Organogel media for on-bead screening in combinatorial catalysis

Poly(vinylidene fluoride) (PVdF) forms thermoreversible gels with a number of dipolar aprotic solvents. Gels were prepared containing chromogenic substrates, subject to transformation by polymer-bound catalysts. When the catalysts were mixed with inactive beads and applied to the surface of the gels, the active beads were identifiable through colour changes. Active beads could also be visualised by thermographic imaging. These methods hold promise for catalyst discovery from split-and-mix combinatorial libraries.     

Genetic algorithm-assisted combinatorial search for a new green phosphor for use in tricolor white LEDs

An evolutionary optimization process involving a genetic algorithm and combinatorial chemistry was employed for the development of green phosphors which are suitable for tricolor white-light-emitting diodes. To accomplish a high luminescent efficiency at 400 nm excitation, we screened a seven-cation oxide system including Tb, Gd, Ce, Mg, Si, Al, and B. The combination of a genetic algorithm and combinatorial chemistry enhanced the searching efficiency when applied for phosphor screening. As a result, the optimized composition was Tb(0.01)Gd(0.02)Ce(0.04)B(0.1)Si(0.83)O(delta), The luminance of this borosilicate glass was 67% that of ZnS:Cu,Al at 400-nm excitation.     

Multiplexed detection of nucleic acids in a combinatorial screening chip

Multiplexed diagnostic testing has the potential to dramatically improve the quality of healthcare. Simultaneous measurement of health indicators and/or disease markers reduces turnaround time and analysis cost and speeds up the decision making process for diagnosis and treatment. At present, however, most diagnostic tests only provide information on a single indicator or marker. Development of efficient diagnostic tests capable of parallel screening of infectious disease markers could significantly advance clinical and diagnostic testing in both developed and developing parts of the world. Here, we report the multiplexed detection of nucleic acids as disease markers within discrete wells of a microfluidic chip using molecular beacons and total internal reflection fluorescence microscopy (TIRFM). Using a 4 × 4 array of 200 pL wells, we screened for the presence of four target single stranded oligonucleotides encoding for conserved regions of the genomes of four common viruses: human immunodeficiency virus-1 (HIV-1), human papillomavirus (HPV), Hepatitis A (Hep A) and Hepatitis B (Hep B). Target oligonucleotides are accurately detected and discriminated against alternative oligonucleotides with different sequences. This combinatorial chip represents a versatile platform for the development of clinical diagnostic tests for simultaneous screening, detection and monitoring of a wide range of biological markers of disease and health using minimal sample size.     

High-throughput screening for combinatorial thin-film library of thermoelectric materials

A high-throughput method has been developed to evaluate the Seebeck coefficient and electrical resistivity of combinatorial thin-film libraries of thermoelectric materials from room temperature to 673 K. Thin-film samples several millimeters in size were deposited on an integrated Al2O3 substrate with embedded lead wires and local heaters for measurement of the thermopower under a controlled temperature gradient. An infrared camera was used for real-time observation of the temperature difference Delta T between two electrical contacts on the sample to obtain the Seebeck coefficient. The Seebeck coefficient and electrical resistivity of constantan thin films were shown to be almost identical to standard data for bulk constantan. High-throughput screening was demonstrated for a thermoelectric Mg-Si-Ge combinatorial library.     

Method for combinatorial screening of moisture vapor transmission rate

A high-throughput method for screening the moisture vapor transmission rate of barrier films was developed. This moisture high-throughput screening (MHTS) technique is based upon a Nafion-crystal violet (CVN) sensor that changes color from yellow to green upon absorption of water. Using an appropriate set of known standards, the slope of absorbance (at 630 nm) as a function of time can be converted into moisture vapor transmission rate (MVTR) values that agree with those obtained using ASTM F1290. High-throughput screening was demonstrated by depositing 20 emulsion-based poly(vinylidene chloride) films, using a 48-well template, of varying thicknesses onto the CVN sensor film and aging at 40 degrees C and 90% relative humidity for 72 h. MVTR values were accurately determined to a level of 0.9 g/m(2).day, at which point side-diffusion of moisture between the barrier and sensor films prevented observation of lower values. Larger sample size and edge-sealing are two proposed methods for improving the sensitivity of MHTS.     

