The guanidiniocarbonylpyrrole–fluorophore conjugates as theragnostic tools for dipeptidyl peptidase III monitoring and inhibition

References

• Abramić, M., Šimaga, S., Osmak, M., Cicin-Sain, L., Vukelic, B., Vlahoviček, K., & Dolovčak, L. (2004). Highly reactive cysteine residues are part of the substrate binding site of mammalian dipeptidyl peptidases III. The International Journal of Biochemistry & Cell Biology, 36, 434–446. doi:10.1016/S1357-2725(03)00267-X
   PubMed Web of Science ®Google Scholar
• Agić, D., Brkić, H., Tomić, S., Karačić, Z., Špoljarević, M., Lisjak, M., … Abramić, M. (2017). Validation of flavonoids as potential dipeptidyl peptidase III inhibitors: Experimental and computational approach. Chemical Biology & Drug Design, 89, 619–627. doi:10.1111/cbdd.12887
   PubMed Web of Science ®Google Scholar
• Armitage, B. A. (2005). DNA binders and related subjects: Cyanine dye-DNA interactions: Intercalation, groove binding, and aggregation. Topics in Current Chemistry, 253, 55–76.
   Web of Science ®Google Scholar
• Baršun, M., Jajčanin, N., Vukelić, B., Špoljarić, J., & Abramić, M. (2007). Human dipeptidyl peptidase III acts as a post-proline-cleaving enzyme on endomorphins. Biological Chemistry, 388(3), 343–348. doi:10.1515/BC.2007.039
   PubMed Web of Science ®Google Scholar
• Borštnar, R., Repič, M., Lynn Kamerlin, S. C., Vianello, R., & Mavri, J. (2012). Computational study of the pKa values of potential catalytic residues in the active site of monoamine oxidase B. Journal of Chemical Theory and Computation, 8(10), 3864–3870. doi:10.1021/ct300119u
   PubMed Web of Science ®Google Scholar
• Dhanda, S., Singh, H., Singh, J., & Singh, T. P. (2008). Functional characterization and specific effects of various peptides on enzymatic activity of a DPP-III homologue from goat brain. Journal of Enzyme Inhibition and Medicinal Chemistry, 23(2), 174–181. doi:10.1080/14756360701450996
   PubMed Web of Science ®Google Scholar
• Korshun, V. A., Stetsenko, D. A., & Gait, M. J. (2002). Novel uridin-2′-yl carbamates: Synthesis, incorporation into oligodeoxyribonucleotides, and remarkable fluorescence properties of 2′-pyren-1-ylmethylcarbamate. ChemInform, 1, 1092–1104. doi:10.1002/chin.200235214
   Google Scholar
• Kostenko, E., Dobrikov, M., Pyshnyi, D., Petyuk, V., Komarova, N., Vlassov, V., & Zenkova, M. (2001). 5'-bis-pyrenylated oligonucleotides displaying excimer fluorescence provide sensitive probes of RNA sequence and structure. Nucleic Acids Research, 29(17), 3611–3620. doi:10.1093/nar/29.17.3611
   PubMed Web of Science ®Google Scholar
• Kumar, P., Reithofer, V., Reisinger, M., Wallner, S., Pavkov-Keller, T., Macheroux, P., & Gruber, K. (2016). Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition. Scientific Reports, 6, 23787. doi:10.1038/srep23787
   PubMed Web of Science ®Google Scholar
• Lakowicz, J. R. (1999). Principles of fluorescence spectroscopy. New York, NY: Kluwer Academic/Plenum.
   Google Scholar
• Lehrer, S. S. (1997). Intramolecular pyrene excimer fluorescence: A probe of proximity and protein conformational change. Methods in Enzymology, 278, 286–295.
   PubMed Web of Science ®Google Scholar
• Mačak Safranko, Z., Sobočanec, S., Šarić, A., Jajčanin-Jozić, N., Krsnik, Z., Aralica, G., … Abramić, M. (2015). The effect of 17 beta-estradiol on the expression of dipeptidyl peptidase III and heme oxygenase 1 in liver of CBA/H mice. Journal of Endocrinological Investigation, 38, 471–479. doi:10.1007/s40618-014-0217-z
   PubMed Web of Science ®Google Scholar
• Mahara, A., Iwase, R., Sakamoto, T., Yamana, K., Yamaoka, T., & Murakami, A. (2002). Bispyrene-conjugated 2'-O-methyloligonucleotide as a highly specific RNA-recognition probe. Angewandte Chemie International Edition, 41(19), 3648–3650. doi:10.1002/1521-3773(20021004)41:19<3648::AID-ANIE3648>3.0.CO;2-Y
   PubMed Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. doi:10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Matić, J., Šupljika, F., Tir, N., Piotrowski, P., Schmuck, C., Abramić, M., … Tomić, S. (2016). Guanidiniocarbonyl-pyrrole-aryl conjugates as inhibitors of human dipeptidyl peptidase III: Combined experimental and computational study. RSC Advances, 6(86), 83044–83052. doi:10.1039/C6RA16966J
   Web of Science ®Google Scholar
• Matovina, M., Agić, D., Abramić, M., Matić, S., Karačić, Z., & Tomić, S. (2017). New findings about human dipeptidyl peptidase III based on mutations found in cancer. RSC Advances, 7(58), 36326–36334. doi:10.1039/C7RA02642K
   Web of Science ®Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. doi:10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Mycek, M.-A., & Pogue, B. W. (2003). Handbook of biomedical fluorescence. Boca Raton, FL: CRC Press.
