The systematic discovery of effective drug combinations is a challenging problem in modern pharmacology, driven by the combinatorial growth of potential pairings and dosage configurations. Network medicine, modeling diseases and drugs as interconnected modules of the human protein-protein interactome, has emerged as a new paradigm for understanding disease mechanisms and drug action. In this work, we propose a quantum annealing-based algorithm for identifying effective drug combinations. Underlying our approach is the biologically motivated principle of `Complementary Exposure', which posits that therapeutic drug combinations target distinct yet complementary regions of a disease module. We translate this into a quadratic unconstrained binary optimisation problem. We test our method for Diabetes Mellitus, Rheumatoid Arthritis, Asthma, and Brain Neoplasms, relying on experimentally validated drug combinations for these diseases. Our simulated quantum annealing experiments reveal that low-energy configurations align with biologically plausible combinations which may serve as prioritized candidates for subsequent experimental validation.
The systematic discovery of effective drug combinations is a challenging problem in modern pharmacology, driven by the combinatorial growth of potential pairings and dosage configurations. Network medicine, modeling diseases and drugs as interconnected modules of the human protein-protein interactome, has emerged as a new paradigm for understanding disease mechanisms and drug action. In this work, we propose a quantum annealing-based algorithm for identifying effective drug combinations. Underlying our approach is the biologically motivated principle of `Complementary Exposure', which posits that therapeutic drug combinations target distinct yet complementary regions of a disease module. We translate this into a quadratic unconstrained binary optimisation problem. We test our method for Diabetes Mellitus, Rheumatoid Arthritis, Asthma, and Brain Neoplasms, relying on experimentally validated drug combinations for these diseases. Our simulated quantum annealing experiments reveal that low-energy configurations align with biologically plausible combinations which may serve as prioritized candidates for subsequent experimental validation.
Scientific and technological advances in medicine and systems biology have unequivocally shown that health and disease must be viewed in the context of the interplay among multiple molecular and environmental factors. Understanding the effects of cellular interconnection on disease progression may lead to the identification of novel disease genes and pathways, and hence influence precision diagnostics and therapeutics. To accomplish this goal, the emerging field of network medicine applies network science approaches to investigate disease pathogenesis, integrating information from relevant Omics databases, including protein-protein interaction, correlation-based, gene regulatory, and Bayesian networks. However, this requires analysing and computing large amounts of data. Moreover, if we are to efficiently search for new drugs and new drug combinations, there is a pressing need for computational methods that could allow us to access the immense chemical compound space until now largely unexplored. Finally, at the microscopic level, drug-target chemistry simulation is ultimately a quantum problem, and hence it requires a quantum solution. As we will discuss, quantum computing may be a key ingredient in enabling the full potential of network medicine. We propose to combine network medicine and quantum algorithms in a novel research field, quantum network medicine, to lay the foundations of a new era of disease prevention and drug design.
Artificial intelligence (AI) has greatly expanded the generative capacity of drug discovery, yet the ability to translate large candidate pools into structured, resource-aware decisions remains limited. This review addresses this emerging optimization bottleneck by examining quantum annealing as a potential decision-optimization layer within hybrid computational workflows. We focus on discrete, constraint-dominated tasks-such as compound subset selection, combinatorial design, and multi-objective prioritization-that can be formulated as quadratic unconstrained binary optimization (QUBO) problems. Rather than positioning quantum annealing as a predictive tool, we analyze its role as a complementary optimization interface integrated with AI-generated scores. We further discuss practical implementation considerations, including embedding overhead, noise, scalability, and benchmarking challenges. By emphasizing workflow-level design and rigorous evaluation, this review provides a pragmatic framework for assessing annealing-based optimization in drug discovery and related data-intensive scientific domains.
Modelling and predicting protein configurations is crucial for advancing drug discovery, enabling the design of treatments for life-threatening diseases. A critical aspect of this challenge is rotamer optimisation - the determination of optimal side-chain conformations given a fixed protein backbone. This problem, involving the internal degrees of freedom of amino acid side-chains, significantly influences the protein's overall structure and function. In this work, we develop a resource-efficient optimisation algorithm to compute the ground state energy of protein structures, with a focus on side-chain configuration. We formulate the rotamer optimisation problem as a Quadratic Unconstrained Binary Optimisation problem and map it to an Ising model, enabling efficient quantum encoding. Building on this formulation, we propose a quantum algorithm based on the Quantum Approximate Optimisation Algorithm to explore the conformational space and identify low-energy configurations. To benchmark our approach, we conduct a classical study using custom-built libraries tailored for structural characterisation and energy optimisation. Our quantum method demonstrates a reduction in computational cost compared to classical simulated annealing techniques, offering a scalable and promising framework for protein structure optimisation in the quantum era.
