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  1. Article ; Online: Searching possible SARS-CoV-2 main protease inhibitors in constituents from herbal medicines using

    Rasul, Hezha O / Thomas, Noel Vinay / Ghafour, Dlzar D / Aziz, Bakhtyar K / Salgado M, Guillermo / Mendoza-Huizar, L H / Candia, Lorena Gerli

    Journal of biomolecular structure & dynamics

    2023  Volume 42, Issue 8, Page(s) 4234–4248

    Abstract: The largest threat to civilization since the Second World War is the spread of the new coronavirus disease (COVID-19). Therefore, there is an urgent need for innovative therapeutic medicines to treat COVID-19. Reusing bio-actives is a workable and ... ...

    Abstract The largest threat to civilization since the Second World War is the spread of the new coronavirus disease (COVID-19). Therefore, there is an urgent need for innovative therapeutic medicines to treat COVID-19. Reusing bio-actives is a workable and efficient strategy in the battle against new epidemics because the process of developing new drugs is time-consuming. This research aimed to identify which herbal remedies had the highest affinity for the receptor and assess a variety of them for potential targets to suppress the SARS-CoV-2 M
    MeSH term(s) Molecular Docking Simulation ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; Molecular Dynamics Simulation ; Humans ; Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/chemistry ; Coronavirus 3C Proteases/metabolism ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; COVID-19 Drug Treatment ; Plants, Medicinal/chemistry ; Herbal Medicine ; Protein Binding ; COVID-19/virology ; Computer Simulation ; Binding Sites ; Pentacyclic Triterpenes/chemistry ; Pentacyclic Triterpenes/pharmacology ; Lupanes
    Chemical Substances Coronavirus 3C Proteases (EC 3.4.22.28) ; Protease Inhibitors ; Antiviral Agents ; Pentacyclic Triterpenes ; lupeol (O268W13H3O) ; Lupanes
    Language English
    Publishing date 2023-06-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2220040
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Identification of natural diterpenes isolated from Azorella species targeting dispersin B using in silico approaches.

    Rasul, Hezha O / Sabir, Dana Khdr / Aziz, Bakhtyar K / Guillermo Salgado, M / Mendoza-Huizar, L H / Belhassan, Assia / Candia, Lorena Gerli / Villada, Wilson Cardona / Thomas, Noel Vinay / Ghafour, Dlzar D

    Journal of molecular modeling

    2023  Volume 29, Issue 6, Page(s) 182

    Abstract: Context: A bacterial biofilm is a cluster of bacterial cells embedded in a self-produced matrix of extracellular polymeric substances such as DNA, proteins, and polysaccharides. Several diseases have been reported to cause by bacterial biofilms, and ... ...

    Abstract Context: A bacterial biofilm is a cluster of bacterial cells embedded in a self-produced matrix of extracellular polymeric substances such as DNA, proteins, and polysaccharides. Several diseases have been reported to cause by bacterial biofilms, and difficulties in treating these infections are of concern. This work aimed to identify the inhibitor with the highest binding affinity for the receptor protein by screening various inhibitors obtained from Azorella species for a potential target to inhibit dispersin B. This work shows that azorellolide has the highest binding affinity (- 8.2 kcal/mol) among the compounds tested, followed by dyhydroazorellolide, mulinone A, and 7-acetoxy-mulin-9,12-diene which all had a binding affinity of - 8.0 kcal/mol. To the best of our knowledge, this is the first study to evaluate and contrast several diterpene compounds as antibacterial biofilm chemicals.
    Methods: Here, molecular modelling techniques tested 49 diterpene compounds of Azorella and six FDA-approved antibiotics medicines for antibiofilm activity. Since protein-like interactions are crucial in drug discovery, AutoDock Vina was initially employed to carry out structure-based virtual screening. The drug-likeness and ADMET properties of the chosen compounds were examined to assess the antibiofilm activity further. Lipinski's rule of five was then applied to determine the antibiofilm activity. Then, molecular electrostatic potential was used to determine the relative polarity of a molecule using the Gaussian 09 package and GaussView 5.08. Following three replica molecular dynamic simulations (using the Schrodinger program, Desmond 2019-4 package) that each lasted 100 ns on the promising candidates, binding free energy was estimated using MM-GBSA. Structural visualisation was used to test the binding affinity of each compound to the crystal structure of dispersin B protein (PDB: 1YHT), a well-known antibiofilm compound.
    MeSH term(s) Molecular Docking Simulation ; Apiaceae/chemistry ; Molecular Dynamics Simulation ; Anti-Bacterial Agents/pharmacology ; Diterpenes/pharmacology ; Diterpenes/chemistry
    Chemical Substances Anti-Bacterial Agents ; Diterpenes
    Language English
    Publishing date 2023-05-20
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1284729-X
    ISSN 0948-5023 ; 1610-2940
    ISSN (online) 0948-5023
    ISSN 1610-2940
    DOI 10.1007/s00894-023-05592-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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