Viral protein-human protein

Last updated: 2022 Feb 23
Total hit(s): 31
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The molecular interaction (MI) energy values between the Omicron Spike protein-RBD and ACE2 is 749.8 kcal.mol-1. This is 1.4 times delta variant MI (538.1) and 2.7 times alpha variant MI (276.9). The strong interaction can be contributed to mutations to lysine (K) at N440K, T478K and Q493K in the Omicron variant, which bind to the contact site acidic amino acids of ACE2. Covid-19 variants transmissible strength can be contributed by basic amino acids, especially lysine. Basic amino acids at the interaction site of S-RBD increased the binding affinity with ACE-2.
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 		35026638
(Talanta)
PMID
35026638
Date of Publishing: 2022 Apr 1
Title Quantitative in silico analysis of SARS-CoV-2 S-RBD omicron mutant transmissibility
Author(s) name Hanai T.
Journal Talanta
Impact factor
10.5
Citation count: 5
Date of Entry 2022 Feb 23

The K417N mutation of Omicron reduces ACE2 binding affinity, but new mutations Q493R, G496S and Q498R, have a compensatory effect on the strength of ACE2 binding and hence Omicron has similar binding affinities of Delta variant. The Omicron spike protein exhibits a measurable increase in affinity for ACE2 relative to the ancestral Wuhan strain, the ACE2 affinity is similar for Delta and Omicron variants.
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 		Pre-print (bioRXiv)
Title SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
Impact factor
N/A
Date of Entry 2022 Jan 10

The RBD of 2019-nCoV S protein binds with human ACE2 with an affinity (KD) 15.2nM which is similar to SARS-CoV and ACE2 binding affinity of 15nM. The RBD of 2019-nCoV is different to that of SARS-CoV. But this did not result in any change with its interaction with ACE2 receptor but had an impact on the cross-reactivity of neutralizing antibodies.
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 		32065055
(Emerg Microbes Infect)
PMID
32065055
Date of Publishing: 2020
Title Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody
Author(s) nameTian X, Li C et al.
Journal Emerg Microbes Infect
Impact factor
5.84
Citation count: 655
Date of Entry 2021 Nov 20

SARS-CoV-2 RBD interacts with the N-linked glycan on Asn90 of ACE2 which is absent in SARS-CoV-1.MD simulation of SARS-CoV-2 with ACE2 indicate unbinding forces range from 70 to 105pN and removal of the N-linked glycan reduced unbinding forces to 50-70pN The difference in ACE2 binding between SARS-CoV-2 and SARS-CoV-1 and could help develop new strategies to block SARS-CoV-2 entry.
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 		32766576
(bioRxiv)
PMID
32766576
Date of Publishing: 2020 Jul 31
Title Biomechanical characterization of SARS-CoV-2 spike RBD and human ACE2 protein-protein interaction
Author(s) nameCao W, Dong C et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 1
Date of Entry 2021 Oct 30

MD simulation of the glycosylated trimer spike of SARS-CoV-2 in complex with glycosylated, soluble, human ACE 2 reveals that glycan at N546 of ACE2 interacts with N0074 and N0165 in the S protein. To develop ACE2 as a possible decoy therapy, understanding the influence of ACE2 polymorphisms on glycosylation and S binding is crucial.Modifications of ACE2 glycosylation could lead to more potent biologics that are more competitive inhibitors of S binding.The study provides a foundation for the development of immunogens, vaccines, antibodies, and inhibitors, as well as new information on the mechanisms that allow for glycan microheterogeneity.In order to produce treatments, detailed investigations of the influence of new polymorphisms in S and natural and designed-for-biologics variants of ACE2 on glycosylation and binding properties are necessary.
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 		32743578
(bioRxiv)
PMID
32743578
Date of Publishing: 2020 Jul 24
Title Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor
Author(s) nameZhao P, Praissman JL et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 1
Date of Entry 2021 Oct 30

Molecular interaction studies of SARS-CoV-2 RBD with different variants of hACE2. No major divergence of the interaction interface of SARS-CoV-2 RBD with hACE2
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 		32410735
(Biochem Biophys Res Commun)
PMID
32410735
Date of Publishing: 2020 Jun 30
Title Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS -Cov , hot-spot analysis and effect of the receptor polymorphism
Author(s) nameOthman H, Bouslama Z et al.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 69
Date of Entry 2021 Aug 2

