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The enterovirus protease inhibitor rupintrivir exerts cross-genotypic anti-norovirus activity and clears cells from the norovirus replicon. Antimicrob Agents Chemother 2014; 58:4675-81. [PMID: 24890597 DOI: 10.1128/aac.02546-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Potent and safe inhibitors of norovirus replication are needed for the treatment and prophylaxis of norovirus infections. We here report that the in vitro anti-norovirus activity of the protease inhibitor rupintrivir is extended to murine noroviruses and that rupintrivir clears human cells from their Norwalk replicon after only two passages of antiviral pressure. In addition, we demonstrate that rupintrivir inhibits the human norovirus (genogroup II [GII]) protease and further explain the inhibitory effect of the molecule by means of molecular modeling on the basis of the crystal structure of the Norwalk virus protease. The combination of rupintrivir with the RNA-dependent RNA polymerase inhibitors 2'-C-methylcytidine and favipiravir (T-705) resulted in a merely additive antiviral effect. The fact that rupintrivir is active against noroviruses belonging to genogroup I (Norwalk virus), genogroup V (murine norovirus), and the recombinant 3C-like protease of a GII norovirus suggests that the drug exerts cross-genotypic anti-norovirus activity and will thus most likely be effective against the clinically relevant human norovirus strains. The design of antiviral molecules targeting the norovirus protease could be a valuable approach for the treatment and/or prophylaxis of norovirus infections.
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Tan J, George S, Kusov Y, Perbandt M, Anemüller S, Mesters JR, Norder H, Coutard B, Lacroix C, Leyssen P, Neyts J, Hilgenfeld R. 3C protease of enterovirus 68: structure-based design of Michael acceptor inhibitors and their broad-spectrum antiviral effects against picornaviruses. J Virol 2013; 87:4339-51. [PMID: 23388726 PMCID: PMC3624371 DOI: 10.1128/jvi.01123-12] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 01/05/2013] [Indexed: 11/20/2022] Open
Abstract
We have determined the cleavage specificity and the crystal structure of the 3C protease of enterovirus 68 (EV68 3C(pro)). The protease exhibits a typical chymotrypsin fold with a Cys...His...Glu catalytic triad; its three-dimensional structure is closely related to that of the 3C(pro) of rhinovirus 2, as well as to that of poliovirus. The phylogenetic position of the EV68 3C(pro) between the corresponding enzymes of rhinoviruses on the one hand and classical enteroviruses on the other prompted us to use the crystal structure for the design of irreversible inhibitors, with the goal of discovering broad-spectrum antiviral compounds. We synthesized a series of peptidic α,β-unsaturated ethyl esters of increasing length and for each inhibitor candidate, we determined a crystal structure of its complex with the EV68 3C(pro), which served as the basis for the next design round. To exhibit inhibitory activity, compounds must span at least P3 to P1'; the most potent inhibitors comprise P4 to P1'. Inhibitory activities were found against the purified 3C protease of EV68, as well as with replicons for poliovirus and EV71 (50% effective concentration [EC(50)] = 0.5 μM for the best compound). Antiviral activities were determined using cell cultures infected with EV71, poliovirus, echovirus 11, and various rhinovirus serotypes. The most potent inhibitor, SG85, exhibited activity with EC(50)s of ≈180 nM against EV71 and ≈60 nM against human rhinovirus 14 in a live virus-cell-based assay. Even the shorter SG75, spanning only P3 to P1', displayed significant activity (EC(50) = 2 to 5 μM) against various rhinoviruses.
