The hyperpolarization-activated nucleotide gated (HCN) channel plays a key role in developing neuropathic pain by regulating through hyperexcitability and rapid signaling. Neuropathic pain defines as the damage or disfunction to the somatosensory nervous system, which alters both central and peripheral nervous system. They are composed of four known subtypes: HCN1-HCN4, which HCN2 significantly contributing to neuropathic pain. These are primarily found in brain, heart and non-excitable tissues. Current drugs, such as opioids, cause serious complications including tolerance, addiction, and respiratory depression with prolonged use. Conotoxins are small venom peptides derived from marine cone snails of different families, and some are known to act as analgesics by inhibiting Voltage gated ion channels. There are currently no known conotoxins which target HCN channels. This structure based drug design study aimed to identify conotoxins which target HCN channels using computational and AI techniques.
Experimental structures of active and inactive HCN1, selected conotoxins (ω-conotoxin MVIIA, α-conotoxin MII, к-conotoxin PVIIA) and homology modelled HCN2 were used together with molecular docking and deep learning methods to predict HCN-conotoxin interactions. Subsequently, in silico mutational analysis was employed to identify toxin mutants with enhanced subtype selectivity.
Results revealed that all three families of conotoxins interact with HCN1 and HCN2. Particularly, MVIIA showed the highest binding affinity, interacting at the extracellular domain of HCN structures and may act as modulators, while kappa conotoxin may act as an inhibitor. Furthermore, MII exhibits the lowest affinity, although computational mutational studies revealed the substitution of leucine at residue 14 may improve its interaction profile.
Overall, this computer aided study provides novel insights into the potential interaction between conotoxins and HCN channels. In future, experimental validation employing cryo-electron microscopy and invitro assays will pave the way for predicting more interacting poses and involve in drug discovery.