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Starvaggi J, Previti S, Zappalà M, Ettari R. The Inhibition of NS2B/NS3 Protease: A New Therapeutic Opportunity to Treat Dengue and Zika Virus Infection. Int J Mol Sci 2024; 25:4376. [PMID: 38673962 PMCID: PMC11050111 DOI: 10.3390/ijms25084376] [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: 03/17/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024] Open
Abstract
In the global pandemic scenario, dengue and zika viruses (DENV and ZIKV, respectively), both mosquito-borne members of the flaviviridae family, represent a serious health problem, and considering the absence of specific antiviral drugs and available vaccines, there is a dire need to identify new targets to treat these types of viral infections. Within this drug discovery process, the protease NS2B/NS3 is considered the primary target for the development of novel anti-flavivirus drugs. The NS2B/NS3 is a serine protease that has a dual function both in the viral replication process and in the elusion of the innate immunity. To date, two main classes of NS2B/NS3 of DENV and ZIKV protease inhibitors have been discovered: those that bind to the orthosteric site and those that act at the allosteric site. Therefore, this perspective article aims to discuss the main features of the use of the most potent NS2B/NS3 inhibitors and their impact at the social level.
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Affiliation(s)
| | | | | | - Roberta Ettari
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (J.S.); (S.P.); (M.Z.)
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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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Santos LH, Caffarena ER, Ferreira RS. pH and non-covalent ligand binding modulate Zika virus NS2B/NS3 protease binding site residues: Discoveries from MD and constant pH MD simulations. J Biomol Struct Dyn 2022; 40:10359-10372. [PMID: 34180376 DOI: 10.1080/07391102.2021.1943528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Zika virus (ZIKV) is a global health concern and has been linked to severe neurological pathologies. Although no medication is available yet, many efforts to develop antivirals and host cell binding inhibitors led to attractive drug-like scaffolds, mainly targeting the nonstructural NS2B/NS3 protease (NS2B/NS3pro). NS2B/NS3pro active site has several titratable residues susceptible to pH changes and ligand binding; hence, understanding these residues' protonation is essential to drug design efforts targeting the active site. Here we use in silico methods to probe non-covalent binding and its effect on pKa shifts of the active site residues on a ligand-free protease and with a non-peptidic competitive inhibitor (Ki=13.5 µM). By applying constant pH molecular dynamics, we found that the catalytic residues of the unbound NS2B/NS3pro achieved the protonation needed for the serine protease mechanism over the pH value of 8.5. Nevertheless, the protease in the holo state achieved this same scenario at lower pH values. Also, non-covalent binding affected the catalytic triad (H51, D75, and S135) by stabilizing their distances and interaction network. Thus, NS2B/NS3pro residues configuration for activity might be both pH-dependent and influenced by ligand binding. However, compound presence within the binding site destabilized the NS2B, interfering with the closed and active conformation necessary for substrate binding and catalysis. Our outcomes provide valuable insights into non-covalent inhibitor behavior and its effect on protease active site residues, impacting optimization and design of novel compounds. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lucianna H Santos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ernesto R Caffarena
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brazil
| | - Rafaela S Ferreira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Yu X, Shan C, Zhu Y, Ma E, Wang J, Wang P, Shi PY, Cheng G. A mutation-mediated evolutionary adaptation of Zika virus in mosquito and mammalian host. Proc Natl Acad Sci U S A 2021; 118:e2113015118. [PMID: 34620704 PMCID: PMC8545446 DOI: 10.1073/pnas.2113015118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2021] [Indexed: 01/18/2023] Open
Abstract
Zika virus (ZIKV) caused millions of infections during its rapid and expansive spread from Asia to the Americas from 2015 to 2017. Here, we compared the infectivity of ZIKV mutants with individual stable substitutions which emerged throughout the Asian ZIKV lineage and were responsible for the explosive outbreaks in the Americas. A threonine (T) to alanine (A) mutation at the 106th residue of the ZIKV capsid (C) protein facilitated the transmission by its mosquito vector, as well as infection in both human cells and immunodeficient mice. A mechanistic study showed that the T106A substitution rendered the C a preferred substrate for the NS2B-NS3 protease, thereby facilitating the maturation of structural proteins and the formation of infectious viral particles. Over a complete "mosquito-mouse-mosquito" cycle, the ZIKV C-T106A mutant showed a higher prevalence of mosquito infection than did the preepidemic strain, thus promoting ZIKV dissemination. Our results support the contribution of this evolutionary adaptation to the occasional widespread reemergence of ZIKV in nature.
