CBP-HSF2 structural and functional interplay in Rubinstein-Taybi neurodevelopmental disorder

Patients carrying autosomal dominant mutations in the histone/lysine acetyl transferases CBP or EP300 develop a neurodevelopmental disorder: Rubinstein-Taybi syndrome (RSTS). The biological pathways underlying these neurodevelopmental defects remain elusive. Here, we unravel the contribution of a stress-responsive pathway to RSTS. We characterize the structural and functional interaction between CBP/EP300 and heat-shock factor 2 (HSF2), a tuner of brain cortical development and major player in prenatal stress responses in the neocortex: CBP/EP300 acetylates HSF2, leading to the stabilization of the HSF2 protein. Consequently, RSTS patient-derived primary cells show decreased levels of HSF2 and HSF2-dependent alteration in their repertoire of molecular chaperones and stress response. Moreover, we unravel a CBP/EP300-HSF2-N-cadherin cascade that is also active in neurodevelopmental contexts, and show that its deregulation disturbs neuroepithelial integrity in 2D and 3D organoid models of cerebral development, generated from RSTS patient-derived iPSC cells, providing a molecular reading key for this complex pathology.

Orofacial Myofunctional Therapy in Obstructive Sleep Apnea Syndrome: A Pathophysiological Perspective

Obstructive sleep apnea (OSA) syndrome is a multi-factorial disorder. Recently identified pathophysiological contributing factors include airway collapsibility, poor pharyngeal muscle responsiveness, a low arousal threshold, and a high loop gain. Understanding the pathophysiology is of pivotal importance to select the most effective treatment option. It is well documented that conventional treatments (continuous positive airway pressure (CPAP), upper airway surgery, and dental appliance) may not always be successful in the presence of non-anatomical traits, especially in mild to moderate OSA. Orofacial myofunctional therapy (OMT) consists of isotonic and isometric exercises targeted to oral and oropharyngeal structures, with the aim of increasing muscle tone, endurance, and coordinated movements of pharyngeal and peripharyngeal muscles. Recent studies have demonstrated the efficacy of OMT in reducing snoring, apnea-hypopnea index, and daytime sleepiness, and improving oxygen saturations and sleep quality. Myofunctional therapy helps to reposition the tongue, improve nasal breathing, and increase muscle tone in pediatric and adult OSA patients. Studies have shown that OMT prevents residual OSA in children after adenotonsillectomy and helps adherence in CPAP-treated OSA patients. Randomized multi-institutional studies will be necessary in the future to determine the effectiveness of OMT in a single or combined modality targeted approach in the treatment of OSA. In this narrative review, we present up-to-date literature data, focusing on the role of OSA pathophysiology concepts concerning pharyngeal anatomical collapsibility and muscle responsiveness, underlying the response to OMT in OSA patients.

Structural Impacts of Drug-Resistance Mutations Appearing in HIV-2 Protease

The use of antiretroviral drugs is accompanied by the emergence of HIV-2 resistances. Thus, it is important to elucidate the mechanisms of resistance to antiretroviral drugs. Here, we propose a structural analysis of 31 drug-resistant mutants of HIV-2 protease (PR2) that is an important target against HIV-2 infection. First, we modeled the structures of each mutant. We then located structural shifts putatively induced by mutations. Finally, we compared wild-type and mutant inhibitor-binding pockets and interfaces to explore the impacts of these induced structural deformations on these two regions. Our results showed that one mutation could induce large structural rearrangements in side-chain and backbone atoms of mutated residue, in its vicinity or further. Structural deformations observed in side-chain atoms are frequent and of greater magnitude, that confirms that to fight drug resistance, interactions with backbone atoms should be favored. We showed that these observed structural deformations modify the conformation, volume, and hydrophobicity of the binding pocket and the composition and size of the PR2 interface. These results suggest that resistance mutations could alter ligand binding by modifying pocket properties and PR2 stability by impacting its interface. Our results reinforce the understanding of the effects of mutations that occurred in PR2 and the different mechanisms of PR2 resistance.

Molecular Chirality in Classical Spacetime: Solving the Controversy about the Spinning Cone Model of Rotating Molecules

The spinning cone is a model of rotating molecules used by Barron in 1986 in relation to asymmetric synthesis and to parity violation. He considered that the non-translating cone spinning about its symmetry axis has false chirality (i.e., it is not chiral), whereas Mislow concluded in 1999 that it is indeed chiral and severely criticized the true versus false chirality nomenclature introduced by Barron, who still disagreed in 2013 with the conclusion of Mislow. Here, it is shown that this controversy comes from an ambiguity in the spinning cone model and that in fact both authors were right. Light is thrown on the true chirality versus false chirality controversy with a very recently published result, which was thus unavailable to both authors: this is a new definition of chirality that encompasses the one introduced by Lord Kelvin at the end of the 19th century.

