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Motivation: Cytochrome P450s are a family of enzymes responsible for the metabolism of approximately 90% of FDA-approved drugs. Medicinal chemists often want to know which atoms of a molecule-its metabolized sites-are oxidized by Cytochrome P450s in order to modify their metabolism. Consequently, there are several methods that use literature-derived, atom-resolution data to train models that can predict a molecule's sites of metabolism. There is, however, much more data available at a lower resolution, where the exact site of metabolism is not known, but the region of the molecule that is oxidized is known. Until now, no site-of-metabolism models made use of region-resolution data., Results: Here, we describe XenoSite-Region, the first reported method for training site-of-metabolism models with region-resolution data. Our approach uses the Expectation Maximization algorithm to train a site-of-metabolism model. Region-resolution metabolism data was simulated from a large site-of-metabolism dataset, containing 2000 molecules with 3400 metabolized and 30 000 un-metabolized sites and covering nine Cytochrome P450 isozymes. When training on the same molecules (but with only region-level information), we find that this approach yields models almost as accurate as models trained with atom-resolution data. Moreover, we find that atom-resolution trained models are more accurate when also trained with region-resolution data from additional molecules. Our approach, therefore, opens up a way to extend the applicable domain of site-of-metabolism models into larger regions of chemical space. This meets a critical need in drug development by tapping into underutilized data commonly available in most large drug companies., Availability and Implementation: The algorithm, data and a web server are available at http://swami.wustl.edu/xregion., (© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

In a typical high-throughput screening (HTS) campaign, less than 1 % of the small-molecule library is characterized by confirmatory experiments. As much as 99 % of the library's molecules are set aside--and not included in downstream analysis--although some of these molecules would prove active were they sent for confirmatory testing. These missing experimental measurements prevent active molecules from being identified by screeners. In this study, we propose managing missing measurements using imputation--a powerful technique from the machine learning community--to fill in accurate guesses where measurements are missing. We then use these imputed measurements to construct an imputed visualization of HTS results, based on the scaffold tree visualization from the literature. This imputed visualization identifies almost all groups of active molecules from a HTS, even those that would otherwise be missed. We validate our methodology by simulating HTS experiments using the data from eight quantitative HTS campaigns, and the implications for drug discovery are discussed. In particular, this method can rapidly and economically identify novel active molecules, each of which could have novel function in either binding or selectivity in addition to representing new intellectual property.

As part of the SAR profiling of the indole-oxoacetic piperazinyl benzamide class of HIV-1 attachment inhibitors, substitution at the C7 position of the lead 4-fluoroindole 2 with various 5- and 6-membered heteroaryl moieties was explored. Highly potent (picomolar) inhibitors of pseudotyped HIV-1 in a primary, cell-based assay were identified and select examples were shown to possess nanomolar inhibitory activity against M- and T-tropic viruses in cell culture. These C7-heteroaryl-indole analogs maintained the ligand efficiency (LE) of 2 and were also lipophilic efficient as measured by LLE and LELP. Pharmacokinetic studies of this class of inhibitor in rats showed that several possessed substantially improved IV clearance and half-lives compared to 2. Oral exposure in the rat correlated with membrane permeability as measured in a Caco-2 assay where the highly permeable 1,2,4-oxadiazole analog 13 exhibited the highest exposure., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

7-(2H-Tetrazol-5-yl)-1H-indole 3 was found to be a potent inhibitor of HIV-1 attachment but the compound lacked oral bioavailability in rats. The cause of the low exposure was believed to be poor absorption attributed to the acidic nature of the tetrazole moiety and, in an effort to address this liability, three more lipohilic tetrazole analogs, N-acetoxymethyl 4, N-pivaloyloxymethyl 5, and N-methyl 6, were evaluated as potential oral prodrugs in rats. Prodrug 5 was ineffective in improving the plasma concentration of 3 in vivo but compound 4 provided a 15-fold enhancement of the plasma concentration of 3. Most interestingly, oral dosing of analog 6 afforded a substantial increase in the plasma concentration of the parent in rats when compared to dosing of parent. This represents a novel example of a methyl tetrazole that acts as a prodrug for a free NH tetrazole-containing compound., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

A series of substituted carboxamides at the indole C7 position of the previously described 4-fluoro-substituted indole HIV-1 attachment inhibitor 1 was synthesized and the SAR delineated. Heteroaryl carboxamide inhibitors that exhibited pM potency in the primary cell-based assay against a pseudotype virus expressing a JRFL envelope were identified. The simple methyl amide analog 4 displayed a promising in vitro profile, with its favorable HLM stability and membrane permeability translating into favorable pharmacokinetic properties in preclinical species., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Public databases that store the data from small-molecule screens are a rich and untapped resource of chemical and biological information. However, screening databases are unorganized, which makes interpreting their data difficult. We propose a method of inferring workflow graphs--which encode the relationships between assays in screening projects--directly from screening data and using these workflows to organize each project's data. On the basis of four heuristics regarding the organization of screening projects, we designed an algorithm that extracts a project's workflow graph from screening data. Where possible, the algorithm is evaluated by comparing each project's inferred workflow to its documentation. In the majority of cases, there are no discrepancies between the two. Most errors can be traced to points in the project where screeners chose additional molecules to test based on structural similarity to promising molecules, a case our algorithm is not yet capable of handling. Nonetheless, these workflows accurately organize most of the data and also provide a method of visualizing a screening project. This method is robust enough to build a workflow-oriented front-end to PubChem and is currently being used regularly by both our lab and our collaborators. A Python implementation of the algorithm is available online, and a searchable database of all PubChem workflows is available at http://swami.wustl.edu/flow.

