This study explores how targeting hydrogen-bonding and vibrational dynamics clarifies the mechanisms through which biological information becomes meaningful in the contexts of health and disease. By focusing on chemically defined interactions, this framework emphasizes how physical constraints at the molecular level shape signaling behavior and cellular outcomes and may form the basis for new therapeutic modalities that serve as both treatments and prophylactic interventions.

Objective: We investigate whether hydrogen-bond–mediated tuning of vibrational frequencies in effector–receptor interactions can modulate signal transduction efficiency. Amplification of signal transduction thereby reveals therapeutic opportunities to influence signaling through controlled perturbation of hydrogen-bond networks.

Method: We performed a comparative analysis of information transmission from genetic encoding to post-translational modification, to assess how cells integrate intrinsic and environmental cues while maintaining signaling fidelity. Emphasis was placed on chemical mechanisms underlying signal propagation, including ionic fluxes, second messengers, scaffolding and adaptor proteins, and molecular switches.

Results: Findings demonstrate that vibrational frequency contributes to molecular functional outcomes and that hydrogen-bond organization plays a central role in directing cellular information flow. Proton-coupled hydrogen-bond dynamics emerged as a regulator of cellular state. Local proton release associated with ATP hydrolysis can reduce pH, perturb hydrogen-bond networks, and alter enzyme conformation and activity, modulate ion channels and signaling pathways including Ca²⁺ signaling—and influence gene regulatory processes.

Conclusions: Disrupted signaling fidelity has profound consequences on cellular behavior, contributing to a wide spectrum of pathological conditions including inflammation, infection, neurodegeneration, and autoimmunity. High-fidelity signaling depends on chemically encoded mechanisms such as temporal gating, spatial compartmentalization, and feedback regulation to preserve specificity, amplification and to ensure signal clarity. Examples from calcium signaling, immunological synapse formation, and neurotransmission illustrate how cells maintain reliable information transfer under dynamic conditions. These observations suggest that therapeutic strategies targeting the chemical determinants of signaling accuracy—rather than isolated pathway components—may provide a complementary approach to disease modulation by restoring information flow at its molecular origin.