Original Research
Frontiers in Drug Discovery ·
Volume 6 - 2026 | https://doi.org/10.3389/fddsv.2026.1922953
Virtual screening of phytochemicals against multiple protein targets of Alzheimer’s disease
- Samuel Mesfin1
- Naamah Bloch1
- Abraham O. Samson1*corresponding author
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
Abstract
Alzheimer’s disease (AD) is a multifactorial neurodegenerative disorder for which current approved therapies provide temporary symptomatic relief, and no disease-modifying treatments are approved. Given the complex pathology of AD and the growing interest in multitarget therapeutic strategies, we performed structure-based virtual screening to identify phytochemicals capable of modulating multiple AD-related targets. A virtual library of 2,847 phytochemical compounds was docked against ten key proteins implicated in AD identified by literature mining, including: amyloid beta (Aβ), acetylcholinesterase (AChE), apolipoprotein E4 (APOE4), β-secretase (BACE1), butyrylcholinesterase (BChE), brain derived neurotrophic factor (BDNF), cyclin dependent kinase 5 (CDK5), glycogen synthase kinase three beta (GSK3β) and presenilin 1/2 (PSEN1/2). Docking results showed potential strong binding of 96 compounds at multiple key targets, and molecular dynamics simulations of the representative compounds Lactucopicrin, Oleanolic acid and Rutecarpine in complex with AChE and GSK3β demonstrated stable protein-ligand complexes, comparable to the known AChE-ligand, Donepezil, and the GSK3β-ligand, QQA. Post-docking filters based on multitarget and heavy atoms count narrowed the selection to 36 compounds. These 36 compounds were classified into families of Alkaloids (Rutecarpine, Sanguinarine, Strychnine), Steroidal alkaloids (Tomatidine, Cyclopamine, Jervine, Verticine, Verticinone), Steroidal sapogenins (Diosgenin, Hecogenin, Yamogenin, Tigogenin, Smilagenin, Sarsasapogenin, Neogitogenin, Ruscogenin), Triterpenoids/sterols (alpha-Spinasterin, Fucosterol, Stigmasterol, Beta-Sitosterol, gamma-Sitosterol, Isofucosterol, Germanicol, Lupeol, Beta-Amyrin, alpha-Amyrin, Taraxerol, Friedelin, Tetrahymanol, Tingenone, Parkeol, Methylenecycloartanol, Ursolic Acid, Oleanolic Acid, Obacunone), and Sesquiterpene (Lactucopicrin). Multiple compounds were supported by the literature, which shows that they can inhibit amyloid aggregation, tau phosphorylation, neuroinflammation, and cholinergic dysfunction, thus lending credibility to our claims. Collectively, our findings suggest that several of the identified multitarget phytochemicals are promising candidates for further experimental validation in AD therapy.
Keywords
Introduction
Alzheimer’s disease (AD) is a complex neurodegenerative disorder and the leading cause of dementia (Monteiro et al., 2023). While the etiology and pathogenesis of AD is not completely understood, it is characterized by protein aggregation of amyloid-beta (Aβ) outside neurons, and of microtube-associated protein tau (MAPT) inside neurons, leading to progressive memory and cognitive impairments (Monteiro et al., 2023; Chen Z.-L. et al., 2023). AD is broadly classified into familial (FAD), which accounts for less than 5% of cases, and sporadic (SAD), representing more than 95% of AD cases (Andrade-Guerrero et al., 2023). The leading cause of early-onset FAD is hereditary mutations in genes encoding the amyloid precursor protein (APP), or γ-secretase, leading to increased cleavage of APP, and overproduction of aggregation-prone Aβ fragments central to AD pathogenesis (Raulin et al., 2022). Sequential proteolysis of the APP is initiated by β-secretase (BACE1), and subsequent cleavage by γ-secretase subunits (PSEN1 and PSEN2) releases Aβ peptides. These peptides self-aggregate, first into soluble oligomers (protofibrils), and later into insoluble fibrils and extracellular plaques (Hampel et al., 2021; Hur, 2022). Experimental evidence shows that these soluble Aβ oligomeric protofibrils are neurotoxic, and linked to neuronal damage, including cholinergic neurons (Hampel et al., 2021; Nasb et al., 2024; Maatuk and Samson, 2013). Cholinergic neurodegeneration leads to acetylcholine deficits, crucial for learning and memory, and its deficiency weakens compromised brain areas in AD (Chen et al., 2022). Furthermore, acetylcholine hydrolysis by cholinesterase enzymes (AChE and BChE) exacerbate the condition (Zhou and Huang, 2022). In addition, Aβ binds to neuronal receptors, such as NMDA and AMPA, leading to calcium influx, and activates intracellular signaling pathways, that impair synaptic function. Aβ also induces production of reactive oxygen species (ROS) leading to oxidative stress that damages cellular components, impairs mitochondrial functions, and contributes to neuronal injury and death (Zhang et al., 2024). In parallel, Aβ toxicity induces kinase/phosphatase dysregulation and promotes tau hyperphosphorylation leading to the formation of neurofibrillary tangles (Xing et al., 2025; Zhang et al., 2023). These tangles disrupt microtubule stability and axonal transport, further impairing neuronal function and promoting neurodegeneration (Xing et al., 2025). Sporadic Alzheimer’s disease (SAD), the predominant form of AD, is driven by complex genetic and environmental factors (Andrade-Guerrero et al., 2023). The strongest risk factor is genetic variations of Apolipoprotein E4 (APOE4), that can impair clearance of insoluble Aβ, compared to APOE3/2 alleles (Allwright et al., 2023; Bassal et al., 2025). APOE4 also increases the risk of Parkinson’s disease (PD), and exacerbates α-synuclein toxic effects (Raulin et al., 2022). Moreover, APOE4 is associated with higher incidence of cardiovascular disease (Dunk et al., 2025), indicating its significant potential in multiple interconnected diseases risk factors.
Currently, there is no cure against AD, and approved drugs provide only temporary symptomatic relief without halting disease progression (Reddi Sree et al., 2025). Despite efforts in therapeutic research for AD, the conventional single target strategy has failed to provide promising treatment. Instead, multi-target therapeutic strategies have been suggested for the treatment of complex diseases like AD (Kumar et al., 2022; Pathak and Kabra, 2024; Yoo et al., 2025; Jangid et al., 2024; Takomthong et al., 2025; Iqbal et al., 2023).
Computer aided drug discovery techniques have become powerful tools in modern drug discovery. Among these, molecular docking enables rapid screening and identification of lead compounds, accelerating drug discovery and can significantly lower the cost and time required for the discovery of an effective drug (Adelusi et al., 2022; Sadybekov et al., 2023; Singh et al., 2024). In addition, ADMET (absorption, distribution, metabolism, excretion and toxicity) prediction enables to flag candidates with poor pharmacokinetics and toxicity profile, avoiding costly failure in later stages. Similarly, molecular dynamics simulation can be used to assess binding stability of docking poses over time (Adelusi et al., 2022). Notably, the availability of large chemical databases such as PubChem, ZINC, and other public libraries represents a major opportunity, enabling virtual screening over vast, structurally diverse molecules, which can improve chances of finding novel scaffolds and of discovering new hits (Korn et al., 2023). In the past, we have used these tools to identify drugs for repurposing in AD using FDA-approved drug libraries (Ben Zaken et al., 2025).
Natural products also play an important role in modern drug discovery due to their high structural diversity, and broad biological activity. These characteristics have shown higher success rates in clinical trials, compared with synthetic compounds (Butler et al., 2025; Domingo-Fernández et al., 2024). In particular, phytochemicals have shown much promise in drug discovery, because of their structural diversity, and their multitarget biological activities (Sharifi-Rad et al., 2022).
Here, we virtually screen 2,847 phytochemicals against multiple biological targets of AD using molecular docking. Then, we apply a multi-target filter followed by low heavy atoms count to identify the most promising candidates, for experimental validation in future studies.
Methods
Target identification
To identify protein targets strongly associated with Alzheimer’s disease (AD), we used a widely adopted strategy in biomedical research based on normalized PubMed association scores (Wang et al., 2020; G et al., 2022; Raj et al., 2024). Briefly, we first obtained a list of 20,594 protein coding human genes from NCBI’s gene resource (www.ncbi.nlm.nih.gov/datasets/gene/taxon/9606/?gene_type=protein-coding, retrieved in February 2025). Then, for each gene, we counted the number of citations returned in a PubMed search using the term: “gene name” [All Fields] (e.g., “amyloid beta precursor protein” [All Fields]). Then, we counted the number of co-citations returned in a combined PubMed search for the gene name, and for AD, using the term: “gene name” [All Fields] AND “Alzheimer’s Disease” [MeSH Terms] (e.g., “amyloid beta precursor protein” [All Fields] and “Alzheimer’s Disease” [MeSH Terms]). Then, the co-citation count was divided by the gene citation count to obtain normalized associations score. Normalization accounts for citation trends, such as highly cited genes, and rare mentions. In addition, the normalized score was multiplied by a penalty factor to reduce the contribution of genes with very low citation counts, to produce the adjusted associations scores. The genes were then ranked based on this Adjusted Score to highlight those with significant literature association. Importantly, an in-house python script was used to automate the citation counts for all protein-coding human genes. Normalized association and adjusted score for ranking was calculated as: where C = number of gene-AD co-citations, T = number of gene citations. Finally, the top ten protein targets most associated with AD were used for molecular docking.
Normalized Score N = C T × 100
Adjusted Score A = N × 1 − 100 T + 100
Target preparation
For each target, a representative PDB structure with human sequence, a complete chain, and the best resolution was retrieved (Wang S. et al., 2022). Then, PDB files were prepared for molecular docking, by removing native ligands, non-standard residues, non-target chains, and water molecules; adding polar hydrogens, and Kollman charges; and converting the files to PDBQT format. For this purpose, visualization tools such as ChimeraX, PyMol and AutoDock Tools were used (Houston et al., 2015; Meng et al., 2023).
To explore the entire surface of protein targets, we employed blind docking. Table 1 lists the PDB IDs and grid box parameters (grid center and grid size), which covers the entire volume of the target protein. The grid box parameters were set using AutoDock Tools (Houston et al., 2015).
TABLE 1. PDB ID and AutoDock grid-box settings of targeted proteins.
| Protein | PDBID | Resolution (Å) | Grid Centre (Å) | Grid size (Å) | ||||
|---|---|---|---|---|---|---|---|---|
| X | Y | Z | X | Y | Z | |||
| Aβ | 6SZF | Solution NMR | −8.79 | 3.34 | −11.43 | 92 | 100 | 93 |
| AChE | 4EY7 | 2.35 | −6.25 | −39.43 | 31.76 | 126 | 126 | 126 |
| APOE4 | 6NCO | 1.71 | −5.42 | −11.63 | 17.64 | 126 | 100 | 126 |
| BACE 1 | 5HU1 | 1.50 | 25.15 | 12.50 | 22.70 | 126 | 126 | 126 |
| BChE | 4TPK | 2.70 | −5.30 | 8.50 | 19.02 | 126 | 126 | 126 |
| BDNF | 1BND | 2.30 | 15.17 | −2.23 | 44.36 | 126 | 100 | 126 |
| CDK5 | 7VDP | 2.09 | 50.40 | −35.86 | 57.20 | 126 | 126 | 126 |
| GSK3β | 6V6L | 2.19 | 1.98 | 14.46 | −11.31 | 126 | 126 | 126 |
| PSEN1 | 8KCS | 2.40 | 167.34 | 174.10 | 156.71 | 126 | 126 | 126 |
| PSEN2 | 7Y5X | 3.00 | 108.38 | 109.92 | 95.28 | 126 | 126 | 126 |
In addition to the primary protein-ligand complexes used in this study, two additional experimentally characterized co-crystal structures, namely, AChE complexed with tacrine (PDB ID: 7XN1) and GSK3β complexed with ANP (also known as SB216763; PDB ID: 1PYX), were incorporated into the docking validation dataset to further evaluate the reliability and reproducibility of the docking protocol. The grid box parameters for AChE (PDB ID: 7XN1) were set to a grid center of X = 55.84, Y = −32.94, and Z = −30.23 Å, with grid dimensions of X = 126, Y = 126, and Z = 126 Å. Similarly, the grid box parameters for GSK3β (PDB ID: 1PYX) were set to a grid center of X = 28.17, Y = 7.84, and Z = 38.91 Å, with grid dimensions of X = 126, Y = 126, and Z = 126 Å.
Preparation of the ligand library
A ligand library consisting of 2,847 phytochemicals was retrieved from the PubChem database “KEGG: Phytochemicals” (retrieved from https://pubchem.ncbi.nlm.nih.gov/classification/#hid=5 in February 2025). The ligands obtained in SDF format were prepared for molecular docking by removing water, adding polar hydrogens, allowing rotatable bonds to be rotatable, adding Gasteiger charges, and converting to PDBQT format suitable for AutoDock Vina. Ligand preparation was performed using Open Babel 3.1.1, and automated using an in-house python script (Houston et al., 2015).
Molecular docking
Following target and ligand preparation, AutoDock vina_1.2.7 was utilized to dock the ligands to the target proteins (Trott and Olson, 2010). An in-house python script was used to automate the docking process. The default setting of AutoDock Vina, including the number of poses (N = 9), exhaustiveness (8), and spacing angstrom (0.375) were left unchanged. For each ligand, the pose with the lowest binding energy was picked as the best pose. Co-crystalized ligands were used to validate our docking settings.
