Molecular Docking


Last updated: 2021 Aug 2
Total hit(s): 19
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Original Article
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Reporting molecular interaction details of hydroxychloroquine (HCQ) with the RBD of SARS-CoV-2 S Protein. ~
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: 6
Date of Entry 2021 Aug 2


Reporting 7 ( cnCoVP-1, cnCoVP-2, cnCoVP-3, cnCoVP-4, cnCoVP-5, cnCoVP-6 and cnCoVP-7) out of 500 generated chimeric peptides against SARS-CoV-2 Spike RBD and recognizing chimeric peptide cnCoVP-1 and cnCoVP-4 to be potential candidates. 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.
32802318
()
PMID
32802318
Title Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain
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.
32802318
()
PMID
32802318
Title Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain
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
()
PMID
32802318
Title Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain
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.
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: 6
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.
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: 1
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: 1
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: 42
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: 1
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.
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: 72
Date of Entry 14_45_39 Jul


Reporting strong interaction between S2 subunit of SARS-nCoV-2 with tumor suppressor protein p53 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: 4


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: 32


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: 32


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: 32


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: 32


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: 32


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: 32


Reporting strong interaction between S2 subunit of SARS-nCoV-2 with tumor suppressor protein BRCA-2 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: 4


Reporting strong interaction between S2 subunit of SARS-nCoV-2 with tumor suppressor protein BRCA-1 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: 4