共查询到20条相似文献,搜索用时 31 毫秒
1.
XIAO Hong SHI Ya-wei WANG Li-li YUAN Jing-mingInstitute of Biotechnology Key Laboratory of Chemical Biology Molecular Engineering of National Ministry of Education Shanxi University Taiyuan P. R. China 《高等学校化学研究》2007,23(2):191-195
IntroductionProtein kinase Cα(PKCα) widely existed in thecells of human being and animals is one kind of serine/threonine kinase that can be rapidly activated by a vari-ety of factors such as Ca2 , cAMP and hormone, re-sulting in the signal transmissio… 相似文献
2.
A cyclic peptide, Tyr-Lys-c[-Lys-Thr-Glu(betaAla)-]-Val, incorporating a beta-Ala lactam side chain linker and designed to target the PDZ domains of the postsynaptic density protein 95 (PSD-95), has been synthesized and structurally characterized by NMR while free and bound to the PDZ1 domain of PSD-95. While bound, the lactam linker of the peptide makes a number of unique contacts outside the canonical PDZ binding motif, providing a novel target for PDZ-domain specificity as well as producing a 10-fold enhancement in binding affinity. Additionally, the cyclization greatly enhances the enzymatic stability, increasing the duration that the peptide inhibits the association between PSD-95 and glutamate receptors, effectively inhibiting the clustering of kainate receptors for over 14 hr after application. Highly specific regulation of kainate receptor action may provide a novel route for treatment of drug addiction and epilepsy. 相似文献
3.
[reaction: see text] Conformationally constrained side chain-bridged cyclic peptides were prepared using bis-carboxylic acid ring spacers. These macrocyles were designed to inhibit protein-protein interactions mediated by the third PDZ domain (PDZ3) of a mammalian neuronal protein, PSD-95. Isothermal titration calorimetry (ITC) experiments measured dissociation constants in the low micromolar range. For each compound, the change in entropy (TdeltaS) of binding either is comparable in magnitude to the enthalpy change (deltaH) or is the predominant driving force for association. 相似文献
4.
We present a novel homogeneous (“mix‐incubate‐read”) droplet microfluidic assay for specific protein detection in picoliter volumes by fluorescence polarization (FP), for the first time demonstrating the use of FP in a droplet microfluidic assay. Using an FP‐based assay we detect streptavidin concentrations as low as 500 nM and demonstrate that an FP assay allows us to distinguish droplets containing 5 μM rabbit IgG from droplets without IgG with an accuracy of 95%, levels relevant for hybridoma screening. This adds to the repertoire of droplet assay techniques a direct protein detection method which can be performed entirely inside droplets without the need for labeling of the analyte molecules. 相似文献
5.
Songling Ma Jiwon Choi Xuemei Jin Hyun-Yi Kim Ji-Hye Yun Weontae Lee Kang-Yell Choi Kyoung Tai No 《Journal of computer-aided molecular design》2018,32(5):643-655
The Wnt/β-catenin signaling pathway plays a significant role in the control of osteoblastogenesis and bone formation. CXXC finger protein 5 (CXXC5) has been recently identified as a negative feedback regulator of osteoblast differentiation through a specific interaction with Dishevelled (Dvl) protein. It was reported that targeting the Dvl–CXXC5 interaction could be a novel anabolic therapeutic target for osteoporosis. In this study, complex structure of Dvl PDZ domain and CXXC5 peptide was simulated with molecular dynamics (MD). Based on the structural analysis of binding modes of MD-simulated Dvl PDZ domain with CXXC5 peptide and crystal Dvl PDZ domain with synthetic peptide–ligands, we generated two different pharmacophore models and applied pharmacophore-based virtual screening to discover potent inhibitors of the Dvl–CXXC5 interaction for the anabolic therapy of osteoporosis. Analysis of 16 compounds selected by means of a virtual screening protocol yielded four compounds that effectively disrupted the Dvl–CXXC5 interaction in the fluorescence polarization assay. Potential compounds were validated by fluorescence spectroscopy and nuclear magnetic resonance. We successfully identified a highly potent inhibitor, BMD4722, which directly binds to the Dvl PDZ domain and disrupts the Dvl–CXXC5 interaction. Overall, CXXC5–Dvl PDZ domain complex based pharmacophore combined with various traditional and simple computational methods is a promising approach for the development of modulators targeting the Dvl–CXXC5 interaction, and the potent inhibitor BMD4722 could serve as a starting point to discover or design more potent and specific the Dvl–CXXC5 interaction disruptors. 相似文献
6.
