1
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Yuan S, Jiang SC, Zhang ZW, Fu YF, Zhu F, Li ZL, Hu J. Abuse of Amantadine in Poultry May Be Associated with Higher Fatality Rate of H5N1 Infections in Humans. J Med Virol 2022; 94:2588-2597. [PMID: 35170774 DOI: 10.1002/jmv.27664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/12/2022] [Indexed: 11/07/2022]
Abstract
Amantadine, an anti-viral drug, has been widely used in human anti-influenza treatments. However, several highly-pathogenic avian influenza viruses show amantadine-resistance mutations in the viral matrix 2 (M2) protein. Here we analyzed global H5N1 sequencing data and calculate possible correlations between frequencies of key mutations in M2 and the mortality rates. We found that frequency of L26I/V27A mutation in M2 (isolated from both human and avian hosts) is linearly correlated with the mortality rates of human H5N1 infections. The significant correlation between M2 mutations in avians and the mortality rates in humans suggest that the pre-existence of L26I/V27A in birds may determine patient fatalities after trans-infections from avian to human hosts. 100% prevalence of L26I/V27A mutation increased the mortality rates from 51% (95% CI 37%-65%) to 89% (95% CI 88%-90%). Mutations involving Leu26 or Val27 were identified to be the major mutations emerging from drug selection pressure. Thus the emergence of the super H5N1 virus with a fatality over 90% may be attributed to the abuse of amantadine in poultry, especially in some southeast Asian countries. A more stringent control to anti-viral veterinary drugs is imperative. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Si-Cong Jiang
- Chengdu KangHong Pharmaceutical Group Comp. Ltd., Chengdu, 610036, China
| | - Zhong-Wei Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu-Fan Fu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Feng Zhu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Zi-Lin Li
- Department of Cardiovascular Surgery, Xijing Hospital, Medical University of the Air Force, Xi'an, 710032, China
| | - Jing Hu
- School of Medicine, Northwest University, Xi'an, 710069, China
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2
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Tzitzoglaki C, Wright A, Freudenberger K, Hoffmann A, Tietjen I, Stylianakis I, Kolarov F, Fedida D, Schmidtke M, Gauglitz G, Cross TA, Kolocouris A. Binding and Proton Blockage by Amantadine Variants of the Influenza M2WT and M2S31N Explained. J Med Chem 2017; 60:1716-1733. [DOI: 10.1021/acs.jmedchem.6b01115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Christina Tzitzoglaki
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
| | - Anna Wright
- Institute
of Molecular Biophysics and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
| | - Kathrin Freudenberger
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - Anja Hoffmann
- Department
of Virology and Antiviral Therapy, Jena University Hospital, Hans Knoell Strasse 2, D-07745 Jena, Germany
| | - Ian Tietjen
- Department
of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ioannis Stylianakis
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
| | - Felix Kolarov
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - David Fedida
- Department
of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michaela Schmidtke
- Department
of Virology and Antiviral Therapy, Jena University Hospital, Hans Knoell Strasse 2, D-07745 Jena, Germany
| | - Günter Gauglitz
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - Timothy A. Cross
- Institute
of Molecular Biophysics and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
- Department
of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Antonios Kolocouris
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
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3
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Boron nitride nanotube as a delivery system for platinum drugs: Drug encapsulation and diffusion coefficient prediction. Eur J Pharm Sci 2016; 88:291-7. [DOI: 10.1016/j.ejps.2016.04.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 04/08/2016] [Accepted: 04/10/2016] [Indexed: 12/25/2022]
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Ioannidis H, Drakopoulos A, Tzitzoglaki C, Homeyer N, Kolarov F, Gkeka P, Freudenberger K, Liolios C, Gauglitz G, Cournia Z, Gohlke H, Kolocouris A. Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM. J Chem Inf Model 2016; 56:862-76. [DOI: 10.1021/acs.jcim.6b00079] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Harris Ioannidis
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Drakopoulos
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Christina Tzitzoglaki
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Nadine Homeyer
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Felix Kolarov
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Paraskevi Gkeka
- Biomedical
Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Kathrin Freudenberger
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Christos Liolios
- Demokritos, National Center for Scientific Research, 15310 Athens, Greece
| | - Günter Gauglitz
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Antonios Kolocouris
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
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5
