Synthetic Peptide Libraries: From Random Mixtures to In Vivo Testing

Author(s): Annamaria Sandomenico, Andrea Caporale, Nunzianna Doti*, Simon Cross, Gabriele Cruciani, Angela Chambery, Sandro De Falco, Menotti Ruvo*

Journal Name: Current Medicinal Chemistry

Volume 27 , Issue 6 , 2020

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Abstract:

Combinatorially generated molecular repertoires have been largely used to identify novel bioactive compounds. Ever more sophisticated technological solutions have been proposed to simplify and speed up such process, expanding the chemical diversity space and increasing the prospect to select new molecular entities with specific and potent activities against targets of therapeutic relevance. In this context, random mixtures of oligomeric peptides were originally used and since 25 years they represent a continuous source of bioactive molecules with potencies ranging from the sub-nM to microM concentration. Synthetic peptide libraries are still employed as starting “synthetic broths” of structurally and chemically diversified molecular fragments from which lead compounds can be extracted and further modified. Thousands of studies have been reported describing the application of combinatorial mixtures of synthetic peptides with different complexity and engrafted on diverse structural scaffolds for the identification of new compounds which have been further developed and also tested in in vivo models of relevant diseases. We briefly review some of the most used methodologies for library preparation and screening and the most recent case studies appeared in the literature where compounds have reached at least in vivo testing in animal or similar models. Recent technological advancements in biotechnology, engineering and computer science have suggested new options to facilitate the discovery of new bioactive peptides. In this instance, we anticipate here a new approach for the design of simple but focused tripeptide libraries against druggable cavities of therapeutic targets and its complementation with existing approaches.

Keywords: Peptide libraries, in vivo testing, Divide-couple-recombine, Solid phase peptide synthesis, Random mixtures, Iterative deconvolution.

[1]
Merrifield, R.B. Solid phase peptide synthesis. I. The synthesis of a tetrapeptide. J. Am. Chem. Soc., 1963, 85(14), 2149-2154.
[http://dx.doi.org/10.1021/ja00897a025]
[2]
Geysen, H.M.; Rodda, S.J.; Mason, T.J. A priori delineation of a peptide which mimics a discontinuous antigenic determinant. Mol. Immunol., 1986, 23(7), 709-715.
[http://dx.doi.org/10.1016/0161-5890(86)90081-7] [PMID: 2432410]
[3]
Houghten, R.A.; Bray, M.K.; Degraw, S.T.; Kirby, C.J. Simplified procedure for carrying out simultaneous multiple hydrogen fluoride cleavages of protected peptide resins. Int. J. Pept. Protein Res., 1986, 27(6), 673-678.
[http://dx.doi.org/10.1111/j.1399-3011.1986.tb01064.x] [PMID: 3759338]
[4]
Lam, K.S.; Salmon, S.E.; Hersh, E.M.; Hruby, V.J.; Kazmierski, W.M.; Knapp, R.J. A new type of synthetic peptide library for identifying ligand-binding activity. Nature, 1991, 354(6348), 82-84.
[http://dx.doi.org/10.1038/354082a0] [PMID: 1944576]
[5]
Furka, A.; Sebestyén, F.; Asgedom, M.; Dibó, G. General method for rapid synthesis of multicomponent peptide mixtures. Int. J. Pept. Protein Res., 1991, 37(6), 487-493.
[http://dx.doi.org/10.1111/j.1399-3011.1991.tb00765.x] [PMID: 1917305]
[6]
Houghten, R.A.; Pinilla, C.; Blondelle, S.E.; Appel, J.R.; Dooley, C.T.; Cuervo, J.H. Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery. Nature, 1991, 354(6348), 84-86.
[http://dx.doi.org/10.1038/354084a0] [PMID: 1719428]
[7]
Akagawa, K.; Satou, J.; Kudo, K. Exploration of structural frameworks for reactive and enantioselective peptide catalysts by library screenings. exploration of structural frameworks for reactive and enantioselective peptide catalysts by library screenings. J. Org. Chem., 2016, 81(19), 9396-9401.
[http://dx.doi.org/10.1021/acs.joc.6b01591] [PMID: 27662499]
[8]
Akagawa, K.; Sakai, N.; Kudo, K. Histidine-containing peptide catalysts developed by a facile library screening method. Angew. Chem. Int. Ed. Engl., 2015, 54(6), 1822-1826.
[http://dx.doi.org/10.1002/anie.201410268] [PMID: 25521645]
[9]
Pinilla, C.; Appel, J.; Blondelle, S.; Dooley, C.; Dörner, B.; Eichler, J.; Ostresh, J.; Houghten, R.A. A review of the utility of soluble peptide combinatorial libraries. Biopolymers, 1995, 37(3), 221-240.
[http://dx.doi.org/10.1002/bip.360370306] [PMID: 7718744]
[10]
Liu, R.; Li, X.; Lam, K.S. Combinatorial chemistry in drug discovery. Curr. Opin. Chem. Biol., 2017, 38, 117-126.
