Rhodanine as a scaffold in drug discovery: a critical review of its biological activities and mechanisms of target modulation

INTRODUCTION: Rhodanine-based compounds have been associated with numerous biological activities. After many years of research in drug discovery, they have gained a reputation as being pan assay interference compounds (PAINS) and frequent hitters in screening campaigns. Rhodanine-based compounds are also aggregators that can non-specifically interact with target proteins as well as Michael acceptors and interfere photometrically in biological assays due to their color. AREAS COVERED: The authors review the recently reported biological activities of rhodanine-based compounds. Furthermore, the article provides details of their synthesis and occurrence in compound libraries through high-throughput screening (HTS) and virtual high-throughput screening (VHTS). Additionally, the authors provide the reader with possible mechanisms of non-specific target modulation, analysis of the crystal structures of enzyme-rhodanine complexes and a comparison of rhodanine and thiazolidine-2,4-dione moieties. EXPERT OPINION: The biological activity of compounds possessing a rhodanine moiety should be considered very critically despite the convincing data obtained in biological assays. In addition to the lack of selectivity, unusual structure-activity relationship profiles and safety and specificity problems mean that rhodanines are generally not optimizable.     

Advances in high-throughput mass spectrometry

The evolution of high-throughput drug discovery is readily apparent as the pharmaceutical industry continues to stress the rapid progression of new chemical entities and biological agents through drug discovery and development pipelines. Mass spectrometry and high performance liquid chromatography-mass spectrometry have played an instrumental role in the support and advancement of all facets of high-throughput drug discovery. The introduction of new instrumentation has extended the breadth of mass spectrometric-based capabilities from the characterization of high-throughput organic synthesis products to early adsorption, distribution, metabolism and excretion profiling. Additionally, advances in the capacity and throughput of mass spectrometry systems have concurrently led to the introduction of data management tools to address automated data reduction, archival and mining, as well as analytical data integration to chemical and biological databases.     

Synthesis of HDAC Inhibitor Libraries via Microscale Workflow

An integrated workflow has been established that enables the synthesis, purification, and subsequent biological testing of compound libraries on a microgram scale. This approach utilizes mass directed preparative HPLC in conjunction with charged aerosol detection (CAD) to generate solutions of investigational compounds at high purity and standardized concentrations, facilitating high fidelity biological testing. This new workflow successfully delivered libraries of histone deacetylase (HDAC) inhibitors that afforded biological data consistent with that obtained from standard scale parallel medicinal chemistry techniques. The advantages of this new approach to library synthesis include greatly reduced material requirements and amenability to high-throughput experimentation.     

Surface activity profiling of drugs applied to the prediction of blood-brain barrier permeability

The present study describes a novel in vitro platform for physicochemical profiling of compounds, based on their impact on the air/water interfacial tension. Interfacial partitioning coefficient, cross-sectional area, and critical micelle concentration were derived from the Gibbs adsorption isotherms recorded for 76 structurally diverse drugs. An approximation for the membrane partitioning coefficient, K(memb), is introduced and calculated for the measured compounds. This methodology provides a fully automatic, high-throughput screening technique for compound characterization, yielding precise thermodynamic information on the partitioning behavior of molecules at air/water interfaces, which can be directly related to their anisotropic interaction with lipid bilayers in biological membranes. The latter represents the barrier for the passive entry of compounds into cells. The surface activity profiles are shown to correlate to the ability of the compounds to pass passively through the blood-brain barrier.     

Rhodanine as a scaffold in drug discovery: a critical review of its biological activities and mechanisms of target modulation

Introduction: Rhodanine-based compounds have been associated with numerous biological activities. After many years of research in drug discovery, they have gained a reputation as being pan assay interference compounds (PAINS) and frequent hitters in screening campaigns. Rhodanine-based compounds are also aggregators that can non-specifically interact with target proteins as well as Michael acceptors and interfere photometrically in biological assays due to their color.

Areas covered: The authors review the recently reported biological activities of rhodanine-based compounds. Furthermore, the article provides details of their synthesis and occurrence in compound libraries through high-throughput screening (HTS) and virtual high-throughput screening (VHTS). Additionally, the authors provide the reader with possible mechanisms of non-specific target modulation, analysis of the crystal structures of enzyme–rhodanine complexes and a comparison of rhodanine and thiazolidine-2,4-dione moieties.

Expert opinion: The biological activity of compounds possessing a rhodanine moiety should be considered very critically despite the convincing data obtained in biological assays. In addition to the lack of selectivity, unusual structure–activity relationship profiles and safety and specificity problems mean that rhodanines are generally not optimizable.     

