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PubMed2002

Structure-based approaches to drug design and virtual screening.

Structure-based design has made an important contribution to drug discovery for many years. Recently, the increasing availability of structural data and the affordability of high-performance computing platforms have broadened the applicability of these methods. In particular, virtual screening has been adopted as an effective paradigm for lead discovery that fits in well alongside high-throughput screening programs. Structure-based virtual screening relies on fast and accurate computational methods for the prediction of receptor-ligand binding modes and binding affinities. In this paper, recent technical advances in the field of molecular docking and de novo design are reviewed, in particular, the development of flexible receptor models, docking of combinatorial libraries and novel scoring methods.

Animals↗

PubMed2006

Application of the ferrous oxidation-xylenol orange assay for the screening of 5-lipoxygenase inhibitors.

5-Lipoxygenase (5-LO) is the key enzyme involved in leukotriene synthesis and its improper regulation is implicated in several inflammatory diseases. A rapid and sensitive assay for 5-LO activity suitable for high-throughput format is not yet available. In this study, we examined whether the ferrous oxidation-xylenol orange (FOX) assay could be applicable for the high-throughput screening of 5-LO inhibitors. Using insect cell lysates overexpressing rat 5-LO, the effects of cofactors of 5-LO such as ATP, Ca2+, and L-alpha-phosphatidylcholine (PC) on the color development of FOX reagents were investigated. ATP quenched substantially color development by hydroperoxide, an intermediate of 5-LO reaction, and an optimum concentration of ATP with little interference was determined as 20 microM. Ethylenediaminetetraacetate (0.4 mM) also affected the complex formation with FOX reagents. On the other hand, neither Ca2+ nor PC influenced complex formation with FOX reagents. Under optimized assay conditions, zileuton, a 5-LO-specific inhibitor, exhibited inhibitory potency (IC50 values of 0.1-0.2 microM) similar to that determined by the conventional spectrophotometric assay. Taken together, this study shows that the FOX assay with some modifications can be employed for high-throughput assay format for the measurement of 5-LO activity at the stage of primary screening.

Animals↗

PubMed2000

Improved method for rapid determination of vitamin A in small samples of breast milk by high-performance liquid chromatography.

Employing a short, potassium hydroxide (KOH) saponification (25 min) and rapid extraction with n-hexane-toluene (1:1) and a <4-min retention time, a convenient, rapid, accurate and precise determination of vitamin A in breast milk was developed. The recovery rate was 102.3 +/- 2.5% and the small relative standard deviation (intra-assay 1.9%, inter-assay 2.3%) resulted in high precision. The amount of breast milk needed is very low (1 ml) which makes the method suitable for the use in free field studies with large sample sizes. The simple extraction and separation steps allow a high throughput screening under routine laboratory conditions.

Chromatography, High Pressure Liquid↗

PubMed2005

High-throughput solution-based medicinal library screening against human serum albumin.

High-throughput screening of combinatorial libraries has evolved from studying large diverse libraries to analyzing small, structurally similar, focused libraries. This paradigm shift has generated a need for rapid screening technologies to screen both diverse and focused libraries in a simple, efficient, and inexpensive manner. We have proactively addressed these needs by developing a high-throughput, solution-based method combining size exclusion (SEC), two-dimensional liquid chromatography (2-D LC), and mass spectrometry (MS) for determining the relative binding of drug candidates in small, focused medicinal libraries against human serum albumin (HSA). Two types of libraries were used to evaluate the performance of the system. The first consisted of five diverse ligands with a wide range of hydrophobicities and whose association constants to HSA cover 3 orders of magnitude. A beta-lactam library composed of structurally similar compounds was used to further confirm the validity of the methodology. The ability to distinguish site-specific interactions of drugs competing for individual domains of the HSA receptor is also demonstrated. Comparison of chromatographic profiles of the library components before and after incubation with the receptor using multiple reaction monitoring allowed a ranking of the ligands according to their relative binding affinities. The observed rankings correlate closely with literature values of the association constants between the respective ligands and HSA. This simple, rugged methodology can screen a wide spectrum of chemical entities from combinatorial mixtures in less than 6 min.

