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ligands were built using maestro 8.5 build panel and prepared by ligprep 2.2 version v22208 ( schrdinger , llc .
, usa ) application that uses optimized potentials for liquid simulations ( opls ) 2005 force field . the protein was prepared by deleting a chain of the dimer before docking the ligands into the active site of the protein .
further the crystallographically observed water molecules and the active site of the protein was defined for generating the grid .
the energy minimized ligands were docked into the prepared grid using glide ( glide 4.5 , schrdinger , inc . ) on a linux based ( redhat linux enterprise rhel 5 ) workstation . the qikprop program ( qikprop 3.1 , schrdinger , inc . )
the neutralizing step is essential , as qikprop is unable to neutralize a structure and no properties will be generated in the normal mode .
it performs grid - based ligand docking with energetics and searches for favourable interactions between one or more typically small ligand molecules and a typically larger receptor molecule , usually a protein .
the glide score of 31 ligands were obtained after performing the ligand docking on a linux based ( red hat linux enterprise rhel 5 ) workstation ( table 1 ) .
hydrophobic interaction as depicted by the hydrophobic enclosure reward that indicates the surrounding of the ligand lipophilic atoms or group by the lipophilic protein atoms .
benzoxazinones derivatives used for the docking study one of the main goals in drug discovery is the identification of innovative small molecular scaffolds exhibiting high binding affinity and selectivity for the target together with a reasonable absorption , distribution , metabolism and excretion ( adme ) profile , lead and/or drug likeness .
such chemical entities are likely to be able to enter higher phases of the drug development process .
this has resulted in a paradigm shift in identifying the drug likeness properties of lead molecules early in the drug discovery process .
thus , in vitro approaches are now widely used to investigate the adme properties of new chemical entities and , more recently , computational ( in silico ) modeling has been investigated as a tool to optimize selection of the most suitable candidates for drug development .
the program was processed in normal mode , and predicted the properties for the best - fit molecules ( ligand nos .
7 , 17 , 21 and 28 ) , consisting of principal descriptors and physiochemical properties with analysis of the log p ( octanol / water ) , % human oral absorption , lipinski 's rule of five violation , cns activity ( tables 2 and 
 3 ) .
it also evaluates the acceptability of the analogues based on lipinski 's rule of 5 that are essential for rational drug design .
it performs grid - based ligand docking with energetics and searches for favourable interactions between one or more typically small ligand molecules and a typically larger receptor molecule , usually a protein .
the glide score of 31 ligands were obtained after performing the ligand docking on a linux based ( red hat linux enterprise rhel 5 ) workstation ( table 1 ) .
hydrophobic interaction as depicted by the hydrophobic enclosure reward that indicates the surrounding of the ligand lipophilic atoms or group by the lipophilic protein atoms .
one of the main goals in drug discovery is the identification of innovative small molecular scaffolds exhibiting high binding affinity and selectivity for the target together with a reasonable absorption , distribution , metabolism and excretion ( adme ) profile , lead and/or drug likeness .
such chemical entities are likely to be able to enter higher phases of the drug development process .
this has resulted in a paradigm shift in identifying the drug likeness properties of lead molecules early in the drug discovery process .
thus , in vitro approaches are now widely used to investigate the adme properties of new chemical entities and , more recently , computational ( in silico ) modeling has been investigated as a tool to optimize selection of the most suitable candidates for drug development .
the program was processed in normal mode , and predicted the properties for the best - fit molecules ( ligand nos .
7 , 17 , 21 and 28 ) , consisting of principal descriptors and physiochemical properties with analysis of the log p ( octanol / water ) , % human oral absorption , lipinski 's rule of five violation , cns activity ( tables 2 and 
 3 ) .
it also evaluates the acceptability of the analogues based on lipinski 's rule of 5 that are essential for rational drug design .
the intermolecular hydrogen bonding interaction of the best - fit ligands were found to be associated with tyr473 , ser289 , hie449 , hip323 , ser342 and gly284 amino acid residue at the receptor active site ( figs . 1 to 6 ) . among all the observed interaction with similar binding pattern , the presence of methyl carboxypentyl side chain ( lig .
