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PubMed2004

Using NMR for ligand discovery and optimization.

Several recent technology-driven advances in the area of NMR have rekindled an interest in the application of the technology to problems in drug discovery and development. A unique aspect of NMR is that it has applicability in broadly different areas of the drug discovery and optimization processes. NMR techniques for screening aimed at the discovery of novel ligands or low molecular weight structures for fragment-based build up procedures are being applied commonly in the industry. Application of NMR in structure-guided drug design and metabonomics are also becoming routine. We present an overview of some of the most recent NMR developments in these areas.

Drug Design↗

PubMed2004

Multiplex polymerase chain reaction analysis of Glu-1 high-molecular-mass glutenin genes from wheat by capillary electrophoresis with laser-induced fluorescence detection.

The unique bread-making properties of wheat are closely correlated with composition and quantity of high-molecular-mass (HMW) glutenin subunits encoded by the Glu-1 genes. We report the development of a multiplex polymerase chain reaction (PCR) method to identify bread wheat genotypes carrying HMW glutenin allele composition of Glu-1 complex loci (Glu-A1, Glu-B1 and Glu-D1) by capillary electrophoresis(CE) with laser-induced fluorescence (LIF) detection. Two triplex primer sets of HMW glutenin subunit genes were examined. An automated and rapid CE-LIF technique is helpful in the multiplex PCR optimization process. Two fluorescent intercalating dyes (EnhanCE, and YO-PRO-1) are compared for detection of DNA fragments. Amplified DNA fragments of HMW glutenin Glu-1 genes were well separated both by agarose slab-gel electrophoresis and CE, and revealed minor differences between the sequences of 1Ax2*, 1Axnull, 1Bx6, 1Bx7, 1Bx17 and 1Dx5 genes. Moreover, CE technique requires samples of smaller volumes in comparison to slab-gel electrophoresis, and data can be obtained in less than 20 min. There was a very high concordance in the assessment of the molecular size of PCR-generated DNA markers. Fast and accurate identification of molecular markers of Glu-1 genes by CE-LIF can be an efficient alternative to standard procedure separation for early selection of useful wheat genotypes with good bread-making quality.

Base Sequence↗

PubMed2005

Oscillatory transverse electric field enhances mass transfer and protein capacity in ion-exchange electrochromatography.

Ion-exchange electrochromatography with an oscillatory electric field perpendicular to mobile-phase flow driven by pressure (pIEEC) was developed with a column design of rectangle cross-section. The effect of electric field strength on the dynamic binding capacity (DBC) was examined by frontal analysis of bovine serum albumin (BSA) adsorption to the packed beds of DEAE Sepharose FF in Tris-glycine buffer (pH 8.2). It was shown that the DBC at 10% breakthrough (Q(10)) in the pIEEC increased linearly with increasing the electric field strength. For example, with a packed-bed height of 15mm and electric potential gradient of 38V/cm, Q(10) increased four times over that in normal ion-exchange chromatography. So, the transverse electric field has created significant electro-kinetic mass transports (electroosmosis and electrophoresis) that intensified exterior liquid-film and intraparticle mass transfers, leading to the increased protein binding capacity. Due to the increased capacity in the pIEEC, partial resolution of BSA and IgG under an overload condition was realized without any process optimization. The results have revealed that an electric potential gradient of 20V/cm was enough to greatly enhance the DBC in the pIEEC, and when necessary, high electric field strength can be realized with a low applied voltage because the side distance of the column is usually an order of magnitude smaller than its height. The use of low voltage to carry out electrochromatography is a significant advantage of the pIEEC over conventional electrochromatography with axial electric field.

Adsorption↗

PubMed2006

Chromatographic refolding of recombinant human interferon gamma by an immobilized sht GroEL191-345 column.

