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Huang L, Liang Y, Hou H, Tang M, Liu X, Ma YN, Liang S. Prokaryotic Expression and Affinity Purification of DDX3 Protein. Protein Pept Lett 2024; 31:236-246. [PMID: 38303525 DOI: 10.2174/0109298665285625231222075700] [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: 10/05/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND DDX3 is a protein with RNA helicase activity that is involved in a variety of biological processes, and it is an important protein target for the development of broad-spectrum antiviral drugs, multiple cancers and chronic inflammation. OBJECTIVES The objective of this study is to establish a simple and efficient method to express and purify DDX3 protein in E. coli, and the recombinant DDX3 should maintain helicase activity for further tailor-made screening and biochemical function validation. METHODS DDX3 cDNA was simultaneously cloned into pET28a-TEV and pNIC28-Bsa4 vectors and transfected into E. coli BL21 (DE3) to compare one suitable prokaryotic expression system. The 6×His-tag was fused to the C-terminus of DDX3 to form a His-tagging DDX3 fusion protein for subsequent purification. Protein dissolution buffer and purification washing conditions were optimized. The His-tagged DDX3 protein would bind with the Ni-NTA agarose by chelation and collected by affinity purification. The 6×His-tag fused with N-terminal DDX3 was eliminated from DDX3 by TEV digestion. A fine purification of DDX3 was performed by gel filtration chromatography. RESULTS The recombinant plasmid pNIC28-DDX3, which contained a 6×His-tag and one TEV cleavage site at the N terminal of DDX3 sequence, was constructed for DDX3 prokaryotic expression and affinity purification based on considering the good solubility of the recombinant His-tagging DDX3, especially under 0.5 mM IPTG incubation at 18°C for 18 h to obtain more soluble DDX3 protein. Finally, the exogenous recombinant DDX3 protein was obtained with more than 95% purity by affinity purification on the Ni-NTA column and removal of miscellaneous through gel filtration chromatography. The finely-purified DDX3 still retained its ATPase activity. CONCLUSION A prokaryotic expression pNIC28-DDX3 system is constructed for efficient expression and affinity purification of bioactive DDX3 protein in E. coli BL21(DE3), which provides an important high-throughput screening and validation of drugs targeting DDX3.
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Affiliation(s)
- Lan Huang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, Section 3 of Renmin South Road, Chengdu, Sichuan, 610041, P.R. China
| | - Yue Liang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, Section 3 of Renmin South Road, Chengdu, Sichuan, 610041, P.R. China
| | - Huijin Hou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, Section 3 of Renmin South Road, Chengdu, Sichuan, 610041, P.R. China
| | - Min Tang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, Section 3 of Renmin South Road, Chengdu, Sichuan, 610041, P.R. China
| | - Xinpeng Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, Section 3 of Renmin South Road, Chengdu, Sichuan, 610041, P.R. China
| | - Yan-Ni Ma
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, Section 3 of Renmin South Road, Chengdu, Sichuan, 610041, P.R. China
| | - Shufang Liang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, Section 3 of Renmin South Road, Chengdu, Sichuan, 610041, P.R. China
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2
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Brai A, Poggialini F, Pasqualini C, Trivisani CI, Vagaggini C, Dreassi E. Progress towards Adjuvant Development: Focus on Antiviral Therapy. Int J Mol Sci 2023; 24:9225. [PMID: 37298177 PMCID: PMC10253057 DOI: 10.3390/ijms24119225] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
In recent decades, vaccines have been extraordinary resources to prevent pathogen diffusion and cancer. Even if they can be formed by a single antigen, the addition of one or more adjuvants represents the key to enhance the response of the immune signal to the antigen, thus accelerating and increasing the duration and the potency of the protective effect. Their use is of particular importance for vulnerable populations, such as the elderly or immunocompromised people. Despite their importance, only in the last forty years has the search for novel adjuvants increased, with the discovery of novel classes of immune potentiators and immunomodulators. Due to the complexity of the cascades involved in immune signal activation, their mechanism of action remains poorly understood, even if significant discovery has been recently made thanks to recombinant technology and metabolomics. This review focuses on the classes of adjuvants under research, recent mechanism of action studies, as well as nanodelivery systems and novel classes of adjuvants that can be chemically manipulated to create novel small molecule adjuvants.
