Library Of Candidates Research Articles

A reliable computational workflow for the selection of optimal screening libraries.

BackgroundThe experimental screening of compound collections is a common starting point in many drug discovery projects. Successes of such screening campaigns critically depend on the quality of the screened library. Many libraries are currently available from different vendors yet the selection of the optimal screening library for a specific project is challenging. We have devised a novel workflow for the rational selection of project-specific screening libraries.ResultsThe workflow accepts as input a set of virtual candidate libraries and applies the following steps to each library: (1) data curation; (2) assessment of ADME/T profile; (3) assessment of the number of promiscuous binders/frequent HTS hitters; (4) assessment of internal diversity; (5) assessment of similarity to known active compound(s) (optional); (6) assessment of similarity to in-house or otherwise accessible compound collections (optional). For ADME/T profiling, Lipinski’s and Veber’s rule-based filters were implemented and a new blood brain barrier permeation model was developed and validated (85 and 74 % success rate for training set and test set, respectively). Diversity and similarity descriptors which demonstrated best performances in terms of their ability to select either diverse or focused sets of compounds from three databases (Drug Bank, CMC and CHEMBL) were identified and used for diversity and similarity assessments. The workflow was used to analyze nine common screening libraries available from six vendors. The results of this analysis are reported for each library providing an assessment of its quality. Furthermore, a consensus approach was developed to combine the results of these analyses into a single score for selecting the optimal library under different scenarios.ConclusionsWe have devised and tested a new workflow for the rational selection of screening libraries under different scenarios. The current workflow was implemented using the Pipeline Pilot software yet due to the usage of generic components, it can be easily adapted and reproduced by computational groups interested in rational selection of screening libraries. Furthermore, the workflow could be readily modified to include additional components. This workflow has been routinely used in our laboratory for the selection of libraries in multiple projects and consistently selects libraries which are well balanced across multiple parameters.Graphical abstract.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-015-0108-0) contains supplementary material, which is available to authorized users.

Tuned Classical Thermal Aromatization Furnishing an Estrogenic Benzoacridine

The diversity-oriented doubling strategy, which generates two 12-arylbenzoacridines from a single triarylmethanol precursor was developed to construct a library of drug candidates for the identification of biologically active compounds. Exploration of this 12-arylbenzoacridine library furnished a 4′-OH derivative as an estrogenic compound.

Novel HIV-1 Integrase Inhibitor Development by Virtual Screening Based on QSAR Models.

HIV-1 integrase (IN) plays an important role in the life cycle of HIV and is responsible for integration of the virus into the human genome. We present computational approaches used to design novel HIV-1 IN inhibitors. We created an IN inhibitor database by collecting experimental data from the literature. We developed quantitative structure-activity relationship (QSAR) models of HIV-1 IN strand transfer (ST) inhibitors using this database. The prediction accuracy of these models was estimated by external 5-fold cross-validation as well as with an additional validation set of 308 structurally distinct compounds from the publicly accessible BindingDB database. The validated models were used to screen a small combinatorial library of potential synthetic candidates to identify hits, with a subsequent docking approach applied to further filter out compounds to arrive at a small set of potential HIV-1 IN inhibitors. As result, 236 compounds with good druglikeness properties and with correct docking poses were identified as potential candidates for synthesis. One of the six compounds finally chosen for synthesis was experimentally confirmed to inhibit the ST reaction with an IC50(ST) of 37 µM. The IN inhibitor database is available for download from http://cactus.nci.nih.gov/download/iidb/.

In vitro screen of a small molecule inhibitor drug library identifies multiple compounds that synergize with oncolytic myxoma virus against human brain tumor-initiating cells.