Heparin binding accelerates the aggregation of pathological amyloid proteins in the brain. Comparative study to the docking score of SARS-CoV-2 S1-heparin complex to amyloid forming proteins shows molecular interaction of the SARS-COV-2 Spike S1 RBD and Heparin shows a high docking score of -282.57. By targeting the binding and aggregation process of the S1 and Heparin, neurodegenration can be prevented.
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 		33789211
(Biochem Biophys Res Commun)
PMID
33789211
Date of Publishing: 2021 May 21
Title SARS-CoV-2 spike protein interactions with amyloidogenic proteins: Potential clues to neurodegeneration
Author(s) name Idrees D, Kumar V.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 18
Date of Entry 2021 Aug 12

SARS-CoV-2 S1 RBD binds heparin binding proteins including A, -synuclein, tau, prion, and TDP-43 RRM. The heparin binding site of S1 protein assists the binding to amyloid proteins to the viral surface and initate aggregation of these proteins, leading to neurodegenration in brain. This provides a reasonable explanation for the neurodegenerative distresses caused by a COVID infection. Increase in Kd as the temperature increased from 25 C to 40 C, showed a decrease in binding affinity for SARS-CoV-2 S1 protein complexes.
Increase in temperature usually disrupts the noncovalent interactions between a protein-protein complex, but, the decrease in binding affinity across the temperatures was less apparent for the -Syn complex with S1. This anomaly suggests a stable interaction between -synuclein to SARS-CoV-2 S1 protein.
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 		33789211
(Biochem Biophys Res Commun)
PMID
33789211
Date of Publishing: 2021 May 21
Title SARS-CoV-2 spike protein interactions with amyloidogenic proteins: Potential clues to neurodegeneration
Author(s) name Idrees D, Kumar V.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 18
Date of Entry 2021 Aug 12

Molecular interaction studies of SARS-CoV-2 RBD with different variants of hACE2. No major divergence of the interaction interface of SARS-CoV-2 RBD with hACE2
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 		PMC
Title Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS -Cov , hot-spot analysis and effect of the receptor polymorphism
Impact factor
N/A
Date of Entry 2021 Jul 28

Molecular interaction studies of RBD from SARS-CoV-2 and SARS-CoV with different ACE2 orthologues Q493 might be responsible for higher affinity due to a better satisfaction of the Van der Waals by the longer polar side chain of asparagine.
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 		32410735
(Biochem Biophys Res Commun)
PMID
32410735
Date of Publishing: 2020 Jun 30
Title Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS -Cov , hot-spot analysis and effect of the receptor polymorphism
Author(s) nameOthman H, Bouslama Z et al.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 69
Date of Entry 2021 Jul 28

Molecular interaction studies of SARS-CoV-2 RBD with different variants of hACE2. No major divergence of the interaction interface of SARS-CoV-2 RBD with hACE2
✍
 		PMC
Title Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS -Cov , hot-spot analysis and effect of the receptor polymorphism
Impact factor
N/A
Date of Entry 2021 Jul 28

Molecular interaction study between polymorphic spike protein and human ACE2 reveals affinity and stability of ACE2 to spike protein of SARS-CoV-2 for a mutants I468V, N638S, R708Q is -65.09 kcal/mol, -65.09kcal/mol and -64.99 kcal/mol, respectively. The variants in the spike protein of SARS-CoV-2 and hACE2 would provide a database for tracking the adaptive mutation of SARS-CoV-2 and potential recombination events across different species.
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 		33542420
(Sci Rep)
PMID
33542420
Date of Publishing: 2021 Feb 4
Title Dynamics of binding ability prediction between spike protein and human ACE2 reveals the adaptive strategy of SARS-CoV-2 in humans
Author(s) nameXue X, Shi J et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 6
Date of Entry 2021 Jul 28

