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  1. Article ; Online: Evolutionary and Structural Insights about Potential SARS-CoV-2 Evasion of Nirmatrelvir.

    Yang, Kai S / Leeuwon, Sunshine Z / Xu, Shiqing / Liu, Wenshe Ray

    Journal of medicinal chemistry

    2022  Volume 65, Issue 13, Page(s) 8686–8698

    Abstract: The U.S. FDA approval of PAXLOVID, a combination therapy of nirmatrelvir and ritonavir has significantly boosted our morale in fighting the COVID-19 pandemic. Nirmatrelvir is an inhibitor of the main protease ( ... ...

    Abstract The U.S. FDA approval of PAXLOVID, a combination therapy of nirmatrelvir and ritonavir has significantly boosted our morale in fighting the COVID-19 pandemic. Nirmatrelvir is an inhibitor of the main protease (M
    MeSH term(s) Coronavirus 3C Proteases ; Humans ; Pandemics ; SARS-CoV-2/genetics ; Viral Nonstructural Proteins/chemistry ; COVID-19 Drug Treatment
    Chemical Substances Viral Nonstructural Proteins ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Language English
    Publishing date 2022-06-22
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.2c00404
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.B 151: Show issues Location:
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  2. Article: A Designed, Highly Efficient Pyrrolysyl-tRNA Synthetase Mutant Binds o-Chlorophenylalanine Using Two Halogen Bonds

    Vatansever, Erol C. / Yang, Kai S. / Geng, Zhi Zachary / Qiao, Yuchen / Li, Pingwei / Xu, Shiqing / Liu, Wenshe Ray

    Journal of molecular biology. 2022 Mar. 05,

    2022  

    Abstract: As one of the most valuable tools for genetic code expansion, pyrrolysyl-tRNA synthetase (PylRS) is structurally related to phenylalanyl-tRNA synthetase (PheRS). By introducing mutations that mimic ligand interactions in PheRS into PylRS, we designed a ... ...

    Abstract As one of the most valuable tools for genetic code expansion, pyrrolysyl-tRNA synthetase (PylRS) is structurally related to phenylalanyl-tRNA synthetase (PheRS). By introducing mutations that mimic ligand interactions in PheRS into PylRS, we designed a PylRS mutant. This mutant, designated as oClFRS, recognizes a number of o-substituted phenylalanines for their genetic incorporation at amber codon. Its efficiency in catalyzing genetic incorporation of o-chlorophenylalanine (o-ClF) is better than that for Nᵋ-tert-butyloxycarbonyl-lysine catalyzed by PylRS. The crystal structure of oClFRS bound with o-ClF shows that o-ClF binds deeply into a hydrophobic but catalytically inactive pocket in the active site and involves two halogen bonds to achieve strong interactions. The shift of o-ClF to a catalytically active position in the oClFRS active site will be necessary for its activation. This is the first reported aminoacyl-tRNA synthetase that involves two halogen bonds for ligation recognition and might represent an alternative route to develop aminoacyl-tRNA synthetase mutants that are selective for noncanonical amino acids over native amino acids.
    Keywords active sites ; crystal structure ; genetic code ; halogens ; hydrophobicity ; ligands ; molecular biology ; mutants ; phenylalanine-tRNA ligase ; stop codon
    Language English
    Dates of publication 2022-0305
    Publishing place Elsevier Ltd
    Document type Article
    Note Pre-press version
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2022.167534
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: An Enhanced Hybrid Screening Approach to Identify Potent Inhibitors for the SARS-CoV-2 Main Protease From the NCI Compound Library.

    Li, Shuhua G / Yang, Kai S / Blankenship, Lauren R / Cho, Chia-Chuan D / Xu, Shiqing / Wang, Hongbin / Liu, Wenshe Ray

    Frontiers in chemistry

    2022  Volume 10, Page(s) 816576

    Abstract: The emergence and rapid spread of SARS-CoV-2, the pathogen of COVID-19, have caused a worldwide public health crisis. The SARS-CoV-2 main protease (Mpro) is an essential enzyme for the virus and therefore an appealing target for the development of ... ...

    Abstract The emergence and rapid spread of SARS-CoV-2, the pathogen of COVID-19, have caused a worldwide public health crisis. The SARS-CoV-2 main protease (Mpro) is an essential enzyme for the virus and therefore an appealing target for the development of antivirals to treat COVID-19 patients. Recently, many
    Language English
    Publishing date 2022-02-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711776-5
    ISSN 2296-2646
    ISSN 2296-2646
    DOI 10.3389/fchem.2022.816576
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A Designed, Highly Efficient Pyrrolysyl-tRNA Synthetase Mutant Binds o-Chlorophenylalanine Using Two Halogen Bonds.

