Quantitative structure-affinity relationship of 5-HT1A receptor ligands by the classification tree method

The influence of molecular structure of 346 ligands on their affinity for 5-HT_1A receptors was investigated. It was shown that the effectiveness of the proposed novel approach for interpretation of decision tree models compared favourably with the PLS method. In the context of the proposed approach, molecular fragments and their values of the relative influence on the affinity for 5-HT_1A receptors were defined.     

A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A,a selective kappa opioid receptor agonist

Combined ligand-based and target-based drug design approaches provide a synergistic advantage over either method individually. Therefore, we set out to develop a powerful virtual screening model to identify novel molecular scaffolds as potential leads for the human KOP (hKOP) receptor employing a combined approach. Utilizing a set of recently reported derivatives of salvinorin A, a structurally unique KOP receptor agonist, a pharmacophore model was developed that consisted of two hydrogen bond acceptor and three hydrophobic features. The model was cross-validated by randomizing the data using the CatScramble technique. Further validation was carried out using a test set that performed well in classifying active and inactive molecules correctly. Simultaneously, a bovine rhodopsin based “agonist-bound” hKOP receptor model was also generated. The model provided more accurate information about the putative binding site of salvinorin A based ligands. Several protein structure-checking programs were used to validate the model. In addition, this model was in agreement with the mutation experiments carried out on KOP receptor. The predictive ability of the model was evaluated by docking a set of known KOP receptor agonists into the active site of this model. The docked scores correlated reasonably well with experimental pK _i values. It is hypothesized that the integration of these two independently generated models would enable a swift and reliable identification of new lead compounds that could reduce time and cost of hit finding within the drug discovery and development process, particularly in the case of GPCRs.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

A homology-based model of the human 5-HT2A receptor derived from an in silico activated G-protein coupled receptor

A homology-based model of the 5-HT_2A receptor was produced utilizing an activated form of the bovine rhodopsin (Rh) crystal structure [1,2]. In silico activation of the Rh structure was accomplished by isomerization of the 11-cis-retinal (1) chromophore, followed by constrained molecular dynamics to relax the resultant high energy structure. The activated form of Rh was then used as a structural template for development of a human 5-HT_2A receptor model. Both the 5-HT_2A receptor and Rh are members of the G-protein coupled receptor (GPCR) super-family. The resulting homology model of the receptor was then used for docking studies of compounds representing a cross-section of structural classes that activate the 5-HT_2A receptor, including ergolines, tryptamines, and amphetamines. The ligand/receptor complexes that ensued were refined and the final binding orientations were observed to be compatible with much of the data acquired through both diversified ligand design and site directed mutagenesis.     

New guanidinium-based carboxylate receptors derived from 5-amino-pyrrole-2-carboxylate: synthesis and first binding studies

The syntheses of two new guanidinium-based carboxylate receptors 2a,b derived from 5-amino pyrrole-2-carboxylate 4 are described. These receptors bind N-acetyl alanine carboxylate and O-acetyl lactate efficiently in aqueous DMSO as could be shown by NMR studies. However, compared to previously reported guanidiniocarbonyl pyrrole receptors 1, the reversal in the direction of the amide group in 2a,b changes both the substrate selectivity (amides are now preferred over esters) and their relative binding affinities. Both effects can be explained based on the calculated complex structure.     

Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors

G-protein coupled receptors (GPCRs) comprise a large superfamily of proteins that are targets for nearly 50% of drugs in clinical use today. In the past, the use of structure-based drug design strategies to develop better drug candidates has been severely hampered due to the absence of the receptor’s three-dimensional structure. However, with recent advances in molecular modeling techniques and better computing power, atomic level details of these receptors can be derived from computationally derived molecular models. Using information from these models coupled with experimental evidence, it has become feasible to build receptor pharmacophores. In this study, we demonstrate the use of the Hybrid Structure Based (HSB) method that can be used effectively to screen and identify prospective ligands that bind to GPCRs. Essentially; this multi-step method combines ligand-based methods for building enriched libraries of small molecules and structure-based methods for screening molecules against the GPCR target. The HSB method was validated to identify retinal and its analogues from a random dataset of ∼300,000 molecules. The results from this study showed that the 9 top-ranking molecules are indeed analogues of retinal. The method was also tested to identify analogues of dopamine binding to the dopamine D2 receptor. Six of the ten top-ranking molecules are known analogues of dopamine including a prodrug, while the other thirty-four molecules are currently being tested for their activity against all dopamine receptors. The results from both these test cases have proved that the HSB method provides a realistic solution to bridge the gap between the ever-increasing demand for new drugs to treat psychiatric disorders and the lack of efficient screening methods for GPCRs. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Enantiomeric separations of amino acids with inductively coupled plasma carbon emission detection

A chiral crown ether column with a pH 1.9 perchloric acid buffered aqueous mobile phase is used to separate amino acid enantiomers by high performance liquid chromatography. An inductively coupled plasma atomic emission spectrometer coupled to the chromatographic system is used as a detector by monitoring the carbon atomic emission line at 193.09 nm. Seven underivatized amino acids are separated and detected resulting in an average mass detection limit of 5 ng (2.5 ng carbon). The chiral crown ether column resolves compounds with a primary amino group near the chiral center by forming a complex between the crown ether and an ammonium ion moiety from the sample. The -form amino acid always elutes faster than its antipode. The carbon emission detector provides nearly identical sensitivities and similar detection limits for any compounds with comparable mass percents of carbon. Quantification is performed on unknown ratios of amino acids using an internal standard without the need for a calibration curve. Summing the calculated amounts of and amino acid and comparing to the known mixture quantity results in an average error of 1.0% for the seven amino acids separated.     

Sensitive analysis of amino acids with carrier-mediated single drop microextraction in-line coupled with capillary electrophoresis

In order to analyze amino acids sensitively without derivatization, we have developed carrier-mediated single drop microextraction (SDME). Nonane-1-sulfonic acid was added to an acidic sample donor solution as a carrier to form neutral ion pair complexes with amino acids. The ion pair complexes were extracted to the organic phase, covering a drop of an aqueous basic acceptor phase hanging at the tip of a capillary, and then back-extracted to the basic acceptor phase, where both the amino acids and the carrier have negative charges and the ion pair complexes are broken. The resulting extract of enriched amino acids was injected into the capillary and analyzed by capillary electrophoresis. With 20-min SDME with agitation of the donor phase, enrichment factors of four aromatic amino acids were up to 120-fold, yielding the LOD of 70-500 nM. The linear dynamic ranges for corrected peak areas were 1-100 μM with linear correlation coefficients larger than 0.9959. With internal standardization, the intraday RSDs of migration times and corrected peak areas were 0.01-0.04% and 2.0-3.7%, respectively. The capabilities of sample cleanup including desalting and preconcentration of carrier-mediated SDME were demonstrated with the analysis of human urine after minimal pretreatment of acidification and centrifugation.     

Electromembrane extraction of amino acids from body fluids followed by capillary electrophoresis with capacitively coupled contactless conductivity detection

Electromembrane extraction (EME) proved to be a simple and rapid pretreatment method for analysis of amino acids and related compounds in body fluid samples. Body fluids were acidified to the final concentration of 2.5 M acetic acid and served as donor solutions. Amino acids, present as cations in the donor solutions, migrated through a supported liquid membrane (SLM) composed of 1-ethyl-2-nitrobenzene/bis-(2-ethylhexyl)phosphonic acid (85:15 (v/v)) into the lumen of a porous polypropylene hollow fiber (HF) on application of electric field. The HF was filled with 2.5 M acetic acid serving as the acceptor solution. Matrix components in body fluids were efficiently retained on the SLM and did not interfere with subsequent analysis. Capillary electrophoresis with capacitively coupled contactless conductivity detection was used for determination of 17 underivatized amino acids in background electrolyte solution consisting of 2.5 M acetic acid. Parameters of EME, such as composition of SLM, pH and composition of donor and acceptor solution, agitation speed, extraction voltage, and extraction time were studied in detail. At optimized conditions, repeatability of migration times and peak areas of 17 amino acids was better than 0.3% and 13%, respectively, calibration curves were linear in a range of two orders of magnitude (r(2)=0.9968-0.9993) and limits of detection ranged from 0.15 to 10 μM. Endogenous concentrations of 12 amino acids were determined in EME treated human serum, plasma, and whole blood. The method was also suitable for simple and rapid pretreatment and determination of elevated concentrations of selected amino acids, which are markers of severe inborn metabolic disorders.     