Impacts of drug resistance mutations on the structural asymmetry of the HIV-2 protease

Background

Drug resistance is a severe problem in HIV treatment. HIV protease is a common target for the design of new drugs for treating HIV infection. Previous studies have shown that the crystallographic structures of the HIV-2 protease (PR2) in bound and unbound forms exhibit structural asymmetry that is important for ligand recognition and binding. Here, we investigated the effects of resistance mutations on the structural asymmetry of PR2. Due to the lack of structural data on PR2 mutants, the 3D structures of 30 PR2 mutants of interest have been modeled using an in silico protocol. Structural asymmetry analysis was carried out with an in-house structural-alphabet-based approach.

Results

The systematic comparison of the asymmetry of the wild-type structure and a large number of mutants highlighted crucial residues for PR2 structure and function. In addition, our results revealed structural changes induced by PR2 flexibility or resistance mutations. The analysis of the highlighted structural changes showed that some mutations alter protein stability or inhibitor binding.

Conclusions

This work consists of a structural analysis of the impact of a large number of PR2 resistant mutants based on modeled structures. It suggests three possible resistance mechanisms of PR2, in which structural changes induced by resistance mutations lead to modifications in the dimerization interface, ligand recognition or inhibitor binding.

0579 Non Intrusive and Unattended Sleep Analyzer Effectively Screens Patients Suspected of Sleep Apnea: A Comparison With Polysomnography

Introduction

Sleep Apnea Syndrome (SAS) is largely underdiagnosed due to the cost and availability of Polysomnography (PSG). We aimed at evaluating the diagnosis of SAS with the WITHINGS Sleep Apnea Detector (SAD), a non-intrusive pressure and sound sensor placed under the mattress.

Methods

118 patients (67 F, 49 years, BMI 33kg/m²) suspected of SAS had an in-laboratory PSG together with Sleep Apnea Detector. From the pressure signal, Sleep Apnea Detector derives respiratory and cardiac signals and movements. From the microphone, snoring and snorting are detected. These features are used to detect sleep periods with a Random Forest classifier and apnea and hypopnea events with a Convolutional Neural Network. The Total Sleep Time (TST) and Apnea Hypopnea Index (AHI) deduced (TSTsad, AHIsad) are compared with the PSG results scored according to AASM rules (TSTpsg, AHIpsg). AHI and TST were compared using bias and Mean Absolute Error (MAE). Sensitivity, specificity, likelihood ratios (LR) and AUROC were calculated for AHI thresholds of 15 and 30/hr.

Results

The average (SD) TSTpsg was 367 (61) minutes. Sleep Apnea Detector overestimated TST by 25 minutes, 7.0% of the average duration in the sample. The precision is acceptable, with a MAE=53 minutes. Average AHIpsg was 32.5 (30.1) and AHIsad 32.8 (29.9). The bias was 0.3 (95% CI [-2.7, 3.3]), MAE=10.3. The sensitivity (Se15) and specificity (Sp15) and their 95% confidence intervals were Se15=88.0% [79.0, 94.1] and Sp15=88.6% [73.3, 96.8]. Positive and negative LR were respectively LR+15=7.70 and LR-15=0.136. AUROC15=0.926. At the 30 threshold, Se30=86.0% [73.3, 94.2] and Sp30=91.2% [81.8, 96.7]. Positive and negative LR were LR+30=9.75 and LR-30=0.153. AUROC30=0.954.

Conclusion

Sleep Apnea Detector has excellent sensitivity and specificity, low bias and good precision. Thus it can be used as an unattended SAS screening device in patients likely to suffer from SAS.

Support

WITHINGS

CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity

BACKGROUND

Endocrine disrupting chemicals (EDCs) are xenobiotics that mimic the interaction of natural hormones and alter synthesis, transport, or metabolic pathways. The prospect of EDCs causing adverse health effects in humans and wildlife has led to the development of scientific and regulatory approaches for evaluating bioactivity. This need is being addressed using high-throughput screening (HTS) in vitro approaches and computational modeling.

OBJECTIVES

In support of the Endocrine Disruptor Screening Program, the U.S. Environmental Protection Agency (EPA) led two worldwide consortiums to virtually screen chemicals for their potential estrogenic and androgenic activities. Here, we describe the Collaborative Modeling Project for Androgen Receptor Activity (CoMPARA) efforts, which follows the steps of the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP).

