Abstract: Helminths have a significant impact on the health and economy of communities, particularly in tropical and subtropical regions. Helminths have adapted to live in different niches, such as the liver, intestine, lungs, and blood vessels, and many of them undertake a multiorgan migratory path in the human host to reach their final destination. For this purpose, helminths secrete a range of molecules that facilitate their penetration, migration, and establishment in the host. Furthermore, helminths have developed a number of mechanisms allowing them to evade the host immune responses, shaping and skewing it towards a regulatory phenotype that ensures long-term parasite survival while causing as little damage as possible to the host. Parasitic helminth proteins therefore are at the forefront of research efforts for the development of control tools (drug targets and vaccines), and more recently as a novel source of drugs to treat inflammatory and metabolic disorders that are now rife in populations that are (almost paradoxically) free of helminth infections. A proteogenomics approach, combining proteomics data with genome sequencing, can provide invaluable data for the annotation of genes and proteins of helminths. This is an exciting new approach in the field of helminthology that can help to identify novel peptides and proteins involved in host–parasite interactions. Protein–protein interaction analyses can provide valuable information for understanding the molecular host–parasite interface. Although the immunomodulatory properties of helminths have been appreciated for some time, characterization of the individual bioactive proteins exerting these effects is still in its infancy. Taking advantage of genomic and proteomic big data will capitalize on this unique opportunity to characterize the helminth-derived pharmacopoeia for allergic and autoimmune diseases.

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