Advanced Molecular Modeling Techniques Applied to Ion Channels Blockers - Ion Channels and Their Inhibitors - page 59

2.1 Exploration of the Binding Sites on Ion Channels

The binding site of the ion channel can vary since the channel receptors usually
have three domains; the extracellular-loop domain, the transmembrane domain, and
the cytoplasmic domain. Molecular docking helps to predict the putative binding
site or suggest novel interactions. For example, the cardiac inwardly rectifying K+
(Kir) channels, spermine is a blocker of the Kir2.1 potassium channel, which
selected to bind in the cytoplasmic site surrounding by Asp255, Glu299, and
Glu224, rather than the pore center in transmembrane domain [ 37 ]. On the contrary,
carvedilol binds in the channel pore, where the binding site located at the cytosolic
portion of inner helix containing Cys166, causing the carvedilol to preferably block
Kir6.xs and Kir3.xs over the Kir2.xs [ 44 ].
When a combined method of docking followed by MD simulations can often
allow greater insight, such as helping to identify multiple binding sites of the Kir6.2
channel and binding modes of imidazoline derivatives were revealed from docking/MD
study when each blocker is accommodated in different site [ 51 ]. The open-state Kv1.5
actually contains two binding sites inside the channel pore for bupivacaine, which are
at the selectivity filter (upper cavity) and a narrower ProValPro-bends (lower cavity)
[ 42 ]. Putative binding site predicted by docking is confirmed by specific experiment.
After amiloride and its derivatives were docked into the human acid-sensing ion channel
(hASIC-1), the putative potential binding site was experimentally confirmed using
whole-cell patch clamp [ 52 ]. A complex of the tarantula toxin PcTx1/hASIC-1a is
first introduced by docking/MD technique. Moreover, novel binding recognition is
also revealed when four domains participated in the binding but only two subunits of
hASIC-1a directly interact with the PcTx1 [ 44 ].
For the Cys-loop family, when docking the -aminobutyric acid (GABA) into the

specific site of the GABA receptor, the binding pocket is any region that supports
cation-

g

interaction [ 39 ]. The glycine receptor (GlyR) is a target for ginkgolide A
and ginkgolide X, where docking predicts that the putative binding site is formed by
the 6 0 M2, 2 0 ,10 0 and 13 0 residues, instead of only 6 0 M2 residue [ 53 ]. Docking
diverse molecules consisting of agonists and antagonists into

p

7-nAChR showed
that the putative binding site consists of evolutionary conserved residues Ser34,
Gln55, Ser146 and Tyr166. Virtual mutations of S34A/T/Y, G55A/E/N, S146A/T/Y,
and Y166A/F/S generate class-specific residues that form H-bond to antagonists
indicating the high sensitivity of ligand binding. In a large pocket such as that of the
hERG potassium ion channel, where diverse molecule can bind and activate the
gating mechanism, docking of propafenone derivatives into the closed and open
state of the hERG provided the first insight into ligand binding [ 38 ].

a

2.2 Exploration of the Bound Blocker Conformation

Molecular docking can also be used to identify the blocker binding conformation to
the ion channel. The gating modifier toxins such as Hanatoxin (HaTx1) bind