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Martini 3, the latest version of the widely used Martini force field for coarse-grained molecular dynamics simulations, is a promising tool to investigate proteins in phospholipid bilayers. However, simulating other lipid environments, such as detergent micelles, presents challenges due to the absence of validated parameters for their constituent molecules. Here, we propose parameters for the micelle-forming surfactant, dodecylphosphocholine (DPC). These result in micelle assembly with aggregation numbers in agreement with experimental values. However, we identified a lack of hydrophobic interactions between transmembrane helix protein dimers and the tails of DPC molecules, preventing insertion and stabilization of the protein in the micelles. This problem was also observed for protein insertion by self-assembling 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) or dipalmitoylphosphatidylcholine (DPPC) bilayers. We propose the reduction of the non-bonded interactions between protein and water beads by 10% as a simple and effective solution to this problem that enables protein encapsulation in phospholipid micelles and bilayers without altering protein dimerization or bilayer structure.Abstract Figure

SUMMARYNeural stem cell (NSC) proliferation and differentiation in the mammalian brain decreases to minimal levels postnatally. Nevertheless, neurogenic niches persist in the adult cortex and hippocampus in rodents, primates and humans, with adult NSC differentiation sharing key regulatory mechanisms with development. Adult neurogenesis impairments have been linked to Alzheimer’s Disease (AD) pathology. Addressing these impairments is a promising new avenue for therapeutic intervention based on neurogenesis. However, this possibility has been hindered by technical difficulties of using in-vivo models to conduct screens, including working with scarce NSCs in the adult brain and differences between human and mouse models or ethical limitations. In our study, we use a combination of mouse and human stem cell models to circumvent these issues and perform comprehensive characterization of a novel neurogenic compound usingin vitroscreening. Our work focuses on the brain-derived neurotrophic factor (BDNF) pathway, a pivotal neurotrophin in the regulation of neuronal growth and differentiation via its receptor tyrosine receptor kinase B (TrkB). We describe the design, chemical synthesis and biological characterization of ENT-A011, a steroidal dehydroepiandrosterone (DHEA) derivative and BDNF mimetic with neuroprotective and neurogenic actions. The compound is able to increase proliferation of mouse primary adult hippocampal NSCs and embryonic cortical NSCs, in the absence of EGF/FGF, while reducing Amyloid-β (Aβ) induced cell death, acting specifically through TrkB activation. The compound is also able to increase astrocytic gene markers involved in NSC maintenance, protect hippocampal neurons from Αβ toxicity and prevent synapse loss after Aβ treatment. To provide a translational link to human cells, we also used neural progenitor cells (NPCs) differentiated from three human induced pluripotent stem cell lines from healthy and AD donors. Our findings suggest that ENT-A011 successfully induces proliferation and prevents cell death after Aβ toxicity of human NPCs. Additionally, using RNAseq profiling, we demonstrate that the compound acts through a core gene network shared with BDNF. Our work characterizes a novel synthetic BDNF mimetic with potential neurogenic and neuroprotective actions in Alzheimer’s disease via stem cell-based screening, demonstrating the promise of stem cell systems for short-listing competitive candidates for further testing.

The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of a community effort, the “Billion molecules against Covid-19 challenge”, to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 potentially active molecules, which were subsequently ranked to find ‘consensus compounds’. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (Nsp12 domain), and (alpha) spike protein S. Overall, 27 potential inhibitors were experimentally confirmed by binding-, cleavage-, and/or viral suppression assays and are presented here. All results are freely available and can be taken further downstream without IP restrictions. Overall, we show the effectiveness of computational techniques, community efforts, and communication across research fields (i.e., protein expression and crystallography, in silico modeling, synthesis and biological assays) to accelerate the early phases of drug discovery.

