Development of plasmin-selective inhibitors and studies of their structure-activity relationship

Various compounds were synthesized by combining three components at positions P1, P1' and P2'. Of these, N-(trans-4-aminomethylcyclohexanecarbonyl)-Tyr(O-2-bromobenzylo xycarbonyl)- octylamide inhibited plasmin selectively with IC50 values of 0.80 and 0.23 microM towards S-2251 and fibrin, respectively. This compound also inhibited plasma kallikrein, urokinase, thrombin and trypsin with IC50 values of 10, > 50, > 50 and 1.6 microM, respectively.     

Development of a quantitative structure-activity relationship model for inhibition of gram-positive bacterial cell growth by biarylamides

A set of compounds consisting of a new and diverse collection of biarylamides was examined using quantitative structure-activity relationship techniques for the purpose of developing a model to describe inhibition of gram-positive bacterial growth (minimum inhibition concentration). The model was sought in order to obtain insight for designing new molecules. A detailed analysis of the underlying structure-activity relationship helped provide insight concerning which structural features of the molecules modulated the activity of the compounds against gram-positive organisms.     

A structure-activity relationship study of brusatol, an antitumor quassinoid

Analogues of brusatol (2) were prepared and examined for their cytotoxic activity by using P-388 murine leukemia cells. The following structure-activity relationships were noted: (i) an enone carbonyl oxygen or an enolic oxygen at C-2 is essential, but an oxygen at C-3 not essential for the activity; (ii) the C-11 β-hydroxyl group is important for the activity; and (iii) the length of the ester alkoxy side chain at C-21 seems to have a slight effect on the activity.     

Wavelet frequency spectrum and its application in analyzing an oscillating chemical system

Based on the continuous wavelet transform (CWT), three types frequency spectra, wavelet frequency spectrum (WFS), point frequency spectrum (PFS) and time frequency spectrum (TFS), were developed. Two data sets were simulated and treated with the proposed spectra, the results indicated that WFS could extract the frequency information, which was like Fourier analysis but more accurate, PFS could obtain the frequency at any moment, TFS could show frequency change with time. These abilities of PFS and TFS were impossible for Fourier analysis. An oscillating chemical signal was processed with WFS and TFS. From the processed results, two points could be learned about the oscillating chemical reaction: one was the oscillating chemical reaction was a mixture one including two or more complex kinetics processes, the velocity of the switch from the reduced state (RS) to the oxidized state (OS) was faster than the reverse switch (from OS to RS); the other was increase of KBrO₃ could decrease the velocities of both switches, which led to the oscillating period became longer.     

Development of a pressure-driven nanofluidic control system and its application to an enzymatic reaction

A novel air-pressure-based nanofluidic control system was developed and its performance was examined. We found that the flow in a 100 nm scale nanochannel on a chip (called an extended nanospace channel) could be controlled within the pressure range of 0.003–0.4 MPa, flow rate range of 0.16–21.2 pL/min, and residence time range of 24 ms–32.4 s by using the developed nanofluidic control system. Furthermore, we successfully demonstrated an enzyme reaction in which the fluorogenic substrate TokyoGreen-β-galactoside (TG-β-gal) was hydrolyzed to the fluorescein derivative TokyoGreen (TG) and β-galactose by the action of β-galactosidase enzyme as a calalyst in a Y-shaped extended nanospace channel. The parameters for the reaction kinetics, such as K _m, V _max and k _cat, were estimated for the nanofluidic reaction, and these values were compared with the results of bulk and microfluidic reactions. A comparison showed that the enzyme reaction rate in the Y-shaped extended nanospace channel increased by a factor of about two compared with the rates in the bulk and micro spaces. We thought that this nanospatial property resulted from the activated protons of water molecules in the extended nanospace. This assumption was supported by the result that the pH dependence of the maximum enzyme activity in the Y-shaped extended nanospace channel was slightly different from that in the bulk and micro spaces. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

New approach to molecular docking and its application to virtual screening of chemical databases

This paper describes the validation of a molecular docking method and its application to virtual database screening. The code flexibly docks ligand molecules into rigid receptor structures using a tabu search methodology driven by an empirically derived function for estimating the binding affinity of a protein-ligand complex. The docking method has been tested on 70 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. The lowest energy geometry produced by the docking protocol is within 2.0 A root mean square of the experimental binding mode for 79% of the complexes. The method has been applied to the problem of virtual database screening to identify known ligands for thrombin, factor Xa, and the estrogen receptor. A database of 10,000 randomly chosen "druglike" molecules has been docked into the three receptor structures. In each case known receptor ligands were included in the study. The results showed good separation between the predicted binding affinities of the known ligand set and the database subset.     

