Biophysical and Dynamic Characterization of Fine-Tuned Binding of the Human Respiratory Syncytial Virus M2-1 Core Domain to Long RNAs.

The human respiratory syncytial virus (hRSV) M2-1 protein functions as a processivity and antitermination factor of the viral polymerase complex. Here, the first evidence that the hRSV M2-1 core domain (cdM2-1) alone has an unfolding activity for long RNAs is presented and the biophysical and dynamic characterization of the cdM2-1/RNA complex is provided. The main contact region of cdM2-1 with RNA was the α1-α2-α5-α6 helix bundle, which suffered local conformational changes and promoted the RNA unfolding activity. This activity may be triggered by base-pairing recognition. RNA molecules wrap around the whole cdM2-1, protruding their termini over the domain. The α2-α3 and α3-α4 loops of cdM2-1 were marked by an increase in picosecond internal motions upon RNA binding, even though they are not directly involved in the interaction. The results revealed that the cdM2-1/RNA complex originates from a fine-tuned binding, contributing to the unraveling interaction aspects necessary for M2-1 activity.IMPORTANCE The main outcome is the molecular description of the fine-tuned binding of the cdM2-1/RNA complex and the provision of evidence that the domain alone has unfolding activity for long RNAs. This binding mode is essential in the understanding of the function in the full-length protein. Human respiratory syncytial virus (hRSV), an orthopneumovirus, stands out for the unique role of its M2-1 protein as a transcriptional antitermination factor able to increase RNA polymerase processivity.

Study protocol to investigate biomolecular muscle profile as predictors of long-term urinary incontinence in women with gestational diabetes mellitus.

BACKGROUND: Pelvic floor muscles (PFM) and rectus abdominis muscles (RAM) of pregnant diabetic rats exhibit atrophy, co-localization of fast and slow fibers and an increased collagen type I/III ratio. However, the role of similar PFM or RAM hyperglycemic-related myopathy in women with gestational diabetes mellitus (GDM) remains poorly investigated. This study aims to assess the frequency of pelvic floor muscle disorders and pregnancy-specific urinary incontinence (PS-UI) 12 months after the Cesarean (C) section in women with GDM. Specifically, differences in PFM/RAM hyperglycemic myopathy will be evaluated. METHODS: The Diamater is an ongoing cohort study of four groups of 59 pregnant women each from the Perinatal Diabetes Research Centre (PDRC), Botucatu Medical School (FMB)-UNESP (São Paulo State University), Brazil. Diagnosis of GDM and PS-UI will be made at 24-26 weeks, with a follow-up at 34-38 weeks of gestation. Inclusion in the study will occur at the time of C-section, and patients will be followed at 24-48 h, 6 weeks and 6 and 12 months postpartum. Study groups will be classified as (1) GDM plus PS-UI; (2) GDM without PS-UI; (3) Non-GDM plus PS-UI; and (4) Non-GDM without PS-UI. We will analyze relationships between GDM, PS-UI and hyperglycemic myopathy at 12 months after C-section. The mediator variables to be evaluated include digital palpation, vaginal squeeze pressure, 3D pelvic floor ultrasound, and 3D RAM ultrasound. RAM samples obtained during C-section will be analyzed for ex-vivo contractility, morphological, molecular and OMICS profiles to further characterize the hyperglycemic myopathy. Additional variables to be evaluated include maternal age, socioeconomic status, educational level, ethnicity, body mass index, weight gain during pregnancy, quality of glycemic control and insulin therapy. DISCUSSION: To our knowledge, this will be the first study to provide data on the prevalence of PS-UI and RAM and PFM physical and biomolecular muscle profiles after C-section in mothers with GDM. The longitudinal design allows for the assessment of cause-effect relationships between GDM, PS-UI, and PFMs and RAMs myopathy. The findings may reveal previously undetermined consequences of GDM.