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Klimochkin YN, Shiryaev VA, Leonova MV. Antiviral properties of cage compounds. New prospects. Russ Chem Bull 2016. [DOI: 10.1007/s11172-015-1035-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Homeyer N, Ioannidis H, Kolarov F, Gauglitz G, Zikos C, Kolocouris A, Gohlke H. Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations. J Chem Inf Model 2016; 56:110-26. [PMID: 26690735 DOI: 10.1021/acs.jcim.5b00467] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The development of novel anti-influenza drugs is of great importance because of the capability of influenza viruses to occasionally cross interspecies barriers and to rapidly mutate. One class of anti-influenza agents, aminoadamantanes, including the drugs amantadine and rimantadine now widely abandoned due to virus resistance, bind to and block the pore of the transmembrane domain of the M2 proton channel (M2TM) of influenza A. Here, we present one of the still rare studies that interprets thermodynamic profiles from isothermal titration calorimetry (ITC) experiments in terms of individual energy contributions to binding, calculated by the computationally inexpensive implicit solvent/implicit membrane molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach, for aminoadamantane compounds binding to M2TM of the avian "Weybridge" strain. For all eight pairs of aminoadamantane compounds considered, the trend of the predicted relative binding free energies and their individual components, effective binding energies and changes in the configurational entropy, agrees with experimental measures (ΔΔG, ΔΔH, TΔΔS) in 88, 88, and 50% of the cases. In addition, information yielded by the MM-PBSA approach about determinants of binding goes beyond that available in component quantities (ΔH, ΔS) from ITC measurements. We demonstrate how one can make use of such information to link thermodynamic profiles from ITC with structural causes on the ligand side and, ultimately, to guide decision making in lead optimization in a prospective manner, which results in an aminoadamantane derivative with improved binding affinity against M2TM(Weybridge).
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Affiliation(s)
- Nadine Homeyer
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf, Germany
| | - Harris Ioannidis
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens , 15771 Athens, Greece
| | - Felix Kolarov
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität Tübingen , 72076 Tübingen, Germany
| | - Günter Gauglitz
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität Tübingen , 72076 Tübingen, Germany
| | - Christos Zikos
- Demokritos, National Center for Scientific Research , 15310 Athens, Greece
| | - Antonios Kolocouris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens , 15771 Athens, Greece
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf, Germany
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7
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Recent progress and challenges in the computer-aided design of inhibitors for influenza A M2 channel proteins. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0964-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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8
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Wanka L, Iqbal K, Schreiner PR. The lipophilic bullet hits the targets: medicinal chemistry of adamantane derivatives. Chem Rev 2013; 113:3516-604. [PMID: 23432396 PMCID: PMC3650105 DOI: 10.1021/cr100264t] [Citation(s) in RCA: 441] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lukas Wanka
- Institute of Organic Chemistry, Justus-Liebig University Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany; Fax +49(641)9934309
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314-6399, USA
| | - Khalid Iqbal
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314-6399, USA
| | - Peter R. Schreiner
- Institute of Organic Chemistry, Justus-Liebig University Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany; Fax +49(641)9934309
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9
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Replica exchange molecular dynamics simulation of chitosan for drug delivery system based on carbon nanotube. J Mol Graph Model 2013; 39:183-92. [DOI: 10.1016/j.jmgm.2012.11.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 10/29/2012] [Accepted: 11/03/2012] [Indexed: 11/21/2022]
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10
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Hong M, DeGrado WF. Structural basis for proton conduction and inhibition by the influenza M2 protein. Protein Sci 2012; 21:1620-33. [PMID: 23001990 DOI: 10.1002/pro.2158] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 09/10/2012] [Accepted: 09/11/2012] [Indexed: 12/20/2022]
Abstract
The influenza M2 protein forms an acid-activated and drug-sensitive proton channel in the virus envelope that is important for the virus lifecycle. The functional properties and high-resolution structures of this proton channel have been extensively studied to understand the mechanisms of proton conduction and drug inhibition. We review biochemical and electrophysiological studies of M2 and discuss how high-resolution structures have transformed our understanding of this proton channel. Comparison of structures obtained in different membrane-mimetic solvents and under different pH using X-ray crystallography, solution NMR, and solid-state NMR spectroscopy revealed how the M2 structure depends on the environment and showed that the pharmacologically relevant drug-binding site lies in the transmembrane (TM) pore. Competing models of proton conduction have been evaluated using biochemical experiments, high-resolution structural methods, and computational modeling. These results are converging to a model in which a histidine residue in the TM domain mediates proton relay with water, aided by microsecond conformational dynamics of the imidazole ring. These mechanistic insights are guiding the design of new inhibitors that target drug-resistant M2 variants and may be relevant for other proton channels.
