BiSim Tool: a binding simulation tool to aid and simplify ligand-binding assay design and development

Ligand-binding assays (LBAs) rely on the reversible, noncovalent binding between the analyte of interest and the assay reagents, and understanding their dynamic equilibrium is key to building robust LBA methods. Although the dynamic interplay of free and bound fractions can be calculated using mathematical models, these are not routinely applied. This approach is costly in terms of both assay development time and reagents, and can result in an under-exploration of the possible parameter combinations. Therefore, we have created a user-friendly simulation tool to facilitate LBA development (the BiSim Tool). We describe the models driving the mathematical simulations and the main features of our software solution by means of case studies, illustrating the tool's value in drug development. To support drug development for all patients worldwide, the BiSim Tool is now available as an open-source code project and as a free web-based tool at https://proteinbindingsimulation.shinyapps.io/BiSim-ProteinBindingSimulation [1]. Ligand-binding assays (LBAs) are essential for analyzing the interaction between an analyte and assay reagents through reversible, noncovalent binding. Understanding the dynamic equilibrium between free and bound fractions in LBAs is crucial for developing effective assay methods. Despite the importance, mathematical models to calculate this dynamic interplay are not commonly used in practice. We developed a new user-friendly simulation tool, BiSim, to make the application of mathematical models in LBA development more accessible. The tool and its underlying mathematical models are explained through case studies, such as determining assay performance requirements, predicting expected complex formation, time-to-equilibrium and assay optimization. BiSim is available as an open-source code project, allowing for wide accessibility and the possibility of community improvements. Additionally, a free web-based service hosts the BiSim Tool, ensuring easy access for users without the need for software installation: https://proteinbindingsimulation.shinyapps.io/BiSim-ProteinBindingSimulation. The combination of detailed use cases and the freely available tool provide a valuable resource for researchers and developers in drug development, saving both time and development costs.