Surveying implicit solvent models for estimating small molecule absolute hydration free energies

Implicit solvent models are powerful tools in accounting for the aqueous environment at a fraction of the computational expense of explicit solvent representations. Here, we compare the ability of common implicit solvent models (TC, OBC, OBC2, GBMV, GBMV2, GBSW, GBSW/MS, GBSW/MS2 and FACTS) to reproduce experimental absolute hydration free energies for a series of 499 small neutral molecules that are modeled using AMBER/GAFF parameters and AM1‐BCC charges. Given optimized surface tension coefficients for scaling the surface area term in the nonpolar contribution, most implicit solvent models demonstrate reasonable agreement with extensive explicit solvent simulations (average difference 1.0–1.7 kcal/mol and R 2 = 0.81–0.91) and with experimental hydration free energies (average unsigned errors = 1.1–1.4 kcal/mol and R 2 = 0.66–0.81). Chemical classes of compounds are identified that need further optimization of their ligand force field parameters and others that require improvement in the physical parameters of the implicit solvent models themselves. More sophisticated nonpolar models are also likely necessary to more effectively represent the underlying physics of solvation and take the quality of hydration free energies estimated from implicit solvent models to the next level. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87097/1/21876_ftp.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/87097/2/JCC_21876_sm_suppinfo.pd

Assessing the quality of absolute hydration free energies among CHARMM‐compatible ligand parameterization schemes

Multipurpose atom‐typer for CHARMM (MATCH), an atom‐typing toolset for molecular mechanics force fields, was recently developed in our laboratory. Here, we assess the ability of MATCH‐generated parameters and partial atomic charges to reproduce experimental absolute hydration free energies for a series of 457 small neutral molecules in GBMV2, Generalized Born with a smooth SWitching (GBSW), and fast analytical continuum treatment of solvation (FACTS) implicit solvent models. The quality of hydration free energies associated with small molecule parameters obtained from ParamChem, SwissParam, and Antechamber are compared. Given optimized surface tension coefficients for scaling the surface area term in the nonpolar contribution, these automated parameterization schemes with GBMV2 and GBSW demonstrate reasonable agreement with experimental hydration free energies (average unsigned errors of 0.9–1.5 kcal/mol and R 2 of 0.63–0.87). GBMV2 and GBSW consistently provide slightly more accurate estimates than FACTS, whereas Antechamber parameters yield marginally more accurate estimates than the current generation of MATCH, ParamChem, and SwissParam parameterization strategies. Modeling with MATCH libraries that are derived from different CHARMM topology and parameter files highlights the importance of having sufficient coverage of chemical space within the underlying databases of these automated schemes and the benefit of targeting specific functional groups for parameterization efforts to maximize both the breadth and the depth of the parameterized space. © 2013 Wiley Periodicals, Inc. Ligand parameterization for molecular mechanics simulations is computationally intensive, requiring long multistep optimization procedures. Recently there has been an influx of automated parameterization tools for the CHARMM force field. These tools radically speed up the process, but it remains unclear whether accuracy is sacrificed to a significant extent. The research presented in this article uses a set of 457 small molecules to quantify the accuracy of four automated parameterization tools by computing absolute hydration free energies.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/97284/1/23199_ftp.pd

Geography and Location Are the Primary Drivers of Office Microbiome Composition.

In the United States, humans spend the majority of their time indoors, where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices. Our data elucidate several important features of microbial communities in BEs. First, under normal office environmental conditions, bacterial communities do not differ on the basis of surface material (e.g., ceiling tile or carpet) but do differ on the basis of the location in a room (e.g., ceiling or floor), two features that are often conflated but that we are able to separate here. We suspect that previous work showing differences in bacterial composition with surface material was likely detecting differences based on different usage patterns. Next, we find that offices have city-specific bacterial communities, such that we can accurately predict which city an office microbiome sample is derived from, but office-specific bacterial communities are less apparent. This differs from previous work, which has suggested office-specific compositions of bacterial communities. We again suspect that the difference from prior work arises from different usage patterns. As has been previously shown, we observe that human skin contributes heavily to the composition of BE surfaces. IMPORTANCE Our study highlights several points that should impact the design of future studies of the microbiology of BEs. First, projects tracking changes in BE bacterial communities should focus sampling efforts on surveying different locations in offices and in different cities but not necessarily different materials or different offices in the same city. Next, disturbance due to repeated sampling, though detectable, is small compared to that due to other variables, opening up a range of longitudinal study designs in the BE. Next, studies requiring more samples than can be sequenced on a single sequencing run (which is increasingly common) must control for run effects by including some of the same samples in all of the sequencing runs as technical replicates. Finally, detailed tracking of indoor and material environment covariates is likely not essential for BE microbiome studies, as the normal range of indoor environmental conditions is likely not large enough to impact bacterial communities

The accuracy of the Jamaican national physician register: a study of the status of physicians registered and their countries of training

