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PubMed2000

Mixed-mode anion-cation exchange/hydrophilic interaction liquid chromatography-electrospray mass spectrometry as an alternative to reversed phase for small molecule drug discovery

Within pharmaceutical drug discovery, significant needs currently exist for the analysis and purification of structurally diverse samples prior to or immediately following high-throughput screening. These processes are required to facilitate rapid and accurate biological profiling, structural determination, and resupply of new drug candidates. Reversed-phase high-performance liquid chromatography (RP-HPLC) coupled with electrospray ionization mass spectrometry (ESI-MS) for both analytical and preparative applications has become the small molecule separation/detection tool of choice for meeting many of these needs. However, the separation selectivity provided by RP-HPLC has been limited to the hydrophobicity-based resolution of relatively nonpolar sample components, and for high-throughput drug discovery applications, no sufficient alternative procedures have been identified. In this investigation, a mixed-mode anion-cation exchange/hydrophilic interaction chromatography (ACE-HILIC) method has been developed to provide both direct compatibility with ESI-MS and evaporative light-scattering detection (ELSD) and separation selectivity highly orthogonal to RP-HPLC. The technique employed silica-based small-pore weak ion exchange resins eluted with a combined aqueous and pH gradient. A diverse set of dipeptide probes was employed for the elucidation of the relative contributions of three retention mechanisms. ACE-HILIC-ESI-MS-ELSD should prove useful for the analysis and purification of compounds from both biological (e.g., natural products) and synthetic (e.g., combinatorial chemistry) sources of molecular diversity.

Journal Article↗
PubMed2006

The purines: potent and versatile small molecule inhibitors and modulators of key biological targets.

The goal of this review is to highlight the wide range of biological activities displayed by purines, with particular emphasis on new purine-based agents which find potential application as chemical-biology tools and/or therapeutic agents. The expanding interest in the biological properties of polyfunctionalized purine derivatives issues, in large part, from the development of rapid high-throughput screening essays for new protein targets, and the corresponding development of efficient synthetic methodology adapted to the construction of highly diverse purine libraries. Purine-based compounds have found new applications as inducers of interferon and lineage-committed cell dedifferentiation, agonists and antagonists of adenosine receptors, ligands of corticotropin-releasing hormone receptors, and as inhibitors of HSP90, Src kinase, p38alpha MAP kinase, sulfotransferases, phosphodiesterases, and Cdks. The scope of application of purines in biology is most certainly far from being exhausted. Testing purine derivatives against the multitude of biological targets for which small molecule probes have not yet been found should thus be a natural reflex.

Antiviral Agents↗
PubMed2003

Human beta-secretase activity in yeast detected by a novel cellular growth selection system.

Sequential processing of the transmembrane amyloid precursor protein (APP) by the beta-secretase BACE and by the gamma-secretase causes secretion of Abeta peptides. Extracellular aggregation of these peptides in the brain is a major hallmark of Alzheimer's disease. For therapeutic purposes and the development of specific inhibitors, it is important to characterize these secretases. We have established a cellular growth selection system for functional expression of human BACE in the yeast Saccharomyces cerevisiae. A fragment of APP bearing the beta-site, the transmembrane domain and the cytosolic tail was fused to the C-terminus of the yeast enzyme invertase, which is normally secreted to allow cell growth in the presence of sucrose as the sole carbon source. The resulting invertase-APP fusion protein was expressed as a type-I transmembrane protein in intracellular compartments of yeast cells lacking endogenous invertase. In these cells, co-expression of human BACE restored cell growth on selective plates upon cleavage of the invertase-APP fusion protein. The cellular growth selection system presented here can be generally applied to screen for secretases that specifically cleave membrane-bound substrates. Furthermore, this system provides the basis for a high-throughput screen for identifying secretase inhibitors that are active in eukaryotic cells.

Amyloid Precursor Protein Secretases↗
PubMed1999

Affinity NMR.

