Abstract
Molecular dynamics simulations were performed in aqueous solution to elucidate an atomistic level picture of complex formation between cucurbit[7]uril (CB7) and three standard aromatic amino acids: tyrosine, tryptophan, and phenylalanine. It was found that all three amino acids formed stable host–guest complexes with CB7, in which the side chain was included inside the hydrophobic cavity and the ammonium and carboxylate groups were excluded. The major forces driving complexation, as calculated from the MM-PBSA method, were the electrostatic and van der Waal interactions. To better understand the effect of pH and the roles of the ammonium and carboxylate groups in the complexation process, simulations were performed for phenylalanine considering different protonation state (at low and high pH) as well as for the deaminated and decarboxylated forms of phenylalanine. The results showed that, compared to phenylalanine at neutral pH (exists as zwitterion), low pH resulted in an increased complex stability for the cationic form, deamination and high pH reduced the stability, while decarboxylation did not result in a significant change. Results from quantum-chemical calculations correlated well with the simulation data.
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Wu, G.: Amino acids: metabolism, functions, and nutrition. Amino Acids 37, 1–17 (2009). https://doi.org/10.1007/s00726-009-0269-0
Maeda, J., Higashiyama, M., Imaizumi, A., Nakayama, T., Yamamoto, H., Daimon, T., Yamakado, M., Imamura, F., Kodama, K.: Possibility of multivariate function composed of plasma amino acid profiles as a novel screening index for non-small cell lung cancer: a case control study. BMC Cancer 10, 690 (2010). https://doi.org/10.1186/1471-2407-10-690
Aliu, E., Kanungo, S., Arnold, G.L.: Amino acid disorders. Ann. Transl. Med. 6, 471 (2018). https://doi.org/10.21037/atm.2018.12.12
Kessler, H.: Conformation and biological activity of cyclic peptides. Angew. Chem. Int. Ed. 21, 512–523 (1982). https://doi.org/10.1002/anie.198205121
Sewald, N., Jakubke, H.: Peptides: Chemistry and Biology, 2nd edn. Wiley-VCH, Weinheim (2009)
Venkatesan, K., Rual, J.-F., Vazquez, A., Stelzl, U., Lemmens, I., Hirozane-Kishikawa, T., Hao, T., Zenkner, M., Xin, X., Goh, K.-I., Yildirim, M.A., Simonis, N., Heinzmann, K., Gebreab, F., Sahalie, J.M., Cevik, S., Simon, C., de Smet, A.-S., Dann, E., Smolyar, A., Vinayagam, A., Yu, H., Szeto, D., Borick, H., Dricot, A., Klitgord, N., Murray, R.R., Lin, C., Lalowski, M., Timm, J., Rau, K., Boone, C., Braun, P., Cusick, M.E., Roth, F.P., Hill, D.E., Tavernier, J., Wanker, E.E., Barabási, A.-L., Vidal, M.: An empirical framework for binary interactome mapping. Nat. Methods 6, 83–90 (2009). https://doi.org/10.1038/nmeth.1280
Still, W.C.: Discovery of sequence-selective peptide binding by synthetic receptors using encoded combinatorial libraries. Acc. Chem. Res. 29, 155–163 (1996). https://doi.org/10.1021/ar950166i
Peczuh, M.W., Hamilton, A.D.: Peptide and protein recognition by designed molecules. Chem. Rev. 100, 2479–2494 (2000). https://doi.org/10.1021/cr9900026
Baell, J.B., Huang, D.C.S.: Prospects for targeting the Bcl-2 family of proteins to develop novel cytotoxic drugs. Biochem. Pharmacol. 64, 851–863 (2002). https://doi.org/10.1016/S0006-2952(02)01148-6
Boger, D.L., Desharnais, J., Capps, K.: Solution-phase combinatorial libraries: modulating cellular signaling by targeting protein–protein or protein–DNA interactions. Angew. Chem. Int. Ed. 42, 4138–4176 (2003). https://doi.org/10.1002/anie.200300574
Wright, A.T., Griffin, M.J., Zhong, Z., McCleskey, S.C., Anslyn, E.V., McDevitt, J.T.: Differential receptors create patterns that distinguish various proteins. Angew. Chem. Int. Ed. 44, 6375–6378 (2005). https://doi.org/10.1002/anie.200501137
