DFT guided design of novel quinone bioisosteres as inhibitors of the clathrin N-terminal domain-amphiphysin protein-protein interaction. Dihydroquinazolin-4(1H)-ones and quinazolin-3(4H)-ones

The sesquiterpene quinone, bolinaquinone (8) and naphthoquinone (9) inhibit the clathrin N-terminal-amphiphysin protein interaction (NTD-PPI). They are potential chemical tools to study clathrin mediated endocytosis. However, Quinones are known PAINS (pan assay interference compounds) and their use in chemical biology studies is fraught with complications. Quinone bioisosteres are poorly defined. We chose to apply high level DFT calculations (DSD-PBEPB86, def2-TZVPP) to leads 8 and 9 to determine their electronic and geometric properties. It was noted that the C1-C4 dicarbonyl moieties were inconsistent in their symmetry, the side chain possessed low level nucleophilicity and was conformationally off-set relative to the quinone moiety. Investigations of 3-substituted piperazin-2,5-ones, which visually resemble many of the key quinone features revealed the presence of symmetrical H-bond acceptor (in vacuo), no nucleophilicity associated with the side chain, and only a slight conformational off-set. Screening for NTD-PPI, Dynamin and clathrin mediated endocytosis activity, revealed no activity. Examination of the dihydroquinazolin-4(1H)-ones and quinazolin-3(4H)-ones indicated a broad match with the electronic and conformational disposition of 8 and 9. Screening revealed analogues within both compound classes as moderate NTD-PPI inhibitors (selected analogues returned NTD-PPI IC₅₀ 15-35 μ M). Molecular docking studies were performed to examine potential binding modalities within the clathrin NTD. DFT calculations have allowed the identification, and subsequent synthesis of small libraries of dihydroquinazolin-4(1H)-ones and quinazolin-3(4H)-ones as non-quinone based inhibitors of the NTD-PPI and from this design and DFT-screen additional core heterocyclic scaffolds that might act as quinone bioisosteres.

Clathrin terminal domain; DFT calculation and analysis; Dihydroquinazolin-4(1H)-Ones and quinazolin-3(4H)-Ones; Molecular docking; Quinone.