Identifying small-molecule lead compounds: the screening approach to drug discovery

High-Content Phenotypic Screen of a Focused TCAMS Drug Library Identifies Novel Disruptors of the Malaria Parasite Calcium Dynamics

The search for new antimalarial drugs with unexplored mechanisms of action is currently one of the main objectives to combat the resistance already in the clinic. New drugs should target specific mechanisms that once initiated lead inevitably to the parasite's death and clearance and cause minimal toxicity to the host. One such new mode of action recently characterized is to target the parasite's calcium dynamics. Disruption of the calcium homeostasis is associated with compromised digestive vacuole membrane integrity and release of its contents, leading to programmed cell death-like features characterized by loss of mitochondrial membrane potential and DNA degradation. Intriguingly, chloroquine (CQ)-treated parasites were previously reported to exhibit such cellular features. Using a high-throughput phenotypic screen, we identified 158 physiological disruptors (hits) of parasite calcium distribution from a small subset of approximately 3000 compounds selected from the GSK TCAMS (Tres Cantos Anti-Malarial Set) compound library. These compounds were then extensively profiled for biological activity against various CQ- and artemisinin-resistant Plasmodium falciparum strains and stages. The hits were also examined for cytotoxicity, speed of antimalarial activity, and their possible inhibitory effects on heme crystallization. Overall, we identified three compounds, TCMDC-136230, -125431, and -125457, which were potent in inducing calcium redistribution but minimally inhibited heme crystallization. Molecular superimposition of the molecules by computational methods identified a common pharmacophore, with the best fit assigned to TCMDC-125457. There were low cytotoxicity or CQ cross-resistance issues for these three compounds. IC₅₀ values of these three compounds were in the low micromolar range. In addition, TCMDC-125457 demonstrated high efficacy when pulsed in a single-dose combination with artesunate against tightly synchronized artemisinin-resistant ring-stage parasites. These results should add new drug options to the current armament of antimalarial drugs as well as provide promising starting points for development of drugs with non-classical modes of action.

Isolation and identification of Streptomyces sp. Act4Zk, a good producer of Staurosporine and some derivatives

In this study, strain Streptomyces sp. Act4Zk was isolated based on a method developed for the isolation of myxobacteria. Due to the low efficiency of the majority of conventional DNA extraction techniques, for molecular identification of the strain Streptomyces sp. Act4Zk, a new technique for DNA extraction of Actinobacteria was developed. In order to explore potential bioactivities of the strain, extracts of the fermented broth culture were prepared by an organic solvent (i.e. ethyl acetate) extraction method using. These ethyl acetate extracts were subjected to HPLC fractionation against standard micro-organisms, followed by LC/MS analysis. Based on morphological, physiological, biochemical and 16S rRNA gene sequence data, strain Streptomyces sp. Act4Zk is likely to be a new species of Streptomyces, close to Streptomyces genecies and Streptomyces roseolilacinus. Antimicrobial assay indicated high antifungal activity as well as antibacterial activity against Mycobacterium smegmatis and Gram-positive bacteria for the new strain. HPLC and LC/MS analyses of the extracts led to the identification of three different compounds and confirmed our hypothesis that the interesting species of the genus Streptomyces being a good producer of staurosporine and some derivatives.

Modeling and Statistical Optimization of Culture Conditions for Improvement of Antifungal Compounds Production by Streptomyces albidoflavus S19 Strain of Wastewater Origin

BACKGROUND

The actinomycetes strains isolated from unexplored ecosystems are a promising alternative for the biosynthesis of novel antimicrobial compounds. Depending on the interesting antifungal activity of the studied strain S19, the statistical method seems to be an effective tool for optimizing the production of anticandidal molecules.

INTRODUCTION

This study was conducted in order to optimize the culture parameters (medium nutrients concentrations and initial pH value) affecting the production of antifungal metabolites from S. albidoflavus strain S19 (obtained from wastewater collected in Bejaia region, Algeria) using Response Surface Metho-dology (RSM). The best conditions for anti-Candida albicans compounds biosynthesis were determined.

METHODS AND RESULTS

The antimicrobial producer strain S. albidoflavus S19 was identified on the basis of morphological, chemicals characters and physiological characteristics along with 16S rRNA gene se-quencing analysis.Response Surface Methodology by Central Composite Design (CCD) was employed to improve the anti-C. albicans agents production through the optimization of medium parameters. The highest antifungal ac-tivity was obtained by using a mixture of 2g l-1 starch, 4g l-1 yeast extract, 2g l-1 peptone at pH 11.

CONCLUSION

The strain S19 isolated from wastewater showed a significant anti-C. albicans activity and this study revealed the effectiveness of RSM and CCD for increasing bioactive compounds production, rising the diameter of inhibition zones from 13 to 34 mm.

