Neglected tropical diseases (NTDs) caused by Leishmania and Schistosoma species continue to impose a significant health burden in endemic regions, largely due to limited therapeutic options, drug resistance, and incomplete understanding of parasite biology at the molecular level. A major restriction in the development of targeted interventions is the structural inaccessibility of parasite membrane-associated proteins, which are central to host invasion, nutrient transport, immune evasion, and survival. Recent advances in cryogenic electron microscopy (cryo-EM) have expanded the structural biology toolkit available for studying difficult parasite proteins, particularly large and membrane-associated macromolecular assemblies. However, experimentally resolved cryo-EM structures remain limited for many of the Leishmania and Schistosoma targets relevant to therapeutic and vaccine development. This review therefore distinguishes experimentally determined structures from partial structural information and computational models and examines how potential cryo-EM approaches may address unresolved structural questions. We discuss current structural knowledge of selected parasite targets, approaches for recombinant expression and membrane-protein stabilization, membrane-mimetic systems for structural characterization, and computational methods that complement experimental structural biology. We further examine how experimentally supported structural information, complemented by computational predictions where appropriate, could contribute to structure-guided drug discovery, vaccine design, and targeted nanomedicine. At present, however, the direct translation of parasite structural information into rational nanotherapeutic design remains limited. Key gaps include the scarcity of experimentally resolved parasite membrane protein structures, challenges in their expression and structural characterization, and limited integration of structural biology with nanoparticle engineering. Resolving these gaps may improve the prospects for structure-informed therapeutic and nanomedicine applications against leishmaniasis, schistosomiasis, and other NTDs.

Recombinant proteins are used to characterize parasite enzymes, membrane proteins, antigens, and protein complexes, but some targets are difficult to recover in a soluble and functional form. Expression can be affected by codon usage, intrinsically disordered or low-complexity regions, transmembrane segments, disulfide-bond formation, post-translational processing, and multidomain organization. This review compares bacterial, yeast, insect-cell, mammalian-cell, Leishmania tarentolae, and cell-free expression systems and examines construct design, codon optimization and harmonization, fusion partners, chaperones, expression regulation, and computational tools. It distinguishes results reported for parasite proteins from recommendations based on general recombinant-protein studies. Experimentally determined Plasmodium falciparum structures illustrate the use of X-ray crystallography, solution NMR, and cryo-electron microscopy; the ribosome example is identified as a parasite-derived complex rather than a recombinant product. Molecular docking, molecular dynamics simulations, and binding-energy calculations are discussed as tools for developing and prioritizing hypotheses, not as substitutes for experimental testing. The review links target features to initial construct and host choices and identifies the protein-quality checks needed before structural or functional conclusions are drawn.