Affinity and Selectivity of ShK Toxin for the Kv1 Potassium Channels from Free Energy Simulations

Abstract

The voltage-gated potassium channel Kv1.3 is an attractive target for treatment of autoimmune diseases. ShK toxin from sea anemone is one of the most potent blockers of Kv1.3, and therefore ShK and its analogues have been proposed as therapeutic leads for such diseases. Increasing the selectivity of the proposed leads for Kv1.3 over other Kv1 channels is a major issue in this endeavor. Here we study binding of ShK toxin to Kv1 channels using free energy simulation methods. Homology models for Kv1.1 and Kv1.3 channels are constructed using the crystal structure of Kv1.2. The initial poses for the Kv1.x-ShK complexes are obtained using HADDOCK, which are then refined via molecular dynamics simulations. The binding mode in each complex is characterized by identifying the strongly interacting residues, which compare well with available mutagenesis studies. For each complex, the potential of mean force is calculated from umbrella sampling simulations, and the corresponding absolute binding free energy is determined. The computed binding free energies are in good agreement with the experimental data, which increases the confidence on the model complexes. The insights gained on Kv1.x-ShK binding modes will be valuable in the development of new ShK analogues with better selectivity properties.

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

“…(1) Small molecule conformational sampling [73][74][75][76]; (2) Protein-folding [77][78][79] and large-scale protein conformational sampling [80][81][82][83]; (3) Protein-protein/peptide-peptide interactions [84][85][86][87][88][89][90][91][92]; (4) DNA conformational changes [93] and DNA-DNA interactions [94][95][96]; (5) Binding and association free-energies [97][98][99][100][101][102][103][104][105][106][107]; (6) Adsorption on and permeation through lipid bilayers [108][109][110][111][112][113][114][115][116][117] …”

CHAPTER 10. Case Study 2: Transforming a Toxin into a Therapeutic: the Sea Anemone Potassium Channel Blocker ShK Toxin for Treatment of Autoimmune Diseases

“…The initial poses for the Kv1.xÀShK complexes were obtained using HADDOCK, 22 and then rened via molecular dynamics simulations (in fact the Kv1.3-ShK structure from this study is the one shown in Figure 10.2c). 23 The binding mode in each complex was characterized by identifying the strongly interacting residues, which compare well with the results of mutagenesis studies referred to above. For each complex, the potential of mean force was calculated from umbrella sampling simulations, and the corresponding absolute binding free energy was determined.…”

“…The computed binding free energies were in remarkably good agreement with the experimental data. 23 We will return to this point in Section 10.6, but we note here that the power of this approach is demonstrated by our recent results with a new ShK analogue containing an additional C-terminal amidated Lys residue. ShK-Kamide is a potent blocker of Kv1.3 and, in contrast to ShK and ShK-amide, it is selective for Kv1.3.…”

“…New approaches to calculating the affinities of peptides for various channels, described in Section 10.3.1, 23,24 are also contributing to the design of new ShK analogues that are amenable to recombinant expression. 42 Findings over the past decade also point to a role of Kv1.3 channels in the regulation of peripheral insulin sensitivity and glucose metabolism.…”

Structural Similarity between Defense Peptide from Wheat and Scorpion Neurotoxin Permits Rational Functional Design

“…It was shown that peptides containing the so-called "functional dyad" usually display potassium channel-blocking activity, although for several molecules, the dyad was shown to be insufficient (59 -62). Moreover, the importance of some other residues, which often serve for higher binding affinity and better blocking ability, was also shown (63)(64)(65).…”