Identification of promiscuous small molecule activators in high-throughput enzyme activation screens

It is recognized that high-throughput enzyme inhibition screens often return nonspecific inhibitors as "hits". Recently, high-throughput screens for enzyme activators have led to the identification of several compounds with novel and potent biological activity. Here, we show that enzyme activation screens can also uncover compounds that activate multiple enzymes in a nonspecific fashion. Described herein are the general structural features of such compounds and methods to differentiate between specific and general enzyme activation.     

Imaged-based high-throughput screening for anti-angiogenic drug discovery

Recent developments in high-content screening (HCS) technologies make it an attractive alternative for anti-angiogenic drug discovery. HCS integrates high-throughput methodologies with automated multicolor fluorescence microscopy to collect quantitative morphological and molecular data from complex biological systems. Organotypic systems based on primary vascular cells model many facets of angiogenesis. The adaptation of these complex in vitro assay systems to high-throughput HCS formats with automated image acquisition enables large-scale chemical library screening campaigns. These HCS principles can be extended further to allow small molecule compounds in in vivo model organisms such as zebrafish. In this review we discuss the latest developments within automated image-based high-throughput screening of chemical libraries for anti-angiogenic compounds.     

Initial compound selection for sequential screening

Initial leads for drug development often originate from high-throughput screening (HTS), where hundreds of thousands of compounds are tested for biological activity. As the number of both targets for screening and compounds available for screening increase, there is a need to consider methods for making this process more efficient. One approach is to screen sequentially, whereby a relatively small set of compounds is assayed and the results are statistically analyzed to produce a mathematical model. The model is used to predict activity and select additional compounds for screening. The new compound bioassay results are added to the results for the initial set and a new model is determined. The process iterates. The focus of this review is on how to select the initial screening set (ISS). It is presumed that the size and quality of the initial set will affect the subsequent model building and, hence, the efficiency of finding active compounds.     

Clinical status of anti-cancer agents derived from marine sources

The chemical, biological and ecological diversity of the marine ecosystem has contributed immensely in the discovery of extremely potent compounds that have shown potent activities in antitumor, analgesia, antiinflammatory, immunomodulation, allergy, anti-viral etc. The compounds of marine origin are diverse in structural class from simple linear peptides to complex macrocyclic polyethers. The recent advances in the sophisticated instruments for the isolation and characterization of marine natural products and development of high-throughput screening, have substantially increased the rate of discovery of various compounds of biomedical application. Didemnin was the first marine peptide that entered in human clinical trials in US for the treatment of cancer and other compounds such as dolastatin-10, soblidotin, didemnin B, ecteinascidin 743, girolline, aplidine, cryptophycins (also arenastatin A), bryostatin 1, ILX 651, kahalalide F, E7389, discodermolide, ES-285 (spisulosine), HTI-286 (hemiasterlin derivative), squalamine, KRN-7000, vitilevuamide, Laulimalide, Curacin A, diazonamide, peloruside A, eleutherobin, sarcodictyin, thiocoraline, salicylihalimides A, ascididemnin, CGX-1160, CGX-1007dictyodendrins, GTS-21 (aka DMBX), manoalide, IPL-576,092 (aka HMR-4011A) have entered in the clinical trials. This article summarize clinical status and synthetic advances of some of these compounds.     

Synthesis,preformulation and liposomal formulation of cholesteryl carborane esters with various fatty chains

The elevated expression of LDL receptor on tumor cells provides one attractive approach for targeted drug delivery to tumor cells. Suitable antitumor compounds, however, need to be synthesized and developed which mimic the native cholesteryl esters (as major constituent of LDL) in chemical structure for targeted delivery to tumor cells through the over-expressed LDL receptors. In the present study, new antitumor compounds were designed containing cholesterol, fatty chain and carborane which is used as the antitumor unit. Three new compounds were synthesized with a three-step reaction scheme. Similar to the native cholesteryl esters, these compounds are extremely hydrophobic and, before any further biological studies, suitable liposomal formulations for these new compounds are required. Various liposomal formulations as well as the preformulation characterization of these new compounds were thus examined. The incorporation efficiency of the compounds in liposomes was found to vary significantly depending on the type of fatty chain attached and the ratio of cholesterol:phospholipid used as the excipients of liposomal formulation.     

CE-108, a new macrolide tetraene antibiotic

In the search for strains producing antifungal compounds, a new tetraene macrolide CE-108 (3) has been isolated from culture broth of Streptomyces diastaticus 108. In addition, the strain also produces the previously described tetraene rimocidin (1) and also the aromatic polyketide oxytetracycline. Both tetraene compounds, structurally related, are produced in a ratio between 25 to 35% (CE-108 compared to rimocidin), although it can be inverted toward CE-108 production by changing the composition of the fermentation medium. This paper deals with the characterization of the producer strain, fermentation, purification, structure determination and biological properties of the new macrolide tetraene CE-108.     

