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  • Professional Practice Paper

  • Proteoforms of the SARS-CoV-2 nucleocapsid protein are primed to proliferate the virus and attenuate the antibody response

    • Authors : Corinne A., Lutomski (2020)

  • The SARS-CoV-2 nucleocapsid (N) protein is the most immunogenic of the structural proteins and plays essential roles in several stages of the virus lifecycle. It is comprised of two major structural domains: the RNA binding domain, which interacts with viral and host RNA, and the oligomerization domain which assembles to form the viral core. Here, we investigate the assembly state and RNA binding properties of the full-length nucleocapsid protein&#x...
  • Periodicals (Báo – Tạp chí)

  • De novo 3D models of SARS-CoV-2 RNA elements and smallmolecule-binding RNAs to aid drug discovery

    • 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 ...
  • Periodicals (Báo – Tạp chí)

  • The repurposed drugs suramin and quinacrine inhibit cooperatively in vitro SARS-CoV-2 3CLpro

    • Authors : Eberle, Raphael J. (2020)

  • The causative agent of COVID-19 (SARS-CoV-2) has spread worldwide resulting in a pandemic of unprecedented magnitude. To date, no clinically safe drug or vaccine is available and the development of molecules to combat SARS-CoV-2 infections is imminent. A well-known strategy to identify molecules with inhibitory potential against SARS-CoV-2 proteins is the repurposing of clinically developed drugs, e.g., anti-parasitic drugs. The results described in this study dem...
  • Journal article

  • An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 Mpro inhibitor

    • 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...
  • Journal article

  • Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors

    • Authors : Oliveira, A. Sofia F.; Ibarra, Amaurys Avila; Bermudez, Isabel (2020)

  • The binding of the Y674-R685 loop of the S protein to three nAChRs, namely the human α4β2 and α7 subtypes and the muscle-like αβγδ receptor from Tetronarce californica. Our results indicate that Y674-R685 has affinity for nAChRs and the region responsible for binding contains the PRRA motif, a four-residue insertion not found in other SARS-like coronaviruses. In particular, R682 has a key role in the stabilisation of the complexes as it&#x...
  • Periodicals (Báo – Tạp chí)

  • Air and surface measurements of SARS-CoV-2 inside a bus during normal operation

    • 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 ...
  • Periodicals (Báo – Tạp chí)

  • Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases

    • 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...
  • Periodicals (Báo – Tạp chí)

  • Closing coronavirus spike glycoproteins by structure-guided design

    • 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&...
  • Journal article

  • In silico approach toward the identification of unique peptides from viral protein infection: Application to COVID-19

    • 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 ...