Conceptual organization of the deCODE biostructures Fragments of Life library.

<p>The current ∼1,400-compound library contains chemically tractable natural small molecule metabolites (FOL-Nat), metabolite-like compounds and their bioisosteres (FOL-NatD), and biaryl mimetics of protein architecture (FOL-Biaryl). The FOL-Nat members include any natural molecule of molecular weight <350 daltons that exists as a substrate, natural product, or allosteric regulator of any metabolic pathway in any cell type, such as the biosynthetic pathways for the neurotransmitter serotonin (<b>1</b>) and the plant hormone auxin (<b>2</b>). The FOL-Nat members also include secondary metabolites such as bestatin (<b>3</b>), a secondary metabolite of <i>Streptomyces olivoreticuli </i><a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000530#pcbi.1000530-Schorlemmer1" target="_blank">[38]</a>. FOL-NatD fragments are defined as heteroatom-containing derivatives, isosteres, or analogs of any FOL-Nat molecule. For example, fragments <b>4–7</b> contain the indole scaffold, which is known to be a privileged building block for drug molecules <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000530#pcbi.1000530-Costantino1" target="_blank">[39]</a>. To emulate protein architecture, the FOL-Biaryl fragments were selected from a variety of biaryl compounds that are potential mimics of protein α, β, or γ turns <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000530#pcbi.1000530-Biros1" target="_blank">[40]</a>–<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000530#pcbi.1000530-Saraogi1" target="_blank">[42]</a>. These include a compound (<b>8</b>) whose structure in an energy-minimized state can be seen to mimic the architecture on an α-turn of a protein structure (here, residues Ser65-Ile66-Leu67-Lys68 of PDB ID:1RTP) and, similarly, a compound (<b>9</b>) whose structure mimics the β-turn of a protein structure (residues Ala20-Ala21-Asp22-Ser23).</p

<i>B. pseudomallei</i> inorganic pyrophosphatase with bound ligand at an oligomeric interface.

<p>Homo-hexameric bacterial inorganic pyrophosphatase is a dimer of trimers (blue and green). The illustration shows the hexamer structure in a complex with three ligand fragment molecules (red spheres and stick structures represent fragment FOL 110), each of which is located at one of three “dimer of trimer” interfaces (1.5 ligands per monomer) (PDBID:3EJ0). The location of one pyrophosphate substrate (cyan spheres) at the active site of one of the monomers is indicated here based on the superimposed structure of the hexamer with pyrophosphate bound in the active site (PDBID:3EIY). The binding sites of the ligands (red) are clearly seen in a pocket formed by the homo-oligomeric assemblage, which is distant from the active site where pyrophosphate (cyan) binds.</p

Structural genomics projects worldwide submitting to the Protein Data Bank.

<p>Note: Some centers with fewer than ten released structures in the PDB (<a href="http://www.rcsb.org/pdb/" target="_blank">www.rcsb.org/pdb/</a>) are not shown.</p><p>PSI, Protein Structure Initiative.</p

Examples of how target protein structure can assist drug discovery and development.

<p>Examples of how target protein structure can assist drug discovery and development.</p

From Cells to Mice to Target: Characterization of NEU-1053 (SB-443342) and Its Analogues for Treatment of Human African Trypanosomiasis

Human African trypanosomiasis is a neglected tropical disease that is lethal if left untreated. Existing therapeutics have limited efficacy and severe associated toxicities. 2-(2-(((3-((1<i>H</i>-Benzo­[<i>d</i>]­imidazol-2-yl)­amino)­propyl)­amino)­methyl)-4,6-dichloro-1<i>H</i>-indol-1-yl)­ethan-1-ol (NEU-1053) has recently been identified from a high-throughput screen of >42,000 compounds as a highly potent and fast-acting trypanocidal agent capable of curing a bloodstream infection of Trypanosoma brucei in mice. We have designed a library of analogues to probe the structure–activity relationship and improve the predicted central nervous system (CNS) exposure of NEU-1053. We report the activity of these inhibitors of T. brucei, the efficacy of NEU-1053 in a murine CNS model of infection, and identification of the target of NEU-1053 via X-ray crystallography

Urea-Based Inhibitors of Trypanosoma brucei Methionyl-tRNA Synthetase: Selectivity and in Vivo Characterization

Urea-based methionyl-tRNA synthetase inhibitors were designed, synthesized, and evaluated for their potential toward treating human African trypanosomiasis (HAT). With the aid of a homology model and a structure–activity-relationship approach, low nM inhibitors were discovered that show high selectivity toward the parasite enzyme over the closest human homologue. These compounds inhibit parasite growth with EC₅₀ values as low as 0.15 μM while having low toxicity to mammalian cells. Two compounds (<b>2</b> and <b>26</b>) showed excellent membrane permeation in the MDR1-MDCKII model and encouraging oral pharmacokinetic properties in mice. Compound <b>2</b> was confirmed to enter the CNS in mice. Compound <b>26</b> had modest suppressive activity against Trpanosoma brucei rhodesiense in the mouse model, suggesting that more potent analogues or compounds with higher exposures need to be developed. The urea-based inhibitors are thus a promising starting point for further optimization toward the discovery of orally available and CNS active drugs to treat HAT

Typical binding mode of an UBI to <i>Tb</i>MetRS.

