Molecular recognition of natural compounds by MR1 and their implication in MAIT cell activation elucidated through McMD-based dynamic docking simulations

Major histocompatibility complex class I-related protein 1 (MR1), presents bacteria-derived ligands to T cell receptors (TCRs) as antigens as a defense against bacterial infections through activation of mucosal-associated invariant T cells (MAIT cells). Since mammals do not produce riboflavin (RBF, vitamin B2) themselves, unlike bacteria, MR1 can present the intermediates of RBF synthesis as a marker of non-self to initiate an immune response. Here, we have performed multicanonical molecular dynamics-based dynamic docking simulations to analyze the binding mechanism of RBF and two of its derivatives, photolumazine I (PLI) and III (PLIII) with MR1. We found that PLI and PLIII bind with high specificity in a manner similar to a known high-affinity ligand, RL-6-Me-7-OH. In contrast, RBF binds in multiple less specific, non-productive configurations. Subsequent structural analyses revealed that PLI and PLIII support productive TCR engagement and MAIT cell activation, while RBF fails to activate MAIT cells. Consequently, an immune response is triggered against PLI and PLIII, but not against RBF. These findings uncover the distinct binding mechanisms between the three compounds and MR1 and highlight their differential effects on MAIT cell activation in the context of bacterial infection.