    Vatansever, Erol C / Yang, Kai S / Geng, Zhi Zachary / Qiao, Yuchen / Li, Pingwei / Xu, Shiqing / Liu, Wenshe Ray

    Journal of molecular biology

    2022  Volume 434, Issue 8, Page(s) 167534

    Abstract: As one of the most valuable tools for genetic code expansion, pyrrolysyl-tRNA synthetase (PylRS) is structurally related to phenylalanyl-tRNA synthetase (PheRS). By introducing mutations that mimic ligand interactions in PheRS into PylRS, we designed a ... ...

    Abstract As one of the most valuable tools for genetic code expansion, pyrrolysyl-tRNA synthetase (PylRS) is structurally related to phenylalanyl-tRNA synthetase (PheRS). By introducing mutations that mimic ligand interactions in PheRS into PylRS, we designed a PylRS mutant. This mutant, designated as oClFRS, recognizes a number of o-substituted phenylalanines for their genetic incorporation at amber codon. Its efficiency in catalyzing genetic incorporation of o-chlorophenylalanine (o-ClF) is better than that for N
    MeSH term(s) Amino Acyl-tRNA Synthetases/chemistry ; Amino Acyl-tRNA Synthetases/genetics ; Genetic Code ; Halogens/chemistry ; Lysine/analogs & derivatives ; Lysine/chemistry ; Lysine/genetics ; Methanosarcina/enzymology ; Mutation ; Phenylalanine/chemistry ; Phenylalanine/genetics ; Protein Binding
    Chemical Substances Halogens ; Phenylalanine (47E5O17Y3R) ; Amino Acyl-tRNA Synthetases (EC 6.1.1.-) ; pyrrolysine (H3214Y96LP) ; Lysine (K3Z4F929H6)
    Language English
    Publishing date 2022-03-09
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2022.167534
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Corrigendum: Drug Repurposing for the SARS-CoV-2 Papain-Like Protease.

    Cho, Chia-Chuan / Li, Shuhua G / Lalonde, Tyler J / Yang, Kai S / Yu, Ge / Qiao, Yuchen / Xu, Shiqing / Liu, Wenshe Ray

    ChemMedChem

    2022  Volume 17, Issue 5, Page(s) e202200053

    Language English
    Publishing date 2022-02-08
    Publishing country Germany
    Document type Published Erratum
    ZDB-ID 2218496-X
    ISSN 1860-7187 ; 1860-7179
    ISSN (online) 1860-7187
    ISSN 1860-7179
    DOI 10.1002/cmdc.202200053
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A Novel Y-Shaped, S-O-N-O-S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease.

    Yang, Kai S / Blankenship, Lauren R / Kuo, Syuan-Ting Alex / Sheng, Yan J / Li, Pingwei / Fierke, Carol A / Russell, David H / Yan, Xin / Xu, Shiqing / Liu, Wenshe Ray

    ACS chemical biology

    2023  Volume 18, Issue 3, Page(s) 449–455

    Abstract: As the COVID-19 pathogen, SARS-CoV-2 relies on its main protease ( ... ...

    Abstract As the COVID-19 pathogen, SARS-CoV-2 relies on its main protease (M
    MeSH term(s) Humans ; COVID-19 ; SARS-CoV-2 ; Viral Nonstructural Proteins/chemistry ; Antiviral Agents/pharmacology ; Antiviral Agents/chemistry ; Protease Inhibitors/chemistry ; Molecular Docking Simulation
    Chemical Substances nirmatrelvir and ritonavir drug combination ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Viral Nonstructural Proteins ; Antiviral Agents ; Protease Inhibitors
    Language English
    Publishing date 2023-01-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ISSN 1554-8937
    ISSN (online) 1554-8937
    DOI 10.1021/acschembio.2c00695
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Drug Repurposing for the SARS-CoV-2 Papain-Like Protease.

    Cho, Chia-Chuan / Li, Shuhua G / Lalonde, Tyler J / Yang, Kai S / Yu, Ge / Qiao, Yuchen / Xu, Shiqing / Ray Liu, Wenshe

    ChemMedChem

    2021  Volume 17, Issue 1, Page(s) e202100455

    Abstract: As the pathogen of COVID-19, SARS-CoV-2 encodes two essential cysteine proteases that process the pathogen's two large polypeptide products pp1a and pp1ab in the human cell host to form 15 functionally important, mature nonstructural proteins. One of the ...