Multitarget filter
After molecular docking, the top 100 ligands (of 2,847 phytochemical compounds) were retained for each target based on their binding energy for further screening. Top ligands that targeted three or more protein were considered multitarget ligands.
Other physicochemical descriptors, including log P, molecular weight, hydrogen bond donors/acceptors, and total polar surface area (TPSA), were also considered using relaxed criteria rather than strict drug-like cutoff thresholds, allowing compounds with potentially favorable characteristics outside conventional drug-likeness ranges to be retained. This is because adherence to strict drug-like filter cutoffs can reduce exploration of chemical space and exclude potentially effective compounds (Kattuparambil et al., 2025) and, moreover, relaxing conventional physicochemical filters have been shown to expand accessible chemical diversity and capture novel scaffolds in drug discovery (Alzyoud et al., 2022).
Interaction analysis
To understand the binding mechanism and interacting residues, interaction analysis was performed for selected ligands using Protein-Ligand Interaction Profiler (PLIP), an automated web-based tool to analyze protein-ligand interactions based on the PDB file format of protein-ligand complexes (Schake et al., 2025).
Molecular dynamics simulation
To understand the stability of the protein-ligand complex over time, molecular dynamics simulations were performed for selected ligands commonly targeting Acetylcholinesterase (AChE) and glycogen synthase kinase three beta (GSK3β). We Followed protocols from previous studies (Vander Meersche et al., 2024) and gromacs tutorial (Lemkul, 2018). Briefly, the crystal structure of the targets was processed, and missing atoms were fixed using PDBfixer. Gromacs compatible protein topology was generated using charmm36 force field and charmm-modified tip3p water model. The terminal residues were assigned their standard protonation states, with the N-terminus protonated (NH3 +) and the C-terminus deprotonated (COO−), to represent physiological ionization states and ensure proper electrostatic interactions during molecular dynamics simulations. Prior to processing the ligand topology, the pdbqt format of the poses was converted to mol2 format, suitable for CGenFF processing, and all hydrogens were added to make suitable for all atom MD simulations. Ligand structures were processed using ‘perl sort_mol2_bonds.pl’ script, downloaded from gromacs tutorial, to ensure consistent connectivity and compatibility with the CHARMM/CGenFF topology generation. Then, CGenFF server was used to generate gromacs compatible ligand topology and parameter files and, the ligand coordinate file was converted to its gromacs format. The protein-ligand complex was built by merging the ligand and protein coordinate files and the system topology was updated to include ligand specific parameters and atom count. The system was then placed in a dodecahedral simulation box with a 1.0 nm buffer from the protein surface and solvated with TIP3P water models and neutralized with Na+/Cl− ions. To optimize the system’s geometry, energy minimization was performed using the steepest descent algorithm for 50,000 steps. Equilibration was then performed following the application of positional restraints to the heavy atoms of the ligand, allowing the solvent and protein to relax while maintaining the ligand in its binding site. Subsequently, we conducted equilibration in a canonical ensemble (NVT) for 100 ps with a 2fs time step using leap-frog integrator. Similarly, equilibration in an isothermal-isobaric thermodynamic ensemble (NPT) was followed by employing leap-frog integrator. The temperature was maintained at 300 K using the modified Berendsen thermostat with a constant time of 0.1 ps. During NPT equilibration, we maintained the pressure at 1 bar using the isotropic Berendsen barostat with a constant time of 2 ps. The final MD simulations were carried out with a time step of 2 fs and total simulation time of 50 ns. Covalent bonds involving hydrogen atoms were constrained using the LINCS algorithm in all the simulations. Long-range electrostatic interactions were managed using the Particle-Mesh Ewald (PME) method. FDA approved acetylcholinesterase inhibitor drugs, Donepezil (Lilienfeld, 2002; Shiget et al., 2001), and clinical inhibitors of GSK3β (Ramurthy et al., 2020) was used as a standard comparison. The obtained MD trajectories were subjected to the analysis of root mean square deviation (RMSD); root mean square fluctuations (RMSF) and radius of gyration (Rg) to assess the overall behavior of the protein and the local flexibility of its backbone.
Results
Protein Targets strongly Associated with Alzheimer’s Disease (AD). To identify top genes associated with AD, we used a widely adopted strategy in biomedical research based on normalized PubMed association scores (Wang et al., 2020; Grissa et al., 2022; Raj et al., 2024). Our literature-mining approach identified the top target proteins associated with AD. PubMed literature count for the top genes and their cooccurrence with AD is presented in Table 2. This table presents the number of publications mentioning each gene, and their co-occurrence with AD.
TABLE 2. Protein Targets strongly Associated with Alzheimer’s Disease.
| Gene ID | GeneName | PubMed citations | Normalized association (%) | |
|---|---|---|---|---|
| Gene | Gene and AD | |||
| PSEN1 | Presenilin 1 | 6,253 | 4,460 | 71.3 |
| PSEN2 | Presenilin 2 | 1,479 | 963 | 65.1 |
| AβPP | Amyloid beta precursor protein | 908 | 434 | 47.8 |
| BACE | Beta-secretase 1 | 441 | 211 | 47.8 |
| MAPT | Microtubule associated protein tau | 2,548 | 811 | 31.8 |
| APOE4 | Apolipoprotein E | 19683 | 4,797 | 24.4 |
| AChE | Acetylcholinesterase | 22994 | 4,317 | 18.8 |
| BChE | Butyrylcholinesterase | 7,684 | 1,233 | 16.0 |
| CDK5 | Cyclin dependent kinase 5 | 2,644 | 327 | 12.4 |
| GSK3β | Glycogen synthase kinase 3 beta | 10445 | 777 | 7.4 |
| BDNF | Brain derived neurotrophic factor | 29895 | 983 | 3.3 |
The most frequently associated genes include γ secretase subunits, Presenilin 1 and 2 (PSEN1 and PSEN2), Amyloid precursor protein (APP), and β secretase enzymes (BACE 1) with a normalized PubMed association of 71%, 65%, 48% respectively. These top genes collectively represent a cascade of amyloidogenic pathway in AD. Mutations in PSEN1/PSEN2 alters cleavage site preference of γ-secretases, resulting to the increased production of longer and aggregation prone Aβ peptides (Willumsen et al., 2023; Kurth et al., 2023; Cai et al., 2015; Liu et al., 2024). Mutations in PSEN1 are the predominant cause of familial Alzheimer’s disease (fAD), whereas PSEN2 mutations are much rarer (Xiao et al., 2021). APP is the substrate for β and γ-secretases and central to Aβ production in AD (Sirisi et al., 2024). The Swedish mutation in APP makes its β-site to be more accessible to β-secretase enzymes (BACE1) and increases its cleavage efficiency, associated to increased production of Aβ (Zhang et al., 2017). Collectively, these top genes are major drivers of familial Alzheimer’s disease (FAD). Following, are microtubule associated protein tau (MAPT), apolipoprotein E4 (APOE4), acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), with normalized association of 32%, 24%, 19% and 16% respectively. Hyperphosphorylation of tau and its aggregation into neurofibrillary tangles is a hallmark feature of AD (Giovinazzo et al., 2021). Glycogen synthase kinase three beta (GSK3β) and cyclin dependent kinase 5 (CDK5) are the major kinase proteins responsible for hyperphosphorylation of MAPT (Giovinazzo et al., 2021; Jayapalan and Natarajan, 2013). Hyperphosphorylation of MAPT decreases its binding affinity to microtubules resulting in its destabilization and cellular dysfunction (Man et al., 2023).
Apolipoprotein E4 (APOE4, 24.4%) is the strongest genetic risk factor in AD. It reduces clearance of Aβ and promotes its accumulation and aggregation (Raulin et al., 2022), enhance tau phosphorylation and aggregation (Koutsodendris et al., 2023) and disrupt blood brain barrier (BBB), increasing permeability and enabling entry of neurotoxic agents (Reas et al., 2024; Kirchner et al., 2023). The cholinesterase enzymes (AChE and BChE) are responsible for hydrolyzing acetylcholine, a neurotransmitter critical for learning and memory, and cause cholinergic deficits contributing to cognitive dysfunction in AD (Chen et al., 2022; Sridhar and Gumpeny, 2024). BChE activity increases in later stage AD and compensates for lost AChE, further lowering acetylcholine levels. Glycogen synthase kinase three beta (GSK3β, 7.4%) and Cyclin dependent kinase (CDK 5, 12.4%) are the most common kinases driving tau hyperphosphorylation in AD (Rekha et al., 2025; Fu et al., 2025). GSK3β phosphorylates tau at multiple sites associated with reduced microtubule binding, increased aggregation, and formation of neurofibrillary tangles. Brain derived neurotrophic factor is responsible for promoting neuron survival and plasticity and its depletion is associated with cognitive decline (Ismail et al., 2020; Gao et al., 2022). Overall, our PubMed co-occurrence analysis have identified significantly AD associated genes, and this result is in agreement with previous studies (Grissa et al., 2022). The PubMed-normalized frequencies reflect not only literature prevalence but also the centrality of these genes in known AD molecular mechanisms.
Molecular docking validation
To validate our molecular docking setup, we predicted the binding affinity, of the native ligands with their respective target, namely, Donepezil with AChE (PDB ID: 4EY7, Kd = 8 nM) (Cheung et al., 2012), KQP with APOE4 (PDB ID: 6NCO, Kd = 30 μM) (Petros et al., 2019), Verubecestat with BACE1 (PDB ID: 5HU1, Ki = 2.2 nM) (Scott et al., 2016), 65L with CDK5 (PDB ID: 7VDP, IC50 = 2.3 nM) (Daniels et al., 2022), QQA with GSK3β (PDB ID: 6V6L, EC50 = 130 nM) (Ramurthy et al., 2020), and Osugacestat (a.k.a. BMS906024) with PSEN1 (PDB ID: 8KCS, IC50 = 21.7 nM) (Guo et al., 2025), Tacrine with AChE (PDB ID: 7XN1, IC50 = 44.6 nM) (Alrouji et al., 2024)) and ANP (a.k.a SB216763) with GSK3β (PDB ID: 1PYX, IC50 = 34.3 nM) (Hopkins et al., 2014). The redocked co-crystalized ligand’s predicted binding affinities were compared with experimental binding data. Redocking accuracy was further assessed by calculating the RMSD between the predicted and crystallographic ligand poses. Redocking of co-crystallized ligand into their corresponding receptor yielded RMSD values ≤ 2.1Å (Table 3), indicating that the docking protocol reproduced the experimentally observed binding poses (Gupta et al., 2019). The correlation between the experimental and predicted ΔG values shown in Table 3 was moderately strong (R = 0.61). This correlation is acceptable, particularly since Kd values were unavailable for some ligands, and Ki, IC50, and EC50 values were used to calculate ΔG. As such, the correlation attests to the precision molecular docking.
TABLE 3. Predicted and experimental free-energy values (ΔG) of ligand/receptor pairs.
| PDBID | Predicted ΔG (kcal/mol) | Redocked pose RMSD (Å) | Experimental ΔG (kcal/mol) |
|---|---|---|---|
| 4EY7 | −11.8 | 2.0 | −11.1 |
| 7XN1 | −9.1 | 0.0 | −11.0 |
| 6NCO | −6.3 | 1.9 | −6.2 |
| 5HU1 | −8.3 | 0.7 | −11.9 |
| 7VDP | −8.4 | 1.9 | −11.8 |
| 6V6L | −8.4 | 1.3 | −9.4 |
| 1PYX | −7.8 | 1.8 | −10.2 |
| 8KCS | −9.2 | 1.3 | −10.5 |
Molecular docking and multitarget screening
Molecular docking is an efficient technique to identify potential binding compounds to the biological target of interest (Alrouji et al., 2024). Here, a total of 2,847 phytochemicals retrieved from PubChem database were subjected to molecular docking using AutoDock Vina. The top 100 ligands of each target were retained based on docking binding affinity scores, resulting 362 unique phytochemical compounds. The fact that only 362, and not close to 1,000, different ligands bind to the top 10 protein targets, indicates that only a portion of the ligands bind to multiple targets, at the same time. Next, we screened based on multitarget binding and retained ligands that target three or more AD targets, reducing the dataset to 96 unique phytochemicals (Supplementary Table S1).
Following, we excluded ligands with more than 33 heavy atoms. Ligands with less heavy atoms are associated with better ligand efficiency metrics (Hopkins et al., 2014). In addition, ligands with heavy atoms counts in the range 10–33, are associated with better prediction scores of BBB penetration (>0.6), using the cubic polynomial function F(x)=(0.0000443x3−0.004556x2+0.12775x−0.463)/0.624231) developed by Weaver and coworkers (Gupta et al., 2019). This reduced the final dataset to 36 ligands with 33 heavy atoms, or less. Figure 1 describes the general procedure followed in our virtual screening.

Molecular docking results of the top hits of all phytochemicals to the AD targets are presented in Figure 2. To visualize the binding site, multitarget ligands were superimposed against their respective targets and visualized using PyMol.

Our docking result showed that top ligands of cholinesterase enzymes, AChE and BChE (Figures 2B,E respectively), potentially bind very strongly at the entrance of the gorge leading to the catalytic site occluding access to the active site (Žužek, 2024). Ligands may either effectively blocking the entrance peripheral anionic site (PAS) or occupying the catalytic active site (CAS), thus potentially preventing acetylcholine from reaching the active site, and from undergoing catalytic breakdown (Žužek, 2024). Our top ranked AChE ligands exhibited favorable binding energies (ΔG between - 11.0 and −9.0 kcal/mol) comparable to the co-crystallized AChE inhibitor, Donepezil (ΔG = −11.8 kcal/mol) approved by the FDA, supporting their promising potential as lead compounds for experimental validation of AChE inhibitors.
