title: Small molecule regulation of protein conformation by binding in the Flap of HIV protease.
abstract: The fragment indole-6-carboxylic acid (1F1), previously identified as a flap site binder in a fragment-based screen against HIV protease (PR), has been cocrystallized with pepstatin-inhibited PR and with apo-PR. Another fragment, 3-indolepropionic acid (1F1-N), predicted by AutoDock calculations and confirmed in a novel inhibition of nucleation crystallization assay, exploits the same interactions in the flap site in two crystal structures. Both 1F1 and 1F1-N bind to the closed form of apo-PR and to pepstatin:PR. In solution, 1F1 and 1F1-N raise the Tm of apo-PR by 3.5-5 °C as assayed by differential scanning fluorimetry (DSF) and show equivalent low-micromolar binding constants to both apo-PR and pepstatin:PR, assayed by backscattering interferometry (BSI). The observed signal intensities in BSI are greater for each fragment upon binding to apo-PR than to pepstatin-bound PR, consistent with greater conformational change in the former binding event. Together, these data indicate that fragment binding in the flap site favors a closed conformation of HIV PR.
authors.affiliation: Deparatment of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute , 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States.
authors.forename: Theresa
authors.initials: T
authors.lastname: Tiefenbrunn
authors.forename: Stefano
authors.initials: S
authors.lastname: Forli
authors.forename: Michael M
authors.initials: MM
authors.lastname: Baksh
authors.forename: Max W
authors.initials: MW
authors.lastname: Chang
authors.forename: Meaghan
authors.initials: M
authors.lastname: Happer
authors.forename: Ying-Chuan
authors.initials: YC
authors.lastname: Lin
authors.forename: Alexander L
authors.initials: AL
authors.lastname: Perryman
authors.forename: Jin-Kyu
authors.initials: JK
authors.lastname: Rhee
authors.forename: Bruce E
authors.initials: BE
authors.lastname: Torbett
authors.forename: Arthur J
authors.initials: AJ
authors.lastname: Olson
authors.forename: John H
authors.initials: JH
authors.lastname: Elder
authors.forename: M G
authors.initials: MG
authors.lastname: Finn
authors.forename: C David
authors.initials: CD
authors.lastname: Stout
mesh_terms: D018360:Crystallography, X-Ray; D015658:HIV Infections / Q000188:drug therapy / Q000201:enzymology / Q000821:virology; D016333:HIV Protease / Q000737:chemistry* / Q000378:metabolism; D017320:HIV Protease Inhibitors / Q000737:chemistry* / Q000494:pharmacology*; D015497:HIV-1 / Q000187:drug effects / Q000201:enzymology*; D006801:Humans; D007211:Indoles / Q000737:chemistry / Q000494:pharmacology; D062105:Molecular Docking Simulation; D010436:Pepstatins / Q000737:chemistry / Q000494:pharmacology; D011422:Propionates / Q000737:chemistry / Q000494:pharmacology; D011487:Protein Conformation / Q000187:drug effects*
chemical_list: D017320:HIV Protease Inhibitors; D007211:Indoles; D010436:Pepstatins; D011422:Propionates; D016333:HIV Protease; C095446:3-(indol-3-yl)propionic acid; C031375:pepstatin
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