In silico identification of small molecule modulators for disruption of Hsp90–Cdc37 protein–protein interaction interface for cancer therapeutic application

Abstract

The protein–protein interactions (PPIs) in the biological systems are important to maintain a number of cellular processes. Several disorders including cancer may be developed due to dysfunction in the assembly of PPI networks. Hence, targeting intracellular PPIs can be considered as a crucial drug target for cancer therapy. Among the enormous and diverse group of cancer-enabling PPIs, the Hsp90–Cdc37 is prominent for cancer therapeutic development. The successful inhibition of Hsp90–Cdc37 PPI interface can be an important therapeutic option for cancer management. In the current study, a set of more than sixty thousand compounds belong to four databases were screened through a multi-steps molecular docking study in Glide against the Hsp90–Cdc37 interaction interface. The Glide-score and Prime-MM-GBSA based binding free energy of DCZ3112, standard Hsp90–Cdc37 inhibitor were found to be −6.96 and −40.46 kcal/mol, respectively. The above two parameters were used as cut-off score to reduce the chemical space from all successfully docked molecules. Furthermore, the in-silico pharmacokinetics parameters, common-feature pharmacophore analyses and the molecular binding interactions were used to wipe out the inactive molecules. Finally, four molecules were found to be important to modulate the Hsp90–Cdc37 interface. The potentiality of the final four molecules was checked through several drug-likeness characteristics. The molecular dynamics (MD) simulation study explained that all four molecules retained inside the interface of Hsp90–Cdc37. The binding free energy of each molecule obtained from the MD simulation trajectory was clearly explained the strong affection towards the Hsp90–Cdc37. Hence, the proposed molecule might be crucial for successful inhibition of the Hsp90–Cdc37 interface.

Communicated by Ramaswamy H. Sarma

Keywords:

• Protein–protein interactions
• Hsp90–Cdc37 interface
• virtual screening
• molecular docking
• molecular dynamics

Acknowledgements

Authors are grateful to the Researchers Supporting Project No. (RSP-2020/161), King Saud University, Riyadh, Saudi Arabia.

Computational resource

The CHPC (www.chpc.ac.za), Cape Town, South Africa is thankfully acknowledged for computational resources and tools.

Disclosure statement

No potential conflict of interest was reported by the authors.