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AI-driven identification of a selective dual function inhibitor blocking HK2 activity and HK2-VDAC1 interaction
Wenying Shan1, Shao-Lin Zhang2, Yehuda G Assaraf3
1Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China; MoE Frontiers Science Centre for Precision Oncology, University of Macau, Taipa, Macau SAR, China.
Abstract:
Selective inhibition of hexokinase 2 (HK2) represents a promising therapeutic strategy due to the pivotal role of HK2 in the Warburg effect, enhancement of glycolysis and anti-apoptosis via HK2-Voltage-Dependent Anion Channel 1 (VDAC1) protein-protein interaction. Moreover, HK2 initiates glycolysis to generate lactate, hence this central enzyme can be pharmacologically targeted to enhance therapy outcomes. Currently, no HK2 inhibitors (HK2is) exist in the clinic. Herein, we employed GCVec, an artificial intelligence (AI)-based compound-protein interaction (CPI) prediction tool, along with molecular docking, to identify the HK2i, 106. This compound exhibited an IC50 of 0.79 ± 0.07 μM and a consistent Kd of 0.41 ± 0.03 μM against HK2 enzyme. It also apparently blocked HK2-VDAC1 interaction as indicated by the disrupted colocalization of HK2-GFP and VDAC1-mCherry. Furthermore, 106 demonstrated enhanced anticancer efficacy under hypoxia in tumor cells with elevated HIF-1α/HK2 and VDAC1 levels. Compound 106 selectively targeted SW480 colorectal cancer cells with high HK2 expression, achieving a growth inhibition IC50 value of 5.00 ± 0.94 μM. Consistently, knockout of HK2 in these tumor cells significantly rescued the IC50 values and eliminated the glycolytic inhibition induced by 106. We further showed that 106 reduced lactate and ATP levels and induced markers of apoptosis, including increased p-AMPK/AMPK ratio and increased Bax levels, as well as decreased Bcl2 levels. Collectively, our findings highlight the potential of GCVec in identifying 106, a first in class dual-function HK2i which emerges as a promising lead compound for further development into a possible anticancer therapeutic agent.
Insights
A novel artificial intelligence tool identified compound 106, a selective hexokinase 2 inhibitor (HK2i). This compound shows promise as an anticancer therapeutic by blocking glycolysis and inducing apoptosis in cancer cells.
Area of Science:
- Biochemistry and Molecular Biology
- Cancer Research and Therapeutics
- Computational Chemistry and Drug Discovery
Background:
- Hexokinase 2 (HK2) plays a crucial role in the Warburg effect, promoting glycolysis and conferring anti-apoptotic properties through interaction with Voltage-Dependent Anion Channel 1 (VDAC1).
- Targeting HK2 is a promising strategy for cancer therapy, as it initiates glycolysis and lactate production, but no clinical HK2 inhibitors (HK2is) are currently available.
Purpose of the Study:
- To identify novel HK2 inhibitors (HK2is) using an AI-based compound-protein interaction (CPI) prediction tool (GCVec) combined with molecular docking.
- To evaluate the efficacy of the identified compound, 106, as a potential anticancer therapeutic agent.
Main Methods:
- Utilized GCVec AI tool and molecular docking to predict and identify potential HK2 inhibitors.
- Assessed compound 106's inhibitory activity against HK2 enzyme (IC50, Kd) and its effect on HK2-VDAC1 interaction.
- Evaluated compound 106's anticancer efficacy in SW480 colorectal cancer cells, including its impact on glycolysis, lactate production, ATP levels, and apoptosis markers.
Main Results:
- Compound 106 demonstrated potent inhibition of HK2 enzyme with IC50 of 0.79 ± 0.07 μM and Kd of 0.41 ± 0.03 μM.
- Compound 106 effectively blocked HK2-VDAC1 interaction and showed enhanced anticancer efficacy under hypoxia in cancer cells with high HK2/VDAC1 levels.
- Selective inhibition of SW480 colorectal cancer cells (IC50 = 5.00 ± 0.94 μM), reduced lactate and ATP, and induced apoptosis markers (increased p-AMPK/AMPK, Bax; decreased Bcl2).
Conclusions:
- GCVec successfully identified compound 106, a novel dual-function HK2 inhibitor.
- Compound 106 exhibits significant anticancer potential by targeting HK2-mediated glycolysis and inducing apoptosis.
- Compound 106 represents a promising lead compound for the development of new anticancer therapeutics.
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