Assessing the Martini 3 protein model: A review of its path and potential.

Coarse-grained (CG) protein models have become indispensable tools for studying many biological protein details, from conformational dynamics to the organization of protein macro-complexes, and even the interaction of proteins with other molecules. The Martini force field is one of the most widely used CG models for bio-molecular simulations, partly because of the enormous success of its protein model. With the recent release of a new and improved version of the Martini force field - Martini 3 - a new iteration of its protein model was also made available. The Martini 3 protein force field is an evolution of its Martini 2 counterpart, aimed at improving many of the shortcomings that had been previously identified. In this mini-review, we first provide a general overview of the model and then focus on the successful advances made in the short time since its release, many of which would not have been possible before. Furthermore, we discuss reported limitations, potential directions for model improvement and comment on what the likely future development and application avenues are.

CHEK2 germline variants identified in familial nonmedullary thyroid cancer lead to impaired protein structure and function.

Approximately 5 to 15% of nonmedullary thyroid cancers (NMTC) present in a familial form (familial nonmedullary thyroid cancers [FNMTC]). The genetic basis of FNMTC remains largely unknown, representing a limitation for diagnostic and clinical management. Recently, germline mutations in DNA repair-related genes have been described in cases with thyroid cancer (TC), suggesting a role in FNMTC etiology. Here, two FNMTC families were studied, each with two members affected with TC. Ninety-four hereditary cancer predisposition genes were analyzed through next-generation sequencing, revealing two germline CHEK2 missense variants (c.962A > C, p.E321A and c.470T > C, p.I157T), which segregated with TC in each FNMTC family. p.E321A, located in the CHK2 protein kinase domain, is a rare variant, previously unreported in the literature. Conversely, p.I157T, located in CHK2 forkhead-associated domain, has been extensively described, having conflicting interpretations of pathogenicity. CHK2 proteins (WT and variants) were characterized using biophysical methods, molecular dynamics simulations, and immunohistochemistry. Overall, biophysical characterization of these CHK2 variants showed that they have compromised structural and conformational stability and impaired kinase activity, compared to the WT protein. CHK2 appears to aggregate into amyloid-like fibrils in vitro, which opens future perspectives toward positioning CHK2 in cancer pathophysiology. CHK2 variants exhibited higher propensity for this conformational change, also displaying higher expression in thyroid tumors. The present findings support the utility of complementary biophysical and in silico approaches toward understanding the impact of genetic variants in protein structure and function, improving the current knowledge on CHEK2 variants' role in FNMTC genetic basis, with prospective clinical translation.

SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility.

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is having a devastating social and economic impact around the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss of vaccine and natural immunity, as well as increased transmissibility. All VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes. The spike glycoprotein binds to angiotensin-converting enzyme 2 (ACE2) via its receptor binding domain (RBD) initiating the infection process. Attempting to understand the effect of RBD mutations in VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect the RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of four VOCs (Alpha, Beta, Delta, and Omicron). Our results show that the wt RBD presents two distinct conformations: an "open" conformation where it is free to bind ACE2; and a "closed" conformation, where the RBM ridge blocks the binding surface. The Alpha and Beta variants shift the open/closed equilibrium towards the open conformation by roughly 20%, likely increasing ACE2 binding affinity. Simulations of the Delta and Omicron variants showed extreme results, with the closed conformation being rarely observed. The Delta variant also differed substantially from the other variants, alternating between the open conformation and an alternative "reversed" one, with a significantly changed orientation of the RBM ridge. This alternate conformation could provide a fitness advantage due to increased availability for ACE2 binding, and by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the Omicron and Delta variants, impact RBD conformational dynamics in a direction that promotes efficient binding to ACE2 and, in the case of Delta, may assist antibody escape.

