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We have investigated the lithium capacity of the 2H phase of niobium sulfide (NbS2) using density functional theory calculations and experiments. Theoretically, this material is found to allow the intercalation of a double layer of Li in between each NbS2 layer when in equilibrium with metal Li. The resulting specific capacity (340.8 mAh/g for the pristine material, 681.6 mAh/g for oxidized material) can reach more than double the specific capacity of graphite anodes. The presence of various defects leads to an even higher capacity with a partially reversible conversion of the material, indicating that the performance of the anodes is robust with respect to the presence of defects. Experiments in battery prototypes with NbS2-based anodes find a first specific capacity of about 1,130 mAh/g, exceeding the theoretical predictions.
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Two new monooxygenase biocatalysts, the Baeyer-Villiger monooxygenase BVMO145 and the flavin monooxygenase FMO401 from Almac library, have been found to catalyse the enantiodivergent oxidation of sulfides bearing N-heterocyclic substituents into sulfoxides under mild and green conditions. The biocatalyst BVMO145 provides (S)-sulfoxides while the flavin monooxygenase FMO401 affords (R)-sulfoxides with good conversions and high ee.
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Enzymatic peptide synthesis is a powerful alternative to solid-phase methods, as enzymes can have high regio- and stereoselectivity and high yield and require mild reaction conditions. This is beneficial in formulation research due to the rise of nucleic acid therapies. Peptide nucleic acids (PNAs) have a high affinity toward DNA and RNA, and their solubility and cellular delivery can be improved via conjugation to peptides. Here, we designed and assessed the viability of the papain enzyme to conjugate four PNA-peptide models in water and an organic solvent using QM/MM metadynamics. We found that the reactions in water yield better results, where three conjugates could potentially be synthesized by the enzyme, with the first transition state as the rate-limiting step, with an associated energy of 14.53 kcal mol-1, although with a slight endergonic profile. The results highlight the importance of considering the enzyme pockets and different substrate acceptivities and contribute to developing greener, direct, and precise synthetic routes for nucleic acid-based therapies. By exploring the enzyme's potential in conjunction with chemical synthesis, current protocols can be simplified for the synthesis of longer nucleic acids and peptide sequences (and, by extension, proteins) from smaller oligo or peptide blocks.
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Teoria da Densidade Funcional , Papaína , Ácidos Nucleicos Peptídicos , Peptídeos , Solventes , Água , Ácidos Nucleicos Peptídicos/química , Papaína/química , Papaína/metabolismo , Água/química , Solventes/química , Peptídeos/química , Simulação de Dinâmica MolecularRESUMO
van der Waals heterojunctions based on transition-metal dichalcogenides (TMDs) offer advanced strategies for manipulating light-emitting and light-harvesting behaviors. A crucial factor determining the light-material interaction is in the band alignment at the heterojunction interface, particularly the distinctions between type-I and type-II alignments. However, altering the band alignment from one type to another without changing the constituent materials is exceptionally difficult. Here, utilizing Bi2O2Se with a thickness-dependent band gap as a bottom layer, we present an innovative strategy for engineering interfacial band configurations in WS2/Bi2O2Se heterojunctions. In particular, we achieve tuning of the band alignment from type-I (Bi2O2Se straddling WS2) to type-II and finally to type-I (WS2 straddling Bi2O2Se) by increasing the thickness of the Bi2O2Se bottom layer from monolayer to multilayer. We verified this band architecture conversion using steady-state and transient spectroscopy as well as density functional theory calculations. Using this material combination, we further design a sophisticated band architecture incorporating both type-I (WS2 straddles Bi2O2Se, fluorescence-quenched) and type-I (Bi2SeO5 straddles WS2, fluorescence-recovered) alignments in one sample through focused laser beam (FLB). By programming the FLB trajectory, we achieve a predesigned localized fluorescence micropattern on WS2 without changing its intrinsic atomic structure. This effective band architecture design strategy represents a significant leap forward in harnessing the potential of TMD heterojunctions for multifunctional photonic applications.
