Sequence : Nsp1

Total row(s): 15
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Key Findings
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Original Article
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Phylogenetic analysis of Israeli and Non-Israeli SARS-CoV-2 sequences revealed that the Israeli SARS-CoV-2 Strain containing P681H mutation originated from the B.1.1.50 Pangolin lineage. The B.1.1.50 Pangolin lineage had the majority of the sequences are from Israel (70%), Palestine (12%), and the UK (12%)
Pre-print (medRXiv)
Date of Publishing 2021 Mar 25
Title A unique SARS-CoV-2 spike protein P681H strain detected in Israel
Author(s) nameNeta S. Zuckerman, Shay Fleishon et al.
Date of Entry 2021 Jun 14


The study reports a newly identified SARS-CoV-2 Strain from Israel. The strain included a non-synonymous mutation in the S protein: P681H (C23604A) and additional four synonymous mutations, Nsp3:C7765T, Nsp12b: C13821T, Nsp16:T21111C, and C29545A. Phylogenetic analysis was also performed to find the lineage and transmission patterns of the viral strain.
In vitro-neutralization assays were also assessed to find the effect of mutations on viral infectivity.
Pre-print (medRXiv)
Title A unique SARS-CoV-2 spike protein P681H strain detected in Israel
Author(s) name -
Date of Entry 2021 Jun 14


Indian metadata was analyzed to associate the frequent mutations and co-mutation patterns with COVID-19 patient status (deceased, symptomatic, mild, and asymptomatic groups). Patient status was reported for only 806 sequences where 95 were marked as deceased, and 631, 49, 31 were marked as symptomatic, mild, and asymptomatic, respectively
Pre-print (bioRXiv)
Date of Publishing 2021 Mar 25
Title Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India
Author(s) nameNupur Biswas, Priyanka Mallick et al.
Date of Entry 2021 Jun 14


Mutation analysis of 2213 complete genomes from six geographical regions worldwide revealed 3178 polymorphic sites. Of these polymorphic sites, 58.5% (1861 sites) were non-synonymous, compared with the reference genome, Wuhan-Hu-1. Seven frequent non-synonymous mutations were observed in the global population of SARS-CoV-2. SARS-CoV-2 from six regions around the world (United States of America (US), Latin America (LA), Europe (EU), Africa (AF), Asia (AS), and Oceania (OC)) were taken randomly from NCBI and GISAID databases up to November 13, 2020, for the analysis.
DnaSP v5.1 software was used to determine the number of polymorphisms.
The difference between synonymous and non-synonymous substitutions (dN/dS) was evaluated using the software MEGA v6.0.
dN frequencies were obtained using Jalview v2.11 software.
P323L substitution in nsp12 (replication/transcription of the SARS-CoV-2 genome) provides structural stability, S447N substitution is located in the RBM (S protein) increases the affinity for the ACE-2 receptor, G614 substitution makes the virus 2.4 times more infectious.
33572190
(Pathogens)
PMID
33572190
Date of Publishing: 2021 Feb 9
Title Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging
Author(s) nameFlores-Alanis A, Cruz-Rangel A et al.
Journal Pathogens
Impact factor
3.31
Citation count: 11


62 mutations identified, including 30 mis-sense mutations, in 22 Moroccan patient isolates showed that Spike_D614G and NSP12_P323L mutations were present in all the analyzed sequences, whereas N_G204R and N_R203K were present in 9 sequences. Link to Clock Diagram depicting Mutation Evolution Rate in Morrocan Isolates,
33558859
(Biosaf Health)
PMID
33558859
Date of Publishing: 2021 Feb 3
Title Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco
Author(s) nameBadaoui B, Sadki K et al.
Journal Biosaf Health
Impact factor
Cant find
Citation count: 3