METHODS

The CoMPARA list of screened chemicals built on CERAPP's list of 32,464 chemicals to include additional chemicals of interest, as well as simulated ToxCast™ metabolites, totaling 55,450 chemical structures. Computational toxicology scientists from 25 international groups contributed 91 predictive models for binding, agonist, and antagonist activity predictions. Models were underpinned by a common training set of 1,746 chemicals compiled from a combined data set of 11 ToxCast™/Tox21 HTS in vitro assays.

RESULTS

The resulting models were evaluated using curated literature data extracted from different sources. To overcome the limitations of single-model approaches, CoMPARA predictions were combined into consensus models that provided averaged predictive accuracy of approximately 80% for the evaluation set.

DISCUSSION

The strengths and limitations of the consensus predictions were discussed with example chemicals; then, the models were implemented into the free and open-source OPERA application to enable screening of new chemicals with a defined applicability domain and accuracy assessment. This implementation was used to screen the entire EPA DSSTox database of ∼875,000 chemicals, and their predicted AR activities have been made available on the EPA CompTox Chemicals dashboard and National Toxicology Program's Integrated Chemical Environment. https://doi.org/10.1289/EHP5580.

CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity

BACKGROUND

Endocrine disrupting chemicals (EDCs) are xenobiotics that mimic the interaction of natural hormones and alter synthesis, transport, or metabolic pathways. The prospect of EDCs causing adverse health effects in humans and wildlife has led to the development of scientific and regulatory approaches for evaluating bioactivity. This need is being addressed using high-throughput screening (HTS) in vitro approaches and computational modeling.

OBJECTIVES

In support of the Endocrine Disruptor Screening Program, the U.S. Environmental Protection Agency (EPA) led two worldwide consortiums to virtually screen chemicals for their potential estrogenic and androgenic activities. Here, we describe the Collaborative Modeling Project for Androgen Receptor Activity (CoMPARA) efforts, which follows the steps of the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP).

METHODS

The CoMPARA list of screened chemicals built on CERAPP's list of 32,464 chemicals to include additional chemicals of interest, as well as simulated ToxCast™ metabolites, totaling 55,450 chemical structures. Computational toxicology scientists from 25 international groups contributed 91 predictive models for binding, agonist, and antagonist activity predictions. Models were underpinned by a common training set of 1,746 chemicals compiled from a combined data set of 11 ToxCast™/Tox21 HTS in vitro assays.

RESULTS

The resulting models were evaluated using curated literature data extracted from different sources. To overcome the limitations of single-model approaches, CoMPARA predictions were combined into consensus models that provided averaged predictive accuracy of approximately 80% for the evaluation set.

DISCUSSION

The strengths and limitations of the consensus predictions were discussed with example chemicals; then, the models were implemented into the free and open-source OPERA application to enable screening of new chemicals with a defined applicability domain and accuracy assessment. This implementation was used to screen the entire EPA DSSTox database of ∼ 875,000 chemicals, and their predicted AR activities have been made available on the EPA CompTox Chemicals dashboard and National Toxicology Program's Integrated Chemical Environment. https://doi.org/10.1289/EHP5580.

New physiological bench test reproducing nocturnal breathing pattern of patients with sleep disordered breathing

Previous studies have shown that Automatic Positive Airway Pressure devices display different behaviors when connected to a bench using theoretical respiratory cycle scripts. However, these scripts are limited and do not simulate physiological behavior during the night. Our aim was to develop a physiological bench that is able to simulate patient breathing airflow by integrating polygraph data. We developed an algorithm analyzing polygraph data and transformed this information into digital inputs required by the bench hardware to reproduce a patient breathing profile on bench. The inputs are respectively the simulated respiratory muscular effort pressure input for an artificial lung and the sealed chamber pressure to regulate the Starling resistor. We did simulations on our bench for a total of 8 hours and 59 minutes for a breathing profile from the demonstration recording of a Nox T3 Sleep Monitor. The simulation performance results showed that in terms of relative peak-valley amplitude of each breathing cycle, simulated bench airflow was biased by only 1.48% ± 6.80% compared to estimated polygraph nasal airflow for a total of 6,479 breathing cycles. For total respiratory cycle time, the average bias ± one standard deviation was 0.000 ± 0.288 seconds. For patient apnea events, our bench simulation had a sensitivity of 84.7% and a positive predictive value equal to 90.3%, considering 149 apneas detected both in polygraph nasal simulated bench airflows. Our new physiological bench would allow personalizing APAP device selection to each patient by taking into account individual characteristics of a sleep breathing profile.