Because binding ligands are directly detected and identified, the diffusion-based NMR method and NOE pumping approach promise to greatly simplify deconvolution in drug screening. An additional advantage of these techniques is that low-affinity ligands, which might be missed by high-throughput screening, can be detected and could serve as synthetic precursors for higher affinity ligands. The biggest challenge to NMR methodology lies in its sensitivity. Compared with other techniques, such as MS (25), NMR methods for screening mixtures are limited by their relative insensitivity. Because of issues such as solubility, stability, and mass limitation, it is not in general judicious to simply increase the concentration of the mixture. Improvements in hardware and software are necessary to extend the applicability of the affinity NMR method to the screening of larger and more complex mixtures. A boost in sensitivity and screening capacity of NMR technique is possible by the implementation of microcoil (26) and flow probe techniques. An upsurge in the capabilities of mixture analysis could be achieved with a combination of independent and complementary techniques (e.g., HPLC, MS) (27). As a unique, nondestructive, and versatile tool, NMR will continue on its fast track of development in the support of drug discovery.

Drug Evaluation, Preclinical↗
PubMed2000

The design and development of an integrated natural products screening database.

We designed and developed NEXUS--a new natural products screening database and related suite of software applications--to utilize the spectacular increases in assay capacity of the modern high throughput screening (HTS) environment. NEXUS not only supports seamless integration with separate HTS systems, but supports user-customized integration with external laboratory automation, particularly sample preparation systems. Designed and developed based on a detailed process model for natural products drug discovery, NEXUS comprises two integrated parts: (1) a single schema of Oracle tables and callable procedures and functions, and (2) software "front-ends" to the database developed using Microsoft Excel and Oracle Discovery/2000. Many of the back-end processing functions were written in Programming Language/Structured Query Language (PL/SQL) to provide an Application Programmer's Interface, which allows end users to create custom applications with little input from information technology professionals.

Biological Products↗
PubMed2007

Past, present, and future of high content screening and the field of cellomics.

High content screening (HCS) was created in 1996 to offer a new platform that could be used to permit relatively high-throughput screening of cells, in which each cell in an array would be analyzed at a sub-cellular resolution using multicolored, fluorescence-based reagents for both specificity and sensitivity. We developed HCS with the perspective of the history of the development of the automated DNA sequencers that revolutionized the field of genomics. Furthermore, HCS was based on a history of important developments in modern cytology. HCS integrates the instrumentation, application software, reagents, sample preparation, and informatics/bioinformatics required to rapidly flow from producing data, generating information, and ultimately creating new cellular knowledge. The HCS platform is beginning to have an important impact on early drug discovery, basic research in systems cell biology, and is expected to play a role in personalized medicine.

Animals↗
PubMed2002

Rapid screening for alpha1-antitrypsin deficiency in patients with chronic obstructive pulmonary disease using dried blood specimens.

We describe two reliable methods for high-throughput screening of proteinase inhibitor (PI) S and PI Z alpha(1)-antitrypsin (alpha(1)-AT) deficiency alleles from dried blood spot (DBS) specimens using the LightCycler fluorimetric analyzer. The method was used to study 72 patients with chronic obstructive pulmonary disease. Results were confirmed with DNA sequencing. The alpha(1)-AT concentration in DBS was determined with immune nephelometry. Sixteen patients (22%) showed no PI Z or PI S mutations. Five patients (7%) had a heterozygous genotype consisting of a PI S allele and a normal allele for the Z and S positions (non-S non-Z). Twenty-five patients (35%) had a heterozygous genotype consisting of a PI Z and a non-S non-Z allele. Two (3%) had the PI SS genotype, 2 (3%) the PI SZ, and 20 (28%) the PI ZZ. All patients with two normal alpha(1)-AT alleles and 10 heterozygous carriers of one normal and one deficient allele had alpha(1)-AT levels that fell within the alpha(1)-AT DBS normal range (1.8-3.1 mg/dl). Two patients with the rare PI MM(malton)- and PI MM(heerlen)-deficient variants showed deficient alpha(1)-AT levels; PI S and PI Z were not detected. Processing 32 samples requires only 40 minutes. This single-step, cost-effective technology is optimal for working with small amounts of DNA, as are present in DBS. The method is suitable for large-scale screening, in cases where PI type is important.

Adult↗
PubMed2001

Antibody-based fluorescence polarization assay to screen combinatorial libraries for sweet taste compounds.

Technological advances in instrumentation, chemical synthesis methods, molecular biology and biochemistry have fueled the recent growth in high throughput screening. Assays are available in a vast range for formats, including fluorescence, luminescence, absorbance, and scintillation detection. Antibodies represent a powerful tool for novel compound discovery and their utility in this regard should not be underestimated. We have designed a fluorescence polarization immunoassay for the identification of novel sweeteners. The assay is based on monoclonal antibodies that bind superpotent sweet taste compounds and libraries of suitable test compounds can be rapidly screened using these antibodies as "artificial taste receptors."

