Genome-wide biochemical analysis of Arabidopsis protein phosphatase using a wheat cell-free system

Plant genome possesses over 100 protein phosphatase (PPase) genes that are key regulators of signal transduction via phosphorylation/dephosphorylation event. Here we report a comprehensive functional analysis of protein serine/threonine, dual-specificity and tyrosine phosphatases using recombinant PPases produced by wheat cell-free protein synthesis system. Eighty-two recombinant PPases were successfully produced using Arabidopsis full-length cDNA as templates. In vitro PPase assay was performed using phosphorylated myelin basic protein as substrate. Among the AtPPases examined, 26 serine/threonine, three dual-specificity and one tyrosine PPases exhibited catalytic activity, including 20 serine/threonine and one dual-specificity PPases that showed in vitro activities for the first time. Our study demonstrates genome-wide biochemical analysis of AtPPases using wheat cell-free system, and provides new information and insights on enzyme activities.

Structured summary of protein interactions

PTP1dephosphorylatesMBP by phosphatase assay (View interaction).AtPP2CdephosphorylatesMBP by phosphatase assay (View interaction).POLTEdephosphorylatesMBP by phosphatase assay (View interaction).TOPP8dephosphorylatesMBP by phosphatase assay (View interaction).HAB1dephosphorylatesMBP by phosphatase assay (View interaction).ABI2dephosphorylatesMBP by phosphatase assay (View interaction).At1g34750dephosphorylatesMBP by phosphatase assay (View interaction).At1g43900dephosphorylatesMBP by phosphatase assay (View interaction).At3g15260dephosphorylatesMBP by phosphatase assay (View interaction).At5g53140dephosphorylatesMBP by phosphatase assay (View interaction).At1g18030dephosphorylatesMBP by phosphatase assay (View interaction).At3g06270dephosphorylatesMBP by phosphatase assay (View interaction).At2g25070dephosphorylatesMBP by phosphatase assay (View interaction).At3g02750dephosphorylatesMBP by phosphatase assay (View interaction).At5g10740dephosphorylatesMBP by phosphatase assay (View interaction).at4g26080dephosphorylatesMBP by phosphatase assay (View interaction).At4g28400dephosphorylatesMBP by phosphatase assay (View interaction).At5g06750dephosphorylatesMBP by phosphatase assay (View interaction).At4g31860dephosphorylatesMBP by phosphatase assay (View interaction).At3g17250dephosphorylatesMBP by phosphatase assay (View interaction).At4g38520dephosphorylatesMBP by phosphatase assay (View interaction).At3g05640dephosphorylatesMBP by phosphatase assay (View interaction).At5g66080dephosphorylatesMBP by phosphatase assay (View interaction).At1g79630dephosphorylatesMBP by phosphatase assay (View interaction).At2g30170dephosphorylatesMBP by phosphatase assay (View interaction).At5g24940dephosphorylatesMBP by phosphatase assay (View interaction).     

Potent mGluR5 antagonists: pyridyl and thiazolyl-ethynyl-3,5-disubstituted-phenyl series

We report the synthesis of four series of 3,5-disubstituted-phenyl ligands targeting the metabotropic glutamate receptor subtype 5: (2-methylthiazol-4-yl)ethynyl (1a-j,), (6-methylpyridin-2-yl)ethynyl (2a-j), (5-methylpyridin-2-yl)ethynyl (3a-j,), and (pyridin-2-yl)ethynyl (4a-j,). The compounds were evaluated for antagonism of glutamate-mediated mobilization of internal calcium in an mGluR5 in vitro assay. All compounds were found to be full antagonists and exhibited low nanomolar to subnanomolar activity.     

A monovalent agonist of TrkA tyrosine kinase receptors can be converted into a bivalent antagonist

Background

Receptor tyrosine kinases (RTK) act through dimerization. Previously it was thought that only bivalent ligands could be agonistic, whereas monovalent ligands should be antagonistic. This notion changed after the demonstration that monovalent ligands can be agonistic, including our report of a small molecule monovalent ligand “D3” that is a partial agonist of the NGF receptor TrkA. A bivalent “D3-linker-D3” was expected to increase agonism.

