Active site similarity between human and <Emphasis Type="Italic">Plasmodium falciparum</Emphasis> phosphodiesterases: considerations for antimalarial drug design

Abstract  

The similarity between Plasmodium falciparum phosphodiesterase enzymes (PfPDEs) and their human counterparts have been examined and human PDE9A was found to be a suitable template for the construction of homology models for each of the four PfPDE isoforms. In contrast, the architecture of the active sites of each model was most similar to human PDE1. Molecular docking was able to model cyclic guanosine monophosphate (cGMP) substrate binding in each case but a docking mode supporting cyclic adenosine monophosphate (cAMP) binding could not be found. Anticipating the potential of PfPDE inhibitors as anti-malarial drugs, a range of reported PDE inhibitors including zaprinast and sildenafil were docked into the model of PfPDEα. The results were consistent with their reported biological activities, and the potential of PDE1/9 inhibitor analogues was also supported by docking.     

The central proline rich region of POB1/REPS2 plays a regulatory role in epidermal growth factor receptor endocytosis by binding to 14-3-3 and SH3 domain-containing proteins

Background  

The human POB1/REPS2 (Partner of RalBP1) protein is highly conserved in mammals where it has been suggested to function as a molecular scaffold recruiting proteins involved in vesicular traffic and linking them to the actin cytoskeleton remodeling machinery. More recently POB1/REPS2 was found highly expressed in androgen-dependent prostate cancer cell lines, while one of its isoforms (isoform 2) is down regulated during prostate cancer progression.     

Adaptation of cAMP signaling system in SH-SY5Y neuroblastoma cells following expression of a constitutively active stimulatory G protein alpha, Q227L Gsalpha

Heterotrimeric GTP-binding proteins (G protein) are known to participate in the transduction of signals from ligand activated receptors to effector molecules to elicit cellular responses. Sustained activation of cAMP-G protein signaling system by agonist results in desensitization of the pathway at receptor levels, however it is not clear whether such receptor responses induce other changes in post-receptor signaling path that are associated with maintenance of AMP levels, i.e. cAMP-forming adenylate cyclase (AC), cAMP-degrading cyclic nucleotide phosphodiesterase (PDE) and cAMP-dependent protein kinase (PKA). Experiments were performed to determine the expression of AC, PDE, and PKA isoforms in SH-SY5Y neuroblastoma cells, in which cAMP system was activated by expressing a constitutively activated mutant of stimulatory G protein (Q227L Gsalpha). Expression of ACI mRNA was increased, but levels of ACVIII and ACIX mRNA were decreased. All of the 4 expressed isoforms of PDE (PDE1C, PDE2, PDE 4A, and PDE4B) were increased in mRNA expression; the levels of PKA RIalpha, RIbeta, and RIIbeta were increased moderately, however, those of RIIalpha and Calpha were increased remarkably. The activities of AC, PDE and PKA were also increased in the SH-SY5Y cells expressing Q227L Gsalpha. The similar changes in expression and activity of AC, PDE and PKA were observed in the SH-SY5Y cells treated with dbcAMP for 6 days. Consequently, it is concluded that the cAMP system adapts at the post-receptor level to a sustained activation of the system by differential expression of the isoforms of AC, PDE, and PKA in SH-SY5Y neuroblastoma. We also showed that an increase in cellular cAMP concentration might mediate the observed changes in the cAMP system.     

Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and proteome array screening

Background  

The mitotic exit network (MEN) is a group of proteins that form a signaling cascade that is essential for cells to exit mitosis in Saccharomyces cerevisiae. The MEN has also been implicated in playing a role in cytokinesis. Two components of this signaling pathway are the protein kinase Dbf2 and its binding partner essential for its kinase activity, Mob1. The components of MEN that act upstream of Dbf2-Mob1 have been characterized, but physiological substrates for Dbf2-Mob1 have yet to be identified.     

The protein kinase DYRK1A phosphorylates the splicing factor SF3b1/SAP155 at Thr434, a novel in vivo phosphorylation site

Background  

The U2 small nuclear ribonucleoprotein particle (snRNP) component SF3b1/SAP155 is the only spliceosomal protein known to be phosphorylated concomitant with splicing catalysis. DYRK1A is a nuclear protein kinase that has been localized to the splicing factor compartment. Here we describe the identification of DYRK1A as a protein kinase that phosphorylates SF3b1in vitro and in cultivated cells.     

