Common Structural Pattern for Flecainide Binding in Atrial-Selective K(v)1.5 and Na(v)1.5 Channels: A Computational Approach

Atrial fibrillation (AF) is the most common cardiac arrhythmia. Its treatment includes antiarrhythmic drugs (AADs) to modulate the function of cardiac ion channels. However, AADs have been limited by proarrhythmic effects, non-cardiovascular toxicities as well as often modest antiarrhythmic efficacy. Theoretical models showed that a combined blockade of Na(v)1.5 (and its current, I(Na)) and K(v)1.5 (and its current, I(Kur)) ion channels yield a synergistic anti-arrhythmic effect without alterations in ventricles. We focused on K(v)1.5 and Na(v)1.5 to search for structural similarities in their binding site (BS) for flecainide (a common blocker and widely prescribed AAD) as a first step for prospective rational multi-target directed ligand (MTDL) design strategies. We present a computational workflow for a flecainide BS comparison in a flecainide-K(v)1.5 docking model and a solved structure of the flecainide-Na(v)1.5 complex. The workflow includes docking, molecular dynamics, BS characterization and pattern matching. We identified a common structural pattern in flecainide BS for these channels. The latter belongs to the central cavity and consists of a hydrophobic patch and a polar region, involving residues from the S6 helix and P-loop. Since the rational MTDL design for AF is still incipient, our findings could advance multi-target atrial-selective strategies for AF treatment.