Chemical approaches to define the structure-activity relationship of heparin-like glycosaminoglycans

Heparin, the drug of choice for the prevention and treatment of thromboembolic disorders, has been shown to interact with many proteins. Despite its widespread medical use, little is known about the precise sequences that interact with specific proteins. The minimum heparin binding sequence for FGF1 and FGF2 necessary to promote signaling was investigated. A characteristic pentasaccharide sequence, DEFGH, is required to accelerate the inhibition of thrombin and factor Xa in the blood-coagulation cascade. The first synthetic heparin pentasaccharide drug has been approved in Europe and the US and is sold under the trade name Arixtra. Other oligosaccharides with different composition are under clinical investigation. The enormous interest in the assembly of heparin oligosaccharides will stimulate the development of new synthetic approaches. Heparin-oligosaccharide-synthesis automation similar to that of DNA or peptide synthesis will play an important role.     

Development of vial wall sorptive extraction and its application to determination of progesterone in human serum

A novel sample preparation method, vial wall sorptive extraction (VWSE), which uses a vial whose internal wall is coated with polydimethylsiloxane (PDMS), was developed. The method was applied to the determination of progesterone in human serum sample. Human serum sample (0.5 mL) spiked with progesterone-¹³C₂ was pipetted into the VWSE device and vortex mixing was performed for 30 min. Then, the serum sample was removed and the vial rinsed with purified water. Fifty microliter of methanol as liquid desorption (LD) solvent was pipetted into the VWSE device and vortex mixing was performed for 10 min. Then, the extract was analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The correlation coefficient (r) of the calibration curve over the concentration range of 0.5–200 ng mL⁻¹ was 0.999. The limit of detection (LOD) and the limit of quantification (LOQ) were 0.1 and 0.5 ng mL⁻¹, respectively. The relative recoveries were 97.9% (RSD: 4.4%, n = 6) and 102.8% (RSD: 1.1%, n = 6) for progesterone spiked at 5 and 50 ng mL⁻¹, respectively. This simple, accurate, sensitive, and selective analytical method is applicable to the trace analysis of a minute amount of sample.     

Development and validation of an improved method for the quantitation of sertraline in human plasma using LC-MS-MS and its application to bioequivalence studies

A rapid and sensitive LC-MS-MS method for the quantitation of sertraline in human plasma was developed and validated. Sertraline and the internal standard, telmisartan, were cleaned up by protein precipitation from 100 μL of plasma sample, and analyzed on a TC-C18 column (5 μm, 150 × 4.6 mm i.d.) using 70% acetonitrile and 30% 10 mM ammonium acetate (0.1% formic acid) as mobile phase. The method was demonstrated to be linear from 0.1 ng/mL to 50 ng/mL with the lower limit of quantitation of 0.1 ng/mL. Intra- and inter-day precision were below 4.40% and 3.55%. Recoveries of sertraline at low, medium, and high levels were 88.0 ± 2.3%, 88.2 ± 1.9%, and 90.0 ± 2.0%, respectively. The method was successfully applied to a bioequivalence study of sertraline after a single oral administration of 50 mg sertraline hydrochloride tablets.     

Synthesis and structure-activity relationship study of monotesone-A, an antifungal component of Monotes engleri

The synthesis of (+/-)-monotesone-A, an antifungal component of Monotes engleri, as well as its four structural analogues were accomplished starting from the corresponding MOM-protected phloracetophenone and benzaldehyde derivatives. Antifungal activities of the five flavanone derivatives were studied against Candida albicans (14053 and ATCC 10231), Candida inconspicua, Candida dubliniensis and Candida krusei.     

Synthesis and structure-activity relationship study of isoglobotrihexosylceramide analogues

Invariant natural killer T (iNKT) cells are innate T lymphocytes that express T cell receptors binding to exogenous and endogenous glycosphingolpid antigens presented by a nonpolymorphic, non-MHC antigen presenting molecule, CD1d. The endogenous glycosphingolipid metabolite, isoglobotrihexosylceramide (iGb3), is the first known natural ligand for both human and mouse iNKT cells, whose activity has been confirmed in a variety of iNKT cell clones generated by different investigators, representing the majority of the iNKT cell population. The signaling pathway mediated by T cell receptor is largely influenced by the structural variation of glycosphingolpid antigens, leading to multiple and varied biological functions of iNKT cells. In order to investigate the structural requirements behind iGb3 triggered iNKT cell activation, the structure-activity relationship (SAR) of iGb3 needs to be characterized. In this study, iGb3 analogues containing 2' ', 3' ', 4' ' and 6' ' deoxy terminal galactose were synthesized for probing the SAR between iGb3 and TCR. The biological assays on the synthetic iGb3 analogues were performed with use of the murine iNKT cell hybridoma DN32.D3. The results showed that the 2' ' and 3' ' hydroxyl groups of terminal galactose play more important roles for the recognition of iGb3 by TCR; while 4' ' and 6' ' hydroxyl groups were not as crucial for this recognition. These studies might help to understand the general structural requirements for natural endogenous ligands recognized by iNKT cells.     

