Discovery of High-Affinity Amyloid Ligands Using a Ligand-Based Virtual Screening Pipeline.

Fibrillar protein aggregates are characteristic of neurodegenerative diseases but represent difficult targets for ligand design, because limited structural information about the binding sites is available. Ligand-based virtual screening has been used to develop a computational method for the selection of new ligands for Aß(1-42) fibrils, and five new ligands have been experimentally confirmed as nanomolar affinity binders. A database of ligands for Aß(1-42) fibrils was assembled from the literature and used to train models for the prediction of dissociation constants based on chemical structure. The virtual screening pipeline consists of three steps: a molecular property filter based on charge, molecular weight, and logP; a machine learning model based on simple chemical descriptors; and machine learning models that use field points as a 3D description of shape and surface properties in the Forge software. The three-step pipeline was used to virtually screen 698 million compounds from the ZINC15 database. From the top 100 compounds with the highest predicted affinities, 46 compounds were experimentally investigated by using a thioflavin T fluorescence displacement assay. Five new Aß(1-42) ligands with dissociation constants in the range 20-600 nM and novel structures were identified, demonstrating the power of this ligand-based approach for discovering new structurally unique, high-affinity amyloid ligands. The experimental hit rate using this virtual screening approach was 10.9%.

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale.

The development of accurate transferable force fields is key to realizing the full potential of atomistic modeling in the study of biological processes such as protein-ligand binding for drug discovery. State-of-the-art transferable force fields, such as those produced by the Open Force Field Initiative, use modern software engineering and automation techniques to yield accuracy improvements. However, force field torsion parameters, which must account for many stereoelectronic and steric effects, are considered to be less transferable than other force field parameters and are therefore often targets for bespoke parametrization. Here, we present the Open Force Field QCSubmit and BespokeFit software packages that, when combined, facilitate the fitting of torsion parameters to quantum mechanical reference data at scale. We demonstrate the use of QCSubmit for simplifying the process of creating and archiving large numbers of quantum chemical calculations, by generating a dataset of 671 torsion scans for druglike fragments. We use BespokeFit to derive individual torsion parameters for each of these molecules, thereby reducing the root-mean-square error in the potential energy surface from 1.1 kcal/mol, using the original transferable force field, to 0.4 kcal/mol using the bespoke version. Furthermore, we employ the bespoke force fields to compute the relative binding free energies of a congeneric series of inhibitors of the TYK2 protein, and demonstrate further improvements in accuracy, compared to the base force field (MUE reduced from 0.560.390.77 to 0.420.280.59 kcal/mol and R2 correlation improved from 0.720.350.87 to 0.930.840.97).

Hybrid Alchemical Free Energy/Machine-Learning Methodology for the Computation of Hydration Free Energies.

A methodology that combines alchemical free energy calculations (FEP) with machine learning (ML) has been developed to compute accurate absolute hydration free energies. The hybrid FEP/ML methodology was trained on a subset of the FreeSolv database and retrospectively shown to outperform most submissions from the SAMPL4 competition. Compared to pure machine-learning approaches, FEP/ML yields more precise estimates of free energies of hydration and requires a fraction of the training set size to outperform standalone FEP calculations. The ML-derived correction terms are further shown to be transferable to a range of related FEP simulation protocols. The approach may be used to inexpensively improve the accuracy of FEP calculations and to flag molecules which will benefit the most from bespoke force field parametrization efforts.

Assessment of Binding Affinity via Alchemical Free-Energy Calculations.

Free-energy calculations have seen increased usage in structure-based drug design. Despite the rising interest, automation of the complex calculations and subsequent analysis of their results are still hampered by the restricted choice of available tools. In this work, an application for automated setup and processing of free-energy calculations is presented. Several sanity checks for assessing the reliability of the calculations were implemented, constituting a distinct advantage over existing open-source tools. The underlying workflow is built on top of the software Sire, SOMD, BioSimSpace, and OpenMM and uses the AMBER 14SB and GAFF2.1 force fields. It was validated on two datasets originally composed by Schrödinger, consisting of 14 protein structures and 220 ligands. Predicted binding affinities were in good agreement with experimental values. For the larger dataset, the average correlation coefficient Rp was 0.70 ± 0.05 and average Kendall's τ was 0.53 ± 0.05, which are broadly comparable to or better than previously reported results using other methods.

