Investigation of the mechanisms of hERG1 blocker toxins as anti-cancer agent with molecular modeling techniques

Abstract

Ion channels are membrane-inserted proteins which regulate the movement of ions through cell membrane. Potassium (K+) ion channels ubiquitously exist in almost all species and locate in cell membranes. Members of this channel family play important roles in cellular signaling, including various processes. It is well-known that K+ ion channels involved in signaling pathways lead to cell proliferation or apoptosis. Because of their location on cell surface and their well-known pharmacology, they can be used as potential targets in anticancer therapies. The human ether-a-go-go related gene 1 (hERG1) K+ channels play crucial role in the heart, different regions of brain, endocrine cells, smooth muscle cells, and numerous tumor cells. It is known that the inherited mutations of hERG1 gene may lead to the disorder of cardiac repolarization (i.e., long QT syndrome (LQTS)), which may result in sudden cardiac death. It is known that K+ ion channels involved in signaling pathways lead to cell proliferation or apoptosis and some specific toxins were investigated for diverse therapeutic applications on targeting the hERG1 K+ channel. Thus, investigation of channel/toxin interactions mechanisms in atomic level is an important topic for the development of toxin-based therapeutics. Thus, in the first part of this thesis, the interaction mechanisms of two toxins named as BeKm-1 and BmTx3b with the closed-state hERG1 channel have been studied by using different molecular modeling techniques including protein-protein docking and molecular dynamics (MD) simulations. The crucial residues of toxins in channel interactions have been elucidated. It is found that R1, K6, K18, R20, K23 and R27 residues in BeKm-1 and F1, K7, K19, K20 and K28 in BmTx3b are the important residues involved in the strong interactions with the closed-state hERG1 K+ channel. The results of this study can be used by medicinal chemists in the designing of diverse therapeutic applications of natural or synthetic peptides targeting the closed state hERG1 K+ channels. In the second part of the thesis, the information that obtained from hERG-BeKm-1 and hERG-BmTx3b interactions, was used to design de novo peptides. The designed de novo peptides were investigated on open-state hERG. In addition to de novo peptides, peptidomimetics and FDA-approved molecules were included in the study to increase the number of molecules studied. It is believed that the data obtained in the thesis study will provide guidance for hERG inhibition for therapeutic purposes. In this way, it is expected to be able to eliminate various types of disease without causing sudden cardiac death.