scholarly journals Peptide-Based Biosensor for Express Diagnostics of Coronavirus Respiratory Infections

Proceedings ◽  
2020 ◽  
Vol 60 (1) ◽  
pp. 52
Author(s):  
Tatiana Zimina ◽  
Vladimir Karasev ◽  
Viktor Luchinin ◽  
Alexander Kolobov ◽  
Ivan Mandrik ◽  
...  
Keyword(s):  
Respiratory Infections ◽  
Microfluidic Channel ◽  
Viral Proteins ◽  
Cell Receptor ◽  
Amino Acid Residues ◽  
Viral Particles ◽  
Diagnostic Approaches ◽  
Ionic Hydrogen Bonds ◽  
Prompt Action ◽  
Spread Of Infection

At the end of year 2019 the first reports appeared of a new coronavirus and on 31st December 2019 WHO declared a public health emergency of international concern. To date (as of 6:08 pm CET, 24th November 2020) according to WHO the new coronavirus, now called severe acute respiratory syndrome (SARS)-CoV-2, has infected 58,900,547 people and killed 1,393,305 people worldwide. It is extremely important to develop means for express diagnostics to ensure prompt action to limit the spread of infection. One of the diagnostic approaches, is the detection of viral particles in swabs. This approach can be realized using a biosensor with specific ligands, based on peptide molecules complementary to surface viral proteins. The concept of the so-called Systems of Conjugated Ionic-Hydrogen Bonds (abbreviated—SSIVS, CIHBS) implemented in the Protein-3D computer program, was applied to analyze the spatial structures of the bonds between the SARS-CoV-2 spike protein and the ACE-2 (Angiotensin converting enzyme 2) receptor, in order to reveal the perspective peptide sequences. There are two clearly marked areas of contact of the spike with the cell receptor—upper and lower, which are visualized in the SSIVS form, and the complex formed at this site is strong enough to ensure its attachment to the coronavirus spike and can compete for binding with the ACE-2 receptor. Two peptides were developed that form a spatial structure complementary to the coronavirus spike: of eight (No. one) and of 15 (No. two) amino acid residues. The peptides were covalently bound to biochip platforms via neutral linkers to form sites with peptides No. one and No. two. The third site has a neutral hydrophilic surface to serve as a reference. The platform was integrated with a microfluidic channel and was used as a flow through device. The detection of bound viral particles was carried out using UV excitation and direct registration of viral proteins fluorescence. The preliminary laboratory tests demonstrated the efficiency of the biosensor.

scholarly journals The Crossroads between Host Copper Metabolism and Influenza Infection

2021 ◽  
Vol 22 (11) ◽  
pp. 5498
Author(s):  
Ludmila V. Puchkova ◽  
Irina V. Kiseleva ◽  
Elena V. Polishchuk ◽  
Massimo Broggini ◽  
Ekaterina Yu. Ilyechova
Keyword(s):  
Respiratory Infections ◽  
Influenza Infection ◽  
Copper Metabolism ◽  
Viral Proteins ◽  
Metabolic System ◽  
Copper Status ◽  
Viral Particles ◽  
Viral Respiratory Infections ◽  
Genetic Constructs ◽  
Host Metabolism

Three main approaches are used to combat severe viral respiratory infections. The first is preemptive vaccination that blocks infection. Weakened or dead viral particles, as well as genetic constructs carrying viral proteins or information about them, are used as an antigen. However, the viral genome is very evolutionary labile and changes continuously. Second, chemical agents are used during infection and inhibit the function of a number of viral proteins. However, these drugs lose their effectiveness because the virus can rapidly acquire resistance to them. The third is the search for points in the host metabolism the effect on which would suppress the replication of the virus but would not have a significant effect on the metabolism of the host. Here, we consider the possibility of using the copper metabolic system as a target to reduce the severity of influenza infection. This is facilitated by the fact that, in mammals, copper status can be rapidly reduced by silver nanoparticles and restored after their cancellation.

scholarly journals Mimicry between respiratory virus proteins and some human immune proteins

2020 ◽  
Vol 10 (2) ◽  
pp. 305-314
Author(s):  
I. N. Zhilinskaya
Keyword(s):  
Immune Response ◽  
Immune System ◽  
Amino Acid ◽  
Measles Virus ◽  
Respiratory Infections ◽  
Viral Proteins ◽  
Cellular Protein ◽  
Amino Acid Sequences ◽  
Host Immune System ◽  
Human Immune