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Affiliation(s)
- Mei Hong
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
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11
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Rungnim C, Arsawang U, Rungrotmongkol T, Hannongbua S. Molecular dynamics properties of varying amounts of the anticancer drug gemcitabine inside an open-ended single-walled carbon nanotube. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.08.050] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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12
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New Adamantane Derivatives Can Overcome Resistance of Influenza A(H1N1)pdm2009 and A(H3N2) Viruses to Remantadine. Bull Exp Biol Med 2012; 153:233-5. [DOI: 10.1007/s10517-012-1684-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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13
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Triple combination antiviral drug (TCAD) composed of amantadine, oseltamivir, and ribavirin impedes the selection of drug-resistant influenza A virus. PLoS One 2011; 6:e29778. [PMID: 22220216 PMCID: PMC3248427 DOI: 10.1371/journal.pone.0029778] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 12/03/2011] [Indexed: 11/19/2022] Open
Abstract
Widespread resistance among circulating influenza A strains to at least one of the anti-influenza drugs is a major public health concern. A triple combination antiviral drug (TCAD) regimen comprised of amantadine, oseltamivir, and ribavirin has been shown to have synergistic and broad spectrum activity against influenza A strains, including drug resistant strains. Here, we used mathematical modeling along with three different experimental approaches to understand the effects of single agents, double combinations, and the TCAD regimen on resistance in influenza in vitro, including: 1) serial passage at constant drug concentrations, 2) serial passage at escalating drug concentrations, and 3) evaluation of the contribution of each component of the TCAD regimen to the suppression of resistance. Consistent with the modeling which demonstrated that three drugs were required to suppress the emergence of resistance in influenza A, treatment with the TCAD regimen resulted in the sustained suppression of drug resistant viruses, whereas treatment with amantadine alone or the amantadine-oseltamivir double combination led to the rapid selection of resistant variants which comprised ∼100% of the population. Furthermore, the TCAD regimen imposed a high genetic barrier to resistance, requiring multiple mutations in order to escape the effects of all the drugs in the regimen. Finally, we demonstrate that each drug in the TCAD regimen made a significant contribution to the suppression of virus breakthrough and resistance at clinically achievable concentrations. Taken together, these data demonstrate that the TCAD regimen was superior to double combinations and single agents at suppressing resistance, and that three drugs at a minimum were required to impede the selection of drug resistant variants in influenza A virus. The use of mathematical modeling with multiple experimental designs and molecular readouts to evaluate and optimize combination drug regimens for the suppression of resistance may be broadly applicable to other infectious diseases.
