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Showing 2451 to 2454 of 5186 entries
Published on June 26, 2020
Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach.
Abstract: Campylobacter jejuni (C. jejuni) is considered to be one of the most frequent causes of bacterial gastroenteritis globally, especially in young children. The genome of C. jejuni contains many proteins with unknown functions termed as hypothetical proteins (HPs). These proteins might have essential biological role to show the full spectrum of this bacterium. Hence, our study aimed to determine the functions of HPs, pertaining to the genome of C. jejuni. An in-silico work flow integrating various tools were performed for functional assignment, three-dimensional structure determination, domain architecture predictors, subcellular localization, physicochemical characterization, and protein-protein interactions (PPIs). Sequences of 267 HPs of C. jejuni were analyzed and successfully attributed the function of 49 HPs with higher confidence. Here, we found proteins with enzymatic activity, transporters, binding and regulatory proteins as well as proteins with biotechnological interest. Assessment of the performance of various tools used in this analysis revealed an accuracy of 95% using receiver operating characteristic (ROC) curve analysis. Functional and structural predictions and the results from ROC analyses provided the validity of in-silico tools used in the present study. The approach used for this analysis leads us to assign the function of unknown proteins and relate them with the functions that have already been described in previous literature.
Published on June 26, 2020
Impact of Food and Drink Administration Vehicles on Paediatric Formulation Performance: Part 1-Effects on Solubility of Poorly Soluble Drugs.
Abstract: Food and drinks are commonly used to facilitate administration of paediatric medicines to improve palatability and enhance patient compliance. However, the impact of this practice on drug solubility and on oral drug bioavailability is not usually studied. Based on recommended strategies for oral administration of paediatric medicines with food and drink vehicles, the aims of this study were (i) to measure the physicochemical properties of (soft) food and drink vehicles, commonly mixed with paediatric medicines prior to administration, and (ii) to assess the impact of the co-administered vehicles on the solubility of two poorly soluble paediatric drugs. Montelukast (sodium) and mesalazine were selected as the model compounds. Distinct differences were observed between the physicochemical properties (i.e. pH, surface tension, osmolality, viscosity and buffer capacity) and macronutrient composition (i.e. fat, sugar and protein content) of the different soft foods and drinks, not only among vehicle type but also within vehicles of the same subtype. Solubility studies of the two model compounds in selected drinks and soft foods resulted in considerably different drug solubility values in each vehicle. The solubility of the drugs was significantly affected by the vehicle physicochemical properties and macronutrient composition, with the solubility of montelukast being driven by the pH, fat and protein content of the vehicles and the solubility of mesalazine by vehicle osmolality, viscosity and sugar content. This vehicle-dependent impact on drug solubility could compromise its bioavailability, and ultimately affect the safety and/or efficacy of the drug and should be taken into consideration during paediatric product development.
Published on June 26, 2020
Glecaprevir and Maraviroc are high-affinity inhibitors of SARS-CoV-2 main protease: possible implication in COVID-19 therapy.
Abstract: Due to the lack of efficient therapeutic options and clinical trial limitations, the FDA-approved drugs can be a good choice to handle Coronavirus disease (COVID-19). Many reports have enough evidence for the use of FDA-approved drugs which have inhibitory potential against target proteins of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we utilized a structure-based drug design approach to find possible drug candidates from the existing pool of FDA-approved drugs and checked their effectiveness against the SARS-CoV-2. We performed virtual screening of the FDA-approved drugs against the main protease (Mpro) of SARS-CoV-2, an essential enzyme, and a potential drug target. Using well-defined computational methods, we identified Glecaprevir and Maraviroc (MVC) as the best inhibitors of SARS-CoV-2 Mpro. Both drugs bind to the substrate-binding pocket of SARS-CoV-2 Mpro and form a significant number of non-covalent interactions. Glecaprevir and MVC bind to the conserved residues of substrate-binding pocket of SARS-CoV-2 Mpro. This work provides sufficient evidence for the use of Glecaprevir and MVC for the therapeutic management of COVID-19 after experimental validation and clinical manifestations.
Published on June 26, 2020
Targeting hub genes and pathways of innate immune response in COVID-19: A network biology perspective.
