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Voss S, Rademann J, Nitsche C. Characterisation of ten NS2B-NS3 proteases: Paving the way for pan-flavivirus drugs. Antiviral Res 2024; 226:105878. [PMID: 38582134 DOI: 10.1016/j.antiviral.2024.105878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/29/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
Flaviviruses can cause severe illness in humans. Effective and safe vaccines are available for some species; however, for many flaviviruses disease prevention or specific treatments remain unavailable. The viral replication cycle depends on the proteolytic activity of the NS2B-NS3 protease, which releases functional viral proteins from a non-functional polyprotein precursor, rendering the protease a promising drug target. In this study, we characterised recombinant NS2B-NS3 proteases from ten flaviviruses including three unreported proteases from the Usutu, Kyasanur forest disease and Powassan viruses. All protease constructs comprise a covalent Gly4-Ser-Gly4 linker connecting the NS3 serine protease domain with its cofactor NS2B. We conducted a comprehensive cleavage site analysis revealing areas of high conversion. While all proteases were active in enzymatic assays, we noted a 1000-fold difference in catalytic efficiency across proteases from different flaviviruses. Two bicyclic peptide inhibitors displayed anti-pan-flaviviral protease activity with inhibition constants ranging from 10 to 1000 nM.
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Affiliation(s)
- Saan Voss
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Jörg Rademann
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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Santos NP, Santos LH, Torquato Quezado de Magalhães M, Lei J, Hilgenfeld R, Salgado Ferreira R, Bleicher L. Characterization of an Allosteric Pocket in Zika Virus NS2B-NS3 Protease. J Chem Inf Model 2022; 62:945-957. [DOI: 10.1021/acs.jcim.1c01326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Naiá Porã Santos
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Lucianna Helene Santos
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Mariana Torquato Quezado de Magalhães
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Jian Lei
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck 23562, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck 23562, Germany
| | - Rafaela Salgado Ferreira
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Lucas Bleicher
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
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Structure and Dynamics of Zika Virus Protease and Its Insights into Inhibitor Design. Biomedicines 2021; 9:biomedicines9081044. [PMID: 34440248 PMCID: PMC8394600 DOI: 10.3390/biomedicines9081044] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/04/2021] [Accepted: 08/16/2021] [Indexed: 12/16/2022] Open
Abstract
Zika virus (ZIKV)—a member of the Flaviviridae family—is an important human pathogen. Its genome encodes a polyprotein that can be further processed into structural and non-structural proteins. ZIKV protease is an important target for antiviral development due to its role in cleaving the polyprotein to release functional viral proteins. The viral protease is a two-component protein complex formed by NS2B and NS3. Structural studies using different approaches demonstrate that conformational changes exist in the protease. The structures and dynamics of this protease in the absence and presence of inhibitors were explored to provide insights into the inhibitor design. The dynamic nature of residues binding to the enzyme cleavage site might be important for the function of the protease. Due to the charges at the protease cleavage site, it is challenging to develop small-molecule compounds acting as substrate competitors. Developing small-molecule compounds to inhibit protease activity through an allosteric mechanism is a feasible strategy because conformational changes are observed in the protease. Herein, structures and dynamics of ZIKV protease are summarized. The conformational changes of ZIKV protease and other proteases in the same family are discussed. The progress in developing allosteric inhibitors is also described. Understanding the structures and dynamics of the proteases are important for designing potent inhibitors.
