乙酰胆碱酯酶敏感性的变化与家蝇抗药性的关系

结合抗性机理, 对四个家蝇(Musca domestica vicina)品系头部的乙酰胆碱酯酶(AchE)对底物和抑制剂反应的动力学进行了研究.结果表明, AchE敏感性的降低是引起两个有机磷药剂(OP)抗性品系DDVP-R和Trichl-R对OP交互抗性的一个主要因子.Trichl-R对二氯苯醚菊酯无抗性, 而二氯苯醚菊酯抗性品系2Cl—R对所测定的OP有负交互抗性, 并且它的AchE对OP的敏感性较正常品系(NP)AchE的敏感性要高.AchE敏感性的变化, 反应在酶结构上, 主要是酶对抑制剂的亲和性(K_d)的变化, 而磷酸化速率(K₂)影响不大.同时对AchE的底物和抑制剂结合位点及结构变化进行了分析和探讨.     

Towards the development of antimicrobial drugs acting by inhibition of pathogen attachment to host cells: a need for polyvalency

The development of inhibitors of microbial attachment to target cells has been proposed recently as a possible novel approach to antimicrobial chemoprophylaxis and treatment. In this paper an attempt is made to contend that such artificial inhibitors must be polyvalent, i.e. capable of binding to the pathogen or its target by multiple bonds.     

QSAR study on 1-benzyl-4[w(substituted phthalimido)alkyl]piperidines:acetyl cholinesterase inhibitors.

QSAR studies on a series of 18 piperidine derivatives, which act as acetyl cholinesterase (AchE) inhibitors, have been performed using van der Waals volume (V omega) and topochemical index (tau). Significant correlations have been obtained, which make it clear that AchE inhibition activity is controlled dominantly by topo chemical index.     

Sulfamide derivatives as transition state analogue inhibitors for carboxypeptidase A

3-Phenyl-2-sulfamoyloxypropionic acid (2), 2-benzyl-3-sulfamoylpropionic acid (3), and N-(N-hydroxysulfamoyl)phenylalanine (5) have been synthesized and evaluated as inhibitors for carboxypeptidase A (CPA) to find that they inhibit the enzyme competitively with the Ki values in the microM range, suggesting that their binding modes to CPA are analogous to each other, and resemble the binding mode of N-sulfamoylphenylalanine (1) that has been established by the X-ray crystallographic method to form a complex with CPA in a manner reminiscent of the binding of a transition state in the catalytic pathway. It was concluded thus that they are a new type of transition state analogue inhibitors for CPA. (R)-N-Hydroxy-N-sulfamoyl-beta-phenylalanine (8) was shown to be also a potent CPA inhibitor (Ki = 39 microM), the high potency of which may be ascribed to the involvement of the hydroxyl in the binding of CPA, most likely forming bidentate coordinative bonds to the zinc ion in CPA together with the sulfamoyl oxygen atom.     

Purification of Acetylcholinesterase from Sea Urchin (Hemicentrotus pulcherrimus) Embryos by Affinity Chromatography

Only one form of acetylcholinesterase (AchE) was detected in Hemicentrotus pulcherrimus embryos. In H. pulcherrimus embryos as well as in the other sea urchin embryos, AchE activity begins to increase rapidly after gastrula stage.
Purification of AchE from plutei has been carried out by the procedure including affinity chromatography. Purified AchE had the activity 14,600 times higher than that of homogenate, and the final yield of AchE was 8%. The enzyme seems to be electrophoretically homogeneous, and has a molecular weight of 3 × 10⁵ as determined by Sepharose CL–6B column chromatography.     

Response surface methodology in docking study of small molecule BACE-1 inhibitors

Computational evaluation of ligand-receptor binding via docking strategy is a well established approach in structure-based drug design. This technique has been applied frequently in developing molecules of biological interest. However, any procedure would require an optimization set up to be more efficient, economic and time-saving. Advantages of modern statistical optimization methods over conventional one-factor-at-a-time studies have been well revealed. The optimization by experimental design provides a combination of factor levels simultaneously satisfying the requirements considered for each of the responses and factors. In this study, response surface method was applied to optimize the prominent factors (number of genetic algorithm runs, population size, maximum number of evaluations, torsion degrees for ligand and number of rotatable bonds in ligand) in AutoDock4.2-based binding study of small molecule β-secretase inhibitors as anti-alzheimer agents. Results revealed that a number of rotatable bonds in ligand and maximum number of docking evaluations were determinant variables affecting docking outputs. The interference between torsion degrees for ligand and number of genetic algorithm runs for docking procedure was found to be the significant interaction term in our model. Optimized docking outputs exhibited a high correlation with experimental fluorescence resonance energy transfer-based IC(50)s for β-secretase inhibitors (R(2)?=?0.9133).     

