Viral protein-human protein

Last updated: 2022 Jun 27
Total hit(s): 32
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Original Article
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Structural superimposition of the RBD region of Spike glycoprotein of SARS-CoV-2 wild and its variants - Omicron, Delta AY.1 & 2 and AY. 3, showed structural changes around the antibody binding regions. Protein structure prediction showed Omicron's polarity, non-polarity, and hydrophobicity characteristics changed from the wild SARS-CoV-2. Omicron and Delta AY.3 are expected to be more pathogenic due to their RBD structures' greater instability.
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 		35690234
(Microb Pathog)
PMID
35690234
Date of Publishing: 2022 Jun 8
Title The influence of new SARS-CoV-2 variant Omicron (B.1.1.529) on vaccine efficacy, its correlation to Delta variants: A computational approach
Author(s) nameRanjan P, Neha et al.
Journal Microb Pathog
Impact factor
2.64
Citation count: 1
Date of Entry 2022 Jun 27

Structural analysis was done to show the position of mutated residues in the Lambda spike regions (NTD and RBD). Three mutations (G75V, T76I, and RSYLTPGD246-253N) were presentin theN-terminal domain (NTD)and the deletion mutation (RSYLTPGD246-253N)mutation was observedin a loop structure(loop 5).Another protein region (Receptor binding domain) containstwo mutations (L452Q and F490S). In addition, the T859N mutation wasfound in a specificSpikesubunit (S2heptad repeat 1). Loop 5 contains 246-260 residues, which was a loop structure designated in a previous study.
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 		Pre-print (bioRXiv)
Title SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance
Impact factor
N/A
Date of Entry 2021 Dec 15

The cryo-EM structure of the S protein of the Alpha variant in the apo form and receptor ACE-2 bound form were charecterised. The A570D mutation modulates the opening and closing of the receptor binding domain (RBD) by introducing a salt bridge. The N501Y mutation increases ACE-2 binding affinity by introducing pi-pi interaction.
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 		Pre-print (bioRXiv)
Title Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations
Impact factor
N/A
Date of Entry 2021 Sep 13

Neuropilin-1 b1 domain binds with SARS-CoV-2 S1 C-end rule (CendR) peptide (7 residues -679-NSPRRAR-685) with an affinity of 20.3 µM at pH 7.5, and 13.0 µM at pH 5.5. In NRP1-depleted Caco-2 cells, viral uptake is halved compared to control cells. Blocking the interaction of NRP1-b1 with SARS-CoV-2 S1 CendR with inhibitors like EG00229 can lead to new anti COVID-19 therapeutics.
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 		33082294
(Science)
PMID
33082294
Date of Publishing: 2020 Nov 13
Title Neuropilin-1 is a host factor for SARS-CoV-2 infection
Author(s) nameDaly JL, Simonetti B et al.
Journal Science
Impact factor
20.57
Citation count: 477
Date of Entry 2021 Aug 2

Monovalent hACE2 decoy CTC-445.2 binds to all the three RBDs of a single spike protein with a low nanomolar affinity and high specificity. The divalent CTC-445.2d shows about ~10 fold increase in the binding. De novo protein design approach to generate decoys is independent to traditional therapeutics and has the potential to better overcome mutational viral evasion.
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 		33154107
(Science)
PMID
33154107
Date of Publishing: 2020 Dec 4
Title De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2
Author(s) nameLinsky TW, Vergara R et al.
Journal Science
Impact factor
20.57
Citation count: 75
Date of Entry 2021 Jul 28

Binding of monoclonal antibody, B6-Fab to SARS-CoV/SARS-CoV-2 spike stem helix peptide, sterically interferes with the spike protein's fusion of the membrane. B6 binds to the hydrophobic core of the stem helix bundle and disrupts its quaternary structure. It prevents S2 subunit refolding from the pre- to the post-fusion state and blocks viral entry. This study unveils an unexpected target for next-generation structure-guided design of a pan-beta-coronavirus vaccine.
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 		33981021
(Nat Struct Mol Biol)
PMID
33981021
Date of Publishing: 2021 May 12
Title Structural basis for broad coronavirus neutralization
Author(s) nameSauer MM, Tortorici MA et al.
Journal Nat Struct Mol Biol
Impact factor
9.8
Citation count: 46
Date of Entry 2021 Jul 28

