Abstract
This article deals with the synthesis in solid phase and characterization of a nucleoamino amide, based on a phenylalaninamide moiety which was N-conjugated to a thymine nucleobase. In analogy to the natural nucleobase–amino acid conjugates, endowed with a wide range of biological properties, the nucleoamino amide interacts with single-stranded nucleic acids as verified in DNA- and RNA-binding assays conducted by CD and UV spectroscopies. These technologies were used to show also that this conjugate binds serum proteins altering significantly their secondary structure, as evidenced by CD and UV using BSA as a model. The biomolecular recognition seems to rely on the ability of the novel compound to bind aromatic and heteroaromatic moieties in protein and nucleic acids, not hindered by its propensity to self-assemble in aqueous solution, behavior suggested by dynamic light scattering (DLS) and CD spectroscopy in concentration- and temperature-dependent experiments. Finally, the high stability in human serum concurs to define the picture of the nucleoamino amide: this enzymatically stable drug candidate could interfere with protein and single-stranded nucleic acid-driven biological processes, particularly those associated with mRNA poly(A) tail, and its self-assembling nature, in analogy to other l-Phe-based systems, discloses new scenarios in drug delivery technology.
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References
Cangelosi VM, Zakharov LN, Johnson DW (2010) Supramolecular “transmetalation” leads to an unusual self-assembled P2L3 cryptand. Angew Chem Int Ed 49:1248–1251
Dobryszycki P, Kołodziejczyk R, Krowarsch D, Gapiński J, Ozyhar A, Kochman M (2004) Unfolding and refolding of juvenile hormone binding protein. Biophys J 86:1138–1148
Dolman NP, More JC, Alt A, Knauss JL, Troop HM, Bleakman D, Collingridge GL, Jane DE (2006) Structure-activity relationship studies on N3-substituted willardiine derivatives acting as AMPA or kainate receptor antagonists. J Med Chem 49:2579–2592
Du X, Zhou J, Guvench O, Sangiorgi FO, Li X, Zhou N, Xu B (2014) Supramolecular assemblies of a conjugate of nucleobase, amino acids, and saccharide act as agonists for proliferation of embryonic stem cells and development of zygotes. Bioconjug Chem 25:1031–1035
Esposito G, Teta R, Miceli R, Ceccarelli LS, Della Sala G, Camerlingo R, Irollo E, Mangoni A, Pirozzi A, Costantino V (2015) Isolation and assessment of the in vitro anti-tumor activity of smenothiazole A and B, chlorinated thiazole-containing peptide/polyketides from the Caribbean sponge, Smenospongia aurea. Mar Drugs 13:444–459
Giri P, Kumar GS (2010) Molecular recognition of poly(A) targeting by protoberberine alkaloids: in vitro biophysical studies and biological perspectives. Mol BioSyst 6:81–88
Goerbitz CH (2006) The structure of nanotubes formed by diphenylalanine, the core recognition motif of Alzheimer's â-amyloid polypeptide. Chem Commun 2332–2334
Gospodarska E, Kupniewska-Kozak A, Goch G, Dadlez M (2011) The structure of nanotubes formed by diphenylalanine, the core recognition motif of Alzheimer’s beta-amyloid polypeptide. Biochim Biophys Acta 1814:592–609
Karst JC, Sotomayor Pérez AC, Guijarro JI, Raynal B, Chenal A, Ladant D (2010) Calmodulin-induced conformational and hydrodynamic changes in the catalytic domain of Bordetella pertussis adenylate cyclase toxin. Biochemistry 49:318–328
Katritzky AR, Mohapatra PP, Singh S, Clemens N, Kirichenko K (2005) Synthesis of α-amino amides via α-amino imidoylbenzotriazoles. J Serb Chem Soc 70:319–327
