Conformational changes of peptidoglycan fragments during their interactions with vancomycin

• Authors: Rafał Ślusarz , Magdalena Ślusarz , Justyna Samaszko , Janusz Madaj
• Languages of publication: EN

Abstracts

EN

Six complexes of vancomycin and peptidoglycan precursors were studied via molecular dynamics simulations. The interactions between the antibiotic and peptidoglycan fragments were identified and described in detail. All six studied modifications of the peptidoglycan precursor resulted in a weakening of the interaction with vancomycin when comparing to the native D-Ala-D-Ala-terminated fragment. It was confirmed that the N-terminus of the vancomycin is directly responsible for peptidoglycan recognition and antimicrobial activity. In simulated systems, the saccharide part of the antibiotic interacts with peptide precursors, thus it could also be important for antimicrobial activity. The complex terminated with D-Lac is the only one in which there is a weak interaction with the sugar moiety in the simulated systems. Analysis of conformational changes is a major scope of this work. The lack of interactions resulting from modification of the peptidoglycan precursors (D-Lac, D-Ser or other substitution) would be counterbalanced by proper modifications of the vancomycin moiety, especially the saccharide part of vancomycin.

Keywords

EN

Modified peptidoglycan; Molecular dynamics of sugar; RMSd; Trajectory analysis; Vancomycin interaction

• Publisher: De Gruyter Open
• Journal: Open Chemistry
• Year: 2011
• Volume: 9
• Issue: 3
• Pages: 422-431