Structural characterization of SARS-CoV-2S 2P trimer complexed with C105 Fabs, state 2 (3RBD "up") shows mutations in the spike protein do not effect the RBD-binding of mAb C105. Anti-SARS-CoV-2 antibody class derived form VH3-53/VH3-66 have a structural basis for eliciting neutralizing antibodies. The RBD and S1A epitopes are not affected by the common mutations in various SARS_CoV-2 isolates, so the various vaccines and antibody therapeutics would be effective against the COVID-19.
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 		32645326
(Cell)
PMID
32645326
Date of Publishing: 2020 Aug 20
Title Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies
Author(s) nameBarnes CO, West AP Jr et al.
Journal Cell
Impact factor
27.35
Citation count: 387
Date of Entry 2021 Jul 28

Polycolonal IgGs and Fabs from COVID-19 convalescent patients recognise different RBD epitopes of different coronaviruses. Structural characterization of SARS-CoV-2S 2P trimer complexed with C105 Fabs, state 1 (2RBD "up"), recognises both S1A and RBD epitopes on SARS-CoV-2 spike. It reveals an epitope that blocks ACE2 receptor binding. Mutations in the spike protein do not effect the RBD-binding mAb C105. The RBD and S1A epitopes are not affected by the common mutations in various SARS_CoV-2 isolates, so the various vaccines and antibody therapeutics would be effective against the COVID-19.
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 		32645326
(Cell)
PMID
32645326
Date of Publishing: 2020 Aug 20
Title Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies
Author(s) nameBarnes CO, West AP Jr et al.
Journal Cell
Impact factor
27.35
Citation count: 387
Date of Entry 2021 Jul 28

Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 . Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The cryo-EM structures show a small but significant effect of the N501Y mutation on Fab ab1 binding and neutralization, but with no measurable effects on VH ab8 binding or neutralization.
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 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain and Fab ab1 and VH ab8 Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. Despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
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 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to VH ab8 (focused refinement of RBD and VH ab8). Y501 shows increased ACE2 affinity and increased infectivity. Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. Despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to VH ab8. Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The cryo-EM structures show a small but significant effect of the N501Y mutation on Fab ab1 binding and neutralization, but with no measurable effects on VH ab8 binding or neutralization.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (class 2). IC50 for wild-type is greater than that for N501Y. IC50 of soluble ACE2-mFC neutralization is 0.066 μg/ml for unmutated pseudotyped virus and 0.0074 μg/ml for N501Y pseudotyped virus. Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (class 1). Residue 501 interacts with Ser30 of Fab ab1, thus N501Y mutation would have a small effect on the antibody binding epitope. Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. Despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain. Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The comparison of neutralization profiles shows that the IC50for neutralization of the N501Y mutant is lower, suggesting that full-length spikes bearing the N501Y mutation bind ACE2-mFc to a higher extent.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain (focused refinement of RBD and ACE2). Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The cryo-EM methods to identify the footprints of antibodies produced byt the vaccinesis a critical tool to prevent and treact COVID-19.
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 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

3C1 heavy chain shares a small overlapping epitope on the RBM loop 502–505 region (including V503, G504, and Y505) with ACE2. IC50 value for 3C1 is 3.127 µg/mL.(weak neutralization potency). NONE
✍
 		33431876
(Nat Commun)
PMID
33431876
Date of Publishing: 2021 Jan 11
Title Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections
Author(s) nameZhang C, Wang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 31