The complexity and challenges of the International Classification of Diseases, Ninth Revision, Clinical Modification to International Classification of Diseases, 10th Revision, Clinical Modification transition in EDs.

Beginning October 2015, the Center for Medicare and Medicaid Services will require medical providers to use the vastly expanded International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM) system. Despite wide availability of information and mapping tools for the next generation of the ICD classification system, some of the challenges associated with transition from ICD-9-CM to ICD-10-CM are not well understood. To quantify the challenges faced by emergency physicians, we analyzed a subset of a 2010 Illinois Medicaid database of emergency department ICD-9-CM codes, seeking to determine the accuracy of existing mapping tools in order to better prepare emergency physicians for the change to the expanded ICD-10-CM system. We found that 27% of 1830 codes represented convoluted multidirectional mappings. We then analyzed the convoluted transitions and found that 8% of total visit encounters (23% of the convoluted transitions) were clinically incorrect. The ambiguity and inaccuracy of these mappings may impact the workflow associated with the translation process and affect the potential mapping between ICD codes and Current Procedural Codes, which determine physician reimbursement.

Footprinting molecular electrostatic potential surfaces for calculation of solvation energies.

A liquid is composed of an ensemble of molecules that populate a large number of different states, so calculation of the solvation energy of a molecule in solution requires a method for summing the interactions with the environment over all of these states. The surface site interaction model for the properties of liquids at equilibrium (SSIMPLE) simplifies the surface of a molecule to a discrete number of specific interaction sites (SSIPs). The thermodynamic properties of these interaction sites can be characterised experimentally, for example, through measurement of association constants for the formation of simple complexes that feature a single H-bonding interaction. Correlation of experimentally determined solution phase H-bond parameters with gas phase ab initio calculations of maxima and minima on molecular electrostatic potential surfaces (MEPS) provides a method for converting gas phase calculations on isolated molecules to parameters that can be used to estimate solution phase interaction free energies. This approach has been generalised using a footprinting technique that converts an MEPS into a discrete set of SSIPs (each described by a polar interaction parameter, εi). These SSIPs represent the molecular recognition properties of the entire surface of the molecule. For example, water is described by four SSIPs, two H-bond donor sites and two H-bond acceptor sites. A liquid mixture is described as an ensemble of SSIPs that represent the components of the mixture at appropriate concentrations. Individual SSIPs are assumed to be independent, so speciation of SSIP contacts can be calculated based on properties of the individual SSIP interactions, which are given by the sum of a polar (εiεj) and a non-polar (E(vdW)) interaction term. Results are presented for calculation the free energies of transfer of a range of organic molecules from the pure liquid into water, from the pure liquid into n-hexadecane, from n-hexadecane into water, from n-octanol into water, and for the transfer of water from pure water into a range of organic liquids. The agreement with experiment is accurate to within 1.6-3.9 kJ mol(-1) root mean square difference, which suggests that the SSIMPLE approach is a promising method for estimation of solvation energies in more complex systems.

On the frontline: pediatric obesity in the emergency department.

Obesity among children is rising at an alarming rate. This study examines pediatric emergency department visits for children aged 2 to 17 years to determine the prevalence of normal, overweight, and obesity as well as to characterize discharge diagnosis and level of service among the different groups. The electronic emergency department medical record and billing service data were used in the review process. Body mass index (BMI) and percentiles were calculated using the Centers for Disease Control formulas with overweight being defined as BMI between 85th and 94th sex- and age-specific percentiles and obesity as greater than 95th sex- and age-specific percentile. The study was reviewed and approved by the institutional review board. Of the 596 patients meeting inclusion criteria, there was a predominance of African American and Hispanic patients. Approximately 53% (313) of patients were classified as normal weight, while 46% (272) of patients were either overweight or obese. The percentages of overweight and obesity were similar across racial/ethnic classifications, with a slight predominance of obesity among minority groups (30% and 35%, respectively, in minority groups vs 28% and 25%, respectively, in nonminority groups). There were no statistically significant differences between discharge diagnosis and level of service among the different weight categories. Rates of overweight and obesity in this predominately minority pediatric population were significantly greater than the published national rates. The impact of the epidemic of childhood obesity mandates the need for innovative strategies of weight control and reduction. Emergency departments routinely treat high-risk pediatric populations and can therefore serve as a resource for screening and early referral that has been previously untapped in combating childhood obesity.