Brain tumor-initiating cells (BTICs) are stem-like cells hypothesized to form a disease reservoir that mediates tumor recurrence in high-grade gliomas. Oncolytic virotherapy uses replication-competent viruses to target and kill malignant cells and has been evaluated in clinic for glioma therapy with limited results. Myxoma virus (MyxV) is a safe and highly effective oncolytic virus (OV) in conventional glioma models but, as seen with other OVs, is only modestly effective for patient-derived BTICs. The objective of this study was to determine whether MyxV treatment against human BTICs could be improved by combining chemotherapeutics and virotherapy. A 73-compound library of drug candidates in clinical use or preclinical development was screened to identify compounds that sensitize human BTICs to MyxV treatment in vitro, and synergy was evaluated mathematically in lead compounds using Chou-Talalay analyses. The effects of combination therapy on viral gene expression and viral replication were also assessed. Eleven compounds that enhance MyxV efficacy were identified, and 6 were shown to synergize with the virus using Chou-Talalay analyses. Four of the synergistic compounds were shown to significantly increase viral gene expression, indicating a potential mechanism for synergy. Three highly synergistic compounds (axitinib, a VEGFR inhibitor; rofecoxib, a cyclooxygenase-2 inhibitor; and pemetrexed, a folate anti-metabolite) belong to classes of compounds that have not been previously shown to synergize with oncolytic viruses in vitro. This study has identified multiple novel drug candidates that synergistically improve MyxV efficacy in a preclinical BTIC glioma model.

Synthesis and characterisation of self-assembled and self-adjuvanting asymmetric multi-epitope lipopeptides of ovalbumin.

Designing a lipopeptide (LP) vaccine with a specific asymmetric arrangement of epitopes may result in an improved display of antigens, increasing host-cell recognition and immunogenicity. This study aimed to synthesise and characterise the physicochemical properties of a library of asymmetric LP-based vaccine candidates that contained multiple CD4(+) and CD8(+) T-cell epitopes from the model protein antigen, ovalbumin. These fully synthetic vaccine candidates were prepared by microwave-assisted solid phase peptide synthesis. The C12 or C16 lipoamino acids were coupled to the N or C terminus of the OVA CD4 peptide epitope. The OVA CD4 LPs and OVA CD8 peptide constructs were then conjugated using azide-alkyne Huisgen cycloaddition to give multivalent synthetic vaccines. Physiochemical characterisation of these vaccines showed a tendency to self-assemble in aqueous media. Changes in lipid length and position induced self-assembly with significant changes to their morphology and secondary structure as shown by transmission electron microscopy and circular dichroism.

Active immunisation of mice with GnRH lipopeptide vaccine candidates: Importance of T helper or multi-dimer GnRH epitope

Active immunisation against gonadotropin releasing hormone (GnRH) is a potential alternative to surgical castration. This study focused on the development of a GnRH subunit lipopeptide vaccine. A library of vaccine candidates that contained one or more (up to eight) copies of monomeric or dimeric GnRH peptide antigen, an adjuvanting lipidic moiety based on lipoamino acids, and an additional T helper epitope, was synthesised by solid phase peptide synthesis. The candidates were evaluated in vivo in order to determine the minimal components of this vaccine necessary to induce a systemic immune response. BALB/c mice were immunised with GnRH lipopeptide conjugates, co-administered with or without Complete Freund’s Adjuvant, followed by two additional immunisations. Significant GnRH-specific IgG titres were detected in sera obtained from mice immunised with four of the seven lipopeptides tested, with an increase in titres observed after successive immunisations. This study highlights the importance of for epitope optimisation and delivery system design when producing anti-hapten antibodies in vivo. The results of this study also contribute to the development of future clinical and veterinary immunocontraceptives.

Improved metal-adhesive polymers from copper(I)-catalyzed azide-alkyne cycloaddition.

Electrically conductive adhesive polymers offer many potential advantages relative to Sn-Pb solders, including reduced toxicity, low cost, low processing temperatures, and the ability to make application-specific formulations. Polymers generated from the copper(I)-catalyzed cycloaddition (CuAAC) reaction between multivalent azides and alkynes have previously been identified as strong metal-binding adhesives. Herein we demonstrate that the performance of these materials can be remarkably improved by the incorporation of a flexibility-inducing difunctionalized component and a tertiary amine additive in optimized concentrations. The best formulations were identified by means of rapid adhesion testing of a library of potential candidates by using a custom-built instrument and validated in an American Society for Testing and Materials (ASTM)-standard lap-shear test. Characteristic phase transitions were identified by differential scanning calorimetry (DSC) for adhesives with and without the additives as a function of curing temperature. The incorporation of flexible components was found to more than double the strength of the adhesive. Moreover, the adhesive was made electrically conductive by the inclusion of 20 wt% silver-coated copper flakes and further improved in this regard by the incorporation of multiwalled carbon nanotubes in the formulation.

