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  1. Article ; Online: Prediction of the binding location between the nuclear inhibitor of DNA binding and differentiation 2 (ID2) and HSPA5.

    Elfiky, Abdo A

    Pathology, research and practice

    2024  Volume 255, Page(s) 155217

    Abstract: Glucose-regulated protein 78 (GRP78), also termed HSPA5, was widely studied in cancer. It was recently approved that GRP78 has nuclear localization potential that sheds light on its role in cancer development. The inhibitor of DNA binding and ... ...

    Abstract Glucose-regulated protein 78 (GRP78), also termed HSPA5, was widely studied in cancer. It was recently approved that GRP78 has nuclear localization potential that sheds light on its role in cancer development. The inhibitor of DNA binding and differentiation 2 (ID2) is the nuclear component that associates with GRP78. The interaction between these two proteins is not understood clearly. In the current study, the binding pattern of GRP78/ID2 is predicted using computational methods. Protein-protein docking is used along with molecular dynamics simulation. The substrate binding domain β of GRP78 can stably interact with the loop region (C42-S60) of ID2 as predicted in this study. This paves the way for a possible destabilizer for this association and cancer eradication.
    MeSH term(s) Humans ; DNA ; Endoplasmic Reticulum Chaperone BiP/metabolism ; Inhibitor of Differentiation Protein 2/metabolism ; Neoplasms/metabolism ; Proteins
    Chemical Substances DNA (9007-49-2) ; Endoplasmic Reticulum Chaperone BiP ; ID2 protein, human ; Inhibitor of Differentiation Protein 2 ; Proteins ; HSPA5 protein, human
    Language English
    Publishing date 2024-02-17
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 391889-0
    ISSN 1618-0631 ; 0344-0338
    ISSN (online) 1618-0631
    ISSN 0344-0338
    DOI 10.1016/j.prp.2024.155217
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Dual targeting of RdRps of SARS-CoV-2 and the mucormycosis-causing fungus: an

    Elfiky, Abdo A

    Future microbiology

    2022  Volume 17, Page(s) 755–762

    Abstract: During the past few months, mucormycosis has been associated with SARS-CoV-2 infections. Molecular docking combined with molecular dynamics simulation is utilized to test nucleotide-based inhibitors against the RdRps of SARS-CoV-2 solved structure ... ...

    Abstract During the past few months, mucormycosis has been associated with SARS-CoV-2 infections. Molecular docking combined with molecular dynamics simulation is utilized to test nucleotide-based inhibitors against the RdRps of SARS-CoV-2 solved structure and
    MeSH term(s) Antiviral Agents/chemistry ; COVID-19/drug therapy ; Fungi ; Humans ; Molecular Docking Simulation ; Mucormycosis/drug therapy ; RNA-Dependent RNA Polymerase ; SARS-CoV-2
    Chemical Substances Antiviral Agents ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
    Language English
    Publishing date 2022-05-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2254620-0
    ISSN 1746-0921 ; 1746-0913
    ISSN (online) 1746-0921
    ISSN 1746-0913
    DOI 10.2217/fmb-2022-0083
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Reply to a letter to the editor.

    Elfiky, Abdo A

    Life sciences

    2020  Volume 252, Page(s) 117715

    Keywords covid19
    Language English
    Publishing date 2020-04-22
    Publishing country Netherlands
    Document type Letter ; Comment
    ZDB-ID 3378-9
    ISSN 1879-0631 ; 0024-3205
    ISSN (online) 1879-0631
    ISSN 0024-3205
    DOI 10.1016/j.lfs.2020.117715
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Triple

    Hassan, Abdel-Moniem S / Elfiky, Abdo A / Elgohary, Alaa M

    Future microbiology

    2024  Volume 19, Page(s) 9–19

    Abstract: Aim: ...