Cationic equilibrium ring-opening polymerization of bicyclic monomers and its application to chemical recycling

Spiro orthoesters give poly(cyclic orthoester)s by single ring-opening polymerization in the presence of acid catalysts, and this process undergoes the equilibrium polymerization. We have applied the function of equilibrium polymerization to chemical recycling of polymeric materials. Crosslinked poly(cyclic orthoester)s, prepared by radical additions of poly(cyclic orthoester)s possessing exomethylene groups and dithiols, efficiently decrosslinked to bifunctional spiro orthoesters in the presence of CF₃CO₂H in CH₂Cl₂. The dithiol-linked bifunctional spiro orthoester monomers, prepared by the radical additions of spiro orthoester possessing exomethylene group and dithiols, afforded the corresponding crosslinked polymers in the presence of CF₃CO₂H as a catalyst in bulk. The decrosslinking of the obtained crosslinked polymer proceeded quantitatively to obtain the corresponding bifunctional monomer at room temperature in CH₂Cl₂. Further, an acid-catalyzed reversible crosslinking-decrosslinking of a polymer having a spiro orthoester group in the side chain was carried out. The copolymer obtained by the radical copolymerization of 2-methylene-1,4,6-trioxaspiro[4.6]undecane with acrylonitrile was treated with CF₃CO₂H at −10 °C in CH₂Cl₂ to afford the crosslinked polymer quantitatively. The crosslinked polymer was then treated with CF₃CO₂H at room temperature at a low concentration in CH₂Cl₂ to recover the original polymer.     

Studying the explanatory capacity of artificial neural networks for understanding environmental chemical quantitative structure-activity relationship models

Although artificial neural networks (ANNs) have been shown to exhibit superior predictive power in the study of quantitative structure-activity relationships (QSARs), they have also been labeled a "black box" because they provide little explanatory insight into the relative influence of the independent variables in the predictive process so that little information on how and why compounds work can be obtained. Here, we have turned our interests to their explanatory capacities; therefore, a method was proposed for assessing the relative importance of variables indicating molecular structure, on the basis of axon connection weights and partial derivatives of the ANN output with respect to its input, which can identify variables that significantly contribute to network predictions, and providing a variable selection method for ANNs. We show that, by extending this approach to ANNs, the "black box" mechanics of ANNs can be greatly illuminated, thereby making it very useful in understanding environmental chemical QSAR models.     

Development of potent and selective plasmin and plasma kallikrein inhibitors and studies on the structure-activity relationship

Based on structure-activity relationship studies, we designed and synthesized plasmin (PL) and plasma kallikrein (PK) inhibitors. Trans-(4-aminomethylcyclohexanecarbonyl)-Tyr(O-Pic)-octylamide inhibited PL, PK, urokinase (UK) and thrombin (TH) with IC50 values of 0.53, 30, 5.3 and > 400 microm, respectively. Trans-(4-aminomethylcyclohexanecarbonyl)-Tyr(O-2-Pyrim)-4-carboxyanilide inhibited PL, PK, UK and TH with IC50 values of 36, 0.56, 440 and > 1,000 microM, respectively.     

CoMFA and CoMSIA 3D-quantitative structure-activity relationship model on benzodiazepine derivatives, inhibitors of phosphodiesterase IV

Recently, we reported structurally novel PDE4 inhibitors based on 1,4-benzodiazepine derivatives. The main interest in developing bezodiazepine-based PDE4 inhibitors is in their lack of adverse effects of emesis with respect to rolipram-like compounds. A large effort has thus been made toward the structural optimization of this series. In the absence of structural information on the inhibitor binding mode into the PDE4 active site, 2D-QSAR (H-QSAR) and two 3D-QSAR (CoMFA and CoMSIA) methods were applied to improve our understanding of the molecular mechanism controlling the PDE4 affinity of the benzodiazepine derivatives. As expected, the CoMSIA 3D contour maps have provided more information on the benzodiazepine interaction mode with the PDE4 active site whereas CoMFA has built the best tool for activity prediction. The 2D pharmacophoric model derived from CoMSIA fields is consistent with the crystal structure of the PDE4 active site reported recently. The combination of the 2D and 3D-QSAR models was used not only to predict new compounds from the structural optimization process, but also to screen a large library of bezodiazepine derivatives.     

The vanadium content of human dental enamel and its relationship to caries

A method for the determination of vanadium in dental enamel based on neutron activation analysis is described. After rapid dissolution of the irradiated sample in perchloric acid,⁵²V is quickly separated by solvent extraction from mixed perchloric-hydrochloric medium with N-benzoyl-N-phenyl hydroxylamine (BPHA) reagent in toluene in 95% yield. The technique was applied to samples from a low caries area of Dalmatia, Zemunik (DMFT<2), and a normal area, Novigrad (DMFT>5), in the same region. No significant differences in vanadium content were found between the two areas, nor between deciduous and permanent teeth. The levels in other areas of Yugoslavia were found to be similar, with a mean concentration of 3.7±1.5 ng·g⁻¹ for 37 samples, with a nearly normal distribution; a few impacted teeth gave lower values. The method can also be adapted to the analysis of bone and biological materials generally.