Intuitive Understanding of sigma Delocalization in Loose and sigma Localization in Tight Helical Conformations of a Saturated Chain Oligosilanes

Conformational effects on the amp; 963; electron delocalization in oligosilanes are addressed by Hartree Fock and time dependent density functional theory calculations B3LYP, 6 311G at MP2 optimized geometries of permethylated uniformly helical linear oligosilanes all amp; 969; SinR2n 2 up to n 16 and for backbone dihedral angles amp; 969; 55 180 . The extent of amp; 963; delocalization is judged by the partition ratio of the highest occupied molecular orbital and is reflected in the dependence of its shape and energy and of UV absorption spectra on n. The results agree with known spectra of all transoid loose helix conformers all [ 165] SinMe2n 2 and reveal a transition at amp; 969; amp; 8776;90 from the amp; 963; delocalized limit at amp; 969; 180 toward and close to the physically non realizable amp; 963; localized tight helix limit amp; 969; 0 with entirely different properties. The distinction is also obtained in the Hückel Ladder H and C models of amp; 963; delocalization. An easy intuitive way to understand the origin of the two contrasting limits is to first view the linear chain as two subchains with alternating primary and vicinal interactions amp; 963; hyperconjugation , one consisting of the odd and the other of the even amp; 963; SiSi bonds, and then allow the two subchains to interact by geminal interactions amp; 963; conjugatio

Regular treatment with salmeterol and inhaled steroids for chronic asthma: serious adverse events

Epidemiological evidence has suggested a link between beta(2)-agonists and increased asthma mortality. There has been much debate about possible causal links for this association, and whether regular (daily) long-acting beta(2)-agonists are safe.ObjectivesThe aim of this review is to assess the risk of fatal and non-fatal serious adverse events in trials that randomised patients with chronic asthma to regular salmeterol with inhaled corticosteroids versus the same dose of inhaled corticosteroids alone.Search strategyTrials were identified using the Cochrane Airways Group Specialised Register of trials. Web sites of clinical trial registers were checked for unpublished trial data and Food and Drug Administration (FDA) submissions in relation to salmeterol were also checked. The date of the most recent search was October 2008.Selection criteriaControlled parallel design clinical trials on patients of any age and severity of asthma were included if they randomised patients to treatment with regular salmeterol and inhaled corticosteroids (in separate or combined inhalers), and were of at least 12 weeks duration.Data collection and analysisTwo authors independently selected trials for inclusion in the review. Outcome data were independently extracted by two authors. Unpublished data on mortality and serious adverse events were obtained from the sponsors, and from FDA submissions.Main resultsThe review included 30 studies (10,873 participants) in adults and adolescents, and three studies (1,173 participants) in children. The overall risk of bias was low and data on serious adverse events were obtained from all studies.Six deaths occurred in 5,710 adults on regular salmeterol with inhaled corticosteroids, and five deaths in 5,163 adults on regular inhaled corticosteroids at the same dose. The difference was not statistically significant (Peto OR 1.05; 95% CI 0.32 to 3.47) and the absolute difference between groups in risk of death of any cause was 0.00005 (95% CI -0.002 to 0.002). No deaths were reported in 1,173 children, and no deaths were reported to be asthma-related.Non-fatal serious adverse events of any cause were reported in 134 adults on regular salmeterol with inhaled corticosteroids, compared to 103 adults on regular inhaled corticosteroids; again this was not a significant increase (Peto OR 1.17; 95% CI 0.90 to 1.52). The absolute difference in the risk of non-fatal serious adverse events was 0.003 (95% CI -0.002 to 0.009).There were three of 586 children with serious adverse events on regular salmeterol with inhaled corticosteroids, compared to four out of 587 on regular inhaled corticosteroids: there was no significant difference between treatments (Peto OR 0.75; 95% CI 0.17 to 3.31).Asthma-related serious adverse events were reported in 23 and 21 adults in each group respectively, a non-significant difference (Peto OR 0.95; 95% CI 0.52 to 1.73), and only one event was reported in children.Authors' conclusionsNo significant differences have been found in fatal or non-fatal serious adverse events in trials in which regular salmeterol has been randomly allocated with inhaled corticosteroids, in comparison to inhaled corticosteroids at the same dose. Although 10,873 adults and 1,173 children have been included in trials, the number of patients suffering adverse events is too small, and the results are too imprecise to confidently rule out a relative increase in all-cause mortality or non-fatal adverse events. It is therefore not possible to determine whether the increase in all-cause non-fatal serious adverse events reported in the previous meta-analysis on regular salmeterol alone is abolished by the additional use of regular inhaled corticosteroids. The absolute difference between groups in the risk of serious adverse events was small. There were no asthma-related deaths and few asthma-related serious adverse events. Clinical decisions and information for patients regarding regular use of salmeterol have to take into account the balance between known symptomatic benefits of salmeterol and the degree of uncertainty and concern associated with its potential harmful effects

Inhaled steroids with and without regular salmeterol for asthma: serious adverse events.

