Representative snapshots taken from the MD simulation of ligand 1 within the new binding pocket (cyan, after 100 ns; magenta, after 800ns), fitted onto the starting geometry of the docked complex (green).

<p>Representative snapshots taken from the MD simulation of ligand 1 within the new binding pocket (cyan, after 100 ns; magenta, after 800ns), fitted onto the starting geometry of the docked complex (green).</p

Model of the apo-NR4A1 (green cylinders) in dimerization with apo-RXR-α (blue cylinders) at the NBS of a cognate NBRE, DNA (CPK colors) indicates the NBS sequences (Red) and the location of the <i>bis</i>-indole 1 (CPK spheres) post-superimposition of the NR4A1 45ns complex.

<p>Model of the apo-NR4A1 (green cylinders) in dimerization with apo-RXR-α (blue cylinders) at the NBS of a cognate NBRE, DNA (CPK colors) indicates the NBS sequences (Red) and the location of the <i>bis</i>-indole 1 (CPK spheres) post-superimposition of the NR4A1 45ns complex.</p

Clustering (above) and DASH, [35] (below) analyses of the 4.1 μs simulation of NR4A1.

<p>The clustering results are color-coded to indicate the population of the cluster in the given time period. The blue vertical dashed lines indicate transitions detected by DASH. The red dashed boxes indicate the clusters/conformations in which the binding pocket discussed below was found.</p

The structures of known small-molecule modulators of NR4A1.

<p>The structures of known small-molecule modulators of NR4A1.</p

Apo-NR4A1 (blue, PDB:2QW4) compared to a snapshot of NR4A1 after 45ns simulation in the presence of 1 (green).

<p>The blue double headed arrows indicate the axes of the helices 1 and 9 in the apo-structure. The regions of the protein that rearrange on ligand binding are denoted by the ellipses (Red; adjacent to the binding site. Violet; remote loop ²⁵F FQELVLPHFGKEDAGD-D⁴⁰).</p

Clustering of pockets that occur in the crystal structure and different snapshots of the MD simulation.

<p>Each vertex represents one pocket. Vertices are connected if the pockets are located in similar regions of the protein surface and have a mutual overlap of at least 30%. Vertex labels consist of the cluster number (0–14, c = crystal) and the pocket number (as identified by PocketPicker,³⁶ sorted by size in ascending order). Vertex colors and sizes correspond to the number of the snapshots (red: crystal) and the pocket sizes, respectively. Clusters <b>1</b>–<b>3</b> contain pockets that are present both in the crystal structure and in some snapshots. Pockets of clusters <b>4–10</b> are not present or smaller than 100 ų in the crystal structure. Cluster <b>4</b> (light green) represents a potential binding site. Clusters <b>5–10</b> represent pockets whose shapes or sizes render ligand binding unlikely.</p

The predicted binding site (blue/blue grey spheres) is located close to the N-terminus of NR4A1.

<p>The flexible loop that is stabilized by ligand binding is indicated by the red ellipse.</p

Side-chains addressing the S1 pocket of trypsin.

<p>Known inhibitors of trypsin exhibiting pyrimidin-2-amine <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002380#pcbi.1002380-PeterlinMasic1" target="_blank">[51]</a> (<i>left</i>) and the pyridin-2-amine <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002380#pcbi.1002380-Feng1" target="_blank">[52]</a> (<i>right</i>) side-chains (grey circles). These moieties were also suggested by DOGS as bioisosters for side-chains of the reference ligands addressing the S1 pocket of trypsin.</p

Bioisosteric replacement.

<p>Side-chains addressing the S1 pocket present in the reference compounds (<i>left</i>) and surrogates suggested by DOGS found in top-scored 200 designs (<i>right</i>).</p

Reduced graph representation.

<p>(<b>A</b>) An example of a reduced graph representation. Dashed lines connect atoms or rings of the molecule (<i>left</i>) with their corresponding vertex of the reduced graph (<i>right</i>). For clarity only some lines are shown. (<b>B</b>) Examples of polycyclic (‘amalgamated’) substructures translated to a single vertex in the reduced graph. (<b>C</b>) Edges of order two are used to connect fused rings (<i>bottom</i>) in order to distinguish the shown cases of neighbored rings in reduced graph representation.</p