Heitmann, L.M., Taylor, A.B., Hart, P.J., Urbach, A.R.: Sequence-specific recognition and cooperative dimerization of N-terminal aromatic peptides in aqueous solution by a synthetic host. J. Am. Chem. Soc. 128, 12574–12581 (2006). https://doi.org/10.1021/ja064323s
Murray, J.K., Gellman, S.H.: Targeting protein–protein interactions: lessons from p53/MDM2. Pept. Sci. 88, 657–686 (2007). https://doi.org/10.1002/bip.20741
Grauer, A., König, B.: Peptidomimetics: a versatile route to biologically active compounds. Eur. J. Org. Chem. 2009, 5099–5111 (2009). https://doi.org/10.1002/ejoc.200900599
Uhlenheuer, D.A., Petkau, K., Brunsveld, L.: Combining supramolecular chemistry with biology. Chem. Soc. Rev. 39, 2817–2826 (2010). https://doi.org/10.1039/B820283B
Chinai, J.M., Taylor, A.B., Ryno, L.M., Hargreaves, N.D., Morris, C.A., Hart, P.J., Urbach, A.R.: Molecular recognition of insulin by a synthetic receptor. J. Am. Chem. Soc. 133, 8810–8813 (2011). https://doi.org/10.1021/ja201581x
Mutihac, L., Lee, J.H., Kim, J.S., Vicens, J.: Recognition of amino acids by functionalized calixarenes. Chem. Soc. Rev. 40, 2777–2796 (2011). https://doi.org/10.1039/C0CS00005A
McGovern, R.E., Fernandes, H., Khan, A.R., Power, N.P., Crowley, P.B.: Protein camouflage in cytochrome c–calixarene complexes. Nat. Chem. 4, 527–533 (2012). https://doi.org/10.1038/nchem.1342
Dang, D.T., Nguyen, H.D., Merkx, M., Brunsveld, L.: Supramolecular control of enzyme activity through cucurbit[8]uril-mediated dimerization. Angew. Chem. Int. Ed. 52, 2915–2919 (2013). https://doi.org/10.1002/anie.201208239
Nimse, S.B., Kim, T.: Biological applications of functionalized calixarenes. Chem. Soc. Rev. 42, 366–386 (2013). https://doi.org/10.1039/C2CS35233H
Hamley, I.W.: Small bioactive peptides for biomaterials design and therapeutics. Chem. Rev. 117, 14015–14041 (2017). https://doi.org/10.1021/acs.chemrev.7b00522
Biedermann, F., Rauwald, U., Cziferszky, M., Williams, K.A., Gann, L.D., Guo, B.Y., Urbach, A.R., Bielawski, C.W., Scherman, O.A.: Benzobis(imidazolium)–cucurbit[8]uril complexes for binding and sensing aromatic compounds in aqueous solution. Chem. Eur. J. 16, 13716–13722 (2010). https://doi.org/10.1002/chem.201002274
Bush, M.E., Bouley, N.D., Urbach, A.R.: Charge-mediated recognition of N-terminal tryptophan in aqueous solution by a synthetic host. J. Am. Chem. Soc. 127, 14511–14517 (2005). https://doi.org/10.1021/ja0548440
Bier, D., Rose, R., Bravo-Rodriguez, K., Bartel, M., Ramirez-Anguita, J.M., Dutt, S., Wilch, C., Klärner, F.-G., Sanchez-Garcia, E., Schrader, T., Ottmann, C.: Molecular tweezers modulate 14–3-3 protein–protein interactions. Nat. Chem. 5, 234–239 (2013). https://doi.org/10.1038/nchem.1570
Martins, J.N., Lima, J.C., Basílio, N.: Selective recognition of amino acids and peptides by small supramolecular receptors. Molecules 26, 106 (2021). https://doi.org/10.3390/molecules26010106
Assaf, K.I., Nau, W.M.: Cucurbiturils: from synthesis to high-affinity binding and catalysis. Chem. Soc. Rev. 44, 394–418 (2015). https://doi.org/10.1039/C4CS00273C
Barrow, S.J., Kasera, S., Rowland, M.J., del Barrio, J., Scherman, O.A.: Cucurbituril-based molecular recognition. Chem. Rev. 115, 12320–12406 (2015). https://doi.org/10.1021/acs.chemrev.5b00341
Caso, J.V., Russo, L., Palmieri, M., Malgieri, G., Galdiero, S., Falanga, A., Isernia, C., Iacovino, R.: Investigating the inclusion properties of aromatic amino acids complexing beta-cyclodextrins in model peptides. Amino Acids 47, 2215–2227 (2015). https://doi.org/10.1007/s00726-015-2003-4
Li, C., Ma, J., Zhao, L., Zhang, Y., Yu, Y., Shu, X., Li, J., Jia, X.: Molecular selective binding of basic amino acids by a water-soluble pillar[5]arene. Chem. Commun. 49, 1924–1926 (2013). https://doi.org/10.1039/C3CC38622H
