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  1. Article ; Online: Correction to: Molecular characterization and complete genome of alstroemeria mosaic virus (AlMV).

    Mosquera-Yuqui, Francisco / Garrido, Patricia / Flores, Francisco J

    Virus genes

    2019  Volume 56, Issue 1, Page(s) 94

    Abstract: The original version of this article unfortunately contained an error in the length of AIMV genome sequence. ...

    Abstract The original version of this article unfortunately contained an error in the length of AIMV genome sequence.
    Language English
    Publishing date 2019-11-27
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ZDB-ID 639496-6
    ISSN 1572-994X ; 0920-8569
    ISSN (online) 1572-994X
    ISSN 0920-8569
    DOI 10.1007/s11262-019-01717-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2397: 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)
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  2. Article ; Online: Molecular characterization and complete genome of alstroemeria mosaic virus (AlMV).

    Mosquera-Yuqui, Francisco / Garrido, Patricia / Flores, Francisco J

    Virus genes

    2019  Volume 56, Issue 1, Page(s) 87–93

    Abstract: Even though alstroemeria mosaic virus (AlMV) is one of the most important viruses affecting alstroemeria plants, its genome is only partially available in public sequence databases. High throughput sequencing (HTS) of RNA from alstroemeria plants with ... ...

    Abstract Even though alstroemeria mosaic virus (AlMV) is one of the most important viruses affecting alstroemeria plants, its genome is only partially available in public sequence databases. High throughput sequencing (HTS) of RNA from alstroemeria plants with symptoms of mosaic and streaking, collected in Lasso-Ecuador, indicated the presence of AlMV and lily symptomless virus. In this study, we aimed to assemble and characterize the complete genome sequence of AlMV. Reads from Illumina sequencing of ribosomal RNA-depleted total RNA were assembled into contigs that were mapped to the sunflower chlorotic mottle virus genome, revealing the 9774 [corrected] bp complete genome sequence of AlMV. Multiple sequence alignment of the AlMV polyprotein with close homologs allowed the identification of ten mature proteins P1, HC-Pro, P3, 6K1, CI, 6K2, NIa-VPg, NIa-Pro, NIb and CP. Furthermore, several potyvirus motifs were identified in the AlMV polyprotein including those related to potyvirus aphid transmission
    MeSH term(s) Alstroemeria/virology ; Base Sequence ; Genome, Viral ; Phylogeny ; Plant Diseases/virology ; Potyvirus/classification ; Potyvirus/genetics ; Potyvirus/isolation & purification ; Viral Proteins/genetics
    Chemical Substances Viral Proteins
    Language English
    Publishing date 2019-11-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 639496-6
    ISSN 1572-994X ; 0920-8569
    ISSN (online) 1572-994X
    ISSN 0920-8569
    DOI 10.1007/s11262-019-01712-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2397: 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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  3. Article ; Online: Targeting the 3CLpro and RdRp of SARS-CoV-2 with phytochemicals from medicinal plants of the Andean Region: molecular docking and molecular dynamics simulations.

    Mosquera-Yuqui, Francisco / Lopez-Guerra, Nicolas / Moncayo-Palacio, Eduardo A

    Journal of biomolecular structure & dynamics

    2020  Volume 40, Issue 5, Page(s) 2010–2023

    Abstract: Given the highly contagious nature of SARS-CoV-2, it has resulted in an unprecedented number of COVID-19 infected and dead people worldwide. Since there is currently no vaccine available in the market, the identification of potential drugs is urgently ... ...

    Abstract Given the highly contagious nature of SARS-CoV-2, it has resulted in an unprecedented number of COVID-19 infected and dead people worldwide. Since there is currently no vaccine available in the market, the identification of potential drugs is urgently needed to control the pandemic. In this study, 92 phytochemicals from medicinal plants growing in the Andean region were screened against SARS-CoV-2 3 C-like protease (3CLpro) and RNA-dependent RNA polymerase (RdRp) in their active sites through molecular docking. The cutoff values were set from the lowest docking scores of the FDA-approved drugs that are being used to treat COVID-19 patients (remdesivir, lopinavir, and ritonavir). Compounds with docking scores that were lower than cutoff values were validated by molecular dynamics simulation with GROMACS, using root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and intermolecular hydrogen bonds (H-bonds). Furthermore, binding free energies were estimated using the MM-PBSA method, and ADMET profiles of potential inhibitors were assessed. Computational analyses revealed that the interaction with hesperidin (theoretical binding energies, ΔG
    MeSH term(s) Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Phytochemicals/pharmacology ; Plants, Medicinal ; RNA-Dependent RNA Polymerase ; SARS-CoV-2 ; COVID-19 Drug Treatment
    Chemical Substances Phytochemicals ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
    Keywords covid19
    Language English
    Publishing date 2020-10-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1835716
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2093: 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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  4. Article: Phylodynamics and Coat Protein Analysis of Babaco Mosaic Virus in Ecuador.

    Mosquera-Yuqui, Francisco / Flores, Francisco J / Moncayo, Eduardo A / Garzón-Proaño, Brighitte A / Méndez, Miguel A / Guevara, Fiama E / Quito-Avila, Diego F / Viera, William / Cornejo-Franco, Juan F / Izquierdo, Andrés R / Noceda, Carlos

    Plants (Basel, Switzerland)

    2022  Volume 11, Issue 13

    Abstract: Babaco is a fast-growing herbaceous shrub with great commercial potential because of the organoleptic properties of its fruit. Babaco mosaic virus (BabMV) is a potexvirus in the ... ...