Eventos adversos asociados al cuidado de la salud en adultos internados en dos hospitales de alta complejidad de Argentina / Healthcare-associated harm in adult patients hospitalized in two tertiary care centers in Argentina

Resumen El daño asociado al cuidado de la salud es relevante y altamente prevenible. El Global Trigger Tool es la principal metodología en uso para su cuantificación. Los objetivos del trabajo fueron cuantificar mediante dicha herramienta el daño asociado al cuidado durante la internación, caracterizar los tipos de daño involucrados, identificar los factores asociados y describir la utilización de la información recabada. Se trata de un estudio longitudinal retrospectivo. Se detectaron 266 eventos adversos totales entre los dos hospitales: 138 eventos en el Hospital A, y 128 eventos en el Hospital B. Esto es 61.3 eventos cada 1000 días paciente, y 62.5 eventos cada 1000 días paciente en A y B respectivamente, p = 0.3. En términos generales, construyendo una sola población de los dos hospitales, se hallaron 32 eventos adversos cada 100 admisiones, y 64.3 eventos cada 1000 días/pacientes. Los eventos estaban asociados en orden decreciente de frecuencia a: medicación (45.5%), infecciones (32.4%), procedimientos sin infección (15.2%), tromboembolismo pulmonar (4.8%), úlceras por presión (1.4%), dispositivos (0.7%). Las variables asociadas fueron polimedicación y polimorbilidad. Los factores asociados a la aparición de eventos adversos fueron el sexo femenino (OR: 2.1), la administración de medicamentos de alto riesgo (OR 2.3), la edad ≥ 80 años (OR 2.6) y el registro de ≥ 3 transferencias entre salas durante la internación (OR 2.9). Las tasas de daño observadas son comparables a las tasas evaluadas por el mismo método en estudios internacionales.

Abstract The damage associated with health care is relevant and highly preventable. The Global Trigger Tool is a leading methodology in use for its quantification. Our study aimed to quantify, through this tool, the damage associated with care during hospitalization, characterize the types of damage involved, identify the associated factors and describe the use of the information collected. We conducted a retrospective longitudinal study. A total of 266 adverse events were detected between the two hospitals: 138 events in Hospital A, and 128 in Hospital B, the patient days analyzed in each hospital were 2089 and 2046 respectively. This is 61.3 events every 1000 patient days, and 62.5 events every 1000 patient days in A and B respectively, p = 0.3. In general terms, constructing a single population of the two hospitals, 32 adverse events were found every 100 admis sions, and 64.3 events every 1000 days / patients. The events were associated in decreasing order of frequency with: medication (45.5%), infections (32.4%), procedures without infection (15.2%), pulmonary thromboembolism (4.8%), pressure ulcers (1.4%), devices (0.7%). The associated variables were polypharmacy and polymorbid ity. Factors associated with the occurrence of adverse events were female gender (OR: 2.1), administration of high-risk medications (OR 2.3), age ≥ 80 years (OR 2.6), and registration of ≥ 3 transfers between wards during hospitalization (OR 2.9). The observed damage rates are comparable to the rates evaluated by the same method in international studies.

[Healthcare-associated harm in adult patients hospitalized in two tertiary care centers in Argentina]. / Eventos adversos asociados al cuidado de la salud en adultos internados en dos hospitales de alta complejidad de Argentina.

The damage associated with health care is relevant and highly preventable. The Global Trigger Tool is a leading methodology in use for its quantification. Our study aimed to quantify, through this tool, the damage associated with care during hospitalization, characterize the types of damage involved, identify the associated factors and describe the use of the information collected. We conducted a retrospective longitudinal study. A total of 266 adverse events were detected between the two hospitals: 138 events in Hospital A, and 128 in Hospital B, the patient days analyzed in each hospital were 2089 and 2046 respectively. This is 61.3 events every 1000 patient days, and 62.5 events every 1000 patient days in A and B respectively, p = 0.3. In general terms, constructing a single population of the two hospitals, 32 adverse events were found every 100 admissions, and 64.3 events every 1000 days / patients. The events were associated in decreasing order of frequency with: medication (45.5%), infections (32.4%), procedures without infection (15.2%), pulmonary thromboembolism (4.8%), pressure ulcers (1.4%), devices (0.7%). The associated variables were polypharmacy and polymorbidity. Factors associated with the occurrence of adverse events were female gender (OR: 2.1), administration of high-risk medications (OR 2.3), age = 80 years (OR 2.6), and registration of = 3 transfers between wards during hospitalization (OR 2.9). The observed damage rates are comparable to the rates evaluated by the same method in international studies.

