Molecular docking analysis and molecular dynamics simulation study of ameltolide analogous as a sodium channel blocker

Maryam IMAN; Atefeh SAADABADI; Asghar DAVOOD

Article Details

Molecular docking analysis and molecular dynamics simulation study of ameltolide analogous as a sodium channel blocker

Authors:

Maryam IMAN | Atefeh SAADABADI | Asghar DAVOOD

Publisher:

TUBITAK

Journal:

Turkish Journal of Chemistry 2015 Vol.39 Issue 2

Document Type:

Article

Publication Date:

8/2015

Document Language:

Turkish

Document ID (Org No.):

2000726921

Frequency:

Bimonthly

eISSN:

1303-6130

pISSN:

1300-0527

Abstract:

 

Fifteen compounds related to ameltolide with sodium channel inhibitory  activity were subjected to a molecular docking study. The chemical  structures of all compounds were built using the program HyperChem and  conformational studies were performed with a semiempirical method followed  by the PM3 method. A docking study was performed using the program AutoDock  on all the compounds. To confirm the binding mode of inhibitors, molecular  dynamics simulations were performed using GROMACS 4.5.5, based upon the  docked conformation of ameltolide. The docking analyses indicated that these  compounds interacted mainly with residues II-S6 and III-S6 of NaV1.2 by  making hydrogen bonds and (\pi -\pi ) interactions with domains I, III,  and IV in the channel's inner pore. Our docking study reveals that amide  linker plays a major role in the drug--receptor interaction. The results of  molecular dynamic simulations confirmed the binding mode of ligands, the  accuracy of docking, and the reliability of active conformations obtained by  AutoDock.

 

Fifteen compounds related to ameltolide with sodium channel inhibitory  activity were subjected to a molecular docking study. The chemical  structures of all compounds were built using the program HyperChem and  conformational studies were performed with a semiempirical method followed  by the PM3 method. A docking study was performed using the program AutoDock  on all the compounds. To confirm the binding mode of inhibitors, molecular  dynamics simulations were performed using GROMACS 4.5.5, based upon the  docked conformation of ameltolide. The docking analyses indicated that these  compounds interacted mainly with residues II-S6 and III-S6 of NaV1.2 by  making hydrogen bonds and (\pi -\pi ) interactions with domains I, III,  and IV in the channel's inner pore. Our docking study reveals that amide  linker plays a major role in the drug--receptor interaction. The results of  molecular dynamic simulations confirmed the binding mode of ligands, the  accuracy of docking, and the reliability of active conformations obtained by  AutoDock.

Article Details

Molecular docking analysis and molecular dynamics simulation study of ameltolide analogous as a sodium channel blocker

Authors: Maryam IMAN | Atefeh SAADABADI | Asghar DAVOOD

Publisher: TUBITAK

Journal: Turkish Journal of Chemistry 2015 Vol.39 Issue 2

Document Type: Article

Publication Date: 8/2015

Document Language: Turkish

Document ID (Org No.): 2000726921

Frequency: Bimonthly

eISSN: 1303-6130

pISSN: 1300-0527

Issues

Authors:

Maryam IMAN | Atefeh SAADABADI | Asghar DAVOOD

Publisher:

TUBITAK

Journal:

Turkish Journal of Chemistry 2015 Vol.39 Issue 2

Document Type:

Article

Publication Date:

8/2015

Document Language:

Turkish

Document ID (Org No.):

2000726921

Frequency:

Bimonthly

eISSN:

1303-6130

pISSN:

1300-0527