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  1. Article: Effects of Dimerization, Dendrimerization, and Chirality in p-BthTX-I Peptide Analogs on the Antibacterial Activity and Enzymatic Inhibition of the SARS-CoV-2 PL

    Bitencourt, Natália Vitória / Righetto, Gabriela Marinho / Camargo, Ilana Lopes Baratella Cunha / de Godoy, Mariana Ortiz / Guido, Rafael Victorio Carvalho / Oliva, Glaucius / Santos-Filho, Norival Alves / Cilli, Eduardo Maffud

    Pharmaceutics

    2023  Volume 15, Issue 2

    Abstract: Recent studies have shown that the peptide [des- ... ...

    Abstract Recent studies have shown that the peptide [des-Cys
    Language English
    Publishing date 2023-01-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527217-2
    ISSN 1999-4923
    ISSN 1999-4923
    DOI 10.3390/pharmaceutics15020436
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.

    Noske, Gabriela Dias / de Souza Silva, Ellen / de Godoy, Mariana Ortiz / Dolci, Isabela / Fernandes, Rafaela Sachetto / Guido, Rafael Victório Carvalho / Sjö, Peter / Oliva, Glaucius / Godoy, Andre Schutzer

    The Journal of biological chemistry

    2023  Volume 299, Issue 3, Page(s) 103004

    Abstract: SARS-CoV-2 is the causative agent of COVID-19. The main viral protease ( ... ...

    Abstract SARS-CoV-2 is the causative agent of COVID-19. The main viral protease (M
    MeSH term(s) Humans ; COVID-19/genetics ; SARS-CoV-2/genetics ; Antiviral Agents/pharmacology ; Lactams ; Leucine ; Nitriles ; Protease Inhibitors/pharmacology
    Chemical Substances 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; ensitrelvir (PX665RAA3H) ; Antiviral Agents ; Lactams ; Leucine (GMW67QNF9C) ; Nitriles ; Protease Inhibitors
    Language English
    Publishing date 2023-02-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2023.103004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Enzymatic versatility and thermostability of a new aryl-alcohol oxidase from Thermothelomyces thermophilus M77.

    Kadowaki, Marco Antonio Seiki / Higasi, Paula Miwa Rabelo / de Godoy, Mariana Ortiz / de Araújo, Evandro Ares / Godoy, Andre Schutzer / Prade, Rolf Alexander / Polikarpov, Igor

    Biochimica et biophysica acta. General subjects

    2020  Volume 1864, Issue 10, Page(s) 129681

    Abstract: Background Fungal aryl-alcohol oxidases (AAOx) are extracellular flavoenzymes that belong to glucose-methanol-choline oxidoreductase family and are responsible for the selective conversion of primary aromatic alcohols into aldehydes and aromatic ... ...

    Abstract Background Fungal aryl-alcohol oxidases (AAOx) are extracellular flavoenzymes that belong to glucose-methanol-choline oxidoreductase family and are responsible for the selective conversion of primary aromatic alcohols into aldehydes and aromatic aldehydes to their corresponding acids, with concomitant production of hydrogen peroxide (H
    MeSH term(s) Alcohol Oxidoreductases/chemistry ; Alcohol Oxidoreductases/metabolism ; Ascomycota/chemistry ; Ascomycota/enzymology ; Ascomycota/metabolism ; Binding Sites ; Calcium/metabolism ; Crystallography, X-Ray ; Enzyme Stability ; Hydrogen Peroxide/metabolism ; Models, Molecular ; Protein Conformation ; Substrate Specificity ; Temperature
    Chemical Substances Hydrogen Peroxide (BBX060AN9V) ; Alcohol Oxidoreductases (EC 1.1.-) ; aryl-alcohol oxidase (EC 1.1.3.7) ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2020-07-10
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 60-7
    ISSN 1872-8006 ; 1879-2596 ; 1879-260X ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    ISSN (online) 1872-8006 ; 1879-2596 ; 1879-260X ; 1879-2642 ; 1879-2618 ; 1879-2650
    ISSN 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    DOI 10.1016/j.bbagen.2020.129681
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  4. Article ; Online: A fast and easy strategy for lytic polysaccharide monooxygenase-cleavable His

    Kadowaki, Marco Antonio Seiki / Magri, Silvia / de Godoy, Mariana Ortiz / Monclaro, Antonielle Vieira / Zarattini, Marco / Cannella, David

    Enzyme and microbial technology

    2020  Volume 143, Page(s) 109704

    Abstract: Lytic polysaccharide monooxygenases (LPMOs) are industrially important enzymes able to enhance the enzymatic lignocellulose saccharification in synergism with classical glycoside hydrolases. Fungal LPMOs have been classified as AA9, AA11, and AA13-16 ... ...

