Molecular modeling of multi-target analogs of huperzine A and applications in Alzheimer’s disease

Context: Given the diverse pathophysiological mechanisms underlying Alzheimer’s disease, it is improbable that a single targeted drug will prove successful as a therapeutic strategy. Therefore, exploring various hypotheses in drug design is imperative. The sequestration of Fe(II) and Zn(II) cations stands out as a crucial mechanism based on the mitigation of reactive oxygen species. Moreover, inhibiting acetylcholinesterase represents a pivotal strategy to enhance acetylcholine levels in the synaptic cleft. This research aims to investigate the analogs of Huperzine A, documented in scientific literature, considering of these two hypotheses. Consequently, the speciation chemistry of these structures with Fe(II) and Zn(II) was scrutinized using quantum chemistry calculations, molecular docking simulations, and theoretical predictions of pharmacokinetics properties. From the pharmacokinetic properties, only two analogs, HupA-A1 and HupA-A2, exhibited a theoretical permeability across the blood-brain barrier; on the other hand, from a thermodynamic standpoint, the enantiomers of HupA-A2 showed negligible chelation values. The enantiomers with the most favorable interaction parameters were S′R′HupA-A1 (ΔGBIND = −40.0 kcal mol−1, fitness score = 35.5) and R′R′HupA-A1 (ΔGBIND = −35.5 kcal mol−1, fitness score = 22.61), being compared with HupA (ΔGBIND = −41.75 kcal mol−1, fitness score = 39.95). From this study, some prime candidates for promising drug were S′R′HupA-A1 and R′R′HupA-A1, primarily owing to their favorable thermodynamic chelating capability and potential anticholinesterase mechanism. Methods: Quantum chemistry calculations were carried out at B3LYP/6-31G(d) level, considering the IEF-PCM(UFF) implicit solvent model for water. The coordination compounds were assessed using the Gibbs free energy variation and hard and soft acid theory. Molecular docking calculations were conducted using the GOLD program, based on the crystal structure of the acetylcholinesterase protein (PDB code = 4EY5), where the ChemScore function was employed with the active site defined as the region within a 15-Å radius around the centroid coordinates (X = −9.557583, Y = −43.910473, Z = 31.466687). Pharmacokinetic properties were predicted using SwissADME, focusing on Lipinski’s rule of five. Graphical Abstract: (Figure presented.)