Theoretical study on N(sp2)+–C(sp2)–H···O hydrogen bonds in the context of drug discovery

C–H···O hydrogen bonds are regarded as weak and overlooked in structure-based drug design. Here, we demonstrate through quantum-chemical calculations that N(sp 2 )⁺–C(sp 2 )–H···O hydrogen bonds involving pyridinium ions exhibit strong and directional interactions with carbonyl oxygen atoms. Density-functional-theory (DFT) and natural-bond-orbital (NBO) analyses indicated that cationization increases the positive charge on adjacent sp 2 C–H protons, thereby enhancing their proton-donating ability. Fragment-based symmetry-adapted-perturbation-theory (F-SAPT) analyses revealed that these interactions remain significant even when the pyridine nitrogen is partially positively charged via interaction with another hydrogen-bond donor. Geometric criteria were established from a theoretical study and applied to a survey of protein–ligand complexes in the Protein Data Bank, and 55 protein kinase–inhibitor complexes exhibiting N(sp 2 )⁺–C(sp 2 )–H···O hydrogen bonds were identified. These findings indicate that N(sp 2 )⁺–C(sp 2 )–H···O hydrogen bonds are recurrent in protein–ligand complexes and provide a novel strategy for enhancing binding affinity in drug design.