Antimalarial and Structural Studies of Pyridine-Containing Inhibitors of 1‑Deoxyxylulose-5-phosphate Reductoisomerase

1-Deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) in the nonmevalonate isoprene biosynthesis pathway is a target for developing antimalarial drugs. Fosmidomycin, a potent DXR inhibitor, showed safety as well as efficacy against <i>Plasmodium falciparum</i> malaria in clinical trials. On the basis of our previous quantitative structure–activity relationship (QSAR) and crystallographic studies, several novel pyridine-containing fosmidomycin derivatives were designed, synthesized, and found to be highly potent inhibitors of <i>P. falciparum</i> DXR (<i>Pf</i>DXR) having <i>K</i>_i values of 1.9–13 nM, with the best one being ∼11× more active than fosmidomycin. These compounds also potently block the proliferation of multidrug resistant <i>P. falciparum</i> with EC₅₀ values as low as 170 nM. A 2.3 Å crystal structure of <i>Pf</i>DXR in complex with one of the inhibitors is reported, showing that the flexible loop of the protein undergoes conformational changes upon ligand binding and a hydrogen bond and favorable hydrophobic interactions between the pyridine group and the <i>Pf</i>DXR account for the enhanced activity

Specific residue variations detected in the EVD68 VP1 protein from the 2014 outbreak strains.

<p><b>(A)</b> VP1 protein alignment based on the Clade B subcluster. The alignment was performed with MEGA5 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144208#pone.0144208.ref036" target="_blank">36</a>]. Hyphens indicate residues identical to those in CA/AFP/11-1767; “X” indicates unidentified amino acid due to unidentified nucleotides in the submitted CA/AFP/v12T04950 sequence. Numbers indicate protein positions. Sequence CQ5585 is missing the fragment surrounding position 290. The subtree for the subclustered Clade B strains is extracted from the tree in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144208#pone.0144208.g001" target="_blank">Fig 1</a>. (<b>B)</b> Structures of viral proteins VP1 (green), VP2 (purple), and VP3 (cyan) in the surface model. The remodeling was based on the published EVD68 structure (PDB: 4WM8) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144208#pone.0144208.ref020" target="_blank">20</a>]. Positions 218 and 290, located on the surface of VP1, are labeled in red. Position 99 is shown in red instead of 98 since the latter is missing in the published EVD68 structure. (<b>C)</b> Position 194, is located beneath the viral surface and is essential for β-sheet formation, which may be important for supporting EVD68 virion “canyon” formation. Left panel: the surface model of VP1 rotated 120° from the model shown in Fig 2B; right panel: a cartoon model of the β-sheet in which residue 194 interacts with residue 183.</p

Evolutionary selection on the 18 clade-specific positions.

<p>After sequence alignment, the dN-dS values for each clade were calculated for these clade-specific positions with the help of MEGA5 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144208#pone.0144208.ref036" target="_blank">36</a>]. Values >0 indicate positive selection, while values <0 indicate purifying selection. Each codon with dN-dS = 0 in this study shared conserved nucleotides and thus was considered as purifyingly selected. Clade D was excluded from this analysis because only two strains contained full-length VP1.</p

Amino acid variation in the VP1 residues of different EV68 clades.

<p>The comparison was performed with the full-length EV68 VP1 region (306 amino acids) from 117 EVD68 sequences. The clade classification is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144208#pone.0144208.g001" target="_blank">Fig 1</a>. Values in the lower-left indicate the average number of different amino acids between the clades, with the range in parentheses. Values in the upper-right indicate the relative percentage of the VP1 region that differs among the clades. Sequence alignment and calculation were performed using MEGA5 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144208#pone.0144208.ref036" target="_blank">36</a>].</p><p>Amino acid variation in the VP1 residues of different EV68 clades.</p

Host-receptor binding and/or viral antigenicity correlate with EVD68 clade classification.

