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1.
The search for the possible binding site of manzamine A to glycogen synthase kinase 3β(GSK-3β) was performed by molecular docking followed by molecular dynamics simulation and calculations of the Gibbs free energy of inhibitor—kinase binding. The cavity between the glycine-rich loop, the loop C, and the activation loop is the most likely site of interaction.  相似文献   

2.
The conformational change associated with the interfacial activation of Rhizomucor miehei lipase involves the displacement of an α-helical lid (residues 82–96) away from the active site on moving from water (high dielectric) to lipid (low dielectric). The presence of two media of very different dielectric properties suggests that electrostatic interactions play an important role in this process. We have used linearized Poisson–Boltzmann calculations to examine the key electrostatic interactions which contribute to lid stability in the closed and open states. It is the two charged residues of the lid, Arg86 and Asp91, that form the strongest electrostatic interactions with the rest of the protein. We identify key residues whose interactions with the lid are significantly perturbed by the change in the dielectric of the medium: Asp61, Arg80, Lys109, Glu117 and the active-site residues Asp203 and Asp256, all of which lie within approximately 20 ? of the lid. We suggest that these residues are good candidates for site-specific mutation studies, which could help elucidate their role in the lipase activation mechanism. Received: 27 May 1998 / Accepted: 17 September 1998 / Published online: 7 December 1998  相似文献   

3.
A series of nine 5-arylidenerhodanine derivatives was prepared in good yields and purity without the use of a solvent or catalyst under microwave-assisted condensation with some substituted isatins. All 5-arylidenerhodanines were evaluated as possible inhibitors of the CK1α/β, CDK5/p25, and GSK-3α/β kinases. None of them showed substantive inhibitory activity against these kinases when evaluated at the concentration of 10 μM.  相似文献   

4.
Glycosyl hydrolase family 16 (GHF16) truncated Fibrobacter succinogenes (TFs) and GHF17 barley 1,3-1,4-β-d-glucanases (β-glucanases) possess different structural folds, β-jellyroll and (β/α)8, although they both catalyze the specific hydrolysis of β-1,4 glycosidic bonds adjacent to β-1,3 linkages in mixed β-1,3 and β-1,4 β-d-glucans or lichenan. Differences in the active site region residues of TFs β-glucanase and barley β-glucanase create binding site topographies that require different substrate conformations. In contrast to barley β-glucanase, TFs β-glucanase possesses a unique and compact active site. The structural analysis results suggest that the tyrosine residue, which is conserved in all known 1,3-1,4-β-d-glucanases, is involved in the recognition of mixed β-1,3 and β-1,4 linked polysaccharide.  相似文献   

5.
17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1) catalyzes the last step of the estrogen biosynthesis, namely the reduction of estrone to the biologically potent estradiol. As such it is a potentially attractive drug target for the treatment of estrogen-dependent diseases like breast cancer and endometriosis. 17β-HSD1 belongs to the bisubstrate enzymes and exists as an ensemble of conformations. These principally differ in the region of the βFαG′-loop, suggesting a prominent role in substrate and inhibitor binding. Although several classes of potent non-steroidal 17β-HSD1 inhibitors currently exist, their binding mode is still unclear. We aimed to elucidate the binding mode of bis(hydroxyphenyl)arenes, a highly potent class of 17β-HSD1 inhibitors, and to rank these compounds correctly with respect to their inhibitory potency, two essential aspects in drug design. Ensemble docking experiments resulted in a steroidal binding mode for the closed enzyme conformations and in an alternative mode for the opened and occluded conformers with the inhibitors placed below the NADPH interacting with it synergically via π–π stacking and H-bond formation. Both binding modes were investigated by MD simulations and MM-PBSA binding free energy estimations using as representative member for this class compound 1 (50 nM). Notably, only the alternative binding mode proved stable and was energetically more favorable, while when simulated in the steroidal binding mode compound 1 was displaced from the active site. In parallel, ab initio studies of small NADPH-inhibitor complexes were performed, which supported the importance of the synergistic interaction between inhibitors and cofactor.  相似文献   

