A Symmetric Inhibitor Binds HIV-1 Protease Asymmetrically

Biochemistry. 1993 Jan 26;32(3):937-47. doi: 10.1021/bi00054a027.


Potential advantages of C2-symmetric inhibitors designed for the symmetric HIV-1 protease include high selectivity, potency, stability, and bioavailability. Pseudo-C2-symmetric monools and C2-symmetric diols, containing central hydroxymethylene and (R,R)-dihydroxyethylene moieties flanked by a variety of hydrophobic P1/P1' side chains, were studied as HIV-1 protease inhibitors. The monools and diols were synthesized in 8-10 steps from D-(+)-arabitol and D-(+)-mannitol, respectively. Monools with ethyl or isobutyl P1/P1' side chains were weak inhibitors of recombinant HIV-1 protease (Ki > 10 microM), while benzyl P1/P1' side chains afforded a moderately potent inhibitor (apparent Ki = 230 nM). Diols were 100-10,000x more potent than analogous monools, and a wider range of P1/P1' side chains led to potent inhibition. Both classes of compounds exhibited lower apparent Ki values under high-salt conditions. Surprisingly, monool and diol HIV-1 protease inhibitors were potent inhibitors of porcine pepsin, a prototypical asymmetric monomeric aspartic protease. These results were evaluated in the context of the pseudosymmetric structure of monomeric aspartic proteases and their evolutionary kinship with the retroviral proteases. The X-ray crystal structure of HIV-1 protease complexed with a symmetric diol was determined at 2.6 A. Contrary to expectations, the diol binds the protease asymmetrically and exhibits 2-fold disorder in the electron density map. Molecular dynamics simulations were conducted beginning with asymmetric and symmetric HIV-1 protease/inhibitor model complexes. A more stable trajectory resulted from the asymmetric complex, in agreement with the observed asymmetric binding mode. A simple four-point model was used to argue more generally that van der Waals and electrostatic force fields can commonly lead to an asymmetric association between symmetric molecules.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Alcohols / chemistry
  • Alcohols / metabolism
  • Dipeptides / chemical synthesis
  • Dipeptides / chemistry
  • Dipeptides / metabolism
  • Dipeptides / pharmacology*
  • Glycols / chemical synthesis
  • Glycols / metabolism
  • Glycols / pharmacology*
  • HIV Protease / drug effects*
  • HIV Protease / metabolism
  • HIV Protease Inhibitors / chemical synthesis
  • HIV Protease Inhibitors / metabolism
  • HIV Protease Inhibitors / pharmacology*
  • HIV-1 / enzymology*
  • Hydrogen Bonding
  • Models, Molecular
  • Pepsin A / antagonists & inhibitors
  • Protein Conformation
  • Recombinant Proteins / metabolism
  • Sensitivity and Specificity
  • Structure-Activity Relationship


  • Alcohols
  • Dipeptides
  • Glycols
  • HIV Protease Inhibitors
  • Recombinant Proteins
  • SK&F 108361
  • phenylalanylphenylalanine
  • HIV Protease
  • Pepsin A