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Eruera AR, McSweeney AM, McKenzie-Goldsmith GM, Opel-Reading HK, Thomas SX, Campbell AC, Stubbing L, Siow A, Hubert JG, Brimble MA, Ward VK, Krause KL. Crystal Structure of Inhibitor-Bound GII.4 Sydney 2012 Norovirus 3C-Like Protease. Viruses 2023; 15:2202. [PMID: 38005879 PMCID: PMC10674469 DOI: 10.3390/v15112202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Norovirus is the leading cause of viral gastroenteritis worldwide, and there are no approved vaccines or therapeutic treatments for chronic or severe norovirus infections. The structural characterisation of the norovirus protease and drug development has predominantly focused upon GI.1 noroviruses, despite most global outbreaks being caused by GII.4 noroviruses. Here, we determined the crystal structures of the GII.4 Sydney 2012 ligand-free norovirus protease at 2.79 Å and at 1.83 Å with a covalently bound high-affinity (IC50 = 0.37 µM) protease inhibitor (NV-004). We show that the active sites of the ligand-free protease structure are present in both open and closed conformations, as determined by their Arg112 side chain orientation. A comparative analysis of the ligand-free and ligand-bound protease structures reveals significant structural differences in the active site cleft and substrate-binding pockets when an inhibitor is covalently bound. We also report a second molecule of NV-004 non-covalently bound within the S4 substrate binding pocket via hydrophobic contacts and a water-mediated hydrogen bond. These new insights can guide structure-aided drug design against the GII.4 genogroup of noroviruses.
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Affiliation(s)
- Alice-Roza Eruera
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (A.-R.E.); (A.M.M.); (G.M.M.-G.); (S.X.T.)
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (H.K.O.-R.); (A.C.C.)
| | - Alice M. McSweeney
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (A.-R.E.); (A.M.M.); (G.M.M.-G.); (S.X.T.)
| | - Geena M. McKenzie-Goldsmith
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (A.-R.E.); (A.M.M.); (G.M.M.-G.); (S.X.T.)
| | - Helen K. Opel-Reading
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (H.K.O.-R.); (A.C.C.)
| | - Simone X. Thomas
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (A.-R.E.); (A.M.M.); (G.M.M.-G.); (S.X.T.)
| | - Ashley C. Campbell
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (H.K.O.-R.); (A.C.C.)
| | - Louise Stubbing
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street and 3b Symonds Street, Auckland 1142, New Zealand; (L.S.); (A.S.); (J.G.H.); (M.A.B.)
| | - Andrew Siow
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street and 3b Symonds Street, Auckland 1142, New Zealand; (L.S.); (A.S.); (J.G.H.); (M.A.B.)
| | - Jonathan G. Hubert
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street and 3b Symonds Street, Auckland 1142, New Zealand; (L.S.); (A.S.); (J.G.H.); (M.A.B.)
| | - Margaret A. Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street and 3b Symonds Street, Auckland 1142, New Zealand; (L.S.); (A.S.); (J.G.H.); (M.A.B.)
| | - Vernon K. Ward
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (A.-R.E.); (A.M.M.); (G.M.M.-G.); (S.X.T.)
| | - Kurt L. Krause
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (H.K.O.-R.); (A.C.C.)
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Ling C, Jin Z, Yeung J, da Silva EB, Chang YC, He T, Yim W, O'Donoghue AJ, Jokerst JV. Valence-driven colorimetric detection of norovirus protease via peptide-AuNP interactions. Chem Commun (Camb) 2023; 59:12459-12462. [PMID: 37782049 DOI: 10.1039/d3cc04142e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
We report here a colorimetric method for rapid detection of norovirus based on the valence-driven peptide-AuNP interactions. We engineered a peptide sequence named K1 with a cleavage sequence in between two lysine residues. The positively charged lysine groups aggregated the negatively charged nanoparticles leading to a purple color change. There was a red color when the cleavage sequence was digested by the Southampton norovirus 3C-like protease (SV3CP)-a protease involved in the life cycle of Human norovirus (HNV). The limit of detection was determined to be 320 nM in Tris buffer. We further show that the sensor has good performance in exhaled breath condensate, urine, and faecal matter. This research provides a potential easy and quick way to selectively detect HNV.
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Affiliation(s)
- Chuxuan Ling
- Department of Nano and Chemical Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Zhicheng Jin
- Department of Nano and Chemical Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Justin Yeung
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yu-Ci Chang
- Program in Materials Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tengyu He
- Program in Materials Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wonjun Yim
- Program in Materials Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jesse V Jokerst
- Department of Nano and Chemical Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
- Program in Materials Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Radiology, University of California, San Diego, La Jolla, CA 92093, USA
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3
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Kovalevsky A, Aniana A, Coates L, Bonnesen PV, Nashed NT, Louis JM. Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors. J Biol Chem 2023:104886. [PMID: 37271339 PMCID: PMC10238122 DOI: 10.1016/j.jbc.2023.104886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/06/2023] Open
Abstract
The effect of mutations of the catalytic dyad residues of SARS-CoV-2 main protease (MProWT) on the thermodynamics of binding of covalent inhibitors comprising nitrile [nirmatrelvir (NMV), NBH2], aldehyde (GC373) and ketone (BBH1) warheads to MPro is examined together with room temperature X-ray crystallography. When lacking the nucleophilic C145, NMV binding is ∼400-fold weaker corresponding to 3.5 kcal/mol and 13.3 °C decreases in free energy (ΔG) and thermal stability (Tm), respectively, relative to MProWT. The H41A mutation results in a 20-fold increase in the dissociation constant (Kd), and 1.7 kcal/mol and 1.4 °C decreases in ΔG and Tm, respectively. Increasing the pH from 7.2 to 8.2 enhances NMV binding to MProH41A, whereas no significant change is observed in binding to MProWT. Structures of the four inhibitor complexes with MPro1-304/C145A show that the active site geometries of the complexes are nearly identical to that of MProWT with the nucleophilic sulfur of C145 positioned to react with the nitrile or the carbonyl carbon. These results support a two-step mechanism for the formation of the covalent complex involving an initial non-covalent binding followed by a nucleophilic attack by the thiolate anion of C145 on the warhead carbon. Noncovalent inhibitor ensitrelvir (ESV) exhibits a binding affinity to MProWT that is similar to NMV but differs in its thermodynamic signature from NMV. The binding of ESV to MProC145A also results in a significant, but smaller, increase in Kd and decrease in ΔG and Tm, relative to NMV.
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Affiliation(s)
- Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA.
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Peter V Bonnesen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nashaat T Nashed
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA.
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He S, Nahhas AF, Habib AH, Alshehri MA, Alshamrani S, Asiri SA, Alnamshan MM, Helmi N, Al-Dhuayan I, Almulhim J, Alharbi AM, Su D, Kumari A, Rahaman A. Identification of compelling inhibitors of human norovirus 3CL protease to combat gastroenteritis: A structure-based virtual screening and molecular dynamics study. Front Chem 2022; 10:1034911. [PMID: 36247661 PMCID: PMC9561104 DOI: 10.3389/fchem.2022.1034911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Human noroviruses (NV) are the most prevalent cause of sporadic and pandemic acute gastroenteritis. NV infections cause substantial morbidity and death globally, especially amongst the aged, immunocompromised individuals, and children. There are presently no authorized NV vaccines, small-molecule therapies, or prophylactics for humans. NV 3 C L protease (3CLP) has been identified as a promising therapeutic target for anti-NV drug development. Herein, we employed a structure-based virtual screening method to screen a library of 700 antiviral compounds against the active site residues of 3CLP. We report three compounds, Sorafenib, YM201636, and LDC4297, that were revealed to have a higher binding energy (BE) value with 3CLP than the control (Dipeptidyl inhibitor 7) following a sequential screening, in-depth molecular docking and visualization, physicochemical and pharmacological property analysis, and molecular dynamics (MD) study. Sorafenib, YM201636, and LDC4297 had BEs of -11.67, -10.34, and -9.78 kcal/mol with 3CLP, respectively, while control had a BE of -6.38 kcal/mol. Furthermore, MD simulations of the two best compounds and control were used to further optimize the interactions, and a 100 ns MD simulation revealed that they form stable complexes with 3CLP. The estimated physicochemical, drug-like, and ADMET properties of these hits suggest that they might be employed as 3CLP inhibitors in the management of gastroenteritis. However, wet lab tests are a prerequisite to optimize them as NV 3CLP inhibitors.
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Affiliation(s)
- Shan He
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, China
- Institute for Nano Scale and Technology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
- Suzhou Ultra-Water-Cleaning Tech, Pty, Ltd., Suzhou, Jiangsu, China
| | - Alaa F. Nahhas
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Ali Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Saleh Alshamrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Saeed A. Asiri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mashael M. Alnamshan
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Nawal Helmi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, University of Jeddah, Jeddah, Saudi Arabia
| | - Ibtesam Al-Dhuayan
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Jawaher Almulhim
- Department of Biological Sciences, King Faisal University, Alahsa, Saudi Arabia
| | - Ahmed M. Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Dongxiao Su
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, China
- *Correspondence: Dongxiao Su, ; Ankita Kumari, ; Abdul Rahaman,
| | - Ankita Kumari
- School of Food Science and Engineering, South china University of Technology, Guangzhou, China
- *Correspondence: Dongxiao Su, ; Ankita Kumari, ; Abdul Rahaman,
| | - Abdul Rahaman
- School of Food Science and Engineering, South china University of Technology, Guangzhou, China
- *Correspondence: Dongxiao Su, ; Ankita Kumari, ; Abdul Rahaman,
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5
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Zhao B, Hu L, Song Y, Patil K, Ramani S, Atmar RL, Estes MK, Prasad BVV. Norovirus Protease Structure and Antivirals Development. Viruses 2021; 13:v13102069. [PMID: 34696498 PMCID: PMC8537771 DOI: 10.3390/v13102069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 11/30/2022] Open
Abstract
Human norovirus (HuNoV) infection is a global health and economic burden. Currently, there are no licensed HuNoV vaccines or antiviral drugs available. The protease encoded by the HuNoV genome plays a critical role in virus replication by cleaving the polyprotein and is an excellent target for developing small-molecule inhibitors. The current strategy for developing HuNoV protease inhibitors is by targeting the enzyme’s active site and designing inhibitors that bind to the substrate-binding pockets located near the active site. However, subtle differential conformational flexibility in response to the different substrates in the polyprotein and structural differences in the active site and substrate-binding pockets across different genogroups, hamper the development of effective broad-spectrum inhibitors. A comparative analysis of the available HuNoV protease structures may provide valuable insight for identifying novel strategies for the design and development of such inhibitors. The goal of this review is to provide such analysis together with an overview of the current status of the design and development of HuNoV protease inhibitors.
