Structural insights into the interactions of repositioning and known drugs for Alzheimer’s disease with hen egg white lysozyme by MM-GBSA

Abstract

Six drugs (dapsone, diltiazem, timolol, rosiglitazone, mesalazine, and milnacipran) that were predicted by network-based polypharmacology approaches as potential anti-Alzheimer’s drugs, have been subjected in this study for in silico and in vitro evaluation to check their potential against protein fibrillation, which is a causative factor for multiple diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington disease, cardiac myopathy, type-II diabetes mellitus and many others. Molecular docking and thereafter molecular dynamics (MD) simulations revealed that diltiazem, rosiglitazone, and milnacipran interact with the binding residues such as Asp52, Glu35, Trp62, and Asp101, which lie within the fibrillating region of HEWL. The MM-GBSA analysis revealed −7.86, −5.05, and −10.29 kcal/mol as the binding energy of diltiazem, rosiglitazone, and milnacipran. The RMSD and RMSF calculations revealed significant stabilities of these ligands within the binding pocket of HEWL. While compared with two reported ligands inhibiting HEWL fibrillation, milnacipran depicted almost similar binding potential with one of the known ligands (Ligand binding affinity −10.66 kcal/mol) of HEWL. Furthermore, secondary structure analyses revealed notable inhibition of the secondary structural changes with our candidate ligand; especially regarding retention of the 3/10 α-helix both by DSSP simulation, Circular dichroism, and FESEM-based microscopic image analyses. Taking further into experimental validation, all three ligands inhibited fibrillation in HEWL in simulated conditions as revealed by blue shift in Congo red assay and later expressing percentage inhibition in ThioflavinT assay as well. However, dose-dependent kinetics revealed that the antifibrillatory effects of drugs are more pronounced at low protein concentrations.

Communicated by Ramaswamy H. Sarma

Keywords:

• Protein fibrillation
• drug repositioning
• MM-GBSA
• Congo Red
• ThioflavinT

Acknowledgment

The authors thank both Bose Institute, Kolkata and Dr. B.C. Roy College of Pharmacy & Allied Health Sciences, Durgapur, WB, India for providing necessary infrastructures to carry out the studies for this project.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Authors’ contributions

AKH, PM, SB: Conceived, designed and performed the simulations and the entire experiments, AKH: MD and MM-GBSA, writing the manuscript; SK and PM: Experimentation and writing the manuscript; DR: Provided molecules, simulations and financial support; AH: CD experiments and data analyses; PD, ShB, AD, SK, RM, AC and SM: Setting up the drug-protein reactions, batch and concentration dependent studies; optimizations, CR and ThT assays, SM, PM, SB: FESEM studies and data analyses.

Additional information

Funding

The project is funded by an intramural grant of the Bose Institute (order no. R/16/21/164 and R/16/21/165 dated 02.11.2021)