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Jeyaram RA, Anu Radha C. N1 neuraminidase of H5N1 avian influenza A virus complexed with sialic acid and zanamivir - A study by molecular docking and molecular dynamics simulation. J Biomol Struct Dyn 2022; 40:11434-11447. [PMID: 34369311 DOI: 10.1080/07391102.2021.1962407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Development of antiviral drugs is an urgent need to control and prevent the presently circulating H5N1 avian influenza virus which is affects the human respiratory tract. The complex crystal structure of N1-N-acetylneuranamic acid (sialic acid, SIA) is not available as complex and hence SIA and zanamivir (ZMR) are docked into the binding site of N1 neuraminidase. Based on the analysis, the initial complex structures have been simulated for 120 ns to get insight into the binding modes and interaction between protein-ligand complex systems. NAMD pair interaction energy and MM-PBSA binding free energy are calculated and show that there are two possible binding modes (BM1 and BM2) for N1-SIA and a single binding mode (BM1) for and N1-ZMR complex structures respectively. BM1 of N1-SIA is the most preferred binding mode. On contrary to the currently available drugs in which the chair conformation is distorted, in both the binding modes of N1-SIA, the binding pocket of N1 neuraminidase is able to accommodate SIA in 2C5 chair conformation which is the preferred conformation of SIA in solution state. In N1-ZMR complex, ZMR is bind in a distorted chair conformation. The neuraminidase binding pocket is also able to accommodate galactose of SIAα(2→3)GAL and SIAα(2→6)GAL. RMSD, RMSF and hydrogen bonding analyses have been carried out to identify the conformational flexibility and structural stability of each complex system. All the analyses show that SIA can be used as an inhibitor for N1 neuraminidase of H5N1 influenza viral infection. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- R A Jeyaram
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, India
| | - C Anu Radha
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, India
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Lalithamaheswari B, Anu Radha C. Structural and conformational dynamics of human milk oligosaccharides, lacto- N-fucopentaose I and II, through molecular dynamics simulation. J Carbohydr Chem 2022. [DOI: 10.1080/07328303.2022.2150203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- B. Lalithamaheswari
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C. Anu Radha
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Parasuraman P, Selvin JFA, Gromiha MM, Fukui K, Veluraja K. Investigation on the binding specificity of Agrocybe cylindracea galectin towards α(2,6)-linked sialyllactose by molecular modeling and molecular dynamics simulations. J Carbohydr Chem 2019. [DOI: 10.1080/07328303.2019.1631323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | | | - M. Michael Gromiha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Kazuhiko Fukui
- National Institute of Advanced Industrial Science and Technology (AIST), Molecular Profiling Research Center for Drug Discovery (molprof), Tokyo, Japan
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Jeyaram RA, Priyadarzini TRK, Anu Radha C, Siva Shanmugam NR, Ramakrishnan C, Gromiha MM, Veluraja K. Molecular dynamics simulation studies on influenza A virus H5N1 complexed with sialic acid and fluorinated sialic acid. J Biomol Struct Dyn 2019; 37:4813-4824. [DOI: 10.1080/07391102.2019.1568304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- R. A. Jeyaram
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, India
| | | | - C. Anu Radha
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, India
| | - N. R. Siva Shanmugam
- Department of Biotechnology, Indian Institute of Technology, Madras, Chennai, India
| | - C. Ramakrishnan
- Department of Biotechnology, Indian Institute of Technology, Madras, Chennai, India
| | - M. Michael Gromiha
- Department of Biotechnology, Indian Institute of Technology, Madras, Chennai, India
| | - K. Veluraja
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, India
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Theoretical Studies on the Electronic Structure Parameters and Reactive Activity of Neu5Gc and Neu5Ac under Food Processing Solvent Environment. Molecules 2019; 24:molecules24020313. [PMID: 30654545 PMCID: PMC6359032 DOI: 10.3390/molecules24020313] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 11/19/2022] Open
Abstract
The animal product hazard factor N-glycolylneuraminic (Neu5Gc) and brain nutrient substance N-acetylneuraminic acid (Neu5Ac) were studied at the M062X/6-311 + G(d,p) geometry optimization level. We considered the electronic structure parameters with different solvents: (benzene ε = 2.27, acetic acid ε = 6.25, ethanol ε = 24.85, lactic acid ε = 22.00, formic acid ε = 51.1, water ε = 78.35). The maximum molecular surface electrostatic potentials, which were 62.77 for Neu5Gc and 60.90 kcal/mol for Neu5Ac, are both located on the carboxyl group hydrogen. The orbital analysis showed that the amide group and carboxyl group confer the sites with susceptibility to nucleophilic and electrophilic attack, respectively. The solvent effect showed that polar solvents, such as formic acid and water, can enhance the two molecules’ nucleophilic activity. To better understand the roles of the hydroxyl group in the two molecules, the independent gradient model theory confirmed the four intramolecular hydrogen bonds of Neu5Gc at gas phase, whereas Neu5Ac only has two. The lowest bond dissociation energy in solvent occurs at O7-H, which is 104.03 kcal/mol in water for Neu5Gc and 104.57 kcal/mol in lactic acid for Neu5Ac. The lowest proton affinity value for Neu5Gc (20.34 kcal/mol) and Neu5Ac (20.76 kcal/mol) was both occur at the carboxyl group O6-H under ethanol. The antioxidant mechanisms of the two sialic acid are prone to sequential proton-loss electron transfer under polar or non-polar solvents.
