1
|
Ferdoush J, Abdul Kadir R, Simay Kaplanoglu S, Osborn M. SARS-CoV-2 and UPS with potentials for therapeutic interventions. Gene 2024; 912:148377. [PMID: 38490508 DOI: 10.1016/j.gene.2024.148377] [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: 01/19/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
The Ubiquitin proteasome system (UPS), an essential eukaryotic/host/cellular post-translational modification (PTM), plays a critical role in the regulation of diverse cellular functions including regulation of protein stability, immune signaling, antiviral activity, as well as virus replication. Although UPS regulation of viral proteins may be utilized by the host as a defense mechanism to invade viruses, viruses may have adapted to take advantage of the host UPS. This system can be manipulated by viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to stimulate various steps of the viral replication cycle and facilitate pathogenesis, thereby causing the respiratory disease COVID-19. Many SARS-CoV-2 encoded proteins including open reading frame 3a (ORF3a), ORF6, ORF7a, ORF9b, and ORF10 interact with the host's UPS machinery, influencing host immune signaling and apoptosis. Moreover, SARS-CoV-2 encoded papain-like protease (PLpro) interferes with the host UPS to facilitate viral replication and to evade the host's immune system. These alterations in SARS-CoV-2 infected cells have been revealed by various proteomic studies, suggesting potential targets for clinical treatment. To provide insight into the underlying causes of COVID-19 and suggest possible directions for therapeutic interventions, this paper reviews the intricate relationship between SARS-CoV-2 and UPS. Promising treatment strategies are also investigated in this paper including targeting PLpro with zinc-ejector drugs, as well as targeting viral non-structural protein (nsp12) via heat treatment associated ubiquitin-mediated proteasomal degradation to reduce viral pathogenesis.
Collapse
Affiliation(s)
- Jannatul Ferdoush
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA.
| | - Rizwaan Abdul Kadir
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Selin Simay Kaplanoglu
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Morgan Osborn
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| |
Collapse
|
2
|
Das R, Sinnarasan VSP, Paul D, Venkatesan A. A Machine Learning Approach to Identify Potential miRNA-Gene Regulatory Network Contributing to the Pathogenesis of SARS-CoV-2 Infection. Biochem Genet 2024; 62:987-1006. [PMID: 37515735 DOI: 10.1007/s10528-023-10458-x] [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: 01/04/2023] [Accepted: 07/14/2023] [Indexed: 07/31/2023]
Abstract
Worldwide, many lives have been lost in the recent outbreak of coronavirus disease. The pathogen responsible for this disease takes advantage of the host machinery to replicate itself and, in turn, causes pathogenesis in humans. Human miRNAs are seen to have a major role in the pathogenesis and progression of viral diseases. Hence, an in-silico approach has been used in this study to uncover the role of miRNAs and their target genes in coronavirus disease pathogenesis. This study attempts to perform the miRNA seq data analysis to identify the potential differentially expressed miRNAs. Considering only the experimentally proven interaction databases TarBase, miRTarBase, and miRecords, the target genes of the miRNAs have been identified from the mirNET analytics platform. The identified hub genes were subjected to gene ontology and pathway enrichment analysis using EnrichR. It is found that a total of 9 miRNAs are deregulated, out of which 2 were upregulated (hsa-mir-3614-5p and hsa-mir-3614-3p) and 7 were downregulated (hsa-mir-17-5p, hsa-mir-106a-5p, hsa-mir-17-3p, hsa-mir-181d-5p, hsa-mir-93-3p, hsa-mir-28-5p, and hsa-mir-100-5p). These miRNAs help us to classify the diseased and healthy control patients accurately. Moreover, it is also found that crucial target genes (UBC and UBB) of 4 signature miRNAs interact with viral replicase polyprotein 1ab of SARS-Coronavirus. As a result, it is noted that the virus hijacks key immune pathways like various cancer and virus infection pathways and molecular functions such as ubiquitin ligase binding and transcription corepressor and coregulator binding.
Collapse
Affiliation(s)
- Rajesh Das
- Department of Bioinformatics, Pondicherry University, RV Nagar, Kalapet, Puducherry, 605014, India
| | | | - Dahrii Paul
- Department of Bioinformatics, Pondicherry University, RV Nagar, Kalapet, Puducherry, 605014, India
| | - Amouda Venkatesan
- Department of Bioinformatics, Pondicherry University, RV Nagar, Kalapet, Puducherry, 605014, India.