The top ligands of CDK5 and GSK3β preferentially docked strongly (ΔG between −10.0 to −8.4 kcal/mol and −10.3 to −8.6 kcal/mol respectively) inside the canonical ATP-binding pocket (Figures 2G,H), a well-characterized active site where many of the classical CDK5 and GSK3β inhibitors bind to prevent phosphorylation of downstream substrates (Gao et al., 2021; Zeb et al., 2019; Balboni et al., 2023; Shri et al., 2023). As such, our top and multitarget ligands may act similarly by occluding ATP-binding competitively thus potentially reducing CDK5 and GSK3β mediated phosphorylation. Notably, recent studies, have also identified highly potent CDK5 and GSK3β inhibitors at the same binding site, by employing structure guided design and cell-based assays (Balboni et al., 2023; Azm et al., 2025; Alhassan, 2025; Pandya et al., 2024; Daniels et al., 2022). These inhibitors, which were co-crystallized in the native PDB structures of CDK5 (Daniels et al., 2022) (PDB ID 7VDP, ligand ID: 65L) and GSK3β (Ramurthy et al., 2020) (PDB ID: 6V6L, ligand ID: QQA) were redocked and used as a standard internal reference of our molecular docking. The co-crystallized inhibitors were also predicted to bind in their native ATP binding-site with binding energies similar to those our top multitarget ligands. As such, our top ranked ligands exhibited favorable binding energies to CDK5 and GSK3β comparable, or better, to the co-crystallized inhibitors 65L (ΔG = −8.4 kcal/mol), and QQA (ΔG = −8.4 kcal/mol), supporting their promising potential as lead compounds for experimental validation.
The top ligands of PSEN1 (Figure 2I) potentially bind strongly (ΔG between −10.8 to −8.7 kcal/mol) at the active site cavity like many other γ-secretase inhibitors (GSIs), including the former drug candidates Semagacestat and Avagacestat, that have been shown to occlude the active site of PSEN1, and inhibit formation of Aβ peptides (Yang et al., 2021). Moreover, the top ligands predicted binding energies were comparable, or higher, than those of Osugacestat (ΔG -9.2 kcal/mol), the co-crystallized inhibitor of PSEN1 (PDB ID 8KCS, ligand ID: Q70) (Guo et al., 2025). As such, our top ligands are promising candidates for experimental validation of γ-secretase inhibitors.
The top ligands of BACE1 (Figure 2D) potentially binds at the active site determined by high-resolution X-ray crystallography, like other BACE1 inhibitors (Pettus et al., 2020; Rueeger et al., 2021). The predicted binding energies of our top ligands of BACE1 (ΔG between −9.3 to −8.1 kcal/mol) were comparable or better to those of Verubecestat (ΔG −8.3 kcal/mol), the co-crystalized ligand of BACE1 PDB structure (PDB ID 5HU1, ligand ID: 66F) (Scott et al., 2016). Like Verubecestat our top ligands may competitively block APP substrate access to the catalytic site, thereby disrupting amyloid-β generation via BACE1 cleavage, pending experimental verification.
The top ligands of APOE4 potentially binds strongly (ΔG between −9.6 and −7.4 kcal/mol), with binding poses and affinities comparable with the previously identified APOE4 stabilizer, co-crystallized in the native PDB structure (PDB ID 6NCO, ligand ID: KQP) (Petros et al., 2019), (Figure 2C). Like KQP, our top ligands may also contribute to stabilizing the APOE4 pending experimental validation.
Collectively, the higher binding affinity to these targets can be attributed to the presence of well-defined pocket, or groove-like architectures, on the protein structures, which provide shape complementarity and persistent interaction hotspots (Cucuzza et al., 2023; Spassov, 2024).
Supplementary Table S1 lists 96 multitarget ligands that potentially bind to 3, or more, biological targets, including Aβ, AChE, APOE4, BACE1, BChE, BDNF, CDK5, GSK3β, PSEN1 and PSEN2. The multitarget ligands that potentially bind to more than a single target, are promiscuous, and have been reported to play an important role in polypharmacology (Haupt et al., 2013). The multitarget ligands are often considered for drug repurposing strategies, and have shown increasing success rates (Haupt et al., 2013; Comajuncosa-Creus et al., 2024). The multitarget ligands exhibit remarkable adaptation to multiple binding sites and have been known to expand rational design of polypharmacologic drugs (Duran-Frigola et al., 2017). Polypharmacology is a new paradigm shift in drug discovery for complex diseases where multiple proteins and pathways are involved in the onset and development of the disease, due to cumulative efficacy at all of its individual targets (Kabir and Muth, 2022). Hence, multitarget (promiscuous) ligands are considered promising in polypharmacology to address several key disease drivers simultaneously (Kabir and Muth, 2022; Abdelsayed, 2025) and, due to this, current research supports the concept of polypharmacology and intentionally incorporating promiscuity in molecules to make them polypharmacologic (Kabir and Muth, 2022). However, the promiscuity of multitarget ligands also potentially increase adverse effects due to non-specific pharmacological activity (Abdelsayed, 2025). Highly promiscuous ligands may exert unintended off-target effects and may pose toxicity. Thus, moderate multitarget ligands, binding some, but not all targets, may be advantageous, and balance therapeutic efficacy versus off-target toxicity. Therefore, not all multitarget phytochemicals may be beneficial for therapeutic use in AD, and moderately promiscuous ligand may be preferred, as seen later in our discussion.
Supplementary Table S1 also lists the physicochemical descriptors that broadly influence the ADMET (absorption, distribution, metabolism, excretion and toxicity) properties of small molecules and commonly used to define drug-likeness (Leeson et al., 2021; Rawat et al., 2024). For comparison, the physicochemical properties of our top hits, including with co-crystallized approved AChE inhibitor (Donepezil) and clinical inhibitors of APOE4 (KQP), BACE1 (Verubecestat), CDK5 (65L), GSK3β (QQA) and PSEN1 (Osugacestat) are presented in Supplementary Table S1. Multiple studies consistently shown that successful CNS drugs exhibit narrower physicochemical space than general drugs mainly to cross the blood brain barrier (BBB). Analysis of CNS drugs tend to exhibit lower molecular weight, topological polar surface area, moderate lipophilicity and smaller number of hydrogen bond donors and acceptors to facilitate passive diffusion across the BBB and enhance membrane permeability (Dehnbostel et al., 2024; Kenny, 2022; Markowicz-Piasecka et al., 2022; Odi et al., 2020). Finally, lower heavy atom counts are often associated with improved BBB permeability because they correlate with lower molecular weight and lower polarity (Gupta et al., 2019). While the strict rules are for oral bioavailability, it also affects the general ADMET properties of molecules. Here, we propose to focus on the smallest ligands, with less than 33 heavy atoms. This measure considers ligand efficiency (LE) metrics per heavy atom, where smaller compounds with good potency are preferred. Figure 3 shows 36 multitarget ligands and contain 33 or less heavy atoms, and that bind three, or more, AD protein targets. These 36 multitarget ligands emerge as promising polypharmacologic agents for experimental validation.

Notably, of our smallest 36 top multitarget ligands, 11 fulfill Lipinski’s rule of five for oral availability, 11 have no violations (Rutecarpine, Sanguinarine, Strychnine, Cyclopamine, Lactucopicrin, Hecogenin, Jervine, Ruscogenin, Verticine, Verticinone, Obacunone (Lipinski et al., 2001) and 25 have one violation (logP). Of the remaining 60 top multitarget ligands, for example, Amentoflavone, Robustaflavone, Cassiamin C and Ginkgetin have more than one violation (Lipinski et al., 2001). In comparison, the FDA approved Donepezil and other co-crystalized inhibitors also fulfill Lipinski’s rule of five. Rutecarpine, which potentially binds to AChE, CDK5 and GSK3β, is the smallest molecule, with narrow physicochemical properties space, making it an attractive CNS relevant molecule (Xu et al., 2022). Here, we focus on the 36 top ligands, with the lowest number of heavy atoms.
Interaction analysis
To better understand the binding patterns of the complexes, we performed interaction analysis for selected molecules utilizing Protein-Ligand Interaction Profiler (PLIP), an automated web-based tool to analyze protein-ligand interactions based on the PDB file format of protein-ligand complexes (Schake et al., 2025). The protein ligand complex was first formed from the AutoDock Vina docking results using PyMol and then provided to PLIP for interaction analysis. Molecules commonly targeting AChE and GSK3β (Lactucopicrin, Oleanolic acid and Rutecarpine) were used for interaction analysis and their interactions were compared with the co-crystalized ligands. The hydrogen bond interacting residues identified by PLIP were highlighted using PyMol in the protein’s structure (Figure 4).

Accordingly, Lactucopicrin formed hydrogen bonds with TYR72, TYR124 and SER293 of AChE (Figure 4A). TYR72 and TYR124 are part of the peripheral anionic site located at the entrance of the active site gorge known to modulate substrate passage and inhibitor binding (de Almeida et al., 2023). Molecules binding to these regions such as Kaempferol, induce conformational changes and inhibit catalytic activity of AChE (Shi et al., 2023). Oleanolic Acid formed hydrogen bond with ARG247 of AChE (Figure 4B), a residue identified as part of the acyl loop door and binding to this site can participate in a non-competitive inhibition mechanism of the enzyme’s activity (Moghadam et al., 2021). Rutecarpine formed π-π stacking interactions with residues TRP286 and TYR341 of the active site of AChE (Figure 4C), similarly as the native ligand, Donepezil (Gondal et al., 2023). Notably, TRP286 also formed π-π stacking interactions with Rutecarpine, lactucopicrin and donepezil, indicating its hotspot recurrent interacting residues. In comparison, the native AChE ligand Donepezil formed hydrogen bonding with PHE295 (Figure 4D), similar to previous reports (Gupta et al., 2024), validating the setup of our molecular docking experiments, and of our other prediction.
Similarly, the same ligands form multiple interactions with active site residues of GSK3β. Lactucopicrin forms hydrogen bonds with ASP200 and LYS85 (Figure 4E) and oleanolic acid formed salt bridges with ARG141 and ARG144 (Figure 4F). The native ligand QQA formed hydrogen bond with ASP133 and VAL135 (Figure 4G). The identified residues are part of the ATP binding pocket and previously reported to be consistent interacting residues in small molecule inhibitors of GSK3β (Alhassan, 2025; Lu et al., 2018).
Unlike hydrophobic interactions, which are the predominant interactions in protein-ligand complexes and largely non-directional and entropy driven, hydrogen bonds are highly directional, with defined donor acceptor distances and angles that govern ligand specificity in biological recognition (Ferreira de Freitas and Schapira, 2017; Bissantz et al., 2010). As such, ligands forming hydrogen bond at the functional site of the receptors may be effective in orienting the ligand in fixed functional positions.
Molecular dynamics simulations
To better evaluate ligand binding stability, molecular dynamics (MD) simulations were performed for the selected phytochemicals targeting both AChE and GSK3β (Lactucopicrin, Oleanolic Acid, and Rutecarpine). Importantly, the AChE backbone remained globally stable in complex with these ligands, exhibiting maximum backbone RMSD values of approximately 2.5 Å (Figure 5A), consistent with structurally stable protein-ligand complexes (Weng et al., 2021; Verma et al., 2022). Notably, Rutecarpine derivatives have been shown to inhibit AChE (Wang et al., 2010). Likewise, Oleanolic acid was found to inhibit AChE (Stępnik et al., 2023). Also, lactucopicrin have been shown to inhibit AChE (Venkatesan et al., 2017). In GSK3β, ligand binding displayed lower backbone RMSD compared to the apo (unbound) form (Figure 5B), indicating reduced conformational fluctuations upon ligand binding. Interestingly, Rutecarpine has been shown to ameliorate spatial memory deficits and enhance synaptic plasticity in AD mice by modulating the GSK-3β signaling pathway (Li et al., 2023). Likewise, Oleanolic acid alleviates cerebral ischemia/reperfusion injury via regulation of the GSK-3β/HO-1 signaling pathway (Lin et al., 2021). Notably, throughout the simulation Lactucopicrin demonstrated greater structural stability than the co-crystallized control ligand, QQA, in GSK3β (Figures 5B,D,F). RMSF analysis revealed residue-level fluctuations generally below 1.0 Å for both AChE and GSK3β complexes (Figures 5C,D), supporting overall structural stability. Consistently, radius of gyration (Rg) analysis demonstrated preserved global compactness of both protein structures throughout the simulations (Figures 5E,F), further confirming the structural integrity of the ligand-bound systems.

Collectively, our MD simulation results indicate that Lactucopicrin, Oleanolic Acid, and Rutecarpine exhibit similar, or even improved dynamic stability, compared to both apo proteins and co-crystallized reference inhibitors, supporting the potential of our phytochemicals as promising candidates for experimental evaluation in AD therapy.
