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.     

Evaluation of the surface free energy of spin‐coated photodefinable epoxy

The surface free energy of crosslinked photodefinable epoxy (PDE) was evaluated from the advancing contact angles measured by the sessile drop method. Poly(tetrafluoroethylene) (PTFE) was used as a reference material in the evaluation of the surface free energies by various models. Pure water, diiodomethane, formamide, ethylene glycol, diethylene glycol, glycerol, 1‐bromonaphthalene, decane, and tetradecane were used as the probing liquids. The surface free energies for PDE and PTFE were calculated to be 43.6 and 21.2 mJ/m², respectively. The contact‐angle measurements indicated the isotropy of the PDE surface with respect to the surface free energy. The PDE coating was further characterized with scanning electron microscopy and atomic force microscopy. The PDE surface was treated chemically and by reactive ion etching (RIE) to determine their impact on the wettability and adhesion. The treatments resulted in decreased contact angles between the crosslinked PDE surface and water as the polarity of the surface increased from about 9% to 18 and 43% by the chemical and RIE treatments, respectively. On the contrary, the surface free energy of the treated PDEs, as calculated by the geometric mean model, did not change markedly (to 47.4 and 41.8 mJ/m² by the chemical and RIE treatments, respectively). Consequently, the contact angles of diiodomethane and the PDE solution on the treated surfaces did not decrease noticeably. The stud‐pull test showed improved adhesion strength for PDE that was left less crosslinked and, therefore, had residual affinity against the sequential PDE layer. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2137–2149, 2002     

Identification of biologically active PDE11-selective inhibitors using a yeast-based high-throughput screen

The biological roles of cyclic nucleotide phosphodiesterase 11 (PDE11) enzymes are poorly understood, in part due to the lack of selective inhibitors. To address the need for such compounds, we completed an ~200,000 compound high-throughput screen (HTS) for PDE11 inhibitors using a yeast-based growth assay, and identified 4 potent and selective PDE11 inhibitors. One compound, along with two structural analogs, elevates cAMP and cortisol levels in human adrenocortical cells, consistent with gene association studies that link PDE11 activity to adrenal function. As such, these compounds can immediately serve as chemical tools to study PDE11 function in cell culture, and as leads to develop therapeutics for the treatment of adrenal insufficiencies. Our results further validate this yeast-based HTS platform for the discovery of potent, selective, and biologically active PDE inhibitors.     

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.     

ONIOM investigation of nucleotide selectivity in phosphodiesterases 3 and 4

The cyclic nucleotide phosphodiesterases (PDEs) are drug‐targeted enzymes that down regulate cyclic nucleotide concentrations in the cell by catalyzing the hydrolysis of the O3′‐phosphorous bond, yielding the noncyclic nucleotides. Selectivity for cAMP versus cGMP (cyclic 3′,5′‐adenosine/‐guanosine monophosphate) as the favored substrate is primarily attributed to the orientation of a conserved glutamine residue which binds to the adenine/guanine ring. We use ONIOM hybrid quantum methods to accurately describe substrate binding within the catalytic sites of the cAMP‐specific PDE4 and the cGMP‐inhibited, dual‐specific PDE3 in order to understand subtle aspects of substrate selectivity. We estimate PDE4's net preference for cAMP binding to be about 16 kcal/mol; the cause of cAMP's known preference resides both in its fixed glutamine orientation (Gln 369 in PDE4D) and in the differential free energy of solvation, which disfavors the binding of cGMP relative to cAMP by about 15 kcal/mol. Also, we discuss the contributing role played by Asn 321, held in place by a partner Asp 167, in the deselection of cGMP by PDE4. PDE3's conserved glutamine (Gln 988 in PDE3B) is free to take on either a cGMP‐favorable or cAMP‐favorable orientation. We find that enthalpies of binding favor cGMP for PDE3, but only by the same amount as free energies of solvation disfavor cGMP binding. Comparison of the PDE3‐cAMP and ‐cGMP complexes and energetics reveals cAMP to be more susceptible to the attack of the hydroxide nucleophile in PDE3. We identify a key threonine residue (Thr 952) as responsible for PDE3's kinetic relative disfavor of cGMP hydrolysis by causing Gln 988 to tilt out of cGMP's purine plane. Our results are consistent with the PDE3's kinetic specificity for cAMP hydrolysis and the known competitive inhibition of PDE3 by cGMP. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

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.     

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.     