Using Nearest Feature Line and Tunable Nearest Neighbor methods for prediction of protein subcellular locations

The subcellular location of a protein is closely correlated with it biological function. In this paper, two new pattern classification methods termed as Nearest Feature Line (NFL) and Tunable Nearest Neighbor (TNN) have been introduced to predict the subcellular location of proteins based on their amino acid composition alone. The simulation experiments were performed with the jackknife test on a previously constructed data set, which consists of 2,427 eukaryotic and 997 prokaryotic proteins. All protein sequences in the data set fall into four eukaryotic subcellular locations and three prokaryotic subcellular locations. The NFL classifier reached the total prediction accuracies of 82.5% for the eukaryotic proteins and 91.0% for the prokaryotic proteins. The TNN classifier reached the total prediction accuracies of 83.6 and 92.2%, respectively. It is clear that high prediction accuracies have been achieved. Compared with Support Vector Machine (SVM) and Nearest Neighbor methods, these two methods display similar or even higher prediction accuracies. Hence, we conclude that NFL and TNN can be used as complementary methods for prediction of protein subcellular locations.     

On-line preconcentration with a novel alkyl phosphinic acid extraction resin coupled with inductively coupled plasma mass spectrometry for determination of trace rare earth elements in seawater

A newly synthesized alkyl phosphinic acid resin (APAR) was used for on-line preconcentration of trace rare earth elements (REES, lanthanides including yttrium) and then determined by inductively coupled plasma mass spectrometry. REEs in seawater could be on-line concentrated on the APAR packed column (4.6 mm i.d. × 50 mm in length), and eluted from the column with 0.5 mL 0.1 mol L⁻¹ nitric acid within 30 s. An enrichment factor of nearly 400 was achieved for all REEs when the seawater sample volume was 200 mL, while the matrix and coexisting spectrally interfering ions such as barium, tin and antimony could be simultaneously separated. The detection limits of this proposed method for REEs were in the range from 1.43 pg L⁻¹ of holmium to 12.7 pg L⁻¹ of lanthanum. The recoveries of REEs were higher than 97.9%, and the precision of the relative standard deviation (R.S.D., n = 6) was less than 5%. The method has been applied to the determination of soluble REEs in seawater.     

Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins

Understanding of proteins adaptive to hypersaline environment and identifying them is a challenging task and would help to design stable proteins. Here, we have systematically analyzed the normalized amino acid compositions of 2121 halophilic and 2400 non-halophilic proteins. The results showed that halophilic protein contained more Asp at the expense of Lys, Ile, Cys and Met, fewer small and hydrophobic residues, and showed a large excess of acidic over basic amino acids. Then, we introduce a support vector machine method to discriminate the halophilic and non-halophilic proteins, by using a novel Pearson VII universal function based kernel. In the three validation check methods, it achieved an overall accuracy of 97.7%, 91.7% and 86.9% and outperformed other machine learning algorithms. We also address the influence of protein size on prediction accuracy and found the worse performance for small size proteins might be some significant residues (Cys and Lys) were missing in the proteins.     

