Cytotoxic monastrol derivatives as adjective inhibitors of drug-resistant Eg5: a molecular dynamics perspective

Abstract

The mitotic kinesin Eg5 is a motor protein involved in the formation of bipolar spindle and cell division. Eg5 is overexpressed in various cancer cells and Eg5 targeting agents are promising candidates for cancer therapy. Subsequent to the discovery of monastrol as a small-molecule Eg5 modulator, numerous inhibitors/modulators have been reported from which a few entered clinical trials. Mutagenic investigations specified declined sensitivity of Eg5 allosteric site to monastrol due to the occurrence of drug-resistant mutations in some cell cultures. Accordingly, identification of tight binders to the mutant Eg5 allosteric site is an invaluable strategy to devise more efficient Eg5 modulators. We have previously synthesized a few dihydropyrimidinethione (DHPMT)-based 5-carboxamide monastrol derivatives (1-5) with higher cytotoxicities against AGS (IC₅₀ 9.90-98.48 µM) and MCF-7 (IC₅₀ 15.20-149.13 µM) cancer cell lines than monastrol. Within a current study, a structural insight was offered into the binding mechanism of intended derivatives inside the mutant Eg5 loop5/α2/α3 allosteric pocket. Molecular docking of the DHPMT R and S-enantiomers unraveled top-scored Eg5 complexes. Molecular dynamics (MD) simulations were carried out on 5 superior complexes as (R)-2/D130V-Eg5, (R)-4/D130V-Eg5, (R)-5/D130V-Eg5, (R)-5/L214I-Eg5, (R)-5/R119L-Eg5, and the control groups monastrol/D130V-Eg5, monastrol/L214I-Eg5, monastrol/R119L-Eg5. Free energy calculations were conducted through conformational sampling of MD-driven binding trajectories. Our results provided structural details on probable interaction mechanism of the cytotoxic DHPMTs that are difficult to address experimentally. The outputs of the current study propose new monastrol derivatives as probable resistance-overwhelming Eg5 modulators.

Communicated by Ramaswamy H. Sarma

HIGHLIGHTS

• MD simulations revealed that R-enantiomer of 5 overwhelmed drug-resistant D130V-Eg5.

• Induced fit L5 loop conformation led to the accommodation of 5 inside Eg5 allosteric site.

• Cooperative lipophilic contacts accommodated DHPMTs inside D130V-Eg5 allosteric site.

• Ser120 pointed toward 5 and made a stable H-bond particularly within the 60-100 ns.

• Major fluctuations of D130V-Eg5 allosteric pocket occurred at L5 loop upon binding to 5.

Keywords:

• Kinesin Eg5
• monastrol
• mutation
• allosteric pocket
• molecular dynamics

Authors’ contributions

Nima Razzaghi-Asl contributed to the conceptualization and design of the study. Material preparation, data collection and analysis were performed by Sara Shahabipour and Amir Naser Shamkhali. The first draft of the manuscript was written by Nima Razzaghi-Asl and Amir Naser Shamkhali commented on previous versions of the manuscript. All the authors read and approved the final manuscript.

Disclosure statement

Authors declare that there is no conflict of interest(s).

Additional information

Funding

This work was supported by Ardabil University of Medical Sciences under Grant number IR.ARUMS.REC.1399.595.