High Impact: The Role of Promiscuous Binding Sites in Polypharmacology

The literature focuses on drug promiscuity, which is a drug’s ability to bind to several targets, because it plays an essential role in polypharmacology. However, little work has been completed regarding binding site promiscuity, even though its properties are now recognized among the key factors that impact drug promiscuity. Here, we quantified and characterized the promiscuity of druggable binding sites from protein-ligand complexes in the high quality Mother Of All Databases while using statistical methods. Most of the sites (80%) exhibited promiscuity, irrespective of the protein class. Nearly half were highly promiscuous and able to interact with various types of ligands. The corresponding pockets were rather large and hydrophobic, with high sulfur atom and aliphatic residue frequencies, but few side chain atoms. Consequently, their interacting ligands can be large, rigid, and weakly hydrophilic. The selective sites that interacted with one ligand type presented less favorable pocket properties for establishing ligand contacts. Thus, their ligands were highly adaptable, small, and hydrophilic. In the dataset, the promiscuity of the site rather than the drug mainly explains the multiple interactions between the drug and target, as most ligand types are dedicated to one site. This underlines the essential contribution of binding site promiscuity to drug promiscuity between different protein classes.

Gait Monitoring and Walk Distance Estimation With an Accelerometer During 6-Minute Walk Test

BACKGROUND

The 6-min walk test (6MWT) encompasses potential and untapped information related to exercise capacity. However, this test does not yield any information about gait pattern. Recently, we used a ventilatory polygraph to reveal respiratory adaptation during the 6MWT with subjects having high or low body mass index (BMI). In this study, we aimed to determine gait parameters with the same device, which integrates an accelerometer.

METHODS

Using a 30-m corridor, steps and U-turns were detected with a custom-made algorithm, compared to video recordings as a reference method, and analyzed offline. From the vertical acceleration signal, we were able to determine cadence and step length, and we could calculate the total distance covered in 6 min (6MWD). We then compared these variables between subjects with low BMI (n = 13 subjects) or high BMI (n = 29 subjects).

RESULTS

Steps and U-turn detection correlated with video results (r = 0.99, P < .001 for both). The 6MWD calculation was also in line with classical measurements (r = 0.99, P < .001). High BMI subjects had a significantly lower 6MWD, cadence, and step length than controls (P < .001 for each). Walking speed was more closely correlated with step length (r = 0.92) than with cadence (r = 0.64) for both groups.

CONCLUSION

Our results demonstrated that a ventilatory polygraph with an embedded accelerometer can be used to detect steps and U-turns, and to calculate 6MWD. This method is sufficiently sensitive to characterize significant BMI-dependent differences in gait pattern during a 6MWT and appears to be a promising tool for routine clinical use.

Statistical Profiling of One Promiscuous Protein Binding Site: Illustrated by Urokinase Catalytic Domain

While recent literature focuses on drug promiscuity, the characterization of promiscuous binding sites (ability to bind several ligands) remains to be explored. Here, we present a proteochemometric modeling approach to analyze diverse ligands and corresponding multiple binding sub-pockets associated with one promiscuous binding site to characterize protein-ligand recognition. We analyze both geometrical and physicochemical profile correspondences. This approach was applied to examine the well-studied druggable urokinase catalytic domain inhibitor binding site, which results in a large number of complex structures bound to various ligands. This approach emphasizes the importance of jointly characterizing pocket and ligand spaces to explore the impact of ligand diversity on sub-pocket properties and to establish their main profile correspondences. This work supports an interest in mining available 3D holo structures associated with a promiscuous binding site to explore its main protein-ligand recognition tendency.

The Cytochrome P450 3A4 has three Major Conformations: New Clues to Drug Recognition by this Promiscuous Enzyme

We computed the channels of the 3A4 isoform of the cytochrome P450 3A4 (CYP) on the basis of 24 crystal structures extracted from the Protein Data Bank (PDB). We identified three major conformations (denoted C, O1 and O2) using an enhanced version of the CCCPP software that we developed for the present work, while only two conformations (C and O² ) are considered in the literature. We established the flowchart of definition of these three conformations in function of the structural and physicochemical parameters of the ligand. The channels are characterized with qualitative and quantitative parameters, and not only with their surrounding secondary structures as it is usually done in the literature.

