Unraveling Protein-Metabolite Interactions in Precision Nutrition: A Case Study of Blueberry-Derived Metabolites Using Advanced Computational Methods Article Swipe
Dipendra Bhandari
,
Adepu Kiran Kumar
,
Andriy Anishkin
,
Colin D. Kay
,
Erin E. Young
,
Kyle M. Baumbauer
,
Anuradha Ghosh
,
Sree V. Chintapalli
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.3390/metabo14080430
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.3390/metabo14080430
Metabolomics, the study of small-molecule metabolites within biological systems, has become a potent instrument for understanding cellular processes. Despite its profound insights into health, disease, and drug development, identifying the protein partners for metabolites, especially dietary phytochemicals, remains challenging. In the present study, we introduced an innovative in silico, structure-based target prediction approach to efficiently predict protein targets for metabolites. We analyzed 27 blood serum metabolites from nutrition intervention studies’ blueberry-rich diets, known for their health benefits, yet with elusive mechanisms of action. Our findings reveal that blueberry-derived metabolites predominantly interact with Carbonic Anhydrase (CA) family proteins, which are crucial in acid-base regulation, respiration, fluid balance, bone metabolism, neurotransmission, and specific aspects of cellular metabolism. Molecular docking showed that these metabolites bind to a common pocket on CA proteins, with binding energies ranging from −5.0 kcal/mol to −9.0 kcal/mol. Further molecular dynamics (MD) simulations confirmed the stable binding of metabolites near the Zn binding site, consistent with known compound interactions. These results highlight the potential health benefits of blueberry metabolites through interaction with CA proteins.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3390/metabo14080430
- https://www.mdpi.com/2218-1989/14/8/430/pdf?version=1723713129
- OA Status
- gold
- Cited By
- 3
- References
- 75
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4401324621
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Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4401324621Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3390/metabo14080430Digital Object Identifier
- Title
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Unraveling Protein-Metabolite Interactions in Precision Nutrition: A Case Study of Blueberry-Derived Metabolites Using Advanced Computational MethodsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-08-03Full publication date if available
- Authors
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Dipendra Bhandari, Adepu Kiran Kumar, Andriy Anishkin, Colin D. Kay, Erin E. Young, Kyle M. Baumbauer, Anuradha Ghosh, Sree V. ChintapalliList of authors in order
- Landing page
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https://doi.org/10.3390/metabo14080430Publisher landing page
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https://www.mdpi.com/2218-1989/14/8/430/pdf?version=1723713129Direct link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://www.mdpi.com/2218-1989/14/8/430/pdf?version=1723713129Direct OA link when available
- Concepts
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In silico, Metabolite, Metabolomics, Docking (animal), Biochemistry, Chemistry, Small molecule, Metabolism, Computational biology, Protein–protein interaction, Biology, Bioinformatics, Medicine, Gene, NursingTop concepts (fields/topics) attached by OpenAlex
- Cited by
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3Total citation count in OpenAlex
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2025: 2, 2024: 1Per-year citation counts (last 5 years)
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75Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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