Differences in Conformational Dynamics between Plasmodium falciparum and Human Hsp90 Orthologues Enable the Structure-Based Discovery of Pathogen-Selective Inhibitors

Abstract

ABSTRACT:The high sequence conservation of druggable pockets of closely related proteins can make it challenging to develop selective inhibitors. We designed a new drug discovery approach that exploits both the static and dynamic differences of two orthologues. We applied it, as a proof of concept, to identify compounds that discriminate between the molecular chaperone Hsp90 of the protozoan pathogen Plasmodium falciparum (Pf) and that of its human host. We found that the ATP-binding pocket has a Pf-specific extension, whose sequence lining is identical in human Hsp90 but which differs by tertiary structure and dynamics. Using these insights for a structure-based drug screen, we discovered novel 7-azaindole compounds that exclusively bind the recombinant Nterminal domain of PfHsp90 but not of human Hsp90 nor of a PfHsp90 mutant with "human-like" dynamics. Moreover, these compounds preferentially inhibit the growth of yeast complemented by PfHsp90 and block the growth of Pf in culture.

Identification and characterization of the antiplasmodial activity of Hsp90 inhibitors

“…0.79 Å over equivalent Cα atoms) [36]. Despite this similarity, however, a close analysis of their ATP binding sites reveals significant differences between the two chaperones’ binding sites [59, 60]. The P. falciparum nucleotide-binding site has an extended pocket that is absent in the human chaperone (Fig.…”

Targeting the Hsp90 C-terminal domain to induce allosteric inhibition and selective client downregulation

“…Two cytosolic isoforms are present, constitutively active Hsp90β and the stress-inducible Hsp90α [1–3]. Hsp90 facilitates protein homeostasis by enhancement of protein stability through reduction of aggregation and misfolding [4,5] via its chaperone cycle. This conformationally-dynamic, multi-domain protein functions as an obligate dimer and has ATPase activity.…”

Hsp90 Inhibitors in Parasitic Nematodes: Prospects and Challenges

“…Much of the emphasis on Hsp90 in protozoan parasites has focused on its potential as a drug target [15], as there is a pressing need for novel therapeutics to combat drug resistant strains of the malaria parasite, P. falciparum, and to target neglected tropical diseases such as human African trypanosomiasis (or sleeping sickness), caused by Trypanosoma brucei. Studies in mouse models of malaria infection have shown synergy between existing anti-malarial compounds, such as chloroquine, and Hsp90 inhibitors [16], while recent work has identified structural differences between P. falciparum and human Hsp90 that could be exploited for drug design [17]. An in silico structure-activity screen identified compounds that bound preferentially to the parasite Hsp90.…”

“…Recent work on T. brucei Hsp83 [18] and on Hsp90 from the malaria parasite, P. falciparum, [17] provides good examples of this approach. However, as discussed previously, at least for some parasitic nematodes, differences in the function of Hsp90 between parasite and host may provide a chink in the armor suitable for exploitation.…”