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Huang Y, Fang Y, Jie H, Yang H, Zhou W, Chen Y, Zhong B. Network pharmacology and molecular docking to scientifically validate the potential mechanism of Lonicerae japonicae flos in the clinical treatment of COVID-19. Nat Prod Res 2024; 38:3699-3706. [PMID: 37732603 DOI: 10.1080/14786419.2023.2260070] [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: 04/03/2023] [Accepted: 09/10/2023] [Indexed: 09/22/2023]
Abstract
Using network pharmacology and molecular docking, we predicted the potential mechanisms of Lonicerae japonicae flos (LJF) therapy for COVID-19. A total of 493 component-related targets and 6,233 COVID-19-related genes were identified, and 267 core genes with overlapping of the two types of genes were identified. The target AKT1, CASP3, IL1B, IL6, PTGS2, TNF and JUN were the hub genes in PPI network according to MCODE score. Component-Target analysis showed the close relationship between targets and components. The results of functional enrichment analyses revealed that LJF exerted pharmacological effects on COVID-19 by regulating IL-17 signalling pathway, TNF signalling pathway, AGE-RAGE signalling pathway in diabetic complications, and Toll-like receptor signalling pathway. Finally, molecular docking confirmed a strong binding affinity between the 7 main active components with the hub genes. The findings suggested that beta-sitosterol, kaempferol and luteolin might be the promising leading components due to their good molecular docking scores.
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Affiliation(s)
- Yisheng Huang
- Department of Anesthesiology, Ganzhou People's Hospital, Ganzhou, P.R. China
- Department of Anesthesiology, Nanfang Hospital Affiliated to Southern Medical University, Guangzhou, P.R. China
| | - Yan Fang
- Department of Anesthesiology, Ganzhou People's Hospital, Ganzhou, P.R. China
| | - Huanhuan Jie
- Department of Anesthesiology, Ganzhou People's Hospital, Ganzhou, P.R. China
| | - Hongbiao Yang
- Department of Anesthesiology, Ganzhou People's Hospital, Ganzhou, P.R. China
| | - Wen Zhou
- Department of Anesthesiology, Ganzhou People's Hospital, Ganzhou, P.R. China
| | - Yijian Chen
- Department of Anesthesiology, Ganzhou People's Hospital, Ganzhou, P.R. China
| | - Baolin Zhong
- Department of Anesthesiology, Ganzhou People's Hospital, Ganzhou, P.R. China
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Huynh DTN, Nguyen HT, Hsieh CM. Taiwan Chingguan Yihau may improve post-COVID-19 respiratory complications through PI3K/AKT, HIF-1, and TNF signaling pathways revealed by network pharmacology analysis. Mol Divers 2024:10.1007/s11030-024-10993-8. [PMID: 39382736 DOI: 10.1007/s11030-024-10993-8] [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: 06/08/2024] [Accepted: 09/14/2024] [Indexed: 10/10/2024]
Abstract
The emergence of new SARS-CoV-2 variants with a higher contagious capability and faster transmissible speed has imposed an incessant menace on global health and the economy. The SARS-CoV-2 infection might reoccur and last much longer than expected. Thence, there is a high possibility that COVID-19 can cause long-term health problems. This condition needs to be investigated thoroughly, especially the post-COVID-19 complications. Respiratory tract disorders are common and typical complications after recovery. Until now, there has been a lack of data on specialized therapeutic medicine for post-COVID-19 complications. The clinical efficacy of NRICM101 has been demonstrated in hospitalized COVID-19 patients. This herbal medicine may also be a promising therapy for post-COVID-19 complications, thanks to its phytochemical constituents. The potential pharmacological mechanisms of NRICM101 in treating post-COVID-19 respiratory complications were investigated using network pharmacology combined with molecular docking, and the results revealed that NRICM101 may exert a beneficial effect through the three primary pathways: PI3K/AKT, HIF-1, and TNF signaling pathways. Flavonoids (especially quercetin) have a predominant role and synergize with other active compounds to produce therapeutic effectiveness. Most of the main active compounds exist in three chief herbal ingredients, including Liquorice root (Glycyrrhiza glabra), Scutellaria root (Scutellaria baicalensis), and Mulberry leaf (Morus alba). To our knowledge, this is the first study of the NRICM101 effect on post-COVID-19 respiratory complications. Our findings may provide a better understanding of the potential mechanisms of NRICM101 in treating SARS-CoV-2 infection and regulating the immunoinflammatory response to improve post-COVID-19 respiratory complications.
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Affiliation(s)
- Dung Tam Nguyen Huynh
- College of Pharmacy, Taipei Medical University, Taipei, 11031, Taiwan
- Can Tho University of Medicine and Pharmacy, Can Tho City, 94117, Vietnam
| | - Hien Thi Nguyen
- Department of Nutrition and Food Safety, Faculty of Public Health, Can Tho University of Medicine and Pharmacy, Can Tho City, 94117, Vietnam
| | - Chien-Ming Hsieh
- College of Pharmacy, Taipei Medical University, Taipei, 11031, Taiwan.
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Jaiswal A, Shrivastav S, Kushwaha HR, Chaturvedi R, Singh RP. Oncogenic potential of SARS-CoV-2-targeting hallmarks of cancer pathways. Cell Commun Signal 2024; 22:447. [PMID: 39327555 PMCID: PMC11426004 DOI: 10.1186/s12964-024-01818-0] [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: 07/01/2024] [Accepted: 09/04/2024] [Indexed: 09/28/2024] Open
Abstract
The 2019 outbreak of SARS-CoV-2 has caused a major worldwide health crisis with high rates of morbidity and death. Interestingly, it has also been linked to cancer, which begs the issue of whether it plays a role in carcinogenesis. Recent studies have revealed various mechanisms by which SARS-CoV-2 can influence oncogenic pathways, potentially promoting cancer development. The virus encodes several proteins that alter key signaling pathways associated with cancer hallmarks. Unlike classical oncogenic viruses, which transform cells through viral oncogenes or by activating host oncogenes, SARS-CoV-2 appears to promote tumorigenesis by inhibiting tumor suppressor genes and pathways while activating survival, proliferation, and inflammation-associated signaling cascades. Bioinformatic analyses and experimental studies have identified numerous interactions between SARS-CoV-2 proteins and cellular components involved in cancer-related processes. This review explores the intricate relationship between SARS-CoV-2 infection and cancer, focusing on the regulation of key hallmarks driving initiation, promotion and progression of cancer by viral proteins. By elucidating the underlying mechanisms driving cellular transformation, the potential of SARS-CoV-2 as an oncovirus is highlighted. Comprehending these interplays is essential to enhance our understanding of COVID-19 and cancer biology and further formulating strategies to alleviate SARS-CoV-2 influence on cancer consequences.
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Affiliation(s)
- Aishwarya Jaiswal
- Cancer Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sanah Shrivastav
- SRM Institute of Science and Technology, Delhi-NCR Campus, Ghaziabad, Uttar Pradesh, India
| | - Hemant R Kushwaha
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
- Special Centre for Systems Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
- Special Centre for Systems Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Rana P Singh
- Cancer Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
- Special Centre for Systems Medicine, Jawaharlal Nehru University, New Delhi, India.
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA.
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Tramontozzi C, Riccio A, Pauciullo S, La Frazia S, Rossi A, Santoro MG. Indomethacin inhibits human seasonal coronaviruses at late stages of viral replication in lung cells: Impact on virus-induced COX-2 expression. J Virus Erad 2024; 10:100387. [PMID: 39399815 PMCID: PMC11470169 DOI: 10.1016/j.jve.2024.100387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 08/29/2024] [Indexed: 10/15/2024] Open
Abstract
Coronaviruses (CoV), zoonotic viruses periodically emerging worldwide, represent a constant potential threat to humans. To date, seven human coronaviruses (HCoV) have been identified: HCoV-229E, HCoV-NL63, HCoV-OC43 and HCoV-HKU1, globally circulating in the human population (seasonal coronaviruses, sHCoV), and three highly-pathogenic coronaviruses, SARS-CoV, MERS-CoV and SARS-CoV-2. Although sHCoV generally cause only mild respiratory diseases, severe complications may occur in specific populations, highlighting the need for broad-spectrum anti-coronavirus drugs. Herein we show that indomethacin (INDO), a non-steroidal anti-inflammatory drug widely used in the clinic for its potent anti-inflammatory and analgesic properties, effectively inhibits the replication of Alpha-coronavirus HCoV-229E and Beta-coronavirus HCoV-OC43 in human lung-derived cells. Indomethacin does not interfere with HCoV binding or entry into target cells, but acts at late stages of the virus life cycle, inhibiting viral RNA synthesis and infectious viral particles production. Although INDO anti-inflammatory action is mediated by blocking cyclooxygenase-1 and -2 (COX-1/2) enzymatic activity, the antiviral effect appears to be cyclooxygenase-independent and is not mimicked by the potent COX-1/2 inhibitor aspirin. Interestingly we found that both seasonal HCoVs markedly (>100 fold) induce the expression of the pro-inflammatory mediator COX-2 in lung cells; notably, INDO-treatment was found to effectively inhibit virus-induced COX-2 expression at the transcriptional level, revealing an additional mechanism to prevent COX-2-mediated inflammatory reactions in HCoV-infected lung cells, besides COX activity inhibition. Altogether the results indicate that indomethacin, possessing both potent anti-inflammatory properties and a direct antiviral activity against HCoV, could be effective in the treatment of Alpha- and Beta-coronavirus infections.
