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Reduced expression and/or activity of Kv1.5 channels (encoded by KCNA5) is a common hallmark in human or experimental pulmonary arterial hypertension (PAH). Likewise, genetic variants in KCNA5 have been found in PAH patients, but their functional consequences and potential impact on the disease are largely unknown. Herein, we aimed to characterize the functional consequences of 7 KCNA5 variants found in a cohort of PAH patients. Potassium currents were recorded by patch-clamp technique in HEK293 cells transfected with WT or mutant Kv1.5 cDNA. Flow cytometry, western blot and confocal microscopy techniques were used for measuring protein expression and cell apoptosis in HEK293 and human pulmonary artery smooth muscle cells (hPASMC). KCNA5 variants found in PAH patients (namely, p.Arg184Pro and p.Gly384Arg) resulted in a clear loss of potassium channel function as assessed by electrophysiological and molecular modelling analyses. The p.Arg184Pro variant also resulted in a pronounced reduction of Kv1.5 expression. Transfection with p.Arg184Pro or p.Gly384Arg variants decreased apoptosis of hPASMCs compared with the WT, demonstrating that KCNA5 dysfunction in both variants affects cell viability. Thus, in addition to affecting channel activity, both variants were associated with impaired apoptosis, a crucial process linked to the disease. The estimated prevalence of dysfunctional KCNA5 variants in the PAH population analyzed was around 1 %. Our data indicate that some KCNA5 variants found PAH patients have critical consequences for channel function supporting the idea that KCNA5 pathogenic variants may be a causative or contributing factor for PAH.

AntiMicrobial Resistance (AMR) is a worldwide health emergency. ESKAPE pathogens include the most relevant AMR bacterial families. In particular, Gram-negative bacteria stand out due to their cell envelope complexity which exhibits strong resistance to antimicrobials. A key element for AMR is the chemical structure of lipid A, modulating the physico-chemical properties of the membrane and permeability to antibiotics. Liposomes are used as models of bacterial membrane infective vesicles. In this work, coarse-grained molecular dynamics simulations were used to model liposomes from ESKAPE Gram-negative bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa). We captured the role of lipid A, cardiolipin and cholesterol on liposome morphology and physico-chemical properties. Additionally, the reported antimicrobial peptides Cecropin B1, JB95, and PTCDA1-kf, were used to unveil their implications on membrane disruption. This study opens a promising starting point to understand molecular keys of bacterial membranes and to promote the discovery of new antimicrobials to overcome AMR.

AntiMicrobial Resistance (AMR) has dramatically increased over the past three decades becoming a worldwide health emergency.Strains of particular concern are known by the acronym ESKAPE, which groups Gram-(+) bacteria: Enterococcus faecium, Staphylococcus aureus; and, Gram-(-) bacterias: Klebsiella pneumoniae (K.p.), Acinetobacter baumannii (A.b.),Pseudomonas aeruginosa (P.a.), and Enterobacter species (e.g., Escherichia coli, E.c.). In particular, Gram-(-) bacteria are highlighted due to their cell envelope complexity which exhibits strong resistance to antimicrobials. Their cell wall contains the periplasm membrane and a thin peptidoglycan layer encased by the outer membrane (OM). The OM acts as protective and selective barrier to most small drugs. Its mechanisms of resistance involve chemical alterations of lipopolysaccharides (LPS), which face the external environment and are indispensable for the bacterial survival.The LPS structure is composed by three main chemical units: a lipid A, a core oligosaccharide and an O-antigen. A key element for AMR is the chemical structure of the lipid A moiety whose changes (e.g., acyl chain length, saturation, branching, and charged head groups) induce physico-chemical property modifications such as fluidity, charge balance, and permeability to antibiotics.3 Liposomes are used as biological membrane models which by tuning their lipid composition can mimic membrane vesicles of pathogenic bacteria, and thus,help to understand AMR mechanisms and to promote drug discovery. Nevertheless, although great progress has been made on the development of computational membrane models to understand resistance mechanisms at molecular level, computational studies with liposomes are scarce.In this work, coarse-grained (CG) molecular dynamics (MD) simulations were used to model liposomes from ESKAPE Gram-(-) bacteria (K.p., A.b., P.a., E.c.). We captured the role of lipid A and cholesterol on liposome morphology and physico-chemical properties.