[http://dx.doi.org/10.1016/j.cbpa.2017.03.017] [PMID: 28494316]
[11]
Lam, K.S.; Lebl, M.; Krchnák, V. The “One-Bead-One-Compound” combinatorial library method. Chem. Rev., 1997, 97(2), 411-448.
[http://dx.doi.org/10.1021/cr9600114] [PMID: 11848877]
[12]
Martínez-Ceron, M.C.; Giudicessi, S.L.; Saavedra, S.L.; Gurevich-Messina, J.M.; Erra-Balsells, R.; Albericio, F.; Cascone, O.; Camperi, S.A. Latest advances in OBOC peptide libraries. improvements in screening strategies and enlarging the family from linear to cyclic libraries. Curr. Pharm. Biotechnol., 2016, 17(5), 449-457.
[http://dx.doi.org/10.2174/1389201017666160114095553] [PMID: 26778455]
[13]
Rahbarnia, L.; Farajnia, S.; Babaei, H.; Majidi, J.; Veisi, K.; Ahmadzadeh, V.; Akbari, B. Evolution of phage display technology: from discovery to application. J. Drug Target., 2017, 25(3), 216-224.
[http://dx.doi.org/10.1080/1061186X.2016.1258570] [PMID: 27819143]
[14]
Hansson, M.; Samuelson, P.; Gunneriusson, E.; Ståhl, S. Surface display on gram positive bacteria. Comb. Chem. High Throughput Screen., 2001, 4(2), 171-184.
[http://dx.doi.org/10.2174/1386207013331183] [PMID: 11281833]
[15]
Boder, E.T.; Wittrup, K.D. Yeast surface display for screening combinatorial polypeptide libraries. Nat. Biotechnol., 1997, 15(6), 553-557.
[http://dx.doi.org/10.1038/nbt0697-553] [PMID: 9181578]
[16]
Mattheakis, L.C.; Bhatt, R.R.; Dower, W.J. An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc. Natl. Acad. Sci. USA, 1994, 91(19), 9022-9026.
[http://dx.doi.org/10.1073/pnas.91.19.9022] [PMID: 7522328]
[17]
Falciani, C.; Pini, A.; Bracci, L. Oligo-branched peptides for tumor targeting: from magic bullets to magic forks. Expert Opin. Biol. Ther., 2009, 9(2), 171-178.
[http://dx.doi.org/10.1517/14712590802620501] [PMID: 19236247]
[18]
Pini, A.; Falciani, C.; Bracci, L. Branched peptides as therapeutics. Curr. Protein Pept. Sci., 2008, 9(5), 468-477.
[http://dx.doi.org/10.2174/138920308785915227] [PMID: 18855698]
[19]
Pande, J.; Szewczyk, M.M.; Grover, A.K. Phage display: concept, innovations, applications and future. Biotechnol. Adv., 2010, 28(6), 849-858.
[http://dx.doi.org/10.1016/j.biotechadv.2010.07.004] [PMID: 20659548]
[20]
Tucker, A.T.; Leonard, S.P.; DuBois, C.D.; Knauf, G.A.; Cunningham, A.L.; Wilke, C.O.; Trent, M.S.; Davies, B.W. Discovery of next-generation antimicrobials through bacterial self-screening of surface-displayed peptide libraries. Cell, 2018, 172(3), 618-628. e613
[http://dx.doi.org/10.1016/j.cell.2017.12.009]
[21]
Boucher, H.W.; Talbot, G.H.; Bradley, J.S.; Edwards, J.E.; Gilbert, D.; Rice, L.B.; Scheld, M.; Spellberg, B.; Bartlett, J. Bad bugs, no drugs: no ESKAPE! An update from the infectious diseases society of America. Clin. Infect. Dis., 2009, 48(1), 1-12.
[http://dx.doi.org/10.1086/595011] [PMID: 19035777]
[22]
Scott, C.P.; Abel-Santos, E.; Wall, M.; Wahnon, D.C.; Benkovic, S.J. Production of cyclic peptides and proteins in vivo. Proc. Natl. Acad. Sci. USA, 1999, 96(24), 13638-13643.
[http://dx.doi.org/10.1073/pnas.96.24.13638] [PMID: 10570125]
[23]
Tavassoli, A. SICLOPPS cyclic peptide libraries in drug discovery. Curr. Opin. Chem. Biol., 2017, 38, 30-35.
[http://dx.doi.org/10.1016/j.cbpa.2017.02.016] [PMID: 28258013]
[24]
Miranda, E.; Nordgren, I.K.; Male, A.L.; Lawrence, C.E.; Hoakwie, F.; Cuda, F.; Court, W.; Fox, K.R.; Townsend, P.A.; Packham, G.K.; Eccles, S.A.; Tavassoli, A. A cyclic peptide inhibitor of HIF-1 heterodimerization that inhibits hypoxia signaling in cancer cells. J. Am. Chem. Soc., 2013, 135(28), 10418-10425.