Boisguerin P Leben R Ay B Radziwill G Moelling K Dong L Volkmer-Engert R 《Chemistry & biology》2004,11(4):449-459
SPOT synthesis permits parallel synthesis and screening of thousands of cellulose membrane-bound peptides to study protein-protein interactions in a proteomic context. Recognition of C-terminal residues is one of the most common binding features of PDZ domains. Unfortunately, most solid support-bound peptide libraries lack a free C terminus due to C-terminal fixation on the solid support. To overcome this restriction, we developed a robust methodology based on our previous strategy for generating peptides with authentic C termini. To validate this improved method, we screened a human peptide library of 6223 C termini with the syntrophin PDZ domain. Furthermore, using the same library, new peptide ligands derived from membrane proteins and receptors were found for the ERBIN PDZ domain. Finally, we identified the protein kinase breakpoint cluster region, which is known as a negative regulator of cell proliferation and oncogenic transformation, as an ERBIN ligand. 相似文献
7.
Like other protein-protein interaction domains, PDZ domains are involved in many key cellular processes. These processes often require that specific multiprotein complexes be assembled, a task that PDZ domains accomplish by binding to specific peptide motifs in target proteins. However, a growing number of experimental studies show that PDZ domains (like other protein-protein interaction domains) can engage in a variety of interactions and bind distinct peptide motifs. Such promiscuity in ligand recognition raises intriguing questions about the molecular and thermodynamic mechanisms that can sustain it. To identify possible sources of promiscuity and selectivity underlying PDZ domain interactions, we performed molecular dynamics simulations of 20 to 25 ns on a set of 12 different PDZ domain complexes (for the proteins PSD-95, Syntenin, Erbin, GRIP, NHERF, Inad, Dishevelled, and Shank). The electrostatic, nonpolar, and configurational entropy binding contributions were evaluated using the MM/PBSA method combined with a quasi-harmonic analysis. The results revealed that PDZ domain interactions are characterized by overwhelmingly favorable nonpolar contributions and almost negligible electrostatic components, a mix that may readily sustain promiscuity. In addition, despite the structural similarity in fold and in recognition modes, the entropic and other dynamical aspects of binding were remarkably variable not only across PDZ domains but also for the same PDZ domain bound to distinct ligands. This variability suggests that entropic and dynamical components can play a role in determining selectivity either of PDZ domain interactions with peptide ligands or of PDZ domain complexes with downstream effectors. 相似文献
8.
The human cardiac troponin (hcTn) has been implicated in diverse cardiovascular diseases (CDs). The protein function is regulated by the inter-subunit interaction between the N-terminal domain of hcTnC and the C-terminal switch peptide of hcTnI; disruption of the interaction has been recognized as a potential therapeutic strategy for CDs. Here, we report use of biogenic medicines as small-molecule competitors to directly disrupt the protein–protein interaction by competitively targeting the core binding site (CBS) of hcTnC NTD domain. A multistep virtual screening protocol is performed against a biogenic compound library to identify competitor candidates and competition assay is employed to verify the screening results. Consequently, two compounds Collismycin and Compound e are identified as strong competitors (CC50 < 10 μM) with hcTnI for hcTnC CBS site, while other tested compounds are found to have moderate (CC50 = 10–100 μM), low (CC50 > 100 μM) or no (CC50 = N.D.) potency. The competitor ligands are anchored at the core groove of hcTnC CBS site through aromatic and hydrophobic interactions, while few peripheral hydrogen bonds are formed to further confer specificity for domain–compound recognition. These molecular-level findings would benefit from further in vitro and in vivo studies at cellular and animal levels, which can help to practice the ultimate therapeutic purpose. 相似文献
9.
[structure: see text] Isothermal titration calorimetry (ITC) is used to study the thermodynamic consequences of systematically modifying the hydrophobic character of a single residue in a series of protein-binding ligands. By substituting standard and nonproteinogenic aliphatic amino acids for the C-terminal valine of the hexapeptide KKETEV, binding to the third PDZ domain (PDZ3) of the PSD-95 protein is characterized by distinct changes in the Gibbs free energy (DeltaG), enthalpy (DeltaH), and entropy (TDeltaS) parameters. One notable observation is that peptide binding affinity can be improved with a nonstandard residue. 相似文献
10.
