Developing a Comparative Docking Protocol for the Prediction of Peptide Selectivity Profiles: Investigation of Potassium Channel Toxins

Po-Chia Chen,Serdar Kuyucak

doi:10.3390/toxins4020110

Abstract

During the development of selective peptides against highly homologous targets, a reliable tool is sought that can predict information on both mechanisms of binding and relative afﬁnities. These tools must ﬁrst be tested on known proﬁles before application on novel therapeutic candidates. We therefore present a comparative docking protocol in HADDOCK using critical motifs, and use it to “predict” the various selectivity proﬁles of several major αKTX scorpion toxin families versus Kv1.1, Kv1.2 and Kv1.3. By correlating results across toxins of similar proﬁles, a comprehensive set of functional residues can be identiﬁed. Reasonable models of channel-toxin interactions can be then drawn that are consistent with known afﬁnity and mutagenesis. Without biological information on the interaction, HADDOCK reproduces mechanisms underlying the universal binding of αKTX-2 toxins, and Kv1.3 selectivity of αKTX-3 toxins. The addition of constraints encouraging the critical lysine insertion conﬁrms these ﬁndings, and gives analogous explanations for other families, including models of partial pore-block in αKTX-6. While qualitatively informative, the HADDOCK scoring function is not yet sufﬁcient for accurate afﬁnity-ranking. False minima in low-afﬁnity complexes often resemble true binding in high-afﬁnity complexes, despite steric/conformational penalties apparent from visual inspection. This contamination signiﬁcantly complicates energetic analysis, although it is usually possible to obtain correct ranking via careful interpretation of binding-well characteristics and elimination of false positives. Aside from adaptations to the broader potassium channel family, we suggest that this strategy of comparative docking can be extended to other channels of interest with known structure, especially in cases where a critical motif exists to improve docking effectiveness.

Highlights

The inhibition of potassium channels by peptides from animal venoms is a subject of broad interest for its physiological and therapeutic applications [1]
As pore-Lys insertion is a common characteristic amongst αKTx toxins [9,63], we define a distance between its amine and the centre of the plane formed by tyrosine carbonyls in the selectivity filter (TVGYG)
We note that the role of external space in selectivity has been previously examined between Kv 1.3 and KCa 1.1 channels [15], and will apply such considerations to this study

Summary

Introduction

The inhibition of potassium channels by peptides from animal venoms is a subject of broad interest for its physiological and therapeutic applications [1]. The distribution of channels being ubiquitous and varied, efficient and safe targetting relies upon the selective binding of pharmacological agents to specific subtypes involved. These include Kv 1.3 and KCa 3.1 in T-cell mediated diseases [2,3,4], Kv 1.4 and 4.x in neuropathic pain [5,6], and others. The similarity of basic functional motifs across the various folding patterns is remarkable, indicating a strong association with the particular characteristics of the channel surface These toxins offer a wide-range of affinities against individual sub-types—a characteristic that underlies current efforts to design pharmaceutically useful toxins

Methods

Results

Conclusion