Antibodies↗
PubMed2025

Integrating RNA sequencing with deep learning-based metabolic toxicity prediction: A new perspective on screening prioritized liquid crystal monomers.

Nearly 99 % of liquid crystal monomers (LCMs) toxicological data remains gaps, especially to aquatic organisms. Herein, this study proposes a rapid and high-throughput screening method for identifying priority LCMs in natural water. Using six fluorinated LCMs (LCMsF) with significant enrichment characteristics in zebrafish as examples, RNA sequencing revealed that LCMsF-induced metabolic disturbances are predominant, including 28 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway abnormalities attributed to 498 differentially expressed genes. Notably, the intricate sequencing process resulted in the inability to rapid identify additional 857 LCMsF that may induce metabolic disturbances. To address this, LCMsT-MTP, a predictive deep learning model based on RNA sequencing, was developed. This model integrates a comprehensive representation of LCMsF structures and metabolic toxicity target sequences. LCMsT-MTP improves upon traditional methods that are limited to single targets and mechanisms by facilitating the simultaneous identification of 21 metabolic toxicities induced by LCMsF. In addition, the LCMsT-MTP model was further applied to non-fluorinated LCMs (LCMsNone F) that satisfy the applicability domains test. Accordingly, a metabolic toxicity priority list of LCMs was proposed, with ∼95 % of LCMs classified as high or medium risk. Priority list validation by molecular dynamics confirmed that the interactions of LCMsF/LCMsNone F and metabolic toxicity targets in representative KEGG pathways were distinct.

Animals↗
PubMed2005

Engineering the E. coli beta-galactosidase for the screening of antiviral protease inhibitors.

Site-specific proteolysis is essential in many fundamental cellular and viral processes. It has been previously shown that the Escherichia coli beta-galactosidase can be useful for the high-throughput screening of human immunodeficiency virus type 1 protease inhibitors. Here, by using crystallographic and functional data of the bacterial enzyme, we have identified a new accommodation site between amino acids 581 and 582, in a solvent-exposed and flexible beta-turn of domain III. The placement of the model peptide reproducing the matrix-capsid (p17/p24) gag cleavage sequence renders a highly active and efficiently digested chimeric construct. The use of this insertion site, that increases the cleavage potential of this reporter enzyme, can improve the sensitivity and dynamic range of the antiviral drug assay. This simple and highly specific analytical test may also be extended to the screening of other specific protease inhibitors by a convenient colorimetric assay.

Amino Acid Substitution↗
PubMed2001

Comparison of chromatographic and spectroscopic methods used to rank compounds for aqueous solubility.

Rapid methods for ranking the solubility of compounds in aqueous media using commercial, 96-well ultraviolet-visible (UV-vis) and nephelometric plate readers are described. The methods were evaluated using commercially available compounds from a variety of structural classes as well as a series of structurally related compounds derived from combinatorial synthesis. Samples were predissolved in dimethyl sulfoxide (DMSO) and then added to the study solvent to attain a final concentration of DMSO in the aqueous solution of 5%. Comparison of filtration of the samples through nylon and poly(tetrafluoroethylene) (PTFE) membranes is also described. The solubility of the compounds determined using the UV-vis plate reader in the absorption mode (with samples filtered with the PTFE filter) as well as in the light scattering mode was in good agreement with that determined by high-performance liquid chromatography, with an average correlation of 0.95. Solubility data obtained using a 96-well nephelometer was also comparable (r(2) = 0.97). The nonequilibrium methods described in this study can be used to rapidly rank compounds from combinatorial libraries for solubility and can also give a general assessment of solubility prior to running additional high throughput screens in a drug discovery environment.

Chromatography, High Pressure Liquid↗
PubMed2006

Histamine H3 receptor antagonists: from target identification to drug leads.

