Computational design principles for bioactive dendrimer based constructs as antagonists of the TLR4-MD-2-LPS complex

Biomaterials

Volumn 32, Issue 33, 2011, Pages 8702-8711

  Barata, Teresa ^a,b   Teo, Ian ^a   Lalwani, Sanjiv ^c   Simanek, Eric ^c   Zloh, Mire ^b   Shaunak, Sunil ^a  

^a HAMMERSMITH HOSPITAL   (United Kingdom)

^b UNIVERSITY OF LONDON   (United Kingdom)

^c TEXAS CHRISTIAN UNIVERSITY   (United States)

Author keywords

Cytokines; Dendrimer; TLR4 MD 2 LPS complex; Triazine polyamidoamine

Indexed keywords

ACCELERATED DESIGN; CELL-SURFACE INTERACTIONS; CHEMICAL ENTITY; CHEMICAL SPECIES; COMPUTATIONAL DESIGN; COMPUTER AIDED; CYTOKINES; DESIGN PRINCIPLES; GLYCOSYLATED; LIPOPOLYSACCHARIDES; LOW COSTS; MALIGNANT DISEASE; PAMAM DENDRIMER; POLYAMIDOAMINE DENDRIMERS; POLYAMIDOAMINES; RABBIT MODELS; TLR4-MD-2-LPS COMPLEX; TOLL-LIKE RECEPTOR 4; WOUND HEALING;

CELL MEMBRANES; POLYDISPERSITY; STRUCTURAL DESIGN; SYNTHESIS (CHEMICAL); TISSUE;

DENDRIMERS;

BACTERIUM LIPOPOLYSACCHARIDE; DENDRIMER; GLUCOSAMINE; POLYAMIDOAMINE; TOLL LIKE RECEPTOR 4; TRIAZINE;

ARTICLE; BIOLOGICAL ACTIVITY; COMPUTER AIDED DESIGN; CONTROLLED STUDY; DENSITY; HUMAN; HUMAN CELL; HYDROPHILICITY; MOLECULAR MODEL; MOLECULAR STABILITY; PRIORITY JOURNAL; STATIC ELECTRICITY;

ANIMALS; BIOCOMPATIBLE MATERIALS; CICATRIX; DENDRIMERS; DISEASE MODELS, ANIMAL; LIPOPOLYSACCHARIDES; LYMPHOCYTE ANTIGEN 96; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; RABBITS; TOLL-LIKE RECEPTOR 4;

BACTERIA (MICROORGANISMS); ORYCTOLAGUS CUNICULUS;

EID: 80052967040     PISSN: 01429612     EISSN: 18785905     Source Type: Journal    
DOI: 10.1016/j.biomaterials.2011.07.085     Document Type: Article

References (30)

