Hydrophobic contacts involved in the binding of RR compounds.

<p>Docking poses obtained for the two structurally-related compounds, (A) <b>RR4</b> (yellow) and (B) <b>RR6</b> (cyan) highlighting the binding differences (thick sticks correspond to residues that are inversely involved). Binding mode of compound having a stretched structure as for <b>RR11</b> (C) and for <b>RR20</b> (D) depicted as blue and orange sticks, respectively. Comparison of the binding mode for the inhibitory compound <b>RR3</b> (E) and the activator <b>RR28</b> (F) assuming a common binding site for both. Residues making halogen bonds are depicted in yellow sticks. All residues contributing to hydrophobic contacts (either with backbone or sidechain atoms) are depicted in solvent accessible surface and in thin sticks (all compounds are not oriented identically).</p

Detailed analysis of the binding mode for best-ranked hit compounds.

<p>(A) Overlay of the docking poses from all selected hits at the dimerization interface. Compounds are depicted in sticks and CD73 as solvent accessible surface (yellow and pink for differentiating the two monomers). (B) Overlay of the three most active compounds, <b>RR3</b> (green) <b>RR6</b> (cyan) and <b>RR16</b> (purple). Main polar interactions involved in the binding of <b>RR3</b> (C), <b>RR6</b> (D) and <b>RR16</b> (E) viewed in the same orientation. (F) Binding pose of hit compound <b>RR11</b> (blue) holding an extended and dimeric structure.</p

Structure-based drug design including cavity selection and dynamics of the enzyme target.

<p>(A) Flowchart illustrating the global strategy for developing allosteric CD73 inhibitors. (B) Five cavities detected using Fpocket on the closed dimeric form of CD73 (4H2G) and shown in colored mesh representations. (C) Top view of superimposed structures of CD73 during the TMD simulation highlighting the large rotating motion of N-domains (centers of mass depicted as spheres in arc shape). (D) Volumes changes and mean local hydrophobic densities observed during TMD for the blue cavity from panel “B” located at the dimerization interface. (E) Target cavity (mesh representation) outside the substrate binding site (AMP and Zn ions are depicted in cyan sticks). (F) Illustration of the target binding site in complex with one hit compound (green sticks) obtained by docking (Glu543 residues are depicted as spheres).</p

Hydrophobic contacts involved in the binding of RR compounds.

<p>Docking poses obtained for the two structurally-related compounds, (A) <b>RR4</b> (yellow) and (B) <b>RR6</b> (cyan) highlighting the binding differences (thick sticks correspond to residues that are inversely involved). Binding mode of compound having a stretched structure as for <b>RR11</b> (C) and for <b>RR20</b> (D) depicted as blue and orange sticks, respectively. Comparison of the binding mode for the inhibitory compound <b>RR3</b> (E) and the activator <b>RR28</b> (F) assuming a common binding site for both. Residues making halogen bonds are depicted in yellow sticks. All residues contributing to hydrophobic contacts (either with backbone or sidechain atoms) are depicted in solvent accessible surface and in thin sticks (all compounds are not oriented identically).</p

Determination of the kinetics inhibition profiles for the most representative compounds.

<p>Secondary plots and double-reciprocal of steady state rate constants as a function of AMP concentration in the absence (circles) or with increasing concentrations of hit compounds (squares, triangles and stars). (A): <b>RR3</b> at 0, 0.4, 0.8 and 1.6 μM; (B): <b>RR4</b> at 0, 0.3, 0.6 and 1.2 μM; (C): <b>RR6</b> at 0, 0.25, 0.5 and 1.0 μM; (D): <b>RR20</b> at 0, 0.3, 0.6 and 1.2 μM.</p

Comparison of hit compounds by using conventional metrics used in drug design.

<p>Inhibition constants (<i>K</i>_i) are expressed as pK_i (A) and ligand (B), ligand-lipophilicity (C), binding and surface (D) efficiencies correspond to LE, LLE, BEI and SEI, respectively. Note that for compounds exhibiting a mixed inhibition mode, two inhibition constants (“a” and “b”) were determined as for <b>RR2</b> and <b>RR16</b>.</p

Enzymatic inhibition assay in the presence of RR compounds using the purified recombinant enzyme.

<p>Red bars indicate the most active <b>RR</b> compounds promoting an enzyme inhibition as efficiently as APCP (5 μM) used as a positive control (green bar). Values of inhibitions are means from three independent experiments ± SD and negative values reflect enzyme activation.</p

Binding mode of hit compound RR28 linking both enzyme monomers.

<p>Residues are depicted in yellow or pink thin sticks according to the monomer they belong and <b>RR28</b> in thick pink sticks.</p

An Engineered Device for Indoleacetic Acid Production under Quorum Sensing Signals Enables <i>Cupriavidus pinatubonensis</i> JMP134 To Stimulate Plant Growth

The environmental effects of chemical fertilizers and pesticides have encouraged the quest for new strategies to increase crop productivity with minimal impacts on the natural medium. Plant growth promoting rhizobacteria (PGPR) can contribute to this endeavor by improving fitness through better nutrition acquisition and stress tolerance. Using the neutral (non PGPR) rhizobacterium <i>Cupriavidus pinatubonensis</i> JMP134 as the host, we engineered a regulatory forward loop that triggered the synthesis of the phytohormone indole-3-acetic acid (IAA) in a manner dependent on quorum sensing (QS) signals. Implementation of the device in JMP134 yielded synthesis of IAA in an autoregulated manner, improving the growth of the roots of inoculated <i>Arabidopsis thaliana</i>. These results not only demonstrated the value of the designed genetic module, but also validated <i>C. pinatubonensis</i> JMP134 as a suitable vehicle for agricultural applications, as it is amenable to genetic manipulations

Electron microscopic analysis of Aedesin-treated bacteria.

<p><i>E. coli</i> were either untreated (A,D) or incubated with VG26-61 (B,E) or Aedesin (C,F), respectively for 2 h at 37°C, prepared as indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105441#s2" target="_blank">Materials and Methods</a> and analyzed by transmission (A–C) and scanning (D–F) electron microscopy.</p