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Affiliation(s)
- Jinzhi Tan
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
- German Centre for Infection Research, University of Lübeck, Lübeck, Germany
| | - Shyla George
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
- German Centre for Infection Research, University of Lübeck, Lübeck, Germany
| | - Yuri Kusov
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
- German Centre for Infection Research, University of Lübeck, Lübeck, Germany
| | - Markus Perbandt
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
- Laboratory for Structural Biology of Infection and Inflammation, Universities of Lübeck and Hamburg, Hamburg, Germany
| | - Stefan Anemüller
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
- German Centre for Infection Research, University of Lübeck, Lübeck, Germany
| | - Jeroen R. Mesters
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
- German Centre for Infection Research, University of Lübeck, Lübeck, Germany
| | - Helene Norder
- Department of Clinical Microbiology, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Bruno Coutard
- Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 6098, Centre National de la Recherche Scientifique and Universités d'Aix-Marseille I et II, Marseille, France
| | - Céline Lacroix
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Pieter Leyssen
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Johan Neyts
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
- German Centre for Infection Research, University of Lübeck, Lübeck, Germany
- Laboratory for Structural Biology of Infection and Inflammation, Universities of Lübeck and Hamburg, Hamburg, Germany
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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Kikuchi Y, Saika H, Yuasa K, Nagahama M, Tsuji A. Isolation and Biochemical Characterization of Two Forms of RD21 from Cotyledons of Daikon Radish (Raphanus sativus). J Biochem 2008; 144:789-98. [DOI: 10.1093/jb/mvn132] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Mladenovic M, Junold K, Fink RF, Thiel W, Schirmeister T, Engels B. Atomistic insights into the inhibition of cysteine proteases: first QM/MM calculations clarifying the regiospecificity and the inhibition potency of epoxide- and aziridine-based inhibitors. J Phys Chem B 2008; 112:5458-69. [PMID: 18393547 DOI: 10.1021/jp711287c] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epoxides and aziridines are important building blocks for inhibitors of cysteine proteases which are promising drug targets for many diseases. In spite of the large amount of experimental data concerning inhibition potency, structure-activity relationships, and structural arrangements of enzyme-inhibitor complexes, little is known about the basic principles which connect the substitution pattern with the resulting activities. To shed some light on this issue which is essential for the rational design of improved compounds, we have studied the inhibition processes theoretically for various inhibitors using quantum mechanical/molecular mechanical hybrid approaches and classical molecular dynamics simulations. The careful analysis of the computational results allows insight into the interactions which govern the regio- and stereospecificity of the interactions. Known structure-activity relationships are rationalized in terms of the same interactions that determine the measured pH dependencies. Inconsistencies in existing X-ray structures are resolved through comparison with the computed structures, which leads to a reassessment of the factors that control the inhibition potency. Similarities and differences in the mode of action of epoxide- and aziridine-based inhibitors are elucidated. Finally the small reaction barriers computed for the irreversible step in E64 analogues call into question the commonly accepted two-step model of inhibition since the second, irreversible step is predicted to be so fast that suitably oriented enzyme-inhibitor complexes will react rather than dissociate and equilibrate.
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Affiliation(s)
- Milena Mladenovic
- Institut für Organische Chemie, and Institut für Pharmazie und Lebensmittelchemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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Yang H, Xie W, Xue X, Yang K, Ma J, Liang W, Zhao Q, Zhou Z, Pei D, Ziebuhr J, Hilgenfeld R, Yuen KY, Wong L, Gao G, Chen S, Chen Z, Ma D, Bartlam M, Rao Z. Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS Biol 2005; 3:e324. [PMID: 16128623 PMCID: PMC1197287 DOI: 10.1371/journal.pbio.0030324] [Citation(s) in RCA: 462] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Accepted: 07/13/2005] [Indexed: 01/07/2023] Open
Abstract
The genus Coronavirus contains about 25 species of coronaviruses (CoVs), which are important pathogens causing highly prevalent diseases and often severe or fatal in humans and animals. No licensed specific drugs are available to prevent their infection. Different host receptors for cellular entry, poorly conserved structural proteins (antigens), and the high mutation and recombination rates of CoVs pose a significant problem in the development of wide-spectrum anti-CoV drugs and vaccines. CoV main proteases (M(pro)s), which are key enzymes in viral gene expression and replication, were revealed to share a highly conservative substrate-recognition pocket by comparison of four crystal structures and a homology model representing all three genetic clusters of the genus Coronavirus. This conclusion was further supported by enzyme activity assays. Mechanism-based irreversible inhibitors were designed, based on this conserved structural region, and a uniform inhibition mechanism was elucidated from the structures of Mpro-inhibitor complexes from severe acute respiratory syndrome-CoV and porcine transmissible gastroenteritis virus. A structure-assisted optimization program has yielded compounds with fast in vitro inactivation of multiple CoV M(pro)s, potent antiviral activity, and extremely low cellular toxicity in cell-based assays. Further modification could rapidly lead to the discovery of a single agent with clinical potential against existing and possible future emerging CoV-related diseases.