Discussion
The 36 top multitarget phytochemicals are classified into: Alkaloids (Rutecarpine, Sanguinarine, Strychnine), Steroidal alkaloids (Tomatidine, Cyclopamine, Jervine, Verticine, Verticinone), Steroidal sapogenins (Diosgenin, Hecogenin, Yamogenin, Tigogenin, Smilagenin, Sarsasapogenin, Neogitogenin, Ruscogenin), Triterpenoids/sterols (Alpha-spinasterin, Fucosterol, Stigmasterol, Beta-sitosterol, Gamma-sitosterol, Isofucosterol, Germanicol, Lupeol, Beta-amyrin, Alpha-amyrin, Taraxerol, Friedelin, Tetrahymanol, Tingenone, Parkeol, Methylenecycloartanol, Ursolic acid, Oleanolic acid, Obacunone), and Sesquiterpene (Lactucopicrin).
The list of top 36 final phytochemicals along with their chemical structure are presented in Table 4.
TABLE 4. Classification of chemical structures of 36 multitarget phytochemicals.
| Classification | Phytochemical ligand | Structure | Protein targets |
|---|---|---|---|
| Alkaloids | Rutecarpine | Chemical structure diagram showing a fused ring system with one indole ring, a benzene ring, and a diazepinone ring, representing the molecular structure of the compound benzodiazepine. | 3 |
| Sanguinarine | Line drawing illustrating a molecular structure with three fused aromatic rings, two five-membered rings containing oxygen atoms, and a central nitrogen atom bonded to a methyl group and positively charged. | 4 | |
| Strychnine | Chemical structure diagram of a compound containing a fused ring system with two nitrogen atoms, two ketone groups, and a phenyl ring attached, depicted in black lines on a white background. | 3 | |
| Steroidal alkaloids | Tomatidine | Chemical structure illustration showing a steroid backbone with multiple fused rings, an amine group, an oxygen atom within a ring, and a hydroxyl group attached to the rightmost ring. | 8 |
| Cyclopamine | Chemical structure diagram showing interconnected hexagonal and pentagonal rings with nitrogen, oxygen, and hydroxyl groups, indicating a complex organic molecule. Bonds and chiral centers are represented with standard line notation. | 6 | |
| Jervine | Chemical structure diagram showing penicillin’s core fused rings, including a β-lactam ring, thiazolidine ring, and attached side chains, with nitrogen, oxygen, and hydroxyl functional groups represented by standard skeletal formulas. | 5 | |
| Verticine | Chemical structure diagram displaying a complex polycyclic molecule with multiple rings, hydroxyl groups labeled OH, and a single nitrogen atom, likely representing a steroidal alkaloid or related compound. | 4 | |
| Verticinone | Chemical structure diagram showing a pentacyclic molecule with multiple rings, labeled with one nitrogen atom, two hydroxyl groups, and a ketone functional group attached to different carbon atoms, depicted using solid and dashed wedges for stereochemistry. | 4 | |
| Steroidal sapogenins | Diosgenin | Structural formula diagram showing a complex organic molecule with four fused rings, two oxygen atoms forming part of rings on the left, and a hydroxyl group attached to the rightmost ring. | 7 |
| Hecogenin | Chemical structure diagram showing a multicyclic organic molecule with multiple hexagonal and pentagonal rings, several chiral centers, two ketone groups, two oxygen-containing rings, and a hydroxyl group attached to the rightmost ring. | 6 | |
| Tigogenin | Chemical structure diagram showing a multi-ring steroid framework with a hydroxyl group attached to the rightmost ring and two oxygen atoms integrated in the leftmost ring system. | 6 | |
| Smilagenin | Chemical structure diagram showing a multi-ring steroid molecule with four fused rings, one of which contains an oxygen atom, and a hydroxyl group attached to one end. | 4 | |
| Ruscogenin | Chemical structure diagram showing a steroid molecule with fused cyclohexane rings, two hydroxyl groups attached at different positions, and an oxygen atom forming an ether bridge within one ring. | 4 | |
| Yamogenin | Chemical structure diagram showing a multi-ringed steroid framework with a fused lactone ring on the left and a hydroxyl group attached to a six-membered ring on the right. | 4 | |
| Neogitogenin | Chemical structure diagram showing rings, oxygen atoms, and hydroxyl groups, representing a steroid molecule with fused rings, oxygen bridges, and two OH groups attached to different carbon atoms. | 3 | |
| Sarsasapogenin | Chemical structure diagram showing a steroid molecule with four fused rings, one containing an oxygen atom, and a hydroxyl group (OH) attached to the rightmost ring. | 3 | |
| Triterpenoids | Alpha-spinasterin | Chemical structure diagram of cholesterol showing four fused hydrocarbon rings, a branched hydrocarbon tail on the left, and a hydroxyl group attached to the rightmost ring. | 3 |
| Fucosterol | Chemical structure diagram showing a complex polycyclic ring system with side chains and a hydroxyl group labeled as OH attached to the rightmost ring. | 3 | |
| Isofucosterol | Chemical structure diagram depicting cholesterol, showing four fused hydrocarbon rings, a branched hydrocarbon tail on the left, several methyl groups, and a hydroxyl group attached to the right end of the structure. | 4 | |
| Stigmasterol | Chemical structure diagram illustrating cholecalciferol, also known as vitamin D3, with several hexagonal and pentagonal rings, multiple methyl groups, and a hydroxyl group attached at the right end. | 3 | |
| Beta-sitosterol | Chemical structure diagram showing a multi-ring molecule with several hexagonal rings fused together, a branched hydrocarbon side chain, and a hydroxyl group (-OH) attached to the rightmost carbon ring. | 4 | |
| Gamma-sitosterol | Chemical structure diagram displaying a complex organic molecule with four fused rings, a branched hydrocarbon tail, multiple chiral centers, and a hydroxyl group attached to one ring, characteristic of cholesterol. | 5 | |
| Germanicol | Chemical structure diagram showing a multi-ring steroid molecule with interconnected hexagonal and pentagonal rings, methyl groups, and a hydroxyl group attached at the terminal right position. | 9 | |
| Lupeol | Chemical structure diagram of a steroid molecule showing four fused carbon rings with several methyl and hydroxyl groups attached, indicated by wedge and dash lines representing stereochemistry. | 3 | |
| Beta-amyrin | Chemical structure diagram showing a steroid backbone with four fused rings and a hydroxyl group attached at the end of the rightmost ring, representing a molecule of cholesterol. | 10 | |
| Alpha-amyrin | Chemical structure diagram of cholesterol, displaying four fused carbon rings with various side groups and a hydroxyl group (OH) attached at the end, represented using standard line notation. | 7 | |
| Taraxerol | Chemical structure diagram showing a polycyclic hydrocarbon skeleton with four fused rings, multiple methyl groups, and a single hydroxyl group attached to the side, representing the molecular structure of cholesterol. | 8 | |
| Friedelin | Chemical structure diagram showing a four-ring fused steroid backbone with three six-membered rings and one five-membered ring, including methyl groups and a ketone functional group on the right ring. | 3 | |
| Tetrahymanol | Skeletal chemical structure diagram showing several fused rings and a hydroxyl group (OH) attached on the right, representing a sterol molecule such as cholesterol. | 7 | |
| Tingenone | Line drawing of a steroid molecule showing four fused rings, with branches indicating ketone and hydroxyl groups, and dashed bonds showing stereochemistry at several positions. | 3 | |
| Parkeol | Chemical structure diagram of cholesterol showing a four-ring fused system with a hydroxyl group, a branched alkyl side chain, and multiple stereochemical indicators throughout the rings and substituents. | 3 | |
| Methylenecycloartanol | Chemical structure diagram displaying interconnected hexagonal and pentagonal rings with a branched side chain and a hydroxyl group (OH) attached at the right end, commonly representing cholesterol. | 3 | |
| Ursolic acid | Structural diagram of ursolic acid, a pentacyclic triterpenoid molecule with five fused rings, a hydroxyl group on the left, and a carboxyl group with a double-bonded oxygen on the upper right. | 4 | |
| Oleanolic acid | Chemical structure diagram showing a tetracyclic steroid framework with a hydroxyl group on the left and a carboxylic acid group on the right, depicting ursolic acid. | 3 | |
| Obacunone | Chemical structure diagram showing a complex polycyclic molecule with several fused rings, multiple oxygen atoms as carbonyl and ether groups, and a phenyl ring attached on the left side. | 5 | |
| Sesquiterpene | Lactucopicrin | Chemical structure diagram displaying a molecule with fused rings, ketone, carboxylic acid, and ester functional groups, as well as a phenol group attached by an ester linkage on the left. | 3 |
Alkaloids (Rutecarpine, Sanguinarine, Strychnine)
Alkaloids constitute a major class of nitrogen-containing natural products characterized by extensive structural diversity and a wide range of pharmacological as well as toxicological activities (Kita et al., 2025). Due to their ability to interact with multiple cellular signaling pathways and molecular targets, many alkaloids have demonstrated significant neuroprotective, anti-inflammatory, antioxidant, and neuromodulatory effects relevant to the pathogenesis of AD (Liu et al., 2023). Among the compounds investigated in this study, Rutecarpine has emerged as a particularly promising candidate with multimodal neuroprotective potential. Rutecarpine has been reported to ameliorate spatial memory deficits and prevent tau protein hyperphosphorylation through inhibition of glycogen synthase kinase-3β (GSK3β). In addition, it has been shown to improve cognitive impairment by restoring mitochondrial function via activation of the AMPK/PGC1α signaling pathway (Gong and Jia, 2023). Consistent with these findings, Rutecarpine may exert beneficial effects in AD by suppressing platelet activation, reducing oxidative stress, and attenuating neuroinflammatory signaling while concurrently inhibiting the PI3K/Akt/GSK3β pathway implicated in tau hyperphosphorylation, thereby potentially alleviating cerebrovascular dysfunction and broader AD-associated neurodegenerative processes (Cao et al., 2024). Importantly, our molecular screening further supports these mechanistic insights, as Rutecarpine demonstrated a strong binding affinity toward GSK3β with a docking score of −9.4 kcal/mol, in agreement with previous experimental and computational studies (Huang et al., 2021).
In contrast, other alkaloids in this group are primarily associated with toxicity rather than therapeutic potential. Strychnine, a well-known neurotoxic compound, has been studied in the context of strychnine-sensitive glycine receptors, which are implicated in inhibitory neurotransmission and may be indirectly relevant to neurophysiological dysfunction in AD (Bukanova et al., 2016). However, due to its potent cytotoxic, vasoconstrictive and hypertensive effects, Strychnine is more likely to exacerbate neurovascular damage and contribute to disease pathology than to provide therapeutic benefit (Vezikov and Simpson, 2026). Similarly, Sanguinarine has been shown to induce apoptosis through reactive oxygen species generation in parasitic models (Li et al., 2022), reflecting its strong cytotoxic potential. Taken together, while certain alkaloids such as Rutecarpine demonstrate promising multitarget neuroprotective mechanisms relevant to AD, many compounds within this chemical class exhibit pronounced toxicity, limiting their suitability for direct therapeutic repurposing in AD.
Steroidal alkaloids (Tomatidine, Cyclopamine, Jervine, Verticine, Verticinone)
Steroidal alkaloids are major class of nitrogen containing natural products with structural diversity and broad pharmacological and toxicological activities (Daley and Cordell, 2021). Steroidal alkaloids identified among our top-ranked compounds have been increasingly associated with modulation of key pathological processes involved in AD, including tau hyperphosphorylation, amyloid processing, neuroinflammation, oxidative stress, and neuronal survival, highlighting their potential as multifunctional therapeutic.
Tomatidine, a steroidal alkaloid abundant in unripe tomatoes, has demonstrated neuroprotective effects, ameliorated cognitive deficits and reduced tau hyperphosphorylation (Zhang et al., 2025). In addition, Tomatidine significantly attenuated neuroinflammation and prevented microglial activation (Kita et al., 2025) both of which are key contributors to AD progression. These findings support its role as a multitarget neuroprotective agent capable of modulating multiple disease-relevant pathways. Likewise, Cyclopamine modulates γ-secretase-mediated cleavage of amyloid precursor protein by altering its subcellular trafficking and lysosomal degradation (Vorobyeva et al., 2014). Likewise, Cyclopamine rescues structural and behavioral deficits in a Drosophila model of AD (Nguyen et al., 2017).
On the other hand, Jervine, another steroidal alkaloid, is a potent dual-binding site inhibitors of both acetylcholinesterase and butyrylcholinesterase (Zheng et al., 2019). Jervine Verticine and Verticinone have been shown to inhibit both AChE and BChE and prevent Aβ aggregation (Zhu et al., 2026). Verticine and Verticinone also exhibit anti-inflammation, hepatoprotective, antitussive, and anticancer effects (Yin et al., 2019). However, Jervine, Verticine, and Verticinone have also shown cytotoxic and anti-tumor effects, potentially limiting their application in AD (Zheng et al., 2019).
Steroidal alkaloids are particularly noteworthy because their steroid-like hydrophobic scaffolds may facilitate interactions with membrane-associated proteins and signaling pathways implicated in neuronal survival and neuroinflammation. In addition, the presence of nitrogen-containing functional groups may enhance their capacity to interact with catalytically active residues within disease-associated protein targets and intercalate into DNA double-strands to modulate gene expression. Such structural features may contribute to multitarget pharmacological behavior increasingly considered advantageous for AD therapeutics. (Passos et al., 2022).