Phosphodiesterase 4D contributes to angiotensin II-induced abdominal aortic aneurysm through smooth muscle cell apoptosis

Abdominal aortic aneurysm (AAA) is a permanent expansion of the abdominal aorta that has a high mortality but limited treatment options. Phosphodiesterase (PDE) 4 family members are cAMP-specific hydrolyzing enzymes and have four isoforms (PDE4A-PDE4D). Several pan-PDE4 inhibitors are used clinically. However, the regulation and function of PDE4 in AAA remain largely unknown. Herein, we showed that PDE4D expression is upregulated in human and angiotensin II-induced mouse AAA tissues using RT-PCR, western blotting, and immunohistochemical staining. Furthermore, smooth muscle cell (SMC)-specific Pde4d knockout mice showed significantly reduced vascular destabilization and AAA development in an experimental AAA model. The PDE4 inhibitor rolipram also suppressed vascular pathogenesis and AAA formation in mice. In addition, PDE4D deficiency inhibited caspase 3 cleavage and SMC apoptosis in vivo and in vitro, as shown by bulk RNA-seq, western blotting, flow cytometry and TUNEL staining. Mechanistic studies revealed that PDE4D promotes apoptosis by suppressing the activation of cAMP-activated protein kinase A (PKA) instead of the exchange protein directly activated by cAMP (Epac). Additionally, the phosphorylation of BCL2-antagonist of cell death (Bad) was reversed by PDE4D siRNA in vitro, which indicates that PDE4D regulates SMC apoptosis via the cAMP-PKA-pBad axis. Overall, these findings indicate that PDE4D upregulation in SMCs plays a causative role in AAA development and suggest that pharmacological inhibition of PDE4 may represent a potential therapeutic strategy.Subject terms: Aneurysm, Apoptosis     

A comparison of relaxation processes in structurally related van der Waals glass formers: the role of internal degrees of freedom

Depolarized dynamic light scattering (DLS), dielectric relaxation (DS), and deuterium NMR studies of fragile van der Waals glass forming liquids phenylphthalein-dimethylether (PDE) and cresolphthalein-dimethylether (KDE) are presented. In PDE a new dielectric loss process was found, which can be attributed to the 180 degrees flip of the phenyl rings. The previous finding that the distribution of the structural relaxation times measured for PDE and KDE by DS is substantially narrower than that measured by DLS is explained by partial decoupling of the dynamics of the dipole moment from the structural relaxation of the sample. The dynamics of PDE and KDE is compared with the previous studies of two other structurally similar liquids: 1,1'-di(4-methoxy-5-methylphenyl)cyclohexane (BMMPC) and 1,1'-bis(p-methoxyphenyl)cyclohexane (BMPC) in order to relate dynamical features with the chemical structure of the material. The evidence for the intramolecular character of the secondary relaxations observed in BMPC and PDE is presented.     

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.     

CoMFA and CoMSIA 3D-quantitative structure-activity relationship model on benzodiazepine derivatives, inhibitors of phosphodiesterase IV

Recently, we reported structurally novel PDE4 inhibitors based on 1,4-benzodiazepine derivatives. The main interest in developing bezodiazepine-based PDE4 inhibitors is in their lack of adverse effects of emesis with respect to rolipram-like compounds. A large effort has thus been made toward the structural optimization of this series. In the absence of structural information on the inhibitor binding mode into the PDE4 active site, 2D-QSAR (H-QSAR) and two 3D-QSAR (CoMFA and CoMSIA) methods were applied to improve our understanding of the molecular mechanism controlling the PDE4 affinity of the benzodiazepine derivatives. As expected, the CoMSIA 3D contour maps have provided more information on the benzodiazepine interaction mode with the PDE4 active site whereas CoMFA has built the best tool for activity prediction. The 2D pharmacophoric model derived from CoMSIA fields is consistent with the crystal structure of the PDE4 active site reported recently. The combination of the 2D and 3D-QSAR models was used not only to predict new compounds from the structural optimization process, but also to screen a large library of bezodiazepine derivatives.     