Background: Bioanalytical support of drug-discovery efforts increasingly requires more complex multiple component analysis, including the bioanalysis of drugs, prodrugs and metabolites. Just as the physiochemical properties of these components may differ widely from each other, optimal LC and MS conditions, including polarity, can also vary greatly among the analytes of interest, thus presenting significant challenges during quantitative LC-MS-based bioanalysis. A single compromised method for the determination of all analytes may sacrifice sensitivity or chromatographic conditions for one analyte in order to achieve adequate results for another. Manually switching between assay conditions to analyze samples under separately optimized conditions for individual compounds can be time consuming., Results: The method presented here addresses the problem of differential analyte optimization using a multiplexed approach for simultaneous quantitative bioanalysis of multiple analytes in the same sample, employing a mixed mode of both turbulent- and laminar-flow chromatography., Conclusion: The approach is illustrated with the quantitation of a lipophilic drug and its hydrophilic phosphate ester prodrug in a biological matrix under individually optimized LC-MS conditions.

The chimpanzee has recently been characterized as a surrogate for oxidative drug metabolism in humans and as a pharmacokinetic model for the selection of drug candidates. In the current study, the glucuronidation of acetaminophen, morphine and oestradiol was evaluated in the chimpanzee to extend the characterization of this important animal model. Following oral administration of acetaminophen (600 mg) to chimpanzees (n=2), pharmacokinetics were comparable with previously reported human values, namely mean oral clearance 0.91 vs. 0.62+/-0.05 l h-1 kg-1, apparent volume of distribution 2.29 vs. 1.65+/-0.25 l kg-1, and half-life 1.86 vs. 1.89+/-7h, for chimpanzee vs. human, respectively. Urinary excretions (percentage of dose) of acetaminophen, acetaminophen glucuronide and acetaminophen sulfate were also similar between chimpanzees and humans, namely 2.3 vs. 5.0, 63.1 vs. 54.7, and 25.0 vs. 32.3%, respectively. Acetaminophen, oestradiol and morphine glucuronide formation kinetics were investigated using chimpanzee (n=2) and pooled human liver microsomes (n=10). V(max) (app) and K(m)(app) (or S(50)(app)) for acetaminophen glucuronide, morphine 3- and 6-glucuronide, and oestradiol 3- and 17-glucuronide formation were comparable in both species. Eadie-Hofstee plots of oestradiol 3-glucuronide formation in chimpanzee microsomes were characteristic of autoactivation kinetics. Western immunoblot analysis of chimpanzee liver microsomes revealed a single immunoreactive band when probed with anti-human UGT1A1, anti-human UGT1A6, and anti-human UGT2B7. Taken collectively, these data demonstrate similar glucuronidation characteristics in chimpanzees and humans.

In recent years training for specialist registrars (SpRs) in GU medicine has undergone a number of changes. In addition, the speciality in general is undergoing modernization and change and issues of workforce planning and consultant job availability have been of particular importance to SpRs. In March 2003 a postal survey of SpRs in the UK was undertaken to evaluate training, future career plans and working patterns. A 59% (69/117) response rate was achieved and overall most SpRs expressed satisfaction with their training. However, a number of concerns were raised with aspects of training, which are discussed in this paper. Nearly half of SpRs will consider working part time in the future and almost two-thirds are interested in job sharing. This is the first survey of its kind in GU medicine and the results are informative to all involved with SpR training programmes and workforce planning in the speciality.

The study objective was to investigate self-reported sexual practices among HIV-positive people in Wales in order to estimate the extent of unprotected sex and to develop services that assist positive people reduce the risk of sexual spread of HIV. A cross-sectional postal questionnaire survey was conducted between February and July 1999 at all open-access HIV outpatient facilities in Wales. All HIV-positive people attending during the study period were invited to enroll in the study. Data were obtained on 104/141 (74%) enrolled patients including 70 (67%) homo/bisexual men. Most (79/104, 76%) were sexually active and 42% (33/79) had casual partners. One in six (13/79, 16.5%) sexually active people reported unprotected high-risk sex with HIV-negative or unknown status partners, the majority (9/13, 69%) of whom were male homosexuals. It is important that health professionals specifically address issues of sexual behaviour with HIV positive people during consultation. A renewed safer sex campaign targeting men who have sex with men is urgently needed.

This study compared the BDProbeTec ET Chlamydia trachomatis amplified DNA assay on urine specimens with culture of genital swabs for the detection of C. trachomatis in patients attending the Department of Genitourinary Medicine (GUM), Cardiff Royal Infirmary. Almost twice as many patients tested positive by BDProbeTec ET than by culture. A similar difference was found for both males and females. The case notes of those patients positive by BDProbeTec ET alone were analysed and a significantly greater number were found to have risk indicators for C. trachomatis infection when compared with age and sex comparable controls, providing clinical validation of our findings. The BDProbeTec ET assay was easy to use, more importantly, the test format features an internal control integral with every sample. The cost per true positive was calculated as comparable with culture. We conclude that the BDProbeTec ET assay is a superior alternative to culture for identifying patients infected with C. trachomatis in the GUM clinic setting.