Skip to main content
Log in

A molecular dynamics study of the complexation of tryptophan, phenylalanine and tyrosine amino acids with cucurbit[7]uril

  • Original Article
  • Published:
Journal of Inclusion Phenomena and Macrocyclic Chemistry Aims and scope Submit manuscript

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.

Graphical abstract

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Scheme 1
Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  1. Wu, G.: Amino acids: metabolism, functions, and nutrition. Amino Acids 37, 1–17 (2009). https://doi.org/10.1007/s00726-009-0269-0

    Article  CAS  PubMed  Google Scholar 

  2. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Kessler, H.: Conformation and biological activity of cyclic peptides. Angew. Chem. Int. Ed. 21, 512–523 (1982). https://doi.org/10.1002/anie.198205121

    Article  Google Scholar 

  5. Sewald, N., Jakubke, H.: Peptides: Chemistry and Biology, 2nd edn. Wiley-VCH, Weinheim (2009)

    Book  Google Scholar 

  6. 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

    Article  CAS  PubMed  Google Scholar 

  7. 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

    Article  CAS  Google Scholar 

  8. 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

    Article  CAS  PubMed  Google Scholar 

  9. 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

    Article  CAS  PubMed  Google Scholar 

  10. 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

    Article  CAS  Google Scholar 

  11. 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

    Article  CAS  Google Scholar 

  12. 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

    Article  CAS  PubMed  Google Scholar 

  13. 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

    Article  CAS  Google Scholar 

  14. 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

    Article  CAS  Google Scholar 

  15. 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

    Article  CAS  PubMed  Google Scholar 

  16. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. 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

    Article  CAS  PubMed  Google Scholar 

  18. 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

    Article  CAS  PubMed  Google Scholar 

  19. 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

    Article  CAS  Google Scholar 

  20. Nimse, S.B., Kim, T.: Biological applications of functionalized calixarenes. Chem. Soc. Rev. 42, 366–386 (2013). https://doi.org/10.1039/C2CS35233H

    Article  CAS  PubMed  Google Scholar 

  21. 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

    Article  CAS  PubMed  Google Scholar 

  22. 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

    Article  CAS  PubMed  Google Scholar 

  23. 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

    Article  CAS  PubMed  Google Scholar 

  24. 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

    Article  CAS  PubMed  Google Scholar 

  25. 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

    Article  CAS  Google Scholar 

  26. 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

    Article  CAS  PubMed  Google Scholar 

  27. 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

    Article  CAS  PubMed  Google Scholar 

  28. 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

    Article  CAS  PubMed  Google Scholar 

  29. 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

    Article  CAS  Google Scholar 

  30. 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

    Article  CAS  PubMed  Google Scholar 

  31. Kaifer, A.E.: Toward reversible control of cucurbit[n]uril complexes. Acc. Chem. Res. 47, 2160–2167 (2014). https://doi.org/10.1021/ar5001204

    Article  CAS  PubMed  Google Scholar 

  32. 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

    Article  CAS  Google Scholar 

  33. 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

    Article  CAS  PubMed  Google Scholar 

  34. 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

    Article  CAS  Google Scholar 

  35. 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

    Article  CAS  Google Scholar 

  36. 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

    Article  CAS  Google Scholar 

  37. 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

    Article  CAS  PubMed  Google Scholar 

  38. 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

    Article  CAS  Google Scholar 

  39. 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

    Article  CAS  PubMed  Google Scholar 

  40. 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

    Article  CAS  Google Scholar 

  41. 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

    Article  CAS  Google Scholar 

  42. 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

    Article  CAS  Google Scholar 

  43. 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)

    Google Scholar 

  44. 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

    Article  CAS  PubMed  Google Scholar 

  45. 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

    Article  CAS  PubMed  Google Scholar 

  46. 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

    Article  CAS  Google Scholar 

  47. 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

    Article  CAS  Google Scholar 

  48. 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

    Article  CAS  Google Scholar 

  49. 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

    Article  CAS  Google Scholar 

  50. 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

    Article  CAS  PubMed  Google Scholar 

  51. 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

    Article  CAS  PubMed  Google Scholar 

  52. 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

    Article  CAS  Google Scholar 

  53. 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

    Article  CAS  Google Scholar 

  54. 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

    Article  CAS  Google Scholar 

  55. 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

    Article  CAS  Google Scholar 

  56. 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

    Article  CAS  Google Scholar 

  57. 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)

    Google Scholar 

  58. 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

    Article  CAS  Google Scholar 

  59. 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

    Article  CAS  Google Scholar 

  60. 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

    Article  CAS  PubMed  Google Scholar 

  61. 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

    Article  CAS  Google Scholar 

  62. 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

    Article  CAS  PubMed  Google Scholar 

  63. 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

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors wish to acknowledge financial support from the Hashemite University.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Khaled Bodoor.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10847-021-01113-2

Keywords

Navigation