3D-QSAR comparative molecular field analysis on opioid receptor antagonists: pooling data from different studies

J Med Chem. 2005 Mar 10;48(5):1620-9. doi: 10.1021/jm049117e.


Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were constructed using comparative molecular field analysis (CoMFA) on a series of opioid receptor antagonists. To obtain statistically significant and robust CoMFA models, a sizable data set of naltrindole and naltrexone analogues was assembled by pooling biological and structural data from independent studies. A process of "leave one data set out", similar to the traditional "leave one out" cross-validation procedure employed in partial least squares (PLS) analysis, was utilized to study the feasibility of pooling data in the present case. These studies indicate that our approach yields statistically significant and highly predictive CoMFA models from the pooled data set of delta, mu, and kappa opioid receptor antagonists. All models showed excellent internal predictability and self-consistency: q(2) = 0.69/r(2) = 0.91 (delta), q(2) = 0.67/r(2) = 0.92 (mu), and q(2) = 0.60/r(2) = 0.96 (kappa). The CoMFA models were further validated using two separate test sets: one test set was selected randomly from the pooled data set, while the other test set was retrieved from other published sources. The overall excellent agreement between CoMFA-predicted and experimental binding affinities for a structurally diverse array of ligands across all three opioid receptor subtypes gives testimony to the superb predictive power of these models. CoMFA field analysis demonstrated that the variations in binding affinity of opioid antagonists are dominated by steric rather than electrostatic interactions with the three opioid receptor binding sites. The CoMFA steric-electrostatic contour maps corresponding to the delta, mu, and kappa opioid receptor subtypes reflected the characteristic similarities and differences in the familiar "message-address" concept of opioid receptor ligands. Structural modifications to increase selectivity for the delta over mu and kappa opioid receptors have been predicted on the basis of the CoMFA contour maps. The structure-activity relationships (SARs) together with the CoMFA models should find utility for the rational design of subtype-selective opioid receptor antagonists.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Least-Squares Analysis
  • Ligands
  • Models, Molecular
  • Naltrexone / analogs & derivatives*
  • Naltrexone / chemistry*
  • Narcotic Antagonists*
  • Quantitative Structure-Activity Relationship*
  • Receptors, Opioid / chemistry*
  • Receptors, Opioid, delta / antagonists & inhibitors
  • Receptors, Opioid, delta / chemistry
  • Receptors, Opioid, kappa / antagonists & inhibitors
  • Receptors, Opioid, kappa / chemistry
  • Receptors, Opioid, mu / antagonists & inhibitors
  • Receptors, Opioid, mu / chemistry
  • Static Electricity


  • Ligands
  • Narcotic Antagonists
  • Receptors, Opioid
  • Receptors, Opioid, delta
  • Receptors, Opioid, kappa
  • Receptors, Opioid, mu
  • Naltrexone
  • naltrindole