    Abstract Lytic polysaccharide monooxygenases (LPMOs) are industrially important enzymes able to enhance the enzymatic lignocellulose saccharification in synergism with classical glycoside hydrolases. Fungal LPMOs have been classified as AA9, AA11, and AA13-16 families showing a diverse specificity for substrates such as soluble and insoluble beta-glucans, chitin, starch, and xylan, besides cellulose. These enzymes are still not fully characterized, and for example this is testify by their mechanism of oxidation regularly reviewed multiple times in the last decade. Noteworthy is that despite the extremely large abundance in the entire Tree of Life, our structural and functional knowledge is based on a restricted pool of LPMO, and probably one of the main reason reside in the challenging posed by their heterologous expression. Notably, the lack of a simple cloning protocol that could be universally applied to LPMO, hinders the conversion of the ever-increasing available genomic information to actual new enzymes. Here, we provide an easy and fast protocol for cloning, expression, and purification of active LPMOs in the following architecture: natural signal peptide, LPMO enzyme, TEV protease site, and His
    MeSH term(s) Cloning, Molecular ; Fungal Proteins/genetics ; Humans ; Mixed Function Oxygenases/genetics ; Polysaccharides ; Xylans
    Chemical Substances Fungal Proteins ; Polysaccharides ; Xylans ; Mixed Function Oxygenases (EC 1.-)
    Language English
    Publishing date 2020-11-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 423729-8
    ISSN 1879-0909 ; 0141-0229
    ISSN (online) 1879-0909
    ISSN 0141-0229
    DOI 10.1016/j.enzmictec.2020.109704
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  5. Article: Enzymatic versatility and thermostability of a new aryl-alcohol oxidase from Thermothelomyces thermophilus M77

    Kadowaki, Marco Antonio Seiki / Higasi, Paula Miwa Rabelo / de Godoy, Mariana Ortiz / de Araújo, Evandro Ares / Godoy, Andre Schutzer / Prade, Rolf Alexander / Polikarpov, Igor

    Biochimica et biophysica acta. 2020 Oct., v. 1864, no. 10

    2020  

    Abstract: BackgroundFungal aryl-alcohol oxidases (AAOx) are extracellular flavoenzymes that belong to glucose-methanol-choline oxidoreductase family and are responsible for the selective conversion of primary aromatic alcohols into aldehydes and aromatic aldehydes ...

    Abstract BackgroundFungal aryl-alcohol oxidases (AAOx) are extracellular flavoenzymes that belong to glucose-methanol-choline oxidoreductase family and are responsible for the selective conversion of primary aromatic alcohols into aldehydes and aromatic aldehydes to their corresponding acids, with concomitant production of hydrogen peroxide (H₂O₂) as by-product. The H₂O₂ can be provided to lignin degradation pathway, a biotechnological property explored in biofuel production. In the thermophilic fungus Thermothelomyces thermophilus (formerly Myceliophthora thermophila), just one AAOx was identified in the exo-proteome.MethodsThe glycosylated and non-refolded crystal structure of an AAOx from T. thermophilus at 2.6 Å resolution was elucidated by X-ray crystallography combined with small-angle X-ray scattering (SAXS) studies. Moreover, biochemical analyses were carried out to shed light on enzyme substrate specificity and thermostability.ResultsThis flavoenzyme harbors a flavin adenine dinucleotide as a cofactor and is able to oxidize aromatic substrates and 5-HMF. Our results also show that the enzyme has similar oxidation rates for bulky or simple aromatic substrates such as cinnamyl and veratryl alcohols. Moreover, the crystal structure of MtAAOx reveals an open active site, which might explain observed specificity of the enzyme.ConclusionsMtAAOx shows previously undescribed structural differences such as a fully accessible catalytic tunnel, heavy glycosylation and Ca²⁺ binding site providing evidences for thermostability and activity of the enzymes from AA3_2 subfamily.General significanceStructural and biochemical analyses of MtAAOx could be important for comprehension of aryl-alcohol oxidases structure-function relationships and provide additional molecular tools to be used in future biotechnological applications.
    Keywords Myceliophthora thermophila ; X-ray diffraction ; acids ; active sites ; alcohols ; aldehydes ; aryl-alcohol oxidase ; binding sites ; calcium ; catalytic activity ; crystal structure ; enzyme activity ; enzyme substrates ; flavin-adenine dinucleotide ; fuel production ; glycosylation ; hydrogen peroxide ; lignin ; oxidation ; small-angle X-ray scattering ; structure-activity relationships ; substrate specificity ; thermal stability ; thermophilic fungi
    Language English
    Dates of publication 2020-10
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 840755-1
    ISSN 0304-4165
    ISSN 0304-4165
    DOI 10.1016/j.bbagen.2020.129681
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  6. Article ; Online: LPMO-oxidized cellulose oligosaccharides evoke immunity in Arabidopsis conferring resistance towards necrotrophic fungus B. cinerea.