Insights into Interactions of Flavanones with Target Human Respiratory Syncytial Virus M2-1 Protein from STD-NMR, Fluorescence Spectroscopy, and Computational Simulations.

The human Respiratory Syncytial Virus (hRSV) is the most frequent agent of respiratory infections in infants and children with no currently approved vaccine. The M2-1 protein is an important transcriptional antitermination factor and a potential target for viral replication inhibitor development. Hesperetin (HST) and hesperidin (HSD) are flavonoids from the flavanone group, naturally found in citrus and have, as one of their properties, antiviral activity. The present study reports on the interactions between hRSV M2-1 and these flavanones using experimental techniques in association with computational tools. STD-NMR results showed that HST and HSD bind to M2-1 by positioning their aromatic rings into the target protein binding site. Fluorescence quenching measurements revealed that HST had an interaction affinity greater than HSD towards M2-1. The thermodynamic analysis suggested that hydrogen bonds and van der Waals interactions are important for the molecular stabilization of the complexes. Computational simulations corroborated with the experimental results and indicated that the possible interaction region for the flavonoids is the AMP-binding site in M2-1. Therefore, these results point that HST and HSD bind stably to a critical region in M2-1, which is vital for its biological function, and thus might play a possible role antiviral against hRSV.

M2-2 gene as a new alternative molecular marker for phylogenetic, phylodynamic, and evolutionary studies of hRSV.

The human Respiratory Syncytial Virus (hRSV) is the main causative agent of acute respiratory infections (ARI), such as pneumonia and bronchiolitis. One of the factors that lead to success in viral replication is the interaction of the M2-2 protein with the ribosomal complex. This interaction is responsible for the phase change of viral activity, acting as an inhibitor or inducer of viral replication, according to the concentration of mRNA. Based on the importance of M2-2 gene and protein have to viral physiology, we performed here evaluations of genetic diversity, phylogenetic reconstructions, phylodynamics, and selection test. Our results suggested an alternative way of classifying this virus in clades A and B, based on a new phylogenetic marker, the M2-2 gene. Therefore, our study is the first one to investigate the dynamics of the evolutionary diversification process of hRSV from the perspective of the M2-2 viral gene. In our study was also identified that the M2-2 gene is under the effect of purifying selection originated by population genetic bottlenecks. Therefore, the M2-2 gene demonstrated an interesting potential to be applied in evolutionary studies involving hRSV, recovering phylogenetic signals and traits of natural selection under the evolution of this virus.

Hesperetin targets the hydrophobic pocket of the nucleoprotein/phosphoprotein binding site of human respiratory syncytial virus.

The human Respiratory Syncytial Virus (hRSV) is one of the most common causes of acute respiratory diseases such as bronchiolitis and pneumonia in children worldwide. Among the viral proteins, the nucleoprotein (N) stands out for forming the nucleocapsid (NC) that functions as a template for replication and transcription by the viral polymerase complex. The NC/polymerase recognition is mediated by the phosphoprotein (P), which establishes an interaction of its C-terminal residues with a hydrophobic pocket in the N-terminal domain of N (N-NTD). The present study consists of biophysical characterization of N-NTD and investigation of flavonoids binding to this domain using experimental and computational approaches. Saturation transfer difference (STD)-NMR measurements showed that among the investigated flavonoids, only hesperetin (Hst) bound to N-NTD. The binding epitope mapping of Hst suggested that its fused aromatic ring is buried in the protein binding site. STD-NMR and fluorescence anisotropy experiments showed that Hst competes with P protein C-terminal dipeptides for the hRSV nucleoprotein/phosphoprotein (N/P) interaction site in N-NTD, indicating that Hst binds to the hydrophobic pocket in this domain. Computational simulations of molecular docking and dynamics corroborated with experimental results, presenting that Hst established a stable interaction with the N/P binding site. The outcomes presented herein shed light on literature reports that described a significant antireplicative activity of Hst against hRSV, revealing molecular details that can provide the development of a new strategy against this virus.

