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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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Jino Blessy J, Siva Shanmugam NR, Veluraja K, Michael Gromiha M. Investigations on the binding specificity of β-galactoside analogues with human galectin-1 using molecular dynamics simulations. J Biomol Struct Dyn 2022; 40:10094-10105. [PMID: 34219624 DOI: 10.1080/07391102.2021.1939788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Galectin-1 (Gal-1) is the first member of galectin family, which has a carbohydrate recognition domain, specifically binds towards β-galactoside containing oligosaccharides. Owing its association with carbohydrates, Gal-1 is involved in many biological processes such as cell signaling, adhesion and pathological pathways such as metastasis, apoptosis and increased tumour cell survival. The development of β-galactoside based inhibitors would help to control the Gal-1 expression. In the current study, we carried out molecular dynamics (MD) simulations to examine the structural and dynamic behaviour Gal-1-thiodigalactoside (TDG), Gal-1-lactobionic acid (LBA) and Gal-1-beta-(1→6)-galactobiose (G16G) complexes. The analysis of glycosidic torsional angles revealed that β-galactoside analogues TDG and LBA have a single binding mode (BM1) whereas G16G has two binding modes (BM1 and BM2) for interacting with Gal-1 protein. We have computed the binding free energies for the complexes Gal-1-TDG, Gal-1-LBA and Gal-1-G16G using MM/PBSA and are -6.45, -6.22 and -3.08 kcal/mol, respectively. This trend agrees well with experiments that the binding of Gal-1 with TDG is stronger than LBA. Further analysis revealed that the interactions due to direct and water-mediated hydrogen bonds play a significant role to the structural stability of the complexes. The result obtained from this study is useful to formulate a set of rules and derive pharmacophore-based features for designing inhibitors against galectin-1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- J Jino Blessy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - N R Siva Shanmugam
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - K Veluraja
- PSN college of Engineering and Technology, Tirunelveli, Tamilnadu, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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Núñez-Franco R, Peccati F, Jiménez-Osés G. A Computational Perspective on Molecular Recognition by Galectins. Curr Med Chem 2021; 29:1219-1231. [PMID: 34348610 DOI: 10.2174/0929867328666210804093058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/17/2021] [Accepted: 06/28/2021] [Indexed: 11/22/2022]
Abstract
This article presents an overview of recent computational studies dedicated to the analysis of binding between galectins and small-molecule ligands. We first present a summary of the most popular simulation techniques adopted for calculating binding poses and binding energies, and then discuss relevant examples reported in the literature for the three main classes of galectins (dimeric, tandem and chimera). We show that simulation of galectin-ligand interactions is a mature field which has proven invaluable for completing and unraveling experimental observations. Future perspectives to further improve the accuracy and cost-effectiveness of existing computational approaches will involve the development of new schemes to account for solvation and entropy effects, which represent the main current limitations to the accuracy of computational results.
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Affiliation(s)
- Reyes Núñez-Franco
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio. Spain
| | - Francesca Peccati
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio. Spain
| | - Gonzalo Jiménez-Osés
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio. Spain
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Dogan A, Uyar A, Hasar S, Keles OF. The protective effects of the Lactarius deliciosus and Agrocybe cylindracea mushrooms on histopathology of carbon tetrachloride induced oxidative stress in rats. Biotech Histochem 2021; 97:143-151. [PMID: 33970727 DOI: 10.1080/10520295.2021.1918349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
We investigated the protective effects of L. deliciosus and A. cylindracea supplementation against carbon tetrachloride (CCI4) induced oxidative stress by measuring levels of adenosine deaminase (ADA) and myeloperoxidase (MPO), and by observing histopathological changes in liver and kidney tissues of rats. We divided 36 rats into six groups: control, CCl4, L. deliciosus, A. cylindracea, CCl4 + L. deliciosus, and CCl4 + A. cylindracea. We found that administration of CCI4, A. cylindracea, and CCl4 + A. cylindracea increased MPO and ADA levels. We observed severe hepato-renal degenerative and necrotic lesions in the CCI4, A. cylindracea and CCl4 + A. cylindracea groups. Severe lesions of the liver and kidney were not observed with A. cylindracea administration. CCI4 induced hepato-renal lesions were ameliorated by L. deliciosus extract supplementation. L. deliciosus could be an important dietary antioxidant for preventing histologic lesions in liver and kidney due to CCI4 induced oxidative stress in rats.
