuclear Zinc(II) Model Phosphatases

A series of pyrazolate-based dizinc(II) complexes has been synthesized and investigated as functional models for phosphoesterases, focusing on correlations between hydrolytic activity and molecular parameters of the bimetallic core. The Zn...Zn distance, the (bridging or nonbridging) position of the Zn-bound hydroxide nucleophile, and individual metal ion coordination numbers are controlled by the topology of the compartmental ligand scaffold. Species distributions of the various dizinc complexes in solution have been determined potentiometrically, and structures in the solid state have been elucidated by X-ray crystallography. The hydrolysis of bis(p-nitrophenyl)phosphate (BNPP) promoted by the dinuclear phosphoesterase model complexes has been investigated in DMSO/buffered water (1:1) at 50 degrees C as a function of complex concentration, substrate concentration, and pH. Coordination of the phosphodiester has been followed by ESI mass spectrometry, and bidentate binding could be verified crystallographically in two cases. Drastic differences in hydrolytic activity are observed and can be attributed to molecular properties. A significant decrease of the pK(a) of zinc-bound water is observed if the resulting hydroxide is involved in a strongly hydrogen-bonded intramolecular O(2)H(3) bridge, which can be even more pronounced than for a bridging hydroxide. Irrespective of the pK(a) of the Zn-bound water, a hydroxide in a bridging position evidently is a relatively poor nucleophile, while a nonbridging hydroxide position is more favorable for hydrolytic activity. Additionally, the metal array has to provide a sufficient number of coordination sites for activating both the substrate and the nucleophile, where phosphate diesters such as BNPP preferentially bind in a bidentate fashion, requiring a third site for water binding. Product inhibition of the active site by the liberated (p-nitrophenyl)phosphate is observed, and the product-inhibited complex could be characterized crystallographically. In that complex, the phosphate monoester is found to cap a rectangular array of four zinc ions composed of two bimetallic entities.

PDE2 inhibition by the PI3 kinase inhibitor LY294002 and analogues

Synthetic 2-morpholinochromones, including the known PI3-kinase inhibitor LY294002, have been evaluated in vitro as inhibitors of isolated human platelet phosphodiesterases. Inhibition of the cAMP-phosphodiesterases, PDE2 and PDE3 by LY294002 is reported for the first time. Preliminary screening across a range of 2-morpholinochromones has revealed structural features for optimised PDE2 inhibition.

Effects of Phosphodiesterase V Inhibition on Nitric Oxide-Mediated Relaxation Responses in Guinea Pig Trachea

In the present study, we aimed to evaluate the effects of PDE V inhibition on NO-mediated relaxation responses in isolated guinea pig trachea. Under the NANC conditions, tracheal preparations were contracted with histamine (100 microm/l). When contraction had reached a plateau, relaxation responses to electrical field stimulation (EFS, 60 V, 0.5 ms, 5-10 Hz) were determined before and after incubation of the tracheal ring with L-NAME (1 mmol/l), a NO synthase inhibitor. L-NAME significantly inhibited the relaxation responses and this inhibitory effect was reversed by L-arginine (1 mmol/l), a precursor of NO, but was not affected by D-arginine. In addition, cumulative application of the NO donors, 3-morpholino-sydnonimine (SIN-1) and sodium nitroprusside (SNP), caused concentration-dependent relaxation of tissues precontracted with histamine. The selective PDE type V inhibitor zaprinast at EC50 concentration (30 micromol/l) significantly potentiated EFS-induced NANC relaxations and relaxant responses to SIN-1 and SNP. In conclusion, these data support the hypothesis that NO is a mediator of NANC relaxations of guinea pig tracheal rings and PDE V inhibition potentiates NO-mediated relaxation.

Subcellular targeting and function of osteoblast nucleotide pyrophosphatase phosphodiesterase 1

The ectonucleoside pyrophosphatase phosphodiesterase 1 (NPP1/PC-1) is a member of the NPP enzyme family that is critical in regulating mineralization. In certain mineralizing sites of bone and cartilage, membrane-limited vesicles [matrix vesicles (MVs)] provide a sheltered internal environment for nucleation of calcium-containing crystals, including hydroxyapatite. MV formation occurs by budding of vesicles from the plasma membrane of mineralizing cells. The MVs are enriched in proteins that promote mineralization. Paradoxically, NPP1, the type II transmembrane protein that generates the potent hydroxyapatite crystal growth inhibitor inorganic pyrophosphate (PPi), is also enriched in MVs. Although osteoblasts express NPP1, NPP2, and NPP3, only NPP1 is enriched in MVs. Therefore, this study uses mineralizing human osteoblastic SaOS-2 cells, a panel of NPP1 mutants, and NPP1 chimeras with NPP3, which does not concentrate in MVs, to investigate how NPP1 preferentially targets to MVs. We demonstrated that a cytosolic dileucine motif (amino acids 49–50) was critical in localizing NPP1 to regions of the plasma membrane that budded off into MVs. Moreover, transposition of the NPP1 cytoplasmic dileucine motif and flanking region (AAASLLAP) to NPP3 conferred to NPP3 the ability to target to the plasma membrane and, subsequently, concentrate in MVs. Functionally, the cytosolic tail dileucine motif NPP1 mutants lost the ability to support MV PPiconcentrations and to suppress calcification. The results identify a specific targeting motif in the NPP1 cytosolic tail that delivers PPi-generating NPP activity to osteoblast MVs for control of calcification.