Secretory protein profiling reveals TNF-α inactivation by selective and promiscuous Sec61 modulators

Cotransins are cyclic heptadepsipeptides that bind the Sec61 translocon to inhibit cotranslational translocation of a subset of secreted and type I transmembrane proteins. The few known cotransin-sensitive substrates are all targeted to the translocon by?a cleavable signal sequence, previously shown to be a critical determinant of cotransin sensitivity. By profiling two cotransin variants against a panel of secreted and transmembrane proteins, we demonstrate that cotransin side-chain differences profoundly affect substrate selectivity. Among the most sensitive substrates we identified is the proinflammatory cytokine tumor necrosis factor alpha (TNF-α). Like all type II transmembrane proteins, TNF-α is targeted to the translocon by its membrane-spanning domain, indicating that a cleavable signal sequence is not strictly required for cotransin sensitivity. Our results thus reveal an unanticipated breadth of translocon substrates whose expression is inhibited by Sec61 modulators.     

Identification of nitrated tyrosine residues of protein kinase G-Iα by mass spectrometry

The nitration of tyrosine to 3-nitrotyrosine is an oxidative modification of tyrosine by nitric oxide and is associated with many diseases, and targeting of protein kinase G (PKG)-I represents a potential therapeutic strategy for pulmonary hypertension and chronic pain. The direct assignment of tyrosine residues of PKG-I has remained to be made due to the low sensitivity of the current proteomic approach. In order to assign modified tyrosine residues of PKG-I, we nitrated purified PKG-Iα expressed in insect Sf9 cells by use of peroxynitrite in vitro and analyzed the trypsin-digested fragments by matrix-assisted laser desorption/ionization–time of flight mass spectrometry and liquid chromatography-tandem mass spectrometry. Among the 21 tyrosine residues of PKG-Iα, 16 tyrosine residues were assigned in 13 fragments; and six tyrosine residues were nitrated, those at Y71, Y141, Y212, Y336, Y345, and Y567, in the peroxynitrite-treated sample. Single mutation of tyrosine residues at Y71, Y212, and Y336 to phenylalanine significantly reduced the nitration of PKG-Iα; and four mutations at Y71, Y141, Y212, and Y336 (Y4F mutant) reduced it additively. PKG-Iα activity was inhibited by peroxynitrite in a concentration-dependent manner from 30 μM to 1 mM, and this inhibition was attenuated in the Y4F mutant. These results demonstrated that PKG-Iα was nitrated at multiple tyrosine residues and that its activity was reduced by nitration of these residues.     

Computational explorations to gain insight into the structural features of TNF-α receptor I inhibitors

TNF-α is a crucial cytokine in the process of inflammatory diseases. The adverse effect of TNF-α is mostly mediated by interaction of TNF-α with TNF-α receptor type I (TNFR1); therefore, discovery of molecules which can bind to TNFR1 preventing TNF-α-receptor complex formation would be of great interest. In the current study, using GRID/GOLPE program, a 3D-QSAR study was conducted on a series of synthetic TNFR1 binders, which resulted in a 3D-QSAR model with appropriate power of predictivity in internal (r²?=?0.94 and q²_LOO?=?0.74) and external (r²?=?0.66 and SDEP?=?0.42) validations. The structural features of TNFR1 inhibitors essential for exerting activity were explored by analyzing the contour maps of the 3D-QSAR model showing that steric interactions and hydrogen bonds are responsible for exerting TNFR1 inhibitory activity. To propose potential chemical entities for TNFR1 inhibition, PubChem database was searched and the selected compounds were virtually tested for anti-TNFR1 activity using the generated model, resulting in two potential anti-TNFR1 compounds. Finally, the possible interactions of the compounds with TNFR1 were investigated using docking studies. The findings in the current work can pave the way for designing more potent anti-TNFR1 inhibitors.     

Phase transition of lipid-like monolayer characterized by second harmonic generation

Phase transition of a lipid-like hemicyanine compound characterized by second harmonic generation is studied carefully. The phase transition is assigned as the first order transition between solid state and liquid state. The transition temperature increases with an increase in the surface molecular concentration. A monolayer structure parameter a which is very sensitive to the phase transition is introduced.     

A new method for determination of antithrombotic activity of egg white protein hydrolysate by microplate reader

A new method for the determination of antithrombotic activity of egg white protein hydrolysate(EWPH)was developed using amicroplate reader.Reaction was carried out at 37℃ and pH 7.2 with fibrinogen concentration 0.1%.Microplate reading wasconducted at 405 nm.Inhibition rate of EWPH on thrombin activity showed linearity(R~2=0.9971),when the inhibition rate was inthe range of 10-90%.The lower limit of detection(LLD,at 99.7%probability)and the biological limit of detection(BLD,at 99.7%probability)of the method were 10.643 and 40 mg/mL,respectively.The repeatability standard deviation(R.S.D.)was 1.08%.Thestandard deviation of the method was 0.027 AT-U.     

