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  1. Article ; Online: Structural Insights into SARS-CoV-2 Nonstructural Protein 1 Interaction with Human Cyclophilin and FKBP1 to Regulate Interferon Production.

    Vankadari, Naveen / Ghosal, Debnath

    The journal of physical chemistry letters

    2024  Volume 15, Issue 4, Page(s) 919–924

    Abstract: The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 coronavirus and the perpetual rise of new variants warrant investigation of the molecular and structural details of the infection process and modulation of the host defense ...

    Abstract The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 coronavirus and the perpetual rise of new variants warrant investigation of the molecular and structural details of the infection process and modulation of the host defense by viral proteins. This Letter reports the combined experimental and computational approaches to provide key insights into the structural and functional basis of Nsp1's association with different cyclophilins and FKBPs in regulating COVID-19 infection. We demonstrated the real-time stability and functional dynamics of the Nsp1-CypA/FKBP1A complex and investigated the repurposing of potential inhibitors that could block these interactions. Overall, we provided insights into the inhibitory role Nsp1 in downstream interferon production, a key aspect for host defense that prevents the SARS-CoV-2 or related family of corona virus infection.
    MeSH term(s) Humans ; SARS-CoV-2/metabolism ; COVID-19 ; Cyclophilins ; Viral Nonstructural Proteins/metabolism ; Interferons
    Chemical Substances Cyclophilins (EC 5.2.1.-) ; Viral Nonstructural Proteins ; Interferons (9008-11-1)
    Language English
    Publishing date 2024-01-19
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c02959
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Arbidol: A potential antiviral drug for the treatment of SARS-CoV-2 by blocking trimerization of the spike glycoprotein.

    Vankadari, Naveen

    International journal of antimicrobial agents

    2020  Volume 56, Issue 2, Page(s) 105998

    Abstract: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic is a global public health emergency, and new therapeutics are needed. This article reports the potential drug target and mechanism of action of Arbidol (umifenovir) to treat ... ...

    Abstract The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic is a global public health emergency, and new therapeutics are needed. This article reports the potential drug target and mechanism of action of Arbidol (umifenovir) to treat coronavirus disease 2019 (COVID-19). Molecular dynamics and structural analysis were used to show how Arbidol targets the SARS-CoV-2 spike glycoprotein and impedes its trimerization, which is key for host cell adhesion and hijacking, indicating the potential of Arbidol to treat COVID-19. It is hoped that knowledge of the potential drug target and mechanism of action of Arbidol will help in the development of new therapeutics for SARS-CoV-2.
    MeSH term(s) Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Betacoronavirus/drug effects ; Betacoronavirus/isolation & purification ; Biopolymers/chemistry ; COVID-19 ; Coronavirus Infections/drug therapy ; Coronavirus Infections/virology ; Humans ; Indoles/chemistry ; Indoles/pharmacology ; Pandemics ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/virology ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/antagonists & inhibitors
    Chemical Substances Antiviral Agents ; Biopolymers ; Indoles ; Spike Glycoprotein, Coronavirus ; umifenovir (93M09WW4RU)
    Keywords covid19
    Language English
    Publishing date 2020-04-28
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1093977-5
    ISSN 1872-7913 ; 0924-8579
    ISSN (online) 1872-7913
    ISSN 0924-8579
    DOI 10.1016/j.ijantimicag.2020.105998
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3368: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  3. Article ; Online: Structure of Furin Protease Binding to SARS-CoV-2 Spike Glycoprotein and Implications for Potential Targets and Virulence.

    Vankadari, Naveen

    The journal of physical chemistry letters

    2020  Volume 11, Issue 16, Page(s) 6655–6663

    Abstract: The COVID-19 pandemic is an urgent global health emergency, and the presence of Furin site in the SARS-CoV-2 spike glycoprotein alters virulence and warrants further molecular, structural, and biophysical studies. Here we report the structure of Furin in ...