In pursuit of the ideal antifungal agent for Candida infections: high-throughput screening of small molecules

Candida infections have created a great burden on the public healthcare sector. The situation is worsened by recent epidemiological changes. Furthermore, the current arsenal of antifungal agents is limited and associated with undesirable drawbacks. Therefore, new antifungal agents that surpass the existing ones are urgently needed. High-throughput screening of small molecule libraries enables rapid hit identification and, possibly, increases hit rate. Moreover, the identified hits could be associated with unrecognized or multiple drug targets, which would provide novel insights into the biological processes of the pathogen. Hence, it is proposed that high-throughput screening of small molecules is particularly important in the pursuit of the ideal antifungal agents for Candida infections.

In silico systems biology approaches for the identification of antimicrobial targets

Classical antibiotic discovery efforts have relied mainly on molecular library screening coupled with target-based lead optimization. The conventional approaches are unable to tackle the emergence of antibiotic resistance and are failing to provide understanding of multiple mechanisms behind drug actions and the off-target effects. These insufficiencies have prompted researchers to focus on a multidisciplinary approach of systems biology-based antibiotic discovery. Systems biology is capable of providing a big-picture view for therapeutic targets through interconnected networks of biochemical reactions derived from both experimental and computational techniques. In this chapter, we have compiled software tools and databases that are typically used for target identification through in silico analyses. We have also identified enzyme- and broad-spectrum metabolite-based drug targets that have emerged through in silico systems microbiology.

Screening of actinomycetes from earthworm castings for their antimicrobial activity and industrial enzymes

Actinomycetes from earthworm castings were isolated and screened for their antimicrobial activity and industrial enzymes. A total of 48 isolates were obtained from 12 samples of earthworm castings. Highest numbers of isolates were recovered from forest site (58.33 %) as compared to grassland (25%) and agricultural land (16.66%). The growth patterns, mycelial coloration of abundance actinomycetes were documented. The dominant genera Identified by cultural, morphological and physiological characteristics were Streptomyces (60.41%) followed by Streptosporangium (10.41%),Saccharopolyspora (6.25%) and Nocardia (6.25%). Besides these, other genera like Micromonospora, Actinomadura, Microbispora, Planobispora and Nocardiopsis were also recovered but in low frequency. Among the 48 isolates, 52.08% were found active against one or more test organisms. Out of 25 active isolates 16% showed activity against bacterial, human fungal as well as phytopathogens. Among 48 isolates 38, 32, 21, 20, 16 and 14 produced enzyme amylase, caseinase, cellulase, gelatinase, xylanase and lipase respectively while 10 isolates produced all the enzymes. More interestingly 2, 3, and 1 isolates produced amylase, xylanase and lipase at 45°C respectively. In the view of its antimicrobial activity as well as enzyme production capability the genus Streptomyces was dominant. The isolate EWC 7(2) was most promising on the basis of its interesting antimicrobial activity and was identified as Streptomyces rochei. The results of these findings have increased the scope of finding industrially important actinomycetes from earthworm castings and these organisms could be promising sources for industrially important molecules or enzymes.

In Vitro Susceptibility of C. albicans and C. neoformens to Potential Metabolites from Streptomycetes

Forty two Streptomycetes isolates from soils of Kodachadri region in Western ghats were recovered by soil dilution technique. Cross streak method was followed for primary screening of antifungal activity. Positive isolates were subjected to secondary screening by cold extraction of fermentation broth in butanol solvent. Six isolates exhibited broad spectrum antifungal activity against all the tested yeast pathogens like Candida albicans, Candida lipolytica, Cryptococcus neoformens and Saccharomyces cerevisiae. One isolate showed excellent antifungal activity against all test organisms with maximum zone of inhibition 60 mm each incase of C. neoformens and C. albicans. Partial characterization of antifungal metabolite by TLC resulted in a purple spot with an R(f) value 0.50. The UV absorption spectra at 218 nm indicated possible chemical nature of the active metabolite as polyene group and purity was assessed by analytical HPLC.