Most frequent and prevalent mutation reported, with reference to Wuhan sequence (hCoV-19/Wuhan/WIV04/2019), was P323L in the non-structural protein 12 (94.7%) whereas the second frequent mutation was D614G in the Spike glycoprotein region (92.6%), followed by G71S in the non-structural protein 5 (70%). SARS-CoV-2 Genome sequences generated in the study (Refer Supplementary Table 1 and 2)
33359061
(Int J Infect Dis)
PMID
33359061
Date of Publishing: 2020 Dec 21
Title Molecular epidemiology of COVID-19 in Oman: A molecular andsurveillance study for the early transmission of COVID-19 in thecountry
Author(s) nameAl-Mahruqi S, Al-Wahaibi A et al.
Journal Int J Infect Dis
Impact factor
3.42
Citation count: 5


Compared to the SARS-CoV-2 reference genome (GenBank accession number: MN996528.1), the SARS-CoV-2 genome of Bangladesh, BCSIR-NILMRC-006, (accession number: MT539159) had eight mutations. A unique mutation was observed in the non-structural protein NSP2 of the ORF1ab gene.
32972934
(Microbiol Resour Announc)
PMID
32972934
Date of Publishing: 2020 Sep 24
Title Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh
Author(s) nameAkter S, Banu TA et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 7


Compared to the SARS-CoV-2 reference genome (GenBank accession number: MN996528.1), the SARS-CoV-2 genome of Bangladesh, BCSIR-NILMRC-007, (accession number: MT539158) had six mutations.
32972934
(Microbiol Resour Announc)
PMID
32972934
Date of Publishing: 2020 Sep 24
Title Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh
Author(s) nameAkter S, Banu TA et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 7


Compared to the SARS-CoV-2 reference genome (GenBank accession number: MN996528.1), the SARS-CoV-2 genome of Bangladesh, BCSIR-NILMRC-008, (accession number: MT539160) had six mutations.
32972934
(Microbiol Resour Announc)
PMID
32972934
Date of Publishing: 2020 Sep 24
Title Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh
Author(s) nameAkter S, Banu TA et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 7


Mutation analysis of 2492 SARS-CoV-2 genomes (belonging to 58 different countries representing six continents and five different climatic zones) revealed 1516 nucleotide variations, 744 amino acid substitutions, and 12 deletion sites. The pattern of mutations was different among the six different continents (Europe, Asia, North America, South America, Africa, and Australia) and five different climatic zones (temperate, tropical, diverse, dry, and continental). Sequences under analysis were retrieved from GISAID database (up to 30 March 2020). NCBI reference strain, Wuhan-Hu-1 (Accession NC_045512) was used as a reference genome for the analysis. Mutation analysis reveals diverse mutation pattern. Importantly, four mutations (Q57H, D614G, L3606F, P4714L) were common to all geographical and climatic conditions.
32814791
(Sci Rep)
PMID
32814791
Date of Publishing: 2020 Aug 19
Title Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity
Author(s) nameIslam MR, Hoque MN et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 98


A209C mutation in the nsp16 of SARS-CoV-2, in the adenosine binding pocket might influence the RNA cap binding. A distant (25 ) ligand-binding site unique to SARS-CoV-2 was discovered which can be targeted for antiviral development.
32709886
(Nat Commun)
PMID
32709886
Date of Publishing: 2020 Jul 24
Title Structural basis of RNA cap modification by SARS-CoV-2
Author(s) nameViswanathan T, Arya S et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 75
Date of Entry 2021 Oct 27


Compared to the SARS-CoV-2 reference genome (MN908947.3), the SARS-CoV-2 isolate, CHRF_nCoV19_0001/Bangladesh (accession number: MT476385), was observed to have nine mutations.
32527780
(Microbiol Resour Announc)
PMID
32527780
Date of Publishing: 2020 Jun 11
Title Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh
Author(s) nameSaha S, Malaker R et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 17


