- Journal article
Authors : Tragni, Vincenzo (2021) - The rapid spread of new SARS-CoV-2 variants needs the development of rapid tools for
predicting the affinity of the mutated proteins responsible for the infection, i.e., the SARS CoV-2 spike protein, for the human ACE2 receptor, aiming to understand if a variant can be
more efficient in invading host cells. Here we show how our computational pipeline,
previously used for studying SARS-CoV-2 spike receptor binding domain (RB...
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- Journal article
Authors : Fornasier, Emanuele (2021) - The SARS-CoV-2 main protease (Mpro) has a pivotal role in mediating viral genome replication and
transcription of coronavirus, making it a promising target for drugs against Covid-19 pandemic.
Here we present a crystal structure of Mpro disclosing new structural features of key regions of the
enzyme. We show that the oxyanion loop, involved in substrate recognition and enzymatic activity,
can adopt a new conformation, which is stable&#...
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- Periodicals (Báo – Tạp chí)
Authors : Di Carlo, Piero; Chiacchiaretta, Piero; Sinjari, Bruna (2020) - Transmission pathways of SARS-CoV-2 are through aerosol, droplet and touching infected material. Indoor locations are more likely environments for the diffusion of the virus contagion among people, but direct detection of SARS-CoV-2 in air or on surfaces is quite sparse, especially regarding public transport. In fact, an important demand is to know how and if it is safe to use them. To understand the possible spreading of COVID-19 inside a ...
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- Journal article
Authors : Zaidman, Daniel; Gehrtz, Paul; Filep, Mihajlo (2020) - Present covalentizer, a computational pipeline for creating irreversible inhibitors based on complex structures of targets with known reversible binders. For each ligand, we create a custom-made focused library of covalent analogs. We use covalent docking, to dock these tailored covalent libraries and to find those that can bind covalently to a nearby cysteine while keeping some of the main interactions of the original molecule. We found ~11,000 cysteine...
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- Journal article
Authors : Yadav, Ruchi (2023) - SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19
34 pandemic. Its ~30 kb RNA genome is translated into two large polyproteins subsequently cleaved
35 by viral papain-like protease and main protease (Mpro/nsp5). Polyprotein processing is essential
36 yet incompletely understood. We studied Mpro-mediated processing of the nsp7-10/11
37 polyprotein, whose mature products are cofactors of the viral replicase, identifying the&#...
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- Periodicals (Báo – Tạp chí)
Authors : McCallum, Matthew; Walls, Alexandra C; Corti, Davide (2020) - The recent spillover of SARS-CoV-2 in the human population resulted in the ongoing COVID-19 pandemic which has already caused 4.9 million infections and more than 326,000 fatalities. To initiate infection the SARS-CoV-2 spike (S) glycoprotein promotes attachment to the host cell surface, determining host and tissue tropism, and fusion of the viral and host membranes. Although SARS-CoV- 2 S is the main target of neutralizing antibodies and the focus&...
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- Journal article
Authors : Almasy, Katherine M. (2021) - Human coronaviruses have become an increasing threat to global health; three highly pathogenic strains have emerged since the early 2000s, including most recently SARS-CoV-2, the cause of COVID-19. A better understanding of the molecular mechanisms of coronavirus pathogenesis is needed, including how these highly virulent strains differ from those that cause milder, common-cold like disease. While significant progress has been made in understanding how SARS-CoV-2 ...
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- Periodicals (Báo – Tạp chí)
Authors : Rangan, Ramya (2020) - he rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosetta’s FARFAR2 algorithm ...
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- Journal Article
Authors : Weidenbacher, Payton A.-B. (2023) - With the SARS-CoV-2 virus still circulating and evolving, there remains an outstanding question if variant-specific
vaccines represent the optimal path forward, or if other strategies might be more efficacious towards providing broad
protection against emerging variants. Here, we examine the efficacy of strain-specific variants of our previously
reported, pan-sarbecovirus vaccine candidate, DCFHP-alum, a ferritin nanoparticle functionalized with an engineered
form ...
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- Journal Article
Authors : Baboo, Sabyasachi (2023) - UBR4 is an E3 ligase (E3) of the N-degron pathway and is involved in
neurodevelopment, age-associated muscular atrophy and cancer progression. The location
and mechanistic classification of the E3 module within the 600 kDa protein UBR4 remains
unknown. Herein, we identify and characterize, at a biochemical and structural level, a distinct
E3 module within human UBR4 consisting of a novel “hemiRING” zinc finger, a helical-rich
UBR ...
