2.5 | Docking of bupivacaine and ropivacaine
In order to study the binding site and mode of local anesthetics in
Kv1.5 ion channel, we used a systematic pipeline that includes docking
simulations in each binding site followed by molecular dynamics
simulations (MDs) and clustering of conformers. Briefly, two binding
sites were selected in the Kv1.5 homology model, the central cavity and
one side pocket. We carry out the docking of local anesthetics into only
one side pocket because the other three are integrated by the same
residues due to the tetrameric nature of the functional channel. The
local anesthetics (S-bupivacaine and ropivacaine (INN name implies that
it is the S-enantiomer)) were sketched and prepared with using LigPrep
(Schrödinger Release 2017-1, New York, USA) included in the Maestro
suite (Schrödinger Release 2017-1, New York, USA), with the force field
OPLS-AA (Kaminski, Friesner et al. , 2001). The nitrogen atom of
the piperidine ring was protonated for both ligands. The charges were
maintained during the parametrization process before docking and MDs.
The docking simulations were performed with Glide (Friesner, Murphyet al. , 2006) using the standard precision scoring function,
obtaining 10 poses per docking simulation. The centre of the grid
boxes for each binding site was focused using the interacting residues
identified by the functional alanine mutagenesis approach for each local
anesthetic. All molecular docking runs were performed with the outer box
edge of the grid setting as 30 Å, thus ensuring that the binding site
residues were included in each grid box. The best poses according to the
docking score were analyzed and the one that present the best
correlation with the experimental findings were further studied by
molecular dynamics simulations.