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Affiliation(s)
- Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Ketki Patil
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
| | - Robert L. Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - B. V. Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
- Correspondence: ; Tel.: +1-713-798-5686
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6
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Structure-based discovery and structural basis of a novel broad-spectrum natural product against main protease of coronavirus. J Virol 2021; 96:e0125321. [PMID: 34586857 PMCID: PMC8754229 DOI: 10.1128/jvi.01253-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Over the past 20 years, the severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome CoV (MERS-CoV), and SARS-CoV-2 emerged, causing severe human respiratory diseases throughout the globe. Developing broad-spectrum drugs would be invaluable in responding to new, emerging coronaviruses and to address unmet urgent clinical needs. Main protease (Mpro; also known as 3CLpro) has a major role in the coronavirus life cycle and is one of the most important targets for anti-coronavirus agents. We show that a natural product, noncovalent inhibitor, shikonin, is a pan-main protease inhibitor of SARS-CoV-2, SARS-CoV, MERS-CoV, human coronavirus (HCoV)-HKU1, HCoV-NL63, and HCoV-229E with micromolar half maximal inhibitory concentration (IC50) values. Structures of the main protease of different coronavirus genus, SARS-CoV from the betacoronavirus genus and HCoV-NL63 from the alphacoronavirus genus, were determined by X-ray crystallography and revealed that the inhibitor interacts with key active site residues in a unique mode. The structure of the main protease inhibitor complex presents an opportunity to discover a novel series of broad-spectrum inhibitors. These data provide substantial evidence that shikonin and its derivatives may be effective against most coronaviruses as well as emerging coronaviruses of the future. Given the importance of the main protease for coronavirus therapeutic indication, insights from these studies should accelerate the development and design of safer and more effective antiviral agents. IMPORTANCE The current pandemic has created an urgent need for broad-spectrum inhibitors of SARS-CoV-2. The main protease is relatively conservative compared to the spike protein and, thus, is one of the most promising targets in developing anti-coronavirus agents. We solved the crystal structures of the main protease of SARS-CoV and HCoV-NL63 that bound to shikonin. The structures provide important insights, have broad implications for understanding the structural basis underlying enzyme activity, and can facilitate rational design of broad-spectrum anti-coronavirus ligands as new therapeutic agents.
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Rathnayake AD, Kim Y, Dampalla CS, Nguyen HN, Jesri ARM, Kashipathy MM, Lushington GH, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-Guided Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease. J Med Chem 2020; 63:11945-11963. [PMID: 32945669 DOI: 10.1021/acs.jmedchem.0c01252] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Acute gastroenteritis caused by noroviruses has a major impact on public health worldwide in terms of morbidity, mortality, and economic burden. The disease impacts most severely immunocompromised patients, the elderly, and children. The current lack of approved vaccines and small-molecule therapeutics for the treatment and prophylaxis of norovirus infections underscores the need for the development of norovirus-specific drugs. The studies described herein entail the use of the gem-dimethyl moiety as a means of improving the pharmacological activity and physicochemical properties of a dipeptidyl series of transition state inhibitors of norovirus 3CL protease, an enzyme essential for viral replication. Several compounds were found to be potent inhibitors of the enzyme in biochemical and cell-based assays. The pharmacological activity and cellular permeability of the inhibitors were found to be sensitive to the location of the gem-dimethyl group.
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Affiliation(s)
- Athri D Rathnayake
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Chamandi S Dampalla
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Abdul-Rahman M Jesri
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Maithri M Kashipathy
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | | | - Kevin P Battaile
- NYX, New York Structural Biology Center, Upton, New York 11973, United States
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
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Discovery of M Protease Inhibitors Encoded by SARS-CoV-2. Antimicrob Agents Chemother 2020; 64:AAC.00872-20. [PMID: 32669265 PMCID: PMC7449189 DOI: 10.1128/aac.00872-20] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/09/2020] [Indexed: 12/27/2022] Open
Abstract
The coronavirus (CoV) disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome CoV-2 (SARS-CoV-2) is a health threat worldwide. Viral main protease (Mpro, also called 3C-like protease [3CLpro]) is a therapeutic target for drug discovery. Herein, we report that GC376, a broad-spectrum inhibitor targeting Mpro in the picornavirus-like supercluster, is a potent inhibitor for the Mpro encoded by SARS-CoV-2, with a half-maximum inhibitory concentration (IC50) of 26.4 ± 1.1 nM. In this study, we also show that GC376 inhibits SARS-CoV-2 replication with a half-maximum effective concentration (EC50) of 0.91 ± 0.03 μM. Only a small portion of SARS-CoV-2 Mpro was covalently modified in the excess of GC376 as evaluated by mass spectrometry analysis, indicating that improved inhibitors are needed. Subsequently, molecular docking analysis revealed that the recognition and binding groups of GC376 within the active site of SARS-CoV-2 Mpro provide important new information for the optimization of GC376. Given that sufficient safety and efficacy data are available for GC376 as an investigational veterinary drug, expedited development of GC376, or its optimized analogues, for treatment of SARS-CoV-2 infection in human is recommended.
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9
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Guo J, Douangamath A, Song W, Coker AR, Chan AE, Wood SP, Cooper JB, Resnick E, London N, Delft FV. In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors. J Struct Biol X 2020; 4:100031. [PMID: 32743543 PMCID: PMC7365090 DOI: 10.1016/j.yjsbx.2020.100031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/15/2020] [Accepted: 07/07/2020] [Indexed: 11/16/2022] Open
Abstract
Outbreaks of human epidemic nonbacterial gastroenteritis are mainly caused by noroviruses. Viral replication requires a 3C-like cysteine protease (3CLpro) which processes the 200 kDa viral polyprotein into six functional proteins. The 3CLpro has attracted much interest due to its potential as a target for antiviral drugs. A system for growing high-quality crystals of native Southampton norovirus 3CLpro (SV3CP) has been established, allowing the ligand-free crystal structure to be determined to 1.3 Å in a tetrameric state. This also allowed crystal-based fragment screening to be performed with various compound libraries, ultimately to guide drug discovery for SV3CP. A total of 19 fragments were found to bind to the protease out of the 844 which were screened. Two of the hits were located at the active site of SV3CP and showed good inhibitory activity in kinetic assays. Another 5 were found at the enzyme's putative RNA-binding site and a further 11 were located in the symmetric central cavity of the tetramer.
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Affiliation(s)
- Jingxu Guo
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, UK
| | - Alice Douangamath
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Weixiao Song
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, UK
| | - Alun R. Coker
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, UK
| | - A.W. Edith Chan
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, UK
| | - Steve P. Wood
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, UK
| | - Jonathan B. Cooper
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, UK
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, UK
| | - Efrat Resnick
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nir London
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Frank von Delft
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
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10
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Ozaki K, Matsushima Y, Nagasawa K, Aso J, Saraya T, Yoshihara K, Murakami K, Motoya T, Ryo A, Kuroda M, Katayama K, Kimura H. Molecular Evolution of the Protease Region in Norovirus Genogroup II. Front Microbiol 2020; 10:2991. [PMID: 31993031 PMCID: PMC6971112 DOI: 10.3389/fmicb.2019.02991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/10/2019] [Indexed: 11/13/2022] Open
Abstract
Noroviruses are a major cause of viral epidemic gastroenteritis in humans worldwide. The protease (Pro) encoded in open reading frame 1 (ORF1) is an essential enzyme for proteolysis of the viral polyprotein. Although there are some reports regarding the evolutionary analysis of norovirus GII-encoding genes, there are few reports focused on the Pro region. We analyzed the molecular evolution of the Pro region of norovirus GII using bioinformatics approaches. A time-scaled phylogenetic tree of the Pro region constructed using a Bayesian Markov chain Monte Carlo method indicated that the common ancestor of GII diverged from GIV around 1680 CE [95% highest posterior density (HPD), 1607-1749]. The GII Pro region emerged around 1752 CE (95%HPD, 1707-1794), forming three further lineages. The evolutionary rate of GII Pro region was estimated at more than 10-3 substitutions/site/year. The distribution of the phylogenetic distances of each genotype differed, and showed genetic diversity. Mapping of the negative selection and substitution sites of the Pro structure showed that the substitution sites in the Pro protein were mostly produced under neutral selection in positions structurally adjacent to the active sites for proteolysis, whereas negative selection was observed in residues distant from the active sites. The phylodynamics of GII.P4, GII.P7, GII.P16, GII.P21, and GII.P31 indicated that their effective population sizes increased during the period from 2005 to 2016 and the increase in population size was almost consistent with the collection year of these genotypes. These results suggest that the Pro region of the norovirus GII evolved rapidly, but under no positive selection, with a high genetic divergence, similar to that of the RNA-dependent RNA polymerase (RdRp) region and the VP1 region of noroviruses.