3C1 binds to core region of RBD. Humanized version of the 2H2/3C1 MAbs neutralize SARS-CoV-2 in vitro with IC50 of 12 ng/mL. 2H2 is the strongest (0.0007µ/ml ) and 3C1 the weakest (µg/mL) in terms of their neutralization potency. Antibody can target RBD domain, if only the epitope is uncovered with enough space to accommodate the Fab so as to allow RBD to grab Fab regardless it is in the up or down conformation. 3C1 Fab is bound to the side of RBD of S trimer.
✍
 		33431876
(Nat Commun)
PMID
33431876
Date of Publishing: 2021 Jan 11
Title Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections
Author(s) nameZhang C, Wang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 31

3C1 binds to core region of RBD. IC50 value for 3C1 is 3.127 µg/mL.(weak neutralization potency) In the humanized complex of 3C1 adn 2H2, 2H2 retains its neutralization potency.
✍
 		33431876
(Nat Commun)
PMID
33431876
Date of Publishing: 2021 Jan 11
Title Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections
Author(s) nameZhang C, Wang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 31

Structure of S-3C1-F1 with one RBD in up configuration and two RBDs in down configuration, where the up configuration RBD is bound to 3C1 fab. 3C1 binds to core region of RBD. It displayed high binding affinity toward SARS-CoV RBD with KD of 1.0 nM. 3C1 Fab is bound to the side of RBD of S trimer.
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 		33431876
(Nat Commun)
PMID
33431876
Date of Publishing: 2021 Jan 11
Title Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections
Author(s) nameZhang C, Wang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 31

Structure of S-2H2-F3b with three RBDs in up configuration and each RBD is bound to 2H2 Fab. 2H2 binds to T470 to T478 of the RBM within RBD. 2H2 is bound on the top of the RBD of S trimer
✍
 		33431876
(Nat Commun)
PMID
33431876
Date of Publishing: 2021 Jan 11
Title Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections
Author(s) nameZhang C, Wang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 31

2H2 binds to T470 to T478 of the RBM within RBD of SARS-CoV-2 Spike protein. IC50 values for 2H2 is 0.0007µ/ml and has strongest neutralization capacity compared to other MAbs 2G3, 8D3, and 3C1. 2H2 is bound on the top of the RBD of S trimer
✍
 		33431876
(Nat Commun)
PMID
33431876
Date of Publishing: 2021 Jan 11
Title Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections
Author(s) nameZhang C, Wang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 31

Structure of S-2H2-F1 with one RBD in up configuration and two RBDs in down configuration, where only the RBD in up configuration is bound to 2H2 Fab. Allosteric rearrangements of the S trimer is caused by Fab. 2H2 is bound on the top of the RBD of S trimer
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 		33431876
(Nat Commun)
PMID
33431876
Date of Publishing: 2021 Jan 11
Title Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections
Author(s) nameZhang C, Wang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 31

Structural characterization of S-2H2-F3a with two RBDs in up configuration and one RBD in down configuration, where each RBD is bound to 2H2 Fab. Humanized version of the 2H2/3C1 MAbs neutralize SARS-CoV-2 in vitro with IC50 of 12 ng/mL. High potency of 2H2 is detected on blocking the interaction between RBD and ACE2. Antibody can target RBD domain, if only the epitope is uncovered with enough space to accommodate the Fab so as to allow RBD to grab Fab regardless it is in the up or down conformation. 2H2 is bound on the top of RBD of S trimer.
✍
 		33431876
(Nat Commun)
PMID
33431876
Date of Publishing: 2021 Jan 11
Title Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections
Author(s) nameZhang C, Wang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 31

Structural characterisation of SARS-CoV-2 spike S1 protein in complex with CR3022 Fab CR3022 epitope can be used as a major target for therapeutic antibodies.
✍
 		32585135
(Cell Host Microbe)
PMID
32585135
Date of Publishing: 2020 Sep 9
Title Neutralization of SARS-CoV-2 by destruction of the Prefusion Spike
Author(s) nameHuo J, Zhao Y et al.
Journal Cell Host Microbe
Impact factor
10.45
Citation count: 144