Dates

published

1 - 6 - 2011

online

22 - 3 - 2011

Contributors

author

Rafał Ślusarz

• University of Gdańsk

author

Magdalena Ślusarz

• University of Gdańsk

author

Justyna Samaszko

• University of Gdańsk

author

Janusz Madaj

• University of Gdańsk

References

• [1] D. Kahne, C. Leimkuhler, W. Lu, C. Walsh, Chem. Rev. 105, 425 (2005) http://dx.doi.org/10.1021/cr030103a[Crossref]
• [2] D.H. Williams, B. Bardsley, Angew. Chem. Int. Ed. 38, 1172 (1999) http://dx.doi.org/10.1002/(SICI)1521-3773(19990503)38:9<1172::AID-ANIE1172>3.0.CO;2-C[Crossref]
• [3] P.E. Reynolds, Eur. J. Clin. Microbiol. Infect. Dis. 8, 943 (1989) http://dx.doi.org/10.1007/BF01967563[Crossref]
• [4] M. Arthur, P. Reynolds, P. Courvalin, Trends Microbiol. 4, 401 (1996) http://dx.doi.org/10.1016/0966-842X(96)10063-9[Crossref]
• [5] M. Fines, B. Périchon, P. Reynolds, D.F. Sahm, P. Courvalin, Antimicrob. Agents Chemother. 43, 2161 (1999) [PubMed]
• [6] R. Leclercq, S. Dutka-Malen, J. Duval, P. Courvalin, Antimicrob. Agents Chemother. 36, 2005 (1992) [PubMed]
• [7] S.J. McKessar, A.M. Berry, J.M. Bell, J.D. Turnidge, J.C. Paton, Antimicrob. Agents Chemother. 44, 3224 (2000) http://dx.doi.org/10.1128/AAC.44.11.3224-3228.2000[Crossref]
• [8] F. Navarro, P. Courvalin, Antimicrob. Agents Chemother. 38, 1788 (1994)
• [9] B. Périchon, P. Reynolds, P. Courvalin, Antimicrob. Agents Chemother. 41, 2016 (1997) [PubMed]
• [10] T.D.H. Bugg, G.D. Wright, S. Dutka-Malen, M. Arthur, P. Courvalin, C.T. Walsh, Biochemistry 30, 10408 (1991) http://dx.doi.org/10.1021/bi00107a007[Crossref]
• [11] P.E. Reynolds, P. Courvalin, Antimicrob. Agents Chemother. 49, 21 (2005) http://dx.doi.org/10.1128/AAC.49.1.21-25.2005[Crossref]
• [12] M. Arthur, P. Courvalin, Antimicrob. Agents Chemother. 37, 1563 (1993) [PubMed]
• [13] D.P. Levine, Clin. Infect. Dis. 42Suppl. 1, 5 (2006) http://dx.doi.org/10.1086/491709[Crossref]
• [14] C.T. Walsh, S.L. Fisher, I.-S. Park, M. Prahalad, Z. Wu, Chem. Biol. 3, 21 (1996) http://dx.doi.org/10.1016/S1074-5521(96)90079-4[Crossref]
• [15] D. Billot-Klein, L. Gutmann, S. Sable, E. Guitet, J. van Heijenoort, J. Bacteriol. 176, 2398 (1994)
• [16] P.E. Reynolds, H.A. Snaith, A.J. Maguire, S. Dutka-Malen, P. Courvalin, Biochem. J. 301, 5 (1994)
• [17] J.C. Barna, D.H. Wiliams, Annu. Rev. Microbiol. 38, 339 (1984) http://dx.doi.org/10.1146/annurev.mi.38.100184.002011[Crossref]
• [18] R. Kannan, C.M. Harris, T.M. Harris, J.P. Waltho, N.J. Skelton, D.H. Williams, J. Am. Chem. Soc. 110, 2946 (1988) http://dx.doi.org/10.1021/ja00217a042[Crossref]
• [19] J.P. Waltho, D.H. Williams, D.J.H. Stone, N.J. Skelton, J. Am. Chem. Soc. 110, 5638 (1988) http://dx.doi.org/10.1021/ja00225a009[Crossref]
• [20] D.A. Beauregard, D.H. Williams, M.N. Gwynn, D.J.C. Knowles, Antimicrob. Agents Chemother. 39, 781 (1995)
• [21] P. Groves, M.S. Searle, J.P. MacKay, D.H. Williams, Structure 2, 747 (1994) http://dx.doi.org/10.1016/S0969-2126(94)00075-1[Crossref]
• [22] J.-G. Lee, C. Sagui, C. Roland, Int. J. Quantum Chem. 110, 2894 (2010) http://dx.doi.org/10.1002/qua.22926[Crossref]
• [23] J.P. MacKay, U. Gerhard, D.A. Beauregard, M.S. Westweil, M.S. Searle, D.H. Williams, J. Am. Chem. Soc. 116, 4581 (1994) http://dx.doi.org/10.1021/ja00090a006[Crossref]
• [24] P.J. Loll, A.E. Bevivino, B.D. Korty, P.H. Axelsen, J. Am. Chem. Soc. 119, 1516 (1997) http://dx.doi.org/10.1021/ja963566p[Crossref]
• [25] D.A. Case, T.A. Darden, T.E. III Cheatham, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, K.M. Merz, D.A. Pearlman, M. Crowley, R.C. Walker, W. Zhang, B. Wang, S. Hayik, A. Roitberg, G. Seabra, K.F. Wong, F. Paesani, X. Wu, S. Brozell, V. Tsui, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, P. Beroza, D.H. Mathews, C. Schafmeister, W.S. Ross, P.A. Kollman, AMBER 9 (University of California, San Francisco, 2006)
• [26] M Basma, S. Sundara, D. Calgan, T. Venali, R.J. Woods, J. Comput. Chem. 22, 1125 (2001) http://dx.doi.org/10.1002/jcc.1072[Crossref]
• [27] K.N. Kirschner, R.J. Woods, Proc. Natl. Acad. Sci. USA 98, 10541 (2001) http://dx.doi.org/10.1073/pnas.191362798[Crossref]
• [28] Y. Duan, C. Wu, S. Chowdhury, M.C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Comput. Chem. 24, 1999 (2003) http://dx.doi.org/10.1002/jcc.10349[Crossref]
• [29] M.W. Schmidt, K.K. Baldridge, J.A. Boatz, S.T. Elbert, M.S. Gordon, J.H. Jensen, S. Koseki, N. Matsunaga, K.A. Nguyen, S. Su, T.L. Windus, M. Dupuis, J.A. Montgomery, J. Comput. Chem. 14, 1347 (1993) http://dx.doi.org/10.1002/jcc.540141112[Crossref]
• [30] C.L. Bayly, P. Cieplak, W.D. Cornell, P.A. Kollman, J. Phys. Chem. 97, 10269 (1993) http://dx.doi.org/10.1021/j100142a004[Crossref]
• [31] Y. Nitanai, K. Kakoi, K. Aoki, PDB accession code 1FVM (2000), DOI: 10.2210/pdb1fvm/pdb [Crossref]
• [32] V. Tsui, D.A. Case, Biopol. Nucl. Acid. Sci. 56, 275 (2001)
• [33] C.P. Sosa, T. Hewitt, M.S. Lee, D.A. Case, J. Mol. Struct. (Theochem) 549, 193 (2001) http://dx.doi.org/10.1016/S0166-1280(01)00497-3[Crossref]
• [34] P.A. Kollman, I. Massova, C. Reyes, B. Kuhn, B.S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, T.E. Cheatham, Acc. Chem. Res. 33, 889 (2000) http://dx.doi.org/10.1021/ar000033j[Crossref]
• [35] S.S. Leung, J. Tirado-Rives, W.L. Jorgensen, Bioorg. Med. Chem. Lett. 19, 1236 (2009) http://dx.doi.org/10.1016/j.bmcl.2008.12.072[Crossref]
• [36] S.S. Leung, J. Tirado-Rives, W.L. Jorgensen, Bioorg. Med. Chem. 17, 5874 (2009) http://dx.doi.org/10.1016/j.bmc.2009.07.006[Crossref]
• [37] Z. Yang, E.R. Vorpagel, J. Laskin, J. Am. Chem. Soc. 130, 13013 (2008) http://dx.doi.org/10.1021/ja802643g[Crossref]
• [38] D. Billot-Klein, D. Blanot, L. Gutmann, J. van Heijenoort, Biochem. J. 304, 1021 (1994)
• [39] M. Batchelor, D. Zhou, M.A. Cooper, C. Abell, T. Rayment, Org. Biomol. Chem. 8, 142 (2010) http://dx.doi.org/10.1039/b919347b[Crossref]
• [40] J.B. Hamburger, A.J. Hoertz, A. Lee, R.J. Senturia, D.G. McCafferty, P.J. Loll, Proc. Natl. Acad. Sci. USA 106, 13759 (2009) http://dx.doi.org/10.1073/pnas.0904686106[Crossref]
• [41] B. Périchon, P. Courvalin, Antimicrob. Agents Chemother. 53, 4580 (2009) http://dx.doi.org/10.1128/AAC.00346-09[Crossref]
• [42] J.C. Poully, F. Lecomte, N. Nieuwjaer, B. Manil, J.P. Schermann, C. Desfrançois, F. Calvo, G. Grégoire, Phys. Chem. Chem. Phys. 12, 3606 (2010) http://dx.doi.org/10.1039/b923787a[Crossref]
• [43] Z. Yang, E.R. Vorpagel, J. Laskin, Chem. Eur. J. 15, 2081 (2009) http://dx.doi.org/10.1002/chem.200802010[Crossref]

Identifiers

DOI

10.2478/s11532-011-0015-9