Antimicrobial resistance (AMR) represents a major threat to global public health in the 21st century, dramatically increasing the pandemic expectations in the coming years. The ongoing need to develop new antimicrobial treatments that are effective against multi-drug-resistant pathogens has led the research community to investigate innovative strategies to tackle AMR. The bacterial cell envelope has been identified as one of the key molecular players responsible for antibiotic resistance, attracting considerable interest as a potential target for novel antimicrobials effective against AMR, to be used alone or in combination with other drugs. However, the multicomponent complexity of bacterial membranes provides a heterogeneous morphology, which is typically difficult to study at the molecular level by experimental techniques, in spite of the significant development of fast and efficient experimental protocols. In recent years, computational modeling, in particular, molecular dynamics simulations, has proven to be an effective tool to reveal key aspects in the architecture and membrane organization of bacterial cell walls. Here, after a general overview about bacterial membranes, AMR mechanisms, and experimental approaches to study AMR, we review the state-of-the-art computational approaches to investigate bacterial AMR envelopes, including their limitations and challenges ahead. Representative examples illustrate how these techniques improve our understanding of bacterial membrane resistance mechanisms, hopefully leading to the development of novel antimicrobial drugs escaping from bacterial resistance strategies.

The innate immunity TLR4/MD-2 system is a membrane receptor of paramount importance as therapeutic target. Its assembly, upon binding of Gram-negative bacteria lipopolysaccharide (LPS), and also dependent on the membrane composition, finally triggers the immune response cascade. We here combine ab-initio calculations, molecular docking, all-atom molecular dynamics simulations, and thermodynamics calculations to provide the most realistic and complete 3D models of the active full TLR4 complex embedded into a realistic membrane to date. Our studies reveal functional and structural insights into the transmembrane domain behavior in different membrane environments, the ectodomain bouncing movement, and the dimerization patterns of the intracellular TIR domain. Our work provides TLR4 models as reasonable 3D structures for the (TLR4/MD-2/LPS) 2 architecture accounting for the active (agonist) state of the TLR4, and pointing to a signal transduction mechanism across cell membrane. These observations unveil relevant molecular aspects involved in the TLR4 innate immune pathways and will promote the discovery of new TLR4 modulators.

Poly(3,4-ethylenedioxythiophene) (PEDOT) is one of the most important conductive polymers utilized in a variety of applications in organic electronics and bioelectronics and energy storage. PEDOT chains are believed to be rather short, but detailed knowledge of their length is missing because of the challenges in its experimental determination due to insolubility of PEDOT films. Here, we report a molecular dynamics (MD) study of in situ oxidative chemical polymerization and simultaneous crystallization of molecularly doped PEDOT focusing on the determination of its chain lengths at different polymerization temperatures. We find the average chain length to be 6, 7, and 11 monomers for 298, 323 and 373 K, respectively. At the same time, the length distribution is rather broad, for example, between 2 and 16 monomer units for T = 323 K. We demonstrate that the limiting factor determining the chain length is the diffusivity of the reactants (PEDOT monomers and oligomers). We also study the polymer film formation during solvent evaporation, and we find that although crystallization starts and proceeds already during the polymerization and doping phases, it mostly occurs during the evaporation phase. Finally, we believe that our results providing the oligomer chain length and polymerization and crystallization mechanisms obtained by means of MD “computational microscopy” provide an important insight into the morphology of PEDOT that cannot be obtained by other means.

