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Pianka J, Gruba N, Lesner A. Novel tools to study West Nile virus NS3 protease activity. Bioorg Chem 2023; 133:106426. [PMID: 36801793 DOI: 10.1016/j.bioorg.2023.106426] [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: 11/23/2022] [Revised: 01/11/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023]
Abstract
West Nile Virus (WNV) belongs to a group of pathogenic viruses called flaviviruses. West Nile virus infection can be mild, causing so-called West Nile Fever (WNF) or severe neuroinvasive form of the disease (WNND), and ultimately even death. There are currently no known medications to prevent West Nile virus infection. Only symptomatic treatment is used. To date, there are no unequivocal tests enabling a quick and unambiguous assessment of WN virus infection. The aim of the research was to obtain specific and selective tools for determining the activity of the West Nile virus serine proteinase. Using the methods of combinatorial chemistry with iterative deconvolution, the substrate specificity of the enzyme in non-primed and primed positions was determined. The FRET ABZ-Ala-Lys-Gln-Arg-Gly-Gly-Thr-Tyr(3-NO2)-NH2 substrate was obtained, characterized by kinetic parameters (KM = 4.20 ± 0.32 × 10-5 M) as for the majority of proteolytic enzymes. The obtained sequence was used to develop and synthesize highly sensitive functionalized quantum dot-based protease probes (QD). A QD WNV NS3 protease probe was obtained to detect an increase in fluorescence of 0.05 nmol enzyme in the assay system. This value was at least 20 times lower than that observed with the optimized substrate. The obtained result may be the basis for further research on the potential use of the WNV NS3 protease in the diagnosis of West Nile virus infection.
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Affiliation(s)
- Joanna Pianka
- University of Gdansk, Faculty of Chemistry, Wita Stwosza 63 Street, PL 80-308 Gdańsk, Poland
| | - Natalia Gruba
- University of Gdansk, Faculty of Chemistry, Wita Stwosza 63 Street, PL 80-308 Gdańsk, Poland.
| | - Adam Lesner
- University of Gdansk, Faculty of Chemistry, Wita Stwosza 63 Street, PL 80-308 Gdańsk, Poland
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Pant S, Jena NR. C-Terminal Extended Hexapeptides as Potent Inhibitors of the NS2B-NS3 Protease of the ZIKA Virus. Front Med (Lausanne) 2022; 9:921060. [PMID: 35872792 PMCID: PMC9306491 DOI: 10.3389/fmed.2022.921060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
The Zika virus (ZIKV) protease is an attractive drug target for the design of novel inhibitors to control the ZIKV infection. As the protease substrate-binding site contains acidic residues, inhibitors with basic residues can be beneficial for the inhibition of protease activities. Molecular dynamics (MD) simulation and molecular mechanics with generalized Born and surface area solvation (MM/GBSA) techniques are employed herein to design potent peptide inhibitors and to understand the nature of the basic residues that can potentially stabilize the acidic residues of the protease substrate-binding site. It is found that the inclusion of K, R, and K at P1, P2, and P3 positions, respectively, and Y at the P4 position (YKRK) would generate a highly stable tetrapeptide-protease complex with a ΔGbind of ~ −80 kcal/mol. We have also shown that the C-terminal extension of this and the second most stable tetrapeptide (YRRR) with small polar residues, such as S and T would generate even more stable hexapeptide-protease complexes. The modes of interactions of these inhibitors are discussed in detail, which are in agreement with earlier experimental studies. Thus, this study is expected to aid in the design of novel antiviral drugs against the ZIKV.
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Affiliation(s)
- Suyash Pant
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Nihar R. Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design and Manufacturing, Jabalpur, India
- *Correspondence: Nihar R. Jena
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Voss S, Nitsche C. Targeting the protease of West Nile virus. RSC Med Chem 2021; 12:1262-1272. [PMID: 34458734 PMCID: PMC8372202 DOI: 10.1039/d1md00080b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/17/2021] [Indexed: 01/04/2023] Open
Abstract
West Nile virus infections can cause severe neurological symptoms. During the last 25 years, cases have been reported in Asia, North America, Africa, Europe and Australia (Kunjin). No West Nile virus vaccines or specific antiviral therapies are available to date. Various viral proteins and host-cell factors have been evaluated as potential drug targets. The viral protease NS2B-NS3 is among the most promising viral targets. It releases viral proteins from a non-functional polyprotein precursor, making it a critical factor of viral replication. Despite strong efforts, no protease inhibitors have reached clinical trials yet. Substrate-derived peptidomimetics have facilitated structural elucidations of the active protease state, while alternative compounds with increased drug-likeness have recently expanded drug discovery efforts beyond the active site.
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Affiliation(s)
- Saan Voss
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
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Peptide derivatives as inhibitors of NS2B-NS3 protease from Dengue, West Nile, and Zika flaviviruses. Bioorg Med Chem 2019; 27:3963-3978. [DOI: 10.1016/j.bmc.2019.07.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 07/18/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022]
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Gruba N, Rodriguez Martinez JI, Grzywa R, Wysocka M, Skoreński M, Burmistrz M, Łęcka M, Lesner A, Sieńczyk M, Pyrć K. Substrate profiling of Zika virus NS2B-NS3 protease. FEBS Lett 2016; 590:3459-3468. [PMID: 27714789 DOI: 10.1002/1873-3468.12443] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/12/2016] [Accepted: 09/22/2016] [Indexed: 01/05/2023]
Abstract
Zika virus (ZIKV), isolated from macaques in Uganda in 1947, was not considered to be a dangerous human pathogen. However, this view has recently changed as ZIKV infections are now associated with serious pathological disorders including microcephaly and Guillain-Barré syndrome. Similar to other viruses in the Flaviviridae family, ZIKV expresses the serine protease NS3 which is responsible for viral protein processing and replication. Herein, we report the expression of an active NS3pro domain fused with the NS2B cofactor (NS2BLN NS3pro ) in a prokaryotic expression system and profile its specificity for synthesized FRET-type substrate libraries. Our findings pave way for screening potential intracellular substrates of NS3 and for developing specific inhibitors of this ZIKV protease.
