Coarse-grained modeling study of nonpeptide RGD ligand density and PEG molecular weight on the conformation of poly(γ-glutamyl-glutamate) paclitaxel conjugates

Journal of Molecular Modeling

Volumn 17, Issue 11, 2011, Pages 2973-2987

  Peng, Lili X ^a   Das, Sanjib K ^b   Yu, Lei ^b   Howell, Stephen B ^c   Gough, David A ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b Biomedical Group   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Active targeting; Coarse grained modeling; Nonpeptide RGD; Paclitaxel; Poly(ethylene glycol); Polymer

Indexed keywords

MACROGOL 10000; MACROGOL 2000; PACLITAXEL; POLY(GAMMA GLUTAMYL GLUTAMATE) PACLITAXEL POLY(ETHYLENE GLYGLYCOL) NONPEPTIDE RGD; POLYETHYLENE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; DENSITY GRADIENT; DRUG DELIVERY SYSTEM; DRUG FORMULATION; HYDROPHILICITY; MOLECULAR DYNAMICS; MOLECULAR WEIGHT; PRIORITY JOURNAL; SURFACE PROPERTY;

CIRCULAR DICHROISM; DIPEPTIDES; GLUTAMATES; LIGANDS; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR WEIGHT; PACLITAXEL; PARTICLE SIZE; POLYETHYLENE GLYCOLS; POLYMERS; PROTEINS;

EID: 80255131078     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-0989-4     Document Type: Article

References (41)