Characterization of theEscherichia coliAntifungal Protein PPEBL21

An antifungal protein isolated from Escherichia coli BL21 (PPEBL21) and predicted to be alcohol dehydrogenase (ADH) was subjected to biological characterization. The PPEBL21, indeed, demonstrated propionaldehyde-specific ADH activity. The Km and Vmax of PPEBL21 were found to be 644.8 μM and 1.2 U/mg, respectively. In-gel activity assay also showed that PPEBL21 was a propionaldehyde-specific ADH. The pI of PPEBL21 was observed to be 7.8. PPEBL21 was found to be stable up to a temperature of 40°C with optimum activity at pH 7.5. The decrease in pH decreased the activity of PPEBL21. These results suggested that PPEBL21 having alcohol dehydrogenase activity and stability at significantly high temperature might be an important lead antifungal molecule. Experiments were performed to identify the possible target of PPEBL21 in the pathogen A. fumigatus. Results revealed that PPEBL21 inhibited completely the expression of a 16 kDa protein in A. fumigatus. The 16 kDa protein of A. fumigatus targeted by PPEBL21 was identified as a hypothetical protein by peptide mass fingerprinting. It is thus hypothesized that a 16 kDa factor is essentially required by A. fumigatus for survival and its impaired synthesis due to treatment with PPEBL21 may lead to the death of pathogen.

Chemical genetic screening of KRAS-based synthetic lethal inhibitors for pancreatic cancer

Pancreatic cancer is one of the deadliest diseases largely due to difficulty in early diagnosis and the lack of effective treatments. KRAS is mutated in more than 90% of pancreatic cancer patients, and oncogenic KRAS contributes to pancreatic cancer tumorigenesis and progression. In this report, using an oncogenic KRASV12-based pancreatic cancer cell model, we developed a chemical genetic screen to identify small chemical inhibitors that selectively target pancreatic cancer cells with gain-of-function KRAS mutation. After screening ~3,200 compounds, we identified one compound that showed selective synthetic lethality against the KRASV12 transformed human pancreatic ductal epithelial cell over its isogenic parental cell line. These selective KRASV12-synthetic lethal compounds may serve as leads for subsequent development of clinically-effective treatments for pancreatic cancer.

Variable-pitch dispensing workstation and its application to the preparation of microsensor arrays

We have developed an 8-ch capillary-based dispensing workstation with a variable capillary pitch mechanism. The capillary intervals can be varied from 1 to 9 mm to dispense different solutions simultaneously at an arbitrary dispensing pitch, allowing direct dispensing from microplates to integrated analytical systems. To evaluate the precision of its dispensing performance, droplets of Rhodamine G dye were dispensed onto glass slides and the values of the optical volume were analyzed. The error in the dispensed volume proved to be 0.54 nL when dispensing 20 nL. In dispensing small volumes, the volume error for this workstation was found to be about 100-fold less than that seen in conventional dispensers. Even highly viscous solutions containing 50% glycerol could be dispensed with precision. Rapid dispensing was also achieved. Moreover, the application of the workstation to preparing addressable 8 x 12 microsensor array chips was demonstrated, providing an independent and reproducible spot array.

Identification of an agent selectively targeting DPC4 (deleted in pancreatic cancer locus 4)-deficient pancreatic cancer cells

One of the most common types of genetic alterations in cancer is the loss-of-function mutations in tumor-suppressor genes. Such mutations are usually very specific to cancer cells and present attractive and unique opportunities for therapeutic interventions. However, for various reasons, antitumor agents that target loss-of-function mutations have not been readily identified. In this report, using the deleted in pancreatic cancer locus 4 (DPC4) gene in pancreatic cancer as an example, we show the feasibility of a novel screening strategy, which we have named Pharmacological Synthetic Lethal Screening, for the identification of agents that selectively target cancer cells with loss-of-function mutations. We created DPC4 isogenic cell lines through the restoration of wild-type DPC4 in a pancreatic cancer cell line, BxPC-3, whose DPC4 gene was homozygously deleted. The isogenic cell lines were then used in the Pharmacological Synthetic Lethal Screening to evaluate compound libraries for antiproliferative activity and selectivity against DPC4 deficiency. After screening 19,590 compounds, we identified one lead compound, UA62001, which showed 4.6-fold selectivity against DPC4 deficiency in the DPC4 isogenic cell lines. UA62001 selectivity was also seen in another set of DPC4 isogenic cell lines generated by small interfering RNA knockdown. In addition, UA62001 was evaluated in commonly used pancreatic cancer cell lines. A fairly good correlation between DPC4 deficiency and UA62001 sensitivity was observed. Cell cycle analysis indicates that UA62001 arrests cells in S and G(2)-M phases. The results of microarray gene expression profiling and quantitative real-time reverse transcription-PCR suggest that cyclin B/CDC2 and minichromosome maintenance complexes might be the downstream cellular targets of UA62001.

