Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β₄₂ monomer: insights from molecular dynamics simulations

Abstract

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-β₄₂ (Aβ₄₂) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aβ₄₂ aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aβ₄₂. MD simulations reveal that C1 stabilizes native α-helix conformation of Aβ₄₂ by interacting with key residues in the central helix region (13–26) with hydrogen bonds and π–π interactions. C1 lowers the solvent-accessible surface area of the central hydrophobic core (CHC), KLVFF (16–20), that confirms burial of hydrophobic residues leading to the dominance of helical conformation in the CHC region. The binding free energy analysis with MM–PBSA demonstrates that Ala2, Phe4, Tyr10, Gln15, Lys16, Leu17, Val18, Phe19, Phe20, Glu22, and Met35 contribute maximum to binding free energy (−43.1 kcal/mol) between C1 and Aβ₄₂ monomer. Overall, MD simulations reveal that C1 inhibits Aβ₄₂ aggregation by stabilizing native helical conformation and inhibiting the formation of aggregation-prone β-sheet conformation. The present results will shed light on the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aβ₄₂.

Keywords:

• Alzheimer’s disease
• amyloid β-peptide
• Aβ₄₂ aggregation
• molecular dynamics simulations
• MM–PBSA

Acknowledgments

Bhupesh Goyal gratefully acknowledges Science and Engineering Research Board (SERB), Department of Science & Technology, Government of India for the award of SERB Start-Up Research Grant (Young Scientists) (Sanction No: SB/FT/CS-013/2014). The authors acknowledge Department of Chemistry, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India for providing research facilities. Dr P. Kolandaivel, UGC BSR Fellow, Department of Physics, Bharathiar University, Tamil Nadu is acknowledged for the DFT calculations. The authors acknowledge National Param Supercomputing Facility (NPSF), CDAC, Pune for providing the computational facilities.