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Affiliation(s)
| | - Anna Riccio
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Pauciullo
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Simone La Frazia
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Antonio Rossi
- Institute of Translational Pharmacology, CNR, Rome, Italy
| | - M. Gabriella Santoro
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- Institute of Translational Pharmacology, CNR, Rome, Italy
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Aghajani Mir M. Illuminating the pathogenic role of SARS-CoV-2: Insights into competing endogenous RNAs (ceRNAs) regulatory networks. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105613. [PMID: 38844190 DOI: 10.1016/j.meegid.2024.105613] [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: 03/07/2024] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
The appearance of SARS-CoV-2 in 2019 triggered a significant economic and health crisis worldwide, with heterogeneous molecular mechanisms that contribute to its development are not yet fully understood. Although substantial progress has been made in elucidating the mechanisms behind SARS-CoV-2 infection and therapy, it continues to rank among the top three global causes of mortality due to infectious illnesses. Non-coding RNAs (ncRNAs), being integral components across nearly all biological processes, demonstrate effective importance in viral pathogenesis. Regarding viral infections, ncRNAs have demonstrated their ability to modulate host reactions, viral replication, and host-pathogen interactions. However, the complex interactions of different types of ncRNAs in the progression of COVID-19 remains understudied. In recent years, a novel mechanism of post-transcriptional gene regulation known as "competing endogenous RNA (ceRNA)" has been proposed. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and viral ncRNAs function as ceRNAs, influencing the expression of associated genes by sequestering shared microRNAs. Recent research on SARS-CoV-2 has revealed that disruptions in specific ceRNA regulatory networks (ceRNETs) contribute to the abnormal expression of key infection-related genes and the establishment of distinctive infection characteristics. These findings present new opportunities to delve deeper into the underlying mechanisms of SARS-CoV-2 pathogenesis, offering potential biomarkers and therapeutic targets. This progress paves the way for a more comprehensive understanding of ceRNETs, shedding light on the intricate mechanisms involved. Further exploration of these mechanisms holds promise for enhancing our ability to prevent viral infections and develop effective antiviral treatments.
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Affiliation(s)
- Mahsa Aghajani Mir
- Deputy of Research and Technology, Babol University of Medical Sciences, Babol, Iran.
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Xu Y, Yi H, Kuang Q, Zheng X, Xu D, Gong L, Yang L, Xiang B. Nucleotide metabolism-related host proteins RNA polymerase II subunit and uridine phosphorylase 1 interacting with porcine epidemic diarrhea virus N proteins affect viral replication. Front Vet Sci 2024; 11:1417348. [PMID: 38933700 PMCID: PMC11200923 DOI: 10.3389/fvets.2024.1417348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly infectious pathogen that targets pig intestines to cause disease. It is globally widespread and causes huge economic losses to the pig industry. PEDV N protein is the protein that constitutes the core of PEDV virus particles, and most of it is expressed in the cytoplasm, and a small part can also be expressed in the nucleus. However, the role of related proteins in host nucleotide metabolic pathways in regulating PEDV replication have not been fully elucidated. In this study, PEDV-N-labeled antibodies were co-immunoprecipitated and combined with LC-MS to screen for host proteins that interact with N proteins. Bioinformatics analyses showed that the selected host proteins were mainly enriched in metabolic pathways. Moreover, co-immunoprecipitation and confocal microscopy confirmed that the second-largest subunit of RNA polymerase II (RPB2) and uridine phosphorylase 1 (UPP1) interacted with the N protein. RPB2 is the main subunit of RNA polymerase II and plays an important role in eukaryotic transcription. UPP1 is an enzyme that catalyzes reversible phosphorylation of uridine to uracil and ribo-1-phosphate to promote catabolism and bio anabolism. RPB2 overexpression significantly promoted viral replication, whereas UPP1 overexpression significantly inhibited viral replication. Studies on interactions between the PEDV N and host proteins are helpful in elucidating the pathogenesis and immune escape mechanism of PEDV.
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Affiliation(s)
- Yifan Xu
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Heyou Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiyuan Kuang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiaoyu Zheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Dan Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lang Gong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Liangyu Yang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Bin Xiang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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Moshawih S, Jarrar Q, Bahrin AA, Lim AF, Ming L, Goh HP. Evaluating NSAIDs in SARS-CoV-2: Immunomodulatory mechanisms and future therapeutic strategies. Heliyon 2024; 10:e25734. [PMID: 38356603 PMCID: PMC10864964 DOI: 10.1016/j.heliyon.2024.e25734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) are widely recognized for their analgesic and anti-inflammatory properties. Amidst the SARS-CoV-2 pandemic, the role of NSAIDs in modulating viral and bacterial infections has become a critical area of research, sparking debates and necessitating a thorough review. This review examines the multifaceted interactions between NSAIDs, immune responses, and infections. Focusing on the immunomodulatory mechanisms of NSAIDs in SARS-CoV-2 and their implications for other viral and bacterial infections, we aim to provide clarity and direction for future therapeutic strategies. NSAIDs demonstrate a dual role in infectious diseases. They reduce inflammation by decreasing neutrophil recruitment and cytokine release, yet potentially compromise antiviral defense mechanisms. They also modulate cytokine storms in SARS-CoV-2 and exhibit the potential to enhance anti-tumor immunity by inhibiting tumor-induced COX-2/PGE2 signaling. Specific NSAIDs have shown efficacy in inhibiting viral replication. The review highlights NSAIDs' synergy with other medications, like COX inhibitors and immunotherapy agents, in augmenting therapeutic effects. Notably, the World Health Organization's analysis found no substantial link between NSAIDs and the worsening of viral respiratory infections. The findings underscore NSAIDs' complex role in infection management. Understanding these interactions is crucial for optimizing therapeutic approaches in current and future pandemics. However, their dual nature warrants cautious application, particularly in vulnerable populations. NSAIDs present a paradoxical impact on immune responses in viral and bacterial infections. While offering potential benefits, their usage in infectious diseases, especially SARS-CoV-2, demands a nuanced understanding to balance therapeutic advantages against possible adverse effects.
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Affiliation(s)
- Said Moshawih
- PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Qais Jarrar
- Department of Applied Pharmaceutical Sciences and Clinical Pharmacy, Faculty of Pharmacy, Isra University, Amman, Jordan
| | - Abdul Alim Bahrin
- PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Ai Fern Lim
- PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Long Ming
- School of Medical and Life Sciences, Sunway University, Sunway City, 47500, Malaysia
| | - Hui Poh Goh
- PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
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Chatterjee S, Sanjeev BS. Over-representation analysis of angiogenic factors in immunosuppressive mechanisms in neoplasms and neurological conditions during COVID-19. Microb Pathog 2023; 185:106386. [PMID: 37865274 DOI: 10.1016/j.micpath.2023.106386] [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: 07/10/2023] [Revised: 09/27/2023] [Accepted: 10/09/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Recent studies emphasized the necessity to identify key (human) biological processes and pathways targeted by the Coronaviridae family of viruses, especially Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronavirus Disease (COVID-19) caused up to 33-55 % death rates in COVID-19 patients with malignant neoplasms and Alzheimer's disease. Given this scenario, we identified biological processes and pathways involved in various diseases which are most likely affected by COVID-19. METHODS The COVID-19 DisGeNET data set (v4.0) contains the associations between various diseases and human genes known to interact with viruses from Coronaviridae family and were obtained from the IntAct Coronavirus data set annotated with DisGeNET data. We constructed the disease-gene network to identify genes that are involved in various comorbid diseased states. Communities from the disease-gene network were identified using Louvain method and functional enrichment through over-representation analysis methodology was used to discover significant biological processes and pathways shared between COVID-19 and other diseases. RESULT The COVID-19 DisGeNET data set (v4.0) comprised of 828 human genes and 10,473 diseases (including various phenotypes) that together constituted nodes in the disease-gene network. Each of the 70,210 edges connects a human gene with an associated disease. The top 10 genes linked to most number of diseases were VEGFA, BCL2, CTNNB1, ALB, COX2, AGT, HLA-A, HMOX1, FGF2 and COMT. The most vulnerable group of patients thus discovered had comorbid conditions such as carcinomas, malignant neoplasms and Alzheimer's disease. Finally, we identified 15 potentially useful biological processes and pathways for improved therapies. Vascular endothelial growth factor (VEGF) is the key mediator of angiogenesis in cancer. It is widely distributed in the brain and plays a crucial role in brain inflammation regulating the level of angiopoietins. With a degree of 1899, VEGFA was associated with maximum number of diseases in the disease-gene network. Previous studies have indicated that increased levels of VEGFA in the blood results in dyspnea, Pulmonary Edema (PE), Acute Lung Injury (ALI) and Acute Respiratory Distress Syndrome (ARDS). In case of COVID-19 patients with neoplasms and other neurological symptoms, our results indicate VEGFA as a therapeutic target for inflammation suppression. As VEGFs are known to disproportionately affect cancer patients, improving endothelial permeability and vasodilation with anti-VEGF therapy could lead to suppression of inflammation and also improve oxygenation. As an outcome of our study, we make case for clinical investigations towards anti-VEGF therapies for such comorbid conditions affected by COVID-19 for better therapeutic outcomes.
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Affiliation(s)
- S Chatterjee
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, India.
| | - B S Sanjeev
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, India.
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Rahman MS, Hossain MS. Eicosanoids Signals in SARS-CoV-2 Infection: A Foe or Friend. Mol Biotechnol 2023:10.1007/s12033-023-00919-4. [PMID: 37878227 DOI: 10.1007/s12033-023-00919-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023]
Abstract
SARS-CoV-2 mediated infection instigated a scary pandemic state since 2019. They created havoc comprising death, imbalanced social structures, and a wrecked global economy. During infection, the inflammation and associated cytokine storm generate a critical pathological situation in the human body, especially in the lungs. By the passage of time of infection, inflammatory disorders, and multiple organ damage happen which might lead to death, if not treated properly. Until now, many pathological parameters have been used to understand the progress of the severity of COVID-19 but with limited success. Bioactive lipid mediators have the potential of initiating and resolving inflammation in any disease. The connection between lipid storm and inflammatory states of SARS-CoV-2 infection has surfaced and got importance to understand and mitigate the pathological states of COVID-19. As the role of eicosanoids in COVID-19 infection is not well defined, available information regarding this issue has been accumulated to address the possible network of eicosanoids related to the initiation of inflammation, promotion of cytokine storm, and resolution of inflammation, and highlight possible strategies for treatment and drug discovery related to SARS-CoV-2 infection in this study. Understanding the involvement of eicosanoids in exploration of cellular events provoked by SARS-CoV-2 infection has been summarized as an important factor to deescalate any upcoming catastrophe imposed by the lethal variants of this micro-monster. Additionally, this study also recognized the eicosanoid based drug discovery, treatment, and strategies for managing the severity of SARS-COV-2 infection.