Designing new high performances materials based on conducting polymers necessitates the development of multiscale models to investigate the charge transport in large realistic systems. In this work, we utilize Coarse-Grained (CG) Molecular Dynamics (MD) simulations to generate morphologies of Poly(3,4-ethylenedioxythiophene) (PEDOT) doped with Tosylate (TOS) ions, and we develop a backmapping protocol to retrieve the atomistic details of the molecules afterwards. We demonstrate that the proposed protocol corrects for the nanostructure distortions induced by Coarse-Graining the system, namely a wrong density and an over-estimated stacking distance. Quantum chemical calculations are performed on the systems obtained after backmapping in order to calculate hopping rates for charge transport, and charge mobilities as a function of the PEDOT chain length and hydration level are then calculated by solving a master equation for transport. The results are identical to the calculations performed on PEDOT morphologies obtained by direct All-Atomistic (AA) MD simulations: the mobility increases with the chain length and decreases with the hydration level, this last effect being more pronounced for short chains. This definitely shows that the workflow CG MD backmapping mobility calculations is in position to calculate charge mobility in PEDOT based materials, paving the way for theoretical investigations of transport in more complex materials such as PEDOT doped with Polystyrene Sulfonate (PSS).

Among all conducting polymers, PEDOT or poly(3,4-ethylenedioxythiophene) has a special place within the field of organic electronics due to its outstanding conductivity, stability, and processability. Since PEDOT was first synthesized in the late 1980s, a massive amount of knowledge has been accumulated about its morphological, structural, electrical, and optical properties, along with its applications in various devices. Notably, however, is that the vast majority of the reports in the field are purely experimental, without any theoretical support from simulation and modeling. In many other fields of material science, molecular modeling has already become a standard tool for guiding the experimental work. For PEDOT, the lack of the theoretical understanding of many important aspects of the material properties and device functionality leads to misconceptions and controversial issues hindering the progress in the field. The purpose of this Perspective is to fill the knowledge gaps and to present the current state-of-the art of the theoretical understanding of PEDOT. As theoretical understanding is essential to correctly interpretate experimental results and for the design of materials and devices with better performance, this Perspective targets equally experimental and theoretical communities working on PEDOT and related materials. We also hope that this Perspective will attract further attention of the computational community, which would help to bring the theoretical understanding of PEDOT to the levels already achieved in many other fields of material science., Funding Agencies|Swedish Research CouncilSwedish Research CouncilEuropean Commission [2016-05990, 2017-04474, 2019-04424]; Swedish Government Strategic Research Area in Materials Science on Advanced Functional Materials at Linkoping University (Faculty Grant SFO-Mat-LiU) [2009-00971]

New multi-target indole and naphthalene derivatives containing the oxadiazolone scaffold as a bioisostere of the melatonin acetamido group have been developed. The novel compounds were characterized at melatonin receptors MTR and MTR, quinone reductase 2 (QR2), lipoxygenase-5 (LOX-5), and monoamine oxidases (MAO-A and MAO-B), and also as radical scavengers. We found that selectivity within the oxadiazolone series can be modulated by modifying the side chain functionality and co-planarity with the indole or naphthalene ring. In phenotypic assays, several oxadiazolone-based derivatives induced signalling mediated by the transcription factor NRF2 and promoted the maturation of neural stem-cells into a neuronal phenotype. Activation of NRF2 could be due to the binding of indole derivatives to KEAP1, as deduced from surface plasmon resonance (SPR) experiments. Molecular modelling studies using the crystal structures of QR2 and the KEAP1 Kelch-domain, as well as the recently described X-ray free-electron laser (XFEL) structures of chimeric MTR and MTR, provided a rationale for the experimental data and afforded valuable insights for future drug design endeavours.

