Protein structure based strategies for antigen discovery and vaccine development against malaria and other pathogens

The review surveys potential "structural antigens" which represent small protein domains that can be chemically synthesized and, isolated from the context of the whole protein, can fold in the same native structure. They include natively unfolded protein regions, small globular domains, alpha-helical coiled coils and regions with tandem repeats forming structures ranging from the collagen triple helices to solenoid-like arrangements. We also describe and compare new strategies for development of vaccine that use the concept of structural epitopes. One type of approach is based on engineering artificial mini-proteins able to mimic structural epitopes of natural proteins. The review compares the "engineering" methodologies with "bioinformatics" approaches that became possible recently, after the sequencing of the genomes of many pathogens, and involve genome-wide bioinformatics searches for "structural antigens". In particular, based on the known P. falciparum genome, we identified putative alpha-helical coiled coil regions, 30-40 amino acids long, in proteins presented in asexual malaria blood stages. Peptides of such regions frequently fold into the "native" structure. A hundred such peptides were synthesized and all of them were recognized at various degrees (5-80%) by a panel of sera from donors living in malaria-endemic areas. The results obtained demonstrate that a bioinformatics/chemical synthesis strategy can rapidly lead to the identification of new proteins that can be targets of potential vaccines and/or drugs against malaria and other infectious organisms.