El daño asociado al cuidado de la salud es relevante y altamente prevenible. El Global Trigger Tool es la principal metodología en uso para su cuantificación. Los objetivos del trabajo fueron cuantificar mediante dicha herramienta el daño asociado al cuidado durante la internación, caracterizar los tipos de daño involucrados, identificar los factores asociados y describir la utilización de la información recabada. Se trata de un estudio longitudinal retrospectivo. Se detectaron 266 eventos adversos totales entre los dos hospitales: 138 eventos en el Hospital A, y 128 eventos en el Hospital B. Esto es 61.3 eventos cada 1000 días paciente, y 62.5 eventos cada 1000 días paciente en A y B respectivamente, p = 0.3. En términos generales, construyendo una sola población de los dos hospitales, se hallaron 32 eventos adversos cada 100 admisiones, y 64.3 eventos cada 1000 días/pacientes. Los eventos estaban asociados en orden decreciente de frecuencia a: medicación (45.5%), infecciones (32.4%), procedimientos sin infección (15.2%), tromboembolismo pulmonar (4.8%), úlceras por presión (1.4%), dispositivos (0.7%). Las variables asociadas fueron polimedicación y polimorbilidad. Los factores asociados a la aparición de eventos adversos fueron el sexo femenino (OR: 2.1), la administración de medicamentos de alto riesgo (OR 2.3), la edad = 80 años (OR 2.6) y el registro de = 3 transferencias entre salas durante la internación (OR 2.9). Las tasas de daño observadas son comparables a las tasas evaluadas por el mismo método en estudios internacionales.

Parainfluenza Fusion Peptide Promotes Membrane Fusion by Assembling into Oligomeric Porelike Structures.

Paramyxoviruses are enveloped viruses harboring a negative-sense RNA genome that must enter the host's cells to replicate. In the case of the parainfluenza virus, the cell entry process starts with the recognition and attachment to target receptors, followed by proteolytic cleavage of the fusion glycoprotein (F) protein, exposing the fusion peptide (FP) region. The FP is responsible for binding to the target membrane, and it is believed to play a crucial role in the fusion process, but the mechanism by which the parainfluenza FP (PIFP) promotes membrane fusion is still unclear. To elucidate this matter, we performed biophysical experimentation of the PIFP in membranes, together with coarse grain (CG) and atomistic (AA) molecular dynamics (MD) simulations. The simulation results led to the pinpointing of the most important PIFP amino acid residues for membrane fusion and show that, at high concentrations, the peptide induces the formation of a water-permeable porelike structure. This structure promotes lipid head intrusion and lipid tail protrusion, which facilitates membrane fusion. Biophysical experimental results validate these findings, showing that, depending on the peptide/lipid ratio, the PIFP can promote fusion and/or membrane leakage. Our work furthers the understanding of the PIFP-induced membrane fusion process, which might help foster development in the field of viral entry inhibition.

Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies.

Understanding SARS-CoV-2 evolution and host immunity is critical to control COVID-19 pandemics. At the core is an arms-race between SARS-CoV-2 antibody and angiotensin-converting enzyme 2 (ACE2) recognition, a function of the viral protein spike. Mutations in spike impacting antibody and/or ACE2 binding are appearing worldwide, imposing the need to monitor SARS-CoV2 evolution and dynamics in the population. Determining signatures in SARS-CoV-2 that render the virus resistant to neutralizing antibodies is critical. We engineered 25 spike-pseudotyped lentiviruses containing individual and combined mutations in the spike protein, including all defining mutations in the variants of concern, to identify the effect of single and synergic amino acid substitutions in promoting immune escape. We confirmed that E484K evades antibody neutralization elicited by infection or vaccination, a capacity augmented when complemented by K417N and N501Y mutations. In silico analysis provided an explanation for E484K immune evasion. E484 frequently engages in interactions with antibodies but not with ACE2. Importantly, we identified a novel amino acid of concern, S494, which shares a similar pattern. Using the already circulating mutation S494P, we found that it reduces antibody neutralization of convalescent and post-immunization sera, particularly when combined with E484K and with mutations able to increase binding to ACE2, such as N501Y. Our analysis of synergic mutations provides a signature for hotspots for immune evasion and for targets of therapies, vaccines and diagnostics.

