Connectivity Map-based drug repositioning evaluation of verapamil as a therapeutic agent for Parkinson's disease

doi:10.12092/j.issn.1009-2501.2026.01.002

Abstract

Abstract:

AIM: To screen small molecule compounds that modulate the expression of transcription factors related to hub genes in the pathogenesis of Parkinson's disease (PD). METHODS: Gene expression profiling data from PD patients were analyzed to find the hub genes for PD pathogenesis and the transcription factors that regulate their expression. Connectivity Map (CMap) was used to screen for potential small molecule drugs that could modulate transcription factors. 6-hydroxydopamine (6-OHDA)-injured PC12 cell and 6-OHDA-induced PD mice model were used to evaluate the potential role of the small molecule for modulating transcription factor expression and treating PD. RESULTS: The predicted results showed Verapamil (Ver) as a potential drug candidate. In vitro, Ver protected PC12 cells from 6-OHDA injury and regulated 6-OHDA-induced expressions of transcription factors such as PAX5, LEF1, MTF1, IKZF3, and SP140, as well as the expressions of PD pathogenic genes such as ITGA6, CDH1, CD40, ESR1, SMAD3, and CXCR4. In PD mice, Ver exerted inhibitory effects on α-Syn expression. However, Ver had weak effects on PD pathogenic genes and their transcription factors described above. CONCLUSION: Ver's therapeutic effect on PD partly depends on its regulatory effect on PD pathogenic genes and their related transcription factors.

Key words: Parkinson's disease, transcription factors, Connectivity Map, verapamil, 6-hydroxydopamine

CLC Number:

Jile XIN, Jing LIU, Xinyi ZHANG, Jiayuan GUO, Wenzhuo HAN, Yixin SUN, Le ZHAO, Weisheng FENG, Xiaoke ZHENG. Connectivity Map-based drug repositioning evaluation of verapamil as a therapeutic agent for Parkinson's disease[J]. Chinese Journal of Clinical Pharmacology and Therapeutics, 2026, 31(1): 14-27.

Figures/Tables 12

Fig.1 Differential gene expression analysis A: Box diagram of normalization of samples. The box plot illustrates the transcriptional expression values of the 12 samples in the Parkinson's disease (PD) expression profile dataset GSE169755. B: Differential expression analysis. The volcano plot displays differentially expressed genes (DEGs) associated with PD onset in the GSE169755 dataset. Red dots indicate downregulated genes, while blue dots represent upregulated genes.

Fig.2 Protein-protein interaction (PPI) network and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis A: PPI network constructed from PD-onset-associated DEGs. Node color closer to red and larger node size indicate higher criticality. B: GO enrichment analysis results. C: KEGG analysis results.

Fig.3 PPI network of hub pathways implicated in PD onset

Fig.4 Transcription factors that regulate hub genes implicated in PD onset and screening of small molecules that regulate the expression of transcription factors A: Regulatory network of transcription factors interacting with PD-associated genes. B: Connectivity Map (CMap) screening for potential small-molecule drugs that modulate the aforementioned transcription factors. The CMap prediction results indicated that verapamil (Ver) exhibited a raw_cs value of -100, the lowest among all compounds, making it the optimal therapeutic candidate.

Fig.5 Protective effect of verapamil (Ver) against 6-hydroxydopamine (6-OHDA)-induced cytotoxicity in PC12 cells ($ \overline{x} $±s, n=3) A: Cytotoxic effects of 6-OHDA on PC12 cells. B: Effects of Ver on the growth rate of 6-OHDA-induced damaged PC12 cells. C: Effects of Ver on the apoptosis rate of 6-OHDA-induced damaged PC12 cells. bP<0.05, cP<0.01, compared with the control group; fP<0.01, compared with the 6-OHDA group.

Fig.6 The regulatory effects of Ver on the expression of transcription factors such as PAX5, LEF1, MTF1, IKZF3, and SP140 in 6-OHDA exposed PC12 cells ($ \overline{x} $±s, n=3) bP<0.05, cP<0.01, compared with the control group; eP<0.05, fP<0.01, compared with the 6-OHDA group.

Fig.7 The regulatory effects of Ver on the expression of hub genes implicated in PD onset, such as ITGA6, CDH1, CD40, ESR1, SMAD3, and CXCR4 in 6-OHDA exposed PC12 cells ($ \overline{x} $±s, n=3) cP<0.01, compared with the control group; fP<0.01, compared with the 6-OHDA group.

Fig.8 Effect of Ver on tyrosine hydroxylase (TH) expression in a 6-OHDA-induced rat model of Parkinson’s disease ($ \overline{x} $±s, n=6) cP<0.01, compared with the control group; fP<0.01, compared with the 6-OHDA group. Scale bar=100 μm; the white arrow represent the TH-positive neuronal cell with brown color.

Fig.9 Effect of Ver on α-synuclein expression in a 6-OHDA induced rat model of PD ($ \overline{x} $±s, n=6) cP<0.01, compared with the control group; fP<0.01, compared with the 6-OHDA group. MFI: mean fluorescence intensity; Scale bar=50 μm; the white arrow represent the α-Syn-positive neuronal cell with red fluorescence.

Fig.10 Western blot detection of the effect of Ver on the expression of TH and α-Syn in the substantia nigra compacta of the 6-OHDA-induced PD mouse model ($ \overline{x} $±s, n=6) cP<0.01, compared with the control group; fP<0.01, compared with the 6-OHDA group.

Fig.11 The regulatory effects of Ver on the expression of transcription factors such as PAX5, LEF1, MTF1, IKZF3, and SP140 in a 6-OHDA induced rat model of PD ($ \overline{x} $±s, n=6) cP<0.01, compared with the control group; fP<0.01, compared with the 6-OHDA group.

Fig.12 The regulatory effects of Ver on the expression of hub genes implicated in PD onset, such as ITGA6, CDH1, CD40, ESR1, SMAD3, and CXCR4 in the 6-OHDA induced rat model of PD ($ \overline{x} $±s, n=6) bP<0.05, cP<0.01, compared with the control group; fP<0.01, compared with the 6-OHDA group.

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