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.

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.

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.

Comment on "Bad Language": Resolving some Ambiguities about Chirality.

In this comment on the Essay entitled "Bad Language" by Dunitz I add new elements which enlighten the discussion. I hope that they contribute to suppress ambiguities and preconceived ideas about chirality.

Four Major Channels Detected in the Cytochrome P450 3A4: A Step toward Understanding Its Multispecificity.

We computed the network of channels of the 3A4 isoform of the cytochrome P450 (CYP) on the basis of 16 crystal structures extracted from the Protein Data Bank (PDB). The calculations were performed with version 2 of the CCCPP software that we developed for this research project. We identified the minimal cost paths (MCPs) output by CCCPP as probable ways to access to the buried active site. The algorithm of calculation of the MCPs is presented in this paper, with its original method of visualization of the channels. We found that these MCPs constitute four major channels in CYP3A4. Among the many channels proposed by Cojocaru et al. in 2007, we found that only four of them open in 3A4. We provide a refined description of these channels together with associated quantitative data.

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.

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.

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.

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.

Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models.

MOTIVATION: Identifying protein cavities, channels and pockets accessible to ligands is a major step to predict potential protein-ligands complexes. It is also essential for preparation of protein-ligand docking experiments in the context of enzymatic activity mechanism and structure-based drug design. RESULTS: We introduce a new method, implemented in a program named CCCPP, which computes the void parts of the proteins, i.e. cavities, channels and pockets. The present approach is a variant of the alpha shapes method, with the advantage of taking into account the size and the shape of the ligand. We show that the widely used spherical model of ligands is most of the time inadequate and that cylindrical shapes are more realistic. The analysis of the void parts of the protein is done via a network of channels depending on the ligand. The performance of CCCPP is tested with known substrates of cytochromes P450 (CYP) 1A2 and 3A4 involved in xenobiotics metabolism. The test results indicate that CCCPP is able to find pathways to the buried heminic P450 active site even for high molecular weight CYP 3A4 substrates such as two ketoconazoles together, an experimentally observed situation. AVAILABILITY: Free binaries are available through a software repository at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html CONTACT: michel.petitjean@univ-paris-diderot.fr.

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.

Modulation of soleus corticospinal excitability during Achilles tendon vibration.

Soleus (SOL) corticospinal excitability has been reported to increase during Achilles tendon vibration. The aim of the present study was to further investigate SOL corticospinal excitability and elucidate the changes to intracortical mechanisms during Achilles tendon vibration. Motor-evoked potentials (MEPs) were elicited in the SOL by transcranial magnetic stimulation (TMS) of the corresponding motor cortical area of the leg with and without 50-Hz Achilles tendon vibration. SOL input-output curves were determined. Paired-pulse protocols were also performed to investigate short-interval intracortical inhibition (SICI) and intracortical facilitation (ICF) by conditioning test TMS pulses with sub-threshold TMS pulses at inter-stimulus intervals of 3 and 13 ms, respectively. During Achilles tendon vibration, motor threshold was lower than in the control condition (43 ± 13 vs. 49 ± 11 % of maximal stimulator output; p = 0.008). Input-output curves were also influenced by vibration, i.e. there was increased maximal MEP amplitude (0.694 ± 0.347 vs. 0.268 ± 0.167 mV; p < 0.001), decreased TMS intensity to elicit a MEP of half the maximal MEP amplitude (100 ± 13 vs. 109 ± 9 % motor threshold; p = 0.009) and a strong tendency for decreased slope constant (0.076 ± 0.04 vs. 0.117 ± 0.04; p = 0.068). Vibration reduced ICF (98 ± 61 vs. 170 ± 105 % of test MEP amplitude; p = 0.05), but had no effect on SICI (53 ± 26 vs. 48 ± 22 % of test MEP amplitude; p = 0.68). The present results further document the increased vibration-induced corticospinal excitability in the soleus muscle and suggest that this increase is not mediated by changes in SICI or ICF.