4-Methylesculetin, a natural coumarin with intestinal anti-inflammatory activity, elicits a glutathione antioxidant response by different mechanisms.

4-methylesculetin (4 ME) is a natural antioxidant coumarin with protective effects on the intestinal inflammation, in which oxidative stress plays a key role in its aetiology and pathophysiology. Based on this, we examined the antioxidant molecular mechanisms involved in the intestinal anti-inflammatory activity of the 4 ME. For this purpose, we investigated the effects of the 4 ME on the modulation of gene expression and antioxidant-related enzyme activities in TNBS model of intestinal inflammation as well as the molecular interaction between 4 ME and glutathione reductase. Our results showed that 4 ME modulated glutathione-related enzymes, mainly increasing glutathione reductase activity. These effects were related to upregulation of glutathione reductase and Nrf2 gene expression. Fluorescence and nuclear magnetic resonance data showed that interaction between 4 ME and glutathione reductase is collisional, hydrophobic and spontaneous, in which C4 methyl group is the second epitope most buried into glutathione reductase. Molecular modelling calculation showed Lys70-B, Arg81-A, Glu381-B, Asp443-A, Ser444-A, Glu447-B and Ser475-A participated in electrostatic interaction, Lys70-B, Glu381-B and Arg81-A acted in the hydrophobic interactions and Trp73, Phe377 and Ala446 are responsible for the hydrogen bonds. Based on this, our results showed 4 ME acted by different mechanisms to control oxidative stress induced by intestinal damage, controlling the imbalance between myeloperoxidase activity and glutathione production, upregulating the glutathione S-transferase and glutathione reductase activities, preventing the Nrf2 and glutathione gene expression downregulation with consequent glutathione maintenance. Finally, 4 ME interacted at molecular level with glutathione reductase, stabilizing its enzymatic activity and reducing oxidative stress to take place in intestinal inflammatory process.

Expression and purification of human respiratory syncytial virus recombinant fusion protein.

The Human Respiratory Syncytial Virus (HRSV) fusion protein (F) was expressed in Escherichia coli BL21A using the pET28a vector at 37 degrees C. The protein was purified from the soluble fraction using affinity resin. The structural quality of the recombinant fusion protein and the estimation of its secondary structure were obtained by circular dichroism. Structural models of the fusion protein presented 46% of the helices in agreement with the spectra by circular dichroism analysis. There are only few studies that succeeded in expressing the HRSV fusion protein in bacteria. This is a report on human fusion protein expression in E. coli and structure analysis, representing a step forward in the development of fusion protein F inhibitors and the production of antibodies.

Binding investigation between M2-1protein from hRSV and acetylated quercetin derivatives: 1H NMR, fluorescence spectroscopy, and molecular docking.

The human Respiratory Syncytial Virus (hRSV) is the main responsible for occurrences of respiratory diseases as pneumonia and bronchiolitis in children and elderly. M2-1 protein from hRSV is an important antitermination factor for transcription process that prevents the premature dissociation of the polymerase complex, making it a potential target for developing of inhibitors of the viral replication. The present study reports the interaction of the M2-1 tetramer with pera (Q1) and tetracetylated (Q2) quercetin derivatives, which were synthesized with the objective of generating stronger bioactive compounds against oxidation process. Fluorescence experiments showed binding constants of the M2-1/compounds complexes on order of 104M-1 with one ligand per monomeric unit, being the affinity of Q2 stronger than Q1. The thermodynamic analysis revealed values of ΔH>0 and ΔS>0, suggesting that hydrophobic interactions play a key role in the formation of the complexes. Molecular docking calculations indicated that binding sites for the compounds are in contact interfaces between globular and zinc finger domains of the monomers and that hydrogen bonds and stacking interactions are important contributions for stabilization of the complexes. Thus, the interaction of the acetylated quercetin derivatives in the RNA-binding sites of M2-1 makes these potential candidates for viral replication inhibitors.