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Hill ME, Yildiz M, Hardy JA. Cysteine Disulfide Traps Reveal Distinct Conformational Ensembles in Dengue Virus NS2B-NS3 Protease. Biochemistry 2018; 58:776-787. [PMID: 30472839 DOI: 10.1021/acs.biochem.8b00978] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The dengue virus protease (NS2B-NS3pro) plays a critical role in the dengue viral life cycle, making it an attractive drug target for dengue-related pathologies, including dengue hemorrhagic fever. A number of studies indicate that NS2B-NS3pro undergoes a transition between two widely different conformational states: an "open" (inactive) conformation and a "closed" (active) conformation. For the past several years, the equilibrium between these states and the resting conformation of NS2B-NS3pro have been debated, although a strong consensus is emerging. To investigate the importance of such conformational states, we developed versions of NS2B-NS3pro that allow us to trap the enzyme in various distinct conformations. Our data from these variants suggest that the enzymatic activity appears to be dependent on the movement of NS2B and may rely on the flexibility of the protease core. Locking the enzyme into the "closed" conformation dramatically increased activity, strongly suggesting that the "closed" conformation is the active conformation. The observed resting state of the enzyme depends largely on the construct used to express the NS2B-NS3pro complex. In an "unlinked" construct, in which the NS2B and NS3 regions exist as independent, co-expressed polypeptides, the enzyme rests predominantly in a "closed", active conformation. In contrast, in a "linked" construct, in which NS2B and NS3 are attached by a nine-amino acid linker, NS2B-NS3pro adopts a more relaxed, alternative conformation. Nevertheless, even the unlinked construct samples both the "closed" and other alternative conformations. Given our findings, and the more realistic resemblance of NS2B-NS3pro to the native enzyme, these data strongly suggest that studies should focus on the "unlinked" constructs moving forward. Additionally, the results from these studies provide a more detailed understanding of the various poses of the dengue virus NS2B-NS3 protease and should help guide future drug discovery efforts aimed at this enzyme.
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Affiliation(s)
- Maureen E Hill
- Department of Chemistry , University of Massachusetts , 374 LGRT, 710 North Pleasant Street , Amherst , Massachusetts 01003 , United States
| | - Muslum Yildiz
- Department of Chemistry , University of Massachusetts , 374 LGRT, 710 North Pleasant Street , Amherst , Massachusetts 01003 , United States
| | - Jeanne A Hardy
- Department of Chemistry , University of Massachusetts , 374 LGRT, 710 North Pleasant Street , Amherst , Massachusetts 01003 , United States
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Tian YS, Zhou Y, Takagi T, Kameoka M, Kawashita N. Dengue Virus and Its Inhibitors: A Brief Review. Chem Pharm Bull (Tokyo) 2018; 66:191-206. [PMID: 29491253 DOI: 10.1248/cpb.c17-00794] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The global occurrence of viral infectious diseases poses a significant threat to human health. Dengue virus (DENV) infection is one of the most noteworthy of these infections. According to a WHO survey, approximately 400 million people are infected annually; symptoms deteriorate in approximately one percent of cases. Numerous foundational and clinical investigations on viral epidemiology, structure and function analysis, infection source and route, therapeutic targets, vaccines, and therapeutic drugs have been conducted by both academic and industrial researchers. At present, CYD-TDV or Dengvaxia® is the only approved vaccine, but potent inhibitors are currently under development. In this review, an overview of the viral life circle and the history of DENVs is presented, and the most recently reported antiviral candidates and newly discovered promising targets are focused and summarized. We believe that these successes and failures have enabled progress in anti-DENV drug discovery and hope that our review will stimulate further innovation in this area.
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Affiliation(s)
- Yu-Shi Tian
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Yi Zhou
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Masanori Kameoka
- Department of International Health, Kobe University Graduate School of Health Sciences
| | - Norihito Kawashita
- Graduate School of Pharmaceutical Sciences, Osaka University.,Faculty of Sciences and Engineering, Kindai University
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A conformational switch high-throughput screening assay and allosteric inhibition of the flavivirus NS2B-NS3 protease. PLoS Pathog 2017; 13:e1006411. [PMID: 28542603 PMCID: PMC5462475 DOI: 10.1371/journal.ppat.1006411] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 06/07/2017] [Accepted: 05/15/2017] [Indexed: 12/02/2022] Open
Abstract
The flavivirus genome encodes a single polyprotein precursor requiring multiple cleavages by host and viral proteases in order to produce the individual proteins that constitute an infectious virion. Previous studies have revealed that the NS2B cofactor of the viral NS2B-NS3 heterocomplex protease displays a conformational dynamic between active and inactive states. Here, we developed a conformational switch assay based on split luciferase complementation (SLC) to monitor the conformational change of NS2B and to characterize candidate allosteric inhibitors. Binding of an active-site inhibitor to the protease resulted in a conformational change of NS2B and led to significant SLC enhancement. Mutagenesis of key residues at an allosteric site abolished this induced conformational change and SLC enhancement. We also performed a virtual screen of NCI library compounds to identify allosteric inhibitors, followed by in vitro biochemical screening of the resultant candidates. Only three of these compounds, NSC135618, 260594, and 146771, significantly inhibited the protease of Dengue virus 2 (DENV2) in vitro, with IC50 values of 1.8 μM, 11.4 μM, and 4.8 μM, respectively. Among the three compounds, only NSC135618 significantly suppressed the SLC enhancement triggered by binding of active-site inhibitor in a dose-dependent manner, indicating that it inhibits the conformational change of NS2B. Results from virus titer reduction assays revealed that NSC135618 is a broad spectrum flavivirus protease inhibitor, and can significantly reduce titers of DENV2, Zika virus (ZIKV), West Nile virus (WNV), and Yellow fever virus (YFV) on A549 cells in vivo, with EC50 values in low micromolar range. In contrast, the cytotoxicity of NSC135618 is only moderate with CC50 of 48.8 μM on A549 cells. Moreover, NSC135618 inhibited ZIKV in human placental and neural progenitor cells relevant to ZIKV pathogenesis. Results from binding, kinetics, Western blot, mass spectrometry and mutagenesis experiments unambiguously demonstrated an allosteric mechanism for inhibition of the viral protease by NSC135618.
