CytoSIP: an annotated structural atlas for interactions involving cytokines or cytokine receptors.

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  • Additional Information
    • Source:
      Publisher: Nature Publishing Group UK Country of Publication: England NLM ID: 101719179 Publication Model: Electronic Cited Medium: Internet ISSN: 2399-3642 (Electronic) Linking ISSN: 23993642 NLM ISO Abbreviation: Commun Biol Subsets: MEDLINE
    • Publication Information:
      Original Publication: London, United Kingdom : Nature Publishing Group UK, [2018]-
    • Subject Terms:
      Polymorphism, Single Nucleotide* ; Receptors, Cytokine*/metabolism ; Receptors, Cytokine*/chemistry ; Receptors, Cytokine*/genetics ; Cytokines*/metabolism ; Cytokines*/genetics ; Cytokines*/chemistry; Humans ; Databases, Protein ; Phenotype
    • Abstract:
      Therapeutic agents targeting cytokine-cytokine receptor (CK-CKR) interactions lead to the disruption in cellular signaling and are effective in treating many diseases including tumors. However, a lack of universal and quick access to annotated structural surface regions on CK/CKR has limited the progress of a structure-driven approach in developing targeted macromolecular drugs and precision medicine therapeutics. Herein we develop CytoSIP (Single nucleotide polymorphisms (SNPs), Interface, and Phenotype), a rich internet application based on a database of atomic interactions around hotspots in experimentally determined CK/CKR structural complexes. CytoSIP contains: (1) SNPs on CK/CKR; (2) interactions involving CK/CKR domains, including CK/CKR interfaces, oligomeric interfaces, epitopes, or other drug targeting surfaces; and (3) diseases and phenotypes associated with CK/CKR or SNPs. The database framework introduces a unique tri-level SIP data model to bridge genetic variants (atomic level) to disease phenotypes (organism level) using protein structure (complexes) as an underlying framework (molecule level). Customized screening tools are implemented to retrieve relevant CK/CKR subset, which reduces the time and resources needed to interrogate large datasets involving CK/CKR surface hotspots and associated pathologies. CytoSIP portal is publicly accessible at https://CytoSIP.biocloud.top , facilitating the panoramic investigation of the context-dependent crosstalk between CK/CKR and the development of targeted therapeutic agents.
      (© 2024. The Author(s).)
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    • Accession Number:
      0 (Receptors, Cytokine)
      0 (Cytokines)
    • Publication Date:
      Date Created: 20240524 Date Completed: 20240524 Latest Revision: 20240527
    • Publication Date:
      20240527
    • Accession Number:
      PMC11126726
    • Accession Number:
      10.1038/s42003-024-06289-0
    • Accession Number:
      38789577