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Affiliation(s)
- Xi Yu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
- Shenzhen Center for Disease Control and Prevention, Institute of Pathogenic Organisms, Shenzhen 518055, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chao Shan
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
| | - Yibin Zhu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
- Shenzhen Center for Disease Control and Prevention, Institute of Pathogenic Organisms, Shenzhen 518055, China
| | - Enhao Ma
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jinglin Wang
- Yunnan Tropical and Subtropical Animal Viral Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming 650224, China
| | - Penghua Wang
- Department of Immunology, School of Medicine, the University of Connecticut Health Center, Farmington, CT 06030
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China;
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
- Shenzhen Center for Disease Control and Prevention, Institute of Pathogenic Organisms, Shenzhen 518055, China
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Mechanisms of Action for Small Molecules Revealed by Structural Biology in Drug Discovery. Int J Mol Sci 2020; 21:ijms21155262. [PMID: 32722222 PMCID: PMC7432558 DOI: 10.3390/ijms21155262] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 12/26/2022] Open
Abstract
Small-molecule drugs are organic compounds affecting molecular pathways by targeting important proteins. These compounds have a low molecular weight, making them penetrate cells easily. Small-molecule drugs can be developed from leads derived from rational drug design or isolated from natural resources. A target-based drug discovery project usually includes target identification, target validation, hit identification, hit to lead and lead optimization. Understanding molecular interactions between small molecules and their targets is critical in drug discovery. Although many biophysical and biochemical methods are able to elucidate molecular interactions of small molecules with their targets, structural biology is the most powerful tool to determine the mechanisms of action for both targets and the developed compounds. Herein, we reviewed the application of structural biology to investigate binding modes of orthosteric and allosteric inhibitors. It is exemplified that structural biology provides a clear view of the binding modes of protease inhibitors and phosphatase inhibitors. We also demonstrate that structural biology provides insights into the function of a target and identifies a druggable site for rational drug design.
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Identification and structural characterization of small molecule fragments targeting Zika virus NS2B-NS3 protease. Antiviral Res 2020; 175:104707. [PMID: 31953156 DOI: 10.1016/j.antiviral.2020.104707] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 11/23/2022]
Abstract
Zika virus (ZIKV) NS2B-NS3 protease is a validated antiviral target as it is essential for maturation of viral proteins. However, its negatively charged active site hinders the development of orthosteric small-molecule inhibitors. Fragment-based drug discovery (FBDD) is a powerful tool to generate novel chemical starting points against difficult drug targets. In this study, we scre ened a fragment compound library against the Zika protease using a primary thermal shift assay and identified twenty-two fragments which (bind to and) stabilize the protease. We then determined the X-ray crystal structures of two hits from different classes, all of which bind to the S1 pocket of the protease. We confirmed that these two fragments bind to the protease without inducing significant conformational changes using solution NMR spectroscopy. These fragment scaffolds serve as the starting point for subsequent lead compound development.
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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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Nitsche C, Onagi H, Quek JP, Otting G, Luo D, Huber T. Biocompatible Macrocyclization between Cysteine and 2-Cyanopyridine Generates Stable Peptide Inhibitors. Org Lett 2019; 21:4709-4712. [DOI: 10.1021/acs.orglett.9b01545] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Hideki Onagi
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Jun-Ping Quek
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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Majerová T, Novotný P, Krýsová E, Konvalinka J. Exploiting the unique features of Zika and Dengue proteases for inhibitor design. Biochimie 2019; 166:132-141. [PMID: 31077760 DOI: 10.1016/j.biochi.2019.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
Zika and Dengue viruses have attracted substantial attention from researchers in light of recent outbreaks of Dengue fever and increases in cases of congenital microcephaly in areas with Zika incidence. This review summarizes the current state of knowledge about Zika and Dengue proteases. These enzymes have several interesting features: 1) NS3 serine protease requires the activating co-factor NS2B, which is anchored in the membrane of the endoplasmic reticulum; 2) NS2B displays extensive conformational dynamics; 3) NS3 is a multidomain protein with proteolytic, NTPase, RNA 5' triphosphatase and helicase activity and has many protein-protein interaction partners; 4) NS3 is autoproteolytically released from its precursor. Attempts to design tight-binding and specific active-site inhibitors are complicated by the facts that the substrate pocket of the NS2B-NS3 protease is flat and the active-site ligands are charged. The ionic character of potential active-site inhibitors negatively influences their cell permeability. Possibilities to block cis-autoprocessing of the protease precursor have recently been considered. Additionally, potential allosteric sites on NS2B-NS3 proteases have been identified and allosteric compounds have been designed to impair substrate binding and/or block the NS2B-NS3 interaction. Such compounds could be specific to viral proteases, without off-target effects on host serine proteases, and could have favorable pharmacokinetic profiles. This review discusses various groups of inhibitors of these proteases according to their mechanisms of action and chemical structures.
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Affiliation(s)
- Taťána Majerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic
| | - Pavel Novotný
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic
| | - Eliška Krýsová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic.
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