Methylation profile of genes CDKN2A (p14 and p16), DAPK1, CDH1, and ADAM23 in head and neck cancer.

Hypermethylation in the promoter region has been associated with a loss of gene function that may give a selective advantage to neoplastic cells. In this study, the methylation pattern of genes CDKN2A (alias p14, p14(ARF), p16, p16(INK4a)), DAPK1, CDH1, and ADAM23 was analyzed in 43 samples of head and neck tumors using methylation-specific polymerase chain reaction. In the oropharynx, there was a statistically significant association between hypermethylation of the DAPK1 gene and the occurrence of lymph node metastases, and in the larynx there was statistically significant evidence of an association between hypermethylation of the ADAM23 gene and advanced stages of the tumors. Thus, a correlation was observed between hypermethylation of the promoter region of genes DAPK1 and ADAM23 and the progression of head and neck cancer.

Structure and functional dynamics characterization of the ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domain by combining molecular dynamics with excited normal modes.

The human respiratory syncytial virus (hRSV) is the major cause of lower respiratory tract infection in children and elderly people worldwide. Its genome encodes 11 proteins including SH protein, whose functions are not well known. Studies show that SH protein increases RSV virulence degree and permeability to small compounds, suggesting it is involved in the formation of ion channels. The knowledge of SH structure and function is fundamental for a better understanding of its infection mechanism. The aim of this study was to model, characterize, and analyze the structural behavior of SH protein in the phospholipids bilayer environment. Molecular modeling of SH pentameric structure was performed, followed by traditional molecular dynamics (MD) simulations of the protein immersed in the lipid bilayer. Molecular dynamics with excited normal modes (MDeNM) was applied in the resulting system in order to investigate long time scale pore dynamics. MD simulations support that SH protein is stable in its pentameric form. Simulations also showed the presence of water molecules within the bilayer by density distribution, thus confirming that SH protein is a viroporin. This water transport was also observed in MDeNM studies with histidine residues of five chains (His22 and His51), playing a key role in pore permeability. The combination of traditional MD and MDeNM was a very efficient protocol to investigate functional conformational changes of transmembrane proteins that act as molecular channels. This protocol can support future investigations of drug candidates by acting on SH protein to inhibit viral infection. Graphical Abstract The ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domainᅟ.

Molecular models of NS3 protease variants of the Hepatitis C virus.

BACKGROUND: Hepatitis C virus (HCV) currently infects approximately three percent of the world population. In view of the lack of vaccines against HCV, there is an urgent need for an efficient treatment of the disease by an effective antiviral drug. Rational drug design has not been the primary way for discovering major therapeutics. Nevertheless, there are reports of success in the development of inhibitor using a structure-based approach. One of the possible targets for drug development against HCV is the NS3 protease variants. Based on the three-dimensional structure of these variants we expect to identify new NS3 protease inhibitors. In order to speed up the modeling process all NS3 protease variant models were generated in a Beowulf cluster. The potential of the structural bioinformatics for development of new antiviral drugs is discussed. RESULTS: The atomic coordinates of crystallographic structure 1CU1 and 1DY9 were used as starting model for modeling of the NS3 protease variant structures. The NS3 protease variant structures are composed of six subdomains, which occur in sequence along the polypeptide chain. The protease domain exhibits the dual beta-barrel fold that is common among members of the chymotrypsin serine protease family. The helicase domain contains two structurally related beta-alpha-beta subdomains and a third subdomain of seven helices and three short beta strands. The latter domain is usually referred to as the helicase alpha-helical subdomain. The rmsd value of bond lengths and bond angles, the average G-factor and Verify 3D values are presented for NS3 protease variant structures. CONCLUSIONS: This project increases the certainty that homology modeling is an useful tool in structural biology and that it can be very valuable in annotating genome sequence information and contributing to structural and functional genomics from virus. The structural models will be used to guide future efforts in the structure-based drug design of a new generation of NS3 protease variants inhibitors. All models in the database are publicly accessible via our interactive website, providing us with large amount of structural models for use in protein-ligand docking analysis.