Methods

Dimeric analogs were synthesized and tested in binding, biochemical, and biological assays.

Results

One analog, 1-ss, binds TrkA with higher affinity than D3 and induces or stabilizes receptor dimers. However, 1-ss exhibited antagonistic activity, through two mechanisms. One mechanism is that 1-ss blocks NGF binding, unlike D3 which is non-competitive. Inhibition of NGF binding may be due to the linker of 1-ss filling the inter-receptor space that NGF traverses before docking. In a second mechanism, 1-ss acts as a pure antagonist, inhibiting NGF-independent TrkA activity in cells over-expressing receptors. Inhibition is likely due to 1-ss “freezing” the TrkA dimer in the inactive state.

Conclusions

Dimerization of an RTK can result in antagonism, through two independent mechanisms.

General significance

we report a small molecule monovalent agonist being converted to a bivalent antagonist.     

Characterization of a Wnt-binding site of the WIF-domain of Wnt inhibitory factor-1

A Wnt-binding site of the WIF-domain of Wnt inhibitory factor-1 was localized by structure-guided arginine-scanning mutagenesis in combination with surface plasmon resonance assays. Our observation that substitution of some residues of WIF resulted in an increased affinity for Wnt5a, but decreased affinity for Wnt3a, suggests that these residues may define the specificity spectrum of WIF for Wnts. These results hold promise for a more specific targeting of Wnt family members with WIF variants in various forms of cancer.

Structured summary of protein interactions

WIFbinds to Wnt7a by surface plasmon resonance (View Interaction)WIFbinds to Wnt4 by surface plasmon resonance (View Interaction)WIF and Wnt3aphysically interact by competition binding (View Interaction 1, 2, 3, 4,5, 6)WIFbinds to Wnt9b by surface plasmon resonance (View Interaction)WIFbinds to Wnt5a by surface plasmon resonance (View Interaction)WIFbinds to Wnt11 by surface plasmon resonance (View Interaction)WIFbinds to Wnt3a by surface plasmon resonance (View Interaction)Wnt-5a and WIFphysically interact by competition binding (View Interaction 1,2, 3, 4, 5, 6)     

Dammarane saponins from Gynostemma pentaphyllum

Dammarane-type saponins (1-7), together with five known compounds, were isolated from the aerial parts of Gynostemma pentaphyllum. Compounds 1-4, 6 and 7 induced the phosphorylation of ERK protein in primary rat cortical neurons, which indicates their potential neuroactivity. On the other hand, no induction of ERK phosphorylation was observed for HEK293 cells following treatment with saponins 1, 3, 4 and 7.     

Synthesis, transport and antiviral activity of Ala-Ser and Val-Ser prodrugs of cidofovir

We report the synthesis and biological evaluation of Ala-(Val-)l-Ser-CO₂R prodrugs of 1, where a dipeptide promoiety is conjugated to the P(OH)₂ group of cidofovir (1) via esterification by the Ser side chain hydroxyl group and an ethyl group (4 and 5) or alone (6 and 7). In a murine model, oral administration of 4 or 5 did not significantly increase total cidofovir species in the plasma compared to 1 or 2, but 7 resulted in a 15-fold increase in a rat model and had an in vitro EC₅₀ value against human cytomegalovirus comparable to 1. Neither 6 nor 7 exhibited toxicity up to 100 μM in KB or HFF cells.     

Acyl-CoA binding domain containing 3 (ACBD3) recruits the protein phosphatase PPM1L to ER-Golgi membrane contact sites

The metal-dependent protein phosphatase family (PPM) governs a number of signaling pathways. PPM1L, originally identified as a negative regulator of stress-activated protein kinase signaling, was recently shown to be involved in the regulation of ceramide trafficking at ER-Golgi membrane contact sites. Here, we identified acyl-CoA binding domain containing 3 (ACBD3) as an interacting partner of PPM1L. We showed that this association, which recruits PPM1L to ER-Golgi membrane contact sites, is mediated by a GOLD (Golgi dynamics) domain in ACBD3. These results suggested that ACBD3 plays a pivotal role in ceramide transport regulation at the ER-Golgi interface.

