Noncovalent Interaction Thresholds Control Translocation and Cytotoxicity: A Combined Computational–Experimental Study

Designing membrane-permeable drugs requires a precise understanding of noncovalent interactions governing cellular uptake. We propose a molecular thermodynamic–dynamic (MTD) framework that quantifies interaction thresholds dictating permeation efficiency, using polychlorinated biphenyls (PCBs) as structurally tunable probes. Our results reveal that optimal permeability occurs within a defined differential binding energy (ΔG = −3.6 to −6.8 kcal/mol for H-/X-bonding), facilitating membrane translocation through a binding-flip mechanism. Beyond this range, excessive binding affinity (ΔG < −7.5 kcal/mol) leads to kinetic trapping at the membrane surface. Notably, the membrane permeation coefficients exhibit a strong linear correlation with differential binding energy (R² = 0.93), as revealed by five distinct transition states, including a rate-limiting vertical rotation step (ΔG = 2.4 kcal/mol). These findings yield two critical design principles: (i) intermediate differential binding (−4.0 to −5.0 kcal/mol) maximizes permeability, aligning with optimal ranges in FDA-approved membrane-permeable drugs, and (ii) targeted X-bonding modulation precisely controls membrane interaction specificity.