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Affiliation(s)
- Mohammad Sharifur Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka, 1000, Bangladesh.
| | - Mohammad Salim Hossain
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
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Yang G, Yue Z, Pan P, Li Y. In Memory of the Virologist Jianguo Wu, 1957-2022. Viruses 2023; 15:1754. [PMID: 37632095 PMCID: PMC10457867 DOI: 10.3390/v15081754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
It is with deep sorrow that we mourn the passing of the virologist Professor Jianguo Wu [...].
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Affiliation(s)
- Ge Yang
- Foshan Institute of Medical Microbiology, Foshan 528315, China
| | - Zhaoyang Yue
- Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou 510632, China
| | - Pan Pan
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou 510632, China
- The First Affiliated Hospital of Jinan University, Guangzhou 510632, China
| | - Yongkui Li
- Foshan Institute of Medical Microbiology, Foshan 528315, China
- Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou 510632, China
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Chen X. A Tribute to Professor Jianguo Wu. Viruses 2023; 15:1720. [PMID: 37632062 PMCID: PMC10457838 DOI: 10.3390/v15081720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
It has been a couple of months since Professor Jianguo Wu left us [...].
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Affiliation(s)
- Xin Chen
- Guangdong Provincial Key Laboratory of Virology, Key Laboratory of Viral Pathogenesis & Infection Prevention and Control, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China
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Fan S, Wang H, Wu D, Liu L. Pharmaceutical approaches for COVID-19: An update on current therapeutic opportunities. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2023; 73:157-173. [PMID: 37307372 DOI: 10.2478/acph-2023-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/18/2022] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2, a newly discovered coronavirus, has been linked to the COVID-19 pandemic and is currently an important public health issue. Despite all the work done to date around the world, there is still no viable treatment for COVID-19. This study examined the most recent evidence on the efficacy and safety of several therapeutic options available including natural substances, synthetic drugs and vaccines in the treatment of COVID-19. Various natural compounds such as sarsapogenin, lycorine, biscoclaurine, vitamin B12, glycyrrhizic acid, riboflavin, resveratrol and kaempferol, various vaccines and drugs such as AZD1222, mRNA-1273, BNT162b2, Sputnik V, and remdesivir, lopinavir, favipiravir, darunavir, oseltamivir, and umifenovir, resp., have been discussed comprehensively. We attempted to provide exhaustive information regarding the various prospective therapeutic approaches available in order to assist researchers and physicians in treating COVID-19 patients.
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Affiliation(s)
- Sijia Fan
- 1Department of Intensive Care Unit, South China Hospital, Health Science Center Shenzhen University Guangdong, Shenzhen 518116, P. R. China
| | - Hongling Wang
- 2Department of Cardiothoracic Surgery 940th Hospital of Joint Logistic Support Force of PLA, Lanzhou, Gansu, 730050, P. R. China
| | - Dean Wu
- 3Department of Respiratory Medicine, The Third People's Hospital of Gansu Province Lanzhou University, Lanzhou, Gansu 730050, P. R. China
| | - Lu Liu
- 4The First Pulmonary and Critical Care Medicine, The Fourth Affiliated Hospital of China Medical University, Shenyang Liaoning, 110032, P. R. China
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Mariniello DF, Allocca V, D’Agnano V, Villaro R, Lanata L, Bagnasco M, Aronne L, Bianco A, Perrotta F. Strategies Tackling Viral Replication and Inflammatory Pathways as Early Pharmacological Treatment for SARS-CoV-2 Infection: Any Potential Role for Ketoprofen Lysine Salt? MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248919. [PMID: 36558048 PMCID: PMC9782495 DOI: 10.3390/molecules27248919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
COVID-19 is an infective disease resulting in widespread respiratory and non-respiratory symptoms prompted by SARS-CoV-2 infection. Interaction between SARS-CoV-2 and host cell receptors prompts activation of pro-inflammatory pathways which are involved in epithelial and endothelial damage mechanisms even after viral clearance. Since inflammation has been recognized as a critical step in COVID-19, anti-inflammatory therapies, including both steroids and non-steroids as well as cytokine inhibitors, have been proposed. Early treatment of COVID-19 has the potential to affect the clinical course of the disease regardless of underlying comorbid conditions. Non-steroidal anti-inflammatory drugs (NSAIDs), which are widely used for symptomatic relief of upper airway infections, became the mainstay of early phase treatment of COVID-19. In this review, we discuss the current evidence for using NSAIDs in early phases of SARS-CoV-2 infection with focus on ketoprofen lysine salt based on its pharmacodynamic and pharmacokinetic features.
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Affiliation(s)
- Domenica Francesca Mariniello
- Department of Translational Medical Sciences, University of Campania “L. Vanvitelli”, 80131 Naples, Italy
- U.O.C. Clinica Pneumologica “L. Vanvitelli”, A.O. dei Colli, Ospedale Monaldi, 80131 Naples, Italy
| | - Valentino Allocca
- Department of Translational Medical Sciences, University of Campania “L. Vanvitelli”, 80131 Naples, Italy
- U.O.C. Clinica Pneumologica “L. Vanvitelli”, A.O. dei Colli, Ospedale Monaldi, 80131 Naples, Italy
| | - Vito D’Agnano
- Department of Translational Medical Sciences, University of Campania “L. Vanvitelli”, 80131 Naples, Italy
- U.O.C. Clinica Pneumologica “L. Vanvitelli”, A.O. dei Colli, Ospedale Monaldi, 80131 Naples, Italy
| | - Riccardo Villaro
- Section of Infectious Diseases, Department of Clinical Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy
| | - Luigi Lanata
- Medical Deptartment, Dompé Farmaceutici SpA, 20122 Milan, Italy
| | | | - Luigi Aronne
- Department of Translational Medical Sciences, University of Campania “L. Vanvitelli”, 80131 Naples, Italy
- U.O.C. Clinica Pneumologica “L. Vanvitelli”, A.O. dei Colli, Ospedale Monaldi, 80131 Naples, Italy
| | - Andrea Bianco
- Department of Translational Medical Sciences, University of Campania “L. Vanvitelli”, 80131 Naples, Italy
- U.O.C. Clinica Pneumologica “L. Vanvitelli”, A.O. dei Colli, Ospedale Monaldi, 80131 Naples, Italy
| | - Fabio Perrotta
- Department of Translational Medical Sciences, University of Campania “L. Vanvitelli”, 80131 Naples, Italy
- U.O.C. Clinica Pneumologica “L. Vanvitelli”, A.O. dei Colli, Ospedale Monaldi, 80131 Naples, Italy
- Correspondence:
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14
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Henri J, Minder L, Mohanasundaram K, Dilly S, Goupil-Lamy A, Di Primo C, Slama Schwok A. Neuropeptides, New Ligands of SARS-CoV-2 Nucleoprotein, a Potential Link between Replication, Inflammation and Neurotransmission. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228094. [PMID: 36432196 PMCID: PMC9698730 DOI: 10.3390/molecules27228094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
Abstract
This work identifies new ligands of the nucleoprotein N of SARS-CoV-2 by in silico screening, which used a new model of N, built from an Alphafold model refined by molecular dynamic simulations. The ligands were neuropeptides, such as substance P (1-7) and enkephalin, bound at a large site of the C-terminal or associated with the N-terminal β-sheet. The BA4 and BA5 Omicron variants of N also exhibited a large site as in wt N, and an increased flexibility of the BA5 variant, enabling substance P binding. The binding sites of some ligands deduced from modeling in wt N were assessed by mutation studies in surface plasmon resonance experiments. Dynamic light scattering showed that the ligands impeded RNA binding to N, which likely inhibited replication. We suggest that the physiological role of these neuropeptides in neurotransmission, pain and vasodilation for cholecystokinin and substance P could be altered by binding to N. We speculate that N may link between viral replication and multiple pathways leading to long COVID-19 symptoms. Therefore, N may constitute a "danger hub" that needs to be inhibited, even at high cost for the host. Antivirals targeted to N may therefore reduce the risk of brain fog and stroke, and improve patients' health.
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Affiliation(s)
- Julien Henri
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR-CNRS 7238, Sorbonne Université, F-75005 Paris, France
| | - Laetitia Minder
- Institut Européen de Chimie et Biologie (IECB), CNRS, INSERM UAR 3033, US001, Univ. Bordeaux, F-33000 Bordeaux, France
| | - Kevin Mohanasundaram
- Saint Antoine Hospital, Centre de Recherche Saint Antoine, Sorbonne Université, Biology and Cancer Therapeutics, INSERM U938, F-75231 Paris, France
| | - Sébastien Dilly
- Saint Antoine Hospital, Centre de Recherche Saint Antoine, Sorbonne Université, Biology and Cancer Therapeutics, INSERM U938, F-75231 Paris, France
| | - Anne Goupil-Lamy
- Biovia, Dassault Systèmes, 10 Rue Marcel Dassault, CS40501, CEDEX, F-78946 Vélizy-Villacoublay, France
| | - Carmelo Di Primo
- CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, Univ. Bordeaux, F-33000 Bordeaux, France
| | - Anny Slama Schwok
- Saint Antoine Hospital, Centre de Recherche Saint Antoine, Sorbonne Université, Biology and Cancer Therapeutics, INSERM U938, F-75231 Paris, France
- Correspondence: or
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15
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García-García T, Fernández-Rodríguez R, Redondo N, de Lucas-Rius A, Zaldívar-López S, López-Ayllón BD, Suárez-Cárdenas JM, Jiménez-Marín Á, Montoya M, Garrido JJ. Impairment of antiviral immune response and disruption of cellular functions by SARS-CoV-2 ORF7a and ORF7b. iScience 2022; 25:105444. [PMID: 36310646 PMCID: PMC9597514 DOI: 10.1016/j.isci.2022.105444] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/20/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022] Open
Abstract
SARS-CoV-2, the causative agent of the present COVID-19 pandemic, possesses eleven accessory proteins encoded in its genome, and some have been implicated in facilitating infection and pathogenesis through their interaction with cellular components. Among these proteins, accessory protein ORF7a and ORF7b functions are poorly understood. In this study, A549 cells were transduced to express ORF7a and ORF7b, respectively, to explore more in depth the role of each accessory protein in the pathological manifestation leading to COVID-19. Bioinformatic analysis and integration of transcriptome results identified defined canonical pathways and functional groupings revealing that after expression of ORF7a or ORF7b, the lung cells are potentially altered to create conditions more favorable for SARS-CoV-2, by inhibiting the IFN-I response, increasing proinflammatory cytokines release, and altering cell metabolic activity and adhesion. Based on these results, it is plausible to suggest that ORF7a or ORF7b could be used as biomarkers of progression in this pandemic.