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Affiliation(s)
- Keita Ozaki
- Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan
- Niitaka Co., Ltd., Osaka, Japan
| | - Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | | | - Jumpei Aso
- Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka, Japan
| | - Takeshi Saraya
- Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka, Japan
| | - Keisuke Yoshihara
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Takumi Motoya
- Ibaraki Prefectural Institute of Public Health, Mito, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Graduate School of Infection Control Sciences, Kitasato Institute for Life Sciences, Kitasato University, Minato, Japan
| | - Hirokazu Kimura
- Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
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11
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A new antiviral scaffold for human norovirus identified with computer-aided approaches on the viral polymerase. Sci Rep 2019; 9:18413. [PMID: 31804593 PMCID: PMC6895199 DOI: 10.1038/s41598-019-54903-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
Human norovirus is the leading cause of acute gastroenteritis worldwide, affecting every year 685 million people. In about one third of cases, this virus affects children under five years of age, causing each year up to 200,000 child deaths, mainly in the developing countries. Norovirus outbreaks are associated with very significant economic losses, with an estimated societal cost of 60 billion dollars per year. Despite the marked socio-economic consequences associated, no therapeutic options or vaccines are currently available to treat or prevent this infection. One promising target to identify new antiviral agents for norovirus is the viral polymerase, which has a pivotal role for the viral replication and lacks closely homologous structures in the host. Starting from the scaffold of a novel class of norovirus polymerase inhibitors recently discovered in our research group with a computer-aided method, different new chemical modifications were designed and carried out, with the aim to identify improved agents effective against norovirus replication in cell-based assays. While different new inhibitors of the viral polymerase were found, a further computer-aided ligand optimisation approach led to the identification of a new antiviral scaffold for norovirus, which inhibits human norovirus replication at low-micromolar concentrations.
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12
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Resnick E, Bradley A, Gan J, Douangamath A, Krojer T, Sethi R, Geurink PP, Aimon A, Amitai G, Bellini D, Bennett J, Fairhead M, Fedorov O, Gabizon R, Gan J, Guo J, Plotnikov A, Reznik N, Ruda GF, Díaz-Sáez L, Straub VM, Szommer T, Velupillai S, Zaidman D, Zhang Y, Coker AR, Dowson CG, Barr HM, Wang C, Huber KVM, Brennan PE, Ovaa H, von Delft F, London N. Rapid Covalent-Probe Discovery by Electrophile-Fragment Screening. J Am Chem Soc 2019; 141:8951-8968. [PMID: 31060360 PMCID: PMC6556873 DOI: 10.1021/jacs.9b02822] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covalent probes can display unmatched potency, selectivity, and duration of action; however, their discovery is challenging. In principle, fragments that can irreversibly bind their target can overcome the low affinity that limits reversible fragment screening, but such electrophilic fragments were considered nonselective and were rarely screened. We hypothesized that mild electrophiles might overcome the selectivity challenge and constructed a library of 993 mildly electrophilic fragments. We characterized this library by a new high-throughput thiol-reactivity assay and screened them against 10 cysteine-containing proteins. Highly reactive and promiscuous fragments were rare and could be easily eliminated. In contrast, we found hits for most targets. Combining our approach with high-throughput crystallography allowed rapid progression to potent and selective probes for two enzymes, the deubiquitinase OTUB2 and the pyrophosphatase NUDT7. No inhibitors were previously known for either. This study highlights the potential of electrophile-fragment screening as a practical and efficient tool for covalent-ligand discovery.
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Affiliation(s)
| | - Anthony Bradley
- Department of Chemistry , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , U.K.,Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K
| | | | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K
| | | | - Ritika Sethi
- Structural Biology Research Center , VIB , Brussels , Belgium.,Structural Biology Brussels , Vrije Universiteit Brussel , Brussels , Belgium
| | - Paul P Geurink
- Oncode Institute and Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC Leiden , The Netherlands
| | - Anthony Aimon
- Department of Chemistry , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , U.K.,Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K
| | | | - Dom Bellini
- School of Life Sciences , University of Warwick , Coventry , U.K
| | | | | | | | | | - Jin Gan
- Oncode Institute and Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC Leiden , The Netherlands
| | - Jingxu Guo
- Division of Medicine , University College London , Gower Street , London WC1E 6BT , U.K
| | | | | | | | | | | | | | | | | | | | - Alun R Coker
- Division of Medicine , University College London , Gower Street , London WC1E 6BT , U.K
| | | | | | | | | | - Paul E Brennan
- School of Life Sciences , University of Warwick , Coventry , U.K.,Alzheimer's Research UK Oxford Drug Discovery Institute , University of Oxford , NDMRB, Roosevelt Drive , Oxford OX3 7FZ , U.K
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC Leiden , The Netherlands
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K.,Department of Biochemistry , University of Johannesburg , Auckland Park 2006 , South Africa
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13
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Galasiti Kankanamalage AC, Weerawarna PM, Rathnayake AD, Kim Y, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Putative structural rearrangements associated with the interaction of macrocyclic inhibitors with norovirus 3CL protease. Proteins 2019; 87:579-587. [PMID: 30883881 DOI: 10.1002/prot.25682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/12/2019] [Accepted: 03/13/2019] [Indexed: 12/17/2022]
Abstract
Human noroviruses are the primary cause of outbreaks of acute gastroenteritis worldwide. The problem is further compounded by the current lack of norovirus-specific antivirals or vaccines. Noroviruses have a single-stranded, positive sense 7 to 8 kb RNA genome which encodes a polyprotein precursor that is processed by a virus-encoded 3C-like cysteine protease (NV 3CLpro) to generate at least six mature nonstructural proteins. Processing of the polyprotein is essential for virus replication, consequently, NV 3CLpro has emerged as an attractive target for the discovery of norovirus therapeutics and prophylactics. We have recently described the structure-based design of macrocyclic transition state inhibitors of NV 3CLpro. In order to gain insight and understanding into the interaction of macrocyclic inhibitors with the enzyme, as well as probe the effect of ring size on pharmacological activity and cellular permeability, additional macrocyclic inhibitors were synthesized and high resolution cocrystal structures determined. The results of our studies tentatively suggest that the macrocyclic scaffold may hamper optimal binding to the active site by impeding concerted cross-talk between the S2 and S4 subsites.
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Affiliation(s)
| | | | | | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Kansas
| | | | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, Illinois
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Kansas
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Kansas
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14
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Muzzarelli KM, Kuiper B, Spellmon N, Brunzelle J, Hackett J, Amblard F, Zhou S, Liu P, Kovari IA, Yang Z, Schinazi RF, Kovari LC. Structural and Antiviral Studies of the Human Norovirus GII.4 Protease. Biochemistry 2019; 58:900-907. [PMID: 30605321 DOI: 10.1021/acs.biochem.8b01063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Norovirus is the leading cause of acute gastroenteritis worldwide with a yearly reported 700 million cases driving a $60 billion global socioeconomic burden. With no United States Food and Drug Administration approved therapeutics and the chance for severe chronic infection and life-threatening complications, researchers have identified the protease as a potential target. However, drug development has focused on the norovirus GI.1 strain despite its accounting for less than 5% of all outbreaks. Our lab aims to change focus for norovirus drug design from GI.1 to the highly infective GII.4, responsible for more than 50% of all outbreaks worldwide. With the first published crystal structure of the norovirus GII.4 protease, we have identified several significant differences in the structure and active site that have hindered development of a potent inhibitor targeting the norovirus GII.4 protease. With these new insights, we have begun designing compounds that demonstrate increased inhibition of the clinically most relevant norovirus GII.4 strain.
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Affiliation(s)
- Kendall M Muzzarelli
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Benjamin Kuiper
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Nicholas Spellmon
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Joseph Brunzelle
- Synchrotron Research Center, Life Science Collaborative Access Team , Northwestern University , Argonne , Illinois United States
| | - Justin Hackett
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics , Emory University School of Medicine , Atlanta , Georgia 30322 , United States
| | - Shaoman Zhou
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics , Emory University School of Medicine , Atlanta , Georgia 30322 , United States
| | - Peng Liu
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics , Emory University School of Medicine , Atlanta , Georgia 30322 , United States
| | - Iulia A Kovari
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Zhe Yang
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics , Emory University School of Medicine , Atlanta , Georgia 30322 , United States
| | - Ladislau C Kovari
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
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15
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Kuiper BD, Muzzarelli KM, Keusch BJ, Holcomb J, Amblard F, Liu P, Zhou S, Kovari IA, Yang Z, Schinazi RF, Kovari LC. Expression, Purification and Characterization of a GII.4 Norovirus Protease from Minerva Virus. Infect Disord Drug Targets 2019; 18:224-232. [PMID: 29779487 DOI: 10.2174/1871526518666180521091158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 04/30/2018] [Accepted: 05/15/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noroviruses are the leading cause of acute gastroenteritis worldwide. Norovirus proteases, which are responsible for cleavage of the viral polyprotein, have become an attractive drug target to treat norovirus infections. Genogroup II (GII) noroviruses are responsible for a majority of outbreaks; however, limited data exists regarding GII norovirus proteases. METHODS We report here successful expression, purification, characterization, and inhibition of the Minerva virus protease (MVpro), a genogroup II genotype 4 (GII.4) norovirus protease. We observed MVpro as both a monomer and dimer in solution through sizeexclusion chromatography. In addition, MVpro cleaves the synthetic substrate mimicking the MVpro NS2/NS3 cleavage site more efficiently than other norovirus proteases such as the Norwalk virus protease (GI.1) and the MD145 protease (GII.4). RESULTS AND CONCLUSION Compound A, a potent inhibitor of MVpro, is a good starting point for the design of inhibitors to target GII.4 noroviruses. Furthermore, the results presented here will allow for future characterization of MVpro inhibitors as they are synthesized.
