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  1. Article ; Online: Nanofactories for Controlled Synthesis and Delivery of Nucleoside Analogue Therapeutics.

    Ebrahimi, Kourosh H

    Chembiochem : a European journal of chemical biology

    2020  Volume 21, Issue 22, Page(s) 3186–3188

    Abstract: The ultimate nanomedicine will be a cell-like machinery capable of reaching a specific target in the body and performing a desired therapeutic action in a controlled fashion. To make such machinery a reality, we need to combine fundamental knowledge and ... ...

    Abstract The ultimate nanomedicine will be a cell-like machinery capable of reaching a specific target in the body and performing a desired therapeutic action in a controlled fashion. To make such machinery a reality, we need to combine fundamental knowledge and technological developments in different areas including polymer chemistry, biology, enzymology, and biochemical engineering. In this viewpoint, I put forward my vision of creating a nanofactory as a step towards developing cell-like nanomedicines. To make the proposed nanofactory a reality there are many challenges ahead. I propose plausible solutions to address some of the main challenges.
    MeSH term(s) Animals ; Drug Delivery Systems ; Humans ; Nanomedicine ; Nucleosides/chemical synthesis ; Nucleosides/chemistry
    Chemical Substances Nucleosides
    Keywords covid19
    Language English
    Publishing date 2020-09-16
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2020469-3
    ISSN 1439-7633 ; 1439-4227
    ISSN (online) 1439-7633
    ISSN 1439-4227
    DOI 10.1002/cbic.202000382
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Ancient complexes of iron and sulfur modulate oncogenes and oncometabolism.

    Nghi, Hoang Thao / Shahmohammadi, Sayeh / Ebrahimi, Kourosh H

    Current opinion in chemical biology

    2023  Volume 76, Page(s) 102338

    Abstract: Inorganic complexes of iron and sulfur, that is, iron-sulfur [FeS] clusters, have played a fundamental role in life on Earth since the prebiotic period. These clusters were involved in elementary reactions leading to the emergence of life and, since then, ...

    Abstract Inorganic complexes of iron and sulfur, that is, iron-sulfur [FeS] clusters, have played a fundamental role in life on Earth since the prebiotic period. These clusters were involved in elementary reactions leading to the emergence of life and, since then, gained function in processes, such as respiration, replication, transcription, and the immune response. We discuss how three [FeS] proteins involved in the innate immune response play a role in oncogene expression/function and oncometabolism. Our analysis highlights the importance of future research into understanding the [FeS] clusters' roles in cancer progression and proliferation. The outcomes of these studies will help identify new targets and develop new anticancer therapeutics.
    MeSH term(s) Iron/metabolism ; Oncogenes ; Sulfur/metabolism ; Iron-Sulfur Proteins/genetics ; Iron-Sulfur Proteins/metabolism
    Chemical Substances Iron (E1UOL152H7) ; Sulfur (70FD1KFU70) ; Iron-Sulfur Proteins
    Language English
    Publishing date 2023-06-07
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1439176-4
    ISSN 1879-0402 ; 1367-5931
    ISSN (online) 1879-0402
    ISSN 1367-5931
    DOI 10.1016/j.cbpa.2023.102338
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4986: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Corrigendum: Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2.

    Dragelj, Jovan / Mroginski, Maria Andrea / Ebrahimi, Kourosh H

    Chembiochem : a European journal of chemical biology

    2022  Volume 23, Issue 15, Page(s) e202200362

    Language English
    Publishing date 2022-07-06
    Publishing country Germany
    Document type Published Erratum
    ZDB-ID 2020469-3
    ISSN 1439-7633 ; 1439-4227
    ISSN (online) 1439-7633
    ISSN 1439-4227
    DOI 10.1002/cbic.202200362
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  4. Article ; Online: VITAS, a sensitive

    Alharbi, Aws Fahd / Kim, Hayun / Chumroo, Dhirish / Ji, Yuxuan / Hakil, Mohammed / Ebrahimi, Kourosh H

    Chemical communications (Cambridge, England)

    2023  Volume 59, Issue 36, Page(s) 5419–5422

    Abstract: To discover new broad-spectrum antiviral nucleotide analogues from natural resources or through protein engineering, we have developed a ... ...

    Abstract To discover new broad-spectrum antiviral nucleotide analogues from natural resources or through protein engineering, we have developed a sensitive
    MeSH term(s) Antiviral Agents/pharmacology ; Biological Products ; Nucleotides ; Protein Engineering
    Chemical Substances Antiviral Agents ; Biological Products ; Nucleotides
    Language English
    Publishing date 2023-05-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d3cc00638g
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A lipidomic view of SARS-CoV-2.