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Affiliation(s)
- Tránsito García-García
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Raúl Fernández-Rodríguez
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Natalia Redondo
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Ana de Lucas-Rius
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Sara Zaldívar-López
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Blanca Dies López-Ayllón
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - José M. Suárez-Cárdenas
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Ángeles Jiménez-Marín
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - María Montoya
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
- Corresponding author
| | - Juan J. Garrido
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
- Corresponding author
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16
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Remuzzi G, Schiaffino S, Santoro MG, FitzGerald GA, Melino G, Patrono C. Drugs for the prevention and treatment of COVID-19 and its complications: An update on what we learned in the past 2 years. Front Pharmacol 2022; 13:987816. [PMID: 36304162 PMCID: PMC9595217 DOI: 10.3389/fphar.2022.987816] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/12/2022] [Indexed: 12/15/2022] Open
Abstract
The COVID-19 Committee of the Lincei Academy has reviewed the scientific evidence supporting the efficacy and safety of existing and new drugs/biologics for the preventing and treating of COVID-19 and its complications. This position paper reports what we have learned in the field in the past 2 years. The focus was on, but not limited to, drugs and neutralizing monoclonal antibodies, anti-SARS-CoV-2 agents, anti-inflammatory and immunomodulatory drugs, complement inhibitors and anticoagulant agents. We also discuss the risks/benefit of using cell therapies on COVID-19 patients. The report summarizes the available evidence, which supports recommendations from health authorities and panels of experts regarding some drugs and biologics, and highlights drugs that are not recommended, or drugs for which there is insufficient evidence to recommend for or against their use. We also address the issue of the safety of drugs used to treat underlying concomitant conditions in COVID-19 patients. The investigators did an enormous amount of work very quickly to understand better the nature and pathophysiology of COVID-19. This expedited the development and repurposing of safe and effective therapeutic interventions, saving an impressive number of lives in the community as well as in hospitals.
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Affiliation(s)
- Giuseppe Remuzzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | | | - Maria Gabriella Santoro
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- Institute of Translational Pharmacology, CNR, Rome, Italy
| | - Garret A. FitzGerald
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Philadelphia, Philadelphia, PA, United States
| | - Gennaro Melino
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Carlo Patrono
- Department of Pharmacology, Catholic University of the Sacred Heart, Rome, Italy
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Manan A, Pirzada RH, Haseeb M, Choi S. Toll-like Receptor Mediation in SARS-CoV-2: A Therapeutic Approach. Int J Mol Sci 2022; 23:10716. [PMID: 36142620 PMCID: PMC9502216 DOI: 10.3390/ijms231810716] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 01/18/2023] Open
Abstract
The innate immune system facilitates defense mechanisms against pathogen invasion and cell damage. Toll-like receptors (TLRs) assist in the activation of the innate immune system by binding to pathogenic ligands. This leads to the generation of intracellular signaling cascades including the biosynthesis of molecular mediators. TLRs on cell membranes are adept at recognizing viral components. Viruses can modulate the innate immune response with the help of proteins and RNAs that downregulate or upregulate the expression of various TLRs. In the case of COVID-19, molecular modulators such as type 1 interferons interfere with signaling pathways in the host cells, leading to an inflammatory response. Coronaviruses are responsible for an enhanced immune signature of inflammatory chemokines and cytokines. TLRs have been employed as therapeutic agents in viral infections as numerous antiviral Food and Drug Administration-approved drugs are TLR agonists. This review highlights the therapeutic approaches associated with SARS-CoV-2 and the TLRs involved in COVID-19 infection.
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Affiliation(s)
- Abdul Manan
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | | | - Muhammad Haseeb
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
- S&K Therapeutics, Ajou University Campus Plaza 418, 199 Worldcup-ro, Yeongtong-gu, Suwon 16502, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
- S&K Therapeutics, Ajou University Campus Plaza 418, 199 Worldcup-ro, Yeongtong-gu, Suwon 16502, Korea
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18
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Short-term celecoxib (celebrex) adjuvant therapy: a clinical trial study on COVID-19 patients. Inflammopharmacology 2022; 30:1645-1657. [PMID: 35834150 PMCID: PMC9281238 DOI: 10.1007/s10787-022-01029-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/22/2022] [Indexed: 11/21/2022]
Abstract
Background It is known that severe acute respiratory coronavirus 2 (SARS-CoV-2) is the viral strain responsible for the recent coronavirus disease 2019 (COVID-19) pandemic. Current documents have demonstrated that the virus causes a PGE2 storm in a substantial proportion of patients via upregulating cyclooxygenase-2 (COX-2) and downregulating prostaglandin E2 (PGE2)-degrading enzymes within the host cell. Aim Herein, we aimed to study how short-term treatment with celecoxib (Celebrex), a selective COX-2 inhibitor, affects demographic features, early symptoms, O2 saturation, and hematological indices of cases with COVID-19. Methods A total of 67 confirmed COVID-19 cases with a mild or moderate disease, who had been referred to an institutional hospital in south-eastern Iran from October 2020 to September 2021, were enrolled. Demographic characteristics, symptoms, and hematological indices of the patients were recorded within different time periods. One-way ANOVA or Kruskal–Wallis tests were used to determine differences between data sets based on normal data distribution. Results O2 saturation was statistically different between the control group and patients receiving celecoxib (p = 0.039). There was no marked difference between the groups in terms of the symptoms they experienced (p > 0.05). On the first days following Celebrex therapy, analysis of complete blood counts showed that white blood cell (WBC) counts were markedly lower in patients treated with a high dose of celecoxib (0.4 g/day) than in controls (p = 0.026). However, mean lymphocyte levels in patients receiving a high dose of celecoxib (0.4 g/day) were markedly higher than in patients receiving celecoxib with half of the dose (0.2 g/day) for one week or the untreated subjects (p = 0.004). Changes in platelet count also followed the WBC alteration pattern. Conclusion Celecoxib is a relatively safe, inexpensive, and widely available drug with non-steroidal anti-inflammatory properties. The therapeutic efficacy of celecoxib depends on the administrated dose. Celecoxib might improve disease-free survival in patients with COVID-19.
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19
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Plasma Oxylipins and Their Precursors Are Strongly Associated with COVID-19 Severity and with Immune Response Markers. Metabolites 2022; 12:metabo12070619. [PMID: 35888743 PMCID: PMC9319897 DOI: 10.3390/metabo12070619] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
COVID-19 is characterised by a dysregulated immune response, that involves signalling lipids acting as mediators of the inflammatory process along the innate and adaptive phases. To promote understanding of the disease biochemistry and provide targets for intervention, we applied a range of LC-MS platforms to analyse over 100 plasma samples from patients with varying COVID-19 severity and with detailed clinical information on inflammatory responses (>30 immune markers). The second publication in a series reports the results of quantitative LC-MS/MS profiling of 63 small lipids including oxylipins, free fatty acids, and endocannabinoids. Compared to samples taken from ward patients, intensive care unit (ICU) patients had 2−4-fold lower levels of arachidonic acid (AA) and its cyclooxygenase-derived prostanoids, as well as lipoxygenase derivatives, exhibiting negative correlations with inflammation markers. The same derivatives showed 2−5-fold increases in recovering ward patients, in paired comparison to early hospitalisation. In contrast, ICU patients showed elevated levels of oxylipins derived from poly-unsaturated fatty acids (PUFA) by non-enzymatic peroxidation or activity of soluble epoxide hydrolase (sEH), and these oxylipins positively correlated with markers of macrophage activation. The deficiency in AA enzymatic products and the lack of elevated intermediates of pro-resolving mediating lipids may result from the preference of alternative metabolic conversions rather than diminished stores of PUFA precursors. Supporting this, ICU patients showed 2-to-11-fold higher levels of linoleic acid (LA) and the corresponding fatty acyl glycerols of AA and LA, all strongly correlated with multiple markers of excessive immune response. Our results suggest that the altered oxylipin metabolism disrupts the expected shift from innate immune response to resolution of inflammation.
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20
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A Review on SARS-CoV-2 Genome in the Aquatic Environment of Africa: Prevalence, Persistence and the Future Prospects. WATER 2022. [DOI: 10.3390/w14132020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The COVID-19 pandemic (Coronavirus disease 2019) remains problematic in all its manifestations on the global stage where countless events of human-to-human exposure have led to fatal cases; thus, the aftermath being an unprecedented public health concern, with inaccessible health care and the instability of economies and financial institutions. These pose massive obstacles that can insatiably devour existing human resources causing negative impacts, especially in developing countries. Tracking the origin, dissemination and mutating strains of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) on population-wide scales is a somewhat overwhelming task, with the urgent need to map the dissemination and magnitude of SARS-CoV-2 in near real-time. This review paper focuses on the poor sanitation of some waterbodies and wastewater management policies in low-income African countries, highlighting how these contribute to the COVID-19 pandemic on the continent. Since the outbreak of the novel coronavirus pandemic, there has been an upsurge in scientific literature and studies concerning SARS-CoV-2 with different opinions and findings. The current paper highlights the challenges and also summarizes the environmental aspects related to the monitoring and fate of the SARS-CoV-2 genomes in the aquatic milieu of Sub-Saharan Africa.
