Cancers are the second leading cause of death in Slovenia and other developed countries worldwide, making them one of the biggest public health concerns. Targeted therapy is a form of molecular medicine that interferes with specific cell structures involved in carcinogenesis. It functions through various mechanisms, including inhibition of tumour cell proliferation. The latter is achieved by inhibiting cell structures that are required for cell division. One of these is the human voltage-gated potassium channel of the 'ether-à-go-go' family (hEAG1), which is responsible for regulating the cell cycle. Indirectly, it forms the mitotic spindle. In addition, hEAG1 is involved in the regulation of resting membrane potential in cells. However, the channel is overexpressed in more than 70% of all cancers. The channel is responsible for cell survival, growth, and division, and thus its inhibition leads to cancer cell death. Structurally, the hEAG1 channel is a tetrameric transmembrane protein that is physiologically most abundant in neurons. Its structure is very similar to that of the hERG channel, which repolarizes cardiac cells. Selective inhibition of the hEAG1 channel remains a challenge because most of its ligands bind simultaneously to the hERG channel and additionally increase the risk of cardiac arrhythmias.
In this master’s thesis, we used various computational methods to discover new selective hEAG1 channel inhibitors. By visually examining the structures of hEAG1 and hERG channels and analysing their amino acid sequences, we compared the two channels. The regions where we found structural differences were used to form binding pockets in the channels. In the hEAG1, two particularly specific pockets were used to perform virtual screening using molecular docking. Both binding pockets were part of the voltage sensor domain. We then generated pharmacophore models for the top hundred virtual hits. Pocket 1 solely exhibited hydrophobic interactions with the ligands, while pocket 2 offered the possibility of also forming an ionic interaction and hydrogen bonds through a donor and an acceptor. We then examined the specificity of amino acids surrounding the binding pocket by comparing them to the hERG channel. We concluded that there are three specific amino acids in pocket 1 and two specific amino acids in pocket 2 in the hEAG1 channel. Considering the result of molecular docking, we decided that the hit compounds are not worth testing in vitro because it is not likely possible to successfully bind into the pockets with high affinity or strong interactions and achieve a sufficient level of selectivity.
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