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  1. Article: Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS

    Loschwitz, Jennifer / Jäckering, Anna / Keutmann, Monika / Olagunju, Maryam / Olubiyi, Olujide O. / Strodel, Birgit

    Data in Brief. 2021 Apr., v. 35

    2021  

    Abstract: We provide general AMBER force field (GAFF) parameters for 160 organic molecules including drugs, natural products, and steroids, which can be employed without further processing in molecular dynamics (MD) simulations using GROMACS. We determined these ... ...

    Abstract We provide general AMBER force field (GAFF) parameters for 160 organic molecules including drugs, natural products, and steroids, which can be employed without further processing in molecular dynamics (MD) simulations using GROMACS. We determined these parameters based on quantum mechanical (QM) calculations involving geometry optimization at the HF6-31G* level of theory. For each molecule we provide a coordinate file of the three-dimensional molecular structure, the topology and the parameter file. The applicability of these parameters was demonstrated by MD simulations of these molecules bound to the active site of the main protease of the coronavirus SARS-CoV-2, 3CLᵖʳᵒ, which is a main player during viral replication causing COVID-19.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; active sites ; data collection ; geometry ; molecular dynamics ; proteinases ; quantum mechanics ; topology ; virus replication
    Language English
    Dates of publication 2021-04
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 2786545-9
    ISSN 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2021.106948
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS.

    Loschwitz, Jennifer / Jäckering, Anna / Keutmann, Monika / Olagunju, Maryam / Olubiyi, Olujide O / Strodel, Birgit

    Data in brief

    2021  Volume 35, Page(s) 106948

    Abstract: We provide general AMBER force field (GAFF) parameters for 160 organic molecules including drugs, natural products, and steroids, which can be employed without further processing in molecular dynamics (MD) simulations using GROMACS. We determined these ... ...

    Abstract We provide general AMBER force field (GAFF) parameters for 160 organic molecules including drugs, natural products, and steroids, which can be employed without further processing in molecular dynamics (MD) simulations using GROMACS. We determined these parameters based on quantum mechanical (QM) calculations involving geometry optimization at the HF6-31G* level of theory. For each molecule we provide a coordinate file of the three-dimensional molecular structure, the topology and the parameter file. The applicability of these parameters was demonstrated by MD simulations of these molecules bound to the active site of the main protease of the coronavirus SARS-CoV-2, 3CL
    Language English
    Publishing date 2021-03-15
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2786545-9
    ISSN 2352-3409 ; 2352-3409
    ISSN (online) 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2021.106948
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Novel inhibitors of the main protease enzyme of SARS-CoV-2 identified via molecular dynamics simulation-guided in vitro assay.

    Loschwitz, Jennifer / Jäckering, Anna / Keutmann, Monika / Olagunju, Maryam / Eberle, Raphael J / Coronado, Monika Aparecida / Olubiyi, Olujide O / Strodel, Birgit

    Bioorganic chemistry

    2021  Volume 111, Page(s) 104862

    Abstract: For the COVID-19 pandemic caused by SARS-CoV-2, there are currently no effective drugs or vaccines to treat this coronavirus infection. In this study, we focus on the main protease enzyme of SARS-CoV-2, ... ...

    Abstract For the COVID-19 pandemic caused by SARS-CoV-2, there are currently no effective drugs or vaccines to treat this coronavirus infection. In this study, we focus on the main protease enzyme of SARS-CoV-2, 3CL
    MeSH term(s) Antiviral Agents/metabolism ; Binding Sites ; Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/metabolism ; Enzyme Assays ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protease Inhibitors/metabolism ; Protein Binding ; SARS-CoV-2/enzymology ; Small Molecule Libraries/metabolism
    Chemical Substances Antiviral Agents ; Ligands ; Protease Inhibitors ; Small Molecule Libraries ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Language English
    Publishing date 2021-03-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 120080-x
    ISSN 1090-2120 ; 0045-2068
    ISSN (online) 1090-2120
    ISSN 0045-2068
    DOI 10.1016/j.bioorg.2021.104862
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4207: 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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  4. Book ; Online: Novel Inhibitors of the Main Protease of SARS-CoV-2 Identified via a Molecular Dynamics Simulation-Guided in Vitro Assay

    Loschwitz, Jennifer / Jäckering, Anna / Keutmann, Monika / Olagunju, Maryam / Eberle, Raphael J. / Coronado, Monika A. / Olubiyi, Olujide O. / Strodel, Birgit

    2020  

    Abstract: ... For the COVID-19 pandemic caused by SARS-CoV-2, there are currently no effective drugs or vaccines to treat this coronavirus infection. In this study, we focus on the main protease enzyme of SARS-CoV-2, 3CL pro , which is critical for viral ... ...

