Challenges
Datasets
Workspaces
Papers
Discussions
Leaderboard
Log inSign up
Challenges
Datasets
Workspaces
Papers
Discussions
Leaderboard
Blog
Job Board
Q3AS

© 2026 Aqora Quantum S.A.S.

TermsPrivacyLegal Notice

The European Physical Journal D

Quantum drug discovery: a hybrid quantum graph neural network–variational quantum eigensolver framework for serine neutralization

Javier Villalba-Díez

Published Jul 1, 2025• 6 citations
Publisher

Abstract

Abstract Quantum computing has emerged as a powerful tool for modeling molecular systems with high accuracy, accelerating the search for novel therapeutic targets. In this study, we present a two-stage hybrid workflow that combines a Quantum Graph Neural Network with a Variational Quantum Eigensolver to identify potent serine neutralizers in the QM9 dataset. In the first stage, an advanced quantum graph neural network architecture incorporating attention layers, self-distillation, and an adaptive learning-rate schedule is trained to predict ionization potentials and binding free energies. Across five independent random-seed trials, our adaptive-thresholded QGNN–VQE pipeline achieves an average $$R^2$$ R 2 of $$0.990 \pm 0.008$$ 0.990 ± 0.008 and a mean absolute error of $$0.034 \pm 0.001$$ 0.034 ± 0.001 eV ( $$\approx 0.79 \pm 0.03$$ ≈ 0.79 ± 0.03 kcal/mol) on the QM9 validation set, demonstrating robust, chemical-accuracy-level predictions. Building on these high-precision predictions, the second stage employs a QAOA-inspired hybrid ranking scheme that merges quantum graph neural network outputs, feature-space similarity (via and cosine similarity), and variational quantum eigensolver-derived energy stability. This $$\alpha $$ α -weighted ( $$\alpha = 0.95$$ α = 0.95 ) scoring framework is applied to over 133,000 molecules, efficiently parsed in parallel. The final ranked list is validated through an improved bijection test, featuring an adaptive similarity threshold to ensure both structural and functional robustness. The top-scoring candidate identified by our pipeline is 5,6,7-tetrahydro-4 H-pyrazolo[4,3-c]pyridin-4-one, highlighting the efficacy of quantum-enhanced modeling in pinpointing complex pharmacological targets. These findings underscore the transformative potential of hybrid quantum-classical workflows in drug discovery, offering a flexible blueprint for advanced screening of other critical biomolecular interactions in the rapidly expanding field of quantum biology. GraphicAbstract VQE for Serine Neutralization

DOI
10.1140/epjd/s10053-025-01024-8

Related papers

A Hybrid Quantum-Classical Machine Learning Framework for Accelerated Drug Discovery

Sriramadasu Sri Sainadh, Saigeetha S.B., Jeeru Bharath Reddy +4 more

The pharmaceutical industry faces mounting challenges in drug discovery, where exploring a chemical space exceeding 10 60 possible compounds remains computationally prohibitive. Traditional in-silico screening approaches struggle to capture the quantum mechanical interactions that determine molecular behavior. To overcome these limitations, this study introduces a hybrid quantum–classical machine learning framework that uniquely integrates molecular graph theory with quantum-enhanced learning for accelerated drug discovery. Using the QM9 benchmark dataset containing 133,885 molecules of low-to-medium structural complexity, we extract Laplacian eigenvalue spectra as topological descriptors that preserve both connectivity and electronic information. These features are jointly processed by Random Forest (RF), Support Vector Machine (SVM), and a Variational Quantum Classifier (VQC) in a weighted ensemble architecture designed for balanced generalization. The Quantum Graph Neural Network (QGNN) component achieves 97.5% accuracy, while the hybrid ensemble attains 100.0% accuracy, confirming strong predictive reliability. Although quantum training requires roughly 3.2× longer computation, it captures high-dimensional correlations that classical methods overlook. Overall, the proposed framework bridges the gap between theoretical quantum computing and practical pharmaceutical modeling, providing a scalable, physics-inspired pathway toward intelligent molecular screening and next-generation drug discovery systems.