Cross-reactivity of B6 monoclonal antibody with the spike glycoproteins of SARS-CoV-2, SARS-COV, MERS and HKU4 is because of the strict conservation of 3 of the 4 hydrophobic residues in the stem helix except for the substitution of F1238MERS-CoV with Y1137SARS-CoV/Y1155SARS-CoV-2 or W1240 OC43/W1237HKU1. B6 binding sterically interferes with S fusogenic conformational changes and blocks viral entry through inhibition of membrane fusion
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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

Surface plasmon resonance (SPR) was used to compare the kinetics of SARS-CoV-2 S protein both D614 and D614G binding to human ACE2. D614G decreases the affinity for ACE2 by increasing the rate of dissociation. The increased infectivity of D614G is not explained by greater ACE2 binding strength.
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 		32991842
(Cell)
PMID
32991842
Date of Publishing: 2020 Oct 29
Title Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Author(s) nameYurkovetskiy L, Wang X et al.
Journal Cell
Impact factor
27.35
Citation count: 434
Date of Entry 2021 Jun 15

Complex of ACE2 receptor and N501Y spike protein ectodomains shows Y501 inserted into a cavity at the binding interface near Y41 of ACE2 providing a structural explanation for the increased ACE2 affinity of the N501Y mutant, and its increased infectivity, but the mutation does note cause large structural changes. 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

Molecular docking experiments with ORF7a and the LFA-1 and Mac-1 I domains reveal E26 (Glu26) in SARS-CoV2 ORF7a forms hydrogen bonds with L205 in LFA-1 and R208 in Mac-1 and thereby interaction between SARS-CoV-2 and leukocytes could result in a modified immune response. ORF7a-mediated effects on immune cells such as T lymphocytes and macrophages (leukocytes) could help understand the disease further and develop effective treatments.
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 		33305306
(Biosci Rep)
PMID
33305306
Date of Publishing: 2020 Dec 11
Title Structural assessment of SARS-CoV2 accessory protein ORF7a predicts LFA-1 and Mac-1 binding potential
Author(s) nameNizamudeen ZA, Xu ER et al.
Journal Biosci Rep
Impact factor
2.51
Citation count: 7

The residues (Asp 1165, Leu 1166, Asn 1173) of the S2 subunit of SARS-CoV-2 have a strong interaction with p53 protein residues- Thr 281, Arg 270, Arg 277, His 175. Further experimental research is required to unveil the impact of COVID-19 in cancer patients and to explore the functional role of these interactions.
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 		32619819
(Transl Oncol)
PMID
32619819
Date of Publishing: 2020 Oct
Title S2 Subunit of SARS-nCoV-2 Interacts with Tumor Suppressor Protein p53 and BRCA: an In Silico Study
Author(s) name Singh N, Bharara Singh A.
Journal Transl Oncol
Impact factor
3.3
Citation count: 8

Amino acid residues Asp 1165, Leu 1166, Ser 1175 of S2 subunit of SARS-CoV-2 show strong interactions with Glu 916, Leu 938, Arg 1117 of BRCA-2 protein. Further experimental research is required to unveil the impact of COVID-19 in cancer patients and to explore the functional role of these interactions.
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 		32619819
(Transl Oncol)
PMID
32619819
Date of Publishing: 2020 Oct
Title S2 Subunit of SARS-nCoV-2 Interacts with Tumor Suppressor Protein p53 and BRCA: an In Silico Study
Author(s) name Singh N, Bharara Singh A.
Journal Transl Oncol
Impact factor
3.3
Citation count: 8

Amino acid residues Asp 1165, Gly 1171, Asn 1173 of S2 subunit of spike protein of SARS-COV-2 have interactions with Lys 1648, Arg 1649, His 1672 of BRCA-1 protein. Further experimental research is required to unveil the impact of COVID-19 in cancer patients and to explore the functional role of these interactions.
✍
 		32619819
(Transl Oncol)
PMID
32619819
Date of Publishing: 2020 Oct
Title S2 Subunit of SARS-nCoV-2 Interacts with Tumor Suppressor Protein p53 and BRCA: an In Silico Study
Author(s) name Singh N, Bharara Singh A.
Journal Transl Oncol
Impact factor
3.3
Citation count: 8