Some engineering parameters for Propionic acid fermentation coupled with Ultrafiltration

The effect of circulation rate on permeate flux, the energy requirements for heating or cooling, the reactor homogeneity, and cell activity are discussed for a continuous culture system with cell recycle. The fermentation system was a continuous stirred-tank reactor with an ultrafiltration membrane unit for cell recycle. The membranes have a tubular configuration and are composed of a carbon support coated with zirconium oxide. The permeate flux obtained for a long-run fermentation with Propionibacterium acidi-propionici was higher when the circulation rate was increased: 5.13 L/m²-h for a circulation rate of 0.810 m³/h and 7.09 L/m²-h for 1.104 m³/h. The temperature rise inside the fermenter for different circulation rates was studied, allowing determination of the need of input or output of energy for temperature control. Residence time distribution studies showed that, with a circulation rate of 0.606 m³/h, the dead volume was 9.2%, whereas at 1.104 m³/h the reactor behavior was almost ideal. The influence of the circulation rate on loss of cell activity is also discussed, and rheological studies are suggested as an indirect indicator of cell viability. We hereby express our recognition for the ongoing collaborations with James Gaddy (University of Arkansas) and Gerard Goma (INSA, Toulouse, France).     

Rapid determination of p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values of 20 amino acids by CZE with UV and capacitively coupled contactless conductivity detections

A rapid and universal capillary zone electrophoresis (CZE) method was developed to determine the dissociation constants (pK _a) of the 20 standard proteogenic amino acids. Since some amino acids are poorly detected by UV, capacitively coupled contactless conductivity detection (C⁴D) was used as an additional detection mode. The C⁴D coupling proved to be very successful on a conventional CE-UV instrument, neither inducing supplementary analyses nor instrument modification. In order to reduce the analysis time for pK _a determination, two strategies were applied: (i) a short-end injection to reduce the effective length, and (ii) a dynamic coating procedure to generate a large electroosmotic flow (EOF), even at pH values as low as 1.5. As a result, the analysis time per amino acid was less than 2 h, using 22 optimized buffers covering a pH range from 1.5 to 12.0 at a constant ionic strength of 50 mM. pK _a values were calculated using an appropriate mathematical model describing the relationship between effective mobility and pH. The obtained pK _a values were in accordance with the literature. Figure a UV (1) and C⁴D (2) detectors placed on-line on the CE capillary. b Curve of effective mobility as a function of pH for histidine     

Direct determination of mercury in cosmetic samples by isotope dilution inductively coupled plasma mass spectrometry after dissolution with formic acid

A new method was proposed for the accurate determination of mercury in cosmetic samples based on isotopic dilution (ID)-photochemical vapor generation (PVG)-inductively coupled plasma mass spectrometry (ICP MS) measurement. Cosmetic samples were directly dissolved in formic acid solution and subsequently subjected to PVG for the reduction of mercury into vapor species following by ICP MS detection. Therefore, the risks of analyte contamination and loss were avoided. Highly enriched ²⁰¹Hg isotopic spike is added to cosmetics and the isotope ratios of ²⁰¹Hg/²⁰²Hg were measured for the quantitation of mercury. With ID calibration, the influences originating from sample matrixes for the determination of mercury in cosmetic samples have been efficiently eliminated. The effects of several experimental parameters, such as the concentration of the formic acid, and the flow rates of carrier gas and sample were investigated. The method provided good reproducibility and the detection limits were found to be 0.6 pg mL⁻¹. Finally, the developed method was successfully applied for the determination of mercury in six cosmetic samples and a spike test was performed to verify the accuracy of the method.     

Functionalization of chitosan with 3,4-dihydroxybenzoic acid for the adsorption/collection of uranium in water samples and its determination by inductively coupled plasma-mass spectrometry