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Chlorpromazine, a Clinically Approved Drug, Inhibits SARS-CoV-2 Nucleocapsid-Mediated Induction of IL-6 in Human Monocytes. Molecules 2022; 27:molecules27123651. [PMID: 35744777 PMCID: PMC9228867 DOI: 10.3390/molecules27123651] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic, caused by the rapidly spreading SARS-CoV-2 virus, led to the unprecedented mobilization of scientists, resulting in the rapid development of vaccines and potential pharmaceuticals. Although COVID-19 symptoms are moderately severe in most people, in some cases the disease can result in pneumonia and acute respiratory failure as well as can be fatal. The severe course of COVID-19 is associated with a hyperinflammatory state called a cytokine storm. One of the key cytokines creating a proinflammatory environment is IL-6, which is secreted mainly by monocytes and macrophages. Therefore, this cytokine has become a target for some therapies that inhibit its biological action; however, these therapies are expensive, and their availability is limited in poorer countries. Thus, new cheaper drugs that can overcome the severe infections of COVID-19 are needed. Here, we show that chlorpromazine inhibits the expression and secretion of IL-6 by monocytes activated by SARS-CoV-2 virus nucleocapsid protein and affects the activity of NF-κB and MEK/ERK signaling. Our results, including others, indicate that chlorpromazine, which has been used for several decades as a neuroleptic, exerts antiviral and immunomodulatory activity, is safe and inexpensive, and might be a desirable drug to support the therapy of patients with COVID-19.
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22
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Rahman S, Shishir MA, Hosen MI, Khan MJ, Arefin A, Khandaker AM. The status and analysis of common mutations found in the SARS-CoV-2 whole genome sequences from Bangladesh. GENE REPORTS 2022; 27:101608. [PMID: 35399222 PMCID: PMC8977224 DOI: 10.1016/j.genrep.2022.101608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/18/2022]
Abstract
Rapid emergence of covid-19 variants by continuous mutation made the world experience continuous waves of infections and as a result, a huge number of death-toll recorded so far. It is, therefore, very important to investigate the diversity and nature of the mutations in the SARS-CoV-2 genomes. In this study, the common mutations occurred in the whole genome sequences of SARS-CoV-2 variants of Bangladesh in a certain timeline were analyzed to better understand its status. Hence, a total of 78 complete genome sequences available in the NCBI database were obtained, aligned and further analyzed. Scattered Single Nucleotide Polymorphisms (SNPs) were identified throughout the genome of variants and common SNPs such as: 241:C>T in the 5′UTR of Open Reading Frame 1A (ORF1A), 3037: C>T in Non-structural Protein 3 (NSP3), 14,408: C>T in ORF6 and 23,402: A>G, 23,403: A>G in Spike Protein (S) were observed, but all of them were synonymous mutations. About 97% of the studied genomes showed a block of tri-nucleotide alteration (GGG>AAC), the most common non-synonymous mutation in the 28,881–28,883 location of the genome. This block results in two amino acid changes (203–204: RG>KR) in the SR rich motif of the nucleocapsid (N) protein of SARS-CoV-2, introducing a lysine in between serine and arginine. The N protein structure of the mutant was predicted through protein modeling. However, no observable difference was found between the mutant and the reference (Wuhan) protein. Further, the protein stability changes upon mutations were analyzed using the I-Mutant2.0 tool. The alteration of the arginine to lysine at the amino acid position 203, showed reduction of entropy, suggesting a possible impact on the overall stability of the N protein. The estimation of the non-synonymous to synonymous substitution ratio (dN/dS) were analyzed for the common mutations and the results showed that the overall mean distance among the N-protein variants were statistically significant, supporting the non-synonymous nature of the mutations. The phylogenetic analysis of the selected 78 genomes, compared with the most common genomic variants of this virus across the globe showed a distinct cluster for the analyzed Bangladeshi sequences. Further studies are warranted for conferring any plausible association of these mutations with the clinical manifestation.
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Key Words
- +ssRNA, positive single-stranded RNA
- ACE2, Angiotensin-Converting Enzyme 2
- Block mutation
- CDK, Cyclin Dependent Kinases
- COX2, Cyclooxygenase 2
- CTD, C-terminal Domain
- CoVs, Coronaviruses
- Common mutations
- DGHS, General of Health Services
- ECM, Extracellular Matrix Protein
- ERGIC, ER-Golgi intermediate compartment
- GSK3, Glycogen Synthase Kinase 3
- IRF3, Interferon Regulatory Factor 3
- NFkB, Nuclear Factor kappa B
- NSP, Nonstructural Protein
- NTD, N-terminal Domain
- ORFs, Open Reading Frames
- PLP, Papain-like Protease
- RBD, Receptor-Binding Domain
- RTC, Replication–Transcription Complex
- RdRp, RNA-dependent RNA polymerase
- SARS-CoV-2
- SNP, Single Nucleotide Polymorphism
- SR rich motif
- TMPRSS2, Transmembrane Protease Serine 2
- sgRNAs, Sub-genomic RNAs
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Affiliation(s)
- Sadniman Rahman
- Branch of Genetics and Molecular Biology, Department of Zoology, University of Dhaka, Bangladesh
| | | | - Md Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Miftahul Jannat Khan
- Department of Anesthesiology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | | | - Ashfaqul Muid Khandaker
- Branch of Genetics and Molecular Biology, Department of Zoology, University of Dhaka, Bangladesh
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Rhoades R, Solomon S, Johnson C, Teng S. Impact of SARS-CoV-2 on Host Factors Involved in Mental Disorders. Front Microbiol 2022; 13:845559. [PMID: 35444632 PMCID: PMC9014212 DOI: 10.3389/fmicb.2022.845559] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/14/2022] [Indexed: 11/23/2022] Open
Abstract
COVID-19, caused by SARS-CoV-2, is a systemic illness due to its multiorgan effects in patients. The disease has a detrimental impact on respiratory and cardiovascular systems. One early symptom of infection is anosmia or lack of smell; this implicates the involvement of the olfactory bulb in COVID-19 disease and provides a route into the central nervous system. However, little is known about how SARS-CoV-2 affects neurological or psychological symptoms. SARS-CoV-2 exploits host receptors that converge on pathways that impact psychological symptoms. This systemic review discusses the ways involved by coronavirus infection and their impact on mental health disorders. We begin by briefly introducing the history of coronaviruses, followed by an overview of the essential proteins to viral entry. Then, we discuss the downstream effects of viral entry on host proteins. Finally, we review the literature on host factors that are known to play critical roles in neuropsychiatric symptoms and mental diseases and discuss how COVID-19 could impact mental health globally. Our review details the host factors and pathways involved in the cellular mechanisms, such as systemic inflammation, that play a significant role in the development of neuropsychological symptoms stemming from COVID-19 infection.
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Affiliation(s)
- Raina Rhoades
- Department of Biology, Howard University, Washington, DC, United States
| | - Sarah Solomon
- Department of Biology, Howard University, Washington, DC, United States
| | - Christina Johnson
- Department of Biology, Howard University, Washington, DC, United States
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Cardiac injury on admission linked to worse outcomes in hospitalized COVID-19 patients. VOJNOSANIT PREGL 2022. [DOI: 10.2298/vsp210602012z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Objectives: To explore the relationships between cardiac injury and COVID-19
severity and mortality in patients. Methods: All consecutive patients with
laboratory-confirmed COVID-19 were included and followed up until discharge
or death from January 30, 2020, to April 5, 2020. Results: A total of 256
COVID-19 patients were included, and 24 (9.4%) had cardiac injury on
admission. Patients with cardiac injury were older (72.76 vs. 55.76) and
more likely to be male (82.8% vs. 42.2%), more likely to be smokers (31.0%
vs. 12.5%) and more likely to have chronic cardiovascular disease (24.1% vs.
7.8%), chronic pulmonary disease (17.2% vs. 3.0%) and chronic kidney disease
(10.3% vs. 2.2%). Laboratory findings suggested that patients with cardiac
injury were more likely to have leukocyte counts >10?109/L and higher levels
of lymphopenia, direct bilirubin, myohemoglobin, blood urea nitrogen,
C-reactive protein, and pro-hormone BNP but lower levels of serum total
protein and estimated glomerular filtration rates. Patients with cardiac
injury experienced more complications (72.4% vs. 47.8%), including acute
respiratory distress syndrome (20.7% vs. 2.7%), acute kidney injury (10.3
vs. 0.4%), severe COVID-19 (58.6% vs. 11.6%) and death (55.2% vs. 3.9%).
Multivariate analyses showed that cardiac injury was associated with an
increased risk of severe COVID-19 (HR=8.71, 95% CI 2.37-32.04) and death
(HR=20.84, 95% CI 1.32-328.22). Conclusion: Cardiac injury on admission is
associated with a higher risk of disease progression and death.
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25
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The potential role of COVID-19 in the induction of DNA damage. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108411. [PMID: 35690420 PMCID: PMC8767986 DOI: 10.1016/j.mrrev.2022.108411] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/30/2021] [Accepted: 01/17/2022] [Indexed: 01/07/2023]
Abstract
The coronavirus disease-2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is challenging global health and economic systems. In some individuals, COVID-19 can cause a wide array of symptoms, affecting several organs, such as the lungs, heart, bowels, kidneys and brain, causing multiorgan failure, sepsis and death. These effects are related in part to direct viral infection of these organs, immunological deregulation, a hypercoagulatory state and the potential for development of cytokine storm syndrome. Since the appearance of COVID-19 is recent, the long-term effects on the health of recovered patients remain unknown. In this review, we focused on current evidence of the mechanisms of DNA damage mediated by coronaviruses. Data supports that these viruses can induce DNA damage, genomic instability, and cell cycle deregulation during their replication in mammalian cells. Since the induction of DNA damage and aberrant DNA repair mechanisms are related to the development of chronic diseases such as cancer, diabetes, neurodegenerative disorders, and atherosclerosis, it will be important to address similar effects and outcomes in recovered COVID-19 patients.