Polimedicación, prescripción inapropiada y eventos adversos a fármacos en ancianos hospitalizados: un problema de seguridad del paciente / Polymedication, inappropriate prescription and adverse events to drugs in hospitalized elderly: a patient safety problem / Polimedicação, prescrição inadequada e eventos adversos a medicamentos em idosos hospitalizados: um problema para a segurança do paciente

RESUMEN Introducción: La esperanza de vida ha ido en aumento y la posibilidad de padecer una o más patologías crónicas, por ejemplo, diabetes mellitus, hipertensión arterial, etc. es alta. La respuesta a los medicamentos en los adultos mayores es marcadamente diferente que en los adultos no ancianos pues se trata de un organismo donde las consecuencias directas del envejecimiento son de relevancia (reducción de la capacidad metabólica del hígado, reducción de la capacidad de filtrado del riñón, hipoclorhidria, entre otros). Objetivo: Analizar la polifarmacia, la prescripción inapropiada y los eventos adversos en adultos mayores hospitalizados. Materiales y métodos: Estudio descriptivo de corte transversal. Resultados: Se estudiaron 318 pacientes. La frecuencia de pacientes polimedicados fue 89 % (283). La prescripción inapropiada, 18,9 %. Los fármacos mayormente presentes en los esquemas de pacientes polimedicados fueron benzodiacepinas, AINEs, anticoagulantes y antihipertensivos. Los pacientes con eventos adversos han sido 179 (56,3 %), de ese porcentaje un 30,2 % (54) ha recibido tratamiento con otro medicamento para resolver el evento producido por un medicamento, eso es la llamada cascada de prescripción o de medicamentos. Conclusiones: La polimedicación es alta y causa eventos adversos, es necesario insistir en el trabajo integral para reducir este problema sanitario.

SUMMARY Introduction: Life expectancy has been increasing and the possibility of suffering from one or more chronic pathologies, for example, diabetes mellitus, arterial hypertension, etc. is high. The response to medications in older adults is markedly different than in non-elderly adults since it is an organism where the direct consequences of aging are relevant (reduction of the metabolic capacity of the liver, reduction of the filtering capacity of the kidney, hypochlorhydria, among others). Objective: To analyze polypharmacy, inappropriate prescription, and adverse events in hospitalized older adults. Materials and methods: Descriptive cross-sectional study. Results: 318 patients were studied. The frequency of polymedicated patients was 89 % (283). Inappropriate prescription, 18.9 %. The drugs most present in the regimens of polymedicated patients were benzodiazepines, NSAIDs, anticoagulants and antihypertensives. Patients with adverse events have been 179 (56.3 %), of that percentage 30.2 % (54) have received treatment with another drug to resolve the event produced by a drug, which is the so-called prescription or prescription cascade. Conclusions: Polypharmacy is high and causes adverse events, it is necessary to insist on comprehensive work to reduce this health problem.

RESUMO Introdução: A expectativa de vida vem aumentando e a possibilidade de sofrer de uma ou mais patologias crónicas, como por exemplo, diabetes mellitus, hipertensão arterial etc. é alta. A resposta aos medicamentos em idosos é marcadamente diferente da de adultos não idosos, pois é um organismo onde as consequências diretas do envelhecimento são relevantes (redução da capacidade metabólica do fígado, redução da capacidade de filtragem do rim, hipocloridria, entre outros). Objetivo: Analisar polifarmácia, prescrição inadequada e eventos adversos em idosos hospitalizados. Materiais e métodos: Estudo transversal descritivo. Resultados: 318 pacientes foram estudados. A frequência de pacientes polimedicados foi de 89% (283). Prescrição inadequada, 18,9%. Os medicamentos mais presentes nos esquemas dos pacientes polimedicados foram benzodiazepínicos, AINEs, anticoagulantes e anti--hipertensivos. Os pacientes com eventos adversos foram 179 (56,3%), desse percentual 30,2% (54) receberam tratamento com outro medicamento para resolução do evento produzido por um medicamento, que é a chamada prescrição ou receita em cascata. Conclusões: A polifarmácia é elevada e causa eventos adversos, é necessário insistir em um trabalho abrangente para reduzir esse problema de saúde.

