Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors

The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa. The descriptors are derived from traditional approaches quantifying the compounds' intrinsic physicochemical properties, together with, bacterium-specific from ensemble docking of compounds targeting specific MexB binding pockets, and all-atom molecular dynamics simulations in different subregions of the OM model. Using these descriptors and the measured inhibitory concentrations, we design a statistical protocol to identify predictors of OM permeation/inhibition. We find consistent rules across most of our data highlighting the role of the interaction between the compounds and the OM. An implementation of the rules uncovered in our study is shown, and it demonstrates the accuracy of our approach in a set of previously unseen compounds. Our analysis sheds new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa, and opens the gate to similar data-driven studies in other Gram-negative pathogens.

Direct Modulators of K-Ras-Membrane Interactions

Protein-membrane interactions (PMIs) are ubiquitous in cellular signaling. Initial steps of signal transduction cascades often rely on transient and dynamic interactions with the inner plasma membrane leaflet to populate and regulate signaling hotspots. Methods to target and modulate these interactions could yield attractive tool compounds and drug candidates. Here, we demonstrate that the conjugation of a medium-chain lipid tail to the covalent K-Ras(G12C) binder MRTX849 at a solvent-exposed site enables such direct modulation of PMIs. The conjugated lipid tail interacts with the tethered membrane and changes the relative membrane orientation and conformation of K-Ras(G12C), as shown by molecular dynamics (MD) simulation-supported NMR studies. In cells, this PMI modulation restricts the lateral mobility of K-Ras(G12C) and disrupts nanoclusters. The described strategy could be broadly applicable to selectively modulate transient PMIs.

Structural origin of the enhanced ionic conductivity upon Nb doping in Sr11Mo4O23 defective double perovskite

We report a substantial enhancement of the oxide-ion conductivity in Sr₁₁Mo₄O₂₃ achieved by Nb doping the Mo sites. This series responds to the formula: Sr₁₁Mo_4-xNb_xO_23-δ (with x = 0.0, 0.5 and 1.0). The original structure can be related to the conventional double perovskite; however, it presents a broken corner sharing connectivity of the octahedral framework, hence leading to a complex and highly defective network. The samples were prepared via citrate precursor method, followed by thermal treatments at 1300 °C for 12 hours in air. The crystal structures were refined from X-ray and neutron powder diffraction (NPD) data. A phase transition from tetragonal to cubic symmetry is identified in a temperature-dependent NPD study, driven by an oxygen delocalization effect. The ionic conductivity measured by impedance spectroscopy is enhanced upon Nb-doping; the x = 1 doped phase exhibits a threefold increase compared to the pristine Sr₁₁Mo₄O₂₃ oxide, with conductivity values of 7.6 × 10^-3 and 2.7 × 10^-2 S·cm^-1 at 650 and 800 °C, which are even greater than for YSZ in the 650-800 °C temperature range, and close to those reported for other state-of-the art solid-oxide electrolytes.

Broadly targeted CD8⁺ T cell responses restricted by major histocompatibility complex E

Major histocompatibility complex E (MHC-E) is a highly conserved, ubiquitously expressed, nonclassical MHC class Ib molecule with limited polymorphism that is primarily involved in the regulation of natural killer (NK) cells. We found that vaccinating rhesus macaques with rhesus cytomegalovirus vectors in which genes Rh157.5 and Rh157.4 are deleted results in MHC-E-restricted presentation of highly varied peptide epitopes to CD8αβ(+) T cells, at ~4 distinct epitopes per 100 amino acids in all tested antigens. Computational structural analysis revealed that MHC-E provides heterogeneous chemical environments for diverse side-chain interactions within a stable, open binding groove. Because MHC-E is up-regulated to evade NK cell activity in cells infected with HIV, simian immunodeficiency virus, and other persistent viruses, MHC-E-restricted CD8(+) T cell responses have the potential to exploit pathogen immune-evasion adaptations, a capability that might endow these unconventional responses with superior efficacy.