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Affiliation(s)
- Natalia Gruba
- Department of Biochemistry, Faculty of Chemistry, University of Gdansk, Poland
| | | | - Renata Grzywa
- Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Magdalena Wysocka
- Department of Biochemistry, Faculty of Chemistry, University of Gdansk, Poland
| | - Marcin Skoreński
- Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Michał Burmistrz
- Department of Microbiology, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Maria Łęcka
- Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Adam Lesner
- Department of Biochemistry, Faculty of Chemistry, University of Gdansk, Poland.
| | - Marcin Sieńczyk
- Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland.
| | - Krzysztof Pyrć
- Department of Microbiology, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland. .,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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Majerle A, Gaber R, Benčina M, Jerala R. Function-based mutation-resistant synthetic signaling device activated by HIV-1 proteolysis. ACS Synth Biol 2015; 4:667-72. [PMID: 25393958 PMCID: PMC4487218 DOI: 10.1021/sb5002483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
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The
high mutation rate of the human immunodeficiency virus type
1 (HIV-1) virus is a major problem since it evades the function of
antibodies and chemical inhibitors. Here, we demonstrate a viral detection
strategy based on synthetic biology principles to detect a specific
viral function rather than a particular viral protein. The resistance
caused by mutations can be circumvented since the mutations that cause
the loss of function also incapacitate the virus. Many pathogens encode
proteases that are essential for their replication and that have a
defined substrate specificity. A genetically encoded sensor composed
of a fused membrane anchor, viral protease target site, and an orthogonal
transcriptional activator was engineered into a human cell line. The
HIV-1 protease released the transcriptional activator from the membrane,
thereby inducing transcription of the selected genes. The device was
still strongly activated by clinically relevant protease mutants that
are resistant to protease inhibitors. In the future, a similar principle
could be applied to detect also other pathogens and functions.
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Affiliation(s)
- Andreja Majerle
- Laboratory
of Biotechnology, National Institute of Chemistry, Hajdrihova
19, 1000 Ljubljana, Slovenia
| | - Rok Gaber
- Laboratory
of Biotechnology, National Institute of Chemistry, Hajdrihova
19, 1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Laboratory
of Biotechnology, National Institute of Chemistry, Hajdrihova
19, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Laboratory
of Biotechnology, National Institute of Chemistry, Hajdrihova
19, 1000 Ljubljana, Slovenia
- EN-FIST Centre
of Excellence, Trg OF 13, 1000 Ljubljana, Slovenia
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Context-Dependent Cleavage of the Capsid Protein by the West Nile Virus Protease Modulates the Efficiency of Virus Assembly. J Virol 2015; 89:8632-42. [PMID: 26063422 DOI: 10.1128/jvi.01253-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/02/2015] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED The molecular mechanisms that define the specificity of flavivirus RNA encapsulation are poorly understood. Virions composed of the structural proteins of one flavivirus and the genomic RNA of a heterologous strain can be assembled and have been developed as live attenuated vaccine candidates for several flaviviruses. In this study, we discovered that not all combinations of flavivirus components are possible. While a West Nile virus (WNV) subgenomic RNA could readily be packaged by structural proteins of the DENV2 strain 16681, production of infectious virions with DENV2 strain New Guinea C (NGC) structural proteins was not possible, despite the very high amino acid identity between these viruses. Mutagenesis studies identified a single residue (position 101) of the DENV capsid (C) protein as the determinant for heterologous virus production. C101 is located at the P1' position of the NS2B/3 protease cleavage site at the carboxy terminus of the C protein. WNV NS2B/3 cleavage of the DENV structural polyprotein was possible when a threonine (Thr101 in strain 16681) but not a serine (Ser101 in strain NGC) occupied the P1' position, a finding not predicted by in vitro protease specificity studies. Critically, both serine and threonine were tolerated at the P1' position of WNV capsid. More extensive mutagenesis revealed the importance of flanking residues within the polyprotein in defining the cleavage specificity of the WNV protease. A more detailed understanding of the context dependence of viral protease specificity may aid the development of new protease inhibitors and provide insight into associated patterns of drug resistance. IMPORTANCE West Nile virus (WNV) and dengue virus (DENV) are mosquito-borne flaviviruses that cause considerable morbidity and mortality in humans. No specific antiflavivirus therapeutics are available for treatment of infection. Proteolytic processing of the flavivirus polyprotein is an essential step in the replication cycle and is an attractive target for antiviral development. The design of protease inhibitors has been informed by insights into the molecular details of the interactions of proteases and their substrates. In this article, studies of the processing of WNV and DENV capsid proteins by the WNV protease identified an unexpected contribution of the sequence surrounding critical residues within the cleavage site on protease specificity. This demonstration of context-dependent protease cleavage has implications for the design of chimeric flaviviruses, new therapeutics, and the interpretation of flavivirus protease substrate specificity studies.
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