A non-polyene antifungal antibiotic from Streptomyces albidoflavus PU 23

In all 312 actinomycete strains were isolated from water and soil samples from different regions. All these isolates were purified and screened for their antifungal activity against pathogenic fungi. Out of these, 22% of the isolates exhibited activity against fungi. One promising strain, Streptomyces albidoflavus PU 23 with strong antifungal activity against pathogenic fungi was selected for further studies. Antibiotic was extracted and purified from the isolate. Aspergillus spp. was most sensitive to the antibiotic followed by other molds and yeasts. The antibiotic was stable at different temperatures and pH tested and there was no significant loss of the antifungal activity after treatment with various detergents and enzymes. Synergistic effect was observed when the antibiotic was used in combination with hamycin. The antibiotic was fairly stable for a period of 12 months at 4 degree C. The mode of action of the antibiotic seems to be by binding to the ergosterol present in the fungal cell membrane resulting in the leakage of intracellular material and eventually death of the cell. The structure of the antibiotic was determined by elemental analysis and by ultraviolet (UV), Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR) and liquid chromatography mass spectra (LCMS). The antibiotic was found to be a straight chain polyhydroxy, polyether, non-proteinic compound with a single double bond, indicating a nonpolyene antifungal antibiotic.

Mechanism targeted discovery of antitumor marine natural products

Antitumor drug discovery programs aim to identify chemical entities for use in the treatment of cancer. Many strategies have been used to achieve this objective. Natural products have always played a major role in anticancer medicine and the unique metabolites produced by marine organisms have increasingly become major players in antitumor drug discovery. Rapid advances have occurred in the understanding of tumor biology and molecular medicine. New insights into mechanisms responsible for neoplastic disease are significantly changing the general philosophical approach towards cancer treatment. Recently identified molecular targets have created exciting new means for disrupting tumor-specific cell signaling, cell division, energy metabolism, gene expression, drug resistance and blood supply. Such tumor-specific treatments could someday decrease our reliance on traditional cytotoxicity-based chemotherapy and provide new less toxic treatment options with significantly fewer side effects. Novel molecular targets and state-of-the-art, molecular mechanism-based screening methods have revitalized antitumor research and these changes are becoming an ever-increasing component of modern antitumor marine natural products research. This review describes marine natural products identified using tumor-specific mechanism-based assays for regulators of angiogenesis, apoptosis, cell cycle, macromolecule synthesis, mitochondrial respiration, mitosis, multidrug efflux and signal transduction. Special emphasis is placed on natural products directly discovered using molecular mechanism-based screening.

Text Influenced Molecular Indexing (TIMI): a literature database mining approach that handles text and chemistry

We present an application of a novel methodology called Text Influenced Molecular Indexing (TIMI) to mine the information in the scientific literature. TIMI is an extension of two existing methodologies: (1) Latent Semantic Structure Indexing (LaSSI), a method for calculating chemical similarity using two-dimensional topological descriptors, and (2) Latent Semantic Indexing (LSI), a method for generating correlations between textual terms. The singular value decomposition (SVD) of a feature/object matrix is the fundamental mathematical operation underlying LSI, LaSSI, and TIMI and is used in the identification of associations between textual and chemical descriptors. We present the results of our studies with a database containing 11,571 PubMed/MEDLINE abstracts which show the advantages of merging textual and chemical descriptors over using either text or chemistry alone. Our work demonstrates that searching text-only databases limits retrieved documents to those that explicitly mention compounds by name in the text. Similarly, searching chemistry-only databases can only retrieve those documents that have chemical structures in them. TIMI, however, enables search and retrieval of documents with textual, chemical, and/or text- and chemistry-based queries. Thus, the TIMI system offers a powerful new approach to uncovering the contextual scientific knowledge sought by the medical research community.

marvin: A Platform for Chemoinformatics Software Development

A strategy for a new type of platform for chemoinformatics software development and its first implementation are presented. The basic task of such a platform is to apply sequences of computational methods to high numbers of molecules. The implementation presented is based on four major components: (a) the application manager, responsible for running programs and for data management; (b) executable applications that supply limited pieces of functionality; (c) syntax definitions for data and control files and (d) the runtime library which comprises routines for data handling and user interface. This simple concept is implemented in the software package marvin. Different computational methods are available within marvin, including parts of commercial software packages (e.g. molecular modeling, bioinformatics, statistics, etc.) as well as newly developed and innovative algorithms. The basic layout of marvin is described and a simple example illustrates its application.

Liquid chromatography/tandem mass spectrometric quantification with metabolite screening as a strategy to enhance the early drug discovery process

Throughput for early discovery drug metabolism studies can be increased with the concomitant acquisition of metabolite screening information and quantitative analysis using ultra-fast gradient chromatographic methods. Typical ultra-fast high-performance liquid chromatography (HPLC) parameters used during early discovery pharmacokinetic (PK) studies, for example, employ full-linear gradients over 1-2 min at very high flow rates (1.5-2 mL/min) on very short HPLC columns (2 x 20 mm). These conditions increase sample throughput by reducing analytical run time without sacrificing chromatographic integrity and may be used to analyze samples generated from a variety of in vitro and in vivo studies. This approach allows acquisition of more information about a lead candidate while maintaining rapid analytical turn-around time. Some examples of this approach are discussed in further detail.