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Affiliation(s)
- Annalaura Brai
- Department of Biotechnologies, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy; (A.B.); (F.P.); (C.P.); (C.V.)
| | - Federica Poggialini
- Department of Biotechnologies, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy; (A.B.); (F.P.); (C.P.); (C.V.)
| | - Claudia Pasqualini
- Department of Biotechnologies, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy; (A.B.); (F.P.); (C.P.); (C.V.)
| | - Claudia Immacolata Trivisani
- Department of Biotechnologies, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy; (A.B.); (F.P.); (C.P.); (C.V.)
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Chiara Vagaggini
- Department of Biotechnologies, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy; (A.B.); (F.P.); (C.P.); (C.V.)
| | - Elena Dreassi
- Department of Biotechnologies, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy; (A.B.); (F.P.); (C.P.); (C.V.)
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3
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Del Rosario García-Lozano M, Dragoni F, Gallego P, Mazzotta S, López-Gómez A, Boccuto A, Martínez-Cortés C, Rodríguez-Martínez A, Pérez-Sánchez H, Manuel Vega-Pérez J, Antonio Del Campo J, Vicenti I, Vega-Holm M, Iglesias-Guerra F. Piperazine-derived small molecules as potential Flaviviridae NS3 protease inhibitors. In vitro antiviral activity evaluation against Zika and Dengue viruses. Bioorg Chem 2023; 133:106408. [PMID: 36801791 DOI: 10.1016/j.bioorg.2023.106408] [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: 07/27/2022] [Revised: 01/23/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Since 2011 Direct Acting antivirals (DAAs) drugs targeting different non-structural (NS) viral proteins (NS3, NS5A or NS5B inhibitors) have been approved for clinical use in HCV therapies. However, currently there are not licensed therapeutics to treat Flavivirus infections and the only licensed DENV vaccine, Dengvaxia, is restricted to patients with preexisting DENV immunity. Similarly to NS5 polymerase, the NS3 catalytic region is evolutionarily conserved among the Flaviviridae family sharing strong structural similarity with other proteases belonging to this family and therefore is an attractive target for the development of pan-flavivirus therapeutics. In this work we present a library of 34 piperazine-derived small molecules as potential Flaviviridae NS3 protease inhibitors. The library was developed through a privileged structures-based design and then biologically screened using a live virus phenotypic assay to determine the half-maximal inhibitor concentration (IC50) of each compound against ZIKV and DENV. Two lead compounds, 42 and 44, with promising broad-spectrum activity against ZIKV (IC50 6.6 µM and 1.9 µM respectively) and DENV (IC50 6.7 µM and 1.4 µM respectively) and a good security profile were identified. Besides, molecular docking calculations were performed to provide insights about key interactions with residues in NS3 proteases' active sites.
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Affiliation(s)
- María Del Rosario García-Lozano
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain; SeLiver Group at the Institute of Biomedicine of Seville (IBIS), Virgen del Rocío University Hospital CSIC University of Seville, Seville, Spain
| | - Filippo Dragoni
- Department of Medical Biotechnologies, Siena University Hospital, Policlinico Le Scotte, Viale Bracci 16, 53100 Siena, Italy
| | - Paloma Gallego
- Unit for Clinical Management of Digestive Diseases and CIBERehd, Valme University Hospital, 41014 Seville, Spain
| | - Sarah Mazzotta
- Department of Chemistry, University of Milan, 20133 Milan, Italy
| | - Alejandro López-Gómez
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
| | - Adele Boccuto
- Department of Medical Biotechnologies, Siena University Hospital, Policlinico Le Scotte, Viale Bracci 16, 53100 Siena, Italy; VisMederi Research srl, Siena, Italy
| | - Carlos Martínez-Cortés
- Structural Bioinformatics and High Performance Computing (BIO-HPC) Research Group, UCAM Universidad Católica de Murcia, 30107 Murcia, Spain
| | - Alejandro Rodríguez-Martínez
- Department of Physical Chemistry and Institute of Biotechnology, University of Granada, Campus Fuentenueva sn, 18071 Granada, Spain
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing (BIO-HPC) Research Group, UCAM Universidad Católica de Murcia, 30107 Murcia, Spain
| | - José Manuel Vega-Pérez
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
| | | | - Ilaria Vicenti
- Department of Medical Biotechnologies, Siena University Hospital, Policlinico Le Scotte, Viale Bracci 16, 53100 Siena, Italy.
