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1
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Lee JH, Sergi C, Kast RE, Kanwar BA, Bourbeau J, Oh S, Sohn MG, Lee CJ, Coleman MD. Aggravating mechanisms from COVID-19. Virol J 2024; 21:228. [PMID: 39334442 PMCID: PMC11430051 DOI: 10.1186/s12985-024-02506-8] [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: 08/08/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces immune-mediated diseases. The pathophysiology of COVID-19 uses the following three mechanisms: (1) inflammasome activation mechanism; (2) cGAS-STING signaling mechanism; and (3) SAMHD1 tetramerization mechanism, which leads to IFN-I production. Interactions between the host and virus govern induction, resulting in multiorgan impacts. The NLRP3 with cGAS-STING constitutes the primary immune response. The expression of SARS-CoV-2 ORF3a, NSP6, NSP7, and NSP8 blocks innate immune activation and facilitates virus replication by targeting the RIG-I/MDA5, TRIF, and cGAS-STING signaling. SAMHD1 has a target motif for CDK1 to protect virion assembly, threonine 592 to modulate a catalytically active tetramer, and antiviral IFN responses to block retroviral infection. Plastic and allosteric nucleic acid binding of SAMHD1 modulates the antiretroviral activity of SAMHD1. Therefore, inflammasome activation, cGAS-STING signaling, and SAMHD1 tetramerization explain acute kidney injury, hepatic, cardiac, neurological, and gastrointestinal injury of COVID-19. It might be necessary to effectively block the pathological courses of diverse diseases.
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Affiliation(s)
- Jong Hoon Lee
- Science and Research Center, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Department of Geriatrics, Gyeonggi Medical Center Pocheon Hospital, 1648 Pocheon-ro Sin-eup-dong, Pocheon-si, Gyeonggi-do, 11142, Republic of Korea.
| | - Consolato Sergi
- Division of Anatomical Pathology, Children's Hospital of Eastern Ontario (CHEO), University of Ottawa, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
| | - Richard E Kast
- IIAIGC Study Center, 11 Arlington Ct, Burlington, 05408 VT, USA
| | - Badar A Kanwar
- Haider Associates, 1999 Forest Ridge Dr, Bedford, TX, 76021, USA
| | - Jean Bourbeau
- Respiratory Epidemiology and Clinical Research Unit, McGill University Health Centre, Montréal, QC, Canada
| | - Sangsuk Oh
- Department of Food Engineering, Food Safety Laboratory, Memory Unit, Ewha Womans University, Seoul, 03670, Korea
| | - Mun-Gi Sohn
- Department of Food Science, KyungHee University College of Life Science, Seoul, 17104, Republic of Korea
| | - Chul Joong Lee
- Department of Anesthesiology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Michael D Coleman
- College of Health and Life Sciences, Aston University, Birmingham, B4 7ET, UK.
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2
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Diogo MA, Cabral AGT, de Oliveira RB. Advances in the Search for SARS-CoV-2 M pro and PL pro Inhibitors. Pathogens 2024; 13:825. [PMID: 39452697 PMCID: PMC11510351 DOI: 10.3390/pathogens13100825] [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: 08/20/2024] [Revised: 09/19/2024] [Accepted: 09/22/2024] [Indexed: 10/26/2024] Open
Abstract
SARS-CoV-2 is a spherical, positive-sense, single-stranded RNA virus with a large genome, responsible for encoding both structural proteins, vital for the viral particle's architecture, and non-structural proteins, critical for the virus's replication cycle. Among the non-structural proteins, two cysteine proteases emerge as promising molecular targets for the design of new antiviral compounds. The main protease (Mpro) is a homodimeric enzyme that plays a pivotal role in the formation of the viral replication-transcription complex, associated with the papain-like protease (PLpro), a cysteine protease that modulates host immune signaling by reversing post-translational modifications of ubiquitin and interferon-stimulated gene 15 (ISG15) in host cells. Due to the importance of these molecular targets for the design and development of novel anti-SARS-CoV-2 drugs, the purpose of this review is to address aspects related to the structure, mechanism of action and strategies for the design of inhibitors capable of targeting the Mpro and PLpro. Examples of covalent and non-covalent inhibitors that are currently being evaluated in preclinical and clinical studies or already approved for therapy will be also discussed to show the advances in medicinal chemistry in the search for new molecules to treat COVID-19.
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Affiliation(s)
| | | | - Renata Barbosa de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.A.D.); (A.G.T.C.)
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3
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Prokop JW, Alberta S, Witteveen-Lane M, Pell S, Farag HA, Bhargava D, Vaughan RM, Frisch A, Bauss J, Bhatti H, Arora S, Subrahmanya C, Pearson D, Goodyke A, Westgate M, Cook TW, Mitchell JT, Zieba J, Sims MD, Underwood A, Hassouna H, Rajasekaran S, Tamae Kakazu MA, Chesla D, Olivero R, Caulfield AJ. SARS-CoV-2 Genotyping Highlights the Challenges in Spike Protein Drift Independent of Other Essential Proteins. Microorganisms 2024; 12:1863. [PMID: 39338537 PMCID: PMC11433680 DOI: 10.3390/microorganisms12091863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/22/2024] [Accepted: 08/27/2024] [Indexed: 09/30/2024] Open
Abstract
As of 2024, SARS-CoV-2 continues to propagate and drift as an endemic virus, impacting healthcare for years. The largest sequencing initiative for any species was initiated to combat the virus, tracking changes over time at a full virus base-pair resolution. The SARS-CoV-2 sequencing represents a unique opportunity to understand selective pressures and viral evolution but requires cross-disciplinary approaches from epidemiology to functional protein biology. Within this work, we integrate a two-year genotyping window with structural biology to explore the selective pressures of SARS-CoV-2 on protein insights. Although genotype and the Spike (Surface Glycoprotein) protein continue to drift, most SARS-CoV-2 proteins have had few amino acid alterations. Within Spike, the high drift rate of amino acids involved in antibody evasion also corresponds to changes within the ACE2 binding pocket that have undergone multiple changes that maintain functional binding. The genotyping suggests selective pressure for receptor specificity that could also confer changes in viral risk. Mapping of amino acid changes to the structures of the SARS-CoV-2 co-transcriptional complex (nsp7-nsp14), nsp3 (papain-like protease), and nsp5 (cysteine protease) proteins suggest they remain critical factors for drug development that will be sustainable, unlike those strategies targeting Spike.