A chitosan resin derivatized with 3,4-dihydroxybenzoic acid moiety (CCTS-DHBA resin) was newly synthesized for the collection/concentration of trace uranium by using cross-linked chitosan (CCTS) as base material, and the adsorption behavior of uranium as well as 60 elements on the resin was examined by passing the sample solutions through a mini-column packed with the resin. After the elution of the collected elements on the resin with 1 M HNO₃, the eluates were measured by inductively coupled plasma-mass spectrometry (ICP-MS).The CCTS-DHBA resin can adsorb several metal cations and several oxoanionic elements at appropriate pH. Among these metal ions, uranium shows an excellent adsorption behavior on this resin. Uranium as UO₂²⁺ species can be adsorbed on the resin by chelating mechanism with adsorption capacity of 330 mg g⁻¹ resin. Through the column treatment, the complete removal of large amounts of alkali and alkaline earth matrices without any loss of adsorption efficiency over prolonged usage were achieved with this resin.The CCTS-DHBA resin was applied to the adsorption/collection of uranium in tap water, river water and seawater samples with satisfactory results. The validation of the proposed method was carried out by analyzing uranium in the standard reference materials of SLRS-4, CASS-4, and NASS-5 after passing through the CCTS-DHBA resin, and the results showed good agreement with the certified values.     

GPCR‐CA: A cellular automaton image approach for predicting G‐protein–coupled receptor functional classes

Given an uncharacterized protein sequence, how can we identify whether it is a G‐protein–coupled receptor (GPCR) or not? If it is, which functional family class does it belong to? It is important to address these questions because GPCRs are among the most frequent targets of therapeutic drugs and the information thus obtained is very useful for “comparative and evolutionary pharmacology,” a technique often used for drug development. Here, we present a web‐server predictor called “GPCR‐CA,” where “CA” stands for “Cellular Automaton” (Wolfram, S. Nature 1984, 311, 419), meaning that the CA images have been utilized to reveal the pattern features hidden in piles of long and complicated protein sequences. Meanwhile, the gray‐level co‐occurrence matrix factors extracted from the CA images are used to represent the samples of proteins through their pseudo amino acid composition (Chou, K.C. Proteins 2001, 43, 246). GPCR‐CA is a two‐layer predictor: the first layer prediction engine is for identifying a query protein as GPCR on non‐GPCR; if it is a GPCR protein, the process will be automatically continued with the second‐layer prediction engine to further identify its type among the following six functional classes: (a) rhodopsin‐like, (b) secretin‐like, (c) metabotrophic/glutamate/pheromone; (d) fungal pheromone, (e) cAMP receptor, and (f) frizzled/smoothened family. The overall success rates by the predictor for the first and second layers are over 91% and 83%, respectively, that were obtained through rigorous jackknife cross‐validation tests on a new‐constructed stringent benchmark dataset in which none of proteins has ≥40% pairwise sequence identity to any other in a same subset. GPCR‐CA is freely accessible at http://218.65.61.89:8080/bioinfo/GPCR‐CA , by which one can get the desired two‐layer results for a query protein sequence within about 20 seconds. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

高效液相色谱-电喷雾串联质谱法测定饲料中的N-氨基甲酰-L-谷氨酸

建立了高效液相色谱-电喷雾串联质谱(HPLC-ESI-MS/MS)测定饲料中N-氨基甲酰-L-谷氨酸(NCG)含量的方法。饲料样品经甲醇提取、混合型强阴离子交换反相固相萃取(PXA)柱净化、HPLC分离后,采用ESI-MS/MS在正离子多反应监测(MRM)模式下进行检测,以碎片离子m/z 148.0和m/z 84.0进行定性,以碎片离子m/z 130.0进行定量。NCG的检出限(S/N >3)为24 μg/kg,定量限(S/N >10)为80 μg/kg,在20~1000 μg/L的质量浓度范围内峰面积与含量的线性关系良好,相关系数为0.9999。对饲料中NCG在80、200、500 mg/kg等3个添加水平下的回收率进行了测定,分别为104.0%、103.5%、95.3%,相对标准偏差分别为7.5%、6.3%、5.8%。结果表明,该方法操作简单,净化效果好,快速,灵敏度和准确度高,符合对饲料样品中NCG检测分析的要求。     

Synthesis of novel chitosan resin derivatized with serine diacetic acid moiety and its application to on-line collection/concentration of trace elements and their determination using inductively coupled plasma-atomic emission spectrometry