Cavity Versus Ligand Shape Descriptors: Application to Urokinase Binding Pockets

We analyzed 78 binding pockets of the human urokinase plasminogen activator (uPA) catalytic domain extracted from a data set of crystallized uPA-ligand complexes. These binding pockets were computed with an original geometric method that does NOT involve any arbitrary parameter, such as cutoff distances, angles, and so on. We measured the deviation from convexity of each pocket shape with the pocket convexity index (PCI). We defined a new pocket descriptor called distributional sphericity coefficient (DISC), which indicates to which extent the protein atoms of a given pocket lie on the surface of a sphere. The DISC values were computed with the freeware PCI. The pocket descriptors and their high correspondences with ligand descriptors are crucial for polypharmacology prediction. We found that the protein heavy atoms lining the urokinases binding pockets are either located on the surface of their convex hull or lie close to this surface. We also found that the radii of the urokinases binding pockets and the radii of their ligands are highly correlated (r = 0.9).

A Fast Algorithm to Compute Conical Pockets in Proteins. Application to the Structural Characterization of γ-Carbonic Anhydrases

Some major proteins families, such as carbonic anhydrases (CAs), have a conical cavity at the active site. No algorithm was available to compute conical cavities, so we needed to design one. The fast algorithm we designed let us show on a set of 717 CAs extracted from the PDB database that γ-CAs are characterized by active site cavity cone angles significantly larger than those of α-CAs and β-CAs: the generatrix-axis angles are greater than 60° for the γ-CAs while they are smaller than 50° for the other CAs. Free binaries of the CONICA software implementing the algorithm are available through a software repository at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html.

Short-term effect of volume recruitment-derecruitment manoeuvre on chest-wall motion in Duchenne muscular dystrophy

Because progressive respiratory muscle weakness leads to decreased chest-wall motion with eventual ribcage stiffening, the purpose was to compare vital capacity (VC) and contributions of chest-wall compartments before and after volume recruitment-derecruitment manoeuvres (VRDM) in Duchenne muscular dystrophy (DMD). We studied nine patients with DMD and VC lower than 30% of predicted. VRDM was performed using 15 insufflations-exsufflations of +30 to -30 cmH₂O. VC and three-dimensional chest-wall motion were measured, as well as oxygen saturation, transcutaneous partial pressure of carbon dioxide and the rapid shallow breathing index (respiratory rate/tidal volume) before (baseline) and immediately and 1 hour after VRDM. VC increased significantly immediately after VRDM (108% ± 7% of baseline, p = 0.018) but returned to baseline within 1 hour, and the rapid shallow breathing index increased significantly. The non-dominant side systematically increased immediately after VRDM ( p = 0.0077), and in the six patients with abnormal breathing asymmetry (difference >10% of VC) at baseline, this asymmetry was corrected immediately and/or 1 hour after VRDM. VRDM improved VC and reduced chest-wall motion asymmetry, but this beneficial effect waned rapidly with respiratory muscle fatigue, suggesting that VRDM may need to be repeated during the day to produce lasting benefits.

New Respiratory Inductive Plethysmography (RIP) Method for Evaluating Ventilatory Adaptation during Mild Physical Activities

The pneumotachometer is currently the most accepted device to measure tidal breathing, however, it requires the use of a mouthpiece and thus alteration of spontaneous ventilation is implied. Respiratory inductive plethysmography (RIP), which includes two belts, one thoracic and one abdominal, is able to determine spontaneous tidal breathing without the use of a facemask or mouthpiece, however, there are a number of as yet unresolved issues. In this study we aimed to describe and validate a new RIP method, relying on a combination of thoracic RIP and nasal pressure signals taking into account that exercise-induced body movements can easily contaminate RIP thoracic signals by generating tissue motion artifacts. A custom-made time domain algorithm that relies on the elimination of low amplitude artifacts was applied to the raw thoracic RIP signal. Determining this tidal ventilation allowed comparisons between the RIP signal and simultaneously-recorded airflow signals from a calibrated pneumotachometer (PT). We assessed 206 comparisons from 30 volunteers who were asked to breathe spontaneously at rest and during walking on the spot. Comparisons between RIP signals processed by our algorithm and PT showed highly significant correlations for tidal volume (Vt), inspiratory (Ti) and expiratory times (Te). Moreover, bias calculated using the Bland and Altman method were reasonably low for Vt and Ti (0.04 L and 0.02 s, respectively), and acceptable for Te (<0.1 s) and the intercept from regression relationships (0.01 L, 0.06 s, 0.17 s respectively). The Ti/Ttot and Vt/Ti ratios obtained with the two methods were also statistically correlated. We conclude that our methodology (filtering by our algorithm and calibrating with our calibration procedure) for thoracic RIP renders this technique sufficiently accurate to evaluate tidal ventilation variation at rest and during mild to moderate physical activity.

