Viral protein, Others


Last updated: 2021 Aug 12
Total hit(s): 10
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Based on the intermolecular contact maps (COCOMAPS tool) of ACE2-S complex structure, three short peptides (pep1c, pep1d, pep1e) were designed to block virus-host interaction in the early stages of SARS-CoV-2 infection. New therapeutics for oral administration against SARS-CoV-2 infection can be developed using these peptides, which could be an alternative to traditional drug development.
33918595
(Molecules)
PMID
33918595
Date of Publishing: 2021 Apr 9
Title Native Structure-Based Peptides as Potential ProteinProtein Interaction Inhibitors of SARS-CoV-2 Spike Protein and Human ACE2 Receptor
Author(s) nameOdolczyk N, Marzec E et al.
Journal Molecules
Impact factor
3.01
Citation count: 1
Date of Entry 2021 Aug 12


The study compares the similarities and differences in the structure of heparin sulfate (HS) in human and bat lungs. Also, discusses about the binding capacity of spike protein of SARS-CoV-2 with homosapiens and chiroptera's lung heparin sulfate. The spike glycoprotein of COVID 19 binds 3.5 times stronger to the human lung heparin(HS) sulfate than bat lung heparin sulfate. The molecular weight of the heparin sulfate is more important than the sulfation level for lung HS binding to SARS-CoV-2 virus spike protein.
33712145
(Carbohydr Polym)
PMID
33712145
Date of Publishing: 2021 May 15
Title Heparan sulfates from bat and human lung and their binding to the spike protein of SARS-CoV-2 virus
Author(s) nameYan L, Song Y et al.
Journal Carbohydr Polym
Impact factor
6.23
Citation count: 1
Date of Entry 2021 Aug 11


Host protein arginine methyltransferases (PRMTs) methylates SARS-CoV-2 N protein at residues R95 and R177 within RGG/RG motifs.Type I PRMT inhibitor (MS023) or substitution of R95 or R177 with lysine inhibits interaction of N protein with the 5-UTR of SARS-CoV-2 genomic RNA, a property required for viral packaging. Type I PRMT inhibitors (MS023), cancer drug canditates, have found to reduce SARS-CoV-2 production by inhibiting the methylation of arginine in the N protein of SARS-CoV-2 and hence are promising antivirals.
34029587
(J Biol Chem)
PMID
34029587
Date of Publishing: 2021 May 23
Title Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication
Author(s) nameCai T, Yu Z et al.
Journal J Biol Chem
Impact factor
3.96
Citation count: 1
Date of Entry 2021 Jul 28


SARS-CoV-2 receptor-binding domain (RBD) binds to human ACE2 receptor (hACE2) more strongly than that of bat ACE2 2 from Rhinolophus macrotis (bACE2-Rm). Glycosylation modification in bACE2-Rm doesn't influence the binding of SARS-CoV-2 RBD with bACE2-Rm.ns.
Patch 2 interaction in bACE2-Rm and hACE2 was highly conserved compared to Patch 1 interaction which showed significant differences in both.
In bACE2-Rm, residues Y41 and E42 are significant within the interface of SARS-CoV-2 RBD, whereas the residues in human include Y41 and Q42.
Most of the residues involved in ACE2 homodimer formation were conserved in both human and bats, indicating possible conservation of ACE2 dimer attributes during evolution.
33335073
(Proc Natl Acad Sci U S A)
PMID
33335073
Date of Publishing: 2021 Jan 5
Title Cross-species recognition of SARS-CoV-2 to bat ACE2
Author(s) nameLiu K, Tan S et al.
Journal Proc Natl Acad Sci U S A
Impact factor
9.35
Citation count: 1


