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(12) United States Patent (10) Patent No.: US 6,884,842 B2 Soane Et Al

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(12) United States Patent (10) Patent No.: US 6,884,842 B2 Soane Et Al USOO6884.842B2 (12) United States Patent (10) Patent No.: US 6,884,842 B2 Soane et al. (45) Date of Patent: Apr. 26, 2005 (54) MOLECULAR COMPOUNDS HAVING 5,630,978 A 5/1997 Domb COMPLEMENTARY SURFACESTO 5,663,387 A 9/1997 Singh TARGETS 5,728.296 A 3/1998 Hjerten et al. 5,814.223 A 9/1998 Hjerten et al. (75) Inventors: David S. Soane, Piedmont, CA (US); 5,834,0255,821,311. A 11/199810/1998 deMosbach Garavilla et al.et al. Stephen E. Barry, Oakland, CA (US); 5858.2962Y- a-2 A 1. f1999 Domb Andrew Goodwin, Oakland, CA (US); 5,872,198. A 2/1999 Mosbach et al. David A. Offord, Castro Valley, CA 5,914,367 A 6/1999 Dordick et al. (US); Michael G. Perrott, San 5,916,445 A 6/1999 Hjerten et al. Francisco, CA (US) 5,916,596 A 6/1999 Desai et al. 5,959,050 A 9/1999 Mosbach et al. (73) Assignee: Alnis BioSciences, Inc., Emeryville, 5,994,110 A 11/1999 Mosbach et al. CA (US) 6,051,372 A 4/2000 Bayerl et al. 6,127,154 A 10/2000 Mosbach et al. (*) Notice: Subject to any disclaimer, the term of this 6,177,513 B1 1/2001 Takeuchi et al. patent is extended or adjusted under 35 6.217.901 B1 4/2001 Perrott et al. U.S.C. 154(b) by 179 days. FOREIGN PATENT DOCUMENTS DE 19627 162 C1 8/1997 (21) Appl. No.: 10/055,837 DE 198 23432 A1 3/1999 (22) Filed: Oct. 26, 2001 St. 29, 3.E. (65) Prior Publication Data WO WO 88/09981 12/1988 WO WO 93/05068 3/1993 US 2003/0153001 A1 Aug. 14, 2003 WO WO 93/09075 5/1993 WO WO 94/11403 5/1994 Related U.S. Application Data WO WO 94/14835 7/1994 WO WO 94/26381 11/1994 (63) Continuation of application No. 09/172.921, filed on Oct. WO WO95/21673 8/1995 14, 1998, now abandoned. WO WO 96/37527 11/1996 (60) Provisional application No. 60/103,616, filed on Oct. 9, WO WO 97/22366 6/1997 1998, and provisional application No. 60/061,805, filed on Oct. 14, 1997. OTHER PUBLICATIONS (51) Int. Cl." ........................ coso. 63.48. Cosg 63/91. Ananthapadmanabhan, KP "Surfactant solutions. Adsorp C08G 89/00; CO8H 1/00 tion and aggregation properties’ Interactions of Surfactants 52) U.S. C. 525,541 525/542. 525/54.23 with Polymers and Proteins, E. D. Goddard and K. P. (52) Oa - 1 - O - - - - - - - - - - - - - - - - - - /54.1; /54.2; /54.23; Ananthapadmanabhanm eds., CRC Press, Boca Raton, 526/238.1; 526/238.2; 526/238.23; 424/450; Chapter 2, pp. 5-58 (1993). 424/489; 424/499 Antoniettiapler Z, etpp al., “Synthesis(1993) and properties of model-mi (58) Field of Search ............................... 525/54.1, 54.2, cronetworks' Makromol. Chem., Macromol. Symp., 489, 499 (Continued) (56) References Cited Primary Examiner Nathan M. Nutter U.S. PATENT DOCUMENTS (74) Attorney, Agent, or Firm-Jacqueline S. Larson 4,075,411 A 2/1978 Dickstein (57) ABSTRACT 4,097,470 A 6/1978 Drobnik et al. 4,107,288 A 8/1978 Oppenheim et al. Synthetic polymer complements (SPCs) are provided, as 4,127,730 A 11/1978 Wulff et al. well as methods for their synthesis and use. The SPCs may 4,622,362. A 11/1986 Rembaum have Surfaces that include functional groups that are comple 4,770906 A 9/1988 Harwell et al. mentary to Surface Sites of targets Such as nanostructures or 4,800,162 A 1/1989 Matson macromolecular targets, and may be capable of Specifically 5,057.427 A 10/1991 Wald et al. 5,077.217. A 12/1991 Matson et al. interacting with Such targets. The positions of the functional 5,110,833 A 5/1992 Mosbach groups in one embodiment are stabilized by a polymer 5,152.978. A 10/1992 Baba et al. network. The SPCs are formed by contacting the target with 5,200,315 A 4/1993 Sutton et al. a set of monomers which Self-assemble on the target, and 5,310,648 A 5/1994 Arnold et al. then are polymerized into a network to form the Synthetic 5,349,036 A 9/1994 Simpson et al. polymer complement. At least a portion of the Surface of the 5,455,027 A 10/1995 Zalipsky et al. resulting SPC thus may include an imprint of the target. The 5,459,127 A 10/1995 Felgner et al. complex of the SPC and the target may be the desired 5,459,176 A 10/1995 Bae et al. product. Alternatively, the target is released, for example, by 5,461,1755,510,118 A 10/19954/1996 BoschFischer et et al. al. controllablylabl expandingding and contractingg the crosslinked net 5,534.270 A 7/1996 De Castro work. The SPC is isolated and used in many applications. 