| | - Margarita Vega-Holm
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain.
| | - Fernando Iglesias-Guerra
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
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4
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Heaton SM, Gorry PR, Borg NA. DExD/H-box helicases in HIV-1 replication and their inhibition. Trends Microbiol 2023; 31:393-404. [PMID: 36463019 DOI: 10.1016/j.tim.2022.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022]
Abstract
Antiretroviral therapy (ART) reduces human immunodeficiency virus type 1 (HIV-1) infection, but selection of treatment-refractory variants remains a major challenge. HIV-1 encodes 16 canonical proteins, a small number of which are the singular targets of nearly all antiretrovirals developed to date. Cellular factors are increasingly being explored, which may present more therapeutic targets, more effectively target certain aspects of the viral replication cycle, and/or limit viral escape. Unlike most other positive-sense RNA viruses that encode at least one helicase, retroviruses are limited to the host repertoire. Accordingly, HIV-1 subverts DEAD-box helicase 3X (DDX3X) and numerous other cellular helicases of the Asp-Glu-x-Asp/His (DExD/H)-box family to service multiple aspects of its replication cycle. Here we review DDX3X and other DExD/H-box helicases in HIV-1 replication and their inhibition.
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Affiliation(s)
- Steven M Heaton
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Current affiliation: RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, 1-chōme-7-22 Suehirochō, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan.
| | - Paul R Gorry
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
| | - Natalie A Borg
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
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5
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Naineni SK, Robert F, Nagar B, Pelletier J. Targeting DEAD-box RNA helicases: The emergence of molecular staples. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1738. [PMID: 35581936 DOI: 10.1002/wrna.1738] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 12/29/2022]
Abstract
RNA helicases constitute a large family of proteins that play critical roles in mediating RNA function. They have been implicated in all facets of gene expression pathways involving RNA, from transcription to processing, transport and translation, and storage and decay. There is significant interest in developing small molecule inhibitors to RNA helicases as some family members have been documented to be dysregulated in neurological and neurodevelopment disorders, as well as in cancers. Although different functional properties of RNA helicases offer multiple opportunities for small molecule development, molecular staples have recently come to the forefront. These bifunctional molecules interact with both protein and RNA components to lock them together, thereby imparting novel gain-of-function properties to their targets. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Sai Kiran Naineni
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Francis Robert
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Bhushan Nagar
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
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6
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Proteins from Tenebrio molitor: An interesting functional ingredient and a source of ACE inhibitory peptides. Food Chem 2022; 393:133409. [PMID: 35751205 DOI: 10.1016/j.foodchem.2022.133409] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/30/2022] [Accepted: 06/04/2022] [Indexed: 11/22/2022]
Abstract
The angiotensin-converting enzyme (ACE) inhibitory potential of the main protein fractions from Tenebrio molitor larvae (TML) was examined to evaluate their use as a novel antihypertensive functional food. Both fractions contained YAN tripeptide, previously reported as responsible for ACE inhibition. Although YAN has been synthesized and was used as a standard for LC-MS/MS quantification and IC50 against ACE was determined, low yields of YAN from TML did not explain adequately the activity of the whole protein fraction. LC-HRMS/MS investigation led to the identification of other three peptides, which were evaluated in silico, synthesized and tested against ACE. Among them, tetrapeptide NIKY showed the most promising activity (52 µM), highlighting once more the potential of TML and paving the way for exploitation in novel foods.