Structured summary of protein interactions

ACBD3 and PPM1Lcolocalize by fluorescence microscopy (View interaction)FYCO1physically interacts with PPM1L by pull down (View interaction)SEC14L2physically interacts with PPM1L by pull down (View interaction)ACBD3physically interacts with PPM1L by pull down (View interaction)SEC14L1physically interacts with PPM1L by pull down (View interaction)PPM1Lphysically interacts with ACBD3 by two hybrid (View interaction)     

The C-terminal domain of human Rev1 contains independent binding sites for DNA polymerase η and Rev7 subunit of polymerase ζ

Human Rev1 is a translesion synthesis (TLS) DNA polymerase involved in bypass replication across sites of DNA damage and postreplicational gap-filling. Rev1 plays an essential structural role in TLS by providing a binding platform for other TLS polymerases that insert nucleotides across DNA lesions (polη, polι, polκ) and extend the distorted primer-terminus (pol?). We use NMR spectroscopy to demonstrate that the Rev1 C-terminal domain utilizes independent interaction interfaces to simultaneously bind a fragment of the ’inserter’ polη and Rev7 subunit of the ’extender’ pol?, thereby serving as a cassette that may accommodate several polymerases making them instantaneously available for TLS.

Structured summary of protein interactions

REV1, REV3 and REV7physically interact by nuclear magnetic resonance (View interaction), molecular sieving (View interaction) and isothermal titration calorimetry (View interaction).REV3 and REV7bind by molecular sieving (View interaction)REV1 and Polη-RIR peptidebind by nuclear magnetic resonance (View interaction)REV1, REV3, REV7 and Polη-RIR peptidephysically interact by nuclear magnetic resonance (View interaction).     

The crystal structure of galactitol-1-phosphate 5-dehydrogenase from Escherichia coli K12 provides insights into its anomalous behavior on IMAC processes

Endogenous galactitol-1-phosphate 5-dehydrogenase (GPDH) (EC 1.1.1.251) from Escherichia coli spontaneously interacts with Ni²⁺-NTA matrices becoming a potential contaminant for recombinant, target His-tagged proteins. Purified recombinant, untagged GPDH (rGPDH) converted galactitol into tagatose, and d-tagatose-6-phosphate into galactitol-1-phosphate, in a Zn²⁺- and NAD(H)-dependent manner and readily crystallized what has permitted to solve its crystal structure. In contrast, N-terminally His-tagged GPDH was marginally stable and readily aggregated. The structure of rGPDH revealed metal-binding sites characteristic from the medium-chain dehydrogenase/reductase protein superfamily which may explain its ability to interact with immobilized metals. The structure also provides clues on the harmful effects of the N-terminal His-tag.

Structured summary of protein interactions

GPDH and GPDHbind by molecular sieving (View interaction)GPDH and GPDHbind by x-ray crystallography (View interaction)GPDH and GPDHbind by cosedimentation in solution (View interaction)     

Characterizing the neurite outgrowth inhibitory effect of Mani

Mani (myelin-associated neurite-outgrowth inhibitor) protein is implicated in both axonal guidance and axonal regeneration after central nervous system (CNS) injury. Here, we applied a neurite outgrowth assay, coupled with a siRNA-driven investigation and immunocytochemistry, to unveil Mani’s axonal outgrowth inhibitory effect in embryonic rat cortical primary neurons in vitro. We further demonstrate Mani’s neuronal localization in comparison with a principal subunit, Cdc27, of the anaphase promoting complex (APC). Considering the protein structure of Mani obtained via a series of bio-computational studies, we propose a Cdc27-Mani-APC-related signalling pathway may be involved in CNS axon regeneration.

