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  1. Article: VSFlow: an open-source ligand-based virtual screening tool.

    Jung, Sascha / Vatheuer, Helge / Czodrowski, Paul

    Journal of cheminformatics

    2023  Volume 15, Issue 1, Page(s) 40

    Abstract: Ligand-based virtual screening is a widespread method in modern drug design. It allows for a rapid screening of large compound databases in order to identify similar structures. Here we report an open-source command line tool which includes a ... ...

    Abstract Ligand-based virtual screening is a widespread method in modern drug design. It allows for a rapid screening of large compound databases in order to identify similar structures. Here we report an open-source command line tool which includes a substructure-, fingerprint- and shape-based virtual screening. Most of the implemented features fully rely on the RDKit cheminformatics framework. VSFlow accepts a wide range of input file formats and is highly customizable. Additionally, a quick visualization of the screening results as pdf and/or pymol file is supported.
    Language English
    Publishing date 2023-03-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 2486539-4
    ISSN 1758-2946
    ISSN 1758-2946
    DOI 10.1186/s13321-023-00703-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Targeting oncogenic KRasG13C with nucleotide-based covalent inhibitors.

    Goebel, Lisa / Kirschner, Tonia / Koska, Sandra / Rai, Amrita / Janning, Petra / Maffini, Stefano / Vatheuer, Helge / Czodrowski, Paul / Goody, Roger S / Müller, Matthias P / Rauh, Daniel

    eLife

    2023  Volume 12

    Abstract: Mutations within Ras proteins represent major drivers in human cancer. In this study, we report the structure-based design, synthesis, as well as biochemical and cellular evaluation of nucleotide-based covalent inhibitors for KRasG13C, an important ... ...

    Abstract Mutations within Ras proteins represent major drivers in human cancer. In this study, we report the structure-based design, synthesis, as well as biochemical and cellular evaluation of nucleotide-based covalent inhibitors for KRasG13C, an important oncogenic mutant of Ras that has not been successfully addressed in the past. Mass spectrometry experiments and kinetic studies reveal promising molecular properties of these covalent inhibitors, and X-ray crystallographic analysis has yielded the first reported crystal structures of KRasG13C covalently locked with these GDP analogues. Importantly, KRasG13C covalently modified with these inhibitors can no longer undergo SOS-catalysed nucleotide exchange. As a final proof-of-concept, we show that in contrast to KRasG13C, the covalently locked protein is unable to induce oncogenic signalling in cells, further highlighting the possibility of using nucleotide-based inhibitors with covalent warheads in KRasG13C-driven cancer.
    MeSH term(s) Humans ; Nucleotides ; Kinetics ; ras Proteins/genetics ; Signal Transduction ; Neoplasms/drug therapy ; Neoplasms/genetics
    Chemical Substances Nucleotides ; ras Proteins (EC 3.6.5.2)
    Language English
    Publishing date 2023-03-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.82184
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Fragtory: Pharmacophore-Focused Design, Synthesis, and Evaluation of an sp

    Bührmann, Mike / Kallepu, Shivakrishna / Warmuth, Jonas D / Wiese, Jan N / Ehrt, Christiane / Vatheuer, Helge / Hiller, Wolf / Seitz, Carina / Levy, Laura / Czodrowski, Paul / Sievers, Sonja / Müller, Matthias P / Rauh, Daniel

    Journal of medicinal chemistry

    2023  Volume 66, Issue 9, Page(s) 6297–6314

    Abstract: Fragment-based drug discovery has played an important role in medicinal chemistry and pharmaceutical research. Despite numerous demonstrated successes, the limited diversity and overrepresentation of planar, ... ...

    Abstract Fragment-based drug discovery has played an important role in medicinal chemistry and pharmaceutical research. Despite numerous demonstrated successes, the limited diversity and overrepresentation of planar, sp
    MeSH term(s) Pharmacophore ; Drug Discovery ; Proteins ; Protein Binding ; Ligands ; Drug Design
    Chemical Substances Proteins ; Ligands
    Language English
    Publishing date 2023-05-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.3c00187
    Database MEDical Literature Analysis and Retrieval System OnLINE

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