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Potential drug-like inhibitors of group 1 influenza neuraminidase identified through computer-aided drug design. (English) Zbl 1366.92039
Summary: Pandemic (H1N1) influenza poses an imminent threat. Nations have stockpiled inhibitors of the influenza protein neuraminidase in hopes of protecting their citizens, but drug-resistant strains have already emerged, and novel therapeutics are urgently needed. In the current work, the computer program AutoGrow is used to generate novel predicted neuraminidase inhibitors. Given the great flexibility of the neuraminidase active site, protein dynamics are also incorporated into the computer-aided drug-design process. Several potential inhibitors are identified that are predicted to bind to neuraminidase better than currently approved drugs.
Reviewer: Reviewer (Berlin)
92C40 Biochemistry, molecular biology
92C50 Medical applications (general)
92C60 Medical epidemiology
AutoDock; DOCK; LUDI
Full Text: DOI
[1] Abdel-Ghafar, A.N.; Chotpitayasunondh, T.; Gao, Z.; Hayden, F.G.; Nguyen, D.H.; de Jong, M.D.; Naghdaliyev, A.; Peiris, J.S.; Shindo, N.; Soeroso, S.; Uyeki, T.M., Update on Avian influenza A (H5N1) virus infection in humans, N. engl. J. med., 358, 261-273, (2008)
[2] Amaro, R.E.; Baron, R.; McCammon, J.A., An improved relaxed complex scheme for receptor flexibility in computer-aided drug design, J. comput.-aided mol. des., 22, 693-705, (2008)
[3] Amaro, R.E.; Schnaufer, A.; Interthal, H.; Hol, W.; Stuart, K.D.; McCammon, J.A., Discovery of drug-like inhibitors of an essential RNA-editing ligase in trypanosoma brucei, Proc. natl. acad. sci., 105, 17278-17283, (2008)
[4] Amaro, R.E.; Minh, D.D.; Cheng, L.S.; Lindstrom, W.M.; Olson, A.J.; Lin, J.H.; Li, W.W.; McCammon, J.A., Remarkable loop flexibility in Avian influenza N1 and its implications for antiviral drug design, J. am. chem. soc., 129, 7764-7765, (2007)
[5] Baker, A.T.; Varghese, J.N.; Laver, W.G.; Air, G.M.; Colman, P.M., Three-dimensional structure of neuraminidase of subtype N9 from an Avian influenza virus, Proteins, 2, 111-117, (1987)
[6] Beigel, J.H.; Farrar, J.; Han, A.M.; Hayden, F.G.; Hyer, R.; de Jong, M.D.; Lochindarat, S.; Nguyen, T.K.; Nguyen, T.H.; Tran, T.H.; Nicoll, A.; Touch, S.; Yuen, K.Y., Avian influenza A (H5N1) infection in humans, N. engl. J. med., 353, 1374-1385, (2005)
[7] Bohm, H.-J., The computer program LUDI: a new method for the de novo design of enzyme inhibitors, J. comput.-aided mol. des., 6, 61, (1992)
[8] Bohm, H.J., A novel computational tool for automated structure-based drug design, J. mol. recogn.: JMR, 6, 131, (1993)
[9] Bohm, H.J., On the use of LUDI to search the fine chemicals directory for ligands of proteins of known three-dimensional structure, J. comput.-aided mol. des., 8, 623-632, (1994)
[10] Bursulaya, B.D.; Totrov, M.; Abagyan, R.; Brooks, C.L., Comparative study of several algorithms for flexible ligand docking, J. comput. aided mol. des., 17, 755-763, (2003)
[11] Cheng, L.S.; Amaro, R.E.; Xu, D.; Li, W.W.; Arzberger, P.W.; McCammon, J.A., Ensemble-based virtual screening reveals potential novel antiviral compounds for Avian influenza neuraminidase, J. med. chem., 51, 3878-3894, (2008)
[12] Christen, M.; Hunenberger, P.H.; Bakowies, D.; Baron, R.; Burgi, R.; Geerke, D.P.; Heinz, T.N.; Kastenholz, M.A.; Krautler, V.; Oostenbrink, C.; Peter, C.; Trzesniak, D.; van Gunsteren, W.F., The GROMOS software for biomolecular simulation: GROMOS05, J. comput. chem., 26, 1719-1751, (2005)
[13] Colman, P.M., Influenza virus neuraminidase: structure, antibodies, and inhibitors, Protein sci., 3, 1687-1696, (1994)
[14] Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; van Gunsteren, W.F.; Mark, A.E., Peptide folding: when simulation meets experiment, Angew. chem. int. ed., 38, 236-240, (1999)
[15] Dawood, F.S.; Jain, S.; Finelli, L.; Shaw, M.W.; Lindstrom, S.; Garten, R.J.; Gubareva, L.V.; Xu, X.; Bridges, C.B.; Uyeki, T.M., Emergence of a novel swine-origin influenza A (H1N1) virus in humans, N. engl. J. med., 360, 2605-2615, (2009)