Abstract: The current pandemic of 2019 novel coronavirus disease (COVID-19) caused by a novel virus strain, 2019-nCoV/SARS-CoV-2 have posed a serious threat to global public health and economy. It is largely unknown how the human immune system responds to this infection. A better understanding of the immune response to SARS-CoV-2 will be important to develop therapeutics against COVID-19. Here, we have used transcriptomic profile of human alveolar adenocarcinoma cells (A549) infected with SARS-CoV-2 and employed a network biology approach to generate human-virus interactome. Network topological analysis discovers 15 SARS-CoV-2 targets, which belongs to a subset of interferon (IFN) stimulated genes (ISGs). These ISGs (IFIT1, IFITM1, IRF7, ISG15, MX1, and OAS2) can be considered as potential candidates for drug targets in the treatments of COVID-19. We have identified significant interaction between ISGs and TLR3 agonists, like poly I: C, and imiquimod, and suggests that TLR3 agonists can be considered as a potential drug for drug repurposing in COVID-19. Our network centric analysis suggests that moderating the innate immune response is a valuable approach to target COVID-19.
Published on June 26, 2020
Building a PubMed knowledge graph.
Abstract: PubMed((R)) is an essential resource for the medical domain, but useful concepts are either difficult to extract or are ambiguous, which has significantly hindered knowledge discovery. To address this issue, we constructed a PubMed knowledge graph (PKG) by extracting bio-entities from 29 million PubMed abstracts, disambiguating author names, integrating funding data through the National Institutes of Health (NIH) ExPORTER, collecting affiliation history and educational background of authors from ORCID((R)), and identifying fine-grained affiliation data from MapAffil. Through the integration of these credible multi-source data, we could create connections among the bio-entities, authors, articles, affiliations, and funding. Data validation revealed that the BioBERT deep learning method of bio-entity extraction significantly outperformed the state-of-the-art models based on the F1 score (by 0.51%), with the author name disambiguation (AND) achieving an F1 score of 98.09%. PKG can trigger broader innovations, not only enabling us to measure scholarly impact, knowledge usage, and knowledge transfer, but also assisting us in profiling authors and organizations based on their connections with bio-entities.
Published on June 26, 2020
Antioxidant, Physicochemical, and Cellular Secretion of Glucagon-Like Peptide-1 Properties of Oat Bran Protein Hydrolysates.
Abstract: The aim of this work was to determine the physicochemical and biological activities of hydrolyzed proteins from sonicated oat brans. In addition to the control bran sample, two types of pre-treatment procedures-namely, ultrasonic bath and probe-type sonication-were performed to extract proteins, followed by hydrolysis with various proteases. Physicochemical analyses showed that Flavourzyme-hydrolysates had greater amounts of aromatic amino acids, Papain-hydrolysates low surface charges (-0.78 to -1.32 mV) compared to the others (-3.67 to -9.17 mV), and Alcalase-hydrolysates a higher surface hydrophobicity. The hydrolysates had good radical scavenging activities but, as the ultrasonic pre-treatment of the brans showed, in certain cases there was a reduction in activities of up to 22% for ROO(*) and HO(*) and 15% for O2(*-) radicals. In anti-diabetic tests, the maximum inhibition of alpha-amylase was 31.8%, while that of dipeptidyl peptidase-4 was 53.6%. In addition, the secretion of glucagon-like peptide-1 in NCI-H716 cells was enhanced by 11.5% in the presence of hydrolysates.
Published on June 25, 2020
Preliminary Virtual Screening Studies to Identify GRP78 Inhibitors Which May Interfere with SARS-CoV-2 Infection.
Abstract: SARS-CoV-2 Spike protein was predicted by molecular docking to bind the host cell surface GRP78, which was suggested as a putative good molecular target to inhibit Covid-19. We aimed to confirm that GRP78 gene expression was increased in blood of SARS-CoV-2 (+) versus SARS-CoV-2 (-) pneumonia patients. In addition, we aimed to identify drugs that could be repurposed to inhibit GRP78, thus with potential anti-SARS-CoV-2 activity. Gene expression studies were performed in 10 SARS-CoV-2 (-) and 24 SARS-CoV-2 (+) pneumonia patients. A structure-based virtual screen was performed with 10,761 small molecules retrieved from DrugBank, using the GRP78 nucleotide binding domain and substrate binding domain as molecular targets. Results indicated that GRP78 mRNA levels were approximately four times higher in the blood of SARS-CoV-2 (+) versus SARS-CoV-2 (-) pneumonia patients, further suggesting that GRP78 might be a good molecular target to treat Covid-19. In addition, a total of 409 compounds were identified with potential as GRP78 inhibitors. In conclusion, we found preliminary evidence that further proposes GRP78 as a possible molecular target to treat Covid-19 and that many clinically approved drugs bind GRP78 as an off-target effect. We suggest that further work should be urgently carried out to confirm if GRP78 is indeed a good molecular target and if some of those drugs have potential to be repurposed for SARS-CoV-2 antiviral activity.