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Affiliation(s)
- Abdulahad Dogan
- Department of Biochemistry, Faculty of Pharmacy, Van Yuzuncu Yil University, Van, Turkey
| | - Ahmet Uyar
- Department of Pathology, Faculty of Veterinary Medicine, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Songul Hasar
- Department of Biology, Institute of Natural and Applied Sciences, Van Yuzuncu Yil University, Van, Turkey
| | - Omer Faruk Keles
- Department of Pathology, Faculty of Veterinary Medicine, Van Yuzuncu Yil University, Van, Turkey
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Physicochemical characterization of a polysaccharide from Agrocybe aegirita and its anti-ageing activity. Carbohydr Polym 2020; 236:116056. [DOI: 10.1016/j.carbpol.2020.116056] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/27/2020] [Accepted: 02/20/2020] [Indexed: 12/20/2022]
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Jeyaram RA, Radha CA, Gromiha MM, Veluraja K. Design of fluorinated sialic acid analog inhibitor to H5 hemagglutinin of H5N1 influenza virus through molecular dynamics simulation study. J Biomol Struct Dyn 2019; 38:3504-3513. [PMID: 31594458 DOI: 10.1080/07391102.2019.1677500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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.
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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
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - K Veluraja
- 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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Dumpati R, Ramatenki V, Vadija R, Vellanki S, Vuruputuri U. Structural insights into suppressor of cytokine signaling 1 protein- identification of new leads for type 2 diabetes mellitus. J Mol Recognit 2018; 31:e2706. [PMID: 29630758 DOI: 10.1002/jmr.2706] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/22/2017] [Accepted: 02/04/2018] [Indexed: 12/23/2022]
Abstract
The study considers the Suppressor of cytokine signaling 1 (SOCS1) protein as a novel Type 2 diabetes mellitus (T2DM) drug target. T2DM in human beings is also triggered by the over expression of SOCS proteins. The SOCS1 acts as a ubiquitin ligase (E3), degrades Insulin Receptor Substrate 1 and 2 (IRS1 and IRS2) proteins, and causes insulin resistance. Therefore, the structure of the SOCS1 protein was evaluated using homology-modeling and molecular dynamics methods and validated using standard computational protocols. The Protein-Protein docking study of SOCS1 with its natural substrates, IRS1 and IRS2, and subsequent solvent accessible surface area analysis gave insight into the binding region of the SOCS1 protein. The in silico active site prediction tools highlight the residues Val155 to Ile211 in SOCS1 being implicated in the ubiquitin mediated protein degradation of the proteins IRS1 and IRS2. Virtual screening in the active site region, using large structural databases, results in selective lead structures with 3-Pyridinol, Xanthine, and Alanine moieties as Pharmacophore. The virtual screening study shows that the residues Glu149, Gly187, Arg188, Leu191, and Ser205 of the SOCS1 are important for binding. The docking study with current anti-diabetic therapeutics shows that the drugs Glibenclamide and Glyclopyramide have a partial affinity towards SOCS1. The predicted ADMET and IC50 properties for the identified ligands are within the acceptable range with drug-like properties. The structural data of SOCS1, its active site, and the identified lead structures are expedient in the development of new T2DM therapeutics.
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Affiliation(s)
- Ramakrishna Dumpati
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana State, India
| | - Vishwanath Ramatenki
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana State, India
| | - Rajender Vadija
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana State, India
| | - Santhiprada Vellanki
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana State, India
| | - Uma Vuruputuri
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana State, India
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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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Making Use of Genomic Information to Explore the Biotechnological Potential of Medicinal Mushrooms. MEDICINAL AND AROMATIC PLANTS OF THE WORLD 2017. [DOI: 10.1007/978-981-10-5978-0_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Tang Y, Zhang H. Theoretical understanding of bio-interfaces/bio-surfaces by simulation: A mini review. BIOSURFACE AND BIOTRIBOLOGY 2016. [DOI: 10.1016/j.bsbt.2016.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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