Docking and scoring--theoretically easy, practically impossible?

Structure-based Drug Design (SBDD) is an essential part of the modern medicinal chemistry, and has led to the acceleration of many projects, and even to drugs on the market. Programs that perform docking and scoring of ligands to receptors are powerful tools in the drug designer's armoury that enhance the process of SBDD. They are even deployed on the desktop of many bench chemists. It is timely to review the state of the art, to understand how good our docking programs are, and what are the issues. In this review we would like to provide a guide around the reliable aspects of docking and scoring and the associated pitfalls aiming at an audience of medicinal chemists rather than modellers. For convenience, we will divide the review into two parts: docking and scoring. Docking concerns the preparation of the receptor and the ligand(s), the sampling of conformational space and stereochemistry (if appropriate). Scoring concerns the evaluation of all of the ligand-receptor poses generated by docking. The two processes are not truly independent, and this will be discussed here in detail. The preparation of the receptor and ligand(s) before docking requires great care. For the receptor, issues of protonation, tautomerisation and hydration are key, and we will discuss current approaches to these issues. Even more important is the degree of sampling: can the algorithms reproduce what is observed experimentally? If they can, are the scoring algorithms good enough to recognise this pose as the best? Do the scores correlate with observed binding affinity? How does local knowledge of the target (for example hinge-binding to a kinase) affect the accuracy of the predictions? We will review the key findings from several evaluation studies and present conclusions about when and how to interpret and trust the results of docking and scoring. Finally, we will present an outline of some of the latest developments in the area of scoring functions.

Reliability and validity of the CMT neuropathy score as a measure of disability

OBJECTIVE

To determine the validity and reliability of the Charcot-Marie-Tooth disease (CMT) neuropathy score (CMTNS) in patients with inherited neuropathy.

BACKGROUND

Natural history studies and potential treatment trials for patients with various forms of CMT are limited by the lack of quantitative methodologies to monitor disease progression. Most cases of CMT can be considered length-dependent axonal neuropathies because disability for even the demyelinating forms correlates with length-dependent axonal degeneration. The total neuropathy score (TNS) is a validated composite measure of disability in length-dependent axonal neuropathies but is weighted toward predominantly sensory neuropathies. Thus, the authors have devised a CMTNS, modified from the TNS, to provide a single measure to quantify CMT disability.

METHODS

The authors measured inter- and intrainvestigator reliability of the CMTNS and performed a validation of the score with the Neuropathy Impairment Score (NIS), patient self-assessment scores, an ambulation index, and other measures of disability.

RESULTS

Inter- and intrainvestigator reliability was more than 95% in the 60 patients evaluated. Patients could be divided into mild (CMTNS, < or =10), moderate (CMTNS, 11 to 20), and severe (CMTNS, > or =21) categories and demonstrated excellent correlations among all measures of disability.

CONCLUSION

The Charcot-Marie-Tooth disease (CMT) neuropathy score is a validated measure of length-dependent axonal and demyelinating CMT disability and can be investigated as an end point for longitudinal studies and clinical trials of CMT.

'Take the stairs instead of the escalator': effect of environmental prompts on community stair use and implications for a national 'Small Steps' campaign

The US government initiated a national health campaign targeting 100 'small step' lifestyle changes to combat obesity. Small Step #67 advocates stair instead of escalator usage in public settings. The aim of this study is to evaluate the effects of motivational signs prompting stair use over escalator use on pedestrians' stair usage in commuter settings. Eight studies, testing the effects of motivational prompts on stair vs. escalator usage in public settings, were reviewed. Participant and study attributes were descriptively coded. Effect size was calculated as the change in percent units of stair users during the intervention phases vs. the baseline phase. The average study included approximately 45,000 observations that were recorded across an average of 15 weeks of intervention. The mean +/- SD change in percent units of stair users was 2.8% +/- 2.4% (P < 0.001), and effects were twice as large in females (4.8%) as in males (2.4%). The number of stairs/building, baseline stair use, and total intervention weeks predicted change in stair use, although the effects were clinically miniscule. In a hypothetical city intervention, we projected that a 2.8% increase in stair usage would result in a weight loss and/or weight gain prevention of 300 g/person/year among new stair users. In sum, point-of-decision motivational signs may help communities attain Small Step #67. However, the singular impact of this community intervention on correcting energy imbalance may be minimal, having slight impact itself on reducing the national obesity prevalence.