1. Tomalia D.A., Baker H., Dewald J., Hall M., Kallos G., Martin S., et al. A new class of polymers - Starburst-dendritic macromolecules. Polym J 1985, 17:117-132.
2. Krasteva N., Besnard I., Guse B., Bauer R.E., Mallen K., Yasuda A., et al. Self-assembled gold nanoparticle/dendrimer composite films for vapor sensing applications. Nano Lett 2002, 2:551-555.
3. Stiriba S.E., Frey H., Haag R. Dendritic polymers in biomedical applications: from potential to clinical use in diagnostics and therapy. Angew Chem Int Ed Engl 2002, 41:1329-1334.
4. Ribourdouille Y., Engel G.D., Richard-Plouet M., Gade L.H. A strongly positive dendrimer effect in asymmetric catalysis: allylic aminations with pyrphos-palladium functionalised PPI and PAMAM dendrimers. Chem Commun (Camb) 2003, 11:1228-1229.
5. Astruc D., Boisselier E., Ornelas C. Dendrimers designed for functions: from physical, photophysical, and supramolecular properties to applications in sensing, catalysis, molecular electronics, photonics, and nanomedicine. Chem Rev 2010, 110:1857-1959.
6. Shaunak S., Thomas S., Gianasi E., Godwin A., Jones E., Teo I., et al. Polyvalent dendrimer glucosamine conjugates prevent scar tissue formation. Nat Biotechnol 2004, 22:977-984.
7. Kim J.I., Lee C.J., Jin M.S., Lee C.H., Paik S.G., Lee H., et al. Crystal structure of CD14 and its implications for LPS signaling. J Biol Chem 2005, 280:11347-11351.
8. Kim H.M., Park B.S., Kim J.I., Kim S.E., Lee J., Oh S.C., et al. Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist eritoran. Cell 2007, 130:906-917.
9. Park B.S., Song D.H., Kim H.M., Choi B.S., Lee H., Lee J.O. The structural basis of LPS recognition by the TLR4-MD-2 complex. Nature 2009, 458:1191-1195.
10. Meng J., Lien E., Golenbock D.T. MD-2-mediated ionic interactions between lipid A and TLR4 are essential for receptor activation. J Biol Chem 2010, 285:8695-8702.
11. Barata T.S., Teo I., Brocchini S., Zloh M., Shaunak S. Partially glycosylated dendrimers block MD-2 and prevent TLR4-MD-2-LPS complex mediated cytokine responses. PLoS Comput Biol 2011, 7(6):e1002095. 10.1371/journal.pcbi.1002095.
12. Esfand R., Tomalia D.A. Poly(amidoamine) (PAMAM) dendrimers: from biomimicry to drug delivery and biomedical applications. Drug Discov Today 2001, 6:427-436.
13. Chouai A., Simanek E.E. Kilogram-scale synthesis of a second-generation dendrimer based on 1,3,5-triazine using green and industrially compatible methods with a single chromatographic step. J Org Chem 2008, 73:2357-2366.
14. Lalwani S., Chouai A., Perez L.M., Santiago V., Shaunak S., Simanek E.E. Mimicking PAMAM dendrimers with amphoteric, hybrid triazine dendrimers: a comparison of dispersity and stability. Macromolecules 2009, 42:6723-6732.
15. Lalwani S., Venditto V.J., Chouai A., Rivera G.E., Shaunak S., Simanek E.E. Electrophoretic behavior of anionic triazine and PAMAM dendrimers: methods for improving resolution and assessing purity using capillary electrophoresis. Macromolecules 2009, 42:3152-3161.
16. Barata TS, Brocchini S, Teo I, Shaunak S, Zloh M. From sequence to 3D structure of hyperbranched molecules: application to surface modified PAMAM dendrimers. J Mol Model doi:10.1007/s00894-011-0966-y.
17. Barata T.S., Shaunak S., Teo I., Zloh M., Brocchini S. Structural studies of biologically active glycosylated polyamidoamine (PAMAM) dendrimers. J Mol Model 2011, 17:2051-2060.
18. Halgren T.A., Nachbar R.B. MMF94: the Merck molecular force field. Bridging the gap - From small organics to proteins. Abstr papers Am Chem Soc 1996, 211:70.
19. Fariborz M., Nigel G.J.R., Wayne C.G., Rob L., Mark L., Craig C., et al. Macromodel - an integrated software system for modelling organic and bioorganic molecules using molecular mechanics. J Comput Chem 1990, 11:440-467.
20. Jorgensen W.L., Tirado-Rives J. Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proc Natl Acad Sci 2005, 102:6665-6670.
21. Still W.C., Tempczyk A., Hawley R.C., Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 2002, 112:6127-6129.
22. Zloh M., Shaunak S., Balan S., Brocchini S. Identification and insertion of 3-carbon bridges in protein disulfide bonds: a computational approach. Nat Protoc 2007, 2:1070-1083.
23. Levy R.M., Gallicchio E. Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modelling electrostatic effects. Annu Rev Phys Chem 2003, 49:531-567.
24. Pedretti A., Villa L., Vistoli G. VEGA - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. J Comput Aided Mol Des 2004, 18:167-173.
25. Islam M.T., Shi X., Balogh L., Baker J.R. HPLC separation of different generations of PAMAM dendrimers modified with various terminal groups. Anal Chem 2005, 77:2063-2070.
26. Shaunak S., Godwin A., Choi J.W., Balan S., Pedone E., Vijayarangam D., et al. Site-specific PEGylation of native disulfide bonds in therapeutic proteins. Nat Chem Biol 2006, 2:312-313.
27. Brocchini S., Balan S., Godwin A., Choi J.W., Zloh M., Shaunak S. PEGylation of native disulfide bonds in proteins. Nat Protoc 2006, 1:2241-2252.
28. Balan S., Choi J.W., Godwin A., Teo I., Laborde C.M., Heidelberger S., et al. Site-specific PEGylation of protein disulfide bonds using a three-carbon bridge. Bioconjug Chem 2007, 18:61-76.
29. Choe J., Kelker M.S., Wilson I.A. Crystal structure of human TLR3 ectodomain. Science 2005, 309:581-585.
30. Jin M.S., Kim S.E., Heo J.Y., Lee M.E., Kim H.M., Paik S.G., et al. Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide. Cell 2007, 130:1071-1082.