scholarly journals CRISPR Screening: Molecular Tools for Studying Virus–Host Interactions

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2258
Author(s):  
Vladimir Chulanov ◽  
Anastasiya Kostyusheva ◽  
Sergey Brezgin ◽  
Natalia Ponomareva ◽  
Vladimir Gegechkori ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Viral Infections ◽  
Whole Genome ◽  
Molecular Tools ◽  
Host Interactions ◽  
Drug Candidates ◽  
Complex Interactions ◽  
Recent Developments ◽  
Novel Drug

CRISPR/Cas is a powerful tool for studying the role of genes in viral infections. The invention of CRISPR screening technologies has made it possible to untangle complex interactions between the host and viral agents. Moreover, whole-genome and pathway-specific CRISPR screens have facilitated identification of novel drug candidates for treating viral infections. In this review, we highlight recent developments in the fields of CRISPR/Cas with a focus on the use of CRISPR screens for studying viral infections and identifying new candidate genes to aid development of antivirals.

scholarly journals Trace Elements as Immunoregulators in SARS-CoV-2 and Other Viral Infections

2021 ◽  
Author(s):  
Karthick Dharmalingam ◽  
Amandeep Birdi ◽  
Sojit Tomo ◽  
Karli Sreenivasulu ◽  
Jaykaran Charan ◽  
...  
Keyword(s):  
Immune Response ◽  
Trace Elements ◽  
Viral Entry ◽  
Viral Infections ◽  
Inhibitory Effect ◽  
Antioxidants Activity ◽  
Host Immune Responses ◽  
Complex Interactions ◽  
Downstream Processes

AbstractNutritional deficiency is associated with impaired immunity and increased susceptibility to infections. The complex interactions of trace elements with the macromolecules trigger the effective immune response against the viral diseases. The outcome of various viral infections along with susceptibility is affected by trace elements such as zinc, selenium, iron, copper, etc. due to their immuno-modulatory effects. Available electronic databases have been comprehensively searched for articles published with full text available and with the key words “Trace elements”, “COVID-19”, “Viral Infections” and “Immune Response” (i.e. separately Zn, Se, Fe, Cu, Mn, Mo, Cr, Li, Ni, Co) appearing in the title and abstract. On the basis of available articles we have explored the role of trace elements in viral infections with special reference to COVID-19 and their interactions with the immune system. Zinc, selenium and other trace elements are vital to triggerTH1 cells and cytokine-mediated immune response for substantial production of proinflammatory cytokines. The antiviral activity of some trace elements is attributed to their inhibitory effect on viral entry, replication and other downstream processes. Trace elements having antioxidants activity not only regulate host immune responses, but also modify the viral genome. Adequate dietary intake of trace elements is essential for activation, development, differentiation and numerous functions.

scholarly journals Viruses and Type 1 Diabetes: From Enteroviruses to the Virome

2021 ◽  
Vol 9 (7) ◽  
pp. 1519
Author(s):  
Sonia R. Isaacs ◽  
Dylan B. Foskett ◽  
Anna J. Maxwell ◽  
Emily J. Ward ◽  
Clare L. Faulkner ◽  
...  
Keyword(s):  
Type 1 Diabetes ◽  
Viral Infections ◽  
Antiviral Drug ◽  
Virus Detection ◽  
Detection Methods ◽  
Islet Autoimmunity ◽  
Comprehensive Overview ◽  
Drug Candidates

For over a century, viruses have left a long trail of evidence implicating them as frequent suspects in the development of type 1 diabetes. Through vigorous interrogation of viral infections in individuals with islet autoimmunity and type 1 diabetes using serological and molecular virus detection methods, as well as mechanistic studies of virus-infected human pancreatic β-cells, the prime suspects have been narrowed down to predominantly human enteroviruses. Here, we provide a comprehensive overview of evidence supporting the hypothesised role of enteroviruses in the development of islet autoimmunity and type 1 diabetes. We also discuss concerns over the historical focus and investigation bias toward enteroviruses and summarise current unbiased efforts aimed at characterising the complete population of viruses (the “virome”) contributing early in life to the development of islet autoimmunity and type 1 diabetes. Finally, we review the range of vaccine and antiviral drug candidates currently being evaluated in clinical trials for the prevention and potential treatment of type 1 diabetes.