解吸附电晕束电离质谱法快速筛选保健食品中非法添加的5型磷酸二酯酶抑制剂

建立了解吸附电晕束离子源(DCBI)结合离子阱质谱快速检测保健食品中非法添加的3种磷酸二酯酶5(PDE5)抑制剂(伐地那非、西地那非、他达拉非)的方法。采用一级质谱筛选,二级质谱确证,对样品中非法添加物进行定性鉴别;通过二级特征碎片离子进行半定量分析,并与传统高效液相色谱-紫外(HPLC-UV)定量检测法对比。对12个市售保健品进行检测,DCBI-MS定性检测结果与HPLC-UV检测结果一致,有7个样品检出他达拉非,3个样品检出西地那非,1个样品检出伐地那非。通过研究3种PDE5抑制剂的二级质谱裂解规律,推测一个样品中含有羟基豪莫西地那非。本方法快速准确,适用于大批量复杂基质样品中PDE5抑制剂的筛查。     

Synthesis and cyclic AMP phosphodiesterase 4 isoenzyme inhibitory activity of heterocycle condensed purines

To reverse the adverse reactions of alkylxanthines and to develop novel inhibitors of cyclic AMP phosphodiesterase 4 (PDE4), a series of heterocycle [a]-, [b]-, [c,d]-, and [i]-condensed purines were designed and synthesized. Although all compounds did not display PDE1 and PDE3 inhibitory activities, several heterocycle [i]-condensed purines strongly inhibited PDE4. Especially, dl-3,4-dipropyl-8-methyl-4,5,7,8-tetrahydro-1H-imidazo[2,1-i]purin-5-one (dl-7c) exhibited comparable PDE4 inhibitory activity (IC(50)=1.9 microM) to rolipram and denbufylline (DBF).     

Design,Synthesis, and Evaluation of Dihydropyranopyrazole Derivatives as Novel PDE2 Inhibitors for the Treatment of Alzheimer’s Disease

Phosphodiesterase 2 (PDE2) has been regarded as a novel target for the treatment of Alzheimer’s disease (AD). In this study, we obtained (R)-LZ77 as a hit compound with moderate PDE2 inhibitory activity (IC₅₀ = 261.3 nM) using a high-throughput virtual screening method based on molecular dynamics. Then, we designed and synthesized 28 dihydropyranopyrazole derivatives as PDE2 inhibitors. Among them, compound (+)-11h was the most potent PDE2 inhibitor, with an IC₅₀ value of 41.5 nM. The molecular docking of PDE2-(+)-11h reveals that the 4-(trifluoromethyl)benzyl)oxyl side chain of the compound enters the H-pocket and forms strong hydrophobic interactions with L770/L809/F862, which improves inhibitory activity. The above results may provide insight for further structural optimization of highly potent PDE2 inhibitors and may lay the foundation for their use in the treatment of AD.     

Quantification of benzo[a]pyrene diol epoxide DNA-adducts by stable isotope dilution liquid chromatography/tandem mass spectrometry

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants found in car exhausts, charbroiled food, and tobacco smoke. Three pathways for the metabolic activation of B[a]P to ultimate carcinogens have been proposed. The most widely accepted pathway involves cytochrome-P450 (CYP) 1A1- and/or 1B1-mediated formation of B[a]P-7,8-oxide, which undergoes epoxide hydrolase-mediated metabolism to the proximate carcinogen B[a]P-7,8-dihydro-7,8-diol. Further CYP1A1- and/or CYP1B1-mediated activation of the dihydrodiol results in the formation of 7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (B[a]PDE), the ultimate carcinogen. In previous studies, it was demonstrated that (+)-anti-B[a]PDE was the most potent tumorigen of the CYP-derived B[a]PDE diastereomers. We have developed a stable isotope dilution, liquid chromatography multiple reaction monitoring/mass spectrometry (LC-MRM/MS) assay for all eight (+/-)-anti-B[a]PDE-derived dGuo and dAdo DNA-adducts. The LC-MRM/MS assay was rigorously validated and used to show that (+)-anti-trans-B[a]PDE-dGuo was the major adduct formed when naked DNA and human bronchoalveolar adenocarcinoma H358 cells were treated with (+/-)-anti-B[a]PDE. The preference for DNA-adducts derived from (+)-anti-B[a]PDE was even more apparent in cellular DNA. Thus, the increased potency of (+)-anti-B[a]PDE as a tumorigen is most likely due its ability to preferentially form DNA-adducts when compared with (-)-anti-B[a]PDE. Also, the adduct profile suggests that this occurs by binding of (+)-anti-B[a]PDE to DNA in a manner that facilitates covalent binding to dGuo rather than dAdo residues.     

