An innovative toolbox based on Pd-catalysis for protease inhibitor synthesis, applied to the discovery of pan-anti-flaviviral compounds

Protease inhibitors can potently block the viral replication cycle. In the context of flaviviruses, NS2B-NS3 protease is a promising viral drug target because of its well conserved backbone among flaviviral species, opening the perspective of developing pan-anti-flaviviral NS2B-NS3 inhibitors. All reported NS2B-NS3 inhibitors, however, suffer from low potency and/or poor biopharmaceutical properties. Structural optimization has proven to be slow and challenging, in part because synthetic methodology for fast, chemically versatile and diversity-oriented modification is lacking. To address these challenges, we propose a methodology to assemble protease inhibitors with varying warheads and side chains in just 2 steps from common starting materials, and apply it to the discovery of pan-anti-flaviviral compounds. First, selected amide/carbamate and aldehyde building blocks will be condensed in a reported three-component reaction with phenylsulfinic acid and benzotriazole, delivering individual 'masked' N-acylimines. These will be further submitted to innovative cross-coupling steps, in which warheads will be introduced. Once the methodology is optimized and the scope is determined, at least 10 additional analogues of a known NS2B-NS3 inhibitor will be prepared with variations in the warhead, P1 side chain and P2-P3 moieties will be synthesized. They will be subjected to enzymatic affinity determination, binding kinetics analysis and cellular assays. Experimental data will be used to validate a Molecular Dynamics study of NS2B-NS3 inhibitors. The project is envisaged to deliver significant societal, scientific R&I, and economic impacts by managing flavivirus infections and creating business cases for industrial R&I in Europe.