Control of peptide nanotube diameter by chemical modifications of an aromatic residue involved in a single close contact.

Supramolecular self-assembly is an attractive pathway for bottom-up synthesis of novel nanomaterials. In particular, this approach allows the spontaneous formation of structures of well-defined shapes and monodisperse characteristic sizes. Because nanotechnology mainly relies on size-dependent physical phenomena, the control of monodispersity is required, but the possibility of tuning the size is also essential. For self-assembling systems, shape, size, and monodispersity are mainly settled by the chemical structure of the building block. Attempts to change the size notably by chemical modification usually end up with the loss of self-assembly. Here, we generated a library of 17 peptides forming nanotubes of monodisperse diameter ranging from 10 to 36 nm. A structural model taking into account close contacts explains how a modification of a few Å of a single aromatic residue induces a fourfold increase in nanotube diameter. The application of such a strategy is demonstrated by the formation of silica nanotubes of various diameters.

Isokinetic testing of evertor and invertor muscles in patients with chronic ankle instability.

Ankle sprains are among the most common sport-related injuries and can lead to chronic ankle instability. Impaired sensorimotor function of the ankle musculature is often suggested as a cause. The current study sought to assess and compare the isokinetic performance and electromyographic patterns of evertor and invertor muscles in patients with chronic ankle instability and in a control group. Twelve patients with chronic ankle instability and twelve healthy subjects were included. Isokinetic eccentric and concentric testing at various angular velocities was performed for eversion and inversion movements. The corresponding myoelectric activities of the fibularis longus and tibialis anterior muscles were quantified from surface electromyographic recordings by computing average root mean square values. Patients had lower myoelectric activity of the evertor and invertor muscles than controls did; this difference could account for the eccentric weakness associated with ankle instability. Functional strength ratios revealed a dynamic strength imbalance in unstable ankle patients and that may contribute to recurrent injury. Our findings suggest that rehabilitation programs for unstable ankle patients must be focused on the motor control of eccentric contractions of the ankle evertors and invertors, to boost these muscles' contribution to ankle stabilization.

Postural control and ventilatory drive during voluntary hyperventilation and carbon dioxide rebreathing.

The present study sought to establish links between hyperventilation and postural stability. Eight university students were asked to stand upright under two hyperventilation conditions applied randomly: (1) a metabolic hyperventilation induced by 5 min of hypercapnic-hyperoxic rebreathing (CO(2)-R); and, (2) a voluntary hyperventilation (VH) of 3 min imposed by a metronome set at 25 cycles per min. Recordings were obtained with eyes open, with the subjects standing on a force plate over 20-s periods. Ventilatory response, displacements in the centre of pressure in both the frontal and sagittal planes and fluctuations in the three planes of the ground reaction force were monitored in the time and frequency domains. Postural changes related to respiratory variations were quantified by coherence analysis. Myoelectric activities of the calf muscles were recorded using surface electromyography. Force plate measurements revealed a reduction in postural stability during both CO(2)-R and VH conditions, mainly in the sagittal plane. Coherence analysis provided evidence of a ventilatory origin in the vertical ground reaction force fluctuations during VH. Electromyographic analyses showed different leg muscles strategies, assuming the existence of links between the control of respiration and the control of posture. Our results suggest that the greater disturbing effects caused by voluntary hyperventilation on body balance are more compensated when respiration is under automatic control. These findings may have implications for understanding the organisation of postural and respiratory activities and suggest that stability of the body may be compromised in situations in which respiratory demand increases and requires voluntary control.

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.

High frequency repetitive Transcranial Magnetic Stimulation promotes long lasting phrenic motoneuron excitability via GABAergic networks.

