Pharmacology and Biochemistry insight into Small-Conductance Calcium-Activated Potassium Channels: A Structural and Bioinformatic Approach

Abstract

The Small-conductance calcium-activated potassium channels (SK) are of significant interest in physiology and pharmacology. In neurons, these channels are involved in the medium duration afterhyperpolarization (mAHP) that occurs after the repolarization of the plasma membrane, thereby modulating the frequency of action potential. These tetrameric channels open in response to an increase in free calcium in the cytoplasm via calmodulin. These proteins have already been identified as being involved in central and peripheral nervous system pathologies, such as atrial fibrillation, ataxia, seizures, schizophrenia, depression and behavioural disorders. The KCNN1-4 genes encode three isoforms of small conductance calcium-activated potassium channels (SK1, SK2 and SK3) and one isoform of medium-conductance calcium-activated potassium channel (SK4). These isoforms are constitutively expressed in many tissues but are expressed differently in the central nervous system. Additionally, SK channels are involved in cell migration and are overexpressed in certain cancerous tissues, highlighting their role in cancer physiology and metastasis. However, the mechanisms related to cancer are not well understood. For all these reasons, SK channels represent prime targets for treating neurological diseases or cancers.

Several peptides and alkaloid molecules are known to bind SK channels with high specificity. However, their difficulty in crossing the blood-brain barrier and, in some cases, their high toxicity make them poor candidates for drug development. No drug to date is capable of targeting a single isoform in a specific interaction. Furthermore, the mechanisms of action of these compounds remain unknown.

In this thesis, I combined structural bioinformatics, modelling, pharmacology, and biochemistry to describe the interactions between drugs and SK channels and contributed to the design of new compounds. We also identified a clear common binding site among all molecules and highlighted conserved interactions between alkaloids and peptides. We highlighted conserved phenylalanines on SK1, SK2 and SK3 involved in the interactions with all drugs tested in this paper. Moreover, our models explain the difference in affinity between SK2 and SK3 for peptides, paving the way for creating new isoform-specific drugs. As with SK4 previously, a Cryo-EM study of these proteins could definitively validate our predictions. Consequently, we also developed a purification protocol in order to observe the first Cryo-TEM illumination of SK3 during this thesis.