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26
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Haslbauer JD, Zinner C, Stalder AK, Schneeberger J, Menter T, Bassetti S, Mertz KD, Went P, Matter MS, Tzankov A. Vascular Damage, Thromboinflammation, Plasmablast Activation, T-Cell Dysregulation and Pathological Histiocytic Response in Pulmonary Draining Lymph Nodes of COVID-19. Front Immunol 2021; 12:763098. [PMID: 34966385 PMCID: PMC8710573 DOI: 10.3389/fimmu.2021.763098] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022] Open
Abstract
Although initial immunophenotypical studies on peripheral blood and bronchoalveolar lavage samples have provided a glimpse into the immunopathology of COVID-19, analyses of pulmonary draining lymph nodes are currently scarce. 22 lethal COVID-19 cases and 28 controls were enrolled in this study. Pulmonary draining lymph nodes (mediastinal, tracheal, peribronchial) were collected at autopsy. Control lymph nodes were selected from a range of histomorphological sequelae [unremarkable histology, infectious mononucleosis, follicular hyperplasia, non-SARS related HLH, extrafollicular plasmablast activation, non-SARS related diffuse alveolar damage (DAD), pneumonia]. Samples were mounted on a tissue microarray and underwent immunohistochemical staining for a selection of immunological markers and in-situ hybridization for Epstein Barr Virus (EBV) and SARS-CoV-2. Gene expression profiling was performed using the HTG EdgeSeq Immune Response Panel. Characteristic patterns of a dysregulated immune response were detected in COVID-19: 1. An accumulation of extrafollicular plasmablasts with a relative paucity or depletion of germinal centers. 2. Evidence of T-cell dysregulation demonstrated by immunohistochemical paucity of FOXP3+, Tbet+ and LEF1+ positive T-cells and a downregulation of key genes responsible for T-cell crosstalk, maturation and migration as well as a reactivation of herpes viruses in 6 COVID-19 lymph nodes (EBV, HSV). 3. Macrophage activation by a M2-polarized, CD163+ phenotype and increased incidence of hemophagocytic activity. 4. Microvascular dysfunction, evidenced by an upregulation of hemostatic (CD36, PROCR, VWF) and proangiogenic (FLT1, TEK) genes and an increase of fibrin microthrombi and CD105+ microvessels. Taken together, these findings imply widespread dysregulation of both innate and adoptive pathways with concordant microvascular dysfunction in severe COVID-19.
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Affiliation(s)
- Jasmin D. Haslbauer
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Carl Zinner
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Anna K. Stalder
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Jan Schneeberger
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Thomas Menter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Stefano Bassetti
- Department of Internal Medicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Philip Went
- Pathology, Cantonal Hospital Graubünden, Chur, Switzerland
| | - Matthias S. Matter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Alexandar Tzankov
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
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27
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Fremont-Smith M, Gherlone N, Smith N, Tisdall P, Ricke DO. Models for COVID-19 Early Cardiac Pathology Following SARS-CoV-2 Infection. Int J Infect Dis 2021; 113:331-335. [PMID: 34592443 PMCID: PMC8473263 DOI: 10.1016/j.ijid.2021.09.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/01/2021] [Accepted: 09/22/2021] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES The clinical manifestations of COVID-19 associated cardiac complications are heterogeneous, ranging from asymptomatic to severe symptoms, including arrhythmias and cardiogenic shock. For COVID-19 patients with cardiac sequela, only a small subset of patients have myocarditis; the pathogenesis of cardiac sequela caused by SARS-CoV-2 other than microthrombi associated sequela remains to be determined. METHODS Retrospective analysis of 71 heart autopsy specimens from COVID-19 and putative COVID-19 in the NIH COVID Digital Pathology Repository. RESULTS The most consistent observation was localized myocardial cell death not associated with either myocarditis or microthrombi. Red blood cells were typically absent from capillaries but, when observed, were predominately in linear clusters (stacks) of adjacent cells. CONCLUSIONS Based on our retrospective analysis, we propose that localized ischemia and subsequent cell death by anoxia contributes to the cardiac pathogenesis in some COVID-19 patients. We propose two new models predicting vasoconstriction of cardiac pericyte cells induced by elevated histamine from hyper-activated mast cells or direct infection. We propose that impeded blood flow and cell death by anoxia are initial steps in the development of SARS-CoV-2 induced cardiac injury in COVID-19 patients independent of microthrombi or myocarditis.
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Affiliation(s)
| | - Nicole Gherlone
- AMITA Health Saint Joseph Hospital Chicago, Chicago, IL 60657, USA.
| | - Nora Smith
- Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, MA, 02420, USA.
| | | | - Darrell O Ricke
- Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, MA, 02420, USA.
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28
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Ricke DO. Hyperactivated Mast Cells Pathogenesis Hypothesis for COVID-19 Cutaneous Manifestations. JID INNOVATIONS 2021; 1:100052. [PMID: 34458884 PMCID: PMC8381631 DOI: 10.1016/j.xjidi.2021.100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Darrell O. Ricke
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, Massachusetts, USA
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29
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Pilkington SM, Watson REB. Should we look beyond the interferon signature in chilblain-like lesions associated with COVID-19? Br J Dermatol 2021; 185:1090-1091. [PMID: 34748213 PMCID: PMC8653276 DOI: 10.1111/bjd.20784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 01/10/2023]
Abstract
Linked Article: Frumholtz et al. Br J Dermatol 2021;185:1176–1185.
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Affiliation(s)
- S M Pilkington
- Centre for Dermatology Research, School of Biological Sciences, The University of Manchester & Salford Royal NHS Foundation Trust, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - R E B Watson
- Centre for Dermatology Research, School of Biological Sciences, The University of Manchester & Salford Royal NHS Foundation Trust, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
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30
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Chowdhury UN, Faruqe MO, Mehedy M, Ahmad S, Islam MB, Shoombuatong W, Azad A, Moni MA. Effects of Bacille Calmette Guerin (BCG) vaccination during COVID-19 infection. Comput Biol Med 2021; 138:104891. [PMID: 34624759 PMCID: PMC8479467 DOI: 10.1016/j.compbiomed.2021.104891] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022]
Abstract
The coronavirus disease 2019 (COVID-19) is caused by the infection of highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as the novel coronavirus. In most countries, the containment of this virus spread is not controlled, which is driving the pandemic towards a more difficult phase. In this study, we investigated the impact of the Bacille Calmette Guerin (BCG) vaccination on the severity and mortality of COVID-19 by performing transcriptomic analyses of SARS-CoV-2 infected and BCG vaccinated samples in peripheral blood mononuclear cells (PBMC). A set of common differentially expressed genes (DEGs) were identified and seeded into their functional enrichment analyses via Gene Ontology (GO)-based functional terms and pre-annotated molecular pathways databases, and their Protein-Protein Interaction (PPI) network analysis. We further analysed the regulatory elements, possible comorbidities and putative drug candidates for COVID-19 patients who have not been BCG-vaccinated. Differential expression analyses of both BCG-vaccinated and COVID-19 infected samples identified 62 shared DEGs indicating their discordant expression pattern in their respected conditions compared to control. Next, PPI analysis of those DEGs revealed 10 hub genes, namely ITGB2, CXCL8, CXCL1, CCR2, IFNG, CCL4, PTGS2, ADORA3, TLR5 and CD33. Functional enrichment analyses found significantly enriched pathways/GO terms including cytokine activities, lysosome, IL-17 signalling pathway, TNF-signalling pathways. Moreover, a set of identified TFs, miRNAs and potential drug molecules were further investigated to assess their biological involvements in COVID-19 and their therapeutic possibilities. Findings showed significant genetic interactions between BCG vaccination and SARS-CoV-2 infection, suggesting an interesting prospect of the BCG vaccine in relation to the COVID-19 pandemic. We hope it may potentially trigger further research on this critical phenomenon to combat COVID-19 spread.
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Affiliation(s)
- Utpala Nanda Chowdhury
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Mehedy
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Shamim Ahmad
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - M. Babul Islam
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - A.K.M. Azad
- Faculty of Science, Engineering & Technology, Swinburne University of Technology Sydney, Australia
| | - Mohammad Ali Moni
- School of Health and Rehabilitation Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD 4072, Australia,Corresponding author
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31
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Tarczewska A, Kolonko-Adamska M, Zarębski M, Dobrucki J, Ożyhar A, Greb-Markiewicz B. The method utilized to purify the SARS-CoV-2 N protein can affect its molecular properties. Int J Biol Macromol 2021; 188:391-403. [PMID: 34371045 PMCID: PMC8343380 DOI: 10.1016/j.ijbiomac.2021.08.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/30/2022]
Abstract
One of the main structural proteins of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the nucleocapsid protein (N). The basic function of this protein is to bind genomic RNA and to form a protective nucleocapsid in the mature virion. The intrinsic ability of the N protein to interact with nucleic acids makes its purification very challenging. Therefore, typically employed purification methods appear to be insufficient for removing nucleic acid contamination. In this study, we present a novel purification protocol that enables the N protein to be prepared without any bound nucleic acids. We also performed comparative structural analysis of the N protein contaminated with nucleic acids and free of contamination and showed significant differences in the structural and phase separation properties of the protein. These results indicate that nucleic-acid contamination may severely affect molecular properties of the purified N protein. In addition, the notable ability of the N protein to form condensates whose morphology and behaviour suggest more ordered forms resembling gel-like or solid structures is described.