6.
Specificity and efficiency of thiored oxin action upon the 2-oxoacid dehydrogenase complexes are studied by using a number of thiored oxins and complexes. Bacterial and mammalian pyruvate and 2-oxoglutarate dehydrogenase systems display similar row of preference to thioredoxins that may result from thioredoxin binding to the homologous or common dihydrolipoamide dehydrogenase components of the complexes. The most sensitive tothioredoxin is the complex whose component exhibits the highest sequence similarity to eukaryotic thioredoxin reductase. Hence, thioredoxin binding to the complexes may be related to that in the thioredoxin reductase, a dihydrolipoamide dehydrogenase homolog. The highest potency of mitochondrial thioredoxin to affect the mitochondiral complexes is revealed. A 96–100% conservation of the mitochondrial thioredoxin structure is shown within the four known sequences and the N-terminus of the pigheart protein determined. Eleven thioredoxins tested biochemically are analyzed by multiple sequence alignment and homology modeling. Their effects correlate with the residues at the contact between the α 3/310 and α 1 helices, the length of the α 1 helix and charges in the α2–β3 and β4–β5 linkers. Polarization of the thioredoxin molecule and its active site surroundings are characterized. Thioredoxins with a highly polarized surface around the essential disulfide bridge (mitochondiral, pea f, and Arabidopsis thaliana h3) show low cross-reactivity as compared to the species with a decreased polarization of this area (e.g., from Escherichia coli). The strongest polarization of the whole molecule results in the highest magnitude of the electrostatic dipole vector of mitochondrial thioredoxin. Thiored oxins with the dipole orientation similar to that of the latter have the affinities for the 2-oxoacid dehydrogenase complexes, proportional to the dipole magnitudes. Thioredoxin with an opposite dipole orientation shows no effect. Activating and inhibitory thioredoxin disulfides are distinguished by the charges of the residues 13/14 (α1 helix(, 51 (α2–β3 linker), and 83/85 (β4–β5 linker), changing the dipole direction. The results show that the thioredoxin-target interplay may be controlled by the long-range interactions between the electrostatic dipole vectors of the proteins and the degree of their interface polarization.  相似文献   

7.
Molecular phylogenetic analysis of a novel thermophilic eubacterium isolated from an Iranian hot spring using 16S rDNA sequence showed that the new isolate belongs to genera Geobacillus. DNA pol I gene from this isolate was amplified, cloned, sequenced, and the three-dimensional (3D) structure of deduced amino acid sequence was predicted. Sequence analysis revealed the gene is 2,631 bp long, encodes a protein of 876 amino acids with a calculated molecular mass of 99 kDa, and belongs to family A DNA polymerases. Comparison of 3′–5′exonuclease domain of Klenow fragment (KF) with corresponding region of newly identified DNA pol I (MF), the large fragment of Bacillus stearothermophilus DNA pol I (BF) and Klentaq1, revealed not only deletions in three regions compared to KF, but that three of the four critical metal-binding residues in KF (Asp355, Glu357, Asp424, and Asp501) are altered in MF as well. Predicted 3D structure and sequence alignments between MF and BF showed that all critical residues in the polymerase active site are conserved.  相似文献   

8.
The inclusion interaction between quercetin and β-cyclodextrin (β-CD) binding site has been investigated, based on PM3 and ONIOM2 methods. The obtained results clearly indicate that the orientation in which the B ring of the guest molecule located near the secondary hydroxyls of the β-CD cavity is preferred in the binding energy. Moreover, Analyses regarding the complex structures suggest that one hydrogen bond between 7-hydroxy group (OH) of quercetin and 6-OH of β-CD is formed. This hydrogen bond interaction plays an important role in the bound quercetin/β-CD complex.  相似文献   