Amazonian mid- to high-latitude glaciation on Mars: Supply-limited ice sources, ice accumulation patterns, and concentric crater fill glacial flow and ice sequestration

Concentric crater fill (CCF) occurs in the interior of impact craters in mid- to high latitudes on Mars and is interpreted to have formed by glacial ice flow and debris covering. We use the characteristics and orientation of deposits comprising CCF, the thickness of pedestal deposits in mid- to high-latitude pedestal craters (Pd), the volumes of the current polar caps, and information about regional slopes and ice rheology to address questions about (1) the maximum thickness of regional ice deposits during the Late Amazonian, (2) the likelihood that these deposits flowed regionally, (3) the geological regions and features most likely to induce ice-flow, and (4) the locations and environments in which ice is likely to have been sequestered up to the present. We find that regional ice flow under Late Amazonian climate conditions requires ice thicknesses exceeding many hundreds of meters for slopes typical of the vast majority of the surface of Mars, a thickness for the mid-latitudes that is well in excess of the total volume available from polar ice reservoirs. This indicates that although conditions for mid- to high-latitude glaciation may have persisted for tens to hundreds of millions of years, the process is “supply limited”, with a steady state reached when the polar ice cap water ice supply becomes exhausted.Impact craters are by far the most abundant landform with associated slopes (interior wall and exterior rim) sufficiently high to induce glacial ice flow under Late Amazonian climate conditions, and topographic slope data show that Amazonian impact craters have been clearly modified, undergoing crater interior slope reduction and floor shallowing. We show that these trends are the predictable response of ice deposition and preferential accumulation and retention in mid- to high-latitude crater interiors during episodes of enhanced spin–axis obliquity. We demonstrate that flow from a single episode of an inter-crater terrain layer comparable to Pedestal Crater deposit thicknesses (~50m) cannot fill the craters in a time period compatible with the interpreted formation times of the Pedestal Crater mantled ice layers. We use a representative obliquity solution to drive an ice flow model and show that a cyclical pattern of multiply recurring layers can both fill the craters with a significant volume of ice, as well as transport debris from the crater walls out into the central regions of the craters. The cyclical pattern of waxing and waning mantling layers results in a rippled pattern of surface debris extending out into the crater interiors that would manifest itself as an observable concentric pattern, comparable in appearance to concentric crater fill. In this scenario, the formation of mantling sublimation till layers seals the accumulating ice and sequesters it from significant temperature variations at diurnal, annual and spin–axis/orbital cycle time scales, to produce ancient ice records preserved today below CCF crater floors.Lack of meltwater features associated with concentric crater fill provides evidence that the Late Amazonian climate did not exceed the melting temperature in the mid- to high-latitudes for any significant period of time. Continued sequestration of ice with time in CCF and related deposits (lobate debris aprons and lineated valley fill) further reduces the already supply-limited polar ice sources, suggesting that there has been a declining reservoir of available ice with each ensuing glacial period. Together, these deposits represent a candidate library of climate chemistry and global change dating from the Late Amazonian, and a non-polar water resource for future exploration.

Selective Chromium(VI) Ligands Identified Using Combinatorial Peptoid Libraries

Hexavalent chromium [Cr(VI)] is a worldwide water contaminant that is currently without cost-effective and efficient remediation strategies. This is in part due to a lack of ligands that can bind it amid an excess of innocuous ions in aqueous solution. We present herein the design and application of a peptoid-based library of ligand candidates for toxic metal ions. A selective screening process was used to identify members of the library that can bind to Cr(VI) species at neutral pH and in the presence of a large excess of spectator ions. There were 11 sequences identified, and their affinities were compared using titrations monitored with UV-vis spectroscopy. To identify the interactions involved in coordination and specificity, we evaluated the effects of sequence substitutions and backbone variation in the highest affinity structure. Additional characterization of the complex formed between this sequence and Cr(VI) was performed using NMR spectroscopy. To evaluate the ability of the developed sequences to remediate contaminated solutions, the structures were synthesized on a solid-phase resin and incubated with environmental water samples that contained simulated levels of chromium contamination. The synthetic structures demonstrated the ability to reduce the amount of toxic chromium to levels within the range of the EPA contamination guidelines. In addition to providing some of the first selective ligands for Cr(VI), these studies highlight the promise of peptoid sequences as easily prepared components of environmental remediation materials.

