Crystallographic fragment-based drug discovery: Use of a brominated fragment library targeting HIV protease

Chemical Biology and Drug Design

Volumn 83, Issue 2, 2014, Pages 141-148

  Tiefenbrunn, Theresa ^a   Forli, Stefano ^a   Happer, Meaghan ^a   Gonzalez, Ana ^b   Tsai, Yingssu ^b,c   Soltis, Michael ^b   Elder, John H ^a   Olson, Arthur J ^a   Stout, Charles D ^a  

^a ILTAB   (United States)

^b SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

fragment binding; HIV protease; structure based drug design; X ray crystallography

Indexed keywords

2 NAPHTHOIC ACID DERIVATIVE; BENZOIC ACID DERIVATIVE; BROMINE DERIVATIVE; DIMETHYL SULFOXIDE; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE INHIBITOR;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; CRYSTALLIZATION; DRUG DESIGN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; WORKFLOW; X RAY CRYSTALLOGRAPHY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

FRAGMENT BINDING; HIV PROTEASE; STRUCTURE-BASED DRUG DESIGN; X-RAY CRYSTALLOGRAPHY;

ALLOSTERIC REGULATION; BINDING SITES; BROMINE; CRYSTALLOGRAPHY, X-RAY; DRUG EVALUATION, PRECLINICAL; HIV PROTEASE; HIV-1; HUMANS; HYDROXYBENZOATE ETHERS; MOLECULAR DOCKING SIMULATION; NAPHTHALENES; PROTEASE INHIBITORS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; SMALL MOLECULE LIBRARIES;

EID: 84892534600     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/cbdd.12227     Document Type: Article

References (16)

1. Bauman J.D., Patel D., Arnold E., (2011) Fragment screening and HIV therapeutics. Top Curr Chem; 317: 181-200.
2. Blaney J., Nienaber V., Burley S.K.,. (2006) Fragment-based Lead Discovery and Optimization Using X-Ray Crystallography, Computational Chemistry, and High-throughput Organic Synthesis. In:, Jahnke W., Erlanson D. A., editors. Fragment-Based Approaches in Drug Discovery. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA; p. 215-248.
3. Hardegger L.A., Kuhn B., Spinnler B., Anselm L., Ecabert R., Stihle M., Gsell B., Thoma R., Diez J., Benz J., Plancher J.-M., Hartmann G., Banner D.W., Haap W., Diederich F., (2011) Systematic investigation of halogen bonding in protein-ligand interactions. Angewandte Chemie Int Ed; 50: 314-318.
4. Wilcken R., Liu X., Zimmermann M.O., Rutherford T.J., Fersht A.R., Joerger A.C., Boeckler F.M., (2012) Halogen-enriched fragment libraries as leads for drug rescue of mutant p53. J Am Chem Soc; 134: 6810-6818.
5. Perryman A.L., Zhang Q., Soutter H.H., Rosenfeld R., McRee D.E., Olson A.J., Elder J.H., Stout C.D., (2010) Fragment-based screen against HIV protease. Chem Biol Drug Des; 75: 257-268.
6. Tiefenbrunn T., Forli S., Baksh M.M., Chang M.W., Happer M., Lin Y.-C., Perryman A.L., Rhee J.-K., Torbett B.E., Olson A.J., Elder J.H., Finn M.G., Stout C.D., et al,. (2013) Small molecule regulation of protein conformation by binding in the flap of HIV protease. ACS Chem Biol; 8: 1223-1231.
7. Lee T., Laco G.S., Torbett B.E., Fox H.S., Lerner D.L., Elder J.H., Wong C.H., et al,. (1998) Analysis of the S3 and S3′ subsite specificities of feline immunodeficiency virus (FIV) protease: development of a broad-based protease inhibitor efficacious against FIV, SIV, and HIV in vitro and ex vivo. Proc Natl Acad Sci USA; 95: 939-944.
8. Tsai Y., McPhillips S.E., Gonzalez A., McPhillips T.M., Zinn D., Cohen A.E., Feese M.D., Bushnell D., Tiefenbrunn T., Stout C.D., Ludaescher B., Hedman B., Hodgson K.O., Soltis S.M., et al,. (2013) AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery. Acta Crystallogr D Biol Crystallogr; 69: 796-803.
9. Kabsch W., (2010) Xds. Acta Crystallogr D Biol Crystallogr; 66: 125-132.
10. Kabsch W., (2010) Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr D Biol Crystallogr; 66: 133-144.
11. Collaborative (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr; 50: 760-763.
12. Read R.J., Schierbeek A.J., (1988) A phased translation function. J App Crystallogr; 21: 490-495.
13. Emsley P., Lohkamp B., Scott W.G., Cowtan K., (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr; 66: 486-501.
14. Murshudov G.N., Vagin A.A., Dodson E.J., (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr; 53: 240-255.
15. McRee D.E., (2004) Differential evolution for protein crystallographic optimizations. Acta Crystallogr D Biol Crystallogr; 60: 2276-2279.
16. McPhillips T.M., McPhillips S.E., Chiu H.J., Cohen A.E., Deacon A.M., Ellis P.J., Garman E., Gonzalez A., Sauter N.K., Phizackerley R.P., Soltis S.M., Kuhn P., et al,. (2002) Blu-Ice and the distributed control system: software for data acquisition and instrument control at macromolecular crystallography beamlines. J Synchrotron Radiat; 9: 401-406.