Small molecule regulation of protein conformation by binding in the flap of HIV protease

Theresa Tiefenbrunn; Stefano Forli; Michael M. Baksh; Max W. Chang; Meaghan Happer; Ying Chuan Lin; Alexander L. Perryman; Jin Kyu Rhee; Bruce E. Torbett; Arthur J. Olson; John H. Elder; M. G. Finn; C. David Stout

doi:10.1021/cb300611p

Small molecule regulation of protein conformation by binding in the flap of HIV protease

Theresa Tiefenbrunn, Stefano Forli, Michael M. Baksh, Max W. Chang, Meaghan Happer, Ying Chuan Lin, Alexander L. Perryman, Jin Kyu Rhee, Bruce E. Torbett, Arthur J. Olson, John H. Elder, M. G. Finn, C. David Stout

Department of Food Science & Biotechnology

Research output: Contribution to journal › Article › peer-review

30 Scopus citations

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 T_m 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.

Original language	English
Pages (from-to)	1223-1231
Number of pages	9
Journal	ACS Chemical Biology
Volume	8
Issue number	6
DOIs	https://doi.org/10.1021/cb300611p
State	Published - 21 Jun 2013

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@article{fa9a87f8b25c492cae397352af972840,

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.",

author = "Theresa Tiefenbrunn and Stefano Forli and Baksh, {Michael M.} and Chang, {Max W.} and Meaghan Happer and Lin, {Ying Chuan} and Perryman, {Alexander L.} and Rhee, {Jin Kyu} and Torbett, {Bruce E.} and Olson, {Arthur J.} and Elder, {John H.} and Finn, {M. G.} and Stout, {C. David}",

year = "2013",

month = jun,

day = "21",

doi = "10.1021/cb300611p",

language = "English",

volume = "8",

pages = "1223--1231",

journal = "ACS Chemical Biology",

issn = "1554-8929",

publisher = "American Chemical Society",

number = "6",

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T1 - Small molecule regulation of protein conformation by binding in the flap of HIV protease

AU - Tiefenbrunn, Theresa

AU - Forli, Stefano

AU - Baksh, Michael M.

AU - Chang, Max W.

AU - Happer, Meaghan

AU - Lin, Ying Chuan

AU - Perryman, Alexander L.

AU - Rhee, Jin Kyu

AU - Torbett, Bruce E.

AU - Olson, Arthur J.

AU - Elder, John H.

AU - Finn, M. G.

AU - Stout, C. David

PY - 2013/6/21

Y1 - 2013/6/21

N2 - 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.

AB - 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.

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Small molecule regulation of protein conformation by binding in the flap of HIV protease

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