Systems biology data analysis methodology in pharmacogenomics

Pharmacogenetics aims to elucidate the genetic factors underlying the individual's response to pharmacotherapy. Coupled with the recent (and ongoing) progress in high-throughput genotyping, sequencing and other genomic technologies, pharmacogenetics is rapidly transforming into pharmacogenomics, while pursuing the primary goals of identifying and studying the genetic contribution to drug therapy response and adverse effects, and existing drug characterization and new drug discovery. Accomplishment of both of these goals hinges on gaining a better understanding of the underlying biological systems; however, reverse-engineering biological system models from the massive datasets generated by the large-scale genetic epidemiology studies presents a formidable data analysis challenge. In this article, we review the recent progress made in developing such data analysis methodology within the paradigm of systems biology research that broadly aims to gain a 'holistic', or 'mechanistic' understanding of biological systems by attempting to capture the entirety of interactions between the components (genetic and otherwise) of the system.     

Antiplasmodial drug targets: a patent review (2000 – 2013)

Introduction: New antimalarials with novel modes of action are crucial in countering the challenge of emerging drug-resistant Plasmodium falciparum. Equally significant is the identification and characterization of the targets these compounds inhibit. Biochemical evidence from seminal studies, whole genome clues and high-throughput chemical screening data provide starting points worth exploring in target identification efforts. Several proteins and biochemical processes/pathways critical to parasite survival have since been profiled and patented.

Areas covered: In this review, an analysis of patents describing the characterization of different enzymatic and/or biosynthetic targets in P. falciparum over the last fourteen years is presented. The review also details structures, biological evaluation, potential modes of action and therapeutic utilities of small molecule antiplasmodial compounds from ongoing research, designed to inhibit these targets.

Expert opinion: Though various strategies to address antimalarial drug resistance exist, direct inhibition of unrelated targets and non-genome coded processes potentially present the most effective options. Additionally, interest in peptides as antimalarials merits further exploration especially in view of their unique low susceptibility to resistance, wider spectrum of action and faster activity. Finally, target-based optimization and chemical validation of novel targets can be facilitated by routine phenotypic whole-cell screening of antiplasmodial hits against any new target(s).     

Development and implementation of a miniaturized high-throughput time-resolved fluorescence energy transfer assay to identify small molecule inhibitors of polo-like kinase 1

Polo-like kinase (Plk) 1 is a key enzyme involved in regulating the mammalian cell cycle that is also a validated anticancer drug target. Nonetheless, there are relatively few readily available potent and selective small molecule inhibitors of Plk1. To increase the availability of pharmacologically valuable Plk1 inhibitors, we describe herein the development, variability assessment, validation, and implementation of a 384-well automated, miniaturized high-throughput time-resolved fluorescence energy transfer screening assay designed to identify Plk1 kinase inhibitors. Using a small molecule library of pharmaceutically active compounds to gauge high-throughput assay robustness and reproducibility, we found nine general kinase inhibitors, including H-89, which was selected as the minimum control. We then interrogated a 97,101 compound library from the National Institutes of Health repository for small molecule inhibitors of Plk1 kinase activity. The initial primary hit rate in a single 10 microM concentration format was 0.21%. Hit compounds were subjected to concentration-response confirmation and interference assays. Identified in the screen were seven compounds with 50% inhibitory concentration (IC50) values below 1 microM, 20 compounds with IC50 values between 1 microM and 5 microM, and eight compounds with IC50 values between 5 and 10 microM, which could be assigned to seven distinct chemotype classes. Hit compounds were also examined for their ability to inhibit other kinases such as protein kinase D, focal adhesion kinase, rho-associated coiled coil protein kinase 2, c-jun NH2-terminal kinase 3, and protein kinase A via experimentation or data-mining. These compounds should be useful as probes for the biological activity of Plk1 and as leads for the development of new selective inhibitors of Plk1.     

Identification and validation of hits from high throughput screens for CFTR modulators

These are exciting times with the appearance of small molecule compounds in clinical trials which target the basic defects caused by mutation in the CFTR gene. This progress was enabled by years of basic research probing the molecular and cellular consequences caused by mutation and the development of methods by which to study the primary anion transport defect in a high-throughput manner by robotics. Future progress with the development of new, more effective corrector compounds is needed. Such discovery will require further progress in defining the molecular targets for effective intervention using a multidisciplinary approach, merging computational, molecular, proteomic and cell biological methods. There is also an urgent need to develop means to link the right therapeutic compound to the right patients given the heterogeneity of the CF patient population. We envision a time when mid to high-throughput methods will be married with stem cell biology to enable testing a compendium of compounds on cells derived from each individual patient. Given the rate of progress in this field- this scenario may exist in the not too distant future.     