    Abstract Babaco is a fast-growing herbaceous shrub with great commercial potential because of the organoleptic properties of its fruit. Babaco mosaic virus (BabMV) is a potexvirus in the family
    Language English
    Publishing date 2022-06-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants11131646
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Targeting the 3CLpro and RdRp of SARS-CoV-2 with phytochemicals from medicinal plants of the Andean Region

    Mosquera-Yuqui, Francisco / Lopez-Guerra, Nicolas / Moncayo-Palacio, Eduardo A.

    Journal of Biomolecular Structure and Dynamics

    molecular docking and molecular dynamics simulations

    2020  , Page(s) 1–14

    Keywords Molecular Biology ; Structural Biology ; General Medicine ; covid19
    Language English
    Publisher Informa UK Limited
    Publishing country uk
    Document type Article ; Online
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1835716
    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 2093: 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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  6. Article: Targeting the 3CLpro and RdRp of SARS-CoV-2 with phytochemicals from medicinal plants of the Andean Region: molecular docking and molecular dynamics simulations

    Mosquera-Yuqui, Francisco / Lopez-Guerra, Nicolas / Moncayo-Palacio, Eduardo A

    J Biomol Struct Dyn

    Abstract: Given the highly contagious nature of SARS-CoV-2, it has resulted in an unprecedented number of COVID-19 infected and dead people worldwide. Since there is currently no vaccine available in the market, the identification of potential drugs is urgently ... ...

    Abstract Given the highly contagious nature of SARS-CoV-2, it has resulted in an unprecedented number of COVID-19 infected and dead people worldwide. Since there is currently no vaccine available in the market, the identification of potential drugs is urgently needed to control the pandemic. In this study, 92 phytochemicals from medicinal plants growing in the Andean region were screened against SARS-CoV-2 3 C-like protease (3CLpro) and RNA-dependent RNA polymerase (RdRp) in their active sites through molecular docking. The cutoff values were set from the lowest docking scores of the FDA-approved drugs that are being used to treat COVID-19 patients (remdesivir, lopinavir, and ritonavir). Compounds with docking scores that were lower than cutoff values were validated by molecular dynamics simulation with GROMACS, using root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and intermolecular hydrogen bonds (H-bonds). Furthermore, binding free energies were estimated using the MM-PBSA method, and ADMET profiles of potential inhibitors were assessed. Computational analyses revealed that the interaction with hesperidin (theoretical binding energies, ΔGbind = -15.18 kcal/mol to 3CLpro and ΔGbind = -9.46 kcal/mol to RdRp) remained stable in both enzymes, unveiling its remarkable potential as a possible multitarget antiviral agent to treat COVID-19. Importantly, lupinifolin with an estimated binding affinity to 3CLpro higher than hesperidin (ΔGbind = -20.93 kcal/mol) is also a potential inhibitor of the 3CLpro. These two compounds displayed suitable pharmacological and structural properties to be drug candidates, demonstrating to be worthy of further research. Communicated by Ramaswamy H. Sarma.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #883009
    Database COVID19

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  7. Article: Phylodynamics and Coat Protein Analysis of Babaco Mosaic Virus in Ecuador

    Mosquera-Yuqui, Francisco / Flores, Francisco J. / Moncayo, Eduardo A. / Garzón-Proaño, Brighitte A. / Méndez, Miguel A. / Guevara, Fiama E. / Quito-Avila, Diego F. / Viera, William / Cornejo-Franco, Juan F. / Izquierdo, Andrés R. / Noceda, Carlos

    Plants. 2022 June 22, v. 11, no. 13

    2022  

    Abstract: Babaco is a fast-growing herbaceous shrub with great commercial potential because of the organoleptic properties of its fruit. Babaco mosaic virus (BabMV) is a potexvirus in the family Alphaflexiviridae affecting babaco in all the provinces that produce ... ...

    Abstract Babaco is a fast-growing herbaceous shrub with great commercial potential because of the organoleptic properties of its fruit. Babaco mosaic virus (BabMV) is a potexvirus in the family Alphaflexiviridae affecting babaco in all the provinces that produce this crop in Ecuador. BabMV was recently described but it has been affecting babaco for decades and, since many potexviruses are serologically indistinguishable, it may have been previously misidentified as papaya mosaic virus. Based on the coat protein (CP) gene, we aimed to study the distribution and epidemiological patterns of BabMV in babaco and chamburo over the years and to model its three-dimensional structure. Sequences of the CP were obtained from thirty-six isolates from plants collected in the main babaco-producing provinces of Ecuador between 2016 and 2021. The evolution rate of BabMV was estimated at 1.21 × 10⁻³ nucleotide substitutions site⁻¹ year⁻¹ and a time of origin of the most recent common ancestor around 1958.80. From molecular dynamics simulations, compared to other proteins of BabMV—RDRP, TGB1, and Alkb domain—the CP exhibited a higher flexibility with the C and N terminals as the most flexible regions. The reconstructed viral distribution provides dispersion patterns which have implications for control approaches of BabMV.
    Keywords Papaya mosaic virus ; ancestry ; coat proteins ; evolution ; fruits ; genes ; molecular dynamics ; shrubs ; viruses ; Ecuador
    Language English
    Dates of publication 2022-0622
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants11131646
    Database NAL-Catalogue (AGRICOLA)

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