Design, synthesis, in silico, and in vitro evaluation of pyrrol-2-yl-phenyl allylidene hydrazine carboximidamide derivatives as AChE/BACE 1 dual inhibitors

Abstract

Alzheimer's disease (AD) manifests as a progressive decline in cognitive function and mental behavior. Targeting two crucial enzymes associated with AD, acetylcholinesterase (AChE) and BACE 1 (Beta-site APP Cleaving Enzyme), in combination, holds promise for therapeutic breakthroughs. In this study, 40 derivatives of pyrrol-2-yl-phenyl allylidene hydrazine carboximidamide were designed based on prior research. These derivatives underwent synthesis and assessment for their inhibitory potential against AChE and BACE 1. ADME predictions indicated favorable physicochemical properties for these compounds. The findings offer novel avenues for exploring the dual inhibition of AChE and BACE 1 as a promising therapeutic strategy for AD.

Fig. 1. US FDA approved drugs for the treatment of Alzheimer's disease.

Fig. 2. Design strategy using molecular hybridization approach.

Fig. 3. (A) X-ray crystallographic structure of AChE (4EY7, ribbon form); (B) prominent amino acid residues surrounded by co-crystallized ligand (E20) bound to chain A and B; (C) surface model of 4EY7 bounded co-crystallized ligand (red color).

Fig. 4. (A) X-ray crystallographic structure of BACE 1 (6UWP, ribbon form); (B) prominent amino acid residues surrounded by co-crystallized ligand (QKA) bound to chain A and B; (C) surface model of 6UWP bounded co-crystallized ligand (red color).

Scheme 1. Reagents and conditions: (i) substituted benzyl bromide, KOH, DMF, ultra-sonication, 25–27 °C, 1 h (ii) substituted benzaldehyde, ethanolic NaOH, ultra-sonication, 20–25 °C, 30 min (iii) aminoguanidine·HCl, conc. HCl, EtOH, ultra-sonication, 30–35 °C, 2.0 h.

Fig. 5. Docking validation of 4EY7 and 6UWP (A) redocked pose of Donepezil (red) in 4EY7 (AChE) superimposed on the co-crystallized ligand (yellow) (RMSD: 0.14 Å, Glide score: 14.56); (B) redocked pose of QKA (red) in 6UWP (BACE 1) superimposed on the co-crystallized ligand (green) (RMSD: 0.08 Å, Glide score: 9.64); (C) and (D) show overlapping of all of the docked compounds within the active site of 4EY7 and 6UWP, respectively.

Fig. 6. (A) 2D interaction plot of 1j in AChE (Glide score-12.26 kcal mol⁻¹); (B) 2D interaction plot of 1j in BACE 1 (Glide score-8.03 kcal mol⁻¹).

Fig. 7. (A) 2D interaction plot of 2h in 4EY7 (Glide score-12.59 kcal mol⁻¹); (B) 2D interaction plot of 2h in BACE 1 (Glide score-7.94 kcal mol⁻¹).

Fig. 8. (A) 3D interaction plot of 3e in 4EY7 (Glide score-11.47 kcal mol⁻¹); (B) H-bond surface model (donor/acceptor) of 4EY7 bound with 3e.

Fig. 9. (A) Secondary structure view of 4EY7 with docked compound 3e within the active site (green color); (B) 3D interaction plot of 3e in 6UWP (Glide score-9.87 kcal mol⁻¹).

Fig. 10. (A) H-bond surface model (donor/acceptor) of 6UWP bound with 3e; (B) secondary structure view of 6UWP with docked compound 3e within the active site (green color).

Fig. 11. Molecular dynamics studies of 3e-AChE (4EY7) docked complex. [A] Comparative RMSD of AChE (protein backbone) and compound 1d in the protein–ligand complex throughout the simulation period of 100 ns. [B] Graphical representation showing protein RMSF throughout the simulation period of 100 ns. [C] Histogram showing interaction fractions with active amino acid residues. [D and E] Timeline representation showing interaction with all the amino acid residues at each time frame.

Fig. 12. Molecular dynamics studies of 3e-BACE 1 (6UWP) docked complex [A] comparative RMSD of BACE 1 (protein backbone) and compound 3e in the protein–ligand complex throughout the simulation period of 100 ns. [B] Graphical representation showing protein RMSF throughout the simulation period of 100 ns. [C] Histogram showing interaction fractions with active amino acid residues; [D and E] timeline representation showing interaction with all the amino acid residues at each time frame.