Quantum Reactivity-Guided Optimization of ATP-Competitive Ligands through Multiscale Simulation

ATP-binding pockets impose stringent geometric and electronic constraints on small-molecule ligands, requiring preservation of key anchoring interactions while permitting only limited scaffold modification. Rational optimization of ATP-competitive inhibitors therefore remains challenging, particularly when electronic reactivity and metabolic liability must be balanced against binding stability. We explored a multiscale, quantum-informed computational strategy to address this challenge using the receptor tyrosine kinase-like orphan receptor 1 (ROR1) pseudokinase domain, an underexplored intracellular cancer target that retains a druggable ATP-binding pocket, as a chemically informative model system. Using Ponatinib as an internal reference scaffold, eight Fukui-guided analogs (DM1- DM8) were designed through density functional theory analyses integrating Mulliken, Löwdin and Hirshfeld charge partitioning with Fukui function mapping. These calculations identified electronically reactive and metabolically labile regions amenable to site-specific modification at C10, C11, C32, and C35, while preserving the alkyne and carbonyl motifs responsible for anchoring interactions within the ATP-binding pocket. To establish a robust energetic and dynamical baseline, 1 μs all-atom molecular dynamics simulations were performed for the ROR1 pseudokinase domain in both apo and Ponatinib-bound states. The designed analogs were subsequently evaluated using 250 ns simulations combined with relative MM-PBSA binding free-energy analysis, revealing a narrow binding-energy range (ΔG_bind ≈ -37 to -45 kcal mol^-1) comparable to Ponatinib (-41.78 ± 5.65 kcal mol^-1 at 250 ns; -40.23 ± 5.61 kcal mol^-1 at 1 μs). Interaction fingerprint analysis confirmed conservation of the hinge-anchored Glu71-Ile103-Asp181 network and the Phe100-Tyr102 aromatic clamp across the series. In silico ADME profiling differentiated developability among energetically similar compounds, identifying DM3-DM5 as the most balanced analogs. Collectively, quantum-mechanical reactivity descriptors can delineate electronically feasible scaffold modification sites within ATP-binding pocketspositions where chemical perturbation is tolerated without disrupting anchoring pharmacophore interactionsproviding substantively complementary information distinct from, classical energy-based scoring or empirical SAR.