Primer pairs for a real-time RT-PCR test specific for the nsp1 gene of SARS-CoV-2.
32501535
(J Med Virol)
PMID
32501535
Date of Publishing: 2020 Nov
Title Identification of nsp1 gene as the target of SARS-CoV-2 real time RT-PCR using nanopore whole genome sequencing
Author(s) nameChan WM, Ip JD et al.
Journal J Med Virol
Impact factor
2.07
Citation count: 19


Probe for a real-time RT-PCR test specific for the nsp1 gene of SARS-CoV-2.
32501535
(J Med Virol)
PMID
32501535
Date of Publishing: 2020 Nov
Title Identification of nsp1 gene as the target of SARS-CoV-2 real time RT-PCR using nanopore whole genome sequencing
Author(s) nameChan WM, Ip JD et al.
Journal J Med Virol
Impact factor
2.07
Citation count: 19


Sequence alignment of SARS-CoV-2 Nsp15 with SARS-Co-V, MERS-Co-V, HCoV229E, MHV show that the active site residues are conserved both in terms of sequence and conformation. Structural comparisons suggest that inhibitors of SARS-CoV Nsp15 have good chance to inhibit the SARS-CoV-2 homolog, but inhibitors of MERS-CoV NendoU are unlikely to inhibit the enzyme.
32304108
(Protein Sci)
PMID
32304108
Date of Publishing: 2020 Jul
Title Crystal structure of Nsp15 endoribonuclease NendoU from SARSCoV2
Author(s) nameKim Y, Jedrzejczak R et al.
Journal Protein Sci
Impact factor
2.4
Citation count: 132



Structure : Nsp1

Total row(s): 20
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Key Findings
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Original Article
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The pseudoknot at the entry to the mRNA channel is a key structural characteristic for translation of the SARS-CoV-2 RNA genome. It specifically interacts with ribosomal proteins (Rabbit 80S ribosome) and 18S rRNA and causes ribosomal pausing prior to -1 frameshifting and the translating ribosome structure. Here, rabbit 80S ribosome colliding in another ribosome stalled by the SARS-CoV-2 pseudoknot is structurally characterized. Interfering with the frameshifting process at the level of nascent chain interactions with the ribosomal tunnel at the level of RNA folding leads to the formation of the frameshift stimulatory pseudoknot, representing a viable strategy in the search for new drugs against SARS-CoV-2.
34029205
(Science)
PMID
34029205
Date of Publishing: 2021 Jun 18
Title Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome
Author(s) nameBhatt PR, Scaiola A et al.
Journal Science
Impact factor
20.57
Citation count: 31
Date of Entry 2021 Aug 11


The pseudoknot at the entry to the mRNA channel is a key structural characteristic for translation of the SARS-CoV-2 RNA genome. It specifically interacts with ribosomal proteins (Rabbit 80S ribosome) and 18S rRNA and causes ribosomal pausing prior to -1 frameshifting and the translating ribosome structure. By cryo-electron microscopy the structure of rabbit 80S ribosome in complex with eRF1 and ABCE1, stalled at the STOP codon in the mutated SARS-CoV-2 slippery site is studied. Interfering with the frameshifting process at the level of nascent chain interactions with the ribosomal tunnel at the level of RNA folding leads to the formation of the frameshift stimulatory pseudoknot, representing a viable strategy in the search for new drugs against SARS-CoV-2.
34029205
(Science)
PMID
34029205
Date of Publishing: 2021 Jun 18
Title Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome
Author(s) nameBhatt PR, Scaiola A et al.
Journal Science
Impact factor
20.57
Citation count: 31
Date of Entry 2021 Aug 11


