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  1. Article ; Online: A multi-stage virtual screening of FDA-approved drugs reveals potential inhibitors of SARS-CoV-2 main protease.

    Mandour, Yasmine M / Zlotos, Darius P / Alaraby Salem, M

    Journal of biomolecular structure & dynamics

    2020  Volume 40, Issue 5, Page(s) 2327–2338

    Abstract: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing global health emergency. Repurposing of approved pharmaceutical drugs for COVID-19 treatment represents an attractive approach to ... ...

    Abstract Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing global health emergency. Repurposing of approved pharmaceutical drugs for COVID-19 treatment represents an attractive approach to quickly identify promising drug candidates. SARS-CoV-2 main protease (M
    MeSH term(s) Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; COVID-19/drug therapy ; Coronavirus 3C Proteases ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Pharmaceutical Preparations ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; SARS-CoV-2
    Chemical Substances Antiviral Agents ; Pharmaceutical Preparations ; Protease Inhibitors ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Keywords covid19
    Language English
    Publishing date 2020-10-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1837680
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Two-photon absorption of fluorescent protein chromophores incorporating non-canonical amino acids: TD-DFT screening and classical dynamics.

    Alaraby Salem, M / Brown, Alex

    Physical chemistry chemical physics : PCCP

    2015  Volume 17, Issue 38, Page(s) 25563–25571

    Abstract: Two-photon spectroscopy of fluorescent proteins is a powerful bio-imaging tool characterized by deep tissue penetration and little damage. However, two-photon spectroscopy has lower sensitivity than one-photon microscopy alternatives and hence a protein ... ...

    Abstract Two-photon spectroscopy of fluorescent proteins is a powerful bio-imaging tool characterized by deep tissue penetration and little damage. However, two-photon spectroscopy has lower sensitivity than one-photon microscopy alternatives and hence a protein with a large two-photon absorption cross-section is needed. We use time-dependent density functional theory (TD-DFT) at the B3LYP/6-31+G(d,p) level of theory to screen twenty-two possible chromophores that can be formed upon replacing the amino-acid Tyr66 that forms the green fluorescent protein (GFP) chromophore with a non-canonical amino acid. A proposed chromophore with a nitro substituent was found to have a large two-photon absorption cross-section (29 GM) compared to other fluorescent protein chromophores as determined at the same level of theory. Classical molecular dynamics are then performed on a nitro-modified fluorescent protein to test its stability and study the effect of the conformational flexibility of the chromophore on its two-photon absorption cross-section. The theoretical results show that the large cross-section is primarily due to the difference between the permanent dipole moments of the excited and ground states of the nitro-modified chromophore. This large difference is maintained through the various conformations assumed by the chromophore in the protein cavity. The nitro-derived protein appears to be very promising as a two-photon absorption probe.
    MeSH term(s) Amino Acids/chemistry ; Amino Acids/metabolism ; Green Fluorescent Proteins/chemistry ; Green Fluorescent Proteins/metabolism ; Molecular Dynamics Simulation ; Photons ; Protein Stability
    Chemical Substances Amino Acids ; Green Fluorescent Proteins (147336-22-9)
    Language English
    Publishing date 2015-10-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c5cp03875h
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: A multi-stage virtual screening of FDA-approved drugs reveals potential inhibitors of SARS-CoV-2 main protease

    Mandour, Yasmine M / Zlotos, Darius P / Alaraby Salem, M

    J Biomol Struct Dyn

    Abstract: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing global health emergency. Repurposing of approved pharmaceutical drugs for COVID-19 treatment represents an attractive approach to ... ...

