Identification of Natural αβ-tubulin Inhibitors Using Integrated Virtual Screening and Machine Learning Strategies

Abstract

Microtubules play a crucial role in cell division and are composed of α-tubulin and β-tubulin heterodimeric subunits; they control the segregation of chromosomes during mitosis. Multiple isotypes of β-tubulin exist in humans, which are tissue-specific. Among them, the β-tubulin subunit is widely expressed in cancer cells that leads to resistance against taxane-based anticancer agents such as paclitaxel, which stabilizes microtubules by binding into the taxane-binding site of the αβ-tubulin heterodimer, addressing the gap, the present study discussed about the potential natural compounds capable of binding at the taxane site of αβ-tubulin heterodimer by exploring alternative scaffolds, offer a potential route to overcome the resistance. A database of 340 natural compounds from the COCONUT natural compound database was screened against the taxane-binding site of αβ-tubulin (PDB: 1JFF) by using AutoDock Vina. Seven potential candidates showing binding affinity of −10.1 kcal/mol or stronger, further integrated with machine learning-based classification was applied to these hits to narrow down these 7 active natural compounds, of which withanolide A and 27-O-acetyl-withaferin A had binding affinities of −10.6 kcal/mol and −10.4 kcal/mol. This study employed molecular docking along with integrated machine learning based virtual screening to check the binding mechanism and stabilization of the potential hits at the taxane binding site of αβ-tubulin heterodimer, molecular docking revealed favorable binding affinities in the taxane binding site of αβ-tubulin heterodimer, Molecular dynamics (MD) simulation evaluated through RMSD, SASA, Rg analysis, showed that both withanolide A and 27-O-acetyl-withaferin A significantly reduced the structural fluctuation and influenced the stability of the αβ-tubulin heterodimer relative to the αβ-tubulin heterodimer ( apo), SASA and Rg valued remained the same as the αβ-tubulin heterodimer (apo) for both withanolide A and 27-O-acetyl-withaferin A, which indicates that stabilizing effect is confined to the ligand binding site rather than extending across the whole protein, principal component analysis, revealed αβ-tubulin heterodimer (apo) has explored a wide conformational range. In contrast, ligand-bound complexes occupied the narrower overlapping region, which indicates reduced structural stability on binding of the ligand. In conclusion, the study identified natural scaffolds against the multi-drug resistant αβ-tubulin, which offer a promising foundation for designing new therapeutic approaches for tumors associated with β-tubulin overexpression.