9.
Ion-electron reaction based fragmentation methods (ExD) in tandem mass spectrometry (MS), such as electron capture dissociation (ECD) and electron transfer dissociation (ETD) represent a powerful tool for biological analysis. ExD methods have been used to differentiate the presence of the isoaspartate (isoAsp) from the aspartate (Asp) in peptides and proteins. IsoAsp is a β3-type amino acid that has an additional methylene group in the backbone, forming a Cα–Cβ bond within the polypeptide chain. Cleavage of this bond provides specific fragments that allow differentiation of the isomers. The presence of a Cα–Cβ bond within the backbone is unique to β-amino acids, suggesting a similar application of ExD toward the analysis of peptides containing other β-type amino acids. In the current study, ECD and ETD analysis of several β-amino acid containing peptides was performed. It was found that N–Cβ and Cα–Cβ bond cleavages were rare, providing few c and z type fragments, which was attributed to the instability of the Cβ radical. Instead, the electron capture resulted primarily in the formation of a and y fragments, representing an alternative fragmentation pathway, likely initiated by the electron capture at a backbone amide nitrogen protonation site within the β amino acid residues.  相似文献   

10.

Background  

Recently there has been increased interest in pancreatic cholesterol esterase due to correlation between enzymatic activity in vivo and absorption of dietary cholesterol. Cholesterol esterase plays a role in digestive lipid absorption in the upper intestinal tract, though its role in cholesterol absorption in particular is controversial. Serine lipases, acetylcholinesterase, butyrylcholinesterase, and cholesterol esterase belong to a large family of proteins called the α/β-hydrolase fold, and they share the same catalytic machinery as serine proteases in that they have an active site serine residue which, with a histidine and an aspartic or glutamic acid, forms a catalytic triad. The aim of this work is to study the stereoselectivity of the acyl chain binding site of the enzyme for four diastereomers of an inhibitor.  相似文献   

11.
Pseudo[3]rotaxane type complexation of α- and β-cyclodextrins (α- and β-CDs, respectively) with N,N′-Diheptyl-4,4′-bipyridinium (diheptyl viologen; HV2+) was investigated. A spectral displacement method using p-nitrophenol as a dye revealed that α-CD and HV2+ formed a 2:1 host-guest complex with stability constants being 3280 and 976 M−1 as the first and second steps of complexation, respectively. 1H-NMR spectra strongly indicated that α-CD accommodated the heptyl groups of HV2+. Although previous studies based on circular dichroism spectroscopy suggested the primary hydroxy side of α-CD faced to the positively charged bipyridinium moiety od HV2+, 2D-NMR studies clearly demonstrated that the secondary hydroxy side of α-CD faced to the bipyridinium moiety. β-CD also formed a 2:1 complex with HV2+ with a similar fashion.  相似文献   

12.
Glycogen Synthase Kinase 3 (GSK-3) is a member of cellular kinase with various functions, such as glucose regulation, cellular differentiation, neuronal function and cell apoptosis. It has been proved as an important therapeutic target in type 2 diabetes mellitus and Alzheimer's disease. To better understand their structure–activity relationships and mechanism of action, an integrated computational study, including three dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, and molecular dynamics (MD), was performed on 79 (5-Imidazol-2-yl-4-phenylpyrimidin-2-yl)[2-(2-pyridylamino)ethyl]amine GSK-3 inhibitors. In this paper, we constructed 3D-QSAR using comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) method. The results showed that the CoMFA model (q 2 = 0.743, r2 = 0.980) and the CoMSIA model (q2 = 0.813, r2 = 0.976) had stable and reliable predictive ability. The electrostatic and H-bond donor fields play important roles in the models. The contour maps of the model visually showed the relationship between the activity of compounds and their three-dimensional structure. Molecular docking was used to identify the key amino acid residues at the active site of GSK-3 and explore its binding mode with ligands. Based on 3D-QSAR models, contour maps and the binding feature between GSK-3 and inhibitor, we designed 10 novel compounds with good potential activity and ADME/T profile. Molecular dynamics simulation results validated that Ile62, Val70 and Lys85 located in the active site play a key role for GSK-3 complexed with inhibitors. These results might provide important information for designing GSK-3 inhibitors with high activity.  相似文献   