Inhibition of S-adenosylhomocysteine hydrolase by acyclic sugar adenosine analogue D-eritadenine. Crystal structure of S-adenosylhomocysteine hydrolase complexed with D-eritadenine

D-eritadenine (DEA) is a potent inhibitor (IC(50) = 7 nm) of S-adenosyl-l-homocysteine hydrolase (AdoHcyase). Unlike cyclic sugar Ado analogue inhibitors, including mechanism-based inhibitors, DEA is an acyclic sugar Ado analogue, and the C2' and C3' have opposite chirality to those of the cyclic sugar Ado inhibitors. Crystal structures of DEA alone and in complex with AdoHcyase have been determined to elucidate the DEA binding scheme to AdoHcyase. The DEA-complexed structure has been analyzed by comparing it with two structures of AdoHcyase complexed with cyclic sugar Ado analogues. The DEA-complexed structure has a closed conformation, and the DEA is located near the bound NAD(+). However, a UV absorption measurement shows that DEA is not oxidized by the bound NAD(+), indicating that the open-closed conformational change of AdoHcyase is due to the substrate/inhibitor binding, not the oxidation state of the bound NAD. The adenine ring of DEA is recognized by four essential hydrogen bonds as observed in the cyclic sugar Ado complexes. The hydrogen bond network around the acyclic sugar moiety indicates that DEA is more tightly connected to the protein than the cyclic sugar Ado analogues. The C3'-H of DEA is pointed toward C4 of the bound NAD(+) (C3'...C4 = 3.7 A), suggesting some interaction between DEA and NAD(+). By placing DEA into the active site of the open structure, the major forces to stabilize the closed conformation of AdoHcyase are identified as the hydrogen bonds between the backbone of His-352 and the adenine ring, and the C3'-H...C4 interaction. DEA has been believed to be an inactivator of AdoHcyase, but this study indicates that DEA is a reversible inhibitor. On the basis of the complexed structure, selective inhibitors of AdoHcyase have been designed.     

The crystal state binding of dithionite to deoxy-hemoglobin.

The crystal state binding of sodium dithionite to deoxyhemoglobin is reported. Dithionite has been used extensively to deoxygenate hemoglobin and myoglobin and there has been considerable interest among users of dithionite about its effect on protein structure and binding site(s). We have determined that dithionite binds to deoxygenated hemoglobin crystals at the interface of two molecules in the crystal lattice. Specific residues involved in hydrogen bonds or salt interactions with dithionite include His116 and His117 of the beta 2 subunit and Lys16 of the alpha 1 subunit of the adjacent hemoglobin molecule. No binding was observed at the symmetry related His116 and 117 beta 1 residues. We have shown that dithionite does not affect the native hemoglobin structure or the binding of several allosteric inhibitors to hemoglobin and can be used to mount T state crystals in the air.     

X-ray structure of a novel matrix metalloproteinase inhibitor complexed to stromelysin

A new class of matrix metalloproteinase (MMP) inhibitors has been identified by screening a collection of compounds against stromelysin. The inhibitors, 2,4,6-pyrimidine triones, have proven to be potent inhibitors of gelatinases A and B. An X-ray crystal structure of one representative compound bound to the catalytic domain of stromelysin shows that the compounds bind at the active site and ligand the active-site zinc. The pyrimidine triones mimic substrates in forming hydrogen bonds to key residues in the active site, and provide opportunities for placing appropriately chosen groups into the S1' specificity pocket of MMPS: A number of compounds have been synthesized and assayed against stromelysin, and the variations in potency are explained in terms of the binding mode revealed in the X-ray crystal structure.     

Synthesis and efficacy of 1-[bis(4-fluorophenyl)-methyl]piperazine derivatives for acetylcholinesterase inhibition, as a stimulant of central cholinergic neurotransmission in Alzheimer's disease

The cholinergic hypothesis of Alzheimer's disease (AD) has spurred the development of numerous structural classes of compounds with different pharmacological profile aimed at increasing central cholinergic neurotransmission. Thus proving a symptomatic treatment for this disease are cholinomimetics with the pharmacological profile of acetyl cholinesterase (AchE) inhibitors. The novel bioactive 1-[bis(4-fluorophenyl)-methyl]piperazine derivatives were synthesized under mild conditions using different aryl/alkyl halides and heterocyclic alkyl halides with 1-[bis(4-fluorophenyl)-methyl]piperazine in the presence of powdered potassium carbonate in N,N-dimethylformamide. All the synthesized compounds were characterized by spectroscopic techniques, elemental analysis and were screened for their efficacy as AchE inhibitor. Some derivatives in this class showed good inhibition against AchE as compared to neostigmine as standard.     

