Membrane proteins structures: A review on computational modeling tools.

BACKGROUND: Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic organisms' genomes. In humans, their importance is emphasized as they represent 50% of all known drug targets. Nevertheless, experimental determination of their three-dimensional (3D) structure has proven to be both time consuming and rather expensive, which has led to the development of computational algorithms to complement the available experimental methods and provide valuable insights. SCOPE OF REVIEW: This review highlights the importance of membrane proteins and how computational methods are capable of overcoming challenges associated with their experimental characterization. It covers various MP structural aspects, such as lipid interactions, allostery, and structure prediction, based on methods such as Molecular Dynamics (MD) and Machine-Learning (ML). MAJOR CONCLUSIONS: Recent developments in algorithms, tools and hybrid approaches, together with the increase in both computational resources and the amount of available data have resulted in increasingly powerful and trustworthy approaches to model MPs. GENERAL SIGNIFICANCE: Even though MPs are elementary and important in nature, the determination of their 3D structure has proven to be a challenging endeavor. Computational methods provide a reliable alternative to experimental methods. In this review, we focus on computational techniques to determine the 3D structure of MP and characterize their binding interfaces. We also summarize the most relevant databases and software programs available for the study of MPs.

Effect of tolbutamide on tetraethylammonium-induced postsynaptic zinc signals at hippocampal mossy fiber-CA3 synapses.

The application of tetraethylammonium (TEA), a blocker of voltage-dependent potassium channels, can induce long-term potentiation (LTP) in the synaptic systems CA3-CA1 and mossy fiber-CA3 pyramidal cells of the hippocampus. In the mossy fibers, the depolarization evoked by extracellular TEA induces a large amount of glutamate and also of zinc release. It is considered that zinc has a neuromodulatory role at the mossy fiber synapses, which can, at least in part, be due to the activation of presynaptic ATP-dependent potassium (KATP) channels. The aim of this work was to study properties of TEA-induced zinc signals, detected at the mossy fiber region, using the permeant form of the zinc indicator Newport Green. The application of TEA caused a depression of those signals that was partially blocked by the KATP channel inhibitor tolbutamide. After the removal of TEA, the signals usually increased to a level above baseline. These results are in agreement with the idea that intense zinc release during strong synaptic events triggers a negative feedback action. The zinc depression, caused by the LTP-evoking chemical stimulation, turns into potentiation after TEA washout, suggesting the existence of a correspondence between the observed zinc potentiation and TEA-evoked mossy fiber LTP.

Predicting Hot Spots Using a Deep Neural Network Approach.

Targeting protein-protein interactions is a challenge and crucial task of the drug discovery process. A good starting point for rational drug design is the identification of hot spots (HS) at protein-protein interfaces, typically conserved residues that contribute most significantly to the binding. In this chapter, we depict point-by-point an in-house pipeline used for HS prediction using only sequence-based features from the well-known SpotOn dataset of soluble proteins (Moreira et al., Sci Rep 7:8007, 2017), through the implementation of a deep neural network. The presented pipeline is divided into three steps: (1) feature extraction, (2) deep learning classification, and (3) model evaluation. We present all the available resources, including code snippets, the main dataset, and the free and open-source modules/packages necessary for full replication of the protocol. The users should be able to develop an HS prediction model with accuracy, precision, recall, and AUROC of 0.96, 0.93, 0.91, and 0.86, respectively.

An Overview of Antiretroviral Agents for Treating HIV Infection in Paediatric Population.

Paediatric Acquired ImmunoDeficiency Syndrome (AIDS) is a life-threatening and infectious disease in which the Human Immunodeficiency Virus (HIV) is mainly transmitted through Mother-To- Child Transmission (MTCT) during pregnancy, labour and delivery, or breastfeeding. This review provides an overview of the distinct therapeutic alternatives to abolish the systemic viral replication in paediatric HIV-1 infection. Numerous classes of antiretroviral agents have emerged as therapeutic tools for downregulation of different steps in the HIV replication process. These classes encompass Non- Nucleoside Analogue Reverse Transcriptase Inhibitors (NNRTIs), Nucleoside/Nucleotide Analogue Reverse Transcriptase Inhibitors (NRTIs/NtRTIs), INtegrase Inhibitors (INIs), Protease Inhibitors (PIs), and Entry Inhibitors (EIs). Co-administration of certain antiretroviral drugs with Pharmacokinetic Enhancers (PEs) may boost the effectiveness of the primary therapeutic agent. The combination of multiple antiretroviral drug regimens (Highly Active AntiRetroviral Therapy - HAART) is currently the standard therapeutic approach for HIV infection. So far, the use of HAART offers the best opportunity for prolonged and maximal viral suppression, and preservation of the immune system upon HIV infection. Still, the frequent administration of high doses of multiple drugs, their inefficient ability to reach the viral reservoirs in adequate doses, the development of drug resistance, and the lack of patient compliance compromise the complete HIV elimination. The development of nanotechnology-based drug delivery systems may enable targeted delivery of antiretroviral agents to inaccessible viral reservoir sites at therapeutic concentrations. In addition, the application of Computer-Aided Drug Design (CADD) approaches has provided valuable tools for the development of anti-HIV drug candidates with favourable pharmacodynamics and pharmacokinetic properties.