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14
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Tran L, Choi SB, Al-Najjar BO, Yusuf M, Wahab HA, Le L. Discovery of potential M2 channel inhibitors based on the amantadine scaffold via virtual screening and pharmacophore modeling. Molecules 2011; 16:10227-55. [PMID: 22158591 PMCID: PMC6264534 DOI: 10.3390/molecules161210227] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 12/06/2011] [Accepted: 12/08/2011] [Indexed: 01/20/2023] Open
Abstract
The M2 channel protein on the influenza A virus membrane has become the main target of the anti-flu drugs amantadine and rimantadine. The structure of the M2 channel proteins of the H3N2 (PDB code 2RLF) and 2009-H1N1 (Genbank accession number GQ385383) viruses may help researchers to solve the drug-resistant problem of these two adamantane-based drugs and develop more powerful new drugs against influenza A virus. In the present study, we searched for new M2 channel inhibitors through a combination of different computational methodologies, including virtual screening with docking and pharmacophore modeling. Virtual screening was performed to calculate the free energies of binding between receptor M2 channel proteins and 200 new designed ligands. After that, pharmacophore analysis was used to identify the important M2 protein-inhibitor interactions and common features of top binding compounds with M2 channel proteins. Finally, the two most potential compounds were determined as novel leads to inhibit M2 channel proteins in both H3N2 and 2009-H1N1 influenza A virus.
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Affiliation(s)
- Linh Tran
- School of Biotechnology, Ho Chi Minh International University, Quarter 6, Linh Trung, Thu Duc District, Ho Chi Minh City 70000, Vietnam; (L.T.)
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia; (S.B.C.); (B.O.A.-N.); (M.Y.)
| | - Sy Bing Choi
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia; (S.B.C.); (B.O.A.-N.); (M.Y.)
| | - Belal O. Al-Najjar
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia; (S.B.C.); (B.O.A.-N.); (M.Y.)
| | - Muhammad Yusuf
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia; (S.B.C.); (B.O.A.-N.); (M.Y.)
| | - Habibah A. Wahab
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia; (S.B.C.); (B.O.A.-N.); (M.Y.)
- Authors to whom correspondence should be addressed; (L.L.); or (H.A.W.); Tel.: +84-906-578-836; Fax: +84-37-244-271
| | - Ly Le
- School of Biotechnology, Ho Chi Minh International University, Quarter 6, Linh Trung, Thu Duc District, Ho Chi Minh City 70000, Vietnam; (L.T.)
- Authors to whom correspondence should be addressed; (L.L.); or (H.A.W.); Tel.: +84-906-578-836; Fax: +84-37-244-271
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15
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Le L, Leluk J. Study on phylogenetic relationships, variability, and correlated mutations in M2 proteins of influenza virus A. PLoS One 2011; 6:e22970. [PMID: 21829678 PMCID: PMC3149066 DOI: 10.1371/journal.pone.0022970] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 07/11/2011] [Indexed: 11/30/2022] Open
Abstract
M2 channel, an influenza virus transmembrane protein, serves as an important target for antiviral drug design. There are still discordances concerning the role of some residues involved in proton transfer as well as the mechanism of inhibition by commercial drugs. The viral M2 proteins show high conservativity; about 3/4 of the positions are occupied by one residue in over 95%. Nine M2 proteins from the H3N2 strain and possibly two proteins from H2N2 strains make a phylogenic cluster closely related to 2RLF. The variability range is limited to 4 residues/position with one exception. The 2RLF protein stands out by the presence of 2 serines at the positions 19 and 50, which are in most other M2 proteins occupied by cysteines. The study of correlated mutations shows that there are several positions with significant mutational correlation that have not been described so far as functionally important. That there are 5 more residues potentially involved in the M2 mechanism of action. The original software used in this work (Consensus Constructor, SSSSg, Corm, Talana) is freely accessible as stand-alone offline applications upon request to the authors. The other software used in this work is freely available online for noncommercial purposes at public services on bioinformatics such as ExPASy or NCBI. The study on mutational variability, evolutionary relationship, and correlated mutation presented in this paper is a potential way to explain more completely the role of significant factors in proton channel action and to clarify the inhibition mechanism by specific drugs.