Procedia Computer Science•Jan 1, 2026•0 citations

Quantum-Enhanced Computational Drug Discovery: Leveraging Variational Quantum Algorithms for Accurate Binding Affinity Prediction and Lead Optimization in Complex Biological Targets

Hande Selvi Yanık

Accurate prediction of binding affinities and efficient lead optimization remain central challenges in computational drug discovery, particularly for complex biological targets characterized by rugged energy landscapes, conformational heterogeneity, and high-dimensional interaction spaces. Classical computational methods—such as molecular docking, force-field–based simulations, and deep learning models—have made substantial progress, yet they often struggle to capture quantum-mechanical effects and long-range correlations critical to molecular recognition. This study explores a quantum-enhanced framework that integrates Variational Quantum Algorithms (VQAs), quantum-inspired Hamiltonian modeling, and hybrid quantum–classical optimization workflows to improve the fidelity and scalability of drug discovery pipelines. By encoding molecular interactions into parameterized quantum circuits, the framework leverages quantum superposition and entanglement to explore complex chemical space more efficiently, enabling refined estimation of binding energies and accelerated identification of high-quality leads. Preliminary simulations indicate that VQA-based estimators outperform classical baselines for challenging protein–ligand systems, reducing prediction error while maintaining computational tractability. These findings highlight the emerging potential of quantum technologies to enable more accurate, data-efficient, and mechanistically grounded drug discovery for next-generation therapeutics.

Next frontier.•Nov 28, 2025•0 citations

Quantum Machine Learning for Drug Discovery: From Molecular Descriptors to Explainable Quantum Pharmacology

Volkan Erol

Recent advances in quantum machine learning (QML) have opened new pathways for accelerating early-stage drug discovery through molecular representation in Hilbert space [1]–[3]. In this work, we present a hybrid quantum–classical framework that integrates quantum kernel estimation and variational quantum neural networks (QNNs) for ligand–target binding prediction [4], [5].A synthetic dataset reflecting the statistical behavior of the BindingDB database [6] was constructed to evaluate quantum descriptors and kernel performance under controlled conditions. The proposed quantum feature maps translate seven key molecular descriptors—molecular weight (MW), logP, hydrogen bond donors (HBD), acceptors (HBA), rotatable bonds (RB), aromatic rings (AR), and topological polar surface area (TPSA)—into entangled qubit states [7], [8].Comparative analyses with classical baselines (SVR, Random Forest, and deep neural networks) revealed that quantum embeddings achieve competitive predictive accuracy (RMSE ≈ 0.06) with improved stability under bootstrap resampling [9]. Quantum kernel alignment and sensitivity studies demonstrated that aromaticity and polarity jointly determine the representational power of QML models [10].Beyond performance, we emphasize Explainable Quantum Pharmacology (EQP)—a paradigm in which interpretability, reproducibility, and physicochemical causality are as essential as accuracy [11].Our findings establish a reproducible, interpretable, and computationally efficient foundation for hybrid QML pipelines in molecular modeling, paving the way for next-generation AI-driven drug discovery.

•Oct 10, 2025•0 citations

Computational Precision Medicine Through Quantum-Enhanced Molecular Modeling

Chidi Ijeoma Nosiri, Paul Okoli, Echerou Leonard Nnadi +2 more

The exorbitant costs, protracted timelines, and elevated attrition rates associated with traditional drug-discovery pipelines underscore the pressing necessity for computational frameworks that can elucidate biomolecular interactions with quantum-level precision and practical scalability. This study introduces a Hybrid Quantum Classical (HQC) framework that combines quantum variational algorithms, classical molecular dynamics, and quantum-assisted machine-learning optimization into a single drug-screening workflow. It builds on the basic idea of Quantum Molecular Simulation (QMS). In the suggested design, quantum processors are used to selectively fix high-fidelity electronic interactions in reactive binding sites, while classical engines model the large-scale conformational dynamics of biomolecular environments. An adaptive quantum-machine-learning layer speeds up convergence even more by learning how structure and energy are related from quantum-refined descriptors. Benchmark tests against oncogenic targets like EGFR, BCR-ABL1, and p53 show that our method is up to 27% more accurate at converging binding energy and takes 4.3 times less time to compute than standard density-functional-theory and standalone QMS methods. The HQC framework makes quantum drug simulation possible for real-world drug discovery by reducing the limitations of current quantum hardware while keeping electronic-scale accuracy. This study demonstrates that hybrid quantum-classical modeling is a scalable and hardware-compatible approach for advancing next-generation computational drug design and precision therapeutics.