A double blind, placebo controlled trial of inert cellulose powder for the relief of symptoms of hay fever in adults

OBJECTIVE

An inert cellulose powder has been on sale in the UK since 1994 as a remedy for hay fever but no scientific trials have been conducted previously. It is applied to the inside of the nose where it forms a gelatinous coating. The principal aim was to determine if there is a significant difference in the amount and type of rescue medication required for adult hay fever sufferers to control their symptoms while using either the inert cellulose powder or a placebo. The second objective was to see whether the cellulose powder resulted in an improvement in symptom control.

RESEARCH DESIGN

A double blind, placebo controlled study was conducted of 97 adult hay fever sufferers, over the grass pollen season of 2004. Participants (selectively recruited to be living within the catchment area of a 50-km radius from Worcester, UK) were assigned randomly to two groups (A, Active and B, Placebo) matched by age by decades and gender. Of those completing the trial, group A had 19 males and 28 females and group B had 21 males and 29 females. There were no significant differences between the groups in age distributions, severity of symptoms over the last 2 years or in medication taken. They completed daily symptom diary score cards and were allowed to take any medications they wished in addition to the inert cellulose powder or placebo because medication use was taken as an outcome measure. Results were analysed in relation to pollen counts.

RESULTS

Significant differences were found in the amounts of rescue medication taken by the active and placebo groups (p < 0.05). More people in the placebo group took rescue treatments than those in the active group. No significant differences were found (p < 0.01) between the active and placebo groups in Likert scores for any of the rhinitis nasal symptoms or in the total Likert symptom daily scores. No adverse events were reported during the study.

CONCLUSIONS

The amount of rescue medication taken by the placebo group was significantly more than that taken by the active group both overall, considering all types of medication, and also in the individual cases of antihistamines, nasal sprays and eye drops. These results provide evidence that the inert cellulose powder reduces the need to take rescue medication for the symptoms of hay fever.

Phase contrast X-ray imaging of mice and rabbit lungs: a comparative study

The significant degree of X-ray phase contrast created by air-tissue interfaces, coupled with the poor radiographic contrast of conventional chest radiographs, makes the inflated lung an ideal candidate for investigating the potential diagnostic improvement afforded by phase contrast X-ray imaging. In small animals these methods highlight the lung airways and lobe boundaries and reveal the lung tissue as a speckled intensity pattern not seen in other soft tissues. We have compared analyser-based and propagation-based phase contrast imaging modalities, together with conventional radiographic imaging, to ascertain which technique shows the greatest image enhancement for various lung sizes. The conventional radiographic image of a mouse was obtained on a Siemens Nova 3000 mammography system, whilst phase contrast images of mice and rabbit chests were acquired at the medical imaging beamline (20B2) at the SPring-8 synchrotron radiation research facility in Japan. For mice aged 1 day, 1 week and 1 month old it was determined that analyser-based imaging showed the greatest overall image contrast, however, for an adult rabbit both techniques yielded excellent contrast. The success of these methods in creating high quality images for rabbit lungs raises the possibility of improving human lung imaging using phase contrast techniques.

Dynamic imaging of the lungs using x-ray phase contrast

High quality real-time imaging of lungs in vivo presents considerable challenges. We demonstrate here that phase contrast x-ray imaging is capable of dynamically imaging the lungs. It retains many of the advantages of simple x-ray imaging, whilst also being able to map weakly absorbing soft tissues based on refractive index differences. Preliminary results reported herein show that this novel imaging technique can identify and locate airway liquid and allows lung aeration in newborn rabbit pups to be dynamically visualized.

