Alzheimer’s Disease: Exploring Pathophysiological Hypotheses and the Role of Machine Learning in Drug Discovery
Abstract
:1. Introduction
2. Hypothesis of the Development of Alzheimer’s Disease
2.1. The Amyloid Hypothesis
2.2. Tau Hypothesis
2.3. Neuroinflammation Hypothesis
2.4. Mitochondrial Dysfunction Hypothesis
2.5. Other Hypotheses for the Development of Alzheimer’s
2.6. Unification Hypothesis
Pathway of Unification Hypothesis
3. Emerging Therapeutic Targets in Alzheimer’s Disease Research
4. The Use of Artificial Intelligence in Alzheimer’s Research
4.1. Virtual Screening of Active Compounds Targeting Therapeutic Sites
4.2. Advantages of AI-Assisted Molecular Docking and Molecular Dynamics
4.3. Modeling the Interaction of Key Hypotheses in Alzheimer’s Development Using AI
4.4. AI Applications in Patient Monitoring in Clinical Studies
4.5. AI-Assisted Diagnosis and Computer Vision
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
MDPI | Multidisciplinary Digital Publishing Institute |
DOAJ | Directory of open access journals |
TLA | Three-letter acronym |
LD | Linear dichroism |
AD | Alzheimer’s disease |
Amyloid-beta | |
ML | Machine learning |
AI | Artificial intelligence |
ROS | Reactive oxygen species |
CNNs | Convolutional neural networks |
LBVS | Ligand-based virtual screening |
SVMs | Support vector machines |
RFs | Random forests |
ANNs | Artificial neural networks |
DNNs | Deep neural networks |
NLP | Natural language processing |
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Hypothesis | Overview |
---|---|
Amyloid Hypothesis | Key Mechanism:
Accumulation of -amyloid peptides forming senile plaques, triggering neuroinflammation and synaptic dysfunction. Evidence: Identification of plaques; toxic soluble oligomers [20]. Therapeutic Targets: Enzymes regulating production and clearance; targeting oligomers. |
Tau Hypothesis | Key Mechanism: Abnormal tau protein forms neurofibrillary tangles, disrupting microtubules and leading to neuronal death. Evidence: Presence of hyperphosphorylated tau; correlation with disease progression [64]. Therapeutic Targets: Inhibitors of tau aggregation; microtubule stabilizers. |
Neuroinflammation Hypothesis | Key Mechanism: Chronic activation of microglia releases pro-inflammatory cytokines, damaging neurons. Evidence: Elevated cytokines and chemokines in AD brains; microglial activation [6]. Therapeutic Targets: Modulators of microglial activity; anti-inflammatory agents. |
Mitochondrial Dysfunction Hypothesis | Key Mechanism: Impaired mitochondrial function leads to energy deficits and oxidative stress. Evidence: Mitochondrial abnormalities; increased oxidative damage in neurons [69]. Therapeutic Targets: Antioxidants; enhancers of mitochondrial biogenesis; mitophagy inducers. |
Synaptic Dysfunction Hypothesis | Key Mechanism: Alterations in synaptic function impair neuron communication, leading to cognitive decline. Evidence: Synaptic loss observed in AD; links to cognitive deficits [49]. Therapeutic Targets: Agents restoring synaptic function; neurotrophic factors. |
Oxidative Stress Hypothesis | Key Mechanism: Excess reactive oxygen species cause cellular damage and apoptosis. Evidence: Presence of oxidative damage in AD brains; lipid peroxidation [50]. Therapeutic Targets: Antioxidants; compounds reducing oxidative stress. |
Neurovascular Hypothesis | Key Mechanism: Vascular dysfunction reduces cerebral blood flow, contributing to neurodegeneration. Evidence: Blood–brain barrier breakdown; reduced flow in AD patients [5]. Therapeutic Targets: Vascular health agents; improving blood–brain barrier integrity. |
Endoplasmic Reticulum Stress Hypothesis | Key Mechanism: Accumulation of misfolded proteins induces ER stress and neuronal death. Evidence: Elevated ER stress markers; unfolded protein response activation [55]. Therapeutic Targets: Modulators of protein folding; ER stress reducers. |
Epigenetic Hypothesis | Key Mechanism: Epigenetic modifications alter gene expression affecting neuronal function. Evidence: DNA methylation changes; histone modifications in AD brains [70]. Therapeutic Targets: Epigenetic modulators; drugs targeting gene expression. |
Metal Hypotheses (Zinc and Aluminum) | Key Mechanism: Dysregulated metal ions contribute to protein aggregation and toxicity. Evidence: Altered metal levels in AD brains; metals interact with and tau [59]. Therapeutic Targets: Metal chelators; normalizing metal homeostasis. |
Lifestyle Factors Hypothesis | Key Mechanism: Diet, physical activity, and sleep patterns influence AD risk. Evidence: Epidemiological links between lifestyle and AD incidence [61]. Therapeutic Targets: Lifestyle interventions; dietary modifications. |
AI Approach | Description |
---|---|
Supervised Learning | Supervised learning involves training models on labeled data to predict outcomes such as disease progression based on clinical data [90]. This method is useful for tasks such as prognosis estimation in Alzheimer’s patients. |
Unsupervised Learning | Unsupervised learning is applied to analyze high-dimensional and unlabeled datasets, such as genomic and proteomic sequences [91]. It is particularly useful in discovering novel patterns, classifications, and subgrouping of patients without predefined labels. |