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Women in developing countries still face enormous challenges when accessing reproductive health care. Access to voluntary family planning empowers women allowing them to complete their education and join the paid workforce. This effectively helps to end poverty, hunger and promotes good health for all. According to the United Nations (UN) organization, in 2022, an estimated 257 million women still lacked access to safe and effective family planning methods globally. One of the main barriers is the associated cost of modern contraceptive methods. Funded by the Bill & Melinda Gates Foundation, Almac Group worked on the development of a novel biocatalytic route to etonogestrel and levonorgestrel, two modern contraceptive APIs, with the goal of substantially decreasing the cost of production and so enabling their use in developing nations. This present work combines the selection and engineering of a carbonyl reductase (CRED) enzyme from Almac's selectAZyme™ panel, with process development, to enable efficient and economically viable bioreduction of ethyl secodione to (13R,17S)-secol, the key chirality introducing intermediate en route to etonogestrel and levonorgestrel API. CRED library screening returned a good hit with an Almac CRED from Bacillus weidmannii, which allowed for highly stereoselective bioreduction at low enzyme loading of less than 1% w/w under screening assay conditions. However, the only co-solvent tolerated was DMSO up to â¼30% v/v, and it was impossible to achieve reaction completion with any enzyme loading at substrate titres of 20 g L-1 and above, due to the insolubility of the secodione. This triggered a rapid enzyme engineering program fully based on computational mutant selection. A small panel of 93 CRED mutants was rationally designed to increase the catalytic activity as well as thermal and solvent stability. The best mutant, Mutant-75, enabled a reaction at 45 °C to go to completion at 90 g L-1 substrate titre in a buffer/DMSO/heptane reaction medium fed over 6 h with substrate DMSO stock solution, with a low enzyme loading of 3.5% w/w wrt substrate. In screening assay conditions, Mutant-75 also showed a 2.2-fold activity increase. Our paper shows which computations and rational decisions enabled this outcome.
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PURPOSE: There are no clinical treatments to prevent/revert age-related alterations associated with oocyte competence decline in the context of advanced maternal age. Those alterations have been attributed to oxidative stress and mitochondrial dysfunction. Our study aimed to test the hypothesis that in vitro maturation (IVM) medium supplementation with antioxidants (resveratrol or phloretin) may revert age-related oocyte competence decline. METHODS: Bovine immature oocytes were matured in vitro for 23 h (young) and 30 h (aged). Postovulatory aged oocytes (control group) and embryos obtained after fertilization were examined and compared with oocytes supplemented with either 2 µM of resveratrol or 6 µM phloretin (treatment groups) during IVM. RESULTS: Aged oocytes had a significantly lower mitochondrial mass and proportion of mitochondrial clustered pattern, lower ooplasmic volume, higher ROS, lower sirtuin-1 protein level, and a lower blastocyst rate in comparison to young oocytes, indicating that postovulatory oocytes have a lower quality and developmental competence, thus validating our experimental model. Supplementation of IVM medium with antioxidants prevented the generation of ROS and restored the active mitochondrial mass and pattern characteristic of younger oocytes. Moreover, sirtuin-1 protein levels were also restored but only following incubation with resveratrol. Despite these findings, the blastocyst rate of treatment groups was not significantly different from the control group, indicating that resveratrol and phloretin could not restore the oocyte competence of postovulatory aged oocytes. CONCLUSION: Resveratrol and phloretin can both revert the age-related oxidative stress and mitochondrial dysfunction during postovulatory aging but were insufficient to enhance embryo developmental rates under our experimental conditions.
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The CRISPR/Cas9 system has emerged as a promising platform for gene editing; however, the lack of an efficient and safe delivery system to introduce it into cells continues to hinder clinical translation. Here, we report a rationally designed gene-editing nanoparticle (NP) formulation for brain applications: an sgRNA:Cas9 ribonucleoprotein complex is immobilized on the NP surface by oligonucleotides that are complementary to the sgRNA. Irradiation of the formulation with a near-infrared (NIR) laser generates heat in the NP, leading to the release of the ribonucleoprotein complex. The gene-editing potential of the formulation was demonstrated in vitro at the single-cell level. The safety and gene editing of the formulation were also demonstrated in the brains of reporter mice, specifically in the subventricular zone after intracerebral administration and in the olfactory bulb after intranasal administration. The formulation presented here offers a new strategy for the spatially controlled delivery of the CRISPR system to the brain.