Minichaperone sht GroEL191-345 was covalently coupled to NHS-activated Sepharose Fast Flow gel. Refolding of recombinant human interferon gamma (rhIFN-gamma) was carried out on a chromatographic column packed with immobilized minichaperone. The effects of salt concentration, urea concentration gradient, elution flow rate and protein loading on the refolding efficiency were investigated. The results indicated that immobilized sht GroEL191-345 chromatography was an effective protocol for the refolding of rhIFN-gamma. When loading 100 microl denatured rhIFN-gamma (17.8 mg/ml), the protein mass recovery and total activity obtained in this optimal process reached 74.25% and 6.74 x 10(6)IU/ml, respectively with the immobilized minichaperone column which was reused for 10 times with 25% decrease of renaturation capacity.

Chaperonin 60↗

PubMed2006

Sequential uniform designs for fingerprints development of Ginkgo biloba extracts by capillary electrophoresis.

A sequential procedure for the method of development of fingerprints based on a uniform design approach has been described in this paper. The sequential uniform design is used to reach the global optimum for a separation. The procedure is illustrated through developing the fingerprint of a Ginkgo biloba extract by capillary electrophoresis (CE) with diode array detection (DAD). The local overlap index (LOVI) is proposed as a criterion to evaluate the separation quality of two-dimensional hyphenated data in the optimization process. The successful application of the described techniques, including a sequential procedure, the CE-DAD hyphenated method and the LOVI criterion, shows their practicality in the fingerprint development of herbal medicines. However, some critical remarks on their use can also be made.

Buffers↗

PubMed2005

Brain aging: reorganizing discoveries about the aging mind.

New discoveries challenge the long-held view that aging is characterized by progressive loss and decline. Evidence for functional reorganization, compensation and effective interventions holds promise for a more optimistic view of neurocognitive status in later life. Complexities associated with assigning function to age-specific activation patterns must be considered relative to performance and in light of pathological aging. New biological and genetic markers, coupled with advances in imaging technologies, are enabling more precise characterization of healthy aging. This interdisciplinary, cognitive neuroscience approach reveals dynamic and optimizing processes in aging that might be harnessed to foster the successful aging of the mind.

Aging↗

PubMed2004

A topological sub-structural approach for predicting human intestinal absorption of drugs.

The human intestinal absorption (HIA) of drugs was studied using a topological sub-structural approach (TOPS-MODE). The drugs were divided into three classes according to reported cutoff values for HIA. "Poor" absorption was defined as HIA < or =30%, "high" absorption as HIA > or =80%, whereas "moderate" absorption was defined between these two values (30% < HIA < 79%). Two linear discriminant analyses were carried out on a training set of 82 compounds. The percentages of correct classification, for both models, were 89.02%. The predictive power of the models were validated by three test: a leave-one-out cross validation procedure (88.9% and 87.9%), an external prediction set of 127 drugs (92.9% and 80.31%) and a test set of 109 oral drugs with bioavailability values reported (93.58% and 91.84%). Finally, positive and negative sub-structural contributions to the HIA were identified and their possibilities in the lead generation and optimization process were evaluated.

Biological Availability↗

PubMed2006

Controlled release of cephalexin through gellan gum beads: effect of formulation parameters on entrapment efficiency, size, and drug release.

Gellan gum beads containing cephalexin were prepared by extruding the dispersion of cephalexin and gellan gum into a solution containing a mixture of calcium and zinc ions (counterions). Beads were prepared by changing experimental variables such as pH of the counterion solution and amount of cephalexin loading in order to optimize process variables on the final % drug entrapment efficiency, release rates, size, and morphology of the beads. Absence of chemical interactions between drug, anionic polymer, and counterions after production of beads was confirmed by Fourier transform infrared spectroscopy. Differential scanning calorimetry was used to understand the crystalline nature of the drug after its successful entrapment. These data indicated the amorphous dispersion of cephalexin in the polymer matrix. Beads were spherical in shape, with the average bead size ranging from 925 to 1183 microm as measured by the laser light scattering technique. Cephalexin entrapment of up to 69.24% was achieved. In vitro release studies were performed in 0.1 N HCl or pH 7.4 phosphate buffer and the release of cephalexin was achieved up to 6 h. Dynamic swelling studies were performed in 0.1 N HCl or pH 7.4 phosphate buffer. Diffusion coefficients were calculated for spherical geometry. The release data have been fitted to an empirical relation to estimate the transport parameters. Mathematical modeling studies were performed for spherical geometry by solving Fick's equation to compute concentration profiles. These results were correlated with the release profiles.

