102 research outputs found

    Molecular simulations on proteins of biomedical interest : A. Ligand-protein hydration B. Cytochrome P450 2D6 and 2C9 C. Myelin associated glycoprotein (MAG)

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    TOPIC 1: Water molecules mediating polar interactions in ligand–protein complexes contribute to both binding affinity and specificity. To account for such water molecules in computer-aided drug discovery, we performed an extensive search in the Cambridge Structural Database (CSD) to identify the geometrical criteria defining interactions of water molecules with ligand and protein. In addition, ab initio calculations were used to derive the propensity of ligand hydration. Based on these information we developed an algorithm (AcquaAlta) to reproduce water molecules bridging polar interactions between ligand and protein moieties. This approach was validated using 20 crystal structures and yielded a match of 76% between experimental and calculated water positions. The solvation algorithm was then applied to the docking of oligopeptides to the periplasmic oligopeptide binding protein A (OppA), supported by a pharmacophore-based alignment tool. TOPIC 2: Drug metabolism, toxicity, and interaction profile are major issues in the drug discovery and lead optimization processes. The Cytochromes P450 (CYPs) 2D6 and 2C9 are enzymes involved in the oxidative metabolism of a majority of the marketed drugs. By identifying the binding mode using pharmacophore pre-alignement and automated flexible docking, and quantifying the binding affinity by multi-dimensional QSAR, we validated a model family of 56 compounds (46 training, 10 test) and 85 (68 training, 17 test) for CYP2D6 and CYP2C9, respectively. The correlation with the experimental data (cross- validated r2 = 0.811 for CYP2D6 and 0.687 for CYP2C9) suggests that our approach is suited for predicting the binding affinity of compounds towards the CYP2D6 and CYP2C9. The models were challenged by Y-scrambling, and by testing an external dataset of binding compounds (15 compounds for CYP2D6 and 40 for CYP2C9) and not binding compounds (64 compounds for CYP2D6 and 56 for CYP2C9). TOPIC 3: After injury, neurites from mammalian adult central nervous systems are inhibited to regenerate by inhibitory proteins such as the myelin-associated glycoprotein (MAG). The block of MAG with potent glycomimetic antagonists could be a fruitful approach to enhance axon regeneration. Libraries of MAG antagonists were derived and synthesized starting from the (general) sialic acid moiety. The binding data were rationalized by docking studies, molecular dynamics simulations and free energy perturbations on a homology model of MAG. The pharmacokinetic profile (i.e. stability in cerebrospinal fluid, logD, and blood-brain barrier permeation) of these compounds has been thoroughly investigated to evaluate the drug-likeness of the identified antagonists

    From the ganglioside GQ1ba to glycomimetic antagonists of the myelin-associated glycoprotein (MAG)

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    The tetrasaccharide 4, a substructure of ganglioside GQ1bα, shows a remarkable affinity for the myelinassociated glycoprotein (MAG) and was therefore selected as starting point for a lead optimization program. In our search for structurally simplified and pharmacokinetically improved mimics of 4, antagonists with modifications of the core disaccharide GalÎČ(1-3)GalNAc, as well as the terminal α(2-3)- and the internal α(2-6)-linked neuraminic acid were synthesized and tested in target-based binding assays. Compared to the reference tetrasaccharide 4, the most potent antagonist 17 exhibits a 360-fold improved affinity. Furthermore, pharmacokinetic parameters such as stability in the cerebrospinal fluid, logD and permeation through the BBB indicate the drug-like properties of antagonist 17

    Impact of nonstationarities on short heart rate variability recordings during obstructive sleep apnea

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    Obstructive sleep apnea (OSA) is a sleep disorder characterized by breathing pauses due to collapse of the upper airways. During OSA the autonomic modulation, as noninvasively assessed through heart period (HP) variability, is altered in a time-varying way even though time-varying properties of HP fluctuations are often disregarded by HP variability studies. We performed a time domain analysis computed over very short epochs corresponding to the sole OSA events explicitly accounting for HP variability nonstationarities. Length-matched epochs were extracted during OSA and quiet sleep (SLEEP) in 13 subjects suffering from OSA (11 males, age 55±11, apnea-hypopnea index 44±19). Mean HP, variance and variance of the residual after exponential detrending were assessed as well as the parameters a and b of the exponential fitting in the form y(n)=a·exp(b·n). HP mean and the parameter a increased during OSA compared to SLEEP. The variance of the residual was significantly lower than original variance during both OSA and SLEEP, while the dispersion of the parameter b was significantly larger. Nonstationarities were evident during both SLEEP and OSA but more dramatically apparent during OSA, thus stressing the need of accounting for them when the autonomic control during OSA is under scrutiny

    Expanding Thurston Maps

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    We study the dynamics of Thurston maps under iteration. These are branched covering maps ff of 2-spheres S2S^2 with a finite set post(f)\mathop{post}(f) of postcritical points. We also assume that the maps are expanding in a suitable sense. Every expanding Thurston map f S2→S2f\: S^2 \to S^2 gives rise to a type of fractal geometry on the underlying sphere S2S^2. This geometry is represented by a class of \emph{visual metrics} ϱ\varrho that are associated with the map. Many dynamical properties of the map are encoded in the geometry of the corresponding {\em visual sphere}, meaning S2S^2 equipped with a visual metric ϱ\varrho. For example, we will see that an expanding Thurston map is topologically conjugate to a rational map if and only if (S2,ϱ)(S^2, \varrho) is quasisymmetrically equivalent to the Riemann sphere C^\widehat{\mathbf{C}}. We also obtain existence and uniqueness results for ff-invariant Jordan curves C⊂S2\mathcal{C}\subset S^2 containing the set post(f)\mathop{post}(f). Furthermore, we obtain several characterizations of Latt\`{e}s maps

    stairs and fire

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    Investigating cardiovascular and cerebrovascular variability in postural syncope by means of extended Granger causality

