The mechanism of cyclic nucleotide hydrolysis in the phosphodiesterase catalytic site

The cyclic nucleotide phosphodiesterase superfamily of enzymes (PDEs) catalyzes the stereospecific hydrolysis of the second messengers adenosine and guanosine 3',5'- cyclic monophosphate (cAMP, cGMP) to produce 5'-AMP and 5'-GMP, respectively. The PDEs are targets of high-throughput screening to determine selective inhibitors for a variety of therapeutic purposes. The catalytic pocket where the hydrolysis takes place is a highly conserved region and has several residues which are absolutely conserved across the PDE families. In this study, we consider a model cyclic substrate in which the adenine/guanine base has been replaced with a hydrogen atom, and we present results of a quantum computational investigation of the hydrolysis reaction as it occurs within the PDE catalytic site using the ONIOM hybrid (B3LYP/6-31g(d):PM3) method. We characterize the bound substrate, the bound hydrolyzed product, and the transition state which connects them for our model cyclic substrate placed in a truncated model of the PDE4D2 catalytic site. We address the role that the conserved histidine proximal to the bimetal system of the catalytic site, along with its conserved glutamine partner, plays in the generation of the hydroxide nucleophile. Our study provides computational evidence for several key features of the cAMP/cGMP hydrolysis mechanism as it occurs within the protein environment across the PDE superfamily.     

Combined 2D and 3D-QSAR,molecular modelling and docking studies of pyrazolodiazepinones as novel phosphodiesterase 2 inhibitors

Selective inhibition of phosphodiesterase 2 (PDE2) in cells where it is located elevates cyclic guanosine monophosphate (cGMP) and acts as novel analgesic with antinociceptive activity. Three-dimensional quantitative structure–activity relationship (QSAR) studies for pyrazolodiazepinone inhibitors exhibiting PDE2 inhibition were performed using comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and Topomer CoMFA, and two-dimensional QSAR study was performed using a Hologram QSAR (HQSAR) method. QSAR models were generated using training set of 23 compounds and were validated using test set of nine compounds. The optimum partial least squares (PLS) for CoMFA-Focusing, CoMSIA-SDH, Topomer CoMFA and HQSAR models exhibited good ‘leave-one-out’ cross validated correlation coefficient (q²) of 0.790, 0.769, 0.840 and 0.787, coefficient of determination (r²) of 0.999, 0.964, 0.979 and 0.980, and high predictive power (r²_pred) of 0.796, 0.833, 0.820 and 0.803 respectively. Docking studies revealed that those inhibitors able to bind to amino acid Gln859 by cGMP binding orientation called ‘glutamine-switch’, and also bind to the hydrophobic clamp of PDE2 isoform, could possess high selectivity for PDE2. From the results of all the studies, structure–activity relationships and structural requirements for binding to active site of PDE2 were established which provide useful guidance for the design and future synthesis of potent PDE2 inhibitors.     

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.     

咪唑并吡啶类化合物结构及PDE抑制活性的三维构效关系研究

对咪唑并吡啶类化合物作为环核苷酸磷酸二酯酶(PDE)的抑制剂的抑制活性进行了比较分子力场分析.结果表明,立体效应和静电作用场是描述对PDE抑制活性和进行结构性能关系研究的最重要的结构参数,提出了对该类化合物进行结构修饰的方法,并由新建立的三维定量构效关系模型对该类化合物的PDE抑制活性进行了预报.     

磷酸二酯酶2 (PDE2)结构及其选择性抑制剂的研究进展

磷酸二酯酶2 (PDE2)主要分布在大脑、心脏细胞中, 作为潜在的药物靶标, 通过水解细胞内第二信使cAMP和cGMP, 对维持cAMP和cGMP的水平起着重要的作用, 其选择性抑制剂有望在内皮渗透性和改善记忆力等方面发挥作用. 综述了PDE2的组织分布、生理功能、催化区域和调节区域晶体结构的特点以及选择性的抑制剂. 最后, 根据药物设计发展的趋势对未来PDE2抑制剂的设计进行了展望.     

Additional evidence for the cyclic GMP signaling pathway resulting in the photophobic behavior of Stentor coeruleus.

