Human macrophages differentiated in the presence of vitamin D3 restrict dengue virus infection and innate responses by downregulating mannose receptor expression

ABSTARCT: Severe dengue disease is associated with high viral loads and overproduction of pro-inflammatory cytokines, suggesting impairment in the control of dengue virus (DENV) and the mechanisms that regulate cytokine production. Vitamin D3 has been described as an important modulator of immune responses to several pathogens. Interestingly, increasing evidence has associated vitamin D with decreased DENV infection and early disease recovery, yet the molecular mechanisms whereby vitamin D reduces DENV infection are not well understood. METHODS AND PRINCIPAL FINDINGS: Macrophages represent important cell targets for DENV replication and consequently, they are key drivers of dengue disease. In this study we evaluated the effect of vitamin D3 on the differentiation of monocyte-derived macrophages (MDM) and their susceptibility and cytokine response to DENV. Our data demonstrate that MDM differentiated in the presence of vitamin D3 (D3-MDM) restrict DENV infection and moderate the classical inflammatory cytokine response. Mechanistically, vitamin D3-driven differentiation led to reduced surface expression of C-type lectins including the mannose receptor (MR, CD206) that is known to act as primary receptor for DENV attachment on macrophages and to trigger of immune signaling. Consequently, DENV bound less efficiently to vitamin D3-differentiated macrophages, leading to lower infection. Interestingly, IL-4 enhanced infection was reduced in D3-MDM by restriction of MR expression. Moreover, we detected moderate secretion of TNF-α, IL-1β, and IL-10 in D3-MDM, likely due to less MR engagement during DENV infection. CONCLUSIONS/SIGNIFICANCE: Our findings reveal a molecular mechanism by which vitamin D counteracts DENV infection and progression of severe disease, and indicates its potential relevance as a preventive or therapeutic candidate

Investigation of the Differences in Activity between Hydroxycycloalkyl N1 Substituted Pyrazole Derivatives As Inhibitors of B-Raf Kinase by Using Docking, Molecular Dynamics, QM/MM, and Fragment-Based De Novo Design: Study of Binding Mode of Diastereomer Compounds

Caballero, J (Caballero, Julio)1; Alzate-Morales, JH (Alzate-Morales, Jans H.)1; Vergara-Jaque, A (Vergara-Jaque, Ariela)1. Addresses: 1. Univ Talca, Ctr Bioinformat & Simulac Mol, Talca, ChileN1 substituted pyrazole derivatives show diverse B-Raf kinase inhibitory activities when different hydroxy-substituted cycloalkyl groups are placed at this position. Docking, molecular dynamics (MD) simulations, and hybrid calculation methods (Quantum Mechanics/Molecular Mechanics (QM/MM)) were performed on the complexes, in order to explain these differences. Docking of the inhibitors showed the same orientation that X-ray crystal structure of the analogous (1E)-5-[1-(4-piperidinyl)-3-(4-pyridinyl)-1H-pyrazol-4-yl]-2,3-dihydro-1H-inden-1-one oxirne. MD simulations of the most active diastereomer compounds containing cis- and trans-3-hydroxycyclohexyl substituents showed stable interactions with residue Ile463 at the entrance of the B-Raf active site. On the other hand, the less active diastereomer compounds containing cis- and trans-2-hydroxycyclopentyl substituents showed interactions with inner residues Asn580 and Ser465. We found that the differences in activity can be explained by considering the dynamic interactions between the inhibitors and their surrounding residues within the B-Raf binding site. We also explained the activity trend by using a testing scoring function derived from more reliable QM/MM calculations. In addition, we search for new inhibitors from a virtual screening carried out by fragment-based de novo design. We generated a set of approximately 200 virtual compounds, which interact with Ile463 and fulfill druglikeness properties according to Lipinski, Veber, and Chose rules

Association of nicotinic acid with a poly(amidoamine) dendrimer studied by molecular dynamics simulations