5,587,143 A 12/1996 Wong 5,587.273 A 12/1996 Yan et al. 36 Claims, 31 Drawing Sheets US 6,884.842 B2 Page 2 OTHER PUBLICATIONS Hermanson, Greg T., Bioconjugation Techniques, Academic Press: San Diego, pp. 57–59, 183-185, 620–622, (1996). Antonietti, Markus, "Polymerization in microemulsions-a Jansen et al., “Molecular design using the minireceptor new approach to ultrafine, highly functionalized polymer concept” J. Chem. Inf Comput. Sci., 37.812-818 (1997). dispersions” Macromol. Chem. Phys., 196:441–446 (1995). Joynes et al., “Novel polymerizable mono- and divalent Arshady et al., “Synthesis of Substrate-Selective polymers quaternary ammonium cationic Surfactants: 1. Synthesis, by host-guest polymerization' Makromol. Chem., Structural characterization and homopolymerization' Poly 182.687–692 (1981). mer; 37:1453–1462 (1996). Ayala et al., “Protein extraction and activity in reverse Kempe et al., “Binding Studies on Substrate and enantio micelles of a nonionic detergent’ Biotechnology and Selective molecularly imprinted polymers' Analytical Let Bioengineering, 39.806-814 (1992). ters, 24:1137–1145 (1991). Bishop et al., “Self-assembled monolayers: recent develop Kriz et al., “Introducing biomimetic Sensors based on ments and applications' Curr: Op. Colloid and Interface molecularly imprinted polymers as recognition elements' Sciences, 1: 127-136 (Feb. 1996). Anal. Chem, 67:21.42–2144 (1995). Boone, Travis D., “Overview of modeling efforts in support Lewis et al., “Automated Site-directed drug design using of microencapsulated polymer mandrel formation' J. MoS molecular lattices” J. Mol. Graph., 10:66–78 (1992). cow Phys. Soc., 8:79–86 (1998). March, Jerry, "Reactions, mechanisms, and Structure' Bunin et al., “The combinatorial Synthesis and chemical and Advanced Organic Chemistry, 3rd ed., Wiley-Interscience, biological evaluation of a 1,4-benzodiazepine library” Proc. New York, pp. 346-347 (1985). Natl. Acad. Sci. U.S.A., 91:4708–4712 (1994). Mayes et al., “Molecularly imprinted polymer beads; Sus Chiannilkulchai et al., “Doxorubicin-loaded nanoparticles: pension polymerization using a liquid perfluorocarbon as the Increased efficiency in murine hepatic metastases' Sel. Can dispersing phase” Anal. Chem., 68:3769–3774 (1996). cer Therpies, 5:1-11 (1990). Martinek et al., “The principles of enzyme stabilization. II. Clark et al., “Proligand: An approach to de novo molecular Increase in the thermostability of enzymes as a result of design. 1. Application to the design of organic molecules' J. multipoint noncovalent interaction with a polymeric Sup Comput. Aided Mol. Des, 9:13–32 (1995). port” Biochemica et Biophysica Acta, 485:13–28 (1977). Corpart et al., “Formation and polymerization of microemul Middleman, S., “Mixing in stirred tanks' Fundamentals of Sions containing a mixture of cationic and anionic mono Polymer Processing, McGraw-Hill, Inc., pp. 340-349 mers” Colloid & Polymer Science, 27.1:1055–1067 (1993). (1977). Duéek, K., ed., “Responsive gels: Volume transitions I' Monfardini et al., "Stabilization of Substances in circulation” Advances in Polymer Science, vol. 109, Springer Verlag Bioconjugate Chemistry, 9:418-450 (1998). (1993) (Table of Contents). Mosbach, Klaus, “Molecular imprinting Trends Biochem. Duéek, K., ed., “Responsive gels: Volume transitions II' Sci., 19:9-14 (1994). Advances in Polymer Science, vol. 110, Springer Verlag Mosbach et al., “The emerging technique of molecular (1993) (Table of Contents). imprinting and its future impact on biotechnology’ Biotech Eisenberg et al., “Electrolyte solutions” Physical Chemistry nology, 14:163–170 (1996). with Applications to the Life Sciences Benjamin/Cummings, O'Shannessy et al., “Molecular recognition in synthetic Menlo Park, CA, Chapter 8, pp. 337-340 (1979). polymers” Journal of Molecular Recognition, 2:1-5 (1989). Ekberg et al., “Molecular imprinting: a technique for pro Paradkar et al., “Aqueous-like activity of C-chymotrypsin ducing specific separation materials' Tibetch 7.92–96 dissolved in nearly anhydrous organic Solvents' J. Am. (1989). Chem. Soc., 116:5009–5010 (1994). Fodor et al., “Light-directed, Spatially addressable parallel Pauling, Linus "A theory of the Structure and process of chemical synthesis” Science, 251:767-773 (1991). formation of antibodies' J. Am. 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