Dynamical Rearrangement of Human Epidermal Growth Factor Receptor 2 upon Antibody Binding: Effects on the Dimerization.

Human epidermal growth factor 2 (HER2) is a ligand-free tyrosine kinase receptor of the HER family that is overexpressed in some of the most aggressive tumours. Although it is known that HER2 dimerization involves a specific region of its extracellular domain, the so-called "dimerization arm", the mechanism of dimerization inhibition remains uncertain. However, uncovering how antibody interactions lead to inhibition of HER2 dimerization is of key importance in understanding its role in tumour progression and therapy. Herein, we employed several computational modelling techniques for a molecular-level understanding of the interactions between HER and specific anti-HER2 antibodies, namely an antigen-binding (Fab) fragment (F0178) and a single-chain variable fragment from Trastuzumab (scFv). Specifically, we investigated the effects of antibody-HER2 interactions on the key residues of "dimerization arm" from molecular dynamics (MD) simulations of unbound HER (in a total of 1 µs), as well as ScFv:HER2 and F0178:HER2 complexes (for a total of 2.5 µs). A deep surface analysis of HER receptor revealed that the binding of specific anti-HER2 antibodies induced conformational changes both in the interfacial residues, which was expected, and in the ECDII (extracellular domain), in particular at the "dimerization arm", which is critical in establishing protein-protein interface (PPI) interactions. Our results support and advance the knowledge on the already described trastuzumab effect on blocking HER2 dimerization through synergistic inhibition and/or steric hindrance. Furthermore, our approach offers a new strategy for fine-tuning target activity through allosteric ligands.

Computational Approaches in Antibody-drug Conjugate Optimization for Targeted Cancer Therapy.

Cancer has become one of the main leading causes of morbidity and mortality worldwide. One of the critical drawbacks of current cancer therapeutics has been the lack of the target-selectivity, as these drugs should have an effect exclusively on cancer cells while not perturbing healthy ones. In addition, their mechanism of action should be sufficiently fast to avoid the invasion of neighbouring healthy tissues by cancer cells. The use of conventional chemotherapeutic agents and other traditional therapies, such as surgery and radiotherapy, leads to off-target interactions with serious side effects. In this respect, recently developed target-selective Antibody-Drug Conjugates (ADCs) are more effective than traditional therapies, presumably due to their modular structures that combine many chemical properties simultaneously. In particular, ADCs are made up of three different units: a highly selective Monoclonal antibody (Mab) which is developed against a tumour-associated antigen, the payload (cytotoxic agent), and the linker. The latter should be stable in circulation while allowing the release of the cytotoxic agent in target cells. The modular nature of these drugs provides a platform to manipulate and improve selectivity and the toxicity of these molecules independently from each other. This in turn leads to generation of second- and third-generation ADCs, which have been more effective than the previous ones in terms of either selectivity or toxicity or both. Development of ADCs with improved efficacy requires knowledge at the atomic level regarding the structure and dynamics of the molecule. As such, we reviewed all the most recent computational methods used to attain all-atom description of the structure, energetics and dynamics of these systems. In particular, this includes homology modelling, molecular docking and refinement, atomistic and coarse-grained molecular dynamics simulations, principal component and cross-correlation analysis. The full characterization of the structure-activity relationship devoted to ADCs is critical for antibody-drug conjugate research and development.

Computational studies of G protein-coupled receptor complexes: Structure and dynamics.

G protein-coupled receptors (GPCRs) are ubiquitously expressed transmembrane proteins associated with a wide range of diseases such as Alzheimer's, Parkinson, schizophrenia, and also implicated in in several abnormal heart conditions. As such, this family of receptors is regarded as excellent drug targets. However, due to the high number of intracellular signaling partners, these receptors have a complex interaction networks and it becomes challenging to modulate their function. Experimentally determined structures give detailed information on the salient structural properties of these signaling complexes but they are far away from providing mechanistic insights into the underlying process. This chapter presents some of the computational tools, namely molecular dynamics, molecular docking, and molecular modeling and related analyses methods that have been used to complement experimental findings.

SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots.

We present SpotOn, a web server to identify and classify interfacial residues as Hot-Spots (HS) and Null-Spots (NS). SpotON implements a robust algorithm with a demonstrated accuracy of 0.95 and sensitivity of 0.98 on an independent test set. The predictor was developed using an ensemble machine learning approach with up-sampling of the minor class. It was trained on 53 complexes using various features, based on both protein 3D structure and sequence. The SpotOn web interface is freely available at: http://milou.science.uu.nl/services/SPOTON/ .

[Successful treatment of a case of extense verrucous chromoblastomychosis with surgical exeresis associated with the use of ketoconazole]. / Tratamiento exitoso de un caso de cromoblatomicosis verrucosa extensa con exéresis quirúrgica asociada a uso de ketoconazol.