Distal symmetric polyneuropathy: a definition for clinical research: report of the American Academy of Neurology, the American Association of Electrodiagnostic Medicine, and the American Academy of Physical Medicine and Rehabilitation

The objective of this report was to develop a case definition of distal symmetric polyneuropathy to standardize and facilitate clinical research and epidemiologic studies. A formalized consensus process was employed to reach agreement after a systematic review and classification of evidence from the literature. The literature indicates that symptoms alone have relatively poor diagnostic accuracy in predicting the presence of polyneuropathy; signs are better predictors of polyneuropathy than symptoms; and single abnormalities on examination are less sensitive than multiple abnormalities in predicting the presence of polyneuropathy. The combination of neuropathic symptoms, signs, and electrodiagnostic findings provides the most accurate diagnosis of distal symmetric polyneuropathy. A set of case definitions was rank ordered by likelihood of disease. The highest likelihood of polyneuropathy (useful for clinical trials) occurs with a combination of multiple symptoms, multiple signs, and abnormal electrodiagnostic studies. A modest likelihood of polyneuropathy (useful for field or epidemiologic studies) occurs with a combination of multiple symptoms and multiple signs when the results of electrodiagnostic studies are not available. A lower likelihood of polyneuropathy occurs when electrodiagnostic studies and signs are discordant. For research purposes, the best approach to defining distal symmetric polyneuropathy is a set of case definitions rank ordered by estimated likelihood of disease. The inclusion of this formalized case definition in clinical and epidemiologic research studies will ensure greater consistency of case selection.

On the origin of speckle in x-ray phase contrast images of lung tissue

Phase contrast x-ray imaging of small animal lungs reveals a speckled intensity pattern not seen in other tissues, making the lungs highly visible in comparison to other organs. Although bearing a superficial resemblance to alveoli, the cause of this speckle has not been established. With a view to determining the mechanism for the formation of speckle, this paper details the results of propagation-based phase contrast experiments performed on mice lungs, together with packed glass microspheres used to emulate lung tissue. These experimental studies are compared to numerical simulations, based on wave propagation techniques. We find that speckle arises from focusing effects, with multiple alveoli acting as aberrated compound refractive lenses. Both experiments and modelling suggest that this speckle-formation phenomenon may lead to better screening methods for human lungs than conventional radiography.

Medical phase contrast x-ray imaging: current status and future prospects

The exploitation of phase contrast appears to offer the tantalising possibility of creating the biggest change in medical x-ray imaging since the invention of computed tomography. A considerable number of experiments performed by researchers across four continents have produced some extraordinary images. These images have demonstrated greatly enhanced contrast over conventional methods revealing soft tissue discrimination at micron scale resolutions. Contrast improvements can be achieved at doses rather less than those required by conventional x-ray imaging. The use of synchrotrons has revealed the possibilities offered by these techniques but unfortunately the application of these ideas in a clinical context requires that technology be pushed to its limits in a number of areas including x-ray sources, optics and detectors. The current state of the art is reviewed.

Medical phase contrast x-ray imaging: current status and future prospects

The exploitation of phase contrast appears to offer the tantalising possibility of creating the biggest change in medical x-ray imaging since the invention of computed tomography. A considerable number of experiments performed by researchers across four continents have produced some extraordinary images. These images have demonstrated greatly enhanced contrast over conventional methods revealing soft tissue discrimination at micron scale resolutions. Contrast improvements can be achieved at doses rather less than those required by conventional x-ray imaging. The use of synchrotrons has revealed the possibilities offered by these techniques but unfortunately the application of these ideas in a clinical context requires that technology be pushed to its limits in a number of areas including x-ray sources, optics and detectors. The current state of the art is reviewed.

Self-assembled uniaxial and biaxial multilayer structures in chiral smectic liquid crystals frustrated between ferro- and antiferroelectricity

With a view to obtain a molecular model for the subphases produced by the frustration between ferro- and antiferroelectricity in chiral smectic liquid crystals, we report results on two compounds and observe (i) the staircase character of uniaxial Sm C(*)(alpha) itself in the bulk and (ii) the multipeaked characteristic reflection bands due to the modulated helical structures just above the Sm C(*)(A) temperature range. We suggest the emergence of several uniaxial and biaxial subphases. The results show that both types of subphases can be specified by q(T) = [F] / ( [A] + [F] ) in the zero-order approximation; [A] and [F] are the numbers of antiferroelectric and ferroelectric orderings in the unit cell. We consider the basis of both types of subphases, particularly the description of the short-pitch helical structure of Sm C(*)(alpha), in terms of the molecular models so far proposed and emphasize the important role played by the discrete flexoelectric polarization.