Steroidal sapogenins (Diosgenin, Hecogenin, Yamogenin, Tigogenin, Smilagenin, Sarsasapogenin, Neogitogenin, Ruscogenin)
Steroidal sapogenins are a structurally related class of steroid-derived natural products characterized by a hydrophobic steroidal core and varying oxygen-containing substituents that confer distinct biological activities. In this study, the steroidal sapogenins potentially bind to multiple AD protein target, in agreement with their neuroprotective, anti-inflammatory, antioxidant, and multitarget pharmacological properties relevant to the pathogenesis of Alzheimer’s disease (AD). In general, steroidal sapogenins have been shown to suppress neuroinflammatory signaling, while simultaneously attenuating oxidative stress and apoptotic pathways (Passos et al., 2022). In addition, steroidal sapogenins have demonstrated neuroprotective activity in both cellular and animal models of neurodegeneration (Sun et al., 2015). Among these compounds, Diosgenin reduces amyloid-β (Aβ) accumulation, suppresses oxidative stress and neuroinflammatory responses, and significantly improves spatial learning and memory performance (Som et al., 2022). Diosgenin also enhances cognitive function in healthy adults (Tohda et al., 2017). Ruscogenin also reduces neuroinflammation in rodents and attenuates ischemia-related BBB dysfunction via NF-κB and anti-inflammatory mechanisms (Cao et al., 2016). Moreover, Ruscogenin reduces oxidative stress and pro-inflammatory cytokine production in microglial cells in Parkinson’s disease mouse models, resulting in significant neuroprotective effects (Wu et al., 2023). In our study, Diosgenin strongly binds to amyloidogenic pathway associated proteins such as BACE1 and PSEN1, tau pathology associated proteins such as CDK5 and with the strong genetic factor protein APOE4 associated to altered clearance of Aβ. Notably, Hecogenin has also been computationally predicted as a potential BACE1 inhibitors (Padmanabhan et al., 2023). Yamogenin exhibits antidepressant effects and inhibits endoplasmic reticulum stress and microglial activation in lipopolysaccharide-induced mice (Chen P.-L. et al., 2023). Sarsasapogenin, another steroidal sapogenin, has shown to significantly inhibit key enzymes involved in pathogenesis of AD such as AChE, BChE, BACE1, and significantly inhibits Aβ42 fibrillization (Kashyap et al., 2020). Smilagenin is structural isomer of Sarsasapogenin and is likely to induce similar effects. Sarsasapogenin-derived timosaponin has also been proposed as novel Aβ-lowering modulators of APP processing (Sy et al., 2016). Collectively, these observations suggest that other top-ranked steroidal sapogenins identified in our study may exert therapeutic effects through multiple complementary mechanisms, including inhibition of amyloidogenic processing, modulation of tau-associated signaling pathways, suppression of neuroinflammatory cytokine production, attenuation of oxidative stress, and preservation of BBB integrity. Such multitarget activity is particularly advantageous in AD, a highly multifactorial neurodegenerative disorder involving interconnected pathological processes rather than a single dominant molecular driver. Consequently, steroidal sapogenins represent a promising class of naturally derived compounds for further investigation, and experimental validation, as multifunctional therapeutic candidates for AD.
Triterpenoids/sterols (Alpha-spinasterin, Fucosterol, Stigmasterol, Beta-sitosterol, Gamma-sitosterol, Isofucosterol, Germanicol, Lupeol, Beta-amyrin, Alpha-amyrin, Taraxerol, Friedelin, Tetrahymanol, Tingenone, Parkeol, Methylenecycloartanol, Ursolic Acid, Oleanolic Acid, Obacunone)
Triterpenoids represent a diverse class of naturally occurring terpenoid-derived compounds that have attracted increasing attention because of their broad pharmacological activities, particularly their antioxidant, anti-inflammatory, anti-apoptotic, and cytoprotective effects (Ling et al., 2022). These biological effects are highly relevant to the pathogenesis of Alzheimer’s disease (AD), in which oxidative stress, chronic neuroinflammation, synaptic dysfunction, and progressive neuronal degeneration collectively contribute to cognitive decline. Notably, many of our top ranked and multitarget triterpenoids identified in our study are supported by previous experimental evidence demonstrating neuroprotective activity in neurodegenerative disease models. Among these compounds, Ursolic acid has shown to improve spatial and recognition memory, to enhance adult hippocampal neurogenesis, and to restore synaptic marker expression in an Aβ injected mouse models (Mirza et al., 2021). Additional studies further showed that Ursolic acid attenuates Aβ-induced behavioral abnormalities, including aggression-like phenotypes, and promotes the clearance of toxic Aβ species from the brain (Wang N. et al., 2022). Oleanolic acid, a structural isomer of Ursolic acid, has similarly shown neuroprotective effect through inhibition of tau hyperphosphorylation and neuroinflammation, leading to improved cognitive function (Liu et al., 2025). Stigmasterol ameliorates neuroinflammation in an AD mouse model and attenuates inflammatory response of microglia via NF-κB, and NLRP3 signaling by AMPK activation (Jie et al., 2022). Likewise, β-Sitosterol ameliorates the cognitive deficits and neuropathological hallmarks in an AD mouse model (Ye et al., 2020). Fucosterol provides protection against amyloid β-induced neurotoxicity, reduces intracellular levels of amyloid β in a cellular model of AD (Gan et al., 2019).
These collective observations reinforce the concept that triterpenoid scaffolds possess multifunctional neuroprotective properties that extend across several neurodegenerative disease mechanisms.
Importantly, AD is a highly multifactorial disorder involving simultaneous dysregulation of amyloid processing, tau phosphorylation, oxidative stress, mitochondrial dysfunction, synaptic degeneration, and chronic neuroinflammation. Consequently, compounds capable of modulating multiple pathological pathways are increasingly recognized as promising therapeutic candidates. In this context, the multitarget interactions observed for the triterpenoids and sterol-like compounds identified in our study suggest that these molecules may attenuate AD pathology through coordinated modulation of several disease-associated protein targets. Their combined antioxidant, anti-inflammatory, and neuroprotective properties therefore support their potential utility as multifunctional therapeutic candidates for AD.
Sesquiterpene (Lactucopicrin)
Lactucopicrin is a sesquiterpene lactone that has been reported to exert strong anti-inflammatory and neuroactive properties relevant to the pathogenesis of Alzheimer’s disease (AD). Lactucopricrin has been identified as a potent inhibitor of the NF-κB inflammatory pathway, a central regulator of neuroinflammatory responses, suggesting anti-inflammatory potentialy (Ávila-Gálvez et al., 2025). In addition, it has been shown to inhibit AChE, which is typically impaired in AD (Jaśkiewicz et al., 2022).
Consistent with these findings, our molecular docking results demonstrate that Lactucopicrin binds strongly to multiple AD-relevant targets, including AChE, with a binding energy of −9.5 kcal/mol. This strong binding affinity supports previously reported mechanistic evidence and further suggests that Lactucopicrin may exert neuroprotective effects through a combination of anti-inflammatory and cholinesterase inhibitory mechanisms, both of which are highly relevant to AD pathology.
Generally, the appearance of many phytochemicals in our top and multitarget hits with experimental evidence neuroprotection in AD and other neurodegeneration disease models shows the robustness of our screening approach and, as such, our other top and multitarget phytochemicals may potentially be relevant for the treatment of Alzheimer’s disease.
Overall, several of the identified phytochemicals, including Rutecarpine, Diosgenin, Oleanolic acid, Ursolic acid, Lactucopicrin, Hecogenin, Sarsasapogenin, Fucosterol, β-Sitosterol, and Stigmasterol, have previously been reported to exhibit neuroprotective or AD-relevant activities through diverse mechanisms. Our multitarget virtual screening therefore provides additional mechanistic hypotheses by identifying molecular targets through which these compounds may exert their experimentally observed pharmacological effects.
Limitations
As a potential limitation to this study, it is crucial to note that our findings are based on computational work. For example, molecular docking is inherently limited by the accuracy of scoring functions. Therefore, the beneficial or deleterious effect of these phytochemicals in AD treatment remains to be validated experimentally and clinically. In addition, clinical validation is required to evaluate the overall effect of promising candidates for repurposing.
Another possible limitation to this study is that the literature-mining method used in this study is based on normalized PubMed association scores and is thus subject to the current state of the published literature. As a result, well-studied genes may receive higher association scores than lesser studied genes with emerging roles in AD. Although this strategy provides an objective and reproducible way to rank heavily studied targets, it may be biased against new or poorly studied proteins.
As another potential limitation to this study, multitarget phytochemicals do not necessarily indicate a better chance at AD treatment. In fact, multitarget phytochemicals could indicate less discriminate selectivity, and more potential toxicity. Thus, a balance between too much selectivity, and too little selectivity can be required to identify promising candidates.
In addition, molecular dynamics simulations were performed for 50 ns in a single run for each protein-ligand complex. Although the results consistently supported complex stability, replicate and extended simulation could provide additional confidence in the observed dynamic behavior.
Finally, as a limitation of this paper, the potential candidates for phytochemical treatment of AD include the top 96 ligands, but not automatically any other members of their drug families.
Conclusion
In conclusion, our integrated computational analysis highlights that multiple natural product families including alkaloids, steroidal alkaloids, steroidal sapogenins, triterpenoids/sterols, and sesquiterpenes exhibit consistent multitarget interactions with key proteins involved in Alzheimer’s disease pathology, including Aβ, AChE, BChE, APOE4, BACE1, BDNF, CDK5, GSK3β, PSEN1 and PSEN2. Some of our claims are supported by the literature, which shows that phytochemicals can inhibit amyloid aggregation, tau phosphorylation, neuroinflammation, and cholinergic dysfunction. Finally, the view that some of our claims are supported by literature lends credibility to our unsupported findings, and several of the identified structurally diverse phytochemicals represent a valuable source of multitarget-directed lead compounds for further development in AD therapeutics.
Generative AI statement
The author(s) declared that generative AI was not used in the creation of this manuscript.
Any alternative text (alt text) provided alongside figures in this article has been generated by Frontiers with the support of artificial intelligence and reasonable efforts have been made to ensure accuracy, including review by the authors wherever possible. If you identify any issues, please contact us.
Publisher’s note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
Supplementary material
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fddsv.2026.1922953/full#supplementary-material
Supplementary material Supplementary material at the source
Footnotes
Edited by: Marco A. Loza-Mejía, Universidad La Salle, Mexico
Reviewed by: Adam Dawria, King Khalid University, Saudi Arabia
Anguraj Moulishankar, Acharya and BM Reddy College of Pharmacy, India
Statements
- Conflict of interest
The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
- Funding
The author(s) declared that financial support was received for this work and/or its publication. Katz Foundation, Ginzburg Foundation.
- Data availability
The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.
- Author contributions
SM: Conceptualization, Data curation, Formal Analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Validation, Visualization, Writing – original draft, Writing – review and editing. NB: Project administration, Writing – original draft, Writing – review and editing. AS: Conceptualization, Formal Analysis, Funding acquisition, Investigation, Methodology, Resources, Supervision, Validation, Visualization, Writing – original draft, Writing – review and editing.