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Encéfalo , Sistemas CRISPR-Cas , Edição de Genes , Raios Infravermelhos , Edição de Genes/métodos , Sistemas CRISPR-Cas/genética , Animais , Encéfalo/metabolismo , Camundongos , Ribonucleoproteínas/metabolismo , Ribonucleoproteínas/química , Ribonucleoproteínas/genética , Nanopartículas/química , HumanosRESUMO
Platelet-rich plasma (PRP) has emerged as a promising therapy in regenerative medicine. However, the lack of standardization in PRP preparation protocols presents a challenge in achieving reproducible and accurate results. This study aimed to optimize the PRP preparation protocol by investigating the impact of two different anticoagulants, sodium citrate (SC) and ethylenediaminetetraacetic acid (EDTA), and resuspension media, plasma versus sodium chloride (NaCl). Platelet recovery rates were calculated and compared between groups, in addition to platelet activity and vascular endothelial growth factor (VEGF) released into plasma after PRP activation. The platelet recovery rate was higher with EDTA in comparison to SC (51.04% vs. 29.85%, p = 0.005). Platelet activity was also higher, with a higher expression of two platelet antibodies, platelet surface P-Selectin (CD62p) and PAC-1, in the EDTA group. The concentration of VEGF was higher with SC in comparison to EDTA (628.73 vs. 265.44 pg/mL, p = 0.013). Platelet recovery rates and VEGF levels were higher in PRP resuspended in plasma when compared to NaCl (61.60% vs. 48.61%, p = 0.011 and 363.32 vs. 159.83 pg/mL, p = 0.005, respectively). Our study reinforces the superiority of EDTA (as anticoagulant) and plasma (for resuspension) in obtaining a higher platelet recovery and preserving platelet functionality during PRP preparation.
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Age-related changes in the mitochondrial status of human cumulus cells (hCCs) impact oocyte quality; however, the relationship between hCC mitochondrial (dys)function and reproductive aging remains poorly understood. This study aimed to establish the interplay between hCC mitochondrial dysfunction and women's reproductive potential. In this investigation, 266 women were enrolled and categorized into two groups based on their age: a young group (<35 years old) and an advanced maternal age (AMA) group (≥35 years old). Comprehensive analysis of reproductive outcomes was conducted in our population. Various mitochondrial-related parameters were analyzed across distinct subsets. Specifically, mitochondrial membrane potential (∆Ψm) and mitochondrial mass were examined in 53 samples, mtDNA content in 25 samples, protein levels in 23 samples, bioenergetic profiles using an XF24 Extracellular Flux Analyzer in 6 samples, and levels of reactive oxygen species (ROS) and adenosine triphosphate (ATP) in 39 and 43 samples, respectively. In our study, the reproductive potential of AMA women sharply decreased, as expected. Additionally, an impairment in the mitochondrial function of hCCs in older women was observed; however, no differences were found in terms of mitochondrial content. Regarding oxidative phosphorylation, metabolic profiling of hCCs from AMA women indicated a decrease in respiratory capacity, which was correlated with an age-dependent decrease in the ATP synthase (ATP5A1) protein level. However, intracellular ROS and ATP levels did not differ between groups. In conclusion, our study indicates that age-related dysfunction in hCCs is associated with impaired mitochondrial function, and, although further studies are required, ATP synthase could be relevant in this impairment.
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Células do Cúmulo , Doenças Mitocondriais , Humanos , Feminino , Idoso , Adulto , Células do Cúmulo/metabolismo , Trifosfato de Adenosina/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Mitocôndrias/metabolismoRESUMO
Nucleic acid technologies with designed intracellular delivery systems are some of the most promising therapies of the future. Small interfering (si)RNAs inhibit gene expression and protein synthesis and may complement current vaccines with faster design and production. Although successful delivery remains an issue, delivery peptides may help to fill this gap. Here, we address this issue by applying bioinformatic approaches to design new putative cell delivery peptides and siRNAs for COVID-19 variants and other related viral diseases. Of the 29,880 RNA sequences analyzed, 62 were identified in silico as able to target the virus mRNA sequence, and from the 9,984 peptide sequences analyzed, 10 were selected as delivery peptides. From the latter, we further performed in vitro studies of the two best-ranked peptides and compared them with the broadly used TAT delivery peptide. One of them, seq5, displayed better internalization results with about double intensity signal compared to TAT after a 1 h incubation time in GFP-HeLa cells. This peptide has, thus, the features of a delivery peptide and could be used for cargo intracellular delivery.
