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Results for “Pharmacology and Toxicology”

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bioRxiv2017

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database

Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review \"alchemical\" approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies (hydration free energies). These approaches use a non-physical pathway to compute free energy differences from a simulation or set of simulations and appear to be a particularly robust and general-purpose approach for this task. We also present an update (version 0.5) to our FreeSolv database of experimental and calculated hydration free energies of neutral compounds and provide input files in formats for several simulation packages. This revision to FreeSolv provides calculated values generated with a single protocol and software version, rather than the heterogeneous protocols used in the prior version of the database. We also further update the database to provide calculated enthalpies and entropies of hydration and some experimental enthalpies and entropies, as well as electrostatic and nonpolar components of solvation free energies.

pharmacology and toxicology↗

bioRxiv2017

Progress Towards a Public Chemogenomic Set for Protein Kinases and a Call for Contributions

Protein kinases are highly tractable targets for drug discovery. However, the biological function and therapeutic potential of the majority of the 500+ human protein kinases remains unknown. We have developed physical and virtual collections of small molecule inhibitors, which we call chemogenomic sets, that are designed to inhibit the catalytic function of almost half the human protein kinases. In this manuscript we share our progress towards generation of a comprehensive kinase chemogenomic set (KCGS), release kinome profiling data of a large inhibitor set (Published Kinase Inhibitor Set 2 (PKIS2)), and outline a process through which the community can openly collaborate to create a KCGS that probes the full complement of human protein kinases.

pharmacology and toxicology↗

bioRxiv2017

Mendelian randomization: a novel approach for the prediction of adverse drug events and drugrepurposing opportunities

Identification of unintended drug effects, specifically drug repurposing opportunities and adverse drug events, maximizes the benefit of a drug and protects the health of patients. However, current observational research methods are subject to several biases. These include confounding by indication, reverse causality, and missing data. We propose that Mendelian randomization (MR) offers a novel approach for the prediction of unintended drug effects. In particular, we advocate the synthesis of evidence from this method and other approaches, in the spirit of triangulation, to improve causal inferences concerning drug effects. MR overcomes some of the limitations associated with the existing methods in this field. Furthermore, it can be applied either pre- or post-approval of the drug and could therefore prevent the potentially harmful exposure of patients in clinical trials and beyond. The potential of MR as a pharmacovigilance and drug repurposing tool is yet to be realized and could both help prevent adverse drug events and identify novel indications for existing drugs in the future.

pharmacology and toxicology↗

bioRxiv2017

Preprint: Environmentally-Friendly Workflow Based on Supercritical Fluid Chromatography and Tandem Mass Spectrometry Molecular Networking For the Discovery of Potent Anti-Viral Leads From Plants

A supercritical fluid chromatography-based targeted purification workflow using tandem mass spectrometry and molecular networking was developed to analyze, annotate and isolate secondary metabolites from complex mixture. This approach was applied for targeted isolation of new antiviral diterpene esters from Euphorbia semiperfoliata whole plant extract. The analysis of bioactive fractions revealed that unknown diterpene esters, including jatrophane esters and phorboids esters, were present in the samples. The purification procedure using semi-preparative-supercritical fluid chromatography led to the isolation and identification of two jatrophane esters (13 and 14) and four 4-deoxyphorbol esters (15-18). Compound 16 was found to display antiviral activity against chikungunya virus (EC50 = 0.45 {micro}M), while compound 15 was found to be a potent and selective inhibitor of HIV-1 replication in a recombinant virus assay (EC50 = 13 nM). This study showed that supercritical fluid chromatography-based workflow and molecular networking can facilitate and accelerate the discovery of bioactive small molecules by targeted molecules of interest, while minimizing the use of toxic solvents.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC=\"FIGDIR/small/106153_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (23K):\norg.highwire.dtl.DTLVardef@191802aorg.highwire.dtl.DTLVardef@1755ab8org.highwire.dtl.DTLVardef@196edf5org.highwire.dtl.DTLVardef@1e0a1e0_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2017

Repurposed High-Throughput Images Enable Biological Activity Prediction For Drug Discovery

We repurpose a High-Throughput (cell) Imaging (HTI) screen of a glucocorticoid receptor assay to predict target protein activity in multiple other seemingly unrelated assays. In two ongoing drug discovery projects, our repurposing approach increased hit rates by 60- to 250-fold over that of the primary project assays while increasing the chemical structure diversity of the hits. Our results suggest that data from available HTI screens are a rich source of information that can be reused to empower drug discovery efforts.

