Fragment-Based Screen against HIV Protease

Authors

  • Alexander L. Perryman,

    1. Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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  • Qing Zhang,

    1. Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
    2. GlaxoSmithKline, R&D China, Building 3, 898 Halei Rd., Zhangjiang Hi-Tech Park, Pudong, Shanghai, China
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  • Holly H. Soutter,

    1. Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
    2. Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA
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  • Robin Rosenfeld,

    1. Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
    2. Active Sight, 11494 Sorrento Valley Road, San Diego, CA 92121, USA
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  • Duncan E. McRee,

    1. Active Sight, 11494 Sorrento Valley Road, San Diego, CA 92121, USA
    2. Sorrento Technologies, 4541 Hidalgo Ave., San Diego, CA 92117, USA
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  • Arthur J. Olson,

    1. Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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  • John E. Elder,

    1. Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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  • C. David Stout

    Corresponding author
    1. Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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  • Data Deposition: Atomic co-ordinates and structure factors have been deposited with the Protein Data Bank (http://www.rcsb.org) for six structures listed in Table 3 (PDB codes 3KF1, 3KF0, 3KFN, 3KFP, 3KFR, and 3KFS).

* Corresponding author: C. David Stout, dave@scripps.edu

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 Å 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 Gly16Gly17Gln18loop where the amide of Gly17is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys14and Leu63. Another fragment, indole-6-carboxylic acid, binds on the ‘outside/top of the flap’ via hydrophobic contacts with Trp42, Pro44, Met46, and Lys55, a hydrogen bond with Val56, and a salt-bridge with Arg57. 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.

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