Potassium channel blocker crafted by ɑ-hairpinin scaffold engineering

Biophysical Journal. 2021. Vol. 120. No. 12. P. 2471–2481.

Tabakmakher V., Gigolaev A., Peigneur S., Krylov N., Tytgat J., Chugunov A., Vassilevski A., Efremov R.

ɑ-Hairpinins are a family of plant defense peptides with a common fold presenting two short ɑ-helices stabilized by two invariant S–S-bridges. We have shown previously that substitution of just two amino acid residues in a wheat ɑ-hairpinin Tk-AMP-X2 leads to Tk-hefu-2 that features specific affinity to voltage-gated potassium channels KV1.3. Here, we utilize a combined molecular modeling approach based on molecular dynamics simulations and Protein Surface Topography technique to improve the affinity of Tk-hefu-2 to KV1.3 while preserving its specificity. An important advance of this work compared to our previous studies is transition from the analysis of various physico-chemical properties of an isolated toxin molecule to its consideration in complex with its target, a membrane-bound ion channel. As a result, a panel of computationally designed Tk-hefu-2 derivatives was synthesized and tested against KV1.3. The most active mutant Tk-hefu-10 showed an IC50 of ∼150 nM being >10 times more active than Tk-hefu-2 and >200 times more active than the original Tk-hefu. We conclude that ɑ-hairpinins provide an attractive disulfide-stabilized scaffold for the rational design of ion channel inhibitors. Furthermore, success rate can be considerably increased by the proposed “target-based” iterative strategy of molecular design.

Keywords: Molecular Dynamics Simulations, Potassium channels, potassium channel blocker

Publication based on the results of: Supercomputer technologies for atomistic modeling of physical processes in condensed matter (2021)