Acecainide↗

PubMed2002

A mammalian two-hybrid screening system for inhibitors of interaction between HIV Nef and the cellular tyrosine kinase Hck.

In the scope of the search for new anti-HIV agents interacting with a new target, we developed a high-throughput screening system to detect the interactions between Nef and Hck. Nef is an accessory protein of HIV, which is involved in the pathogenicity of the acquired immunodeficiency syndrome (AIDS). Nef is also a signaling molecule because it binds to many host molecules. It has especially high affinity to Hck, a member of src family tyrosine kinase. Using a mammalian two-hybrid system, the interaction between Nef and the SH3 domain of Hck induced luciferase activity with high sensitivity and a Nef-PXXP peptide inhibited this interaction; and so did the anticancer drug adriamycin. We also developed another assay system by coexpression of full-length Hck and Nef, and found that Hck kinase was activated depending on the dose of Nef plasmid. Using the second system, we found that adriamycin interfered with the Nef-Hck interaction by reducing the amount of the Hck protein. The mammalian two-hybrid system may show utility in screening inhibitors of Nef-Hck interaction.

3T3 Cells↗

PubMed2005

An offline-addition format for identifying GPCR modulators by screening 384-well mixed compounds in the FLIPR.

Although fluorescence imaging plate reader (FLIPR)-based assays have been widely used in high-throughput screening, improved efficiencies in throughput and fidelity continue to be investigated. This study presents an offline compound addition protocol coupled with a testing strategy using mixtures of compounds in a 384-well format to identify antagonists of the neurokinin-1 receptor expressed in the human astrocytoma cell line (U373 MG). Substance P evoked a concentration-dependent increase in intracellular cellular Ca(2+) with an EC(50) value of 0.30 +/- 0.17 nM, which was inhibited by neurokinin-1 (NK1) antagonists L-733,060 and L-703,606. Test compounds, as mixtures of 10 compounds/well, were added to the cells offline using an automated dispensing unit and incubated prior to performing the assay in the FLIPR. Using the offline protocol, a higher through put of ~200,000 compounds was achieved in an 8-h working day, and several novel structural classes of compounds were identified as antagonists for the NK1 receptor. These studies demonstrate that the offline compound addition format using a mixture of compounds in a 384-well FLIPR assay provides an efficient platform for screening and identifying modulators for G-protein-coupled receptors.

Cell Line, Tumor↗

PubMed2005

Probing the primary screening efficiency by multiple replicate testing: a quantitative analysis of hit confirmation and false screening results of a biochemical assay.

Despite a large body of references on assay development, assay optimization, strategies, and methodologies for high-throughput screening (HTS), there have been few reports on investigations of the efficiency of primary screening in a systematic and quantitative manner for a typical HTS process. Recently, the authors investigated the primary hit comparison and the effect of measurement variability by screening a library of approximately 25,000 random compounds in multiple replicate tests in a nuclear receptor recruitment assay with 2 different assay detection technologies. In this report, we utilized these sets of multiple replicate screening data from a different perspective and conducted a systematic data analysis in order to gain some insights into the hit-finding efficiency of a typical primary screening process. Specifically, hit confirmation, false-positive (declaration) rates, and false-negative rates at different hit cutoff limits were explored and calculated from the 2 different assay formats. Results and analyses provided some quantitative estimation regarding the reliability and efficiency of the primary screening process. For the 2 assay formats tested in this report, the confirmation rate (activity repeated at or above a certain hit limit) was found to be 65% or above. It was also suggested that, at least in this case, applying some hit-selection strategies, it is possible to decrease the number of false-negative or false-positive hits without significantly increasing the efforts in primary screening.

DNA-Binding Proteins↗

PubMed2004

Current progress in natural product-like libraries for discovery screening.

Natural product-like libraries represent an effort to combine the attractive features of natural products and combinatorial libraries for high-throughput screening. Three approaches to natural product-like library design are discussed: (1) Libraries based on core scaffolds from individual natural products, (2) libraries of diverse structures with general structural characteristics of natural products, and (3) libraries of diverse structures based on specific structural motifs from classes of natural products. Examples of successful applications in discovery screening are described for each category. These studies highlight the exciting potential of natural product-like libraries in both chemical biology and drug discovery.