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7
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Harris J, Borg NA. The multifaceted roles of NLRP3-modulating proteins in virus infection. Front Immunol 2022; 13:987453. [PMID: 36110852 PMCID: PMC9468583 DOI: 10.3389/fimmu.2022.987453] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022] Open
Abstract
The innate immune response to viruses is critical for the correct establishment of protective adaptive immunity. Amongst the many pathways involved, the NLRP3 [nucleotide-binding oligomerisation domain (NOD)-like receptor protein 3 (NLRP3)] inflammasome has received considerable attention, particularly in the context of immunity and pathogenesis during infection with influenza A (IAV) and SARS-CoV-2, the causative agent of COVID-19. Activation of the NLRP3 inflammasome results in the secretion of the proinflammatory cytokines IL-1β and IL-18, commonly coupled with pyroptotic cell death. While this mechanism is protective and key to host defense, aberrant NLRP3 inflammasome activation causes a hyperinflammatory response and excessive release of cytokines, both locally and systemically. Here, we discuss key molecules in the NLRP3 pathway that have also been shown to have significant roles in innate and adaptive immunity to viruses, including DEAD box helicase X-linked (DDX3X), vimentin and macrophage migration inhibitory factor (MIF). We also discuss the clinical opportunities to suppress NLRP3-mediated inflammation and reduce disease severity.
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Affiliation(s)
- James Harris
- Cell Biology Assays Team, Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Clayton, VIC, Australia
- Centre for Inflammatory diseases, Department of Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Natalie A. Borg
- Immunity and Immune Evasion Laboratory, Chronic Infectious and Inflammatory Diseases Research, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
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8
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Vesuna F, Akhrymuk I, Smith A, Winnard PT, Lin SC, Panny L, Scharpf R, Kehn-Hall K, Raman V. RK-33, a small molecule inhibitor of host RNA helicase DDX3, suppresses multiple variants of SARS-CoV-2. Front Microbiol 2022; 13:959577. [PMID: 36090095 PMCID: PMC9453862 DOI: 10.3389/fmicb.2022.959577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/27/2022] [Indexed: 12/03/2022] Open
Abstract
SARS-CoV-2, the virus behind the deadly COVID-19 pandemic, continues to spread globally even as vaccine strategies are proving effective in preventing hospitalizations and deaths. However, evolving variants of the virus appear to be more transmissive and vaccine efficacy toward them is waning. As a result, SARS-CoV-2 will continue to have a deadly impact on public health into the foreseeable future. One strategy to bypass the continuing problem of newer variants is to target host proteins required for viral replication. We have used this host-targeted antiviral (HTA) strategy that targets DDX3X (DDX3), a host DEAD-box RNA helicase that is usurped by SARS-CoV-2 for virus production. We demonstrated that targeting DDX3 with RK-33, a small molecule inhibitor, reduced the viral load in four isolates of SARS-CoV-2 (Lineage A, and Lineage B Alpha, Beta, and Delta variants) by one to three log orders in Calu-3 cells. Furthermore, proteomics and RNA-seq analyses indicated that most SARS-CoV-2 genes were downregulated by RK-33 treatment. Also, we show that the use of RK-33 decreases TMPRSS2 expression, which may be due to DDX3s ability to unwind G-quadraplex structures present in the TMPRSS2 promoter. The data presented support the use of RK-33 as an HTA strategy to control SARS-CoV-2 infection, irrespective of its mutational status, in humans.
