In the context of drug design, C-H···O hydrogen bonds have received little attention so far, mostly because they are considered weak relative to other noncovalent interactions such as O-H···O hydrogen bonds, π/π interactions, and van der Waals interactions. Herein, we demonstrate the significance of hydrogen bonds between C-H groups adjacent to an ammonium cation and an oxygen atom (N+-C-H···O hydrogen bonds) in protein-ligand complexes. Quantum chemical calculations revealed details on the strength and geometrical requirements of these N+-C-H···O hydrogen bonds, and a subsequent survey of the Protein Data Bank (PDB) based on these criteria suggested that numerous protein-ligand complexes contain such N+-C-H···O hydrogen bonds. An ensuing experimental investigation into the G9a-like protein (GLP)-inhibitor complex demonstrated that N+-C-H···O hydrogen bonds affect the activity of the inhibitors against the target enzyme. These results should provide the basis for the use of N+-C-H···O hydrogen bonds in drug discovery.

The first synthesis of a CF3-substituted semisquarate was accomplished via nucleophilic trifluoromethylation using CF3SiMe3 and subsequent rhenium-catalyzed allylic alcohol rearrangement. The short-step skeletal-divergent synthesis of trifluoromethylated functional molecules was successfully achieved using the CF3-substituted semisquarate as the platform.

The NAD+-dependent deacetylase SIRT2 represents an attractive target for drug development. Here, we designed and synthesized drug-like SIRT2-selective inhibitors based on an analysis of the putative binding modes of recently reported SIRT2-selective inhibitors and evaluated their SIRT2-inhibitory activity. This led us to develop a more drug-like diketopiperazine structure as a “hydrogen bond (H-bond) hunter” to target the substrate-binding site of SIRT2. Thioamide 53, a conjugate of diketopiperazine and 2-anilinobenzamide which is expected to occupy the “selectivity pocket” of SIRT2, exhibited potent SIRT2-selective inhibition. Inhibition of SIRT2 by 53 was mediated by the formation of a 53-ADP-ribose conjugate, suggesting that 53 is a mechanism-based inhibitor targeting the “selectivity pocket”, substrate-binding site, and NAD+-binding site. Furthermore, 53 showed potent antiproliferative activity toward breast cancer cells and promoted neurite outgrowth of Neuro-2a cells. These findings should pave the way for the discovery of novel therapeutic agents for cancer and neurological disorders.

In situ click chemistry has great potential for identifying enzyme inhibitors. However, conventional in situ click chemistry provides extremely low yields of the products, making it incompatible with direct activity-based assays. Here, to address this issue, we focused on the catalysis of azide–alkyne cycloaddition (AAC) by the metal ion in metalloproteins. We chose 2-ethynyl N-heterocompounds as alkyne fragments which are activated by coordination to the metal ion. For proof of concept, we applied metal ion-catalyzed in situ AAC to identify inhibitors of Fe­(II)-dependent lysine demethylase 5C (KDM5C). The triazole product was obtained in dramatically high yield, dependently on Fe­(II) in KDM5C, and the metalloprotein-catalyzed click reaction was compatible with activity-based high-throughput screening, enabling us to discover a potent KDM5C inhibitor. Thus, metal-catalyzed in situ AAC should be generally applicable to other metalloproteins.

Optimizing linker design is important for ensuring efficient degradation activity of proteolysis‐targeting chimeras (PROTACs). Therefore, developing a straightforward synthetic approach that combines the protein‐of‐interest ligand (POI ligand) and the ligand for E3 ubiquitin ligase (E3 ligand) in various binding styles through a linker is essential for rapid PROTAC syntheses. Herein, a solid‐phase approach for convenient PROTAC synthesis is presented. We designed azide intermediates with different linker lengths to which the E3 ligand, pomalidomide, is attached and performed facile PROTACs synthesis by forming triazole, amide, and urea bonds from the intermediates.