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Affiliation(s)
- Benjamin D Kuiper
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Kendall M Muzzarelli
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Bradley J Keusch
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Joshua Holcomb
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Peng Liu
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Shaoman Zhou
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Iulia A Kovari
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Zhe Yang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Ladislau C Kovari
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, United States
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16
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Ghosh S, Malik YS, Kobayashi N. Therapeutics and Immunoprophylaxis Against Noroviruses and Rotaviruses: The Past, Present, and Future. Curr Drug Metab 2018; 19:170-191. [PMID: 28901254 PMCID: PMC5971199 DOI: 10.2174/1389200218666170912161449] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/25/2016] [Accepted: 03/19/2017] [Indexed: 12/20/2022]
Abstract
Background: Noroviruses and rotaviruses are important viral etiologies of severe gastroenteritis. Noroviruses are the primary cause of nonbacterial diarrheal outbreaks in humans, whilst rotaviruses are a major cause of childhood diarrhea. Although both enteric pathogens substantially impact human health and economies, there are no approved drugs against noroviruses and rotaviruses so far. On the other hand, whilst the currently licensed rotavirus vaccines have been successfully implemented in over 100 countries, the most advanced norovirus vaccine has recently completed phase-I and II trials. Methods: We performed a structured search of bibliographic databases for peer-reviewed research litera-ture on advances in the fields of norovirus and rotavirus therapeutics and immunoprophylaxis. Results: Technological advances coupled with a proper understanding of viral morphology and replication over the past decade has facilitated pioneering research on therapeutics and immunoprophylaxis against noroviruses and rotaviruses, with promising outcomes in human clinical trials of some of the drugs and vaccines. This review focuses on the various developments in the fields of norovirus and rotavirus thera-peutics and immunoprophylaxis, such as potential antiviral drug molecules, passive immunotherapies (oral human immunoglobulins, egg yolk and bovine colostral antibodies, llama-derived nanobodies, and anti-bodies expressed in probiotics, plants, rice grains and insect larvae), immune system modulators, probiot-ics, phytochemicals and other biological substances such as bovine milk proteins, therapeutic nanoparti-cles, hydrogels and viscogens, conventional viral vaccines (live and inactivated whole virus vaccines), and genetically engineered viral vaccines (reassortant viral particles, virus-like particles (VLPs) and other sub-unit recombinant vaccines including multi-valent viral vaccines, edible plant vaccines, and encapsulated viral particles). Conclusions: This review provides important insights into the various approaches to therapeutics and im-munoprophylaxis against noroviruses and rotaviruses..
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Affiliation(s)
- Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, St. Kitts and Nevis, West Indies.,Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Yashpal Singh Malik
- Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
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17
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Kitano M, Hosmillo M, Emmott E, Lu J, Goodfellow I. Selection and Characterization of Rupintrivir-Resistant Norwalk Virus Replicon Cells In Vitro. Antimicrob Agents Chemother 2018; 62:e00201-18. [PMID: 29530860 PMCID: PMC5923142 DOI: 10.1128/aac.00201-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/02/2018] [Indexed: 12/30/2022] Open
Abstract
Human norovirus (HuNoV) is a major cause of nonbacterial gastroenteritis worldwide, yet despite its impact on society, vaccines and antivirals are currently lacking. A HuNoV replicon system has been widely applied to the evaluation of antiviral compounds and has thus accelerated the process of drug discovery against HuNoV infection. Rupintrivir, an irreversible inhibitor of the human rhinovirus 3C protease, has been reported to inhibit the replication of the Norwalk virus replicon via the inhibition of the norovirus protease. Here we report, for the first time, the generation of rupintrivir-resistant human Norwalk virus replicon cells in vitro Sequence analysis revealed that these replicon cells contained amino acid substitutions of alanine 105 to valine (A105V) and isoleucine 109 to valine (I109V) in the viral protease NS6. The application of a cell-based fluorescence resonance energy transfer (FRET) assay for protease activity demonstrated that these substitutions were involved in the enhanced resistance to rupintrivir. Furthermore, we validated the effect of these mutations using reverse genetics in murine norovirus (MNV), demonstrating that a recombinant MNV strain with a single I109V substitution in the protease also showed reduced susceptibility to rupintrivir. In summary, using a combination of different approaches, we have demonstrated that, under the correct conditions, mutations in the norovirus protease that lead to the generation of resistant mutants can rapidly occur.
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Affiliation(s)
- Mitsutaka Kitano
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Edward Emmott
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Jia Lu
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
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18
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Ferla S, Netzler NE, Ferla S, Veronese S, Tuipulotu DE, Guccione S, Brancale A, White PA, Bassetto M. In silico screening for human norovirus antivirals reveals a novel non-nucleoside inhibitor of the viral polymerase. Sci Rep 2018. [PMID: 29515206 PMCID: PMC5841303 DOI: 10.1038/s41598-018-22303-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Human norovirus causes approximately 219,000 deaths annually, yet there are currently no antivirals available. A virtual screening of commercially available drug-like compounds (~300,000) was performed on the suramin and PPNDS binding-sites of the norovirus RNA-dependent RNA polymerase (RdRp). Selected compounds (n = 62) were examined for inhibition of norovirus RdRp activity using an in vitro transcription assay. Eight candidates demonstrated RdRp inhibition (>25% inhibition at 10 µM), which was confirmed using a gel-shift RdRp assay for two of them. The two molecules were identified as initial hits and selected for structure-activity relationship studies, which resulted in the synthesis of novel compounds that were examined for inhibitory activity. Five compounds inhibited human norovirus RdRp activity (>50% at 10 µM), with the best candidate, 54, demonstrating an IC50 of 5.6 µM against the RdRp and a CC50 of 62.8 µM. Combinational treatment of 54 and the known RdRp site-B inhibitor PPNDS revealed antagonism, indicating that 54 binds in the same binding pocket. Two RdRps with mutations (Q414A and R419A) previously shown to be critical for the binding of site-B compounds had no effect on inhibition, suggesting 54 interacts with distinct site-B residues. This study revealed the novel scaffold 54 for further development as a norovirus antiviral.
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Affiliation(s)
- Salvatore Ferla
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom.
| | - Natalie E Netzler
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sebastiano Ferla
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom.,Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, Catania, Italy
| | - Sofia Veronese
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Salvatore Guccione
- Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, Catania, Italy
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Marcella Bassetto
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
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19
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Damalanka VC, Kim Y, Galasiti Kankanamalage AC, Rathnayake AD, Mehzabeen N, Battaile KP, Lovell S, Nguyen HN, Lushington GH, Chang KO, Groutas WC. Structure-guided design, synthesis and evaluation of oxazolidinone-based inhibitors of norovirus 3CL protease. Eur J Med Chem 2018; 143:881-890. [PMID: 29227928 PMCID: PMC5737831 DOI: 10.1016/j.ejmech.2017.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/18/2017] [Accepted: 12/04/2017] [Indexed: 11/29/2022]
Abstract
Acute nonbacterial gastroenteritis caused by noroviruses constitutes a global public health concern and a significant economic burden. There are currently no small molecule therapeutics or vaccines for the treatment of norovirus infections. A structure-guided approach was utilized in the design of a series of inhibitors of norovirus 3CL protease that embody an oxazolidinone ring as a novel design element for attaining optimal binding interactions. Low micromolar cell-permeable inhibitors that display anti-norovirus activity have been identified. The mechanism of action, mode of binding, and structural rearrangements associated with the interaction of the inhibitors and the enzyme were elucidated using X-ray crystallography.
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Affiliation(s)
- Vishnu C Damalanka
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | | | - Athri D Rathnayake
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | | | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
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20
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Galasiti Kankanamalage AC, Kim Y, Rathnayake AD, Alliston KR, Butler MM, Cardinale SC, Bowlin TL, Groutas WC, Chang KO. Design, Synthesis, and Evaluation of Novel Prodrugs of Transition State Inhibitors of Norovirus 3CL Protease. J Med Chem 2017; 60:6239-6248. [DOI: 10.1021/acs.jmedchem.7b00497] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | - Yunjeong Kim
- Department
of Diagnostic Medicine & Pathobiology, Kansas State University
College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Athri D. Rathnayake
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Kevin R. Alliston
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | | | | | - Terry L. Bowlin
- Microbiotix, Inc., Worcester, Massachusetts 01605, United States
| | - William C. Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Kyeong-Ok Chang
- Department
of Diagnostic Medicine & Pathobiology, Kansas State University
College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
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Damalanka VC, Kim Y, Galasiti Kankanamalage AC, Lushington GH, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Design, synthesis, and evaluation of a novel series of macrocyclic inhibitors of norovirus 3CL protease. Eur J Med Chem 2017; 127:41-61. [PMID: 28038326 PMCID: PMC5296247 DOI: 10.1016/j.ejmech.2016.12.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/01/2016] [Accepted: 12/16/2016] [Indexed: 02/01/2023]
Abstract
Norovirus infections have a major impact on public health worldwide, yet there is a current dearth of norovirus-specific therapeutics and prophylactics. This report describes the discovery of a novel class of macrocyclic inhibitors of norovirus 3C-like protease, a cysteine protease that is essential for virus replication. SAR, structural, and biochemical studies were carried out to ascertain the effect of structure on pharmacological activity and permeability. Insights gained from these studies have laid a solid foundation for capitalizing on the therapeutic potential of the series of inhibitors described herein.
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Affiliation(s)
- Vishnu C Damalanka
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | | | | | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
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22
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Xu C, Fu J, Zhu Y. A Narrative Review of Norovirus Gastroenteritis: More Global Attention Is Needed. INTERNATIONAL JOURNAL OF TRAVEL MEDICINE AND GLOBAL HEALTH 2016. [DOI: 10.21859/ijtmgh-040402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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23
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Galasiti Kankanamalage AC, Kim Y, Rathnayake AD, Damalanka VC, Weerawarna PM, Doyle ST, Alsoudi AF, Dissanayake DMP, Lushington GH, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-based exploration and exploitation of the S 4 subsite of norovirus 3CL protease in the design of potent and permeable inhibitors. Eur J Med Chem 2016; 126:502-516. [PMID: 27914364 DOI: 10.1016/j.ejmech.2016.11.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/10/2016] [Accepted: 11/12/2016] [Indexed: 12/17/2022]
Abstract
Human noroviruses are the primary cause of epidemic and sporadic acute gastroenteritis. The worldwide high morbidity and mortality associated with norovirus infections, particularly among the elderly, immunocompromised patients and children, constitute a serious public health concern. There are currently no approved human vaccines or norovirus-specific small-molecule therapeutics or prophylactics. Norovirus 3CL protease has recently emerged as a potential therapeutic target for the development of anti-norovirus agents. We hypothesized that the S4 subsite of the enzyme may provide an effective means of designing potent and cell permeable inhibitors of the enzyme. We report herein the structure-guided exploration and exploitation of the S4 subsite of norovirus 3CL protease in the design and synthesis of effective inhibitors of the protease.