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Affiliation(s)
- Farhad Vesuna
- Division of Cancer Imaging Research, Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ivan Akhrymuk
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Amy Smith
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Paul T Winnard
- Division of Cancer Imaging Research, Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Shih-Chao Lin
- Bachelor Degree Program in Marine Biotechnology, College of Life Sciences, National Taiwan Ocean University, Keelung, Taiwan
| | - Lauren Panny
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Robert Scharpf
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kylene Kehn-Hall
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- Center for Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Venu Raman
- Division of Cancer Imaging Research, Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Departments of Oncology, Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
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9
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Brai A, Trivisani CI, Poggialini F, Pasqualini C, Vagaggini C, Dreassi E. DEAD-Box Helicase DDX3X as a Host Target against Emerging Viruses: New Insights for Medicinal Chemical Approaches. J Med Chem 2022; 65:10195-10216. [PMID: 35899912 DOI: 10.1021/acs.jmedchem.2c00755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years, globalization, global warming, and population aging have contributed to the spread of emerging viruses, such as coronaviruses (COVs), West Nile (WNV), Dengue (DENV), and Zika (ZIKV). The number of reported infections is increasing, and considering the high viral mutation rate, it is conceivable that it will increase significantly in the coming years. The risk caused by viruses is now more evident due to the COVID-19 pandemic, which highlighted the need to find new broad-spectrum antiviral agents able to tackle the present pandemic and future epidemics. DDX3X helicase is a host factor required for viral replication. Selective inhibitors have been identified and developed into broad-spectrum antivirals active against emerging pathogens, including SARS-CoV-2 and most importantly against drug-resistant strains. This perspective describes the inhibitors identified in the last years, highlighting their therapeutic potential as innovative broad-spectrum antivirals.
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Affiliation(s)
- Annalaura Brai
- Department of Biotechnology, Chemistry & Pharmacy, University of Siena, I-53100 Siena Italy
| | | | - Federica Poggialini
- Department of Biotechnology, Chemistry & Pharmacy, University of Siena, I-53100 Siena Italy
| | - Claudia Pasqualini
- Department of Biotechnology, Chemistry & Pharmacy, University of Siena, I-53100 Siena Italy
| | - Chiara Vagaggini
- Department of Biotechnology, Chemistry & Pharmacy, University of Siena, I-53100 Siena Italy
| | - Elena Dreassi
- Department of Biotechnology, Chemistry & Pharmacy, University of Siena, I-53100 Siena Italy
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10
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Vesuna F, Akhrymuk I, Smith A, Winnard PT, Lin SC, Scharpf R, Kehn-Hall K, Raman V. RK-33, a small molecule inhibitor of host RNA helicase DDX3, suppresses multiple variants of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.28.482334. [PMID: 35262079 PMCID: PMC8902879 DOI: 10.1101/2022.02.28.482334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2, the virus behind the deadly COVID-19 pandemic, continues to spread globally even as vaccine strategies are proving effective in preventing hospitalizations and deaths. However, evolving variants of the virus appear to be more transmissive and vaccine efficacy towards them is waning. As a result, SARS-CoV-2 will continue to have a deadly impact on public health into the foreseeable future. One strategy to bypass the continuing problem of newer variants is to target host proteins required for viral replication. We have used this host-targeted antiviral (HTA) strategy that targets DDX3, a host DEAD-box RNA helicase that is usurped by SARS-CoV-2 for virus production. We demonstrated that targeting DDX3 with RK-33, a small molecule inhibitor, reduced the viral load in four isolates of SARS-CoV-2 (Lineage A, and Lineage B Alpha, Beta, and Delta variants) by one to three log orders in Calu-3 cells. Furthermore, proteomics and RNA-seq analyses indicated that most SARS-CoV-2 genes were downregulated by RK-33 treatment. Also, we show that the use of RK-33 decreases TMPRSS2 expression, which may be due to DDX3s ability to unwind G-quadraplex structures present in the TMPRSS2 promoter. The data presented supports the use of RK-33 as an HTA strategy to control SARS-CoV-2 infection, irrespective of its mutational status, in humans.