13.
The X-ray crystal structure of the fluorescent antitumor sulfonamide carbonic anhydrase (CA, EC, 4.2.1.1) inhibitor (4-sulfamoylphenylethyl)thioureido fluorescein (1) in complex with the cytosolic isoform hCA II is reported, together with a modeling study of the adduct of 1 with the tumor-associated isoform hCA IX. Its binding to hCA II is similar to that of other benzesulfonamides, with the ionized sulfonamide coordinated to the Zn2+ ion within the enzyme active site, and also participating in a network of hydrogen bonds with residues Thr199 and Glu106. The scaffold of 1 did not establish polar interactions within the enzyme active site but made hydrophobic contacts (<4.5 A) with Gln92, Val121, Phe131, Val135, Leu198, Thr199, Thr200, and Pro202. The substituted 3-carboxy-amino-phenyl functionality was at van der Waals distance from Phe131, Gly132, and Val135. The bulky tricyclic fluorescein moiety was located at the rim of the active site, on the protein surface, and strongly interacted with the alpha-helix formed by residues Asp130-Val135. All these interactions were preserved in the hCA IX-1 adduct, but the carbonyl moiety of the fluorescein tail of 1 participates in a strong hydrogen bond with the guanidine moiety of Arg130, an amino acid characteristic of the hCA IX active site. This may account for the roughly 2 times higher affinity of 1 for hCA IX over hCA II and may explain why in vivo the compound specifically accumulates only in hypoxic tumors overexpressing CA IX and not in the normal tissues. The compound is in clinical studies as an imaging tool for acute hypoxic tumors.  相似文献   

14.
Glycogen synthase kinase-3 beta (GSK-3β) regulates glycogen metabolism and many different cellulars, including apoptosis, signaling, and neural. It is a crucial therapeutic receptor in heart disease, type 2 diabetes, and Alzheimer's. In this study, using computational methods, flavonoid compounds were investigated for potential inhibitors against GSK-3β. Virtual screening was utilized to investigate flavonoid compounds obtained from the PubChem database. Structure of human heart mitochondria of GSK-3β receptor constructed by homology modeling. Best binding poses were discovered via in silico molecular docking simulation. We surveyed noncovalent interactions among amino acid residues involved in the active site of the modeled Protein and compounds via molecular docking and molecular dynamics (MD).Moreover, ADMET characteristics of best docking conformers have been investigated. The obtained results revealed that compound 1 containing chromenone moiety with binding energy H-bond ?11.4 kcal/mol inhibited effectively binding pocket of the GSK-3β receptor. Moreover, MD simulation analysis (RMSD and radius of gyration indicated complex of the compound and GSK-3β receptor remained stable throughout 100 ns MD simulation, and also analysis of ADMET profiles revealed that selected compounds had good drug-likeness and pharmacokinetic properties. Hence, it was suggested that compounds with chromenone scaffold could potentially inhibit GSK-3β. Structural modification of the chromenone derivatives may result in the discovery of promising candidates for identifying novel drugs as GSK-3β inhibitors.  相似文献   

15.
Summary.  Wittig condensations of α,β-unsaturated carbonyl compounds with ethyl 3-ethoxy-4-(triphenylphosphoranylidene)-2-butenoate gave good to high yields of (2E,4E,6E)-ethyl 3-ethoxy-2,4,6-alkatrienoates. Some of last mentioned compounds were almost quatitatively hydrolysed to (4E,6E)-ethyl 3-oxo-4,6-alkadienoates. This method can therefore be used as an attractive alternative for the preparation of unsaturated conjugated β-keto esters previously prepared in very low yields from α,β-unsaturated carbonyl compounds and ethyl 3-oxo-4-(triphenylphosphoranylidene)butanoate. Present address: Boron Molecular Pty. Ltd., PO Box 756, Noble Park, VIC 3174, Australia. E-mail: cmoorhoff@boronmolecular.com Received June 17, 2002; accepted June 21, 2002  相似文献   