Iconic Research and Engineering Journals•Jul 31, 2023•0 citations

Hybrid Quantum-Classical Algorithms for Drug Discovery and Molecular Simulation

Murali Krishna Pasupuleti

Abstract: This study explores the implementation of hybrid quantum-classical algorithms in the realm of drug discovery and molecular simulation, with an emphasis on optimizing molecular interaction prediction. The integration of quantum computing paradigms, particularly the Variational Quantum Eigensolver (VQE), with classical machine learning techniques is evaluated for its efficacy in simulating molecular systems. Key results demonstrate superior accuracy in predicting binding affinities and reaction energetics using the hybrid models compared to traditional methods. The findings offer significant implications for accelerating the drug development pipeline, particularly in early-stage candidate screening. Keywords: Hybrid computing, Quantum simulation, Molecular interaction, Drug discovery, Variational Quantum Eigensolver, Quantum-classical integration

International Journal of Academic and Industrial Research Innovations(IJAIRI)•Jun 27, 2025•1 citation

Hybrid Quantum-Classical Machine Learning Architectures for Accelerated Drug Discover

Vibhor Pal

Rapid drug development has been increasingly prevalent over the last ten years, and this trend, when combined with efficient regulatory approvals, has in large part been the driver for the rapid availability of innovative drugs to patients worldwide. This work presents a hybrid Variational Quantum Eigen seeker–Neural Network (VQE-NN) model, a single accelerated drug-solving device that leverages the benefits of both traditional and quantum computers. It performs drug class prediction and feature analysis based on the Kaggle Drug Classification dataset, which contains 2,000–3,000 records with categorical, textual, and numerical features. In data preprocessing, the researchers applied text normalization, tokenization, stemming, and TF-IDF-based feature extraction. The hybrid model presented consists of a VQE module for the optimization of molecular representations and a neural network for classification. In addition, the hyperparameters were carefully tuned to ensure the model learns efficiently and converges. The experimental results show the model's remarkable prediction capability as seen from an accuracy of 97.0%, precision of 96.3%, recall of 96.8%, F1-score of 96.5%, and an AUC of 0.9991. In the performance comparison, the VQE-NN model is claimed to be superior to the existing benchmarks, such as Generative RNN and Seq2Seq Autoencoder models. Besides, the research highlights the benefits of the model, which stem from using quantum entanglement and superposition, which allows for the identification of correlations in higher dimensions and offers a scalable, robust, and state-of-the-art framework for drug prediction