<p>(A) The structure of <i>Tb</i>MetRS•<b>Chem 1433</b> is used as the prototypic complex to depict the binding mode of the UBIs in which the R1 moiety binds to the EMP and urea-R2 moiety binds to the AP. R1 and urea-R2 moieties are connected by the <i>N</i>-methylpropanamine linker, which is mostly solvent exposed. <b>Chem 1433</b> is shown in ball and stick model in deep purple. <i>Tb</i>MetRS is shown in surface representation in light pink with residues within a 4.5 Å radius from <b>Chem 1433</b> as stick model in light pink. Also see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002775#pntd.0002775.s003" target="_blank">Figure S3</a> for interactions between <b>Chem 1433</b> and <i>Tb</i>MetRS in the EMP and the AP. (B) Binding of inhibitor is accompanied by movement of multiple residues in the active site compared to the Met-bound M-state (PDB code 4EG1). In the EMP, two subpockets, the EMP-S and the EMP-E, can be discerned. Both subpockets are lined mostly by hydrophobic residues, some shown in stick model in light pink. Superposition of <i>Tb</i>MetRS•Met complex (not shown) onto <i>Tb</i>MetRS•<b>Chem 1433</b> (light pink) showed that Met occupies the EMP-S with the sulfur atom (marked as yellow cross) occupying essentially the same position as one of the <i>meta</i>-Cl in <b>Chem 1433</b>. Val473, Trp474 and Phe522 moved significantly to form the EMP-E. Also see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002775#pntd.0002775.s003" target="_blank">Figure S3A</a> for further details of the interactions within the EMP.</p

Interactions in the EMP.

<p>(A) Superpositions of Met-bound (not shown), <b>Chem 1433</b>-bound (deep purple) and <b>Chem 1444</b>-bound (blue) complexes show that a <i>meta</i>-Cl occupies the same position as the sulfur atom of Met (marked as yellow cross) in the EMP-S. The other <i>meta</i>-substituent occupies the EMP-E. <i>Meta</i>-Cl is preferred over <i>meta</i>-methoxy in the EMP-S. (B) If the <i>ortho</i>-substituent is small (hydroxyl), <i>meta</i>-allyl in <b>Chem 1472</b> (cyan) or <i>meta</i>-I in <b>Chem 1473</b> (orange) is bound to the EMP-S and <i>meta</i>-Cl is bound to the EMP-E. (C) If the <i>ortho</i>-substituent is large, <i>meta</i>-Cl is bound to the EMP-S and <i>meta</i>-butoxy in <b>Chem 1475</b> (green) or <i>meta</i>-ethoxy in <b>Chem 1469</b> (pale blue) is bound to the EMP-E. (D) Superpositions of all 15 UBI complexes indicate a consistent conformation of the EMP is selected for binding in 13 of the complexes (gray). In contrast, two other complexes, compound <b>Chem 1475</b>-bound (green) and compound <b>Chem 1476</b>-bound (brown) with large <i>ortho</i>- and <i>meta</i>-substituents in and near the EMP-E, cause minor adjustment in the conformation of the protein. Residues to the N-terminal of α-9 are displaced by an average of 0.7 Å for their C_α atoms as indicated by the red arrows. Displacement of Phe522 and His523 is also observed. (E) Compound <b>Chem 1540</b> (teal) is an example of inhibitors without the typical 3,5-di-halide substituted phenyl group as R1. The EMP-S is occupied but the fitting of the EMP-E is sub-optimal, resulting in a hydrophobic void and high IC₅₀ value.</p

The simultaneous binding of Chem 1433 and AMPPCP.

<p>(A) The structure of <i>Tb</i>MetRS•<b>Chem 1433</b>•AMPPCP shown with the difference electron density calculated by omitting <b>Chem 1433</b> and AMPPCP, contoured at 3σ (gray is positive density, red is negative density). (B) Residues around 4.5 Å radius of AMPPCP is shown in stick model (light pink) with <b>Chem 1433</b> (deep purple) and AMPPCP (pale green) shown in ball and stick model. Possible hydrogen bonds between AMPPCP and <i>Tb</i>MetRS are shown with a dashed line. Crucially, the secondary amine in the linker of <b>Chem 1433</b> forms a strong hydrogen bond with a β-phosphate oxygen in AMPPCP (2.6 Å). (C) Superposition of <i>Tb</i>MetRS•<b>Chem 1433</b>•AMPPCP and <i>Tb</i>MetRS•MAMP (PDB: 4EG3, protein not depicted) show that the AMP moiety of MAMP (cyan) binds, on average, approximately 1.5 Å deeper into the ribose and adenine pockets (red arrow).</p

5‑Fluoroimidazo[4,5‑<i>b</i>]pyridine Is a Privileged Fragment That Conveys Bioavailability to Potent Trypanosomal Methionyl-tRNA Synthetase Inhibitors

Fluorination is a well-known strategy for improving the bioavailability of drug molecules. However, its impact on efficacy is not easily predicted. On the basis of inhibitor-bound protein crystal structures, we found a beneficial fluorination spot for inhibitors targeting methionyl-tRNA synthetase of Trypanosoma brucei. In particular, incorporating 5-fluoroimidazo­[4,5-<i>b</i>]­pyridine into inhibitors leads to central nervous system bioavailability and maintained or even improved efficacy