Inhibitors of the Plasmodium falciparum Hsp90 towards Selective Antimalarial Drug Design: The Past, Present and Future

Abstract

Malaria is still one of the major killer parasitic diseases in tropical settings, posing a public health threat. The development of antimalarial drug resistance is reversing the gains made in attempts to control the disease. The parasite leads a complex life cycle that has adapted to outwit almost all known antimalarial drugs to date, including the first line of treatment, artesunate. There is a high unmet need to develop new strategies and identify novel therapeutics to reverse antimalarial drug resistance development. Among the strategies, here we focus and discuss the merits of the development of antimalarials targeting the Heat shock protein 90 (Hsp90) due to the central role it plays in protein quality control.

Keywords: Hsp90 inhibitors; Plasmodium falciparum; heat shock protein 90; malaria; molecular chaperone; parasite Hsp90.

Figure 1

The nucleotide-dependent Hsp90 functional cycle and domain organization of P. falciparum Hsp90s. (A) Schematic of the general Hsp90 protein domain organization. (B) The Hsp90 functional cycle begins when Hsp90 is bound to ATP associate with an unfolded/partially folded client protein. Subsequently, the lid region closes over the ATP binding pocket, and the NTD dimerize, adopting a closed conformation. When the MDs associate, there is a repositioning of the catalytic loop in the MDs, which enables ATP hydrolysis. Upon ATP hydrolysis, the correctly folded client protein is released. The Hsp90 homodimer returns to the unbound open conformation and is primed for subsequent rounds of ATP hydrolysis and protein folding. This functional cycle is also modulated by co-chaperones such as HOP, Aha1, and p23. (C) Hsp90 protein models with the domains color codedthe NTDs are (purple), the linker (red), the MDs (blue), and the CTDs (green). The NTD helices H1, H4, and H5 are shown in yellow. Helices involved in dimerization are shown in orange. (D) The schematic of P. falciparum Hsp90 linear domain architecture for the differently localized Hsp90 proteins. Three-dimension (3-D) protein structures were generated by depositing protein sequences to the online PHYRE2 protein fold recognition server (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index, accessed on 18 April 2021). The 3-D model structures were visualized using the Schrodinger Maestro release 2021-3: LLC, New York, NY.

Figure 2

Multiple sequence alignments of Hsp90 proteins. Multiple sequence alignments of Hsp90 proteins from host Homo sapiens with sequences retrieved from NCBI (https://www.ncbi.nlm.nih.gov/protein, accessed on 13 April 2021) with respective accession number HSPC2 (NP_001017963.2) and HSPC4 (AAH66656.1). The P. falciparum Hsp90 protein sequences were retrieved from PlasmoDB (www.plasmoDB.org, accessed on 13 April 2021) with accession numbers PfHsp90 (PF3D7_0708400) and PfGrp94 (PF3D7_1222300), respectively. The model eukaryote Saccharomyces cerevisiae Hsp90 protein sequences were retrieved from https://www.yeastgenome.org/(accessed on 13 April 2021) ScHsc82 (accession numbers: S000004798) and ScHsp82 (Accession number: S000006161). Residues involved in ATP binding are indicated in red boxes [30,31]. The arrowheads represent hydrophobic side pocket one in blue, side pocket two in green, and side pocket three in purple. The QEDGQ insertion of human Grp94 is highlighted in purple. The lid helixes N1, N4, and N5, are highlighted in yellow. The residues that take part in the binding of geldanamycin in the NTD are indicated with green squares. The putative substrate-binding pocket of the MD is shown in cyan. Critical hydrophobic residues in this cavity are indicated with blue squares. Residues involved in hydrogen bonding with gambogic acid are indicated with yellow squares. Critical catalytic loop residues of the MD involved in ATP hydrolysis are indicated with purple squares. Colored bars beneath the MSA indicates the protein domains: Grey is the signal peptide and Pre-N region. The NTDs are indicated with purple bars, the linker with red, the MDs with blue, and the CTDs with green. The conserved residues are shown with white text on black background, and semi-conserved residues are shown with white text on a grey background. The protein sequences were submitted to T-Coffee (http://tcoffee.crg.cat/apps/tcoffee/do:regular; accessed on 14 September 2021)) for alignment. Boxshade (http://www.ch.embnet.org/software/BOX_form.html; accessed on 14 September 2021) conservation level coloring.

Figure 3

Superimposed domains and catalytic loop residues of the four parasite Hsp90 proteins. The 3-dimensional models of the four parasite Hsp90 proteins are superimposed to show catalytic residue structural conformation conservation. Catalytic residues of the other Hsp90 paralogs are thought to interact with the γ phosphate of ATP, enabling its hydrolysis. (A) The NTDs of the four parasite proteins. (B) The MDs of the four parasite proteins. (C) The CTDs of the four parasite proteins. The four parasite proteins superimposed cartoon zoomed-in for the (D) MD and (E) the NTD. The catalytic residues of PfHsp90 are labeled in (D,E). PfHsp90 is shown in purple, PfGrp94 in orange, PfHsp90_A in blue, and PfHsp90_M is shown in green. The non-conserved residues are in the MD of PfHsp90_M, which are Ser513, Asn516, and Arg520. Protein structures 3-D models were created by depositing amino acid sequences on the PHYRE2 protein fold recognition server (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index; accessed on 18 April 2021). The resultant 3-D protein structures were visualized and superimposed using the Schrödinger Maestro Release 2021-3: LLC, New York, NY.

