Enhancing MD simulations: ASGARD's automated analysis for GROMACS.

Molecular Dynamics (MD) simulations are essential in analyzing the physical movement of molecules, with GROMACS being a widely recognized open-source package for this purpose. However, conducting analyses individually in GROMACS can take excessive time and effort. Addressing this challenge, we introduce ASGARD, an innovative workflow designed to streamline and automate the analysis of MD simulation of protein or protein-ligand complex. Unlike the traditional, manual approach, ASGARD enables researchers to generate comprehensive analyses with a single command line, significantly accelerating the research process and avoiding the laborious task of manual report generation. This tool automatically performs a range of analyses post-simulation, including system stability and flexibility assessments through RMSD Fluctuation and Distribution calculations. It further provides dynamic analysis using SASA, DSSP method graphs, and various interaction analyses. A key feature of ASGARD is its user-friendly design; it requires no additional installations or dependencies, making it highly accessible for researchers. In conclusion, ASGARD simplifies the MD simulation analysis process and substantially enhances efficiency and productivity in molecular research by providing an integrated, one-command analysis solution.Communicated by Ramaswamy H. Sarma.

An Interpretable Machine Learning Approach to Predict Sensory Processing Sensitivity Trait in Nursing Students.

Sensory processing sensitivity (SPS) is a personality trait that makes certain individuals excessively sensitive to stimuli. People carrying this trait are defined as Highly Sensitive People (HSP). The SPS trait is notably prevalent among nursing students and nurse staff. Although there are HSP diagnostic tools, there is little information about early detection. Therefore, the aim of this work was to develop a prediction model to identify HSP and provide an individualized nursing assessment. A total of 672 nursing students completed all the evaluations. In addition to the HSP diagnosis, emotional intelligence, communication skills, and conflict styles were evaluated. An interpretable machine learning model was trained to predict the SPS trait. We observed a 33% prevalence of HSP, which was higher in women and people with previous health training. HSP were characterized by greater emotional repair (p = 0.033), empathy (p = 0.030), respect (p = 0.038), and global communication skills (p = 0.036). Overall, sex and emotional intelligence dimensions are important to detect this trait, although personal characteristics should be considered. The present individualized prediction model could help to predict the presence of the SPS trait in nursing students, which may be useful in conducting intervention strategies to avoid the negative consequences and reinforce the positive ones of this trait.

ESSENCE-Dock: A Consensus-Based Approach to Enhance Virtual Screening Enrichment in Drug Discovery.

Drug development is a complex, costly, and time-consuming endeavor. While high-throughput screening (HTS) plays a critical role in the discovery stage, it is one of many factors contributing to these challenges. In certain contexts, virtual screening can complement the HTS, potentially offering a more streamlined approach in the initial stages of drug discovery. Molecular docking is an example of a popular virtual screening technique that is often used for this purpose; however, its effectiveness can vary greatly. This has led to the use of consensus docking approaches that combine results from different docking methods to improve the identification of active compounds and reduce the occurrence of false positives. However, many of these methods do not fully leverage the latest advancements in molecular docking. In response, we present ESSENCE-Dock (Effective Structural Screening ENrichment ConsEnsus Dock), a new consensus docking workflow aimed at decreasing false positives and increasing the discovery of active compounds. By utilizing a combination of novel docking algorithms, we improve the selection process for potential active compounds. ESSENCE-Dock has been made to be user-friendly, requiring only a few simple commands to perform a complete screening while also being designed for use in high-performance computing (HPC) environments.

Piperazine-derived small molecules as potential Flaviviridae NS3 protease inhibitors. In vitro antiviral activity evaluation against Zika and Dengue viruses.

Since 2011 Direct Acting antivirals (DAAs) drugs targeting different non-structural (NS) viral proteins (NS3, NS5A or NS5B inhibitors) have been approved for clinical use in HCV therapies. However, currently there are not licensed therapeutics to treat Flavivirus infections and the only licensed DENV vaccine, Dengvaxia, is restricted to patients with preexisting DENV immunity. Similarly to NS5 polymerase, the NS3 catalytic region is evolutionarily conserved among the Flaviviridae family sharing strong structural similarity with other proteases belonging to this family and therefore is an attractive target for the development of pan-flavivirus therapeutics. In this work we present a library of 34 piperazine-derived small molecules as potential Flaviviridae NS3 protease inhibitors. The library was developed through a privileged structures-based design and then biologically screened using a live virus phenotypic assay to determine the half-maximal inhibitor concentration (IC50) of each compound against ZIKV and DENV. Two lead compounds, 42 and 44, with promising broad-spectrum activity against ZIKV (IC50 6.6 µM and 1.9 µM respectively) and DENV (IC50 6.7 µM and 1.4 µM respectively) and a good security profile were identified. Besides, molecular docking calculations were performed to provide insights about key interactions with residues in NS3 proteases' active sites.

