3D Pharmacophore-Based Discovery of Novel KV10.1 Inhibitors with Antiproliferative Activity.

Žan Toplak,Lucija Peterlin Mašič,Luis A Pardo,Steve Peigneur,Matjaž Novak,Alja Štern,Špela Gubič,Bojana Žegura,Xiaoyi Shi,Štefan Možina,Tihomir Tomašič,Jan Tytgat,Louise Antonia Hendrickx

doi:10.3390/cancers13061244

Abstract

Simple SummaryA novel structural class of inhibitors of the voltage-gated potassium channel KV10.1 was discovered by a ligand-based drug design method using a 3D pharmacophore model. The virtual screening hit compound ZVS-08 inhibited the channel in a voltage-dependent manner consistent with the action of a gating modifier. Structure–activity relationship studies revealed a nanomolar KV10.1 inhibitor that is selective for some KV and NaV channels but exhibits significant inhibition of the hERG channel. KV10.1 inhibitor 1 inhibited the growth of the MCF-7 cell line expressing high levels of KV10.1 and low levels of hERG more potently than the Panc1 cell line (no KV10.1 and high hERG expression). Moreover, the KV10.1 inhibitor 1 induced significant apoptosis in tumour spheroids of Colo-357 cells. This study may provide a basis for the use of computational drug design methods for the discovery of novel KV10.1 inhibitors as new promising anticancer drugs.(1) Background: The voltage-gated potassium channel KV10.1 (Eag1) is considered a near- universal tumour marker and represents a promising new target for the discovery of novel anticancer drugs. (2) Methods: We utilized the ligand-based drug discovery methodology using 3D pharmacophore modelling and medicinal chemistry approaches to prepare a novel structural class of KV10.1 inhibitors. Whole-cell patch clamp experiments were used to investigate potency, selectivity, kinetics and mode of inhibition. Anticancer activity was determined using 2D and 3D cell-based models. (3) Results: The virtual screening hit compound ZVS-08 discovered by 3D pharmacophore modelling exhibited an IC50 value of 3.70 µM against KV10.1 and inhibited the channel in a voltage-dependent manner consistent with the action of a gating modifier. Structural optimization resulted in the most potent KV10.1 inhibitor of the series with an IC50 value of 740 nM, which was potent on the MCF-7 cell line expressing high KV10.1 levels and low hERG levels, induced significant apoptosis in tumour spheroids of Colo-357 cells and was not mutagenic. (4) Conclusions: Computational ligand-based drug design methods can be successful in the discovery of new potent KV10.1 inhibitors. The main problem in the field of KV10.1 inhibitors remains selectivity against the hERG channel, which needs to be addressed in the future also with target-based drug design methods.

Highlights

The voltage-gated potassium channel KV 10.1 (Eag1) is a member of the ether-à-go-go family, which includes the erg and elk subfamilies [1]
The discovery of KV 10.1 inhibitors has been limited to reports of known compounds or drugs that bind to this channel mostly as an off-target (Figure 1)
Limitations of structure-based in silico approaches in the design of KV 10.1 inhibitors can be overcome by ligand-based methods, such as 3D similarity search and pharmacophore modelling

Summary

Introduction

The voltage-gated potassium channel KV 10.1 (Eag1) is a member of the ether-à-go-go family, which includes the erg (eag-related gene, KV 11) and elk (eag-like K+ channel, KV 12) subfamilies [1]. To date, no KV 10.1-specific small-molecule inhibitors have been reported, as most of them inhibit voltage-gated sodium channels or, most importantly, the cardiac hERG channel, posing the risk of cardiac side effects [4]. Recent studies have pointed to a particular structural difference between KV 10.1 and hERG channels, suggesting the possibility of selective targeting of KV 10.1 in cancer therapies [19]. This opens exciting possibilities for further exploration using the published cryo-electron microscopy structures of KV 10.1 and hERG [2,20]

Objectives

Results

Discussion

Conclusion