We report that exo- and endogenous guanosine 3',5'-cyclic monophosphate (cGMP) specifically influenced the photophobic response. In behavioral experiments the slowly hydrolyzable and membrane-permeable analogs of cGMP (8-bromo-cGMP [Br-cGMP] and N6,2'-o-dibutyryl-cGMP) dramatically prolonged the time for ciliary stop response and decreased the duration of ciliary reversal in a dose-dependent manner. When analogs of adenosine 3',5'-cyclic monophosphate (cAMP) (8-bromo-cAMP or N6,2'-o-dibutyryl-cAMP) were used, no essential effects were detected on the kinetics of the photophobic response. Both nonspecific cyclic nucleotide phosphodiesterase (PDE) activity inhibitors (3-isobutyl-1-methylxanthine [IBMX] and 1,3-dimethylxanthine [theophylline]) and the highly specific cGMP-PDE activity inhibitor 1,4-dihydro-5-[2-propoxyphenyl]-7H-1,2,3-triazolo[4,5-d]pyrimidine-7-one (zaprinast) mimicked the effects of cGMP analogs. Treatment of cells with an inhibitor of guanylate cyclase activity (6-anilino-5,8-quinolinedione [LY 83583]) exerted an effect opposite to that of cGMP analogs and PDE activity inhibitors. The positive physiological effect of LY 83583 was significantly diminished in ciliates that were treated simultaneously with Br-cGMP. In an assay of cell cyclic nucleotide content, the exposure of dark-adapted Stentor to light evoked a transient decrease in the basal level of intracellular cGMP. Alterations in internal cGMP levels were more distinct when the intensity of applied illumination was increased. In the presence of IBMX or theophylline the basal content of cGMP was markedly enhanced, and the photoinduced changes in cGMP level were less pronounced. In this paper the possible whole molecular mechanism by which the ciliary orientation in Stentor is controlled by light is presented.     

磷酸二酯酶4b抑制剂定量构效关系及分子对接研究

磷酸二酯酶4(PDE4)是第二信使环磷酸腺苷(cAMP)选择性高亲和力的水解酶,影响气道平滑肌、炎性细胞和免疫细胞的功能,选择性PDE4b抑制剂作为抗炎药治疗哮喘和慢性阻塞性肺病(COPD)因为不会引起恶心呕吐等副反应而受到极大的关注。本文使用比较分子场(CoMFA)方法,对系列嘧啶二芳基取代的PDE4b抑制剂构建了合理的三维定量构效关系(3D-QSAR)模型,使用分子对接方法研究了抑制剂与酶的相互作用,发现该系列化合物的嘧啶环2位引入带有较大电负性基团取代的五元环状烃基可提升活性;嘧啶环4位、5位两个碳原子上建议保留小体积取代基;嘧啶环6位引入带有氢键给体或氢键受体取代的芳烃基可增加化合物活性。本研究可为后续合理设计高效的PDE4b抑制剂提供理论指导。     

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.     

Photosensitive signal transduction induces membrane hyperpolarization in Paramecium bursaria

The protozoan ciliate Paramecium bursaria exhibits membrane hyperpolarization in response to photostimulation, accompanied with an increased swimming speed. The external addition of cyclic nucleotide phosphodiesterase (PDE) inhibitors, either theophylline (1,3-dimethylxanthine) or 3-isobutyl-1-methylxanthin (IBMX), increased in both amplitudes of the membrane hyperpolarization and the increase in swimming speed. Moreover, the addition of membrane permeable cyclic nucleotide analogs, either 8-bromo-adenosine 3',5'-cyclic monophosphate (Br-cAMP) or 8-Br-guanosine 3',5'-cyclic monophosphate (Br-cGMP), increased these amplitudes. On the other hand, the addition of l-cis-diltiazem, known to block the conductance of cyclic nucleotide-gated channels, partially decreased both amplitudes of the membrane hyperpolarization and the increase in swimming speed. An enzyme immunoassay of cellular cyclic nucleotide contents showed that photostimulation induced a rapid increase in adenosine 3',5'-cyclic monophosphate (cAMP), but little increase in guanosine 3',5'-cyclic monophosphate (cGMP), raising the possibility that a rapid increase in cAMP mediates the light-induced hyperpolarization in P. bursaria.     