Differentiation therapy of human cancer: basic science and clinical applications

Current cancer therapies are highly toxic and often nonspecific. A potentially less toxic approach to treating this prevalent disease employs agents that modify cancer cell differentiation, termed 'differentiation therapy.' This approach is based on the tacit assumption that many neoplastic cell types exhibit reversible defects in differentiation, which upon appropriate treatment, results in tumor reprogramming and a concomitant loss in proliferative capacity and induction of terminal differentiation or apoptosis (programmed cell death). Laboratory studies that focus on elucidating mechanisms of action are demonstrating the effectiveness of 'differentiation therapy,' which is now beginning to show translational promise in the clinical setting.

Evaluation of liquid handling conditions in microplates

Liquid handling in higher density microplates (e.g., 1536-well microplates) for more efficient drug screening necessitates carefully selected and optimized parameters. The quality of a liquid handling procedure is dependent on the carryover rate of residual liquids during the pipetting process, the mixing behavior in the wells, foam and bubble formation, and evaporation. We compared and optimized these parameters in 96-, 384-, and 1536-well microplates, and herein we critically evaluate the performance of the CyBi-Well 96/384/1536 automated micropipetting device, which formed the basis of our evaluation studies.

Mass spectrometry innovations in drug discovery and development

This review highlights the many roles mass spectrometry plays in the discovery and development of new therapeutics by both the pharmaceutical and the biotechnology industries. Innovations in mass spectrometer source design, improvements to mass accuracy, and implementation of computer-controlled automation have accelerated the purification and characterization of compounds derived from combinatorial libraries, as well as the throughput of pharmacokinetics studies. The use of accelerator mass spectrometry, chemical reaction interface-mass spectrometry and continuous flow-isotope ratio mass spectrometry are promising alternatives for conducting mass balance studies in man. To meet the technical challenges of proteomics, discovery groups in biotechnology companies have led the way to development of instruments with greater sensitivity and mass accuracy (e.g., MALDI-TOF, ESI-Q-TOF, Ion Trap), the miniaturization of separation techniques and ion sources (e.g., capillary HPLC and nanospray), and the utilization of bioinformatics. Affinity-based methods coupled to mass spectrometry are allowing rapid and selective identification of both synthetic and biological molecules. With decreasing instrument cost and size and increasing reliability, mass spectrometers are penetrating both the manufacturing and the quality control arenas. The next generation of technologies to simplify the investigation of the complex fate of novel pharmaceutical entities in vitro and in vivo will be chip-based approaches coupled with mass spectrometry.

Inhibition of [(3)H]ponasterone a binding by ecdysone agonists in the intact Sf-9 cell line

Ecdysone agonists, including dibenzoylhydrazines, significantly inhibited the binding of [(3)H]ponasterone A ([(3)H]PoA) in intact Sf-9 cells (Spodoptera frugiperda). The amount of [(3)H]PoA binding varied in a concentration-dependent manner. According to the IC(50), concentration at which there is 50% inhibition, the order of potency of typical ecdysone agonists is tebufenozide (RH-5992) > methoxyfenozide (RH-2485) > PoA > 20-hydroxyecdysone > cyasterone > RH-5849, makisterone A > or = inokosterone > ecdysone. The ranking is consistent with that obtained from a cultured integument system of the rice stem borer Chilo suppressalis except for methoxyfenozide. Other compounds whose modes of action are different from that of ecdysteroids, for example respiration inhibitors, plant steroid hormones, and chitin synthesis inhibitors, did not inhibit the binding of [(3)H]PoA significantly. The mammalian hormones estradiol and diethylstilbestrol, and a secondary bile acid, lithocholic acid, significantly inhibited the binding of [(3)H]PoA at 25 microM. However, their binding activity in terms of pIC(50) was either very low or not evaluated.