Biological Factors↗

PubMed2003

Virtual screening of virtual libraries.

Virtual screening of virtual libraries (VSVL) is a rapidly changing area of research. Great efforts are being made to produce better algorithms, selection methods and infrastructure. Yet, the number of successful examples in the literature is not impressive, although the quality of work certainly is high. Why is this? One reason is that these methods tend to be applied at the lead generation stage and therefore there is a large lead-time before successful examples appear in the literature. However, any computational chemist would confirm that these methods are successful and there exists a glut of start-up companies specialising in virtual screening. Moreover, the scientific community would not be focussing so much attention on this area if it were not yielding results. Even so, the paucity of literature data is certainly a hindrance to the development of better methods. The VSVL process is unique within the discovery process, in that it is the only method that can screen the > 10(30) genuinely novel molecules out there. Already, some VSVL methods are evaluating 10(13) compounds, a capacity that high throughput screening can only dream of. There is a huge potential advantage for the company that develops efficient and effective methods, for lead generation, lead hopping and optimization of both potency and ADME properties. To do this, it requires more than the software, it requires confidence to exploit the methodology, to commit synthesis on the basis of it, and to build this approach into the medicinal chemistry strategy. It is a fact that these tools remain quite daunting for the majority of scientists working at the bench. The routine use of these methods is not simply a matter of education and training. Integration of these methods into accessible and robust end user software, without dilution of the science, must be a priority. We have reached a coincidence, where several technologies have the required level of maturity predictive computational chemistry methods, algorithms that manage the combinatorial explosion, high throughput crystallography and ADME measurements and the massive increase in computational horsepower from distributed computing. The author is confident that the synergy of these technologies will bring great benefit to the industry, with more efficient production of higher quality clinical candidates. The future is bright. The future is virtual!

Algorithms↗

PubMed2004

Recent progress in biocatalyst discovery and optimization.

The use of enzymes in industrial catalysis continues to grow because of the considerable advantages of natural catalytic systems. The need for enantiomerically pure fine chemicals and the movement away from chemically burdened technologies will drive the acceptance of enzyme-assisted processes. New technologies for enzyme discovery and optimization have enabled the application of enzymes in harsh industrial conditions and in processes demanding stringent selectivity. These discovery and laboratory evolution methods entail genomic approaches that by their nature engender screening of extremely large numbers of gene types and variants. By extension, the fitness of an individual high-throughput screen requires an intelligent, process-targeted assay amenable to a chosen screening platform.

Biotechnology↗

PubMed2006

Rapid microbiologic and pharmacologic evaluation of experimental compounds against Mycobacterium tuberculosis.

The assessment of physiochemical and pharmacological properties at early stages of drug discovery can accelerate the conversion of hits and leads into candidates for further development. A strategy for streamlined evaluation of compounds against Mycobacterium tuberculosis in the early preclinical stage is presented in this report. As a primary assay to rapidly select experimental compounds with sufficient in vitro activity, the growth inhibition microtiter plate assay was devised as an alternative to current methods. This microdilution plate assay is a liquid culture method based on spectrophotometric readings of the bacillary growth. The performance of this method was compared to the performance of two established susceptibility methods using clinical available tuberculosis (TB) drugs. Data generated from all three assays were similar for all of the tested compounds. A second simple bioassay was devised to assess the oral bioavailability of compounds prior to extensive in vivo efficacy testing. The bioassay estimates drug concentrations in collected serum samples by a microdilution MIC plate method using M. tuberculosis. In the same assay, the MIC of the compound is also determined in the presence of 10% mouse serum as an indication of protein binding. The method was validated using different clinically available TB drugs, and results are discussed in this report. With these methodological advances, screening of compounds against tuberculosis in the preclinical phase will be rapid, can be adapted to semi-high-throughput screening, and will add relevant physicochemical and basic pharmacological criteria to the decision process of drug discovery.

