Network architecture determines delay robustness in the spindle assembly checkpoint

The spindle assembly checkpoint (SAC) ensures accurate chromosome segregation during mitosis by preventing premature activation of the anaphase-promoting complex/cyclosome (APC/C). Despite its critical role in maintaining genomic stability, most mathematical models of the SAC treat underlying biochemical processes as instantaneous, neglecting experimentally observed delays arising from molecular activation, complex assembly, and intracellular transport. How such temporal structure interacts with network architecture to shape checkpoint dynamics remains unclear. Here, we develop a distributed-delay framework and incorporate experimentally motivated delays into multiple mechanistic SAC architectures. Using a gamma-chain formulation, we perform systematic stability and bifurcation analyses across representative models. We find that biologically realistic delays fundamentally reorganize system dynamics, partitioning SAC architectures into two distinct classes: delay-robust designs that preserve strong APC/C inhibition, and delay-sensitive designs in which checkpoint control collapses. Motivated by this classification, we introduce a bistable template architecture that combines mechanistic Mad2 templating with an autocatalytic feedback loop. This design maintains bistability and high inhibition across a broad range of physiological delays and remains resilient under stochastic perturbations. These results identify network architecture as a key determinant of robustness to molecular timing and demonstrate that distributed delays can stabilize, rather than destabilize, checkpoint function by enabling temporal integration and memory-like behavior. More broadly, this work establishes delay-aware design principles for biochemical decision-making systems in which intermediate processes are intrinsically time-distributed.