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Abstract
Sialic acids are cytoprotectors, mainly localized on the surface of cell membranes with multiple and outstanding cell biological functions. The history of their structural analysis, occurrence, and functions is fascinating and described in this review. Reports from different researchers on apparently similar substances from a variety of biological materials led to the identification of a 9-carbon monosaccharide, which in 1957 was designated "sialic acid." The most frequently occurring member of the sialic acid family is N-acetylneuraminic acid, followed by N-glycolylneuraminic acid and O-acetylated derivatives, and up to now over about 80 neuraminic acid derivatives have been described. They appeared first in the animal kingdom, ranging from echinoderms up to higher animals, in many microorganisms, and are also expressed in insects, but are absent in higher plants. Sialic acids are masks and ligands and play as such dual roles in biology. Their involvement in immunology and tumor biology, as well as in hereditary diseases, cannot be underestimated. N-Glycolylneuraminic acid is very special, as this sugar cannot be expressed by humans, but is a xenoantigen with pathogenetic potential. Sialidases (neuraminidases), which liberate sialic acids from cellular compounds, had been known from very early on from studies with influenza viruses. Sialyltransferases, which are responsible for the sialylation of glycans and elongation of polysialic acids, are studied because of their significance in development and, for instance, in cancer. As more information about the functions in health and disease is acquired, the use of sialic acids in the treatment of diseases is also envisaged.
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Affiliation(s)
- Roland Schauer
- Biochemisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| | - Johannis P Kamerling
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
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Murugan V, Parasuraman P, Selvin JFA, Gromiha MM, Fukui K, Veluraja K. Theoretical investigation on the binding specificity of fluorinated sialyldisaccharides Neu5Acα(2–3)Gal and Neu5Acα(2–6)Gal with influenza hemagglutinin H1 – A Molecular Dynamics Study. J Carbohydr Chem 2017. [DOI: 10.1080/07328303.2017.1365153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Veeramani Murugan
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, India
| | - Ponnusamy Parasuraman
- Department of Physical Sciences, Bannari Amman Institute of Technology, Erode, Tamilnadu, India
| | | | - Michael M. Gromiha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu, India
| | - Kazuhiko Fukui
- National Institute of Advanced Industrial Science and Technology (AIST), Molecular Profiling Research Center for Drug Discovery (molprof), 2-4-7 Aomi, Koto-ku, Tokyo, Japan
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Priyadarzini TRK, Selvin JFA, Gromiha MM, Fukui K, Veluraja K. Theoretical investigation on the binding specificity of sialyldisaccharides with hemagglutinins of influenza A virus by molecular dynamics simulations. J Biol Chem 2012; 287:34547-57. [PMID: 22846994 DOI: 10.1074/jbc.m112.357061] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recognition of cell-surface sialyldisaccharides by influenza A hemagglutinin (HA) triggers the infection process of influenza. The changes in glycosidic torsional linkage and the receptor conformations may alter the binding specificity of HAs to the sialylglycans. In this study, 10-ns molecular dynamics simulations were carried out to examine the structural and dynamic behavior of the HAs bound with sialyldisaccharides Neu5Acα(2-3)Gal (N23G) and Neu5Acα(2-6)Gal (N26G). The analysis of the glycosidic torsional angles and the pair interaction energy between the receptor and the interacting residues of the binding site reveal that N23G has two binding modes for H1 and H5 and a single binding mode for H3 and H9. For N26G, H1 and H3 has two binding modes, and H5 and H9 has a single binding mode. The direct and water-mediated hydrogen bonding interactions between the receptors and HAs play dominant roles in the structural stabilization of the complexes. It is concluded from pair interaction energy and Molecular Mechanic-Poisson-Boltzmann Surface Area calculations that N26G is a better receptor for H1 when compared with N23G. N23G is a better receptor for H5 when compared with N26G. However, H3 and H9 can recognize N23G and N26G in equal binding specificity due to the marginal energy difference (≈2.5 kcal/mol). The order of binding specificity of N23G is H3 > H5 > H9 > H1 and N26G is H1 > H3 > H5 > H9, respectively. The proposed conformational models will be helpful in designing inhibitors for influenza virus.
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Affiliation(s)
- Thanu R K Priyadarzini
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu 627 012, India
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