Computer-assisted evaluation of plant-derived β-secretase inhibitors in Alzheimer’s disease

A theoretical screening of phytochemical constituents from Millettia brandisiana as inhibitors against acetylcholinesterase

Alzheimer's disease is one of the causes associated with the early stages of dementia. Nowadays, the main treatment available is to inhibit the actions of the acetylcholinesterase (AChE) enzyme, which has been identified as responsible for the disease. In this study, computational methods were used to examine the structure and therapeutic ability of chemical compounds extracted from Millettia brandisiana natural products against AChE. This plant is commonly known as a traditional medicine in Vietnam and Thailand for the treatment of several diseases. Furthermore, machine learning helped us narrow down the choice of 85 substances for further studies by molecular docking and molecular dynamics simulations to gain deeper insights into the interactions between inhibitors and disease proteins. Of the five top-choice substances, γ-dimethylallyloxy-5,7,2,5-tetramethoxyisoflavone emerges as a promising substance due to its large free binding energy to AChE and the high thermodynamic stability of the resulting complex.

Pharmacophore-Based Screening, Molecular Docking, and Dynamic Simulation of Fungal Metabolites as Inhibitors of Multi-Targets in Neurodegenerative Disorders

Neurodegenerative disorders, such as Alzheimer's disease (AD), negatively affect the economic and psychological system. For AD, there is still a lack of disease-altering treatments and promising cures due to its complex pathophysiology. In this study, we computationally screened the natural database of fungal metabolites against three known therapeutic target proteins of AD. Initially, a pharmacophore-based, drug-likeness category was employed for screening, and it filtered the 14 (A-N) best hits out of 17,544 fungal metabolites. The 14 best hits were docked individually against GSK-3β, the NMDA receptor, and BACE-1 to investigate the potential of finding a multitarget inhibitor. We found that compounds B, F, and L were immuno-toxic, whereas E, H, I, and J had a higher LD50 dose (5000 mg/kg). Among the examined metabolites, the Bisacremine-C (compound I) was found to be the most active molecule against GSK-3β (ΔG: -8.7 ± 0.2 Kcal/mol, Ki: 2.4 × 106 M-1), NMDA (ΔG: -9.5 ± 0.1 Kcal/mol, Ki: 9.2 × 106 M-1), and BACE-1 (ΔG: -9.1 ± 0.2 Kcal/mol, Ki: 4.7 × 106 M-1). It showed a 25-fold higher affinity with GSK-3β, 6.3-fold higher affinity with NMDA, and 9.04-fold higher affinity with BACE-1 than their native ligands, respectively. Molecular dynamic simulation parameters, such as RMSD, RMSF, Rg, and SASA, all confirmed that the overall structures of the targeted enzymes did not change significantly after binding with Bisacremine-C, and the ligand remained inside the binding cavity in a stable conformation for most of the simulation time. The most significant hydrophobic contacts for the GSK-3β-Bisacremine-C complex are with ILE62, VAL70, ALA83, and LEU188, whereas GLN185 is significant for H-bonds. In terms of hydrophobic contacts, TYR184 and PHE246 are the most important, while SER180 is vital for H-bonds in NMDA-Bisacremine-C. THR232 is the most crucial for H-bonds in BACE-1-Bisacremine-C and ILE110-produced hydrophobic contacts. This study laid a foundation for further experimental validation and clinical trials regarding the biopotency of Bisacremine-C.

Antioxidant and anti-Alzheimer activities of Clivia miniata (Lindl) roots, bulbs, and aerial parts: In-vitro and in-silico studies

Clivia miniata (Lindl) is a member of the family Amaryllidaceae known for its chemically diverse alkaloids with a wide range of biological activities. Many reports revealed a direct role of oxidative stress in the early stage of Alzheimer's disease (AD). Meanwhile, β-site amyloid precursor protein cleavage enzyme 1 (BACE-1) is a molecular target for the treatment of AD. We aimed to investigate C. miniata root, bulb, and aerial part chemical profiling, antioxidant, BACE-1, and AChE enzyme inhibitory activities. Results showed that the total root had the most potent radical scavenging activity as compared to the total bulb and aerial part, respectively. Ethanol root extract had the most potent BACE-1 inhibitory activity (IC50 = 0.02 ± 0.001 µg/mL) as compared to the bulb and aerial part (IC50 = 0.93 ± 0.13, 1.80 ± 0.24 µg/mL), respectively. Moreover, the total root extract mitigated AChE enzyme activity more than total bulb and aerial fractions with IC50 values of (0.06 ± 0.02, 0.58 ± 0.3, and 1.89 ± 0.42 µg/mL, respectively. Bioassay-guided acid-base fractionation confirmed superior BACE-1 inhibitory activity of the root fractions particularly, methylene chloride and ethyl acetate fractions with (IC50 values of 0.21 ± 0.60 and 0.01 ± 0.001 µg/mL), respectively. UPLC-MS analysis of ethyl acetate and methylene chloride fractions of C. miniata root led to the identification of eight phenolics and thirteen alkaloids, respectively. Molecular docking studies against BACE-1 protein revealed that lycorine di-hexoside, miniatine, and cliviaaline were the most promising hits. Further investigation of anti-AD potential of the aforementioned small molecules is required.