Small molecules for interference with cell-cell-communication systems in Gram-negative bacteria

Quorum sensing (QS) systems are bacterial cell-to-cell communication systems that use small molecules as signals. Since QS is involved in the regulation of virulence and biofilm formation in several pathogenic bacteria, it has been suggested as a new target for the development of novel antibacterial therapies. As such, interference with the signal receptors by using chemical compounds has been proposed as an alternative strategy for treatment of bacterial infections and has already shown promising results in combination with traditional antibiotic treatments. In Gram-negative bacteria, the best studied QS systems use N-acyl homoserine lactones (AHLs) as signal molecules. This review provides an overview of all new chemical structure types that inhibit AHL-mediated QS systems as reported during the last three years in scientific journals and in the patent literature. The compounds were classified into three main groups depending on their structure: AHL analogues, 2(5H)-furanones, and compounds that are not structurally related to AHLs. We discuss the biological assays used and the different strategies applied to discover these molecules, including new approaches such as molecular docking for in silico identification of lead structures and random high-throughput screening of large libraries of chemicals. Finally, we elaborate on structure-activity relationships and on the new insights in the mechanisms of action of the identified inhibitors, highlighting the potential of these small molecules in medicine.     

Antimycotic Drug Discovery in the Age of Genomics

Genomic-based methodologies are increasingly used at all stages of drug development. The most extensive applications have occurred in early drug discovery stages due to advances in technologies that allow for automated synthesis and characterization of organic compounds, and for high-throughput screening of these molecules against known drug targets. The adaptation of genomic-based methodologies in later stages of drug development presents a more difficult task. In this review we describe how genomics can be used to identify previously uncharacterized pharmacologic actions that provide a basis for the development of new classes of antimycotic agents or for adverse event aversion. Clinically, novel antimycotics are gravely needed. This review provides a perspective on new technologies that will bridge the gap between drug discovery and development that may enable more rapid access to new antimycotic agents.     

Process technologies for purity enhancement of large discovery libraries

The design, synthesis and characterization of structurally diverse compound libraries are key first steps in drug discovery. High-throughput screening of these libraries against protein targets is a useful procedure for identifying hits, which can then be optimized to produce compound leads against these protein targets. For this process to be most successful the initial compounds screened must be of high quality, necessitating high-throughput characterization and purification. This review summarizes recent advances in purification processes for combinatorial chemistry.     

Systems biology of cyanobacterial secondary metabolite production and its role in drug discovery

Background: Cyanobacteria continue to be an important source of compounds that show unprecedented biological activities of pharmaceutical interest. Cyanobacterial metabolites show an interesting and exciting range of biological activities ranging from antimicrobial and immunosuppressant to anticancer and anti-HIV. Objective: This review explores the possibilities of applying systems biology approaches for harnessing these compounds as drug leads, primarily produced through large multimodular non-ribosomal peptide synthetase (NRPS), polyketide synthase (PKS) and mixed NRPS–PKS enzymatic systems. Methods: A brief survey of the strategies for in silico analysis for drug target identification using genomic and high-throughput proteomics data, virtual screening and receptor–ligand docking based approaches are also discussed. Conclusion: We conclude with an outlook on how the field will evolve, especially in partnership with the new engineering-based, more endpoint exploitative paradigm of synthetic biology.     

HierS: hierarchical scaffold clustering using topological chemical graphs

An exhaustive ring-based algorithm, HierS, has been developed in order to provide an intuitive approach to compound clustering for analyzing high-throughput screening results. The recursive algorithm rapidly identifies all possible ring-delimited substructures within a set of compounds. Molecules are grouped by shared ring substructures (scaffolds) so that common scaffolds obtain higher membership. Once all of the scaffolds for a set of compounds are identified, the hierarchical structural relationships between the scaffold structures are established. The complex network of hierarchical relationships is then utilized to navigate compounds in a structurally directed fashion. When the scaffold hierarchy is traversed, over-represented structural features can be rapidly identified so that excess compounds that contain them can be removed without significantly impacting the structural diversity landscape of the compound set. Furthermore, the removed compounds can provide the opportunity to follow-up on active compounds that had previously been discarded because of practical limitations on follow-up capacity. A Web-based interface has been developed that incorporates this algorithm in order to allow for an interactive analysis. In addition, biological data are coupled to scaffolds by the inclusion of activity histograms, which indicate how the compounds in each scaffold class performed in previous high-throughput screening campaigns.