Target Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria

Abstract

Drug-resistant malarial strains have been continuously emerging recently, which posts a great challenge for the global health. Therefore, new antimalarial drugs with novel targeting mechanisms are urgently needed for fighting drug-resistant malaria. NADH-ubiquinone oxidoreductase of Plasmodium falciparum (PfNDH2) represents a viable target for antimalarial drug development. However, the absence of structural information on PfNDH2 limited rational drug design and further development. Herein, we report high resolution crystal structures of the PfNDH2 protein for the first time in Apo-, NADH-, and RYL-552 (a new inhibitor)-bound states. The PfNDH2 inhibitor exhibits excellent potency against both drug-resistant strains in vitro and parasite-infected mice in vivo via a potential allosteric mechanism. Furthermore, it was found that the inhibitor can be used in combination with dihydroartemisinin (DHA) synergistically. These findings not only are important for malarial PfNDH2 protein-based drug development but could also have broad implications for other NDH2-containing pathogenic microorganisms such as Mycobacterium tuberculosis.

FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function

“…Notably, RYL-552 binds three different binding regions within 5jwc far from the NADH/FAD/UQ cofactor-binding area. While two of those regions appear to be poorly resolved, the third ones appears to be a specific binding cavity [45]. By superimposing 5jwc with the analyzed AIF, NDI, and NDH-2, it appears that NDH-2 and NDI might form several interactions with RYL-552 involving 8 and 11 residues, respectively, that appear to be further well conserved in the sampled NDH-2 and NDI-like proteins (although in the latter, the overlapping binding region appears more buried from the local secondary structure), at variance with the AIF showing a lower number of interacting residues (just four, see Supplementary Table S6 and Supplementary Figure S4).…”

“…The main differences between the five structures are at the level of their C-terminus portion. Notably, 5jwc.pdb [45] shows a 70-aa long extra loop (residues 363-433, 5jwc.pdb numbering (Figure 4)).…”

“…Conversely, it was observed that RYL-552 (a quinolinic derivative, see Table 1 and [45]) within NDH-2-like protein from P. falciparum (5jwc), SL827 (a sulphonamide derivative, see Table 1 and [48]) within lipoamide DH from M. tubercolosis (4m52.pdb), and ketopropylthioethanesulphonate within NADPH:2KPCC oxidoreductase from Xanthobacterautotrophicus (1mo9.pdb, [49]) are located at dedicated binding regions involving several species-specific residues not involved in the binding of NADH/FAD/UQ cofactors.…”

Crystal structure of type II NADH:quinone oxidoreductase from Caldalkalibacillus thermarum with an improved resolution of 2.15 Å

“…To date, crystal structures of NDH-2 have been determined for only the following four species: Saccharomyces cerevisiae (Feng et al, 2012;Iwata et al, 2012), Caldalkalibacillus thermarum (Heikal et al, 2014), Staphylococcus aureus (Sena et al, 2015) and P. falciparum (Yang et al, 2017). NDH-2 consists of three domains.…”

Research journey of respirasome

“…In 2012, our group solved the X-ray structures of Ndi1 (NDH2 from yeast) in apo, NADH-, Q-, and NADH-Q-bound states and demonstrated that electron transfer in NDH2 requires two Q molecules and CTD of NDH2 mediates the homodimerization and membrane attachment (Feng et al, 2012). Later on, our group reported the X-ray structures of PfNDH2 (NDH2 from P. falciparum) in its apo, NADH-, and RYL-552 (a new inhibitor)bound states, unveiling the inhibiting mechanism of PfNDH2 and providing accurate information for designing new antimalarial drugs (Yang et al, 2017).…”