pharmacology and toxicology↗

bioRxiv2017

Neutrophil elastase inhibitor sivelestat ameliorates gefitinib-naphthalene-induced acute pneumonitis in mice

Background and objectiveGefitinib, an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI), is an effective therapeutic agent for non-small cell lung cancer with EGFR mutations. It can cause severe acute pneumonitis in some patients. We previously demonstrated that mice with naphthalene-induced airway epithelial injury developed severe gefitinib-induced pneumonitis and that neutrophils played important roles in the development of the disease. This study aimed to investigate the effects of the neutrophil elastase inhibitor sivelestat on gefitinib-induced pneumonitis in mice.\n\nMethodsC57BL/6J mice received naphthalene (200 mg/kg) intraperitoneally on day 0. Gefitinib (250 or 300 mg/kg) was orally administered to mice from day -1 until day 13. Sivelestat (150 mg/kg) was administered intraperitoneally from day 1 until day 13. Bronchoalveolar lavage fluid (BALF) and lung tissues were sampled on day 14.\n\nResultsSivelestat treatment significantly reduced the protein level, neutrophil count, neutrophil elastase activity in BALF, and severity of histopathologic findings on day 14 for mice administered with 250 mg/kg of gefitinib. Moreover, sivelestat treatment significantly improved the survival of mice administered with 300 mg/kg of gefitinib. Conclusions: These results indicate that sivelestat is a promising therapeutic agent for severe acute pneumonitis caused by gefitinib.\n\nSummary statementNeutrophil elastase inhibitor sivelestat is a promising therapeutic agent for severe acute pneumonitis caused by gefitinib.

pharmacology and toxicology↗

bioRxiv2017

Impacts of Bisphenol A and Ethinyl Estradiol on Male and Female CD-1 Mouse Spleen

The endocrine disruptor bisphenol A (BPA) and the pharmaceutical 17-ethinyl estradiol (EE) are synthetic chemicals with estrogen-like activities. Despite ubiquitous human exposure to BPA, and the wide-spread clinical use of EE as oral contraceptive adjuvant, the impact of these estrogenic endocrine disrupting chemicals (EDCs) on the immune system is unclear. Here we report results of in vivo dose response studies that analyzed the histology and microstructural changes in the spleen of adult male and female CD-1 mice exposed to 4 to 40,000 g/kg/day BPA or 0.02 to 2 g/kg/day EE from conception until 12-14 weeks of age. Results of that analysis indicate that both BPA and EE have dose- and sex-specific impacts on the cellular and microanatomical structures of the spleens that reveal minor alterations in immunomodulatory and hematopoietic functions. These findings support previous studies demonstrating the murine immune system as a sensitive target for estrogens, and that oral exposures to BPA and EE have important estrogen-like immunomodulatory affects in both sexes of the CD-1 mouse.

pharmacology and toxicology↗

bioRxiv2017

Consensus rank orderings of molecular fingerprints illustrate the most genuine similarities between marketed drugs and small endogenous human metabolites, but highlight exogenous natural products as the most important natural drug transporter substrates. bioRxiv version.

We compare several molecular fingerprint encodings for marketed, small molecule drugs, and assess how their rank order varies with the fingerprint in terms of the Tanimoto similarity to the most similar endogenous human metabolite as taken from Recon2. For the great majority of drugs, the rank order varies very greatly depending on the encoding used, and also somewhat when the Tanimoto similarity (TS) is replaced by the Tversky similarity. However, for a subset of such drugs, amounting to some 10% of the set and a Tanimoto similarity of ~0.8 or greater, the similarity coefficient is relatively robust to the encoding used. This leads to a metric that, while arbitrary, suggests that a Tanimoto similarity of 0.75-0.8 or greater genuinely does imply a considerable structural similarity of two molecules in the drug-endogenite space. Although comparatively few (<10% of) marketed drugs are, in this sense, robustly similar to an endogenite, there is often at least one encoding with which they are genuinely similar (e.g. TS > 0.75). This is referred to as the Take Your Pick Improved Cheminformatic Analytical Likeness or TYPICAL encoding, and on this basis some 66% of drugs are within a TS of 0.75 to an endogenite.\n\nWe next explicitly recognise that natural evolution will have selected for the ability to transport dietary substances, including plant, animal and microbial secondary metabolites, that are of benefit to the host. These should also be explored in terms of their closeness to marketed drugs. We thus compared the TS of marketed drugs with the contents of various databases of natural products. When this is done, we find that some 80% of marketed drugs are within a TS of 0.7 to a natural product, even using just the MACCS encoding. For patterned and TYPICAL encodings, 80% and 98% of drugs are within a TS of 0.8 to (an endogenite or) an exogenous natural product. This implies strongly that it is these exogeneous (dietary and medicinal) natural products that are more to be seen as the natural substrates of drug transporters (as is recognised, for instance, for the solute carrier SLC22A4 and ergothioneine). This novel analysis casts an entirely different light on the kinds of natural molecules that are to be seen as most like marketed drugs, and hence potential transporter substrates, and further suggests that a renewed exploitation of natural products as drug scaffolds would be amply rewarded.