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COVID-19 , SARS-CoV-2 , Humanos , RNA Interferente Pequeno/genética , SARS-CoV-2/genética , Células HeLa , Peptídeos/metabolismoRESUMO
Background: Chagas disease and human African trypanosomiasis cause substantial death and morbidity, particularly in low- and middle-income countries, making the need for novel drugs urgent. Methodology & results: Therefore, an explainable multitask pipeline to profile the activity of compounds against three trypanosomes (Trypanosoma brucei brucei, Trypanosoma brucei rhodesiense and Trypanosoma cruzi) were created. These models successfully discovered four new experimental hits (LC-3, LC-4, LC-6 and LC-15). Among them, LC-6 showed promising results, with IC50 values ranging 0.01-0.072 µM and selectivity indices >10,000. Conclusion: These results demonstrate that the multitask protocol offers predictivity and interpretability in the virtual screening of new antitrypanosomal compounds and has the potential to improve hit rates in Chagas and human African trypanosomiasis projects.
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Doença de Chagas , Tripanossomicidas , Trypanosoma brucei brucei , Trypanosoma cruzi , Tripanossomíase Africana , Animais , Humanos , Tripanossomíase Africana/tratamento farmacológico , Tripanossomicidas/farmacologia , Doença de Chagas/tratamento farmacológicoRESUMO
The majority of animal studies on methylphenidate (MP) use intraperitoneal (IP) injections, subcutaneous (SC) injections, or the oral gavage route of administration. While all these methods allow for delivery of MP, it is the oral route that is clinically relevant. IP injections commonly deliver an immediate and maximum dose of MP due to their quick absorption. This quick-localized effect can give timely results but will only display a small window of the psychostimulant's effects on the animal model. On the opposite side of the spectrum, a SC injection does not accurately represent the pathophysiology of an oral exposure because the metabolic rate of the drug would be much slower. The oral-gavage method, while providing an oral route, possesses some adverse effects such as potential animal injury and can be stressful to the animal compared to voluntary drinking. It is thus important to allow the animal to have free consumption of MP, and drinking it to more accurately mirror human treatment. The use of a two-bottle drinking method allows for this. Rodents typically have a faster metabolism than humans, which means this needs to be considered when administering MP orally while reaching target pharmacokinetic levels in plasma. With this oral two-bottle approach, the pathophysiological effects of MP on development, behavior, neurochemistry and brain function can be studied. The present review summarizes these effects of oral MP which have important implications in medicine.
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Methionine sulfoxide reductase A (MsrA) enzymes have recently found applications as nonoxidative biocatalysts in the enantioselective kinetic resolution of racemic sulfoxides. This work describes the identification of selective and robust MsrA biocatalysts able to catalyze the enantioselective reduction of a variety of aromatic and aliphatic chiral sulfoxides at 8-64 mM concentration with high yields and excellent ees (up to 99%). Moreover, with the aim to expand the substrate scope of MsrA biocatalysts, a library of mutant enzymes has been designed via rational mutagenesis utilizing in silico docking, molecular dynamics, and structural nuclear magnetic resonance (NMR) studies. The mutant enzyme MsrA33 was found to catalyze the kinetic resolution of bulky sulfoxide substrates bearing non-methyl substituents on the sulfur atom with ees up to 99%, overcoming a significant limitation of the currently available MsrA biocatalysts.
