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  1. Article ; Online: Variable Macro X Domain of SARS-CoV-2 Retains the Ability to Bind ADP-ribose

    David N. Frick / Rajdeep S. Virdi / Nemanja Vuksanovic / Narayan Dahal / Nicholas R Silvaggi

    Abstract: ABSTRACTThe virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that encodes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymers, helicase and main protease, are well ... ...

    Abstract ABSTRACTThe virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that encodes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymers, helicase and main protease, are well conserved between SARS-CoV-2 and the original SARS virus, but several others are not. This study examines one of the most novel proteins encoded by SARS-CoV-2, a macrodomain of nonstructural protein 3 (nsp3). Although 26% of the amino acids in this SARS-CoV-2 macrodomain differ from those seen in other corona-viruses, the protein retains the ability to bind ADP-ribose, which is an important characteristic of beta coronaviruses, and potential therapeutic target.
    Keywords covid19
    Publisher biorxiv
    Document type Article ; Online
    DOI 10.1101/2020.03.31.014639
    Database COVID19

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  2. Article ; Online: Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3.

    Frick, David N / Virdi, Rajdeep S / Vuksanovic, Nemanja / Dahal, Narayan / Silvaggi, Nicholas R

    Biochemistry

    2020  Volume 59, Issue 28, Page(s) 2608–2615

    Abstract: The virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that encodes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymerase, helicase, and main protease, are well conserved ...

    Abstract The virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that encodes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymerase, helicase, and main protease, are well conserved between SARS-CoV-2 and the original SARS virus, but several others are not. This study examines one of the proteins encoded by SARS-CoV-2 that is most different, a macrodomain of nonstructural protein 3 (nsp3). Although 26% of the amino acids in this SARS-CoV-2 macrodomain differ from those observed in other coronaviruses, biochemical and structural data reveal that the protein retains the ability to bind ADP-ribose, which is an important characteristic of beta coronaviruses and a potential therapeutic target.
    MeSH term(s) Adenosine Diphosphate Ribose/metabolism ; Betacoronavirus/chemistry ; COVID-19 ; Coronavirus/chemistry ; Coronavirus Infections/drug therapy ; Coronavirus Infections/virology ; Coronavirus Papain-Like Proteases ; Crystallography, X-Ray ; Drug Delivery Systems ; Humans ; Models, Molecular ; Pandemics ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/virology ; Protein Domains ; SARS-CoV-2 ; Thermodynamics ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/metabolism
    Chemical Substances Viral Nonstructural Proteins ; Adenosine Diphosphate Ribose (20762-30-5) ; Coronavirus Papain-Like Proteases (EC 3.4.22.2) ; papain-like protease, SARS-CoV-2 (EC 3.4.22.2)
    Keywords covid19
    Language English
    Publishing date 2020-07-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.0c00309
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3

    Frick, David N. / Virdi, Rajdeep S. / Vuksanovic, Nemanja / Dahal, Narayan / Silvaggi, Nicholas R.

    Biochemistry

    2020  Volume 59, Issue 28, Page(s) 2608–2615

    Keywords Biochemistry ; covid19
    Language English
    Publisher American Chemical Society (ACS)
    Publishing country us
    Document type Article ; Online
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.0c00309
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3

    Frick, David N / Virdi, Rajdeep S / Vuksanovic, Nemanja / Dahal, Narayan / Silvaggi, Nicholas R

    Biochemistry. 2020 June 24, v. 59, no. 28

    2020  

    Abstract: The virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that encodes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymerase, helicase, and main protease, are well conserved ...