[http://dx.doi.org/10.1021/ja402993u] [PMID: 23796364]
[25]
Naumann, T.A.; Tavassoli, A.; Benkovic, S.J. Genetic selection of cyclic peptide Dam methyltransferase inhibitors. ChemBioChem, 2008, 9(2), 194-197.
[http://dx.doi.org/10.1002/cbic.200700561] [PMID: 18085543]
[26]
Obexer, R.; Walport, L.J.; Suga, H. Exploring sequence space: harnessing chemical and biological diversity towards new peptide leads. Curr. Opin. Chem. Biol., 2017, 38, 52-61.
[http://dx.doi.org/10.1016/j.cbpa.2017.02.020] [PMID: 28319812]
[27]
Rhodes, C.A.; Pei, D. Bicyclic peptides as next-generation therapeutics. Chemistry, 2017, 23(52), 12690-12703.
[http://dx.doi.org/10.1002/chem.201702117] [PMID: 28590540]
[28]
Carney, R.P.; Thillier, Y.; Kiss, Z.; Sahabi, A.; Heleno Campos, J.C.; Knudson, A.; Liu, R.; Olivos, D.; Saunders, M.; Tian, L.; Lam, K.S. Combinatorial library screening with liposomes for discovery of membrane active peptides. combinatorial library screening with liposomes for discovery of membrane active peptides. ACS Comb. Sci., 2017, 19(5), 299-307.
[http://dx.doi.org/10.1021/acscombsci.6b00182] [PMID: 28378995]
[29]
Wang, X.; Zhang, J.; Song, A.; Lebrilla, C.B.; Lam, K.S. Encoding method for OBOC small molecule libraries using a biphasic approach for ladder-synthesis of coding tags. J. Am. Chem. Soc., 2004, 126(18), 5740-5749.
[http://dx.doi.org/10.1021/ja049322j] [PMID: 15125667]
[30]
Liu, R.; Marik, J.; Lam, K.S. A novel peptide-based encoding system for “one-bead one-compound” peptidomimetic and small molecule combinatorial libraries. J. Am. Chem. Soc., 2002, 124(26), 7678-7680.
[http://dx.doi.org/10.1021/ja026421t] [PMID: 12083920]
[31]
Liu, R.; Li, X.; Xiao, W.; Lam, K.S. Tumor-targeting peptides from combinatorial libraries. Adv. Drug Deliv. Rev., 2017, 110-111, 13-37.
[http://dx.doi.org/10.1016/j.addr.2016.05.009] [PMID: 27210583]
[32]
Marasco, D.; Perretta, G.; Sabatella, M.; Ruvo, M. Past and future perspectives of synthetic peptide libraries. Curr. Protein Pept. Sci., 2008, 9(5), 447-467.
[http://dx.doi.org/10.2174/138920308785915209] [PMID: 18855697]
[33]
Pinilla, C.; Martin, R.; Gran, B.; Appel, J.R.; Boggiano, C.; Wilson, D.B.; Houghten, R.A. Exploring immunological specificity using synthetic peptide combinatorial libraries. Curr. Opin. Immunol., 1999, 11(2), 193-202.
[http://dx.doi.org/10.1016/S0952-7915(99)80033-8] [PMID: 10322159]
[34]
Hilpert, K.; Winkler, D.F.; Hancock, R.E. Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion. Nat. Protoc., 2007, 2(6), 1333-1349.
[http://dx.doi.org/10.1038/nprot.2007.160] [PMID: 17545971]
[35]
Schneider, A.C.; Fritz, D.; Vasquez, J.K.; Vollrath, S.B.L.; Blackwell, H.E.; Bräse, S. Microwave-Facilitated SPOT-Synthesis of Antibacterial Dipeptoids. ACS Comb. Sci., 2017, 19(12), 715-737.
[http://dx.doi.org/10.1021/acscombsci.7b00096] [PMID: 29035557]
[36]
Volkmer, R.; Tapia, V.; Landgraf, C. Synthetic peptide arrays for investigating protein interaction domains. FEBS Lett., 2012, 586(17), 2780-2786.
[http://dx.doi.org/10.1016/j.febslet.2012.04.028] [PMID: 22576123]
[37]
López-Pérez, P.M.; Grimsey, E.; Bourne, L.; Mikut, R.; Hilpert, K. Screening and optimizing antimicrobial peptides by using SPOT-synthesis. Front Chem., 2017, 5, 25.
[http://dx.doi.org/10.3389/fchem.2017.00025] [PMID: 28447030]
[38]
Pinilla, C.; Appel, J.R.; Blondelle, S.E.; Dooley, C.T.; Eichler, J.; Ostresh, J.M.; Houghten, R.A. Versatility of positional scanning synthetic combinatorial libraries for the identification of individual compounds. Drug Dev. Res., 1994, 33(2), 133-145.
[http://dx.doi.org/10.1002/ddr.430330210]
[39]
Dooley, C.T.; Houghten, R.A. The use of positional scanning synthetic peptide combinatorial libraries for the rapid determination of opioid receptor ligands. Life Sci., 1993, 52(18), 1509-1517.
