Structure-Based Optimization of N-Substituted Oseltamivir Derivatives as Potent Anti-Influenza A Virus Agents with Significantly Improved Potency against Oseltamivir-Resistant N1-H274Y Variant.

Due to the emergence of highly pathogenic and oseltamivir-resistant influenza viruses, there is an urgent need to develop new anti-influenza agents. Herein, five subseries of oseltamivir derivatives were designed and synthesized to improve their activity toward drug-resistant viral strains by further exploiting the 150-cavity in the neuraminidases (NAs). The bioassay results showed that compound 21h exhibited antiviral activities similar to or better than those of oseltamivir carboxylate (OSC) against H5N1, H5N2, H5N6, and H5N8. Besides, 21h was 5- to 86-fold more potent than OSC toward N1, N8, and N1-H274Y mutant NAs in the inhibitory assays. Computational studies provided a plausible rationale for the high potency of 21h against group-1 and N1-H274Y NAs. In addition, 21h demonstrated acceptable oral bioavailability, low acute toxicity, potent antiviral activity in vivo, and high metabolic stability. Overall, the above excellent profiles make 21h a promising drug candidate for the treatment of influenza virus infection.

[1]  R. Webby,et al.  The avian and mammalian host range of highly pathogenic avian H5N1 influenza. , 2013, Virus research.

[2]  D. M. Ryan,et al.  Rational design of potent sialidase-based inhibitors of influenza virus replication , 1993, Nature.

[3]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[4]  Alan J. Hay,et al.  Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants , 2008, Nature.

[5]  G. Palù,et al.  Antiviral strategies against influenza virus: towards new therapeutic approaches , 2014, Cellular and Molecular Life Sciences.

[6]  T. Sakai,et al.  Low growth ability of recent influenza clinical isolates in MDCK cells is due to their low receptor binding affinities. , 2006, Microbes and infection.

[7]  H. Ågren,et al.  Different Positron Emission Tomography Tau Tracers Bind to Multiple Binding Sites on the Tau Fibril: Insight from Computational Modeling. , 2018, ACS chemical neuroscience.

[8]  S. Genheden,et al.  The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities , 2015, Expert opinion on drug discovery.

[9]  G. Boivin,et al.  Influenza virus resistance to neuraminidase inhibitors. , 2013, Antiviral research.

[10]  Peng Zhan,et al.  Design, Synthesis, and Evaluation of Thiophene[3,2-d]pyrimidine Derivatives as HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors with Significantly Improved Drug Resistance Profiles. , 2016, Journal of medicinal chemistry.

[11]  James M Aramini,et al.  Structures of influenza A proteins and insights into antiviral drug targets , 2010, Nature Structural &Molecular Biology.

[12]  J. McKimm-Breschkin,et al.  Influenza neuraminidase inhibitors: antiviral action and mechanisms of resistance , 2013, Influenza and other respiratory viruses.

[13]  I. Cornella-Taracido,et al.  Causes and Significance of Increased Compound Potency in Cellular or Physiological Contexts. , 2017, Journal of medicinal chemistry.

[14]  Bertrand R. Caré,et al.  Rescue of a H3N2 Influenza Virus Containing a Deficient Neuraminidase Protein by a Hemagglutinin with a Low Receptor-Binding Affinity , 2012, PloS one.

[15]  L. Goracci,et al.  Structural investigation of cycloheptathiophene-3-carboxamide derivatives targeting influenza virus polymerase assembly. , 2013, Journal of medicinal chemistry.

[16]  C. Breneman,et al.  Determining atom‐centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis , 1990 .

[17]  Kousuke Saito,et al.  Neuraminidase inhibitor susceptibility profile of pandemic and seasonal influenza viruses during the 2009-2010 and 2010-2011 influenza seasons in Japan. , 2013, Antiviral research.

[18]  C. Perry,et al.  Oseltamivir , 2012, Drugs.

[19]  K. Goa,et al.  Zanamivir , 1999, Drugs.

[20]  Yuguang Mu,et al.  Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations , 2013, PloS one.

[21]  G. Du,et al.  Structure-activity relationship of flavonoids as influenza virus neuraminidase inhibitors and their in vitro anti-viral activities. , 2008, Bioorganic & medicinal chemistry.

[22]  Giorgio Palù,et al.  Small molecule inhibitors of influenza A and B viruses that act by disrupting subunit interactions of the viral polymerase , 2012, Proceedings of the National Academy of Sciences.

[23]  Robert V. Swift,et al.  Mechanism of 150-cavity formation in influenza neuraminidase , 2011, Nature communications.

[24]  A. Yang,et al.  A practical synthesis of zanamivir phosphonate congeners with potent anti-influenza activity. , 2011, Journal of the American Chemical Society.

[25]  Peter D Gibbons,et al.  Identification, Design and Biological Evaluation of Bisaryl Quinolones Targeting Plasmodium falciparum Type II NADH:Quinone Oxidoreductase (PfNDH2) , 2012, Journal of medicinal chemistry.

[26]  Uko Maran,et al.  Design of Multi-Binding-Site Inhibitors, Ligand Efficiency, and Consensus Screening of Avian Influenza H5N1 Wild-Type Neuraminidase and of the Oseltamivir-Resistant H274Y Variant , 2008, J. Chem. Inf. Model..

