title: Fragment-based screen against HIV protease.
abstract: 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.
authors.affiliation: Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
authors.forename: Alexander L
authors.initials: AL
authors.lastname: Perryman
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhang
authors.forename: Holly H
authors.initials: HH
authors.lastname: Soutter
authors.forename: Robin
authors.initials: R
authors.lastname: Rosenfeld
authors.forename: Duncan E
authors.initials: DE
authors.lastname: McRee
authors.forename: Arthur J
authors.initials: AJ
authors.lastname: Olson
authors.forename: John E
authors.initials: JE
authors.lastname: Elder
authors.forename: C David
authors.initials: CD
authors.lastname: Stout
mesh_terms: D001665:Binding Sites; D002264:Carboxylic Acids / Q000737:chemistry / Q000494:pharmacology; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003511:Cyclohexanols / Q000737:chemistry / Q000494:pharmacology; D016333:HIV Protease / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017320:HIV Protease Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D006801:Humans; D006860:Hydrogen Bonding; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013876:Thiophenes / Q000737:chemistry / Q000494:pharmacology
chemical_list: D002264:Carboxylic Acids; D003511:Cyclohexanols; D017320:HIV Protease Inhibitors; D011994:Recombinant Proteins; D013876:Thiophenes; C088015:benzothiophene; D016333:HIV Protease