Kitamura K, Kinsui EZ, Abe F (2017) Critical role of the proton-dependent oligopeptide transporter (POT) in the cellular uptake of the peptidyl nucleoside antibiotic, blasticidin S. Biochim Biophys Acta 1864:393–398
Lamberth C (2016) Naturally occurring amino acid derivatives with herbicidal, fungicidal or insecticidal activity. Amino Acids 48:929–940
Lilla EA, Yokoyama K (2016) Carbon extension in peptidylnucleoside biosynthesis by radical SAM enzymes. Nat Chem Biol 12:905–907
Lindquist NR, Carter TG, Cangelosi VM, Zakharov LN, Johnson DW (2010) Three’s company: co-crystallization of a self-assembled S(4) metallacyclophane with two diastereomeric metallacycle intermediates. Chem Commun 46:3505–3507
Madonna S, Scarponi C, Doti N, Carbone T, Cavani A, Scognamiglio PL, Marasco D, Albanesi C (2013) Therapeutical potential of a peptide mimicking the SOCS1 kinase inhibitory region in skin immune responses. Eur J Immunol 43:1883–1895
Mik V, Mičková Z, Doležal K, Frébort I, Pospíšil T (2017) Activity of (+)-Discadenine as a plant cytokinin. J Nat Prod 80:2136–2140
Mishra A, Panda JJ, Basu A, Chauhan VS (2008) Nanovesicles based on self-assembly of conformationally constrained aromatic residue containing amphiphilic dipeptides. Langmuir 24:4571–4576
Miyauchi K, Kimura S, Suzuki T (2013) A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat Chem Biol 9:105–111
Mizutani M, Jitsukawa K, Masuda H, Einaga H (1996) Synthesis and X-ray structure of a unique multinuclear complex constructed by a nucleobase-amino acid DL-willardiine. Chem Comm 11:1389–1390
Musumeci D, Rozza L, Merlino A, Paduano L, Marzo T, Massai L, Messori L, Montesarchio D (2015) Interaction of anticancer Ru(III) complexes with single stranded and duplex DNA model systems. Dalton Trans 44:13914–13925
Musumeci D, Roviello V, Roviello GN (2018) DNA- and RNA-binding ability of oligoDapT, a nucleobase-decorated peptide, for biomedical applications. Int J Nanomed 13:2613–2629
Pape VF, Türk D, Szabó P, Wiese M, Enyedy EA, Szakács G (2015) Synthesis and characterization of the anticancer and metal binding properties of novel pyrimidinylhydrazone derivatives. J Inorg Biochem 144:18–30
Pinto B, Rusciano G, D’Errico S, Borbone N, Sasso A, Piccialli V, Mayol L, Oliviero G, Piccialli G (2017) Synthesis and label free characterization of a bimolecular PNA homo quadruplex. Biochim Biophys Acta 1861:1222–1228
Reches M, Gazit E (2006) Controlled patterning of aligned self-assembled peptide nanotubes. Nat Nanotechnol 1:195–200
Roviello GN, Musumeci D (2016) Synthetic approaches to nucleopeptides containing all four nucleobases, and nucleic acid-binding studies on a mixed-sequence nucleo-oligolysine. RSC Adv 6:63578–63585
Roviello GN, Musumeci D, Pedone C, Bucci EM (2010a) Synthesis, characterization and hybridization studies of an alternate nucleo-epsilon/gamma-peptide: complexes formation with natural nucleic acids. Amino Acids 38:103–111
Roviello GN, Di Gaetano S, Capasso D, Cesarani A, Bucci EM, Pedone C (2010b) Synthesis, spectroscopic studies and biological activity of a novel nucleopeptide with Moloney murine leukemia virus reverse transcriptase inhibitory activity. Amino Acids 38:1489–1496
Roviello GN, Crescenzo C, Capasso D, Di Gaetano S, Franco S, Bucci EM, Pedone C (2010c) Synthesis of a novel Fmoc-protected nucleoaminoacid for the solid phase assembly of 4-piperidyl glycine/l-arginine-containing nucleopeptides and preliminary RNA: interaction studies. Amino Acids 39:795–800
Roviello GN, Ricci A, Bucci EM, Pedone C (2011a) Synthesis, biological evaluation and supramolecular assembly of novel analogues of peptidyl nucleosides. Mol BioSyst 7:1773–1778