1. M Ferrari 2005 Cancer nanotechnology: opportunities and challenges Nat Rev Cancer 5 161 171 10.1038/nrc1566 1:CAS:528:DC%2BD2MXhslSnt7o%3D (Pubitemid 40314948)
2. Amiji MM (2007) Nanotechnology for cancer therapy. CRC, Boca Raton
3. R Satchi-Fainaro M Puder JW Davies HT Tran DA Sampson AK Greene G Corfas J Folkman 2004 Targeting angiogenesis with a conjugate of HPMA copolymer and TNP-470 Nat Med 10 225 261 10.1038/nm1002 (Pubitemid 38667615)
4. RJ Kok AJ Schraa EJ Bos HE Moorlag SA Asgeirsdottir M Everts DKF Meijer G Molema 2002 Preparation and functional evaluation of RGD-modified proteins as αVβ3 integrin directed therapeutics Bioconjug Chem 13 128 135 10.1021/bc015561+ 1:CAS:528:DC%2BD3MXos12it7c%3D (Pubitemid 34119644)
5. X Chen C Plasencia Y Hou N Neamati 2005 Synthesis and biological evaluation of dimeric RGD peptide-paclitaxel conjugate as a model for integrin-targeted drug delivery J Med Chem 48 1098 1106 10.1021/jm049165z 1:CAS:528:DC%2BD2MXntFKjtg%3D%3D (Pubitemid 40270453)
6. M Lorger JS Kreuger M O'Neal K Staflin B Felding-Habermann 2009 Activation of tumor cell integrin αVβ3 controls angiogenesis and metastatic growth in the brain Proc Natl Acad Sci USA 106 10666 10671 10.1073/pnas.0903035106 1:CAS:528:DC%2BD1MXos1Sks7c%3D
7. K Temming RM Schiffelers G Molem RJ Kok 2005 RGD-based strategies for selective delivery of therapeutics and imaging agents to the tumour vasculature Drug Resist Updat 8 381 402 10.1016/j.drup.2005.10.002 1:CAS:528: DC%2BD28Xit1Crsr4%3D (Pubitemid 43358061)
8. F Danhier B Vroman N Lecouturier N Crokart V Pourcelle H Freichels C Jérôme J Marchand-Brynaert O Feron V Préat, et al. 2009 Targeting of tumor endothelium by RGD-grafted PLGA-nanoparticles loaded with paclitaxel J Control Release 2 166 173 10.1016/j.jconrel.2009.08.011
9. E Bourguet JL Banères J Parello X Lusinchi JP Girard JP Vidal 2003 Nonpeptide RGD antagonists: a novel class of mimetics, the 5, 8-disubstituted 1-azabicyclo[5.2.0]nonan-2-one Lactam Bioorg Med Chem Lett 13 1561 1564 10.1016/S0960-894X(03)00181-1 1:CAS:528:DC%2BD3sXivFels7g%3D (Pubitemid 36428560)
10. Wang X, Gang Z, Van S, Yu L (2009) Polymer paclitaxel conjugates and methods for treating cancer. USA Patent US20090226393
11. Pujol JL (2005) Phase II study of carboplatin and weekly paclitaxel as first line treatment of elderly patients with non-small cell lung cancer. Clinical Study Report for Study CA139-368
12. Yoshida T (2009) Rollover study of weekly paclitaxel (BMS-181339) in patients with advanced breast cancer. Clinical Study Report for Study CA139-387
13. R Duncan 2003 The dawning era of polymer therapeutics Nat Rev Drug Discov 2 347 360 10.1038/nrd1088 1:CAS:528:DC%2BD3sXjslamtb0%3D (Pubitemid 37361705)
14. KM McNeeley E Karathanasis AV Annapragada RV Bellamkonda 2009 Masking and triggered unmasking of targeting ligands on nanocarriers to improve drug delivery to brain tumors Biomaterials 30 3986 3995 10.1016/j.biomaterials.2009. 04.012 1:CAS:528:DC%2BD1MXmvVykt74%3D
15. OC Farokhzad R Langer 2009 Impact of nanotechnology on drug delivery ACS Nano 3 16 20 10.1021/nn900002m 1:CAS:528:DC%2BD1MXnvFGisQ%3D%3D
16. Y Geng P Dalhaimer S Cai R Tsai M Tewari T Minko DE Discher 2007 Shape effects of filaments versus spherical particles in flow and drug delivery Nat Nanotechnol 2 249 255 10.1038/nnano.2007.70 1:CAS:528:DC%2BD1cXktVGgsbs%3D (Pubitemid 46739812)
17. P Decuzzi R Pasqualini W Arap M Ferrari 2009 Intravascular delivery of particulate systems: does geometry really matter? Pharma Res 26 235 243 10.1007/s11095-008-9697-x 1:CAS:528:DC%2BD1cXhsFSjsr7P
18. S Takeoka 2002 Rolling properties of rGPIbα-conjugated phospholipid vesicles with different membrane flexibilities on vWf surface under flow conditions Biochem Biophys Res Commun 296 765 770 10.1016/S0006-291X(02)00934-8 1:CAS:528:DC%2BD38XmtFShurs%3D
19. WF van Gunsteren 1993 Molecular dynamics studies of proteins Curr Opin Struct Biol 3 277 281 10.1016/S0959-440X(05)80164-2 (Pubitemid 23121000)
20. AE Mark HJC Berendsen WF van Gunsteren 1991 Conformational flexibility of aqueuous monomeric and dimeric insulin: a molecular dynamics study Biochemistry 30 10866 10872 10.1021/bi00109a009 1:CAS:528:DyaK3MXmt1eku74%3D