Regio-controlled synthesis of unsymmetrical pyrazine-fused sinomenine derivatives and discriminate substitution effects on TNF-α inhibitory activity

A unified regio-controlled synthetic protocol combined with the use of Suzuki couplings, in a diverse fashion, has been developed and successfully applied to the synthesis of various pairs of unsymmetrical pyrazine-fused derivatives of sinomenine, a natural immunemodulating alkaloid. Introduction of two vicinal aromatic substituents to the pyrazine functionality resulted in significant improvement of TNF-α inhibitory activity, and a number of new derivatives exhibited even higher inhibition rate than that of positive control SB202190. In addition, discriminate but complicated substitution effects of these sinomenine–pyrazine hybrids have been observed on tumor necrosis factor-α (TNF-α) inhibitory activity.     

Novel pyrrolopyrimidine-based α-helix mimetics: cell-permeable inhibitors of protein−protein interactions

There is considerable interest in developing non-peptidic, small-molecule α-helix mimetics to disrupt α-helix-mediated protein?protein interactions. Herein, we report the design of a novel pyrrolopyrimidine-based scaffold for such α-helix mimetics with increased conformational rigidity. We also developed a facile solid-phase synthetic route that is amenable to divergent synthesis of a large library. Using a fluorescence polarization-based assay, we identified cell-permeable, dual MDMX/MDM2 inhibitors, demonstrating that the designed molecules can act as α-helix mimetics.     

Structure-based design of conformationally constrained cyclic peptidomimetics to target the MLL1-WDR5 protein–protein interaction as inhibitors of the MLL1 methyltransferase activity

We described herein structure-based design,synthesis and evaluation of conformationally constrained,cyclic peptidomimetics to block the MLL1-WDR5 protein–protein interaction as inhibitors of the MLL1 histone methyltransferase activity.Our study has yielded cyclic peptidomimetics with very high binding affinities to WDR5(Kivalues 1 nmol/L) and function as antagonists of the MLL1 histone methyltransferase activity.     

Colorimetric determination of the activity of acetylcholinesterase and its inhibitors by exploiting the iodide-catalyzed oxidation of 3,3′,5,5′-tetramethylbenzidine by hydrogen peroxide

We describe a sensitive and selective colorimetric method for the determination of the activity of the enzyme acetylcholinesterase (AChE) and its inhibitors. Detection is based on the fact that acetylthiocholine iodide (ATCI) catalyzes the oxidation of the substrate 3,3′,5,5′-tetramethylbenzidine (TMB) by H₂O₂ to form a blue product (ox-TMB) with an absorption peak at 652 nm, but that oxidation is suppressed if ACTI previously is hydrolyzed by AChE to form thiocholine which decolorizes ox-TMB. In the presence of inhibitor, the activity of AChE is inhibited, thereby inducing the recovery of the blue coloration. Based on these findings, a highly sensitive method is developed for the determination of AChE and its inhibitors. The assay only requires mixing of buffer, solutions of ATCI, TMB, H₂O₂ and a sample containing AChE and photometric measurement. It works in the 0.05 to 5 mU?mL^?1 enzyme activity range and has a detection limit as low as 30 μU?mL^?1. The inhibitor neostigmine causes 50 % enzyme inhibition in 14.5 nM concentration. This analytical system has a wide scope in that it may be applied to the determination of the activity of various other hydrolases with proper substrates.

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Graphical abstract The blue product formed by the iodide-catalyzed oxidation of 3,3′5,5′-tetramethylbenzidine (TMB) by hydrogen peroxide is decolorized if acetylthiocholine iodide (ATCI) is hydrolyzed by acetylcholinesterase (AChE) to form thiocholine. If, however, AChE is inhibited, color formation will take place again.

     

Synthesis of 1-aryl-3-（3,4-dihydro-2H-chromen-5-yl） ureas as TNF-α inhibitors

A new series of compounds,1-aryl-3-(3,4-dihydro-2H-chromen-5-yl) ureas,have been synthesized and their structures were confirmed by FAB-MS and ~1H NMR.The preliminary pharmacological screening showed that these compounds inhibited TNF-αproduction in lipopolysaccharide (LPS)-stimulated THP-1 cells.     