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Affiliation(s)
- Jeremy W. Prokop
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Sheryl Alberta
- Advanced Technology Lab, Corewell Health, Grand Rapids, MI 49503, USA; (S.A.); (S.P.)
| | - Martin Witteveen-Lane
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - Samantha Pell
- Advanced Technology Lab, Corewell Health, Grand Rapids, MI 49503, USA; (S.A.); (S.P.)
| | - Hosam A. Farag
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - Disha Bhargava
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Robert M. Vaughan
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Austin Frisch
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Jacob Bauss
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Humza Bhatti
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Sanjana Arora
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - Charitha Subrahmanya
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - David Pearson
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - Austin Goodyke
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - Mason Westgate
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - Taylor W. Cook
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Jackson T. Mitchell
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Jacob Zieba
- Genetics and Genome Sciences Program, BioMolecular Science, Michigan State University, East Lansing, MI 48824, USA;
| | - Matthew D. Sims
- Section of Infectious Diseases, Corewell Health, Royal Oak, MI 48073, USA;
- Department of Internal Medicine, Oakland University William Beaumont School of Medicine, Auburn Hills, MI 48309, USA
| | - Adam Underwood
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA;
| | - Habiba Hassouna
- Adult Infectious Disease, Corewell Health, Grand Rapids, MI 49503, USA;
| | - Surender Rajasekaran
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Maximiliano A. Tamae Kakazu
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
- Division of Pulmonary and Critical Care Medicine, Corewell Health, Grand Rapids, MI 49503, USA
| | - Dave Chesla
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Rosemary Olivero
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
- Pediatric Infectious Disease, Helen DeVos Children’s Hospital, Corewell Health, Grand Rapids, MI 49503, USA
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Karahmet Sher E, Alebić M, Marković Boras M, Boškailo E, Karahmet Farhat E, Karahmet A, Pavlović B, Sher F, Lekić L. Nanotechnology in medicine revolutionizing drug delivery for cancer and viral infection treatments. Int J Pharm 2024; 660:124345. [PMID: 38885775 DOI: 10.1016/j.ijpharm.2024.124345] [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: 02/26/2024] [Revised: 06/04/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
Advancements in nanotechnology were vastly applied in medicine and pharmacy, especially in the field of nano-delivery systems. It took a long time for these systems to ensure precise delivery of very delicate molecules, such as RNA, to cells at concentrations that yield remarkable efficiency, with success rates reaching 95.0% and 94.5%. These days, there are several advantages of using nanotechnological solutions in the prevention and treatment of cancer and viral infections. Its interventions improve treatment outcomes both due to increased effectiveness of the drug at target location and by reducing adverse reactions, thereby increasing patient adherence to the therapy. Based on the current knowledge an updated review was made, and perspective, opportunities and challenges in nanomedicine were discussed. The methods employed include comprehensive examination of existing literature and studies on nanoparticles and nano-delivery systems including both in vitro tests performed on cell cultures and in vivo assessments carried out on appropriate animal models, with a specific emphasis on their applications in oncology and virology. This brings together various aspects including both structure and formation as well as its association with characteristic behaviour in organisms, providing a novel perspective. Furthermore, the practical application of these systems in medicine and pharmacy with a focus on viral diseases and malignancies was explored. This review can serve as a valuable guide for fellow researchers, helping them navigate the abundance of findings in this field. The results indicate that applications of nanotechnological solutions for the delivery of medicinal products improving therapeutic outcomes will continue to expand.
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Affiliation(s)
- Emina Karahmet Sher
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom.
| | - Mirna Alebić
- Department of Pharmacy, University Hospital Centre Zagreb, Zagreb 10000, Croatia
| | - Marijana Marković Boras
- Department of Laboratory Diagnostic, University Clinical Hospital Mostar, Mostar 88000, Bosnia and Herzegovina; International Society of Engineering Science and Technology, Nottingham, United Kingdom
| | - Emina Boškailo
- International Society of Engineering Science and Technology, Nottingham, United Kingdom
| | - Esma Karahmet Farhat
- International Society of Engineering Science and Technology, Nottingham, United Kingdom; Department of Food and Nutrition, Faculty of Food Technology, Juraj Strossmayer University of Osijek, Osijek 31000, Croatia
| | - Alma Karahmet
- International Society of Engineering Science and Technology, Nottingham, United Kingdom
| | - Bojan Pavlović
- Faculty of Physical Education and Sports, University of East Sarajevo, Lukavica, Republika Srpska 75327, Bosnia and Herzegovina
| | - Farooq Sher
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom.
| | - Lana Lekić
- Faculty of Health Studies, University of Sarajevo, Sarajevo 71000, Bosnia and Herzegovina
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Aminiranjbar Z, Gultakti CA, Alangari MN, Wang Y, Demir B, Koker Z, Das AK, Anantram MP, Oren EE, Hihath J. Identifying SARS-CoV-2 Variants Using Single-Molecule Conductance Measurements. ACS Sens 2024; 9:2888-2896. [PMID: 38773960 DOI: 10.1021/acssensors.3c02734] [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] [Indexed: 05/24/2024]
Abstract
The global COVID-19 pandemic has highlighted the need for rapid, reliable, and efficient detection of biological agents and the necessity of tracking changes in genetic material as new SARS-CoV-2 variants emerge. Here, we demonstrate that RNA-based, single-molecule conductance experiments can be used to identify specific variants of SARS-CoV-2. To this end, we (i) select target sequences of interest for specific variants, (ii) utilize single-molecule break junction measurements to obtain conductance histograms for each sequence and its potential mutations, and (iii) employ the XGBoost machine learning classifier to rapidly identify the presence of target molecules in solution with a limited number of conductance traces. This approach allows high-specificity and high-sensitivity detection of RNA target sequences less than 20 base pairs in length by utilizing a complementary DNA probe capable of binding to the specific target. We use this approach to directly detect SARS-CoV-2 variants of concerns B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) and further demonstrate that the specific sequence conductance is sensitive to nucleotide mismatches, thus broadening the identification capabilities of the system. Thus, our experimental methodology detects specific SARS-CoV-2 variants, as well as recognizes the emergence of new variants as they arise.