Dissociation of the K-Ras4B/PDEδ complex upon contact with lipid membranes: membrane delivery instead of extraction

K-Ras4B is a small GTPase whose selective membrane localization and clustering into microdomains are mediated by its polybasic farnesylated C-terminus. The importance of the subcellular distribution for the signaling activity of K-Ras4B became apparent from recent in vivo studies, showing that the delta subunit of cGMP phosphodiesterase (PDEδ), which possesses a hydrophobic prenyl-binding pocket, is able to function as a potential binding partner for farnesylated proteins, thereby leading to a modulation of the spatiotemporal organization of K-Ras. Even though PDEδ has been suggested to serve as a cytosolic carrier for Ras, the functional transport mechanism still remains largely elusive. In this study, the effect of PDEδ on the interaction of GDP- and GTP-loaded K-Ras4B with neutral and anionic model biomembranes has been investigated by a combination of different spectroscopic and imaging techniques. The results show that PDEδ is not able to extract K-Ras4B from membranes. Rather, the K-Ras4B/PDEδ complex formed in bulk solution turned out to be unstable in the presence of heterogeneous membranes, resulting in a release of farnesylated K-Ras4B upon membrane contact. With the additional observation of enhanced membrane affinity for the K-Ras4B/PDEδ complex, a molecular mechanism for the PDEδ-K-Ras4B-membrane interaction could be proposed. This includes an effective delivery of PDEδ-solubilized K-Ras4B to the plasma membrane, probably through cytoplasmic diffusion, the dissociation of the K-Ras4B/PDEδ complex upon plasma membrane contact, and finally the membrane binding of released farnesylated K-Ras4B that leads to K-Ras4B-enriched microdomain formation.     

Effects of Extracts and Flavonoids from Drosera rotundifolia L. on Ciliary Beat Frequency and Murine Airway Smooth Muscle

Extracts from Drosera rotundifolia are traditionally used to treat cough symptoms during a common cold. The present study aimed to investigate the impact of extracts from D. rotundifolia and active compounds on the respiratory tract. Tracheal slices of C57BL/6N mice were used ex vivo to examine effects on airway smooth muscle (ASM) and ciliary beat frequency (CBF). Phosphodiesterase (PDE) inhibition assays were carried out to test whether PDE1 or PDE4 are targeted by the active compounds. An ethanol–water extract, as well as an aqueous fraction of this extract, exerted antispasmodic properties against acetylcholine-induced contractions. In addition, contractions induced by 60 mM K⁺ were abrogated by the aqueous fraction. Effects on ASM could be attributed to the flavonoids quercetin, 2″-O-galloylhyperoside and hyperoside. Moreover, the Drosera extract and the aqueous fraction increased the CBF of murine tracheal slices. Quercetin and 2″-O-galloylhyperoside were identified as active compounds involved in the elevation of CBF. Both compounds inhibited PDE1A and PDE4D. The elevation of CBF was mimicked by the subtype-selective PDE inhibitor rolipram (PDE4) and by 8-methoxymethyl-IBMX. In summary, our study shows, for the first time, that a Drosera extract and its flavonoid compounds increase the CBF of murine airways while antispasmodic effects were transferred to ASM.     

Synthesis and Evaluation of PDE5 Inhibitory Activity of Novel Pyrido[2＇,1＇：5,1]pyrazolo[4,3-d]pyrimidin-4-one Derivatives

Novel pyridopyrazolopyrimidinone derivatives were designed and synthesized as potential PDE5 inhibitors. The target compounds demonstrated significant inhibitory activity against human platelet PDE5, but less potent than sildenafil.     

Synthesis and structure-activity relationship of N-arylrolipram derivatives as inhibitors of PDE4 isozymes

Structure activity studies of N-phenylrolipram derivatives have led to the identification of highly potent PDE4 inhibitors. The potential of these inhibitors for cellular activity was routinely assessed in an assay of fMLP induced oxidative burst in human eosinophils. Since first generation PDE4 inhibitors have been plagued with a number of unwanted side effects, parallel structure activity studies for competition with the [3H]-rolipram binding site in rat brain were performed. In this fashion 5-[4-(3-cyclopentyloxy-4-methoxyphenyl)-2-oxo-pyrrolidin-1-yl]-3-(3-methoxybenzyloxy)benzoic acid N',N'-dimethylhydrazide (22) was identified as a potent inhibitor of PDE4 which exhibits >1000 fold selectivity versus PDE3, and is a nanomolar inhibitor in all the cellular assays tested. Studies on the stereoselectivity of PDE4 inhibition of this class of rolipram based compounds revealed, that for example (S)-11 is a more potent inhibitor than (R)-11. This effect can also be observed in primary human cells where the (S)-enantiomer is about 10 fold more potent than the corresponding (R)-enantiomer.