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Affiliation(s)
- Ly Le
- School of Biotechnology, Ho Chi Minh International University, Ho Chi Minh City, Vietnam
| | - Jacek Leluk
- Department of Molecular Biology, Faculty of Biological Sciences, University of Zielona Góra, Zielona Góra, Poland
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16
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Gu RX, Liu LA, Wei DQ, Du JG, Liu L, Liu H. Free energy calculations on the two drug binding sites in the M2 proton channel. J Am Chem Soc 2011; 133:10817-25. [PMID: 21711026 DOI: 10.1021/ja1114198] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Two alternative binding sites of adamantane-type drugs in the influenza A M2 channel have been suggested, one with the drug binding inside the channel pore and the other with four drug molecule S-binding to the C-terminal surface of the transmembrane domain. Recent computational and experimental studies have suggested that the pore binding site is more energetically favorable but the external surface binding site may also exist. Nonetheless, which drug binding site leads to channel inhibition in vivo and how drug-resistant mutations affect these sites are not completely understood. We applied molecular dynamics simulations and potential of mean force calculations to examine the structures and the free energies associated with these putative drug binding sites in an M2-lipid bilayer system. We found that, at biological pH (~7.4), the pore binding site is more thermodynamically favorable than the surface binding site by ~7 kcal/mol and, hence, would lead to more stable drug binding and channel inhibition. This result is in excellent agreement with several recent studies. More importantly, a novel finding of ours is that binding to the channel pore requires overcoming a much higher energy barrier of ~10 kcal/mol than binding to the C-terminal channel surface, indicating that the latter site is more kinetically favorable. Our study is the first computational work that provides both kinetic and thermodynamic energy information on these drug binding sites. Our results provide a theoretical framework to interpret and reconcile existing and often conflicting results regarding these two binding sites, thus helping to expand our understanding of M2-drug binding, and may help guide the design and screening of novel drugs to combat the virus.
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Affiliation(s)
- Ruo-Xu Gu
- State Key Laboratory of Microbial Metabolism, Luc Montagnier Biomedical Research Institute, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai Minhang District, China 200240
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17
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Cady SD, Wang J, Wu Y, DeGrado WF, Hong M. Specific binding of adamantane drugs and direction of their polar amines in the pore of the influenza M2 transmembrane domain in lipid bilayers and dodecylphosphocholine micelles determined by NMR spectroscopy. J Am Chem Soc 2011; 133:4274-84. [PMID: 21381693 PMCID: PMC3078525 DOI: 10.1021/ja102581n] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The transmembrane domain of the influenza M2 protein (M2TM) forms a tetrameric proton channel important for the virus lifecycle. The proton-channel activity is inhibited by amine-containing adamantyl drugs amantadine and rimantadine, which have been shown to bind specifically to the pore of M2TM near Ser31. However, whether the polar amine points to the N- or C-terminus of the channel has not yet been determined. Elucidating the polar group direction will shed light on the mechanism by which drug binding inhibits this proton channel and will facilitate rational design of new inhibitors. In this study, we determine the polar amine direction using M2TM reconstituted in lipid bilayers as well as dodecylphosphocholine (DPC) micelles. (13)C-(2)H rotational-echo double-resonance NMR experiments of (13)C-labeled M2TM and methyl-deuterated rimantadine in lipid bilayers showed that the polar amine pointed to the C-terminus of the channel, with the methyl group close to Gly34. Solution NMR experiments of M2TM in DPC micelles indicate that drug binding causes significant chemical shift perturbations of the protein that are very similar to those seen for M2TM and M2(18-60) bound to lipid bilayers. Specific (2)H-labeling of the drugs permitted the assignment of drug-protein cross peaks, which indicate that amantadine and rimantadine bind to the pore in the same fashion as for bilayer-bound M2TM. These results strongly suggest that adamantyl inhibition of M2TM is achieved not only by direct physical occlusion of the channel, but also by perturbing the equilibrium constant of the proton-sensing residue His37. The reproduction of the pharmacologically relevant specific pore-binding site in DPC micelles, which was not observed with a different detergent, DHPC, underscores the significant influence of the detergent environment on the functional structure of this membrane protein.