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Affiliation(s)
- Zahra Aminiranjbar
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
| | - Caglanaz Akin Gultakti
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Mashari Nasser Alangari
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
- Department of Electrical Engineering, University of Hail, Hail 2240, Saudi Arabia
| | - Yiren Wang
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Zeynep Koker
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Arindam K Das
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
- Department of Computer Science and Electrical Engineering, Eastern Washington University, Cheney, Washington 99004,United States
| | - M P Anantram
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Joshua Hihath
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
- Center for Bioelectronics and Biosensors, School of Electrical, Computer, and Energy Engineering, Arizona State University, Phoenix, Arizona 85287, United States
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6
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Du M, Johnston K, Berrocal V, Li W, Xu X, Yu Z. ULV: A robust statistical method for clustered data, with applications to multi-subject, single-cell omics data. ARXIV 2024:arXiv:2406.06767v1. [PMID: 38947924 PMCID: PMC11213121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Molecular and genomic technological advancements have greatly enhanced our understanding of biological processes by allowing us to quantify key biological variables such as gene expression, protein levels, and microbiome compositions. These breakthroughs have enabled us to achieve increasingly higher levels of resolution in our measurements, exemplified by our ability to comprehensively profile biological information at the single-cell level. However, the analysis of such data faces several critical challenges: limited number of individuals, non-normality, potential dropouts, outliers, and repeated measurements from the same individual. In this article, we propose a novel method, which we call U-statistic based latent variable (ULV). Our proposed method takes advantage of the robustness of rank-based statistics and exploits the statistical efficiency of parametric methods for small sample sizes. It is a computationally feasible framework that addresses all the issues mentioned above simultaneously. We show that our method controls false positives at desired significance levels. An additional advantage of ULV is its flexibility in modeling various types of single-cell data, including both RNA and protein abundance. The usefulness of our method is demonstrated in two studies: a single-cell proteomics study of acute myelogenous leukemia (AML) and a single-cell RNA study of COVID-19 symptoms. In the AML study, ULV successfully identified differentially expressed proteins that would have been missed by the pseudobulk version of the Wilcoxon rank-sum test. In the COVID-19 study, ULV identified genes associated with covariates such as age and gender, and genes that would be missed without adjusting for covariates. The differentially expressed genes identified by our method are less biased toward genes with high expression levels. Furthermore, ULV identified additional gene pathways likely contributing to the mechanisms of COVID-19 severity.
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Affiliation(s)
- Mingyu Du
- Center for Complex Biological Systems, University of California, Irvine, 92697, CA, USA
| | - Kevin Johnston
- Department of Anatomy and Neurobiology, University of California, Irvine, 92697, CA, USA
| | - Veronica Berrocal
- Department of Statistics, University of California, Irvine, 92697, CA, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, 92697, CA, USA
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, University of California, Irvine, 92697, CA, USA
- Center for Neural Circuits Mapping, University of California, Irvine, 92697, CA, USA
| | - Zhaoxia Yu
- Department of Statistics, University of California, Irvine, 92697, CA, USA
- Center for Neural Circuits Mapping, University of California, Irvine, 92697, CA, USA
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7
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Yousefi Rad A, Rastegari AA, Shahanipour K, Monajemi R. Moringa oleifera and Its Biochemical Compounds: Potential Multi-targeted Therapeutic Agents Against COVID-19 and Associated Cancer Progression. Biochem Genet 2024:10.1007/s10528-024-10758-w. [PMID: 38583096 DOI: 10.1007/s10528-024-10758-w] [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: 08/22/2023] [Accepted: 02/23/2024] [Indexed: 04/08/2024]
Abstract
The Coronavirus disease-2019 (COVID-19) pandemic is a global concern, with updated pharmacological therapeutic strategies needed. Cancer patients have been found to be more susceptible to severe COVID-19 and death, and COVID-19 can also lead to cancer progression. Traditional medicinal plants have long been used as anti-infection and anti-inflammatory agents, and Moringa oleifera (M. oleifera) is one such plant containing natural products such as kaempferol, quercetin, and hesperetin, which can reduce inflammatory responses and complications associated with viral infections and multiple cancers. This review article explores the cellular and molecular mechanisms of action of M. oleifera as an anti-COVID-19 and anti-inflammatory agent, and its potential role in reducing the risk of cancer progression in cancer patients with COVID-19. The article discusses the ability of M. oleifera to modulate NF-κB, MAPK, mTOR, NLRP3 inflammasome, and other inflammatory pathways, as well as the polyphenols and flavonoids like quercetin and kaempferol, that contribute to its anti-inflammatory properties. Overall, this review highlights the potential therapeutic benefits of M. oleifera in addressing COVID-19 and associated cancer progression. However, further investigations are necessary to fully understand the cellular and molecular mechanisms of action of M. oleifera and its natural products as anti-inflammatory, anti-COVID-19, and anti-cancer strategies.