Genotyping microarray (gene chip) for the ABCR (ABCA4) gene

Genetic variation in the ABCR (ABCA4) gene has been associated with five distinct retinal phenotypes, including Stargardt disease/fundus flavimaculatus (STGD/FFM), cone-rod dystrophy (CRD), and age-related macular degeneration (AMD). Comparative genetic analyses of ABCR variation and diagnostics have been complicated by substantial allelic heterogeneity and by differences in screening methods. To overcome these limitations, we designed a genotyping microarray (gene chip) for ABCR that includes all approximately 400 disease-associated and other variants currently described, enabling simultaneous detection of all known ABCR variants. The ABCR genotyping microarray (the ABCR400 chip) was constructed by the arrayed primer extension (APEX) technology. Each sequence change in ABCR was included on the chip by synthesis and application of sequence-specific oligonucleotides. We validated the chip by screening 136 confirmed STGD patients and 96 healthy controls, each of whom we had analyzed previously by single strand conformation polymorphism (SSCP) technology and/or heteroduplex analysis. The microarray was >98% effective in determining the existing genetic variation and was comparable to direct sequencing in that it yielded many sequence changes undetected by SSCP. In STGD patient cohorts, the efficiency of the array to detect disease-associated alleles was between 54% and 78%, depending on the ethnic composition and degree of clinical and molecular characterization of a cohort. In addition, chip analysis suggested a high carrier frequency (up to 1:10) of ABCR variants in the general population. The ABCR genotyping microarray is a robust, cost-effective, and comprehensive screening tool for variation in one gene in which mutations are responsible for a substantial fraction of retinal disease. The ABCR chip is a prototype for the next generation of screening and diagnostic tools in ophthalmic genetics, bridging clinical and scientific research.

Outcomes of systematic screening for optic pathway tumors in children with Neurofibromatosis Type 1

Optic pathway tumors (OPT) occur in about 15% of individuals with Neurofibromatosis Type 1 (NF1) and may effect substantial visual loss. Because their growth is not predictable at the time of discovery, neuroimaging for OPT in asymptomatic NF1 patients remains controversial. We evaluated the outcomes of systematic screening by both MRI and ophthalmic examinations for OPT in young children with NF1 seen at multi-disciplinary clinics for Neurofibromatosis and Genetics at one institution between 1996 and 2001. We report on 84 children who presented with NF1 under age 6 years, of whom 13 children presented with either known OPT or abnormal MRI findings and 11 children had OPTs identified by neuroimaging, including two children with abnormal eye examinations at presentation (one with strabismus and one with optic atrophy). Nine OPTs were detected in asymptomatic subjects with normal ophthalmic examinations. Three children with chiasmal lesions enlarging on subsequent MRI were treated with carboplatin and vincristine. After treatment, the vision in each involved eye was intact. In contrast, the 13 children with OPT diagnosed outside of screening guidelines included five children with substantial visual loss. Our observations suggest that early recognition of NF1 promotes appropriate surveillance and allows early intervention to reduce complications of OPT. This analysis supports prospective studies to compare the outcomes of systematic screening with neuroimaging to screening with ophthalmic examinations alone in children with NF1.

Distal symmetrical polyneuropathy: Definition for clinical research

The objective of this report was to develop a case definition of "distal symmetrical polyneuropathy" to standardize and facilitate clinical research and epidemiological studies. A formalized consensus process was employed to reach agreement after a systematic review and classification of evidence from the literature. The literature indicates that symptoms alone have relatively poor diagnostic accuracy in predicting the presence of polyneuropathy; signs are better predictors of polyneuropathy than symptoms; and single abnormalities on examination are less sensitive than multiple abnormalities in predicting the presence of polyneuropathy. The combination of neuropathic symptoms, signs, and electrodiagnostic findings provides the most accurate diagnosis of distal symmetrical polyneuropathy. A set of case definitions was rank ordered by likelihood of disease. The highest likelihood of polyneuropathy (useful for clinical trials) occurs with a combination of multiple symptoms, multiple signs, and abnormal electrodiagnostic studies. A modest likelihood of polyneuropathy (useful for field or epidemiological studies) occurs with a combination of multiple symptoms and multiple signs when the results of electrodiagnostic studies are not available. A lower likelihood of polyneuropathy occurs when electrodiagnostic studies and signs are discordant. For research purposes, the best approach for defining distal symmetrical polyneuropathy is a set of case definitions rank ordered by estimated likelihood of disease. The inclusion of this formalized case definition in clinical and epidemiological research studies will ensure greater consistency of case selection.