Structured summary of protein interactions

MANIphysically interacts with DAZAP2 by two hybrid (View interaction)MANIphysically interacts with FAM168A by two hybrid (View interaction)MANIphysically interacts with YPEL2 by two hybrid (View interaction)MANIphysically interacts with TMTC1 by two hybrid (View interaction)     

Efficient synthesis of 3-O-thia-cPA and preliminary analysis of its biological activity toward autotaxin

The efficient synthesis of 3-O-thia-cPAs (4a-d), sulfur analogues of cyclic phosphatidic acid (cPA), has been achieved. The key step of the synthesis is an intramolecular Arbuzov reaction to construct the cyclic thiophosphate moiety. The present synthetic route enables the synthesis of 4a-d in only four steps from the commercially available glycidol. Preliminary biological experiments showed that 4a-d exhibited a similar inhibitory effect on autotaxin (ATX) as original cPA.     

Myosin filament assembly requires a cluster of four positive residues located in the rod domain

Myosin has an intrinsic ability to organize into ordered thick filaments that mediate muscle contraction. Here, we use surface plasmon resonance and light scattering analysis to further characterize the molecular determinants that guide myosin filament assembly. Both assays identify a cluster of lysine and arginine residues as important for myosin polymerization in vitro. Moreover, in cardiomyocytes, replacement of these charged residues by alanine severely affects the incorporation of myosin into the distal ends of the sarcomere. Our findings show that a novel assembly element with a distinct charge profile is present at the C-terminus of sarcomeric myosins.

Structured summary of protein interactions

WT LMMbinds to WT LMM by surface plasmon resonance (View Interaction)WT LMMbinds to CT2 LMM by surface plasmon resonance (View Interaction)WT LMMbinds to Alanine mutant LMM by surface plasmon resonance (View Interaction)WT LMM and WT LMMbind by light scattering (View Interaction)Alanine mutant LMM and Alanine mutant LMMbind by light scattering (View Interaction)WT LMM and Alanine mutant LMMbind by light scattering (View Interaction)     

Nonenzymic,biogenetic-like cyclization of a trienic acetal

The stereoselective synthesis of the trans,trans trienic acetal 9 is described. Alkylation of the lithio derivative of 2-methyl-1-hexene-5-yne (10) with ethylene oxide gave the acetylenic alcohol 11, which on reduction with sodium in liquid ammonia afforded the trans diene 12. Alkylation of the sodium enolate of acetylacetone with 13, the mesylate derived from 12, gave the dione 14; chlorination of 14 and deacylation of the resulting chloro dione 15 provided the α-chloro ketone 16. Conversion of 16 to the trans,trans acetal 9 was accomplished by means of a Cornforth olefin synthesis. Thus, stereoselective attack by the Grignard reagent derived from 1-ethylenedioxy-4-chlorobutane afforded from 16 the chlorohydrin 17, which on treatment with methanolic base was converted to the trans epoxide 18. Deoxygenation of 18 to give the trans,trans acetal 9 was accomplished via the intermediacy of the iodohydrin 19.     

N,N′-Bis(3-methoxysalicylidene)propane-1,2-diamine mononuclear 4f and heterodinuclear Cu-4f complexes: Synthesis, crystal structure and electrochemical properties

