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  1. Article ; Online: Insights into the mechanism of SARS-CoV-2 main protease autocatalytic maturation from model precursors.

    Aniana, Annie / Nashed, Nashaat T / Ghirlando, Rodolfo / Coates, Leighton / Kneller, Daniel W / Kovalevsky, Andrey / Louis, John M

    Communications biology

    2023  Volume 6, Issue 1, Page(s) 1159

    Abstract: A critical step for SARS-CoV-2 assembly and maturation involves the autoactivation of the main protease ( ... ...

    Abstract A critical step for SARS-CoV-2 assembly and maturation involves the autoactivation of the main protease (MPro
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19/genetics ; Mutation ; Coronavirus 3C Proteases/genetics
    Chemical Substances 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Language English
    Publishing date 2023-11-13
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-023-05469-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Novel HIV PR inhibitors with C4-substituted bis-THF and bis-fluoro-benzyl target the two active site mutations of highly drug resistant mutant PR

    Agniswamy, Johnson / Kneller, Daniel W / Ghosh, Arun K / Weber, Irene T

    Biochemical and biophysical research communications

    2021  Volume 566, Page(s) 30–35

    Abstract: The emergence of multidrug resistant (MDR) HIV strains severely reduces the effectiveness of antiretroviral therapy. Clinical inhibitor darunavir (1) has picomolar binding affinity for HIV-1 protease (PR), however, drug resistant variants like ... ...

    Abstract The emergence of multidrug resistant (MDR) HIV strains severely reduces the effectiveness of antiretroviral therapy. Clinical inhibitor darunavir (1) has picomolar binding affinity for HIV-1 protease (PR), however, drug resistant variants like PR
    MeSH term(s) Catalytic Domain/drug effects ; Darunavir/analogs & derivatives ; Darunavir/pharmacology ; Drug Resistance, Viral ; HIV Infections/drug therapy ; HIV Infections/virology ; HIV Protease/chemistry ; HIV Protease/genetics ; HIV Protease/metabolism ; HIV Protease Inhibitors/chemistry ; HIV Protease Inhibitors/pharmacology ; HIV-1/drug effects ; HIV-1/genetics ; Humans ; Models, Molecular ; Point Mutation/drug effects
    Chemical Substances HIV Protease Inhibitors ; HIV Protease (EC 3.4.23.-) ; p16 protease, Human immunodeficiency virus 1 (EC 3.4.23.-) ; Darunavir (YO603Y8113)
    Language English
    Publishing date 2021-06-07
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 205723-2
    ISSN 1090-2104 ; 0006-291X ; 0006-291X
    ISSN (online) 1090-2104 ; 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2021.05.094
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 116: Show issues Location:
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  3. Article ; Online: Highly drug-resistant HIV-1 protease reveals decreased intra-subunit interactions due to clusters of mutations.

    Kneller, Daniel W / Agniswamy, Johnson / Harrison, Robert W / Weber, Irene T

    The FEBS journal

    2020  Volume 287, Issue 15, Page(s) 3235–3254

    Abstract: Drug-resistance is a serious problem for treatment of the HIV/AIDS pandemic. Potent clinical inhibitors of HIV-1 protease show several orders of magnitude worse inhibition of highly drug-resistant variants. Hence, the structure and enzyme activities were ...

    Abstract Drug-resistance is a serious problem for treatment of the HIV/AIDS pandemic. Potent clinical inhibitors of HIV-1 protease show several orders of magnitude worse inhibition of highly drug-resistant variants. Hence, the structure and enzyme activities were analyzed for HIV protease mutant HIV-1 protease (EC 3.4.23.16) (PR) with 22 mutations (PRS5B) from a clinical isolate that was selected by machine learning to represent high-level drug-resistance. PRS5B has 22 mutations including only one (I84V) in the inhibitor binding site; however, clinical inhibitors had poor inhibition of PRS5B activity with kinetic inhibition value (K
    MeSH term(s) Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Drug Resistance, Viral/genetics ; HIV Protease/chemistry ; HIV Protease/genetics ; HIV Protease/metabolism ; HIV Protease Inhibitors/pharmacology ; Humans ; Models, Molecular ; Molecular Dynamics Simulation ; Mutation ; Protein Conformation
    Chemical Substances HIV Protease Inhibitors ; HIV Protease (EC 3.4.23.-)
    Language English
    Publishing date 2020-01-23
    Publishing country England
    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 2173655-8
    ISSN 1742-4658 ; 1742-464X
    ISSN (online) 1742-4658
    ISSN 1742-464X
    DOI 10.1111/febs.15207
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 260: Show issues Location:
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  4. Article: Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography.