The pseudoknot at the entry to the mRNA channel is a key structural characteristic for translation of the SARS-CoV-2 RNA genome. It specifically interacts with ribosomal proteins (Rabbit 80S ribosome) and 18S rRNA and causes ribosomal pausing prior to -1 frameshifting and the translating ribosome structure was studied by cryo-electron microscopy. The rabbit 80S ribosome is stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot. Interfering with the frameshifting process at the level of nascent chain interactions with the ribosomal tunnel at the level of RNA folding leads to the formation of the frameshift stimulatory pseudoknot, representing a viable strategy in the search for new drugs against SARS-CoV-2.
34029205
(Science)
PMID
34029205
Date of Publishing: 2021 Jun 18
Title Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome
Author(s) nameBhatt PR, Scaiola A et al.
Journal Science
Impact factor
20.57
Citation count: 31
Date of Entry 2021 Aug 11


The pseudoknot at the entry to the mRNA channel is a key structural characteristic for translation of the SARS-CoV-2 RNA genome. It specifically interacts with ribosomal proteins (Rabbit 80S ribosome) and 18S rRNA and causes ribosomal pausing prior to -1 frameshifting and the translating ribosome structure was studied by cryo-electron microscopy to a high resolution. Interfering with the frameshifting process at the level of nascent chain interactions with the ribosomal tunnel at the level of RNA folding leads to the formation of the frameshift stimulatory pseudoknot, representing a viable strategy in the search for new drugs against SARS-CoV-2.
34029205
(Science)
PMID
34029205
Date of Publishing: 2021 Jun 18
Title Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome
Author(s) nameBhatt PR, Scaiola A et al.
Journal Science
Impact factor
20.57
Citation count: 31
Date of Entry 2021 Aug 11


Structure of SARS-CoV-2 Nsp15 endoribonuclease with Uridine-2',3'-Vanadate (UV, a transition state analog), results in the formation of 2′,3′-cyclic phosphodiester. This is critical for further RNA maturation and functions. This structure proposes that Nsp15 should follow a two-step reaction mechanism with the final product being 3UMP.
33564093
(Commun Biol)
PMID
33564093
Date of Publishing: 2021 Feb 9
Title Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Author(s) nameKim Y, Wower J et al.
Journal Commun Biol
Impact factor
~
Citation count: 26
Date of Entry 2021 Aug 2


The structure of Tipiracil (a uracil derivative ) and SARS-CoV-2 Nsp15 endoribonuclease shows Tipiracil competitively inhibits the enzyme action by binding to its active site. Structure illustrates that uracil alone probably has similar inhibitory properties and provides basis for the uracil scaffold-based drug development.
33564093
(Commun Biol)
PMID
33564093
Date of Publishing: 2021 Feb 9
Title Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Author(s) nameKim Y, Wower J et al.
Journal Commun Biol
Impact factor
~
Citation count: 26
Date of Entry 2021 Aug 2


SARS-CoV-2 Nsp15 is inhibited by interactions with the uridine binding pocket in the enzyme's active site. Structure of SARS CoV-2 Nsp15 endoribonuclease in complex with Uridine-5'-Monophosphate shows Nsp15 discriminates between the uracil and purine bases by forming van der Waals contacts with Tyr343 and hydrogen bonds Ser294 (an active site residue ). Nsp15 enzyme is inhibited by the binding of 5'-UMP in the uracil binding pocket.
33564093
(Commun Biol)
PMID
33564093
Date of Publishing: 2021 Feb 9
Title Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Author(s) nameKim Y, Wower J et al.
Journal Commun Biol
Impact factor
~
Citation count: 26
Date of Entry 2021 Aug 2


Structure of SARS-CoV-2 Nsp15 endoribonuclease in complex with 3'-uridine monophosphate shows uracil demonstrates higher affinity for Trp333 site than in uracil-recognition site created by His235, His250, and Thr341. Structure emphasis that since the enzyme's substrate is a larger RNA molecule, the identity of the Trp333-interacting base is inappropriate.
33564093
(Commun Biol)
PMID
33564093
Date of Publishing: 2021 Feb 9
Title Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Author(s) nameKim Y, Wower J et al.
Journal Commun Biol
Impact factor
~
Citation count: 26
Date of Entry 2021 Aug 2