Combinatorial chemistry as a tool for drug discovery

The question 'will combinatorial chemistry deliver real medicines' has been posed [96]. First it is important to realise that the chemical part of the drug discovery process cannot stand alone; the integration of synthesis and biological assays is fundamental to the combinatorial approach. The results presented in Tables 3.1 to 3.8 suggest that so far smaller directed combinatorial libraries have obtained equivalent results to those obtained previously from traditional medicinal chemistry analogue programs. Unfortunately, because of the long time it takes to develop pharmaceutical drugs there are no examples yet of marketed drugs discovered by combinatorial methods. There are interesting examples where active leads have been discovered from the screening of the same library against multiple targets (e.g. libraries 13, 39, 43, 66, 71 and 76). It is now possible to handle much larger libraries of non-oligomeric structures and the chemistry required for such applications is becoming available. Whether combinatorial approaches can also be adapted to deal with all the other requirements of a successful pharmaceutical (lack of toxicity, bioavailability etc.) is open to question but there are already examples such as cassette dosing [235-237]. However we can still be optimistic about the possibility of larger libraries producing avenues of investigation for the medicinal chemist to develop into real drugs. Combinatorial chemistry is an important tool for the medicinal chemist.

Discovering novel chemotherapeutic drugs for the third millennium

There is enormous potential for the discovery of innovative cancer drugs with improved efficacy and selectivity for the third millennium. In this review we show how novel mechanism-based agents are being discovered by focusing on the molecular targets and pathways that are causally involved in cancer formation, maintenance and progression. We also show how new technologies, from genomics through high through-put bioscience, combinatorial chemistry, rational drug design and molecular pharmacodynamic and imaging techniques, are accelerating the pace of cancer drug discovery. The process of contemporary small molecule drug discovery is described and progress and current issues are reviewed. New and potential targets and pathways for therapeutic intervention are illustrated. The first examples of a new generation of molecular therapeutics are now entering hypothesis-testing clinical trials and showing activity. The early years of the new millennium will see a range of exciting new agents moving from bench to bedside and beginning to impact on the management and cure of cancer.

Structure-based identification of small molecule antiviral compounds targeted to the gp41 core structure of the human immunodeficiency virus type 1

Recent X-ray crystallographic determination of the HIV-1 envelope glycoprotein gp41 core structure opened up a new avenue to discover antiviral agents for chemotherapy of HIV-1 infection and AIDS. We have undertaken a systematic study to search for anti-HIV-1 lead compounds targeted to gp41. Using molecular docking techniques to screen a database of 20 000 organic molecules, we found 16 compounds with the best fit for docking into the hydrophobic cavity within the gp41 core and with maximum possible interactions with the target site. Further testing of these compounds by an enzyme-linked immunosorbent assay and virus inhibition assays discerned two compounds (ADS-J1 and ADS-J2) having inhibitory activity at micromolar concentrations on the formation of the gp41 core structure and on HIV-1 infection. These two compounds will be used as leads to design more effective HIV-1 inhibitors targeted to the HIV-1 gp41 core structure.

Optimization of the cost and sensitivity of receptor- and enzyme-based assays

In detecting receptor antagonists or enzyme inhibitors, there are three parameters that often affect the outcome in a predictable quantitative manner: concentrations of the receptors (enzyme), labeled ligand (substrate), and antagonist (inhibitor). The usual goal of assay optimization is to maximize the ability of the assay to detect low concentrations of the analyte. Another question of practical importance, especially in screening of large numbers of samples, would be minimization of the reagent cost. Although the mathematical theory of optimization of the receptor binding assay was developed a long time ago, the resulting formulas (in the general case of unequal affinities of ligand and competitor) were not well suited for practical use. The current availability of computational programs, such as Mathematica, makes possible an efficient solution, both for receptor- and enzyme-based assays. We use a graphical approach to assay optimization and apply it to the following problems: (1) optimization of assay sensitivity, (2) optimization of the reagent cost, and (3) analysis of the entire range of the parameter values since the mathematically optimal values may sometimes be impractical. The computation is extremely simple and the problem can sometimes be solved in several minutes.

Combinatorial mixture synthesis and biological evaluation of dihydrophenyl triazine antifolates

The traditional 'one-pot' three component synthesis was adapted successfully for combinatorial mixtures synthesis of dihydrophenyl triazines, which are nonclassical, dihydrofolate reductase (DHFR) inhibitors. Each library was designed to comprise eight reaction mixture pots and in every pot there were three dihydrophenyl triazines. A total of three libraries were synthesized and the final number of compounds harvested was 64. The products precipitated out of the reaction mixture and could be collected easily and cleansed by washing. Solid supports and further purification processes were not required. The reactions were monitored by TLC and a HPLC method was developed to determine the number of products in each pot. All 24 pots were screened for inhibitory activity against the rat liver DHFR. Two pots showed good inhibitory activity and the products in them were individually synthesized, characterized and biologically tested again. One lead compound was identified amongst all the compounds synthesized, and would be further optimized.