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Chen WN, Nitsche C, Pilla KB, Graham B, Huber T, Klein CD, Otting G. Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets. J Am Chem Soc 2016; 138:4539-46. [PMID: 26974502 DOI: 10.1021/jacs.6b00416] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure-guided drug design relies on detailed structural knowledge of protein-ligand complexes, but crystallization of cocomplexes is not always possible. Here we present a sensitive nuclear magnetic resonance (NMR) approach to determine the binding mode of tightly binding lead compounds in complex with difficult target proteins. In contrast to established NMR methods, it does not depend on rapid exchange between bound and free ligand or on stable isotope labeling, relying instead on a tert-butyl group as a chemical label. tert-Butyl groups are found in numerous protein ligands and deliver an exceptionally narrow and tall (1)H NMR signal. We show that a tert-butyl group also produces outstandingly intense intra- and intermolecular NOESY cross-peaks. These enable measurements of pseudocontact shifts generated by lanthanide tags attached to the protein, which in turn allows positioning of the ligand on the protein. Once the ligand has been located, assignments of intermolecular NOEs become possible even without prior resonance assignments of protein side chains. The approach is demonstrated with the dengue virus NS2B-NS3 protease in complex with a high-affinity ligand containing a tert-butyl group.
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Affiliation(s)
- Wan-Na Chen
- Australian National University , Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Australian National University , Research School of Chemistry, Canberra, ACT 2601, Australia.,Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Kala Bharath Pilla
- Australian National University , Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Bim Graham
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Thomas Huber
- Australian National University , Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Gottfried Otting
- Australian National University , Research School of Chemistry, Canberra, ACT 2601, Australia
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Abstract
The dengue virus and related flaviviruses are an increasing global health threat. In this perspective, we comment on and review medicinal chemistry efforts aimed at the prevention or treatment of dengue infections. We include target-based approaches aimed at viral or host factors and results from phenotypic screenings in cellular assay systems for viral replication. This perspective is limited to the discussion of results that provide explicit chemistry or structure-activity relationship (SAR), or appear to be of particular interest to the medicinal chemist for other reasons. The discovery and development efforts discussed here may at least partially be extrapolated toward other emerging flaviviral infections, such as West Nile virus. Therefore, this perspective, although not aimed at flaviviruses in general, should also be able to provide an overview of the medicinal chemistry of these closely related infectious agents.
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Affiliation(s)
- Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Christoph Nitsche
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Veaceslav Boldescu
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.,Laboratory of Organic Synthesis, Institute of Chemistry of the Academy of Sciences of Moldova , Academiei 3, 2028 Chisinau, Moldova
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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Zhu L, Yang J, Li H, Sun H, Liu J, Wang J. Conformational change study of dengue virus NS2B-NS3 protease using 19F NMR spectroscopy. Biochem Biophys Res Commun 2015; 461:677-80. [DOI: 10.1016/j.bbrc.2015.04.090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 01/31/2023]
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Nitsche C, Holloway S, Schirmeister T, Klein CD. Biochemistry and medicinal chemistry of the dengue virus protease. Chem Rev 2014; 114:11348-81. [PMID: 25268322 DOI: 10.1021/cr500233q] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Christoph Nitsche
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Steven Holloway
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz , Staudingerweg 5, D-55128 Mainz, Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz , Staudingerweg 5, D-55128 Mainz, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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