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The structure of an HIV-1 specific cell entry inhibitor in complex with the HIV-1 gp41 trimeric core.

Zhou G, Ferrer M, Chopra R, Kapoor TM, Strassmaier T, Weissenhorn W, Skehel JJ, Oprian D, Schreiber SL, Harrison SC, Wiley DC
Bioorg Med Chem 8 2219-27 (2000)
Cited: 33 times
EuropePMC logo PMID: 11026535

Abstract

The three-dimensional structure of the complex between an HIV-1 cell-entry inhibitor selected from screening a combinatorial library of non-natural building blocks and the central, trimeric, coiled-coil core of HIV-1 gp41 has been determined by X-ray crystallography. The biased combinatorial library was designed to identify ligands binding in nonpolar pockets on the surface of the coiled-coil core of gp41. The crystal structure shows that the non-peptide moiety of the inhibitor binds to the targeted cavity in two different binding modes. This result suggests a strategy for increasing inhibitor potency by use of a second-generation combinatorial library designed to give simultaneous occupancy of both binding sites.

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  1. A human monoclonal antibody neutralizes diverse HIV-1 isolates by binding a critical gp41 epitope. Miller MD, Geleziunas R, Bianchi E, Lennard S, Hrin R, Zhang H, Lu M, An Z, Ingallinella P, Finotto M, Mattu M, Finnefrock AC, Bramhill D, Cook J, Eckert DM, Hampton R, Patel M, Jarantow S, Joyce J, Ciliberto G, Cortese R, Lu P, Strohl W, Schleif W, McElhaugh M, Lane S, Lloyd C, Lowe D, Osbourn J, Vaughan T, Emini E, Barbato G, Kim PS, Hazuda DJ, Shiver JW, Pessi A. Proc Natl Acad Sci U S A 102 14759-14764 (2005)
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  1. The structural biology of type I viral membrane fusion. Colman PM, Lawrence MC. Nat Rev Mol Cell Biol 4 309-319 (2003)
  2. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Mobley DL, Dill KA. Structure 17 489-498 (2009)
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  5. Development of Small-molecule HIV Entry Inhibitors Specifically Targeting gp120 or gp41. Lu L, Yu F, Cai L, Debnath AK, Jiang S. Curr Top Med Chem 16 1074-1090 (2016)
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  7. Progress in identifying peptides and small-molecule inhibitors targeted to gp41 of HIV-1. Debnath AK. Expert Opin Investig Drugs 15 465-478 (2006)
  8. Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7, and histone demethylases. Bellows ML, Floudas CA. Curr Drug Targets 11 264-278 (2010)
  9. Small-Molecule HIV Entry Inhibitors Targeting gp120 and gp41. Yu F, Jiang S. Adv Exp Med Biol 1366 27-43 (2022)

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  5. A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme. Lilien RH, Stevens BW, Anderson AC, Donald BR. J Comput Biol 12 740-761 (2005)
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  8. Structural characterization of respiratory syncytial virus fusion inhibitor escape mutants: homology model of the F protein and a syncytium formation assay. Morton CJ, Cameron R, Lawrence LJ, Lin B, Lowe M, Luttick A, Mason A, McKimm-Breschkin J, Parker MW, Ryan J, Smout M, Sullivan J, Tucker SP, Young PR. Virology 311 275-288 (2003)
  9. Non-peptide entry inhibitors of HIV-1 that target the gp41 coiled coil pocket. Stewart KD, Huth JR, Ng TI, McDaniel K, Hutchinson RN, Stoll VS, Mendoza RR, Matayoshi ED, Carrick R, Mo H, Severin J, Walter K, Richardson PL, Barrett LW, Meadows R, Anderson S, Kohlbrenner W, Maring C, Kempf DJ, Molla A, Olejniczak ET. Bioorg Med Chem Lett 20 612-617 (2010)
  10. Binding of antifusion peptides with HIVgp41 from molecular dynamics simulations: quantitative correlation with experiment. Strockbine B, Rizzo RC. Proteins 67 630-642 (2007)
  11. Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface. Green DF, Tidor B. Proteins 60 644-657 (2005)
  12. Evaluation of "credit card" libraries for inhibition of HIV-1 gp41 fusogenic core formation. Xu Y, Lu H, Kennedy JP, Yan X, McAllister LA, Yamamoto N, Moss JA, Boldt GE, Jiang S, Janda KD. J Comb Chem 8 531-539 (2006)
  13. Structural similarity between HIV-1 gp41 and SARS-CoV S2 proteins suggests an analogous membrane fusion mechanism. Wu Zhang X, Leng Yap Y. Theochem 677 73-76 (2004)
  14. Your personalized protein structure: Andrei N. Lupas fused to GCN4 adaptors. Deiss S, Hernandez Alvarez B, Bär K, Ewers CP, Coles M, Albrecht R, Hartmann MD. J Struct Biol 186 380-385 (2014)
  15. Identification of Echovirus 1 and coxsackievirus A9 receptor molecules via a novel flow cytometric quantification method. Triantafilou M, Wilson KM, Triantafilou K. Cytometry 43 279-289 (2001)
  16. Computer applications for prediction of protein-protein interactions and rational drug design. Grosdidier S, Totrov M, Fernández-Recio J. Adv Appl Bioinform Chem 2 101-123 (2009)
  17. Design and characterization of an engineered gp41 protein from human immunodeficiency virus-1 as a tool for drug discovery. Stewart KD, Steffy K, Harris K, Harlan JE, Stoll VS, Huth JR, Walter KA, Gramling-Evans E, Mendoza RR, Severin JM, Richardson PL, Barrett LW, Matayoshi ED, Swift KM, Betz SF, Muchmore SW, Kempf DJ, Molla A. J Comput Aided Mol Des 21 121-130 (2007)
  18. Efficient trapping of HIV-1 envelope protein by hetero-oligomerization with an N-helix chimera. Ou W, Silver J. Retrovirology 2 51 (2005)
  19. HIV-1 envelope accessible surface and polarity: clade, blood, and brain. Sowmya G, Shamini G, Anita S, Sakharkar M, Mathura V, Rodriguez H, Levine AJ, Singer E, Commins D, Somboonwit C, Sinnott JT, Sidhu HS, Rajaseger G, Pushparaj PN, Kangueane P, Shapshak P. Bioinformation 6 48-56 (2011)
  20. Ligand-K* Sequence Elimination: A Novel Algorithm for Ensemble-Based Redesign of Receptor-Ligand Binding. Shen, Tian H, Tang D, Yao W, Gao X. IEEE/ACM Trans Comput Biol Bioinform 11 573-578 (2014)


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