<p>Abstract</p> <p>Background</p> <p>The number of physicians per 10,000 population is a basic health indicator used to determine access to health care. Studies from the United States of America and Europe indicate that their physician registration databases may be flawed. Clinical research activities have suggested that the current records of physicians registered to practice in Jamaica may not be accurate. Our objective was to determine whether the Medical Council of Jamaica (MCJ) accurately records and reports the identities, number and specialty designation of physicians in Jamaica. An additional aim was to determine the countries in which these physicians were trained.</p> <p>Methods</p> <p>Data regarding physicians practicing in Jamaica in 2005 were obtained from multiple sources including the MCJ and the telephone directory. Intense efforts at tracing were undertaken in a sub-sample of physicians, internists and paediatricians to further improve the accuracy of the data. Data were analysed using SPSS, version 11.5.</p> <p>Results</p> <p>The MCJ listed 2667 registered physicians of which 118 (4.4%) were no longer practicing in Jamaica. Of the subset of 150 physicians who were more actively traced, an additional 11 were found to be no longer in practice. Thus at least 129 (4.8%) of the physicians on the MCJ list were not actively practising in Jamaica. Twenty-nine qualified physicians who were in practice, but not currently on the Jamaican register, were identified from other data sources. This yielded an estimate of 2567 physicians or 9.68 physicians per 10,000 persons. Seven hundred and twenty six specialists were identified, 118 from the MCJ list only, 452 from other sources, in particular medical associations, and 156 from both the MCJ list and other sources. Sixty-six percent of registered doctors completed medical school at the University of the West Indies (UWI).</p> <p>Conclusion</p> <p>These data suggest that the MCJ list includes some physicians no longer practicing in Jamaica while underestimating the number of specialists. Difficulty in accurately estimating the number of practicing physicians has been reported in studies done in other countries but the under-reporting of the number of specialists is uncommon. Additional consideration should be given to strategies to ensure compliance with the annual registration that is mandated by law and to changing the law to include registration of specialist qualifications.</p

Diversity-Oriented Enzymatic Synthesis of Cyclopropane Building Blocks

While biocatalysis is increasingly incorporated into drug development pipelines, it is less commonly used in the early stages of drug discovery. By engineering a protein to produce a chiral motif with a derivatizable functional handle, biocatalysts can be used to help generate diverse building blocks for drug discovery. Here we show the engineering of two variants of Rhodothermus marinus nitric oxide dioxygenase (RmaNOD) to catalyze the formation of cis- and trans-diastereomers of a pinacolboronate-substituted cyclopropane which can be readily derivatized to generate diverse stereopure cyclopropane building blocks

Diversity-Oriented Enzymatic Synthesis of Cyclopropane Building Blocks

While biocatalysis is increasingly incorporated into drug development pipelines, it is less commonly used in the early stages of drug discovery. By engineering a protein to produce a chiral motif with a derivatizable functional handle, biocatalysts can be used to help generate diverse building blocks for drug discovery. Here we show the engineering of two variants of Rhodothermus marinus nitric oxide dioxygenase (RmaNOD) to catalyze the formation of cis- and trans-diastereomers of a pinacolboronate-substituted cyclopropane which can be readily derivatized to generate diverse stereopure cyclopropane building blocks

IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis.

Dupilumab is a fully human antibody to interleukin-4 receptor α that improves the signs and symptoms of moderate to severe atopic dermatitis (AD). To determine the effects of dupilumab on Staphylococcus aureus colonization and microbial diversity on the skin, bacterial DNA was analyzed from swabs collected from lesional and nonlesional skin in a double-blind, placebo-controlled study of 54 patients with moderate to severe AD randomized (1:1) and treated with either dupilumab (200 mg weekly) or placebo for 16 weeks. Microbial diversity and relative abundance of Staphylococcus were assessed by DNA sequencing of 16S ribosomal RNA, and absolute S.&nbsp;aureus abundance was measured by quantitative PCR. Before treatment, lesional skin had lower microbial diversity and higher overall abundance of S.&nbsp;aureus than nonlesional skin. During dupilumab treatment, microbial diversity increased and the abundance of S.&nbsp;aureus decreased. Pronounced changes were seen in nonlesional and lesional skin. Decreased S.&nbsp;aureus abundance during dupilumab treatment correlated with clinical improvement of AD and biomarkers of type 2 immunity. We conclude that clinical improvement of AD that is mediated by interleukin-4 receptor α inhibition and the subsequent suppression of type 2 inflammation is correlated with increased microbial diversity and reduced abundance of S.&nbsp;aureus

Discovery of Novel Adenosine Receptor Agonists That Exhibit Subtype Selectivity.

A series of N(6)-bicyclic and N(6)-(2-hydroxy)cyclopentyl derivatives of adenosine were synthesized as novel A1R agonists and their A1R/A2R selectivity assessed using a simple yeast screening platform. We observed that the most selective, high potency ligands were achieved through N(6)-adamantyl substitution in combination with 5'-N-ethylcarboxamido or 5'-hydroxymethyl groups. In addition, we determined that 5'-(2-fluoro)thiophenyl derivatives all failed to generate a signaling response despite showing an interaction with the A1R. Some selected compounds were also tested on A1R and A3R in mammalian cells revealing that four of them are entirely A1R-selective agonists. By using in silico homology modeling and ligand docking, we provide insight into their mechanisms of recognition and activation of the A1R. We believe that given the broad tissue distribution, but contrasting signaling profiles, of adenosine receptor subtypes, these compounds might have therapeutic potential.This study was supported by the Swiss National Science Foundation (SNSF professorship PP00P2_123536 and PP00P2_146321 to M.L.), the BBSRC (G.L., BB/G01227X/1 and BB/M00015X/1), an MRC Doctoral Training Partnership (I.W. MR/J003964/1), and the EPSRC (A.K., EP/G500045/1).This is the author accepted manuscript. The final version is available from the American Chemical Society via http://dx.doi.org/10.1021/acs.jmedchem.5b0140

Terminate Lung Cancer (TLC) Study—A Mixed-Methods Population Approach to Increase Lung Cancer Screening Awareness and Low-Dose Computed Tomography in Eastern Kentucky

For low dose CT lung cancer screening to be effective in curbing disease mortality, efforts are needed to overcome barriers to awareness and facilitate uptake of the current evidence-based screening guidelines. A sequential mixed-methods approach was employed to design a screening campaign utilizing messages developed from community focus groups, followed by implementation of the outreach campaign intervention in two high-risk Kentucky regions. This study reports on rates of awareness and screening in intervention regions, as compared to a control region