Biophysical and structural characterization of the recombinant human eIF3L.

The eukaryotic translation initiation factor 3, subunit L (eIF3L) is one of the subunits of the eIF3 complex, an accessory protein of the Polymerase I enzyme and may have an important role in the Flavivirus replication by interaction with a viral non-structural 5 protein. Considering the importance of eIF3L in a diversity of cellular functions, we have produced the recombinant full-length eIF3L protein in Escherichia coli and performed spectroscopic and in silico analyses to gain insights into its hydrodynamic behavior and structure. Dynamic light scattering showed that eIF3L behaves as monomer when it is not interacting with other molecular partners. Circular dichroism experiments showed a typical spectrum of α-helical protein for eIF3L, which is supported by sequence-based predictions of secondary structure and the 3D in silico model. The molecular docking with the K subunit of the eIF3 complex revealed a strong interaction. It was also predicted several potential interaction sites in eIF3L, indicating that the protein is likely capable of interacting with other molecules as experimentally shown in other functional studies. Moreover, bioinformatics analyses showed approximately 8 putative phosphorylation sites and one possible N-glycosylation site, suggesting its regulation by post-translational modifications. The production of the eIF3L protein in E. coli and structural information gained in this study can be instrumental for target-based drug design and inhibitors against Flavivirus replication and to shed light on the molecular mechanisms involved in the eukaryotic translation initiation.

The influence of solutes on the enthalpy/entropy change of the actinomycin D binding to DNA: hydration, energy compensation and long-range deformation on DNA.

The effects of the changes in the temperature and in the water chemical potential on the energetic of the actinomycin D (ACTD) interaction with natural DNA are studied. At reduced water chemical potential, induced by the addition of neutral solute (sucrose), the ACTD-to-DNA binding isotherms show that the drug accesses two types of binding sites: strong and weak. The binding constants to the stronger sites are sensitive to changes in the temperature and in the water chemical potential, while the weak sites are practically insensitive to these changes. The van't Hoff analyses of the binding in different water chemical potential shows that the binding process to the more specific sites is endothermic in phosphate buffer (ΔH(vH) ∼ 1 kcal/mol) and becomes exothermic when the water chemical potential decreases (ΔH(vH) = -11 kcal/mol in sucrose 30%). The number of water molecules released on the binding to the stronger sites, obtained from the slopes of linkage plots in different temperatures, increases with the decrease in the temperature. Ring closure reactions in the presence of neutral solutes have shown that the reduction in the water activity induces DNA unwinding. It was observed that both reduced water chemical potential and small ratios of daunomycin bound per base pairs have the same effects on the ACTD binding isotherms and consequently on the binding thermodynamic parameters. The results presented indicate that the ACTD binding to the recognition site is enthalpycally unfavorable, which should be compensated by the deformation in the DNA. This compensation would probably be the origin of the synergism observed for these two drugs.

Human respiratory syncytial virus in children hospitalized for acute lower respiratory infection.

OBJECTIVE: To evaluate the prevalence and seasonality of human respiratory syncytial virus (HRSV) in children aged 0 to 6 years, hospitalized with acute lower respiratory infection (ALRI) in São José do Rio Preto, SP, Brazil, and the association between age, diagnosis, and HRSV. METHODS: Between May 2004 and September 2005, we studied 290 consecutive episodes of community-acquired ALRI in children aged 0 to 6 years admitted to the Hospital de Base of São José do Rio Preto. In order to detect HRSV, nasopharyngeal secretion samples were collected and RT-PCR molecular analysis was performed. RESULTS: The HRSV prevalence was 29.3% for the cases of hospitalized patients with ALRI. ALRI was common in infants (median age = 13.5 months). HRSV was more frequent in cases of bronchiolitis (64%) and during the first year of life (35%). Episodes of HRSV infection occurred between fall and spring, showing higher frequency in 2004 than in 2005. Clinical and radiological criteria were not sufficient to establish the diagnosis of infection with HRSV. Antibiotic therapy was used in 78.8% of episodes of HRSV. CONCLUSIONS: There was a high prevalence of HRSV in children aged 0 to 6 years who were hospitalized for ALRI, predominantly in younger patients or those with bronchiolitis. The circulation of the virus varied in the two years studied. Our results suggest the need for laboratory diagnosis of HRSV in the clinical practice.

