Paramagnetic relaxation assisted docking of a small indole compound in the HIV-1 gp41 hydrophobic pocket

ACS Chemical Biology

Volumn 6, Issue 3, 2011, Pages 267-274

  Gochin, Miriam ^a,b   Zhou, Guangyan ^a   Phillips, Aaron H ^a  

^a Touro University   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOXYLIC ACID; GLUTAMINE; GLYCOPROTEIN; GLYCOPROTEIN 41; INDOLE DERIVATIVE; LYSINE; PROTON; TRYPTOPHAN; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROGEN BOND; HYDROPHOBICITY; MAGNETISM; MOLECULAR DOCKING; NUCLEAR MAGNETIC RESONANCE; PARAMAGNETISM; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; STRUCTURE ANALYSIS;

ANTI-BACTERIAL AGENTS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; HIV ENVELOPE PROTEIN GP41; HIV-1; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; INDOLES; LIGANDS; MAGNETICS; MODELS, MOLECULAR; STRUCTURE-ACTIVITY RELATIONSHIP;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 79955639492     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb100368d     Document Type: Article

References (33)

1. Chan, D. C., Chutkowski, C. T., and Kim, P. S. (1998) Evidence that a prominent cavity in the coiled coil of HIV type 1 gp41 is an attractive drug target. Proc. Natl. Acad. Sci. U.SA. 95, 15613-15617. (Pubitemid 29018748)
2. Jiang, S., Lu, H., Liu, S., Zhao, Q., He, Y., and Debnath, A. K. (2004) N-Substituted pyrrole derivatives as novel human immunodeficiency virus type 1 entry inhibitors. Antimicrob. Agents Chemother. 48, 4349-4359.
3. Liu, S., Wu, S., and Jiang, S. (2007) HIV entry inhibitors targeting gp41: from polypeptides to small-molecule compounds. Curr. Pharm. Des. 13, 143-162. (Pubitemid 46085289)
4. Frey, G., Rits-Volloch, S., Zhang, X. Q., Schooley, R. T., Chen, B., and Harrison, S. C. (2006) Small molecules that bind the inner core of gp41 and inhibit HIV envelope-mediated fusion. Proc. Natl. Acad. Sci. U.SA. 103, 13938-13943. (Pubitemid 44452961)
5. Cai, L., and Gochin, M. (2007) A novel fluorescence intensity screening assay identifies new low molecular weight inhibitors of the gp41 coiled coil domain of HIV-1. Antimicrob. Agents Chemother. 51 , 2388-2395. (Pubitemid 47047315)
6. Wang, Y., Lu, H., Zhu, Q Jiang, S., and Liao, Y. (2010) Structure-based design, synthesis and biological evaluation of new N-carboxyphenylpyrrole derivatives as HIV fusion inhibitors targeting gp41. Bioorg. Med. Chem. Lett. 20, 189-192.
7. Katritzky, A. R., Tala, S. R., Lu, H., Vakulenko, A. V., Chen, Q.Y., Sivapackiam, J., Pandya, K., Jiang, S., and Debnath, A. K. (2009) Design, synthesis, and structure-activity relationship of a novel series of 2-aryl 5-(4-oxo-3-phenethyl-2-thioxothiazolidinylidenemethyl)furans as HIV-1 entry inhibitors. J. Med. Chem. 52, 7631-7639.
8. Teixeira, C., Barbault, F., Rebehmed, J., Liu, K., Xie, L., Lu, H., Jiang, S., Fan, B., and Maurel, F. (2008) Molecular modeling studies of N-substituted pyrrole derivatives-potential HIV-1 gp41 inhibitors. Bioorg. Med. Chem. 16, 3039-3048. (Pubitemid 351418201)
9. Zhou, G., Wu, D., Hermel, E., Balogh, E., and Gochin, M. (2010) Design, synthesis, and evaluation of indole compounds as novel inhibitors targeting Gp41. Bioorg. Med. Chem. Lett. 20, 1500-1503.
10. Berman, H., Henrick, K., and Nakamura, H. (2003) Announcing the worldwide Protein Data Bank (www.pdb.orgwww.pdb.org). Nat. Struct. Biol.10, 980. (Pubitemid 37500485)
11. Balogh, E., Wu, D., Zhou, G., and Gochin, M. (2009) NMR second site screening for structure determination of ligands bound in the hydrophobic pocket of HIV-1 gp41. J. Am. Chem. Soc. 131, 2821-2823.
12. Stewart, K. D., Huth, J. R., Ng, T. I., McDaniel, K., Hutchinson, R. N., Stoll, V. S., Mendoza, R. R., Matayoshi, E. D., Carrick, R., Mo, H., Severin, J., Walter, K., Richardson, P. L., Barrett, L. W., Meadows, R., Anderson, S., Kohlbrenner, W., Maring, C., Kempf, D. J., Molla, A., and Olejniczak, E. T. (2010) Non-peptide entry inhibitors of HIV-1 that target the gp41 coiled coil pocket. Bioorg. Med. Chem. Lett. 20, 612-617.