Molecular interactions of SARS-CoV-2 S protein's RBD with ACE2 receptor and CR3022 shows CR3022 IgG binding affinity (Kd) and Fab binding affinity (Kd) to SARS-CoV-2 is <0.1 and 115 ±3, respectively. SARS-CoV-2 has a conserved, epitope shared between SARS-CoV-2 and SARS-CoV. The availability of conserved epitopes would allow structure-based design of a SARS-CoV-2 vaccine and also of cross-protective antibody responses against future coronavirus epidemics and pandemics.
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 		32245784
(Science)
PMID
32245784
Date of Publishing: 2020 May 8
Title A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV
Author(s) nameYuan M, Wu NC et al.
Journal Science
Impact factor
20.57
Citation count: 731

Proving that interaction between SARS-CoV-2-CTD and hACE2 Is specific and displays 4-fold stronger affinity compared with the SARS-RBD by real-time surface plasmon resonance (SPR) assays. hACE2 and SARS-CoV-2-CTD binding region leads to ~4-fold higher binding affinity compared with the SARS-RBD. Distinct epitope features between SARS-RBD and SARS-CoV-2-CTD have been , although both can engage hACE2.
✍
 		32275855
(Cell)
PMID
32275855
Date of Publishing: 2020 May 14
Title Structural and functional basis of SARS-CoV-2 entry by using human ACE2
Author(s) nameWang Q, Zhang Y et al.
Journal Cell
Impact factor
27.35
Citation count: 1242

Interaction between SARS-CoV-2-CTD and hACE2 is specific and displays 4-fold stronger affinity compared with the SARS-RBD. Dissociation constants (KD) of SARS-CoV-2-S1 and SARS-CoV-2-CTD binding to hACE2 are 94.6 ±6.5 nM and 133.3 ±5.6 nM, respectively. The virus-receptor engagement is dominated by polar contacts mediated by the hydrophilic residues. A single K353A mutation was sufficient to abolish these interactions.
✍
 		32275855
(Cell)
PMID
32275855
Date of Publishing: 2020 May 14
Title Structural and functional basis of SARS-CoV-2 entry by using human ACE2.
Author(s) nameWang Q, Zhang Y et al.
Journal Cell
Impact factor
27.35
Citation count: 1242

Molecular interactions between gangliosides and the NTD of SARS-CoV-2 S protein show Phe-135, Asn-137 and Arg-158 are major residues in the interaction. The total energy of interaction is -100 kJ.mol^−1. Chloroquine binds to sialic acids and gangliosides with high affinity and S protein is unable to bind to the gangliosides in the presence of chloroquine. CLQ and CLQ-OH, it is the nitrogen-containing ring of the drug that stacks on to the Glc ring. If once, two CLQ-OH (or two CLQ) molecules are bound to a ganglioside , any binding of a SARS-CoV-2 S protein to the same ganglioside is totally prevented. Mechanism of action of hydroxychloroquine (CLQ-OH).
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 		32251731
(Int J Antimicrob Agents)
PMID
32251731
Date of Publishing: 2020 May
Title Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection
Author(s) nameFantini J, Di Scala C et al.
Journal Int J Antimicrob Agents
Impact factor
4.6
Citation count: 253

Structural characterisation of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2 Neutralizing monoclonal antibodies targeting SARS-CoV-2 RBM can prevent the virus from binding to hACE2, and hence are promising antiviral drugs. The functionally important epitopes in SARS-CoV-2 RBM, can guide structure-based design of highly efficacious RBD vaccines.
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 		32225175
(Nature)
PMID
32225175
Date of Publishing: 2020 May
Title Structural basis of receptor recognition by SARS-CoV-2
Author(s) nameShang J, Ye G et al.
Journal Nature
Impact factor
24.36
Citation count: 1576

The critical human ACE2-binding residues of SARS-CoV-2 RBD are L(455), GVEG (482-485), F (486), Q (493), S (494), N (501) Both structural and biochemical data reveal that SARS-CoV-2 RBD recognizes hACE2 better than SARS-CoV RBD does.
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 		32225175
(Nature)
PMID
32225175
Date of Publishing: 2020 May
Title Structural basis of receptor recognition by SARS-CoV-2
Author(s) nameShang J, Ye G et al.
Journal Nature
Impact factor
24.36
Citation count: 1576