ACS Publications. Most Trusted. Most Cited. Most Read
My Activity

Small Molecule Regulation of Protein Conformation by Binding in the Flap of HIV Protease

View Author Information
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
*(T.T.) Phone: 858-784-2110. Fax: 858-784-2857. E-mail: [email protected]
Cite this: ACS Chem. Biol. 2013, 8, 6, 1223–1231
Publication Date (Web):March 29, 2013
Copyright © 2013 American Chemical Society

    Article Views





    Read OnlinePDF (1 MB)
    Supporting Info (1)»


    Abstract Image

    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.

    Supporting Information

    Jump To

    Refinement statistics, chemical structures, rmsd comparisons, AutoDock binding modes, FRET-based inhibition results, electron density. This material is available free of charge via the Internet at

    Accession Codes

    Coordinates and structure factors have been deposited in the Protein Data Bank with accession numbers 4EJ8, 4EJD, 4EJK, and 4EJL.

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system:

    Cited By

    This article is cited by 28 publications.

    1. Zhihui Zhang, Michael M. Baksh, M. G. Finn, David K. Heidary, and Christopher I. Richards . Direct Measurement of Trafficking of the Cystic Fibrosis Transmembrane Conductance Regulator to the Cell Surface and Binding to a Chemical Chaperone. Biochemistry 2017, 56 (1) , 240-249.
    2. Peng Zhan, Christophe Pannecouque, Erik De Clercq, and Xinyong Liu . Anti-HIV Drug Discovery and Development: Current Innovations and Future Trends. Journal of Medicinal Chemistry 2016, 59 (7) , 2849-2878.
    3. Magdalena Korczynska, Daniel D. Le, Noah Younger, Elisabet Gregori-Puigjané, Anthony Tumber, Tobias Krojer, Srikannathasan Velupillai, Carina Gileadi, Radosław P. Nowak, Eriko Iwasa, Samuel B. Pollock, Idelisse Ortiz Torres, Udo Oppermann, Brian K. Shoichet, and Danica Galonić Fujimori . Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. Journal of Medicinal Chemistry 2016, 59 (4) , 1580-1598.
    4. Nanjie Deng, Stefano Forli, Peng He, Alex Perryman, Lauren Wickstrom, R. S. K. Vijayan, Theresa Tiefenbrunn, David Stout, Emilio Gallicchio, Arthur J. Olson, and Ronald M. Levy . Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease. The Journal of Physical Chemistry B 2015, 119 (3) , 976-988.
    5. Hisham M. Dokainish, Yuji Sugita. Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling. International Journal of Molecular Sciences 2021, 22 (1) , 270.
    6. Dean Sherry, Roland Worth, Yasien Sayed. Elasticity-Associated Functionality and Inhibition of the HIV Protease. 2021, 79-108.
    7. David S. Goodsell, Michel F. Sanner, Arthur J. Olson, Stefano Forli. The AutoDock suite at 30. Protein Science 2021, 30 (1) , 31-43.
    8. Thomas R. Weikl, Bahram Hemmateenejad. Accessory mutations balance the marginal stability of the HIV‐1 protease in drug resistance. Proteins: Structure, Function, and Bioinformatics 2020, 88 (3) , 476-484.
    9. Zahara Khanjiwala, Anubha Khale, Arati Prabhu. Docking structurally similar analogues: Dealing with the false-positive. Journal of Molecular Graphics and Modelling 2019, 93 , 107451.
    10. Michael Kammer, Amanda Kussrow, Melissa D. Carter, Samantha L. Isenberg, Rudolph C. Johnson, Robert H. Batchelor, George W. Jackson, Darryl J. Bornhop. Rapid quantification of two chemical nerve agent metabolites in serum. Biosensors and Bioelectronics 2019, 131 , 119-127.
    11. Adriano Luchi, Emilio Angelina, Lucrecia Bogado, Stefano Forli, Arthur Olson, Nélida Peruchena. Flap‐site Fragment Restores Back Wild‐type Behaviour in Resistant Form of HIV Protease. Molecular Informatics 2018, 37 (12)