Cephalexin↗

PubMed2026

Comparative profiling of microbial community structure, enzyme potential, metabolic features, and volatile composition in craft and Jiafan Huangjiu processes.

Craft Huangjiu and Jiafan Huangjiu represent two distinct industrial Huangjiu product outcomes with contrasting volatile profiles. This study compared craft Huangjiu (L70) and Jiafan Huangjiu (L79) to characterize their physicochemical, microbial, gene-level functional, metabolic, and volatile features. Because L70 involved mid-fermentation addition of finished Huangjiu, this comparison was not intended to isolate the sole effect of fermentation interruption versus continued fermentation. L79 showed more extensive carbon and nitrogen utilization, with lower residual substrates and higher ethanol and acetic acid contents than L70, whereas L70 retained a less complete fermentation state. At the volatile level, GC-MS and volatile metabolomics consistently showed an ester-enriched profile in L79 and a more alcohol-dominant profile in L70. FlavorDB-based putative annotation and threshold-based OAV analysis further indicated distinct database-assigned descriptor distributions and potential odor-active compounds, with more OAV > 1 ester-related compounds in L79. Metagenomic analysis showed that L70 was dominated by Lactobacillus acetotolerans, whereas L79 contained higher relative abundances of Saccharomyces cerevisiae, Aspergillus oryzae, Aspergillus flavus, and Fructilactobacillus fructivorans. Metagenomic functional annotation showed higher representation of hydrolysis-related CAZy genes and ester-related enzyme annotations in L79. KEGG-based pathway mapping further indicated greater gene-level potential for ethanol-, acetate-, and acetyl-CoA-related metabolism in L79. Accordingly, the L70 profile should be interpreted as the integrated final-product outcome of process intervention, exogenous input, and subsequent fermentation. The findings provide a comparative basis for future flavor regulation and process optimization in Huangjiu and other fermented alcoholic beverages.

Volatile Organic Compounds↗

PubMed2026

Proteomic characterization of acidic aqueous extracts from Vicia faba L. pod valves identifies chitinase as a major co-extracted protein macromolecule.

Naturally acidic aqueous extracts from Vicia faba L. pod valves are being explored as sustainable, L-DOPA-oriented plant preparations. Pod valves represent an underutilized processing by-product reported to contain L-DOPA, a compound widely used in Parkinson's disease therapy, while acidic aqueous media may help preserve its physicochemical stability. However, the protein macromolecules co-extracted from V. faba pod valves under these conditions remain poorly characterized. This information is relevant because persistent plant proteins may influence extract composition, stability, susceptibility to degradation, and downstream processing requirements. Here, we characterized co-extracted V. faba protein macromolecules in aqueous pod-valve extracts prepared in ultrapure water or naturally acidic media, including 2% Phyllanthus emblica, 5% Punica granatum, and 2% Ribes rubrum. Protein profiles were first evaluated by SDS-PAGE and subsequently analyzed by nanoflow liquid chromatography coupled to high-resolution tandem mass spectrometry (nLC-MS/MS). Protein identifications were complemented with Gene Ontology annotation and a descriptive semi-quantitative assessment of relative protein representation across extraction media. Chitinase was the most represented V. faba-assigned protein macromolecule across the extracts, with additional highly represented proteins including glucan endo-1,3-beta-D-glucosidase, pathogenesis-related proteins, and polyphenol oxidase A1. These co-extracted proteins are mainly associated with plant defense, stress responses, cell-wall remodeling, and oxidative processing, suggesting that they may be relevant for extract quality attributes during handling and storage. This study provides a compositional proteomic reference for the co-extracted protein macromolecules present in acidic aqueous extracts from V. faba pod valves, supporting future studies on extract stability, processing optimization, and the development of standardized plant-based preparations.

Vicia faba↗

PubMed2005

Thymosin-loaded enteric microspheres for oral administration: preparation and in vitro release studies.