    Abstract Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing global health emergency. Repurposing of approved pharmaceutical drugs for COVID-19 treatment represents an attractive approach to quickly identify promising drug candidates. SARS-CoV-2 main protease (Mpro) is responsible for the maturation of viral functional proteins making it a key antiviral target. Based on the recently revealed crystal structures of SARS-CoV-2 Mpro, we herein describe a multi-stage virtual screening protocol including pharmacophore screening, molecular docking and protein-ligand interaction fingerprints (PLIF) post-docking filtration for efficient enrichment of potent SARS-CoV-2 Mpro inhibitors. Potential hits, along with a cocrystallized control were further studied via molecular dynamics. A 150-ns production trajectory was followed by RMSD, free energy calculation, and H-bond analysis for each compound. The applied virtual screening protocol led to identification of five FDA-approved drugs with promising binding modes to key subsites of the substrate-binding pocket of SARS-CoV-2 Mpro. The identified compounds belong to different pharmaceutical classes, including several protease inhibitors, antineoplastic agents and a natural flavonoid. The drug candidates discovered in this study present a potential extension of the recently reported SARS-CoV-2 Mpro inhibitors that have been identified using other virtual screening protocols and may be repurposed for COVID-19 treatment.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #889356
    Database COVID19

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  4. Article ; Online: A multi-stage virtual screening of FDA-approved drugs reveals potential inhibitors of SARS-CoV-2 main protease

    Mandour, Yasmine M. / Zlotos, Darius P. / Alaraby Salem, M.

    Journal of Biomolecular Structure and Dynamics

    2020  , Page(s) 1–12

    Keywords Molecular Biology ; Structural Biology ; General Medicine ; covid19
    Language English
    Publisher Informa UK Limited
    Publishing country uk
    Document type Article ; Online
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1837680
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: New pyrazole derivatives: Synthesis, anti-inflammatory activity, cycloxygenase inhibition assay and evaluation of mPGES.

    Hassan, Ghaneya S / Abdel Rahman, Doaa E / Abdelmajeed, Esraa A / Refaey, Rana H / Alaraby Salem, M / Nissan, Yassin M

    European journal of medicinal chemistry

    2019  Volume 171, Page(s) 332–342

    Abstract: New pyrazole derivatives 2-5 were synthesized and evaluated for their COX-1 and COX-2 inhibitory activity in vitro. All compounds showed good inhibitory activity at a nanomolar level and most compounds exhibited selectivity towards COX-2 inhibition. ... ...

    Abstract New pyrazole derivatives 2-5 were synthesized and evaluated for their COX-1 and COX-2 inhibitory activity in vitro. All compounds showed good inhibitory activity at a nanomolar level and most compounds exhibited selectivity towards COX-2 inhibition. Compounds 2a, 3b, 4a, 5b and 5e exhibited IC
    MeSH term(s) Anti-Inflammatory Agents, Non-Steroidal/chemical synthesis ; Anti-Inflammatory Agents, Non-Steroidal/chemistry ; Anti-Inflammatory Agents, Non-Steroidal/pharmacology ; Cyclooxygenase 1/metabolism ; Cyclooxygenase 2/metabolism ; Cyclooxygenase Inhibitors/chemical synthesis ; Cyclooxygenase Inhibitors/chemistry ; Cyclooxygenase Inhibitors/pharmacology ; Dose-Response Relationship, Drug ; Humans ; Microsomes/drug effects ; Microsomes/enzymology ; Molecular Docking Simulation ; Molecular Structure ; Prostaglandin-Endoperoxide Synthases/metabolism ; Pyrazoles/chemical synthesis ; Pyrazoles/chemistry ; Pyrazoles/pharmacology ; Structure-Activity Relationship
    Chemical Substances Anti-Inflammatory Agents, Non-Steroidal ; Cyclooxygenase Inhibitors ; Pyrazoles ; pyrazole (3QD5KJZ7ZJ) ; Cyclooxygenase 1 (EC 1.14.99.1) ; Cyclooxygenase 2 (EC 1.14.99.1) ; Prostaglandin-Endoperoxide Synthases (EC 1.14.99.1)
    Language English
    Publishing date 2019-03-23
    Publishing country France
    Document type Journal Article
    ZDB-ID 188597-2
    ISSN 1768-3254 ; 0009-4374 ; 0223-5234
    ISSN (online) 1768-3254
    ISSN 0009-4374 ; 0223-5234
    DOI 10.1016/j.ejmech.2019.03.052
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.B 784: Show issues Location:
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