BACKGROUND: Epidemiological evidence has suggested a link between use of beta₂-agonists and increased asthma mortality. Much debate has surrounded possible causal links for this association, and whether regular (daily) long-acting beta₂-agonists (LABAs) are safe, particularly when used in combination with inhaled corticosteroids (ICSs). This is an update of a Cochrane Review that now includes data from two large trials including 11,679 adults and 6208 children; both were mandated by the US Food and Drug Administration (FDA).  OBJECTIVES: To assess risks of mortality and non-fatal serious adverse events (SAEs) in trials that randomised participants with chronic asthma to regular salmeterol and ICS versus the same dose of ICS. SEARCH METHODS: We identified randomised trials using the Cochrane Airways Group Specialised Register of trials. We checked websites of clinical trials registers for unpublished trial data. We also checked FDA submissions in relation to salmeterol. The date of the most recent search was 10 October 2018. SELECTION CRITERIA: We included parallel-design randomised trials involving adults, children, or both with asthma of any severity who were randomised to treatment with regular salmeterol and ICS (in separate or combined inhalers) versus the same dose of ICS of at least 12 weeks in duration. DATA COLLECTION AND ANALYSIS: We conducted the review according to standard procedures expected by Cochrane. We obtained unpublished data on mortality and SAEs from the sponsors, from ClinicalTrials.gov, and from FDA submissions. We assessed our confidence in the evidence according to current GRADE recommendations. MAIN RESULTS: We have included in this review 41 studies (27,951 participants) in adults and adolescents, along with eight studies (8453 participants) in children. We judged that the overall risk of bias was low for all-cause events, and we obtained data on SAEs from all study authors. All except 542 adults (and none of the children) were given salmeterol and fluticasone in the same (combination) inhaler.DeathsEleven of a total of 14,233 adults taking regular salmeterol and ICS died, as did 13 of 13,718 taking regular ICS at the same dose. The pooled Peto odds ratio (OR) was 0.80 (95% confidence interval (CI) 0.36 to 1.78; participants = 27,951; studies = 41; I² = 0%; moderate-certainty evidence). In other words, for every 1000 adults treated for 25 weeks, one death occurred among those on ICS alone, and the corresponding risk among those taking salmeterol and ICS was also one death (95% CI 0 to 2 deaths).No children died, and no adults or children died of asthma, so we remain uncertain about mortality in children and about asthma mortality in any age group.Non-fatal serious adverse eventsA total of 332 adults receiving regular salmeterol with ICS experienced a non-fatal SAE of any cause, compared to 282 adults receiving regular ICS. The pooled Peto OR was 1.14 (95% CI 0.97 to 1.33; participants = 27,951; studies = 41; I² = 0%; moderate-certainty evidence). For every 1000 adults treated for 25 weeks, 21 adults on ICS alone had an SAE, and the corresponding risk for those on salmeterol and ICS was 23 adults (95% CI 20 to 27).Sixty-five of 4229 children given regular salmeterol with ICS suffered an SAE of any cause, compared to 62 of 4224 children given regular ICS. The pooled Peto OR was 1.04 (95% CI 0.73 to 1.48; participants = 8453; studies = 8; I² = 0%; moderate-certainty evidence). For every 1000 children treated for 23 weeks, 15 children on ICS alone had an SAE, and the corresponding risk for those on salmeterol and ICS was 15 children (95% CI 11 to 22).Asthma-related serious adverse eventsEighty and 67 adults in each group, respectively, experienced an asthma-related non-fatal SAE. The pooled Peto OR was 1.15 (95% CI 0.83 to 1.59; participants = 27,951; studies = 41; I² = 0%; low-certainty evidence). For every 1000 adults treated for 25 weeks, five receiving ICS alone had an asthma-related SAE, and the corresponding risk among those on salmeterol and ICS was six adults (95% CI 4 to 8).Twenty-nine children taking salmeterol and ICS and 23 children taking ICS alone reported asthma-related events. The pooled Peto OR was 1.25 (95% CI 0.72 to 2.16; participants = 8453; studies = 8; I² = 0%; moderate-certainty evidence). For every 1000 children treated for 23 weeks, five receiving an ICS alone had an asthma-related SAE, and the corresponding risk among those receiving salmeterol and ICS was seven children (95% CI 4 to 12). AUTHORS' CONCLUSIONS: We did not find a difference in the risk of death or serious adverse events in either adults or children. However, trial authors reported no asthma deaths among 27,951 adults or 8453 children randomised to regular salmeterol and ICS or ICS alone over an average of six months. Therefore, the risk of dying from asthma on either treatment was very low, but we remain uncertain about whether the risk of dying from asthma is altered by adding salmeterol to ICS.Inclusion of new trials has increased the precision of the estimates for non-fatal SAEs of any cause. We can now say that the worst-case estimate is that at least 152 adults and 139 children must be treated with combination salmeterol and ICS for six months for one additional person to be admitted to the hospital (compared to treatment with ICS alone). These possible risks still have to be weighed against the benefits experienced by people who take combination treatment.However more than 90% of prescribed treatment was taken in the new trials, so the effects observed may be different from those seen with salmeterol in combination with ICS in daily practice

Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration

We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We conclude with a brief presentation of some combination methods. \ua9 2013 by the author; licensee MDPI, Basel, Switzerland

Identification of β-strand mediated protein–protein interaction inhibitors using ligand-directed fragment ligation

β-Strand mediated protein–protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators

Computational Characterization of Human Soluble Calcium-Activated Nucleotidase 1

Human soluble calcium-activated nucleotidase 1 (hSCAN-1) represents a new family of apyrase enzymes, the Calcium Activated Nucleotidases (CANs), which catalyze the hydrolysis of various di- and tri-nucleotides. Biologically, apyrases are involved in the regulation of extra-cellular purinergic and pyrimidinergic signaling, which associates their functionality with homeostatic processes such as the maintenance of cellular calcium levels. The enhanced expression of hSCAN-1 itself has recently been associated with stress-related processes (e.g. unfolded protein response), as well as specific disease states (e.g. Desbuquois dysplasia, prostate cancer). From a structural and functional perspective, the CANs differ from other well-characterized nucleotide-phosphate-binding enzymes. We have found that they posses a unique phosphate-binding motif, which lacks the common P-loop and is dominated by ionizable residues. Catalytically, they display highly specific calcium dependence, distinct from the cationic promiscuity of the NTPDase apyrase family. Motivated by the initial success in the redesign of hSCAN-1 into a potentially therapeutic anti-coagulant, we are the first to computationally investigate the active site structure, reactivity, and catalytic mechanism of a member from this novel phosphoryl transfer family. Supported by molecular dynamics simulations, we have revealed a highly symmetric, yet previously unrecognized, second calcium-binding site, which is the key to the family's exclusive calcium activation and explains the unusual, experimentally observed, sigmoidal relationship between calcium concentration and hSCAN-1 activity. We present how the ionizable nature of this binding site can account for additional experimental observations: a narrow pH range for optimal hSCAN-1 activity and a moderate enzymatic inhibition in the presence of sodium. Supported by ab initio QM/MM molecular dynamics simulations, we propose a detailed phosphoryl transfer mechanism for hSCAN-1, which relies upon the loose 8-9-fold coordination around this catalytic calcium. This coordination structure includes two protonated ionizable residues, Asp44 and Asp114, that properly orient the nucleophilic water. A third protonated Asp46 donates its proton, through the substrate, to neutralize the bridging oxygen leaving group. In light of our theoretical results and interpretation, we propose specific mutagenesis intended to enhance the rate of nucleotide hydrolysis and combined mutagenesis/kinetics experiments designed to empirically support our findings

Magnetic circular dichroism of peralkylated tetrasilane conformers

Magnetic circular dichroism (MCD) of five peralkylated tetrasilanes (1–5) conformationally constrained to angles ranging from nearly 0° to 180° and of the open chain tetrasilane Si(4)Me(10) (6) shows a clear conformational dependence and permits the detection of previously hidden transitions. In the tetrasilane CH(2)Si(4)Me(8) (1), with the smallest dihedral angle, comparison of MCD with absorption spectra reveals four low-energy electronic transitions. In the tetrasilanes 2–4, three distinct transitions are apparent. In tetrasilanes 5 and 6, MCD reveals the very weak transition that has been predicted to be buried under the first intense peak and to which the anomalous thermochromism of 6 and other short-chain oligosilanes has been attributed

Revelation of a Catalytic Calcium-Binding Site Elucidates Unusual Metal Dependence of a Human Apyrase

Human soluble calcium-activated nucleotidase 1 (hSCAN-1) represents a new family of apyrase enzymes that catalyze the hydrolysis of nucleotide di- and triphosphates, thereby modulating extracellular purinergic and pyrimidinergic signaling. Among well-characterized phosphoryl transfer enzymes, hSCAN-1 is unique not only in its unusual calcium-dependent activation, but also in its novel phosphate-binding motif. Its catalytic site does not utilize backbone amide groups to bind phosphate, as in the common P-loop, but contains a large cluster of acidic ionizable side chains. By employing a state-of-the-art computational approach, we have revealed a previously uncharacterized catalytic calcium-binding site in hSCAN-1, which elucidates the unusual calcium-dependence of its apyrase activity. In a high-order coordination shell, the newly identified calcium ion organizes the active site residues to mediate nucleotide binding, to orient the nucleophilic water, and to facilitate the phosphoryl transfer reaction. From ab initio QM/MM molecular dynamics simulations with umbrella sampling, we have characterized a reverse protonation catalytic mechanism for hSCAN-1 and determined its free energy reaction profile. Our results are consistent with available experimental studies and provide new detailed insight into the structure–function relationship of this novel calcium-activated phosphoryl transfer enzyme