[http://dx.doi.org/10.1016/0024-3205(93)90113-H] [PMID: 8387136]
[40]
Ostresh, J.M.; Husar, G.M.; Blondelle, S.E.; Dörner, B.; Weber, P.A.; Houghten, R.A. “Libraries from libraries”: chemical transformation of combinatorial libraries to extend the range and repertoire of chemical diversity. Proc. Natl. Acad. Sci. USA, 1994, 91(23), 11138-11142.
[http://dx.doi.org/10.1073/pnas.91.23.11138] [PMID: 7972024]
[41]
Blondelle, S.E.R.A. Houghten. Membrane protecting sequences and new antimicrobial peptides identified through the screening of synthetic peptide combinatorial librariesTechniques in Protein Chemistry; John W. Crabb, E., Ed.; Academic Press V: Orlando., 1994, Vol. 5, pp. 509-516.
[42]
Lau, J.L.; Dunn, M.K. Therapeutic peptides: Historical perspectives, current development trends, and future directions. Bioorg. Med. Chem., 2018, 26(10), 2700-2707.
[http://dx.doi.org/10.1016/j.bmc.2017.06.052] [PMID: 28720325]
[43]
Marino, M.; Ruvo, M.; De Falco, S.; Fassina, G. Prevention of systemic lupus erythematosus in MRL/lpr mice by administration of an immunoglobulin-binding peptide. Nat. Biotechnol., 2000, 18(7), 735-739.
[http://dx.doi.org/10.1038/77296] [PMID: 10888840]
[44]
Verdoliva, A.; Marasco, D.; De Capua, A.; Saporito, A.; Bellofiore, P.; Manfredi, V.; Fattorusso, R.; Pedone, C.; Ruvo, M. A new ligand for immunoglobulin g subdomains by screening of a synthetic peptide library. ChemBioChem, 2005, 6(7), 1242-1253.
[http://dx.doi.org/10.1002/cbic.200400368] [PMID: 15937987]
[45]
Ruvo, M.; Sandomenico, A.; Tudisco, L.; De Falco, S. Branched peptides for the modulation of protein-protein interactions: more arms are better than one? Curr. Med. Chem., 2011, 18(16), 2429-2437.
[http://dx.doi.org/10.2174/092986711795843191] [PMID: 21568915]
[46]
Ponticelli, S.; Marasco, D.; Tarallo, V.; Albuquerque, R.J.; Mitola, S.; Takeda, A.; Stassen, J.M.; Presta, M.; Ambati, J.; Ruvo, M.; De Falco, S. Modulation of angiogenesis by a tetrameric tripeptide that antagonizes vascular endothelial growth factor receptor 1. J. Biol. Chem., 2008, 283(49), 34250-34259.
[http://dx.doi.org/10.1074/jbc.M806607200] [PMID: 18922791]
[47]
Cicatiello, V.; Apicella, I.; Tudisco, L.; Tarallo, V.; Formisano, L.; Sandomenico, A.; Kim, Y.; Bastos-Carvalho, A.; Orlandi, A.; Ambati, J.; Ruvo, M.; Bianco, R.; De Falco, S. Powerful anti-tumor and anti-angiogenic activity of a new anti-vascular endothelial growth factor receptor 1 peptide in colorectal cancer models. Oncotarget, 2015, 6(12), 10563-10576.
[http://dx.doi.org/10.18632/oncotarget.3384] [PMID: 25868854]
[48]
Lonardo, E.; Parish, C.L.; Ponticelli, S.; Marasco, D.; Ribeiro, D.; Ruvo, M.; De Falco, S.; Arenas, E.; Minchiotti, G. A small synthetic cripto blocking Peptide improves neural induction, dopaminergic differentiation, and functional integration of mouse embryonic stem cells in a rat model of Parkinson’s disease. Stem Cells, 2010, 28(8), 1326-1337.
[http://dx.doi.org/10.1002/stem.458] [PMID: 20641036]
[49]
Ung, P.; Winkler, D.A. Tripeptide motifs in biology: targets for peptidomimetic design. J. Med. Chem., 2011, 54(5), 1111-1125.
[http://dx.doi.org/10.1021/jm1012984] [PMID: 21275407]
[50]
Tornatore, L.; Sandomenico, A.; Raimondo, D.; Low, C.; Rocci, A.; Tralau-Stewart, C.; Capece, D.; D’Andrea, D.; Bua, M.; Boyle, E.; van Duin, M.; Zoppoli, P.; Jaxa-Chamiec, A.; Thotakura, A.K.; Dyson, J.; Walker, B.A.; Leonardi, A.; Chambery, A.; Driessen, C.; Sonneveld, P.; Morgan, G.; Palumbo, A.; Tramontano, A.; Rahemtulla, A.; Ruvo, M.; Franzoso, G. Cancer-selective targeting of the NF-κB survival pathway with GADD45β/MKK7 inhibitors. Cancer Cell, 2014, 26(6), 938.