Published on June 25, 2020
Chemical, Physical and Biological Triggers of Evolutionary Conserved Bcl-xL-Mediated Apoptosis.
Abstract: BACKGROUND: The evidence that pan-Bcl-2 or Bcl-xL-specific inhibitors prematurely kill virus-infected or RNA/DNA-transfected cells provides rationale for investigating these apoptotic inducers further. We hypothesized that not only invasive RNA or DNA (biological factors) but also DNA/RNA-damaging chemical or physical factors could trigger apoptosis that have been sensitized with pan-Bcl-2 or Bcl-xL-specific agents; Methods: We tested chemical and physical factors plus Bcl-xL-specific inhibitor A-1155463 in cells of various origins and the small roundworms (C. elegans); Results: We show that combination of a A-1155463 along with a DNA-damaging agent, 4-nitroquinoline-1-oxide (4NQO), prematurely kills cells of various origins as well as C. elegans. The synergistic effect is p53-dependent and associated with the release of Bad and Bax from Bcl-xL, which trigger mitochondrial outer membrane permeabilization. Furthermore, we found that combining Bcl-xL-specific inhibitors with various chemical compounds or physical insults also induced cell death; Conclusions: Thus, we were able to identify several biological, chemical and physical triggers of the evolutionarily conserved Bcl-xL-mediated apoptotic pathway, shedding light on strategies and targets for novel drug development.
Published on June 24, 2020
Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative Against SARS-CoV2: An In Silico Analysis.
Abstract: The pandemic associated with Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV2) and its disease named COVID-19 challenged the scientific community to discover effective therapeutic solutions in a short period. Repurposing existing drugs is one viable approach that emphasizes speed during these urgent times. Famotidine, a class A G protein-coupled receptor antagonist used for the treatment of gastroesophageal reflux was recently identified in an in silico screening. Additionally, a recent retrospective clinical report showed that the treatment with famotidine provided a good outcome in patients infected with SARS-CoV2. A clinical trial testing effectiveness of famotidine in combination with hydroxychloroquine is currently ongoing in the United States (US). In the 1990s, famotidine was described as an antiviral agent against human immunodeficiency virus (HIV). Interestingly, some HIV protease inhibitors are presently being used against SARS-CoV2. However, it is not clear if famotidine could be effective against SARS-CoV2. Thus, by using a computational analysis, we aimed to examine if the antiviral effect of famotidine could be related to the inhibition of proteases involved in the virus replication. Our results showed that famotidine could interact within the catalytic site of the three proteases associated with SARS-CoV2 replication. However, weak binding affinity of famotidine to these proteases suggests that a successful famotidine therapy could likely be achieved only in combination with other antiviral drugs. Finally, analysis of famotidine's pharmacokinetic parameters indicated that its effect against SARS-CoV2 infection could be reached only upon intravenous administration. This work will contribute to the pharmacological knowledge of famotidine as an antiviral agent against SARS-CoV2.
Published on June 23, 2020
In silico analysis for factors affecting anti-malarial penetration into red blood cells.
Abstract: BACKGROUND: Malaria is a parasitic disease that produces significant infection in red blood cells. The objective of this study is to investigate the relationships between factors affecting the penetration of currently available anti-malarials into red blood cells. METHODS: Fifteen anti-malarial drugs listed in the third edition of the World Health Organization malaria treatment guidelines were enrolled in the study. Relationship analysis began with the prioritization of the physicochemical properties of the anti-malarials to create a multivariate linear regression model that correlates the red blood cell penetration. RESULTS: It was found that protein binding was significantly correlated with red blood cell penetration, with a negative coefficient. The next step was repeated analysis to find molecular descriptors that influence protein binding. The coefficients of the number of rotating bonds and the number of aliphatic hydrocarbons are negative, as opposed to the positive coefficients of the number of hydrogen bonds and the number of aromatic hydrocarbons. The p-value was less than 0.05. CONCLUSIONS: Anti-malarials with a small number of hydrogen bonds and aromatic hydrocarbons, together with a high number of rotatable bonds and aliphatic hydrocarbons, may have a higher tendency to penetrate the red blood cells.
Showing 2451 to 2454 of 5186 entries