Two-colour screening in combinatorial chemistry: prospecting for enantioselectivity in a library of steroid-based receptors

The screening of resin-bound combinatorial libraries with pairs of dye-tagged substrates is a powerful strategy for discovering selective receptors. However, implementation has been hampered by a lack of complementary but chemically similar dyes. We now show that the well-established Disperse Red 1 and the recently-introduced Bristol Blue 1 can be used in parallel to synthesise ‘pseudoenantiomeric’ analogues of N-acetyl-α-amino acids and of the anti-inflammatory drug Naproxen. A steroid-based receptor library has been prepared and screened with these substrates. Preliminary results suggest that some members may be highly enantioselective receptors for N-acetyl-α-amino acids.     

Direct screening of a dynamic combinatorial library using mass spectrometry

A dynamic combinatorial library (DCL) screening approach is described that permits direct identification of the effective (from ineffective) combination of building blocks in the equilibrating DCL. The approach uses Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) together with sustained off-resonance irradiation collision activated dissociation (SORI-CAD) to detect noncovalent protein-DCL ligand complexes under native conditions. It was shown that in a single, rapid experiment one could concurrently identify all the ligands of interest from the DCL against a background of inactive DCL ligands while still in the presence of the target protein. This result has demonstrated that mass spectrometry may provide a fast preliminary screening approach to identify DCL candidates for later verification with more traditional but time-consuming analysis. The MS/MS enables DCL mixtures to be effectively deconvoluted without the need for either chromatography, synthesis of DCL sub-libraries, conversion of the DCL to a static library, or disruption of the protein-ligand complexes before analysis--all typically necessary for the current screening method for DCLs.     

Solvent effects on the screening of parallel combinatorial libraries for selectors for chiral chromatography

The correlation between the resin-swelling property and the outcome of the crucial equilibration assay used in our parallel library screening method is investigated. It is found that the incorporation of CHCl3 (an effective swelling solvent for both the polystyrene and TentaGel resins) into the equilibration solvent leads to faster equilibration and thus shorter library screening time. The outcome of the equilibration experiment is also found to depend on the chemical nature of the solid base resins. It appears that polystyrene resin, which has a relatively inert surface, provides higher enantioselectivity than the polar TentaGel resin. The importance of a thoroughly swelled resin for the direct assay of functional groups on the resin is demonstrated.     

Use of catalyst pharmacophore models for screening of large combinatorial libraries

Using a data set comprised of literature compounds and structure-activity data for cyclin dependent kinase 2, several pharmacophore hypotheses were generated using Catalyst and evaluated using several criteria. The two best were used in retrospective searches of 10 three-dimensional databases containing over 1,000,000 proprietary compounds. The results were then analyzed for the efficiency with which the hypotheses performed in the areas of compound prioritization, library prioritization, and library design. First as a test of their compound prioritization capabilities, the pharmacophore models were used to search combinatorial libraries that were known to contain CDK active compounds to see if the pharmacophore models could selectively choose the active compounds over the inactive compounds. Second as a test of their utility in library design again the pharmacophore models were used to search the active combinatorial libraries to see if the key synthons were over represented in the hits from the pharmacophore searches. Finally as a test of their ability to prioritize combinatorial libraries, several inactive libraries were searched in addition to the active libraries in order to see if the active libraries produced significantly more hits than the inactive libraries. For this study the pharmacophore models showed potential in all three areas. For compound prioritization, one of the models selected active compounds at a rate nearly 11 times that of random compound selection though in other cases models missed the active compounds entirely. For library design, most of the key fragments were over represented in the hits from at least one of the searches though again some key fragments were missed. Finally, for library prioritization, the two active libraries both produced a significant number of hits with both pharmacophore models, whereas none of the eight inactive libraries produced a significant number of hits for both models.     

Similarity search profiles as a diagnostic tool for the analysis of virtual screening calculations

An analysis method termed similarity search profiling has been developed to evaluate fingerprint-based virtual screening calculations. The analysis is based on systematic similarity search calculations using multiple template compounds over the entire value range of a similarity coefficient. In graphical representations, numbers of correctly identified hits and other detected database compounds are separately monitored. The resulting profiles make it possible to determine whether a virtual screening trial can in principle succeed for a given compound class, search tool, similarity metric, and selection criterion. As a test case, we have analyzed virtual screening calculations using a recently designed fingerprint on 23 different biological activity classes in a compound source database containing approximately 1.3 million molecules. Based on our predefined selection criteria, we found that virtual screening analysis was successful for 19 of 23 compound classes. Profile analysis also makes it possible to determine compound class-specific similarity threshold values for similarity searching.     