The successful cloning and functional expression of the histamine H(3) receptor in the late 1990 s has greatly facilitated our efforts to identify small molecule, non-imidazole based compounds to permit the evaluation of H(3) antagonists in models of CNS disorders. High-throughput screening identified several series of lead compounds, including a series of imidazopyridines, which led to JNJ-6379490, a compound with high affinity for the human H(3) receptor. Analysis of structural features common to several series of non-imidazole H(3) receptor ligands resulted in a pharmacophore model. This model led to the design of JNJ-5207852, a diamine-based H(3) antagonist with good in vitro and in vivo efficacy but with an undesirable long half-life. However, further modifications of the template provided an understanding of the effect of structural modifications on pharmacokinetic properties, ultimately affording several additional series of compounds including JNJ-10181457, a compound with an improved pharmacokinetic profile. These compounds allowed in vivo pharmacological evaluation to show that H(3) antagonists promote wakefulness, but unlike modafinil and classical psychostimultants, they do not increase locomotor activity or produce any alteration of the EEG power spectral activity in rats. H(3) antagonists also increase extracellular acetylcholine and norepinephrine but not dopamine in rat frontal cortex and show efficacy in various models of learning-memory deficit. In addition, cFos immunoreactivity studies show H(3) antagonists activate neuronal cells in restricted rat brain regions in contrast to widespread activation after modafinil or amphetamine treatment. Therefore, H(3) antagonists are promising clinical candidates for the treatment of excessive day time sleepiness and/or cognitive disorders.

Animals↗
PubMed2005

Fluorometric broad-range screening of compounds with affinity for nucleic acids.

The potential of a nucleic acid-based optical bioprobe for environmental measurements and drug monitoring is described. The sensor employs the long-wavelength intercalating fluorophore TO-PRO-3 (TP3). Compounds that interact with the TP3-DNA complex are indirectly detected by a decrease in the fluorescence intensity. We found that the configuration and length of the DNA dramatically affected the intensity of the fluorescence emitted from the TP3-DNA complex. We compared nucleic acids from different sources and optimized the system for pBR322 plasmid DNA (4363 bp) digested by HindIII restriction endonuclease. This endonuclease has a single recognition site in plasmid pBR322. In the proposed method, we attempt to combine broad-range detection with rapid and simple operation. A fiber-optic capillary fluorescence system was used to analyze toxic aromatic amines, antibiotics, and several kinds of antitumor drugs, using small amounts of sample, down to 10 muL, with a sensitivity comparable to that of current electrochemical methods. The detection limit can be as low as a few ppb or submicromolar. This approach is useful for routine screening in environmental monitoring or for controlling cytotoxic drug administration. The ease of operation and the rapid response allow high-throughput screening.

Amines↗
PubMed2006

Direct sampling of chemical weapons in water by photoionization mass spectrometry.

The vulnerability of water supplies to toxic contamination calls for fast and effective means for screening water samples for multiple threats. We describe the use of photoionization (PI) mass spectrometry (MS) for high-speed, high-throughput screening and molecular identification of chemical weapons (CW) threats and other hazardous compounds. The screening technology can detect a wide range of compounds at subacute concentrations with no sample preparation and a sampling cycle time of approximately 45 s. The technology was tested with CW agents VX, GA, GB, GD, GF, HD, HN1, and HN3, in addition to riot agents and precursors. All are sensitively detected and give simple PI mass spectra dominated by the parent ion. The target application of the PI MS method is as a routine, real-time early warning system for CW agents and other hazardous compounds in air and in water. In this work, we also present comprehensive measurements for water analysis and report on the system detection limits, linearity, quantitation accuracy, and false positive (FP) and false negative rates for concentrations at subacute levels. The latter data are presented in the form of receiver operating characteristic curves of the form of detection probability P(D) versus FP probability P(FP). These measurements were made using the CW surrogate compounds, DMMP, DEMP, DEEP, and DIMP. Method detection limits (3sigma) obtained using a capillary injection method yielded 1, 6, 3, and 2 ng/mL, respectively. These results were obtained using 1-microL injections of water samples without any preparation, corresponding to mass detection limits of 1, 6, 3, and 2 pg, respectively. The linear range was about 3-4 decades and the dynamic range about 4-5 decades. The relative standard deviations were generally <10% at CW subacute concentrations levels.

Chemical Warfare Agents↗
PubMedDate not supplied

PowerMV: a software environment for molecular viewing, descriptor generation, data analysis and hit evaluation.