Repetitive transcranial magnetic stimulation (rTMS) is a promising, innovative, and non-invasive therapy used clinically. Efficacy of rTMS has been demonstrated to ameliorate psychiatric disorders and neuropathic pain through neuromodulation of affected neural circuits. However, little is known about the mechanisms and the specific neural circuits via which rTMS facilitates these functional effects. The aim of this study was to begin revealing the mechanisms by which rTMS may tap into existing neural circuits, by using a well characterized spinal motor circuit - the phrenic circuit. Here we hypothesized that rTMS can be used to enhance phrenic motoneuron excitability in anesthetized Sprague Dawley rats. Multiple acute rTMS protocols were used revealing 10 Hz rTMS protocol induced a robust, long-lasting increase in phrenic motoneuron excitability, functionally evaluated by diaphragm motor evoked potentials (59.1 ± 21.1 % of increase compared to baseline 60 min after 10 Hz protocol against 6.0 ± 5.8 % (p = 0.007) for Time Control, -5.8 ± 7.4 % (p < 0.001) for 3 Hz, and 5.2 ± 12.5 % (p = 0.008) for 30 Hz protocols). A deeper analyze allowed to discriminate "responder" and "non-responder" subgroups among 10 Hz rTMS treated animals. Intravenous injections of GABAA and GABAB receptor agonists prior to 10 Hz rTMS treatment, abolished the enhanced phrenic motoneuron excitability, suggesting GABAergic input plays a mechanistic role in rTMS-induced phrenic excitability. These data demonstrate that a single high frequency rTMS protocol at 10 Hz increases phrenic motoneuron excitability, mediated by a local GABAergic "disinhibition". By understanding how rTMS can be used to affect neural circuits non-invasively we can begin to harness the therapeutic potential of this neuromodulatory strategy to promote recovery after disease or injury to the central nervous system.

Effect of transcranial magnetic stimulation on four types of pressure-programmable valves.

BACKGROUND: Exposure to powerful magnetic fields may alter the settings of programmable ventriculoperitoneal shunt valves or even cause permanent damage to these devices. Transcranial magnetic stimulation (TMS) and magnetic resonance imaging both generate a high-intensity, focal magnetic field. To the best of our knowledge, there is no literature data on the compatibility of TMS with neurosurgical implants. The aim of the present in vitro study was to investigate the effects of TMS on four types of pressure-programmable valves (the Strata 2 from Medtronic, the Polaris from Sophysa, the ProGAV from Miethke, and a cylindrical valve from Codman-Hakim). METHODS: We used a Magpro X100 stimulator (Medtronic) for monophasic or biphasic TMS via a circular or a figure-of-eight coil. Each valve setting was tested before and after exposure to TMS. Experiment 1: The effect of the coil-valve distance (10, 5, 2.5, and 1 cm) was assessed. Experiment 2: We mimicked in situ stimulation with a human mannequin by placing the valve in a retroauricular position, the TMS circular coil on the apex, and figure-of-eight coil centered over the primary motor area site. Temperature changes were monitored throughout the experiments. Experience 3: TMS-induced valve movements were assessed by using an in-house accelerometric setup. RESULTS: Our results primarily demonstrated that the Strata 2 and Codman-Hakim valves' settings were perturbed by TMS. There was no heating effect for any of the valves. However, TMS induced movements of the Strata 2, Polaris, and ProGAV valves. Experiment 1: The unsetting frequencies observed for the Strata 2 and the Codman-Hakim valve showed an influence of the distance, the coil model, and the magnetic field characteristics, whereas the Polaris and ProGAV's settings remained unchanged. Experiment 2: Unsetting occurred for Strata 2 valve with the circular coil only, whereas the Polaris, ProGAV, and Codman-Hakim valves' settings remained stable. Experiment 3: The Strata 2, Polaris, and ProGAV valves showed high-amplitude oscillations during TMS under all stimulation conditions, whereas the Codman-Hakim valve did not move. CONCLUSIONS: Our in vitro experiments showed that TMS can interfere with programmable shunt valves by inducing unsetting or movement. This finding suggests that great care must be taken if applying TMS in hydrocephalic, shunted patients.