AI-Driven Chemical Design: Transforming the Sustainability of the Pharmaceutical Industry
Abstract
:1. Introduction
2. Background Information on AI Models and Key Concepts
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- Deep Neural Networks (DNNs) are versatile architectures composed of multiple hidden layers, capable of learning complex, non-linear relationships in data. They are used for both regression (i.e., predicting solubility or melting point) and classification (i.e., toxic, non-toxic substances). DNNs are especially powerful when working with large, high-dimensional datasets such as molecular fingerprints [14].
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- Extreme Gradient Boosting (XGBoost) is mainly used with structured data and is widely applied in regression tasks (i.e., predicting pharmacokinetic parameters), as well as in classification problems (i.e., drug–target interaction) [15].
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- Support Vector Machines (SVMs) are supervised algorithms that can operate as classifiers or regressors. In drug discovery, they are often used in classification tasks (i.e., active vs. inactive compounds), but they are also applicable in regression settings (i.e., estimating binding affinity or partition coefficients). SVMs perform well in high-dimensional spaces and with small-to-medium-sized datasets [16].
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- Random Forests are ensemble models that build multiple decision trees and average their outputs for regression or vote for classification. They are robust to overfitting, handle missing values well, and are commonly used in tasks such as predicting biodegradability, toxicity, or release profiles in drug delivery systems [17].
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- Mean Absolute Error (MAE) measures the average magnitude of errors between predicted and true values. It is robust to outliers and provides a straightforward interpretation in the same units as the output variable. It is calculated as in (Equation (1)):
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- Root Mean Squared Error (RMSE) is calculated as the square root of the average of the squared differences between the predicted and actual values. This value is more sensitive to outliers than MAE (Equation (2)):
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- Mean Relative Error (MRE) expresses the absolute error as a proportion of the true value, averaged across all samples (Equation (3)):
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- Mean Absolute Percentage Error (MAPE) represents the average percentage difference between the predicted and actual values (Equation (4)):
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- ROC Curves (Receiver Operating Characteristic) are used for binary classification problems. They are graphical representations of the True Positive Rate (Sensitivity) against the False Positive Rate (1 − Specificity) at various threshold settings.
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- AUC (Area Under the ROC Curve) summarises the ROC curve into a single number ranging from 0 to 1. It represents the probability that a randomly chosen positive instance is ranked higher than a randomly chosen negative one. Values equal or below 0.5 indicate that the model has no ability to discriminate between categories.
3. Optimisation of Synthetic Routes
- Molecular Complexity: Many pharmaceutical compounds have intricate structures with multiple functional groups. While these complex structures have been associated with higher selectivity [21], it makes their synthesis challenging.
- Chirality and Selectivity: Over half of drugs require specific stereochemistry [24], meaning that reactions must favour the desired enantiomer or diastereomer, which can reduce the effective yield.
- Purification Losses: Rigorous purification steps are needed to meet regulatory purity requirements, leading to additional material loss [25].
3.1. Biocatalyst Design
3.2. Heterogeneous Catalyst Design
4. Synthesis Optimisation
4.1. Speeding Up the Discovery of Drugs
4.2. Solvent Usage
4.3. Synthetic Pathway Optimisation
5. Artificial Intelligence in Drug Waste Reduction
5.1. Reduction in Drug Waste Through Dosage Optimisation
5.2. Design of Biodegradable Drug Delivery Systems
6. Current Status of Molecular Design for Sustainability and Future Perspectives
7. Conclusions
Funding
Conflicts of Interest
References
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Dataset | Model Prediction | Algorithm | Performance | Refs. |
---|---|---|---|---|
280 million protein sequences from >19,000 families | Protein function | 1.2-billion-parameter neural network | AUC = 0.85 (experimentally validated) | [38] |
BRENDA DATASET (37,624,812 sequences) | Protein activity (model made available as Open Source) | Language model | - | [36,37] |
3.15 billion protein sequences, 236 million protein structures, and 539 million proteins with function annotations | Protein activity | Language model | SS3 > 80% pTM > 0.8 pLDDT > 0.8 RMSD < 1.5 Å (experimentally validated) | [40] |
Protein–small molecule complexes in PDB | Enzyme structure | Deep Neural Network | RMSD < 1.5 Å (experimentally validated) | [41] |