Structure of SARS-CoV-2 Nsp15 endoribonuclease in complex with dinucleoside monophosphate (GpU), which binds to the active site of the enzyme with uracil interacting with Tyr343 and Ser294. This results in the SARS-CoV-2 Nsp15 is inhibition. Complex structure demonstrates location and specificity determinants of the uridine with a 5-phosphoryl group. Nsp15 is shown to bind and hydrolyze 4, 7, and 20 nucleotide long RNA. Comparitive study of Nsp15 and RNase A active site displayed some conserved active site residues and indicated a common catalytic mechanism with a two-step reaction releasing 3UMP, despite distinct RNA binding site organization in both including both sequence and structure dissimilarity.
33564093
(Commun Biol)
PMID
33564093
Date of Publishing: 2021 Feb 9
Title Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Author(s) nameKim Y, Wower J et al.
Journal Commun Biol
Impact factor
~
Citation count: 26
Date of Entry 2021 Aug 2


Structure of SARS-CoV-2 mini RTC assembly by viral RNA-dependent RNA polymerase (nsp12) with a template-primer RNA, nsp7 and nsp8, and two helicase molecules (nsp13-1 and nsp13-2). nsp13-1 stabilizes the mini RTC by contacting with nsp13-2, which anchors the 5'-extension of RNA template, and interacts with nsp7-nsp8-nsp12-RNA.
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: 49


Structural characterisation of SARS-CoV-2 mini replication and transcription complex
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: 49


Structural characterization of SARS-CoV-2 nsp10 in its unbound form and its behavior in a liquid. Nsp10 binds with nsp14 and nsp16 and facilitates the 3-to-5 exoribonuclease and 2-O-methyltransferase activities respectively.
33036230
(Int J Mol Sci)
PMID
33036230
Date of Publishing: 2020 Oct 6
Title Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2
Author(s) nameRogstam A, Nyblom M et al.
Journal Int J Mol Sci
Impact factor
4.21
Citation count: 12


Structure of SARS-CoV-2 nsp16/nsp10 in complex with RNA cap analogue (m7GpppA) and S-adenosylmethionine (SAM), which methylates 2-OH of ribose of the first transcribing nucleotide of the mRNA cap. It causes conformational changes in nsp16 and an alternate ligand binding site in nsp16 which can be a target for antiviral development. The structure also reveals the basis of an induced fit model of the RNA cap binding and 2-O methylation of the first transcribing nucleotide of SARS-CoV-2 genome.
32709886
(Nat Commun)
PMID
32709886
Date of Publishing: 2020 Jul 24
Title Structural basis of RNA cap modification by SARS-CoV-2
Author(s) nameViswanathan T, Arya S et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 75
Date of Entry 2021 Oct 27


The structure of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex in its active form comprises the non-structural protein 12 (nsp12), nsp8, and nsp7, and more than two turns of RNA template-product duplex. The active-site cleft of nsp12 binds to the first turn of RNA. Two copies of nsp8 bind to opposite sides of the cleft and position the second turn of RNA. Long helical extensions in nsp8 protrude along exiting RNA, forming positively charged 'sliding poles'. These sliding poles help in the processivity of RdRp, required for replicating the long genome of coronaviruses. 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: 218


Structural characteirzation of the nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP) The structure of the template-RTP RdRp complex provides a useful model to rationalize how these drugs inhibit the activity of SARS-CoV-2 RdRp.
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: 404


Structural characterization of cryo-EM structure of the apo nsp12-nsp7-nsp8 complex Knowledge of viral replication mechanism as well as the structure of the protiens involved can prove to be fruitful for drug discovery against SARS-CoV-2 virus
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: 404


