Figure 6: Ainsliadimer A (1) is a novel allosteric inhibitor of IKKβ.
From: Ainsliadimer A selectively inhibits IKKα/β by covalently binding a conserved cysteine
(a) (A and B) The two modelled structures used to predict that a Michael acceptor (highlighted using red circle) forms a covalent bond with C46; (C and D) Superimposed structures representing the 250 ns MD simulations in the Orientation-1 and the Orientation-2 systems, respectively. IKKβ is presented in a ribbon model in grey color (sulfur atom of C46 is shown as a yellow sphere), the ligand is shown in a thin line and coloured gradually from deep blue to deep red along the time series. Structural convergence was only observed in the Orientation-2 system, where the compound binds in a relatively stable conformation (highlighted in the black circle) after 180 ns and lasts for the remaining 70 ns (movie S1 records all of the MD simulation trajectories). (b) A representative view of a simulated binding complex. (A) The left side shows the global view of the entire IKKβ structure; the right side shows the focused view of ainsliadimer A (1) in the allosteric binding site. Ainsliadimer A (1) forms a hydrogen bond with the backbone of C46 and interacts favourably with several hydrophobic residues including Trp58, Ile62, Val79, Leu91, Pro92 and Leu94. (c) The number of close contacts (distance <4.5 Å) between any heavy atoms of ainsliadimer A (1) and Trp58. (d) Binding of ainsliadimer A (1) to IKKβ induced conformational change. Stern–Volmer plots for quenching of the intrinsic tryptophan fluorescence of IKKβ by acrylamide are shown. The detailed experimental protocol is described in the Online Methods. (e) The determination of kobs for interaction of IKKβ (0.5 μM) with Probe (15 μM) for different times was calculated as described in Online Methods. (f) Plotting the kobs value for binding of IKKβ as a function of ainsliadimer A (1) concentration.