A novel chelating resin functionalized with serine diacetic acid moiety was synthesized by using chitosan as base material, and applied to the collection/concentration of trace elements in environmental water samples, followed by the determination using inductively coupled plasma-atomic emission spectrometer (ICP-AES). The synthesized resin, crosslinked chitosan serine diacetic acid (CCTS-SDA), showed good adsorption behavior toward trace amounts of Cd, Pb, Cu, Ni, V, Ga, Sc, In, and Th in a wide pH range. Additionally, rare earth elements also can be retained on the resin at neutral pH region. The adsorbed elements can be easily eluted with 1 mol L⁻¹ of nitric acid, and their recoveries were found to be 90-100%. The CCTS-SDA was packed in a mini-column, which was then installed in a computer-controlled auto-pretreatment system (Auto-Pret System) for on-line trace elements collection and determination with ICP-AES. Experimental parameters which related to the improvement of sensitivity and reproducibility were optimized. The limits of detection (LOD) for 13 elements were found to be in sub-ppb level. The proposed method with CCTS-SDA resin was successfully applied to the determination of trace elements in river water samples. The method was validated by determining a certified reference material of river water, SLRS-4.     

A rugged and transferable method for determining blood cadmium,mercury, and lead with inductively coupled plasma-mass spectrometry

A simple, high-throughput method for determining total cadmium, mercury, and lead in blood in cases of suspected exposure, using inductively coupled plasma-mass spectrometry (ICP-MS), has been developed and validated. One part matrix-matched standards, blanks, or aliquots of blood specimens were diluted with 49 parts of a solution containing 0.25% (w/w) tetramethylammonium hydroxide; 0.05% v/v Triton X-100 (blood cell membranes and protein solubilization); 0.01% (w/v) ammonium pyrolidinedithiocarbamate (mercury memory effect prevention and oxidation state stabilization, solubilization by complexation of all three metals); 1% v/v isopropanol (signal enhancement); and 10 μg/L iridium (internal standard). Thus the final dilution factor is 1 + 49. The method provides the basis for the determination of total cadmium, mercury, and lead for assessment of environmental, occupational, accidental ingestion or elevated exposures from other means. Approximately 80 specimens, including blanks, calibration standards, and quality control materials can be processed in an 8-h day. The method has been evaluated by examining reference materials from the National Institute of Standards and Technology, as well as by participation in six rounds of proficiency testing intercomparisons led by the Wadsworth Center of the New York State Department of Health. This method was developed for the purpose of increasing U.S. emergency response laboratory capacity. To this end, 33 U.S. state, and 1 district health department laboratories have validated this method in their own laboratories.     

Determination of Ca, K, Mg, Na, sulfate, phosphate, formate, acetate, propionate, and glycerol in biodiesel by capillary electrophoresis with capacitively coupled contactless conductivity detection

In this work, a new method employing capillary electrophoresis (CE) for the determination of several species in biodiesel is introduced. The concentrations of inorganic species (Na⁺, K⁺, Ca²⁺, Mg²⁺, SO₄²⁻, and PO₄³⁻) and glycerol are of interest to the regulatory authorities due to their ability to form undesirable compounds in engines. Additionally, other species of low molecular weight (e.g., acetate, formate, and propionate) are of interest because they contribute towards increasing the acidity. These species are formed by the degradation of biodiesel and cause damage to engines and the environment. The cation separation was performed in background electrolyte (BGE) composed of 30 mmol L⁻¹ of 2-(n-morpholino)ethanesulfonic acid (MES)/L-histidine (His), pH 6. The separation of anionic species was carried out in similar BGE with 0.2 mmol L⁻¹ cetyltrimethylammonium bromide (CTAB) added. For glycerol, a neutral species, its oxidation with periodate was employed. This well-known reaction is specific to polyols and generates iodate. The amount of iodate produced by the reaction was determined by CE. The separation was carried out in approximately 1 min using BGE composed of 30 mmol L⁻¹ acetic acid, pH 3. The analytical parameters evaluated were: linearity (r > 0.99), the RSD values for area and migration time were < 3.4% and 0.9%, respectively, and recovery was in the range of 89 to 107%.