A comparative analysis on search for amino acid sequences in viral proteins causing respiratory infections (or respiratory infections syndrome) homologous to amino acid sequences from some human immune proteins was performed. The following viruses were used for comparative computer analysis: coronavirus (SARS-CoV), serotype C subgroup adenovirus C (adenoid 71 strain), measles virus (ICHINOSE-BA strain), rubella (Therien strain) and respiratory syncytial (B1 strain) virus. The search for homologous sequences in viral and human immune proteins was carried out by computer comparison of 12 amino acid fragments, which were assigned as homologous at identity in ≥ 8 positions. The data obtained showed that viral proteins contained homologous motifs in several host immune proteins involved in regulating both the inflammatory response and immune response. Mechanistically, all viruses studied were characterized by sequences homologous to host immune proteins such as complement system proteins, integrins, apoptosis inhibitory proteins, interleukins, and toll-like receptors. Such cellular proteins are actively involved in regulating host inflammatory process and immune response formation. Upon that, a set of host immune proteins, to which homologous fragments were found in viral proteins, was individual for each virus. Interestingly, the largest amount of homologous fragments (up to 20) was mainly concentrated in viral proteins with polymerase and protease activity suggesting that these proteins apart to their major role were involved in production of viral nucleic acids and might participate in regulating host immune system. Envelope, internal and non-structural viral proteins, homologous fragments were detected in much smaller quantities (from 1 to 4). In addition, two fragments homologous to various motifs of the same cellular protein were detected in some viral proteins. Thus, the data obtained further support our understanding that signs of immune system disorders in viral infections can result from multi-layered processes associated with modulation of host innate and adaptive immune system, and open up new approaches to study interaction of viruses with host immune system and identify new functions of viral proteins.

scholarly journals Hijacking the Fusion Complex of Human Parainfluenza Virus as an Antiviral Strategy

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
T. C. Marcink ◽  
E. Yariv ◽  
K. Rybkina ◽  
V. Más ◽  
F. T. Bovier ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Target Cell ◽  
Electron Tomography ◽  
Cell Receptor ◽  
Parainfluenza Virus ◽  
F Protein ◽  
Highly Active ◽  
Viral Particles ◽  
Virtual Modeling ◽  
Human Parainfluenza Virus

ABSTRACT The receptor binding protein of parainfluenza virus, hemagglutinin-neuraminidase (HN), is responsible for actively triggering the viral fusion protein (F) to undergo a conformational change leading to insertion into the target cell and fusion of the virus with the target cell membrane. For proper viral entry to occur, this process must occur when HN is engaged with host cell receptors at the cell surface. It is possible to interfere with this process through premature activation of the F protein, distant from the target cell receptor. Conformational changes in the F protein and adoption of the postfusion form of the protein prior to receptor engagement of HN at the host cell membrane inactivate the virus. We previously identified small molecules that interact with HN and induce it to activate F in an untimely fashion, validating a new antiviral strategy. To obtain highly active pretriggering candidate molecules we carried out a virtual modeling screen for molecules that interact with sialic acid binding site II on HN, which we propose to be the site responsible for activating F. To directly assess the mechanism of action of one such highly effective new premature activating compound, PAC-3066, we use cryo-electron tomography on authentic intact viral particles for the first time to examine the effects of PAC-3066 treatment on the conformation of the viral F protein. We present the first direct observation of the conformational rearrangement induced in the viral F protein. IMPORTANCE Paramyxoviruses, including human parainfluenza virus type 3, are internalized into host cells by fusion between viral and target cell membranes. The receptor binding protein, hemagglutinin-neuraminidase (HN), upon binding to its cell receptor, triggers conformational changes in the fusion protein (F). This action of HN activates F to reach its fusion-competent state. Using small molecules that interact with HN, we can induce the premature activation of F and inactivate the virus. To obtain highly active pretriggering compounds, we carried out a virtual modeling screen for molecules that interact with a sialic acid binding site on HN that we propose to be the site involved in activating F. We use cryo-electron tomography of authentic intact viral particles for the first time to directly assess the mechanism of action of this treatment on the conformation of the viral F protein and present the first direct observation of the induced conformational rearrangement in the viral F protein.

scholarly journals A distinct class of plant and animal viral proteins that disrupt mitosis by directly interrupting the mitotic entry switch Wee1-Cdc25-Cdk1

2020 ◽  
Vol 6 (20) ◽  
pp. eaba3418
Author(s):  
Huaibing Jin ◽  
Zhiqiang Du ◽  
Yanjing Zhang ◽  
Judit Antal ◽  
Zongliang Xia ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Viral Proteins ◽  
Plant Viruses ◽  
Amino Acid Residues ◽  
Protein Protein Interactions ◽  
Common Amino Acid ◽  
Mitotic Entry ◽  
Distinct Class ◽  
Barley Yellow Dwarf ◽  
Hiv 1