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Affiliation(s)
- Haitao Yang
- 1Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing, China
- 2National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Weiqing Xie
- 3State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoyu Xue
- 1Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing, China
- 2National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kailin Yang
- 1Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing, China
- 2National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jing Ma
- 1Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing, China
- 2National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wenxue Liang
- 4Shanghai Institute of Hematology, Rui-Jin Hospital affiliated to Shanghai Second Medical University, Shanghai, China
| | - Qi Zhao
- 1Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing, China
- 2National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhe Zhou
- 1Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing, China
- 2National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Duanqing Pei
- 5Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - John Ziebuhr
- 6Institute of Virology and Immunology, University of Würzburg, Würzburg, Germany
| | - Rolf Hilgenfeld
- 7Institute for Biochemistry, University of Lübeck, Lübeck, Germany
| | - Kwok Yung Yuen
- 8Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Luet Wong
- 9Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Guangxia Gao
- 1Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing, China
- 2National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Saijuan Chen
- 4Shanghai Institute of Hematology, Rui-Jin Hospital affiliated to Shanghai Second Medical University, Shanghai, China
| | - Zhu Chen
- 4Shanghai Institute of Hematology, Rui-Jin Hospital affiliated to Shanghai Second Medical University, Shanghai, China
| | - Dawei Ma
- 3State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Mark Bartlam
- 1Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing, China
- 2National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zihe Rao
- 1Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing, China
- 2National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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Powers JC, Asgian JL, Ekici OD, James KE. Irreversible inhibitors of serine, cysteine, and threonine proteases. Chem Rev 2002; 102:4639-750. [PMID: 12475205 DOI: 10.1021/cr010182v] [Citation(s) in RCA: 818] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- James C Powers
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
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Dragovich PS, Prins TJ, Zhou R, Johnson TO, Brown EL, Maldonado FC, Fuhrman SA, Zalman LS, Patick AK, Matthews DA, Hou X, Meador JW, Ferre RA, Worland ST. Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. Part 7: structure-activity studies of bicyclic 2-pyridone-containing peptidomimetics. Bioorg Med Chem Lett 2002; 12:733-8. [PMID: 11858991 DOI: 10.1016/s0960-894x(02)00008-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The structure-based design, chemical synthesis, and biological evaluation of bicyclic 2-pyridone-containing human rhinovirus (HRV) 3C protease (3CP) inhibitors are described. An optimized compound is shown to exhibit antiviral activity when tested against a variety of HRV serotypes (EC(50)'s ranging from 0.037 to 0.162 microM).
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Affiliation(s)
- Peter S Dragovich
- Pfizer Global Research and Development-La Jolla/Agouron Pharmaceuticals, Inc., San Diego, CA 92121-1111, USA.
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Matthews DA, Dragovich PS, Webber SE, Fuhrman SA, Patick AK, Zalman LS, Hendrickson TF, Love RA, Prins TJ, Marakovits JT, Zhou R, Tikhe J, Ford CE, Meador JW, Ferre RA, Brown EL, Binford SL, Brothers MA, DeLisle DM, Worland ST. Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes. Proc Natl Acad Sci U S A 1999; 96:11000-7. [PMID: 10500114 PMCID: PMC34232 DOI: 10.1073/pnas.96.20.11000] [Citation(s) in RCA: 239] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human rhinoviruses, the most important etiologic agents of the common cold, are messenger-active single-stranded monocistronic RNA viruses that have evolved a highly complex cascade of proteolytic processing events to control viral gene expression and replication. Most maturation cleavages within the precursor polyprotein are mediated by rhinovirus 3C protease (or its immediate precursor, 3CD), a cysteine protease with a trypsin-like polypeptide fold. High-resolution crystal structures of the enzyme from three viral serotypes have been used for the design and elaboration of 3C protease inhibitors representing different structural and chemical classes. Inhibitors having alpha,beta-unsaturated carbonyl groups combined with peptidyl-binding elements specific for 3C protease undergo a Michael reaction mediated by nucleophilic addition of the enzyme's catalytic Cys-147, resulting in covalent-bond formation and irreversible inactivation of the viral protease. Direct inhibition of 3C proteolytic activity in virally infected cells treated with these compounds can be inferred from dose-dependent accumulations of viral precursor polyproteins as determined by SDS/PAGE analysis of radiolabeled proteins. Cocrystal-structure-assisted optimization of 3C-protease-directed Michael acceptors has yielded molecules having extremely rapid in vitro inactivation of the viral protease, potent antiviral activity against multiple rhinovirus serotypes and low cellular toxicity. Recently, one compound in this series, AG7088, has entered clinical trials.
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Affiliation(s)
- D A Matthews
- Agouron Pharmaceuticals, Inc., 3565 General Atomics Court, San Diego, CA 92121, USA.
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9
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Meara JP, Rich DH. Mechanistic studies on the inactivation of papain by epoxysuccinyl inhibitors. J Med Chem 1996; 39:3357-66. [PMID: 8765519 DOI: 10.1021/jm950445b] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Analogs of the epoxysuccinyl peptide cysteine proteinase inhibitor, EP-475 (2a), in which the free carboxylate has been replaced by hydroxamic acid, amide, methyl ketone, hydroxyl, and ethyl ester functionalities, have been synthesized. Individual rate constants of inhibition of papain were determined for these inhibitors. The results show that a carbonyl-containing functionality is necessary for good activity. The pH dependence of the inhibition of papain was determined for a nonionizable EP-475 (2a) analog; inhibition was found to depend on two acidic ionizations (pKas of 3.93 and 4.09) of papain. Implications for the mechanism of action of epoxysuccinyl peptides with papain are discussed.
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Affiliation(s)
- J P Meara
- School of Pharmacy, University of Wisconsin, Madison 53705, USA
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