[http://dx.doi.org/10.1016/j.ccell.2014.11.021] [PMID: 28898681]
[51]
Sandomenico, A.; Russo, A.; Palmieri, G.; Bergamo, P.; Gogliettino, M.; Falcigno, L.; Ruvo, M. Small peptide inhibitors of acetyl-peptide hydrolase having an uncommon mechanism of inhibition and a stable bent conformation. J. Med. Chem., 2012, 55(5), 2102-2111.
[http://dx.doi.org/10.1021/jm2013375] [PMID: 22309188]
[52]
Sandomenico, A.; Severino, V.; Apone, F.; De Lucia, A.; Caporale, A.; Doti, N.; Russo, A.; Russo, R.; Rega, C.; Del Giacco, T.; Falcigno, L.; Ruvo, M.; Chambery, A. Trifluoroacetylated tyrosine-rich D-tetrapeptides have potent antioxidant activity. Peptides, 2017, 89, 50-59.
[http://dx.doi.org/10.1016/j.peptides.2017.01.011] [PMID: 28130120]
[53]
Ambati, B.K.; Nozaki, M.; Singh, N.; Takeda, A.; Jani, P.D.; Suthar, T.; Albuquerque, R.J.; Richter, E.; Sakurai, E.; Newcomb, M.T.; Kleinman, M.E.; Caldwell, R.B.; Lin, Q.; Ogura, Y.; Orecchia, A.; Samuelson, D.A.; Agnew, D.W.; St Leger, J.; Green, W.R.; Mahasreshti, P.J.; Curiel, D.T.; Kwan, D.; Marsh, H.; Ikeda, S.; Leiper, L.J.; Collinson, J.M.; Bogdanovich, S.; Khurana, T.S.; Shibuya, M.; Baldwin, M.E.; Ferrara, N.; Gerber, H.P.; De Falco, S.; Witta, J.; Baffi, J.Z.; Raisler, B.J.; Ambati, J. Corneal avascularity is due to soluble VEGF receptor-1. Nature, 2006, 443(7114), 993-997.
[http://dx.doi.org/10.1038/nature05249] [PMID: 17051153]
[54]
Strizzi, L.; Bianco, C.; Normanno, N.; Salomon, D. Cripto-1: a multifunctional modulator during embryogenesis and oncogenesis. Oncogene, 2005, 24(37), 5731-5741.
[http://dx.doi.org/10.1038/sj.onc.1208918] [PMID: 16123806]
[55]
Minchiotti, G. Nodal-dependant Cripto signaling in ES cells: from stem cells to tumor biology. Oncogene, 2005, 24(37), 5668-5675.
[http://dx.doi.org/10.1038/sj.onc.1208917] [PMID: 16123800]
[56]
Winkler, C.; Kirik, D.; Björklund, A. Cell transplantation in Parkinson’s disease: how can we make it work? Trends Neurosci., 2005, 28(2), 86-92.
[http://dx.doi.org/10.1016/j.tins.2004.12.006] [PMID: 15667931]
[57]
Kumaresan, P.R.; Devaraj, S.; Huang, W.; Lau, E.Y.; Liu, R.; Lam, K.S.; Jialal, I. Synthesis and characterization of a novel inhibitor of C-reactive protein-mediated proinflammatory effects. Metab. Syndr. Relat. Disord., 2013, 11(3), 177-184.
[http://dx.doi.org/10.1089/met.2012.0123] [PMID: 23445482]
[58]
Jialal, I.; Devaraj, S.; Smith, G.; Lam, K.S.; Kumaresan, P.R. A novel peptide inhibitor attenuates C-reactive protein’s pro-inflammatory effects in-vivo. Int. J. Cardiol., 2013, 168(4), 3909-3912.
[http://dx.doi.org/10.1016/j.ijcard.2013.06.047] [PMID: 23871616]
[59]
Devaraj, S.; Singh, U.; Jialal, I. The evolving role of C-reactive protein in atherothrombosis. Clin. Chem., 2009, 55(2), 229-238.
[http://dx.doi.org/10.1373/clinchem.2008.108886] [PMID: 19095731]
[60]
Pepys, M.B.; Hirschfield, G.M.; Tennent, G.A.; Gallimore, J.R.; Kahan, M.C.; Bellotti, V.; Hawkins, P.N.; Myers, R.M.; Smith, M.D.; Polara, A.; Cobb, A.J.; Ley, S.V.; Aquilina, J.A.; Robinson, C.V.; Sharif, I.; Gray, G.A.; Sabin, C.A.; Jenvey, M.C.; Kolstoe, S.E.; Thompson, D.; Wood, S.P. Targeting C-reactive protein for the treatment of cardiovascular disease. Nature, 2006, 440(7088), 1217-1221.
[http://dx.doi.org/10.1038/nature04672] [PMID: 16642000]
[61]
Armishaw, C.J.; Banerjee, J.; Ganno, M.L.; Reilley, K.J.; Eans, S.O.; Mizrachi, E.; Gyanda, R.; Hoot, M.R.; Houghten, R.A.; McLaughlin, J.P. Discovery of novel antinociceptive α-conotoxin analogues from the direct in vivo screening of a synthetic mixture-based combinatorial library. ACS Comb. Sci., 2013, 15(3), 153-161.