Citrate ion makes hydrogen bonds with numerous important active site residues, including His235, His250, Lys290, and Thr341, as well as two water molecules and PEG, in the structure of Nsp15/cit at 1.90Å. Structural comparisons suggest that inhibitors of SARS-CoV Nsp15 have good chance to inhibit the SARS-CoV-2 homolog but inhibitors of MERS-CoV NendoU are unlikely to inhibit the enzyme.
32304108
(Protein Sci)
PMID
32304108
Date of Publishing: 2020 Jul
Title Crystal structure of Nsp15 endoribonuclease NendoU from SARSCoV2
Author(s) nameKim Y, Jedrzejczak R et al.
Journal Protein Sci
Impact factor
2.4
Citation count: 132


The crystal structure of Nsp15 monomer features three distinct domains:- N‐terminal domain is composed of an antiparallel β‐sheet, middle domain formed by 10 β‐strands and three short helices and C‐terminal catalytic NendoU domain formed by two antiparallel β‐sheets. The structure of SARS‐CoV‐2 Nsp15 monomer is very similar to other Nsp15s from coronaviruses.
32304108
(Protein Sci)
PMID
32304108
Date of Publishing: 2020 Jul
Title Crystal structure of Nsp15 endoribonuclease NendoU from SARSCoV2
Author(s) nameKim Y, Jedrzejczak R et al.
Journal Protein Sci
Impact factor
2.4
Citation count: 132


Structure of SARS-CoV-2 RNA-dependent RNA polymerase nsp12 in complex with cofactors nsp7 and nsp8 under reducing condition, forms a β hairpin domain (residues N215 to N218) at its N-terminus. This structure aids in antiviral viral study of remdesivir and other antiviral drugs. The structure of RdRp can be used as a source for discovering broad spectrum antivirals.
32277040
(Science)
PMID
32277040
Date of Publishing: 2020 May 15
Title Structure of the RNA-dependent RNA polymerase from COVID-19 virus
Author(s) nameGao Y, Yan L et al.
Journal Science
Impact factor
20.57
Citation count: 515
Date of Entry 2021 Jul 28


Structure of SARS-Cov-2 RNA-dependent RNA polymerase nsp12, in complex with nsp7 and nsp8 reports a conserved polymerase core and a β hairpin domain (residues N215 to N218) at its N-terminus. This structure aids in the study of remdesivir and other drug candidates' antiviral activity. The structure of RdRp can be used as a source for discovering broad spectrum antivirals.
32277040
(Science)
PMID
32277040
Date of Publishing: 2020 May 15
Title Structure of the RNA-dependent RNA polymerase from COVID-19 virus
Author(s) nameGao Y, Yan L et al.
Journal Science
Impact factor
20.57
Citation count: 515
Date of Entry 2021 Jul 28



Drugs : Nsp1

Total row(s): 9
Select item(s)
Key Findings
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Original Article
(hover to see details)
11,000 compounds out of this library was chosen for target-specific virtual screening based on Lipinskis rule of 5. The natural screening suggested two efficient compounds (PubChem ID: 95372568 and 1776037) with dihydroxyphenyl region of the compound, found to be important in the interaction with the viral protein showing promising activity which may act as a potent lead inhibitory molecule against the virus. In combina tion with virtual screening, modelling, drug like liness, molecular docking, and 500 ns cumulative molecular dynamics simulations (100 ns for each complex) along with the decomposition analysis to calculate and confirm the stability and fold, we propose 95372568 and 1776037 as novel compo unds of natural origin capable of getting develop ed into potent lead molecules against SARS-CoV- 2 target protein NSP15.
33963942
(J Mol Model)
PMID
33963942
Date of Publishing: 2021 May 8
Title Analysis of natural compounds against the activity of SARS-CoV-2 NSP15 protein towards an effective treatment against COVID-19: a theoretical and computational biology approach
Author(s) name Motwalli O, Alazmi M.
Journal J Mol Model
Citation count 2
Date of Entry 2021 Sep 5