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Affiliation(s)
- Ali Yousefi Rad
- Department of Biochemistry, Falavarjan Branch, Islamic Azad University, Esfahan, Iran
| | - Ali Asghar Rastegari
- Department of Molecular and Cell Biochemistry, Falavarjan Branch, Islamic Azad University, Esfahan, Iran.
| | - Kahin Shahanipour
- Department of Biochemistry, Falavarjan Branch, Islamic Azad University, Esfahan, Iran
| | - Ramesh Monajemi
- Department of Biology, Falavarjan Branch, Islamic Azad University, Esfahan, Iran
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Wang F, Liu D, Gao D, Yuan J, Zhao J, Yuan S, Cen Y, Lin GQ, Zhao J, Tian P. Discovery of natural catechol derivatives as covalent SARS-CoV-2 3CL pro inhibitors. Int J Biol Macromol 2024; 264:130377. [PMID: 38395279 DOI: 10.1016/j.ijbiomac.2024.130377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a threat to public health, and extensive research by scientists worldwide has also prompted the development of antiviral therapies. The 3C-like protease (3CLpro) is critical for SARS-CoV-2 replication and acts as an effective target for drug development. To date, numerous of natural products have been reported to exhibit inhibitory effects on 3CLpro, which encourages us to identify other novel inhibitors and elucidate their mechanism of action. In this study, we first screened an in-house compound library of 101 natural products using FRET assay, and found that oleuropein showed good inhibitory activity against SARS CoV-2 3CLpro with an IC50 value of 4.18 μM. Further studies revealed that the catechol core is essential for activity and can covalently bind to SARS-CoV-2 3CLpro. Among other 45 catechol derivatives, wedelolactone, capsazepine and brazilin showed better SARS-CoV-2 3CLpro inhibitory activities with IC50 values of 1.35 μM, 1.95 μM and 1.18 μM, respectively. These catechol derivatives were verified to be irreversible covalent inhibitors by time-dependent experiments, enzymatic kinetic studies, dilution and dialysis assays. It also exhibited good selectivity towards different cysteine proteases (SARS-CoV-2 PLpro, cathepsin B and cathepsin L). Subsequently, the binding affinity between brazilin and SARS-CoV-2 3CLpro was determined by SPR assay with KD value of 0.80 μM. Molecular dynamic (MD) simulations study showed the binding mode of brazilin in the target protein. In particular, brazilin displayed good anti-SARS-CoV-2 activity in A549-hACE2-TMPRSS2 cells with EC50 values of 7.85 ± 0.20 μM and 5.24 ± 0.21 μM for full time and post-infection treatments, respectively. This study provides a promising lead compound for the development of novel anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Feng Wang
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China; Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong 510320, China
| | - Dingding Gao
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Jinwei Yuan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Shuai Yuan
- Health and Quarantine Laboratory, Guangzhou Customs District Technology Center, Guangzhou 510700, China
| | - Yixin Cen
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Guo-Qiang Lin
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China; Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong 510320, China; Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Ping Tian
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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9
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Zhu C, Pang S, Liu J, Duan Q. Current Progress, Challenges and Prospects in the Development of COVID-19 Vaccines. Drugs 2024; 84:403-423. [PMID: 38652356 DOI: 10.1007/s40265-024-02013-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2024] [Indexed: 04/25/2024]
Abstract
The COVID-19 pandemic has resulted in over 772 million confirmed cases, including nearly 7 million deaths, according to the World Health Organization (WHO). Leveraging rapid development, accelerated vaccine approval processes, and large-scale production of various COVID-19 vaccines using different technical platforms, the WHO declared an end to the global health emergency of COVID-19 on May 5, 2023. Current COVID-19 vaccines encompass inactivated, live attenuated, viral vector, protein subunit, nucleic acid (DNA and RNA), and virus-like particle (VLP) vaccines. However, the efficacy of these vaccines is diminishing due to the constant mutation of SARS-CoV-2 and the heightened immune evasion abilities of emerging variants. This review examines the impact of the COVID-19 pandemic, the biological characteristics of the virus, and its diverse variants. Moreover, the review underscores the effectiveness, advantages, and disadvantages of authorized COVID-19 vaccines. Additionally, it analyzes the challenges, strategies, and future prospects of developing a safe, broad-spectrum vaccine that confers sufficient and sustainable immune protection against new variants of SARS-CoV-2. These discussions not only offer insight for the development of next-generation COVID-19 vaccines but also summarize experiences for combating future emerging viruses.
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Affiliation(s)
- Congrui Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510000, China
| | - Shengmei Pang
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Jiaqi Liu
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Qiangde Duan
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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10
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Kakavandi S, Hajikhani B, Azizi P, Aziziyan F, Nabi-Afjadi M, Farani MR, Zalpoor H, Azarian M, Saadi MI, Gharesi-Fard B, Terpos E, Zare I, Motamedifar M. COVID-19 in patients with anemia and haematological malignancies: risk factors, clinical guidelines, and emerging therapeutic approaches. Cell Commun Signal 2024; 22:126. [PMID: 38360719 PMCID: PMC10868124 DOI: 10.1186/s12964-023-01316-9] [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: 07/20/2023] [Accepted: 09/13/2023] [Indexed: 02/17/2024] Open
Abstract
Extensive research in countries with high sociodemographic indices (SDIs) to date has shown that coronavirus disease 2019 (COVID-19) may be directly associated with more severe outcomes among patients living with haematological disorders and malignancies (HDMs). Because individuals with moderate to severe immunodeficiency are likely to undergo persistent infections, shed virus particles for prolonged periods, and lack an inflammatory or abortive phase, this represents an overall risk of morbidity and mortality from COVID-19. In cases suffering from HDMs, further investigation is needed to achieve a better understanding of triviruses and a group of related variants in patients with anemia and HDMs, as well as their treatment through vaccines, drugs, and other methods. Against this background, the present study aimed to delineate the relationship between HDMs and the novel COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Besides, effective treatment options for HDM cases were further explored to address this epidemic and its variants. Therefore, learning about how COVID-19 manifests in these patients, along with exploiting the most appropriate treatments, may lead to the development of treatment and care strategies by clinicians and researchers to help patients recover faster. Video Abstract.
