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

Humans Polymorphism, Single Nucleotide Receptors, Cytokine / metabolism Cytokines / metabolism Databases, Protein Phenotype

Journal

Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179

Informations de publication

Date de publication:
24 May 2024
Historique:
received: 23 05 2023
accepted: 03 05 2024
medline: 25 5 2024
pubmed: 25 5 2024
entrez: 24 5 2024
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s42003-024-06289-0 PMID: 38789577
pubmed: 38789577
doi: 10.1038/s42003-024-06289-0
pii: 10.1038/s42003-024-06289-0
doi:

Substances chimiques

Receptors, Cytokine 0
Cytokines 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

630

Informations de copyright

© 2024. The Author(s).

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Auteurs

Lu Wang (L)

Bioinformatics Center, Hunan University College of Biology, Changsha, Hunan, 410082, China.
Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510100, China.
Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, Guangzhou Key Laboratory of Cardiac Pathogenesis and Prevention, Guangzhou, Guangdong, 510100, China.
ORCID: 0000-0002-6288-8880

Fang Sun (F)

Bioinformatics Center, Hunan University College of Biology, Changsha, Hunan, 410082, China.
Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, 410006, China.

Qianying Li (Q)

Bioinformatics Center, Hunan University College of Biology, Changsha, Hunan, 410082, China.

Haojie Ma (H)

Bioinformatics Center, Hunan University College of Biology, Changsha, Hunan, 410082, China.

Juanhong Zhong (J)

Bioinformatics Center, Hunan University College of Biology, Changsha, Hunan, 410082, China.

Huihui Zhang (H)

Bioinformatics Center, Hunan University College of Biology, Changsha, Hunan, 410082, China.
ORCID: 0000-0001-8173-2825

Siyi Cheng (S)

Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510100, China.
Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, Guangzhou Key Laboratory of Cardiac Pathogenesis and Prevention, Guangzhou, Guangdong, 510100, China.

Hao Wu (H)

Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510100, China.
Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, Guangzhou Key Laboratory of Cardiac Pathogenesis and Prevention, Guangzhou, Guangdong, 510100, China.

Yanmin Zhao (Y)

Bioinformatics Center, Hunan University College of Biology, Changsha, Hunan, 410082, China.

Nasui Wang (N)

Division of Endocrinology and Metabolism, The First Affiliated Hospital of Shantou University Medical College, No. 57 Changping Road, Shantou, 515041, China.
ORCID: 0000-0002-1332-187X

Zhongqiu Xie (Z)

Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA.
ORCID: 0000-0002-2869-7669

Mingyi Zhao (M)

Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, 410006, China. mingyi@csu.edu.cn.

Ping Zhu (P)

Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510100, China. tanganqier@163.com.
Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, Guangzhou Key Laboratory of Cardiac Pathogenesis and Prevention, Guangzhou, Guangdong, 510100, China. tanganqier@163.com.

Heping Zheng (H)

Bioinformatics Center, Hunan University College of Biology, Changsha, Hunan, 410082, China. hz5p@hnu.edu.cn.
ORCID: 0000-0002-6961-4938

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › CytoSIP: an annotated structural atlas for...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › CytoSIP: an annotated structural atlas for...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines membranaires › Récepteurs de surface cellulaire › Récepteurs immunologiques › Récepteurs aux cytokines › CytoSIP: an annotated structural atlas for...
questionsmedicales.fr › Facteurs biologiques › Protéines et peptides de signalisation intercellulaire › Cytokines › CytoSIP: an annotated structural atlas for...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › Bases de données de protéines › CytoSIP: an annotated structural atlas for...
questionsmedicales.fr › Phénomènes génétiques › Phénotype › CytoSIP: an annotated structural atlas for...