Body Mass Index-Dependent Ventilatory Parameters From Respiratory Inductive Plethysmography During 6-Minute Walk Test

BACKGROUND

Walking is part of obesity management. Assessment of ventilatory impairments and consequences for gait induced by obesity could be clinically helpful. We aimed to develop a method to accurately monitor ventilation with respiratory inductive plethysmography (RIP) in subjects with high body mass indices (BMIs) during a 6-min walk test (6MWT).

METHODS

25 volunteers were divided into 2 groups based on BMI (<25 or >30 kg/m2) and performed a 6MWT with a calibrated RIP. Ventilatory parameters (tidal volume [V(T)], inspiratory [T(I)] and expiratory [T(E)] times, V(T)/T(I) ratio, and T(I)/Ttot ratio) were determined after processing RIP signals with a custom-made algorithm designed to discriminate tissue motion artifacts and respiratory cycles in the time domain. Six-min walk distance and average speed by minute were collected.

RESULTS

The number of artifacts removed by the algorithm used for artifact removal was higher for high-BMI subjects and was correlated to their individual values (r = 0.66, P < .001). Six-min walk distance was lower for the group with a higher BMI (P = .001). ANOVA revealed effects of exercise for V(T), T(I), and T(E) (P < .001) and also BMI effects in the course of the 6MWT for V(T), T(I), T(E), V(T)/T(I), and T(I)/Ttot (P < .001 for each of them).

CONCLUSIONS

This respiratory monitoring method is sufficiently sensitive to point out differences between rest and exercise as well as locomotor and ventilatory differences relative to BMI during the 6MWT. Thus, this system gives useful information from the 6MWT for clinicians who want to assess respiratory patterns of patients during this commonly used test.

PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins

Predicting protein pocket's ability to bind drug-like molecules with high affinity, i.e. druggability, is of major interest in the target identification phase of drug discovery. Therefore, pocket druggability investigations represent a key step of compound clinical progression projects. Currently computational druggability prediction models are attached to one unique pocket estimation method despite pocket estimation uncertainties. In this paper, we propose ‘PockDrug-Server’ to predict pocket druggability, efficient on both (i) estimated pockets guided by the ligand proximity (extracted by proximity to a ligand from a holo protein structure) and (ii) estimated pockets based solely on protein structure information (based on amino atoms that form the surface of potential binding cavities). PockDrug-Server provides consistent druggability results using different pocket estimation methods. It is robust with respect to pocket boundary and estimation uncertainties, thus efficient using apo pockets that are challenging to estimate. It clearly distinguishes druggable from less druggable pockets using different estimation methods and outperformed recent druggability models for apo pockets. It can be carried out from one or a set of apo/holo proteins using different pocket estimation methods proposed by our web server or from any pocket previously estimated by the user. PockDrug-Server is publicly available at: http://pockdrug.rpbs.univ-paris-diderot.fr.

Postural- and respiratory-related activities of abdominal muscles during post-exercise hyperventilation

The present study focuses on the role of superficial abdominal muscles revealed by electromyographic recordings during the maintenance of a bipedal stance perturbed by post-exercise hyperventilation. Twelve healthy subjects performed six 30-s postural tests: one pre-exercise test while breathing quietly, then one test every minute for the 5 min immediately following a maximum-intensity, incremental cycling exercise test. Displacement of the centre of pressure in the sagittal plane was monitored over time. Myoelectric activities of the obliquus externus (OE), obliquus internus (OI) and rectus abdominis (RA) muscles were recorded by surface electromyography (EMG). Metabolic parameters were measured with a portable telemetric device. The change in ventilatory drive induced by exercise was accompanied by a significant increase in both postural sway parameters and EMG activities. For OE and OI, the increased EMG activities were prominent during expiration, whereas OI was silent during inspiration. OE and RA were activated during both expiration and inspiration. It is concluded that the compensation of respiratory disturbances of the erect posture appears to be less effective when minute ventilation increases. The patterns of muscle activity suggest that abdominal muscles are controlled differentially and that their functional coordination is dependent on the respiratory demand.

Synthetic lethals in HIV: ways to avoid drug resistance : Running title: Preventing HIV resistance

Background

RNA viruses rapidly accumulate genetic variation, which can give rise to synthetic lethal (SL) and deleterious (SD) mutations. Synthetic lethal mutations (non-lethal when alone but lethal when combined in one genome) have been studied to develop cancer therapies. This principle can also be used against fast-evolving RNA-viruses. Indeed, targeting protein sites involved in SD + SL interactions with a drug would render any mutation of such sites, lethal.