    Abstract The virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that encodes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymerase, helicase, and main protease, are well conserved between SARS-CoV-2 and the original SARS virus, but several others are not. This study examines one of the proteins encoded by SARS-CoV-2 that is most different, a macrodomain of nonstructural protein 3 (nsp3). Although 26% of the amino acids in this SARS-CoV-2 macrodomain differ from those observed in other coronaviruses, biochemical and structural data reveal that the protein retains the ability to bind ADP-ribose, which is an important characteristic of beta coronaviruses and a potential therapeutic target.
    Keywords Coronavirus infections ; Orthocoronavirinae ; RNA ; RNA-directed RNA polymerase ; amino acids ; antiviral agents ; genome ; proteinases ; therapeutics ; viral nonstructural proteins ; viruses
    Language English
    Dates of publication 2020-0624
    Size p. 2608-2615.
    Publishing place American Chemical Society
    Document type Article
    Note NAL-light
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.0c00309
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Discovery of Drug-like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3

    Virdi, Rajdeep S. / Bavisotto, Robert V. / Hopper, Nicholas C. / Frick, David N.

    Abstract: The Mac1 domain of the multifunctional SARS-CoV-2 non-structural protein 3 (nsp3) is a potential COVID-19 drug target because it is suspected to enhance the ability of the virus to evade the human immune system The SARS-CoV-2 Mac1 domain binds ADP-ribose ...

    Abstract The Mac1 domain of the multifunctional SARS-CoV-2 non-structural protein 3 (nsp3) is a potential COVID-19 drug target because it is suspected to enhance the ability of the virus to evade the human immune system The SARS-CoV-2 Mac1 domain binds ADP-ribose and proteins harboring this important post-translational modification Small molecules that bind the Mac1 domain in place of ADP-ribose might therefore be useful as molecular probes or scaffolds for antiviral drug discovery Two high throughput screens were used here to identify such ligands in small libraries of drugs and drug-like compounds The first screen used differential scanning fluorimetry (DSF, aka the thermal shift or ThermoFluor assay) to examine the melting temperature of SARS-CoV-2 Mac1 domain in the presence of various compounds In the second screen, various high-resolution SARS-CoV-2 Mac1 structures were used with Autodock VINA to identify potential ligands Numerous hit compounds were either steroids (estradiol valerate & flunisolide), beta-lactams (cefaclor & cefatrizine), or benzimidazoles (telmisartan, rabeprazole, omeprazole, & esomeprazole) Isothermal titration calorimetry was used to confirm that rabeprazole, omeprazole, and compounds in other chemical classes, such as irinotecan, nifedipine, trifluoperazine, bind SARS-CoV-2 Mac1 with an affinity similar to ADP-ribose
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #665871
    Database COVID19

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  6. Article ; Online: Discovery of Drug-like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3

    Virdi, Rajdeep S / Bavisotto, Robert V / Hopper, Nicholas C / Frick, David

    bioRxiv

    Abstract: The Mac1 domain of the multifunctional SARS-CoV-2 non-structural protein 3 (nsp3) is a potential COVID-19 drug target because it is suspected to enhance the ability of the virus to evade the human immune system. The SARS-CoV-2 Mac1 domain binds ADP- ... ...

    Abstract The Mac1 domain of the multifunctional SARS-CoV-2 non-structural protein 3 (nsp3) is a potential COVID-19 drug target because it is suspected to enhance the ability of the virus to evade the human immune system. The SARS-CoV-2 Mac1 domain binds ADP-ribose and proteins harboring this important post-translational modification. Small molecules that bind the Mac1 domain in place of ADP-ribose might therefore be useful as molecular probes or scaffolds for antiviral drug discovery. Two high throughput screens were used here to identify such ligands in small libraries of drugs and drug-like compounds. The first screen used differential scanning fluorimetry (DSF, aka the thermal shift or ThermoFluor assay) to examine the melting temperature of SARS-CoV-2 Mac1 domain in the presence of various compounds. In the second screen, various high-resolution SARS-CoV-2 Mac1 structures were used with Autodock VINA to identify potential ligands. Numerous hit compounds were either steroids (estradiol valerate & flunisolide), beta-lactams (cefaclor & cefatrizine), or benzimidazoles (telmisartan, rabeprazole, omeprazole, & esomeprazole). Isothermal titration calorimetry was used to confirm that rabeprazole, omeprazole, and compounds in other chemical classes, such as irinotecan, nifedipine, trifluoperazine, bind SARS-CoV-2 Mac1 with an affinity similar to ADP-ribose.
    Keywords covid19
    Language English
    Publishing date 2020-07-06
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.07.06.190413
    Database COVID19

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  7. Article: Discovery of Drug-like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3.