Thymosin, a water-soluble polypeptide compound, was encapsulated within enteric microspheres of acrylic acid resin II by modified oil in oil (o/o) emulsion solvent evaporation method. The mixture emulsifier composed of lecithin and Span 80 was critical to the formation of sphere-shaped thymosin microparticles. Optimizing process parameters, such as the volume ratio of organic solvent to water, initial drug feed and polymer concentration, resulted in high drug encapsulation efficiency of 89.7% (6% polymer concentration and 0.5% initial drug feed). In vitro release studies suggested that thymosin release from microspheres exhibited pH dependent profiles. For formulation with 6% polymer concentration and 0.5% initial drug feed, 68.7% thymosin was released within 4h in pH 6.8 PBS buffer, while only 6.5% was observed in acid medium.

Acrylates↗

PubMed2006

Novel interpenetrating network chitosan-poly(ethylene oxide-g-acrylamide) hydrogel microspheres for the controlled release of capecitabine.

This paper describes the synthesis of capecitabine-loaded semi-interpenetrating network hydrogel microspheres of chitosan-poly(ethylene oxide-g-acrylamide) by emulsion crosslinking using glutaraldehyde. Poly(ethylene oxide) was grafted with polyacrylamide by free radical polymerization using ceric ammonium nitrate as a redox initiator. Capecitabine, an anticancer drug, was successfully loaded into microspheres by changing experimental variables such as grafting ratio of the graft copolymer, ratio of the graft copolymer to chitosan, amount of crosslinking agent and percentage of drug loading in order to optimize process variables on drug encapsulation efficiency, release rates, size and morphology of the microspheres. A 2(4) full factorial design was employed to evaluate the combined effect of selected independent variables on percentage of drug release at 5h (response). Regression models were used for the response and data were compared statistically using the analysis of variance (ANOVA). Grafting, interpenetrating network formation and chemical stability of the capecitabine after encapsulation into microspheres was confirmed by Fourier infrared spectra (FTIR). Differential scanning calorimetry (DSC) and X-ray diffractometry (XRD) studies were made on drug-loaded microspheres to investigate the crystalline nature of drug after encapsulation. Results indicated amorphous dispersion of capecitabine in the polymer matrix. Scanning electron microscope (SEM) confirmed spherical shapes and smooth surface morphology of the microspheres. Mean particle size of the microspheres as measured by the laser light scattering technique ranged between 82 and 168microm. Capecitabine was successfully encapsulated into semi-IPN microspheres and percentage of encapsulation efficiency varied from 79 to 87. In vitro release studies were performed in simulated gastric fluid (pH 1.2) for the initial 2h, followed by simulated intestinal fluid (pH 7.4) until complete dissolution. The release of capecitabine was continued up to 10h. Release data were fitted to an empirical relationship to estimate the transport parameters. Dynamic swelling studies were performed in the simulated intestinal fluid and diffusion coefficients were calculated by considering the spherical geometry of the matrices.

Acrylic Resins↗

PubMed2005

Benefit of using biologic parameters (EUD and NTCP) in IMRT optimization for treatment of intrahepatic tumors.

