A high-throughput molecular dynamics screening (HTMDS) approach to the design of novel cyclopeptide inhibitors of ATAD2B based on the non-canonical combinatorial library.

A high-throughput MD screening (HTMDS) process for cyclic peptides (CPs) binders designed with canonical and non-canonical amino acids.698,800 CP candidates with a total of 25,570 ns MD simulations were performed to study the protein-ligand binding interactions and CP design.Some potent CP candidates were obtained with high binding free energies (ΔGbind) estimated by the MM/PBSA approach compared with the standard inhibitor C-38 against the bromodomain (BrD) of ATAD2B.