[http://dx.doi.org/10.1021/co300152x] [PMID: 2341417]
[62]
Peng, L.; Liu, R.; Marik, J.; Wang, X.; Takada, Y.; Lam, K.S. Combinatorial chemistry identifies high-affinity peptidomimetics against alpha4beta1 integrin for in vivo tumor imaging. Nat. Chem. Biol., 2006, 2(7), 381-389.
[http://dx.doi.org/10.1038/nchembio798] [PMID: 16767086]
[63]
Yao, N.; Xiao, W.; Wang, X.; Marik, J.; Park, S.H.; Takada, Y.; Lam, K.S. Discovery of targeting ligands for breast cancer cells using the one-bead one-compound combinatorial method. J. Med. Chem., 2009, 52(1), 126-133.
[http://dx.doi.org/10.1021/jm801062d] [PMID: 19055415]
[64]
Xiao, W.; Wang, Y.; Lau, E.Y.; Luo, J.; Yao, N.; Shi, C.; Meza, L.; Tseng, H.; Maeda, Y.; Kumaresan, P.; Liu, R.; Lightstone, F.C.; Takada, Y.; Lam, K.S. The use of one-bead one-compound combinatorial library technology to discover high-affinity αvβ3 integrin and cancer targeting arginine-glycine-aspartic acid ligands with a built-in handle. Mol. Cancer Ther., 2010, 9(10), 2714-2723.
[http://dx.doi.org/10.1158/1535-7163.MCT-10-0308] [PMID: 20858725]
[65]
Wang, Y.; Xiao, W.; Zhang, Y.; Meza, L.; Tseng, H.; Takada, Y.; Ames, J.B.; Lam, K.S. Optimization of RGD-containing cyclic peptides against αvβ3 integrin. Mol. Cancer Ther., 2016, 15(2), 232-240.
[http://dx.doi.org/10.1158/1535-7163.MCT-15-0544] [PMID: 26719578]
[66]
Xiao, W.; Li, T.; Bononi, F.C.; Lac, D.; Kekessie, I.A.; Liu, Y.; Sanchez, E.; Mazloom, A.; Ma, A.H.; Lin, J.; Tran, J.; Yang, K.; Lam, K.S.; Liu, R. Discovery and characterization of a high-affinity and high-specificity peptide ligand LXY30 for in vivo targeting of α3 integrin-expressing human tumors. EJNMMI Res., 2016, 6(1), 18.
[http://dx.doi.org/10.1186/s13550-016-0165-z] [PMID: 26922417]
[67]
Leung, N.Y.; Wai, C.Y.; Ho, M.H.; Liu, R.; Lam, K.S.; Wang, J.J.; Shu, S.A.; Chu, K.H.; Leung, P.S. Screening and identification of mimotopes of the major shrimp allergen tropomyosin using one-bead-one-compound peptide libraries. Cell. Mol. Immunol., 2017, 14(3), 308-318.
[http://dx.doi.org/10.1038/cmi.2015.83] [PMID: 26364917]
[68]
De Smaele, E.; Zazzeroni, F.; Papa, S.; Nguyen, D.U.; Jin, R.; Jones, J.; Cong, R.; Franzoso, G. Induction of gadd45beta by NF-kappaB downregulates pro-apoptotic JNK signalling. Nature, 2001, 414(6861), 308-313.
[http://dx.doi.org/10.1038/35104560] [PMID: 11713530]
[69]
Papa, S.; Zazzeroni, F.; Bubici, C.; Jayawardena, S.; Alvarez, K.; Matsuda, S.; Nguyen, D.U.; Pham, C.G.; Nelsbach, A.H.; Melis, T.; De Smaele, E.; Tang, W.J.; D’Adamio, L.; Franzoso, G. Gadd45 beta mediates the NF-kappa B suppression of JNK signalling by targeting MKK7/JNKK2. Nat. Cell Biol., 2004, 6(2), 146-153.
[http://dx.doi.org/10.1038/ncb1093] [PMID: 14743220]
[70]
Papa, S.; Monti, S.M.; Vitale, R.M.; Bubici, C.; Jayawardena, S.; Alvarez, K.; De Smaele, E.; Dathan, N.; Pedone, C.; Ruvo, M.; Franzoso, G. Insights into the structural basis of the GADD45beta-mediated inactivation of the JNK kinase, MKK7/JNKK2. J. Biol. Chem., 2007, 282(26), 19029-19041.
[http://dx.doi.org/10.1074/jbc.M703112200] [PMID: 17485467]
[71]
Rega, C.; Russo, R.; Focà, A.; Sandomenico, A.; Iaccarino, E.; Raimondo, D.; Milanetti, E.; Tornatore, L.; Franzoso, G.; Pedone, P.V.; Ruvo, M.; Chambery, A. Probing the interaction interface of the GADD45β/MKK7 and MKK7/DTP3 complexes by chemical cross-linking mass spectrometry. Int. J. Biol. Macromol., 2018, 114, 114-123.