Multitargeted Virtual Screening and Molecular Simulation of Natural Product-like Compounds against GSK3β, NMDA-Receptor, and BACE-1 for the Management of Alzheimer's Disease

The complexity of Alzheimer's disease (AD) and several side effects of currently available medication inclined us to search for a novel natural cure by targeting multiple key regulatory proteins. We initially virtually screened the natural product-like compounds against GSK3β, NMDA receptor, and BACE-1 and thereafter validated the best hit through molecular dynamics simulation (MDS). The results demonstrated that out of 2029 compounds, only 51 compounds exhibited better binding interactions than native ligands, with all three protein targets (NMDA, GSK3β, and BACE) considered multitarget inhibitors. Among them, F1094-0201 is the most potent inhibitor against multiple targets with binding energy -11.7, -10.6, and -12 kcal/mol, respectively. ADME-T analysis results showed that F1094-0201 was found to be suitable for CNS drug-likeness in addition to their other drug-likeness properties. The MDS results of RMSD, RMSF, Rg, SASA, SSE and residue interactions indicated the formation of a strong and stable association in the complex of ligands (F1094-0201) and proteins. These findings confirm the F1094-0201's ability to remain inside target proteins' binding pockets while forming a stable complex of protein-ligand. The free energies (MM/GBSA) of BACE-F1094-0201, GSK3β-F1094-0201, and NMDA-F1094-0201 complex formation were -73.78 ± 4.31 kcal mol^-1, -72.77 ± 3.43 kcal mol^-1, and -52.51 ± 2.85 kcal mol^-1, respectively. Amongst the target proteins, F1094-0201 have a more stable association with BACE, followed by NMDA and GSK3β. These attributes of F1094-0201 indicate it as a possible option for the management of pathophysiological pathways associated with AD.

Neuroprotective Potential of Biflavone Ginkgetin: A Review

Neurological disorders are becoming more common, and there is an intense search for molecules that can help treat them. Several natural components, especially those from the flavonoid group, have shown promising results. Ginkgetin is the first known biflavonoid, a flavonoid dimer isolated from ginkgo (Ginkgo biloba L.). Later, its occurrence was discovered in more than 20 different plant species, most of which are known for their use in traditional medicine. Herein we have summarized the data on the neuroprotective potential of ginkgetin. There is evidence of protection against neuronal damage caused by ischemic strokes, neurotumors, Alzheimer's disease (AD), and Parkinson's disease (PD). Beneficial effects in ischemic strokes have been demonstrated in animal studies in which injection of ginkgetin before or after onset of the stoke showed protection from neuronal damage. AD protection has been the most studied to date. Possible mechanisms include inhibition of reactive oxygen species, inhibition of β-secretase, inhibition of Aβ fibril formation, amelioration of inflammation, and antimicrobial activity. Ginkgetin has also shown positive effects on the relief of PD symptoms in animal studies. Most of the available data are from in vitro or in vivo animal studies, where ginkgetin showed promising results, and further clinical studies should be conducted.

Chemical Composition, Antiaging Activities and Molecular Docking Studies of Essential Oils from Acca sellowiana (Feijoa)

This study aimed to investigate the chemical composition of essential oils isolated from Acca sellowiana (feijoa) leaves and stems and elaborate on their relevance as natural anti-aging, coupled with molecular-docking studies. The isolated oils were analysed using gas chromatography-mass spectrometry analysis and investigated for inhibitory effects against acetylcholinesterase, β -secretase, collagenase, elastase and tyrosinase. Molecular-modelling study was performed using MOE-Dock program to evaluate binding interactions of major components with the above-mentioned targets. The leaf oil revealed the predominance of caryophyllene oxide (24.3%), linalool (7.9%), and spathulenol (6.6%), while the stem oil was presented by caryophyllene oxide (38.1%), α-zingiberene (10.1%) and humulene oxide II (6.0%). The stem oil expressed superior inhibitory activities against acetylcholinesterase (IC 50 =0.15±0.01µg/mL), β -secretase (IC 50 =3.99±0.23µg/mL), collagenase (IC 50 =408.10±20.80 µg/mL), elastase (IC 50 =0.17±0.01 μg/mL) and tyrosinase (IC 50 =8.45 ± 0.40µg/mL). The valuable binding interactions and docking scores were observed for caryophyllene oxide and α-zingiberene with acetylcholinesterase. Besides, α-zingibirene followed by linalool and τ-cadinol revealed tight fitting with collagenase and elastase. Additionally, linalool, spathulenol and τ-cadinol showed the best binding energy to tyrosinase. This study provides valuable scientific data on A. sellowiana as potential candidates for the development of natural antiaging formulations.

Thermodynamic and kinetic studies on antioxidant capacity of amentoflavone: a DFT (density functional theory) computational approach

Density functional theory (DFT) at the theoretical M06-2X/6-311G(d,p) level was used to assess thermodynamics and kinetics in the antioxidative action of amentoflavone (AF). The antioxidative HAT pathway (H-atom transfer) is assigned to this compound in gas, but the SPL-ET (sequential proton loss-electron transfer) is the main route in polar solvents methanol and water. In all four mediums gas, benzene, methanol, and water, 4‴-OH is the most active site in free radical quenching with the lowest BDE (bond dissociation enthalpy) values of 81.8-84.8 kcal/mol, as well as it exerted the PA (proton affinity) values of 29.8-33.0 kcal/mol in methanol and water. Regarding kinetics, when interacted with ^•OOH and ^•NO₂ in gas and methanol, 4‴-OH group is also responsible for the lowest ΔG^# values (Gibbs free energy of activation), and the highest rate constant K values. Acidic assessment also indicated that 4‴-OH is associated with the strongest acidity (the lowest pK_a). Two favorable oriented 4‴-OH and 7-OH groups further exhibited antioxidative activity since they prevented metal ions Zn²⁺ and Fe²⁺ from participating in free radical producing processes, in which the most stable complex [FeAF(H₂O)₄] generated the lowest IE value of -206.2 kcal/mol, and E_gap value of 3.491 kcal/mol, but the highest MIA values of 184.6 kcal/mol in methanol.