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Affiliation(s)
- Sareh Kakavandi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Paniz Azizi
- Psychological and Brain Science Departments, Program in Neuroscience, Indiana University, Bloomington, IN, USA
| | - Fatemeh Aziziyan
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohsen Nabi-Afjadi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Marzieh Ramezani Farani
- Department of Biological Sciences and Bioengineering, Nano Bio High-Tech Materials Research Center, Inha University, Incheon, 22212, Republic of Korea
| | - Hamidreza Zalpoor
- Student Research Committee, Fasa University of Medical Sciences, Fasa, Iran
- Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Maryam Azarian
- Department of Radiology, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | | | | | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co., Ltd., Shiraz, 7178795844, Iran.
| | - Mohammad Motamedifar
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
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11
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Edalat F, Khakpour N, Heli H, Letafati A, Ramezani A, Hosseini SY, Moattari A. Immunological mechanisms of the nucleocapsid protein in COVID-19. Sci Rep 2024; 14:3711. [PMID: 38355695 PMCID: PMC10867304 DOI: 10.1038/s41598-024-53906-3] [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: 09/24/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
The emergence of corona virus disease 2019 (COVID-19), resulting from Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has left an indelible mark on a global scale, causing countless infections and fatalities. This investigation delves into the role of the SARS-CoV-2 nucleocapsid (N) protein within the HEK293 cells, shedding light on its influence over apoptosis, interferon signaling, and cytokines production. The N gene was amplified, inserted into the pAdTrack-CMV vector, and then transfected to the HEK293 cells. Changes in the expression of IRF3, IRF7, IFN-β, BAK, BAX, and BCL-2 genes were evaluated. The levels of proinflammatory cytokines of IL-6, IL-12, IL-1β, and TNF-α were also determined. The N protein exhibited an anti-apoptotic effect by modulating critical genes associated with apoptosis, including BAK, BAX, and BCL-2. This effect potentially prolonged the survival of infected cells. The N protein also played a role in immune evasion by suppressing the interferon pathway, evidenced by the downregulation of essential interferon regulatory factors of IRF3 and IRF7, and IFN-β expression. The N protein expression led to a substantial increase in the production of proinflammatory cytokines of IL-6, IL-12, IL-1β, and TNF-α. The N protein emerged as a versatile factor and was exerted over apoptosis, interferon signaling, and cytokine production. These findings carry potential implications for the development of targeted therapies to combat COVID-19 and mitigate its global health impact.
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Affiliation(s)
- Fahime Edalat
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Niloofar Khakpour
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hossein Heli
- Nanomedicine and Nanobiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arash Letafati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Amin Ramezani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Science, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Younes Hosseini
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran.
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12
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Boonserm P, Somsoros W, Khunrae P, Charupanit K, Limsakul P, Sutthibutpong T. Allosteric Signal within the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein Mediated by a Class 3 Monoclonal Antibody Revealed through Molecular Dynamics Simulations and Protein Residue Networks. ACS OMEGA 2024; 9:4684-4694. [PMID: 38313482 PMCID: PMC10831861 DOI: 10.1021/acsomega.3c07947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/26/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
This study investigated the allosteric action within the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein caused by class 3 monoclonal antibody (mAb) binding. As the emergence of SARS-CoV-2 variants has raised concerns about the effectiveness of treatments by antibodies, targeting the highly conserved class 3 epitopes has become an alternative strategy of antibody design. Simulations of explicitly solvated RBD of the BA.2.75 omicron subvariants were carried out both in the presence and in the absence of bebtelovimab, as a model example of class 3 monoclonal antibodies against the RBD of the SARS-CoV-2 spike protein. The comparative analysis showed that bebtelovimab's binding on two α helices at the epitope region disrupted the nearby interaction network, which triggered a denser interaction network formation on the opposite side of the receptor-binding motif (RBM) region and resulted in a "close" conformation that could prevent the ACE2 binding. A better understanding of this allosteric action could lead to the development of alternative mAbs for further variants of concern. In terms of computational techniques, the communicability matrix could serve as a tool to visualize the effects of allostery, as the pairs of amino acids or secondary structures with high communicability could pinpoint the possible sites to transfer the allosteric signal. Additionally, the communicability gain/loss matrix could help elucidate the consequences of allosteric actions, which could be employed along with other allostery quantification techniques in some previous studies.
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Affiliation(s)
- Patamalai Boonserm
- Department
of Microbiology, Faculty of Science, King
Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Wasusit Somsoros
- Department
of Microbiology, Faculty of Science, King
Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Pongsak Khunrae
- Department
of Microbiology, Faculty of Science, King
Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Krit Charupanit
- Department
of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Praopim Limsakul
- Division
of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
- Center
of Excellence for Trace Analysis and Biosensor (TAB-CoE), Faculty
of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Thana Sutthibutpong
- Theoretical
and Computational Physics Group, Department of Physics, Faculty of
Science, King Mongkut’s University
of Technology Thonburi, Bangkok 10140, Thailand
- Center
of
Excellence in Theoretical and Computational Science (TACS-CoE), Faculty
of Science, King Mongkut’s University
of Technology Thonburi, Bangkok 10140, Thailand
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13
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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.
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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
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14
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Dobrek Ł. A review on the current approaches and perspectives of Covid-19 treatment. POLSKI MERKURIUSZ LEKARSKI : ORGAN POLSKIEGO TOWARZYSTWA LEKARSKIEGO 2024; 52:337-346. [PMID: 39007473 DOI: 10.36740/merkur202403111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
At the beginning of 2020, the world was faced with the challenge of the coronavirus disease 2019 (COVID-19) pandemic announced by the WHO on March 11, caused by the betacoronavirus type 2 of the severe acute respiratory syndrome (SARS-CoV-2), which had profound health, sociological and even economic consequences. The quickly implemented and large-scale research resulted in the introduction of widely available vaccines that reduced the further development of the pandemic and antivirals against SARS-CoV-2. Currently, 11 antiviral drugs (Tixagevimab/Cilgavimab, Regdanvimab, Casirivimab/Imdevimab, Sotrovimab, Nirmatrelvir/Ritonavir, Remdesivir, Molnupiravir, Baricitinib, Anakinra, Tocilizumab, Vilobelimab) have been approved or conditionally approved by the European Medicines Agency and/or by the Food and Drug Administration and are available on the pharmaceutical market. The progress in the pathophysiological description of the SARS-CoV-2 infection has allowed the identif i cation of potential targets for drugs against SARS-CoV-2: inhibitors of intracellular entry of the virus (the interaction between the viral spike (S) protein and the cellular angiotensin converting enzyme-2; ACE2 receptor), inhibitors of viral and cellular proteases, and immunomodulatory drugs (antagonists of pro-inf l ammatory cytokines or complement components). Novel agents against SARS-CoV-2 are also sought among the previously routinely used drugs as their repositioning and among plant-derived compounds. It is expected that ongoing research should result in the introduction of new drugs used in COVID-19 in the near future. The article brief l y describes the current epidemiological situation regarding COVID-19 and the currently used vaccines. Moreover, the paper outlines currently used and researched potential drugs in the pharmacotherapy of this disease.
