Coupling HPLC to on-line, post-column (bio)chemical assays for high-resolution screening of bioactive compounds from complex mixtures

It is challenging to screen and identify bioactive compounds from complex mixtures. We review a recently developed technique that couples high-performance liquid chromatography (HPLC) to on-line, post-column (bio)chemical assays and parallel chemical analysis to screen and identify bioactive compounds from complex mixtures without the need for cumbersome purification and subsequent screening. In this system, HPLC separates complex mixtures and a post-column (bio)chemical assay determines the activity of the individual compounds present in the mixtures. Parallel chemical-detection methods (e.g., diode-array detection, mass spectrometry and nuclear magnetic resonance) identify and quantify the active compounds simultaneously. We focus on relatively widely used on-line, post-column assays for antioxidant screening and less widely used hyphenated systems involving assays based on enzymes and receptors. These strategies have proved to be very useful for rapid profiling and identification of individual active components in mixtures to provide a powerful method for natural product-based drug discovery.     

Data processing in metabolic fingerprinting by CE-UV: application to urine samples from autistic children

Metabolic fingerprinting of biofluids such as urine can be used to detect and analyse differences between individuals. However, before pattern recognition methods can be utilised for classification, preprocessing techniques for the denoising, baseline removal, normalisation and alignment of electropherograms must be applied. Here a MEKC method using diode array detection has been used for high-resolution separation of both charged and neutral metabolites. Novel and generic algorithms have been developed for use prior to multivariate data analysis. Alignment is achieved by combining the use of reference peaks with a method that uses information from multiple wavelengths to align electropherograms to a reference signal. This metabolic fingerprinting approach by MEKC has been applied for the first time to urine samples from autistic and control children in a nontargeted and unbiased search for markers for autism. Although no biomarkers for autism could be determined using MEKC data here, the general approach presented could also be applied to the processing of other data collected by CE with UV-Vis detection.     

Peptide mimetics as enzyme inhibitors: Use of free energy perturbation calculations to evaluate isosteric replacement for amide bonds in a potent HIV protease inhibitor

Summary We present the application of free energy perturbation theory/molecular dynamics to predict the consequence of replacing each of the seven peptide bonds in the potent HIV protease inhibitor JG365: ACE (acetyl)-Ser-Leu-Asn-HEA (hydroxyethylamine analog of Phe-Pro)-Ile-Val-NME (N-methyl) by ethylene or fluoroethylene isosteres. Replacing two of these bonds may well lead to significantly tighter binding; replacing two others is predicted to significantly diminish the binding affinity. Also, for three of the peptide bonds fluoroethylene replacements could lead to increased binding of free energies of the inhibitors. Our results should be considered as predictive since there are, as yet, no experimental results on such peptide replacements as enzyme inhibitors.     

Recent advances in polyhydroxyalkanoate production by mixed aerobic cultures: from the substrate to the final product

Numerous bacteria have been found to exhibit the capacity for intracellular polyhydroxyalkanoates (PHA) accumulation. Current methods for PHA production at the industrial scale are based on their synthesis from microbial isolates in either their wild form or by recombinant strains. High production costs are associated with these methods; thus, attempts have been made to develop more cost-effective processes. Reducing the cost of the carbon substrates (e.g., through feeding renewable wastes) and increasing the efficiency of production technologies (including both fermentation and downstream extraction and recovery) are two such examples of these attempts. PHA production processes based on mixed microbial cultures are being investigated as a possible technology to decrease production costs, since no sterilization is required and bacteria can adapt quite well to the complex substrates that may be present in waste material. PHA accumulation by mixed cultures has been found under various operational conditions and configurations at both bench-scale and full-scale production. The process known as "feast and famine" or as "aerobic dynamic feeding" seems to have a high potential for PHA production by mixed cultures. Enriched cultures submitted to a transient carbon supply can synthesize PHA at levels comparable to those of pure cultures. Indeed, the intracellular PHA content can reach around 70% of the cell dry weight, suggesting that this process could be competitive with pure culture PHA production when fully developed. Basic and applied research of the PHA production process by mixed cultures has been carried out in the past decade, focusing on areas such as microbial characterization, process configuration, reactor operational strategies, process modeling and control, and polymer characterization. This paper presents a review of the PHA production process with mixed cultures, encompassing the findings reported in the literature as well as our own experimental results in relation to each of these areas.     

Generic simple enzyme immunoassay approach to avert small molecule immobilization problems on solid phases: Application to the determination of tobramycin in serum

Generic simple and sensitive universal enzyme immunoassay approach for the determination of small analytes has been developed to avert the problems associated with small molecule immobilization onto solid phases. The developed assay employed a heterogeneous non-competitive binding format. The assay used anti-analyte antibody coupled to polyacrylamide beads as a solid-phase and β-d-galactosidase enzyme-labeled analyte as a label. In this assay, the analyte in a sample was firstly incubated to react with an excess of the antibody-coupled beads, and then the unoccupied antibody binding sites were allowed to react with the enzyme-labeled analyte. Analyte bound to the antibody-coupled beads was separated by centrifugation, and the enzyme activity of the supernatant was measured spectrophotometrically at 420 nm, after reaction with 4-nitrophenyl-β-d-galactopyranoside as a substrate for the enzyme. The signal was directly proportional to the concentration of analyte in the sample. The optimum conditions for the developed assay were established and applied to the determination of tobramycin, as a representative example of the small analytes, in serum samples. The assay limit of detection was 10 ng mL⁻¹ and the effective working range at relative standard deviation of ≤10% was 40-800 ng mL⁻¹. The assay precisions were acceptable; the relative standard deviations were 4.36-5.17 and 5.62-7.40% for intra- and inter-assay precision, respectively. Analytical recovery of tobramycin spiked in serum ranged from 95.89 ± 4.25 to 103.45 ± 4.60%. The assay results correlated well with those obtained by high-performance liquid chromatography (r = 0.992). The assay described herein has great practical value in determination of small analytes because it is sensitive, rapid, and easy to perform in any laboratory. Although the assay was validated for tobramycin, however, it is also anticipated that the same methodology could be used for essentially any analyte for which a selective antibody exists, and an appropriate enzyme conjugate can be made.     

Structural and functional annotation of PR/SET Domain (PRDM) protein family: In-silico study elaborating role of PRDM12 mutation in congenital insensitivity to pain

Congenital insensitivity to pain (CIP), classified as a type of hereditary sensory and autonomic neuropathies, is a rare disease in which the affected individuals fail to perceive sensation of pain. One of the PR/SET Domain Proteins, PRDM12, has been identified in recent past as a candidate gene for congenital insensitivity to pain. In the present study, we performed whole exome sequencing in a Pakistani family with CIP phenotype to ascertain the causative mutation. We identified a previously described alanine repeat duplication in PRDM12 (Ala353_Ala359dup) in this family. After this, we performed structural annotations for PR/SET Domain (PRDM) containing protein family to prognosticate the potential hypothetical structure of PRDM proteins with physical and chemical parameters. Out of nineteen members of this family, four members (PRDM5, PRDM8, PRDM12 and PRDM13) were specially focused because of their role in neurological disorders. Predictions about structure and interactions of these proteins revealed novel interacting molecules and pathways. Detailed in silico analysis of PRDM12 was performed to elaborate importance of its domain structure in interaction with other proteins and its role in pain insensitivity phenotype. These results have substantially enhanced our understanding regarding the etiology of congenital pain insensitivity and would stimulate further research on therapy and prevention.