Evidence for inhibition of HIF-1α prolyl hydroxylase 3 activity by four biologically active tetraazamacrocycles

Hypoxia inducible factor 1 (HIF-1) is central to the hypoxic response in mammals. HIF-1α prolyl hydroxylase 3 (PHD3) degrades HIF through the hydroxylation of HIF-1α. Inhibition of PHD3 activity is crucial for up-regulating HIF-1α levels, thereby acting as HIF-dependent diseases therapy. Macrocyclic polyamines which display high stability on iron-chelating may well inhibit the enzyme activity. Thus inhibition and interaction on catalytic PHD3 by four biologically active tetraazamacrocycles (1-4), which have two types of parent rings to chelate iron(ii) dissimilarly, were studied. The apparent IC(50) values of 2.56, 1.91, 5.29 and 2.44 μM, respectively, showed good inhibition potency of the four compounds. K(I) values were 7.86, 3.69, 1.59 and 2.92 μM for 1-4, respectively. Different inhibition actions of the two groups of compounds were identified. Circular dichroism (CD) and fluorescence spectrometries proved that one type of compound has significant effects on protein conformation while another type does not. Computational methodology was constructed to employ the equilibrium geometry of enzyme active site with the presence of substrate competitive inhibitor. Iron(ii) coordination in the active site by inhibitors of this kind induces conformational change of the enzyme and blocks substrate binding.     

Regulation of β-amylase activity by alkylresorcinols

The effects of two alkylresorcinols, namely, methylresorcinol (MR) and hexylresorcinol (HR), which are chemical analogues of the natural anabiosis factors of some bacteria, on the catalytic activity of β-amylase has been investigated. When water-soluble potato starch is used as a substrate, MR in a concentration ranging from 0.8 to 12.9 mmol/L raises the activity of β-amylase to 170%. HR at a concentration ranging from 0.05 to 0.35 mmol/L stimulates a weak increase in the activity of β-amylase to 115%. A further increase in the concentration (0.75 mmol/L) leads to inhibition by 50%. The interaction of MR with β-amylase allows one to increase the general yield of the hydrolysis products of potato and malt starch by 1.5 to 1.6 times, to enhance the rate of hydrolysis by 4 to 5 times, and to extend the temperature and pH ranges of catalysis. Non-competitive activation in the presence of MR and non-competitive inhibition in the presence of HR are observed upon determining the kinetic parameters of the starch hydrolysis by β-amylase modified with alkylresorcinols.     

Computer-aided design and discovery of protein–protein interaction inhibitors as agents for anti-HIV therapy

Protein–protein interactions (PPI) are involved in most of the essential processes that occur in organisms. In recent years, PPI have become the object of increasing attention in drug discovery, particularly for anti-HIV drugs. Although the use of combinations of existing drugs, termed highly active antiretroviral therapy (HAART), has revolutionized the treatment of HIV/AIDS, problems with these agents, such as the rapid emergence of drug-resistant HIV-1 mutants and serious adverse effects, have highlighted the need for further discovery of new drugs and new targets. Numerous investigations have shown that PPI play a key role in the virus’s life cycle and that blocking or modulating them has a significant therapeutic potential. Here we summarize the recent progress in computer-aided design of PPI inhibitors, mainly focusing on the selection of the drug targets (HIV enzymes and virus entry machinery) and the utilization of peptides and small molecules to prevent a variety of protein–protein interactions (viral–viral or viral–host) that play a vital role in the progression of HIV infection.     

Characterization of a core fragment of the rhesus monkey TRIM5α protein

Background  

Like all tripartite motif (TRIM) proteins, the retroviral restriction factor TRIM5α consists of RING, B-box 2 and coiled-coil domains, with a C-terminal B30.2(SPRY) domain. Although structures have been determined for some individual TRIM domains, the structure of an intact TRIM protein is unknown.     

Synthesis of potent inhibitors of β-ketoacyl-acyl carrier protein synthase III as potential antimicrobial agents

Mycobacterium tuberculosis FabH, an essential enzyme in the mycolic acid biosynthetic pathway, is an attractive target for novel anti-tubercolosis agents. Structure-based design and synthesis of 1-(4-carboxybutyl)-4-(4-(substituted benzyloxy)phenyl)-1H-pyrrole-2-carboxylic acid derivatives 7a-h, a subset of eight potential FabH inhibitors, is described in this paper. The Vilsmeier-Haack reaction was employed as a key step. The structures of all the newly synthesized compounds were identified by IR, 1H-NMR, 13C-NMR, ESI-MS and HRMS. The alamarBlue? microassay was employed to evaluate the compounds 7a-h against Mycobacterium tuberculosis H??Rv. The results demonstrate that the compound 7d possesses good in vitro antimycobacterial activity against Mycobacterium tuberculosis H??Rv (Minimum Inhibitory Concentration value [MIC], 12.5 μg/mL).These compounds may prove useful in the discovery and development of new anti-tuberculosis drugs.     

A Sesquiterpene Lactone from a Medicinal Herb Inhibits Proinflammatory Activity of TNF-α by Inhibiting Ubiquitin-Conjugating Enzyme UbcH5

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