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Affiliation(s)
- Łukasz Dobrek
- FACULTY OF SCIENCE AND TECHNOLOGY, JAN DLUGOSZ UNIVERSITY IN CZESTOCHOWA, CZESTOCHOWA, POLAND
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15
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Liang JJ, Pitsillou E, Hung A, Karagiannis TC. A repository of COVID-19 related molecular dynamics simulations and utilisation in the context of nsp10-nsp16 antivirals. J Mol Graph Model 2024; 126:108666. [PMID: 37976980 DOI: 10.1016/j.jmgm.2023.108666] [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: 09/14/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of establishing systems and infrastructure to develop vaccines, antiviral drugs, and therapeutic antibodies against emerging pathogens. Typical drug discovery processes involve targeting suitable proteins to effect pathogen replication or to attenuate host responses, by examining either large chemical databases or protein-protein interactions. Following initial screens, molecular dynamics (MD) simulations are critical for gaining further insight into molecular interactions. During the COVID-19 pandemic, many research groups made their simulations widely available, as highlighted by the comprehensive D.E. Shaw Research trajectory database. To investigate protein target sites and evaluate potential lead compounds, we performed over 300 MD simulations relating to COVID-19. We organised our simulations into a repository, which is publicly available at https://epimedlab.org/trajectories/. The trajectories cover a large part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteome, and the majority of our MD simulations focused on the identification of potential antivirals. For example, we focused on the S-adenosyl-l-methionine binding site of the nsp10-nsp16 complex, a critical component of viral replication, revealing verbascoside as a potential lead. Moreover, we utilised MD trajectories to explore the interface between the spike protein receptor binding domain and human angiotensin-converting enzyme 2 receptor, with the ultimate aim being investigation of new variants in real-time. Overall, MD simulations are a critical component of the in silico drug discovery process and as highlighted throughout the pandemic, data sharing enables accelerated progress. We have organised our extensive collection of COVID-19 related MD trajectories into an easily accessible repository.
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Affiliation(s)
- Julia J Liang
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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16
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Purandare N, Ghosalkar E, Grossman LI, Aras S. Mitochondrial Oxidative Phosphorylation in Viral Infections. Viruses 2023; 15:2380. [PMID: 38140621 PMCID: PMC10747082 DOI: 10.3390/v15122380] [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: 10/25/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Mitochondria have been identified as the "powerhouse" of the cell, generating the cellular energy, ATP, for almost seven decades. Research over time has uncovered a multifaceted role of the mitochondrion in processes such as cellular stress signaling, generating precursor molecules, immune response, and apoptosis to name a few. Dysfunctional mitochondria resulting from a departure in homeostasis results in cellular degeneration. Viruses hijack host cell machinery to facilitate their own replication in the absence of a bonafide replication machinery. Replication being an energy intensive process necessitates regulation of the host cell oxidative phosphorylation occurring at the electron transport chain in the mitochondria to generate energy. Mitochondria, therefore, can be an attractive therapeutic target by limiting energy for viral replication. In this review we focus on the physiology of oxidative phosphorylation and on the limited studies highlighting the regulatory effects viruses induce on the electron transport chain.
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Affiliation(s)
- Neeraja Purandare
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (N.P.); (E.G.); (L.I.G.)
| | - Esha Ghosalkar
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (N.P.); (E.G.); (L.I.G.)
| | - Lawrence I. Grossman
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (N.P.); (E.G.); (L.I.G.)
| | - Siddhesh Aras
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (N.P.); (E.G.); (L.I.G.)
- Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
- Department of Oncology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
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17
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Sadrolvaezin A, Pezhman A, Zare I, Nasab SZ, Chamani S, Naghizadeh A, Mostafavi E. Systemic allergic contact dermatitis to palladium, platinum, and titanium: mechanisms, clinical manifestations, prevalence, and therapeutic approaches. MedComm (Beijing) 2023; 4:e386. [PMID: 37873514 PMCID: PMC10590457 DOI: 10.1002/mco2.386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 10/25/2023] Open
Abstract
Contact dermatitis (CD) is an inflammatory skin disease of eczema that is elicited by chemicals or metal ions that have toxic effects without eliciting a T-cell response (contact elicitation) or by small reactive chemicals that modify proteins and induce innate and adaptive immune responses (contact allergens). The clinical condition is characterized by localized skin rash, pruritus, redness, swelling, and lesions, which are mainly detected by patch tests and lymphocyte stimulation. Heavy metals such as palladium (Pd), platinum (Pt), and titanium (Ti) are ubiquitous in our environment. These heavy metals have shown CD effects as allergic agents. Immunological responses result from the interaction of cytokines and T cells. Occupational metal CD accounts for most cases of work-related cutaneous disorders. In this systematic review, the allergic effects of heavy metals, including Pd, Pt, and Ti, and the mechanisms, clinical manifestations, prevalence, and therapeutic approaches are discussed in detail. Furthermore, the therapeutic approaches introduced to treat CD, including corticosteroids, topical calcineurin inhibitors, systemic immunosuppressive agents, phototherapy, and antihistamines, can be effective in the treatment of these diseases in the future. Ultimately, the insights identified could lead to improved therapeutic and diagnostic pathways.