    Zarattini, Marco / Corso, Massimiliano / Kadowaki, Marco Antonio / Monclaro, Antonielle / Magri, Silvia / Milanese, Irma / Jolivet, Sylvie / de Godoy, Mariana Ortiz / Hermans, Christian / Fagard, Mathilde / Cannella, David

    Communications biology

    2021  Volume 4, Issue 1, Page(s) 727

    Abstract: Lytic Polysaccharide Monooxygenases (LPMOs) are powerful redox enzymes able to oxidatively cleave recalcitrant polysaccharides. Widely conserved across biological kingdoms, LPMOs of the AA9 family are deployed by phytopathogens to deconstruct cellulose ... ...

    Abstract Lytic Polysaccharide Monooxygenases (LPMOs) are powerful redox enzymes able to oxidatively cleave recalcitrant polysaccharides. Widely conserved across biological kingdoms, LPMOs of the AA9 family are deployed by phytopathogens to deconstruct cellulose polymers. In response, plants have evolved sophisticated mechanisms to sense cell wall damage and thus self-triggering Damage Triggered Immunity responses. Here, we show that Arabidopsis plants exposed to LPMO products triggered the innate immunity ultimately leading to increased resistance to the necrotrophic fungus Botrytis cinerea. We demonstrated that plants undergo a deep transcriptional reprogramming upon elicitation with AA9 derived cellulose- or cello-oligosaccharides (AA9_COS). To decipher the specific effects of native and oxidized LPMO-generated AA9_COS, a pairwise comparison with cellobiose, the smallest non-oxidized unit constituting cellulose, is presented. Moreover, we identified two leucine-rich repeat receptor-like kinases, namely STRESS INDUCED FACTOR 2 and 4, playing a crucial role in signaling the AA9_COS-dependent responses such as camalexin production. Furthermore, increased levels of ethylene, jasmonic and salicylic acid hormones, along with deposition of callose in the cell wall was observed. Collectively, our data reveal that LPMOs might play a crucial role in plant-pathogen interactions.
    MeSH term(s) Arabidopsis/immunology ; Arabidopsis/metabolism ; Arabidopsis/microbiology ; Botrytis/immunology ; Cellulose/metabolism ; Disease Resistance ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Mixed Function Oxygenases/metabolism ; Mixed Function Oxygenases/physiology ; Oligosaccharides/metabolism ; Oligosaccharides/physiology ; Plant Diseases/immunology ; Plant Diseases/microbiology ; Sordariales/metabolism
    Chemical Substances Oligosaccharides ; Cellulose (9004-34-6) ; Mixed Function Oxygenases (EC 1.-)
    Language English
    Publishing date 2021-06-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-021-02226-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Structural basis of nirmatrelvir and ensitrelvir resistance profiles against SARS-CoV-2 Main Protease naturally occurring polymorphisms

    Noske, Gabriela Dias / de Souza Silva, Ellen / de Godoy, Mariana Ortiz / Dolci, Isabela / Fernandes, Rafaela Sachetto / Guido, Rafael Victório Carvalho / Sjö, Peter / Oliva, Glaucius / Godoy, Andre Schutzer

    bioRxiv

    Abstract: SARS-CoV-2 is the causative agent of COVID-19. Mpro is the main viral protease, with a critical role in replication and, therefore, an attractive target for antiviral drug discovery. The clinically approved drug nirmatrelvir from Pfizer, and the clinical ...

    Abstract SARS-CoV-2 is the causative agent of COVID-19. Mpro is the main viral protease, with a critical role in replication and, therefore, an attractive target for antiviral drug discovery. The clinically approved drug nirmatrelvir from Pfizer, and the clinical candidate ensitrelvir from Shionogi Pharmaceuticals had so far showed great potential for treatment of viral infections. Despite the importance of new therapeutics, the broad use of antivirals is often associated with mutation selection and resistance generation. Herein, we characterized 14 naturally occurring polymorphisms that are already in circulation and are within the radius of action of these two antivirals. Nirmatrelvir retained most of its in vitro activity against most polymorphism tested, while mutants G143S and Q189K were associated with higher resistance. For ensitrelvir, higher resistance was observed for polymorphisms M49I, G143S and R188S, but not for Q189K, suggesting a distinct resistance profile difference between the two inhibitors. The crystal structures of selected polymorphism reveal the structural basis for resistance generation. Our data will assist the monitoring of potential resistant strains, support the design of combined therapy to avoid resistance, as well as assist the development of a next generation of Mpro inhibitors.
    Keywords covid19
    Language English
    Publishing date 2022-09-01
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2022.08.31.506107
    Database COVID19

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