    Abstract As the pathogen of COVID-19, SARS-CoV-2 encodes two essential cysteine proteases that process the pathogen's two large polypeptide products pp1a and pp1ab in the human cell host to form 15 functionally important, mature nonstructural proteins. One of the two enzymes is papain-like protease or PL
    MeSH term(s) Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Coronavirus Papain-Like Proteases/antagonists & inhibitors ; Cysteine Proteinase Inhibitors/chemistry ; Cysteine Proteinase Inhibitors/pharmacology ; Drug Repositioning ; Humans ; Inhibitory Concentration 50 ; SARS-CoV-2/drug effects ; Structure-Activity Relationship
    Chemical Substances Antiviral Agents ; Cysteine Proteinase Inhibitors ; Coronavirus Papain-Like Proteases (EC 3.4.22.2) ; papain-like protease, SARS-CoV-2 (EC 3.4.22.2)
    Language English
    Publishing date 2021-10-12
    Publishing country Germany
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2218496-X
    ISSN 1860-7187 ; 1860-7179
    ISSN (online) 1860-7187
    ISSN 1860-7179
    DOI 10.1002/cmdc.202100455
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Azapeptides with unique covalent warheads as SARS-CoV-2 main protease inhibitors.

    Khatua, Kaustav / Alugubelli, Yugendar R / Yang, Kai S / Vulupala, Veerabhadra R / Blankenship, Lauren R / Coleman, Demonta / Atla, Sandeep / Chaki, Sankar P / Geng, Zhi Zachary / Ma, Xinyu R / Xiao, Jing / Chen, Peng-Hsun / Cho, Chia-Chuan D / Sharma, Shivangi / Vatansever, Erol C / Ma, Yuying / Yu, Ge / Neuman, Benjamin W / Xu, Shiqing /
    Liu, Wenshe Ray

    Antiviral research

    2024  Volume 225, Page(s) 105874

    Abstract: The main protease ( ... ...

    Abstract The main protease (M
    MeSH term(s) Humans ; SARS-CoV-2/metabolism ; COVID-19 ; Cysteine ; Cysteine Endopeptidases/metabolism ; Viral Nonstructural Proteins ; Protease Inhibitors/pharmacology ; Antiviral Agents/pharmacology ; Coronavirus 3C Proteases
    Chemical Substances 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Cysteine (K848JZ4886) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Viral Nonstructural Proteins ; Protease Inhibitors ; Antiviral Agents ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Language English
    Publishing date 2024-03-28
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 306628-9
    ISSN 1872-9096 ; 0166-3542
    ISSN (online) 1872-9096
    ISSN 0166-3542
    DOI 10.1016/j.antiviral.2024.105874
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease.

    Geng, Zhi Zachary / Atla, Sandeep / Shaabani, Namir / Vulupala, Veerabhadra R / Yang, Kai S / Alugubelli, Yugendar R / Khatua, Kaustav / Chen, Peng-Hsun Chase / Xiao, Jing / Blankenship, Lauren R / Ma, Xinyu R / Vatansever, Erol C / Cho, Chia-Chuan / Ma, Yuying / Allen, Robert / Ji, Henry / Xu, Shiqing / Liu, Wenshe Ray

    bioRxiv : the preprint server for biology

    2023  

    Abstract: SARS-CoV-2 is the coronavirus pathogen of the currently prevailing COVID-19 pandemic. It relies on its main protease ( ... ...

    Abstract SARS-CoV-2 is the coronavirus pathogen of the currently prevailing COVID-19 pandemic. It relies on its main protease (M
    Language English
    Publishing date 2023-01-18
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.17.524469
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease.

    Geng, Zhi Zachary / Atla, Sandeep / Shaabani, Namir / Vulupala, Veerabhadra / Yang, Kai S / Alugubelli, Yugendar R / Khatua, Kaustav / Chen, Peng-Hsun / Xiao, Jing / Blankenship, Lauren R / Ma, Xinyu R / Vatansever, Erol C / Cho, Chia-Chuan D / Ma, Yuying / Allen, Robert / Ji, Henry / Xu, Shiqing / Liu, Wenshe Ray

    Journal of medicinal chemistry

    2023  Volume 66, Issue 16, Page(s) 11040–11055

    Abstract: SARS-CoV-2, the COVID-19 pathogen, relies on its main protease ( ... ...

    Abstract SARS-CoV-2, the COVID-19 pathogen, relies on its main protease (M
    MeSH term(s) Humans ; COVID-19 ; SARS-CoV-2 ; Antiviral Agents/pharmacology ; Carboxylic Acids ; Protease Inhibitors/pharmacology ; Molecular Docking Simulation
    Chemical Substances 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; nonane (T9W3VH6G10) ; Antiviral Agents ; Carboxylic Acids ; Protease Inhibitors
    Language English
    Publishing date 2023-08-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.3c00221
    Database MEDical Literature Analysis and Retrieval System OnLINE

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