References
- Abdelsayed M. (2025). AI-Driven polypharmacology in small-molecule drug discovery. Int. J. Mol. Sci. 26 (14), 6996. doi:10.3390/ijms26146996
- Adelusi T. I., Oyedele A. Q. K., Boyenle I. D., Ogunlana A. T., Adeyemi R. O., Ukachi C. D. (2022). Molecular modeling in drug discovery. Inf. Med. Unlocked 29, 100880. doi:10.1016/j.imu.2022.100880
- Alhassan H. H. (2025). Integrative machine learning and molecular simulation approaches identify GSK3β inhibitors for neurodegenerative disease therapy. Sci. Rep. 15 (1), 21632. doi:10.1038/s41598-025-04129-7
- Allwright M., Mundell H. D., McCorkindale A. N., Lindley R. I., Austin P. J., Guennewig B. (2023). Ranking the risk factors for Alzheimer’s disease; findings from the UK biobank study. Aging Brain 3, 100081. doi:10.1016/j.nbas.2023.100081
- Alrouji M., Alhumaydhi F. A., Al Abdulmonem W., Sharaf S. E., Shahwan M., Majarisi T. (2024). Identifying β-secretase 1 (BACE1) inhibitors from plant-based compounds: an approach targeting Alzheimer’s therapeutics employing molecular docking and dynamics simulation. Mol. Divers. 28 (5), 2967 – 2980. doi:10.1007/s11030-023-10726-3
- Alzyoud L., Bryce R. A., Al Sorkhy M., Atatreh N., Ghattas M. A. (2022). Structure-based assessment and druggability classification of protein–protein interaction sites. Sci. Rep. 12 (1), 7975. doi:10.1038/s41598-022-12105-8
- Andrade-Guerrero J., Santiago-Balmaseda A., Jeronimo-Aguilar P., Vargas-Rodríguez I., Cadena-Suárez A. R., Sánchez-Garibay C. (2023). Alzheimer’s disease: an updated overview of its genetics. Int. J. Mol. Sci. 24 (4), 3754. doi:10.3390/ijms24043754
- Ávila-Gálvez M. Á., J G Pinto C., Rafael-Pita C., P Silva I., Janowska A. T., Marinho S. (2025). Lactucopicrin: a sesquiterpene lactone with anti-inflammatory activity modulates the crosstalk between NF-kB and AHR pathways. J. Med. Chem. 68 (21), 23406 – 23420. doi:10.1021/acs.jmedchem.5c02294
- Azmal M., Paul J. K., Talukder O. F., Been Haque A. S. N., Ghosh A. (2025). Computational identification of phytochemicals as glycogen synthase kinase 3 beta (GSK3β) inhibitors for therapeutic applications in chronic diseases. Sci. Rep. 15 (1), 34882. doi:10.1038/s41598-025-17343-0
- Balboni B., Masi M., Rocchia W., Girotto S., Cavalli A. (2023). GSK-3β allosteric inhibition: a dead end or a new pharmacological frontier? Int. J. Mol. Sci. 24 (8), 7541. doi:10.3390/ijms24087541
- Bassal R., Rivkin-Natan M., Rabinovich A., Michaelson D. M., Frenkel D., Pinkas-Kramarski R. (2025). APOE4 impairs autophagy and Aβ clearance by microglial cells. Inflamm. Res. 74 (1), 61. doi:10.1007/s00011-025-02016-5
- Ben Zaken K., Mesfin S., Bloch N., Samson A. O. (2025). Virtual screening of drugs against multiple targets of Alzheimer’s disease. J. Alzheimers Dis. 108 (3), 1088 – 1103. doi:10.1177/13872877251387167
- Bissantz C., Kuhn B., Stahl M. (2010). A medicinal chemist’s guide to molecular interactions. J. Med. Chem. 53 (14), 5061 – 5084. doi:10.1021/jm100112j
- Bukanova J. V., Sharonova I. N., Skrebitsky V. G. (2016). Functional modulation of strychnine-sensitive glycine receptors in rat hippocampal pyramidal neurons by amyloid-β protein (1-42). Brain Res. 1651, 61 – 72. doi:10.1016/j.brainres.2016.09.016
- Butler M. S., Capon R.J, Blaskovich M. A. T., Henderson I. R. (2025). Natural product-derived compounds in clinical trials and drug approvals. Nat. Prod. Rep. 43 (1), 20 - 88. doi:10.1039/d5np00031a
- Cai Y., An S. S., Kim S. (2015). Mutations in presenilin 2 and its implications in Alzheimer’s disease and other dementia-associated disorders. Clin. Interv. Aging 10, 1163 – 1172. doi:10.2147/CIA.S85808
- Cao G., Jiang N., Hu Y., Zhang Y., Wang G., Yin M. (2016). Ruscogenin attenuates cerebral ischemia-induced blood-brain barrier dysfunction by suppressing TXNIP/NLRP3 inflammasome activation and the MAPK pathway. Int. J. Mol. Sci. 17 (9). doi:10.3390/ijms17091418
- Cao Q., Dong P., Han H. (2024). Therapeutic effects of the major alkaloid constituents of Evodia rutaecarpa in Alzheimer’s disease. Psychogeriatrics 24 (2), 443 – 457. doi:10.1111/psyg.13051
- Chen Z. R., Huang J. B., Yang S. L., Hong F. F. (2022). Role of cholinergic signaling in Alzheimer’s disease. Molecules 27 (6), 1816. doi:10.3390/molecules27061816
- Chen Z.-L., Singh P. K., Calvano M., Norris E. H., Strickland S. (2023). A possible mechanism for the enhanced toxicity of beta-amyloid protofibrils in Alzheimer’s disease. Proc. Natl. Acad. Sci. 120 (36), e2309389120. doi:10.1073/pnas.2309389120
- Chen P.-L., Xu G. H., Li M., Zhang J. Y., Cheng J., Li C. F. (2023). Yamogenin exhibits Antidepressant-like effects via inhibition of ER stress and microglial activation in LPS-induced mice. ACS Chem. Neurosci. 14 (17), 3173 – 3182. doi:10.1021/acschemneuro.3c00306
- Cheung J., Rudolph M. J., Burshteyn F., Cassidy M. S., Gary E. N., Love J. (2012). Structures of human acetylcholinesterase in complex with pharmacologically important ligands. J. Med. Chem. 55 (22), 10282 – 10286. doi:10.1021/jm300871x
- Comajuncosa-Creus A., Jorba G., Barril X., Aloy P. (2024). Comprehensive detection and characterization of human druggable pockets through binding site descriptors. Nat. Commun. 15 (1), 7917. doi:10.1038/s41467-024-52146-3
- Cucuzza S., Sitnik M., Jurt S., Michel E., Dai W., Müntener T. (2023). Unexpected dynamics in femtomolar complexes of binding proteins with peptides. Nat. Commun. 14 (1), 7823. doi:10.1038/s41467-023-43596-2
- Daley S. K., Cordell G. A. (2021). Alkaloids in contemporary drug discovery to meet global disease needs. Molecules 26 (13), 3800. doi:10.3390/molecules26133800
- Daniels M. H., Malojcic G., Clugston S. L., Williams B., Coeffet-Le Gal M., Pan-Zhou X. R. (2022). Discovery and optimization of highly selective inhibitors of CDK5. J. Med. Chem. 65 (4), 3575 – 3596. doi:10.1021/acs.jmedchem.1c02069
- de Almeida R. B. M., Barbosa D. B., do Bomfim M. R., Amparo J. A. O., Andrade B. S., Costa S. L. (2023). Identification of a novel dual inhibitor of acetylcholinesterase and butyrylcholinesterase: in vitro and in silico studies. Pharm. (Basel) 16 (1), 95. doi:10.3390/ph16010095
- Dehnbostel F. O., Dixit V. A., Preissner R., Banerjee P. (2024). Non-animal models for blood-brain barrier permeability evaluation of drug-like compounds. Sci. Rep. 14 (1), 8908. doi:10.1038/s41598-024-59734-9
- Domingo-Fernández D., Gadiya Y., Preto A. J., Krettler C. A., Mubeen S., Allen A. (2024). Natural products have increased rates of clinical trial success throughout the drug development process. J. Nat. Prod. 87 (7), 1844 – 1851. doi:10.1021/acs.jnatprod.4c00581
- Dunk M. M., Driscoll I., Espeland M. A., Hayden K. M., Liu S., Nassir R. (2025). Relationships between APOE, type 2 diabetes, and cardiovascular disease in postmenopausal women. J. Gerontol. A Biol. Sci. Med. Sci. 80 (2), glae246. doi:10.1093/gerona/glae246
- Duran-Frigola M., Siragusa L., Ruppin E., Barril X., Cruciani G., Aloy P. (2017). Detecting similar binding pockets to enable systems polypharmacology. PLoS Comput. Biol. 13 (6), e1005522. doi:10.1371/journal.pcbi.1005522
- Ferreira de Freitas R., Schapira M. (2017). A systematic analysis of atomic protein-ligand interactions in the PDB. Medchemcomm 8 (10), 1970 – 1981. doi:10.1039/c7md00381a
- Fu K., Lin N., Xu Y., Huang E., He R., Wu Z. (2025). CDK5-mediated hyperphosphorylation of Tau217 impairs neuronal synaptic structure and exacerbates cognitive impairment in Alzheimer’s disease. Transl. Psychiatry 15 (1), 302. doi:10.1038/s41398-025-03551-9
- Grissa D., Junge A., Oprea T. I., Jensen L. J. (2022). Diseases 2.0: a weekly updated database of disease-gene associations from text mining and data integration. Database (Oxford) 2022, baac019. doi:10.1093/database/baac019
- Gan S. Y., Wong L. Z., Wong J. W., Tan E. L. (2019). Fucosterol exerts protection against amyloid β-induced neurotoxicity, reduces intracellular levels of amyloid β and enhances the mRNA expression of neuroglobin in amyloid β-induced SH-SY5Y cells. Int. J. Biol. Macromol. 121, 207 – 213. doi:10.1016/j.ijbiomac.2018.10.021
- Gao G.-B., Sun Y., Fang R. D., Wang Y., Wang Y., He Q. Y. (2021). Post-translational modifications of CDK5 and their biological roles in cancer. Mol. Biomed. 2 (1), 22. doi:10.1186/s43556-021-00029-0
- Gao L., Zhang Y., Sterling K., Song W. (2022). Brain-derived neurotrophic factor in Alzheimer’s disease and its pharmaceutical potential. Transl. Neurodegener. 11 (1), 4. doi:10.1186/s40035-022-00279-0
- Giovinazzo D., Bursac B., Sbodio J. I., Nalluru S., Vignane T., Snowman A. M. (2021). Hydrogen sulfide is neuroprotective in Alzheimer’s disease by sulfhydrating GSK3β and inhibiting Tau hyperphosphorylation. Proc. Natl. Acad. Sci. U. S. A. 118 (4), e2017225118. doi:10.1073/pnas.2017225118
- Gondal H. Y., Tariq S., Akhter S., Raza A. R., Rehman M. F. U., Rubab S. L. (2023). Synthesis, characterization, and in vitro anti-cholinesterase screening of novel indole amines. RSC Adv. 13 (2), 1203 – 1215. doi:10.1039/d2ra05105b
- Gong M., Jia J. (2023). Rutaecarpine mitigates cognitive impairment by balancing mitochondrial function through activation of the AMPK/PGC1α pathway. Mol. Neurobiol. 60 (11), 6598 – 6612. doi:10.1007/s12035-023-03505-6
- Guo X., Li H., Lu X., Liu H., U K., Yan C. (2025). Structural basis of human γ-secretase inhibition by anticancer clinical compounds. Nat. Struct. and Mol. Biol. 32 (4), 719 – 728. doi:10.1038/s41594-024-01439-8
- Gupta M., Lee H. J., Barden C. J., Weaver D. F. (2019). The blood–brain barrier (BBB) score. J. Med. Chem. 62 (21), 9824 – 9836. doi:10.1021/acs.jmedchem.9b01220
- Gupta M., Pant S., Rana P., Kumar A., Prasun C., Nair M. S. (2024). Investigation, scaffold hopping of novel donepezil-based compounds as anti-Alzhiemer’s agents: synthesis, in-silico and pharmacological evaluations. Sci. Rep. 14 (1), 1687. doi:10.1038/s41598-024-51713-4
- Hampel H., Hardy J., Blennow K., Chen C., Perry G., Kim S. H. (2021). The Amyloid-β pathway in Alzheimer’s disease. Mol. Psychiatry 26 (10), 5481 – 5503. doi:10.1038/s41380-021-01249-0
- Haupt V. J., Daminelli S., Schroeder M. (2013). Drug promiscuity in PDB: protein binding site similarity is key. PLoS One 8 (6), e65894. doi:10.1371/journal.pone.0065894
- Hopkins A. L., Keserü G. M., Leeson P. D., Rees D. C., Reynolds C. H. (2014). The role of ligand efficiency metrics in drug discovery. Nat. Rev. Drug Discov. 13 (2), 105 – 121. doi:10.1038/nrd4163
- Houston D. R., Yen L. H., Pettit S., Walkinshaw M. D. (2015). Structure- and ligand-based virtual screening identifies new scaffolds for inhibitors of the oncoprotein MDM2. PLoS One 10 (4), e0121424. doi:10.1371/journal.pone.0121424
- Huang C. J., Huang W. C., Lin W. T., Shu L. H., Sheu J. R., Tran O. T. (2021). Rutaecarpine, an alkaloid from Evodia rutaecarpa, can prevent platelet activation in humans and reduce microvascular thrombosis in mice: crucial role of the PI3K/Akt/GSK3β signal axis through a cyclic Nucleotides/VASP-Independent mechanism. Int. J. Mol. Sci. 22 (20), 11109. doi:10.3390/ijms222011109
- Hur J. Y. (2022). γ-Secretase in Alzheimer’s disease. Exp. Mol. Med. 54 (4), 433 – 446. doi:10.1038/s12276-022-00754-8
- Iqbal D., Rehman M. T., Alajmi M. F., Alsaweed M., Jamal Q. M. S., Alasiry S. M. (2023). 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. Pharm. (Basel) 16 (4), 622. doi:10.3390/ph16040622
- Ismail N. A., Leong Abdullah M. F. I., Hami R., Ahmad Yusof H. (2020). A narrative review of brain-derived neurotrophic factor (BDNF) on cognitive performance in Alzheimer’s disease. Growth factors. 38 (3-4), 210 – 225. doi:10.1080/08977194.2020.1864347