21. V Daggett M Levitt 1992 A model of the molten globule state from molecular dynamics simulations Proc Natl Acad Sci USA 89 5142 5146 10.1073/pnas.89.11.5142 1:CAS:528:DyaK38XltVKlsb8%3D
22. LX Peng A Ivetac S Van G Zhao AS Chaudhari L Yu SB Howell JA McCammon DA Gough 2010 Characterization of a clinical polymer-drug conjugate using multiscale modeling Biopolymers 93 936 951 10.1002/bip.21474 1:CAS:528:DC%2BC3cXht1Wns7%2FI
23. L Monticelli SK Kandasamy X Periole RG Larson DP Tieleman SJ Marrink 2008 The MARTINI coarse-grained force field: extension to proteins J Chem Theory Comput 4 819 834 10.1021/ct700324x 1:CAS:528:DC%2BD1cXks1Onsrg%3D
24. NJ Greenfield 2007 Using circular dichroism spectroscopy spectra to estimate protein secondary structure Nat Protoc 1 2876 2890 10.1038/nprot.2006. 202
25. FC Bernstein TF Koetzle GJ Williams EE Meyer Jr MD Brice JR Rodgers O Kennard T Shimanouchi M Tasumi 1977 J Mol Biol 112 535 10.1016/S0022-2836(77) 80200-3 1:CAS:528:DyaE2sXkvVert7o%3D
26. Frisch MJT et al (1995) Gaussian 94. Gaussian Inc, Pittsburgh
27. WD Cornell C Cieplak CI Bayly PA Kollman 1993 Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation J Am Chem Soc 115 9620 9631 10.1021/ja00074a030 1:CAS:528:DyaK3sXmt1Gmsbk%3D
28. A Onufriev D Bashford DA Case 2004 Exploring protein native states and large-scale conformational changes with a modified Generalized-Born model Proteins 55 383 394 10.1002/prot.20033 1:CAS:528:DC%2BD2cXjtFKhs78%3D (Pubitemid 38437495)
29. J Weiser PS Shenkin WC Still 1999 Approximate atomic surfaces from linear combinations of pairwise overlaps (LPCO) J Comput Chem 20 217 230 10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A 1:CAS:528:DyaK1MXltVCltQ%3D%3D (Pubitemid 129653030)
30. V Hornak R Abel A Okur R Strockbine A Roitberg C Simmerling 2006 Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins 65 712 725 10.1002/prot.21123 1:CAS:528: DC%2BD28XhtFWqt7fM (Pubitemid 44583220)
31. WD Cornell P Cieplak CI Bayly IR Gould KM Merz Jr DM Ferguson DC Spellmeyer T Fox JW Caldwell PA Kollman 1995 A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J Am Chem Soc 117 5179 5197 10.1021/ja00124a002 1:CAS:528:DyaK2MXlsFertrc%3D
32. J Wang RM Rolf JW Caldwell PA Kollman DA Case 2004 Development and testing of a general amber force field J Comput Chem 25 1157 1174 10.1002/jcc.20035 1:CAS:528:DC%2BD2cXksFakurc%3D
33. J Ryckaert G Ciccotti H Berendsen 1977 Numerical integration of the Cartesian equations of motion of a system with constraints; molecular dynamics of n-alkenes J Comp Physiol 23 327 341 1:CAS:528:DyaE2sXktVGhsL4%3D
34. SJ Marrink JH Rissalada S Yefimov DP Tieleman AH de Vries 2007 The MARTINI force field: coarse-grained model for biomolecular simulations J Phys Chem B 111 7812 7824 10.1021/jp071097f 1:CAS:528:DC%2BD2sXmsVKmsLc%3D (Pubitemid 47169693)
35. J Trylska V Tozzini JA McCammon 2005 Exploring global motions and correlations in the ribosome Biophys J 89 1455 1463 10.1529/biophysj.104.058495 1:CAS:528:DC%2BD2MXpvF2kt70%3D (Pubitemid 41233505)
36. SJ Marrink AH de Vries AE Mark 2004 J Phys Chem B 108 750 760 10.1021/jp036508g 1:CAS:528:DC%2BD3sXptlKjsb4%3D
37. LS Cheng RE Amaro D Xu WW Li PW Arzberger JA McCammon 2008 Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase J Med Chem 51 3878 3894 10.1021/jm8001197 1:CAS:528:DC%2BD1cXnt1ymsLs%3D (Pubitemid 351956517)
38. W Humphrey A Dalke K Schulten 1996 VMD - Visual Molecular Dynamics J Mol Graph 14 33 38 10.1016/0263-7855(96)00018-5 1:CAS:528:DyaK28Xis12nsrg%3D (Pubitemid 26152973)
39. E Lindahl B Hess D van der Spoel 2001 GROMACS 3.0: a package for molecular simulation and trajectory analysis J Mol Model 7 306 317 1:CAS:528:DC%2BD3MXnsVGjsL4%3D (Pubitemid 36153547)
40. M Abe Y Kobayashi S Yamamoto Y Daimon A Yamaguchi Y Ikeda H Ichinoki M Notaguchi K Goto T Araki 2005 FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex Science 309 1052 1056 10.1126/science.1115983 1:CAS:528:DC%2BD2MXnsl2ltLs%3D (Pubitemid 41134458)
41. SC Yasui TA Keiderling 1986 Vibrational circular dichroism of polypeptides. VI. Polytyrosine alpha-helical and random-coil results Biopolymers 25 5 15 10.1002/bip.360250103 1:CAS:528:DyaL28XmsVCksQ%3D%3D