Liu, S., Ruspic, C., Mukhopadhyay, P., Chakrabarti, S., Zavalij, P.Y., Isaacs, L.: The cucurbit[n]uril family: prime components for self-sorting systems. J. Am. Chem. Soc. 127, 15959–15967 (2005). https://doi.org/10.1021/ja055013x
Kaifer, A.E.: Toward reversible control of cucurbit[n]uril complexes. Acc. Chem. Res. 47, 2160–2167 (2014). https://doi.org/10.1021/ar5001204
Nau, W.M., Florea, M., Assaf, K.I.: Deep inside cucurbiturils: physical properties and volumes of their inner cavity determine the hydrophobic driving force for host–guest complexation. Isr. J. Chem. 51, 559–577 (2011). https://doi.org/10.1002/ijch.201100044
Biedermann, F., Uzunova, V.D., Scherman, O.A., Nau, W.M., De Simone, A.: Release of high-energy water as an essential driving force for the high-affinity binding of cucurbit[n]urils. J. Am. Chem. Soc. 134, 15318–15323 (2012). https://doi.org/10.1021/ja303309e
Biedermann, F., Nau, W.M., Schneider, H.-J.: The hydrophobic effect revisited: studies with supramolecular complexes imply high-energy water as a noncovalent driving force. Angew. Chem. Int. Ed. 53, 11158–11171 (2014). https://doi.org/10.1002/anie.201310958
Buschmann, H.-J., Schollmeyer, E., Mutihac, L.: The formation of amino acid and dipeptide complexes with α-cyclodextrin and cucurbit[6]uril in aqueous solutions studied by titration calorimetry. Thermochim. Acta 399, 203–208 (2003). https://doi.org/10.1016/S0040-6031(02)00462-8
Buschmann, H.-J., Mutihac, L., Mutihac, R.-C., Schollmeyer, E.: Complexation behavior of cucurbit[6]uril with short polypeptides. Thermochim. Acta 430, 79–82 (2005). https://doi.org/10.1016/j.tca.2005.01.002
Rekharsky, M.V., Yamamura, H., Inoue, C., Kawai, M., Osaka, I., Arakawa, R., Shiba, K., Sato, A., Ko, Y.H., Selvapalam, N., Kim, K., Inoue, Y.: Chiral recognition in cucurbituril cavities. J. Am. Chem. Soc. 128, 14871–14880 (2006). https://doi.org/10.1021/ja063323p
Rajgariah, P., Urbach, A.R.: Scope of amino acid recognition by cucurbit[8]uril. J. Incl. Phenom. Macrocycl. Chem. 62, 251–254 (2008). https://doi.org/10.1007/s10847-008-9464-y
Gamal-Eldin, M.A., Macartney, D.H.: Selective molecular recognition of methylated lysines and arginines by cucurbit[6]uril and cucurbit[7]uril in aqueous solution. Org. Biomol. Chem. 11, 488–495 (2013). https://doi.org/10.1039/C2OB27007B
Biedermann, F., Nau, W.M.: Noncovalent chirality sensing ensembles for the detection and reaction monitoring of amino acids, peptides, proteins, and aromatic drugs. Angew. Chem. Int. Ed. 53, 5694–5699 (2014). https://doi.org/10.1002/anie.201400718
Ma, F., Zheng, X., Xie, L., Li, Z.: Sequence-dependent nanomolar binding of tripeptides containing N-terminal phenylalanine by cucurbit[7]uril: a theoretical study. J. Mol. Liq. 328, 115479 (2021). https://doi.org/10.1016/j.molliq.2021.115479
Kim, J., Jung, I.-S., Kim, S.-Y., Lee, E., Kang, J.-K., Sakamoto, S., Yamaguchi, K., Kim, K.: New cucurbituril homologues: syntheses, isolation, characterization, and X-ray crystal structures of cucurbit[n]uril (n = 5, 7, and 8). J. Am. Chem. Soc. 122, 540–541 (2000). https://doi.org/10.1021/ja993376p
Case, D., Betz, R., Cerutti, D.S., Cheatham, T., Darden, T., Duke, R., Giese, T.J., Gohlke, H., Götz, A., Homeyer, N., Izadi, S., Janowski, P., Kaus, J., Kovalenko, A., Lee, T.-S., LeGrand, S., Li, P., Lin, C., Luchko, T., Kollman, P.: Amber 16. University of California, San Francisco (2016)
Horn, A.H.C.: A consistent force field parameter set for zwitterionic amino acid residues. J. Mol. Model. 20, 2478 (2014). https://doi.org/10.1007/s00894-014-2478-z
Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., Case, D.A.: Development and testing of a general amber force field. J. Comput. Chem. 25, 1157–1174 (2004). https://doi.org/10.1002/jcc.20035