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Affiliation(s)
- Sarah D. Cady
- Department of Chemistry, Iowa State University, Ames, IA 50011
| | - Jun Wang
- Department of Biochemistry & Biophysics, School of Medicine, and Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6059
| | - Yibing Wu
- Department of Biochemistry & Biophysics, School of Medicine, and Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6059
| | - William F. DeGrado
- Department of Biochemistry & Biophysics, School of Medicine, and Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6059
| | - Mei Hong
- Department of Chemistry, Iowa State University, Ames, IA 50011
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Wang J, Qiu JX, Soto C, DeGrado WF. Structural and dynamic mechanisms for the function and inhibition of the M2 proton channel from influenza A virus. Curr Opin Struct Biol 2011; 21:68-80. [PMID: 21247754 PMCID: PMC3039100 DOI: 10.1016/j.sbi.2010.12.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 12/09/2010] [Indexed: 12/11/2022]
Abstract
The M2 proton channel from influenza A virus, a prototype for a class of viral ion channels known as viroporins, conducts protons along a chain of water molecules and ionizable sidechains, including His37. Recent studies highlight a delicate interplay between protein folding, proton binding, and proton conduction through the channel. Drugs inhibit proton conduction by binding to an aqueous cavity adjacent to M2's proton-selective filter, thereby blocking access of proton to the filter, and altering the energetic landscape of the channel and the energetics of proton-binding to His37.
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Affiliation(s)
- Jun Wang
- Department of Chemistry, School of Medicine, University of Pennsylvania, 422 Curvie Blvd, Philadelphia, PA, 19104, USA
| | - Jade Xiaoyan Qiu
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, 422 Curvie Blvd, Philadelphia, PA, 19104, USA
| | - Cinque Soto
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, 422 Curvie Blvd, Philadelphia, PA, 19104, USA
| | - William F. DeGrado
- Department of Chemistry, School of Medicine, University of Pennsylvania, 422 Curvie Blvd, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, 422 Curvie Blvd, Philadelphia, PA, 19104, USA
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Nunthaboot N, Rungrotmongkol T, Malaisree M, Kaiyawet N, Decha P, Sompornpisut P, Poovorawan Y, Hannongbua S. Evolution of Human Receptor Binding Affinity of H1N1 Hemagglutinins from 1918 to 2009 Pandemic Influenza A Virus. J Chem Inf Model 2010; 50:1410-7. [DOI: 10.1021/ci100038g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nadtanet Nunthaboot
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, 44150, Thailand, Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand, Center of Innovative Nanotechnology, Chulalongkorn University, Bangkok, 10330, Thailand, Computational Chemistry Research Unit, Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung 93110, Thailand, and Center of Excellence in Clinical Virology, Faculty
| | - Thanyada Rungrotmongkol
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, 44150, Thailand, Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand, Center of Innovative Nanotechnology, Chulalongkorn University, Bangkok, 10330, Thailand, Computational Chemistry Research Unit, Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung 93110, Thailand, and Center of Excellence in Clinical Virology, Faculty
| | - Maturos Malaisree
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, 44150, Thailand, Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand, Center of Innovative Nanotechnology, Chulalongkorn University, Bangkok, 10330, Thailand, Computational Chemistry Research Unit, Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung 93110, Thailand, and Center of Excellence in Clinical Virology, Faculty
| | - Nopporn Kaiyawet
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, 44150, Thailand, Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand, Center of Innovative Nanotechnology, Chulalongkorn University, Bangkok, 10330, Thailand, Computational Chemistry Research Unit, Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung 93110, Thailand, and Center of Excellence in Clinical Virology, Faculty
| | - Panita Decha
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, 44150, Thailand, Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand, Center of Innovative Nanotechnology, Chulalongkorn University, Bangkok, 10330, Thailand, Computational Chemistry Research Unit, Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung 93110, Thailand, and Center of Excellence in Clinical Virology, Faculty
| | - Pornthep Sompornpisut