[http://dx.doi.org/10.1016/j.ijbiomac.2018.03.090] [PMID: 29572137]
[72]
Tornatore, L.; Capece, D.; D’Andrea, D.; Begalli, F.; Verzella, D.; Bennett, J.; Acton, G.; Campbell, E.A.; Kelly, J.; Tarbit, M.; Adams, N.; Bannoo, S.; Leonardi, A.; Sandomenico, A.; Raimondo, D.; Ruvo, M.; Chambery, A.; Al-Obaidi, M.J.; Kaczmarski, R.S.; Gabriel, I.; Benjamin, R.; Kaiser, M.F.; Oakervee, H.E.; Wechalekar, A.; Apperley, J.F.; Auner, H.; Franzoso, G. Preclinical and clinical proof of concept for a safe and mechanistically effective NF-κB-targeting strategy in multiple myeloma. Br. J. Haematol.,
[73]
Ashby, M.; Petkova, A.; Gani, J.; Mikut, R.; Hilpert, K. Use of peptide libraries for identification and optimization of novel antimicrobial peptides. Curr. Top. Med. Chem., 2017, 17(5), 537-553.
[http://dx.doi.org/10.2174/1568026616666160713125555] [PMID: 27411326]
[74]
Greber, K.E.; Dawgul, M. Antimicrobial peptides under clinical trials. Antimicrobial peptides under clinical trials. Curr. Top. Med. Chem., 2017, 17(5), 620-628.
[http://dx.doi.org/10.2174/1568026616666160713143331] [PMID: 27411322]
[75]
Fox, J.L. Antimicrobial peptides stage a comeback. Nat. Biotechnol., 2013, 31(5), 379-382.
[http://dx.doi.org/10.1038/nbt.2572] [PMID: 23657384]
[76]
Fjell, C.D.; Hiss, J.A.; Hancock, R.E.; Schneider, G. Designing antimicrobial peptides: form follows function. Nat. Rev. Drug Discov., 2011, 11(1), 37-51.
[http://dx.doi.org/10.1038/nrd3591] [PMID: 22173434]
[77]
Bionda, N.; Fleeman, R.M.; de la Fuente-Núñez, C.; Rodriguez, M.C.; Reffuveille, F.; Shaw, L.N.; Pastar, I.; Davis, S.C.; Hancock, R.E.W.; Cudic, P. Identification of novel cyclic lipopeptides from a positional scanning combinatorial library with enhanced antibacterial and antibiofilm activities. Eur. J. Med. Chem., 2016, 108, 354-363.
[http://dx.doi.org/10.1016/j.ejmech.2015.11.032] [PMID: 26703794]
[78]
Houghten, R.A. General method for the rapid solid-phase synthesis of large numbers of peptides: specificity of antigen-antibody interaction at the level of individual amino acids. Proc. Natl. Acad. Sci. USA, 1985, 82(15), 5131-5135.
[http://dx.doi.org/10.1073/pnas.82.15.5131] [PMID: 2410914]
[79]
Jofré, C.; Guzmán, F.; Cárdenas, C.; Albericio, F.; Marshall, S.H. A natural peptide and its variants derived from the processing of infectious pancreatic necrosis virus (IPNV) displaying enhanced antimicrobial activity: a novel alternative for the control of bacterial diseases. Peptides, 2011, 32(5), 852-858.
[http://dx.doi.org/10.1016/j.peptides.2011.01.026] [PMID: 21291934]
[80]
Krauson, A.J.; He, J.; Wimley, A.W.; Hoffmann, A.R.; Wimley, W.C. Synthetic molecular evolution of pore-forming peptides by iterative combinatorial library screening. ACS Chem. Biol., 2013, 8(4), 823-831.
[http://dx.doi.org/10.1021/cb300598k] [PMID: 23394375]
[81]
Rausch, J.M.; Marks, J.R.; Wimley, W.C. Rational combinatorial design of pore-forming beta-sheet peptides. Proc. Natl. Acad. Sci. USA, 2005, 102(30), 10511-10515.
[http://dx.doi.org/10.1073/pnas.0502013102] [PMID: 16020534]
[82]
Rausch, J.M.; Marks, J.R.; Rathinakumar, R.; Wimley, W.C. Beta-sheet pore-forming peptides selected from a rational combinatorial library: mechanism of pore formation in lipid vesicles and activity in biological membranes. Biochemistry, 2007, 46(43), 12124-12139.
[http://dx.doi.org/10.1021/bi700978h] [PMID: 17918962]
[83]
Poirel, L.; Jayol, A.; Nordmann, P. Polymyxins: antibacterial activity, susceptibility testing, and resistance mechanisms encoded by plasmids or chromosomes. Clin. Microbiol. Rev., 2017, 30(2), 557-596.