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Affiliation(s)
- Ali Sadrolvaezin
- Medical Toxicology and Drug Abuse Research CenterBirjand University of Medical SciencesBirjandIran
| | - Arezou Pezhman
- School of MedicineZahedan Azad University of Medical SciencesZahedanIran
| | - Iman Zare
- Research and Development DepartmentSina Medical Biochemistry Technologies Co. Ltd.ShirazIran
| | - Shima Zahed Nasab
- Department of Life Science EngineeringFaculty of New Sciences and TechnologiesUniversity of TehranTehranIran
| | - Sajad Chamani
- Medical Toxicology and Drug Abuse Research CenterBirjand University of Medical SciencesBirjandIran
| | - Ali Naghizadeh
- Medical Toxicology and Drug Abuse Research CenterBirjand University of Medical SciencesBirjandIran
| | - Ebrahim Mostafavi
- Stanford Cardiovascular InstituteStanford University School of MedicineStanfordCaliforniaUSA
- Department of MedicineStanford University School of MedicineStanfordCaliforniaUSA
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18
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Pitsillou E, Beh RC, Liang JJ, Tang TS, Zhou X, Siow YY, Ma Y, Hu Z, Wu Z, Hung A, Karagiannis TC. EpiMed Coronabank Chemical Collection: Compound selection, ADMET analysis, and utilisation in the context of potential SARS-CoV-2 antivirals. J Mol Graph Model 2023; 125:108602. [PMID: 37597309 DOI: 10.1016/j.jmgm.2023.108602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/21/2023]
Abstract
Antiviral drugs are important for the coronavirus disease 2019 (COVID-19) response, as vaccines and antibodies may have reduced efficacy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Antiviral drugs that have been made available for use, albeit with questionable efficacy, include remdesivir (Veklury®), nirmatrelvir-ritonavir (Paxlovid™), and molnupiravir (Lagevrio®). To expand the options available for COVID-19 and prepare for future pandemics, there is a need to investigate new uses for existing drugs and design novel compounds. To support these efforts, we have created a comprehensive library of 750 molecules that have been sourced from in vitro, in vivo, and in silico studies. It is publicly available at our dedicated website (https://epimedlab.org/crl/). The EpiMed Coronabank Chemical Collection consists of compounds that have been divided into 10 main classes based on antiviral properties, as well as the potential to be used for the management, prevention, or treatment of COVID-19 related complications. A detailed description of each compound is provided, along with the molecular formula, canonical SMILES, and U.S. Food and Drug Administration approval status. The chemical structures have been obtained and are available for download. Moreover, the pharmacokinetic properties of the ligands have been characterised. To demonstrate an application of the EpiMed Coronabank Chemical Collection, molecular docking was used to evaluate the binding characteristics of ligands against SARS-CoV-2 nonstructural and accessory proteins. Overall, our database can be used to aid the drug repositioning process, and for gaining further insight into the molecular mechanisms of action of potential compounds of interest.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Raymond C Beh
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Julia J Liang
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Thinh Sieu Tang
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Xun Zhou
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ya Yun Siow
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yinghao Ma
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Zifang Hu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Zifei Wu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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19
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Yevsieieva LV, Lohachova KO, Kyrychenko A, Kovalenko SM, Ivanov VV, Kalugin ON. Main and papain-like proteases as prospective targets for pharmacological treatment of coronavirus SARS-CoV-2. RSC Adv 2023; 13:35500-35524. [PMID: 38077980 PMCID: PMC10698513 DOI: 10.1039/d3ra06479d] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/23/2023] [Indexed: 10/16/2024] Open
Abstract
The pandemic caused by the coronavirus SARS-CoV-2 led to a global crisis in the world healthcare system. Despite some progress in the creation of antiviral vaccines and mass vaccination of the population, the number of patients continues to grow because of the spread of new SARS-CoV-2 mutations. There is an urgent need for direct-acting drugs capable of suppressing or stopping the main mechanisms of reproduction of the coronavirus SARS-CoV-2. Several studies have shown that the successful replication of the virus in the cell requires proteolytic cleavage of the protein structures of the virus. Two proteases are crucial in replicating SARS-CoV-2 and other coronaviruses: the main protease (Mpro) and the papain-like protease (PLpro). In this review, we summarize the essential viral proteins of SARS-CoV-2 required for its viral life cycle as targets for chemotherapy of coronavirus infection and provide a critical summary of the development of drugs against COVID-19 from the drug repurposing strategy up to the molecular design of novel covalent and non-covalent agents capable of inhibiting virus replication. We overview the main antiviral strategy and the choice of SARS-CoV-2 Mpro and PLpro proteases as promising targets for pharmacological impact on the coronavirus life cycle.
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Affiliation(s)
- Larysa V Yevsieieva
- School of Chemistry, V. N. Karazin Kharkiv National University 4 Svobody sq. Kharkiv 61022 Ukraine
| | - Kateryna O Lohachova
- School of Chemistry, V. N. Karazin Kharkiv National University 4 Svobody sq. Kharkiv 61022 Ukraine
| | - Alexander Kyrychenko
- School of Chemistry, V. N. Karazin Kharkiv National University 4 Svobody sq. Kharkiv 61022 Ukraine
| | - Sergiy M Kovalenko
- School of Chemistry, V. N. Karazin Kharkiv National University 4 Svobody sq. Kharkiv 61022 Ukraine
| | - Volodymyr V Ivanov
- School of Chemistry, V. N. Karazin Kharkiv National University 4 Svobody sq. Kharkiv 61022 Ukraine
| | - Oleg N Kalugin
- School of Chemistry, V. N. Karazin Kharkiv National University 4 Svobody sq. Kharkiv 61022 Ukraine
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20
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Rabaan AA, Alenazy MF, Alshehri AA, Alshahrani MA, Al-Subaie MF, Alrasheed HA, Al Kaabi NA, Thakur N, Bouafia NA, Alissa M, Alsulaiman AM, AlBaadani AM, Alhani HM, Alhaddad AH, Alfouzan WA, Ali BMA, Al-Abdulali KH, Khamis F, Bayahya A, Al Fares MA, Sharma M, Dhawan M. An updated review on pathogenic coronaviruses (CoVs) amid the emergence of SARS-CoV-2 variants: A look into the repercussions and possible solutions. J Infect Public Health 2023; 16:1870-1883. [PMID: 37839310 DOI: 10.1016/j.jiph.2023.09.004] [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: 05/04/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
SARS-CoV-2, responsible for COVID-19, shares 79% and 50% of its identity with SARS-CoV-1 and MERS-CoV, respectively. It uses the same main cell attachment and entry receptor as SARS-CoV-1, which is the ACE-2 receptor. However, key residues in the receptor-binding domain of its S-protein seem to give it a stronger affinity for the receptor and a better ability to hide from the host immune system. Like SARS-CoV-1 and MERS-CoV, cytokine storms in critically ill COVID-19 patients cause ARDS, neurological pathology, multiorgan failure, and increased death. Though many issues remain, the global research effort and lessons from SARS-CoV-1 and MERS-CoV are hopeful. The emergence of novel SARS-CoV-2 variants and subvariants raised serious concerns among the scientific community amid the emergence of other viral diseases like monkeypox and Marburg virus, which are major concerns for healthcare settings worldwide. Hence, an updated review on the comparative analysis of various coronaviruses (CoVs) has been developed, which highlights the evolution of CoVs and their repercussions.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan.