Stereoelectronic properties of spiroquinazolinones in differential PDE7 inhibitory activity

A detailed computational study on a series of spiroquinazolinones showing phosphodiesterase 7 (PDE7) inhibitory activity was performed to understand the binding mode and the role of stereoelectronic properties in binding. Our docking studies reproduced the essential hydrogen bonding and hydrophobic interactions for inhibitors of this class of enzymes. The N1 proton of the quinazolinone scaffold was involved in H-bonding to an amide side chain of the conserved glutamine residue in the active site. The central bicyclic ring of the molecules showed hydrophobic and pi-stacking interactions with hydrophobic and aromatic amino acid residues, respectively, present in the PDE7 active site. The docked conformations were optimized with density functional theory (DFT) and DFT electronic properties were calculated. Comparison of molecular electrostatic potential (MEP) plots of inhibitors with the active site of PDE7 suggested that the electronic distribution in the molecules is as important as steric factors for binding of the molecules to the receptor. The hydrogen bonding ability and nucleophilic nature of N1 appeared to be important for governing the interaction with PDE7. For less active inhibitors (pIC(50) < 6.5), the MEP maximum at N1 of the spiroquinazolinone ring was high or low based on the electronic properties of the substituents. All the more active molecules (pIC(50) > 6.5) had MEP highest at N3, not N1. Efficient binding of these inhibitors may need some rearrangement of side chains of active-site residues, especially Asn365. This computational modeling study should aid in design of new molecules in this class with improved PDE7 inhibition.     

Solvent hydrogen bonding and structural effects on the reaction of 2‐halo‐5‐nitropyridines with parasubstituted anilines in dimethylsulfoxide/acetonitrile mixtures

Substitution reactions of some parasubstituted anilines with 2‐chloro‐5‐nitropyridine and 2‐bromo‐5‐nitropyridine were carried out conductometrically in dimethylsulfoxide/acetonitrile mixtures. The correlation of second order rate constants with Hammett's substituent constants yields a fairly linear straight line with a negative slope. The correlation of rate data with Kamlet–Taft's solvatochromic parameters is excellent (100R²= 97%) in both the substrates. The solvation model proposed is well supported by the solvatochromism exhibited by aniline in the solvent mixture under investigation. The molar extinction coefficient (ε_max ) of aniline varies appreciably up to ～25% with the change in composition of the mixture. The multivariate correlation analysis of ε_max (with α, β, π*) suggests that the solvation around NH₂ moiety of aniline through hydrogen bond donor (HBD) property is found to be dominant in the solvation process and consequently in altering the rate. The observation is that the dominance of HBD property in solvation is further confirmed by the cyclic voltammetric oxidation of aniline in the solvent mixture. © 2011 Wiley Peiodicals, Inc. Int J Chem Kinet 43: 409–417, 2011     

Microchip CE‐LIF method for the hydrolysis of L‐glutamine by using L‐asparaginase enzyme reactor based on gold nanoparticle

l ‐Asparaginase (l ‐Asnase) can suppress the growth of malignant cells by rapid depletion of two essential amino acids, l ‐glutamine (l ‐Gln) and l ‐asparagine (l ‐Asn). To study the cytotoxic effect and the secondary complications of l ‐Asnase in the treatment of acute lymphoblastic leukemia, the development of a novel enzyme reactor of l ‐Asnase for the hydrolysis of l ‐Gln, employing the enzyme‐gold nanoparticle conjugates in capillary, was reported in this work. First, a microchip CE (MCE)‐LIF was established for the separation of l ‐amino acids (l ‐Gln and l ‐glutamic acid) and studying the hydrolysis of l ‐Gln by using l ‐Asnase enzyme reactor. Then, using l ‐Gln as target analyte, the enzyme kinetics of l ‐Asnase in free solution, enzyme‐gold nanoparticle conjugates (E‐GNP), and the enzyme‐gold nanoparticle conjugates immobilized in capillary (E‐GNP‐C) were investigated in detail with the proposed MCE‐LIF method. Moreover, for optimizing the enzymatic reaction efficiency, three important parameters, including the length of capillary, the enzyme concentration reacted with gold nanoparticle and the amount of l ‐Asnase immobilized on the gold nanoparticle, have been studied. Owing to the high specific activity, the E‐GNP‐C enzyme reactor exhibited the best performance for the hydrolysis of l ‐Gln.     

Incorporating the excluded solvent volume and surface charges for computing solvation free energy

Gauss's law or Poisson's equation is conventionally used to calculate solvation free energy. However, the near‐solute dielectric polarization from Gauss's law or Poisson's equation differs from that obtained from molecular dynamics (MD) simulations. To mimic the near‐solute dielectric polarization from MD simulations, the first‐shell water was treated as two layers of surface charges, the densities of which are proportional to the electric field at the solvent molecule that is modeled as a hard sphere. The intermediate water was treated as a bulk solvent. An equation describing the solvation free energy of ions using this solvent scheme was derived using the TIP3P water model. © 2013 Wiley Periodicals, Inc.     