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11
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Wang Y, Chen X, Lin S, Gao H, Liu FX, Zhou Z, Yi W. Hexafluoroisopropanol (HFIP)-prompted rearrangement of N-phenoxysulfonamides for the direct assembly of ortho-sulfonamide phenols: A combined experimental and computational study. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2021.153601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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De Colibus L, Stunnenberg M, Geijtenbeek TB. DDX3X structural analysis: Implications in the pharmacology and innate immunity. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:100-109. [PMID: 35647523 PMCID: PMC9133689 DOI: 10.1016/j.crimmu.2022.05.002] [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: 12/13/2021] [Revised: 05/01/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
The human DEAD-Box Helicase 3 X-Linked (DDX3X) is an ATP-dependent RNA helicase involved in virtually every step of RNA metabolism, ranging from transcription regulation in the nucleus to translation initiation and stress granule (SG) formation, and plays crucial roles in innate immunity, as well as tumorigenesis and viral infections. This review discusses latest advances in DDX3X biology and structure-function relationship, including the implications of the recent DDX3X crystal structure in complex with double stranded RNA for RNA metabolism, DDX3X involvement in the cross-talk between innate immune responses and cell stress adaptation, and the roles of DDX3X in controlling cell fate. The human DDX3X, an ATP-dependent RNA helicase, plays a central role in a variety of cellular processes involving RNA. DDX3X is implicated in antiviral signalling pathways. DDX3X interacts with full-length NLRP3 and its NACHT domain. The recent crystal structure of DDX3X in complex with dsRNA offers a model for understanding its binding to the HIV-1 TAR hairpin sequence.
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13
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Targeting DDX3X Helicase Activity with BA103 Shows Promising Therapeutic Effects in Preclinical Glioblastoma Models. Cancers (Basel) 2021; 13:cancers13215569. [PMID: 34771731 PMCID: PMC8582824 DOI: 10.3390/cancers13215569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 01/16/2023] Open
Abstract
Simple Summary In the last ten years, the human helicase protein DDX3X turned out to be an extremely interesting target for the development of potential anticancer drugs. Herein, we discovered BA103, a novel specific inhibitor of the helicase binding site of DDX3X, which is characterized by broad-spectrum anticancer activity. BA103 revealed promising tolerability in fibroblasts and good pharmacokinetic properties. Furthermore, BA103 was able to decrease the expression of β-catenin and to reduce tumor migration. Its capability to pass the blood–brain barrier led us to investigate its potential against glioblastoma, which is a high refractory disease with poor prognosis. High efficacy was proven in both xenograft and orthotopic animal models. Abstract DDX3X is an ATP-dependent RNA helicase that has recently attracted interest for its involvement in viral replication and oncogenic progression. Starting from hit compounds previously identified by our group, we have designed and synthesized a new series of DDX3X inhibitors that effectively blocked its helicase activity. These new compounds were able to inhibit the proliferation of cell lines from different cancer types, also in DDX3X low-expressing cancer cell lines. According to the absorption, distribution, metabolism, elimination properties, and antitumoral activity, compound BA103 was chosen to be further investigated in glioblastoma models. BA103 determined a significant reduction in the proliferation and migration of U87 and U251 cells, downregulating the oncogenic protein β-catenin. An in vivo evaluation demonstrated that BA103 was able to reach the brain and reduce the tumor growth in xenograft and orthotopic models without evident side effects. This study represents the first demonstration that DDX3X-targeted small molecules are feasible and promising drugs also in glioblastoma.
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RNA Helicase DDX3: A Double-Edged Sword for Viral Replication and Immune Signaling. Microorganisms 2021; 9:microorganisms9061206. [PMID: 34204859 PMCID: PMC8227550 DOI: 10.3390/microorganisms9061206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/19/2022] Open
Abstract
DDX3 is a cellular ATP-dependent RNA helicase involved in different aspects of RNA metabolism ranging from transcription to translation and therefore, DDX3 participates in the regulation of key cellular processes including cell cycle progression, apoptosis, cancer and the antiviral immune response leading to type-I interferon production. DDX3 has also been described as an essential cellular factor for the replication of different viruses, including important human threats such HIV-1 or HCV, and different small molecules targeting DDX3 activity have been developed. Indeed, increasing evidence suggests that DDX3 can be considered not only a promising but also a viable target for anticancer and antiviral treatments. In this review, we summarize distinct functional aspects of DDX3 focusing on its participation as a double-edged sword in the host immune response and in the replication cycle of different viruses.