pharmacology and toxicology↗

bioRxiv2017

Transcriptome profiling reveals bisphenol A alternatives activate estrogen receptor alpha in human breast cancer cells

BackgroundPlasticizers with estrogenic activity, such as bisphenol A (BPA), have been reported to have potential adverse health effects in humans. Due to mounting evidence of these health effects and public pressure, BPA is being phased out by the plastics manufacturing industry and replaced by other bisphenol variants in \"BPA-free\" products.\n\nObjectivesWe have compared estrogenic activity of BPA to 6 bisphenol analogues (bisphenol S, BPS; bisphenol F, BPF; bisphenol AP, BPAP; bisphenol AF, BPAF; bisphenol Z, BPZ; bisphenol B, BPB) in three human breast cancer cell lines.\n\nMethodsEstrogenicity was assessed by cell growth in an estrogen receptor (ER)-mediated cell proliferation assay, and by the induction of estrogen response element (ERE)-mediated transcription in a luciferase assay. Gene expression profiles were determined in MCF-7 human breast cancer cells by microarray analysis and confirmed by Illumina-based RNA sequencing.\n\nResultsAll bisphenols showed estrogenic activity in promoting cell growth and inducing ERE-mediated transcription. BPAF was the most potent bisphenol, followed by BPB > BPZ ~ BPA > BPF ~ BPAP > BPS. The addition of ICI 182,780 antagonized the activation of ERs by bisphenols. Data mining of ToxCast high-throughput screening assays confirms our results but also shows divergence in the sensitivities of the assays. The comparison of transcriptome profile alterations resulting from BPA alternatives with an ER gene expression biomarker further indicates that all BPA alternatives act as ER agonists in MCF-7 cells. These results were confirmed by RNA sequencing.\n\nConclusionIn conclusion, BPA alternatives are not necessarily less estrogenic in a human breast cancer cell model. Three bisphenols (BPAF, BPB, and BPZ) were more estrogenic than BPA. The relevance of human exposure to BPA alternatives in hormone-dependent breast cancer risk should be investigated.

pharmacology and toxicology↗

bioRxiv2017

Applying Mondrian Cross-Conformal Prediction to Estimate Prediction Confidence on Large Imbalanced Bioactivity Datasets

Conformal prediction has been proposed as a more rigorous way to define prediction confidence compared to other application domain concepts that have earlier been used for QSAR modelling. One main advantage of such a method is that it provides a prediction region potentially with multiple predicted labels, which contrasts to the single valued (regression) or single label (classification) output predictions by standard QSAR modelling algorithms. Standard conformal prediction might not be suitable for imbalanced datasets. Therefore, Mondrian cross-conformal prediction (MCCP) which combines the Mondrian inductive conformal prediction with cross-fold calibration sets has been introduced. In this study, the MCCP method was applied to 18 publicly available datasets that have various imbalance levels varying from 1:10 to 1:1000 (ratio of active/inactive compounds). Our results show that MCCP in general performed well on cheminformatics datasets with various imbalance levels. More importantly, the method not only provides confidence of prediction and prediction regions compared to standard machine learning methods, but also produces valid predictions for the minority class. In addition, a compound similarity based nonconformity measure was investigated. Our results demonstrate that although it gives valid predictions, its efficiency is much worse than nonconformity measures obtained from supervised learning.