Results

Here, we set up a strategy to detect intragenic pairs of SL and SD at the surface of the protein to predict less escapable drug target sites. For this, we detected SD + SL, studying HIV protease (PR) and reverse transcriptase (RT) sequence alignments from two groups of VIH⁺ individuals: treated with drugs (T) or not (NT). Using a series of statistical approaches, we were able to propose bona fide SD + SL couples. When focusing on spatially close co-variant SD + SL couples at the surface of the protein, we found 5 SD + SL groups (2 in the protease and 3 in the reverse transcriptase), which could be good candidates to form pockets to accommodate potential drugs.

Conclusions

Thus, designing drugs targeting these specific SD + SL groups would not allow the virus to mutate any residue involved in such groups without losing an essential function. Moreover, we also show that the selection pressure induced by the treatment leads to the appearance of new mutations, which change the mutational landscape of the protein. This drives the existence of differential SD + SL couples between the drug-treated and non-treated groups. Thus, new anti-viral drugs should be designed differently to target such groups.

Reviewers

This article was reviewed by Neil Greenspan Csaba Pal and István Simon.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-015-0044-y) contains supplementary material, which is available to authorized users.

PockDrug: A Model for Predicting Pocket Druggability That Overcomes Pocket Estimation Uncertainties

Predicting protein druggability is a key interest in the target identification phase of drug discovery. Here, we assess the pocket estimation methods' influence on druggability predictions by comparing statistical models constructed from pockets estimated using different pocket estimation methods: a proximity of either 4 or 5.5 Å to a cocrystallized ligand or DoGSite and fpocket estimation methods. We developed PockDrug, a robust pocket druggability model that copes with uncertainties in pocket boundaries. It is based on a linear discriminant analysis from a pool of 52 descriptors combined with a selection of the most stable and efficient models using different pocket estimation methods. PockDrug retains the best combinations of three pocket properties which impact druggability: geometry, hydrophobicity, and aromaticity. It results in an average accuracy of 87.9% ± 4.7% using a test set and exhibits higher accuracy (∼5-10%) than previous studies that used an identical apo set. In conclusion, this study confirms the influence of pocket estimation on pocket druggability prediction and proposes PockDrug as a new model that overcomes pocket estimation variability.

Achilles tendon vibration-induced changes in plantar flexor corticospinal excitability

Daily Achilles tendon vibration has been shown to increase muscle force, likely via corticospinal neural adaptations. The aim of the present study was to determine the extent by which corticospinal excitability is influenced during direct Achilles tendon vibration. Motor-evoked potentials (MEPs) were elicited in the soleus (SOL), gastrocnemius medialis (GM) and tibialis anterior (TA) by transcranial magnetic stimulation of the motor cortical area of the leg with and without Achilles tendon vibration at various frequencies (50, 80 and 110 Hz). Contralateral homologues were also investigated. SOL and GM MEP amplitude significantly increased by 226 ± 188 and 66 ± 39%, respectively, during Achilles tendon vibration, without any difference between the tested frequencies. No MEP changes were reported for TA or contralateral homologues. Increased SOL and GM MEP amplitude suggests increased vibration-induced corticospinal excitability independent of vibration frequency.

VIRAPOPS2 supports the influenza virus reassortments

BACKGROUND

For over 400 years, due to the reassortment of their segmented genomes, influenza viruses evolve extremely quickly and cause devastating epidemics. This reassortment arises because two flu viruses can infect the same cell and therefore the new virions' genomes will be composed of segment reassortments of the two parental strains. A treatment developed against parents could then be ineffective if the virions' genomes are different enough from their parent's genomes. It is therefore essential to simulate such reassortment phenomena to assess the risk of apparition of new flu strain.

FINDINGS

So we decided to upgrade the forward simulator VIRAPOPS, containing already the necessary options to handle non-segmented viral populations. This new version can mimic single or successive reassortments, in birds, humans and/or swines. Other options such as the ability to treat populations of positive or negative sense viral RNAs, were also added. Finally, we propose output options giving statistics of the results.

CONCLUSION

In this paper we present a new version of VIRAPOPS which now manages the viral segment reassortments and the negative sense single strain RNA viruses, these two issues being the cause of serious public health problems.