Purine 3′:5′‐cyclic nucleotides with the nucleobase in a syn orientation: cAMP,cGMP and cIMP

Purine 3′:5′‐cyclic nucleotides are very well known for their role as the secondary messengers in hormone action and cellular signal transduction. Nonetheless, their solid‐state conformational details still require investigation. Five crystals containing purine 3′:5′‐cyclic nucleotides have been obtained and structurally characterized, namely adenosine 3′:5′‐cyclic phosphate dihydrate, C₁₀H₁₂N₅O₆P·2H₂O or cAMP·2H₂O, (I), adenosine 3′:5′‐cyclic phosphate 0.3‐hydrate, C₁₀H₁₂N₅O₆P·0.3H₂O or cAMP·0.3H₂O, (II), guanosine 3′:5′‐cyclic phosphate pentahydrate, C₁₀H₁₂N₅O₇P·5H₂O or cGMP·5H₂O, (III), sodium guanosine 3′:5′‐cyclic phosphate tetrahydrate, Na⁺·C₁₀H₁₁N₅O₇P⁻·4H₂O or Na(cGMP)·4H₂O, (IV), and sodium inosine 3′:5′‐cyclic phosphate tetrahydrate, Na⁺·C₁₀H₁₀N₄O₇P⁻·4H₂O or Na(cIMP)·4H₂O, (V). Most of the cyclic nucleotide zwitterions/anions [two from four cAMP present in total in (I) and (II), cGMP in (III), cGMP⁻ in (IV) and cIMP⁻ in (V)] are syn conformers about the N‐glycosidic bond, and this nucleobase arrangement is accompanied by C_rib—H…N_pur hydrogen bonds (rib = ribose and pur = purine). The base orientation is tuned by the ribose pucker. An analysis of data obtained from the Cambridge Structural Database made in the context of syn–anti conformational preferences has revealed that among the syn conformers of various purine nucleotides, cyclic nucleotides and dinucleotides predominate significantly. The interactions stabilizing the syn conformation have been indicated. The inter‐nucleotide contacts in (I)–(V) have been systematized in terms of the chemical groups involved. All five structures display three‐dimensional hydrogen‐bonded networks.     

Influence of hydrogen bonds between sidechains and cooperativity on self‐assembly of the cyclopeptides

The self‐assembly of four cyclic D,L‐octapeptides, [‐(D‐Ala‐Gln)₄‐], [‐(D‐Val‐Gln)₄‐], [‐(D‐Leu‐Gln)₄‐], and [‐(D‐Phe‐Gln)₄‐], was investigated on the theory level in detail. Based on these cyclic peptides, which contain L‐Gln residues and possess C₄ symmetry, a series of oligomers were constructed according to different stacking modes as well as interaction patterns. We employed the semiempirical molecular orbital method AM1 to optimize the structures of all the oligomers, some of which were further studied using density functional method B3PW91/6‐31G to calculate the interaction energies. The studies indicate that when these cyclopeptides aggregate to form oligomers, or even nanotubes, four more hydrogen bonds could form between the sidechains of L‐Gln residues in addition to eight hydrogen bonds formed between the backbones of adjacent two cyclic peptides, a result that would clearly affect the self‐assembling process of cyclic peptides. The main effects can be summarized as follows. First, the dimers of these cyclic peptides with C₄ symmetry are more stable than those with D₄ symmetry due to their additional H‐bonds between Gln sidechains. Second, for the self‐assembly of the cyclopeptides, there is a competition between parallel and antiparallel stacking modes in lower oligomers such as dimers. However, with an increasing degree of oligomerization, energetically there is an increased possibility for the cyclic peptides to take the parallel stacking mode in assembly. Finally, the synergetic effect of weak interactions is the fundamental driving force for cyclic peptides to form stable nanotubes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Emerging Potential of the Phosphodiesterase (PDE) Inhibitor Ibudilast for Neurodegenerative Diseases: An Update on Preclinical and Clinical Evidence