Molecular orientation and the infrared dichroism of a chiral smectic liquid crystal in a homogeneously aligned cell at different temperature and bias fields

The molecular orientation and the dichroic behavior of the vibrational bands of a homogeneously aligned helical cell containing chiral smectic liquid crystal (R)-(-)-1-methylheptyl 4-(4(')-dodecyloxybiphenyl-4-ylcarbonyloxy)-3-fluorobenzoate are studied at various temperatures as a function of the bias field. These temperatures correspond to the various phase states of the sample at zero field. For those bands that exhibit significant dichroism, the field dependencies of the dichroic parameters (the dichroic ratio and the polarization angle of maximum absorbance) are found to be dependent on temperature, phase state, and helical unwinding. For the SmA* and SmC(*)(alpha) phases, the phenyl band dichroic ratio and the corresponding orientational order parameter are found to be almost independent of the bias field. The temperature dependence of the orientational order for zero field is discussed by taking into account the structures of the phases and the molecular tilt angles. The field dependencies of the phenyl band dichroic parameters for the SmC(*)(A) and SmC(*)(gamma) phases yield results about the distribution of directors in the layers of their unit cells and the state of helical unwinding. The azimuthal orientational distribution function of the carbonyl transition moments with respect to the long molecular axis has been determined. It is found that the degrees of the polar and quadrupolar biasing increase with decrease in temperature and the azimuthal biasing angle for the chiral carbonyl group increases significantly with a reduction in temperature.

X-ray refraction effects: application to the imaging of biological tissues

The purpose of this study was to explore the potential of refraction contrast X-ray imaging of biological tissues. Images of dissected mouse lungs, heart, liver and legs were produced using the medical beamline at the Elettra Synchrotron at Trieste, Italy. The technique used was diffraction enhanced imaging. This utilizes a silicon crystal positioned between the tissue sample and the detector to separate refracted X-rays from transmitted and scattered radiation by Bragg diffraction. The contrast in the images produced is related to changes in the X-ray refractive index of the tissues, resulting in remarkable clarity compared with conventional X-ray images based on absorption effects. These changes were greatest at the boundaries between different tissues, giving a marked edge enhancement effect and three-dimensional appearance to the images. The technique provides a way of imaging a property of biological tissues not yet exploited, and further studies are planned to identify specific applications in medical imaging.

Diagnostic DNA testing for X-linked ocular albinism (OA1) with a hierarchical mutation screening protocol

Albinism is a group of inherited conditions in which affected individuals have less than normal pigment in the eyes, skin, and hair compared to others of the same race and ethnic background. The prevalence of all types of albinism in the United States is estimated at 1 in 20,000, based on poor epidemiological data. X-linked Nettleship-Falls ocular albinism (XLOA, OA1) affects approximately 1/150,000 males in the population. XLOA effects reduce visual acuity and nystagmus, result in a mild skin and hair phenotype, and occur mostly in XY males. Female carriers of XLOA have normal visual acuity, but often show iris punctate transillumination and a classic pattern of mosaic retinal pigmentation, coarse and grainy in the macula and becoming increasingly reticular into the periphery of the retinal pigment epithelium. Studies of OA1 have shown linkage of a single gene to markers at Xp22.3-p22.2. About 48% of the reported mutations in the OA1 gene are intragenic deletions and about 43% are point mutations. We present a hierarchical strategy for mutation screening for diagnostic testing for OA1 that comprises two tiers: first, multiplex PCR to detect intragenic deletions in the OA1 gene with denaturing high-performance liquid chromatography (dHPLC), and, second, heteroduplex analysis with dHPLC to scan for mutations, with subsequent sequencing of variants to confirm putative mutations in the OA1 gene. Prenatal diagnosis can be provided for families when the mutation has been firmly identified. We have validated this procedure with positive controls that were identified in patients by Southern blot, single-stranded conformation polymorphism (SSCP), and sequencing. In this hierarchical strategy, these procedures have an analytical sensitivity of > 99%.