- Jangid K., Devi B., Sahoo A., Kumar V., Dwivedi A. R., Thareja S. (2024). Virtual screening and molecular dynamics simulation approach for the identification of potential multi-target directed ligands for the treatment of Alzheimer’s disease. J. Biomol. Struct. Dyn. 42 (1), 509 – 527. doi:10.1080/07391102.2023.2201838
- Jaśkiewicz A., Budryn G., Carmena-Bargueño M., Pérez-Sánchez H. (2022). Evaluation of activity of sesquiterpene lactones and chicory extracts as acetylcholinesterase inhibitors assayed in calorimetric and docking simulation studies. Nutrients 14 (17), 3633. doi:10.3390/nu14173633
- Jayapalan S., Natarajan J. (2013). The role of CDK5 and GSK3B kinases in hyperphosphorylation of microtubule associated protein tau (MAPT) in Alzheimer’s disease. Bioinformation 9 (20), 1023 – 1030. doi:10.6026/97320630091023
- Jie F., Yang X., Yang B., Liu Y., Wu L., Lu B. (2022). Stigmasterol attenuates inflammatory response of microglia via NF-κB and NLRP3 signaling by AMPK activation. Biomed. and Pharmacother. 153, 113317. doi:10.1016/j.biopha.2022.113317
- Kabir A., Muth A. (2022). Polypharmacology: the science of multi-targeting molecules. Pharmacol. Res. 176, 106055. doi:10.1016/j.phrs.2021.106055
- Kashyap P., Muthusamy K., Niranjan M., Trikha S., Kumar S. (2020). Sarsasapogenin: a steroidal saponin from Asparagus racemosus as multi target directed ligand in Alzheimer’s disease. Steroids 153, 108529. doi:10.1016/j.steroids.2019.108529
- Kattuparambil A. A., Chaurasia D. K., Shekhar S., Srinivasan A., Mondal S., Aduri R. (2025). Exploring chemical space for “druglike” small molecules in the age of AI. Front. Mol. Biosci. 12, 2025. doi:10.3389/fmolb.2025.1553667
- Kenny P. W. (2022). Hydrogen-bond donors in drug design. J. Med. Chem. 65 (21), 14261 – 14275. doi:10.1021/acs.jmedchem.2c01147
- Kirchner K., Garvert L., Kühn L., Bonk S., Grabe H. J., Van der Auwera S. (2023). Detrimental effects of ApoE ε4 on blood-brain barrier integrity and their potential implications on the pathogenesis of Alzheimer’s disease. Cells 12 (21), 2512. doi:10.3390/cells12212512
- Kita A., Kawade Y., Murakami H., Ikeda R., Araki R., Yabe T. (2025). Tomatidine attenuates post-stroke cognitive impairment by reducing neuroinflammation through prevention of M1 microglial polarization via NF-κB signaling. J. Pharmacol. Sci. 158 (4), 294 – 302. doi:10.1016/j.jphs.2025.05.011
- Korn M., Ehrt C., Ruggiu F., Gastreich M., Rarey M. (2023). Navigating large chemical spaces in early-phase drug discovery. Curr. Opin. Struct. Biol. 80, 102578. doi:10.1016/j.sbi.2023.102578
- Koutsodendris N., Blumenfeld J., Agrawal A., Traglia M., Grone B., Zilberter M. (2023). Neuronal APOE4 removal protects against tau-mediated gliosis, neurodegeneration and myelin deficits. Nat. Aging 3 (3), 275 – 296. doi:10.1038/s43587-023-00368-3
- Kumar N., Kumar V., Anand P., Kumar V., Ranjan Dwivedi A., Kumar V. (2022). Advancements in the development of multi-target directed ligands for the treatment of Alzheimer’s disease. Bioorg Med. Chem. 61, 116742. doi:10.1016/j.bmc.2022.116742
- Kurth V., Ogorek I., Münch C., Lopez-Rios J., Ousson S., Lehmann S. (2023). Pathogenic Aβ production by heterozygous PSEN1 mutations is intrinsic to the mutant protein and not mediated by conformational hindrance of wild-type PSEN1. J. Biol. Chem. 299 (8), 104997. doi:10.1016/j.jbc.2023.104997
- Leeson P. D., Bento A. P., Gaulton A., Hersey A., Manners E. J., Radoux C. J. (2021). Target-based evaluation of “Drug-Like” properties and ligand efficiencies. J. Med. Chem. 64 (11), 7210 – 7230. doi:10.1021/acs.jmedchem.1c00416
- Lemkul J. A. (2018). From proteins to perturbed hamiltonians: a suite of tutorials for the GROMACS-2018 molecular simulation package [article v1.0]. Living J. Comput. Mol. Sci. 1 (1), 5068. doi:10.33011/livecoms.1.1.5068
- Li J.-Y., Huang H. B., Pan T. X., Wang N., Shi C. W., Zhang B. (2022). Sanguinarine induces apoptosis in Eimeria tenella sporozoites via the generation of reactive oxygen species. Poult. Sci. 101 (5), 101771. doi:10.1016/j.psj.2022.101771
- Li D., Huang Z., Xu X., Li Y. (2023). Promising derivatives of rutaecarpine with diverse pharmacological activities. Front. Chem. 11, 1199799. doi:10.3389/fchem.2023.1199799
- Lilienfeld S. (2002). Galantamine--a novel cholinergic drug with a unique dual mode of action for the treatment of patients with Alzheimer’s disease. CNS Drug Rev. 8 (2), 159 – 176. doi:10.1111/j.1527-3458.2002.tb00221.x
- Lin K., Zhang Z., Zhang Z., Zhu P., Jiang X., Wang Y. (2021). Oleanolic acid alleviates cerebral ischemia/reperfusion injury via regulation of the GSK-3β/HO-1 signaling pathway. Pharm. (Basel) 15 (1), 1. doi:10.3390/ph15010001
- Ling T., Boyd L., Rivas F. (2022). Triterpenoids as reactive oxygen species modulators of cell fate. Chem. Res. Toxicol. 35 (4), 569 – 584. doi:10.1021/acs.chemrestox.1c00428
- Lipinski C. A., Lombardo F., Dominy B. W., Feeney P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 46 (1-3), 3 – 26. doi:10.1016/s0169-409x(00)00129-0
- Liu J.-Y., Guo H. Y., Quan Z. S., Shen Q. K., Cui H., Li X. (2023). Research progress of natural products and their derivatives against Alzheimer’s disease. J. Enzyme Inhibition Med. Chem. 38 (1), 2171026. doi:10.1080/14756366.2023.2171026
- Liu L., Schultz S. A., Saba A., Yang H. S., Li A., Selkoe D. J. (2024). The pathogenicity of PSEN2 variants is tied to Aβ production and homology to PSEN1. Alzheimers Dement. 20 (12), 8867 – 8877. doi:10.1002/alz.14339
- Liu Z., Huang X., Zhang M., Quan Y. S., Wang Y. L., Liu J. Y. (2025). Discovery of oleanolic acid derivatives that inhibit tau protein phosphorylation and neuroinflammation induced by Aβ(25)(-)(35) in vitro and in vivo. Bioorg Chem. 164, 108866. doi:10.1016/j.bioorg.2025.108866
- Lu K., Wang X., Chen Y., Liang D., Luo H., Long L. (2018). Identification of two potential glycogen synthase kinase 3β inhibitors for the treatment of osteosarcoma. Acta Biochimica Biophysica Sinica 50 (5), 456 – 464. doi:10.1093/abbs/gmx142
- Maatuk N., Samson A. O. (2013). Modeling the binding mechanism of Alzheimer’s Aβ1–42 to nicotinic acetylcholine receptors based on similarity with snake α-neurotoxins. NeuroToxicology 34, 236 – 242. doi:10.1016/j.neuro.2012.09.007
- Man V. H., He X., Gao J., Wang J. (2023). Phosphorylation of Tau R2 repeat destabilizes its binding to microtubules: a molecular dynamics simulation study. ACS Chem. Neurosci. 14 (3), 458 – 467. doi:10.1021/acschemneuro.2c00611
- Markowicz-Piasecka M., Markiewicz A., Darłak P., Sikora J., Adla S. K., Bagina S. (2022). Current chemical, biological, and physiological views in the development of successful brain-targeted pharmaceutics. Neurotherapeutics 19 (3), 942 – 976. doi:10.1007/s13311-022-01228-5
- Meng E. C., Goddard T. D., Pettersen E. F., Couch G. S., Pearson Z. J., Morris J. H. (2023). UCSF ChimeraX: tools for structure building and analysis. Protein Sci. 32 (11), e4792. doi:10.1002/pro.4792
- Mirza F. J., Amber S., Sumera, Hassan D., Ahmed T., Zahid S. (2021). Rosmarinic acid and ursolic acid alleviate deficits in cognition, synaptic regulation and adult hippocampal neurogenesis in an Aβ(1-42)-induced mouse model of Alzheimer’s disease. Phytomedicine 83, 153490. doi:10.1016/j.phymed.2021.153490
- Moghadam B., Ashouri M., Roohi H., Karimi-Jafari M. H. (2021). Computational evidence of new putative allosteric sites in the acetylcholinesterase receptor. J. Mol. Graph. Model. 107, 107981. doi:10.1016/j.jmgm.2021.107981
- Monteiro A. R., Barbosa D. J., Remião F., Silva R. (2023). Alzheimer’s disease: insights and new prospects in disease pathophysiology, biomarkers and disease-modifying drugs. Biochem. Pharmacol. 211, 115522. doi:10.1016/j.bcp.2023.115522
- Nasb M., Tao W., Chen N. (2024). Alzheimer’s disease puzzle: delving into pathogenesis hypotheses. Aging Dis. 15 (1), 43 – 73. doi:10.14336/AD.2023.0608
- Nguyen P. (2017). The Phytosterol Cyclopamine Rescues Structural and Behavioral Deficits in a Drosophila Model of Alzheimer’s Disease. Editors Marenda D., Saunders A. (Philadelphia, Pennsylvania: Drexel University).
- Odi R., Bibi D., Wager T., Bialer M. (2020). A perspective on the physicochemical and biopharmaceutic properties of marketed antiseizure drugs-from phenobarbital to cenobamate and beyond. Epilepsia 61 (8), 1543 – 1552. doi:10.1111/epi.16597
- Padmanabhan D., Siddiqui M. H., Natarajan P., Palanisamy S. (2023). Hecogenin a plant derived small molecule as an antagonist to BACE-1: a potential target for neurodegenerative disorders. Metabolites 13 (6), 758. doi:10.3390/metabo13060758
- Pandya V., Rao P., Prajapati J., Rawal R. M., Goswami D. (2024). Pinpointing top inhibitors for GSK3β from pool of indirubin derivatives using rigorous computational workflow and their validation using molecular dynamics (MD) simulations. Sci. Rep. 14 (1), 49. doi:10.1038/s41598-023-50992-7
- Passos F. R. S., Araújo-Filho H. G., Monteiro B. S., Shanmugam S., Araújo A. A. d. S., Almeida J. R. G. d. S. (2022). Anti-inflammatory and modulatory effects of steroidal saponins and sapogenins on cytokines: a review of pre-clinical research. Phytomedicine 96, 153842. doi:10.1016/j.phymed.2021.153842
- Pathak C., Kabra U. D. (2024). A comprehensive review of multi-target directed ligands in the treatment of Alzheimer’s disease. Bioorg Chem. 144, 107152. doi:10.1016/j.bioorg.2024.107152
- Petros A. M., Korepanova A., Jakob C. G., Qiu W., Panchal S. C., Wang J. (2019). Fragment-based discovery of an apolipoprotein E4 (apoE4) stabilizer. J. Med. Chem. 62 (8), 4120 – 4130. doi:10.1021/acs.jmedchem.9b00178
- Pettus L. H., Bourbeau M. P., Bradley J., Bartberger M. D., Chen K., Hickman D. (2020). Discovery of AM-6494: a potent and orally efficacious β-Site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitor with in vivo selectivity over BACE2. J. Med. Chem. 63 (5), 2263 – 2281. doi:10.1021/acs.jmedchem.9b01034
- Raj S., Raj S., Namdeo V., Srivastava A. (2024). Decoding the gene-disease associations in type 2 diabetes: a curated dataset for text mining-based classification. Data Brief. 54, 110418. doi:10.1016/j.dib.2024.110418
- Ramurthy S., Pfister K. B., Boyce R. S., Brown S. P., Costales A. Q., Desai M. C. (2020). Discovery and optimization of novel pyridines as highly potent and selective glycogen synthase kinase 3 inhibitors. Bioorg Med. Chem. Lett. 30 (4), 126930. doi:10.1016/j.bmcl.2019.126930
- Raulin A.-C., Doss S. V., Trottier Z. A., Ikezu T. C., Bu G., Liu C. C. (2022). ApoE in Alzheimer’s disease: pathophysiology and therapeutic strategies. Mol. Neurodegener. 17 (1), 72. doi:10.1186/s13024-022-00574-4
- Rawat K., Tewari D., Bisht A., Chandra S., Tiruneh Y. K., Hassan H. M. (2024). Identification of AChE targeted therapeutic compounds for Alzheimer’s disease: an in-silico study with DFT integration. Sci. Rep. 14 (1), 30356. doi:10.1038/s41598-024-81285-2
- Reas E. T., Solders S. K., Tsiknia A., Triebswetter C., Shen Q., Rivera C. S. (2024). APOE ε4-related blood-brain barrier breakdown is associated with microstructural abnormalities. APOE Alzheimers Dement. 20 (12), 8615 – 8624. doi:10.1002/alz.14302
- Reddi Sree R., Kalyan M., Anand N., Mani S., Gorantla V. R., Sakharkar M. K. (2025). Newer therapeutic approaches in treating Alzheimer’s disease: a comprehensive review. ACS Omega 10 (6), 5148 – 5171. doi:10.1021/acsomega.4c05527
- Rekha A., Afzal M., Babu M. A., Menon S. V., Nathiya D., Supriya S. (2025). GSK-3β dysregulation in aging: implications for tau pathology and Alzheimer’s disease progression. Mol. Cell Neurosci. 133, 104005. doi:10.1016/j.mcn.2025.104005