[http://dx.doi.org/10.1128/CMR.00064-16] [PMID: 28275006]
[84]
Gonzalez-Ruiz, A.; Seaton, R.A.; Hamed, K. Daptomycin: an evidence-based review of its role in the treatment of Gram-positive infections. Infect. Drug Resist., 2016, 9, 47-58.
[PMID: 27143941]
[85]
Vaara, M. New polymyxin derivatives that display improved efficacy in animal infection models as compared to polymyxin B and colistin. Med. Res. Rev., 2018, 38(5), 1661-1673.
[http://dx.doi.org/10.1002/med.21494] [PMID: 29485690]
[86]
Langer, M.; Beck-Sickinger, A.G. Peptides as carrier for tumor diagnosis and treatment. Curr. Med. Chem. Anticancer Agents, 2001, 1(1), 71-93.
[http://dx.doi.org/10.2174/1568011013354877] [PMID: 12678771]
[87]
Salomon, D.S.; Brandt, R.; Ciardiello, F.; Normanno, N. Epidermal growth factor-related peptides and their receptors in human malignancies. Crit. Rev. Oncol. Hematol., 1995, 19(3), 183-232.
[http://dx.doi.org/10.1016/1040-8428(94)00144-I] [PMID: 7612182]
[88]
Geng, L.; Wang, Z.; Jia, X.; Han, Q.; Xiang, Z.; Li, D.; Yang, X.; Zhang, D.; Bu, X.; Wang, W.; Hu, Z.; Fang, Q. HER2 targeting peptides screening and applications in tumor imaging and drug delivery. Theranostics, 2016, 6(8), 1261-1273.
[http://dx.doi.org/10.7150/thno.14302] [PMID: 27279916]
[89]
Zheng, H.; Wang, W.; Li, X.; Wang, Z.; Hood, L.; Lausted, C.; Hu, Z. An automated Teflon microfluidic peptide synthesizer. Lab Chip, 2013, 13(17), 3347-3350.
[http://dx.doi.org/10.1039/c3lc50632k] [PMID: 23835869]
[90]
Wang, W.; Huang, Y.; Liu, J.; Xie, Y.; Zhao, R.; Xiong, S.; Liu, G.; Chen, Y.; Ma, H. Integrated SPPS on continuous-flow radial microfluidic chip. Lab Chip, 2011, 11(5), 929-935.
[http://dx.doi.org/10.1039/c0lc00542h] [PMID: 21270975]
[91]
Xiang, Z.; Yang, X.; Xu, J.; Lai, W.; Wang, Z.; Hu, Z.; Tian, J.; Geng, L.; Fang, Q. Tumor detection using magnetosome nanoparticles functionalized with a newly screened EGFR/HER2 targeting peptide. Biomaterials, 2017, 115, 53-64.
[http://dx.doi.org/10.1016/j.biomaterials.2016.11.022] [PMID: 27888699]
[92]
Cross, S.; Baroni, M.; Goracci, L.; Cruciani, G. GRID-based three-dimensional pharmacophores I: FLAPpharm, a novel approach for pharmacophore elucidation. J. Chem. Inf. Model., 2012, 52(10), 2587-2598.
[http://dx.doi.org/10.1021/ci300153d] [PMID: 22970894]
[93]
Baroni, M.; Cruciani, G.; Sciabola, S.; Perruccio, F.; Mason, J.S. A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): theory and application. J. Chem. Inf. Model., 2007, 47(2), 279-294.
[http://dx.doi.org/10.1021/ci600253e] [PMID: 17381166]
[94]
Cross, S.; Baroni, M.; Carosati, E.; Benedetti, P.; Clementi, S. FLAP: GRID molecular interaction fields in virtual screening. validation using the DUD data set. J. Chem. Inf. Model., 2010, 50(8), 1442-1450.
[http://dx.doi.org/10.1021/ci100221g] [PMID: 20690627]
[95]
von Itzstein, M.; Wu, W.Y.; Kok, G.B.; Pegg, M.S.; Dyason, J.C.; Jin, B.; Van Phan, T.; Smythe, M.L.; White, H.F.; Oliver, S.W. Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature, 1993, 363(6428), 418-423.
[http://dx.doi.org/10.1038/363418a0] [PMID: 8502295]
[96]
Allinger, N.L.; Yuh, Y.H.; Lii, J.H. Molecular mechanics. The MM3 force field for hydrocarbons. J. Am. Chem. Soc., 1989, 111(23), 8551-8566.
[http://dx.doi.org/10.1021/ja00205a001]
[97]
Ruvo, M.; Caporale, A.; Incisivo, M.; Cross, S.; Doti, N.; Focà, A.; Focà, G.; Mascanzoni, F.; Raimondo, D.; Falcigno, L.; Calvanese, L.; D’Auria, G.; Iaccarino, E.; Sandomenico, A.; Chambery, A.; Rega, C.; Cruciani, G. In: 15th Naples Workshop on Bioactive Peptides; Naples. Morelli, G.; Ed, 2016.


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VOLUME: 27
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