3 ) and the affinity was increased by carboxyl oxygen ( as hydrogen bond acceptor ) with a best glide score of -14.54 as compared to the co - crystallized aryloxyphenyl acetic acid which achieved a glide score of -12.50 .
interaction of aryloxyphenylacetic acid ( a ) hydrogen bonding interaction of aryloxyphenylacetic acid where the carboxyl groups interact with the tyr473 , ser 289 , hie449 and hip 323 residue .
( b ) hydrophobic enclosure reward ( -0.28 ) achieved by the hydrophobic group ( phenyl ) of ligand no.7 .
17 ( a ) hydrogen bonding interaction and ( b ) hydrophobic enclosure reward ( -0.15 ) achieved by the hydrophobic group ( phenyl ) of ligand no .
21 ( a ) hydrogen bonding interaction and ( b ) hydrophobic enclosure reward ( -0.26 ) achieved by the hydrophobic group ( phenyl ) of ligand no
interaction of ligand no.28 ( a ) hydrogen bonding interaction and ( b ) hydrophobic enclosure reward ( -0.36 ) achieved by the hydrophobic group ( phenyl ) of ligand no.28 .
interaction of co - crystallized ligand ( a ) hydrogen bonding interaction and ( b ) hydrophobic enclosure reward ( -0.86 ) achieved by the hydrophobic group ( benzisoxazolyl ) of co - crystallized ligand ( -0.86 ) occupying the tyr473 , ser 289 and hie 449 pocket .
graphical picture showing superimposition and binding mode of co - crystallized ligand graphical picture showing superimposition and binding mode of co - crystallized ligand ( co1 ) ( a ) with ligand 21 ( rmsd 1.65 ) and ( b ) with ligand 31 ( rmsd 1.46  ) docked at the active site of hppar receptor .
the docking structures of all the compounds showed that they bind in a very similar pattern with the active site of ppar-. the best results obtained with docking scores are -14.04 , -14.20 , -14.54 and -14.28 of ligand 7 , 17 , 21 and 28 respectively .
based on the glide scores it can be inferred that n - alkyl chain substitution of benzoxazinone nucleus mainly long and branched chain increases the affinity .
further hydroxyl and acyl group substitution of medium length chain gives the best score as the presence of -oh and carbonyl group at the distal side chain assist in hydrogen bond interaction with gly284 and ser342 residue , respectively ( figs . 2 and 3 ) . in comparison with the co -
crystallized ligand ( -0.86 ) , most of the ligand received a poor hydrophobic enclosure reward .
this may be due to the binding orientation of the molecules as all the derivatives present its phenyl acetic acid moiety towards the active site , which is much less hydrophobic than the benzoxazinone nucleus .
based on the overall analysis it may be concluded that the series has the potential for the treatment of type 2 diabetes and the benzoxazinone pharmacophore could be used for further development .
the purpose of the present study is to undertake a docking study of some benzoxazinone derivatives on human peroxisome proliferator activated receptor co - crystallized with an alpha - aryloxyphenylacetic acid agonist using glide 4.5 . 
 the qikprop program was used to obtain the absorption , distribution , metabolism and excretion properties of the analogues . 
 the intermolecular hydrogen bonding interaction of the best - fit ligands were found to be associated with tyr473 , ser289 , hie 449 , hip 323 , ser 342 and gly 284 amino acid residue at the receptor active site . among all the observed interaction with similar binding pattern , the presence of methyl carboxypentyl side chain ( lig . 
 no . 
 21 ) showed additional interaction with ser 342 and the affinity was increased by carboxyl oxygen ( as hydrogen bond acceptor ) with a best glide score of -14.54 as compared to the co - crystallized aryloxyphenyl acetic acid which achieved a glide score of -12.50 .