pharmacology and toxicology↗

bioRxiv2017

Identification and Optimization of 4-Anilinoquinolines as Inhibitors of Cyclin G Associated Kinase

4-Anilinoquinolines were identified as potent and narrow spectrum inhibitors of the cyclin G associated kinase (GAK), an important regulator of viral and bacterial entry into host cells. Optimization of the 4-anilino group and the 6,7-quinoline substituents produced GAK inhibitors with nanomolar activity and over 50,000-fold selectivity relative to other members of the numb-associated kinase (NAK) sub-family. These compounds may be useful tools to explore the therapeutic potential of GAK in prevention of a broad range of infectious diseases.

pharmacology and toxicology↗

bioRxiv2017

Toxicity Of Chlordane At Early Developmental Stage Of Zebrafish

Chlordane is highly toxic organochlorine pesticides that have been widely used throughout the world for decades and posing adverse effects on the environment. Contents detected in tissue and blood samples have resulted in a raising concern for their potential effects on wildlife and humans. In this study, we investigate the potential effect of chlordane on the development of zebrafish embryos. Zebrafish larvae were treated with different concentrations (0, 25, 50, 100, 200 ng/L) of chlordane from 12 hours postfertilization (hpf). Different early stage parameters were observed at 1, 2, 3 and 4 day post-fertilization (dpf). Chlordane-exposed zebrafish larvae appeared significant lower survival rate, developmental and hatching time delay and decreased embryo productivity. The heartbeat rate and blood flow were decreased in a dose dependent manner. These results suggested that exposure to real life of chlordane led to direct morphological and phenotypic changes and effects systems related to development and reproduction even in short-term manner.

pharmacology and toxicology↗

bioRxiv2017

The acute toxicity of Oxydemeton-methyl in zebrafish

Oxydemeton-methyl, is an organothiophosphate insecticide, which is widely used in agricultural and urban pest controls. It exists in the environment and a large amount bioaccumulation in the wildlife due to its strong water solubility and mobility. Although its potentially harmful effect on animals and humans, few studies have focused on the oxydemeton-methyl pollution in the environment. Zebrafish have been used for many years to valuate the pollution status of water and toxicity of chemicals. In the present study, we aimed to investigate the effect of oxydemeton-methyl on the expression level of liver microsomal cytochrome P450, on the activity of NADPH-P450 reductase and reactive oxygen species (ROS) generation in zebrafish. Adult male and female zebrafish were treated with different concentration of oxydemeton-methyl (10, 50, 100 M) for 5, 10, 20 and 30 days. We found that the oxydemeton-methyl exposure significantly increased the P450 levels and the activity of NAPDH-P450 reductase. ROS generation and the DNA damage were augmented in a dose-dependent manner in the zebrafish. These results indicated that oxydemeton-methyl is able to induce strong oxidative stress and hence highly toxic to the zebrafish.

pharmacology and toxicology↗

bioRxiv2017

Detecting Drug-Target Binding In Cells Using Fluorescence Activated Cell Sorting Coupled With Mass Spectrometry Analysis

The assessment of drug-target engagement for determining the efficacy of a compound inside cells remains challenging, particularly for difficult target proteins. Existing techniques are more suited to soluble protein targets. Difficult target proteins include those with challenging in vitro solubility, stability or purification properties that preclude target isolation. Here, we report a novel technique that measures intracellular compound-target complex formation, as well as cellular permeability, specificity and cytotoxicity - the Toxicity-Affinity-Permeability-Selectivity (TAPS) technique. The TAPS assay is exemplified here using human kynurenine 3-monooxygenase (KMO), a challenging intracellular membrane protein target of significant current interest. TAPS confirmed target binding of known KMO inhibitors inside cells. We conclude that the TAPS assay can be used to facilitate intracellular hit validation on most, if not all intracellular drug targets.

pharmacology and toxicology↗

bioRxiv2017

Practical Unidentifiability Of Receptor Density In Target Mediated Drug Disposition Models Can Lead To Over-Interpretation Of Drug Concentration Data

For monoclonal antibodies, mathematical models of target mediated drug disposition (TMDD) are often fit to data in order to estimate key physiological parameters of the system. These parameter estimates can then be used to support drug development by assisting with the assessment of whether the target is druggable and what the first in human dose should be. The TMDD model is almost always over-parameterized given the available data, resulting in the practical unidentifiability of some of the model parameters, including the target receptor density. In particular, when only PK data is available, the receptor density is almost always practically unidentifiable. However, because practical identifiability is not regularly assessed, incorrect interpretation of model fits to the data can be made. This issue is illustrated using two case studies from the literature.