16.
Trivalent lanthanide cations are extensively being used in biochemical experiments to probe various dication-binding sites in proteins; however, the factors governing the binding specificity of lanthanide cations for these binding sites remain unclear. Hence, we have performed systematic studies to evaluate the interactions between La3+ and model Ca2+ - and Mg2+ -binding sites using density functional theory combined with continuum dielectric methods. The calculations reveal the key factors and corresponding physical bases favoring the substitution of trivalent lanthanides for divalent Ca2+ and Mg2+ in holoproteins. Replacing Ca2+ or Mg2+ with La3+ is facilitated by (1) minimizing the solvent exposure and the flexibility of the metal-binding cavity, (2) freeing both carboxylate oxygen atoms of Asp/Glu side chains in the metal-binding site so that they could bind bidentately to La3+, (3) maximizing the number of metal-bound carboxylate groups in buried sites, but minimizing the number of metal-bound carboxylate groups in solvent-exposed sites, and (4) including an Asn/Gln side chain for sites lined with four Asp/Glu side chains. In proteins bound to both Mg2+ and Ca2+, La3+ would prefer to replace Ca2+, as compared to Mg2+. A second Mg2+-binding site with a net positive charge would hamper the Mg2+ --> La3+ exchange, as compared to the respective mononuclear site, although the La3+ substitution of the first native metal is more favorable than the second one. The findings of this work are in accord with available experimental data.  相似文献   

17.
Metallo-β-lactamases (MβLs) are Zn(II)-based bacterial enzymes that hydrolyze β-lactam antibiotics, hampering their beneficial effects. In the most relevant subclass (B1), X-ray crystallography studies on the enzyme from Bacillus Cereus point to either two zinc ions in two metal sites (the so-called ‘3H’ and ‘DCH’ sites) or a single Zn(II) ion in the 3H site, where the ion is coordinated by Asp120, Cys221 and His263 residues. However, spectroscopic studies on the B1 enzyme from B. Cereus in the mono-zinc form suggested the presence of the Zn(II) ion also in the DCH site, where it is bound to an aspartate, a cysteine, a histidine and a water molecule. A structural model of this enzyme in its DCH mononuclear form, so far lacking, is therefore required for inhibitor design and mechanistic studies. By using force field based and mixed quantum–classical (QM/MM) molecular dynamics (MD) simulations of the protein in aqueous solution we constructed such structural model. The geometry and the H-bond network at the catalytic site of this model, in the free form and in complex with two common β-lactam drugs, is compared with experimental and theoretical findings of CphA and the recently solved crystal structure of new B2 MβL from Serratia fonticola (Sfh-I). These are MβLs from the B2 subclass, which features an experimentally well established mono-zinc form, in which the Zn(II) is located in the DCH site. From our simulations the εεδ and δεδ protomers emerge as possible DCH mono-zinc reactive species, giving a novel contribution to the discussion on the MβL reactivity and to the drug design process.  相似文献   

18.
The present study aimed to identify the prospective inhibitors of MurD, a cytoplasmic enzyme that catalyzes the addition of d-glutamate to the UDP-N-acetylmuramoyl-l-alanine nucleotide precursor in Mycobacterium tuberculosis (MTB), using virtual screening, docking studies, pharmacokinetic analysis, Molecular Dynamic (MD) simulation, and Molecular Mechanics Generalized Born and Surface Area (MM-GBSA) analyses. The three dimensional (3D) structure was determined based on the homology technique using a template from Streptococcus agalactiae. The modeled structure had three binding sites, namely; substrate binding site (Val18, Thr19, Asp39, Asp40, Gly75, Asn147, Gln171 and His192), the ATP binding site (Gly123, Lys124, Thr125, Thr126, Glu166, Asp283, and Arg314) and the glutamic acid binding site (Arg382, Ser463, and Tyr470). These residues mentioned above play a critical role in the catalytic activity of the enzyme, and their inhibition could serve as a stumbling block to the normal function of the enzyme. A total of 10,344 obtained from virtual screened of Zinc and PubChem databases. These compounds further screened for Lipinski rule of five, docking studies and pharmacokinetic analysis. Four compounds with good binding energies (ZINC11881196 = −10.33 kcal/mol, ZINC12247644 = −8.90 kcal/mol, ZINC14995379 =−8.42 kcal/mol, and PubChem6185 = −8.20 kcal/mol), better than the binding energies of the ATP (−2.31 kcal/mol) and the ligand with known IC50, Aminothiazole (−7.11 kcal/mol) were selected for the MD simulation and MM-GBSA analyses. The result of the analyses showed that all the four ligands formed a stable complex and had the binding free energies better than the binding energy of ATP. Therefore, these ligands considered as suitable prospective inhibitors of the MurD after experimental validation.  相似文献   