<p><b>(A).</b> Surface models of EVD68 VP1 (green), VP2 (purple), and VP3 (cyan), with clade-specific residues labeled in red. The remodeling was based on the published EVD68 structure (PDB: 4WM8) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144208#pone.0144208.ref020" target="_blank">20</a>]. Positions 140 and 149 are labeled in red to indicate the approximate positions of residues 141, 143, 144, 145, and 148 that are missing in the published structure. <b>(B).</b> Structural alignment of VP1 from the published EVD68 structure (green) or the proposed structure (blue) based on the viral structure of Echovirus 7 (PDB: 2X5I) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144208#pone.0144208.ref038" target="_blank">38</a>]. The alignment was performed with PyMol. (<b>C).</b> Surface model of the proposed EVD68 VP1 structure (blue), with clade-specific residues indicated in red. The panel on the right provides a detailed cartoon model showing clade-specific residues (in red) located on the loops forming the “canyon” responsible for host-receptor interaction. The BC-loop and DE-loop, thought to be critical in both host-receptor binding and viral antigenicity [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144208#pone.0144208.ref040" target="_blank">40</a>], are labeled with orange frames.</p

Phylogenetic analysis of full-length VP1 region of EVD68 strains.

<p>117 full-length EVD68 VP1 sequences were used for the re-construction of the Neighbor-Joining tree (<b>A</b>). Similar clade formation was detected compared to that in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144208#pone.0144208.g001" target="_blank">Fig 1</a>, and each clade was shown as a subtree (<b>B, C, and D,</b> for Clade A, B, and C respectively). The tree was re-constructed with the help of MEGA5 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144208#pone.0144208.ref036" target="_blank">36</a>]. Only bootstrap values >70 were shown. For a clearer presentation of the relationship between strains, only the topology was shown. Circle symbols indicate EVD68 strain from the 2014 outbreak, while square symbols indicate compressed EVD68 clades.</p

Crystallographic Investigation and Selective Inhibition of Mutant Isocitrate Dehydrogenase

Mutations in isocitrate dehydrogenase (IDH), a key enzyme in the tricarboxylic acid cycle, have recently been found in ∼75% glioma and ∼20% acute myeloid leukemia. Different from the wild-type enzyme, mutant IDH1 catalyzes the reduction of α-ketoglutaric acid to d-2-hydroxyglutaric acid. Strong evidence has shown mutant IDH1 represents a novel target for this type of cancer. We found two 1-hydroxypyridin-2-one compounds that are potent inhibitors of R132H and R132C IDH1 mutants with <i>K</i>_i values as low as 120 nM. These compounds exhibit >60-fold selectivity against wild-type IDH1 and can inhibit the production of d-2-hydroxyglutaric acid in IDH1 mutated cells, representing novel chemical probes for cancer biology studies. We also report the first inhibitor-bound crystal structures of IDH1­(R132H), showing these inhibitors have H-bond, electrostatic, and hydrophobic interactions with the mutant enzyme. Comparison with the substrate-bound IDH1 structures revealed the structural basis for the high enzyme selectivity of these compounds

Inhibition of Cancer-Associated Mutant Isocitrate Dehydrogenases by 2‑Thiohydantoin Compounds

Somatic mutations of isocitrate dehydrogenase 1 (IDH1) at R132 are frequently found in certain cancers such as glioma. With losing the activity of wild-type IDH1, the R132H and R132C mutant proteins can reduce α-ketoglutaric acid (α-KG) to d-2-hydroxyglutaric acid (D2HG). The resulting high concentration of D2HG inhibits many α-KG-dependent dioxygenases, including histone demethylases, to cause broad histone hypermethylation. These aberrant epigenetic changes are responsible for the initiation of these cancers. We report the synthesis, structure–activity relationships, enzyme kinetics, and binding thermodynamics of a novel series of 2-thiohydantoin and related compounds, among which several compounds are potent inhibitors of mutant IDH1 with <i>K</i>_i as low as 420 nM. X-ray crystal structures of IDH1­(R132H) in complex with two inhibitors are reported, showing their inhibitor–protein interactions. These compounds can decrease the cellular concentration of D2HG, reduce the levels of histone methylation, and suppress the proliferation of stem-like cancer cells in BT142 glioma with IDH1 R132H mutation

Primary data

Primary data(table1, table2 and table3 in the maintext were extracted from these data, it also contains screening data for tyr99 saturation mutagenesis

Crystal structure analysis of <i>Gka</i>P wild-type and mutant Y99L.

<p>(A) Overlay of the structures of wild-type <i>Gka</i>P (green), and Y99L (purple). (B) Overlay of loop 7 regions of wild-type <i>Gka</i>P (green) and Y99L (purple). The metal ions are shown in red spheres. Distances are shown in Å.</p