The present study discusses the development of an algorithm to generate input files for quantum mechanical (QM) calculations from molecular dynamics (MD) trajectories of protein-carbohydrate complex simulations and QM optimization of binding-site residues of influenza hemagglutinin H1 along with its cell surface receptor sialyldisaccharides Neu5Acα(2→3)Gal (N23G) and Neu5Acα(2→6)Gal (N26G). Five frames from the local minima of MD trajectories were chosen for QM calculations. The geometry optimization was carried out by Gaussian09 software. The optimized geometries were analyzed, and the resultant ab initio molecular structures can be used for inhibitor design and therapeutics of influenza A virus. Copyright © 2015 Taylor & Francis Group, LLC.

Murugan V

Department of Mathematics

School of Advanced Sciences

Vellore Campus

Veluraja K

Department of Physics

M. Michael Gromiha

Parasuraman P

Selvin J.F.A

Priyadarzini T.R.K

Gromiha M.M

Fukui K

Vellore Institute of Technology (VIT) is a private university located in&nbsp;Tamil Nadu, India. Founded in 1984, as Vellore Engineering College, the institution offers 20 undergraduate, 34 postgraduate, four integrated and four research programs. It has campuses in Vellore, Amravati, Bhopal and Chennai.

VIT is one of the top ranked private universities in India according to NIRF, THE and QS Rankings.&nbsp;Govt. of India has recognized&nbsp;VIT, Vellore as an&nbsp;Institution of Eminence. This has allowed VIT to take independent quality initiatives and move up in world ranking.

&nbsp;

&nbsp;

VIT University

Geometry Optimization of Carbohydrate Binding Sites of Influenza: A Quantum Mechanical Approach

Journal of Carbohydrate Chemistry

Influenza epidemics and pandemics are caused by influenza A virus. The cell surface protein of hemagglutinin and neuraminidase is responsible for viral infection and release of progeny virus on the host cell membrane. Now 18 hemagglutinin and 11 neuraminidase subtypes are identified. The avian influenza virus of H5N1 is an emergent threat to public health issues. To control the influenza viral infection it is necessary to develop antiviral inhibitors and vaccination. In the present investigation we carried out 50 ns Molecular Dynamics simulation on H5 hemagglutinin of Influenza A virus H5N1 complexed with fluorinated sialic acid by substituting fluorine atoms at any two hydroxyls of sialic acid by considering combinatorial combination. The binding affinity between the protein–ligand complex system is investigated by calculating pair interaction energy and MM-PBSA binding free energy. All the complex structures are stabilized by hydrogen bonding interactions between the H5 protein and the ligand fluorinated sialic acid. It is concluded from all the analyses that the fluorinated complexes enhance the inhibiting potency against H5 hemagglutinin and the order of inhibiting potency is SIA-F9 ≫ SIA-F2 ≈ SIA-F7 ≈ SIA-F2F4 ≈ SIA-F2F9 ≈ SIA-F7F9 > SIA-F7F8 ≈ SIA-F2F8 ≈ SIA-F8F9 > SIA-F4 ≈ SIA-F4F7 ≈ SIA-F4F8 ≈ SIA-F8 ≈ SIA-F2F7 ≈ SIA > SIA-F4F9. This study suggests that one can design the inhibitor by using the mono fluorinated models SIA-F9, SIA-F2 and SIA-F7 and difluorinated models SIA-F2F4, SIA-F2F9 and SIA-F7F9 to inhibit H5 of H5N1 to avoid Influenza A viral infection. Communicated by Ramaswamy H. Sarma. © 2019, © 2019 Informa UK Limited, trading as Taylor & Francis Group.

Journal of Biomolecular Structure and Dynamics

Design of fluorinated sialic acid analog inhibitor to H5 hemagglutinin of H5N1 influenza virus through molecular dynamics simulation study

In the present study, the hydroxyl groups at the C4 and C7 positions of sialic acid and C6 position of galactose in Neu5Acα(2–3)Gal (N23G) and the hydroxyl groups at the C8 position of sialic acid and C3 and C4 positions of galactose in Neu5Acα(2–6)Gal (N26G) were substituted with fluorine atoms, respectively. Molecular dynamics simulations of 100 ns duration were carried out to investigate the structural and dynamical behavior of H1 bound with the tri-fluorinated N23G and N26G (FN23G and FN26G). Based on energy analysis, it was concluded that FN26G should be a better binder for hemagglutinin (H1) than FN23G and it might act as an inhibitor for influenza. © 2017 Taylor & Francis Group, LLC.

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

Practical Mathematical Optimization Springer Optimization and Its Applications

SOME BASIC OPTIMIZATION THEOREMS

Oriental Journal of Chemistry

Density Functional Theory, Natural Bond Orbital and Atoms in Molecule Analyses on the Hydrogen Bonding Interactions in 2-chloroaniline-Carboxylic Acids

Journal of Computational Chemistry

Convergence in the QM-only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase

Bulletin of the Korean Chemical Society

Importance of Accurate Charges in Binding Affinity Calculations: A Case of Neuraminidase Series

Journal	Data powered by TypesetJournal of Carbohydrate Chemistry
Publisher	Data powered by TypesetTaylor and Francis Inc.
ISSN	07328303
Open Access	No