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Affiliation(s)
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Athri D Rathnayake
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Vishnu C Damalanka
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | | | - Sean T Doyle
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Amer F Alsoudi
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | | | | | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
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24
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Antiviral targets of human noroviruses. Curr Opin Virol 2016; 18:117-25. [PMID: 27318434 DOI: 10.1016/j.coviro.2016.06.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/06/2016] [Accepted: 06/06/2016] [Indexed: 11/20/2022]
Abstract
Human noroviruses are major causative agents of sporadic and epidemic gastroenteritis both in children and adults. Currently there are no licensed therapeutic intervention measures either in terms of vaccines or drugs available for these highly contagious human pathogens. Genetic and antigenic diversity of these viruses, rapid emergence of new strains, and their ability to infect a broad population by using polymorphic histo-blood group antigens for cell attachment, pose significant challenges for the development of effective antiviral agents. Despite these impediments, there is progress in the design and development of therapeutic agents. These include capsid-based candidate vaccines, and potential antivirals either in the form of glycomimetics or designer antibodies that block HBGA binding, as well as those that target essential non-structural proteins such as the viral protease and RNA-dependent RNA polymerase. In addition to these classical approaches, recent studies suggest the possibility of interferons and targeting host cell factors as viable approaches to counter norovirus infection. This review provides a brief overview of this progress.
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25
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Abstract
INTRODUCTION Rapid transmission of norovirus often occurs due to its low infectious dosage, high genetic diversity and its short incubation time. The viruses cause acute gastroenteritis and may lead to death. Presently, no effective vaccine or selective drugs accepted by the United States Food and Drug Administration (FDA) are available for the treatment of norovirus. Advances in the development of norovirus replicon cell lines, GII.4-Sydney HuNoV strain human B cells, and murine and gnotobiotic pig norovirus models have facilitated the discovery of effective small molecule inhibitors in vitro and in vivo. AREAS COVERED This review gives a brief discussion of the biology and replication of norovirus before highlighting the discovery of anti-norovirus molecules. The article coverage includes: an overview of the current state of norovirus drug discovery, the targeting of the norovirus life cycle, the inhibition of structural and nonstructural proteins of norovirus such as proteases and polymerase, and the blockage of virus entry into host cells. Finally, anti-norovirus drugs in the clinical development stage are described. EXPERT OPINION The current approach for the counteraction of norovirus focuses on the inhibition of viral RNA polymerase, norovirus 3C-like protease and the structural proteins VP1 as well as the blockade of norovirus entry. Broad-spectrum anti-norovirus molecules, based on the inhibition of 3C-like protease, have been developed. Other host factors and ways to overcome the development of resistance through mutation are also being examined. A dual approach in targeting viral and host factors may lead to an effective counteraction of norovirus infection. Current successes in developing norovirus replicon harboring cells and norovirus infected human cells, as well as murine norovirus models and other animal models such as piglets have facilitated the discovery of effective drugs and helped our understanding of its mechanism of action.
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Affiliation(s)
- Sahani Weerasekara
- a Department of Chemistry , Kansas State University , Manhattan , KS , USA
| | - Allan M Prior
- b Molecular Sciences Institute, School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa
| | - Duy H Hua
- a Department of Chemistry , Kansas State University , Manhattan , KS , USA
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26
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Weerawarna PM, Kim Y, Galasiti Kankanamalage AC, Damalanka VC, Lushington GH, Alliston KR, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-based design and synthesis of triazole-based macrocyclic inhibitors of norovirus protease: Structural, biochemical, spectroscopic, and antiviral studies. Eur J Med Chem 2016; 119:300-18. [PMID: 27235842 PMCID: PMC4916972 DOI: 10.1016/j.ejmech.2016.04.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/04/2016] [Accepted: 04/06/2016] [Indexed: 01/14/2023]
Abstract
Outbreaks of acute gastroenteritis caused by noroviruses constitute a public health concern worldwide. To date, there are no approved drugs or vaccines for the management and prophylaxis of norovirus infections. A potentially effective strategy for the development of norovirus therapeutics entails the discovery of inhibitors of norovirus 3CL protease, an enzyme essential for noroviral replication. We describe herein the structure-based design of the first class of permeable, triazole-based macrocyclic inhibitors of norovirus 3C-like protease, as well as pertinent X-ray crystallographic, biochemical, spectroscopic, and antiviral studies. Novel triazole-based macrocyclic inhibitors of norovirus 3CL protease were synthesized. The interplay of conformation and activity was probed using NMR and X-ray crystallography. Bound inhibitors assume a β-strand conformation according to X-ray crystal structure. Loss of critical hydrogen bonding interactions was revealed by X-ray crystallography.
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Affiliation(s)
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | | | - Vishnu C Damalanka
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | | | - Kevin R Alliston
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
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27
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Damalanka VC, Kim Y, Alliston KR, Weerawarna PM, Galasiti Kankanamalage AC, Lushington GH, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Oxadiazole-Based Cell Permeable Macrocyclic Transition State Inhibitors of Norovirus 3CL Protease. J Med Chem 2016; 59:1899-913. [PMID: 26823007 DOI: 10.1021/acs.jmedchem.5b01464] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Human noroviruses are the primary causative agents of acute gastroenteritis and a pressing public health burden worldwide. There are currently no vaccines or small molecule therapeutics available for the treatment or prophylaxis of norovirus infections. Norovirus 3CL protease plays a vital role in viral replication by generating structural and nonstructural proteins via the cleavage of the viral polyprotein. Thus, molecules that inhibit the viral protease may have potential therapeutic value. We describe herein the structure-based design, synthesis, and in vitro and cell-based evaluation of the first class of oxadiazole-based, permeable macrocyclic inhibitors of norovirus 3CL protease.
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Affiliation(s)
- Vishnu C Damalanka
- Department of Chemistry, Wichita State University , Wichita, Kansas 67260, United States
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas 66506, United States
| | - Kevin R Alliston
- Department of Chemistry, Wichita State University , Wichita, Kansas 67260, United States
| | - Pathum M Weerawarna
- Department of Chemistry, Wichita State University , Wichita, Kansas 67260, United States
| | | | | | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas , Lawrence, Kansas 66047, United States
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas , Lawrence, Kansas 66047, United States
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas 66506, United States
| | - William C Groutas
- Department of Chemistry, Wichita State University , Wichita, Kansas 67260, United States
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Galasiti Kankanamalage AC, Weerawarna PM, Kim Y, Chang KO, Groutas WC. Anti-norovirus therapeutics: a patent review (2010-2015). Expert Opin Ther Pat 2016; 26:297-308. [PMID: 26881878 PMCID: PMC4948123 DOI: 10.1517/13543776.2016.1153065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Human noroviruses are the primary causative agents of acute gastroenteritis and are a pressing public health burden worldwide. There are currently no vaccines or small molecule therapeutics available for the treatment or prophylaxis of norovirus infections. An improved understanding of norovirus biology, as well as the pathogenic mechanisms underlying the disease, has provided the impetus for a range of intense exploratory drug discovery efforts targeting viral and host factors. AREAS COVERED An overview of norovirus inhibitors disclosed in the patent literature (2010-present) and Clinicaltrials.gov is presented. The review is further enriched and supplemented by recent literature reports. EXPERT OPINION Seminal discoveries made in recent years, including a better understanding of the pathobiology and life cycle of norovirus, the identification and targeting of multiple viral and host factors, the advent of a replicon system and a small animal model for the preclinical evaluation of lead compounds, and the availability of high resolution X-ray crystal structures that can be utilized in structure-based drug design and lead optimization campaigns, collectively suggest that a small molecule therapeutic and prophylactic for norovirus infection is likely to emerge in the not too distant future.
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Affiliation(s)
| | | | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, Manhattan, Kansas 66506, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, Manhattan, Kansas 66506, USA
| | - William C. Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
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29
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Emmott E, Sweeney TR, Goodfellow I. A Cell-based Fluorescence Resonance Energy Transfer (FRET) Sensor Reveals Inter- and Intragenogroup Variations in Norovirus Protease Activity and Polyprotein Cleavage. J Biol Chem 2015; 290:27841-53. [PMID: 26363064 PMCID: PMC4646915 DOI: 10.1074/jbc.m115.688234] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Indexed: 12/22/2022] Open
Abstract
The viral protease represents a key drug target for the development of antiviral therapeutics. Because many protease inhibitors mimic protease substrates, differences in substrate recognition between proteases may affect their sensitivity to a given inhibitor. Here we use a cell-based FRET sensor to investigate the activity of different norovirus proteases upon cleavage of various norovirus cleavage sites inserted into a linker region separating cyan fluorescent protein and yellow fluorescent protein. Using this system, we demonstrate that differences in substrate processing exist between proteases from human noroviruses (genogroups I (GI) and II) and the commonly used murine norovirus (MNV, genogroup V) model. These altered the cleavage efficiency of specific cleavage sites both within and between genogroups. The differences observed between these proteases may affect sensitivity to protease inhibitors and the suitability of MNV as a model system for testing such molecules against the human norovirus protease. Finally, we demonstrate that replacement of MNV polyprotein cleavage sites with the GI or GII equivalents, with the exception of the NS6–7 junction, leads to the production of infectious virus when the MNV NS6 protease, but not the GI or GII proteases, are present.