Caballero, J (reprint author) Univ Talca, Ctr Bioinformat & Simulac Mol, 2 Norte 685,Casilla 721, Talca, Chile.The interaction of poly(amidoamine)-G3 (PAMAM-G3) dendrimer with nicotinic acid (NA) was investigated by using molecular dynamics (MD) simulations. First, sample free energy profiles of NA crossing PAMAM-G3 at pH 6 and 3 were computed using the adaptive biasing force (ABF) method. We found that PAMAM-G3 provides a more appropriate environment for NA inclusion when internal tertiary amine groups are unprotonated (at pH 6). However, when internal tertiary amine groups are protonated (at pH 3), the PAMAM cavities are less hydrophobic; therefore the drug-dendrimer interactions become similar to drug-solvent interactions. Traditional MD simulations were also performed to investigate the structural stability of the PAMAM-NA complexes near the free energy minima at pH 6. We found that association of NA and PAMAM adopts a preferred binding mode around the surface of PAMAM, where hydrogen bond (HB) interactions with the amino and amide NH groups of the nearby monomers are established. These interactions are very stable whether additional van der Waals interactions between pyridine ring of NA and methylene groups of the more external monomers of PAMAM are established. (C) 2012 Elsevier Inc. All rights reserved

Papel de la lactancia materna en la reducción de la retinopatía de la prematuridad: estudio de casos y controles

Introducción: La Retinopatía del Prematuro es una de las principales causas de ceguera prevenible en niños; dado que cada vez existe mayor sobrevida en niños de menor peso y edad gestacional, su prevalencia es mayor. Existe evidencia sobre el papel de la lactancia materna  en su prevención.Objetivo: Determinar la asociación entre la lactancia materna y la presencia de retinopatía de la prematuridad.Diseño del estudio: Estudio observacional analítico de casos y controles.Método: Se incluyeron 295 prematuros del programa de Retinopatía de la Prematuridad en la Clínica Universitaria Bolivariana de la ciudad de Medellín durante los años 2009 a 2014. La población objetivo fueron los niños pretérmino menores de 32 semanas de edad gestacional y peso al nacer menor a 1800 gramos. Como casos se seleccionaron los prematuros que durante su evaluación rutinaria por el Servicio de Retina desarrollaron ROP y como controles, los prematuros que no la desarrollaron, durante el mismo período de observación. Se registró la presencia y estadio de retinopatía del prematuro, el tipo de lactancia (Materna Vs Fórmula) y otras variables relacionadas.Resultados: Los prematuros que recibieron menos lactancia materna durante su estancia hospitalaria tuvieron mayor incidencia de retinopatía del prematuro. En promedio recibieron  21 cc menos  por día (Diferencia de Medias (DM):-21.00; IC 95%: -41.11 a -0.90; p=0.041). En el análisis bivariado, los factores que mostraron relación significativa con la retinopatía del prematuro fueron: Peso al nacer en gramos (DM: -359,091; IC 95%: -435.4 a – 282.633; p=0.00), días de oxigenoterapia  (DM: 33.78; IC 95%: 25.56 a 42.0; p=0.00) y las comorbilidades enfermedad de membrana hialina (OR: 3.015; IC 95%: 1.619 a 5.615; p= 0.00) y hemorragia interventricular (OR: 2.969; IC 95%: 1.434 – 6.144; p=0.02).Conclusión: Los resultados de este estudio sugieren la lactancia materna como factor protector para el desarrollo de la retinopatía del prematuro

Study of differences in the VEGFR2 inhibitory activities between semaxanib and SU5205 using 3D-QSAR, docking, and molecular dynamics simulations