A murine model of cervical spinal cord injury to study post-lesional respiratory neuroplasticity

A cervical spinal cord injury induces permanent paralysis, and often leads to respiratory distress. To date, no efficient therapeutics have been developed to improve/ameliorate the respiratory failure following high cervical spinal cord injury (SCI). Here we propose a murine pre-clinical model of high SCI at the cervical 2 (C2) metameric level to study diverse post-lesional respiratory neuroplasticity. The technique consists of a surgical partial injury at the C2 level, which will induce a hemiparalysis of the diaphragm due to a deafferentation of the phrenic motoneurons from the respiratory centers located in the brainstem. The contralateral side of the injury remains intact and allows the animal recovery. Unlike other SCIs which affect the locomotor function (at the thoracic and lumbar level), the respiratory function does not require animal motivation and the quantification of the deficit/recovery can be easily performed (diaphragm and phrenic nerve recordings, whole body ventilation). This pre-clinical C2 SCI model is a powerful, useful, and reliable pre-clinical model to study various respiratory and non-respiratory neuroplasticity events at different levels (molecular to physiology) and to test diverse putative therapeutic strategies which might improve the respiration in SCI patients.

VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations

SUMMARY

Daily, mutability and recombination of RNA viruses result in the production of million variants. All these rapid genomic changes directly influence the functional sites of the protein, its 3D structure or its drug resistances. Therefore, it is important to simulate these drastic switches to determine their effects on virus populations. Many computer programs are able to simulate specific variations in DNA genomes, but are generally non-adapted to RNA viruses. They simulate site-specific selection pressures, but rarely pressures on covariant or on higher order correlated sites and no at all on synthetic lethal groups. That is why we felt it important to create VIRAPOPS, a forward simulator that models specific RNA virus functions. It was designed for computational biologists, biologists and virologists.

AVAILABILITY AND IMPLEMENTATION

Free binaries are available through a software repository at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html.

Transcranial direct-current stimulation reduced the excitability of diaphragmatic corticospinal pathways whatever the polarity used

We investigated effects of transcranial direct-current stimulation (tDCS) on the diaphragmatic corticospinal pathways in healthy human. Anodal, cathodal, and sham tDCS were randomly applied upon the left diaphragmatic motor cortex in twelve healthy right-handed men. Corticospinal pathways excitability was assessed by means of transcranial magnetic stimulation (TMS) elicited motor-evoked-potential (MEP). For each tDCS condition, MEPs were recorded before (Pre) tDCS then after 10 min (Post1, at tDCS discontinuation in the anodal and cathodal sessions) and 20 min (Post2). As result, both anodal and cathodal tDCS significantly decreased MEP amplitude of the right hemidiaphragm at both Post1 and Post2, versus Pre. MEP amplitude was unchanged versus Pre during the sham condition. The effects of cathodal and anodal tDCS applied to the diaphragm motor cortex differ from those observed during tDCS of the limb motor cortex. These differences may be related to specific characteristics of the diaphragmatic corticospinal pathways as well as to the diaphragm's functional peculiarities compared with the limb muscles.

Acute effects of Achilles tendon vibration on soleus and tibialis anterior spinal and cortical excitability

Prolonged vibration is known to alter muscle performance. Attenuation of Ia afferent efficacy is the main mechanism suggested. However, changes in motor cortex excitability could also be hypothesized. The purpose of the present study was therefore to analyze the acute and outlasting effects of 1 h of Achilles tendon vibration (frequency, 50 Hz) on the soleus (SOL) and tibialis anterior (TA) neuromuscular excitability. Spinal excitability was investigated by means of H-reflexes and F-waves while cortical excitability was characterized by motor evoked potentials (MEPs) obtained by transcranial magnetic stimulation. Twelve subjects performed the experimental procedures 3 times: at the beginning of the testing session (PRE), immediately after 1 h of Achilles tendon vibration (POST), and 1 h after the end of vibration (POST-1H). Prolonged vibration led to acute reduced H-reflex amplitudes for SOL only (46.9% ± 7.7% vs. 32.8% ± 7%; p = 0.006). Mainly presynaptic inhibition mechanisms were thought to be involved because of unchanged F-wave persistence and amplitude mean values, suggesting unaffected motoneuronal excitability. While no acute effects were reported for SOL and TA cortical excitability, both muscles were characterized by an outlasting increase in their MEP amplitude (0.64 ± 0.2 mV vs. 0.43 ± 0.18 mV and 2.17 ± 0.56 mV vs. 1.26 ± 0.36 mV, respectively; p < 0.05). The high modulation of Ia afferent input by vibration led to changes in motor cortex excitability that could contribute to the enhancement in muscular activation capacities reported after chronic use of tendon vibration.