References
- Barre-Sinoussi F, Chermann JC, Rey F, et al. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Rev Invest Clin 2004;56:126–9
- Gallo RC, Salahuddin SZ, Popovic M, et al. Frequent detection and isolation of cytopathic retroviruses (HTLV-III) from patients with AIDS and at risk for AIDS. Science 1984;224:500–3
- Choe H, Farzan M, Sun Y, et al. The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell 1996;85:1135–48
- Dalgleish AG, Beverley PCL, Clapham PR, et al. The CD4 (T4) Antigen is an essential component of the receptor for the AIDS retrovirus. Nature 1984;312:763–7
- Furuta RA, Wild CT, Weng YK, Weiss CD. Capture of an early fusion-active conformation of HIV-1 gp41 (vol 5, pg 276, 1998). Nat Struct Biol 1998;5:612
- He Y, Vassell R, Zaitseva M, et al. Peptides trap the human immunodeficiency virus type 1 envelope glycoprotein fusion intermediate at two sites. J Virol 2003;77:1666–71
- Pancera M, Zhou T, Druz A, et al. Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature 2014;514:455
- LaLonde JM, Kwon YD, Jones DM, et al. Structure-based design, synthesis, and characterization of dual hotspot small-molecule HIV-1 entry inhibitors. J Med Chem 2012;55:4382–96
- Madani N, Schoen A, Princiotto AM, et al. Small-molecule CD4 mimics interact with a highly conserved pocket on HIV-1 gp120. Structure 2008;16:1689–701
- Si ZH, Madani N, Cox JM, et al. Small-molecule inhibitors of HIV-1 entry block receptor-induced conformational changes in the viral envelope glycoproteins. Proc Natl Acad Sci USA 2004;101:5036–41
- Regueiro-Ren A, Xue QM, Swidorski JJ, et al. Inhibitors of human immunodeficiency virus type 1 (HIV-1) attachment. 12. Structure–activity relationships associated with 4-fluoro-6-azaindole derivatives leading to the identification of 1-(4-benzoylpiperazin-1-yl)-2-(4-fluoro-7-1,2,3 triazol-1-yl-1H-pyrrolo 2,3-c pyridin-3-yl)ethane-1,2-dione (BMS-585248). J Med Chem 2013;56:1656–69
- Lin PF, Blair W, Wang T, et al. A small molecule HIV-1 inhibitor that targets the HIV-1 envelope and inhibits CD4 receptor binding. Proc Natl Acad Sci USA 2003;100:11013–18
- Zhao Q, Ma LY, Jiang SB, et al. N-phenyl-N′-(2,2,6,6-tetramethyl-piperidin-4-yl)-oxalamides as a new class of HIV-1 entry inhibitors that prevent gp120 binding to CD4. Virology 2005;339:213–25
- Guttman M, Garcia NK, Cupo A, et al. CD4-induced activation in a soluble HIV-1 Env trimer. Structure 2014;22:974–84
- Hoffman TL, LaBranche CC, Zhang W, et al. Stable exposure of the coreceptor-binding site in a CD4-independent HIV-1 envelope protein. Proc Natl Acad Sci 1999;96:6359–64
- Herschhorn A, Gu C, Espy N, et al. A broad HIV-1 inhibitor blocks envelope glycoprotein transitions critical for entry. Nat Chem Biol 2014;10:U845–89
- Kwon YD, Finzi A, Wu X, et al. Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops. Proc Natl Acad Sci USA 2012;109:5663–8
- Munro JB, Gorman J, Ma X, et al. Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions. Science 2014;346:759–63
- Shrivastava IH, Wendel K, LaLonde JM. Spontaneous rearrangement of the beta20/beta21 strands in simulations of. Biochemistry 2012;51:7783–93
- Shrivastava I, LaLonde JM. Enhanced dynamics of HIV gp120 glycoprotein by small molecule binding. Biochemistry 2011;50:4173–83
- Korkut A, Hendrickson WA. Structural plasticity and conformational transitions of HIV envelope glycoprotein gp120. PLoS One 2012;7:e52170
- Sang P, Yang L-Q, Ji X-L, et al. Insight derived from molecular dynamics simulations into molecular motions, thermodynamics and kinetics of HIV-1 gp120. PLoS One 2014;9:e104714
- Rusert P, Krarup A, Magnus C, et al. Interaction of the gp120 V1V2 loop with a neighboring gp120 unit shields the HIV envelope trimer against cross-neutralizing antibodies. J Exp Med 2011;208:1419–33
- Hanwell MD, Curtis DE, Lonie DC, et al. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform 2012;4:17
- Deshpande N, Addess KJ, Bluhm WF, et al. The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res 2005;33:D233–7
- Pettersen EF, Goddard TD, Huang CC, et al. UCSF chimera – a visualization system for exploratory research and analysis. J Comput Chem 2004;25:1605–12
- Morris GM, Huey R, Lindstrom W, et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 2009;30:2785–91
- Dundas J, Ouyang Z, Tseng J, et al. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 2006;34:W116–8
- Fuhrmann J, Rurainski A, Lenhof HP, Neumann D. A new Lamarckian genetic algorithm for flexible ligand–receptor docking. J Compu Chem 2010;31:1911–18
- Wallace AC, Laskowski RA, Thornton JM. Ligplot – a program to generate schematic diagrams of protein ligand interactions. Protein Eng 1995;8:127–34
- Kwon YD, LaLonde JM, Yang Y, et al. Crystal structures of HIV-1 gp120 envelope glycoprotein in complex with NBD analogues that target the CD4-binding site. PLoS One 2014;9:e85940
- Case DA, Babin V, Berryman JT, et al. AMBER 14. San Francisco (CA): University of California; 2014
- Krautler V, Van Gunsteren WF, Hunenberger PH. A fast SHAKE: algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. J Comput Chem 2001;22:501–8
- Wu XW, Brooks BR. Self-guided Langevin dynamics simulation method. Chem Phys Lett 2003;381:512–18
- Bakan A, Meireles LM, Bahar I. ProDy: protein dynamics inferred from theory and experiments. Bioinformatics 2011;27:1575–7
- Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:33–8