    12. Sergio M. Marques, Lukas Daniel, Tomas Buryska, Zbynek Prokop, Jan Brezovsky, Jiri Damborsky. Enzyme Tunnels and Gates As Relevant Targets in Drug Design. Medicinal Research Reviews 2017, 37 (5) , 1095-1139.
    13. Michael M. Baksh, M.G. Finn. An experimental check of backscattering interferometry. Sensors and Actuators B: Chemical 2017, 243 , 977-981.
    14. Xian-Mei Meng, Wei-Jun Hu, Yu-Guang Mu, Xie-Huang Sheng. Effect of allosteric molecules on structure and drug affinity of HIV-1 protease by molecular dynamics simulations. Journal of Molecular Graphics and Modelling 2016, 70 , 153-162.
    15. Darryl J. Bornhop, Michael N. Kammer, Amanda Kussrow, Robert A. Flowers. Reply to Varma: Elucidation of the signal origin for label-free, free-solution interactions. Proceedings of the National Academy of Sciences 2016, 113 (34)
    16. Dimitrios Xanthopoulos, Eftichia Kritsi, Claudiu T. Supuran, Manthos G. Papadopoulos, Georgios Leonis, Panagiotis Zoumpoulakis. Discovery of HIV Type 1 Aspartic Protease Hit Compounds through Combined Computational Approaches. ChemMedChem 2016, 11 (15) , 1646-1652.
    17. Rosemberg O. Soares, Pedro H.M. Torres, Manuela L. da Silva, Pedro G. Pascutti. Unraveling HIV protease flaps dynamics by Constant pH Molecular Dynamics simulations. Journal of Structural Biology 2016, 195 (2) , 216-226.
    18. Lauren Wickstrom, Nanjie Deng, Peng He, Ahmet Mentes, Crystal Nguyen, Michael K. Gilson, Tom Kurtzman, Emilio Gallicchio, Ronald M. Levy. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data. Journal of Molecular Recognition 2016, 29 (1) , 10-21.
    19. Peter M. U. Ung, Phani Ghanakota, Sarah E. Graham, Katrina W. Lexa, Heather A. Carlson. Identifying binding hot spots on protein surfaces by mixed‐solvent molecular dynamics: HIV‐1 protease as a test case. Biopolymers 2016, 105 (1) , 21-34.
    20. Boshi Huang, Dongwei Kang, Peng Zhan, Xinyong Liu. Fragment-based approaches to anti-HIV drug discovery: state of the art and future opportunities. Expert Opinion on Drug Discovery 2015, 10 (12) , 1271-1281.
    21. Stefano Forli. Charting a Path to Success in Virtual Screening. Molecules 2015, 20 (10) , 18732-18758.
    22. Stefano Forli, Arthur J. Olson. Computational Challenges of Structure-Based Approaches Applied to HIV. 2015, 31-51.
    23. Theresa Tiefenbrunn, C. David Stout. Towards novel therapeutics for HIV through fragment-based screening and drug design. Progress in Biophysics and Molecular Biology 2014, 116 (2-3) , 124-140.
    24. Yu-ming M. Huang, Myungshim Kang, Chia-en A. Chang. Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics. Journal of Molecular Recognition 2014, 27 (9) , 537-548.
    25. Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Diogo Santos-Martins, Arthur J. Olson. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein–ligand binding challenge. Journal of Computer-Aided Molecular Design 2014, 28 (4) , 429-441.
    26. Theresa Tiefenbrunn, Stefano Forli, Meaghan Happer, Ana Gonzalez, Yingssu Tsai, Michael Soltis, John H. Elder, Arthur J. Olson, Charles D. Stout. Crystallographic Fragment-Based Drug Discovery: Use of a Brominated Fragment Library Targeting HIV Protease. Chemical Biology & Drug Design 2014, 83 (2) , 141-148.
    27. Dongwei Kang, Yu'ning Song, Wenmin Chen, Peng Zhan, Xinyong Liu. “Old Dogs with New Tricks”: exploiting alternative mechanisms of action and new drug design strategies for clinically validated HIV targets. Molecular BioSystems 2014, 10 (8) , 1998.
    28. Róisín M. McMahon, Martin J. Scanlon, Jennifer L. Martin. Interrogating Fragments Using a Protein Thermal Shift Assay. Australian Journal of Chemistry 2013, 66 (12) , 1502.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Your Mendeley pairing has expired. Please reconnect