    Kneller, Daniel W / Zhang, Qiu / Coates, Leighton / Louis, John M / Kovalevsky, Andrey

    IUCrJ

    2021  Volume 8, Issue Pt 6, Page(s) 973–979

    Abstract: SARS-CoV-2 emerged at the end of 2019 to cause an unprecedented pandemic of the deadly respiratory disease COVID-19 that continues to date. The viral main protease ( ... ...

    Abstract SARS-CoV-2 emerged at the end of 2019 to cause an unprecedented pandemic of the deadly respiratory disease COVID-19 that continues to date. The viral main protease (M
    Language English
    Publishing date 2021-10-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252521010113
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Room-temperature neutron and X-ray data collection of 3CL M

    Kneller, Daniel W / Phillips, Gwyndalyn / Kovalevsky, Andrey / Coates, Leighton

    Acta crystallographica. Section F, Structural biology communications

    2020  Volume 76, Issue Pt 10, Page(s) 483–487

    Abstract: The replication of SARS-CoV-2 produces two large polyproteins, pp1a and pp1ab, that are inactive until cleavage by the viral chymotrypsin-like cysteine protease enzyme (3CL ... ...

    Abstract The replication of SARS-CoV-2 produces two large polyproteins, pp1a and pp1ab, that are inactive until cleavage by the viral chymotrypsin-like cysteine protease enzyme (3CL M
    MeSH term(s) Betacoronavirus/chemistry ; Betacoronavirus/enzymology ; Betacoronavirus/genetics ; COVID-19 ; Catalytic Domain ; Coronavirus 3C Proteases ; Coronavirus Infections/virology ; Crystallography, X-Ray ; Cysteine Endopeptidases/chemistry ; Cysteine Endopeptidases/genetics ; Humans ; Models, Molecular ; Neutron Diffraction ; Pandemics ; Pneumonia, Viral/virology ; Protein Conformation ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; SARS-CoV-2 ; Temperature ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/genetics
    Chemical Substances Recombinant Proteins ; Viral Nonstructural Proteins ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Keywords covid19
    Language English
    Publishing date 2020-09-15
    Publishing country United States
    Document type Journal Article
    ISSN 2053-230X
    ISSN (online) 2053-230X
    DOI 10.1107/S2053230X20011814
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Revertant mutation V48G alters conformational dynamics of highly drug resistant HIV protease PRS17.

    Burnaman, Shelley H / Kneller, Daniel W / Wang, Yuan-Fang / Kovalevsky, Andrey / Weber, Irene T

    Journal of molecular graphics & modelling

    2021  Volume 108, Page(s) 108005

    Abstract: Drug resistance is a serious problem for controlling the HIV/AIDS pandemic. Current antiviral drugs show several orders of magnitude worse inhibition of highly resistant clinical variant PRS17 of HIV-1 protease compared with wild-type protease. We have ... ...

    Abstract Drug resistance is a serious problem for controlling the HIV/AIDS pandemic. Current antiviral drugs show several orders of magnitude worse inhibition of highly resistant clinical variant PRS17 of HIV-1 protease compared with wild-type protease. We have analyzed the effects of a common resistance mutation G48V in the flexible flaps of the protease by assessing the revertant PRS17
    MeSH term(s) Catalytic Domain ; Drug Resistance, Viral/genetics ; HIV Protease/genetics ; HIV Protease/metabolism ; HIV Protease Inhibitors/pharmacology ; Mutation ; Pharmaceutical Preparations ; Protein Conformation
    Chemical Substances HIV Protease Inhibitors ; Pharmaceutical Preparations ; HIV Protease (EC 3.4.23.-)
    Language English
    Publishing date 2021-08-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1396450-1
    ISSN 1873-4243 ; 1093-3263
    ISSN (online) 1873-4243
    ISSN 1093-3263
    DOI 10.1016/j.jmgm.2021.108005
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    Zs.A 3491: Show issues Location:
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  7. Article ; Online: Direct Observation of Protonation State Modulation in SARS-CoV-2 Main Protease upon Inhibitor Binding with Neutron Crystallography.

    Kneller, Daniel W / Phillips, Gwyndalyn / Weiss, Kevin L / Zhang, Qiu / Coates, Leighton / Kovalevsky, Andrey

    Journal of medicinal chemistry

    2021  Volume 64, Issue 8, Page(s) 4991–5000

    Abstract: The main protease (3CL ... ...