Different potential repurposed drugs, including, chloroquine , hydroxychloroquine, ivermectin, remdesivir, and favipiravir, were screened in the present study. Molecular docking of these drugs with different SARS-CoV-2 target proteins, including spike and membrane proteins, RdRp, nucleoproteins, viral proteases, and nsp14, was performed. Molecular dynamics simulation and MM-PBSA calculation were also conducted. Ivermectin and remdesivir were found to be the most promising drugs.
33746908
(Front Microbiol)
PMID
33746908
Date of Publishing: 2020
Title Molecular Docking Reveals Ivermectin and Remdesivir as Potential Repurposed Drugs Against SARS-CoV-2
Author(s) name Eweas AF, Alhossary AA, Abdel-Moneim AS.
Journal Front Microbiol
Impact factor
4.19
Citation count: 8
Date of Entry 2021 Sep 5


Virulence protein factor Nsp1 was targeted by in silico virtual screening of ligand libraries. Molecular docking simulations of the top6 screened ligands with Nsp1 were used and the ligand-Nsp1 complexes were subjected to molecular dynamics simulations to analyze the behaviours of the ligands in a virtual cell From the analyses, it could be safely concluded that the ligands, viz., ligand1, ligand4 and ligand6 had the maximum binding affinities to the Nsp1 apoprotein. All these ligands could bind to the key amino acid residues, Lys164 and His165, which are vital to exert the activity of the Nsp1 apoprotein.
33612076
(J Biomol Struct Dyn)
PMID
33612076
Date of Publishing: 2021 Feb 22
Title Identification of the binding interactions of some novel antiviral compounds against Nsp1 protein from SARS-CoV-2 (COVID-19) through high throughput screening.
Author(s) name Chowdhury N, Bagchi A.
Journal J Biomol Struct Dyn
Impact factor
3.22
Citation count: 1
Date of Entry 2021 Sep 5


Virtual screening of 970 000 chemical compounds against the ATP-binding site to identify potential inhibitors indicates two of the top drug hits (Cepharanthine,Lumacaftor) have significant activity in inhibiting purified recombinant SARS-CoV-2 helicase. ATPase activity was performed to validate high throughput virtual screening method.
33052685
(J Phys Chem Lett)
PMID
33052685
Date of Publishing: 2020 Nov 5
Title Discovery of COVID-19 Inhibitors Targeting the SARS-CoV-2 Nsp13 Helicase
Author(s) name White MA, Lin W, Cheng X.
Journal J Phys Chem Lett
Impact factor
7.33
Citation count: 23
Date of Entry 2021 Sep 5


The study showed that SARS-CoV-2 NSP14-a bifunctional enzyme ,could be a potential drug target for intervention and four drugs-Saquinavir, Hypericin, Baicalein and Bromocriptine were seen to be able to bind to the N-terminal and C-terminal domains of SARS-CoV-2 NSP 14 were seen as potential drug targets for intervention. The compounds including Saquinavir, Hypericin, Baicalein and Bromocriptine, could bind the N-terminus and C-terminus of the homology model of the SARS-CoV-2 Nsp14, providing as a candidate drug against SARS-CoV-2
32923004
(J Pharm Anal)
PMID
32923004
Date of Publishing: 2020 Sep 7
Title Potential Treatment of Chinese and Western Medicine Targeting Nsp14 of SARS-CoV-2
Author(s) nameLiu C, Zhu X et al.
Journal J Pharm Anal
Impact factor
4.84
Citation count: 12
Date of Entry 2021 Sep 5


In-silico models of Nsp13 helicase and nsp14 were generated using comparative homology modelling. The structures were validated and then used for virtual screening of pre-existing, FDA approved antiviral drugs.This was done to verify that these drugs could be repurposed to be used against SARS-CoV-2 infection.
32875166
(Gene Rep)
PMID
32875166
Date of Publishing: 2020 Dec
Title In silico structure modelling of SARS-CoV-2 Nsp13 helicase and Nsp14 and repurposing of FDA approved antiviral drugs as dual inhibitors
Author(s) name Gurung AB.
Journal Gene Rep
Impact factor
0.61
Citation count: 23
Date of Entry 2021 Sep 5