Ideally, a team of biologists, medicinal chemists and information specialists will evaluate the hits from high throughput screening. In practice, it often falls to nonmedicinal chemists to make the initial evaluation of HTS hits. Chemical genetics and high content screening both rely on screening in cells or animals where the biological target may not be known. There is a need to place active compounds into a context to suggest potential biological mechanisms. Our idea is to build an operating environment to help the biologist make the initial evaluation of HTS data. To this end the operating environment provides viewing of compound structure files, computation of basic biologically relevant chemical properties and searching against biologically annotated chemical structure databases. The benefit is to help the nonmedicinal chemist, biologist and statistician put compounds into a potentially informative biological context. Although there are several similar public and private programs used in the pharmaceutical industry to help evaluate hits, these programs are often built for computational chemists. Our program is designed for use by biologists and statisticians.

Computer Simulation↗
PubMed2004

Neuroprotective effects of a novel poly(ADP-ribose) polymerase-1 inhibitor, 2-[3-[4-(4-chlorophenyl)-1-piperazinyl] propyl]-4(3H)-quinazolinone (FR255595), in an in vitro model of cell death and in mouse 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine model of Parkinson's disease.

The massive activation of poly(ADP-ribose) polymerase-1 (PARP-1) by DNA-damaging stimuli, such as exposure to reactive oxygen species (ROS), can lead to cell injury via severe, irreversible depletion of the NAD and ATP pool, and PARP-1 inhibitors have been expected to rescue neurons from degeneration in a number of disease models. We have recently identified 2-[3-[4-(4-chlorophenyl)-1-piperazinyl] propyl]-4(3H)-quinazolinone (FR255595) as a novel and potent PARP-1 inhibitor through structure-based drug design and high-throughput screening. This compound potently inhibited PARP activity with an IC(50) value of 11 nM and was orally active and highly brain penetrable. Here, we show that prevention of PARP activation by FR255595 protects against both ROS-induced cells injury in vitro and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced nigrostriatal dopaminergic damage in an in vivo Parkinson's disease (PD) model. In cell death models in vitro, exposure of hydrogen peroxide induced cell death with PARP overactivation in PC12 cells and SH-SY5Y cells, and pre- and post-treatment with FR255595 (10(-9)-10(-5) M) significantly reduced PARP activation and cell death. In mouse MPTP model, MPTP (20 mg/kg i.p.) intoxication lead to PARP activation and cell damage in the nigrostriatal dopaminergic pathway, which was significantly ameliorated by oral administration of FR255595 (10-32 mg/kg), both in the substantia nigra and in the striatum via marked reduction of PARP activation, even with delayed treatment. These findings clearly indicate that the novel PARP-1 inhibitor FR255595 exerts neuroprotective effect through its potent PARP-1 inhibitory actions in PD model, suggesting that the drug could be an attractive candidate for several neurodegenerative disorders, including PD.

Animals↗
PubMed2000

The impact of genomics-based technologies on drug safety evaluation.

Determining the potential toxicity of compounds early in the drug discovery process can be extremely beneficial in terms of both time and money conservation. Because of the speed of modern chemical synthesis and screening, to accurately evaluate the large number of compounds being produced, toxicology assays must have both high-fidelity and high-throughput capabilities. In addition, assays must be performed using limited amounts of compound. In the past decade, several new and innovative techniques have been developed that not only allow for high-throughput screening but can also provide detailed information concerning the molecular mechanisms behind toxic effects. Techniques such as hybridization microarrays, real-time polymerase chain reaction, and large-scale sequencing are some of the methods that have been or are starting to be used routinely in pharmaceutical companies. This review examines the contributions of these and related techniques toward toxicity evaluation of potential drug candidates and their future role in the discovery of new therapeutics.

Animals↗
PubMed1997

Rationale and perspectives on the development of fungicides.

Fungicides continue to be essential for the effective control of plant diseases. New classes of fungicides with novel modes of action are being developed in the 1990s. These include the strobilurins, phenylpyrroles, anilinopyrimidines, phenoxyquinolines, and compounds that trigger defense mechanisms in the plant. For the foreseeable future, new toxophores will be identified through a process of random screening, with natural products representing a rich source of fungicide leads. Progress is being made in the development of high-throughput screens comprised of target enzyme sites or cell-based assays; these techniques will improve the probability of discovery. Following the identification of suitable leads, biorational design is used to optimize specific properties. In vivo glasshouse screens and field trials are expected to remain the dominant methods for characterizing new compounds. Low toxicity to humans and wildlife, low environmental impact, low residues in food, and compatibility with integrated pest management (IPM) programs are increasingly important considerations in the selection of fungicides for development.

Journal Article↗