Genotype-phenotype linkage for directed evolution and screening of combinatorial protein libraries

The technologies for screening peptide and protein libraries for studies in the fields of directed protein evolution and functional genomics have advanced with astonishing speed. For screening of functional proteins, three technologies are required: (i) the construction of a gene library (genotype), (ii) the establishment of a linkage between each protein (phenotype) and its encoding gene (genotype), and (iii) the selection of desired proteins (phenotype) from the library. This review highlights the genotype-phenotype linkage technologies, which can be classified into three types; that is, cell-type linkage, virus-type linkage, and array-type linkage methods. These methods are summarized, and their advantages and disadvantages are discussed.     

Development and validation of a screening procedure for the assessment of inhibition using a recombinant enzyme

Myeloperoxidase (MPO, E.C. 1.1.11.7) is a heme-containing enzyme that catalyses the synthesis of hypochlorous acid (HOCl) in the presence of hydrogen peroxide (H2O2) and chlorine anions. The production of HOCl is kept under strict control of neutrophils. However, in several pathological conditions, MPO is leaked in the extracellular fluid, which involves an over-production of reactive oxygen species like HOCl and promotes the damages caused by neutrophils. As a consequence, the inhibition of MPO by various agents has been investigated and a variety of molecules have been evaluated for this activity in different models. The present study aims to describe and validate a rapid screening method based on the taurine assay and using a recombinant MPO. After validation of the stock solutions used during the experiments, the amount of MPO for the completion of the reaction was measured and fixed to an optimal value. The inhibiting concentration at 50% of flufenamic acid (taken as a reference molecule) was then assessed in both a simple tube test and a microplate test and delivered similar results (1.3+/-0.2 microM vs 1.4+/-0.2 microM, P=0.2). Finally, different molecules able to inhibit MPO were evaluated in this rapid assay system providing results comparable to literature. The high throughput screening is undoubtedly a first line assessment method which affords the selection of inhibitors and permits to reduce the number of candidates for a further elucidation of the mechanism of MPO inhibition.     

Rapid screening procedure for the detection of trichothecenes in plasma and urine

A rapid and easy procedure to screen for trichothecenes in plasma and urine is presented. The toxins are extracted using a Clin-Elut column, hydrolyzed to their corresponding parent alcohols and cleaned up with a silica cartridge followed by derivatization for gas chromatographic analysis. The detection of any of the parent alcohols in plasma or urine would indicate an exposure to trichothecenes. Recoveries in urine are between 78 and 119% at levels of 50-1000 ng/ml and recoveries in plasma are between 80 and 116% at levels of 50-500 ng/ml. The limit of detection is better than 25 ppb.     

Drug search for leishmaniasis: a virtual screening approach by grid computing

The trypanosomatid protozoa Leishmania is endemic in ~100 countries, with infections causing ~2 million new cases of leishmaniasis annually. Disease symptoms can include severe skin and mucosal ulcers, fever, anemia, splenomegaly, and death. Unfortunately, therapeutics approved to treat leishmaniasis are associated with potentially severe side effects, including death. Furthermore, drug-resistant Leishmania parasites have developed in most endemic countries. To address an urgent need for new, safe and inexpensive anti-leishmanial drugs, we utilized the IBM World Community Grid to complete computer-based drug discovery screens (Drug Search for Leishmaniasis) using unique leishmanial proteins and a database of 600,000 drug-like small molecules. Protein structures from different Leishmania species were selected for molecular dynamics (MD) simulations, and a series of conformational “snapshots” were chosen from each MD trajectory to simulate the protein’s flexibility. A Relaxed Complex Scheme methodology was used to screen ~2000 MD conformations against the small molecule database, producing >1 billion protein-ligand structures. For each protein target, a binding spectrum was calculated to identify compounds predicted to bind with highest average affinity to all protein conformations. Significantly, four different Leishmania protein targets were predicted to strongly bind small molecules, with the strongest binding interactions predicted to occur for dihydroorotate dehydrogenase (LmDHODH; PDB:3MJY). A number of predicted tight-binding LmDHODH inhibitors were tested in vitro and potent selective inhibitors of Leishmania panamensis were identified. These promising small molecules are suitable for further development using iterative structure-based optimization and in vitro/in vivo validation assays.     

Thin-layer chromatographic screening procedure for some drugs in horse plasma

A thin-layer chromatographic screening procedure for some basic, neutral and acidic drugs was developed using 3 ml of horse plasma. Chloroform-2-propanol (95:5, v/v) was used as the extraction solvent. The drugs were identified by a high-performance thin-layer chromatographic plate and spraying successively with some detection reagents. In this study, the extraction recovery rates and the detection limits were determined at the same time.