Abstract
This study aims to systematically investigate the multi-target mechanisms of cobalamin in the treatment of ischemic stroke using network pharmacology and molecular docking approaches. We screened databases to identify the targets of cobalamin and performed intersected with with ischemic stroke-related targets to construct a “drug-target-disease” interaction network. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to identify key biological processes and signaling pathways. Additionally, molecular docking simulations were performed to assess the binding affinity between cobalamin and hub proteins. Molecular dynamics (MD) simulations were used to assess the stability of the protein–ligand complexes over a 500 ns simulation period. Additionally, ADME (Absorption, Distribution, Metabolism, Excretion) and blood–brain barrier (BBB) permeability predictions were made using ADMETlab 3.0 and admetSAR 3.0. A total of 95 therapeutic targets of cobalamin for ischemic stroke were identified. Network analysis and molecular docking highlighted eight core targets—ALB, TIMP1, PLG, FN1, AGT, SERPINE1, APOE, and SPP1—with high binding affinities to cobalamin. GO analysis suggested that cobalamin regulates inflammatory responses, post-translational modifications, complement binding, and lipoprotein particle binding. KEGG analysis identified complement and coagulation cascades, the PI3K/AKT pathway, and inflammation-related signaling as central to its therapeutic effects. Molecular docking showed strong binding to ALB and TIMP1, which was further confirmed by MD simulations, with minimal conformational changes. The PLG-cobalamin complex exhibited more fluctuations. ADME analysis revealed low passive permeability, particularly across the blood–brain barrier, but moderate distribution and high plasma protein binding. This study provides evidence that cobalamin may offer neuroprotective effects in ischemic stroke by interacting with key target proteins involved in coagulation, inflammation, and lipid metabolism. The findings highlight the potential of cobalamin as a therapeutic agent, although its limited ability to cross the blood–brain barrier may restrict its oral use. Further experimental validation and development of suitable delivery methods are needed to fully realize cobalamin’s potential in stroke therapy.
Data availability
All data analysed during this study are included in the websites mentioned above. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository71 with the dataset identifier PXD062264. The data not published within this article are available from the corresponding author on reasonable request.
Abbreviations
- WHO:
-
World Health Organization
- rt-PA:
-
Recombinant tissue plasminogen activator
- ALB:
-
Albumin
- TIMP1:
-
Tissue inhibitor of metalloproteinases 1
- PLG:
-
Plasminogen
- FN1:
-
Fibronectin 1
- AGT:
-
Angiotensinogen
- SERPINE1:
-
Serpin family E member 1
- APOE:
-
Apolipoprotein E
- SPP1:
-
Secreted Phosphoprotein 1
- PPI:
-
Protein-protein interaction
- GO:
-
Gene ontology
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- FDR:
-
False discovery rate
- DAVID:
-
Database for Annotation, Visualization, and Integrated Discovery
- STRING:
-
Search Tool for the Retrieval of Interacting Genes
- MCC:
-
Maximal clique centrality
- BP:
-
Biological process
- CC:
-
Cellular component
- MF:
-
Molecular function
- MCODE:
-
Molecular Complex Detection
- CytoNCA:
-
Cytoscape Network Centrality Analysis
- VWF:
-
Von Willebrand factor
- CRP:
-
C-reactive protein
- PME:
-
Particle Mesh Ewald
- NVT:
-
Number of particles (N), Volume (V), and Temperature (T) ensemble
- NPT:
-
Number of particles (N), Pressure (P), and Temperature (T) ensemble
- ADMET:
-
Absorption, Distribution, Metabolism, Excretion, and Toxicity
- BBB:
-
Blood–brain barrier
- TPSA:
-
Topological polar surface area
- HIA:
-
Human intestinal absorption
- CGenFF:
-
CHARMM General Force Field
- RMSD:
-
Root mean square deviation
- RMSF:
-
Root mean square fluctuation
- Rg:
-
Radius of gyration
- SASA:
-
Solvent accessible surface area
- MD:
-
Molecular dynamics
- PDB:
-
Protein Data Bank
- MCAO:
-
Middle Cerebral Artery Occlusion
- tHcy:
-
Total homocysteine
- hs-CRP:
-
High-sensitivity C-reactive protein
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Acknowledgements
We thank all investigators contributed to this article. We also give thanks to all patients enrolled in this study.
Funding
This work was supported by the National Natural Science Foundation of China (Grant No. 82171456) awarded to Qin Yang and the 2023 Research Planning Project of the Sichuan Provincial Psychological Society (No. SCSXLXH2023034) awarded to Pingping Liu.
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Q.Y. contributed to the study conception and design and provided critical revisions and editorial input for the manuscript. L. Z. and Y.C. jointly drafted the initial version of the manuscript and developed the primary tables and figures. H.W. and J.W. performed the data analysis. F.X. and P.L. were responsible for data acquisition from the relevant datasets. All authors were involved in the study design, contributed to manuscript revisions, and approved the final version of the manuscript.
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Zhou, L., Cai, Y., Wu, H. et al. Neuroprotective mechanisms of cobalamin in ischemic stroke insights from network pharmacology and molecular simulations. Sci Rep (2026). https://doi.org/10.1038/s41598-026-41564-6
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DOI: https://doi.org/10.1038/s41598-026-41564-6