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- Journal article
Authors : Laffeber, Charlie (2021) - Rapidly spreading new variants of SARS-CoV-2 carry multiple mutations in the viral spike
protein which attaches to the angiotensin converting enzyme 2 (ACE2) receptor on host cells.
Among these mutations are amino acid changes N501Y (lineage B.1.1.7, first identified in the
UK), and the combination N501Y, E484K, K417N (B.1.351, first identified in South Africa),
all located at the interface on the receptor binding domain (RBD). We expe...
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- Periodicals (Báo – Tạp chí)
Authors : Stamatakis, George; Samiotaki, Martina; Mpakali, Anastasia (2020) - Presentation of antigenic peptides by MHCI is central to cellular immune responses against viral pathogens. While adaptive immune responses versus SARS-CoV-2 can be of critical importance to both recovery and vaccine efficacy, how protein antigens from this pathogen are processed to generate antigenic peptides is largely unknown. Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein...
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- Periodicals (Báo – Tạp chí)
Authors : Sinegubova, Maria V. (2020) - The spike (S) protein is one of the three proteins forming the coronaviruses' viral envelope. The S protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has a spatial structure similar to the S proteins of other mammalian coronaviruses, except for a unique receptor-binding domain (RBD), which is a significant inducer of host immune response. Recombinant SARS-CoV-2 RBD is widely used as a highly specific minimal antigen for...
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- Journal article
Authors : Ragotte, Robert J. (2021) - Basigin, or CD147, has been reported as a co-receptor used by SARS-CoV-2 to invade host cells. Basigin also has a well-established role in Plasmodium falciparum malaria infection of human erythrocytes where it is bound by one of the parasite’s invasion ligands, reticulocyte binding protein homolog 5 (RH5). Here, we sought to validate the claim that the receptor binding domain (RBD) of SARS-CoV-2 spike glycoprotein can form a complex with basigi...
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- Journal article
Authors : Orsburn, Benjamin C; Jenkins, Conor; Miller, Sierra M (2020) - We describe a method for rapid in silico selection of diagnostic peptides from newly described viral pathogens and applied this approach to SARS-CoV-2/COVID-19. This approach is multi-tiered, beginning with compiling the theoretical protein sequences from genomic derived data. In the case of SARS-CoV-2 we begin with 496 peptides that would be produced by proteolytic digestion of the viral proteins. To eliminate peptides that would cause cross-reactivity ...
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- Journal article
Authors : Orsburn, Benjamin C; Jenkins, Conor; Miller, Sierra M (2020) - We describe a method for rapid in silico selection of diagnostic peptides from newly described viral pathogens and applied this approach to SARS-CoV-2/COVID-19. This approach is multi-tiered, beginning with compiling the theoretical protein sequences from genomic derived data. In the case of SARS-CoV-2 we begin with 496 peptides that would be produced by proteolytic digestion of the viral proteins. To eliminate peptides that would cause cross-reactivity ...
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- Journal article
Authors : Aguilera, David (2023) - Antiviral compounds are crucial to controlling the SARS-CoV-2 pandemic. Approved drugs have been tested for their efficacy against COVID-19, and new pharmaceuticals are being developed as a complementary tool to vaccines However, there are not any effective treatment against this disease yet. In this work, a cheap and fast purification method of natural tyrosinase from Agaricus bisporus fresh mushrooms was developed in order to evaluate the potential of&...
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- Journal article
Authors : Roy, Urmi (2023) - Among the multiple SARS-CoV-2 variants recently reported, the Delta variant has generated most perilous and widespread effects. Another variant, Omicron, has been identified specifically for its high transmissibility. Omicron contains numerous spike (S) protein mutations and in numbers much larger than those of its predecessor variants. In this report we discuss some essential structural aspects and time-based structure changes of a selected set of spike protein&#...
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- Journal Article
Authors : Ketaren, Natalia E. (2023) - SARS-CoV-2 has infected >40% of the world’s population (Collaborators 2022) resulting in
a devastating loss of life. As the SARS-CoV-2 pandemic enters its endemic phase (Meng,
Irwin et al. 2023, Pilz and Ioannidis 2023), multiple new variants continue to circulate. Since
its initial spread, the rapid adaptation of the virus to selective pressures continues to
produce variants of concern (VoC), of which the omicron variants presently ...
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- Journal article
Authors : Fleming, Aaron M. (2021) - Nanopore devices can directly sequence RNA, and the method has the potential to determine
locations of epitranscriptomic modifications that have grown in significance because of their roles
in cell regulation and stress response. Pseudouridine (Ψ), the most common modification in RNA,
was sequenced with a nanopore system using a protein sensor with a helicase brake in synthetic
RNAs with 100% modification at 18 known human pseudouridinylati...
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