Roviello GN, Di Gaetano S, Capasso D, Franco S, Crescenzo C, Bucci EM, Pedone C (2011b) RNA-binding and viral reverse transcriptase inhibitory activity of a novel cationic diamino acid-based peptide. J Med Chem 54:2095–2101
Roviello GN, Musumeci D, Bucci EM, Pedone C (2011c) Synthesis and characterization of a novel ester-based nucleoamino acid for the assembly of aromatic nucleopeptides for biomedical applications. Int J Pharm 415:206–210
Roviello GN, Musumeci D, Roviello V, Pirtskhalava M, Egoyan A, Mirtskhulava M (2015) Natural and artificial binders of polyriboadenylic acid and their effect on RNA structure. Beilstein J Nanotechnol 6:1338–1347
Roviello GN, Vicidomini C, Di Gaetano S, Capasso D, Musumeci D, Roviello V (2016a) Solid phase synthesis and RNA-binding activity of an arginine-containing nucleopeptide. RSC Adv 6:14140–14148
Roviello GN, Roviello V, Autiero I, Saviano M (2016b) Solid phase synthesis of TyrT, a thymine–tyrosine conjugate with poly(A) RNA-binding ability. RSC Adv 6:27607–27613
Roviello GN, Oliviero G, Di Napoli A, Borbone N, Piccialli G (2018) Synthesis, self-assembly-behavior and biomolecular recognition properties of thyminyl dipeptides. Arab J Chem. https://doi.org/10.1016/j.arabjc.2018.02.014
Rozan P, Kuo YH, Lambein F (2001) Amino acids in seeds and seedlings of the genus Lens. Phytochemistry 58:281–289
Saghyan AS, Simonyan HM, Petrosyan SG, Geolchanyan AV, Roviello GN, Musumeci D, Roviello V (2014) Thiophenyl-substituted triazolyl-thione l-alanine: asymmetric synthesis, aggregation and biological properties. Amino Acids 46:2325–2332
Scognamiglio PL, Di Natale C, Leone M, Poletto M, Vitagliano L, Tell G, Marasco D (2014) G-quadruplex DNA recognition by nucleophosmin: new insights from protein dissection. Biochim Biophys Acta 1840:2050–2059
Song G, Ren J (2010) Recognition and regulation of unique nucleic acid structures by small molecules. Chem Commun 46:7283–7294
Teta R, Irollo E, Della Sala G, Pirozzi G, Mangoni A, Costantino V (2013) Smenamides A and B, chlorinated peptide/polyketide hybrids containing a dolapyrrolidinone unit from the Caribbean sponge Smenospongia aurea. Evaluation of their role as leads in antitumor drug research. Mar Drugs 11:4451–4463
Weckenmann NM, Nachtsheim BJ (2015) Enantioselective synthesis of D-α-(Uracil-5-yl)glycine derivatives and their racemization-free incorporation into a Model-Peptide. Eur J Org Chem 30:6624–6630
Wu D, Zhou J, Shi J, Du X, Xu B (2014) A naphthalene-containing amino acid enables hydrogelation of a conjugate of nucleobase-saccharide-amino acids. Chem Commun 50:1992–1994
Yuan ZY, Lu X, Lei F, Chai YS, Wang YG, Jiang JF, Feng TS, Wang XP, Yu X, Yan XJ, Xing DM, Du LJ (2015) TATA boxes in gene transcription and poly(A) tails in mRNA stability: new perspective on the effects of berberine. Sci Rep. 5:18326. https://doi.org/10.1038/srep18326
Acknowledgements
I thank Prof. Antonio Roviello for his precious suggestions and Mr. Leopoldo Zona for his invaluable technical assistance.
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An abbreviation list and the description of materials and methods, together with the copies of 1H and 13C NMR spectra, two energy-minimized 3D molecular views and some predicted properties of L-PheT are reported in this section
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Roviello, G.N. Novel insights into nucleoamino acids: biomolecular recognition and aggregation studies of a thymine-conjugated l-phenyl alanine. Amino Acids 50, 933–941 (2018). https://doi.org/10.1007/s00726-018-2562-2
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DOI: https://doi.org/10.1007/s00726-018-2562-2