Tunable mechanical behavior of synthetic organogels as biofidelic tissue simulants

Solvent-swollen polymer gels can be utilized as mechanical simulants of biological tissues to evaluate protective systems and assess injury mechanisms. However, a key challenge in this application of synthetic materials is mimicking the rate-dependent mechanical response of complex biological tissues. Here, we characterize the mechanical behavior of tissue simulant gel candidates comprising a chemically crosslinked polydimethylsiloxane (PDMS) network loaded with a non-reactive PDMS solvent, and compare this response with that of tissue from murine heart and liver under comparable loading conditions. We first survey the rheological properties of a library of tissue simulant candidates to investigate the effects of solvent loading percentage, reactive functional group stoichiometry, and solvent molecular weight. We then quantify the impact resistance, energy dissipation capacities, and energy dissipation rates via impact indentation for the tissue simulant candidates, as well as for the murine heart and liver. We demonstrate that by tuning these variables the silicone gels can be engineered to match the impact response of biological tissues. These experiments inform the design principles required for synthetic polymer gels that are optimized to predict the response of specific biological tissues to impact loading, providing insight for further tuning of this gel system to match the impact response of other “soft tissues”.

Combinatorial synthesis of labelled drugs and PET tracers: synthesis of a focused library of11C-carbonyl-labelled acrylamides as potential biomarkers of EGFR expression

Combinatorial synthesis is extensively used in drug development and lead optimisation. However, this approach has rarely been used for positron emission tomography because of limitations in available technologies. [11C]Carbon monoxide is amenable to combinatorial synthesis in transition-metal-catalysed reactions because it can react with a wide variety of electrophiles and nucleophiles, which opens up the possibilities for combinatorial radiochemistry. Herein, we exemplify the combinatorial approach by 11C-labelling a library of epidermal growth factor receptor inhibitors. The selection of candidates was guided by molecular docking. Epidermal growth factor receptor is overexpressed in a variety of tumours, and it has become an important drug target. The 11C-labelling reactions were performed using four substituted vinyl iodides and three different 4-anilino-6-aminoquinazolines using a palladium-mediated reaction with [11C]carbon monoxide using a single set of reaction conditions. In total, 12 labelled acrylamide derivatives were radiolabelled and obtained in 24–61% decay-corrected radiochemical yield (from [11C]carbon monoxide). Starting from 5.6 GBq [11C]carbon monoxide, 0.85 GBq of formulated N-[4-(3-bromo-phenylamino)-quinazolin-6-yl]-acryl[11C]amide [11C]12da was obtained within 47 min from end of bombardment (specific activity of 60 GBq µmol−1). This strategy is an example of how [11C]carbon monoxide can be utilised in the labelling of libraries of drug candidates and positron emission tomography tracers for in vitro and in vivo testing.

Rapid Discovery of Highly Potent and Selective Inhibitors of Histone Deacetylase 8 Using Click Chemistry to Generate Candidate Libraries

To find HDAC8-selective inhibitors, we designed a library of HDAC inhibitor candidates, each containing a zinc-binding group that coordinates with the active-site zinc ion, linked via a triazole moiety to a capping structure that interacts with residues on the rim of the active site. These compounds were synthesized by using click chemistry. Screening identified HDAC8-selective inhibitors including C149 (IC(50) = 0.070 μM), which was more potent than PCI-34058 (6) (IC(50) = 0.31 μM), a known HDAC8 inhibitor. Molecular modeling suggested that the phenylthiomethyl group of C149 binds to a unique hydrophobic pocket of HDAC8, and the orientation of the phenylthiomethyl and hydroxamate moieties (fixed by the triazole moiety) is important for the potency and selectivity. The inhibitors caused selective acetylation of cohesin in cells and exerted growth-inhibitory effects on T-cell lymphoma and neuroblastoma cells (GI(50) = 3-80 μM). These findings suggest that HDAC8-selective inhibitors have potential as anticancer agents.

