Fragment-based screen against HIV protease

Chem Biol Drug Des. 2010 Mar;75(3):257-68. doi: 10.1111/j.1747-0285.2009.00943.x. Epub 2010 Jan 19.


We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 A resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the 'exo site' adjacent to the Gly(16)Gly(17)Gln(18)loop where the amide of Gly(17)is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys(14)and Leu(63). Another fragment, indole-6-carboxylic acid, binds on the 'outside/top of the flap' via hydrophobic contacts with Trp(42), Pro(44), Met(46), and Lys(55), a hydrogen bond with Val(56), and a salt-bridge with Arg(57). 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Carboxylic Acids / chemistry
  • Carboxylic Acids / pharmacology
  • Catalytic Domain
  • Crystallography, X-Ray
  • Cyclohexanols / chemistry
  • Cyclohexanols / pharmacology
  • HIV Protease / chemistry*
  • HIV Protease / genetics
  • HIV Protease / metabolism
  • HIV Protease Inhibitors / chemistry*
  • HIV Protease Inhibitors / pharmacology
  • Humans
  • Hydrogen Bonding
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Thiophenes / chemistry
  • Thiophenes / pharmacology


  • Carboxylic Acids
  • Cyclohexanols
  • HIV Protease Inhibitors
  • Recombinant Proteins
  • Thiophenes
  • benzothiophene
  • HIV Protease