International Journal of Advanced Research in Science Communication and Technology•Jun 30, 2021•2 citations
Abstract Quantum computing has emerged as a powerful tool for modeling molecular systems with high accuracy, accelerating the search for novel therapeutic targets. In this study, we present a two-stage hybrid workflow that combines a Quantum Graph Neural Network with a Variational Quantum Eigensolver to identify potent serine neutralizers in the QM9 dataset. In the first stage, an advanced quantum graph neural network architecture incorporating attention layers, self-distillation, and an adaptive learning-rate schedule is trained to predict ionization potentials and binding free energies. Across five independent random-seed trials, our adaptive-thresholded QGNN–VQE pipeline achieves an average R2R^2R2 R 2 of 0.990±0.0080.990 \pm 0.0080.990±0.008 0.990 ± 0.008 and a mean absolute error of 0.034±0.0010.034 \pm 0.0010.034±0.001 0.034 ± 0.001 eV ( ≈0.79±0.03\approx 0.79 \pm 0.03≈0.79±0.03 ≈ 0.79 ± 0.03 kcal/mol) on the QM9 validation set, demonstrating robust, chemical-accuracy-level predictions. Building on these high-precision predictions, the second stage employs a QAOA-inspired hybrid ranking scheme that merges quantum graph neural network outputs, feature-space similarity (via and cosine similarity), and variational quantum eigensolver-derived energy stability. This α\alpha α α -weighted ( α=0.95\alpha = 0.95α=0.95 α = 0.95 ) scoring framework is applied to over 133,000 molecules, efficiently parsed in parallel. The final ranked list is validated through an improved bijection test, featuring an adaptive similarity threshold to ensure both structural and functional robustness. The top-scoring candidate identified by our pipeline is 5,6,7-tetrahydro-4 H-pyrazolo[4,3-c]pyridin-4-one, highlighting the efficacy of quantum-enhanced modeling in pinpointing complex pharmacological targets. These findings underscore the transformative potential of hybrid quantum-classical workflows in drug discovery, offering a flexible blueprint for advanced screening of other critical biomolecular interactions in the rapidly expanding field of quantum biology. GraphicAbstract VQE for Serine Neutralization
The pharmaceutical industry faces mounting challenges in drug discovery, where exploring a chemical space exceeding 10 60 possible compounds remains computationally prohibitive. Traditional in-silico screening approaches struggle to capture the quantum mechanical interactions that determine molecular behavior. To overcome these limitations, this study introduces a hybrid quantum–classical machine learning framework that uniquely integrates molecular graph theory with quantum-enhanced learning for accelerated drug discovery. Using the QM9 benchmark dataset containing 133,885 molecules of low-to-medium structural complexity, we extract Laplacian eigenvalue spectra as topological descriptors that preserve both connectivity and electronic information. These features are jointly processed by Random Forest (RF), Support Vector Machine (SVM), and a Variational Quantum Classifier (VQC) in a weighted ensemble architecture designed for balanced generalization. The Quantum Graph Neural Network (QGNN) component achieves 97.5% accuracy, while the hybrid ensemble attains 100.0% accuracy, confirming strong predictive reliability. Although quantum training requires roughly 3.2× longer computation, it captures high-dimensional correlations that classical methods overlook. Overall, the proposed framework bridges the gap between theoretical quantum computing and practical pharmaceutical modeling, providing a scalable, physics-inspired pathway toward intelligent molecular screening and next-generation drug discovery systems.
Accurate prediction of binding affinities and efficient lead optimization remain central challenges in computational drug discovery, particularly for complex biological targets characterized by rugged energy landscapes, conformational heterogeneity, and high-dimensional interaction spaces. Classical computational methods—such as molecular docking, force-field–based simulations, and deep learning models—have made substantial progress, yet they often struggle to capture quantum-mechanical effects and long-range correlations critical to molecular recognition. This study explores a quantum-enhanced framework that integrates Variational Quantum Algorithms (VQAs), quantum-inspired Hamiltonian modeling, and hybrid quantum–classical optimization workflows to improve the fidelity and scalability of drug discovery pipelines. By encoding molecular interactions into parameterized quantum circuits, the framework leverages quantum superposition and entanglement to explore complex chemical space more efficiently, enabling refined estimation of binding energies and accelerated identification of high-quality leads. Preliminary simulations indicate that VQA-based estimators outperform classical baselines for challenging protein–ligand systems, reducing prediction error while maintaining computational tractability. These findings highlight the emerging potential of quantum technologies to enable more accurate, data-efficient, and mechanistically grounded drug discovery for next-generation therapeutics.