[16] De Clercq, E., Antiviral agents active against influenza A viruses, Nat. rev. drug discov., 5, 1015-1025, (2006)
[17] De Clercq, E.; Neyts, J., Avian influenza A (H5N1) infection: targets and strategies for chemotherapeutic intervention, Trends pharmacol. sci., 28, 280-285, (2007)
[18] de Jong, M.D.; Tran, T.T.; Truong, H.K.; Vo, M.H.; Smith, G.J.; Nguyen, V.C.; Bach, V.C.; Phan, T.Q.; Do, Q.H.; Guan, Y.; Peiris, J.S.; Tran, T.H.; Farrar, J., Oseltamivir resistance during treatment of influenza A (H5N1) infection, N. engl. J. med., 353, 2667-2672, (2005)
[19] Durrant, J.D.; Amaro, R.E.; McCammon, J.A., Autogrow: a novel algorithm for protein inhibitor design, Chem. biol. drug des., 73, 168-178, (2009)
[20] Ewing, T.J.; Makino, S.; Skillman, A.G.; Kuntz, I.D., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases, J. comput.-aided mol. des., 15, 411, (2001)
[21] Jones, G.; Willett, P.; Glen, R.C.; Leach, A.R.; Taylor, R., Development and validation of a genetic algorithm for flexible docking, J. mol. biol., 267, 727, (1997)
[22] Kiso, M.; Mitamura, K.; Sakai-Tagawa, Y.; Shiraishi, K.; Kawakami, C.; Kimura, K.; Hayden, F.G.; Sugaya, N.; Kawaoka, Y., Resistant influenza A viruses in children treated with oseltamivir: descriptive study, The lancet, 364, 759-765, (2004)
[23] Kobasa, D.; Kodihalli, S.; Luo, M.; Castrucci, M.R.; Donatelli, I.; Suzuki, Y.; Suzuki, T.; Kawaoka, Y., Amino acid residues contributing to the substrate specificity of the influenza A virus neuraminidase, J. virol., 73, 6743-6751, (1999)
[24] Lin, J.H.; Perryman, A.L.; Schames, J.R.; McCammon, J.A., Computational drug design accommodating receptor flexibility: the relaxed complex scheme, J. am. chem. soc., 124, 5632-5633, (2002)
[25] Lipinski, C.A.; Lombardo, F.; Dominy, B.W.; Feeney, P.J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Adv. drug deliv. rev., 46, 3-26, (2001)
[26] Malaisree, M.; Rungrotmongkol, T.; Decha, P.; Intharathep, P.; Aruksakunwong, O.; Hannongbua, S., Understanding of known drug – target interactions in the catalytic pocket of neuraminidase subtype N1, Proteins, 71, 1908-1918, (2008)
[27] Morris, G.M.; Goodsell, D.S.; Halliday, R.S.; Huey, R.; Hart, W.E.; Belew, R.K.; Olson, A.J., Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function, J. comput. chem., 19, 1639-1662, (1998)
[28] Moscona, A., Oseltamivir resistance—disabling our influenza defenses, N. engl. J. med., 353, 2633-2636, (2005)
[29] Oxford, J.; Balasingam, S.; Lambkin, R., A new millennium conundrum: how to use a powerful class of influenza anti-neuraminidase drugs (NAIs) in the community, J. antimicrob. chemother., 53, 133-136, (2004)
[30] Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G., A fast flexible docking method using an incremental construction algorithm, J. mol. biol., 261, 470, (1996)
[31] Rees, D.C.; Congreve, M.; Murray, C.W.; Carr, R., Fragment-based lead discovery, Nat. rev. drug discov., 3, 660-672, (2004)
[32] Russell, R.J.; Haire, L.F.; Stevens, D.J.; Collins, P.J.; Lin, Y.P.; Blackburn, G.M.; Hay, A.J.; Gamblin, S.J.; Skehel, J.J., The structure of H5N1 Avian influenza neuraminidase suggests new opportunities for drug design, Nature, 443, 45-49, (2006)
[33] Schames, J.R.; Henchman, R.H.; Siegel, J.S.; Sotriffer, C.A.; Ni, H.; McCammon, J.A., Discovery of a novel binding trench in HIV integrase, J. med. chem., 47, 1879-1881, (2004)
[34] Varghese, J.N.; Laver, W.G.; Colman, P.M., Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 A resolution, Nature, 303, 35-40, (1983)
[35] Wishart, D.S.; Knox, C.; Guo, A.C.; Shrivastava, S.; Hassanali, M.; Stothard, P.; Chang, Z.; Woolsey, J., Drugbank: a comprehensive resource for in silico drug discovery and exploration, Nucleic acids res., 34, D668-D672, (2006)
[36] Xu, X.; Zhu, X.; Dwek, R.A.; Stevens, J.; Wilson, I.A., Structural characterization of the 1918 influenza virus H1N1 neuraminidase, J. virol., 82, 10493-10501, (2008)
[37] Zhang, X.J.; Baase, W.A.; Matthews, B.W., Multiple alanine replacements within alpha-helix 126-134 of T4 lysozyme have independent, additive effects on both structure and stability, Protein sci., 1, 761-776, (1992)
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