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Squeglia F, Romano M, Ruggiero A, Maga G, Berisio R. Host DDX Helicases as Possible SARS-CoV-2 Proviral Factors: A Structural Overview of Their Hijacking Through Multiple Viral Proteins. Front Chem 2020; 8:602162. [PMID: 33381492 PMCID: PMC7769135 DOI: 10.3389/fchem.2020.602162] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
As intracellular parasites, viruses hijack the host cell metabolic machinery for their replication. Among other cellular proteins, the DEAD-box (DDX) RNA helicases have been shown to be hijacked by coronaviruses and to participate in essential DDX-mediated viral replication steps. Human DDX RNA helicases play essential roles in a broad array of biological processes and serve multiple roles at the virus-host interface. The viral proteins responsible for DDX interactions are highly conserved among coronaviruses, suggesting that they might also play conserved functions in the SARS-CoV-2 replication cycle. In this review, we provide an update of the structural and functional data of DDX as possible key factors involved in SARS-CoV-2 hijacking mechanisms. We also attempt to fill the existing gaps in the available structural information through homology modeling. Based on this information, we propose possible paths exploited by the virus to replicate more efficiently by taking advantage of host DDX proteins. As a general rule, sequestration of DDX helicases by SARS-CoV-2 is expected to play a pro-viral role in two ways: by enhancing key steps of the virus life cycle and, at the same time, by suppressing the host innate immune response.
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
| | - Maria Romano
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics (IGM-CNR), Pavia, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
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Winnard PT, Vesuna F, Raman V. Targeting host DEAD-box RNA helicase DDX3X for treating viral infections. Antiviral Res 2020; 185:104994. [PMID: 33301755 DOI: 10.1016/j.antiviral.2020.104994] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/19/2020] [Accepted: 12/02/2020] [Indexed: 02/06/2023]
Abstract
DDX3X or DDX3, a member of the DEAD (asp, glu, ala, asp) box RNA helicase family of proteins, is a multifunctional protein, which is usurped by several viruses and is vital to their production. To date, 18 species of virus from 12 genera have been demonstrated to be dependent on DDX3 for virulence. In addition, DDX3 has been shown to function within 7 of 10 subcellular regions that are involved in the metabolism of viruses. As such, due to its direct interaction with viral components across most or all stages of viral life cycles, DDX3 can be considered an excellent host target for pan-antiviral drug therapy and has been reported to be a possible broad-spectrum antiviral target. Along these lines, it has been demonstrated that treatment of virally infected cells with small molecule inhibitors of DDX3 blunts virion productions. On the other hand, DDX3 bolsters an innate immune response and viruses have evolved capacities to sequester or block DDX3, which dampens an innate immune response. Thus, enhancing DDX3 production or co-targeting direct viral products that interfere with DDX3's modulation of innate immunity would also diminish virion production. Here we review the evidence that supports the hypothesis that modulating DDX3's agonistic and antagonistic functions during viral infections could have an important impact on safely and efficiently subduing a broad-spectrum of viral infections.
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Affiliation(s)
- Paul T Winnard
- Division of Cancer Imaging Research, The Russell H Morgan Department of Radiology and Radiological Sciences, USA
| | - Farhad Vesuna
- Division of Cancer Imaging Research, The Russell H Morgan Department of Radiology and Radiological Sciences, USA
| | - Venu Raman
- Division of Cancer Imaging Research, The Russell H Morgan Department of Radiology and Radiological Sciences, USA; Department of Oncology, The Johns Hopkins University, School of Medicine, Baltimore, MD, USA; Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands.