Vírus respiratório sincicial humano em crianças hospitalizadas por infecções agudas das vias aéreas inferiores / Human respiratory syncytial virus in children hospitalized for acute lower respiratory infection

OBJETIVO: Avaliar a prevalência e a sazonalidade do vírus respiratório sincicial humano (VRSH) em crianças de 0 a 6 anos hospitalizadas por infecção aguda das vias aéreas inferiores (IVAI) em São José do Rio Preto (SP) e a associação entre faixa etária, diagnóstico e VRSH. MÉTODOS: Entre maio de 2004 e setembro de 2005, foram estudados 290 episódios consecutivos de IVAI adquiridos na comunidade em crianças de 0 a 6 anos internadas no Hospital de Base de São José do Rio Preto. Para identificação do VRSH, foram coletadas amostras de secreção de nasofaringe e realizou-se análise molecular por meio da técnica de RT-PCR. RESULTADOS: A prevalência de VRSH foi de 29,3 por cento nos episódios de IVAI hospitalizados. A IVAI foi frequente em lactentes (mediana de idade = 13,5 meses). O VRSH foi mais frequente nos casos de bronquiolite (64 por cento) e no primeiro ano de vida (35 por cento). Os episódios de infecção por VRSH ocorreram entre o outono e a primavera, com frequência maior em 2004 do que em 2005. Os critérios clínicos e radiológicos não foram suficientes para o diagnóstico de infecção pelo VRSH. Em 78,8 por cento dos episódios de VRSH, houve tratamento com antibiótico. CONCLUSÕES: A prevalência do VRSH em crianças de 0 a 6 anos hospitalizadas por IVAI foi elevada, com predomínio nas mais jovens ou com bronquiolite. A circulação do vírus variou nos dois anos estudados. Os resultados sugerem necessidade de diagnóstico laboratorial do VRSR na prática clínica.

OBJECTIVE: To evaluate the prevalence and seasonality of human respiratory syncytial virus (HRSV) in children aged 0 to 6 years, hospitalized with acute lower respiratory infection (ALRI) in São José do Rio Preto, SP, Brazil, and the association between age, diagnosis, and HRSV. METHODS: Between May 2004 and September 2005, we studied 290 consecutive episodes of community-acquired ALRI in children aged 0 to 6 years admitted to the Hospital de Base of São José do Rio Preto. In order to detect HRSV, nasopharyngeal secretion samples were collected and RT-PCR molecular analysis was performed. RESULTS: The HRSV prevalence was 29.3 percent for the cases of hospitalized patients with ALRI. ALRI was common in infants (median age = 13.5 months). HRSV was more frequent in cases of bronchiolitis (64 percent) and during the first year of life (35 percent). Episodes of HRSV infection occurred between fall and spring, showing higher frequency in 2004 than in 2005. Clinical and radiological criteria were not sufficient to establish the diagnosis of infection with HRSV. Antibiotic therapy was used in 78.8 percent of episodes of HRSV. CONCLUSIONS: There was a high prevalence of HRSV in children aged 0 to 6 years who were hospitalized for ALRI, predominantly in younger patients or those with bronchiolitis. The circulation of the virus varied in the two years studied. Our results suggest the need for laboratory diagnosis of HRSV in the clinical practice.