Average K_a/K_s ratios between the LGTs.

<p>The average K_a/K_s ratios for each of the LGTs and reference genes between strains. The numbers under the bars in represent the LGTs as listed in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004326#pntd.0004326.g001" target="_blank">Fig 1A</a>. The boxes under the bars shows the fate of the corresponding LGT in genus <i>Leishmania</i>–classified as gene acquisition, degradation, acquirement of stop codons and indels respectively. Four LGTs (LmjF.03.0390, LmjF.15.0740, LmjF.23.0260 and LmjF.36.0260) have K_a/K_s ratios ≥1, and these LGTs have frame shift- and major in-frame indels, and contain stop codons.</p

LGTs with large variations in codon bias among their orthologs.

<p>(A) CAI scores of orthologues to LmjF.15.0740, and the fate of the LGT in genus <i>Leishmania</i>. The average CAI score of LmjL.15.0740 and LtrX.15.0740 is significantly lower than the average CAI score of the other orthologs to LmjF.15.0740 (p<0,001). Frame shift indels and stop codons in LmjL.15.0740 and LtrX.15.0740, as well as major in-frame indels in subgenus <i>Viannia</i> and <i>mexicana-</i>complex are indicated in the phylogenetic tree. (B) CAI scores of orthologues to LmjF.23.0260, and the fate of the LGT in genus <i>Leishmania</i>. The average CAI scores of orthologs to LmjF.23.0260 in subgenus <i>Viannia</i> is significantly lower than the average CAI scores of the other orthologs to LmjF.23.0260 (p<0,001). Major in-frame indels, frame shift indels and stop codons in all orthologs of subgenus <i>Viannia</i>, as well as stop codon in <i>L</i>. <i>tarentolae</i> are indicated in the phylogenetic tree. (C) CAI scores of orthologues to LmjF.36.0260, and the fate of the LGT in genus <i>Leishmania</i>. The average CAI scores of orthologs to LmjF.36.0260 in subgenus <i>Viannia</i> is significantly lower than the average CAI scores of the other orthologs to LmjF.23.0260 (p<0,001). LamH.36.0260 displays the lowest CAI score among orthologs of subgenus <i>Leishmania</i>. Major in-frame indels contributing to divergence of orthologs of subgenus <i>Viannia</i>, frame shift indels and stop codons in LamH.36.0260 and gene loss in <i>L</i>. <i>tropica</i> are indicated in the phylogenetic tree. Significance in panel A-C was calculated with a pooled two-sample t-test.</p

Consensus trees with orthologues to LGTs.

<p><b>(A)</b> Phylogenetic tree (congruent with the systematics proposed by Fraga and co-workers from 2010) showing the presence of LGT orthologs in five sequenced genomes of <i>Leishmania</i> and the sequenced genomes of <i>Trypanosoma cruzi</i> and <i>Trypanosoma bruceii</i>. The number of acquired genes (green boxes) and lost genes (red boxes) are presented numerically. (Red boxes*) refers to gene loss of orthologs to universal trypanosomatid LGTs. <b>(B)</b> Consensus tree summarizing the agreement between the phylogenetic trees for the twenty-three LGTs, investigated in detail in this study. Genus <i>Leishmania</i> is divided into the three subgenera <i>Viannia</i>, <i>Sauroleishamania</i> (here represented by only one species and one strain–<i>L</i>. <i>tarentolae</i>) and <i>Leishmania</i>. Subgenera <i>Viannia</i> and <i>Leishmania</i> are further divided into several complexes, and the topology of the consensus tree is completely congruent with the systematics proposed by Fraga and co-workers (2010). The fate of each LGT is illustrated with coloured boxes. “Gene acquisition” (green boxes) and “Gene loss” (red boxes) are based on presence of orthologs in published genomes or amplification of orthologs with PCR. Insertions/deletions (indels) (blue and orange boxes) and presence of stop codons (brown boxes) have been determined by manual inspections of alignments of obtained sequences and are relative to the gene sequence in <i>L</i>. <i>major</i> F. “In-frame Indels” (blue boxes) are insertions or deletions of more than 50 nucleotides not causing any frame-shift. “Frame-shift Indels” (orange boxes) are insertions or deletions that causes frame-shifts. Remnants (black boxes) of orthologs have been identified with synteny analyses (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004326#sec005" target="_blank">Material and Methods</a>).</p

Investigating Pharmacological Similarity by Charting Chemical Space

In this study, biologically relevant areas of the chemical space were analyzed using ChemGPS-NP. This application enables comparing groups of ligands within a multidimensional space based on principle components derived from physicochemical descriptors. Also, 3D visualization of the ChemGPS-NP global map can be used to conveniently evaluate bioactive compound similarity and visually distinguish between different types or groups of compounds. To further establish ChemGPS-NP as a method to accurately represent the chemical space, a comparison with structure-based fingerprint has been performed. Interesting complementarities between the two descriptions of molecules were observed. It has been shown that the accuracy of describing molecules with physicochemical descriptors like in ChemGPS-NP is similar to the accuracy of structural fingerprints in retrieving bioactive molecules. Lastly, pharmacological similarity of structurally diverse compounds has been investigated in ChemGPS-NP space. These results further strengthen the case of using ChemGPS-NP as a tool to explore and visualize chemical space

Selective demethylation and acetylation of phenanthrenequinones.

<p>Reagents and conditions: (i) TMSI, CH₂Cl₂, RT or 60°C. (ii) Ac₂O, pyridine, RT.</p

Synthesis of methoxy-phenanthrenequinones.

<p>Reagents and conditions: (i) MeOH, Fe₂(SO₄)₃, PTSA, 70°C.</p

Structural sets used in the pharmacophore study.

<p>CA-1∼CA-11 and 3a-9b are noted as natural and synthesized compounds, respectively.</p

Demethylation of phenanthrenes.

<p>Reagents and conditions: (i) AlCl₃, benzene, 70°C.</p

ChemGPS-NP analysis of calanquinone A (6a) and denbinobin (6b).

<p>Score plot of the three dimensions (principal components 2–4) consisting of PC2 (yellow; aromaticity etc.), PC3 (green; lipophilicity etc.) and PC4 (orange; flexibility/rigidity), from analysis of most potent compounds <b>6a</b> and <b>6b</b> as medium seagreen cubes in the ChemGPS-NP model addressed by Rosén et al. in 2009 for prediction of MOA. A reference set of known anticancer agents includes alkylating agents (red), anti-metabolites (lime), proteasome inhibitions (cyan), tyrosine kinase inhibitors (orange), topoisomerase I (blue), topoisomerase II (magenta), and tubulin inhibitors (black).</p

The best HypoGen pharmacophore model mapping onto calanquinone A (6a) and its derivatives.

<p>The light and dark green represent active and inactive features, respectively. The models mapped with the compounds <b>6a</b> (A), <b>6b</b> (B), <b>7a</b> (C), <b>7b</b> (D), <b>5a</b> (E) and <b>5b</b> (F) are shown here. Pharmacophore features are colored as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037897#pone-0037897-g007" target="_blank">Figure 7</a>.</p