    Abstract
    For the COVID-19 pandemic caused by SARS-CoV-2, there are currently no effective drugs or vaccines to treat this coronavirus infection. In this study, we focus on the main protease enzyme of SARS-CoV-2, 3CL pro , which is critical for viral replication. We employ explicit solvent molecular dynamics simulations of about 150 compounds docked into 3CL pro ’s binding site and that had emerged as good main protease ligands from our previous in silico screening of over 1.2 million compounds. By incoporating protein dynamics and applying a range of structural descriptors, such as the ability to form specific contacts with the catalytic dyad residues of 3CL pro and the structural fluctuations of the ligands in the binding site, we are able to further refine our compound selection. Fourteen compounds including estradiol shown to be the most promising based on our calculations were procured and screened against recombinant 3CL pro in a fluorescence assay. Eight of these compounds have significant activity in inhibiting the SARS-CoV-2 main protease. Among these are corilagin, a gallotannin, and lurasidone, an antipsychotic drug, which emerged as the most promising natural product and drug, respectively, and might thus be candidates for drug repurposing for the treatment of COVID-19. In addition, we also tested the inhibitory activity of testosterone, and our results reveal testosterone as possessing moderate inhibitory potency against the 3CL pro enzyme, which may thus provide an explanation why older men are more severely affected by COVID-19.
    Keywords covid19
    Publisher American Chemical Society (ACS)
    Publishing country us
    Document type Book ; Online
    DOI 10.26434/chemrxiv.13200281
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  5. Book ; Online: Novel Inhibitors of the Main Protease of SARS-CoV-2 Identified via a Molecular Dynamics Simulation-Guided in Vitro Assay

    Loschwitz, Jennifer / Jäckering, Anna / Keutmann, Monika / Olagunju, Maryam / Eberle, Raphael J. / Coronado, Monika A. / Olubiyi, Olujide O. / Strodel, Birgit

    2020  

    Abstract: ... For the COVID-19 pandemic caused by SARS-CoV-2, there are currently no effective drugs or vaccines to treat this coronavirus infection. In this study, we focus on the main protease enzyme of SARS-CoV-2, 3CL pro , which is critical for viral ... ...

    Abstract
    For the COVID-19 pandemic caused by SARS-CoV-2, there are currently no effective drugs or vaccines to treat this coronavirus infection. In this study, we focus on the main protease enzyme of SARS-CoV-2, 3CL pro , which is critical for viral replication. We employ explicit solvent molecular dynamics simulations of about 150 compounds docked into 3CL pro ’s binding site and that had emerged as good main protease ligands from our previous in silico screening of over 1.2 million compounds. By incoporating protein dynamics and applying a range of structural descriptors, such as the ability to form specific contacts with the catalytic dyad residues of 3CL pro and the structural fluctuations of the ligands in the binding site, we are able to further refine our compound selection. Fourteen compounds including estradiol shown to be the most promising based on our calculations were procured and screened against recombinant 3CL pro in a fluorescence assay. Eight of these compounds have significant activity in inhibiting the SARS-CoV-2 main protease. Among these are corilagin, a gallotannin, and lurasidone, an antipsychotic drug, which emerged as the most promising natural product and drug, respectively, and might thus be candidates for drug repurposing for the treatment of COVID-19. In addition, we also tested the inhibitory activity of testosterone, and our results reveal testosterone as possessing moderate inhibitory potency against the 3CL pro enzyme, which may thus provide an explanation why older men are more severely affected by COVID-19.
    Keywords covid19
    Publisher American Chemical Society (ACS)
    Publishing country us
    Document type Book ; Online
    DOI 10.26434/chemrxiv.13200281.v1
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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  6. Article: Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase.

    Pfaff, Lara / Gao, Jian / Li, Zhishuai / Jäckering, Anna / Weber, Gert / Mican, Jan / Chen, Yinping / Dong, Weiliang / Han, Xu / Feiler, Christian G / Ao, Yu-Fei / Badenhorst, Christoffel P S / Bednar, David / Palm, Gottfried J / Lammers, Michael / Damborsky, Jiri / Strodel, Birgit / Liu, Weidong / Bornscheuer, Uwe T /
    Wei, Ren

    ACS catalysis

    2022  Volume 12, Issue 15, Page(s) 9790–9800

    Abstract: Thermophilic polyester hydrolases (PES-H) have recently enabled biocatalytic recycling of the mass-produced synthetic polyester polyethylene terephthalate (PET), which has found widespread use in the packaging and textile industries. The growing demand ... ...

    Abstract Thermophilic polyester hydrolases (PES-H) have recently enabled biocatalytic recycling of the mass-produced synthetic polyester polyethylene terephthalate (PET), which has found widespread use in the packaging and textile industries. The growing demand for efficient PET hydrolases prompted us to solve high-resolution crystal structures of two metagenome-derived enzymes (PES-H1 and PES-H2) and notably also in complex with various PET substrate analogues. Structural analyses and computational modeling using molecular dynamics simulations provided an understanding of how product inhibition and multiple substrate binding modes influence key mechanistic steps of enzymatic PET hydrolysis. Key residues involved in substrate-binding and those identified previously as mutational hotspots in homologous enzymes were subjected to mutagenesis. At 72 °C, the L92F/Q94Y variant of PES-H1 exhibited 2.3-fold and 3.4-fold improved hydrolytic activity against amorphous PET films and pretreated real-world PET waste, respectively. The R204C/S250C variant of PES-H1 had a 6.4 °C higher melting temperature than the wild-type enzyme but retained similar hydrolytic activity. Under optimal reaction conditions, the L92F/Q94Y variant of PES-H1 hydrolyzed low-crystallinity PET materials 2.2-fold more efficiently than LCC ICCG, which was previously the most active PET hydrolase reported in the literature. This property makes the L92F/Q94Y variant of PES-H1 a good candidate for future applications in industrial plastic recycling processes.
    Language English
    Publishing date 2022-07-27
    Publishing country United States
    Document type Journal Article
    ISSN 2155-5435
    ISSN 2155-5435
    DOI 10.1021/acscatal.2c02275
    Database MEDical Literature Analysis and Retrieval System OnLINE

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