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INTRODUCTION: Polycystic ovary syndrome (PCOS) is a common endocrine disorder often leading to anovulatory infertility. PCOS pathophysiology is still unclear and several potential genetic susceptibility factors have been proposed. The effect of polymorphisms in two genesrelated to follicular recruitment and development, the follicle-stimulating hormone receptor (FSHR) and the estrogen receptor 1 (ESR1), have been studied in different populations with contradictory results. AIMS: To evaluate the influence of FSHR rs6166 (c.2039A>G) and of ESR1 rs2234693 (Pvull c.453-397 T > C) polymorphisms on PCOS risk, phenotype, and response to controlled ovarian stimulation (COS). MATERIALS AND METHODS: Genotyping of the FSHR rs6166 and the ESR1 rs2234693 polymorphisms was performed in PCOS women and a control group undergoing in vitro fertilization (IVF). Demographic, clinical, and biochemical data, genotype frequency, and IVF outcomes were compared between groups. RESULTS: We evaluated 88 PCOS women and 80 controls. There was no significant difference in the genotype distribution of FSHR rs6166 polymorphism between PCOS women and controls (AA 31.8%/AS 48.9%/SS 19.3% in PCOS women vs AA 37.5%/AS 40.0%/SS 22.5% in controls; p = 0.522). The same was true for the ESR1 rs2234693 (CC 24.1%/CT 46.0%/TT 29.9% in PCOS women vs CC 18.8%/CT 48.8%/TT 32.5% in controls; p = 0.697). In PCOS women, we found higher follicle-stimulating hormone (FSH) levels on the third day of the menstrual cycle associated with the SS variant of the FSHR polymorphism (9.2 vs 6.2 ± 1.6 and 5.6 ± 1.6 mUI/mL; p = 0.011). We did not find other associations between the baseline hormonal parameters, antral follicle count, and response measures to COS with FSHR or ESR1 genotypes. We found, however, a need for higher cumulative doses of FSH for COS in patients with the SS variant of the FSHR rs6166 polymorphism (1860.5 ± 627.8 IU for SSvs 1498.1 ± 359.3 for AA and 1425.4 ± 474.8 for SA; p = 0.046 and p = 0.046). CONCLUSION: Our data suggest that in the population, FSHR rs6166and ESR1 rs2234693 polymorphisms do not influence the risk of developing PCOS nor do they influence the patient's phenotype and IVF success. However, the SS variant of the FSHR rs6166 polymorphism may be associated with FSH resistance requiring higher FSH doses for COS.
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In the healthcare sector, resorting to big data and advanced analytics is a great advantage when dealing with complex groups of patients in terms of comorbidities, representing a significant step towards personalized targeting. In this work, we focus on understanding key features and clinical pathways of patients with multimorbidity suffering from Dementia. This disease can result from many heterogeneous factors, potentially becoming more prevalent as the population ages. We present a set of methods that allow us to identify medical appointment patterns within a cohort of 1924 patients followed from January 2007 to August 2021 in Hospital da Luz (Lisbon), and to stratify patients into subgroups that exhibit similar patterns of interaction. With Markov Chains, we are able to identify the most prevailing medical appointments attended by Dementia patients, as well as recurring transitions between these. To perform patient stratification, we applied AliClu, a temporal sequence alignment algorithm for clustering longitudinal clinical data, which allowed us to successfully identify patient subgroups with similar medical appointment activity. A feature analysis per cluster obtained allows the identification of distinct patterns and characteristics. This pipeline provides a tool to identify prevailing clinical pathways of medical appointments within the dataset, as well as the most common transitions between medical specialities within Dementia patients. This methodology, alongside demographic and clinical data, has the potential to provide early signalling of the most likely clinical pathways and serve as a support tool for health providers in deciding the best course of treatment, considering a patient as a whole.
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Demência , Multimorbidade , Humanos , Cadeias de Markov , Comorbidade , Algoritmos , Demência/diagnósticoRESUMO
The use of nucleotides for biomedical applications is an old desire in the scientific community. As we will present here, there are references published over the past 40 years with this intended use. The main problem is that, as unstable molecules, nucleotides require some additional protection to extend their shelf life in the biological environment. Among the different nucleotide carriers, the nano-sized liposomes proved to be an effective strategic tool to overcome all these drawbacks related to the nucleotide high instability. Moreover, due to their low immunogenicity and easy preparation, the liposomes were selected as the main strategy for delivery of the mRNA developed for COVID-19 immunization. For sure this is the most important and relevant example of nucleotide application for human biomedical conditions. In addition, the use of mRNA vaccines for COVID-19 has increased interest in the application of this type of technology to other health conditions. For this review article, we will present some of these examples, especially focused on the use of liposomes to protect and deliver nucleotides for cancer therapy, immunostimulatory activities, enzymatic diagnostic applications, some examples for veterinarian use, and the treatment of neglected tropical disease.
