Peptidomimetic Library

Description

As the name implies, peptidomimetics are organic molecules that mimic the action of peptides. These molecules may structurally resemble peptides but are distinctly different in terms of their side chains or their molecular backbones. Since the mode of action for a small-molecule and a peptidomimetic is similar, confusion sometimes arises with regard to the classification of the molecule as being a peptidomimetic or simply a small organic molecular mimic. Nevertheless, interactions with proteins can be mediated by other molecules with intermediate molecular masses instead of the low molecular weights associated with small-molecules or peptidomimetics.

Publications

i Zubay, G. L. Biochemistry, 4th ed.; Wm. C. Brown Publishers: Dubaque, Iowa, 1998.
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ix (a) Marchesini, S. Secondary Protein Structure: 3.10 helix. http://www.med.unibs.it/~marchesi/310.html (accessed 9/29/05). (b) Janes, R. W. First Year: Basic Biochemistry. http://www.qmul.ac.uk/~ugbt760/bas02new.doc (accessed 9/29/05)
x A Server for b-Turn Types Prediction. http://bioinformatics.uams.edu/raghava/betaturns/method.html (accessed 9/29/05).
xi Sipkins, D. A.; Wei, X.; Wu, J. W.; Runnels, J. M.; Cote, D.; Means, T. K.; Luster, D. A.; Scadden, D. T.; Lin, C. P. Nature 2005, 435, 969-974.
xii Y. Lavrovsky, Y.A. Ivanenkov, K.V. Balakin, A.V. Ivachtchenko. CXCR4 receptor as a promising target for oncolytic drugs. Mini-Reviews in Medicinal Chemistry, 2008, 8, 1075-1087.
xiii (a) K.V. Balakin, Y.A. Ivanenkov, et al. Regulators of Chemokine Receptor Activity as Promising Anticancer Therapeutics. Current Cancer Drug Targets, 2008, 8, 299-340; (b) AMD3100: CXCR4 Chemokine Receptor Antagonist. http://www.sigmaaldrich.com/img/assets/13760/amd3100.pdf (accessed 9/29/05).
xiv Li, L.; Thomas, R. M.; Suzuki, H.; De Brabander, J. K.; Wang, X.; Harran, P. G. Science 2004, 305, 1471-1474.
xv Montalto, M. C.; Collard, C. D.; Buras, J. A.; Reenstra, W. R.; McClaine, R.; Gies, D. R.; Rother, R. P.; Stahl, G. L. J. Immunol. 2001, 166, 4148-4153.
xvi (a) Cochran, A. G. Chemistry & Biology. 2000, 7, R85-R94; (b) Berman, A. E.; Kozlova, N. I.; Morozevich, G. E. Biochemistry (Moscow) 2003, 68, 1284-1299; (c) Newham, P.; Humphries, M. J. Molecular Medicine Today 1996, 96, 304-313.
xvii D’Alessio, P.; Moutet, M.; Coudrier, E.; Darquenne, S.; Chaudiere, J. Free Radical Biology & Medicine 1998, 24, 979-987.
xviii Gadek, T. R.; Burdick, D. J.; McDowell, R. S.; Stanley, M. S.; Marsters, J. C., Jr.; Paris, K. J.; Oare, D. A.; Reynolds, M. E.; Ladner, C.; Zioncheck, K. A.; Lee, W. P.; Gribling, P.; Dennis, M. S.; Skelton, N. J.; Tumas, D. B.; Clark, K. R.; Keating, S. M.; Beresini, M. H.; Tilley, J. W.; Presta, L. G.; Bodary, S. C. Science 2002, 295, 1086-1089.
xix Hippenmeyer, P. J.; Ruminski, R. P.; Rico, J. G.; Sharon, H.; Lu, D.; Griggs, D. W. Anitviral Research 2002, 55, 169-178.
xx (a) Lee, H. B.; Zaccaro, M. C.; Pattarawarapan, M.; Roy, S.; Saragovi, H. U.; Burgess, K. J. Org. Chem. 2004, 69, 701-713; (b) Reyes, S. J.; Burgess, K. Tetrahedron: Asymmetry 2005, 16, 1061-1069; (c) Maliartchouk, S.; Feng, Y.; Ivanisevic, L.; Debeir, T.; Cuello, A. C.; Burgess, K.; Saragovi, H. U. Mol. Pharm. 2000, 57, 385-391; (d) Ogbu, C. O.; Qabar, M. N.; Boatman, P. D.; Urban, J.; Meara, J. P.; Ferguson, M. D.; Tulinsky, J.; Lum, C.; Babu, S.; Blaskovich, M. A.; Nakanishi, H.;