Figure 4

Chemical structure of geldanamycin and its derivatives. 4.1 Geldanamycin (GA) is a natural Hsp90 inhibitor and its derivatives 4.2 17-allylamino-17-demethoxygeldanamycin (17-AAG), 4.3 17-dimethylamino ethylamino-17-demethoxygeldanamycin (17-DMAG), and 4.4 17-allylamino-17-demethoxygeldanamycin hydroquinone hydrochloride (IPI-504). 4.5 17-amino-17-demethoxygeld anamycin (IPI-493) is a major metabolite of both IPI-504 and 17-AAG. The P. falciparum growth inhibition IC50 values are indicated.

Figure 5

The chemical structure of Harmine and the derivatives. The inhibitors, 5.1 Acrisorcin. 5.2 Harmine. 5.3 2-amino-3-phospho propionic acid (APPA) were tested in in parsite growth inhibition studies. The 5.4 N-harmicines 6 and 5.5 O-harmicines 7. 5.6 N,O-bis-harmicines 8 and their derivative 5.7 8b. 5.8 N-harmicines 5 and its derivatives 5.9 5a, 5.10 5b, 5.11 5d, 5.12 5e and 5.13 5f. 5.14 O-harmicines 6 and its derivatives 5.15 6a, 5.16 6d and 5.17 6e. 5.18 Harmicine 27a. Other synthetic compounds 5.19 CP-6. 5.20 CP-7. 5.21 CP-10 were also developed. The respective IC₅₀ values for parasite growth inhibition are shown.

Figure 6

The purines and other derivatives as potential P. falciparum Hsp90 inhibitors. The chemical structures of the compounds are shown with their respective numbering. 6.1 PU3. 6.2 PU-H71. 6.3 MPC-3100. 6.4 CNF2024/BIIB021. 6.5 Debio0932. 6.6 Methyl 1-isopentyl-3-(2-methoxyacetamido)-5-((6-methylhept-5-en-2-yl)amino)-1H-pyrrolo[2,3-b]pyridine-2-carboxylate (IND31119). Two amino-alcohol-carbazole (N-CBZ) 6.7 5E and 6.8 5B. 6.9 Gamitrinib. 6.10 N-ethyl-carboximido adenosine (NECA) and its derivatives 6.11 N-propylcarboxamido adenosine (NPCA), 6.12 N-hydroxyethylcarboxamido adenosine (NEoCA) and 6.13 N-aminoethycarboxamido adenosine (NEaCA). Three purine derivatives 6.14 8-((2,4-Dimethylphenyl)thio)-3-(pent-4-yn-1-yl)-3H-purin-6-amine (PU-H54), 6.15 6-amino-8-[(3,5-dichlorophenyl)thio]-N-(1-methylethyl)-9H-purine-9-propanamine (PU-WS13) and 6.16 8-((2,4-Dichlorophenyl)thio)-9-(pent-4-yn-1-yl)-9H-purin-6-amine (PU-H39). Known parasite growth inhibition IC₅₀ values are indicated. purine and derivatives, 7 a-azandole and amino-alcohol, carbazole derivatives with known parasite growth inhibition IC₅₀ values, are indicated.

Figure 7

Radicicol and derivatives. The chemical structure of radicicol (7.8) derivatives include Radamide (7.9) and synthetic derivatives, compounds 7.1 and 7.2.NVP-AUY922 (7.3) is a resorcinylic isoxazole amine compound, with its derivatives 7.4, 7.5, 7.6 and 7.7 The respective IC₅₀ value for parasite growth inhibition is shown.

Figure 8

The chemical structure of inhibitors targeting the Hsp90 middle and C-terminal domains. The structures of compounds that target the NTD and CTD of Hsp90 and also abrogate co-chaperone interactions are shown. Inhibitors of the coumermycin family 8.1 Novobiocin and its derivatives 8.2 A4, 8.3 4-deshydroxynovobiocin (DHN1) and 8.4 3′-descarbamoyl-4-deshydroxynovobiocin (DHN2). Additional members of the coumermycin family 8.5 Clorobiocin and 8.6 Coumermycin A1 derivative. 8.7 3,4-dihydropyrimidin-2(1H)-one (DHPM). A natural product 8.8 Gambogic acid (GBA) and its derivative 8.9 DAP-19. A diterpene triepozide 8.10 Triptolide (TL). A peptidomimetic compound 8.11 Antp-TPR peptide. A small molecule compound 8.12 1,6-dimethyl-1-3-propylpyrimido(5,4-e)(1,2,4)triazine-5,7-dione (C9). Sansalvamide A compounds 8.13 San-A1 and 8.14 San-A2. Additional co-chaperone inhibitors 8.15 Celastrol, 8.16 Cucurbitacin D and 8.17 Gedunin. 8.18 Violacein.