In silico Analysis of Conformational Changes Induced by Mutation of Aromatic Binding Residues: Consequences for Drug Binding in the hERG K+ Channel

Knape, Kirsten; Linder, Tobias; Wolschann, Peter; Beyer, Anton; Stary-Weinzinger, Anna

doi:10.1371/journal.pone.0028778

Cited by 24 publications

(22 citation statements)

References 51 publications

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“…MD simulations were performed with Gromacs v. 4.5.4. (Hess et al ., ) as described previously (Knape et al ., ). Briefly, the hERG model was embedded in an equilibrated membrane consisting of 280 dioleolylphosphatidylcholine (DOPC) lipids by making use of the g_membed tool (Wolf et al ., ).…”

Section: Methodsmentioning

confidence: 97%

Structure‐activity relationships of pentamidine‐affected ion channel trafficking and dofetilide mediated rescue

Varkevisser

Houtman

Linder

et al. 2013

British J Pharmacology

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BACKGROUND AND PURPOSEDrug interference with normal hERG protein trafficking substantially reduces the channel density in the plasma membrane and thereby poses an arrhythmic threat. The chemical substructures important for hERG trafficking inhibition were investigated using pentamidine as a model drug. Furthermore, the relationship between acute ion channel block and correction of trafficking by dofetilide was studied. EXPERIMENTAL APPROACHhERG and KIR2.1 trafficking in HEK293 cells was evaluated by Western blot and immunofluorescence microscopy after treatment with pentamidine and six pentamidine analogues, and correction with dofetilide and four dofetilide analogues that displayed different abilities to inhibit IKr. Molecular dynamics simulations were used to address mode, number and type of interactions between hERG and dofetilide analogues. KEY RESULTSStructural modifications of pentamidine differentially affected plasma membrane levels of hERG and KIR2.1. Modification of the phenyl ring or substituents directly attached to it had the largest effect, affirming the importance of these chemical residues in ion channel binding. PA-4 had the mildest effects on both ion channels. Dofetilide corrected pentamidine-induced hERG, but not KIR2.1 trafficking defects. Dofetilide analogues that displayed high channel affinity, mediated by pi-pi stacks and hydrophobic interactions, also restored hERG protein levels, whereas analogues with low affinity were ineffective. CONCLUSIONS AND IMPLICATIONSDrug-induced trafficking defects can be minimized if certain chemical features are avoided or 'synthesized out'; this could influence the design and development of future drugs. Further analysis of such features in hERG trafficking correctors may facilitate the design of a non-blocking corrector for trafficking defective hERG proteins in both congenital and acquired LQTS. AbbreviationsER, endoplasmic reticulum; hERG, human ether-a-go-go-related gene; IK1, cardiac inward rectifying K + current; IKr, rapid component of the delayed rectifier K

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Section: Methodsmentioning

confidence: 97%

Structure‐activity relationships of pentamidine‐affected ion channel trafficking and dofetilide mediated rescue

Varkevisser

Houtman

Linder

et al. 2013

British J Pharmacology

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show abstract

“…The protein was embedded in an equilibrated membrane consisting of 280 dioleolylphosphatidylcholine (DOPC) lipids using the g_membed tool [56], which is part of the gromacs package. K + ions were placed in the SF, as described previously [57], at K + sites S0, S2, and S4, with waters placed at S1 and S3 of the SF [38]. Cl − ions were added randomly within the solvent to neutralize the system.…”

Section: Methodsmentioning

confidence: 99%

Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA

2013

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The bacterial potassium channel KcsA, which has been crystallized in several conformations, offers an ideal model to investigate activation gating of ion channels. In this study, essential dynamics simulations are applied to obtain insights into the transition pathways and the energy profile of KcsA pore gating. In agreement with previous hypotheses, our simulations reveal a two phasic activation gating process. In the first phase, local structural rearrangements in TM2 are observed leading to an intermediate channel conformation, followed by large structural rearrangements leading to full opening of KcsA. Conformational changes of a highly conserved phenylalanine, F114, at the bundle crossing region are crucial for the transition from a closed to an intermediate state. 3.9 µs umbrella sampling calculations reveal that there are two well-defined energy barriers dividing closed, intermediate, and open channel states. In agreement with mutational studies, the closed state was found to be energetically more favorable compared to the open state. Further, the simulations provide new insights into the dynamical coupling effects of F103 between the activation gate and the selectivity filter. Investigations on individual subunits support cooperativity of subunits during activation gating.

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“…Three snapshots (15, 33, and 50 nanoseconds) were taken from MD trajectories. The stability of the predicted binding modes of ICA to WT hEAG1 channels in open and closed conformation was confirmed in 50 nanosecond MD simulations as described previously (Knape et al, 2011).…”

Section: Methodsmentioning

confidence: 58%

ICA-105574 Interacts with a Common Binding Site to Elicit Opposite Effects on Inactivation Gating of EAG and ERG Potassium Channels

2013

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Rapid and voltage-dependent inactivation greatly attenuates outward currents in ether-a-go-go-related gene (ERG) K 1 channels. In contrast, inactivation of related ether-a-go-go (EAG) K 1 channels is very slow and minimally reduces outward currents. ICA-105574 (ICA, or 3-nitro-N-[4-phenoxyphenyl]-benzamide) has opposite effects on inactivation of these two channel types. Although ICA greatly attenuates ERG inactivation by shifting its voltage dependence to more positive potentials, it enhances the rate and extent of EAG inactivation without altering its voltage dependence. Here, we investigate whether the inverse functional response to ICA in EAG and ERG channels is related to differences in ICA binding site or to intrinsic mechanisms of inactivation. Molecular modeling coupled with site-directed mutagenesis suggests that ICA binds in a channel-specific orientation to a hydrophobic pocket bounded by the S5/pore helix/S6 of one subunit and S6 of an adjacent subunit. ICA is a mixed agonist of mutant EAG and EAG/ERG chimera channels that inactivate by a combination of slow and fast mechanisms. With the exception of three residues, the specific amino acids that form the putative binding pocket for ICA in ERG are conserved in EAG. Mutations introduced into EAG to replicate the ICA binding site in ERG did not alter the functional response to ICA. Together these findings suggest that ICA binds to the same site in EAG and ERG channels to elicit opposite functional effects. The resultant agonist or antagonist activity is determined solely by channel-specific differences in the mechanisms of inactivation gating.

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In silico Analysis of Conformational Changes Induced by Mutation of Aromatic Binding Residues: Consequences for Drug Binding in the hERG K+ Channel

Cited by 24 publications

References 51 publications

Structure‐activity relationships of pentamidine‐affected ion channel trafficking and dofetilide mediated rescue

Structure‐activity relationships of pentamidine‐affected ion channel trafficking and dofetilide mediated rescue

Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA

ICA-105574 Interacts with a Common Binding Site to Elicit Opposite Effects on Inactivation Gating of EAG and ERG Potassium Channels

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