The case of a 56-year-old man with an extense verrucous chromoblastomycosis of long evolution, with lesions in the right foot that had not been cured with previous treatment, and that was successfully treated by surgical exeresis of all the lesions together with oral ketoconazole, is presented. Literature was reviewed to conclude that the treatment of chromoblastomycosis is still a challenge and that it should be selected for each case in particular.

Tratamiento exitoso de un caso de cromoblatomicosis verrucosa extensa con exéresis quirúrgica asociada a uso de ketoconazol / Successful treatment of a case of extense verrucous chromoblastomychosis with surgical exeresis associated with the use of ketoconazole

Se presentó el caso de un hombre de 56 años de edad con una cromoblastomicosis verrucosa extensa, de larga evolución, con lesiones localizadas en pie derecho, que no había curado con tratamientos previos y fue tratado con éxito mediante exéresis quirúrgica de todas las lesiones junto con ketoconazol oral. Se revisó la literatura para concluir que el tratamiento de la cromoblastomicosis continúa siendo un reto y debe ser seleccionado para cada caso en particular. En pacientes con lesiones exuberantes, la exéresis quirúrgica previa parece ser un proceder de utilidad

Pioderma gangrenoso vegetante asociado con insuficiencia renal / Vegetative pyoderma gangrenosum associated with renal failure

Se presentó el caso de un paciente que desarrolló un pioderma gangrenoso vegetante que concomitaba con una insuficiencia renal aguda, esto lo llevó a un estado de gravedad extrema. El paciente recibió tratamiento inicialmente con antibióticos sistémicos por considerarse el cuadro como una piodermitis, pero no se obtuvo una respuesta satisfactoria. Después fue tratado con Levamizol y alfa interferón, y se logró con este tratamiento mejoría de su estado general y de sus lesiones cutáneas. Se realizó entonces exéresis quirúrgica, con autoinjerto de las lesiones de la cara y el pene, con buenos resultados. Las lesiones pioderma gangrenoso fueron recidivantes, se trataron con prednisona y se obtuvo una rápida resolución de las lesiones en cada ocasión que se presentaron

Liquen escleroso y atrófico extragenital / Extragenital sclerous and atrophic liquem

Se actualizaron algunos aspectos del liquen escleroso y atrófico (LEA) y se presentaron los resultados del estudio clínico-epidemiológico de 12 pacientes con LEA extragenital. Todos los casos revisados pertenecían a la raza blanca y la mayor incidencia se encontró en mujeres mayores de 40 años. La localización de las lesiones fue más frecuente en el tórax

Acne Vulgar e Inmunidad Celular / Acne vulgaris and cellular immunity

Se realizo un estudio prospectivo de la inmunidad celular de 44 pacientes con acne que acudieron a la Consulta Externa del Hospital "General Calixto Garcia" durante el ano 1992, mediante el test de roseta espontanea y de roseta activa, para aportar nuevos elementos que ayuden a esclarecer uno de los aspectos ma controvertidos de la patogenia del acne, el inmunologico. La formacion de roseta espontanea estuvo por debajo de los valores normales en el 64 por ciento de los enfermos, en el de roseta activa tuvieron respuesta normal el 55 por ciento de los casos. Hubo disminucion significativa de la formacion de roseta espontanea y activa en relacion con los grado de intensidad del acne. En los pacientes con acne vulgar estudiados, la inmunidad celular parece estar comprometida y relacionada con los grados de intensidad del acne, hecho muy importante que abriria nuevas perspectivas en la inmunoterapia para el tratamiento de esta afeccion

Pitiriasis rubra pilaris asociada a artritis reumatoidea. Presentación de 1 caso / Pityriasis rubra pilaris associated with rheumatoid arthritis: a case report

Se presentó 1 caso de pitiriasis rubra pilaris eritrodérmica de 10 años de evolución en 1 paciente de 74 años de edad. Se observó que la enfermedad cutánea se asoció con artritis reumatoidea lo que hizo pensar a los autores en el posible papel etiológico de los factores inmunológicos en la pitiriasis rubra pilaris. Durante su evolución también se presentó un carcinoma papilar de vejiga, queratosis seborreicas múltiples, nódulo laríngeo benigno, carcinomas basales y un queratoacantoma. Se impuso tratamiento con methotrexate, pero no resultó satisfactorio para su PRP. Se obtuvo una buena respuesta con el etretinato

Dispositivo para transduçäo de força em uma cadeira de Bonett / Device for strenght transduction in a Bonett chair

Este trabalho propõe um mecanismo de automação para uma Cadeira de Bonett adaptada, visando uma avaliação do ganho real de força obtido através de dois métodos de fortalecimento muscular. DE LORME e DAPRE.

This paper describes a device for the automation of Bonett chair. with the aim to compare the real gain of strength, using two methods of analyzing muscular strengthening, proposed by DE LORME and DAPRE.