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Felicetti T, Manfroni G, Cecchetti V, Cannalire R. Broad-Spectrum Flavivirus Inhibitors: a Medicinal Chemistry Point of View. ChemMedChem 2020; 15:2391-2419. [PMID: 32961008 DOI: 10.1002/cmdc.202000464] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/16/2020] [Indexed: 12/16/2022]
Abstract
Infections by flaviviruses, such as Dengue, West Nile, Yellow Fever and Zika viruses, represent a growing risk for global health. There are vaccines only for few flaviviruses while no effective treatments are available. Flaviviruses share epidemiological, structural, and ecologic features and often different viruses can co-infect the same host. Therefore, the identification of broad-spectrum inhibitors is highly desirable either for known flaviviruses or for viruses that likely will emerge in the future. Strategies targeting both virus and host factors have been pursued to identify broad-spectrum antiflaviviral agents. In this review, we describe the most promising and best characterized targets and their relative broad-spectrum inhibitors, identified by drug repurposing/libraries screenings and by focused medicinal chemistry campaigns. Finally, we discuss about future strategies to identify new broad-spectrum antiflavivirus agents.
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Affiliation(s)
- Tommaso Felicetti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123, Perugia, Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123, Perugia, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123, Perugia, Italy
| | - Rolando Cannalire
- Department of Pharmacy, University of Napoli "Federico II", via D. Montesano 49, 80131, Napoli, Italy
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Riva V, Garbelli A, Brai A, Casiraghi F, Fazi R, Trivisani CI, Boccuto A, Saladini F, Vicenti I, Martelli F, Zazzi M, Giannecchini S, Dreassi E, Botta M, Maga G. Unique Domain for a Unique Target: Selective Inhibitors of Host Cell DDX3X to Fight Emerging Viruses. J Med Chem 2020; 63:9876-9887. [PMID: 32787106 DOI: 10.1021/acs.jmedchem.0c01039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Emerging viruses like dengue, West Nile, chikungunya, and Zika can cause widespread viral epidemics. Developing novel drugs or vaccines against specific targets for each virus is a difficult task. As obligate parasites, all viruses exploit common cellular pathways, providing the possibility to develop broad-spectrum antiviral agents targeting host factors. The human DEAD-box RNA helicase DDX3X is an essential cofactor for viral replication but dispensable for cell viability. Herein, we exploited the presence of a unique structural motif of DDX3X not shared by other cellular enzymes to develop a theoretical model to aid in the design of a novel class of highly selective inhibitors acting against such specific targets, thus limiting off-targeting effects. High-throughput virtual screening led us to identify hit compound 5, endowed with promising antienzymatic activity. To improve its aqueous solubility, 5 and its two enantiomers were synthesized and converted into their corresponding acetate salts (compounds 11, 12, and 13). In vitro mutagenesis and biochemical and cellular assays further confirmed that the developed molecules were selective for DDX3X and were able to suppress replication of West Nile and dengue viruses in infected cells in the micromolar range while showing no toxicity for uninfected cells. These results provide proof of principle for a novel strategy in developing highly selective and broad-spectrum antiviral molecules active against emerging and dangerous viral pathogens. This study paves the way for the development of larger focused libraries targeting such domain to expand SAR studies and fully characterize their mode of interaction.
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Affiliation(s)
- Valentina Riva
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Anna Garbelli
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Annalaura Brai
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Federica Casiraghi
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Roberta Fazi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Claudia I Trivisani
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Adele Boccuto
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Francesco Saladini
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Ilaria Vicenti
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Francesco Martelli
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi di Firenze, Viale Morgnani 48, I-50134 Firenze, Italy
| | - Maurizio Zazzi
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Simone Giannecchini
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi di Firenze, Viale Morgnani 48, I-50134 Firenze, Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Maurizio Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Biotechnology College of Science and Technology, Temple University, Biolife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - Giovanni Maga
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
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