Single and interactive effects of malathion, overwintered green frog tadpoles, and cyanobacteria on gray treefrog tadpoles.

Amphibian population declines around the world are associated with invasive species, pesticides, pathogens, habitat destruction, or a combination of factors. Because contamination is widespread, it represents a relevant environmental stress that can affect the ability of organisms to deal with other factors present in the environment. We examined the effects of the insecticide malathion, larger tadpole competitors (green frogs, Rana clamitans), and a toxic cyanobacteria (Anabaena spp.) on tadpoles of Cope's gray treefrog (Hyla chrysoscelis) reared from hatching through metamorphosis in outdoor mesocosms. The response of mass at metamorphosis and time to metamorphosis was significantly affected by exposure to malathion and presence of overwintered green frog tadpoles. Malathion generally led to increased mass at metamorphosis, earlier time to metamorphosis, and increased activity during larval development. These results likely stem from short-term increases in periphyton associated with malathion exposure (although these effects were nonsignificant). Exposure of gray treefrogs to overwintered green frog tadpoles led to an earlier time to metamorphosis without differences in mass at metamorphosis and was associated with increased activity in gray treefrogs. Survival of gray treefrogs was significantly affected by an interaction of green frog and malathion, indicating nonadditive effects of these treatments. Exposure to cyanobacteria had a significant negative effect on green frogs but no effect on treefrogs. Malathion had the strongest effect on the community, but our results indicated that some factors can interact in ways not predicted by single factors alone.

Electrostatic Complementarity as a Fast and Effective Tool to Optimize Binding and Selectivity of Protein-Ligand Complexes.

Electrostatic interactions between small molecules and their respective receptors are essential for molecular recognition and are also key contributors to the binding free energy. Assessing the electrostatic match of protein-ligand complexes therefore provides important insights into why ligands bind and what can be changed to improve binding. Ideally, the ligand and protein electrostatic potentials at the protein-ligand interaction interface should maximize their complementarity while minimizing desolvation penalties. In this work, we present a fast and efficient tool to calculate and visualize the electrostatic complementarity (EC) of protein-ligand complexes. We compiled benchmark sets demonstrating electrostatically driven structure-activity relationships (SAR) from literature data, including kinase, protein-protein interaction, and GPCR targets, and used these to demonstrate that the EC method can visualize, rationalize, and predict electrostatically driven ligand affinity changes and help to predict compound selectivity. The methodology presented here for the analysis of EC is a powerful and versatile tool for drug design.

A new pyridazine series of GABAA alpha5 ligands.

Screening of the Merck compound collection identified 6 as an unusually simple, low molecular weight hit with moderate affinity for GABAA receptors. The structural novelty of 6, compared to our advanced series of GABAA alpha5 inverse agonists, made it an attractive molecule for further exploration. This paper will describe the evolution of 6 into a new series of ligands with nanomolar affinity and functional selectivity for GABAA alpha5 receptor subtypes.

The Aging Waistline: Impact of the Geriatric Obesity Epidemic on an Urban Emergency Department: Original Communication.

PURPOSE: Reviews adult emergency department (ED) visits for patients age 65 and older during one calendar year; determine the prevalence of weight classifications; identifies trends between BMI and discharge/admitting diagnoses, vital signs, and severity index. METHODS: The electronic medical records system and data from the ED billing service was reviewed for an urban academic institution with an annual volume of 125,000 for patients age > 65. Using a random number table, a retrospective cohort of 328 elderly patients was selected for review, representing a convenience sample of 2.6% of elderly ED visits. Body Mass Index (BMI) was calculated, using the Center for Disease Control (CDC) formula with underweight (<18.5), normal (18.5 - 24.9), overweight (25 - 29.9), and obese (≥30). RESULTS: The majority of the cohort in this study was African-American and Hispanic (60% and 27% respectively), and there were a higher percentage of females than males (60% and 40% respectively). Approximately 29% of the patients were classified as normal weight, 35% classified as overweight, and 36% as obese. The older the patient, the more likely that patient belonged to a lower weight classification (p < 0.01). Those presenting with neurological, pulmonary or gastrointestinal complaints were more likely to be of a higher weight classification (p < 0.05). Patients who were hypertensive on arrival to the ED were more likely to be in a higher weight classification (p < 0.01). CONCLUSION: Those patients with a higher weight classification had a strong correlation with selected abnormal vital signs and disease presentations. EDs are important sources of care for the elderly. EDs can serve as a previously untapped resource for screening and early referral exercise programs aimed at improving physical function/functional status and quality of life in the elderly patient population.