Reactions of H₂L [H₂L = N,N′-bis(3-methoxysalicylidene)propane-1,2-diamine] and Ln(NO₃)₃ · 6H₂O give rise to two different mononuclear 4f complexes, namely, {[(H₂L)La(NO₃)₃(MeOH)] · H₂O}_n (1) and [(H₂L)Nd(NO₃)₃] (2). Further additions of Cu(Ac)₂ · H₂O to the mononuclear 4f complexes yield expected heterodinuclear Cu-4f complexes [LCu(Me₂CO)Ln(NO₃)₃] (3, Ln = Nd; 4, Ln = Eu; 5, Ln = Dy). Complex 1 is a unique 1D polymeric chain structure, and 2 is one of the few structurally characterized discrete hexadentate salen-type mononuclear 4f complexes. Complexes 3-5 are similar to their analogues. However, they are prepared by a reversed synthetic route in contrast to their isomorphic complexes. Electrochemical behavior of heterodinuclear Cu-4f complexes 3-5 has been examined by cyclic voltammetry in acetonitrile. The redox potential of heterodinuclear Cu-4f complexes 3-5 shows significant anodic shift comparing to that of mononuclear copper complex (LCu). A tendency of anodic shift was observed in a sequence of 3 < 4 < 5. This results from the modulating effect of coordination geometry around Cu(II) ion on redox potential.     

Allosteric modulators of human A2B adenosine receptor

Background

Among adenosine receptors (ARs) the A_2B subtype exhibits low affinity for the endogenous agonist compared with the A₁, A_2A, and A₃ subtypes and is therefore activated when concentrations of adenosine increase to a large extent following tissue damages (e.g. ischemia, inflammation). For this reason, A_2B AR represents an important pharmacological target.

Methods

We evaluated seven 1-benzyl-3-ketoindole derivatives (7–9) for their ability to act as positive or negative allosteric modulators of human A_2B AR through binding and functional assays using CHO cells expressing human A₁, A_2A, A_2B, and A₃ ARs.

Results

The investigated compounds behaved as specific positive or negative allosteric modulators of human A_2B AR depending on small differences in their structures. The positive allosteric modulators 7a,b and 8a increased agonist efficacy without any effect on agonist potency. The negative allosteric modulators 8b,c and 9a,b reduced agonist potency and efficacy.

Conclusions

A number of 1-benzyl-3-ketoindole derivatives were pharmacologically characterized as selective positive (7a,b) or negative (8c, 9a,b) allosteric modulators of human A_2B AR.

General significance

The 1-benzyl-3-ketoindole derivatives 7–9 acting as positive or negative allosteric modulators of human A_2B AR represent new pharmacological tools useful for the development of therapeutic agents to treat pathological conditions related to an altered functionality of A_2B AR.     

Dopamine release and molecular modeling study of some coumarin derivatives

4-aryl-2-amino-6-(4-hydroxy-2-oxo-2H-chromen-3-yl)-pyridin-3-carbonitrile (1), 4-aryl-2-oxo-6-(4-hydroxy-2-oxo-2H-chromen-3-yl)-pyridin-3-carbonitriles (2a-2c), 3-(6-aryl-1,2,5,6- tetrahydro-2-thioxopyrimidin-4-yl)-4-hydroxy-2H-chromen-2-one (3a, 3b) and pyrazol-3-yl-4-hydroxycoumarin derivatives (4a-4c, 5, 6a, 6b, 7a, 7b, and 8a-8c) were prepared in order to measure their % change dopamine release in comparison to amphetamine as reference, using PC-12 cells in different concentrations. In addition, the molecular modeling study of the compounds into 3BHH receptor was also demonstrated. The calculated inhibition constant (k_i) implemented in the AutoDock program revealed identical correlation with the experimental results to that obtained binding free energy (ΔG_b) as both parameters revealed reasonable correlation coefficients (R²) being 0.51 involving 10 compounds; (1, 2b, 2c, 3a, 3b, 4a, 4b, 6a, and 8c).     

A concise synthesis of glucuronide metabolites of urolithin-B, resveratrol, and hydroxytyrosol

A simple and direct strategy to chemically synthesize O-β-d-glucuronides of urolithin-B 4, resveratrol 5, and the corresponding hydroxytyrosol derivatives 6, 7 (as a regioisomeric mixture), and 8 is described. The critical glycosylation step has been optimized using a structurally simple phenol, urolithin-B, by modification of several reaction parameters (solvent, promoter, and glucuronide donor). Very high yields have been obtained in the first synthesis of the O-β-d-glucuronide of urolithin-B 4. Extension of these reaction conditions was used for the synthesis of resveratrol-3-O-glucuronide 5 where a higher yield than previously reported was obtained by using the much more common trichloroacetimidate glucuronide donor. Finally, three O-β-d-glucuronides of hydroxytyrosol 6, 7, and 8 have been synthesized for the first time using chemical synthesis.     

