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Jeyaram RA, Radha CA. Investigation on the Binding Properties of N1 Neuraminidase of H5N1 Influenza Virus in Complex with Fluorinated Sialic Acid Analog Compounds—a Study by Molecular Docking and Molecular Dynamics Simulations. BRAZILIAN JOURNAL OF PHYSICS 2022; 52:21. [PMCID: PMC8656140 DOI: 10.1007/s13538-021-01009-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/12/2021] [Indexed: 03/19/2024]
Abstract
Worldwide, only two types of antiviral inhibitors (M2 ion channel protein inhibitor and Neuraminidase inhibitors) are approved to treat the influenza viral infection. But the mutation of amino acid sequence in the viral membrane proteins creates the viral resistance to existing antiviral drugs or inhibitors. So the corresponding antiviral drugs have to be reformulated to match these antigenic variations. Fluorination on the carbon–based molecule significantly enriches its biological properties. Hence this study is motivated to design the fluorinated sialic acid (SIA) analog inhibitors for the neuraminidase of H5N1 influenza A virus by substituting fluorine atom at different hydroxyls (O2, O4, O7, O8, and O9) of sialic acid. 100 ns molecular dynamics simulations are carried out for each protein–ligand complex system. NAMD pair interaction energy and MM–PBSA binding free energy calculations predict two possible binding modes for N1–SIA_F2, N1–SIA_F4, and N1–SIA_F7 complexes and single binding mode for N1–SIA_F8 and N1–SIA_F9 complexes. RMSD, RMSF, and hydrogen bonding analyses are used to understand the conformational flexibility and structural stability of each complex system. It has been concluded that the fluorinated sialic acid drug candidates SIA_F2 and SIA_F7 have better inhibiting potency against the N1 neuraminidase of H5N1 influenza virus.
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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, 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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Bao J, Marathe B, Govorkova EA, Zheng JJ. Drug Repurposing Identifies Inhibitors of Oseltamivir-Resistant Influenza Viruses. Angew Chem Int Ed Engl 2016; 55:3438-41. [PMID: 26833677 PMCID: PMC4807618 DOI: 10.1002/anie.201511361] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/18/2016] [Indexed: 12/14/2022]
Abstract
The neuraminidase (NA) inhibitor, oseltamivir, is a widely used anti-influenza drug. However, oseltamivir-resistant H1N1 influenza viruses carrying the H275Y NA mutation spontaneously emerged as a result of natural genetic drift and drug treatment. Because H275Y and other potential mutations may generate a future pandemic influenza strain that is oseltamivir-resistant, alternative therapy options are needed. Herein, we show that a structure-based computational method can be used to identify existing drugs that inhibit resistant viruses, thereby providing a first line of pharmaceutical defense against this possible scenario. We identified two drugs, nalidixic acid and dorzolamide, that potently inhibit the NA activity of oseltamivir-resistant H1N1 viruses with the H275Y NA mutation at very low concentrations, but have no effect on wild-type H1N1 NA even at a much higher concentration, suggesting that the oseltamivir-resistance mutation itself caused susceptibility to these drugs.
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Affiliation(s)
- Ju Bao
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Bindumadhav Marathe
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Elena A Govorkova
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jie J Zheng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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Bao J, Marathe B, Govorkova EA, Zheng JJ. Drug Repurposing Identifies Inhibitors of Oseltamivir-Resistant Influenza Viruses. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ju Bao
- Department of Structural Biology; St. Jude Children's Research Hospital; Memphis TN 38105 USA
| | - Bindumadhav Marathe
- Department of Infectious Diseases; St. Jude Children's Research Hospital; Memphis TN 38105 USA
| | - Elena A. Govorkova
- Department of Infectious Diseases; St. Jude Children's Research Hospital; Memphis TN 38105 USA
| | - Jie J. Zheng
- Department of Structural Biology; St. Jude Children's Research Hospital; Memphis TN 38105 USA
- Stein Eye Institute; Department of Ophthalmology; David Geffen School of Medicine at UCLA; Los Angeles CA 90095 USA
- Department of Infectious Diseases; St. Jude Children's Research Hospital; Memphis TN 38105 USA
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Tschowri N, Schumacher MA, Schlimpert S, Chinnam NB, Findlay KC, Brennan RG, Buttner MJ. Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development. Cell 2015; 158:1136-1147. [PMID: 25171413 PMCID: PMC4151990 DOI: 10.1016/j.cell.2014.07.022] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 05/27/2014] [Accepted: 07/17/2014] [Indexed: 11/25/2022]
Abstract