Click triazole-based oligopeptides 1-3 were found to self-dimerize (K(dim) ≈ 10-680 M(-1)) in a head-to-tail fashion based on (1)H variable concentration, 2D, and H/D exchange NMR, VPO, CD, FT-IR studies and Gaussian 03 simulations. The dimerization constant K(dim) was shown to increase with increasing number of the amino acid units. Within the same oligomeric series, the K(dim) value is strongly affected by the size of the C-terminal end group. The tripeptides 2 are also excellent organogelators of aromatic solvents. 相似文献
11.
Sturza M Daviero-Minaud S Huvé M Renaut N Tiercelin N Mentré O 《Inorganic chemistry》2011,50(24):12499-12507
The (Ba,Sr)FeO(3-δ) system is known for its strong tendency for oxygen and vacancies to order into several forms including fully ordered pseudobrownmillerites, hexagonal perovskites with segregation of the vacancies in particular anionic layers and low deficient (pseudo)cubic compounds (generally δ < 0.27, Fe(3/4+)). We show for the first time, using a simple chemical process, the easy access to a large amount of vacancies (δ ≈ 0.5, Fe(3+)) within the room-temperature stable tetragonal (pseudocubic) Sr(0.8)Ba(0.2)FeF(~0.1)(O,F)(~2.5.) The drastic effect of the incorporation of a minor amount of fluoride passes through the repartition of local O/F/□ constraints shifting the tolerance factor into the pseudocubic range for highly deficient compounds. It is stable up to 670 K, where an irreversible reoxidation process occurs, leading to the cubic-form. The comparison with the cubic oxide Sr(0.8)Ba(0.2)FeO(~2.7) shows the increase of the resistivity (3D-VRH model) by two decades due to the almost single valent Fe(3+) of the oxofluoride. In addition, the G-type magnetic ordering shows relatively weak moment for Fe(3+) cations (M(Fe) ≈ 2.64(1) μB at room temperature) attributed to incoherent magnetic components expected from local disorder in such anionic-deficient compounds. 相似文献
12.
PDZ domains are important scaffolding modules that typically bind to the C-termini of their interaction partners. Several structures of such complexes have been solved, revealing a conserved binding site in the PDZ domain and an extended conformation of the bound peptide. A compendium of information regarding PDZ complexes demonstrates that dissimilar C-terminal peptides bind to the same PDZ domain, and different PDZ domains can bind the same peptides. A detailed understanding of the PDZ-peptide recognition is needed to elucidate this complexity. To this end, we have designed a family of docking protocols for PDZ domains (termed PDZ-DocScheme) that is based on simulated annealing molecular dynamics and rotamer optimization, and is applicable to the docking of long peptides (20-40 rotatable bonds) to both known PDZ structures and to the more complicated problem of homology models of these domains. The resulting protocol reproduces the structures of PDZ complexes with peptides 4-8 amino acids long within 1-2 A from the experimental structure when the docking is performed to the original structure. If the structure of the target PDZ domain is an apo structure or a homology model, the docking protocol yields structures within 3 A in 9 out of 12 test cases. The automated docking procedure PDZ-DocScheme can serve in the generation of a structural context for validation of PDZ domain specificity from mutagenesis and ligand binding data. 相似文献
13.
Souvik Guha Ibrahim Yussif El-Deeb Shalini Yadav Ranajit Das Dr. Kshatresh Dutta Dubey Mousumi Baruah Dr. Ludovic Gremaud Prof. Dr. Subhabrata Sen 《Chemistry (Weinheim an der Bergstrasse, Germany)》2022,28(63):e202202405
Herein we have reported the discovery of a pentacyclic building block comprised of fused indole-quinoline and piperidinone from the natural product perophoramidine as a formidable anticancer agent. The compounds were synthesized in six steps where the key steps involved a blue LED mediated intramolecular cyclopropanation of the indole intermediates and concomitant reduction of the associated aryl nitro moiety to nitroso in the molecule. Cytotoxicity screening of the compounds against an array of cancer cells that is, MCF7, HCT116 and A549 demonstrated 0.6 to 9 μM IC50s by few of the compounds. γH2AX immunofluorescence assay of the two most potent molecules from the phenotypic screening with anti-γ-H2AX Alexa Fluor 488 antibody revealed extensive DNA damage of the A549 cells which indicated probable PARP inhibition (similar to Perophoramidine). Through molecular docking and molecular dynamic (MD) simulation studies the binding efficiency of our compounds with poly(ADP-ribose)polymerase 1 (PARP 1) enzyme was determined. Chemiluminescent PARP Assay with Histone-coated strips indicated that the most active compounds from the phenotypic screening induced PARP-1 inhibition with IC50s of 1.3→1.5 μM. 相似文献
14.