19.
Cyclodextrins (CDs) are cyclic oligosaccharides that form inclusion complexes with lipophilic molecules through their hydrophobic central cavity. In this study, the effect of α-CD, hydroxylpropyl-β-CD (HP-β-CD) and mixtures of these two CDs on the aqueous solubility of cyclosporine A (CyA) was investigated. Infrared spectroscopy and thermal analysis were used to confirm CyA-CD complex formation. CyA aqueous solubility was increased by 10 and 80 fold in the presence of α-CD and HP β-CD, respectively. The phase-solubility profile for HP-β-CD was linear while that for α-CD had positive deviation from linearity. In the presence of constant concentration of α-CD (15% w/v), aqueous solubility of CyA was further increased upon addition of HP-β-CD up to a concentration of 20% w/v. At higher HP-β-CD concentrations, aqueous solubility of CyA was observed to decrease. Addition of sodium acetate (up to 5% w/v) to aqueous solutions containing 20% w/v HP-β-CD and increasing concentrations of α-CD resulted in a significant reduction in CyA solubility. Complex formation between CyA and both α-CD and HP-β-CD was confirmed by differential scanning calorimetry (DSC). No significant changes were observed in the IR spectra of either CyA or CD following complex formation suggesting chemical interaction between CyA and the CD was unlikely. Phase-solubility studies showed that α-CD had a much greater effect on the solubility of CyA than HP-β-CD. Addition of HP-β-CD to aqueous solutions of α-CD affected the solubility of CyA in these systems. A mixture of 15% w/v α-CD and 20% w/v HP-β-CD was optimal for increasing aqueous solubility of CyA.  相似文献   

20.
Twelve cardiac glycosides and aglycons were isolated from Strophanthus kombe seeds. Of these, eight were identified as cymarin, K-strophanthin-β, K-strophanthoside, periplocymarin, 17α-strophadogenin, erysimin (= helveticoside), erysimoside, and neoglucoerysimoside. Four glycosides, preliminarily designated Sk-x, Sk-y, Sk-z, and Sk-20, were new. Their chemical structures were established as 3β-O-β-D-glucopyranosyl-5β,14β,16β-trihydroxy-19-oxo-17α-card-20(22)enolide (17α-strophadogenin-3-O-β-D-glucoside), 3β-O-β-D-cymaropyranosyl-5β,14β,16β-trihydroxy-19-oxo-17α-card-20(22)enolide (17α-strophadogenin-3-O-β-D-cymaroside), 3β-O-β-D-cymaropyranosyl-4′-O-β-D-glucopyranosyl-6″-O-β-D-glucopyranosyl-5β, 14β,16β-trihydroxy-19-oxo-17α-card-20(22)enolide (17α-strophadogenin-3-O-strophanthotrioside), and 3-O-β-D-digitoxopyranosyl-4′-O-β-D-glucopyranosyl-6″-O-β-D-glucopyranosyl-5β,14β, 19-trihydroxy-card-20(22)enolide (strophanthidol-3-O-gentiobiosyldigitoxoside), respectively. __________ Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 156–159, March–April, 2006.  相似文献   

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