| | - Maha Fahad Alenazy
- Department of Physiology, College of Medicine, King Khalid university hospital, King Saud University, Riyadh 4545, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Maha F Al-Subaie
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Research Center, Dr. Sulaiman Alhabib Medical Group, Riyadh 13328, Saudi Arabia; Department of Infectious Diseases, Dr. Sulaiman Alhabib Medical Group, Riyadh 13328, Saudi Arabia
| | - Hayam A Alrasheed
- Department of pharmacy Practice, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia; Pharmacy Department, King Abdullah Bin Abdulaziz University Hospital, Riyadh 11671, Saudi Arabia
| | - Nawal A Al Kaabi
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, 51900, United Arab Emirates; College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Nanamika Thakur
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Nabiha A Bouafia
- Infection prevention and control centre of Excellence, Prince Sultan Medical Military City, Riyadh 12233, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | | | - Abeer M AlBaadani
- Internal Medicine Department, Infectious Disease Division, London health science Center, London, Ontario N6G0X2, Canada
| | - Hatem M Alhani
- Department of Pediatric Infectious Disease, Maternity and Children Hospital, Dammam 31176, Saudi Arabia; Department of Infection Control, Maternity and Children Hospital, Dammam 31176, Saudi Arabia; Preventive Medicine and Infection Prevention and Control Department, Directorate of Ministry of Health, Dammam 32245, Saudi Arabia
| | - Ali H Alhaddad
- Assistant Agency for Hospital Affairs, Ministry of Health, Riyadh 12382, Saudi Arabia
| | - Wadha A Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait; Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Batool Mohammed Abu Ali
- Infectious disease section, Department of internal medicine, King Fahad Hospital Hofuf, Hofuf 36365, Saudi Arabia
| | - Khadija H Al-Abdulali
- Nursing Department, Home health care, Qatif Health Network, Qatif 31911, Saudi Arabia
| | - Faryal Khamis
- Infection Diseases unit, Department of Internal Medicine, Royal Hospital, Muscat 1331, Oman
| | - Ali Bayahya
- Microbiology Department, Alqunfudah General Hospital, Alqunfudah 28813, Saudi Arabia
| | - Mona A Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia.
| | - Manish Sharma
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, India; Trafford College, Altrincham, Manchester WA14 5PQ, UK.
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21
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Grand RJ. SARS-CoV-2 and the DNA damage response. J Gen Virol 2023; 104:001918. [PMID: 37948194 PMCID: PMC10768691 DOI: 10.1099/jgv.0.001918] [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: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is characterized by respiratory distress, multiorgan dysfunction and, in some cases, death. The virus is also responsible for post-COVID-19 condition (commonly referred to as 'long COVID'). SARS-CoV-2 is a single-stranded, positive-sense RNA virus with a genome of approximately 30 kb, which encodes 26 proteins. It has been reported to affect multiple pathways in infected cells, resulting, in many cases, in the induction of a 'cytokine storm' and cellular senescence. Perhaps because it is an RNA virus, replicating largely in the cytoplasm, the effect of SARS-Cov-2 on genome stability and DNA damage responses (DDRs) has received relatively little attention. However, it is now becoming clear that the virus causes damage to cellular DNA, as shown by the presence of micronuclei, DNA repair foci and increased comet tails in infected cells. This review considers recent evidence indicating how SARS-CoV-2 causes genome instability, deregulates the cell cycle and targets specific components of DDR pathways. The significance of the virus's ability to cause cellular senescence is also considered, as are the implications of genome instability for patients suffering from long COVID.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, The Medical School, University of Birmingham, Birmingham, UK
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22
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Morimoto S. Fine structure of a partition in the spike glycoprotein encoded in the SARS-CoV-2 genome. Biosystems 2023; 232:104990. [PMID: 37611861 DOI: 10.1016/j.biosystems.2023.104990] [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: 04/07/2023] [Revised: 06/23/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023]
Abstract
The gene encoding the spike glycoprotein of the SARS-CoV-2 virus that causes COVID-19 disease, was analyzed through two types of periodic tables (standard and cube) of the genetic code to discover the internal fine structure of the spike (S) protein. The analysis was performed on the Wuhan-Hu-1 SARS-CoV-2 sequence (GenBank accession number NC_045512.2). A partition was detected between codon numbers (three-letter code numbers) 47 and 48 that code amino acids in the S-protein. The population distribution of organized codes and amino acid replacements in the S-protein showed large differences between two regions of the cube-type periodic table. The genetic codes of codon numbers 48-63 (4th plane of the cube table) had a higher frequency than the genetic codes of each of the other three planes (1st-3rd planes). Planes-linkage structures involved in the partition were also analyzed and a simplified model for the S-protein gene was obtained where a planes-linkage of the 4th plane and another planes-linkage of the 1st-3rd planes were linked together in alternate shifts. Most of the code population in the 4th plane and their planes-linkage multiformity gave additional support to the partition between codon numbers 47 and 48 in the S-protein gene. Analysis of real lineages of the SARS-CoV-2 virus through the cube-type periodic table identified distinguishing features of the Omicron lineage that included not only a large code population within the receptor-binding domain of the S-protein, but also large percentage rises in the population of amino acid replacements in the 1st and 2nd planes.
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