    Abstract The COVID-19 pandemic is an urgent global health emergency, and the presence of Furin site in the SARS-CoV-2 spike glycoprotein alters virulence and warrants further molecular, structural, and biophysical studies. Here we report the structure of Furin in complex with SARS-CoV-2 spike glycoprotein, demonstrating how Furin binds to the S1/S2 region of spike glycoprotein and eventually cleaves the viral protein using experimental functional studies, molecular dynamics, and docking. The structural studies underline the mechanism and mode of action of Furin, which is a key process in host cell entry and a hallmark of enhanced virulence. Our whole-exome sequencing analysis shows the genetic variants/alleles in Furin were found to alter the binding affinity for viral spike glycoprotein and could vary in infectivity in humans. Unravelling the mechanisms of Furin action, binding dynamics, and the genetic variants opens the growing arena of bona fide antibodies and development of potential therapeutics targeting the blockage of Furin cleavage.
    MeSH term(s) Amino Acid Sequence ; Animals ; Betacoronavirus/chemistry ; Betacoronavirus/pathogenicity ; CHO Cells ; Catalytic Domain ; Cricetulus ; Furin/chemistry ; Furin/genetics ; Furin/metabolism ; Gene Expression/physiology ; Hexosamines/metabolism ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; Proteolysis ; SARS-CoV-2 ; Serine Proteinase Inhibitors/metabolism ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism ; Virulence/physiology
    Chemical Substances 2,5-dideoxystreptamine ; Hexosamines ; Serine Proteinase Inhibitors ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; FURIN protein, human (EC 3.4.21.75) ; Furin (EC 3.4.21.75)
    Keywords covid19
    Language English
    Publishing date 2020-08-05
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.0c01698
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Overwhelming mutations or SNPs of SARS-CoV-2: A point of caution.

    Vankadari, Naveen

    Gene

    2020  Volume 752, Page(s) 144792

    Abstract: The morbidity of SARS-CoV-2 (COVID-19) is reaching 3 Million landmark causing and a serious public health concern globally and it is enigmatic how several antiviral and antibody treatments were not effective in the different period across the globe. With ...

    Abstract The morbidity of SARS-CoV-2 (COVID-19) is reaching 3 Million landmark causing and a serious public health concern globally and it is enigmatic how several antiviral and antibody treatments were not effective in the different period across the globe. With the drastic increasing number of positive cases around the world WHO raised the importance in the assessment of the risk of spread and understanding genetic modifications that could have occurred in the SARS-CoV-2. Using all available deep sequencing data of complete genome from all over the world (NCBI repository), we identified several hundreds of point mutations or SNPs in SARS-CoV-2 all across the genome. This could be the cause for the constant change and differed virulence with an increase in mortality and morbidity. Among the 12 different countries (one sequence from each country) with complete genome sequencing data, we noted the 47 key point mutations or SNPs located along the entire genome that might have impact in the virulence and response to different antivirals against SARS-CoV-2. In this regard, key viral proteins of spike glycoprotein, Nsp1, RdRp and the ORF8 region got heavily mutated within these 3 months via person-to-person passage. We also discuss what could be the possible cause of this rapid mutation in the SARS-CoV-2.
    MeSH term(s) Americas/epidemiology ; Asia/epidemiology ; Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections/epidemiology ; Coronavirus Infections/virology ; Drug Resistance, Viral ; Europe/epidemiology ; Genome, Viral ; Humans ; Pandemics ; Phylogeny ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/virology ; Point Mutation ; Polymorphism, Single Nucleotide ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics ; Viral Proteins/classification ; Viral Proteins/genetics
    Chemical Substances Spike Glycoprotein, Coronavirus ; Viral Proteins ; spike protein, SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-05-20
    Publishing country Netherlands
    Document type Letter
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2020.144792
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1357: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Overwhelming mutations or SNPs of SARS-CoV-2

    Vankadari, Naveen

    Gene

    A point of caution

    2020  Volume 752, Page(s) 144792

    Keywords Genetics ; General Medicine ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2020.144792
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  6. Article ; Online: Structure of Furin Protease Binding to SARS-CoV-2 Spike Glycoprotein and Implications for Potential Targets and Virulence

    Vankadari, Naveen

    The Journal of Physical Chemistry Letters

    2020  Volume 11, Issue 16, Page(s) 6655–6663

    Keywords General Materials Science ; covid19
    Language English
    Publisher American Chemical Society (ACS)
    Publishing country us
    Document type Article ; Online
    ISSN 1948-7185
    DOI 10.1021/acs.jpclett.0c01698
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  7. Article ; Online: Note: Grid cork and septal cork syringe adapters: An effective tool for efficient greasing of 24-well crystallization trays.