scholarly journals Recent Updates on Research Models and Tools to Study Virus–Host Interactions at the Placenta

Viruses ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 5 ◽  
Author(s):  
Jae Kyung Lee ◽  
Soo-Jin Oh ◽  
Hosun Park ◽  
Ok Sarah Shin
Keyword(s):  
Viral Infections ◽  
Protective Role ◽  
Biological Mechanisms ◽  
Cellular Targets ◽  
Host Interactions ◽  
Wide Range ◽  
Hofbauer Cells ◽  
Maternal Fetal Transmission ◽  
Immunological Barrier

The placenta is a unique mixed organ, composed of both maternal and fetal tissues, that is formed only during pregnancy and serves as the key physiological and immunological barrier preventing maternal–fetal transmission of pathogens. Several viruses can circumvent this physical barrier and enter the fetal compartment, resulting in miscarriage, preterm birth, and birth defects, including microcephaly. The mechanisms underlying viral strategies to evade the protective role of placenta are poorly understood. Here, we reviewed the role of trophoblasts and Hofbauer cells in the placenta and have highlighted characteristics of vertical and perinatal infections caused by a wide range of viruses. Moreover, we explored current progress and future opportunities in cellular targets, pathogenesis, and underlying biological mechanisms of congenital viral infections, as well as novel research models and tools to study the placenta.

scholarly journals Viruses and Type 1 Diabetes: From Enteroviruses to the Virome

2021 ◽  
Author(s):  
Sonia R Isaacs ◽  
Dylan B Foskett ◽  
Anna J Maxwell ◽  
Emily J Ward ◽  
Clare L Faulkner ◽  
...  
Keyword(s):  
Type 1 Diabetes ◽  
Viral Infections ◽  
Antiviral Drug ◽  
Virus Detection ◽  
Detection Methods ◽  
Islet Autoimmunity ◽  
Comprehensive Overview ◽  
Drug Candidates

For over a century, viruses have left a long trail of evidence implicating them as frequent suspects in the development of type 1 diabetes. Through vigorous interrogation of viral infections in individuals with islet autoimmunity and type 1 diabetes using serological and molecular virus detection methods, and mechanistic studies of virus infected human pancreatic β-cells, the prime suspects have been narrowed down to predominantly human enteroviruses. Here we provide a comprehensive overview of evidence supporting the hypothesised role of enteroviruses in the development of islet autoimmunity and type 1 diabetes. We also discuss concerns over the historical focus and investigation bias toward enteroviruses, and summarise current unbiased efforts aimed at characterising the complete population of viruses (the “virome”) contributing early in life to the development of islet autoimmunity and type 1 diabetes. Finally, we review the range of vaccine and antiviral drug candidates currently being evaluated in clinical trials for the prevention and potential treatment of type 1 diabetes.

scholarly journals Identifying Protein Features Responsible for Improved Drug Repurposing Accuracies Using The CANDO Platform: Implications for Drug Design

2018 ◽  
Author(s):  
William Mangione ◽  
Ram Samudrala
Keyword(s):  
Drug Design ◽  
Drug Repurposing ◽  
Biomedical Literature ◽  
Learning Approaches ◽  
Drug Candidates ◽  
Protein Library ◽  
Fold Reduction ◽  
Ligand Interactions ◽  
Novel Drug

Drug repurposing is a valuable tool for combating the slowing rates of novel therapeutic discovery. The Computational Analysis of Novel Drug Opportunities (CANDO) platform performs shotgun repurposing of 2030 indications/diseases using 3733 drugs/compounds to predict interactions with 46,784 proteins and relating them via proteomic interaction signatures. An accuracy is calculated by comparing interaction similarities of drugs approved for the same indications. We performed a unique subset analysis by breaking down the full protein library into smaller subsets and then recombining the best performing subsets into larger supersets. Up to 14% improvement in accuracy is seen upon benchmarking the supersets, representing a 100–1000 fold reduction in the number of proteins considered relative to the full library. Further analysis revealed that libraries comprised of proteins with more equitably diverse ligand interactions are important for describing compound behavior. Using one of these libraries to generate putative drug candidates against malaria results in more drugs that could be validated in the biomedical literature than the list suggested by the full protein library. Our work elucidates the role of particular protein subsets and corresponding ligand interactions that play a role in drug repurposing, with implications for drug design and machine learning approaches to improve the CANDO platform.