Reinforcement Learning | Reinforcement learning is used to simulate and optimize therapeutic strategies by learning from the outcomes of previous simulations [92]. It is increasingly applied to find optimal treatment protocols and intervention strategies for neurodegenerative diseases. |
Model | Description |
---|---|
SVM (Support Vector Machine) | A supervised learning algorithm that seeks an optimal hyperplane to separate data points of different classes with maximal margin [93] |
RF (Random Forest) | An ensemble method composed of multiple decision trees. It reduces overfitting and increases predictive accuracy by averaging the results of numerous weak learners [93]. |
ANNs (Artificial Neural Networks) | Computational models inspired by biological neural networks, capable of recognizing complex patterns in data through interconnected layers of weighted nodes [94]. |
DNNs (Deep Neural Networks) | A type of neural network with multiple hidden layers that can automatically learn hierarchical representations, enabling the extraction of increasingly abstract features [95]. |
LBVS (Ligand-Based Virtual Screening) | A computational approach that uses known active compounds to predict new molecules with similar biological activity, facilitating the discovery of novel candidates [96]. |
Deep Learning Models | A family of advanced neural network architectures (including CNNs, RNNs, and transformers) that learn from large datasets, often without the need for manual feature engineering [97]. |
AlphaFold | An AI system that predicts protein structures from amino acid sequences with high accuracy, providing insights into molecular form and function [98]. |
Systems Biology Models | Integrative computational frameworks that combine data from various biological levels (genomes, proteomes, metabolomes) to model complex biological systems holistically [99]. |
Agent-Based Models | Simulation models where individual entities (agents) follow defined rules, allowing complex global patterns to emerge from local interactions [100]. |
Bayesian Networks | Probabilistic graphical models that represent variables and their conditional dependencies, enabling reasoning under uncertainty and probabilistic inference [101]. |
NLP (Natural Language Processing) | Techniques and models for analyzing, understanding, and generating human language, often applied to tasks like sentiment analysis, machine translation, and information extraction [102]. |
Sensor-Based Monitoring | The use of wearable devices, IoT sensors, and other technologies to continuously capture data streams (e.g., physiological signals, environmental parameters) for subsequent analysis [103]. |
DeepAD | A specialized deep learning approach designed for complex classification and prediction tasks, integrating multiple data types and learning representations at various scales [104]. |
Area of Application | AI Techniques Used | Key Benefits | Challenges |
---|---|---|---|
Virtual Screening of Active Compounds | SVM, RF, ANN, DNN, LBVS | Accelerated identification of potential drug candidates, improved screening efficiency | Data quality, computational resources [108] |
Molecular Docking and Dynamics | Deep Learning Models (AlphaFold, DeepDock, AtomNet, CNNScore, RF-Score) | Enhanced accuracy in predicting protein structures and ligand interactions | Modeling biological flexibility, validation of predictions [113] |
Modeling Disease Hypotheses | Systems Biology Models (EpiSim), Agent-Based Models (Repast Simphony), Bayesian Networks, Reinforcement Learning | Integrated understanding of disease mechanisms, identification of therapeutic targets | Complexity of biological systems, data integration [120] |
Patient Monitoring in Clinical Studies | Wearable Devices, NLP, Sensor-Based Monitoring | Real-time data collection, personalized treatment plans, improved adherence | Data privacy, variability in patient data [134] |
AI-Assisted Diagnosis | Deep Learning Models (DeepAD, VoxCNN, CNNs) | Early detection of structural brain changes, increased diagnostic accuracy | Requirement for large datasets, potential for overfitting [143] |
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Dominguez-Gortaire, J.; Ruiz, A.; Porto-Pazos, A.B.; Rodriguez-Yanez, S.; Cedron, F. Alzheimer’s Disease: Exploring Pathophysiological Hypotheses and the Role of Machine Learning in Drug Discovery. Int. J. Mol. Sci. 2025, 26, 1004. https://doi.org/10.3390/ijms26031004
Dominguez-Gortaire J, Ruiz A, Porto-Pazos AB, Rodriguez-Yanez S, Cedron F. Alzheimer’s Disease: Exploring Pathophysiological Hypotheses and the Role of Machine Learning in Drug Discovery. International Journal of Molecular Sciences. 2025; 26(3):1004. https://doi.org/10.3390/ijms26031004
Chicago/Turabian StyleDominguez-Gortaire, Jose, Alejandra Ruiz, Ana Belen Porto-Pazos, Santiago Rodriguez-Yanez, and Francisco Cedron. 2025. "Alzheimer’s Disease: Exploring Pathophysiological Hypotheses and the Role of Machine Learning in Drug Discovery" International Journal of Molecular Sciences 26, no. 3: 1004. https://doi.org/10.3390/ijms26031004
APA StyleDominguez-Gortaire, J., Ruiz, A., Porto-Pazos, A. B., Rodriguez-Yanez, S., & Cedron, F. (2025). Alzheimer’s Disease: Exploring Pathophysiological Hypotheses and the Role of Machine Learning in Drug Discovery. International Journal of Molecular Sciences, 26(3), 1004. https://doi.org/10.3390/ijms26031004