Animals↗

PubMed1997

Approaches to antibacterial drug discovery.

The discovery of new antibacterial drugs can be based either upon empirical screening methods or structure-based design. Empirical methods utilise both intact bacteria and isolated biochemical targets for high throughput screening of natural product or chemical libraries to detect inhibitor leads. Structure-based methods for drug design are based upon understanding the molecular architecture of the active site in an appropriate target molecule. Empirical methods have been widely applied to screen for antibacterial agents and the introduction of combinatorial methods for the synthesis of chemical libraries considerably expands the potential of empirical screening methods. In contrast, structure-based drug design has not yet been widely applied to the development of antibacterial drugs, although it has proved to be a successful approach in other therapeutic areas. Recent advances in the sequencing of bacterial genomes will assist both empirical and structure-based approaches by identifying new, essential bacterial genes whose products may become the targets of new agents with selective antibacterial activity.

Journal Article↗

PubMed2002

Psychiatric Genomics, inc.

Mental illness affects millions of patients and has been shown to have multiple genetic components. The interaction of environmental factors, such as stress, with the expression of genetic susceptibilities has hampered the development of novel and effective drug treatments. A new approach is described that can discover novel classes of drugs for the treatment of the underlying causes of these diseases rather than their symptoms. This approach screens drug candidates according to their ability to alter the expression of multiple genes in a multiparameter high-throughput screening assay (MPHTS SM) that does not require a prori knowledge of the targets of screening assays. Clinical development of drug candidates will be pursued through partnerships with pharmaceutical companies and/or large biotechnology companies.

Drug Evaluation, Preclinical↗

PubMed2006

A robust screen for inhibitors and enhancers of phosphoinositide-3 kinase (PI3K) activities by ratiometric fluorescence superquenching.

Aberrant regulation of phosphoinositide 3-kinase (PI3K) activity is implicated in various diseases such as cancer and diabetes. Thus, high-throughput screening (HTS) of small-molecule inhibitors for PI3 kinases is an appealing strategy for drug development. Despite the attractiveness of lipid kinases as drug targets, screening for inhibitors for PI3K activities has been hampered by limited assay formats adaptable for HTS. The authors describe a homogeneous, direct, and nonradioactive assay for highly sensitive detection of PI3Kalpha, beta, delta, and gamma activities, which is suitable for HTS. The assay is based on fluorescence superquenching of a conjugated polymer upon metal-ion-mediated association of phosphorylated and dye-labeled substrates. As a result of phosphorylation, quencher and polymer are brought into proximity, and fluorescent energy transfer occurs. This event can be monitored as either fluorescence quench of the polymer or as enhanced emission from the quencher. Ratiometric analysis of the wavelengths eliminates interferences from autofluorescing compounds, which are present in HTS libraries. The platform has been adapted for the 384-well microplate format and delivers Z factors of > 0.6 at substrate conversions as low as 7%. Using this assay platform, several unreported inhibitors and activators of PI3Ks were identified in an 84- compound screen.

Androstadienes↗

PubMed2004

HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.

