Recruiting monomer for dimer formation: resolving the antagonistic mechanisms of novel immune check point inhibitors against Programmed Death Ligand-1 in cancer immunotherapy

The design of small molecule antagonists against Programmed Death Ligand-1 (PD-L1) has been the recent highlight of the immune checkpoint blockade therapy. This interventive approach has been potentiated by the development of BMS compounds; BMS-1001 and BMS-1166, which exert their therapeutic activities by inducing dimerisation of PD-L1; a molecular mechanism that has remained unclear. For the first time, we resolve the dynamical events that underlie the antagonistic mechanisms of BMS-1001 and BMS-1166 when bound to PD-L1 using an all-atom molecular dynamics (MD) simulations approach and free binding energy Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) calculations. Time-scale dynamical findings revealed that upon binding a PD-L1 monomer, the BMS-compounds gradually facilitated the ‘inbound’ motion of another PD-L1 monomer in the same conformational phase space up till dimer formation. Moreover, the non-liganded PD-L1 monomer exhibited the highest structural flexibility and atomistic motions relative to the BMS-liganded monomer as revealed by post-MD trajectory analyses using root mean square deviation (RMSD) and root mean square fluctuations (RMSF) parameters. Trajectory investigations into ligand motions also revealed that the BMS compounds exhibited mechanistic transitions from the monomeric binding site (monomer A) where they were initially bound, to the second monomeric site (monomer B) where they were strongly bound, followed by eventual high-affinity interactions at the tunnel-like binding cleft formed upon the dimerisation of both PD-L1 monomers. These findings present a model that describes the mechanism by which the BMS compounds induce PD-L1 dimerisation and could further enhance the design of highly selective and novel monomeric recruiters of PD-L1 in cancer immunotherapy.