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Affiliation(s)
- Edward Emmott
- From the Division of Virology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 2QQ, United Kingdom
| | - Trevor R Sweeney
- From the Division of Virology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 2QQ, United Kingdom
| | - Ian Goodfellow
- From the Division of Virology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 2QQ, United Kingdom
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Kim Y, Galasiti Kankanamalage AC, Chang KO, Groutas WC. Recent Advances in the Discovery of Norovirus Therapeutics. J Med Chem 2015; 58:9438-50. [PMID: 26258852 DOI: 10.1021/acs.jmedchem.5b00762] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Noroviruses are members of the family Caliciviridae. Norovirus infections are a global health burden that impacts >20 million individuals annually in the U.S. alone. Noroviruses are associated with high morbidity among vulnerable populations, particularly immunocompromised patients. This perspective highlights recent developments related to the discovery and development of norovirus-specific small-molecule therapeutics as well as recent advances in our understanding of norovirus biology and pathogenesis. Most of the work in this area is at the early discovery stage and has been primarily focused on inhibitors of norovirus 3C-like protease and RNA dependent RNA polymerase. However, recent discoveries emanating from basic studies in norovirus research have resulted in the identification of new host-related drug targets that can be exploited. A repurposed compound has been advanced to human clinical studies.
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Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas 66506, United States
| | | | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas 66506, United States
| | - William C Groutas
- Department of Chemistry, Wichita State University , 1845 North Fairmount Avenue, Wichita, Kansas 67260, United States
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31
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Kankanamalage ACG, Kim Y, Weerawarna PM, Uy RAZ, Damalanka VC, Mandadapu SR, Alliston KR, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-guided design and optimization of dipeptidyl inhibitors of norovirus 3CL protease. Structure-activity relationships and biochemical, X-ray crystallographic, cell-based, and in vivo studies. J Med Chem 2015; 58:3144-55. [PMID: 25761614 PMCID: PMC4484267 DOI: 10.1021/jm5019934] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Norovirus infection constitutes the primary cause of acute viral gastroenteritis. There are currently no vaccines or norovirus-specific antiviral therapeutics available for the management of norovirus infection. Norovirus 3C-like protease is essential for viral replication, consequently, inhibition of this enzyme is a fruitful avenue of investigation that may lead to the emergence of antinorovirus therapeutics. We describe herein the optimization of dipeptidyl inhibitors of norovirus 3C-like protease using iterative SAR, X-ray crystallographic, and enzyme and cell-based studies. We also demonstrate herein in vivo efficacy of an inhibitor using the murine model of norovirus infection.
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Affiliation(s)
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506
| | | | | | | | | | - Kevin R. Alliston
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047
| | - Kevin P. Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506
| | - William C. Groutas
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047
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32
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Fernandes H, Leen EN, Cromwell H, Pfeil MP, Curry S. Structure determination of Murine Norovirus NS6 proteases with C-terminal extensions designed to probe protease-substrate interactions. PeerJ 2015; 3:e798. [PMID: 25755927 PMCID: PMC4349150 DOI: 10.7717/peerj.798] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/05/2015] [Indexed: 01/20/2023] Open
Abstract
Noroviruses are positive-sense single-stranded RNA viruses. They encode an NS6 protease that cleaves a viral polyprotein at specific sites to produce mature viral proteins. In an earlier study we obtained crystals of murine norovirus (MNV) NS6 protease in which crystal contacts were mediated by specific insertion of the C-terminus of one protein (which contains residues P5-P1 of the NS6-7 cleavage junction) into the peptide binding site of an adjacent molecule, forming an adventitious protease-product complex. We sought to reproduce this crystal form to investigate protease–substrate complexes by extending the C-terminus of NS6 construct to include residues on the C-terminal (P′) side of the cleavage junction. We report the crystallization and crystal structure determination of inactive mutants of murine norovirus NS6 protease with C-terminal extensions of one, two and four residues from the N-terminus of the adjacent NS7 protein (NS6 1′, NS6 2′, NS6 4′). We also determined the structure of a chimeric extended NS6 protease in which the P4-P4′ sequence of the NS6-7 cleavage site was replaced with the corresponding sequence from the NS2-3 cleavage junction (NS6 4′ 2|3).The constructs NS6 1′ and NS6 2′ yielded crystals that diffracted anisotropically. We found that, although the uncorrected data could be phased by molecular replacement, refinement of the structures stalled unless the data were ellipsoidally truncated and corrected with anisotropic B-factors. These corrections significantly improved phasing by molecular replacement and subsequent refinement.The refined structures of all four extended NS6 proteases are very similar in structure to the mature MNV NS6—and in one case reveal additional details of a surface loop. Although the packing arrangement observed showed some similarities to those observed in the adventitious protease-product crystals reported previously, in no case were specific protease–substrate interactions observed.
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Affiliation(s)
| | - Eoin N Leen
- Department of Life Sciences, Imperial College London , UK
| | | | | | - Stephen Curry
- Department of Life Sciences, Imperial College London , UK
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33
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Herod M, Prince C, Skilton R, Ward V, Cooper J, Clarke I. Structure-based design and functional studies of novel noroviral 3C protease chimaeras offer insights into substrate specificity. Biochem J 2014; 464:461-72. [PMID: 25275273 PMCID: PMC4613530 DOI: 10.1042/bj20140959] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/26/2014] [Accepted: 10/02/2014] [Indexed: 01/30/2023]
Abstract
The norovirus NS6 protease is a key target for anti-viral drug development. Noroviruses encode a 2200 amino acid polyprotein which is cleaved by this critical protease at five defined boundary substrates into six mature non-structural (NS) proteins. Studies of the human norovirus (HNV) NS6 protease, in the context of a full ORF1 polyprotein, have been severely hampered because HNVs are not culturable. Thus, investigations into the HNV NS6 protease have been largely restricted to in vitro assays using Escherichia coli-expressed, purified enzyme. The NS6 protease is formed of two distinct domains joined by a linking loop. Structural data suggest that domain 2 of the protease possesses substantial substrate binding pockets which form the bulk of the interactions with the NS boundaries and largely dictate boundary specificity and cleavage. We have constructed chimaeric murine norovirus (MNV) genomes carrying individual domains from the HNV protease and demonstrated by cell transfection that chimaeric HNV proteases have functional activity in the context of the full-length ORF1 polyprotein. Although domain 2 primarily confers boundary specificity, our data suggest that an inter-domain interaction exists within HNV NS6 protease which influences cleavage of specific substrates. The present study also shows that chimaeric MNVs provide improved models for studying HNV protein function in the context of a full ORF1 polyprotein.
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Affiliation(s)
- Morgan R. Herod
- Molecular Microbiology Group, University of Southampton, Southampton SO16 6YD, U.K
| | - Cynthia A. Prince
- Molecular Microbiology Group, University of Southampton, Southampton SO16 6YD, U.K
| | - Rachel J. Skilton
- Molecular Microbiology Group, University of Southampton, Southampton SO16 6YD, U.K
| | - Vernon K. Ward
- Otago School of Medical Sciences, Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Jonathan B. Cooper
- Laboratory for Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, U.K
| | - Ian N. Clarke
- Molecular Microbiology Group, University of Southampton, Southampton SO16 6YD, U.K
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May J, Viswanathan P, Ng KKS, Medvedev A, Korba B. The p4-p2' amino acids surrounding human norovirus polyprotein cleavage sites define the core sequence regulating self-processing order. J Virol 2014; 88:10738-47. [PMID: 24991013 PMCID: PMC4178882 DOI: 10.1128/jvi.01357-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 06/30/2014] [Indexed: 01/16/2023] Open
Abstract
UNLABELLED Noroviruses (NoV) are members of the family Caliciviridae. The human NoV open reading frame 1 (ORF1) encodes a 200-kDa polyprotein which is cleaved by the viral 20-kDa 3C-like protease (Pro, NS6) into 6 nonstructural proteins that are necessary for viral replication. The NoV ORF1 polyprotein is processed in a specific order, with "early" sites (NS1/2-3 and NS3-4) being cleaved rapidly and three "late" sites (NS4-5, NS5-6, and NS6-7) processed subsequently and less efficiently. Previously, we demonstrated that the NoV polyprotein processing order is directly correlated with the efficiency of the enzyme, which is regulated by the primary amino acid sequences surrounding ORF1 cleavage sites. Using fluorescence resonance energy transfer (FRET) peptides representing the NS2-3 and NS6-7 ORF1 cleavage sites, we now demonstrate that the amino acids spanning positions P4 to P2' (P4-P2') surrounding each site comprise the core sequence controlling NoV protease enzyme efficiency. Furthermore, the NoV polyprotein self-processing order can be altered by interchanging this core sequence between NS2-3 and any of the three late sites in in vitro transcription-translation assays. We also demonstrate that the nature of the side chain at the P3 position for the NS1/2-3 (Nterm/NTPase) site confers significant influence on enzyme catalysis (kcat and kcat/Km), a feature overlooked in previous structural studies. Molecular modeling provides possible explanations for the P3 interactions with NoV protease. IMPORTANCE Noroviruses (NoV) are the prevailing cause of nonbacterial acute gastroenteritis worldwide and pose a significant financial burden on health care systems. Proteolytic processing of the viral nonstructural polyprotein is required for norovirus replication. Previously, the core sequence of amino acids surrounding the scissile bonds responsible for governing the relative processing order had not been determined. Using both FRET-based peptides and full-length NoV polyprotein, we have successfully demonstrated that the core sequences spanning positions P4-P2' surrounding the NS2-3, NS4-5, NS5-6, and NS6-7 cleavage sites contain all of the structural information necessary to control processing order. We also provide insight into a previously overlooked role for the NS2-3 P3 residue in enzyme efficiency. This article builds upon our previous studies on NoV protease enzymatic activities and polyprotein processing order. Our work provides significant additional insight into understanding viral polyprotein processing and has important implications for improving the design of inhibitors targeting the NoV protease.