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Affiliation(s)
- Aneta Tarczewska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Marta Kolonko-Adamska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Mirosław Zarębski
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Jurek Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
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32
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Abdelhafiz AS, Fouad MA, Sayed-Ahmed MM, Kamel MM, Ali A, Fouda M, Khalil MA, Abdel-Moneim AS, Kamal LM. Upregulation of FOXP3 is associated with severity of hypoxia and poor outcomes in COVID-19 patients. Virology 2021; 563:74-81. [PMID: 34478955 PMCID: PMC8397927 DOI: 10.1016/j.virol.2021.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/13/2021] [Accepted: 08/21/2021] [Indexed: 01/08/2023]
Abstract
The levels of messenger RNA (mRNA) transcription of FOXP3, IFN-γ, TNF, IL-6 and COX-2 from both COVID-19 infected and control subjects were evaluated using SYBRTM green real-time polymerase chain reaction (RT-PCR). Severe/critical cases showed significantly lower lymphocyte counts and higher neutrophil counts than the mild or moderate cases. There were significantly lower levels of mRNA expressions of IFN-γ, TNFα and FOXP3 in COVID-19 patients than in the control group. On the other hand, IL-6 and COX-2 expressions were significantly higher in patients suffering from severe disease. FOXP3 expressions were correlated with the severities of hypoxia and were excellent in predicting the disease severity. This was followed by the IL-6, COX-2 and TNFα expressions. FOXP3 expression was the only biomarker to show a significant correlation with patient mortality. It was concluded that SARS-CoV-2 infection is associated with the downregulation of FOXP3 and upregulations of IL-6 and COX-2.
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Affiliation(s)
- Ahmed S Abdelhafiz
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mariam A Fouad
- Pharmacology and Experimental Oncology Unit, National Cancer Institute, Cairo University, Cairo, Egypt; Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Mohamed M Sayed-Ahmed
- Pharmacology and Experimental Oncology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mahmoud M Kamel
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Asmaa Ali
- Department of Pulmonary Medicine, Abbassia Chest Hospital, MOH, Cairo, Egypt
| | - Merhan Fouda
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mahmoud A Khalil
- Department of Tropical Medicine and Infectious Disease, Imbaba Fever Hospital, MOH, Cairo, Egypt
| | - Ahmed S Abdel-Moneim
- Microbiology Department, College of Medicine, Taif University, P.O. Box 1109, Taif, 21944, Saudi Arabia.
| | - Lamyaa M Kamal
- Department of Clinical and Chemical Pathology, Elsahel Teaching Hospital, MOH, Cairo, Egypt
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33
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Sisakht M, Solhjoo A, Mahmoodzadeh A, Fathalipour M, Kabiri M, Sakhteman A. Potential inhibitors of the main protease of SARS-CoV-2 and modulators of arachidonic acid pathway: Non-steroidal anti-inflammatory drugs against COVID-19. Comput Biol Med 2021; 136:104686. [PMID: 34340125 PMCID: PMC8319042 DOI: 10.1016/j.compbiomed.2021.104686] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 02/06/2023]
Abstract
The main protease of SARS-CoV-2 is one of the key targets to develop and design antiviral drugs. There is no general agreement on the use of non-steroidal anti-inflammatory drugs (NSAIDs) in COVID-19. In this study, we investigated NSAIDs as potential inhibitors for chymotrypsin-like protease (3CLpro) and the main protease of the SARS-CoV-2 to find out the best candidates, which can act as potent inhibitors against the main protease. We also predicted the effect of NSAIDs on the arachidonic pathway and evaluated the hepatotoxicity of the compounds using systems biology techniques. Molecular docking was conducted via AutoDock Vina to estimate the interactions and binding affinities between selected NSAIDs and the main protease. Molecular docking results showed the presence of 10 NSAIDs based on lower binding energy (kcal/mol) toward the 3CLpro inhibition site compared to the co-crystal native ligand Inhibitor N3 (-6.6 kcal/mol). To validate the docking results, molecular dynamic (MD) simulations on the top inhibitor, Talniflumate, were performed. To obtain differentially-expressed genes under the 27 NSAIDs perturbations, we utilized the L1000 final Z-scores from the NCBI GEO repository (GSE92742). The obtained dataset included gene expression profiling signatures for 27 NSAIDs. The hepatotoxicity of NSAIDs was studied by systems biology modeling of Disturbed Metabolic Pathways. This study highlights the new application of NSAIDs as anti-viral drugs used against COVID-19. NSAIDs may also attenuate the cytokine storm through the downregulation of inflammatory mediators in the arachidonic acid pathway.
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Affiliation(s)
- Mohsen Sisakht
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Solhjoo
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Mahmoodzadeh
- Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Mohammad Fathalipour
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Endocrinology and Metabolic Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Maryam Kabiri
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.
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34
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Kaidashev I, Shlykova O, Izmailova O, Torubara O, Yushchenko Y, Tyshkovska T, Kyslyi V, Belyaeva A, Maryniak D. Host gene variability and SARS-CoV-2 infection: A review article. Heliyon 2021; 7:e07863. [PMID: 34458641 PMCID: PMC8382593 DOI: 10.1016/j.heliyon.2021.e07863] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/15/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is a global threat that influenced healthcare systems around the world. This virus caused an infection in humans with different clinical signs and syndromes, severity, and mortality. The key components of the COVID-19 molecular pathogenesis are coronavirus entry and replication, antigen presentation, humoral and cellular immunity, cytokine storm, coronavirus immune evasion. The analysis of recent literature displayed possible molecular targets in the key components of the COVID-19 pathogenesis. Some of these targets might have gene polymorphisms that influenced the COVID-19 course. Unfortunately, several findings are still putative or extrapolated from SARS and MERS experimental investigations or clinical trials. We systematised original data about gene polymorphisms of possible molecular targets and associations with the COVID-19 course. Most data were obtained for angiotensin-converting enzymes 1 and 2, TMPRSS2 gene polymorphisms. Only a few results were found for gene polymorphisms of adhesion molecules, interferon system components, cytokines, and transcriptional factors, oxidative stress and metabolic molecules, as well as haemocoagulation. Understanding the host gene variability and its associations with COVID-19 can provide insights into the disease pathogenesis, individual susceptibility to SARS-CoV-2 infection, severity, complications, and mortality prognosis for the disease. Besides, these data might help in the identification of appropriate targets for intervention.
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Affiliation(s)
- I. Kaidashev
- Poltava State Medical University, Poltava, Ukraine
| | - O. Shlykova
- Poltava State Medical University, Poltava, Ukraine
| | - O. Izmailova
- Poltava State Medical University, Poltava, Ukraine
| | - O. Torubara
- Poltava State Medical University, Poltava, Ukraine
| | | | | | - V. Kyslyi
- Poltava State Medical University, Poltava, Ukraine
| | - A. Belyaeva
- Poltava State Medical University, Poltava, Ukraine
| | - D. Maryniak
- Poltava State Medical University, Poltava, Ukraine
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35
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Das JK, Roy S. Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns. Genomics 2021; 113:2177-2188. [PMID: 34019999 PMCID: PMC8131179 DOI: 10.1016/j.ygeno.2021.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/04/2023]
Abstract
The prevailing COVID-19 pandemic has drawn the attention of the scientific community to study the evolutionary origin of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). This study is a comprehensive quantitative analysis of the protein-coding sequences of seven human coronaviruses (HCoVs) to decipher the nucleotide sequence variability and codon usage patterns. It is essential to understand the survival ability of the viruses, their adaptation to hosts, and their evolution. The current analysis revealed a high abundance of the relative dinucleotide (odds ratio), GC and CT pairs in the first and last two codon positions, respectively, as well as a low abundance of the CG pair in the last two positions of the codon, which might be related to the evolution of the viruses. A remarkable level of variability of GC content in the third position of the codon among the seven coronaviruses was observed. Codons with high RSCU values are primarily from the aliphatic and hydroxyl amino acid groups, and codons with low RSCU values belong to the aliphatic, cyclic, positively charged, and sulfur-containing amino acid groups. In order to elucidate the evolutionary processes of the seven coronaviruses, a phylogenetic tree (dendrogram) was constructed based on the RSCU scores of the codons. The severe and mild categories CoVs were positioned in different clades. A comparative phylogenetic study with other coronaviruses depicted that SARS-CoV-2 is close to the CoV isolated from pangolins (Manis javanica, Pangolin-CoV) and cats (Felis catus, SARS(r)-CoV). Further analysis of the effective number of codon (ENC) usage bias showed a relatively higher bias for SARS-CoV and MERS-CoV compared to SARS-CoV-2. The ENC plot against GC3 suggested that the mutational bias might have a role in determining the codon usage variation among candidate viruses. A codon adaptability study on a few human host parasites (from different kingdoms), including CoVs, showed a diverse adaptability pattern. SARS-CoV-2 and SARS-CoV exhibit relatively lower but similar codon adaptability compared to MERS-CoV.
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Affiliation(s)
- Jayanta Kumar Das
- Department of Pediatrics, Johns Hopkins University School of Medicine, MD, USA.
| | - Swarup Roy
- Network Reconstruction & Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, Gangtok, India.
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Lv J, Tu S, Xu L. Detection of Phenotype-Related Mutations of COVID-19 via the Whole Genomic Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1242-1249. [PMID: 33417561 PMCID: PMC8769011 DOI: 10.1109/tcbb.2021.3049836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 11/30/2020] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
The coronavirus disease 2019 (COVID-19) epidemic continues to spread rapidly around the world and nearly 20 millions people are infected. This paper utilises both single-locus analysis and joint-SNPs analysis for detection of significant single nucleotide polymorphisms (SNPs) in the phenotypes of symptomatic versus asymptomatic, the early collection time versus the late collection time, the old versus the young, and the male versus the female. Also, this paper analyses the relationship between any two SNPs via linkage disequilibrium analysis, and visualises the patterns of cumulative mutations of SNPs over collection time. The results are in three folds. First, the SNP which locates at the nucleotide position 4321 is found to be an independent significant locus associated with all the first three phenotypes. Moreover, 12 significant SNPs are found in the first two studies. Second, gene orf1ab containing SNP-4321 is detected to be significantly associated with the first three phenotypes, and the three genes S, ORF3a, and N, are detected to be significant in the first two phenotypes. Third, some of the detected genes or SNPs are related to the SARS-COV-2 as supported by literature survey, which indicates that the results here may be helpful for further investigation.