Neurodegenerative diseases constitute a broad range of central nervous system disorders, characterized by neuronal degeneration. Alzheimer’s disease, Parkinson’s disease, amyolotrophic lateral sclerosis (ALS), and progressive forms of multiple sclerosis (MS) are some of the most frequent neurodegenerative diseases. Despite their diversity, these diseases share some common pathophysiological mechanisms: the abnormal aggregation of disease-related misfolded proteins, autophagosome–lysosome pathway dysregulation, impaired ubiquitin–proteasome system, oxidative damage, mitochondrial dysfunction and excessive neuroinflammation. There is still no effective drug that could halt the progression of neurodegenerative diseases, and the current treatments are mainly symptomatic. In this regard, the development of novel multi-target pharmaceutical approaches presents an attractive therapeutic strategy. Ibudilast, an anti-inflammatory drug firstly developed as an asthma treatment, is a cyclic nucleotide phosphodiesterases (PDEs) inhibitor, which mainly acts by increasing the amount of cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), while downregulating the pro-inflammatory factors, such as tumor necrosis factor-α (TNF-α), macrophage migration inhibitory factor (MIF) and Toll-like receptor 4 (TLR-4). The preclinical evidence shows that ibudilast may act neuroprotectively in neurodegenerative diseases, by suppressing neuroinflammation, inhibiting apoptosis, regulating the mitochondrial function and by affecting the ubiquitin–proteasome and autophagosome–lysosome pathways, as well as by attenuating oxidative stress. The clinical trials in ALS and progressive MS also show some promising results. Herein, we aim to provide an update on the emerging preclinical and clinical evidence on the therapeutic potential of ibudilast in these disorders, discuss the potential challenges and suggest the future directions.     

Solvatochromism and preferential solvation of Brooker's merocyanine in water–methanol mixtures

The excitation energy of Brooker's merocyanine in water–methanol mixtures shows nonlinear behavior with respect to the mole fraction of methanol, and it was suggested that this behavior is related to preferential solvation by methanol. We investigated the origin of this behavior and its relation to preferential solvation using the three‐dimensional reference interaction site model self‐consistent field method and time‐dependent density functional theory. The calculated excitation energies were in good agreement with the experimental behavior. Analysis of the coordination numbers revealed preferential solvation by methanol. The free energy component analysis implied that solvent reorganization and solvation entropy drive the preferential solvation by methanol, while the direct solute–solvent interaction promotes solvation by water. The difference in the preferential solvation effect on the ground and excited states causes the nonlinear excitation energy shift. © 2017 Wiley Periodicals, Inc.     

Effective Homogeneous Hydrolysis of Phosphodiester and DNA Cleavage by Chitosan‐copper Complex

We aimed to explore the role of chitosan‐based metal complexes in catalyzing the hydrolysis of phosphodiesters. To this end, we performed detailed studies on the kinetics of the chitosan copper complex (CSCu)‐catalyzed hydrolysis of bis(4‐nitrophenol) phosphate (BNPP) in Tris‐H⁺ buffer and in an organic solvent. A significant enhancement in the rate of reaction (up to 3×10⁵‐fold acceleration) was observed at pH 8.0 (25°C). The pH dependence of BNPP hydrolysis at pH 5.5–9.5 and the UV spectra revealed that the copper‐bounded water molecules underwent deprotonation to form the active catalytic species CSCu‐OH. The kinetic behavior of BNPP catalytic hydrolysis in the Tris‐H⁺ buffer was consistent with that predicted by the Michaelis‐Menten kinetics model. An intramolecular nucleophilic attack by the copper‐bonded hydroxide group on the same activated phosphodiester substrate was proposed as the catalytic mechanism for CSCu‐catalyzed reaction system. The results of DNA binding and cleavage experiments indicated electrostatic binding mode of CSCu to DNA as well as the strong capability of CSCu to disturb the supercoiled strand of DNA and cleave it to nicked circular form.     

Development of a PDEδ-Targeting PROTACs that Impair Lipid Metabolism

The prenyl-protein chaperone PDEδ modulates the localization of lipidated proteins in the cell, but current knowledge about its biological function is limited. Small-molecule inhibitors that target the PDEδ prenyl-binding site have proven invaluable in the analysis of biological processes mediated by PDEδ, like KRas cellular trafficking. However, allosteric inhibitor release from PDEδ by the Arl2/3 GTPases limits their application. We describe the development of new proteolysis-targeting chimeras (PROTACs) that efficiently and selectively reduce PDEδ levels in cells through induced proteasomal degradation. Application of the PDEδ PROTACs increased sterol regulatory element binding protein (SREBP)-mediated gene expression of enzymes involved in lipid metabolism, which was accompanied by elevated levels of cholesterol precursors. This finding for the first time demonstrates that PDEδ function plays a role in the regulation of enzymes of the mevalonate pathway.