Removal of Human Ether-à-go-go Related Gene (hERG) K⁺ Channel Affinity through Rigidity: A Case of Clofilium Analogues

Abstract

Cardiotoxicity is a side effect that plagues modern drug design and is very often due to the off-target blockade of the human ether-à-go-go related gene (hERG) potassium channel. To better understand the structural determinants of this blockade, we designed and synthesized a series of 40 derivatives of clofilium, a class III antiarrhythmic agent. These were evaluated in radioligand binding and patch-clamp assays to establish structure-affinity relationships (SAR) for this potassium channel. Efforts were especially focused on studying the influence of the structural rigidity and the nature of the linkers composing the clofilium scaffold. It was shown that introducing triple bonds and oxygen atoms in the n-butyl linker of the molecule greatly reduced affinity without significantly modifying the pKa of the essential basic nitrogen. These findings could prove useful in the first stages of drug discovery as a systematic way of reducing the risk of hERG K(+) channel blockade-induced cardiotoxicity.

Structure–Affinity Relationships (SARs) and Structure–Kinetics Relationships (SKRs) of Kv11.1 Blockers

“…Compounds 19,20,24,25,[27][28][29][30][39][40][41][42][43][44][45][46] were newly synthesized in order to obtain compounds with various RT values besides a diverse range of K i and k on values. All other compounds were selected from our in-house library based on their distinct affinities and kinetic parameters, and synthesis of these compounds has been reported in our previously published studies.…”

“…22−25 As shown in Scheme 1, clofilium (4-(4-chlorophenyl)butyldiethyl-heptylammonium) derivatives 19 and 20 were prepared from 4-iodotoluene in a three-step sequence as follows: Sonogashira cross-coupling of 4-iodotoluene and propargyl alcohol, formation of the corresponding tosylate, and displacement of the tosylate with the corresponding secondary amine. 24 To investigate the effect of flexibility in the side chains of aliphatic pyridinium derivatives, several symmetrical 2,6-substituted N-methylated-pyridine compounds with different alkyl chain lengths (24, 25, and 27−30) were synthesized according to Scheme 2. The first series of compounds (S23a− e) were derived from commercially available 2,6-dibromopyridine and 1-alkynes with various lengths via a Sonogashira coupling reaction.…”

Chemical optimization of macrocyclic HIV-1 inactivators for improving potency and increasing the structural diversity at the triazole ring

“…HPLC grade ACN, Millipore-MilliQ water and 0.1% TFA were used as solvents for the HPLC purification. Alkynes a9 - a16 were synthesized from the corresponding benzyl bromides a1 - a8 following the procedures previously described 45 (see below). Alkynes a9 - a16 were used in click reactions without purification because they are volatile and unstable upon storage.…”

Computer Simulations Reveal a Novel Blocking Mode of the hERG Ion Channel by the Antiarrhythmic Agent Clofilium

“…The nitro analog previously mentioned has a protonated tertiary nitrogen, yet the block does not diminish with a great degree. A different result was included in a recent study which performed the synthesis and evaluation of many clofilium analogs, when favoring the tertiary nitrogen generally led to reduced binding affinity . For example, introducing a triple bond in the chlorophenyl‐quaternary nitrogen linker reduced block to IC 50 =40 nM (compound 7, Table S1) and modeling a clofilium analog with a tertiary nitrogen also reduced block to IC 50 =43 nM (compound 90, Table S1).…”

“…Firstly, the “classical binding mode” explains that the aromatic ring is placed upwards into the cleft formed by Thr623, Ser624 and Tyr652, the aliphatic tail points downwards, forming hydrophobic interactions with Phe656, the quaternary nitrogen forms cation‐π interactions with several Tyr652 residues and the chlorine atom forms hydrogen bonds with Thr623 and Ser624, correlating with the channel's slow recovery from clofilium block . This position was also predicted in and firmly established in an ample study regarding binding of many clofilium analogs on hERG …”