13. Gochin, M., Guy, R. K., and Case, M. A. (2003) A metallopeptide assembly of the HIV-1 gp41 coiled coil is an ideal receptor in fluorescence detection of ligand binding. Angew. Chem., Int. Ed. 42, 5325-5328. (Pubitemid 37462644)
14. Carr, H. Y., and Purcell, E. M. (1954) Effects of diffusion on free precession in nuclear magnetic resonance experiments. Phys. Rev. 94, 630-63894, 630-638.
15. Hoult, D. (1976) Solvent peak saturation with single phase and quadrature Fourier transformation. J. Magn. Reson. 21 , 337-347.
16. Meiboom, S., and Gill, D. (1958) Modified spin-echo method for measuring nuclear relaxation times. Rev. Sci. Instrum. 29, 688-691.
17. Mulder, F. A., Skrynnikov, N. R., Hon, B., Dahlquist, F. W., and Kay, L. E. (2001) Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme. J. Am. Chem. Soc. 123, 967-975. (Pubitemid 32151376)
18. Solomon, I., and Bloembergen, N. (1956) Nuclear magnetic interactions in the HF Molecule. J. Chem. Phys. 25, 261-266.
19. Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., and Olson, A. J. (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785-2791.
20. Trott, O., and Olson, A. J. (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31 , 455-461.
21. Schwieters, C. D., Kuszewski, J. J., Tjandra, N., and Clore, G. M. (2003) The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 160, 65-73.
22. Iwahara, J., Schwieters, C. D., and Clore, G. M. (2004) Ensemble approach for NMR structure refinement against (1)H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule. J. Am. Chem. Soc. 126, 5879-5896. (Pubitemid 38621427)
23. Springman, E. B., Celtaxis Inc, personal communication.
24. Welch, B. D., VanDemark, A. P., Heroux, A., Hill, C. P., and Kay, M. S. (2007) Potent D-peptide inhibitors of HIV-1 entry. Proc. Natl. Acad. Sci. U.SA. 104, 16828-16833. (Pubitemid 350210950)
25. Caffrey, M., Cai, M., Kaufman, J., Stahl, S. J., Wingfield, P. T., Covell, D. G., Gronenborn, A. M., and Clore, G. M. (1998) Three- dimensional solution structure of the 44 kDa ectodomain of SIV gp41. EMBO J. 17, 4572-4584. (Pubitemid 28377158)
26. Caffrey, M. (2001) Model for the structure of the HIV-1 gp41 ectodomain: insight into the intermolecular interactions of the gp41 loop. Biochim. Biophys. Acta 1536, 116-122. (Pubitemid 32530810)
27. Jahnke, W., Perez, L. B., Paris, C. G., Strauss, A., Fendrich, G., and Nalin, C. M. (2000) Second-site NMR screening with a spin-labeled first ligand. J. Am. Chem. Soc. 122, 7394-7395. (Pubitemid 30636731)
28. Vazquez, J., De, S. K., Chen, L. H., Riel-Mehan, M., Emdadi, A., Cellitti, J., Stebbins, J. L., Rega, M. F., and Pellecchia, M. (2008) Development ofparamagnetic probes for molecular recognition studies in protein kinases. J. Med. Chem. 51 , 3460-3465. (Pubitemid 351875002)
29. Yu, D., Volkov, A. N., and Tang, C. (2009) Characterizing dynamic protein-protein interactions using differentially scaled paramagnetic relaxation enhancement. J. Am. Chem. Soc. 131 , 17291-17297.
30. Liu, Y., Kahn, R. A., and Prestegard, J. H. (2010) Dynamic structure of membrane-anchored ArfGTP. Nat. Struct.Mol.Biol. 17, 876-881.
31. Volkov, A. N., Worrall, J. A., Holtzmann, E., and Ubbink, M. (2006) Solution structure and dynamics of the complex between cytochrome c and cytochrome c peroxidase determined byparamagnetic NMR. Proc. Natl. Acad. Sci. U.S.A. 103, 18945-18950. (Pubitemid 350002808)
32. He, Y., Liu, S., Jing, W., Lu, H., Cai, D., Chin, D. J., Debnath, A. K., Kirchhoff, F., and Jiang, S. (2007) Conserved residue Lys574 in the cavity of HIV-1 Gp41 coiled-coil domain is critical for six-helix bundle stability and virus entry. J. Biol. Chem. 282, 25631-25639. (Pubitemid 47372795)
33. Bermejo, G. A., Strub, M. P., Ho, C., and Tjandra, N. (2009) Determination of the solution-bound conformation of an amino acid binding protein by NMR paramagnetic relaxation enhancement: use ofa single flexible paramagnetic probe with improved estimation of its sampling space. J. Am. Chem. Soc. 131 , 9532-9537.