    Abstract The main protease (3CL M
    MeSH term(s) Binding Sites ; Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/chemistry ; Coronavirus 3C Proteases/metabolism ; Crystallography/methods ; Crystallography, X-Ray ; Cysteine Proteinase Inhibitors/chemistry ; Cysteine Proteinase Inhibitors/metabolism ; Models, Molecular ; Neutrons ; Oligopeptides/chemistry ; Oligopeptides/metabolism ; Protein Conformation ; Protons
    Chemical Substances Cysteine Proteinase Inhibitors ; Oligopeptides ; Protons ; telaprevir (655M5O3W0U) ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Language English
    Publishing date 2021-03-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.1c00058
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    Zs.B 151: Show issues Location:
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    Zs.MB 1: Show issues

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  8. Article ; Online: HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics.

    Wong-Sam, Andres / Wang, Yuan-Fang / Kneller, Daniel W / Kovalevsky, Andrey Y / Ghosh, Arun K / Harrison, Robert W / Weber, Irene T

    Journal of molecular graphics & modelling

    2022  Volume 117, Page(s) 108315

    Abstract: Antiretroviral drug resistance is a therapeutic obstacle for people with HIV. HIV protease inhibitors darunavir and lopinavir are recommended for resistant infections. We characterized a protease mutant (PR10x) derived from a highly resistant clinical ... ...

    Abstract Antiretroviral drug resistance is a therapeutic obstacle for people with HIV. HIV protease inhibitors darunavir and lopinavir are recommended for resistant infections. We characterized a protease mutant (PR10x) derived from a highly resistant clinical isolate including 10 mutations associated with resistance to lopinavir and darunavir. Compared to the wild-type protease, PR10x exhibits ∼3-fold decrease in catalytic efficiency and K
    MeSH term(s) Crystallography, X-Ray ; Darunavir/pharmacology ; Drug Resistance, Viral/genetics ; HIV Protease/chemistry ; HIV Protease Inhibitors/chemistry ; HIV Protease Inhibitors/pharmacology ; Humans ; Lopinavir/pharmacology ; Molecular Dynamics Simulation ; Mutation
    Chemical Substances HIV Protease Inhibitors ; Lopinavir (2494G1JF75) ; HIV Protease (EC 3.4.23.-) ; p16 protease, Human immunodeficiency virus 1 (EC 3.4.23.-) ; Darunavir (YO603Y8113)
    Language English
    Publishing date 2022-09-01
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 1396450-1
    ISSN 1873-4243 ; 1093-3263
    ISSN (online) 1873-4243
    ISSN 1093-3263
    DOI 10.1016/j.jmgm.2022.108315
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    Zs.A 3491: Show issues Location:
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  9. Article ; Online: Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor.

    Kneller, Daniel W / Gerlits, Oksana / Daemen, Luke L / Pavlova, Anna / Gumbart, James C / Cheng, Yongqiang / Kovalevsky, Andrey

    Physical chemistry chemical physics : PCCP

    2022  Volume 24, Issue 6, Page(s) 3586–3597

    Abstract: Biomacromolecules are inherently dynamic, and their dynamics are interwoven into function. The fast collective vibrational dynamics in proteins occurs in the low picosecond timescale corresponding to frequencies of ∼5-50 ... ...

    Abstract Biomacromolecules are inherently dynamic, and their dynamics are interwoven into function. The fast collective vibrational dynamics in proteins occurs in the low picosecond timescale corresponding to frequencies of ∼5-50 cm
    MeSH term(s) HIV Protease/chemistry ; HIV-1/enzymology ; Molecular Dynamics Simulation ; Neutrons ; Spectrum Analysis ; Vibration
    Chemical Substances HIV Protease (EC 3.4.23.-) ; p16 protease, Human immunodeficiency virus 1 (EC 3.4.23.-)
    Language English
    Publishing date 2022-02-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d1cp05487b
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  10. Article ; Online: Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain.

    Nashed, Nashaat T / Kneller, Daniel W / Coates, Leighton / Ghirlando, Rodolfo / Aniana, Annie / Kovalevsky, Andrey / Louis, John M

    Communications biology

    2022  Volume 5, Issue 1, Page(s) 976

    Abstract: The monomeric catalytic domain (residues 1-199) of SARS-CoV-2 main protease ( ... ...

    Abstract The monomeric catalytic domain (residues 1-199) of SARS-CoV-2 main protease (MPro
    MeSH term(s) Amino Acids ; COVID-19 ; Catalytic Domain ; Coronavirus 3C Proteases ; Humans ; Peptide Hydrolases ; Polyproteins ; SARS-CoV-2/genetics
    Chemical Substances Amino Acids ; Polyproteins ; Peptide Hydrolases (EC 3.4.-) ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Language English
    Publishing date 2022-09-16
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-022-03910-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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