In the present study, the in silico models of SARS-CoV-2 nsp13 helicase and nsp14 protein were elucidated using a comparative homology modelling approach. Simeprevir (SMV), Paritaprevir (PTV) and Grazoprevir (GZR) were the common leads identified which show higher binding affinity to both nsp13 helicase and nsp14 as compared to the control inhibitors and therefore, they might be potential dual-target inhibitors.
32875166
(Gene Rep)
PMID
32875166
Date of Publishing: 2020 Dec
Title In silico structure modelling of SARS-CoV-2 Nsp13 helicase and Nsp14 and repurposing of FDA approved antiviral drugs as dual inhibitors
Author(s) name Gurung AB.
Journal Gene Rep
Impact factor
0.61
Citation count: 23
Date of Entry 2021 Sep 5


The in silico models were further used for virtual screening of the Food and Drug Administration (FDA) approved antiviral drugs. Simeprevir (SMV), Paritaprevir (PTV) and Grazoprevir (GZR) were the common leads identified which show higher binding affinity to both nsp13 helicase and nsp14 as compared to the control inhibitors and therefore, they might be potential dual-target inhibitors.
32875166
(Gene Rep)
PMID
32875166
Date of Publishing: 2020 Dec
Title In silico structure modelling of SARS-CoV-2 Nsp13 helicase and Nsp14 and repurposing of FDA approved antiviral drugs as dual inhibitors
Author(s) name Gurung AB.
Journal Gene Rep
Impact factor
0.61
Citation count: 23
Date of Entry 2021 Sep 5


Identification of a potent inhibitor of Methyltransferase, Endoribonuclease, Phosphatase and Main Protease enzymes of SARS CoV-2 by coumarin derivatives using insilico approach. The in silico studies were performed on maestro 12.0 software (Schrodinger LLC 2019, USA). Two thousand seven hundred fifty-five biologically active coumarin derivative was docked with above receptor proteins of SARS CoV-2.
32835632
(J Biomol Struct Dyn)
PMID
32835632
Date of Publishing: 2020 Aug 24
Title In silico validation of coumarin derivatives as potential inhibitors against Main Protease, NSP10/NSP16-Methyltransferase, Phosphatase and Endoribonuclease of SARS CoV-2
Author(s) name Maurya AK, Mishra N.
Journal J Biomol Struct Dyn
Impact factor
3.22
Citation count: 5
Date of Entry 2021 Sep 5



Diagnostics : Nsp1

Total row(s): 1
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Original Article
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Reporting a novel nsp1 real-time RT-PCR assay for the detection of SARS-CoV-2, based on nanopore sequencing. nsp1 gene was identified as a highlyexpressed gene in all samples via Nanopore wholegenome sequencing. This assay is unique because it target the nsp1 gene which is located at the 5' end of the genome, while the other assays targets the middle or the end of the SARS-CoV-2 genome.
32501535
(J Med Virol)
PMID
32501535
Date of Publishing: 2020 Nov
Title Identification of nsp1 gene as the target of SARS-CoV-2 real time RT-PCR using nanopore whole genome sequencing
Author(s) nameChan WM, Ip JD et al.
Journal J Med Virol
Impact factor
2.07
Citation count: 19



Molecular_interactions : Nsp1

Total row(s): 4
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Original Article
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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: 49


The high-resolution structure of a ternary complex of SARS-CoV-2 nsp16 and nsp10 in the presence of cognate RNA substrate analogue and methyl donor, S-adenosyl methionine (SAM) shows conformational changes associated with substrate binding as the enzyme transitions from a binary to a ternary state. ~
32709886
(Nat Commun)
PMID
32709886
Date of Publishing: 2020 Jul 24
Title Structural basis of RNA cap modification by SARS-CoV-2
Author(s) nameViswanathan T, Arya S et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 75
Date of Entry 2021 Oct 27


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: 218


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: 404