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, 44150, Thailand, Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand, Center of Innovative Nanotechnology, Chulalongkorn University, Bangkok, 10330, Thailand, Computational Chemistry Research Unit, Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung 93110, Thailand, and Center of Excellence in Clinical Virology, Faculty
| | - Yong Poovorawan
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, 44150, Thailand, Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand, Center of Innovative Nanotechnology, Chulalongkorn University, Bangkok, 10330, Thailand, Computational Chemistry Research Unit, Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung 93110, Thailand, and Center of Excellence in Clinical Virology, Faculty
| | - Supot Hannongbua
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, 44150, Thailand, Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand, Center of Innovative Nanotechnology, Chulalongkorn University, Bangkok, 10330, Thailand, Computational Chemistry Research Unit, Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung 93110, Thailand, and Center of Excellence in Clinical Virology, Faculty
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Eleftheratos S, Spearpoint P, Ortore G, Kolocouris A, Martinelli A, Martin S, Hay A. Interaction of aminoadamantane derivatives with the influenza A virus M2 channel-docking using a pore blocking model. Bioorg Med Chem Lett 2010; 20:4182-7. [PMID: 20570509 DOI: 10.1016/j.bmcl.2010.05.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 05/11/2010] [Accepted: 05/13/2010] [Indexed: 01/22/2023]
Abstract
Interaction of aminoadamantanes with the influenza A virus M2 proton channel was analyzed by docking simulations of a series of synthetic aminoadamantane derivatives, of differing binding affinity, into the crystal structure of the transmembrane (M2TM) pore. The pore blocking model tested in the 'gas phase' describes qualitatively the changes on the relative binding affinities of the compounds (although a series of highly hydrophobic ligands which seem to have little capacity for different specific interactions with their receptor). The docking calculations predicted poses in which the adamantane ring is surrounded mainly by the alkyl side chains of Val27 or Ala30 and the ligand's amino group is generally hydrogen bonded with hydroxyls of Ser31 or carbonyls of Val27 or carbonyls of Ala30, the former (Ser31) being the most stable and most frequently observed. The binding of the ligand is a compromise between hydrogen bonding ability, which is elevated by a primary amino group, and apolar interactions, which are increased by the ability of the lipophilic moiety to adequately fill a hydrophobic pocket within the M2TM pore. A delicate balance of these hydrophobic contributions is required for optimal interaction.
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Affiliation(s)
- Stelios Eleftheratos
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
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Rungrotmongkol T, Intharathep P, Malaisree M, Nunthaboot N, Kaiyawet N, Sompornpisut P, Payungporn S, Poovorawan Y, Hannongbua S. Susceptibility of antiviral drugs against 2009 influenza A (H1N1) virus. Biochem Biophys Res Commun 2009; 385:390-4. [DOI: 10.1016/j.bbrc.2009.05.066] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 05/18/2009] [Indexed: 10/20/2022]
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Chapter 7 Influenza A M2. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1554-4516(09)10007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Structural basis for the function and inhibition of an influenza virus proton channel. Nature 2008; 451:596-9. [PMID: 18235504 DOI: 10.1038/nature06528] [Citation(s) in RCA: 481] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 12/06/2007] [Indexed: 12/15/2022]
Abstract
The M2 protein from influenza A virus is a pH-activated proton channel that mediates acidification of the interior of viral particles entrapped in endosomes. M2 is the target of the anti-influenza drugs amantadine and rimantadine; recently, resistance to these drugs in humans, birds and pigs has reached more than 90% (ref. 1). Here we describe the crystal structure of the transmembrane-spanning region of the homotetrameric protein in the presence and absence of the channel-blocking drug amantadine. pH-dependent structural changes occur near a set of conserved His and Trp residues that are involved in proton gating. The drug-binding site is lined by residues that are mutated in amantadine-resistant viruses. Binding of amantadine physically occludes the pore, and might also perturb the pK(a) of the critical His residue. The structure provides a starting point for solving the problem of resistance to M2-channel blockers.
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