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  1. Article ; Online: PARP1pred

    Tassanee Lerksuthirat / Sermsiri Chitphuk / Wasana Stitchantrakul / Donniphat Dejsuphong / Aijaz Ahmad Malik / Chanin Nantasenamat

    EXCLI Journal : Experimental and Clinical Sciences, Vol 22, Pp 84-

    a web server for screening the bioactivity of inhibitors against DNA repair enzyme PARP-1

    2023  Volume 107

    Abstract: Cancer is the leading cause of death worldwide, resulting in the mortality of more than 10 million people in 2020, according to Global Cancer Statistics 2020. A potential cancer therapy involves targeting the DNA repair process by inhibiting PARP-1. In ... ...

    Abstract Cancer is the leading cause of death worldwide, resulting in the mortality of more than 10 million people in 2020, according to Global Cancer Statistics 2020. A potential cancer therapy involves targeting the DNA repair process by inhibiting PARP-1. In this study, classification models were constructed using a non-redundant set of 2018 PARP-1 inhibitors. Briefly, compounds were described by 12 fingerprint types and built using the random forest algorithm concomitant with various sampling approaches. Results indicated that PubChem with an oversampling approach yielded the best performance, with a Matthews correlation coefficient > 0.7 while also affording interpretable molecular features. Moreover, feature importance, as determined from the Gini index, revealed that the aromatic/cyclic/heterocyclic moiety, nitrogen-containing fingerprints, and the ether/aldehyde/alcohol moiety were important for PARP-1 inhibition. Finally, our predictive model was deployed as a web application called PARP1pred and is publicly available at https://parp1pred.streamlitapp.com, allowing users to predict the biological activity of query compounds using their SMILES notation as the input. It is anticipated that the model described herein will aid in the discovery of effective PARP-1 inhibitors.
    Keywords parp-1 ; dna repair ; machine learning ; qsar ; webserver ; cheminformatics ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282 ; Biology (General) ; QH301-705.5
    Subject code 540
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: TRIM29 is required for efficient recruitment of 53BP1 in response to DNA double‐strand breaks in vertebrate cells

    Rakkreat Wikiniyadhanee / Tassanee Lerksuthirat / Wasana Stitchantrakul / Sermsiri Chitphuk / Thanyachai Sura / Donniphat Dejsuphong

    FEBS Open Bio, Vol 10, Iss 10, Pp 2055-

    2020  Volume 2071

    Abstract: Tripartite motif‐containing protein 29 (TRIM29) is involved in DNA double‐strand break (DSB) repair. However, the specific roles of TRIM29 in DNA repair are not clearly understood. To investigate the involvement of TRIM29 in DNA DSB repair, we disrupted ... ...

    Abstract Tripartite motif‐containing protein 29 (TRIM29) is involved in DNA double‐strand break (DSB) repair. However, the specific roles of TRIM29 in DNA repair are not clearly understood. To investigate the involvement of TRIM29 in DNA DSB repair, we disrupted TRIM29 in DT40 cells by gene targeting with homologous recombination (HR). The roles of TRIM29 were investigated by clonogenic survival assays and immunofluorescence analyses. TRIM29 triallelic knockout (TRIM29−/−/−/+) cells were sensitive to etoposide, but resistant to camptothecin. Foci formation assays to assess DNA repair activities showed that the dissociation of etoposide‐induced phosphorylated H2A histone family member X (ɣ‐H2AX) foci was retained in TRIM29−/−/−/+ cells, and the formation of etoposide‐induced tumor suppressor p53‐binding protein 1 (53BP1) foci in TRIM29−/−/−/+ cells was slower compared with wild‐type (WT) cells. Interestingly, the kinetics of camptothecin‐induced RAD51 foci formation of TRIM29−/−/−/+ cells was higher than that of WT cells. These results indicate that TRIM29 is required for efficient recruitment of 53BP1 to facilitate the nonhomologous end‐joining (NHEJ) pathway and thereby suppress the HR pathway in response to DNA DSBs. TRIM29 regulates the choice of DNA DSB repair pathway by facilitating 53BP1 accumulation to promote NHEJ and may have potential for development into a therapeutic target to sensitize refractory cancers or as biomarker of personalized therapies.
    Keywords 53BP1 ; DT40 ; etoposide ; nonhomologous end joining ; TRIM29 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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