Two-dimensional parallel array technology as a new approach to automated combinatorial solid-phase organic synthesis

An automated, 96-well parallel array synthesizer for solid-phase organic synthesis has been designed and constructed. The instrument employs a unique reagent array delivery format, in which each reagent utilized has a dedicated plumbing system. An inert atmosphere is maintained during all phases of a synthesis, and temperature can be controlled via a thermal transfer plate which holds the injection molded reaction block. The reaction plate assembly slides in the X-axis direction, while eight nozzle blocks holding the reagent lines slide in the Y-axis direction, allowing for the extremely rapid delivery of any of 64 reagents to 96 wells. In addition, there are six banks of fixed nozzle blocks, which deliver the same reagent or solvent to eight wells at once, for a total of 72 possible reagents. The instrument is controlled by software which allows the straightforward programming of the synthesis of a larger number of compounds. This is accomplished by supplying a general synthetic procedure in the form of a command file, which calls upon certain reagents to be added to specific wells via lookup in a sequence file. The bottle position, flow rate, and concentration of each reagent is stored in a separate reagent table file. To demonstrate the utility of the parallel array synthesizer, a small combinatorial library of hydroxamic acids was prepared in high throughput mode for biological screening. Approximately 1300 compounds were prepared on a 10 μmole scale (3-5 mg) in a few weeks. The resulting crude compounds were generally >80% pure, and were utilized directly for high throughput screening in antibacterial assays. Several active wells were found, and the activity was verified by solution-phase synthesis of analytically pure material, indicating that the system described herein is an efficient means for the parallel synthesis of compounds for lead discovery. Copyright 1998 John Wiley & Sons, Inc.

Bioactive agents from natural sources: trends in discovery and application

About 30% of the worldwide sales of drugs are based on natural products. Though recombinant proteins and peptides account for increasing sales rates, the superiority of low-molecular mass compounds in human diseases therapy remains undisputed mainly due to more favorable compliance and bioavailability properties. In the past, new therapeutic approaches often derived from natural products. Numerous examples from medicine impressively demonstrate the innovative potential of natural compounds and their impact on progress in drug discovery and development. However, natural products are currently undergoing a phase of reduced attention in drug discovery because of the enormous effort which is necessary to isolate the active principles and to elucidate their structures. To meet the demand of several hundred thousands of test samples that have to be submitted to high-throughput screening (HTS) new strategies in natural product chemistry are necessary in order to compete successfully with combinatorial chemistry. Today, pharmaceutical companies have to spend approximately US $350 million to develop a new drug. Currently, approaches to improve and accelerate the joint drug discovery and development process are expected to arise mainly from innovation in drug target elucidation and lead finding. Breakthroughs in molecular biology, cell biology, and genetic engineering in the 1980 s gave access to understanding diseases on the molecular or on the gene level. Subsequently, constructing novel target directed screening assay systems of promising therapeutic significance, automation, and miniaturization resulted in HTS approaches changing the industrial drug discovery process drastically. Furthermore, elucidation of the human genome will provide access to a dramatically increased number of new potential drug targets that have to be evaluated for drug discovery. HTS enables the testing of an increasing number of samples. Therefore, new concepts to generate large compound collections with improved structural diversity are desirable.

Rapid drug metabolite profiling using fast liquid chromatography, automated multiple-stage mass spectrometry and receptor-binding

Rapid drug metabolite profiling can be achieved using fast chromatographic separation and fast mass spectrometric scanning without compromising the separation efficiency. Fast chromatographic separations of drug and its metabolites can be achieved by eluting from a short narrow-bore guard cartridge column (20 x 2 mm I.D., 3 microns BDS Hypersil C8) at flow-rate of 1.0 ml/min and with a gradient volume greater than 90 column volumes. The need for chromatographic separation is important for automated data dependent multiple-stage mass spectrometry (MSn) experimentation. The total analysis time of 8 min permits profiling of metabolites in a 96-well plate in 13 h. The narrow chromatographic peaks resulting from the high flow-rate require the use of a mass spectrometer capable of fast scan speed due to the need to perform multiple MS experiments within the same chromatographic analysis. A method has been developed for screening potentially biologically active in vitro microsomal metabolites by affinity binding with a receptor. After separation by centrifugal ultrafiltration, the bound ligands are released and characterized by LC-MS. In vitro microsomal metabolites of tamoxifen, raloxifene and adatanserin were screened for potential biological activity using this method. The in vitro metabolites of tamoxifen captured by the receptor include N-demethyltamoxifen and three species of hydroxytamoxifen; these data are consistent with those from a conventional binding study and bioassay. In addition, both hydroxyraloxifene and dihydroxyraloxifene are also recognized by the receptor. The specificity of the molecular recognition process is illustrated by the absence of binding with control microsomal incubate and with adatanserin and its metabolites. Therefore, active metabolites can be rapidly profiled by fast LC, automated MSn, and receptor binding. This information can be obtained quickly and can add value to the drug discovery process.

