PAM-DB: Revealing Protein Activation Mechanisms for Next-Generation Rational Drug Discovery

Abstract

Current rational drug design relies predominantly on computational (CADD/AIDD) methods that model binding thermodynamics and static conformations of target proteins, primarily in their inactive states. However, the kinetic parameters that govern experimental efficacy—such as catalytic turnover and signaling potency—are determined by molecular interactions with transition states (TS), intermediate states (IS), and the entire continuum of conformations along the least free-energy activation pathway. The absence of this dynamic dimension has fundamentally limited the predictive power and success rate of conventional structure-based approaches. Here, we present a structural database that systematically maps the complete activation trajectories of pharmaceutically relevant targets, encompassing TS, IS, and all connecting conformational ensembles. This resource offers multiple strategic advantages for drug discovery: enabling rational targeting of previously “undruggable” proteins, facilitating biased agonism/antagonism design, revealing cryptic allosteric sites in inactive conformations, identifying novel transient pockets along the activation route, rationalizing the mechanisms of existing drugs, predicting mutational effects on activation barriers, and prospectively forecasting drug resistance and off-target liabilities. We demonstrate the utility of this database through representative case studies and provide implementation guidelines for integration into existing discovery pipelines. More detailed information can be found at our website: https://www.momedpamdb.com/en. Terminology The following terms are clarified in this document: Stable state (SS): In this document, this term refers exclusively to, and is synonymous with, the protein’s inactive state (IAS). Note that other states may also be stabilized into meta-stable states by certain means. Unstable state (US): This term encompasses all states other than SS, even if they appear computationally meta-stable on the free energy surface. Activated state (AS): The meta-stable working state of the protein. Transition state (TS): The state with the highest free energy along the least-energy pathway on the free energy surface that connects the inactive state to the activated state of the target protein. Intermediate state (IS): The state(s) located at a local minimum along the least-energy pathway, excluding SS and AS.