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Alzheimer's disease (AD) is a widespread dementia-related disease affecting mankind worldwide. A cholinergic hypothesis is considered the most effective target for treating mild to moderate AD. Present study aims to identify new scaffolds for inhibiting acetylcholinesterase activity. To find Acetylcholinesterase (AChE) inhibitors, we computationally designed and chemically synthesized a series of cation-π inhibitors based on novel scaffolds that potentially block AChE. The cytotoxic effect of inhibitors were determined by MTT. AChE inhibition experiment was performed by Ellman and the Amplex red method in the SH-SY5Y cell line. Further, the experimental data on designed compounds corroborate with various computational studies that further elucidate the binding mode of interactions and binding affinity. The inhibitors were designed to promote dual binding and were incorporated with groups that may facilitate any of the cation- π, hydrophobic and hydrogen-bonding interactions with the conserved and hot-spot residues in the binding site. The inhibitors possessing pyridine-N-methylated pyridinium group and thereby involved in cation- π interactions are highly active relative to the marketed drug Donepezil as well as the designed analogs that lack the group. In vitro enzymatic Ellman assay and Amplex red assay on SH-SY5Y cell line estimated IC50 of the designed compounds in nM range with one having binding affinity higher than Donepezil. Compounds exhibit no significant toxicity up to µM range. Compounds possessing methylidenecyclohexanone scaffolds, with characteristic dual-binding and involving strong cation-π interactions, serves as new leads for AChE and opens a new direction for drug discovery efforts.

Senescence is the major key factor that leads to the loss of neurons throughout aging. Cellular senescence is not the consequence of single cause, but there are multiple aspects which may induce senescence in a cell. Various causes such as gene expression, molecular interactions and protein processing and chromatin organization are described as causal factor for senescence. It is well known that the damage to the nuclear or mitochondrial DNA contributes to the aging either directly by inducing the apoptosis/cellular senescence or indirectly by altering cellular functions. The significant nuclear DNA damage with the age is directly associated with the continuous declining in DNA repair. The continuous decline in expression of topoisomerase 2 beta (Topo IIβ) in cultured cerebellar granule neurons over time indicated the decline in the repair of damage DNA. DNA Topo IIβ is an enzyme that is crucial for solving topological problems of DNA and thus has an important role in DNA repair. The enzyme is predominantly present in non-proliferating cells such as neurons. In this paper, we have studied the genes which were differentially expressed over time in cultured cerebellar granule neurons (CGNs) and identified potential genes associated with the senescence. Our results showed that the two genes neuropeptide Y (Npy) and Slit homolog 2 (Drosophila) (Slit2) gradually increase during aging, and upon suppression of these two genes, there was gradual increase in cell viability along with restoration of the expression of Topo IIβ and potential repair proteins.

A quantum mechanics (QM)/molecular mechanics (MM)-based free energy perturbation (FEP) method, developed recently, provides most accurate estimation of binding affinities. The validity of the method was evaluated for a large set of diverse inhibitors for fructose 1,6-bisphosphatase (FBPase), a target enzyme for type-II diabetes mellitus. The validation set comprises of 22 important structurally different mutations. The calculated relative binding free energies using the QM/MM-based FEP method reproduce the experimental values with exceptional precision of less than ±0.5 kcal/mol. The CPU requirements for QM/MM-based FEP are about fivefold greater than conventional FEP methods, but it is superior in accuracy of predictions. In addition, the QM/MM-based FEP method eliminates the need for time-consuming development of MM force field parameters, which are frequently required for novel inhibitors described by MM. Future automation of the method and parallelization of the code for 128/256/512 cluster computers is expected to enhance the speed and increase its use for drug design and lead optimization. The present application of QM/MM-based FEP method for structurally diverse set of analogs serves to enhance the scope of FEP method and demonstrate the utility of QM/MM-based FEP method for its potential in drug discovery.