PREDICTION OF WELL-CONSERVED HIV-1 LIGANDS USING A MATRIX-BASED ALGORITHM, EPIMATRIX

This preliminary study was undertaken to identify new human leucocyte antigens (HLA) ligands from human immunodeficiency virus type 1 (HIV-1 ) which are highly conserved across HIV-1 clades and which may serve t o induce cross-reactive cytotoxic T lymphocytes (CTLs). EpiMatrix was used to predict putative ligands from HIV-1 for HLA-A2 and HLA-B27. Tw enty-six peptides that were both likely to bind and also highly conser ved across HIV-1 strains in the Los Alamos HIV sequence database were selected for binding assays using the T2 stabilization assay. Two pept ides that were also highly likely to bind (for A2 and B27, as determin ed by EpiMatrix) and well conserved across HIV-1 strains, and had prev iously been described to bind in the published literature, were also s elected to serve as positive controls for the assays. Ten new major hi stocompatibility complex (MHC) ligands were identified among the 26 st udy peptides. the control peptides bound, as expected. These data conf irm that EpiMatrix can be used to screen HIV-1 protein sequences for h ighly conserved regions that are likely to bind to MHC and may prove t o be highly conserved HIV-1 CTL epitopes. (C) 1998 Published by Elsevi er Science Ltd. All rights reserved.