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Affiliation(s)
- Jared May
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA
| | - Prasanth Viswanathan
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA
| | - Kenneth K-S Ng
- Department of Biological Sciences and Alberta Glycomics Centre, University of Calgary, Calgary, Alberta, Canada
| | - Alexei Medvedev
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA
| | - Brent Korba
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA
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35
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Rocha-Pereira J, Neyts J, Jochmans D. Norovirus: targets and tools in antiviral drug discovery. Biochem Pharmacol 2014; 91:1-11. [PMID: 24893351 PMCID: PMC7111065 DOI: 10.1016/j.bcp.2014.05.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 05/23/2014] [Accepted: 05/27/2014] [Indexed: 11/29/2022]
Abstract
The development of antiviral strategies to treat or prevent norovirus infections is a pressing matter. Noroviruses are the number 1 cause of acute gastroenteritis, of foodborne illness, of sporadic gastroenteritis in all age groups and of severe acute gastroenteritis in children less than 5 years old seeking medical assistance [USA/CDC]. In developing countries, noroviruses are linked to significant mortality (~200,000 children <5 years old). Noroviruses are a major culprit for the closure of hospital wards, and associated with increased hospitalization and mortality among the elderly. Transplant patients have significant risk of acquiring persistent norovirus gastroenteritis. Control and prevention strategies are limited to the use of disinfectants and hand sanitizers, whose efficacy is frequently insufficient. Hence, there is an ample need for antiviral treatment and prophylaxis of norovirus infections. The fact that only a handful of inhibitors of norovirus replication have been reported can largely be attributable to the hampering inability to cultivate human noroviruses in cell culture. The Norwalk replicon-bearing cells and the murine norovirus-infected cell lines are the available models to assess in vitro antiviral activity of compounds. Human noroviruses have been shown to replicate (to some extent) in mice, calves, gnotobiotic pigs, and chimpanzees. Infection of interferon-deficient mice with the murine norovirus results in virus-induced diarrhea. Here we review recent developments in understanding which norovirus proteins or host cell factors may serve as targets for inhibition of viral replication. Given the recent advances, significant progress in the search for antiviral strategies against norovirus infections is expected in the upcoming years.
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Affiliation(s)
- Joana Rocha-Pereira
- Rega Institute for Medical Research, KU Leuven - University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Johan Neyts
- Rega Institute for Medical Research, KU Leuven - University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
| | - Dirk Jochmans
- Rega Institute for Medical Research, KU Leuven - University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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36
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Takahashi D, Kim Y, Lovell S, Prakash O, Groutas WC, Chang KO. Structural and inhibitor studies of norovirus 3C-like proteases. Virus Res 2013; 178:437-44. [PMID: 24055466 PMCID: PMC3840063 DOI: 10.1016/j.virusres.2013.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 01/23/2023]
Abstract
Noroviruses have a single-stranded, positive sense 7-8kb RNA genome, which encodes a polyprotein precursor processed by a virus-encoded 3C-like cysteine protease (3CLpro) to generate mature non-structural proteins. Because processing of the polyprotein is essential for virus replication, norovirus 3CLpro has been targeted for the discovery of anti-norovirus small molecule therapeutics. Thus, we performed functional, structural and inhibition studies of norovirus 3CLpro with fluorescence resonance energy transfer (FRET) assay, X-ray crystallography, and NMR spectroscopy with a synthetic protease inhibitor. Three 3CLpro from Norwalk virus (NV, genogroup I), MD145 (genogroup II) and murine norovirus-1 (MNV-1, genogroup V) were optimized for a FRET assay, and compared for the inhibitory activities of a synthetic protease inhibitor (GC376). The apo 3D structures of NV 3CLpro determined with X-ray crystallography and NMR spectroscopy were further analyzed. In addition, the binding mode of NV 3CLpro-GC376 was compared with X-ray crystallography and NMR spectroscopy. The results of this report provide insight into the interaction of NV 3CLpro with substrate/inhibitor for better understanding of the enzyme and antiviral drug development.
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Affiliation(s)
- Daisuke Takahashi
- Department of Biochemistry, Kansas State University, 141 Chalmers Hall, Manhattan, KS 66506, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS 66047
| | - Om Prakash
- Department of Biochemistry, Kansas State University, 141 Chalmers Hall, Manhattan, KS 66506, USA
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506
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37
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Potent inhibition of norovirus by dipeptidyl α-hydroxyphosphonate transition state mimics. Bioorg Med Chem Lett 2013; 23:5941-4. [PMID: 24054123 DOI: 10.1016/j.bmcl.2013.08.073] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/12/2013] [Accepted: 08/15/2013] [Indexed: 12/16/2022]
Abstract
The design, synthesis, and evaluation of a series of dipeptidyl α-hydroxyphosphonates is reported. The synthesized compounds displayed high anti-norovirus activity in a cell-based replicon system, as well as high enzyme selectivity.
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38
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Mandadapu SR, Weerawarna PM, Prior AM, Uy RAZ, Aravapalli S, Alliston KR, Lushington GH, Kim Y, Hua DH, Chang KO, Groutas WC. Macrocyclic inhibitors of 3C and 3C-like proteases of picornavirus, norovirus, and coronavirus. Bioorg Med Chem Lett 2013; 23:3709-12. [PMID: 23727045 PMCID: PMC3750990 DOI: 10.1016/j.bmcl.2013.05.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 04/29/2013] [Accepted: 05/07/2013] [Indexed: 12/18/2022]
Abstract
The design, synthesis, and in vitro evaluation of the first macrocyclic inhibitor of 3C and 3C-like proteases of picornavirus, norovirus, and coronavirus are reported. The in vitro inhibitory activity (50% effective concentration) of the macrocyclic inhibitor toward enterovirus 3C protease (CVB3 Nancy strain), and coronavirus (SARS-CoV) and norovirus 3C-like proteases, was determined to be 1.8, 15.5 and 5.1 μM, respectively.
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Affiliation(s)
| | | | - Allan M. Prior
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
| | | | - Sridhar Aravapalli
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Kevin R. Alliston
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | | | - Yunjeong Kim
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Duy H. Hua
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - William C. Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
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39
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Viswanathan P, May J, Uhm S, Yon C, Korba B. RNA binding by human Norovirus 3C-like proteases inhibits protease activity. Virology 2013; 438:20-7. [PMID: 23399036 DOI: 10.1016/j.virol.2013.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/20/2012] [Accepted: 01/11/2013] [Indexed: 11/28/2022]
Abstract
A highly active, fluorescence-based, in vitro assay for human Norovirus protease from genogroup I and II viruses was optimized utilizing as little as 0.25μM enzyme, pH 7.6, and substrate:enzyme of 50-100. Activity in Tris-HCl or sodium phosphate buffers was 2-fold less than HEPES, and 2-fold lower for buffer concentrations over 10mM. Protease activity at pH 7.6 was 73% (GI) or 63% (GII) of activity at the optimal pH 9.0. Sodium inhibited activity 2-3 fold, while potassium, calcium, magnesium, and manganese inhibited 5-10 fold. Differences in efficiency due to pH, buffer, and cations were due to changes in kcat and not Km. Norovirus protease bound short RNAs representing the 3' or 5' ends of the virus, inhibiting protease activity (IC50 3-5μM) in a non-competitive manner. Previous reports indicated participation of the protease in the Norovirus replicase complex. The current studies provide initial support for a defined role for the viral protease in Norovirus replication.
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Affiliation(s)
- Prasanth Viswanathan
- Georgetown University Medical Center, Department of Microbiology and Immunology, 3900 Reservoir Rd., N.W., Med-Dent Building, RM SW319, Washington, DC 20057, USA
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40
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Structural basis of substrate specificity and protease inhibition in Norwalk virus. J Virol 2013; 87:4281-92. [PMID: 23365454 DOI: 10.1128/jvi.02869-12] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Norwalk virus (NV), the prototype human calicivirus, is the leading cause of nonbacterial acute gastroenteritis. The NV protease cleaves the polyprotein encoded by open reading frame 1 of the viral genome at five nonhomologous sites, releasing six nonstructural proteins that are essential for viral replication. The structural details of how NV protease recognizes multiple substrates are unclear. In our X-ray structure of an NV protease construct, we observed that the C-terminal tail, representing the native substrate positions P5 to P1, is inserted into the active site cleft of the neighboring protease molecule, providing atomic details of how NV protease recognizes a substrate. The crystallographic structure of NV protease with the C-terminal tail redesigned to mimic P4 to P1 of another substrate site provided further structural details on how the active site accommodates sequence variations in the substrates. Based on these structural analyses, substrate-based aldehyde inhibitors were synthesized and screened for inhibition potency. Crystallographic structures of the protease in complex with each of the three most potent inhibitors were determined. These structures showed concerted conformational changes in the S4 and S2 pockets of the protease to accommodate variations in the P4 and P2 residues of the substrate/inhibitor, which could be a mechanism for how the NV protease recognizes multiple sites in the polyprotein with differential affinities during virus replication. These structures further indicate that the mechanism of inhibition by these inhibitors involves covalent bond formation with the side chain of the conserved cysteine in the active site by nucleophilic addition, and such substrate-based aldehydes could be effective protease inhibitors.
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41
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Takahashi D, Hiromasa Y, Kim Y, Anbanandam A, Yao X, Chang KO, Prakash O. Structural and dynamics characterization of norovirus protease. Protein Sci 2013; 22:347-57. [PMID: 23319456 DOI: 10.1002/pro.2215] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/26/2012] [Accepted: 12/30/2012] [Indexed: 01/24/2023]
Abstract
Norovirus protease is an essential enzyme for proteolytic maturation of norovirus nonstructural proteins and has been implicated as a potential target for antiviral drug development. Although X-ray structural studies of the protease give us wealth of structural information including interactions of the protease with its substrate and dimeric overall structure, the role of protein dynamics in the substrate recognition and the biological relevance of the protease dimer remain unclear. Here we determined the solution NMR structure of the 3C-like protease from Norwalk virus (NV 3CLpro), a prototype strain of norovirus, and analyzed its backbone dynamics and hydrodynamic behavior in solution. ¹⁵N spin relaxation and analytical ultracentrifugation analyses demonstrate that NV 3CLpro is predominantly a monomer in solution. Solution structure of NV 3CLpro shows significant structural variation in C-terminal domain compared with crystal structures and among lower energy structure ensembles. Also, ¹⁵N spin relaxation and Carr-Purcell-Meiboom-Gill (CPMG)-based relaxation dispersion analyses reveal the dynamic properties of residues in the C-terminal domain over a wide range of timescales. In particular, the long loop spanning residues T123-G133 show fast motion (ps-ns), and the residues in the bII-cII region forming the large hydrophobic pocket (S2 site) undergo conformational exchanges on slower timescales (μs-ms), suggesting their important role in substrate recognition.