    Virdi, Rajdeep S / Bavisotto, Robert V / Hopper, Nicholas C / Vuksanovic, Nemanja / Melkonian, Trevor R / Silvaggi, Nicholas R / Frick, David N

    bioRxiv : the preprint server for biology

    2020  

    Abstract: Small molecules that bind the SARS-CoV-2 non-structural protein 3 Mac1 domain in place of ADP-ribose could be useful as molecular probes or scaffolds for COVID-19 antiviral drug discovery because Mac1 has been linked to coronavirus' ability to evade ... ...

    Abstract Small molecules that bind the SARS-CoV-2 non-structural protein 3 Mac1 domain in place of ADP-ribose could be useful as molecular probes or scaffolds for COVID-19 antiviral drug discovery because Mac1 has been linked to coronavirus' ability to evade cellular detection. A high-throughput assay based on differential scanning fluorimetry (DSF) was therefore optimized and used to identify possible Mac1 ligands in small libraries of drugs and drug-like compounds. Numerous promising compounds included nucleotides, steroids, beta-lactams, and benzimidazoles. The main drawback to this approach was that a high percentage of compounds in some libraries were found to influence the observed Mac1 melting temperature. To prioritize DSF screening hits, the shapes of the observed melting curves and initial assay fluorescence were examined, and the results were compared with virtual screens performed using Autodock VINA. The molecular basis for alternate ligand binding was also examined by determining a structure of one of the hits, cyclic adenosine monophosphate, with atomic resolution.
    Keywords covid19
    Language English
    Publishing date 2020-09-01
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2020.07.06.190413
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Discovery of Drug-Like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3.

    Virdi, Rajdeep S / Bavisotto, Robert V / Hopper, Nicholas C / Vuksanovic, Nemanja / Melkonian, Trevor R / Silvaggi, Nicholas R / Frick, David N

    SLAS discovery : advancing life sciences R & D

    2020  Volume 25, Issue 10, Page(s) 1162–1170

    Abstract: Small molecules that bind the SARS-CoV-2 nonstructural protein 3 Mac1 domain in place of ADP-ribose could be useful as molecular probes or scaffolds for COVID-19 antiviral drug discovery because Mac1 has been linked to the ability of coronaviruses to ... ...

    Abstract Small molecules that bind the SARS-CoV-2 nonstructural protein 3 Mac1 domain in place of ADP-ribose could be useful as molecular probes or scaffolds for COVID-19 antiviral drug discovery because Mac1 has been linked to the ability of coronaviruses to evade cellular detection. A high-throughput assay based on differential scanning fluorimetry (DSF) was therefore optimized and used to identify possible Mac1 ligands in small libraries of drugs and drug-like compounds. Numerous promising compounds included nucleotides, steroids, β-lactams, and benzimidazoles. The main drawback to this approach was that a high percentage of compounds in some libraries were found to influence the observed Mac1 melting temperature. To prioritize DSF screening hits, the shapes of the observed melting curves and initial assay fluorescence were examined, and the results were compared with virtual screens performed using AutoDock Vina. The molecular basis for alternate ligand binding was also examined by determining a structure of one of the hits, cyclic adenosine monophosphate, with atomic resolution.
    MeSH term(s) Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Binding Sites ; Coronavirus Papain-Like Proteases/chemistry ; Coronavirus Papain-Like Proteases/genetics ; Coronavirus Papain-Like Proteases/metabolism ; Cyclic AMP/chemistry ; Cyclic AMP/metabolism ; High-Throughput Screening Assays/methods ; Ligands ; Models, Molecular ; Molecular Docking Simulation ; Protein Conformation ; Protein Domains ; SARS-CoV-2/chemistry ; SARS-CoV-2/drug effects
    Chemical Substances Antiviral Agents ; Ligands ; Cyclic AMP (E0399OZS9N) ; Coronavirus Papain-Like Proteases (EC 3.4.22.2) ; papain-like protease, SARS-CoV-2 (EC 3.4.22.2)
    Keywords covid19
    Language English
    Publishing date 2020-09-28
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2885123-7
    ISSN 2472-5560 ; 2472-5552
    ISSN (online) 2472-5560
    ISSN 2472-5552
    DOI 10.1177/2472555220960428
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4911: Show issues Location:
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  9. Article ; Online: Development of a Novel, Small-Molecule Brain-Penetrant Histone Deacetylase Inhibitor That Enhances Spatial Memory Formation in Mice.