pharmacology and toxicology↗

bioRxiv2017

High Ambient Temperature Facilitates The Acquisition Of 3,4-Methylenedioxymethamphetamine (MDMA) Self-Administration

RationaleMDMA alters body temperature in rats with a direction that depends on the ambient temperature (TA). The thermoregulatory effects of MDMA and TA may affect intravenous self-administration (IVSA) of MDMA but limited prior reports conflict.\n\nObjectiveTo determine how body temperature responses under high and low TA influence MDMA IVSA.\n\nMethodsMale Sprague-Dawley rats were trained to IVSA MDMA (1.0 mg/kg/infusion; 2-hr sessions; FR5 schedule of reinforcement) under TA 20{degrees}C or 30{degrees}C. Radiotelemetry transmitters recorded body temperature and activity during IVSA.\n\nResultsMDMA intake increased under both TA during acquisition, but to a greater extent in the 30{degrees}C group. The magnitude of hypothermia was initially equivalent between groups but diminished over training in the 30{degrees}C group. Within-session activity was initially lower in the 30{degrees} C group, but by the end of acquisition and maintenance, activity was similar for both groups. When TA conditions were swapped, the hot-trained group increased MDMA IVSA under 20 {degrees}C TA and a modest decrease in drug intake was observed in the cold-trained group under 30 {degrees}C TA. Subsequent non-contingent MDMA (1.0-5.0 mg/kg, i.v.) found that rats with higher MDMA IVSA rates showed blunted hypothermia compared with rats with lower IVSA levels; however, within-session activity did not differ by group. High TA increased intracranial self-stimulation thresholds in a different group of rats and MDMA reduced thresholds below baseline at low, but not high, TA.\n\nConclusionsHigh TA appears to enhance acquisition of MDMA IVSA through an aversive effect and not via thermoregulatory motivation.

pharmacology and toxicology↗

bioRxiv2017

Wheel running increases hyperthermia and mortality rate following 3,4-methylenedioxymethamphetamine (MDMA) in rats

Hyperthermic responses are commonly reported in cases of human medical emergency following recreational use of 3,4-methylenedioxymethamphetamine (MDMA, \"Ecstasy\"), but a precise determination of contributing environmental factors has been elusive given the relative scarcity of threatening and fatal reactions in humans. This study was conducted to determine if elevated physical activity contributes to hyperthermic responses to MDMA in a well controlled animal model. Unrestrained male Wistar rats were monitored with minimally-invasive radiotelemetry techniques following challenge with MDMA (1.0, 5.6 and 10.0 mg/kg, s.c.). Studies were conducted in low (23-25{degrees}C) and high (27{degrees}C) ambient temperature (TA), with and without access to an activity wheel. The study confirmed dose dependent effects on body temperature, chamber activity and wheel activity which were modified by different TA conditions. Increases in wheel and home chamber activity produced by 10 mg/kg MDMA increased the magnitude of hyperthermia under 27{degrees}C TA. Furthermore, greater subject mortality was observed in the wheel-access condition compared with the no-wheel condition. These data provide direct evidence that sustained physical activity increases the hyperthermic response to MDMA and that this is associated with increased lethality. This is the first direct experimental confirmation that increased physical activity may be a risk factor for adverse reactions to MDMA in human user populations.

pharmacology and toxicology↗

bioRxiv2017

Model Based Safety Ranking Of Opioid Drugs Using Adversity Index

Annual ADR report counts of opioid drugs are examined to develop a candidate index of overall safety of a drug. Actual counts for various drugs have been sourced from www.vigiaccess.org. A feature found to be common to all drugs considered is that an exponential function adequately describes the pattern of cumulative counts. In the exponential model, the parameter in the exponent (rate constant) is robust and remains the same whether counts are corrected for exposure or not. We propose use of this rate constant as adversity index of a drug. Drugs in use can be ranked by value of adversity index, lower value suggesting safer drug.\n\nKey pointsCumulative total of annual ADR report counts of opioid drugs follows an exponential pattern. Rate constant in the model is independent of volume of use of the drug. Hence it is a suitable index of overall safety.

pharmacology and toxicology↗