Molecular Docking

Last updated: 2022 Jun 27
Total hit(s): 21
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Binding affinity of ACE2-Omicron RBD is higher(18208) than the ACE2-wild RBD (17910), but less than ACE2-Delta AY.1 & 2 (19084). Omicron had less interactions with human neutralizing antibodies - CR3022, B38, CB6, P2B2F6, and REGN. The Omicron variant has an increased the likelihood of re-infection and immune evasion. The docking analysis of the RBD region of Omicron and Delta variants with the ACE2 receptor and with selected antibodies showed differences in binding affinity when compared with the wild SARS-CoV-2 (original strain) spike-RBD region. Relatively unstable RBD structures of Omicron and Delta AY.3 may cause more pathogenicity.
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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

Molecular dynamics (MD) simulations of a linear polyglycerolsulfate (LPGS) with the wild type and Omicron RBDs reveal LPGS binds to the wild type RBD on the cationic patch away from the RBM, whereas it binds to the cationic patch on the RBM of the Omicron RBD. More research is needed to determine if a tighter binding to HSPG may improve the likelihood of binding to ACE2.
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 		35020256
(Chembiochem)
PMID
35020256
Date of Publishing: 2022 Jan 12
Title Charge Matters: Mutations in Omicron variant favor Binding to Cells
Author(s) nameNie C, Sahoo AK et al.
Journal Chembiochem
Impact factor
2.64
Citation count: 3
Date of Entry 2022 Feb 26

Molecular docking studies of Hydroxychloroquine(HCQ) on the RBD of SARS-CoV-2 Spike protein produced a Vina score of −5.5 kcal mol−1 .The hydroxyl group of HCQ molecule forms a strong hydrogen bonding with Asn501 side chain residing on one part of the receptor binding motif (RBM) of the Spike protein. ~
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 		32696720
(J Biomol Struct Dyn)
PMID
32696720
Date of Publishing: 2020 Jul 22
Title Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19
Author(s) name Sehailia M, Chemat S.
Journal J Biomol Struct Dyn
Impact factor
3.22
Citation count: 25
Date of Entry 2021 Aug 2

Seven chimeric peptides (cnCoVP-1, cnCoVP-2, cnCoVP-3, cnCoVP-4, cnCoVP-5, cnCoVP-6, and cnCoVP-7) were found to block SARS-CoV-2 Spike RBD out of 500 generated. The most promising candidates for preventing RBD of the spike are cnCoVP-1 and cnCoVP-4. Chimeric peptides cnCoVP-1 and cnCoVP-4 are found to partially block the access of SARS-CoV-2 Spike RBD to hACE2, howerver further in vitro and in vivo testing and validation is required.
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 		32802318
(F1000Res)
PMID
32802318
Date of Publishing: 2020
Title Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain
Author(s) nameBarh D, Tiwari S et al.
Journal F1000Res
Impact factor
2.64
Citation count: 25
Date of Entry 2021 Aug 2

Reporting 7 identifed peptides (DBP1, DBP2, DBP3, DBP4, DBP5, DBP6, DBP7) screened from 5 antimicrobial peptide databases of 20 amino acids in length to target against SARS-CoV-2 Spike RBD to exhibit their anti-SARS virus activities and recognizing DBP6 to be a potential peptide. Peptide DBP6 could be a potential drug peptide to be tested for SARS-CoV-2 Spike protein-drug development.
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 		32802318
(F1000Res)
PMID
32802318
Date of Publishing: 2020
Title Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain
Author(s) nameBarh D, Tiwari S et al.
Journal F1000Res
Impact factor
2.64
Citation count: 25
Date of Entry 2021 Aug 2

Reporting 3 designed stretches of hACE2 residue-based peptides (AC26, AC23, AC20) that demonstrates maximum active binding affinity with the Spike SARS-CoV RBD and identifying AC23 and AC20 to be potential sequence based peptide. AC20 and AC23 derived from hACE2 is found to probably block two key critical positions and hence can be further tested for its efficacy and therapeutics target against SARS-CoV-2 Spike RBD
✍
 		32802318
(F1000Res)
PMID
32802318
Date of Publishing: 2020
Title Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain
Author(s) nameBarh D, Tiwari S et al.
Journal F1000Res
Impact factor
2.64
Citation count: 25
Date of Entry 2021 Aug 2

Reporting molecular binding and interaction of tight junction-associated PALS1 structure with Envelope protein C-terminal octapeptides of SARS-CoV and SARS-CoV-2 Key role of E protein C-terminal domain during infection is emphasized.
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 		32891874
(Microbes Infect)
PMID
32891874
Date of Publishing: 2020 Nov-Dec
Title Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis
Author(s) nameDe Maio F, Lo Cascio E et al.
Journal Microbes Infect
Impact factor
2.373
Citation count: 28
Date of Entry 2021 Aug 2

Comparative analysis of the docking scores obtained by molecular docking of SARS-CoV-2 S1 RBD domain to amyloid and heparin to heparin binding proteins. This shows S1-heparin has the highest docking score and as the temperature increases from 25° C to 40° C, the binding affinity for SARS-CoV-2 S1 protein complexes decreases. Targeting the interaction of SARS-CoV-2 spike protein with the brain proteins might be a suitable way to reduce the aggregation process and thus neurodegeneration in COVID-19 patients.
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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

In silico study of bioactive compounds (citronellol, alpha-terpineol, eucalyptol, d-limonene, 3-carene, o-cymene, and alpha-pinene) found in Eucalyptus and Corymbia species essential oil on Mpro by molecular docking. The docking study eucaluptol would act as a possible inhibitor of Mpro.
✍
 		33848890
(J Infect Public Health)
PMID
33848890
Date of Publishing: 2021 May
Title Essential oils as an effective alternative for the treatment of COVID-19: Molecular interaction analysis of protease (M pro) with pharmacokinetics and toxicological properties
Author(s) namePanikar S, Shoba G et al.
Journal J Infect Public Health
Impact factor
2.49
Citation count: 12
Date of Entry 2021 Aug 12