scholarly journals Pathogenetic profiling of COVID-19 and SARS-like viruses

2020 ◽  
Author(s):  
Zulkar Nain ◽  
Humayan Kabir Rana ◽  
Pietro Liò ◽  
Sheikh Mohammed Shariful Islam ◽  
Matthew A Summers ◽  
...  
Keyword(s):  
Viral Infections ◽  
Chemical Interaction ◽  
Interaction Analysis ◽  
Control Measures ◽  
Functional Enrichment ◽  
Drug Candidates ◽  
Prospective Control ◽  
Genetic Mechanisms ◽  
Novel Coronavirus ◽  
Novel Drug

Abstract The novel coronavirus (2019-nCoV) has recently emerged, causing COVID-19 outbreaks and significant societal/global disruption. Importantly, COVID-19 infection resembles SARS-like complications. However, the lack of knowledge about the underlying genetic mechanisms of COVID-19 warrants the development of prospective control measures. In this study, we employed whole-genome alignment and digital DNA–DNA hybridization analyses to assess genomic linkage between 2019-nCoV and other coronaviruses. To understand the pathogenetic behavior of 2019-nCoV, we compared gene expression datasets of viral infections closest to 2019-nCoV with four COVID-19 clinical presentations followed by functional enrichment of shared dysregulated genes. Potential chemical antagonists were also identified using protein–chemical interaction analysis. Based on phylogram analysis, the 2019-nCoV was found genetically closest to SARS-CoVs. In addition, we identified 562 upregulated and 738 downregulated genes (adj. P ≤ 0.05) with SARS-CoV infection. Among the dysregulated genes, SARS-CoV shared ≤19 upregulated and ≤22 downregulated genes with each of different COVID-19 complications. Notably, upregulation of BCL6 and PFKFB3 genes was common to SARS-CoV, pneumonia and severe acute respiratory syndrome, while they shared CRIP2, NSG1 and TNFRSF21 genes in downregulation. Besides, 14 genes were common to different SARS-CoV comorbidities that might influence COVID-19 disease. We also observed similarities in pathways that can lead to COVID-19 and SARS-CoV diseases. Finally, protein–chemical interactions suggest cyclosporine, resveratrol and quercetin as promising drug candidates against COVID-19 as well as other SARS-like viral infections. The pathogenetic analyses, along with identified biomarkers, signaling pathways and chemical antagonists, could prove useful for novel drug development in the fight against the current global 2019-nCoV pandemic.

scholarly journals Roles of glycosaminoglycans as regulators of ligand/receptor complexes

Open Biology ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 180026 ◽  
Author(s):  
Robert G. Smock ◽  
Rob Meijers
Keyword(s):  
Cellular Response ◽  
Molecular Mechanisms ◽  
Gag Protein ◽  
Surface Receptors ◽  
Drug Candidates ◽  
Receptor Complexes ◽  
Tumour Metastasis ◽  
Novel Drug

Glycosaminoglycans (GAGs) play a widespread role in embryonic development, as deletion of enzymes that contribute to GAG synthesis lead to deficiencies in cell migration and tissue modelling. Despite the biochemical and structural characterization of individual protein/GAG interactions, there is no concept available that links the molecular mechanisms of GAG/protein engagements to tissue development. Here, we focus on the role of GAG polymers in mediating interactions between cell surface receptors and their ligands. We categorize several switches that lead to ligand activation, inhibition, selection and addition, based on recent structural studies of select receptor/ligand complexes. Based on these principles, we propose that individual GAG polymers may affect several receptor pathways in parallel, orchestrating a cellular response to an environmental cue. We believe that it is worthwhile to study the role of GAGs as molecular switches, as this may lead to novel drug candidates to target processes such as angiogenesis, neuroregeneration and tumour metastasis.

scholarly journals Recent Developments in New Therapeutic Agents against Alzheimer and Parkinson Diseases: In-Silico Approaches

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2193
Author(s):  
Pedro Cruz-Vicente ◽  
Luís A. Passarinha ◽  
Samuel Silvestre ◽  
Eugenia Gallardo
Keyword(s):  
Clinical Trials ◽  
In Silico ◽  
Symptomatic Relief ◽  
Therapeutic Agents ◽  
Future Perspectives ◽  
Drug Candidates ◽  
Recent Developments ◽  
Progressive Neurodegeneration ◽  
Novel Drug ◽  
Parkinson Diseases