2950 thermophilic protein sequences | Enzyme thermostability | Deep Neural Network and bi-long short-term memory | ACC (%) = 94.34 PR (%) = 93.97 REC (%) = 94.81 REC (%) = 94.36 MCC (%) = 88.73 AUROC (%) = 98.68 | [46] |
Dataset from 21,498 microorganisms | Enzyme optimal temperature (model made available as Open Source) | Random Forest regressor | R2 = 0.94 RMSE = 4.46 | [47] |
Optimal growth temperatures for 96 million host bacterial strains | Enzyme thermostability | Language model | Experimentally validated | [48] |
16,706 unique sequences | Catalytic activity | Generative Adversarial Network | Experimentally validated | [50] |
Dataset | Model Prediction | Algorithm | Performance | Ref. |
---|---|---|---|---|
603 articles | Catalyst synthesis optimisation | Large language model and Bayesian optimisation | Experimentally validated | [64] |
22,000 articles from Web of Science | Catalyst synthesis optimisation | Language model | Average predicted faraday efficiency = 64.15% | [65] |
549 monomer–catalyst pairs for catalyst model | Monomer conversion, dispersity, and average molecular weight | Regression transformer | Pearson correlation = 0.59 (Experimentally validated) | [66] |
Dataset | Model Prediction | Algorithm | Performance | Ref. |
---|---|---|---|---|
186 (simulated systems) + 34 (experimentally verified) | DES formation | Support Vector Machine | Average ROC-AUC score = 0.8 (experimentally validated) | [94] |
237 experimentally validated DESs | Melting temperature | Support Vector Regression | R2 = 0.74, RMSE = 22.5 | [95] |
530 DESs | Heat capacity | Neural Network Multilayer Perceptron | AARD = 4% | [92] |
402 different DES compositions | Diffusion model with self-/cross-attention | R2 = 0.93 (experimentally validated) | [98] | |
435 records | Hydrogen sulphide (H2S) elimination capacity | Cascade neural network | MAE = 0.02 MSE = 0.0031 AARE = 3.03 R2 = 0.99943 (experimentally validated) | [99] |
- | Melting temperature, density, viscosity (model made available as Open Source) | CatBoost | R2 = 0.6–0.91 AARD = 3.14–19.05% (experimentally validated) | [100] |
- | Solubility | Non-linear Support Vector Regression | Experimentally validated | [93] |
1000 labelled mixtures of DESs and NADESs | DES formation | Transformer-based neural network model | F1-Score = 0.82 (experimentally validated) | [101] |
1239 records | DES density | Least-squares Support Vector Regression | R2 = 0.99798 MAPE = 0.26% | [102] |
Dataset | Model Prediction | Algorithm | Performance | Ref. |
---|---|---|---|---|
1141 therapeutic drug-monitoring measurements from 347 patients | Dose-adjusted concentrations of lamotrigine | Extra-trees regression algorithm | MAE = 8.7 μg mL−1 g−1 day Mean Relative Error (%) = 3% (experimentally validated) | [113] |
1099 patients, each described with 280 attributes | Postoperative analgesic requirements | Decision trees | Prediction accuracies of total analgesic consumption of 80.9% (experimentally validated) | [122] |
10,000 bioactive compounds from ChEMBL database | Clearance, volume distribution, half-life, bioavailability | Stacking ensemble model | R2 = 0.92 MAE = 0.062 | [116] |
Simulated pharmacokinetic and pharmacodynamic data | Anaesthetic dosing | Reinforcement learning algorithm | Median episode median performance error of 1.1% ± 0.5 (experimentally validated with retrospective data) | [125] |
210 case data | Increase in flow rate of remifentanil | Long short-term memory | Specificity = 0.73 Sensitivity = 0.66 ROC-AUC = 0.75 | [121] |
13 processed EEG parameters from 200 patients | Anaesthesia scores | Reinforcement learning algorithm | R2 = 0.94 (experimentally validated) | [123] |
Dataset | Model Prediction | Algorithm | Performance | Ref. |
---|---|---|---|---|
540 experimental data points | Release kinetics | Support Vector Machine | R2 = 0.998 RMSE = 0.3701 MSE = 0.137 MAPE = 0.944 (experimentally validated) | [137] |
76 biodegradation curves | Biodegradation kinetics (%) | Long short-term memory neural network | MAPE = 7.6–16.99% MAE = 0.018–0.027 MSE = 0.0004–0.001 RMSE = 6.71–11.33 (experimentally validated with validation dataset) | [139] |
Data from 133 experiments | Polymer properties (Young’s modulus, flammability) | Artificial neural network | MRE = 21% (experimentally validated with molecular dynamic simulations) | [140] |
15,000 data samples | Drug release kinetics | Decision Tree Regression | R2 = 0.94652 RMSE = 6.04 × 10−5 MAE = 4.83 × 10−5 | [141] |
500 datapoints | Drug release kinetics | Random Forest | R2 = 0.99 MAPE = 0.002 (experimentally validated) | [142] |
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Ruiz-Gonzalez, A. AI-Driven Chemical Design: Transforming the Sustainability of the Pharmaceutical Industry. Future Pharmacol. 2025, 5, 24. https://doi.org/10.3390/futurepharmacol5020024
Ruiz-Gonzalez A. AI-Driven Chemical Design: Transforming the Sustainability of the Pharmaceutical Industry. Future Pharmacology. 2025; 5(2):24. https://doi.org/10.3390/futurepharmacol5020024
Chicago/Turabian StyleRuiz-Gonzalez, Antonio. 2025. "AI-Driven Chemical Design: Transforming the Sustainability of the Pharmaceutical Industry" Future Pharmacology 5, no. 2: 24. https://doi.org/10.3390/futurepharmacol5020024
APA StyleRuiz-Gonzalez, A. (2025). AI-Driven Chemical Design: Transforming the Sustainability of the Pharmaceutical Industry. Future Pharmacology, 5(2), 24. https://doi.org/10.3390/futurepharmacol5020024