Many animal viral proteins, e.g., Vpr of HIV-1, disrupt host mitosis by directly interrupting the mitotic entry switch Wee1-Cdc25-Cdk1. However, it is unknown whether plant viruses may use this mechanism in their pathogenesis. Here, we report that the 17K protein, encoded by barley yellow dwarf viruses and related poleroviruses, delays G2/M transition and disrupts mitosis in both host (barley) and nonhost (fission yeast, Arabidopsis thaliana, and tobacco) cells through interrupting the function of Wee1-Cdc25-CDKA/Cdc2 via direct protein-protein interactions and alteration of CDKA/Cdc2 phosphorylation. When ectopically expressed, 17K disrupts the mitosis of cultured human cells, and HIV-1 Vpr inhibits plant cell growth. Furthermore, 17K and Vpr share similar secondary structural feature and common amino acid residues required for interacting with plant CDKA. Thus, our work reveals a distinct class of mitosis regulators that are conserved between plant and animal viruses and play active roles in viral pathogenesis.

scholarly journals M11l

2000 ◽  
Vol 191 (9) ◽  
pp. 1487-1498 ◽  
Author(s):  
Helen Everett ◽  
Michele Barry ◽  
Siow Fong Lee ◽  
Xuejun Sun ◽  
Kathryn Graham ◽  
...  
Keyword(s):  
Amino Acid ◽  
Permeability Transition ◽  
Basic Amino Acid ◽  
Viral Proteins ◽  
Myxoma Virus ◽  
Amino Acid Residues ◽  
Hydrophobic Domain ◽  
Monocyte Apoptosis ◽  
Induced Apoptosis ◽  
Knockout Virus

M11L, a novel 166–amino acid membrane-associated protein expressed by the poxvirus, myxoma virus, was previously found to modulate apoptosis after infection of rabbit leukocytes. Furthermore, infection of rabbits with an M11L knockout virus unexpectedly produced lesions with a profound proinflammatory phenotype. We show here that M11L is antiapoptotic when expressed independently of other viral proteins, and is directed specifically to mitochondria by a short COOH-terminal region that is necessary and sufficient for targeting. This targeting region consists of a hydrophobic domain flanked by basic amino acid residues, adjacent to a positively charged tail. M11L blocks staurosporine-induced apoptosis by preventing mitochondria from undergoing a permeability transition, and the mitochondrial localization of this protein is essential for this function. We show that M11L is specifically required to inhibit the apoptotic response of monocytes/macrophages during virus infection, as cells of this lineage undergo apoptosis when infected with the M11L knockout virus. As monocyte apoptosis is uniquely proinflammatory, we propose that this observation reconciles the paradoxical proapoptotic and proinflammatory phenotypes of the M11L knockout virus. We suggest that apoptosis of tissue macrophages represents an important antiviral defense, and that the inhibition of apoptosis by viral proteins can be directed in a cell-specific fashion.

scholarly journals Infectious Agents and Bone Marrow Failure: A Causal or a Casual Connection?

2021 ◽  
Vol 8 ◽  
Author(s):  
Valentina Giudice ◽  
Antonio M. Risitano ◽  
Carmine Selleri
Keyword(s):  
Bone Marrow ◽  
Bone Marrow Failure ◽  
Indirect Evidence ◽  
Cell Receptor ◽  
Cross Reactivity ◽  
Autoimmune Response ◽  
Hematopoietic Stem ◽  
Immune Mediated ◽  
Viral Particles ◽  
Cellular Components

Acquired bone marrow failure (BMF) syndromes are considered immune-mediated disorders because hematological recovery after immunosuppressive therapies is the strongest indirect evidence of the involvement of immune cells in marrow failure development. Among pathophysiology hypotheses, immune derangement after chronic antigen exposure or cross-reactivity between viral particles and cellular components are the most accepted; however, epitopes against whom these lymphocytes are directed to remain unknown. In this study, we showed that BMF-associated immunodominant clones, namely the most represented T cells carrying an antigen-specific T-cell receptor (TCR) sequence in a random pool, were frequently associated with those described in various infectious diseases, such as cytomegalovirus (CMV) and Mycobacterium tuberculosis infection. We hypothesize that these pathogens might elicit an autoimmune response triggered by cross-reactivity between pathogen-related components and proteins or might be expanded as an unspecific response to a global immune dysregulation during BMF. However, those frequent intracellular pathogens might not only be passengers in marrow failure development, while playing a central role in starting the autoimmune response against hematopoietic stem cells.

scholarly journals Characterizing the retroviral envelope glycoprotein membrane proximal external region and membrane-spanning domains for their roles in helical alignment, fusogenicity, and incorporation into viral particles.