    Abstract Aim:
    MeSH term(s) Humans ; SARS-CoV-2 ; RNA-Dependent RNA Polymerase/genetics ; RNA-Dependent RNA Polymerase/chemistry ; Antiviral Agents/therapeutic use ; Rhizopus oryzae ; COVID-19 ; Molecular Docking Simulation ; Nucleotides ; RNA, Viral
    Chemical Substances RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; Antiviral Agents ; Nucleotides ; RNA, Viral
    Language English
    Publishing date 2024-01-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 2254620-0
    ISSN 1746-0921 ; 1746-0913
    ISSN (online) 1746-0921
    ISSN 1746-0913
    DOI 10.2217/fmb-2023-0103
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Corrigendum to "Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARSCoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study" [Life Sci. 253 (2020) 117592].

    Elfiky, Abdo A

    Life sciences

    2020  Volume 258, Page(s) 118350

    Language English
    Publishing date 2020-08-28
    Publishing country Netherlands
    Document type Published Erratum
    ZDB-ID 3378-9
    ISSN 1879-0631 ; 0024-3205
    ISSN (online) 1879-0631
    ISSN 0024-3205
    DOI 10.1016/j.lfs.2020.118350
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Binding site prediction between lysozyme and glucose-regulated protein 78, a hope to fight amyloidosis.

    Elgharib, Ahmed M / Elshemey, Wael M / Elfiky, Abdo A

    Journal of biomolecular structure & dynamics

    2024  , Page(s) 1–12

    Abstract: Amyloidosis is an extraordinarily vigorous and heterogeneous group of disorders that causes numerous organ failures due to the precipitation of misfolded proteins. Many of these damaged proteins are discarded before causing any fatal diseases due to the ... ...

    Abstract Amyloidosis is an extraordinarily vigorous and heterogeneous group of disorders that causes numerous organ failures due to the precipitation of misfolded proteins. Many of these damaged proteins are discarded before causing any fatal diseases due to the contribution of the protein quality control (PQC) system and its chaperons, including glucose-regulated protein (GRP78). One of the most important enzymatic proteins inside the body is lysozyme, which is reported to have many mutated variants that may cause amyloid fibrils. This study used structural bioinformatics and molecular dynamics simulations to test and suggest binding sites for the human lysozyme protein with GRP78. Multiple sequence alignment (MSA) shows that part of the lysozyme envelope protein (C65-C81 cyclic region) has high similarities (30.77% identity) with the cyclic Pep42. Additionally, the binding between the lysozyme cyclic region (C65-C81) and GRP78 substrate binding domain (SBD) is found favorable. The number and types of interactions vary between each of the mutant isoforms of lysozyme. The more significant the conformational changes in the mutation, the greater its probability of aggregation and the formation of amyloid fibrils. Each mutation leads to different interactions and binding patterns with GRP78. The present computational study suggests a lysozyme-GRP78 binding site, thus paving the way for drug designers to construct suitable carriers that can collect misfolded lysozyme proteins and eliminate them from the body, preventing their aggregation and amyloidogenesis.Communicated by Ramaswamy H. Sarma.
    Language English
    Publishing date 2024-02-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2024.2321238
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Targeting of HPV E6 at the binding sites to the host-cell E6AP, p53, and the endoplasmic reticulum-resident chaperone, GRP78.

    Elfiky, Abdo A / Saied, Hazem R / Ali, Maha A

    Journal of biomolecular structure & dynamics

    2023  , Page(s) 1–11

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2023-10-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2270067
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: SARS-CoV-2 Spike-Heat Shock Protein A5 (GRP78) Recognition may be Related to the Immersed Human Coronaviruses.

    Elfiky, Abdo A

    Frontiers in pharmacology

    2020  Volume 11, Page(s) 577467

    Abstract: The human coronavirus (HCoV), SARS-CoV-2, caused more than 34 M confirmed infections from which more than 1 M deaths are reported until now (the WHO situation report-154). The current pandemic causes severe socio-economic burden. Due to the importance of ...

    Abstract The human coronavirus (HCoV), SARS-CoV-2, caused more than 34 M confirmed infections from which more than 1 M deaths are reported until now (the WHO situation report-154). The current pandemic causes severe socio-economic burden. Due to the importance of understanding of the mode of recognition and viral entry, spike protein shed drug designers as the first look protein target with the first released solved structure on 26 February 2020 (PDB ID: 6VSB). It is proposed that the recognition site for GRP78 is found in SARS-CoV-2 and the immersed human coronaviruses but experimental validation is still required.
    Language English
    Publishing date 2020-12-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2020.577467
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Human papillomavirus E6: Host cell receptor, GRP78, binding site prediction.