Resin-Supported Catalysts for CuAAC Click Reactions in Aqueous or Organic Solvents

The copper-catalyzed azide-alkyne cycloaddition click reaction is a valuable process for the synthesis of libraries of drug candidates, derivatized polymers and materials, and a wide variety of other functional molecules. In some circumstances, the removal of the copper catalyst is both necessary and inconvenient. We describe here two immobilized forms of a Cu-binding ligand that has been shown to accelerate triazole formation under many different conditions, using different resin supports that are appropriate for aqueous or organic solvents. Copper leaching from these resins was modest, allowing them to be reused in many reaction/filtration cycles without recharging with metal ion. The utility of this catalyst form was demonstrated in the convenient synthesis of 20 N-acetylgalactosamine derivatives for biological testing.

DrugLogit: Logistic Discrimination between Drugs and Nondrugs Including Disease-Specificity by Assigning Probabilities Based on Molecular Properties

The increasing knowledge of both structure and activity of compounds provides a good basis for enhancing the pharmacological characterization of chemical libraries. In addition, pharmacology can be seen as incorporating both advances from molecular biology as well as chemical sciences, with innovative insight provided from studying target-ligand data from a ligand molecular point of view. Predictions and profiling of libraries of drug candidates have previously focused mainly on certain cases of oral bioavailability. Inclusion of other administration routes and disease-specificity would improve the precision of drug profiling. In this work, recent data are extended, and a probability-based approach is introduced for quantitative and gradual classification of compounds into categories of drugs/nondrugs, as well as for disease- or organ-specificity. Using experimental data of over 1067 compounds and multivariate logistic regressions, the classification shows good performance in training and independent test cases. The regressions have high statistical significance in terms of the robustness of coefficients and 95% confidence intervals provided by a 1000-fold bootstrapping resampling. Besides their good predictive power, the classification functions remain chemically interpretable, containing only one to five variables in total, and the physicochemical terms involved can be easily calculated. The present approach is useful for an improved description and filtering of compound libraries. It can also be applied sequentially or in combinations of filters, as well as adapted to particular use cases. The scores and equations may be able to suggest possible routes for compound or library modification. The data is made available for reuse by others, and the equations are freely accessible at http://hermes.chem.ut.ee/~alfx/druglogit.html.

Label-free fluorescence method for screening G-quadruplex ligands

G-quadruplex ligands can interfere with the telomere structure, telomere elongation/replication, and proliferation of cancer cells. A key element in the development of potent G-quadruplex ligands is the screening of large chemical libraries of potential candidates. Here, we describe a simple fluorescence method for screening of G-quadruplex ligands. The method is based on the ability of G-quadruplex ligands to displace hemin from G-quadruplex-based DNAzyme, resulting in a decrease of its catalytic activity on the fluorescence-developing reaction between p-hydroxyphenylacetic acid and H 2O 2. The method eliminates the requirement for expensive and time-consuming preparation of labeled DNA. Our method provides a simple, cheap, and sensitive approach to screen G-quadruplex ligands (potential antitumor drugs).

Comparative analysis of epitope predictions: proposed library of putative vaccine candidates for HIV

Designing a vaccine for a disease is one of the crucial tasks that involve millions and billions of dollars, several decades and yet there is no guarantee of successful results. Several pharmaceutical companies are investing their money and time in such activities. Computational biology could be of great help in these activities by proving a library of plausible candidates that might actually show some positive responses. MHC binding peptide prediction is one such area where the immense power of computers could be used to get a breakthrough. In this direction several databases and servers have been developed by many labs to predict the MHC binding peptides. These short peptides on the antigen surface are recognized by the MHC molecule and are presented to the receptors of T-cells for further immune response. Peptides that bind to a given MHC molecule share sequence similarity. Here we present a comparative study of servers that can predict the MHC binding peptides in a given protein sequence of the antigen. Based on this comparative analysis on HIV data, we are able to propose a library of putative vaccine candidates for the env GP-160 protein of HIV-1.