Identification of Kukoamine A, Zeaxanthin, and Clexane as New Furin Inhibitors.

The endogenous protease furin is a key protein in many different diseases, such as cancer and infections. For this reason, a wide range of studies has focused on targeting furin from a therapeutic point of view. Our main objective consisted of identifying new compounds that could enlarge the furin inhibitor arsenal; secondarily, we assayed their adjuvant effect in combination with a known furin inhibitor, CMK, which avoids the SARS-CoV-2 S protein cleavage by means of that inhibition. Virtual screening was carried out to identify potential furin inhibitors. The inhibition of physiological and purified recombinant furin by screening selected compounds, Clexane, and these drugs in combination with CMK was assayed in fluorogenic tests by using a specific furin substrate. The effects of the selected inhibitors from virtual screening on cell viability (293T HEK cell line) were assayed by means of flow cytometry. Through virtual screening, Zeaxanthin and Kukoamine A were selected as the main potential furin inhibitors. In fluorogenic assays, these two compounds and Clexane inhibited both physiological and recombinant furin in a dose-dependent way. In addition, these compounds increased physiological furin inhibition by CMK, showing an adjuvant effect. In conclusion, we identified Kukoamine A, Zeaxanthin, and Clexane as new furin inhibitors. In addition, these drugs were able to increase furin inhibition by CMK, so they could also increase its efficiency when avoiding S protein proteolysis, which is essential for SARS-CoV-2 cell infection.

Social Cognition in Patients with Early-Onset Parkinson's Disease.

Social cognition (SC) deficits have been linked to Parkinson's disease (PD) but have been less well researched than general cognitive processes, especially in early-onset PD (EOPD), despite this population often having greater social and family demands. Most studies focus on recognition of facial emotion, theory of mind (ToM), and decision-making domains, with limited research reporting on social reasoning. The main objective of this work was to compare SC ability across four domains: emotional processing, social reasoning, ToM, and decision-making between patients with EOPD and healthy controls. Twenty-five nondemented patients with EOPD and 25 controls matched for sex, age, and educational level were enrolled. A battery that included six SC tests was administered to all study participants; a decision-making scale was completed by participants' partners. Statistically significant differences were found between patients with EOPD and controls in all subtests across the four SC domains studied. The EOPD group demonstrated worse performance on all tasks, with large effect sizes. Differences remained significant after adjusting for Montreal Cognitive Assessment (MoCA) test scores for all SC subtests except the decision-making scale and the Iowa gambling task. No significant correlations between SC and other clinical PD variables were found. Our study shows that patients with EOPD perform significantly below controls in multiple SC domains affecting recognition of facial emotion, social reasoning, ToM, and decision-making. Only decision-making seems to be mediated by overall cognitive ability. The confounding or contributing effect of other clinical PD variables should be studied further.

Selective Binding of Cyclodextrins with Leflunomide and Its Pharmacologically Active Metabolite Teriflunomide.

The selectivity of encapsulation of leflunomide and teriflunomide by native α-, ß- and γ-cyclodextrins was investigated through 1H NMR and molecular modeling. Thermodynamic analysis revealed the main driving forces involved in the binding. For α-cyclodextrin, the partial encapsulation was obtained while deep penetration was characterized for the other two cyclodextrins, where the remaining polar fragment of the molecule is located outside the macrocyclic cavity. The interactions via hydrogen bonding are responsible for high negative enthalpy and entropy changes accompanying the complexation of cyclodextrins with teriflunomide. These results were in agreement with the molecular modeling calculations, which provide a clearer picture of the involved interactions at the atomic level.

