Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations
Phosphoinositide 3-kinase alpha (PI3KÎ±) is involved in fundamental cellular processes including cell proliferation and differentiation and is frequently mutated in human malignancies. One of the most common mutations is E545K, which results in an amino acid substitution of opposite charge. It has been recently proposed that in this oncogenic charge-reversal mutation, the interactions between the protein catalytic and regulatory subunits are abrogated, resulting in loss of regulation and constitutive PI3KÎ± activity, which can lead to oncogenesis. To assess the mechanism of the PI3KÎ± E545K activating mutation, extensive Molecular Dynamics simulations were performed to examine conformational changes differing between the wild type (WT) and mutant proteins as they occur in microsecond simulations. In the E545KÂ mutantÂ PI3KÎ±, we observe a spontaneous detachment of the nSH2 PI3KÎ± domain (regulatory subunit, p85Î±) from the helical domain (catalytic subunit, p110Î±)Â causing significant loss of communication between the regulatory and catalytic subunits. We examine the allosteric network of the two proteins and show that a cluster of residues around the mutation is important for delivering communication signals between the catalytic and regulatory subunits. Our results demonstrate the dynamical and structuralÂ effects induced by the p110Î± E545K mutation in atomic level detail and indicate a possible mechanism for the loss of regulation that E545K confers on PI3KÎ±.
Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2
Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design data resource (D3R) organizes challenges against blinded experimental data to prospectively test computational methodologies as an opportunity for improved methods and algorithms to emerge. We participated in Grand Challenge 2 to predict the crystallographic poses of 36 Farnesoid X Receptor (FXR)-bound ligands and the relative binding affinities for two designated subsets of 18 and 15 FXR-bound ligands. Here, we present our methodology for pose and affinity predictions and its evaluation after the release of the experimental data. For predicting the crystallographic poses, we used docking and physics-based pose prediction methods guided by the binding poses of native ligands. For FXR ligands with known chemotypes in the PDB, we accurately predicted their binding modes, while for those with unknown chemotypes the predictions were more challenging. Our group ranked #1st (based on the median RMSD) out of 46 groups, which submitted complete entries for the binding pose prediction challenge. For the relative binding affinity prediction challenge, we performed free energy perturbation (FEP) calculations coupled with molecular dynamics (MD) simulations. FEP/MD calculations displayed a high success rate in identifying compounds with better or worse binding affinity than the reference (parent) compound. Our studies suggest that when ligands with chemical precedent are available in the literature, binding pose predictions using docking and physics-based methods are reliable; however, predictions are challenging for ligands with completely unknown chemotypes. We also show that FEP/MD calculations hold predictive value and can nowadays be used in a high throughput mode in a lead optimization project provided that crystal structures of sufficiently high quality are available.
A systematic review of the safety and efficacy of distal coronary artery anastomotic devices in MIDCAB and TECAB surgery
BACKGROUND:Minimally invasive direct coronary artery bypass (MIDCAB) and totally endoscopic coronary artery bypass (TECAB) techniques may improve recovery and reduce hospital stay following coronary artery bypass surgery (CABG). However, working in a limited space with indirect visualisation would greatly benefit from a simple, high-quality and reproducible automated distal anastomotic method. Several devices have been developed; however, their uptake has been limited due to uncertainty around their impact on patient outcomes. METHODS:A systematic review of the literature identified six studies, incorporating 139 subjects undergoing MIDCAB or TECAB surgery using a distal anastomotic device. RESULTS:The overall 30-day mortality was 0.7% (1/137). No cardiac specific mortality was observed. For each outcome of perioperative myocardial infarction (MI), postoperative stroke and haemorrhage, only a single event was observed for each (n=1/136, 1/138 and 1/136, respectively). The overall device failure rates were low, with the use of additional sutures only reported in a single case with the Magnetic Vascular Port (MVP) device. Anastomotic time ranged from a mean of 3.32 minutes with the MVP device to 20 minutes with the C-Port device. CONCLUSIONS:These results demonstrate the overall acceptable early outcomes of distal anastomotic devices for use in minimally invasive coronary bypass surgery. Future research should focus on designing adequately powered, comparative, randomised trials, focusing on major adverse cardiac and cerebrovascular events (MACCE) outcomes in both the short and long-term, with clear case-by-case reasons for device failure and a comparison of anastomotic times. In this way, we may determine whether such devices will facilitate the minimal access and robotic coronary procedures of the future.
Type 1 Diabetes Mellitus and Bariatric Surgery: A Systematic Review and Meta-Analysis
BACKGROUND:Type 1 diabetes mellitus (T1DM) has a rising global prevalence. Although it is vastly outnumbered by type 2 diabetes mellitus rates, it remains a persistent worldwide source of morbidity and mortality. Increasingly, its sufferers are afflicted by obesity and its complications. The objective of the study is to quantify the effects of bariatric surgery on T1DM by appraising the primary outcomes of glycosylated haemoglobin (HbA1c), insulin requirements and body mass index (BMI). Secondary outcomes included blood pressure, triglycerides and cholesterol biochemistry. METHODS:A systematic review of studies reporting pre-operative and post-operative outcomes in T1DM patients undergoing bariatric surgery was done. Data were meta-analysed using random effects modelling. Subgroup analysis and quality scoring were assessed. RESULTS:Bariatric surgery in obese T1DM patients is associated with a significant reduction in insulin requirement (-48.95 units, 95Â % CI of -56.27, -41.62), insulin requirement per kilogramme (-0.391, 95Â % CI of -0.51, -0.27), HbA1c (-0.933, 95Â % CI of -1.604, -0.262) and BMI (-11.04Â kg/m(2), 95Â % CI of -13.49, -8.59). Surgery is also associated with a statistically significant reduction in systolic and diastolic blood pressure and a significant beneficial rise in HDL. Heterogeneity in these results was high, and study quality was low overall. CONCLUSIONS:Bariatric surgery in obese T1DM patients is associated with a significant improvement in insulin requirement and a significant though modest effect on HbA1c. These early results require further substantiation with future studies focusing on higher levels of evidence. This may offer a deeper understanding of diabetogenesis and can contribute to better selection and stratification of diabetic patients for metabolic surgery and future metabolic treatment strategies.
Surgical management of infected cardiac implantable electronic devices
The growing use of cardiac implantable electronic devices (CIED) has led to infections requiring intervention. These are traditionally managed using a percutaneous transvenous approach to fully extract the culpable leads. Indications for such strategies are well-established and range from simple traction to the use of powered extraction tools including laser sheaths. Where such attempts fail, or if there are further complications, then there may be need for a cardiothoracic surgical approach. Limited evidence is currently available on the merits of individual strategies, and these are mainly drawn from case reports or series. Most utilise cardiopulmonary bypass, cardioplegic arrest and entry within the right atrium to allow direct visualisation of any vegetation and safely explant all CIED components whilst avoiding perforation, valvular and paravalvular damage. In this review, we describe a number of these and the unique challenges faced by surgeons when attempting to extract CIED. It is clear that future work should concentrate on creating clear consensus and guidelines on indications, risks and measures of efficacy outcomes for various surgical techniques.