    Ebrahimi, Kourosh H / McCullagh, James S O

    Bioscience reports

    2021  Volume 41, Issue 8

    Abstract: The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which started in late 2019, has caused huge social and economic losses. A growing number of investigators are focusing on understanding the interaction of SARS-CoV-2 ... ...

    Abstract The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which started in late 2019, has caused huge social and economic losses. A growing number of investigators are focusing on understanding the interaction of SARS-CoV-2 with host cellular processes to find therapeutic approaches. New data suggest that lipid metabolism may play a significant role in regulating the response of immune cells like macrophages to viral infection, thereby affecting the outcome of the disease. Therefore, understanding the role of lipid metabolism could help develop new therapeutic approaches to mitigate the social and economic cost of coronavirus disease 2019 (COVID-19).
    MeSH term(s) COVID-19/epidemiology ; COVID-19/immunology ; COVID-19/metabolism ; Homeostasis/immunology ; Humans ; Lipid Metabolism/immunology ; Lipidomics ; Pandemics ; SARS-CoV-2/chemistry
    Language English
    Publishing date 2021-07-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 764946-0
    ISSN 1573-4935 ; 0144-8463
    ISSN (online) 1573-4935
    ISSN 0144-8463
    DOI 10.1042/BSR20210953
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1676: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Multi-structural molecular docking (MOD) combined with molecular dynamics reveal the structural requirements of designing broad-spectrum inhibitors of SARS-CoV-2 entry to host cells.

    Da, Anqi / Wu-Lu, Meritxell / Dragelj, Jovan / Mroginski, Maria Andrea / Ebrahimi, Kourosh H

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 16387

    Abstract: New variants of SARS-CoV-2 that can escape immune response continue to emerge. Consequently, there is an urgent demand to design small molecule therapeutics inhibiting viral entry to host cells to reduce infectivity rate. Despite numerous in silico and ... ...

    Abstract New variants of SARS-CoV-2 that can escape immune response continue to emerge. Consequently, there is an urgent demand to design small molecule therapeutics inhibiting viral entry to host cells to reduce infectivity rate. Despite numerous in silico and in situ studies, the structural requirement of designing viral-entry inhibitors effective against multiple variants of SARS-CoV-2 has yet to be described. Here we systematically screened the binding of various natural products (NPs) to six different SARS-CoV-2 receptor-binding domain (RBD) structures. We demonstrate that Multi-structural Molecular Docking (MOD) combined with molecular dynamics calculations allowed us to predict a vulnerable site of RBD and the structural requirement of ligands binding to this vulnerable site. We expect that our findings lay the foundation for in silico screening and identification of lead molecules to guide drug discovery into designing new broad-spectrum lead molecules to counter the threat of future variants of SARS-CoV-2.
    MeSH term(s) Humans ; COVID-19 ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; SARS-CoV-2 ; Biological Products ; Protein Binding
    Chemical Substances Biological Products
    Language English
    Publishing date 2023-09-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-42015-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Ion-Exchange Chromatography Coupled to Mass Spectrometry in Life Science, Environmental, and Medical Research.

    Ngere, Judith B / Ebrahimi, Kourosh H / Williams, Rachel / Pires, Elisabete / Walsby-Tickle, John / McCullagh, James S O

    Analytical chemistry

    2023  Volume 95, Issue 1, Page(s) 152–166

    MeSH term(s) Environmental Science ; Mass Spectrometry/methods ; Chromatography, High Pressure Liquid/methods ; Chromatography, Ion Exchange/methods ; Biomedical Research
    Language English
    Publishing date 2023-01-27
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.2c04298
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4033: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  8. Article ; Online: Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2.

    Dragelj, Jovan / Mroginski, Maria Andrea / Ebrahimi, Kourosh H

    Chembiochem : a European journal of chemical biology

    2021  Volume 22, Issue 20, Page(s) 2946–2950

    Abstract: Since the emergence of SARS-CoV-2, little attention has been paid to the interplay between the interaction of virus and commensal microbiota. Here, we used molecular docking and dynamics simulations to study the interaction of some of the known ... ...