[27]  David J. Stevens,et al.  The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design , 2006, Nature.

[28]  G. Gao,et al.  Bat-derived influenza-like viruses H17N10 and H18N11 , 2014, Trends in Microbiology.

[29]  Kuo-Chen Chou,et al.  Three new powerful oseltamivir derivatives for inhibiting the neuraminidase of influenza virus. , 2010, Biochemical and biophysical research communications.

[30]  Holger Gohlke,et al.  MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. , 2012, Journal of chemical theory and computation.

[31]  J. Baell,et al.  New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. , 2010, Journal of medicinal chemistry.

[32]  M. Kiso,et al.  A Novel Potent and Highly Specific Inhibitor against Influenza Viral N1-N9 Neuraminidases: Insight into Neuraminidase-Inhibitor Interactions. , 2016, Journal of medicinal chemistry.

[33]  L. Goracci,et al.  Optimization of small-molecule inhibitors of influenza virus polymerase: from thiophene-3-carboxamide to polyamido scaffolds. , 2014, Journal of medicinal chemistry.

[34]  H. Ågren,et al.  The Culprit Is in the Cave: The Core Sites Explain the Binding Profiles of Amyloid-Specific Tracers. , 2016, The journal of physical chemistry letters.

[35]  J. Andrew McCammon,et al.  Characterizing Loop Dynamics and Ligand Recognition in Human- and Avian-Type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-Point Free Energy Calculations , 2009, Journal of the American Chemical Society.

[36]  Andrew G. Watts,et al.  Structural and Functional Analysis of Anti-Influenza Activity of 4-, 7-, 8- and 9-Deoxygenated 2,3-Difluoro- N-acetylneuraminic Acid Derivatives. , 2018, Journal of medicinal chemistry.

[37]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[38]  Jianhua He,et al.  The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site , 2010, Nature Structural &Molecular Biology.

[39]  M. Eichelberger,et al.  Rapid selection of oseltamivir- and peramivir-resistant pandemic H1N1 virus during therapy in 2 immunocompromised hosts. , 2010, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[40]  Virapong Prachayasittikul,et al.  Exploring the chemical space of influenza neuraminidase inhibitors , 2016, PeerJ.

[41]  Peng Zhan,et al.  Structure-Based Optimization of Thiophene[3,2-d]pyrimidine Derivatives as Potent HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors with Improved Potency against Resistance-Associated Variants. , 2017, Journal of medicinal chemistry.

[42]  David Baltimore,et al.  Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance , 2010, Science.

[43]  George F. Gao,et al.  Structural and Functional Analysis of Laninamivir and its Octanoate Prodrug Reveals Group Specific Mechanisms for Influenza NA Inhibition , 2011, PLoS pathogens.

[44]  Vasanthanathan Poongavanam,et al.  Integrative approaches in HIV‐1 non‐nucleoside reverse transcriptase inhibitor design , 2018 .

[45]  P. Kerry,et al.  Serendipitous discovery of a potent influenza virus a neuraminidase inhibitor. , 2014, Angewandte Chemie.

[46]  Gabriele Neumann,et al.  Emergence and pandemic potential of swine-origin H1N1 influenza virus , 2009, Nature.

[47]  M. Schmidtke,et al.  Utilization of the embryonated egg for in vivo evaluation of the anti-influenza virus activity of neuraminidase inhibitors , 2006, Medical Microbiology and Immunology.

[48]  C. D. de Haan,et al.  Oseltamivir analogues bearing N-substituted guanidines as potent neuraminidase inhibitors. , 2014, Journal of medicinal chemistry.

[49]  P. Kollman,et al.  Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.

[50]  Ivan Merelli,et al.  Virtual screening pipeline and ligand modelling for H5N1 neuraminidase. , 2009, Biochemical and biophysical research communications.

[51]  L. Goracci,et al.  A Broad Anti-influenza Hybrid Small Molecule That Potently Disrupts the Interaction of Polymerase Acidic Protein-Basic Protein 1 (PA-PB1) Subunits. , 2015, Journal of medicinal chemistry.

[52]  Peng Zhan,et al.  Optimization of N-Substituted Oseltamivir Derivatives as Potent Inhibitors of Group-1 and -2 Influenza A Neuraminidases, Including a Drug-Resistant Variant. , 2018, Journal of medicinal chemistry.

[53]  Xinyong Liu,et al.  Discovery of N-substituted oseltamivir derivatives as potent and selective inhibitors of H5N1 influenza neuraminidase. , 2014, Journal of medicinal chemistry.

[54]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[55]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[56]  An-Suei Yang,et al.  Synthesis of tamiflu and its phosphonate congeners possessing potent anti-influenza activity. , 2007, Journal of the American Chemical Society.

[57]  G. Ayora-Talavera,et al.  Hemagglutinin variants of influenza A(H1N1)pdm09 virus with reduced affinity for sialic acid receptors , 2014, Archives of Virology.

[58]  A J Elliott,et al.  Systematic structure-based design and stereoselective synthesis of novel multisubstituted cyclopentane derivatives with potent antiinfluenza activity. , 2001, Journal of medicinal chemistry.