Ruan, F.; Cao, B.; Minarik, R.; Little, T.; Nelson, S.; Nguyen, M.; Gall, A.; Kahn, M. Bioorg. Med. Chem. Lett. 1998, 8, 2321; (e) Fink, B. E.; Kym, P. R.; Katzenellenbogen, J. A. J. Am. Chem. Soc. 1998, 120, 4334; (f) Johannesson, P.; Lindeberg, G.; Tong, W.; Gogoll, A.; Karlen, A.; Hallberg, A. J. Med. Chem. 1999, 42, 601; (g) Golebiowski, A.; Klopfenstein, S. R.; Chen, J. J.; Shao, X. Tet. Lett. 2000, 41, 4841-4844; (e) Pfeifer, M. E.; Moehle, K.; Linden, A.; Robinson, J. Helv. Chim. Acta 2000, 83, 444.
xxi (a) Pattarawarapan, M.; Burgess, K. J. Med. Chem. 2003, 46, 5277-5291; (b) Maliartchouk, S.; Feng, Y.; Ivanisevic, L.; Debeir, T.; Cuello, A. C.; Burgess, K.; Saragovi, H. U. Mol. Pharm. 2000, 57, 385-391.
xxii (a) Orner, B. P.; Ernst, J. T.; Hamilton, A. D. J. Am. Chem. Soc. 2001, 123, 5382-5383; (b) (36) Kutzki, O.; Park, H. S.; Ernst, J. T.; Orner, B. P.; Hamilton, A. D. J. Am. Chem. Soc. 2002, 124, 11838-11839; (c) Ernst, J. T.; Becerril, J.; Park, H. S.; Yin, H.; Hamilton, A. D. Angew. Chem. Int. Ed. 2003, 42, 535-539; (d) Yin, H.; Lee, G.; Sedey, K. A.; Rodriguez, J. M.; Wang, H.-G.; Sebti, S. M.; Hamilton, A. D. J. Am. Chem. Soc. 2005, 127, 5463-5468; (e) Yin, H.; Lee, G.; Kutzki, O.; Park, H. S.; Orner, B. P.; Ernst, J. T.; Wang, H.-G.; Sebti, S. M.; Hamilton, A. D. J. Am. Chem. Soc. 2005, 127, 10191-10196; (f) Jacoby, E. Bioorg. Med. Chem. Lett. 2002, 12, 891-893; (g) Horwell, D. C.; Howson, W.; Nolan, W. P.; Ratcliffe, G. S.; Rees, D. C.; Willems, H. Tetrahedron 1995, 51, 203-216.
xxiii Shepherd, N. E.; Abbenante, G.; Fairlie, D. P. Angew. Chem. Int. Ed. 2004, 43, 2687-2690.
xxiv (a) Calvo, J. C.; Choconta, K. C.; Diaz, D.; Orozco, O.; Bravo, M. M.; Espejo, F.; Salazar, L. M.; Guzman, F.; Patarroyo, M. E. J. Med. Chem. 2003, 46, 5389-5394; (b) Peczuh, M. W.; Hamilton, A. D. Chem. Rev. 2000, 100, 2479-2494; (c) Asada, S.; Choi, Y.; Uesugi, M. J. Am. Chem. Soc. 2003, 125, 4992-4993.
xxv Peczuh, M. W.; Hamilton, A. D. Chem. Rev. 2000, 100, 2479-2494.
xxvi Fairlie, D. P.; West, M. L.; Wong, A. K. Curr. Med. Chem. 1998, 5, 29-62.
xxvii (a) Marrone, T. J.; Briggs, J. M.; McCammon, J. A. Annu. Rev. Pharmacol. Toxicol. 1997, 37, 71-90; (b) Joseph-McCarthy, D. Pharmacology & Therapeutics 1999, 84, 179-191.
xxviii McConkey, B. J.; Sobolev, V.; Edelman M. Curr. Sci. 2002, 83, 845-856.
xxix (a) Affinity, December 1998. Molecular Simulations, Inc.: San Diego, 1998. (b) Janin, J. Protein Science 2005, 14, 278-283.
xxx (a) Marrone, T. J.; Briggs, J. M.; McCammon, J. A. Annu. Rev. Pharmacol. Toxicol. 1997, 37, 71-90; (b) Joseph-McCarthy, D. Pharmacology & Therapeutics 1999, 84, 179-191; (c) McConkey, B. J.; Sobolev, V.; Edelman M. Curr. Sci. 2002, 83, 845-856.
xxxi Ajay, W.; Walters, P.; Murcko, M. J. Med. Chem. 1998, 41, 3314.
xxxii (a) Pattarawarapan, M.; Burgess, K. J. Med. Chem. 2003, 46, 5277-5291; (b) Ito, M.; Sakai, N.; Ito, K.; Mizobe, F.; Hanada, K. J. Antibiotics 1999, 52, 224-230; (c) Owolabi, J. B.; Rizkalla, G.; Tehim, A.; Ross, G. M.; Riopelle, R. J. J. Pharm.Expt. Ther. 1999, 289, 1271-1276; (d) Labie, C.; Lafon, C.; Marmouget, C.; Saubusse, P.; Fournier, J. British J. Pharm.1999, 127, 139-144; (d) LeSauteur, L.; Cheung, N. K. V.; Lisbona, R.; Saragovi, H. U. Nature Biotech. 1996, 14, 1120-1122.
xxxiii Nicolaou, K. C.; Snyder, S. A. Classics in Total Synthesis II. Wiley-VCH: Weinheim, Germany, 2003, pp. 365-378.
xxxiv (a) Christopher P. Carron, Debra M. Meyer, Jodi A. Pegg, V. Wayne Engleman, Maureen A. Nickols, Steven L. Settle, William F. Westlin, Peter G. Ruminski, and G. Allen Nickols. Cancer Research, 1998, 58, 1930-1935; (b) C P Carron, D M Meyer, V W Engleman, J G Rico, P G Ruminski, R L Ornberg, W F Westlin and G A Nickols. Journal of Endocrinology (2000) 165, 587–598.