Molecular docking chemical structures from traditional Chinese medicinal compounds to RdRp of SARS-CoV-2, SARS-Co-V, and MERS-Co-V, has found theaflavin has a lower idock score in the catalytic pocket of RdRp in SARSCoV2 (9.11kcal/mol). It has lower binding energy of 8.8kcal/mol when it docks in the catalytic pocket of SARS-CoV-2 RdRp. Theaflavin could inhibit RdRp activity by blocking the active site in the groove and hence can be used as a lead compound for developing a SARS-CoV-2 inhibitor that targets RdRp. Since in vivo effect is not known, further research is needed.
✍
 		32167173
(J Med Virol)
PMID
32167173
Date of Publishing: 2020 Jun
Title The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase
Author(s) nameLung J, Lin YS et al.
Journal J Med Virol
Impact factor
2.07
Citation count: 99
Date of Entry 2021 Aug 11

Molecular docking of astemizole to ACE2 shows that it can bind to ACE2 and inhibit the invasion of SARS-CoV-2 spike pseudoviruses. Astemizole is a potential drug candidate that can be repurposed in anti-coronavirus therapies.
✍
 		33932547
(Microb Pathog)
PMID
33932547
Date of Publishing: 2021 Apr 28
Title Astemizole as a drug to inhibit the effect of SARS-COV-2 in vitro
Author(s) nameWang X, Lu J et al.
Journal Microb Pathog
Impact factor
2.64
Citation count: 2
Date of Entry 2021 Aug 10

Reporting binding and interaction pattern between the modelled viral spike protein SARS-CoV-2 and ACE2 receptor The loops and puntual mutations determine the host receptor specificity for the viral spike protein and also the increased infection and viral spreading.
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 		32210742
(EXCLI J)
PMID
32210742
Date of Publishing: 2020
Title Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An in silico analysis
Author(s) nameOrtega JT, Serrano ML et al.
Journal EXCLI J
Impact factor
2.01
Citation count: 138
Date of Entry 2021 Jul 3

Molecular interactions between the docked Spike glycoprotein of SARSCoV2 with modeled cell surface TLR4 of human 3D structure of interacting protein-TLR4 was generated using homology modeling.
✍
 		32383269
(J Med Virol)
PMID
32383269
Date of Publishing: 2020 Oct
Title In silico studies on the comparative characterization of the interactions of SARSCoV2 spike glycoprotein with ACE2 receptor homologs and human TLRs
Author(s) name Choudhury A, Mukherjee S.
Journal J Med Virol
Impact factor
2.07
Citation count: 162

Molecular interaction between the docked Spike glycoprotein of SARSCoV2 with modeled cell surface TLR6 of human. 3D structure of interacting protein-TLR6 was generated using homology modeling.
✍
 		32383269
(J Med Virol)
PMID
32383269
Date of Publishing: 2020 Oct
Title In silico studies on the comparative characterization of the interactions of SARSCoV2 spike glycoprotein with ACE2 receptor homologs and human TLRs
Author(s) name Choudhury A, Mukherjee S.
Journal J Med Virol
Impact factor
2.07
Citation count: 162

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.
✍
 		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 between the docked Spike glycoprotein of SARSCoV2 with modeled cell surface TLR1 of human . 3D structure of interacting protein-TLR1 was generated using homology modeling.
✍
 		32383269
(J Med Virol)
PMID
32383269
Date of Publishing: 2020 Oct
Title In silico studies on the comparative characterization of the interactions of SARSCoV2 spike glycoprotein with ACE2 receptor homologs and human TLRs
Author(s) name Choudhury A, Mukherjee S.
Journal J Med Virol
Impact factor
2.07
Citation count: 162

Molecular interactions between the docked Spikeglycoprotein of SARSCoV2 with modeled transmembrane ACE2 receptor of human (Homo sapiens) . 3D structure of interacting protein from human was generated using homology modeling.
✍
 		32383269
(J Med Virol)
PMID
32383269
Date of Publishing: 2020 Oct
Title In silico studies on the comparative characterization of the interactions of SARSCoV2 spike glycoprotein with ACE2 receptor homologs and human TLRs
Author(s) name Choudhury A, Mukherjee S.
Journal J Med Virol
Impact factor
2.07
Citation count: 162

Molecular interactions between the docked Spike protein of SARSCoV2 with modeled transmembrane ACE2 receptor of bat (Rhinolophus sinicus) . 3D structure of interacting protein from bat was generated using homology modeling.
✍
 		32383269
(J Med Virol)
PMID
32383269
Date of Publishing: 2020 Oct
Title In silico studies on the comparative characterization of the interactions of SARSCoV2 spike glycoprotein with ACE2 receptor homologs and human TLRs
Author(s) name Choudhury A, Mukherjee S.
Journal J Med Virol
Impact factor
2.07
Citation count: 162

Molecular interactions between the docked Spike glycoprotein of SARSCoV2 with modeled transmembrane ACE2 receptor of pangolin (Manis javanica) 3D structure of interacting protein from pangolin was generated using homology modeling.
✍
 		32383269
(J Med Virol)
PMID
32383269
Date of Publishing: 2020 Oct
Title In silico studies on the comparative characterization of the interactions of SARSCoV2 spike glycoprotein with ACE2 receptor homologs and human TLRs
Author(s) name Choudhury A, Mukherjee S.
Journal J Med Virol
Impact factor
2.07
Citation count: 162

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.
✍
 		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