Conformational and SAR analysis of NAALADase and PSMA inhibitors

Bioorg Med Chem. 2003 Oct 1;11(20):4455-61. doi: 10.1016/s0968-0896(03)00427-9.


Prostate specific membrane antigen (PSMA) is a 110 kDa type II transmembrane protein that is expressed exclusively by prostate tumor cells and as such is a clear cellular target in the development of a new method for fast and reliable diagnosis of prostate cancer. PSMA is highly homologous to the neuropeptidase NAALADase, and it has been shown that inhibitors of NAALADase also strongly bind to PSMA. In an effort to better understand the structural basis of the inhibitory activity of more than 60NAALADase inhibitors synthesized and tested by our group, we used Monte Carlo calculations employing the Merck Molecular Force Field to explore the conformational space available to a set of PSMA inhibitors. Conformational analysis indicated that the lower the number of unique conformations accessible by an inhibitor, the greater the biological activity displayed by the compound against LnCAP cells. This suggests that the difference in activity is largely entropy based. The key conformations associated with high activity are used to develop a simple pharmacophore model that led to the design of new, conformationally restricted analogues with potentially high activity in rational drug design.

MeSH terms

  • Antineoplastic Agents / chemistry*
  • Cell Line, Tumor
  • Entropy
  • Glutamate Carboxypeptidase II / antagonists & inhibitors*
  • Humans
  • Inhibitory Concentration 50
  • Ligands
  • Models, Molecular
  • Molecular Conformation
  • Monte Carlo Method
  • Peptides / chemical synthesis
  • Peptides / pharmacology
  • Prostate-Specific Antigen / antagonists & inhibitors*
  • Protein Binding
  • Structure-Activity Relationship


  • Antineoplastic Agents
  • Ligands
  • Peptides
  • Glutamate Carboxypeptidase II
  • Prostate-Specific Antigen