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    The patterns of Granger causality (GC) between heart period (HP), mean arterial pressure (AP) and cerebral blood flow velocity (FV) were investigated in ten subjects with postural related syncope (PRS). The classic GC measure based on vector autoregressive (VAR) modeling was compared with a novel extended GC (eGC) measure derived from VAR models incorporating instantaneous causal effects among the series. The analysis was performed in the supine and in the upright position during early (ET) and late (LT, close to presyncope) epochs of head-up tilt. Moving from ET to LT, both GC and eGC decreased from AP to HP, and increased from AP to FV, reflecting baroreflex impairment and loss of cerebral autoregulation. The statistical significance of these changes was better assessed using the eGC, thus suggesting the importance of including instantaneous effects in the causality analysis of cardiovascular and cerebrovascular variability during PRS

    A different unhappy triad in the knee. a case of acute simultaneous rupture of Patellar Tendon, Anterior Cruciate Ligament and lateral meniscus treated in one stage and review of literature

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    We present a case report of a 43-year-old male patient with simultaneous ruptured of anterior cruciate ligament (ACL), patellar tendon (PT) and lateral meniscus tear, occurred during a tennis match. This combinate tear is not frequent, and literature reports only few cases. Clinical diagnosis can be difficult and the support of MRI and X-Ray is needed. Surgery was performed within seven days from injury in a one-step fashion. Clinical and radiological outcome treatment was successful

    Nonlinear effects of respiration on the crosstalk between cardiovascular and cerebrovascular control systems

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    Cardiovascular and cerebrovascular regulatory systems are vital control mechanisms responsible for guaranteeing homeostasis and are affected by respiration. This work proposes the investigation of cardiovascular and cerebrovascular control systems and the nonlinear influences of respiration on both regulations through joint symbolic analysis (JSA), conditioned or unconditioned on respiration. Interactions between cardiovascular and cerebrovascular regulatory systems were evaluated as well by performing correlation analysis between JSA indexes describing the two control systems. Heart period, systolic and mean arterial pressure, mean cerebral blood flow velocity and respiration were acquired on a beat-to-beat basis in 13 subjects experiencing recurrent syncope episodes (SYNC) and 13 healthy individuals (non-SYNC) in supine resting condition and during head-up tilt test at 60° (TILT). Results showed that JSA distinguished conditions and groups, whereas time domain parameters detected only the effect of TILT. Respiration affected cardiovascular and cerebrovascular regulatory systems in a nonlinear way and was able to modulate the interactions between the two control systems with different outcome in non-SYNC and SYNC groups, thus suggesting that the analysis of the impact of respiration on cardiovascular and cerebrovascular regulatory systems might improve our understanding of the mechanisms underpinning the development of postural-related syncope

    Validity of the STOP-Bang Questionnaire in Identifying OSA in a Dental Patient Cohort

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    Background and objectives: Obstructive Sleep Apnea represents a widespread problem in the population, but it is often not diagnosed and not considered a true pathology. Different diagnostic tools are available for the diagnosis of sleep apnea. This study aims to demonstrate the ability of the STOP-Bang (Snoring, Tiredness, Observed apnea, high blood Pressure, Body mass index, Age, Neck circumference, and Gender) questionnaire in identifying subjects with Obstructive Sleep Apnea (OSA) Syndrome, highlighting the role of dentists as epidemiological sentinels. Materials and methods: the STOP-Bang questionnaire was administered to a cohort of 1000 patients, assessing three private dental clinics in Italy. Excessive daytime sleepiness was measured using Epworth Sleepiness Scale (ESS) and defined as ≄ 10. Subjects were considered at risk of OSA if they had three or more positive items at STOP-Bang and were invited to undergo further examination with a type 3 polygraph. Presence of OSA was measured with the apnea-hypopnea index (AHI) and defined as AHI ≄ 5. Results: 482/1000 subjects (48.2%) had three or more positive items in the STOP-Bang questionnaire and were considered at risk for Obstructive Sleep Apnea Syndrome (OSAS). Excessive daytime sleepiness (EDS ≄ 10) was more frequent among subjects at risk for OSAS (73/482, 15.1%) vs. those not at risk for OSAS (30/518, 5.8%) (p < 0.0001). Moreover, 153/482 subjects at risk for OSAS (31.7%) accepted further examination with a type 3 polygraph. Presence of OSAS (AHI ≄ 5) was suggested in 121/153 subjects (79.1%, 95% CI 71.6% to 85.1%), with 76/121 subjects (62.8%) needing treatment (AHI ≄ 15). Conclusion: the high prevalence of OSAS highlights the role of dentists as “epidemiological sentinels”. The STOP-Bang questionnaire is a simple and efficacious instrument for screening sleep apnea patients
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