Selective targeting of indel‐inferred differences in spatial structures of highly homologous proteins

Abstract

Recent findings have shown that the protein elongation factor-1alpha (EF-1alpha) from the eukaryotic pathogen Leishmania donovani possesses virulence properties. This was unexpected, since it has greater than 80% sequence identity with its human homologue. Given that EF-1alpha is essential for cell survival, in principle, it can be considered an attractive drug target. However, the challenge is to be able to selectively target the protein so as not to affect function of the human homologue. While a limited number of discrete differences were scattered throughout the sequence, most of the difference between these 2 homologues could be attributed to a 12-amino acid insert present in human EF-1alpha and absent from the leishmania sequence. In the present study, we modeled the spatial differences in structures of human and L. donovani EF-1alpha's inferred by this insertion-deletion (or "indel"). The protein models were used to develop antibodies directed specifically toward the deletion region of the pathogen protein. The strategy described allowed successful selective targeting of this putative leishmania virulence factor while avoiding recognition of the highly similar human EF-1alpha homologue. These findings may establish a new strategy for the development of antagonists directed against certain pathogenic targets having close human homologues.

Complete Cap 4 Formation Is Not Required for Viability inTrypanosoma brucei

“…Insertion-deletion (indel) differences seen in TbMT417 and TbMT511 relative to VP39 are prevalent in other conserved kinetoplastid proteins (8). Indels may confer pathogeneic properties (9) or may allow interactions with other proteins. In the case of the kinetoplastid VP39 homologs, both indels of TbMT511 are contained within the Rossmann fold and could alter the shape of the RNA-binding pocket, effectively extending the path on the surface that connects the MTase active site relative to the cap-binding site.…”

Using a systems biology approach to dissect parasite–host interactions

“…donovani, the principal agent of VL, has been a model organism for identifying selective targets for drug design and for putative virulence factors. For example, the protein elongation factor-1a (EF-1a) from L. donovani shares 82% identity with its human homologue, except for a 12-amino acid deletion [Cherkasov et al, 2005]. This deletion appears to switch the EF-1a function from that of a housekeeping enzyme to a binding and activating protein for the Src-homology 2 domain containing tyrosine phosphatase (SHP-2).…”

“…By activating SHP-2 in human macrophages, L. donovani EF-1a deactivates the internal macrophage environment, thereby favoring parasite survival. Protein homology models were used to develop antibodies specifically against the 12-amino acid deletion, thereby selectively targeting a parasite virulence factor while avoiding the similar human homologue [Cherkasov et al, 2005]. Elongation factor-2 (EF-2) was one of several antigens identified from a 2D gel electrophoresis, matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-TOF-MS), and MALDI-TOF/TOF-MS analysis of a soluble protein fraction of L. donovani promastigotes [Gupta et al, 2007].…”

Finding the Smoking Gun: Protein Tyrosine Phosphatases as Tools and Targets of Unicellular Microorganisms and Viruses

“…L. donovani EF-1 protein sequence shares 82% homology with its human ortholog, and the bulk of the difference between these two orthologs accounts for the 12-aminoacid surface-exposed insert present in the human protein and absent in the L. donovani ortholog. This indel is also present in Giardia lamblia, Trypanosoma brucei, Entamoeba histolytica, Cryptosporidium parvum, Plasmodium knowlesi, Plasmodium falciparum, and in Leishmania braziliensis [63][64][65]. Thus EF-1α-mediated modulation of SHP-1 signaling may not be limited only to leishmaniasis, may contribute to the widely shared mechanism of host-pathogen interaction, and the indel itself may serve as an important novel drug target.…”