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Blessia TF, Rapheal VS, Sharmila DJ. Molecular Dynamics of Sialic Acid Analogues and their Interaction with Influenza Hemagglutinin. Indian J Pharm Sci. 2010;72(4):449-57doi: 10.4103/0250-474X.73919.
Blessia, T. F., Rapheal, V. S., & Sharmila, D. J. (2010). Molecular Dynamics of Sialic Acid Analogues and their Interaction with Influenza Hemagglutinin. Indian journal of pharmaceutical sciences, 72(4), 449-57. https://doi.org/10.4103/0250-474X.73919
Blessia, T Femlin, et al. "Molecular Dynamics of Sialic Acid Analogues and their Interaction with Influenza Hemagglutinin." Indian journal of pharmaceutical sciences vol. 72,4 (2010): 449-57. doi: https://doi.org/10.4103/0250-474X.73919
Blessia TF, Rapheal VS, Sharmila DJ. Molecular Dynamics of Sialic Acid Analogues and their Interaction with Influenza Hemagglutinin. Indian J Pharm Sci. 2010 Jul;72(4):449-57. doi: 10.4103/0250-474X.73919. PMID: 21218055; PMCID: PMC3013563.
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Indian J Pharm Sci. 2010 Jul;72(4):449-57. doi: 10.4103/0250-474X.73919.

Molecular Dynamics of Sialic Acid Analogues and their Interaction with Influenza Hemagglutinin.

Indian journal of pharmaceutical sciences

T Femlin Blessia, V S Rapheal, D J S Sharmila

Affiliations

  1. Department of Bioinformatics, Karunya University, Karunya Nagar, Coimbatore-641 114, India.

PMID: 21218055 PMCID: PMC3013563 DOI: 10.4103/0250-474X.73919

Abstract

Synthetic sialic acid analogues with multiple modifications at different positions(C-1/C-2/C-4/C-8/C-9) are investigated by molecular mechanics and molecular dynamics to determine their conformational preferences and structural stability to interact with their natural receptors. Sialic acids with multiple modifications are soaked in a periodic box of water as solvent. Molecular mechanics and a 2 nanosecond molecular dynamics are done using amber force fields with 30 picosecond equilibrium. Direct and water mediated hydrogen bonds existing in the sialic acid analogues, aiding for their structural stabilization are identified in this study. The accessible conformations of side chain linkages of sialic acid analogues holding multiple substituents are determined from molecular dynamics trajectory at every 1ps interval. Transitions between different minimum energy regions in conformational maps are also noticed in C-1, C-2, C-4, C-8 and C-9 substituents. Docking studies were done to find the binding mode of the sialic acid analogues with Influenza hemagglutinin. This finding provides stereo chemical explanation and conformational preference of sialic acid analogues which may be crucial for the design of sialic acid analogues as inhibitors for different sialic acid specific pathogenic proteins such as influenza toxins and neuraminidases.

Keywords: AMBER; molecular dynamics; molecular mechanics; molecular modeling; sialic acid analogues

References

  1. Biochemistry. 1992 Oct 13;31(40):9609-21 - PubMed
  2. J Comput Chem. 2005 Dec;26(16):1668-88 - PubMed
  3. J Biomol Struct Dyn. 2006 Jun;23(6):641-56 - PubMed
  4. Annu Rev Biochem. 1987;56:365-94 - PubMed
  5. Nature. 1988 Jun 2;333(6172):426-31 - PubMed
  6. Eur J Biochem. 1992 Apr 1;205(1):147-53 - PubMed
  7. J Med Chem. 2006 Jan 26;49(2):534-53 - PubMed
  8. Prog Drug Res. 2008;65:211, 213-49 - PubMed

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