PURPOSE: To investigate whether intensity-modulated radiotherapy (IMRT), optimized using the generalized equivalent uniform dose (gEUD) and normal tissue complication probability (NTCP) models, can increase the safe dose to intrahepatic tumors compared with three-dimensional conformal RT (3D-CRT). A secondary objective was to investigate the optimal beam arrangement for liver IMRT plans. METHODS AND MATERIALS: Planning CT data of 15 patients with intrahepatic tumors, previously treated with 3D-CRT, were used as input. The dose delivered using 3D-CRT had been limited either by tolerance of adjacent organs, which were close to, or overlapped with, the planning target volume (PTV; overlap cases, n = 8), or liver toxicity (nonoverlap, n = 7). IMRT plans were created using the gEUD to maximize the dose across the PTV and the NTCP to maintain the organ-at-risk toxicity to that of the conformal plan. Increased heterogeneity was allowed across the PTV in overlap cases, without compromising the minimal PTV dose of the conformal plan and restricting the maximal dose to within 110% of the mean. Three different beam arrangements were used for each case: seven-field equidistant axial, six-field noncoplanar (predominantly right-sided beams), and a reproduction of the conformal gantry angles. gEUDs were also computed and used for evaluation of the plans (regardless of planning technique) to reflect the response of both high- and low-grade tumors. The IMRT plan that allowed the greatest gEUD across the PTV was used in the comparison with the 3D-CRT plan. RESULTS: The use of IMRT significantly increased the maximal gEUD achievable across the PTV compared with the 3D-CRT plans. This was the case for the assumptions of both high- and low-grade tumors, irrespective of the tumor position within the liver. The mean gEUD increase was 11 Gy (high grade) and 18.0 Gy (low grade) for overlap cases (p = 0.001 and p = 0.003, respectively) and 10 Gy for nonoverlap cases (p = 0.020). When comparing the IMRT beam arrangements, gEUDs were considered equivalent if they differed by less than one fraction (1.5 Gy). In overlap cases (n = 8), an equivalent "best" gEUD value was obtained in 3, 5, and 7 cases for the original conformal angle, seven-field axial, and six-field noncoplanar plan, respectively. The corresponding results were 5, 2, and 3 in the cases without an overlap (n = 7). CONCLUSION: We have successfully used mathematical/biologic models directly as cost functions within the optimizing process to produce IMRT plans that maximize the gEUD while maintaining compliance with a well-defined protocol for the treatment of intrahepatic cancer. For both PTV-organ-at-risk overlap and nonoverlap situations, IMRT has the capacity to improve the maximal dose achievable across the PTV, expressed in terms of the gEUD. The use of multiple noncoplanar beams appears to confer an advantage over fewer beams in cases with PTV-organ-at-risk overlap. When liver toxicity is the dose-limiting factor, high gEUD values are obtained most frequently when the field arrangement is chosen to provide the shortest possible transhepatic path length.

Algorithms↗

PubMed2006

Minimal step length necessary for recovery of forward balance loss with a single step.

Although the boundary conditions necessary to trigger a step in reaction to a forward balance loss have been predicted in previous research, the relationship between minimal step length needed for balance recovery with this single step and the center of mass (COM) motion state (i.e., its position and velocity) remains unknown. The purpose of this paper was to present a theoretical framework within which the minimal step length needed for balance recovery can be estimated. We therefore developed a simplified four-segment sagittal model of human body stepping for balance recovery. The work-energy principle of the Newtonian mechanics was employed in the simulation to determine the amount of excess mechanical energy that can be absorbed as a function of step length and the corresponding eccentric joint work that can be generated in a single step. We found that an increase in initial forward velocity and a greater forward shift of the COM require a corresponding increase in the minimal step length needed for balance recovery. Furthermore, the minimal step length is also a function of the muscle strength at the ankle: the lower the muscle strength, the greater the minimal step length required. Our theoretical framework reduces the complexity associated with previous studies relying on forward dynamics and iterative optimization processes. This method may also be applied to study aspects of balance control such as the prevention of balance loss in the posterior or mediolateral direction.

Accidental Falls↗

PubMed2006

Response surface methodology for the evaluation of glucose-6-phosphate dehydrogenase enrichment process by soybean lecithin reversed micelles.

Glucose-6-phosphate dehydrogenase (G6PD) present in Saccahromyces cerevisiae is an enzyme of the pentose pathway. An effective enrichment of this intracellular enzyme can be achieved with the reversed micellar methodology. In this work, this methodology was employed with soybean lecithin, a biocompatible surfactant. A factorial design was used to evaluate the influence of pH (A) and extraction runs (B) on the G6PD purification factor. After statistical analysis and process optimization, a mathematical model representing G6PD enrichment was obtained: Y=4.89-0.83A+0.092B+0.27AB-1.37B2 with an enzyme purification factor of about 5.2.

Algorithms↗

PubMed2026

Selective monitoring of trace-level catechin and myricetin in herbal and aqueous matrices using magnetic MIP-DSPME: Optimization via design of experiments.

