P049 Human metabolites bind to the P4 pocket of HLA-DRB1∗15:01, with implications for multiple sclerosis susceptibility

Abstract

Aim Models of HLA mediated drug hypersensitivity suggest that binding of small molecules in the peptide binding groove results in changes in conformation of the bound peptide, leading to an aberrant immune response. We hypothesize that naturally occurring small molecules may similarly alter T-cell response in Multiple Sclerosis (MS), where susceptibility is strongly associated with DRB1 ∗ 15:01. We performed virtual screening of the complete Human Metabolite Database (HMDB) for docking in DRB1 ∗ 15:01 and assessed the potential impact on binding of human myelin basic peptide (MBP). Methods Virtual Screening for HLA-DRB1 ∗ 15:01 was conducted on a structure obtained in molecular dynamics simulations of the complex with bound MBP. Valine 89 and phenylalanine 92 of the MBP were identified as P1 and P4 anchor residues. Two independent screenings were conducted to probe pockets P1 and P4 in the structure of DRB1 ∗ 15:01 obtained from the protein data bank (PDB code 1BX2) using the HMDB library (v3.6), which consists of 41993 human metabolites. The virtual screening was conducted with UCSF Chimera v1.10.2, AUTODOCK v4.2, Clipper 1.6.0, Dockblaster 1.6.0 program. Results We observed the binding of metabolites specifically in the P4 pockets of HLA-DRB1 ∗ 15:01. We calculated energy score, vander-waals component, electrostatic component, polar solvation component, molecular charge, heavy atoms, polar contacts (3.3 A), nonpolar contacts (3.3–4.5 A), and number of conformations for the docked DRB1 ∗ 15:01 and metabolite complex. We used Dockblaster (v1.6.0) to select top ranked metabolites and investigate the distribution of their scores. On this basis, we obtained 361 significant metabolites from the docking results in the P4 pocket and ranked them on the basis of their energy score. Further, we found that Phenylalanine MBP92 allows the binding of metabolites in the P4 pocket of DRB1 ∗ 1501 but not Valine MBP of P1 pockets. Conclusions These results suggest that the binding of naturally occurring human metabolites in the P4 pockets of HLA-DRB1 ∗ 15:01 may subtly alters the TCR recognition site of HLA/MBP, possibly by changing the conformation in the normally bound position, or causing a register shift in the bound peptide. This in turn may bring about profound alterations in T-cell responsiveness, resulting in autoimmunity.