Aberrant expression of signaling-related proteins 14-3-3 gamma and RACK1 in fetal Down syndrome brain (trisomy 21)

Although Down Syndrome (DS, trisomy 21) is the most frequent isolated cause of mental retardation, information on brain protein expression and in particular protein expression of signaling-related proteins is limited. Impaired signaling in DS involving different signaling systems has been proposed and the availability of fetal brain along with recent proteome technologies unambiguously identifying individual brain proteins made us study individual signaling factors in the brain. We studied fetal brain cortex of controls (n = 7) and DS (n = 9) from early second trimester of gestation by two-dimensional gel electrophoresis with subsequent matrix-assisted laser/desorption ionization (MALDI) identification followed by quantification with specific software. Four 14-3-3 protein isoforms, mitogen-activated protein kinase 1, receptor for activited kinase 1 (RACK1), constitutive photomorphogenesis (COP9) complex subunit 4 and cAMP-dependent protein kinase type II have been identified. Quantification showed that protein 14-3-3 gamma (means +/- standard deviation of controls: 10.18+/-2.30 and of DS 4.20+/-1.19) and two spots assigned to RACK1 (controls spot 1: 4.15+/-2.45 and DS 1.95+/-0.93; controls spot 2: 5.08+/-2.4 vs. DS: 2.56+/-1.19) were significantly decreased in DS cortex. Reduced 14-3-3 gamma may represent impaired neuronal differentiation, synaptic plasticity and impaired signaling by PKC and Raf while decreased RACK1 (anchoring protein receptor for activated C-kinase) may reflect or generate deranged beta-II- protein kinease C (PKC) function with the putative biological meaning of aberrant migration and neuritic outgrowth in DS early in life.     

Identification of sites phosphorylated by the vaccinia virus B1R kinase in viral protein H5R

Background  

Vaccinia virus gene B1R encodes a serine/threonine protein kinase. In vitro this protein kinase phosphorylates ribosomal proteins Sa and S2 and vaccinia virus protein H5R, proteins that become phosphorylated during infection. Nothing is known about the sites phosphorylated on these proteins or the general substrate specificity of the kinase. The work described is the first to address these questions.     

Anti-cancer activity of novel dibenzo[b,f]azepine tethered isoxazoline derivatives

Background  

Nef is an HIV-1 accessory protein essential for viral replication and AIDS progression. Nef interacts with a multitude of host cell signaling partners, including members of the Src kinase family. Nef preferentially activates Hck, a Src-family kinase (SFK) strongly expressed in macrophages and other HIV target cells, by binding to its regulatory SH3 domain. Recently, we identified a series of kinase inhibitors that preferentially inhibit Hck in the presence of Nef. These compounds also block Nef-dependent HIV replication, validating the Nef-SFK signaling pathway as an antiretroviral drug target. Our findings also suggested that by binding to the Hck SH3 domain, Nef indirectly affects the conformation of the kinase active site to favor inhibitor association.     

Determination of a novel phosphodiesterase4 inhibitor, 3‐[1‐(3cyclopropylmethoxy‐4‐difluoromethoxybenzyl)‐1H‐pyrazol‐3‐yl]‐benzoic acid (PDE‐423) in rat plasma using liquid chromatography–tandem mass spectrometry

A method for determining a novel phosphodiesterase‐4 inhibitor, 3‐[1‐(3cyclopropylmethoxy‐4‐difluoromethoxybenzyl)‐1H‐pyrazol‐3‐yl]‐benzoic acid (PDE‐423), in rat plasma was developed and validated using liquid chromatography–tandem mass spectrometry for further pharmacokinetic study for development as a novel anti‐asthmatic drug. PDE‐423 in the concentration range of 0.02–10 µg/mL was linear with a correlation coefficient of >0.99, and the mean intra‐ and inter‐assay precisions of the assay were 7.50 and 3.86%, respectively. The validated method was used successfully for a pharmacokinetic study of PDE‐423 in rats. Copyright © 2014 John Wiley & Sons, Ltd.     

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction

Background  

Eps15 homology (EH) domains are protein interaction modules binding to peptides containing Asn-Pro-Phe (NPF) motifs and mediating critical events during endocytosis and signal transduction. The EH domain of POB1 associates with Eps15, a protein characterized by a striking string of DPF triplets, 15 in human and 13 in mouse Eps15, at the C-terminus and lacking the typical EH-binding NPF motif.     

Novel isoquinolone PDK1 inhibitors discovered through fragment-based lead discovery

