DockingServer

plumbagin CID_10205 to IGF Receptor

Author: Mr. Prakash Shyam - 10/08/06, 00:22

More docking results of Mr. Prakash Shyam Address: Department of Animal Science, Bharathidasan University, Tiruchirappalli. 620024. India

Abstract: Plumbagin (1,4-Naphthalenedione, 5-hydroxy-2-methyl-(9CI)) is a natural bicyclic naphthoquinone found in a number of medicinal plants, including Plumbago europaea, Plumbago rosea, Plumbago zeylanica and Dionaea muscipula (venus fly trap). Plumbago family has outstanding record of accomplishment in ayurvedic medicine and traditionally used for microbial infections, cancer, and rheumatoid arthritis (Mossa et al., 2004, Srinivas et al., 2004, Ding et al., 2005 and Hsu et al., 2006) in Asian continent. In specific, plumbagin like naphthoquinones have been used for these treatments. However, most of these claims are supported only by anecdotal evidence, there are few scientific reports describing their cytotoxic efficacy, and literature suggesting their mechanisms is scarce.









Result table

Rank
 
Est. Free Energy
of Binding
Est. Inhibition
Constant, Ki
vdW + Hbond
+ desolv Energy
Electrostatic
Energy
Total Intermolec.
Energy
Frequency
 
1
-4.60 kcal/mol
428.09 uM
-5.30 kcal/mol
+0.40 kcal/mol
-4.89 kcal/mol
70
 





Interaction Table

polar
hydrophobic
pi-pi
other
  O3 (3)
  [3.23]		 – ARG1104 (NH1)
  C9 (12)
  [3.88]		 – VAL1023 (CB)
  C3 (6)
  [3.88]		 – HIS1103 (CD2)
  O2 (2)
  [3.59]		 – PHE1027 (CE2)
 
  C8 (11)
  [3.19]		 – MET1024 (CE)
  C4 (7)
  [3.85]		 – HIS1103 (CD2)
  O2 (2)
  [3.80]		 – LEU1096 (CD1)
 
  C10 (13)
  [3.26]		 – MET1024 (CE)
  C2 (5)
  [3.54]		 – PHE1124 (CB)
  O2 (2)
  [3.72]		 – HIS1103 (CD2)
 
  C11 (14)
  [3.32]		 – LEU1096 (CD1, CG)
  C5 (8)
  [3.86]		 – PHE1124 (CB)
  C10 (13)
  [3.49]		 – ASP1123 (CB)
 
  C11 (14)
  [3.60]		 – HIS1103 (CB, CD2, CG)
  C6 (9)
  [3.43]		 – PHE1124 (CB)
  O1 (1)
  [3.62]		 – PHE1124 (CB)
 








Docking calculations were carried out using DockingServer (Bikadi, Hazai, 2009). The MMFF94 force field (Halgren, 1998) was used for energy minimization of ligand molecule (plumbagin CID_10205.pdb) using DockingServer. Gasteiger partial charges were added to the ligand atoms. Non-polar hydrogen atoms were merged, and rotatable bonds were defined.
Docking calculations were carried out on IGF Receptor protein model. Essential hydrogen atoms, Kollman united atom type charges, and solvation parameters were added with the aid of AutoDock tools (Morris, Goodsell et al., 1998). Affinity (grid) maps of 20×20×20 Å grid points and 0.375 Å spacing were generated using the Autogrid program (Morris, Goodsell et al., 1998). AutoDock parameter set- and distance-dependent dielectric functions were used in the calculation of the van der Waals and the electrostatic terms, respectively.
Docking simulations were performed using the Lamarckian genetic algorithm (LGA) and the Solis & Wets local search method (Solis and Wets, 1981). Initial position, orientation, and torsions of the ligand molecules were set randomly. Each docking experiment was derived from 10 different runs that were set to terminate after a maximum of 250000 energy evaluations. The population size was set to 150. During the search, a translational step of 0.2 Å, and quaternion and torsion steps of 5 were applied.



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