Related Experiment Video
Updated: Aug 6, 2025
Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Ensemble-based molecular docking and spectrofluorometric analysis of interaction between cytotoxin and tumor necrosis
Nurhamimah Misuan1, Saharuddin Mohamad2,3, Thibault Tubiana4
1School of Science, Monash University Malaysia, Bandar Sunway, Malaysia.
Abstract:
Cytotoxin (CTX) is a three-finger toxin presents predominantly in cobra venom. The functional site of the toxin is located at its three hydrophobic loop tips. Its actual mechanism of cytotoxicity remains inconclusive as few conflicting hypotheses have been proposed in addition to direct cytolytic effects. The present work investigated the interaction between CTX and death receptor families via ensemble-based molecular docking and fluorescence titration analysis. Multiple sequence alignments of different CTX isoforms obtained a conserved CTX sequence. The three-dimensional structure of the conserved CTX was later determined using homology modelling, and its quality was validated. Ensemble-based molecular docking of CTX was performed with different death receptors, such as Fas-ligand and tumor necrosis factor receptor families. Our results showed that tumor necrosis factor receptor 1 (TNFR1) was the best receptor interacting with CTX attributed to the interaction of all three functional loops and evinced with low HADDOCK, Z-score and RMSD value. The interaction between CTX and TNFR1 was also supported by a concentration-dependent reduction of fluorescence intensity with increasing binding affinity. The possible intermolecular interactions between CTX and TNFR1 were Van der Waals forces and hydrogen bonding. Our findings suggest a possibility that CTX triggers apoptosis cell death through non-covalent interactions with TNFR1.Communicated by Ramaswamy H. Sarma.
Insights
Cobra cytotoxin (CTX) may trigger apoptosis by interacting with tumor necrosis factor receptor 1 (TNFR1). This interaction, involving CTX
Area of Science:
- Biochemistry
- Molecular Biology
- Toxicology
Background:
- Cytotoxin (CTX) is a prominent cobra venom component.
- The precise mechanism of CTX-induced cytotoxicity is not fully understood.
- Existing hypotheses include direct cytolytic effects and interactions with cellular receptors.
Purpose of the Study:
- To investigate the interaction between CTX and death receptor families.
- To elucidate the molecular mechanism of CTX-induced apoptosis.
- To identify specific death receptors that bind to CTX.
Main Methods:
- Ensemble-based molecular docking was employed to predict binding interactions.
- Homology modeling was used to determine the 3D structure of a conserved CTX sequence.
- Fluorescence titration analysis was performed to confirm binding affinity.
Main Results:
- Tumor necrosis factor receptor 1 (TNFR1) showed the highest affinity for CTX.
- Binding involved interactions with all three functional loops of CTX, confirmed by low HADDOCK, Z-score, and RMSD values.
- Fluorescence quenching demonstrated a concentration-dependent binding affinity between CTX and TNFR1, mediated by Van der Waals forces and hydrogen bonding.
Conclusions:
- CTX interacts with TNFR1 through non-covalent forces.
- This interaction suggests a novel mechanism where CTX may induce apoptosis via TNFR1 signaling.
- Further research is warranted to confirm this pathway in vivo.
