Structural Bioinformatics Studies Of Ion Channels

Channel proteins are crucial membrane proteins. Ions and smallmolecules are exchanged between the extra-cellular side and the cytoplasmicside through channel proteins to accomplish various physiological processes.Many channel proteins could be used as drug targets, for instance, influenzavirus proton channel M2and the nicotinic acetylcholine receptor are targetsof the anti-influenza drugs and the anti-Alzheimer’s diseases drugs,respectively. In this study, we performed theoretical studies on these two ionchannels.M2protein is a proton channel embedded in the influenza viral envelopand is of paramount important for the viral infection and replication.Amantadine and rimantadine are two M2channel inhibitors which havebeen used as anti-influenza drugs for decades. However, their inhibitionmechanism is still not clear and they have lost their effects gradually inrecent years because of naturally occurring drug resistant mutations. Wesimulated the interactions between inhibitors and the wild type channel andthe drug resistant mutants to give insight into rational drug design of novelM2inhibitors.In Chapter3, we investigated the dynamic properties of the ligand-M2complexes by molecular dynamics (MD) simulations and calculated thebinding free energies of inhibitors at different binding sites on the protein byumbrella sampling method. We found two different sites co-exist on the protein. However, only the binding site in the channel pore is a thermal siteand could bind inhibitor stably, whereas the binding site on the proteinsurface is a kinetic site where ligand binds and dissociates quickly. Inhibitorsblock the proton conduction by occluding the channel pore. In Chapter4, wesimulated the structures of different drug resistant mutants and calculatedtheir binding free energies with inhibitors. We illustrated the structuralchanges of the channel and the water structure in the channel pore andshowed how these structural changes resulted in ligand binding free energychanges and drug resistance.Nicotinic acetylcholine receptors (nAChRs) are cation channels on theneuron cell which are drug targets for some neurodegenerative diseases (e.g.,the Alzheimer’s disease). Although various nAChR agonists are designed,most of them could not be used as drug candidates because they have lowselectivity for different nAChR subtypes and may result in various sideeffects. Another disadvantage of agonists is that the nAChRs aredesensitized if they exposed in agonist environment for long time. Allostericmodulators of nAChRs could avoid the above two problems, however, theirdesign is difficult.In order to guide rational drug design targeting the nAChRs, in Chapter6, we conducted MD simulations to investigate the interactions betweenJN403(an agonist) and different nAChR subtypes and calculated theirbinding free energies. Our results emphasized the importance of the longrange electrostatic interactions and van der Waals interactions for ligandselectivity. We also designed a new kind of positive allosteric modulatorsand tested their efficacy and potency by biological experiments. Then, weidentified their binding sites at the subunit interfaces of the extracellulardomain, near to the agonist site, by molecular modeling techniques and proposed probable mechanisms for their activity.Our simulations give insights into the rational drug design for these twochannel proteins.