Drug discovery: past, present and future

New drug discovery from early on involved a trial-and-error approach on naturally derived materials and substances until the end of the nineteenth century. The first half of the twentieth century witnessed systematic pharmacological evaluations of both natural and synthetic compounds. However, most new drugs until the 1970s were discovered by serendipity. With the exponential development of molecular biology on one hand and computer technology on the other, it became possible from 1980 onwards to place drug discovery on a rational basis. Cloning of genes has led to the development of methodologies for specific receptor-directed and enzyme-directed drug discoveries. Advances in recombinant DNA and transgenic technologies have enabled the production of human hormonal and other endogenous biomolecules as new drugs. As we understand more about the co-ordinating and regulating powers of the cerebral cortex during the next century, especially of the frontal lobe, man may be able to use bio-feedback training to voluntarily regulate the release of neurotransmitters, hormones, and other molecules involved in the regulation of various physiological processes in health as well as in disease.

Therapeutic peptides and peptidomimetics

Peptidomimetics are one set of probes used in the transition pathway of small molecule drug design. Cyclization of the peptide backbone and its modification with aromatic residues constitutes an effective approach to mimetic drug design and circumvents obstacles associated with delivery and formulation of peptides and peptidomimetics. In the past year, examples of mimicking beta-turn structures has led to combining design strategies with molecular libraries, demonstrating that peptidomimetics can provide valuable clues about receptor similarities not revealed by their endogenous ligands. This information can lead to the development of dual inhibitors. In addition, this work suggests that the use of libraries and rational design need not be mutually exclusive approaches to lead discovery.

Multidimensional chromatography coupled with mass spectrometry for target-based screening

The synthesis of structural analogs and the process of drug discovery have evolved dramatically through recent advances in solid-phase synthesis reagents and automated screening systems. As molecular diversity strategies emerge, the need for automated target-based selection of lead candidates becomes equally important. Multidimensional automated chromatographic techniques coupled to electrospray ionization mass spectrometry facilitate the selection process and provide maximum characterization information in a single screening run. The capture of tightly bound affinity leads by target biomolecules, followed by subsequent release and high-resolution separation with sensitive detection, significantly reduces the time required to identify and characterize lead compounds. This automated multidimensional chromatographic approach coupled with mass spectrometry, Selectronics, was used with several organic and natural libraries to demonstrate an automated target-based screening technique to select for high-affinity binders as potential lead compounds.

Why sequence the genome of Mycobacterium tuberculosis?

Radical measures are required to prevent the grim predictions of the World Health Organisation for the deterioration of the global tuberculosis epidemic in the next century from becoming reality. Study of the nerve centre of the tubercle bacillus, its genome, by means of systematic deoxyribonucleic acid sequence analysis will provide a wealth of information about Mycobacterium tuberculosis that will undoubtedly fuel the next generation of research. In the coming year, this highly cost-effective approach will deliver an unprecedented amount of knowledge to catalyse the development of new, more efficient diagnostic tools and therapeutic interventions to detect, control and, ultimately, eliminate tuberculosis.

Macromolecular versus small-molecule therapeutics: drug discovery, development and clinical considerations

Recent advances in biomedical science in general, and molecular biology in particular, have provided a greater understanding of pathogenesis at the molecular and (sub)cellular level. In turn, this has stimulated the development of macromolecular, mechanism-based therapeutic agents, ranging from recombinant proteins, to oligonucleotides, to genes/gene fragments. The factors essential for the successful development of this new class of therapeutic agents are not necessarily the same as those for the development of conventional small organic molecules. This review mentions several issues relating to the development of macromolecular drugs, and emphasizes the key issue of drug transport and delivery.

Pyrolysis mass spectrometry and its applications in biotechnology

Pyrolysis mass spectrometry is a rapid and high-resolution method for the analysis of otherwise non-volatile material and has been widely applied for discriminating between closely related microbial strains. Recent advances in statistical and neural network methods based on supervised learning have now permitted exploitation of pyrolysis mass spectrometry in the quantitative analysis of many diverse samples of biotechnological interest; the technique may thus be regarded as an 'anything-sensor'.

Fishing for drugs from the sea: status and strategies

Marine organisms represent an enormous, essentially unexploited, resource of natural products. Globally, the race to develop marine-derived drugs is well under way with many pharmaceutical companies positioning themselves to reap large profits by the exploitation of the ocean's rich chemical diversity. Targeted strategies, often in combination with high-throughput screening, are being employed in this hunt for novel pharmacotherapeutic agents. David de Vries and Phil Beart examine the potential, problems and technologies of an international pharmaceutical search that has important ethical considerations.