Catechuic acid and ethyl 2,4,5-trihydroxybenzoate from d-glucose

Synthesis of catechuic acid (1) and ethyl 2,4,5-trihydroxybenzoate (2) from d-glucose-derived β-ketoester is described. The polyhydroxylated β-ketoester obtained from the hydrolysis of sugar β-ketoester 3 was subjected to an aldol-type condensation to get 4 that on enolization, dehydration, and hydrogenation afforded ethyl 2,4,5-trihydroxybenzoate (2). On the other hand, hydrogenation of aldol product 4 afforded polyhydroxylated keto-carbasugar 6, which on mild acid treatment and ester hydrolysis in basic media led to catechuic acid 1. Intermediate 4 is co-related to 3-dehydroshikimic acid, a biochemical intermediate from d-glucose in the synthesis of pro-catechuic acid.     

Antitumor agents 279. Structure-activity relationship and in vivo studies of novel 2-(furan-2-yl)naphthalen-1-ol (FNO) analogs as potent and selective anti-breast cancer agents

In our ongoing modification study of neo-tanshinlactone (1), we discovered 2-(furan-2-yl)naphthalen-1-ol (FNO) derivatives 3 and 4 as a new class of anti-tumor agents. To explore structure-activity relationships (SAR) of this scaffold, 18 new analogs, 6-12 and 14-24, were designed and synthesized. The C11-esters 7 and 12 displayed broad anti-tumor activity (ED₅₀ 1.1-4.3 μg/mL against seven cancer cell lines), while C11-hydroxymethyl 14 showed unique selectivity against the SKBR-3 breast cancer cell line (ED₅₀ 0.73 μg/mL). Compounds 15 and 22 displayed potent and selective anti-breast tumor activity (ED₅₀ 1.7 and 0.85 μg/mL, respectively, against MDA-MB-231). The SAR results demonstrated that the substitutions from the ring-opened lactone ring C of 1 are critical to the anti-tumor potency as well as the apparent tumor-tissue type selectivity. Treatment with 3 in Brca1^f11/f11p53^f5&6/f5&6Cre^c mice models significantly inhibited the proliferation of mammary epithelial cells and branching of mammary glands.     

Synthesis,angiopreventive activity,and in vivo tumor inhibition of novel benzophenone–benzimidazole analogs

Aim

The development of anticancer drugs with specific targets is of prime importance in modern biology. This study investigates the angiopreventive and in vivo tumor inhibition activities of novel synthetic benzophenone–benzimidazole analogs.

Main methods

The multistep synthesis of novel benzophenone–benzimidazole analogs (8a–n) allowing substitution with methoxy, methyl and halogen groups at different positions on the identical chemical backbone and the variations in the number of substituents were synthesized and characterized. The newly synthesized compounds were further evaluated for cytotoxic and antiproliferative effects against Ehrlich ascites carcinoma (EAC) cells. The potent lead compounds were further assessed for antiangiogenic effects in a CAM model and a tumor-induced vasculature in vivo model. The effect of angioprevention on tumor growth was verified in a mouse model.

Key findings

The cytotoxicity studies revealed that compounds 8f and 8n are strongly cytotoxic. Analyzing the structure–activity relationship, we found that an increase in the number of methyl groups in addition to methoxy substitution at the para position of the benzoyl ring in compound 8n resulted in higher potency compared to 8f. Furthermore, neovessel formation in in vivo systems, such as the chorioallantoic membrane (CAM) and tumor-induced mice peritoneum models, was significantly suppressed and reflected the tumor inhibition observed in mice.

Significance

These results suggest the potential clinical application of compound 8n as an antiangiogenic drug for cancer therapy.