P012 Structure directed identification of human metabolite binding in the P4 pocket of MHC class-II DRB1∗15:01 and DRB1∗15:03 and implications for multiple sclerosis risk

Abstract

Aim Robust models of HLA mediated drug hypersensitivity demonstrate that binding of small molecules in the peptide-binding groove may result in changes in conformation or register shift of bound peptide, leading to an altered immune response. We performed virtual screening of the complete Human Metabolite Database (HMDB) for docking to the multiple sclerosis (MS) susceptible DRB1 ∗ 15:01 allele and compared the results to the closely related yet non-susceptible DRB1 ∗ 15:03 allele; and assessed the potential impact on binding of human myelin basic peptide (MBP). Methods The crystal structure of DRB1∗15:01 was obtained from the protein data bank under accession number 1BX2. An in silico DRB1 ∗ 15:03 structure was generated from the known structure of DRB1 ∗ 15:01 by mutating residue Tyr 30 > His 30 . The target proteins ( DRB1 ∗ 15:01 and DRB1 ∗ 15:03 ) were prepared with N-acetyl-D-glucosamine (NAG) for docking with human metabolites using UCSF Chimera (v1.11.2). We conducted independent screenings to probe each pocket of the peptide binding groove for both proteins using HMDB library v3.6, which consists of 41993 human metabolites. Results We observed higher energy scores for metabolite binding to DRB1 ∗ 15:01 than DRB1 ∗ 15:03. We found that 78 and 82 metabolites bind strictly to DRB1 ∗ 15:01 or DRB1 ∗ 15:03 respectively, while 79 metabolites bind to both structures. Structural comparison of docked metabolites with DRB1 ∗ 15:01 and DRB1 ∗ 15:03 complexed with MBP revealed that Phenylalanine MBP 92 allows binding of metabolites in the P4 pocket of DRB1 ∗ 15:01 but Valine MBP 89 abrogates metabolite binding in the P1 pocket. We observed differences in the energy score for the binding of the same metabolites in the P4 pockets of DRB1 ∗ 15:01 and DRB1 ∗ 15:03 or different metabolites in the P4 pockets of DRB1 ∗ 15:01 and DRB1 ∗ 15:03 suggesting stronger binding to DRB1 ∗ 15:01. Further, several of these metabolites have been previously associated with MS. Conclusions Our study confirmed that specific, disease-associated human metabolites bind effectively with the most polymorphic P4 pockets of DRB1 ∗ 15:01, the primary MS susceptible allele in most populations. Our results suggest that endogenous human metabolites bound in specific pockets of HLA may be immunomodulatory and implicated in autoimmune disease.