    Abstract Since the emergence of SARS-CoV-2, little attention has been paid to the interplay between the interaction of virus and commensal microbiota. Here, we used molecular docking and dynamics simulations to study the interaction of some of the known metabolites and natural products (NPs) produced by commensal microbiota with the receptor binding domain (RBD) of the spike glycoprotein of SARS-CoV-2. The results predict that NPs of commensal microbiota such as bile acids and non-ribosomal peptides (NRPs), of which some are siderophores, bind to the wild-type RBD and interfere with its binding to the ACE2 receptor. N501Y mutation, which is present in many of the emerging variants of the virus, abolishes the predicted binding pocket of bile acids and NRPs. Based on these findings, available experimental data showing that bile acids reduce the binding affinity of wild-type RBD to the ACE2 receptor, and the data suggesting that the respiratory tract microbiota affect viral infection we put forward the following proposal: mutations such as N501Y enable the RBD to bind to the ACE2 receptor more effectively in the presence of NPs produced by the respiratory tract bacteria thereby, increasing the infectivity rate of the virus. We hope our data stimulate future works to better understand the interactions of NPs produced by commensal microbiota with respiratory viruses like SARS-CoV-2.
    MeSH term(s) Animals ; Bacteria/metabolism ; Biological Products/metabolism ; COVID-19/genetics ; COVID-19/virology ; Computer Simulation ; Genetic Variation/genetics ; Humans ; Microbiota ; Protein Interaction Domains and Motifs ; Receptors, Virus/metabolism ; SARS-CoV-2/genetics
    Chemical Substances Biological Products ; Receptors, Virus
    Language English
    Publishing date 2021-07-26
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2020469-3
    ISSN 1439-7633 ; 1439-4227
    ISSN (online) 1439-7633
    ISSN 1439-4227
    DOI 10.1002/cbic.202100346
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  9. Article: Interferon‐stimulated gene products as regulators of central carbon metabolism

    Ebrahimi, Kourosh H. / Gilbert‐Jaramillo, Javier / James, William S. / McCullagh, James S.O.

    FEBS journal. 2021 June, v. 288, no. 12

    2021  

    Abstract: In response to viral infections, the innate immune system rapidly activates expression of several interferon‐stimulated genes (ISGs), whose protein and metabolic products are believed to directly interfere with the viral life cycle. Here, we argue that ... ...

    Abstract In response to viral infections, the innate immune system rapidly activates expression of several interferon‐stimulated genes (ISGs), whose protein and metabolic products are believed to directly interfere with the viral life cycle. Here, we argue that biochemical reactions performed by two specific protein products of ISGs modulate central carbon metabolism to support a broad‐spectrum antiviral response. We demonstrate that the metabolites generated by metalloenzymes nitric oxide synthase and the radical S‐adenosylmethionine (SAM) enzyme RSAD2 inhibit the activity of the housekeeping and glycolytic enzyme glyceraldehyde 3‐phosphate dehydrogenase (GAPDH). We discuss that this inhibition is likely to stimulate a range of metabolic and signalling processes to support a broad‐spectrum immune response. Based on these analyses, we propose that inhibiting GAPDH in individuals with deteriorated cellular innate immune response like elderly might help in treating viral diseases such as COVID‐19.
    Keywords COVID-19 infection ; S-adenosylmethionine ; carbon metabolism ; elderly ; genes ; glyceraldehyde-3-phosphate dehydrogenase ; glycolysis ; immune response ; innate immunity ; metabolites ; nitric oxide synthase
    Language English
    Dates of publication 2021-06
    Size p. 3715-3726.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 2173655-8
    ISSN 1742-4658 ; 1742-464X
    ISSN (online) 1742-4658
    ISSN 1742-464X
    DOI 10.1111/febs.15625
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 2006/704: Show issues

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  10. Article ; Online: Density dependent regulation of inflammatory responses in macrophages.

    Vaughan-Jackson, Alun / Stodolak, Szymon / Ebrahimi, Kourosh H / Johnson, Errin / Reardon, Paul K / Dupont, Maeva / Zhang, Shengpan / McCullagh, James S O / James, William S

    Frontiers in immunology

    2022  Volume 13, Page(s) 895488

    Abstract: Macrophage distribution density is tightly regulated within the body, yet the importance of macrophage crowding ... ...

    Abstract Macrophage distribution density is tightly regulated within the body, yet the importance of macrophage crowding during
    MeSH term(s) Humans ; Cell Differentiation ; Induced Pluripotent Stem Cells/metabolism ; Macrophages/metabolism ; Monocytes/metabolism ; Cytokines/metabolism
    Chemical Substances Cytokines
    Language English
    Publishing date 2022-12-16
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2022.895488
    Database MEDical Literature Analysis and Retrieval System OnLINE

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