| Neurodegenerative diseases are irreversible diseases caused by the loss of neurons in cells of the brain and spinal cord,the cause of which is still unclear and there is no specific medicine for a complete cure.In recent years,the number of patients has been increasing.It is estimated that there will be approximately 152 million patients with neurodegenerative diseases in the world in 2050.It is urgent to solve the problem of neurodegenerative diseases.Long-term use of western medicine will not only bring side effects but also produce dependence,which forces people to look for new methods and approaches.However,multiple studies have shown that traditional Chinese medicine plays an important role in the treatment of neurodegenerative diseases.The use of natural products in traditional Chinese medicine to develop new drugs is of great significance for the treatment of neurodegenerative diseases.Falcarindiol is a natural polyacetylene alcohol compound that has demonstrated anti-inflammatory,neurological effects,and potential anticancer properties.GABA_A receptors are important neural receptors and targets of many neural drugs.For example,sedatives,anesthetics,and antiepileptic drugs can all act on GABA_A receptors.Studies have shown that falcarindiol has a certain regulatory effect on GABA_A receptors,but the effect is currently unknown.In this context,we investigated the interaction mechanism of human GABA_A receptor(subunit composed ofα1β2γ2)and falcarindiol by computational simulation.Our assumptions for the study are as follows:1)To determine the stable binding site of falcarindiol on GABA_A receptors.2)How does falcarindiol modulate GABA_Areceptors at the binding site,activating or antagonizing?Therefore,after site prediction and molecular docking of the GABA_A receptor,seven site complexes were obtained for conventional molecular dynamics simulations,calculation of the binding free energy of falcarindiol to the receptor at 7 sites,and determination of the role played by different sites by umbrella sampling simulations.Subsequently,we will analyze how falcarindiol affects the binding of GABA molecules to GABA_A receptor and the conformational changes of GABA_A receptor.The results show that:1)After binding free energy calculations,we identified six sites where falcarindiol binds stably at the receptor.2)Umbrella sampling simulation results show that falcarindiol has a higher energy value for chloride ions to pass through the channel at all 6 sites than that of GABA_A alone.This indicates that the presence of falcarindiol does not facilitate the entry of chloride ions into the cells and acts as an antagonist role.3)GABA molecules were phased out of the receptor within 200 ns in the presence of falcarindiol,the distance between the CA atom of residue SER201 on theβ-subunit loop C and the CA atom of residue LEU128 on theα-subunit becomes larger with time.It shows that the presence of falcarindiol does not favor the binding of GABA molecules to the receptor and acts as an antagonist.4)The transmembrane helix rotates clockwise as seen in the conformational change,while the receptor activator usually causes the helix to rotate counterclockwise with a tendency to open the channel.This indicates that falcarindiol does not make the channel tend to open and thus play an antagonistic role.The clockwise rotation of the helix and the change in the curvature of the amino acid residues both reveal that the falcarindiol at the transmembrane site enables the drive between the helix subunits,the subunit in the extracellular region is driven to rotate clockwise,and loop C on theβsubunit tends to open.In conclusion,we identified the sites where falcarindiol binds stably to the GABA_A receptor by molecular dynamics simulations and corresponding analytical methods,and all of these sites have antagonistic effects on the receptor,finally obtaining three effective sites in the transmembrane structural domain.It will provide a theoretical basis for the subsequent study of the action of polyacetylene alcohol analogues on GABA_A receptor and the corresponding drug development. |