    Belayet, Jawad B / Beamish, Sarah / Rahaman, Mizzanoor / Alanani, Samer / Virdi, Rajdeep S / Frick, David N / Rahman, A F M Towheedur / Ulicki, Joseph S / Biswas, Sreya / Arnold, Leggy A / Roni, M S Rashid / Cheng, Eric Y / Steeber, Douglas A / Frick, Karyn M / Hossain, M Mahmun

    Journal of medicinal chemistry

    2022  Volume 65, Issue 4, Page(s) 3388–3403

    Abstract: Histone acetylation is a prominent epigenetic modification linked to the memory loss symptoms associated with neurodegenerative disease. The use of existing histone deacetylase inhibitor (HDACi) drugs for treatment is precluded by their weak blood-brain ... ...

    Abstract Histone acetylation is a prominent epigenetic modification linked to the memory loss symptoms associated with neurodegenerative disease. The use of existing histone deacetylase inhibitor (HDACi) drugs for treatment is precluded by their weak blood-brain barrier (BBB) permeability and undesirable toxicity. Here, we address these shortcomings by developing a new class of disulfide-based compounds, inspired by the scaffold of the FDA-approved HDACi romidepsin (FK288). Our findings indicate that our novel compound MJM-1 increases the overall level of histone 3 (H3) acetylation in a prostate cancer cell line. In mice, MJM-1 injected intraperitoneally (i.p.) crossed the BBB and could be detected in the hippocampus, a brain region that mediates memory. Consistent with this finding, we found that the post-training i.p. administration of MJM-1 enhanced hippocampus-dependent spatial memory consolidation in male mice. Therefore, MJM-1 represents a potential lead for further optimization as a therapeutic strategy for ameliorating cognitive deficits in aging and neurodegenerative diseases.
    MeSH term(s) Animals ; Brain/metabolism ; Cell Line, Tumor ; Histone Deacetylase Inhibitors/chemical synthesis ; Histone Deacetylase Inhibitors/pharmacokinetics ; Histone Deacetylase Inhibitors/pharmacology ; Mice ; Mice, Inbred BALB C ; Spatial Memory/drug effects
    Chemical Substances Histone Deacetylase Inhibitors
    Language English
    Publishing date 2022-02-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.1c01928
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.B 151: Show issues Location:
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    Zs.MB 1: Show issues

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  10. Article ; Online: Variable Macro X Domain of SARS-CoV-2 Retains the Ability to Bind ADP-ribose

    Frick, David N. / Virdi, Rajdeep S. / Vuksanovic, Nemanja / Dahal, Narayan / Silvaggi, Nicholas R

    bioRxiv

    Abstract: The virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that en-codes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymers, helicase and main protease, are well conserved ... ...

    Abstract The virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that en-codes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymers, helicase and main protease, are well conserved between SARS-CoV-2 and the original SARS virus, but several others are not. This study examines one of the most novel proteins encoded by SARS-CoV-2, a macrodomain of nonstructural protein 3 (nsp3). Although 26% of the amino acids in this SARS-CoV-2 macrodo-main differ from those seen in other coronaviruses, the protein retains the ability to bind ADP-ribose, which is an important characteristic of beta corona-viruses, and potential therapeutic target.
    Keywords covid19
    Language English
    Publishing date 2020-04-02
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.03.31.014639
    Database COVID19

    Full text online

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