Hydrogen bonding penalty upon ligand binding

Ligand binding involves breakage of hydrogen bonds with water molecules and formation of new hydrogen bonds between protein and ligand. In this work, the change of hydrogen bonding energy in the binding process, namely hydrogen bonding penalty, is evaluated with a new method. The hydrogen bonding penalty can not only be used to filter unrealistic poses in docking, but also improve the accuracy of binding energy calculation. A new model integrated with hydrogen bonding penalty for free energy calculation gives a root mean square error of 0.7 kcal/mol on 74 inhibitors in the training set and of 1.1 kcal/mol on 64 inhibitors in the test set. Moreover, an application of hydrogen bonding penalty into a high throughput docking campaign for EphB4 inhibitors is presented, and remarkably, three novel scaffolds are discovered out of seven tested. The binding affinity and ligand efficiency of the most potent compound is about 300 nM and 0.35 kcal/mol per non-hydrogen atom, respectively.     

Interactions of thrombin with benzamidine-based inhibitors.

Trypsin and trypsin-like enzymes cleave C-terminal bonds of the basic amino acids Arg and Lys. Inhibitors of these enzymes have been found not only among Arg and Lys derivatives but also with structurally related benzamidines. Especially cyclic amides of 4-amidinophenylalanine were found to be inhibitors of thrombin. The most potent selective thrombin inhibitor of these type is N alpha-(beta-naphthylsulfonylglycyl)-4-amidinophenylalanine piperidine. From the X-ray crystal structures of thrombin and trypsin-inhibitor complexes the thrombin complexes formed with inhibitors derived from amidinophenylalanine have been modeled. These models allow valuable predictions to design inhibitors of improved selection and binding properties. Most recently, also the X-ray crystal structures of complexes of inhibitors with bovine thrombin have been solved.     

Peptidyl-prolyl isomerase inhibitors

Designed peptidyl-prolyl isomerase (PPIase) inhibitors of Pin1, cyclophilin (CyP), and FK506 binding protein (FKBP) are reviewed. Emphasis is placed on the design, structure, and biological activity of the inhibitors. While CyP and FKBP inhibitors have been explored fairly thoroughly, inhibitors of the relatively new Pin1 cell cycle regulator are in their infancy. Ligands designed for Pin1 and CyP have primarily been ground state analogues: alkenes and bicyclic compounds. For FKBP, more of the focus has been on analogues of bonds at the reactive center, the prolyl amide, because of the idea that the alpha-ketoamide of FK506 is an analogue of the twisted amide in the transition state.     

麦长管蚜在长期镉胁迫下超氧化物歧化酶和乙酰胆碱酯酶基因的表达水平变化

重金属污染已经对生物产生强大的选择压力。为了探索麦长管蚜Sitobion avenae经重金属镉长期胁迫后超氧化物歧化酶（SOD）和乙酰胆碱酯酶（AchE）基因表达的变化规律, 本研究模拟自然环境条件, 用Cd2+溶液浇灌土壤, 通过土壤-小麦-麦长管蚜体系连续处理麦长管蚜20代, 通过PCR扩增得到SOD和AchE基因cDNA片段, 并用Real-time PCR的方法对连续处理5, 10, 15和20代的蚜虫进行基因表达水平的研究。结果表明： 麦长管蚜SOD和AchE基因的表达水平会受Cd的浓度和连续处理世代数的影响。与对照相比, 在5 代和10 代时呈现上调模式, 而在处理20代后, 其表达则受到了抑制。40 mg/kg是关键的浓度, 高于此浓度时, 基因的表达会出现下调模式。由此可见, 低剂量的毒性胁迫会促使超氧化物歧化酶和乙酰胆碱酯酶的表达量增加, 而高剂量胁迫则会限制两种酶的防御作用。     

Kinetics, in silico docking, molecular dynamics, and MM-GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP-binding site inhibitors: the role of water molecules examined

With an aim toward glycogenolysis control in Type 2 diabetes, we have investigated via kinetic experiments and computation the potential of indirubin (IC?? > 50 μM), indirubin-3'-oxime (IC?? = 144 nM), KT5720 (K(i) = 18.4 nM) and staurosporine (K(i) = 0.37 nM) as phosphorylase kinase (PhKγtrnc) ATP-binding site inhibitors, with the latter two revealed as potent inhibitors in the low nM range. Because of lack of structural information, we have exploited information from homologous kinase complexes to direct in silico calculations (docking, molecular dynamics, and MMGBSA) to predict the binding characteristics of the four ligands. All inhibitors are predicted to bind in the same active site area as the ATP adenine ring, with binding dominated by hinge region hydrogen bonds to Asp104:O and Met106:O (all four ligands) and also Met106:NH (for the indirubins). The PhKγtrnc-staurosporine complex has the greatest number of receptor-ligand hydrogen bonds, while for the indirubin-3'-oxime and KT5720 complexes there is an important network of interchanging water molecules bridging inhibitor-enzyme contacts. The MM-GBSA results revealed the source of staurosporine's low nM potency to be favorable electrostatic interactions, while KT5720 has strong van der Waals contributions. KT5720 interacts with the greatest number of protein residues either by direct or 1-water bridged hydrogen bond interactions, and the potential for more selective PhK inhibition based on a KT5720 analogue has been established. Including receptor flexibility in Schr?dinger induced-fit docking calculations in most cases correctly predicted the binding modes as compared with the molecular dynamics structures; the algorithm was less effective when there were key structural waters bridging receptor-ligand contacts.     

Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase.

Crystal structures of the serine-carboxyl proteinase from Pseudomonas sp. 101 (PSCP), complexed with a number of inhibitors, have been solved and refined at high- to atomic-level resolution. All of these inhibitors (tyrostatin, pseudo-tyrostatin, AcIPF, AcIAF, and chymostatin, as well as previously studied iodotyrostatin and pseudo-iodotyrostatin) make covalent bonds to the active site Ser287 through their aldehyde moieties, while their side chains occupy subsites S1-S4 of the enzyme. The mode of binding of the inhibitors is almost identical for their P1 and P2 side chains, while significant differences are observed for P3 and P4 (if present). Kinetic parameters for the binding of these nanomolar inhibitors to PSCP have been established and correlated with the observed mode of binding. The preferences of this enzyme for a larger side chain in P2 as well as Tyr or Phe in P1 are explained by the size, shape, and characteristics of the S2 and S1 regions of the protein structure, respectively. Networks of hydrogen bonds involving glutamic and aspartic acids have been analyzed for the atomic-resolution structure of the native enzyme. PSCP contains a calcium-binding site that consists of Asp328, Asp348, three amide carbonyl groups, and a water molecule, in almost perfect octahedral coordination. The presence of Ca(2+) cation is necessary for the activity of the enzyme.     

Understanding the origins of time-dependent inhibition by polypeptide deformylase inhibitors

The continual bacterial adaptation to antibiotics creates an ongoing medical need for the development of novel therapeutics. Polypeptide deformylase (PDF) is a highly conserved bacterial enzyme, which is essential for viability. It has previously been shown that PDF inhibitors represent a promising new area for the development of antimicrobial agents, and that many of the best PDF inhibitors demonstrate slow, time-dependent binding. To improve our understanding of the mechanistic origin of this time-dependent inhibition, we examined in detail the kinetics of PDF catalysis and inhibition by several different PDF inhibitors. Varying pH and solvent isotope led to clear changes in time-dependent inhibition parameters, as did inclusion of NaCl, which binds to the active site metal of PDF. Quantitative analysis of these results demonstrated that the observed time dependence arises from slow binding of the inhibitors to the active site metal. However, we also found several metal binding inhibitors that exhibited rapid, non-time-dependent onset of inhibition. By a combination of structural and chemical modification studies, we show that metal binding is only slow when the rest of the inhibitor makes optimal hydrogen bonds within the subsites of PDF. Both of these interactions between the inhibitor and enzyme were found to be necessary to observe time-dependent inhibition, as elimination of either leads to its loss.     

Probing the electronic structures and properties of neutral and anionic ScSi n (0,−1) (n = 1–6) clusters using ccCA-TM and G4 theory

We apply molecular docking, molecular dynamics (MD) simulation, and binding free energy calculation to investigate and reveal the binding mechanism between five xanthine inhibitors and DPP-4. The electrostatic and van der Waals interactions of the five inhibitors with DPP-4 are analyzed and discussed. The computed binding free energies using MM-PBSA method are in qualitatively agreement with experimental inhibitory potency of five inhibitors. The hydrogen bonds of inhibitors with Ser630 and Asp663 can stabilize the inhibitors in binding sites. The van der Waals interactions, especially the key contacts with His740, Asn710, Trp629, and Tyr666 have larger contributions to the binding free energy and play important roles in distinguishing the variant bioactivity of five inhibitors.     

X-ray analysis of a thrombin inhibitor-trypsin complex

The three-dimensional structure of a thrombin inhibitor-trypsin complex has been determined by an X-ray analysis at 2.5 A resolution. The result has given experimental support to the mechanisms previously proposed by the authors for the selective inhibition of trypsin, thrombin, factor Xa, and plasmin by inhibitors with an arginine or lysine backbone. The differences in the amino acid sequences at the positions corresponding to Ilc63, Leu99, and Ser190 of trypsin give each enzyme different binding affinities toward inhibitors and result in the selective inhibition. Furthermore, the X-ray analysis has revealed a novel type of interaction between the inhibitor and trypsin. The hydrogen bonds between the inhibitor main chain and trypsin Gly216 play an essential role in the complex formation.