Nsp13-1 stabilizes SARS-CoV-2 replication and transcription (RTC) complex by contacting with nsp13-2, which anchors the 5'-extension of RNA template, and interacting with nsp7-nsp8-nsp12-RNA. Different orientations of nsp13-1 results in different interactions with the two forms of mini RTC. Mini RTC with an nsp12R365A mutation has greater helicase activity compared to individual apsnsp13. Nsp13-1T216A mutation has a decreased helicase activity.
33208736
(Nat Commun)
PMID
33208736
Date of Publishing: 2020 Nov 18
Title Architecture of a SARS-CoV-2 mini replication and transcription complex
Author(s) nameYan L, Zhang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 4


Designing a novel Hydroxychloroquine inspired compound - PMP329 by using molecular dynamics and non-equilibrium alchemical transformation techniques, which has an improved potency for 3CLpro - an important functional protein for SARS-CoV-2 replication. The novel HCQ-inspired compound, PMP329 has been predicted to have high dissociation constant of 70 nanomoles. This calls for a rapid invitro measurement of the activity of PMP329 on 3CLpro as a possible antiviral agent for Covid-19.
32633733
(Chem Commun (Camb))
PMID
32633733
Date of Publishing: 2020 Aug 4
Title Interaction of hydroxychloroquine with SARS-CoV2 functional proteins using all-atoms non-equilibrium alchemical simulations
Author(s) nameProcacci P, Macchiagodena M et al.
Journal Chem Commun (Camb)
Impact factor
~5.996
Citation count: 5


Cryo-electron microscopy structure of the SARS-CoV-2 RdRp with non-structural protein 12 (nsp12), nsp8 and nsp7, and more than two turns of RNA template-product duplex, shows active-site cleft of nsp12 binds to the first turn of RNA and mediates RdRp activity and two copies of nsp8 bind to opposite sides of the cleft and position the second turn of RNA. Nsp8 along the exiting RNA, forms positively charged 'sliding poles' which affect the processivity of RdRp. The active site of nsp12 consists of five conserved motif AE, of which the residues (D760 and D761) of motif C binds to the RNA 3 end and plays a crucial role in RNA synthesis. K58 is located in the nsp8 extension and plays an important role in interaction with RNA.
32438371
(Nature)
PMID
32438371
Date of Publishing: 2020 Aug
Title Structure of replicating SARS-CoV-2 polymerase
Author(s) nameHillen HS, Kokic G et al.
Journal Nature
Impact factor
24.36
Citation count: 74


Structural characterization of Peptide-bound SARS-CoV-2 Nsp9 RNA-replicase. 3C sequence forms β sheet interactions with the N terminus of the protein from the other protomer, as a result N terminal residues move outward by ∼1.6 Ć (residues 6–10). The significance of this is yet to be established.
32592996
(iScience)
PMID
32592996
Date of Publishing: 2020 Jul 24
Title Crystal Structure of the SARS-CoV-2 Non-structural Protein 9, Nsp9
Author(s) nameLittler DR, Gully BS et al.
Journal iScience
Impact factor
4.447
Citation count: 29


The complex cryo-electron microscopy structure of SARS-CoV-2 RdRp with a 50-base template-primer RNA and remdesivir, shows the partial double-stranded RNA template is present in the central channel of RdRp where remdesivir is covalently attached as the first replicated base pair and results in the termination of chain elongation. The conserved protein-RNA interactions and the catalytic active site residues, in the diverse RNA viruses, makes it possible to develop broad spectrum antiviral inhibitors.
32358203
(Science)
PMID
32358203
Date of Publishing: 2020 Jun 26
Title Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir
Author(s) nameYin W, Mao C et al.
Journal Science
Impact factor
20.57
Citation count: 156


The in silico structural analysis of the Boceprevir bound complexes of SARS-CoV-2 Mpro and its R60C mutant revealed that the R60C mutation in the Main protease (Mpro) decreases the stability of protein and affects the binding of inhibitor. The point mutation was observed in Mpro (R60C) of SARS-CoV-2 Vietnam isolate.
32881907
(PLoS One)
PMID
32881907
Date of Publishing: 2020
Title Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight
Author(s) nameKhan MI, Khan ZA et al.
Journal PLoS One
Impact factor
2.87
Citation count: 7