To provide practical means for rapidly scanning the extensive experimental combinatorial chemistry libraries now available for high-throughput screening (HTS), it is essential to establish computational virtual ligand screening (VLS) techniques to rapidly identify out of a large library all active compounds against a particular protein target. Toward this goal we developed HierVLS, a fast hierarchical docking approach that starts with a coarse grain conformational search over a large number of configurations filtered with a fast but crude energy function, followed by a succession of finer grain levels, using successively more accurate but more expensive descriptions of the ligand-protein-solvent interactions to filter successively fewer cases. The final step of this procedure optimizes one configuration of the ligand in the protein site using our most accurate energy expression and description of the solvent, which would be impractical for all conformations and sites sampled in the coarse level. HierVLS is based on the HierDock approach, but rather than allowing an hour or more to determine the best binding site and energy for each ligands (as in HierDock), we have adapted our procedure so that it can lead to reliable results while using only 4 min (866 MHz Pentium III processor) per ligand. To validate the accuracy for HierVLS to predict the experimentally observed binding conformation, we considered 37 cocrystal structures comprising 11 target proteins. We find that HierVLS identifies the correct binding mode for all 37 cocrystals. In addition, the calculated binding energies correlate well with available experimental binding constants. To validate how well HierVLS can identify the correct ligand in an extensive library of decoys, we considered a library of over 10 000 molecules. HierVLS identifies 26 out of the 37 cases in the top 2% ranked by binding affinity among the 10 037 molecules. The failures result from either metal-containing sites on the protein or water-mediated ligand-protein interactions, which we anticipate can be solved within the constraints of practical VLS. We then applied HierVLS to screen a 55000-compound virtual library against the target protein-tyrosine phosphatase 1B (ptp1b). The top 250 compounds by binding affinity included all six ptp1b cocrystal ligands added to the library plus three other experimentally confirmed binders. The best (top 1) binder is an experimentally confirmed positive. We conclude that HierVLS is useful for selecting leads for a particular target out of large combinatorial databases.

Carbonic Anhydrase II↗

PubMed2005

Experimental screening of dihydrofolate reductase yields a "test set" of 50,000 small molecules for a computational data-mining and docking competition.

High-throughput screening (HTS) generates an abundance of data that are a valuable resource to be mined. Dockers and data miners can use "real-world" HTS data to test and further develop their tools. A screen of 50,000 diverse small molecules was carried out against Escherichia coli dihydrofolate reductase (DHFR) and compared with a previous screen of 50,000 compounds against the same target. Identical assays and conditions were maintained for both studies. Prior to the completion of the second screen, the original screening data were publicly released for use as a "training set", and computational chemists and data analysts were challenged to predict the activity of compounds in this second "test set". Upon completion, the primary screen of the test set generated no potent inhibitors of DHFR activity.

Computational Biology↗

PubMed2005

Genotoxicity screening: the slow march to the future.

Genetic toxicology testing in drug discovery and development is slowly moving into the age of high-throughput screening (HTS). This has been helped by the development of new tools, as well as validation studies and data analysis to support their use in hit-to-lead or lead optimisation decisions. This review provides an overview of the current genetic toxicology methodologies and a few HTS methodologies. Comparisons are made between the predictivity of carcinogenesis that can be achieved in screening strategies as well as by the battery of regulatory tests. The importance of false-positive and false-negative calls at different stages in development is considered. There is a good prospect that in genetic toxicology, as in other areas of ADME-Tox, HTS will reduce the growing costs of carrying compounds with undesirable characteristics too far along the drug development process.

Animals↗

PubMed2005

Cyclic nucleotide signalling: a molecular approach to drug discovery for Alzheimer's disease.

The EPAC (exchange protein directly activated by cAMP) proteins are GEFs (guanine nucleotide-exchange factors) that activate Rap GTPases upon binding to cAMP. The involvement of these proteins in a number of diseases, neurodegenerative, inflammatory and metabolic, has started to show how they may prove to be important targets for therapeutic intervention. We first became interested in EPAC when we discovered that the expression levels of both EPAC1 and EPAC2 were altered in those regions of the brain associated with Alzheimer's disease [McPhee, Breslin, Kewney, MacKenzie, Cooreman, Gibson and Hammond (2004) International Patent number WO 2004/096199 A2]. It was known that compounds could be designed to be selective for EPAC over PKA (protein kinase A); however, these compounds were all based around the core structure of cAMP. We decided to screen a small compound library (10000 compounds) to investigate the possibility of developing a compound series outside of the cAMP structure. We subsequently developed a novel, high-throughput screen based on the displacement of [3H]cAMP from the EPAC cAMP-binding site and identified small molecule hits from the Scottish Biomedical Lead Generation Library. These compounds selectively bind to the cAMP-binding sites of EPAC1 and EPAC2 and are structurally dissimilar to cAMP. They have similar affinities for both EPAC1 and EPAC2 and have a high degree of specificity for EPAC over PKA. We believe that these compounds provide a valuable starting point for a drug optimization programme.

Alzheimer Disease↗