   Google Scholar
• Pang, X. L., Shimizu, A., Kurita, S., Zankov, D. P., Takeuchi, K., Yasuda-Yamahara, M., … Ogita, H. (2016). Novel therapeutic role for dipeptidyl peptidase III in the treatment of hypertension. Hypertension, 68(3), 630–641. doi:10.1161/HYPERTENSIONAHA.116.07357
   PubMed Web of Science ®Google Scholar
• Prajapati, S. C., & Chauhan, S. S. (2011). Dipeptidyl peptidase III: A multifaceted oligopeptide N-end cutter. FEBS Journal, 278(18), 3256–3276. doi:10.1111/j.1742-4658.2011.08275.x
   PubMed Web of Science ®Google Scholar
• Prajapati, S. C., & Chauhan, S. S. (2016). Human dipeptidyl peptidase III mRNA variant I and II are expressed concurrently in multiple tumor derived cell lines and translated at comparable efficiency in vitro. Molecular Biology Reports, 43(6), 457–462. doi:10.1007/s11033-016-3996-9
   PubMed Web of Science ®Google Scholar
• Schmuck, C. (2011). A journey through 12 years of interacting molecules: From artificial amino acid receptors to the recognition of biomolecules and switchable nanomaterials. Synlett, 2011(13), 1798–1815. doi:10.1055/s-0030-1260946
   Google Scholar
• Shi, C. H., Wu, J. B., & Pan, D. F. (2016). Review on near-infrared heptamethine cyanine dyes as theranostic agents for tumor imaging, targeting, and photodynamic therapy. Journal of Biomedical Optics, 21(5), 050901. doi:10.1117/1.JBO.21.5.050901
   PubMed Web of Science ®Google Scholar
• Šmidlehner, T., Karačić, Z., Tomić, S., Schmuck, C., & Piantanida, I. (2018). Fluorescent cyanine-guanidiniocarbonyl-pyrrole conjugate with pH-dependent DNA/RNA recognition and DPP III fluorescent labelling and inhibition properties. Monatshefte für Chemie - Chemical Monthly, 149(7), 1307–1313. doi:10.1007/s00706-018-2192-0
   Google Scholar
• Špoljarić, J., Salopek-Sondi, B., Makarević, J., Vukelić, B., Agić, D., Šimaga, S., … Abramić, M. (2009). Absolutely conserved tryptophan in M49 family of peptidases contributes to catalysis and binding of competitive inhibitors. Bioorganic Chemistry, 37(3), 70–76. doi:10.1016/j.bioorg.2009.03.002
   PubMed Web of Science ®Google Scholar
• Tatikolov, A. (2012). Polymethine dyes as spectral-fluorescent probes for biomacromolecules. Journal of Photochemistry and Photobiology C: Photochemistry Reviews, 13(1), 55–90. doi:10.1016/j.jphotochemrev.2011.11.001
   Web of Science ®Google Scholar
• Tomić, A., Berynskyy, M., Wade, R. C., & Tomić, S. (2015). Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding. Molecular Biosystems, 11(11), 3068–3080. doi:10.1039/C5MB00465A
   PubMedGoogle Scholar
• Tomić, A., Gonzalez, M., & Tomić, S. (2012). The large scale conformational change of the human DPP III-substrate prefers the “closed” form. Journal of Chemical Information and Modeling, 52(6), 1583–1594. doi:10.1021/ci300141k
   PubMed Web of Science ®Google Scholar
• Tomić, A., Kovačević, B., & Tomić, S. (2016). Concerted nitrogen inversion and hydrogen bonding to Glu451 are responsible for protein-controlled suppression of the reverse reaction in human DPP III. Physical Chemistry Chemical Physics, 18(39), 27245–27256. doi:10.1039/C6CP04580D
   PubMed Web of Science ®Google Scholar
• Tomić, A., Horvat, G., Ramek, M., Agić, D., Brkić, H., & Tomić, S. (2019). New zinc ion parameters suitable for classical MD simulations of zinc metallopeptidases. Journal of Chemical Information and Modeling, 59(8), 3437–3453. doi:10.1021/acs.jcim.9b00235
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. doi:10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., & Hou, T. (2019). End-point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chemical Reviews, 119(16), 9478. doi:10.1021/acs.chemrev.9b00055
   PubMed Web of Science ®Google Scholar
• Winnik, F. M. (1993). Photophysics of preassociated pyrenes in aqueous polymer-solutions and in other organized media. Chemical Reviews, 93(2), 587–614. doi:10.1021/cr00018a001
   Web of Science ®Google Scholar
• Yamamoto, Y., Hashimoto, J., Shimamura, M., Yamaguchi, T., & Hazato, T. (2000). Characterization of tynorphin, a potent endogenous inhibitor of dipeptidyl peptidaseIII. Peptides, 21(4), 503–508. doi:10.1016/S0196-9781(00)00174-1
   PubMed Web of Science ®Google Scholar
• Yamana, K., Zako, H., Asazuma, K., Iwase, R., Nakano, H., & Murakami, A. (2001). Fluorescence detection of specific RNA sequences using 2'-pyrene-modified oligoribonucleotides. Angewandte Chemie International Edition, 40(6), 1104–1106. doi:10.1002/1521-3773(20010316)40:6<1104::AID-ANIE11040>3.0.CO;2-2
   PubMed Web of Science ®Google Scholar