NDLI: Homology modeling, molecular dynamic simulation, and docking based binding site analysis of human dopamine (D4) receptor

Content Provider	Springer Nature Link
Author	Khoddami, Minasadat Nadri, Hamid Moradi, Alireza Sakhteman, Amirhossein
Copyright Year	2015
Abstract	Human dopamine D4 receptor is a GPCR target in the treatment of neurological and psychiatric conditions such as schizophrenia and Parkinson’s disease. The X-ray structure of this receptor has not been resolved so far. Therefore, a proper 3D structure of D4 could provide a good tool in order to design novel ligands against this target. In this study, homology modeling studies were performed to obtain a reasonable structure of the receptor using known templates. The obtained model was subjected to molecular dynamic simulation within a DPPC membrane system. Some structural features of the receptor such as a conserved disulfide bridge and ionic lock were considered in the modeling experiments. The resulted trajectories of simulation were clustered based on the root mean square deviation of the backbone. Some known ligands and decoys were accordingly docked into the representative frames of each cluster. The best final model was finally selected based on its ability to discriminate between active ligands and inactive decoys (ROC = 0.839). The presented model of human D4 receptor could be a promising starting point in future studies of drug design for the described target. Graphical Abstract Superposition of human D4 model with the crystal structure of D3 at TM regions
Starting Page	1
Ending Page	10
Page Count	10
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	21
Issue Number	2
e-ISSN	09485023
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2015-02-04
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Binding site Docking Homology modeling Human dopamine D4 receptor Molecular dynamic simulation Computer Applications in Chemistry Molecular Medicine Computer Application in Life Sciences Characterization and Evaluation of Materials Theoretical and Computational Chemistry
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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