Structure-based design, synthesis, and memapsin 2 (BACE) inhibitory activity of carbocyclic and heterocyclic peptidomimetics

J Med Chem. 2005 Aug 11;48(16):5175-90. doi: 10.1021/jm050142+.

Abstract

Molecular modeling based on the X-ray crystal structure of the Tang-Ghosh heptapeptide inhibitor 1 (OM99-2) of BACE led to the design and synthesis of a series of constrained P(1)' analogues. A cyclopentane ring was incorporated in 1 spanning the P(1)' Ala methyl group and the adjacent methylene carbon atom of the chain. Progressive truncation at the P(2)'-P(4)' sites led to a potent truncated analogue 5 with good selectivity over Cathepsin D. Using the same backbone replacement concept, a series of cyclopentane, cyclopentanone, tetrahydrofuran, pyrrolidine, and pyrrolidinone analogues were synthesized with considerable variation at the P and P' sites. The cyclopentanone and 2-pyrrolidinone analogues 45 and 57 showed low nM BACE inhibition. X-ray cocrystal structures of two analogues 5 and 45 revealed excellent convergence with the original inhibitor 1 structure while providing new insights into other interactions which could be exploited for future modifications.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amyloid Precursor Protein Secretases
  • Aspartic Acid Endopeptidases / antagonists & inhibitors*
  • Aspartic Acid Endopeptidases / chemistry
  • Binding Sites
  • Cathepsin D / antagonists & inhibitors
  • Crystallography, X-Ray
  • Cyclopentanes / chemical synthesis*
  • Cyclopentanes / chemistry
  • Endopeptidases
  • Furans / chemical synthesis*
  • Furans / chemistry
  • Humans
  • Models, Molecular
  • Molecular Mimicry
  • Peptides / chemistry*
  • Pyrrolidines / chemical synthesis*
  • Pyrrolidines / chemistry
  • Pyrrolidinones / chemical synthesis
  • Pyrrolidinones / chemistry
  • Structure-Activity Relationship

Substances

  • Cyclopentanes
  • Furans
  • Peptides
  • Pyrrolidines
  • Pyrrolidinones
  • Amyloid Precursor Protein Secretases
  • Endopeptidases
  • Aspartic Acid Endopeptidases
  • BACE1 protein, human
  • Cathepsin D