Phosphoinositide-dependent kinase-1 (PDK1) is a critical enzyme in the PI3K/AKT pathway and to the activation of AGC family protein kinases, including S6K, SGK, and PKC. Dysregulation of this pathway plays a key role in cancer cell growth, survival and tumor angiogenesis. As such, inhibitors of PDK1 offer the promise of a new therapeutic modality for cancer treatment. Fragment based drug screening has recently become a viable entry point for hit identification. In this work, NMR spectroscopy fragment screening of PDK1 afforded novel chemotypes as orthogonal starting points from HTS screening hits. Compounds identified as hits by NMR spectroscopy were tested in a biochemical assay, and fragments with activity in both assays were clustered. The Pfizer compound file was mined via substructure and 2D similarity search, and the chemotypes were prioritized by ligand efficiency (LE), SAR mining, chemical attractiveness, and chemical enablement of promising vectors. From this effort, an isoquinolone fragment hit, 5 (IC₅₀ 870 μM, LE = 0.39), was identified as a novel, ligand efficient inhibitor of PDK1 and a suitable scaffold for further optimization. Initially in the absence of crystallographic data, a fragment growing approach efficiently explored four vectors of the isoquinolone scaffold via parallel synthesis to afford a compound with crystallographic data, 16 (IC₅₀ 41.4 μM, LE = 0.33). Subsequent lead optimization efforts provided 24 (IC₅₀ 1.8 μM, LE = 0.42), with greater than fivefold selectivity against other key pathway kinases.     

Molecular transporters for peptides: delivery of a cardioprotective εPKC agonist peptide into cells and intact ischemic heart using a transport system, R7

Background: Recently, we reported a novel oligoguanidine transporter system, polyarginine (R₇), which, when conjugated to spectroscopic probes (e.g., fluorescein) and drugs (e.g., cyclosporin A), results in highly water-soluble conjugates that rapidly enter cells and tissues. We report herein the preparation of the first R₇ peptide conjugates and a study of their cellular and organ uptake and functional activity. The octapeptide ψεRACK was selected for this study as it is known to exhibit selective ε protein kinase C isozyme agonist activity and to reduce ischemia-induced damage in cardiomyocytes. However, ψεRACK is not cell-permeable.Results: Here we show that an R₇-ψεRACK conjugate readily enters cardiomyocytes, significantly outperforming ψεRACK conjugates of the transporters derived from HIV Tat and from Antennapedia. Moreover, R₇-ψεRACK conjugate reduced ischemic damage when delivered into intact hearts either prior to or after the ischemic insult.Conclusions: Our data suggest that R₇ converts a peptide lead into a potential therapeutic agent for the ischemic heart.     

Displacement affinity chromatography of protein phosphatase one (PP1) complexes

Background  

Protein phosphatase one (PP1) is a ubiquitously expressed, highly conserved protein phosphatase that dephosphorylates target protein serine and threonine residues. PP1 is localized to its site of action by interacting with targeting or regulatory proteins, a majority of which contains a primary docking site referred to as the RVXF/W motif.     

Strategic approaches to drug design. II. Modelling studies on phosphodiesterase substrates and inhibitors

Summary Modelling studies have been carried out on the phosphodiesterase (PDE) substrates, adenosine- and guanosine-35-cyclic monophosphates, and on a number of non-specific and type III-specific phosphodiesterase inhibitors. These studies have assisted the understanding of PDE substrate differentiation and the design of potent, selective PDE type III inhibitors.     

Molecular insights into the binding affinity and specificity of the hemagglutinin cleavage loop from four highly pathogenic H5N1 isolates towards the proprotein convertase furin

Abstract  

The furin (FR) complex with each of four different sequences of hemagglutinin from the highly pathogenic H5N1 strains (HPH5), which were identified during the 2004–2010 influenza outbreaks in Thailand, were evaluated by molecular dynamics simulations, so as to compare the specificity and recognition of the enzyme–substrate binding. Relative to the conventional HPH5 inserted (H5Sq1, RERRRKKR), the S5-R or S6-R arginine residue is replaced by the smaller lysine in the H5Sq2 (RERKRKKR) and H5Sq3 (REKRRKKR) strains, respectively, whereas the S3-K lysine residue is deleted in H5Sq4 (RERRR_KR). The molecular dynamics results of the intermolecular interactions, in terms of hydrogen bonds and per-residue decomposition energy, between the substrate and furin revealed that the deletion of the positively charged amino acid at the S3 position in H5Sq4 leads to a notably weaker binding and specificity with the furin active site compared with that of FR–H5Sq1. A slight change in the substrate binding was found in the FR–H5Sq2 and FR–H5Sq3 complexes as a result of the replacement of the arginine with the shorter side-chained lysine (same positive charge). Altogether, the predicted binding free energy of the enzyme–substrate complexes was found to be in the following order: FR–H5Sq1 < FR–H5Sq2 ~ FR–H5Sq3 ≪ FR–H5Sq4.     

Interaction of connexin43 and protein kinase C-delta during FGF2 signaling

Background  

We have recently demonstrated that modulation of the gap junction protein, connexin43, can affect the response of osteoblasts to fibroblast growth factor 2 in a protein kinase C-delta-dependent manner. Others have shown that the C-terminal tail of connexin43 serves as a docking platform for signaling complexes. It is unknown whether protein kinase C-delta can physically interact with connexin43.     

