Secondary pharmacology across therapeutic modalities: A cross-modality principle-based framework for off-target assessment

Secondary pharmacology encompasses the pharmacological effects of a therapeutic agent beyond its intended therapeutic mechanism. While secondary pharmacology assessment is well established for small molecules, the emergence of biologics, peptides and proteins, oligonucleotide therapeutics, targeted protein degraders, and gene and cell therapies, has exposed important limitations of traditional assessment paradigms. Across these modalities, unintended biological activity may arise through different mechanisms, including direct target binding, cross-reactivity, hybridization-dependent transcript modulation, induced protein degradation, altered tissue tropism, and cell-mediated biological responses. Consequently, approaches developed primarily for small molecules are not universally applicable, highlighting gaps in regulatory frameworks, including ICH S7A. This review examines secondary pharmacology practices across therapeutic modalities and identifies modality-specific considerations and shared principles underpinning hazard identification and risk assessment. Despite differences in biological mechanisms and assessment methodologies, several foundational concepts consistently emerge, including mechanistic plausibility, target relevance, exposure context, translational understanding, and integration of multiple lines of evidence. Building on these principles, we propose a cross-modality principle-based framework that distinguishes hazard identification from contextualisation and risk assessment, supporting decision-making through a structured weight of evidence approach. This applied scientific justification aims to improve consistency, translatability, and regulatory alignment while enabling secondary pharmacology assessment to evolve with the therapeutic landscape.