| |
Collapse
|
3
|
Haghir Ebrahim Abadi MH, Ghasemlou A, Bayani F, Sefidbakht Y, Vosough M, Mozaffari-Jovin S, Uversky VN. AI-driven covalent drug design strategies targeting main protease (m pro) against SARS-CoV-2: structural insights and molecular mechanisms. J Biomol Struct Dyn 2024:1-29. [PMID: 38287509 DOI: 10.1080/07391102.2024.2308769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024]
Abstract
The emergence of new SARS-CoV-2 variants has raised concerns about the effectiveness of COVID-19 vaccines. To address this challenge, small-molecule antivirals have been proposed as a crucial therapeutic option. Among potential targets for anti-COVID-19 therapy, the main protease (Mpro) of SARS-CoV-2 is important due to its essential role in the virus's life cycle and high conservation. The substrate-binding region of the core proteases of various coronaviruses, including SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), could be used for the generation of new protease inhibitors. Various drug discovery methods have employed a diverse range of strategies, targeting both monomeric and dimeric forms, including drug repurposing, integrating virtual screening with high-throughput screening (HTS), and structure-based drug design, each demonstrating varying levels of efficiency. Covalent inhibitors, such as Nirmatrelvir and MG-101, showcase robust and high-affinity binding to Mpro, exhibiting stable interactions confirmed by molecular docking studies. Development of effective antiviral drugs is imperative to address potential pandemic situations. This review explores recent advances in the search for Mpro inhibitors and the application of artificial intelligence (AI) in drug design. AI leverages vast datasets and advanced algorithms to streamline the design and identification of promising Mpro inhibitors. AI-driven drug discovery methods, including molecular docking, predictive modeling, and structure-based drug repurposing, are at the forefront of identifying potential candidates for effective antiviral therapy. In a time when COVID-19 potentially threat global health, the quest for potent antiviral solutions targeting Mpro could be critical for inhibiting the virus.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | | | - Fatemeh Bayani
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sina Mozaffari-Jovin
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
| |
Collapse
|
4
|
Gavilán E, Medina-Guzman R, Bahatyrevich-Kharitonik B, Ruano D. Protein Quality Control Systems and ER Stress as Key Players in SARS-CoV-2-Induced Neurodegeneration. Cells 2024; 13:123. [PMID: 38247815 PMCID: PMC10814689 DOI: 10.3390/cells13020123] [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: 11/29/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The COVID-19 pandemic has brought to the forefront the intricate relationship between SARS-CoV-2 and its impact on neurological complications, including potential links to neurodegenerative processes, characterized by a dysfunction of the protein quality control systems and ER stress. This review article explores the role of protein quality control systems, such as the Unfolded Protein Response (UPR), the Endoplasmic Reticulum-Associated Degradation (ERAD), the Ubiquitin-Proteasome System (UPS), autophagy and the molecular chaperones, in SARS-CoV-2 infection. Our hypothesis suggests that SARS-CoV-2 produces ER stress and exploits the protein quality control systems, leading to a disruption in proteostasis that cannot be solved by the host cell. This disruption culminates in cell death and may represent a link between SARS-CoV-2 and neurodegeneration.
Collapse
Affiliation(s)
- Elena Gavilán
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
| | - Rafael Medina-Guzman
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
| | - Bazhena Bahatyrevich-Kharitonik
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
| | - Diego Ruano
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
| |
Collapse
|
5
|
Lear TB, Boudreau ÁN, Lockwood KC, Chu E, Camarco DP, Cao Q, Nguyen M, Evankovich JW, Finkel T, Liu Y, Chen BB. E3 ubiquitin ligase ZBTB25 suppresses beta coronavirus infection through ubiquitination of the main viral protease MPro. J Biol Chem 2023; 299:105388. [PMID: 37890782 PMCID: PMC10679490 DOI: 10.1016/j.jbc.2023.105388] [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: 05/19/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The main protease of severe acute respiratory syndrome coronavirus 2, Mpro, is a key viral protein essential for viral infection and replication. Mpro has been the target of many pharmacological efforts; however, the host-specific regulation of Mpro protein remains unclear. Here, we report the ubiquitin-proteasome-dependent degradation of Mpro protein in human cells, facilitated by the human E3 ubiquitin ligase ZBTB25. We demonstrate that Mpro has a short half-life that is prolonged via proteasomal inhibition, with its Lys-100 residue serving as a potential ubiquitin acceptor. Using in vitro binding assays, we observed ZBTB25 and Mpro bind to each other in vitro, and using progressive deletional mapping, we further uncovered the required domains for this interaction. Finally, we used an orthologous beta-coronavirus infection model and observed that genetic ablation of ZBTB25 resulted in a more highly infective virus, an effect lost upon reconstitution of ZBTB25 to deleted cells. In conclusion, these data suggest a new mechanism of Mpro protein regulation as well as identify ZBTB25 as an anticoronaviral E3 ubiquitin ligase.
Collapse
Affiliation(s)
- Travis B Lear
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Áine N Boudreau
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - Karina C Lockwood
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - Elise Chu
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - Daniel P Camarco
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - Qing Cao
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Matthew Nguyen
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - John W Evankovich
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Toren Finkel
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yuan Liu
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bill B Chen
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
| |
Collapse
|
6
|
Zheng Y, Yang H, Zhang X, Gao C. Regulation of SARS-CoV-2 infection and antiviral innate immunity by ubiquitination and ubiquitin-like conjugation. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194984. [PMID: 37717938 DOI: 10.1016/j.bbagrm.2023.194984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/30/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
A global pandemic COVID-19 resulting from SARS-CoV-2 has affected a significant portion of the human population. Antiviral innate immunity is critical for controlling and eliminating the viral infection. Ubiquitination is extensively involved in antiviral signaling, and recent studies suggest that ubiquitin-like proteins (Ubls) modifications also participate in innate antiviral pathways such as RLR and cGAS-STING pathways. Notably, virus infection harnesses ubiquitination and Ubls modifications to facilitate viral replication and counteract innate antiviral immunity. These observations indicate that ubiquitination and Ubls modifications are critical checkpoints for the tug-of-war between virus and host. This review discusses the current progress regarding the modulation of the SARS-CoV-2 life cycle and antiviral innate immune pathways by ubiquitination and Ubls modifications. This paper emphasizes the arising concept that ubiquitination and Ubls modifications are powerful modulators of virus and host interaction and potential drug targets for treating the infection of SARS-CoV-2.
Collapse
Affiliation(s)
- Yi Zheng
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China.
| | - Huiyu Yang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Xuejing Zhang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Chengjiang Gao
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China.
| |
Collapse
|