Neurodegenerative diseases (ND), including Alzheimer’s (AD) and Parkinson’s Disease (PD), are becoming increasingly more common and are recognized as a social problem in modern societies. These disorders are characterized by a progressive neurodegeneration and are considered one of the main causes of disability and mortality worldwide. Currently, there is no existing cure for AD nor PD and the clinically used drugs aim only at symptomatic relief, and are not capable of stopping neurodegeneration. Over the last years, several drug candidates reached clinical trials phases, but they were suspended, mainly because of the unsatisfactory pharmacological benefits. Recently, the number of compounds developed using in silico approaches has been increasing at a promising rate, mainly evaluating the affinity for several macromolecular targets and applying filters to exclude compounds with potentially unfavorable pharmacokinetics. Thus, in this review, an overview of the current therapeutics in use for these two ND, the main targets in drug development, and the primary studies published in the last five years that used in silico approaches to design novel drug candidates for AD and PD treatment will be presented. In addition, future perspectives for the treatment of these ND will also be briefly discussed.

Antimicrobial Peptides: Vestiges of Past or Modern Therapeutics?

2020 ◽  
Vol 20 (3) ◽  
pp. 183-195 ◽  
Author(s):  
Jyotsna Bhatt Mitra ◽  
Veerendra K. Sharma ◽  
Mukesh Kumar ◽  
Archana Mukherjee
Keyword(s):  
Antimicrobial Peptides ◽  
Structural Diversity ◽  
Antibiotic Resistant ◽  
Drug Candidates ◽  
Wide Range ◽  
Domains Of Life ◽  
History Of ◽  
Mechanism Of Interaction ◽  
Novel Drug

The ubiquitous occurrence of Antimicrobial Peptides (AMPs) in all domains of life emphasizes their crucial role as ancient mediators of host defense. Despite their antiquity and prolonged history of exposure to pathogens, endogenous AMPs continue to serve as effective antibiotics. An "evolutionary arms race" between host and pathogen resulted in structural diversity of AMPs, leading these molecules to retain activity against a wide range of pathogens, including antibiotic-resistant microbes. As the menace of antibiotic resistance continues to render most antibiotics ineffective against pathogens, the search for novel drug candidates has taken the center stage. The ability of AMPs to combat antibiotic-resistant microbes gave rise to a remarkable surge of interest in AMPs as potential therapeutics. Apart from being effective antimicrobials, AMPs have also found application as probes suitable for in-situ diagnosis of infection. Here, we review the evolutionary history of AMPs, their structural diversity, and mechanism of interaction with microbial membranes. We also summarize the role of AMPs as modern pharmaceuticals and challenges to this development.

scholarly journals GPCRs: Lipid-Dependent Membrane Receptors That Act as Drug Targets

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Amitabha Chattopadhyay
Keyword(s):  
Drug Targets ◽  
Membrane Lipids ◽  
Structural Information ◽  
Membrane Receptors ◽  
Future Research ◽  
Membrane Cholesterol ◽  
Drug Candidates ◽  
Basic Biology ◽  
Novel Drug

G protein-coupled receptors (GPCRs) are the largest class of molecules involved in signal transduction across cell membranes and represent major targets in the development of novel drug candidates in all clinical areas. Although there have been some recent leads, structural information on GPCRs is relatively rare due to the difficulty associated with crystallization. A specific reason for this is the intrinsic flexibility displayed by GPCRs, which is necessary for their functional diversity. Since GPCRs are integral membrane proteins, interaction of membrane lipids with them constitutes an important area of research in GPCR biology. In particular, membrane cholesterol has been reported to have a modulatory role in the function of a number of GPCRs. The role of membrane cholesterol in GPCR function is discussed with specific example of the serotonin1A receptor. Recent results show that GPCRs are characterized with structural motifs that preferentially associate with cholesterol. An emerging and important concept is oligomerization of GPCRs and its role in GPCR function and signaling. The role of membrane cholesterol in GPCR oligomerization is highlighted. Future research in GPCR biology would offer novel insight in basic biology and provide new avenues for drug discovery.

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