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  1. Article: Binding modes of potential anti-prion phytochemicals to PrP

    Neupane, Sandesh / Khadka, Jenisha / Rayamajhi, Sandesh / Pandey, Arti S

    Journal of Ayurveda and integrative medicine

    2023  Volume 14, Issue 4, Page(s) 100750

    Abstract: Background: Prion diseases involve the conversion of a normal, cell-surface glycoprotein (PrP: Objective: This study aims to identify potential anti-prion compounds from plant phytochemicals by integrating traditional ethnobotanical knowledge with ... ...

    Abstract Background: Prion diseases involve the conversion of a normal, cell-surface glycoprotein (PrP
    Objective: This study aims to identify potential anti-prion compounds from plant phytochemicals by integrating traditional ethnobotanical knowledge with modern in silico drug design approaches.
    Materials and methods: In the current study medicinal phytochemicals were docked with swapped and non-swapped crystal structures of PrP
    Results: Eleven new phytochemicals were identified based on their binding energies and pharmacokinetic properties. The binding sites and interactions of the known and new anti-prion compounds are similar, and differences in binding modes occur in structures with very subtle differences in side chain conformations. Binding of these compounds poses steric hindrance to neighbouring molecules. Residues shown to be associated with the inhibition of PrP
    Conclusion: Identified compounds might act as potent inhibitors of PrP
    Language English
    Publishing date 2023-07-17
    Publishing country United States
    Document type Journal Article
    ISSN 0975-9476
    ISSN 0975-9476
    DOI 10.1016/j.jaim.2023.100750
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Binding modes of potential anti-prion phytochemicals to PrPC structures in silico

    Neupane, Sandesh / Khadka, Jenisha / Rayamajhi, Sandesh / Pandey, Arti S.

    Journal of Ayurveda and Integrative Medicine. 2023 July, Aug., v. 14, no. 4 p.100750-

    2023  

    Abstract: Prion diseases involve the conversion of a normal, cell-surface glycoprotein (PrPC) into a misfolded pathogenic form (PrPSᶜ). One possible strategy to inhibit PrPSᶜ formation is to stabilize the native conformation of PrPC and interfere with the ... ...

    Abstract Prion diseases involve the conversion of a normal, cell-surface glycoprotein (PrPC) into a misfolded pathogenic form (PrPSᶜ). One possible strategy to inhibit PrPSᶜ formation is to stabilize the native conformation of PrPC and interfere with the conversion of PrPC to PrPSᶜ. Many compounds have been shown to inhibit the conversion process, however, no promising drugs have been identified to cure prion diseases. This study aims to identify potential anti-prion compounds from plant phytochemicals by integrating traditional ethnobotanical knowledge with modern in silico drug design approaches. In the current study medicinal phytochemicals were docked with swapped and non-swapped crystal structures of PrPCin silico to identify potential anti-prions to determine their binding modes and interactions. Eleven new phytochemicals were identified based on their binding energies and pharmacokinetic properties. The binding sites and interactions of the known and new anti-prion compounds are similar, and differences in binding modes occur in structures with very subtle differences in side chain conformations. Binding of these compounds poses steric hindrance to neighbouring molecules. Residues shown to be associated with the inhibition of PrPC to PrPSᶜ conversion form interactions with most of the compounds. Identified compounds might act as potent inhibitors of PrPC to PrPSᶜ conversion. These might be attractive candidates for the development of novel anti-prion therapy although further tests in vitro cell cultures and in vivo mouse models are needed to confirm these findings.
    Keywords Ayurvedic medicine ; computer simulation ; drug design ; ethnobotany ; glycoproteins ; pharmacokinetics ; phytochemicals ; prions ; therapeutics ; anti-Prion ; Terpenes ; Quinones ; Sterols
    Language English
    Dates of publication 2023-07
    Publishing place Elsevier B.V.
    Document type Article ; Online
    Note Pre-press version ; Use and reproduction
    ISSN 0975-9476
    DOI 10.1016/j.jaim.2023.100750
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Chromosome-level organization of the regulatory genome in the Drosophila nervous system.

    Mohana, Giriram / Dorier, Julien / Li, Xiao / Mouginot, Marion / Smith, Rebecca C / Malek, Héléna / Leleu, Marion / Rodriguez, Daniel / Khadka, Jenisha / Rosa, Patrycja / Cousin, Pascal / Iseli, Christian / Restrepo, Simon / Guex, Nicolas / McCabe, Brian D / Jankowski, Aleksander / Levine, Michael S / Gambetta, Maria Cristina

    Cell

    2023  Volume 186, Issue 18, Page(s) 3826–3844.e26

    Abstract: Previous studies have identified topologically associating domains (TADs) as basic units of genome organization. We present evidence of a previously unreported level of genome folding, where distant TAD pairs, megabases apart, interact to form meta- ... ...

    Abstract Previous studies have identified topologically associating domains (TADs) as basic units of genome organization. We present evidence of a previously unreported level of genome folding, where distant TAD pairs, megabases apart, interact to form meta-domains. Within meta-domains, gene promoters and structural intergenic elements present in distant TADs are specifically paired. The associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. These long-range associations occur in a large fraction of neurons but support transcription in only a subset of neurons. Meta-domains are formed by diverse transcription factors that are able to pair over long and flexible distances. We present evidence that two such factors, GAF and CTCF, play direct roles in this process. The relative simplicity of higher-order meta-domain interactions in Drosophila, compared with those previously described in mammals, allowed the demonstration that genomes can fold into highly specialized cell-type-specific scaffolds that enable megabase-scale regulatory associations.
    MeSH term(s) Animals ; Chromatin/genetics ; DNA Packaging ; Drosophila/genetics ; Mammals/genetics ; Neurogenesis ; Neurons ; Transcription Factors ; Drosophila Proteins ; Genome, Insect ; Gene Expression Regulation ; Chromosomes, Insect
    Chemical Substances Chromatin ; Trl protein, Drosophila ; CTCF protein, Drosophila ; Transcription Factors ; Drosophila Proteins
    Language English
    Publishing date 2023-08-02
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2023.07.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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