Poly(3,4-ethylenedioxythiophene) (PEDOT) is a conducting polymer that is used in a wide range of applications such as electronics, optoelectronics, and bio-electronics, where the fundamental understanding of the charge transport, and in particular of the electrical conductivity sigma, is a prerequisite to develop new high performance devices. There are many reports in the literature where the conductivity of archetypical conducting polymer PEDOT doped with tosylate (PEDOT:TOS) exhibits a dry negative temperature coefficient, d sigma/dT < 0, which is strikingly different from the activated-type behavior with d sigma/dT > 0 commonly observed in most conducting polymers. This unusual temperature dependence was attributed to the transition from the photon-assisted hopping to the metallic behavior, which is however difficult to rationalize taking into account that this transition occurs at high temperatures. In order to understand the origin of this unusual behavior, multiscale mobility calculations in PEDOT:TOS for the model of hopping transport were performed, where changes in the morphology and the density of states (DOS) with the temperature were explicitly taken into account. The morphology was calculated using the Molecular Dynamics simulations, and the hopping rates between the chains were calculated quantum-mechanically following the Miller-Abrahams formalism. Our results reproduce the observed negative temperature coefficient, where however the percolation analysis shows that this behavior mainly arises because of the changes in morphology upon heating when the system becomes less ordered. This results in a less efficient pi-pi stacking and hence lower mobility in the system. We therefore conclude that experimentally observed negative mobility temperature coefficient in conducting polymers at high temperatures is consistent with the hopping transport, and does not necessarily reflect the transition to a metallic band-like transport. Based on our multiscale, QC 20191218

This study has been developed within a multidisciplinary project designed to search for multitarget compounds with NRF2 inducing capacity, by inhibiting the Keap1-NRF2 interaction, for the treatment of Alzheimer¿s disease. We have focused on melatonin and resveratrol derivatives, which additionally induce NRF2 transcription factor, master regulator of oxidative stress. For this study, two melatonin (CH213 and CH507) and one resveratrol (PL119) derivatives, which were the ones that duplicated NRF2 expression at concentrations below 10 ¿M, were selected. We found that these compounds were not neurotoxic in the human neuroblastoma cell line SH-SY5Y at the concentration of 100 ¿M. Thereafter, neuroprotection in a tau hyperphosphorylation in vitro model induced by okadaic acid (OA) was studied; compounds CH507 and PLC119 presented significant neuroprotection, while CH213 did not. Nevertheless, neuroprotection of compound CH213 against OA was studied in primary neuronal cultures achieving significant results. Additionally, their potential anti neuroinflammatory effects were studied in primary rat glial cultures exposed to LPS; in this model, only compound CH213 reduced nitric oxide production and IL-1b. CH123 was further studied in an acute model of hippocampal slices, where toxicity was induced by incubation with OA for 6 h and in organotypic hippocampal cultures of 14 months old APPTau mice; in these models, CH213 was able to provide neuroprotection and reduce oxidative stress. Finally, since QR2, also known as MT3, is overexpressed in AD patients, we sought of interest to perform a molecular docking study to evaluate how the compounds could interact with this receptor. In conclusion, CH213 is a melatonin derivative that induces NRF2 with antineuroinflammatory, antioxidant and neuroprotective properties; however, future studies in in vivo AD models need to be conducted to validate the in vitro results here obtained.

The potential of conjugated polymers to compete with inorganic materials in the field of semiconductor is conditional on fine-tuning of the charge carriers mobility. The latter is closely related to the material morphology, and various studies have shown that the bottleneck for charge transport is the connectivity between well-ordered crystallites, with a high degree of pi-pi stacking, dispersed into a disordered matrix. However, at this time there is a lack of theoretical descriptions accounting for this link between morphology and mobility, hindering the development of systematic material designs. Here we propose a computational model to predict charge carriers mobility in conducting polymer PEDOT depending on the physicochemical properties of the system. We start by calculating the morphology using molecular dynamics simulations. Based on the calculated morphology we perform quantum mechanical calculation of the transfer integrals between states in polymer chains and calculate corresponding hopping rates using the Miller-Abrahams formalism. We then construct a transport resistive network, calculate the mobility using a mean-field approach, and analyze the calculated mobility in terms of transfer integrals distributions and percolation thresholds. Our results provide theoretical support for the recent study [Noriega et al., Nat Mater 12, 1038 (2013)] explaining why the mobility in polymers rapidly increases as the chain length is increased and then saturates for sufficiently long chains. Our study also provides the answer to the long-standing question whether the enhancement of the crystallinity is the key to designing high-mobility polymers. We demonstrate, that it is the effective pi-pi stacking, not the long-range order that is essential for the material design for the enhanced electrical performance. This generic model can compare the mobility of a polymer thin film with different solvent contents, solvent additives, dopant species or polymer characteristics, QC 20181213