The optimization of multidrug cancer treatment schedules is a high-dimensional combinatorial optimization problem involving nonlinear tumor dynamics, pharmacokinetic interactions, and stringent toxicity constraints. When exploring large therapeutic search spaces, conventional optimization algorithms often exhibit limited scalability and become trapped in local optima. This simulation study proposes a hybrid quantum-classical optimization framework that employs QA to generate adaptive treatment schedules for precision oncology. The treatment scheduling problem is formulated as a quadratic unconstrained binary optimization (QUBO) model, which encodes drug combinations, dosing intervals, toxicity constraints, and synergistic interactions within an Ising Hamiltonian compatible with D-Wave quantum annealing hardware. Global combinatorial optimization is performed using a D-Wave Advantage quantum annealer, while sequential least squares programming refines continuous dosage parameters under pharmacokinetic and toxicity constraints. Tumor progression is represented using a modified Gompertz growth model coupled with first-order pharmacokinetic dynamics. The proposed framework was evaluated using synthetic Digital Twin datasets generated from clinically realistic pharmacokinetic and tumor growth parameters. Simulation results demonstrated a maximum tumor regression ratio of 0.98 ± 0.02, compared with 0.82 ± 0.05 for standard-of-care protocols, while maintaining a lower cumulative toxicity index (40 ± 5 versus 75 ± 8) and reducing optimization time to less than 2 s for 120-variable scheduling problems. The hybrid framework exhibited near-linear computational scalability and maintained robustness under stochastic dosage perturbations (TRR > 0.95 at σ = 0.25). However, predictive classification performance remained limited (AUC = 0.49), highlighting the need for validation using longitudinal clinical datasets and multimodal patient-specific data. These findings demonstrate the potential of hybrid quantum-classical optimization as a scalable computational framework for adaptive treatment scheduling and personalized precision oncology.
Regenerative medicine requires rapid analysis of the best therapeutic molecules capable of interacting with in vivo undifferentiated mass with complex biology and therapeutic properties that are needed to repair and regenerate tissues. The scalability and efficiency of conventional computational solutions and even recent representations with more advanced classical neural networks are limited when it comes to molecular data that are high dimensional. The combination of quantum computing principles and deep learning neural networks provides a potential avenue to speed this process up, by exploiting quantum parallelism, entanglement and superposition in pattern recognition and simulation of molecules through what is known as Quantum Neural Networks (QNNs). The paper describes how to apply QNNs to facilitate the process of target identification, molecular docking, and compound optimization in regenerative medicine in particular. We introduce a conceptual, hybrid quantum classical model to simulate protein-ligand interactions, screen drug candidates and economize on computational costs relative to classical models. The offered solution marks the conceivably quicker performance in molecular screening, better sensitivity in predicting drug-target interactions, and accommodating complex biological data. QNNs by connecting both quantum computing and biomedical innovation can foreseeably lead to much shorter time-to-discovery, yielding more successfully and personified regenerative treatments.
Abstract : We propose a hybrid quantum–classical framework that integrates variational quantum machine learning (QML) for molecular binding affinity prediction with quantum annealing for Pareto-optimal drug formulation design. Leveraging a four-qubit variational circuit, our QML model achieves superior predictive performance compared to state-of-the-art classical baselines, effectively capturing complex molecular interactions. In parallel, we formulate drug formulation optimization as a Quadratic Unconstrained Binary Optimization (QUBO) problem and solve it using D-Wave’s quantum annealer, enabling efficient identification of Pareto-optimal solutions that balance bioavailability, toxicity, and stability. By unifying predictive modeling and combinatorial optimization within a single pipeline, our framework demonstrates the potential of near-term quantum devices to accelerate and enhance critical stages of drug discovery. These findings underscore the transformative role of NISQ-era algorithms in bridging molecular informatics and formulation design, paving the way for scalable, data-driven pharmaceutical innovation.