2015 ◽  
Author(s):  
◽  
Daniel James Salamango
Keyword(s):  
Leukemia Virus ◽  
Surface Protein ◽  
Surface Proteins ◽  
Target Cells ◽  
Amino Acid Residues ◽  
Specific Domain ◽  
Specific Amino Acid ◽  
Viral Particles ◽  
Membrane Spanning ◽  
Membrane Spanning Domains

Viruses use surface proteins to gain access into target cells to initiate infection. How these surface proteins make it into assembling viral particles and the exact details of the entry process are poorly understood. My work here provides insight into how Murine Leukemia Virus (MLV) acquires its surface protein and how this surface protein initiates entry into the target cell. I have identified that two domains in the surface protein dictate its ability to be acquired by the virus. Further, I have identified that four specific amino acid residues in a specific domain of the protein significantly contribute to the entry mechanism

scholarly journals Recombination and purifying selection preserves covariant movements of mosaic SARS-CoV-2 protein S

2020 ◽  
Author(s):  
Massimiliano S. Tagliamonte ◽  
Nabil Abid ◽  
David A. Ostrov ◽  
Giovanni Chillemi ◽  
Sergei L. Kosakovsky Pond ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Protein S ◽  
Cell Receptor ◽  
The Novel ◽  
Amino Acid Residues ◽  
Dynamic Simulations ◽  
Viral Spread ◽  
Host Cell Receptor ◽  
Pandemic Strains

AbstractIn depth evolutionary and structural analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolated from bats, pangolins, and humans are necessary to assess the role of natural selection and recombination in the emergence of the current pandemic strain. The SARS-CoV-2 S glycoprotein unique features have been associated with efficient viral spread in the human population. Phylogeny-based and genetic algorithm methods clearly show that recombination events between viral progenitors infecting animal hosts led to a mosaic structure in the S gene. We identified recombination coldspots in the S glycoprotein and strong purifying selection. Moreover, although there is little evidence of diversifying positive selection during host-switching, structural analysis suggests that some of the residues emerged along the ancestral lineage of current pandemic strains may contribute to enhanced ability to infect human cells. Interestingly, recombination did not affect the long-range covariant movements of SARS-CoV-2 S glycoprotein monomer in pre-fusion conformation but, on the contrary, could contribute to the observed overall viral efficiency. Our dynamic simulations revealed that the movements between the host cell receptor binding domain (RBD) and the novel furin-like cleavage site are correlated. We identified threonine 333 (under purifying selection), at the beginning of the RBD, as the hinge of the opening/closing mechanism of the SARS-CoV-2 S glycoprotein monomer functional to hACE2 binding. Our findings support a scenario where ancestral recombination and fixation of amino acid residues in the RBD of the S glycoprotein generated a virus with unique features, capable of extremely efficient infection of the human host.

scholarly journals Simultaneous identification of viruses and SARS-CoV-2 variants with programmable DNA nanobait

2021 ◽  
Author(s):  
Filip Boskovic ◽  
Jinbo Zhu ◽  
Ran Tivony ◽  
Alexander Ohmann ◽  
Kaikai Chen ◽  
...  
Keyword(s):  
Respiratory Infections ◽  
Target Selection ◽  
Respiratory Viruses ◽  
Rna Molecules ◽  
Rna Targets ◽  
Diagnostic Approaches ◽  
Syncytial Virus ◽  
Nucleotide Resolution ◽  
Simultaneous Identification ◽  
Multiple Pathogens

Respiratory infections are the major cause of death from infectious disease worldwide. The clinical presentation of many respiratory viruses is indistinguishable; therefore, diagnostic approaches that can identify multiple pathogens are essential for patient management. We aimed to address this challenge with self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid read-out via nanopore sensing. Here, we show this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from SARS-CoV-2, respiratory syncytial virus (RSV), rhinovirus, influenza, and parainfluenza. Our nanobait could be reprogrammed to discriminate viral variants, and we identified several key SARS-CoV-2 variants with single-nucleotide resolution. We increased assay specificity with bespoke nanobait that could identify numerous short RNA targets in the same viral sample in a complex background of the human transcriptome. Notably, we found that the sequence position in the viral RNA secondary structure is critical for nanobait design. Lastly, we show that nanobait could discriminate between samples extracted from oropharyngeal swabs from negative and positive SARS-CoV-2 patients using programmable target cleavage without pre-amplification. Our system allows for multiplexed identification of native RNA molecules, providing a new scalable approach for diagnostics of multiple respiratory viruses in a single assay.

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