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Affiliation(s)
- Daisuke Takahashi
- Department of Biochemistry, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
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42
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Mandadapu SR, Gunnam MR, Tiew KC, Uy RAZ, Prior AM, Alliston KR, Hua DH, Kim Y, Chang KO, Groutas WC. Inhibition of norovirus 3CL protease by bisulfite adducts of transition state inhibitors. Bioorg Med Chem Lett 2012; 23:62-5. [PMID: 23218713 DOI: 10.1016/j.bmcl.2012.11.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/05/2012] [Accepted: 11/07/2012] [Indexed: 01/08/2023]
Abstract
Noroviruses are the most common cause of acute viral gastroenteritis, accounting for >21 million cases annually in the US alone. Norovirus infections constitute an important health problem for which there are no specific antiviral therapeutics or vaccines. In this study, a series of bisulfite adducts derived from representative transition state inhibitors (dipeptidyl aldehydes and α-ketoamides) was synthesized and shown to exhibit anti-norovirus activity in a cell-based replicon system. The ED(50) of the most effective inhibitor was 60 nM. This study demonstrates for the first time the utilization of bisulfite adducts of transition state inhibitors in the inhibition of norovirus 3C-like protease in vitro and in a cell-based replicon system. The approach described herein can be extended to the synthesis of the bisulfite adducts of other classes of transition state inhibitors of serine and cysteine proteases, such as α-ketoheterocycles and α-ketoesters.
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43
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Kim Y, Lovell S, Tiew KC, Mandadapu SR, Alliston KR, Battaile KP, Groutas WC, Chang KO. Broad-spectrum antivirals against 3C or 3C-like proteases of picornaviruses, noroviruses, and coronaviruses. J Virol 2012; 86:11754-62. [PMID: 22915796 PMCID: PMC3486288 DOI: 10.1128/jvi.01348-12] [Citation(s) in RCA: 246] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 08/12/2012] [Indexed: 01/19/2023] Open
Abstract
Phylogenetic analysis has demonstrated that some positive-sense RNA viruses can be classified into the picornavirus-like supercluster, which includes picornaviruses, caliciviruses, and coronaviruses. These viruses possess 3C or 3C-like proteases (3Cpro or 3CLpro, respectively), which contain a typical chymotrypsin-like fold and a catalytic triad (or dyad) with a Cys residue as a nucleophile. The conserved key sites of 3Cpro or 3CLpro may serve as attractive targets for the design of broad-spectrum antivirals for multiple viruses in the supercluster. We previously reported the structure-based design and synthesis of potent protease inhibitors of Norwalk virus (NV), a member of the Caliciviridae family. We report herein the broad-spectrum antiviral activities of three compounds possessing a common dipeptidyl residue with different warheads, i.e., an aldehyde (GC373), a bisulfite adduct (GC376), and an α-ketoamide (GC375), against viruses that belong to the supercluster. All compounds were highly effective against the majority of tested viruses, with half-maximal inhibitory concentrations in the high nanomolar or low micromolar range in enzyme- and/or cell-based assays and with high therapeutic indices. We also report the high-resolution X-ray cocrystal structures of NV 3CLpro-, poliovirus 3Cpro-, and transmissible gastroenteritis virus 3CLpro- GC376 inhibitor complexes, which show the compound covalently bound to a nucleophilic Cys residue in the catalytic site of the corresponding protease. We conclude that these compounds have the potential to be developed as antiviral therapeutics aimed at a single virus or multiple viruses in the picornavirus-like supercluster by targeting 3Cpro or 3CLpro.
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Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas, USA
| | - Kok-Chuan Tiew
- Department of Chemistry, Wichita State University, Wichita, Kansas, USA
| | | | - Kevin R. Alliston
- Department of Chemistry, Wichita State University, Wichita, Kansas, USA
| | - Kevin P. Battaile
- IMCA-CAT Hauptman-Woodward Medical Research Institute, Argonne, Illinois, USA
| | | | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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44
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Leen EN, Baeza G, Curry S. Structure of a murine norovirus NS6 protease-product complex revealed by adventitious crystallisation. PLoS One 2012; 7:e38723. [PMID: 22685603 PMCID: PMC3369882 DOI: 10.1371/journal.pone.0038723] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 05/14/2012] [Indexed: 01/19/2023] Open
Abstract
Murine noroviruses have emerged as a valuable tool for investigating the molecular basis of infection and pathogenesis of the closely related human noroviruses, which are the major cause of non-bacterial gastroenteritis. The replication of noroviruses relies on the proteolytic processing of a large polyprotein precursor into six non-structural proteins (NS1–2, NS3, NS4, NS5, NS6pro, NS7pol) by the virally-encoded NS6 protease. We report here the crystal structure of MNV NS6pro, which has been determined to a resolution of 1.6 Å. Adventitiously, the crystal contacts are mediated in part by the binding of the C-terminus of NS6pro within the peptide-binding cleft of a neighbouring molecule. This insertion occurs for both molecules in the asymmetric unit of the crystal in a manner that is consistent with physiologically-relevant binding, thereby providing two independent views of a protease-peptide complex. Since the NS6pro C-terminus is formed in vivo by NS6pro processing, these crystal contacts replicate the protease-product complex that is formed immediately following cleavage of the peptide bond at the NS6-NS7 junction. The observed mode of binding of the C-terminal product peptide yields new insights into the structural basis of NS6pro specificity.
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Affiliation(s)
- Eoin N. Leen
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Gabriela Baeza
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Stephen Curry
- Department of Life Sciences, Imperial College, London, United Kingdom
- * E-mail:
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45
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Mandadapu SR, Weerawarna PM, Gunnam MR, Alliston KR, Lushington GH, Kim Y, Chang KO, Groutas WC. Potent inhibition of norovirus 3CL protease by peptidyl α-ketoamides and α-ketoheterocycles. Bioorg Med Chem Lett 2012; 22:4820-6. [PMID: 22698498 DOI: 10.1016/j.bmcl.2012.05.055] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 05/10/2012] [Accepted: 05/11/2012] [Indexed: 12/13/2022]
Abstract
A series of structurally-diverse α-ketoamides and α-ketoheterocycles was synthesized and subsequently investigated for inhibitory activity against norovirus 3CL protease in vitro, as well as anti-norovirus activity in a cell-based replicon system. The synthesized compounds were found to inhibit norovirus 3CL protease in vitro and to also exhibit potent anti-norovirus activity in a cell-based replicon system.
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46
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Chang KO, Takahashi D, Prakash O, Kim Y. Characterization and inhibition of norovirus proteases of genogroups I and II using a fluorescence resonance energy transfer assay. Virology 2012; 423:125-33. [PMID: 22200497 PMCID: PMC3259199 DOI: 10.1016/j.virol.2011.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 11/26/2011] [Accepted: 12/01/2011] [Indexed: 01/08/2023]
Abstract
Noroviruses are the major cause of food- or water-borne gastroenteritis outbreaks in humans. The norovirus protease that cleaves a large viral polyprotein to nonstructural proteins is essential for virus replication and an attractive target for antiviral drug development. Noroviruses show high genetic diversity with at least five genogroups, GI-GV, of which GI and GII are responsible for the majority of norovirus infections in humans. We cloned and expressed proteases of Norwalk virus (GI) and MD145 virus (GII) and characterized the enzymatic activities with fluorescence resonance energy transfer substrates. We demonstrated that the GI and GII proteases cleaved the substrates derived from the naturally occurring cleavage site in the open reading frame (ORF) 1 of G1 norovirus with similar efficiency, and that enzymatic activity of both proteases was inhibited by commercial protease inhibitors including chymostatin. The interaction of chymostatin to Norwalk virus protease was validated by nuclear magnetic resonance (NMR) spectroscopy.
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Affiliation(s)
- Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, KS 66506, USA
| | - Daisuke Takahashi
- Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA
| | - Om Prakash
- Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, KS 66506, USA,Corresponding author at: Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA. Fax: + 1 785 532 4039
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47
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Someya Y. From head to toe of the norovirus 3C-like protease. Biomol Concepts 2012; 3:41-56. [DOI: 10.1515/bmc.2011.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 11/02/2011] [Indexed: 01/25/2023] Open
Abstract
AbstractNoroviruses are major causative agents of viral gastroenteritis in humans. Currently, there are no therapeutic medications to treat noroviral infections, nor are there effective vaccines against these pathogens. The viral 3C-like protease is solely responsible for the maturation of viral protein components. The crystal structures of the proteases were resolved at high atomic resolution. The protease was also explored by means of mutagenesis. These studies revealed the active-site amino acid residues and factors determining and affecting substrate specificity as well as the principle of architecting the protease molecule. The possible mechanism of proteolysis was also suggested. Consideration of the data accumulated thus far will be useful for development of therapeutic drugs targeting the viral protease.
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Affiliation(s)
- Yuichi Someya
- 1Department of Virology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-Murayama, Tokyo 208-0011, Japan
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48
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Tiew KC, He G, Aravapalli S, Mandadapu SR, Gunnam MR, Alliston KR, Lushington GH, Kim Y, Chang KO, Groutas WC. Design, synthesis, and evaluation of inhibitors of Norwalk virus 3C protease. Bioorg Med Chem Lett 2011; 21:5315-9. [PMID: 21802286 DOI: 10.1016/j.bmcl.2011.07.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/28/2011] [Accepted: 07/06/2011] [Indexed: 11/19/2022]
Abstract
The first series of peptidyl aldehyde inhibitors that incorporate in their structure a glutamine surrogate has been designed and synthesized based on the known substrate specificity of Norwalk virus 3C protease. The inhibitory activity of the compounds with the protease and with a norovirus cell-based replicon system was investigated. Members of this class of compounds exhibited noteworthy activity both in vitro and in a cell-based replicon system.
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Affiliation(s)
- Kok-Chuan Tiew
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
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