The measurement of cyclic nucleotide phosphodiesterase 4 activities via the quantification of inorganic phosphate with malachite green

A spectrometric method was investigated to measure the activities of recombinant human cyclic nucleotide phosphodiesterase 4 (PDE4), based on the use of malachite green (MLG) to quantify phosphate released from adenosine-5′-monophosphate (AMP) by the action of calf intestinal alkaline phosphatase (CIAP). Glycerol at 2% stabilized the complex between MLG and phosphomolybdate, whose absorbance at 630 nm was proportional to phosphate concentrations with resistance to common substances in PDE4 reaction mixtures except papaverine. CIAP had the Michaelis-Menten constant (K_m) of (12.0 ± 2.1) μM (n = 3) for AMP at pH 7.4, and was resistant to EDTA below 0.20 mM. By the coupled end-point assay at 30.0 U L⁻¹ CIAP with reaction durations within 30 min, the rates to release phosphate in PDE4 reaction mixtures containing 10.0 mM MgCl₂ and 0.10 mM EDTA linearly responded to the amounts of PDE4 over wide ranges. Meanwhile, K_m of PDE4 was (8.8 ± 0.2) μM (n = 2), zinc ion inhibited PDE4 and rolipram had the inhibition constant about 10 nM. These results supported that by the coupled end-point assay, this method was promising to screen of PDE inhibitors that had no interference with the MLG assay of phosphate.     

Synthesis,characterization and ethylene polymerization of 1-(2,6-dimethyl-4-fluorenylphenylimino)-2-aryliminoacenaphthylnickel bromides

A series of 1-(2,6-dimethyl-4-fluorenylphenylimino)-2-aryliminoacenaphthylene compounds (aryl = 2,6-di(Me)Ph (L1), 2,6-di(Et)Ph (L2), 2,6-di(i-Pr)Ph (L3), 2,4,6-tri(Me)Ph (L4), 2,6-di(Et)-4-MePh (L5)) was prepared and used to form their corresponding dibromonickel complexes (D1–D5). Both L1–L5 and D1–D5 were fully characterized by FT-IR and elemental analysis as well as NMR measurements in the case of ligands L1–L5. The molecular structure of the representative complex D5 was confirmed by single crystal X-ray diffraction revealing a distorted trigonal bipyramidal geometry around the nickel center. On activation with either ethylaluminium sesquichloride (Et₃Al₂Cl₃, EASC) or methylaluminoxane (MAO), all nickel complexes exhibited high activities up to 9.82 × 10⁶ g of PE (mol of Ni)⁻¹ h⁻¹ for ethylene polymerization. In comparison with the polyethylenes obtained with related Ni pre-catalysts, the polyethylenes obtained in this work possessed relatively higher molecular weights and lower levels of branching, highlighting the significant influence of the remote fluorenyl substituent.     

Synthesis and thermal behavior of cis- and trans-1-tert-butyl-4,5-dimethyl-2-phenyl-2-(trimethylsiloxy)-1-(trimethylsilyl)-1-silacyclohex-4-ene

The cothermolysis of benzoyl(tert-butyl)bis(trimethylsilyl)silane with 2,3-dimethylbutadiene in a sealed tube at 140 °C for 24 h afforded cis- and trans-1-tert-butyl-4,5-dimethyl-2-phenyl-2-(trimethylsiloxy)-1-(trimethylsilyl)-1-silacyclohex-4-ene (2 and 3) in a ratio of approximately 1:1 in 66% combined yield. When cis-silacyclohex-4-ene 2 was heated in a sealed tube at 250 °C for 24 h, dyotropic ring contraction took place to give 1-[(tert-butyl)(trimethylsiloxy)(trimethylsilyl)silyl]-3,4-dimethyl-1-phenylcyclopent-3-ene (4), but not trans-2-tert-butyl-4,5-dimethyl-2-phenyl-1-(trimethylsiloxy)-1-(trimethylsilyl)-1-silacyclohex-4-ene (6). The thermolysis of trans-silacyclohex-4-ene 3 under the same conditions, however, afforded two products, 1-silyl-1-phenylcyclopent-3-ene 4 and trans-1-tert-butyl-4,5-dimethyl-2-phenyl-1-(trimethylsiloxy)-2-(trimethylsilyl)-1-silacyclohex-4-ene (5). The theoretical calculations were carried out to characterize the transition states and other local minima, and to evaluate the activation energies for the dyotropic rearrangement of 2 to 4 and 6, and 3 to 4 and 5. The energy barriers between 2 and 4, between 3 and 4, and between 3 and 5 were evaluated to be 188, 191, 192 kJ mol⁻¹, respectively. The energy barrier between 2 and 6, however, was calculated to be 201 kJ mol⁻¹ or higher. These results are consistent with the experimental finding that the thermal isomerization of 2 affords only 4, but 3 produces both 4 and 5.