High content pharmacophores from molecular fields: a biologically relevant method for comparing and understanding ligands.

The question of how and why a small molecule binds to a protein is central to ligand-based drug discovery. The traditional way of approaching these questions is pharmacophore analysis. However, pharmacophores as usually applied lack quantitation and subtlety. An improvement is to consider the electrostatic and steric fields of the ligand directly. Molecular fields provide a rich view of the potential interactions that a molecule can make and can be validated through experimental data on molecular interactions and through quantum mechanics calculations. A technique is presented in this review for comparing molecules using molecular fields and assigning similarity scores. This high information content method can be used to align molecules for SAR analysis, to determine the bioactive conformation from ligand data, and to screen large libraries of compounds for structurally unrelated actives. An extension to allow interactive exploration of chemistry space via bioisostere analysis is also reviewed. Examples from the literature showing the success of these methods are presented, and future directions discussed.

Better than random? The chemotype enrichment problem.

Chemotype enrichment is increasingly recognized as an important measure of virtual screening performance. However, little attention has been paid to producing metrics which can quantify chemotype retrieval. Here, we examine two different protocols for analyzing chemotype retrieval: "cluster averaging", where the contribution of each active to the scoring metric is proportional to the number of other actives with the same chemotype, and "first found", where only the first active for a given chemotype contributes to the score. We demonstrate that this latter analysis, common in the qualitative analysis used in the current literature, has important drawbacks when combined with quantitative metrics.

Effects of temperature and perch diameter on arboreal locomotion in the snake Elaphe guttata.

Arboreality is widespread in multiple lineages of snakes and these habitats are important for foraging, escaping predators, and thermoregulation for many species. However, very little is known about factors influencing the arboreal locomotor abilities of snakes. Arboreal performance was assessed in a semi-arboreal snake (Elaphe guttata) using an artificial perch apparatus. Locomotor velocity, body posture, and balance was measured during movement on three perch diameters (3, 6, 10-cm) at three temperatures (10, 20, 30 degrees C). Velocities attained by E. guttata on perches are much slower than those of terrestrial lateral undulation and swimming and somewhat slower than concertina velocities recorded in other species across the same experimental temperatures. At higher temperatures, faster speeds were associated with a more elongated posture. At lower temperatures, snakes displayed a more looped body posture, but still fell more often than at higher temperatures. Our results suggest that temperature has a large influence on both balance and movement by snakes on perches. Although there were no differences in velocities resulting from perch diameter, snakes fell more often from thicker perches. This differs from arboreal velocities attained by limbed vertebrates, which decrease with decreasing perch diameter, suggesting that snakes have a size-relative advantage over limbed animals, such as lizards, when traversing a network of narrow branches. Future studies investigating arboreal locomotion among snakes that vary both phylogenetically and morphologically are needed to assess the potential benefits of limblessness in complex, three-dimensional environments.

FieldScreen: virtual screening using molecular fields. Application to the DUD data set.

FieldScreen, a ligand-based Virtual Screening (VS) method, is described. Its use of 3D molecular fields makes it particularly suitable for scaffold hopping, and we have rigorously validated it for this purpose using a clustered version of the Directory of Useful Decoys (DUD). Using thirteen pharmaceutically relevant targets, we demonstrate that FieldScreen produces superior early chemotype enrichments, compared to DOCK. Additionally, hits retrieved by FieldScreen are consistently lower in molecular weight than those retrieved by docking. Where no X-ray protein structures are available, FieldScreen searches are more robust than docking into homology models or apo structures.

Molecular field extrema as descriptors of biological activity: definition and validation.

The paper describes the generation of four types of three-dimensional molecular field descriptors or 'field points' as extrema of electrostatic, steric, and hydrophobic fields. These field points are used to define the properties necessary for a molecule to bind in a characteristic way into a specified active site. The hypothesis is that compounds showing a similar field point pattern are likely to bind at the same target site regardless of structure. The methodology to test this idea is illustrated using HIV NNRTI and thrombin ligands and validated across seven other targets. From the in silico comparisons of field point overlays, the experimentally observed binding poses of these ligands in their respective sites can be reproduced from pairwise comparisons.