Caballero, J (reprint author), Univ Talca, Ctr Bioinformat & Simulac Mol, 2 Norte 685,Casilla 721, Talca, Chile.Semaxanib (SU5416) and 3[4'-fluorobenzylidene]indolin-2-one (SU5205) are structurally similar drugs that are able to inhibit vascular endothelial growth factor receptor-2 (VEGFR2), but the former is 87 times more effective than the latter. Previously, SU5205 was used as a radiolabelled inhibitor (as surrogate for SU5416) and a radiotracer for positron emission tomography (PET) imaging, but the compound exhibited poor stability and only a moderate IC50 toward VEGFR2. In the current work, the relationship between the structure and activity of these drugs as VEGFR2 inhibitors was studied using 3D-QSAR, docking and molecular dynamics (MD) simulations. First, comparative molecular field analysis (CoMFA) was performed using 48 2-indolinone derivatives and their VEGFR2 inhibitory activities. The best CoMFA model was carried out over a training set including 40 compounds, and it included steric and electrostatic fields. In addition, this model gave satisfactory cross-validation results and adequately predicted 8 compounds contained in the test set. The plots of the CoMFA fields could explain the structural differences between semaxanib and SU5205. Docking and molecular dynamics simulations showed that both molecules have the same orientation and dynamics inside the VEGFR2 active site. However, the hydrophobic pocket of VEGFR2 was more exposed to the solvent media when it was complexed with SU5205. An energetic analysis, including Embrace and MM-GBSA calculations, revealed that the potency of ligand binding is governed by van der Waals contacts. (C) 2011 Elsevier Inc. All rights reserved

The pH sensor of the plant K+-uptake channel KAT1 is built from a sensory cloud rather than from single key amino acids

Gonzalez, W (reprint author), Univ Talca, Ctr Bioinformat & Simulac Mol, 2 Norte 685, Talca 3465548, Chile.The uptake of potassium ions (K+) accompanied by an acidification of the apoplasm is a prerequisite for stomatal opening. The acidification (approximately 2-2.5 pH units) is perceived by voltage-gated inward potassium channels (K-in) that then can open their pores with lower energy cost. The sensory units for extracellular pH in stomatal K-in channels are proposed to be histidines exposed to the apoplasm. However, in the Arabidopsis thaliana stomatal K-in channel KAT1, mutations in the unique histidine exposed to the solvent (His(267)) do not affect the pH dependency. We demonstrate in the present study that His(267) of the KAT1 channel cannot sense pH changes since the neighbouring residue Phe(266) shifts its pK(a) to undetectable values through a cation-pi interaction. Instead, we show that Glu(240) placed in the extracellular loop between transmembrane segments S5 and S6 is involved in the extracellular acid activation mechanism. Based on structural models we propose that this region may serve as a molecular link between the pH- and the voltage-sensor. Like Glu(240), several other titratable residues could contribute to the pH-sensor of KAT1, interact with each other and even connect such residues far away from the voltage-sensor with the gating machinery of the channel

The pH sensor of the plant K plus uptake channel KAT1 is built from a sensory cloud rather than from single key amino acids

The uptake of potassium ions (K+) accompanied by an acidification of the apoplasm is a prerequisite for stomatal opening. The acidification (approximately 2–2.5 pH units) is perceived by voltage-gated inward potassium channels (Kin) that then can open their pores with lower energy cost. The sensory units for extracellular pH in stomatal Kin channels are proposed to be histidines exposed to the apoplasm. However, in the Arabidopsis thaliana stomatal Kin channel KAT1, mutations in the unique histidine exposed to the solvent (His267) do not affect the pH dependency. We demonstrate in the present study that His267 of the KAT1 channel cannot sense pH changes since the neighbouring residue Phe266 shifts its pKa to undetectable values through a cation–p interaction. Instead, we show that Glu240 placed in the extracellular loop between transmembrane segments S5 and S6 is involved in the extracellular acid activation mechanism. Based on structural models we propose that this region may serve as a molecular link between the pH- and the voltage-sensor. Like Glu240, several other titratable residues could contribute to the pH-sensor of KAT1, interact with each other and even connect such residues far away from the voltage-sensor with the gating machinery of the channel