A three-dimensional model of the delta-opioid pharmacophore: comparative molecular modeling of peptide and nonpeptide ligands.
A comparative molecular modeling study of delta-opioid ligands was performed under the assumption that potent peptide and nonpeptide agonists may have common three-dimensional (3D) arrangement of pharmacophore groups upon binding to the delta-receptor. Low-energy conformations of the agonists 7-spiroindanyloxymorphone (SIOM) and 2-methyl-4a-alpha-(3-hydroxyphenyl)-1,2,3,4,4a,5,12, 12a-alpha-octahydro-quinolino[2,3,3-g]isoquinoline (TAN-67), and a partial agonist oxomorphindole (OMI) were determined by high-temperature molecular dynamics (MD). A good spatial overlap was found for the pharmacophore groups of SIOM, TAN-67, and OMI, including the basic nitrogen, phenol hydroxyl, and two aromatic ring. Based on this overlap we proposed a 3D pharmacophore model for nonpeptide delta-opioid agonists with a distance of 7.0 +/- 1.3 A between the two aromatic rings and of 8.2 +/- 1.0 A between the nitrogen and phenyl ring. The potent and highly delta-opioid receptor selective agonist [(2S,3R)-TMT(1)]DPDPE, which shares global backbone constraints of the 14-membered disulfide cycle and a strong preference for the trans rotamer of the TMT(1) side chain, was chosen as a peptide template of the delta-opioid pharmacophore. Extensive MD simulations at 300 K with the AMBER force field were performed for [(2S,3R)-TMT(1)]DPDPE and the less potent [(2S, 3S)-TMT(1)]DPDPE analogue. Multiple MD trajectories were collected for each peptide starting from the x-ray structures of DPDPE and [L-Ala(3)]DPDPE and from models proposed in the literature. Low-energy MD conformations were filtered by the nonpeptide pharmacophore query and then directly superimposed with SIOM, OMI, and TAN-67. Two conformers of [(2S,3R)-TMT(1)]DPDPE that showed the best overlap with the nonpeptide pharmacophore (rms deviation </= 1. 0 A for N,O atoms and centroids of two aromatic rings) were selected as possible delta-receptor binding conformations. These conformations have similar backbone structures, and trans rotamers of the TMT(1) side-chain group. They are reasonably close to the crystal structure of [L-Ala(3)]DPDPE, and differ significantly from the crystal structure of DPDPE. The conformer with a gauche(-) rotamer of Phe(4) is most consistent with structure-activity relationships of delta-opioid peptides. The proposed 3D models were used for rational design of new nonpeptide delta-receptor ligands.
Shenderovich
M D
MD
Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA.
Liao
S
S
Qian
X
X
Hruby
V J
VJ
D000700:Analgesics / Q000737:chemistry; D001665:Binding Sites; D020881:Enkephalin, D-Penicillamine (2,5)- / Q000031:analogs & derivatives / Q000737:chemistry*; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D009025:Morpholines / Q000737:chemistry; D010111:Oxymorphone / Q000031:analogs & derivatives* / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011804:Quinolines / Q000737:chemistry*; D017465:Receptors, Opioid, delta / Q000737:chemistry*; D013141:Spiro Compounds / Q000737:chemistry*; D013329:Structure-Activity Relationship
D000700:Analgesics; D008024:Ligands; D009025:Morpholines; D010455:Peptides; D011804:Quinolines; D017465:Receptors, Opioid, delta; D013141:Spiro Compounds; C094142:TAN 67; C070418:oxymorphindole; C082822:7-spiroindanyloxymorphone; D020881:Enkephalin, D-Penicillamine (2,5)-; D010111:Oxymorphone