Integrated Approach Including Docking, MD Simulations, and Network Analysis Highlights the Action Mechanism of the Cardiac hERG Activator RPR260243

Figures

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  Figure 1. (a) Illustration of the hERG channel in the open state conformation embedded in a lipid membrane model. The VSD encompassing helices S1 to S4 is in blue, the PD with helices S5 and S6, the P-Loop, the SF is in red, and the carboxy-terminal domain is in green. (b) Structural formula of RPR and associated graph representation. Colored circles represent the network nodes corresponding to the center of mass of each numbered region.

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  Figure 2. Scheme representing the action of RPR as a hERG activator. Red arrows refer to impaired transition from one state to another influenced by the drug. The closed states with gating charges Qg = 8e and Qg = 6e are assumed to be at equilibrium.

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  Figure 3. (a) Residues employed in the cluster analysis with respect to those directly implied in the activity of RPR displayed as thick capped sticks. (b) Relative population of the ten clusters identified for each channel model. The extended set of residues shown in panel (a) refers to the representative conformation of the most populated cluster (cluster #1) for each channel model.

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  Figure 4. (a) Binding modes obtained through ensemble docking calculation where only residues 4.5 Å from the ligand are reported. (b) Contact map related to the ensemble docking simulations in (a) showing the presence of the interactions between RPR and residues that form the predicted binding sites during the overall simulations of the bound systems. A contact fraction equal to 1 indicates that the interaction between the ligand and the residue persists during the whole trajectory. The cutoff distance used to identify the interactions between the ligand and the side chain of residues was 4.5 Å. Residues known to affect the RPR activity are shown as sticks in panel (a) and are highlighted with red circles in panel (b).

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  Figure 5. Activation and inactivation paths identified by the network analysis in the hERG closed and open states. Activation paths identified in the unbound (a) and bound (b,c) closed states with Qg = 6e and Qg = 8e, respectively. Inactivation path identified in the unbound (d) and bound (e,f) open states. RPR is schematized as described in Figure 1b. Colored arrows describe the kinematic chain of amino acids: violet arrows refer to the noncanonical activation path that follows the S4 → S1 → S5 → S6 route; red and orange arrows refer to the canonical paths L45 → S5 → S6 starting from the N-term or C-term sides of the loop, respectively; yellow arrows refer to the inactivation path that follows the S4 → S1 → S5 → P-Loop → SF route. Residues are colored based on the Betweenness Centrality values whose legend is indicated in the figure.