CRALBP, cellular retinaldehyde-binding protein, is a retinoid-binding protein necessary for efficient regeneration of rod and cone visual pigments. The C terminus of CRALBP binds to the PDZ domains of EBP50/NHERF-1, which in turn bind to ezrin and actin, proteins localized to the apical processes of the retinal pigment epithelium. In this study, we examined structural features associated with the interaction of the two proteins. The C-terminal amino-acid sequence of 11 orthologous CRALBPs is either ENTAL, ENTAF or EDTAL. Peptides ending in each of these sequences inhibited the interaction of CRALBP and EBP50/NHERF-1 with the use of an overlay assay. Molecular modeling showed that both NTAL and NTAF formed similar networks of H bonds with PDZ1 of EBP50/ NHERF-1, and the side chains of both C-terminal Leu and Phe fit into the peptide-binding groove of PDZ1x CRALBP.11-cis-retinal and EBP50/NHERF-1 migrated as single components when analyzed individually by gel filtration and as a complex when mixed together before gel filtration. Complex formation was abolished by preincubation of EBP50/NHERF-1 with peptide EVENTAL. The ligand absorption spectrum of the complex was identical with that of CRALBP x 11-cis-retinal, demonstrating that complex formation did not perturb the ligand-binding domain of CRALBP. 相似文献
15.
Because of advances in the high-throughput screening technology, identification of a hit that can bind to a target protein
has become a relatively easy task; however, in the process of drug discovery, the following hit-to-lead and lead optimization
still remain challenging. In a typical hit-to-lead and lead optimization process, the analogues of the most promising hits
are synthesized for the development of structure–activity relationship (SAR) analysis, and in turn, in the effort of optimization
of lead compounds, such analysis provides guidance for the further synthesis. The synthesis processes are usually long and
labor-intensive. In silico searching has becoming an alternative approach to explore SAR especially with millions of compounds
ready to be screened and most of them can be easily obtained. Here, we report our discovery of 15 new Dishevelled PDZ domain
inhibitors by using such an approach. In our studies, we first developed a pharmacophore model based on NSC668036, an inhibitor
previously identified in our laboratory; based on the model, we then screened the ChemDiv database by using an algorithm that
combines similarity search and docking procedures; finally, we selected potent inhibitors based on docking analysis and examined
them by using NMR spectroscopy. NMR experiments showed that all the 15 compounds we chose bound to the PDZ domain tighter
than NSC668036. 相似文献
16.
Marsden DM Nicholson RL Skindersoe ME Galloway WR Sore HF Givskov M Salmond GP Ladlow M Welch M Spring DR 《Organic & biomolecular chemistry》2010,8(23):5313-5323
The screening of large arrays of drug-like small-molecules was traditionally a time consuming and resource intensive task. New methodology developed within our laboratories provides an attractive low cost, 3D microarray-assisted screening platform that could be used to rapidly assay thousands of compounds. As a proof-of-principle the platform was exploited to screen a number of quorum sensing analogs. Quorum sensing is used by bacterium to initiate and spread infection; in this context its modulation may have significant clinical value. 3D microarray slides were probed with fluorescently labeled ligand-binding domains of the LuxR homolog CarR from Erwinia carotovora subsp. carotovora. The 3D microarray platform was used to discover the biologically active chloro-pyridine pharmacophore, which was validated using a fluorometric ligand binding assay and ITC. Analogs containing the chloro-pyridine pharmacophore were found to be potent inhibitors of N-acyl-homoserine-lactone (AHL) mediated quorum sensing phenotypes in Serratia (IC(50) = ~5 μM) and Pseudomonas aeruginosa (IC(50) = 10-20 μM). 相似文献
17.
The PDZ domain of proteins mediates a protein-protein interaction by recognizing the hydrophobic C-terminal tail of the target protein. One of the challenges put forth by the DREAM (Discussions on Reverse Engineering Assessment and Methods) 2009 Challenge consists of predicting a position weight matrix (PWM) that describes the specificity profile of five PDZ domains to their target peptides. We consider the primary structures of each of the five PDZ domains as a numerical sequence derived from graph-theoretic models of each of the individual amino acids in the protein sequence. Using available PDZ domain databases to obtain known targets, the graph-theoretic based numerical sequences are then used to train a neural network to recognize their targets. Given the challenge sequences, the target probabilities are computed and a corresponding position weight matrix is derived. In this work we present our method. The results of our method placed second in the DREAM 2009 challenge. 相似文献
18.