The cyclic dinucleotide c-di-GMP is a signaling molecule with diverse functions in cellular physiology. Here, we report that c-di-GMP can assemble into a tetramer that mediates the effective dimerization of a transcription factor, BldD, which controls the progression of multicellular differentiation in sporulating actinomycete bacteria. BldD represses expression of sporulation genes during vegetative growth in a manner that depends on c-di-GMP-mediated dimerization. Structural and biochemical analyses show that tetrameric c-di-GMP links two subunits of BldD through their C-terminal domains, which are otherwise separated by ∼10 Å and thus cannot effect dimerization directly. Binding of the c-di-GMP tetramer by BldD is selective and requires a bipartite RXD-X8-RXXD signature. The findings indicate a unique mechanism of protein dimerization and the ability of nucleotide signaling molecules to assume alternative oligomeric states to effect different functions. c-di-GMP controls development in the multicellular bacteria Streptomyces c-di-GMP developmental signaling is directly mediated by the master regulator BldD A heretofore unseen tetrameric form of c-di-GMP binds BldD to effect its dimerization BldD-(c-di-GMP) represses transcription of sporulation genes during vegetative growth
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Affiliation(s)
- Natalia Tschowri
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Susan Schlimpert
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Naga Babu Chinnam
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kim C Findlay
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Richard G Brennan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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YANG ZHIWEI, WU FEI, LIU JUNXING, WANG SHUQIU, YUAN XIAOHUI. SUSCEPTIBILITY OF COMMERCIAL NEURAMINIDASE INHIBITORS AGAINST 2013 A/H7N9 INFLUENZA VIRUS: A DOCKING AND MOLECULAR DYNAMICS STUDY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The latest influenza A ( H 7 N 9) virus attracted a worldwide attention due to the first report of human infections and the continuing reported cases in China. In this work, homology modeling, docking and molecular dynamics simulations were combined to study the interactions between neuraminidase ( N 9_2013, from novel A/ H 7 N 9 virus) and agents zanamivir, oseltamivir, peramivir. It was found that N 9_2013 protein is structurally close to the template (PDB code: 1F8B), especially the active site. The binding properties of N 9_2013 protein were nearly identical to those of template. As a result, the three available drugs should be still efficacious for the new emerging A ( H 7 N 9) virus. However, the stabilities of docked complexes and binding affinities (Eint) were slightly reduced, in contrast to the corresponding inhibitor-template complexes, with the values of -82.27 (-84.30), -78.84 (-80.28) and -77.52 (-81.94) kcal mol-1, respectively. Besides, R292K mutation might induce the resistance of the novel virus to the commercial inhibitors. Thus, it arouses the need for continuous monitoring of antiviral drug susceptibilities.
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Affiliation(s)
- ZHIWEI YANG
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, P. R. China
| | - FEI WU
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, P. R. China
| | - JUNXING LIU
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, P. R. China
| | - SHUQIU WANG
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, P. R. China
| | - XIAOHUI YUAN
- Institute of Biomedicine, Jinan University, Guangzhou 510632, P. R. China
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Homeyer N, Gohlke H. Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method. Mol Inform 2012; 31:114-22. [DOI: 10.1002/minf.201100135] [Citation(s) in RCA: 603] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 11/26/2011] [Indexed: 11/06/2022]
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Crystal structure of a putative transcriptional regulator SCO0520 from Streptomyces coelicolor A3(2) reveals an unusual dimer among TetR family proteins. ACTA ACUST UNITED AC 2011; 12:149-57. [PMID: 21625866 DOI: 10.1007/s10969-011-9112-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 05/14/2011] [Indexed: 10/18/2022]
Abstract
A structure of the apo-form of the putative transcriptional regulator SCO0520 from Streptomyces coelicolor A3(2) was determined at 1.8 Å resolution. SCO0520 belongs to the TetR family of regulators. In the crystal lattice, the asymmetric unit contains two monomers that form an Ω-shaped dimer. The distance between the two DNA-recognition domains is much longer than the corresponding distances in the known structures of other TetR family proteins. In addition, the subunits in the dimer have different conformational states, resulting in different relative positions of the DNA-binding and regulatory domains. Similar conformational modifications are observed in other TetR regulators and result from ligand binding. These studies provide information about the flexibility of SCO0520 molecule and its putative biological function.
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