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The normalized compression distance (NCD) is a similarity measure between a pair of finite objects based on compression. Clustering methods usually use distances (e.g., Euclidean distance, Manhattan distance) to measure the similarity between objects. The NCD is yet another distance with particular characteristics that can be used to build the starting distance matrix for methods such as hierarchical clustering or K-medoids. In this work, we propose Zgli, a novel Python module that enables the user to compute the NCD between files inside a given folder. Inspired by the CompLearn Linux command line tool, this module iterates on it by providing new text file compressors, a new compression-by-column option for tabular data, such as CSV files, and an encoder for small files made up of categorical data. Our results demonstrate that compression by column can yield better results than previous methods in the literature when clustering tabular data. Additionally, the categorical encoder shows that it can augment categorical data, allowing the use of the NCD for new data types. One of the advantages is that using this new feature does not require knowledge or context of the data. Furthermore, the fact that the new proposed module is written in Python, one of the most popular programming languages for machine learning, potentiates its use by developers to tackle problems with a new approach based on compression. This pipeline was tested in clinical data and proved a promising computational strategy by providing patient stratification via clusters aiding in precision medicine.
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Compressão de Dados , Doenças não Transmissíveis , Espondilartrite , Humanos , Algoritmos , Compressão de Dados/métodos , Análise por ConglomeradosRESUMO
Intensive efforts have been made to provide better treatments to cancer patients. Currently, nanoparticle-based drug delivery systems have gained propulsion, as they can overcome the drawbacks of free drugs. However, drug stability inside the nanocapsule must be ensured to prevent burst release. To overcome this, drugs conjugated to amphiphilic copolymers, assembled into nanoparticles, can provide a sustained release if endogenously degraded. Thus, we have designed and assessed the drug release viability of polymer-drug conjugates by the human Carboxylesterase 2, for a targeted drug activation. We performed molecular dynamics simulations applying a quantum mechanics/molecular mechanics potential to study the degradation profiles of 30 designed conjugates, where six were predicted to be hydrolyzed by this enzyme. We further analyzed the enzyme-substrate environment to delve into what structural features may lead to successful hydrolysis. These findings contribute to the development of new medicines ensuring effective cancer treatments with fewer side effects.
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Nanopartículas , Neoplasias , Humanos , Polímeros/química , Portadores de Fármacos/química , Nanopartículas/química , Sistemas de Liberação de MedicamentosRESUMO
We describe an approach based on non-equilibrium molecular dynamics (NEMD) simulations to calculate the ionic mobility of solid ion conductors such as solid electrolytes from first-principles. The calculations are carried out in finite slabs of the material, where an electric field is applied and the dynamic response of the mobile ions is measured. We compare our results with those obtained from diffusion calculations, under the non-interacting ion approximation, and with experiment. This method is shown to provide good quantitative estimates for the ionic mobilities of two silver conductors, [Formula: see text]-AgI and [Formula: see text]-RbAg[Formula: see text]I[Formula: see text]. In addition to being convenient and numerically robust, this method accounts for ion-ion correlations at a much lower computational cost than exact approaches.
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Amanita phalloides is one of the most toxic mushrooms worldwide, being responsible for the majority of human fatal cases of mushroom intoxications. α-Amanitin, the most deleterious toxin of A. phalloides, inhibits RNA polymerase II (RNAP II), causing hepatic and renal failure. Herein, we used cyclosporine A after it showed potential to displace RNAP II α-amanitin in silico. That potential was not confirmed either by the incorporation of ethynyl-UTP or by the monitoring of fluorescent RNAP II levels. Nevertheless, concomitant incubation of cyclosporine A with α-amanitin, for a short period, provided significant protection against its toxicity in differentiated HepaRG cells. In mice, the concomitant administration of α-amanitin [0.45 mg/kg intraperitoneal (i.p.)] with cyclosporine A (10 mg/kg i.p. plus 2 × 10 mg/kg cyclosporine A i.p. at 8 and 12 h post α-amanitin) resulted in the full survival of α-amanitin-intoxicated mice, up to 30 days after the toxin's administration. Since α-amanitin is a substrate of the organic-anion-transporting polypeptide 1B3 and cyclosporine A inhibits this transporter and is a potent anti-inflammatory agent, we hypothesize that these mechanisms are responsible for the protection observed. These results indicate a potential antidotal effect of cyclosporine A, and its safety profile advocates for its use at an early stage of α-amanitin intoxications.