    Vankadari, Naveen

    The Review of scientific instruments

    2018  Volume 89, Issue 10, Page(s) 106103

    Abstract: Applying grease to seal the well surface of the crystallization plate through traditional approaches in the hanging drop vapor diffusion method is a laborious process and known to cause air bubble formation. Here we report a simple design of adapters to ... ...

    Abstract Applying grease to seal the well surface of the crystallization plate through traditional approaches in the hanging drop vapor diffusion method is a laborious process and known to cause air bubble formation. Here we report a simple design of adapters to the regular syringes for applying grease to the 24-well crystallization tray. This newly developed tool overcomes the difficulties faced with the traditional greasing methods, such as uneven distribution and excess of grease on the wells. The use of new adapters expedites the process of greasing by 4-5 times which is quick and reliable and can be cost effective in terms of time and labor. In addition, this tool reduces the time and effort required for greasing the wells. Here we demonstrate two types of adaptors (grid cork and septal cork), and the effectiveness of both the adaptors was further corroborated by crystallization trials.
    Language English
    Publishing date 2018-11-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209865-9
    ISSN 1089-7623 ; 0034-6748
    ISSN (online) 1089-7623
    ISSN 0034-6748
    DOI 10.1063/1.5029860
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    Z 4' 46/112: Show issues

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  8. Article ; Online: Arbidol

    Vankadari, Naveen

    International Journal of Antimicrobial Agents

    A potential antiviral drug for the treatment of SARS-CoV-2 by blocking trimerization of the spike glycoprotein

    2020  Volume 56, Issue 2, Page(s) 105998

    Keywords Microbiology (medical) ; Pharmacology (medical) ; Infectious Diseases ; General Medicine ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 1093977-5
    ISSN 1872-7913 ; 0924-8579
    ISSN (online) 1872-7913
    ISSN 0924-8579
    DOI 10.1016/j.ijantimicag.2020.105998
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3368: 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)
    Zs.MO 500: Show issues

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  9. Article: Arbidol: A potential antiviral drug for the treatment of SARS-CoV-2 by blocking trimerization of the spike glycoprotein

    Vankadari, Naveen

    Int J Antimicrob Agents

    Abstract: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic is a global public health emergency, and new therapeutics are needed. This article reports the potential drug target and mechanism of action of Arbidol (umifenovir) to treat ... ...

    Abstract The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic is a global public health emergency, and new therapeutics are needed. This article reports the potential drug target and mechanism of action of Arbidol (umifenovir) to treat coronavirus disease 2019 (COVID-19). Molecular dynamics and structural analysis were used to show how Arbidol targets the SARS-CoV-2 spike glycoprotein and impedes its trimerization, which is key for host cell adhesion and hijacking, indicating the potential of Arbidol to treat COVID-19. It is hoped that knowledge of the potential drug target and mechanism of action of Arbidol will help in the development of new therapeutics for SARS-CoV-2.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #291695
    Database COVID19

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  10. Article ; Online: Arbidol: A potential antiviral drug for the treatment of SARS-CoV-2 by blocking the trimerization of viral spike glycoprotein ?

    Vankadari, Naveen

    International Journal of Antimicrobial Agents

    Abstract: Abstract The SARS-CoV-2 pandemic is an urgent global public health emergency and warrants investigating studies on bonafide antivirals for combat. Here we report the drug target and mechanism of action of potential antiviral drug Arbidol for SARS-CoV-2 ... ...

    Abstract Abstract The SARS-CoV-2 pandemic is an urgent global public health emergency and warrants investigating studies on bonafide antivirals for combat. Here we report the drug target and mechanism of action of potential antiviral drug Arbidol for SARS-CoV-2 infections. Our structural and molecular dynamics studies show how Arbidol targets the SARS-CoV-2 spike glycoprotein and impede the trimerization of spike glycoprotein, which is a key for host cell adhesion and hijacking, thus placing Arbidol as a potential drug for repurposing. This study also abets in the development of other new therapeutics for COIVD-19 disease based on Arbidol binding mode and using structure-guided drug designing.
    Keywords covid19
    Publisher Elsevier
    Document type Article ; Online
    DOI 10.1016/j.ijantimicag.2020.105998
    Database COVID19

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