Eyüp Başaran 《中国化学会会志》2023,70(7):1580-1590
In this research, two new series of N-arylsulfonyl hydrazone compounds ( 14 – 25 ) possessing a sulfonate moiety were synthesized and characterized by elemental analysis and various spectroscopic techniques including fourier transform infrared (FT-IR), 1H-, and 13C nuclear magnetic resonance (NMR). These compounds synthesized as target molecules ( 14 – 25 ) were tested for their in vitro acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibition activities and antioxidant potential. The antioxidant capacities of the tested molecules were determined by four different assays. The IC50 values of the screened molecules were determined in the range of 60.14 ± 0.25–84.81 ± 1.09 μM against AChE and in the range of 70.11 ± 0.67–93.60 ± 0.47 μM against BChE. In the AChE assay, 4-hydroxybenzaldehyde-based compound 25 (60.14 ± 0.25 μM) showed the highest activity in comparison to rivastigmine (501 ± 3.08 μM). This compound (71.42 ± 0.19 μM) is also one of the compounds with the highest activity against BChE. In the BChE assay, 2-hydroxybenzaldehyde-based compound 19 (70.11 ± 0.67 μM) indicated the highest activity in comparison to rivastigmine (19.95 ± 0.20 μM). In antioxidant activity studies, the tested molecules showed lower activities than the standard compounds (butylated hydroxytoluene and α-tocopherol). Consequently, some novel compounds can be used as potential inhibitor candidates in future studies. 相似文献
19.
Sirtuins are nicotinamide dinucleotide-dependent class III histone deacetylases catalyzing various physiological processes involved in cell proliferation, differentiation, apoptosis, and ageing. This makes them attractive targets in drug research. In order to simplify sirtuin substrates for assay development, two N(?)-acetyllysine derivatives, N(?)-acetyl-N(α)-(4-methyl-7-methoxycoumarin)lysine amide, and N(?)-acetyl-N(α)-(4-methyl-7-methoxycoumarin)lysine methyl ester were synthesized and evaluated as substrates for human SIRT1 in a capillary electrophoresis-based enzyme assay. Substrate, deacetylated product, and the coproduct nicotinamide were separated in a 200 mM phosphate/Tris buffer at pH 2.85. Field-amplified sample injection was employed to achieve sufficient assay sensitivity. While the ester derivative was not recognized by the enzyme, the amide substrate was effectively converted to the deacetylated product. The assay was subsequently validated with respect to range, linearity, limit of detection, and limit of quantification. Michaelis-Menten kinetic parameters, K(m) = 83 μM and V(max) = 6.8 μM/min were determined. The applicability of the assay for inhibitor screening was demonstrated using the known inhibitors sirtinol and the suramin derivate NF258. Resveratrol did not increase the deacetylation rate at concentrations of up to 200 μM. Docking experiments revealed the necessity of an amide function at the C-terminus of nonpeptide substrates while more structural freedom is tolerated at the N-terminus of N(?) -acetyllysine. 相似文献
20.
We describe the development and validation of a high-resolution screening (HRS) platform which couples gradient reversed-phase
high-performance liquid chromatography (RP-HPLC) on-line to estrogen receptor α (ERα) affinity detection using fluorescence
polarization (FP). FP, which allows detection at high wavelengths, limits the occurrence of interference from the autofluorescence
of test compounds in the bioassay. A fluorescein-labeled estradiol derivative (E2-F) was synthesized and a binding assay was
optimized in platereader format. After subsequent optimization in flow-injection analysis (FIA) mode, the optimized parameters
were translated to the on-line HRS bioassay. Proof of principle was demonstrated by separating a mixture of five compounds
known to be estrogenic (17β-estradiol, 17α-ethinylestradiol and the phytoestrogens coumestrol, coumarol and zearalenone),
followed by post-column bioaffinity screening of the individual affinities for ERα. Using the HRS-based FP setup, we were
able to screen affinities of off-line-generated metabolites of zearalenone for ERα. It is concluded that the on-line FP-based
bioassay can be used to screen for the affinity of compounds without the disturbing occurrence of autofluorescence. 相似文献