The organic electronic ion pump (OEIP) has been developed as an “iontronic” tool for delivery of biological signaling compounds. OEIPs rely on electrophoretically “pumping” charged compounds, either at neutral or shifted pH, through an ion-selective channel. Significant shifts in pH lead to an abundance of H+ or OH–, which are delivered along with the intended substance. While this method has been used to transport various neurotransmitters, the role of pH has not been explored. Here we present an investigation of the role of pH on OEIP transport efficiency using the neurotransmitter γ-aminobutyric acid (GABA) as the model cationic delivery substance. GABA transport is evaluated at various pHs using electrical and chemical characterization and compared to molecular dynamics simulations, all of which agree that pH 3 is ideal for GABA transport. These results demonstrate a useful method for optimizing transport of other substances and thus broadening OEIP applications., Funding agencies: EU Seventh Framework Programme [607896]; Knut and Alice Wallenberg Foundation [2012.0302]; Onnesjo Foundation

A recently synthesized self-doped conducting oligomer, salt of bis[3,4-ethylenedioxythiophene]3thiophene butyric acid, ETE-S, is a novel promising material for green energy applications. Recently, it has been demonstrated that it can polymerize in vivo, in plant systems, leading to a formation of long-range conducting wires, charge storage and supercapacitive behaviour of living plants. Here we investigate the morphology of ETE-S combining the experimental characterisation using Grazing Incidence Wide Angle X-ray Scattering (GIWAXS) and atomistic molecular dynamics (MD) simulations. The GIWAXS measurements reveal a formation of small crystallites consisting of π–π stacked oligomers (with the staking distance 3.5 Å) that are further organized in h00 lamellae. These experimental results are confirmed by MD calculations, where we calculated the X-ray diffraction pattern and the radial distribution function for the distance between ETE-S chains. Our MD simulations also demonstrate the formation of the percolative paths for charge carriers that extend throughout the whole structure, despite the fact that the oligomers are short (6–9 rings) and crystallites are thin along the π–π stacking direction, consisting of only two or three π–π stacked oligomers. The existence of the percolative paths explains the previously observed high conductivity in in vivo polymerized ETE-S. We also explored the geometrical conformation of ETE-S oligomers and the bending of their aliphatic chains as a function of the oligomer lengths., Funding agencies: Swedish Energy Agency [38332-1]; Knut and Alice Wallenberg Foundation; Marie Sklodowska Curie Individual Fellowship (MSCA-IF-EF-ST) [702641]

Coarse grained (CG) modeling has been applied to study the influence of the Trastuzumab monoclonal antibody on the structure and dynamics of the full ErbB2 receptor dimer, including the lipid bilayer. The usage of CG models to study such complexes is almost mandatory, at present, due to the large size of the whole system. We will show that the Martini model performs satisfactorily well, giving results well-matched with those obtained by atomistic models as well as with the experimental information existing on homolog receptors. For example, the extra and intracellular domains approach the bilayer surface in both the monomer and dimer cases. The Trastuzumab-Fab hinders the interaction of the receptors with the lipid bilayer. Another interesting effect of the antibody is the disruption of the antiparallel arrangement of the juxtamembrane segments in the dimer case. These findings might help to understand the effect of the antibody on the receptor bioactivity. Springer International Publishing Switzerland 2014