    Elfiky, Abdo A

    Journal of medical virology

    2020  Volume 92, Issue 12, Page(s) 3759–3765

    Abstract: Human papillomavirus (HPV) is the main cervical cancer-promoting element that is transmitted through sexual routes. Anal, head, and throat cancers are also reported to be accompanied by HPV infection. E6 is one of the HPV nonstructural proteins, which is ...

    Abstract Human papillomavirus (HPV) is the main cervical cancer-promoting element that is transmitted through sexual routes. Anal, head, and throat cancers are also reported to be accompanied by HPV infection. E6 is one of the HPV nonstructural proteins, which is responsible for cell differentiation by targeting tumor suppressor genes, p105Rb and p53. E6 was reported to be stabilized by two chaperone proteins; glucose-regulated protein 78 (GRP78) and heat shock protein 90. GRP78 is responsible for the unfolded protein response of the cells, and it was reported to be upregulated in many cancers, including cervical cancer. It was reported that knocking out GRP78 destabilizes E6 leading to faster degradation of E6 in vivo. The current work predicts the possible binding mode between E6 and GRP78 based on sequence and structural similarities.
    Keywords covid19
    Language English
    Publishing date 2020-03-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 752392-0
    ISSN 1096-9071 ; 0146-6615
    ISSN (online) 1096-9071
    ISSN 0146-6615
    DOI 10.1002/jmv.25737
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Natural products may interfere with SARS-CoV-2 attachment to the host cell.

    Elfiky, Abdo A

    Journal of biomolecular structure & dynamics

    2020  Volume 39, Issue 9, Page(s) 3194–3203

    Abstract: SARS-CoV-2 has been emerged in December 2019 in China, causing deadly (5% mortality) pandemic pneumonia, termed COVID-19. More than one host-cell receptor is reported to be recognized by the viral spike protein, among them is the cell-surface Heat Shock ... ...

    Abstract SARS-CoV-2 has been emerged in December 2019 in China, causing deadly (5% mortality) pandemic pneumonia, termed COVID-19. More than one host-cell receptor is reported to be recognized by the viral spike protein, among them is the cell-surface Heat Shock Protein A5 (HSPA5), also termed GRP78 or BiP. Upon viral infection, HSPA5 is upregulated, then translocating to the cell membrane where it is subjected to be recognized by the SARS-CoV-2 spike. In this study, some natural product compounds are tested against the HSPA5 substrate-binding domain β (SBDβ), which reported to be the recognition site for the SARS-CoV-2 spike. Molecular docking and molecular dynamics simulations are used to test some natural compounds binding to HSPA5 SBDβ. The results show high to a moderate binding affinity for the phytoestrogens (Diadiazin, Genistein, Formontein, and Biochanin A), chlorogenic acid, linolenic acid, palmitic acid, caffeic acid, caffeic acid phenethyl ester, hydroxytyrosol, cis-p-Coumaric acid, cinnamaldehyde, thymoquinone, and some physiological hormones such as estrogens, progesterone, testosterone, and cholesterol to the HSPA5 SBDβ. Based on its binding affinities, the phytoestrogens and estrogens are the best in binding HSPA5, hence may interfere with SARS-CoV-2 attachment to the stressed cells. These compounds can be successful as anti-COVID-19 agents for people with a high risk of cell stress like elders, cancer patients, and front-line medical staff.Communicated by Ramaswamy H. Sarma.
    MeSH term(s) Aged ; Binding Sites ; Biological Products ; COVID-19 ; Humans ; Molecular Docking Simulation ; SARS-CoV-2
    Chemical Substances Biological Products
    Keywords covid19
    Language English
    Publishing date 2020-05-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1761881
    Database MEDical Literature Analysis and Retrieval System OnLINE

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