Recent advances in quantum machine learning (QML) have opened new pathways for accelerating early-stage drug discovery through molecular representation in Hilbert space [1]–[3]. In this work, we present a hybrid quantum–classical framework that integrates quantum kernel estimation and variational quantum neural networks (QNNs) for ligand–target binding prediction [4], [5].A synthetic dataset reflecting the statistical behavior of the BindingDB database [6] was constructed to evaluate quantum descriptors and kernel performance under controlled conditions. The proposed quantum feature maps translate seven key molecular descriptors—molecular weight (MW), logP, hydrogen bond donors (HBD), acceptors (HBA), rotatable bonds (RB), aromatic rings (AR), and topological polar surface area (TPSA)—into entangled qubit states [7], [8].Comparative analyses with classical baselines (SVR, Random Forest, and deep neural networks) revealed that quantum embeddings achieve competitive predictive accuracy (RMSE ≈ 0.06) with improved stability under bootstrap resampling [9]. Quantum kernel alignment and sensitivity studies demonstrated that aromaticity and polarity jointly determine the representational power of QML models [10].Beyond performance, we emphasize Explainable Quantum Pharmacology (EQP)—a paradigm in which interpretability, reproducibility, and physicochemical causality are as essential as accuracy [11].Our findings establish a reproducible, interpretable, and computationally efficient foundation for hybrid QML pipelines in molecular modeling, paving the way for next-generation AI-driven drug discovery.
The exorbitant costs, protracted timelines, and elevated attrition rates associated with traditional drug-discovery pipelines underscore the pressing necessity for computational frameworks that can elucidate biomolecular interactions with quantum-level precision and practical scalability. This study introduces a Hybrid Quantum Classical (HQC) framework that combines quantum variational algorithms, classical molecular dynamics, and quantum-assisted machine-learning optimization into a single drug-screening workflow. It builds on the basic idea of Quantum Molecular Simulation (QMS). In the suggested design, quantum processors are used to selectively fix high-fidelity electronic interactions in reactive binding sites, while classical engines model the large-scale conformational dynamics of biomolecular environments. An adaptive quantum-machine-learning layer speeds up convergence even more by learning how structure and energy are related from quantum-refined descriptors. Benchmark tests against oncogenic targets like EGFR, BCR-ABL1, and p53 show that our method is up to 27% more accurate at converging binding energy and takes 4.3 times less time to compute than standard density-functional-theory and standalone QMS methods. The HQC framework makes quantum drug simulation possible for real-world drug discovery by reducing the limitations of current quantum hardware while keeping electronic-scale accuracy. This study demonstrates that hybrid quantum-classical modeling is a scalable and hardware-compatible approach for advancing next-generation computational drug design and precision therapeutics.
Abstract: This study explores the implementation of hybrid quantum-classical algorithms in the realm of drug discovery and molecular simulation, with an emphasis on optimizing molecular interaction prediction. The integration of quantum computing paradigms, particularly the Variational Quantum Eigensolver (VQE), with classical machine learning techniques is evaluated for its efficacy in simulating molecular systems. Key results demonstrate superior accuracy in predicting binding affinities and reaction energetics using the hybrid models compared to traditional methods. The findings offer significant implications for accelerating the drug development pipeline, particularly in early-stage candidate screening. Keywords: Hybrid computing, Quantum simulation, Molecular interaction, Drug discovery, Variational Quantum Eigensolver, Quantum-classical integration
Rapid drug development has been increasingly prevalent over the last ten years, and this trend, when combined with efficient regulatory approvals, has in large part been the driver for the rapid availability of innovative drugs to patients worldwide. This work presents a hybrid Variational Quantum Eigen seeker–Neural Network (VQE-NN) model, a single accelerated drug-solving device that leverages the benefits of both traditional and quantum computers. It performs drug class prediction and feature analysis based on the Kaggle Drug Classification dataset, which contains 2,000–3,000 records with categorical, textual, and numerical features. In data preprocessing, the researchers applied text normalization, tokenization, stemming, and TF-IDF-based feature extraction. The hybrid model presented consists of a VQE module for the optimization of molecular representations and a neural network for classification. In addition, the hyperparameters were carefully tuned to ensure the model learns efficiently and converges. The experimental results show the model's remarkable prediction capability as seen from an accuracy of 97.0%, precision of 96.3%, recall of 96.8%, F1-score of 96.5%, and an AUC of 0.9991. In the performance comparison, the VQE-NN model is claimed to be superior to the existing benchmarks, such as Generative RNN and Seq2Seq Autoencoder models. Besides, the research highlights the benefits of the model, which stem from using quantum entanglement and superposition, which allows for the identification of correlations in higher dimensions and offers a scalable, robust, and state-of-the-art framework for drug prediction