Enfermedad de Devic. Reporte de caso y revisión de literatura / Devic's disease. A case report and literature review

Resumen La neuromielitis óptica (NMO) o enfermedad de Devic, es una enfermedad inflamatoria infrecuente del sistema nervioso central (SNC) que afecta predominantemente el nervio óptico y la médula espinal. El mecanismo de la enfermedad es dado por la producción de anticuerpos IgG cuyo principal blanco inmunitario es el canal acuaporina 4 (AQP4), los cuales desencadenan un proceso inflamatorio y desmielinizante en dichas estructuras. Presentamos el caso de una paciente, quien desarrolló episodios sensitivos crónicos fluctuantes con afección visual, sin mejoría con el tratamiento convencional; durante el abordaje diagnóstico se encontraron lesiones desmielinizantes y anticuerpos anti-AQP4 positivos, por lo que se concluyó el diagnóstico de NMO, y respondió de manera positiva al tratamiento con anticuerpos monoclonales.

Abstract Optic neuromyelitis or Devic's disease is a rare inflammatory disease of the central nervous system (CNS) that predominantly affects the optic nerve and spinal cord. The mechanism of the disease is given by the production of IgG antibodies whose main target is the acuaporine channel 4 (AQP4) that trigger an inflammatory and demyelinating process in the aforementioned structures. We present the case of a patient who developed chronic and fluctuating sensitive episodes with visual impairment, without improvement after conventional treatment. During the diagnostic approach we found demyelinating lesions and positive AQP4-antibodies, this lead to a diagnosis of optic neuromyelitis. A positive response was obtained to the therapy with monoclonal antibodies.

[Clinical and demographic characteristics of patients with multiple sclerosis]. / Características clínicas y demográficas de los pacientes con esclerosis múltiple.

BACKGROUND: Multiple sclerosis (MS) is a disease whose physiopathogenesis shows a complex interaction of genetic and environmental factors. Given that those factors have not been documented in our country, we describe the clinical and demographic characteristics from a sample of patients with MS. METHODS: We carried out an observational, descriptive, cross-sectional, and retrolective study in a Center for Demyelinating Diseases. We took the information from the clinical records of a sample of patients with multiple sclerosis, who arrived to the center from April 2014 to July 2015. RESULTS: We obtained data from 313 patients, out of which 65.5 % were women. Mean age was 41 years (SD 11.22). Minimum age of diagnosis was 12 years and maximum, 66 years; mean age of diagnosis was 32 years (SD 9.72). With regards to clinical variables, 3.4 % presented radiologically isolated syndrome (RIS), 82 % relapsing-remitting MS (RRMS), 13.9 % secondary-progressive MS (SPMS), and 0.8 % primary-progressive MS (PPMS). Of all the patients, 10 % had first or second degree relatives with diagnosis of this disease; 16 % had foreign ancestors; 27 % were smokers. Treatment consisted of glatiramer acetate, 28 %; intramuscular interferon beta 1a, 18 %; subcutaneous interferon beta 1a, 16 %; subcutaneous interferon beta 1b, 30 %; fingolimod, 3 %; and others, 5 %. CONCLUSIONS: Clinical and demographic characteristics are similar to those reported in international literature. More studies would be needed to typify Mexican population with MS.

Introducción: la esclerosis múltiple (EM) es una enfermedad que presenta una compleja interacción de factores genéticos y ambientales en su fisiopatogenia. Dado que esos factores han sido poco abordados en México, describimos las características clínicas y demográficas de una muestra de pacientes con EM. Métodos: estudio observacional, descriptivo, transversal y retrolectivo, realizado en un hospital de tercer nivel. Se obtuvo información de expedientes clínicos de una muestra de pacientes con el diagnóstico de EM, captados de abril de 2014 a julio de 2015. Resultados: se obtuvieron datos de 313 pacientes, 65.5 % mujeres, con edad promedio de 41 años (DE 11.22). La edad mínima del diagnóstico fue de 12 años y la máxima de 66; el promedio de edad del diagnóstico fue 32 años (DE 9.72). De la variante clínica 3.4 % tuvo síndrome neurológico aislado (CIS), EM remitente-recurrente 82 %, EM secundaria progresiva 13.9 % y EM primaria progresiva 0.8 %. El 10 % de los pacientes tenía parentesco de primer o segundo grado con diagnóstico de EM. El 16 % tuvo ascendencia extranjera. El 27 % tenía hábito tabáquico. Los tratamientos utilizados fueron el acetato de glatiramero 28 %, interferon beta 1a IM 18 %, interferon beta 1a SC 16 %, interferon beta 1b SC 30 %, fingolimod 3 % y otros 5 %. Conclusiones: las características clínicas y demográficas son similares a lo reportado en la literatura internacional. Se requieren más estudios para caracterizar mejor a la población mexicana con EM.