Bayly, C.I., Cieplak, P., Cornell, W., Kollman, P.A.: A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 97, 10269–10280 (1993). https://doi.org/10.1021/j100142a004
Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L.: Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983). https://doi.org/10.1063/1.445869
York, D.M., Darden, T.A., Pedersen, L.G.: The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J. Chem. Phys. 99, 8345–8348 (1993). https://doi.org/10.1063/1.465608
Ryckaert, J.-P., Ciccotti, G., Berendsen, H.J.C.: Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327–341 (1977). https://doi.org/10.1016/0021-9991(77)90098-5
Humphrey, W., Dalke, A., Schulten, K.: VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996). https://doi.org/10.1016/0263-7855(96)00018-5
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E.: UCSF Chimera: a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). https://doi.org/10.1002/jcc.20084
Rawashdeh, A.M.M., El-Barghouthi, M.I., Assaf, K.I., Al-Gharabli, S.I.: Complexation of N-methyl-4-(p-methyl benzoyl)-pyridinium methyl cation and its neutral analogue by cucurbit[7]uril and β-cyclodextrin: a computational study. J. Incl. Phenom. Macrocycl. Chem. 64, 357–365 (2009). https://doi.org/10.1007/s10847-009-9574-1
El-Barghouthi, M.I., Assaf, K.I., Rawashdeh, A.M.M.: Molecular dynamics of methyl viologen-cucurbit[n]uril complexes in aqueous solution. J. Chem. Theory Comput. 6, 984–992 (2010). https://doi.org/10.1021/ct900622h
Malhis, L.D., Bodoor, K., Assaf, K.I., Al-Sakhen, N.A., El-Barghouthi, M.I.: Molecular dynamics simulation of a cucurbituril based molecular switch triggered by pH changes. Comput. Theor. Chem. 1066, 104–112 (2015). https://doi.org/10.1016/j.comptc.2015.05.010
El-Barghouthi, M.I., Abdel-Halim, H.M., Haj-Ibrahim, F.J., Bodoor, K., Assaf, K.I.: Molecular dynamics of nor-Seco-cucurbit[10]uril complexes. J. Incl. Phenom. Macrocycl. Chem. 82, 323–333 (2015). https://doi.org/10.1007/s10847-015-0488-9
El-Barghouthi, M.I., Abdel-Halim, H.M., Haj-Ibrahim, F.J., Assaf, K.I.: Molecular dynamics simulation study of the structural features and inclusion capacities of cucurbit[6]uril derivatives in aqueous solutions. Supramol. Chem. 27, 80–89 (2015). https://doi.org/10.1080/10610278.2014.910601
Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., et al.: Gaussian 16, Revision A.03. Gaussian, Inc., Wallingford, CT (2016)
Becke, A.D.: Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648–5652 (1993). https://doi.org/10.1063/1.464913
Lee, C., Yang, W., Parr, R.G.: Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37, 785–789 (1988). https://doi.org/10.1103/PhysRevB.37.785
Marenich, A.V., Cramer, C.J., Truhlar, D.G.: Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J. Phys. Chem. B 113, 6378–6396 (2009). https://doi.org/10.1021/jp810292n
Zhao, Y., Truhlar, D.: The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor. Chem. Acc. 120, 215–241 (2008). https://doi.org/10.1021/acs.jctc.6b00637
Grimme, S.: Supramolecular binding thermodynamics by dispersion-corrected density functional theory. Chem. Eur. J. 18, 9955–9964 (2012). https://doi.org/10.1002/chem.201200497
Lee, J.W., Lee, H.H.L., Ko, Y.H., Kim, K., Kim, H.I.: Deciphering the specific high-affinity binding of cucurbit[7]uril to amino acids in water. J. Phys. Chem. B. 119, 4628–4636 (2015). https://doi.org/10.1021/acs.jpcb.5b00743
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Bodoor, K., El-Barghouthi, M.I., Assaf, K.I. et al. A molecular dynamics study of the complexation of tryptophan, phenylalanine and tyrosine amino acids with cucurbit[7]uril. J Incl Phenom Macrocycl Chem 102, 159–168 (2022). https://doi.org/10.1007/s10847-021-01113-2
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DOI: https://doi.org/10.1007/s10847-021-01113-2