Droplet microfluidics with magnetic beads: a new tool to investigate drug–protein interactions

In this study, we give the proof of concept for a method to determine binding constants of compounds in solution. By implementing a technique based on magnetic beads with a microfluidic device for segmented flow generation, we demonstrate, for individual droplets, fast, robust and complete separation of the magnetic beads. The beads are used as a carrier for one binding partner and hence, any bound molecule is separated likewise, while the segmentation into small microdroplets ensures fast mixing, and opens future prospects for droplet-wise analysis of drug candidate libraries. We employ the method for characterization of drug-protein binding, here warfarin to human serum albumin. The approach lays the basis for a microfluidic droplet-based screening device aimed at investigating the interactions of drugs with specific targets including enzymes and cells. Furthermore, the continuous method could be employed for various applications, such as binding assays, kinetic studies, and single cell analysis, in which rapid removal of a reactive component is required.

A sandwiched microarray platform for benchtop cell-based high throughput screening

The emergence of combinatorial chemistries and the increased discovery of natural compounds have led to the production of expansive libraries of drug candidates and vast numbers of compounds with potentially interesting biological activities. Despite broad interest in high throughput screening (HTS) across varied fields of biological research, there has not been an increase in accessible HTS technologies. Here, we present a simple microarray sandwich system suitable for screening chemical libraries in cell-based assays at the benchtop. The microarray platform delivers chemical compounds to isolated cell cultures by ‘sandwiching’ chemical-laden arrayed posts with cell-seeded microwells. In this way, an array of sealed cell-based assays was generated without cross-contamination between neighbouring assays. After chemical exposure, cell viability was analyzed by fluorescence detection of cell viability assays on a per microwell basis using a standard microarray scanner. We demonstrate the efficacy of the system by generating four hits from toxicology screens towards MCF-7 human breast cancer cells. Three of the hits were identified in a combinatorial screen of a library of natural compounds in combination with verapamil, a P-glycoprotein inhibitor. A fourth hit, 9-methoxy-camptothecin, was identified by screening the natural compound library in the absence of verapamil. The method developed here miniaturizes existing HTS systems and enables the screening of a wide array of individual or combinatorial libraries in a reproducible and scalable manner. We anticipate broad application of such a system as it is amenable to combinatorial drug screening in a simple, robust and portable platform.

SURVIVAL OF THE WEAKEST

EVOLUTION MAY BE based on “survival of the fittest,” but when it comes to selecting the best catalysts, that dictum doesn’t always hold. A research team has shown that one can select the best catalysts from combinatorial libraries of candidates by instead using the principle of “survival of the weakest”—that is, the most unstable catalytic intermediates make for the best catalysts. The approach could make it possible to discover catalysts more quickly for syntheses of drugs and other products. It has been difficult to find selection methods to separate the cream of the crop (the fastest catalysts) from the dross when screening libraries to identify highly active catalysts. Now, theoretical chemist F. Matthias Bickelhaupt of Free University of Amsterdam, catalysis specialist Joost N. H. Reek of the University of Amsterdam, and coworkers have developed an innovative selection strategy for such experiments based on survival of the weakest intermediates ( Nat. Chem., DOI: 10.1038/nchem.614). The researchers ...

A Simplified Assay Method for Determining the Binding Affinities of DNA Binding Molecules to Duplex DNA

Chemotherapy is a crucial anticancer strategy. Numerous compounds have been developed as potential candidates for anticancer drug, and many of these compounds, including FDAapproved anti-cancer drugs such as doxorubicin, daunorubicin and amsacrine, are known to reversibly interact with DNA to form drug/DNA complexes. 1 Large libraries of compounds of DNA-binding molecules have been synthesized by combinatorial chemistry. 2 However, the selection of viable candidates among the many compounds contained in these libraries is one of the major bottlenecks in drug discovery. 3 To overcome this problem, high-throughput screening (HTS) methods are used to screen large libraries of potential drug candidates for biological activity. 4 Generally, the anticancer drug’s biological activity is correlated with its binding affinities to DNA. 5 In the past, typical screening processes have included mass spectroscopy, nuclear magnetic resonance, light scattering, and electrochemistry. 6 Un