A novel dispersive solid-phase microextraction approach utilizing a magnetic molecularly imprinted polymer (MMIP) integrated with HPLC-UV detection was developed for the concurrent quantification of catechin and myricetin in herbal extracts and aqueous samples. The sorbent was engineered as a core-shell nanocomposite, consisting of a selective polymer layer deposited onto Fe3O4@SiO2-APTMS magnetic nanoparticles. Dual-template imprinting using catechin and myricetin generated complementary binding cavities within the polymer framework. Experimental variables influencing extraction were systematically screened and subsequently optimized. A Plackett-Burman design was first applied to identify the most influential factors, with pH and sorption time identified as the dominant variables. These parameters were subsequently fine-tuned using a central composite design, and the optimization process was completed in only 30 experimental runs. The sorption characteristics of the imprinted sorbent (MMIP) were compared with those of its non-imprinted counterpart (MNIP). The MMIP demonstrated markedly higher maximum binding capacities (Qmax), reaching 119.3 mg g-1 for myricetin and 112.1 mg g-1 for catechin, whereas the corresponding values for the MNIP were 32.55 and 32.08 mg g-1, respectively. Moreover, the affinity constants (KL = 0.760-0.950 L mg-1) were approximately 2.3-fold higher for the MMIP, confirming its stronger and more selective interactions with the target analytes. The selectivity coefficients for the targeted flavonoids relative to structurally related compounds, including ferulic acid, p-coumaric acid, melatonin, and curcumin, exceeded 3.5 for the MMIP, whereas the corresponding values for the MNIP were close to 1.1, demonstrating the high molecular recognition capability of the imprinted sorbent. Method validation demonstrated limits of detection (LODs) of 0.33-0.59 ng mL-1 and limits of quantification (LOQs) of 1.10-1.96 ng mL-1, and excellent linearity over the concentration range of 5.0-5500 ng mL-1 (R2 > 0.998). The method achieved recoveries of 93.96% to 105.69% with RSDs below 5.5%, while the preconcentration factors ranged from 209 to 229. Furthermore, the sorbent retained more than 95% of its extraction efficiency after four consecutive reuse cycles and more than 80% after six cycles, demonstrating excellent stability and reusability. The proposed method was successfully applied to the analysis of six medicinal plant extracts and water samples, showing negligible matrix interference and superior sensitivity, selectivity, and operational simplicity compared with conventional solid-phase extraction methods.

Flavonoids↗

PubMed2006

Microfluidic light scattering as a tool to study the structure of aqueous polymer solutions.

A small-angle light scattering (SALS) apparatus, coupled with a specially designed microfluidic device is shown to monitor the formation and subsequent size distribution of giant multilamellar vesicles of a diblock copolymer in aqueous solution. The closed-face design, fabricated between glass slides using a UV-curable optical adhesive, incorporates multiple inlets, a mixing system, and a viewing window to perform on-line SALS. The mixing of each component is tested using polystyrene latex microspheres. Vesicles of the block copolymer, EO6BO11 in aqueous solution are formed on the SALS chip and the pair distance distribution function determined using an inverse Fourier transformation of the scattered intensity to quantify the population and distribution for a range of vesicle sizes. These experiments provide demonstrations of how SALS on a microfluidic device can be used as a rapid screening tool to optimize processing conditions for a range of polymer solutions.

Coloring Agents↗

PubMed2006

Biosorption of cadmium by various types of dried sludge: an equilibrium study and investigation of mechanisms.

Batch equilibrium sorption experiments were used for screening for cost-effective four types of sludge, which were DWS (drinking water treatment plant sludge), LLS (landfill leachate sludge), ADSS (anaerobically digested sewage sludge), and SS (sewage sludge). SS removed cadmium most efficiently from aqueous solution (0.38 mmol/g), and showed the highest desorption efficiency (26.3%). Only the SS can be fitted by Langmuir isotherm model (r2 = 0.996). The FT-IR spectra of SS and cadmium loaded SS indicated that carboxyl groups were major binding sites of cadmium binding sites. In kinetic experiment, it was found that the uptake of the metal by the SS was accompanied with proton release, indicating that the metal binding occurs via an ion exchange as well as by electrostatic interaction between carboxylate groups and cadmium ions. This sorbent may have a potential for use as high-value biosorbent of heavy metals and it deserves further investigations into the details of practical application, for example on the development of desorption methods and on sorption process optimization.

Adsorption↗