MARTINI coarse-grained model for crystalline cellulose microfibers

Commercial-scale biofuel production requires a deep understanding of the structure and dynamics of its principal target: cellulose. However, an accurate description and modeling of this carbohydrate structure at the mesoscale remains elusive, particularly because of its overwhelming length scale and configurational complexity. We have derived a set of MARTINI coarse-grained force field parameters for the simulation of crystalline cellulose fibers. The model is adapted to reproduce different physicochemical and mechanical properties of native cellulose Iβ. The model is able not only to handle a transition from cellulose Iβ to another cellulose allomorph, cellulose IIII, but also to capture the physical response to temperature and mechanical bending of longer cellulose nanofibers. By developing the MARTINI model of a solid cellulose crystalline fiber from the building blocks of a soluble cellobiose coarse-grained model, we have provided a systematic way to build MARTINI models for other crystalline biopolymers.

Envisioning the future of transhumant pastoralism through participatory scenario planning: a case study in Spain

Transhumance is a practice of nomadic pastoralism that was once common in Mediterranean Europe. This livestock-rearing system is associated with the maintenance of cultural landscapes and the delivery of a wide range of ecosystem services. Although transhumance is still practised in Spain on a small scale, its future is highly uncertain because of socioeconomic constraints and other drivers of change. A participatory scenario-planning exercise with 68 participants, including shepherds, decision-makers, veterinarians, environmental experts, intermediaries from the wool and meat markets, and researchers, was used to envision plausible futures for transhumance and to enlighten policy-making for the maintenance of this practice along the Conquense Drove Road, one of the largest foot-based transhumant social-ecological networks still in use in Spain. Specifically, the aims were to: (1) analyse the drivers influencing the future of transhumance, (2) depict the current situation of transhumance, (3) envision future scenarios for this activity, (4) analyse ecosystem services’ trade-offs between different scenarios and their effect on human wellbeing, and (5) provide some insights for policy-making related to the maintenance of transhumance. Four plausible future scenarios were built, each showing clear trade-offs in the delivery of 19 ecosystem services, such as food, fibre, ecological connectivity, soil fertility, air quality, fire prevention, cultural identity, local ecological knowledge and cultural exchanges, as well as the different dimensions of human wellbeing. As a result of the participatory process, nine management strategies were identified for the maintenance of transhumance. Priority was given to the implementation of payment schemes for ecosystem services, the enhancement of social capital among transhumants and institutional coordination, the improvement of product marketing, and the restoration and conservation of drove roads. Finally, the implications of the current reform of the Common Agricultural Policy in the European Union for the maintenance of transhumance are discussed.

Subjective response to antipsychotics in schizophrenic patients: clinical implications and related factors

Awad defined subjective response to medication as the subjective interpretation of the physiological changes that follow its intake. This response is involved in drug compliance and may relate to clinical outcome of the disease. This study examined the variables hypothesized to be related to subjective response to antipsychotics. Sixty schizophrenic in-patients were evaluated with a protocol that examined compliance, hospitalizations, psychopathology, familial and social relationships, degree of autonomy and motivation for life during the year prior to the study. Overall functioning in the previous year was assessed with the Global Assessment Scale (GAS), psychopathology with the Brief Psychopathology Rating Scale (BPRS), insight with the Birchwood scale and side-effects with the Uscandinavian Kociety of Usypharmacology (UKU) side-effects rating scale. Subjective response was evaluated with the Drug Attitude Inventory (DAI-30). The multiple regression analysis revealed that insight and the BPRS paranoid subscale predicted subjective response to antipsychotics (R2=0.31). No relationship was found between subjective response and sociodemographic variables or side-effects. A positive subjective response was related to drug compliance and variables that indicate a more benign clinical course over the previous year. Subjective response to antipsychotics in schizophrenia is related to insight and paranoid ideation.