Reducción de prescripción inapropiada y eventos adversos a medicamentos en ancianos hospitalizados / Reduction of inappropriate prescriptions and adverse effects to medications in hospitalized elderly patients

La combinación de prescripción inapropiada de medicamentos (PIM) y prescripción apropiada omitida (PPO) en ancianos requiere intervenciones múltiples para reducir su magnitud y los subsecuentes eventos adversos. Este estudio tiene como objetivo evaluar la PIM, la PPO, y los eventos adversos a medicamentos (EAM) antes y después de la intervención de un farmacéutico clínico sobre la prescripción del médico. En un estudio de tipo pre-post, se analizó la prescripción de un total de 16 542 fármacos realizada a 1262 pacientes aplicando los criterios STOPP-START (screening tool of older people's prescriptions/screening tool to alert to right treatment). La intervención consistió en la difusión de los criterios STOPP-START en todas las áreas del hospital mediante clases y publicaciones y las sugerencias diarias del farmacéutico clínico al médico responsable sobre la prescripción a cada paciente. Antes de la intervención, la PIM fue 48.9% al ingreso y 46.1% al egreso y luego de la intervención 47.4% al ingreso y 16.7% al egreso. La PPO antes de la intervención fue 10% al ingreso y 7.6% al egreso; después de la intervención fue 12.2% al ingreso y 7.8% al egreso. El porcentaje de pacientes con EAM fue 50.9% antes de la intervención y 34.4% después. Las readmisiones a emergencias fueron 12.2% y 4.7% antes y después de la intervención. La PIM, los EAM, el error de conciliación, la interacción medicamentosa clínicamente grave y el delirio fueron reducidos significativamente. Se concluye que, coincidiendo con buena parte de la literatura internacional, la intervención obtuvo resultados positivos.

Together, potentially inappropriate prescribing of medications (PIP) and appropriate prescribing omission (APO) constitute a problem that requires multiple interventions to reduce its size and the occurrence of adverse drug events (ADE). This study aims to assess PIP, APO, ADE before and after the intervention of a clinical pharmacist over medical prescriptions for elderly hospitalized patients. In a before-after study, a total of 16 542 prescriptions for 1262 patients were analyzed applying the criteria defined in both STOPP- START (screening tool of older people's prescriptions and screening tool to alert to right treatment). The intervention consisted in lectures and publications on STOPP-START criteria made available to all the areas of the hospital and suggestions made by the clinical pharmacist to the physician on each individual prescription. Before intervention, PIM was 48.9% on admission and 46.1% at discharge, while after the intervention it was 47.4% on admission and 16.7% at discharge. APO was 10% on admission and 7.6% at discharge, while after intervention it was 12.2% on admission and 7.9% at discharge. ADE were 50.9% before and 34.4% after intervention. The frequency of return to emergency was 12.2% and 4.7% before and after intervention. PIM, EAM, conciliation error, clinically serious drug interaction, and delirium were reduced to statistically significant levels. In line with various international studies, the intervention showed to attain positive results.

[Reduction of inappropriate prescriptions and adverse effects to medications in hospitalized elderly patients]. / Reducción de prescripción inapropiada y eventos adversos a medicamentos en ancianos hospitalizados.

Together, potentially inappropriate prescribing of medications (PIP) and appropriate prescribing omission (APO) constitute a problem that requires multiple interventions to reduce its size and the occurrence of adverse drug events (ADE). This study aims to assess PIP, APO, ADE before and after the intervention of a clinical pharmacist over medical prescriptions for elderly hospitalized patients. In a before-after study, a total of 16 542 prescriptions for 1262 patients were analyzed applying the criteria defined in both STOPP- START (screening tool of older people's prescriptions and screening tool to alert to right treatment). The intervention consisted in lectures and publications on STOPP-START criteria made available to all the areas of the hospital and suggestions made by the clinical pharmacist to the physician on each individual prescription. Before intervention, PIM was 48.9% on admission and 46.1% at discharge, while after the intervention it was 47.4% on admission and 16.7% at discharge. APO was 10% on admission and 7.6% at discharge, while after intervention it was 12.2% on admission and 7.9% at discharge. ADE were 50.9% before and 34.4% after intervention. The frequency of return to emergency was 12.2% and 4.7% before and after intervention. PIM, EAM, conciliation error, clinically serious drug interaction, and delirium were reduced to statistically significant levels. In line with various international studies, the intervention showed to attain positive results.