Self-compassion is considered a protective factor that promotes positive psychology, happiness, emotional regulation and embodiment. Self‐compassion offers an approach wherein individuals in dance can pursue optimal participation and performance without compromising health and well‐being. The present study aimed to explore self-compassion among recreational dancers and discover possible differences between tango and ballet. More specifically the study examined: i) the levels of self-compassion in recreational tango and ballet dancers; ii) differences in self-compassion according to demographic characteristics; and iii) differences between tango and ballet dancers. The research was based on several adults from various cities in Greece who participated in tango and ballet for recreational reasons during their leisure time. One hundred and ninety-one dancers (20 men and 171 women), between the ages of 17 and 62, completed the self-compassion scale of Mantzios, Wilson and Giannou (2015), which consists of twenty-six items. The answers were given on a five-point Likert scale, while the reliability of the scale was successfully tested. In addition, the questionnaire contained the collection of other data such as demographic characteristics. According to the first aim, the high scores on self-compassion among recreational dancers showed a relationship between self-compassion and dance, and a positive influence of ballet and tango practice. The second hypothesis was partially confirmed as statistically significant differences emerged only between the age groups with those over forty years of age to show higher levels of self-compassion. Regarding the third aim of the research, differences were found between types of dance. Tango participants showed higher levels of self-compassion than ballet participants. Specific dance teaching interventions are discussed based on somatic and embodiment theory, to create healthier mental, emotional and behavioral patterns for dancers, schools, academies or companies. Received: 2 August 2022 / Accepted: 20 October 2022 / Published: 5 November 2022

Phosphoinositide 3-kinase alpha (PI3Kα) 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 PI3Kα activity, which can lead to oncogenesis. To assess the mechanism of the PI3Kα 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 E545K mutant PI3Kα, we observe a spontaneous detachment of the nSH2 PI3Kα domain (regulatory subunit, p85α) from the helical domain (catalytic subunit, p110α) 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 structural effects induced by the p110α E545K mutation in atomic level detail and indicate a possible mechanism for the loss of regulation that E545K confers on PI3Kα.

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.

Kinases are intensely pursued as drug targets for cancer treatment. Usually, kinase inhibitors target the active center (ATP binding site). However, the similarity of this site across many kinases often results in non-selective inhibition. Accordingly, an alternative approach is being pursued for the identification of allosteric inhibitors targeting relatively less conserved binding sites, thus higher selectivity can be attained. PI3Kα is the most frequently mutated kinase in human cancers, with 80% of the mutations occurring in two hotspots of the PIK3CA gene, which encodes the catalytic subunit of PI3Kα: 1) the H1047R mutation, which is found at the kinase (membrane binding) domain and 2) the E545K mutation, which is found at the helical domain (amino acid replacement with charge reversal). To assess the activation mechanisms of PIK3CA mutants, extensive microsecond Molecular Dynamics (MD) simulations were performed to examine conformational differences between the wild type (WT) and mutant proteins. The MD results were used to predict alterations in the allosteric networks of the WT upon each of the mutation. Binding site analysis of allosteric action in the kinase domain identified cavities in the vicinity of the H1047R mutation and the membrane-binding region. Virtual screening and subsequent biochemical assays were used to identify several PI3Kα inhibitors acting at a micromolar concentration. The effect of the inhibitors on WT and H1047R mutant PI3Kα-membrane associations was subsequently studied by SPR experiments, which showed that these small molecules alter the protein-membrane affinity, unlike other known PI3Kα inhibitors such as wortmannin. It was also observed that the inhibitory concentration remained unchanged even under conditions of increased ATP concentration, indicating that these inhibitors are non-competitive. The most promising small molecules were further tested in vivo using xenografts and genetically modified mouse models. Micro PET/CT imaging of the tumors showed reduction in volume after treatment. Immunohistochemical analysis of the xenografts showed reduction of proliferation and increase in apoptosis after treatment, in comparison to the controls. Details about the results with the E545K will be presented at the meeting. Note: This abstract was not presented at the meeting. Citation Format: Zoe Cournia, Paraskevi Gkeka, Hari Leontiadou, Ioannis Galdadas, Christina Athanasiou, Antriana Papadimitropoulou, Vasiliki Lazani, Maria Pavlaki, Bogos Agianian, Savvas Christoforidis, Argiris Efstratiadis. Νovel small molecule modulators of the hotspot PIK3CA mutants identified by computational and experimental approaches [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3918.

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, 95 % CI of −56.27, −41.62), insulin requirement per kilogramme (−0.391, 95 % CI of −0.51, −0.27), HbA1c (−0.933, 95 % CI of −1.604, −0.262) and BMI (−11.04 kg/m2, 95 % 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.

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.

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.