- Rueeger H., Lueoend R., Machauer R., Veenstra S. J., Holzer P., Hurth K. (2021). Synthesis of the potent, selective, and efficacious β-Secretase (BACE1) inhibitor NB-360. J. Med. Chem. 64 (8), 4677 – 4696. doi:10.1021/acs.jmedchem.0c02143
- Sadybekov A. V., Katritch V. (2023). Computational approaches streamlining drug discovery. Nature 616 (7958), 673 – 685. doi:10.1038/s41586-023-05905-z
- Schake P., Bolz S. N., Linnemann K., Schroeder M. (2025). PLIP 2025: introducing protein–protein interactions to the protein–ligand interaction profiler. Nucleic Acids Res. 53 (W1), W463 – W465. doi:10.1093/nar/gkaf361
- Scott J. D., Li S. W., Brunskill A. P. J., Chen X., Cox K., Cumming J. N. (2016). Discovery of the 3-Imino-1,2,4-thiadiazinane 1,1-Dioxide derivative verubecestat (MK-8931)–A β-Site amyloid precursor protein cleaving enzyme 1 inhibitor for the treatment of Alzheimer’s disease. J. Med. Chem. 59 (23), 10435 – 10450. doi:10.1021/acs.jmedchem.6b00307
- Sharifi-Rad J., Rapposelli S., Sestito S., Herrera-Bravo J., Arancibia-Diaz A., Salazar L. A. (2022). Multi-target mechanisms of phytochemicals in Alzheimer’s disease: effects on oxidative stress, neuroinflammation and protein aggregation. J. Pers. Med. 12 (9), 1515. doi:10.3390/jpm12091515
- Shi W., Zhang G., Liao Y., Fei X., Gong D., Hu X. (2023). Anti-acetylcholinesterase mechanism of kaempferol and its synergistic effect with galanthamine hydrobromide. Food Biosci. 56, 103174. doi:10.1016/j.fbio.2023.103174
- Shigeta M., Homma A. (2001). Donepezil for Alzheimer’s disease: pharmacodynamic, pharmacokinetic, and clinical profiles. CNS Drug Rev. 7 (4), 353 – 368. doi:10.1111/j.1527-3458.2001.tb00204.x
- Shri S. R., Manandhar S., Nayak Y., Pai K. S. R. (2023). Role of GSK-3β inhibitors: new promises and opportunities for Alzheimer’s disease. Adv. Pharm. Bull. 13 (4), 688 – 700. doi:10.34172/apb.2023.071
- Singh K., Bhushan B., Singh B. (2024). Advances in drug discovery and design using computer-aided molecular modeling. Curr. Comput. Aided Drug Des. 20 (5), 697 – 710. doi:10.2174/1573409920666230914123005
- Sirisi S., Sánchez-Aced É., Belbin O., Lleó A. (2024). APP dyshomeostasis in the pathogenesis of Alzheimer’s disease: implications for current drug targets. Alzheimers Res. Ther. 16 (1), 144. doi:10.1186/s13195-024-01504-w
- Som S., Antony J., Dhanabal S., Ponnusankar S. (2022). Neuroprotective role of diosgenin, a NGF stimulator, against Aβ (1-42) induced neurotoxicity in animal model of Alzheimer’s disease. Metab. Brain Dis. 37 (2), 359 – 372. doi:10.1007/s11011-021-00880-8
- Spassov D. S. (2024). Binding affinity determination in drug design: insights from lock and key, induced fit, conformational selection, and inhibitor trapping models. Int. J. Mol. Sci. 25 (13), 7124. doi:10.3390/ijms25137124
- Sridhar G. R., Gumpeny L. (2024). Emerging significance of butyrylcholinesterase. World J. Exp. Med. 14 (1), 87202. doi:10.5493/wjem.v14.i1.87202
- Stępnik K., Kukula-Koch W., Plazinski W., Rybicka M., Gawel K. (2023). Neuroprotective properties of oleanolic acid-computational-driven molecular research combined with in vitro and in vivo experiments. Pharm. (Basel) 16 (9), 1234. doi:10.3390/ph16091234
- Sun A., Xu X., Lin J., Cui X., Xu R. (2015). Neuroprotection by saponins. Phytother. Res. 29 (2), 187 – 200. doi:10.1002/ptr.5246
- Sy L. K., Lok C. N., Wang J. Y., Liu Y., Cheng L., Wan P. K. (2016). Identification of “sarsasapogenin-aglyconed” timosaponins as novel Aβ-lowering modulators of amyloid precursor protein processing. Chem. Sci. 7 (5), 3206 – 3214. doi:10.1039/c5sc02377g
- Takomthong P., Waiwut P., Boonyarat C. (2025). Targeting multiple pathways with virtual screening to identify the multi-target agent for Alzheimer’s disease treatment. J. Comput. Aided Mol. Des. 39 (1), 24. doi:10.1007/s10822-025-00602-7
- Tohda C., Yang X., Matsui M., Inada Y., Kadomoto E., Nakada S. (2017). Diosgenin-rich yam extract enhances cognitive function: a placebo-controlled, randomized, double-blind, crossover study of healthy adults. Nutrients 9 (10). doi:10.3390/nu9101160
- Trott O., Olson A. J. (2010). AutoDock vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31 (2), 455 – 461. doi:10.1002/jcc.21334
- Vander Meersche Y., Cretin G., Gheeraert A., Gelly J. C., Galochkina T. (2024). ATLAS: protein flexibility description from atomistic molecular dynamics simulations. Nucleic Acids Res. 52 (D1), D384 – d392. doi:10.1093/nar/gkad1084
- Venkatesan R., Shim W. S., Yeo E. J., Kim S. Y. (2017). Lactucopicrin potentiates neuritogenesis and neurotrophic effects by regulating Ca2+/CaMKII/ATF1 signaling pathway. J. Ethnopharmacol. 198, 174 – 183. doi:10.1016/j.jep.2016.12.035
- Verma A. K., Majid A., Hossain M. S., Ahmed S. F., Ashid M., Bhojiya A. A. (2022). Identification of 1, 2, 4-Triazine and its derivatives against lanosterol 14-Demethylase (CYP51) property of candida albicans: influence on the development of new antifungal therapeutic strategies. Front. Med. Technol. 4, 845322. doi:10.3389/fmedt.2022.845322
- Vezikov L. V., Simpson M. (2026). Plant Alkaloids Toxicity, in Statpearls. Treasure Island (FL) ineligible companies: StatPearls Publishing Copyright © 2026, StatPearls Publishing LLC.
- Vorobyeva A. G., Lee R., Miller S., Longen C., Sharoni M., Kandelwal P. J. (2014). Cyclopamine modulates γ-secretase-mediated cleavage of amyloid precursor protein by altering its subcellular trafficking and lysosomal degradation. J. Biol. Chem. 289 (48), 33258 – 33274. doi:10.1074/jbc.M114.591792
- Wang B., Mai Y. C., Li Y., Hou J. Q., Huang S. L., Ou T. M. (2010). Synthesis and evaluation of novel rutaecarpine derivatives and related alkaloids derivatives as selective acetylcholinesterase inhibitors. Eur. J. Med. Chem. 45 (4), 1415 – 1423. doi:10.1016/j.ejmech.2009.12.044
- Wang C. C. N., Jin J., Chang J. G., Hayakawa M., Kitazawa A., Tsai J. J. P. (2020). Identification of most influential co-occurring gene suites for gastrointestinal cancer using biomedical literature mining and graph-based influence maximization. BMC Med. Inf. Decis. Mak. 20 (1), 208. doi:10.1186/s12911-020-01227-6
- Wang S., Lin H., Huang Z., He Y., Deng X., Xu Y. (2022). CavitySpace: a database of potential ligand binding sites in the human proteome. Biomolecules 12 (7), 967. doi:10.3390/biom12070967
- Wang N., Wang E., Wang R., Muhammad F., Li T., Yue J. (2022). Ursolic acid ameliorates amyloid β-induced pathological symptoms in Caenorhabditis elegans by activating the proteasome. Neurotoxicology 88, 231 – 240. doi:10.1016/j.neuro.2021.12.004
- Weng Y. L., Naik S. R., Dingelstad N., Lugo M. R., Kalyaanamoorthy S., Ganesan A. (2021). Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 main protease complexes reveal the role of lateral pocket in enhancing the ligand affinity. Sci. Rep. 11 (1), 7429. doi:10.1038/s41598-021-86471-0
- Willumsen N., Arber C., Lovejoy C., Toombs J., Alatza A., Weston P. S. J. (2023). The PSEN1 E280G mutation leads to increased amyloid-β43 production in induced pluripotent stem cell neurons and deposition in brain tissue. Brain Commun. 5 (1), fcac321. doi:10.1093/braincomms/fcac321
- Wu Q., Wang M., Chen W., Wang K., Wang Y. (2023). Assessing neuroprotective efficacy of phytochemical saponin ruscogenin in both in vitro and in vivo model. Arabian J. Chem. 16 (6), 104693. doi:10.1016/j.arabjc.2023.104693
- Xiao X., Liu H., Liu X., Zhang W., Zhang S., Jiao B. (2021). APP, PSEN1, and PSEN2 variants in Alzheimer’s disease: systematic Re-evaluation according to ACMG guidelines. Front. Aging Neurosci. 13, 695808. doi:10.3389/fnagi.2021.695808
- Xing H., Yue S., Qin R., Du X., Wu Y., Zhangsun D. (2025). Recent advances in drug development for Alzheimer’s disease: a comprehensive review. Int. J. Mol. Sci. 26 (8), 3905. doi:10.3390/ijms26083905
- Xu M., Li L., Liu H., Lu W., Ling X., Gong M. (2022). Rutaecarpine attenuates oxidative stress-induced traumatic brain injury and reduces secondary injury via the PGK1/KEAP1/NRF2 signaling pathway. Front. Pharmacol. 13, 807125. doi:10.3389/fphar.2022.807125
- Yang G., Zhou R., Guo X., Yan C., Lei J., Shi Y. (2021). Structural basis of γ-secretase inhibition and modulation by small molecule drugs. Cell 184 (2), 521 – 533.e14. doi:10.1016/j.cell.2020.11.049
- Ye J. Y., Li L., Hao Q. M., Qin Y., Ma C. S. (2020). β-Sitosterol treatment attenuates cognitive deficits and prevents amyloid plaque deposition in amyloid protein precursor/presenilin 1 mice. Korean J. Physiol. Pharmacol. 24 (1), 39 – 46. doi:10.4196/kjpp.2020.24.1.39
- Yin Z., Zhang J., Guo Q., Chen L., Zhang W., Kang W. (2019). Pharmacological effects of verticine: current status. Evid. Based Complement. Altern. Med. 2019, 2394605. doi:10.1155/2019/2394605
- Yoo J., Lee J., Ahn B., Han J., Lim M. H. (2025). Multi-target-directed therapeutic strategies for Alzheimer’s disease: controlling amyloid-β aggregation, metal ion homeostasis, and enzyme inhibition. Chem. Sci. 16 (5), 2105 – 2135. doi:10.1039/d4sc06762b
- Zeb A., Son M., Yoon S., Kim J. H., Park S. J., Lee K. W. (2019). Computational simulations identified two candidate inhibitors of Cdk5/p25 to abrogate Tau-associated neurological disorders. Comput. Struct. Biotechnol. J. 17, 579 – 590. doi:10.1016/j.csbj.2019.04.010
- Zhang S., Wang Z., Cai F., Zhang M., Wu Y., Zhang J. (2017). BACE1 cleavage site selection critical for amyloidogenesis and Alzheimer’s pathogenesis. J. Neurosci. 37 (29), 6915 – 6925. doi:10.1523/JNEUROSCI.0340-17.2017
- Zhang Y., Chen H., Li R., Sterling K., Song W. (2023). Amyloid β-based therapy for Alzheimer’s disease: challenges, successes and future. Signal Transduct. Target. Ther. 8 (1), 248. doi:10.1038/s41392-023-01484-7
- Zhang J., Zhang Y., Wang J., Xia Y., Zhang J., Chen L. (2024). Recent advances in Alzheimer’s disease: mechanisms, clinical trials and new drug development strategies. Signal Transduct. Target Ther. 9 (1), 211. doi:10.1038/s41392-024-01911-3
- Zhang W. G., Ding J., Wang L., Wu C. J., Mao J. Y., Ding K. (2025). Tomatidine ameliorates diabetes-induced cognitive impairment and tau hyperphosphorylation through the AMPK-TFEB pathway. J. Neurochem. 169 (5), e70087. doi:10.1111/jnc.70087
- Zheng B., Wang C., Song W., Ye X., Xiang Z. (2019). Pharmacokinetics and enterohepatic circulation of jervine, an antitumor steroidal alkaloid from Veratrum nigrum in rats. J. Pharm. Anal. 9 (5), 367 – 372. doi:10.1016/j.jpha.2019.04.004
- Zhou S., Huang G. (2022). The biological activities of butyrylcholinesterase inhibitors. Biomed. Pharmacother. 146, 112556. doi:10.1016/j.biopha.2021.112556
- Zhu M.-M., Wang L. N., Liu Y. M., Zhu D. R., Wang B. C., Ma R. X. (2026). Rare steroidal alkaloids with multifunctional anti-AD activities from Fritillaria taipaiensis. J. Mol. Struct. 1362, 145717. doi:10.1016/j.molstruc.2026.145717
- Žužek M. C. (2024). Advances in cholinesterase inhibitor Research-An overview of preclinical studies of selected Organoruthenium(II) complexes. Int. J. Mol. Sci. 25 (16), 9049. doi:10.3390/ijms25169049
Citation
Mesfin, S., et al. (2026). Virtual screening of phytochemicals against multiple protein targets of Alzheimer’s disease. Frontiers in Drug Discovery, Volume 6. https://doi.org/
- Received
- Accepted
- Published
- Volume
- 6 - 2026
Copyright
Copyright © 2026 Mesfin, Bloch and Samson.
License: https://creativecommons.org/licenses/by/4.0/
*Correspondence: Abraham O. Samson
Article metrics
- Views
- 0
- Downloads
- 0
- Citations
- 0
- Shares
- 0