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Affiliation(s)
- Jinxiong Lv
- Center for Cognitive Machines and Computational Health (CMaCH)Department of Computer Science and EngineeringShanghai Jiao Tong UniversityShanghai200240China
| | - Shikui Tu
- Center for Cognitive Machines and Computational Health (CMaCH)Department of Computer Science and EngineeringShanghai Jiao Tong UniversityShanghai200240China
| | - Lei Xu
- Center for Cognitive Machines and Computational Health (CMaCH)Department of Computer Science and EngineeringShanghai Jiao Tong UniversityShanghai200240China
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Gorkhali R, Koirala P, Rijal S, Mainali A, Baral A, Bhattarai HK. Structure and Function of Major SARS-CoV-2 and SARS-CoV Proteins. Bioinform Biol Insights 2021; 15:11779322211025876. [PMID: 34220199 PMCID: PMC8221690 DOI: 10.1177/11779322211025876] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/25/2021] [Indexed: 01/20/2023] Open
Abstract
SARS-CoV-2 virus, the causative agent of COVID-19 pandemic, has a genomic organization consisting of 16 nonstructural proteins (nsps), 4 structural proteins, and 9 accessory proteins. Relative of SARS-CoV-2, SARS-CoV, has genomic organization, which is very similar. In this article, the function and structure of the proteins of SARS-CoV-2 and SARS-CoV are described in great detail. The nsps are expressed as a single or two polyproteins, which are then cleaved into individual proteins using two proteases of the virus, a chymotrypsin-like protease and a papain-like protease. The released proteins serve as centers of virus replication and transcription. Some of these nsps modulate the host’s translation and immune systems, while others help the virus evade the host immune system. Some of the nsps help form replication-transcription complex at double-membrane vesicles. Others, including one RNA-dependent RNA polymerase and one exonuclease, help in the polymerization of newly synthesized RNA of the virus and help minimize the mutation rate by proofreading. After synthesis of the viral RNA, it gets capped. The capping consists of adding GMP and a methylation mark, called cap 0 and additionally adding a methyl group to the terminal ribose called cap1. Capping is accomplished with the help of a helicase, which also helps remove a phosphate, two methyltransferases, and a scaffolding factor. Among the structural proteins, S protein forms the receptor of the virus, which latches on the angiotensin-converting enzyme 2 receptor of the host and N protein binds and protects the genomic RNA of the virus. The accessory proteins found in these viruses are small proteins with immune modulatory roles. Besides functions of these proteins, solved X-ray and cryogenic electron microscopy structures related to the function of the proteins along with comparisons to other coronavirus homologs have been described in the article. Finally, the rate of mutation of SARS-CoV-2 residues of the proteome during the 2020 pandemic has been described. Some proteins are mutated more often than other proteins, but the significance of these mutation rates is not fully understood.
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Affiliation(s)
- Ritesh Gorkhali
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | | | - Sadikshya Rijal
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | - Ashmita Mainali
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | - Adesh Baral
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
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Wu F, Chen Y, You K, Tan S, Xu Y, Wang PH, Liu S, Li YX. Generation of WAe001-A-58 human embryonic stem cell line with inducible expression of the SARS-CoV-2 nucleocapsid protein. Stem Cell Res 2021; 53:102197. [PMID: 33771478 PMCID: PMC7835078 DOI: 10.1016/j.scr.2021.102197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 11/20/2022] Open
Abstract
Excessive prostaglandin E2 (PGE2) is the key pathological basis for COVID-19 and a Celebrex treatment of hospitalized COVID-19 patients with comorbidities led to 100% discharged rate and zero death (Hong et al. 2020). It is also suggested that SARS-CoV-2 infected multiple organs and the SARS-CoV nucleocapsid (N) protein transcriptionally drives the expression of the host COX-2 gene. In order to test whether SARS-CoV-2 N protein activates COX-2 transcription in multiple human relevant cell types, an expression inducible human embryonic stem cell line was generated by piggyBac transposon system. This cell line maintained its pluripotency, differentiation potentials, normal morphology and karyotype.
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Affiliation(s)
- Feima Wu
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yan Chen
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Kai You
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Shenglin Tan
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yingying Xu
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Pei-Hui Wang
- Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shiming Liu
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Yin-Xiong Li
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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Oz M, Lorke DE, Kabbani N. A comprehensive guide to the pharmacologic regulation of angiotensin converting enzyme 2 (ACE2), the SARS-CoV-2 entry receptor. Pharmacol Ther 2021; 221:107750. [PMID: 33275999 PMCID: PMC7854082 DOI: 10.1016/j.pharmthera.2020.107750] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023]
Abstract
The recent emergence of coronavirus disease-2019 (COVID-19) as a global pandemic has prompted scientists to address an urgent need for defining mechanisms of disease pathology and treatment. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent for COVID-19, employs angiotensin converting enzyme 2 (ACE2) as its primary target for cell surface attachment and likely entry into the host cell. Thus, understanding factors that may regulate the expression and function of ACE2 in the healthy and diseased body is critical for clinical intervention. Over 66% of all adults in the United States are currently using a prescription drug and while earlier findings have focused on possible upregulation of ACE2 expression through the use of renin angiotensin system (RAS) inhibitors, mounting evidence suggests that various other widely administered drugs used in the treatment of hypertension, heart failure, diabetes mellitus, hyperlipidemias, coagulation disorders, and pulmonary disease may also present a varied risk for COVID-19. Specifically, we summarize mechanisms on how heparin, statins, steroids and phytochemicals, besides their established therapeutic effects, may also interfere with SARS-CoV-2 viral entry into cells. We also describe evidence on the effect of several vitamins, phytochemicals, and naturally occurring compounds on ACE2 expression and activity in various tissues and disease models. This comprehensive review aims to provide a timely compendium on the potential impact of commonly prescribed drugs and pharmacologically active compounds on COVID-19 pathology and risk through regulation of ACE2 and RAS signaling.
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Key Words
- adam17, a disintegrin and metalloprotease 17
- ace, angiotensin i converting enzyme
- ace-inh., angiotensin i converting enzyme inhibitor
- ampk, amp-activated protein kinase
- ang-ii, angiotensin ii
- arb, angiotensin ii type 1-receptor blocker
- ards, acute respiratory distress syndrome
- at1-r, angiotensin ii type 1-receptor
- βarb, β-adrenergic receptor blockers
- bk, bradykinin
- ccb, calcium channel blockers
- ch25h, cholesterol-25-hydroxylase
- copd, chronic obstructive lung disease
- cox, cyclooxygenase
- covid-19, coronavirus disease-2019
- dabk, [des-arg9]-bradykinin
- erk, extracellular signal-regulated kinase
- 25hc, 25-hydroxycholesterol
- hs, heparan sulfate
- hspg, heparan sulfate proteoglycan
- ibd, inflammatory bowel disease
- map, mitogen-activated protein
- mers, middle east respiratory syndrome
- mrb, mineralocorticoid receptor blocker
- nos, nitric oxide synthase
- nsaid, non-steroid anti-inflammatory drug
- ras, renin-angiotensin system
- sars-cov, severe acute respiratory syndrome coronavirus
- sh, spontaneously hypertensive
- s protein, spike protein
- sirt1, sirtuin 1
- t2dm, type 2 diabetes mellitus
- tcm, traditional chinese medicine
- tmprss2, transmembrane protease, serine 2
- tnf, tumor necrosis factor
- ufh, unfractionated heparin
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Affiliation(s)
- Murat Oz
- Department of Pharmacology and Therapeutics, Faculty of Pharmacy, Kuwait University, Safat 13110, Kuwait.
| | - Dietrich Ernst Lorke
- Department of Anatomy and Cellular Biology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates; Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Nadine Kabbani
- School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
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Antiviral Properties of the NSAID Drug Naproxen Targeting the Nucleoprotein of SARS-CoV-2 Coronavirus. Molecules 2021; 26:molecules26092593. [PMID: 33946802 PMCID: PMC8124269 DOI: 10.3390/molecules26092593] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
There is an urgent need for specific antiviral treatments directed against SARS-CoV-2 to prevent the most severe forms of COVID-19. By drug repurposing, affordable therapeutics could be supplied worldwide in the present pandemic context. Targeting the nucleoprotein N of the SARS-CoV-2 coronavirus could be a strategy to impede viral replication and possibly other essential functions associated with viral N. The antiviral properties of naproxen, a non-steroidal anti-inflammatory drug (NSAID) that was previously demonstrated to be active against Influenza A virus, were evaluated against SARS-CoV-2. Intrinsic fluorescence spectroscopy, fluorescence anisotropy, and dynamic light scattering assays demonstrated naproxen binding to the nucleoprotein of SARS-Cov-2 as predicted by molecular modeling. Naproxen impeded recombinant N oligomerization and inhibited viral replication in infected cells. In VeroE6 cells and reconstituted human primary respiratory epithelium models of SARS-CoV-2 infection, naproxen specifically inhibited viral replication and protected the bronchial epithelia against SARS-CoV-2-induced damage. No inhibition of viral replication was observed with paracetamol or the COX-2 inhibitor celecoxib. Thus, among the NSAID tested, only naproxen combined antiviral and anti-inflammatory properties. Naproxen addition to the standard of care could be beneficial in a clinical setting, as tested in an ongoing clinical study.
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Hatakeyama D, Masuda T, Miki R, Ohtsuki S, Kuzuhara T. In-vitro acetylation of SARS-CoV and SARS-CoV-2 nucleocapsid proteins by human PCAF and GCN5. Biochem Biophys Res Commun 2021; 557:273-279. [PMID: 33894414 PMCID: PMC8030717 DOI: 10.1016/j.bbrc.2021.03.173] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022]
Abstract
Recently, the novel coronavirus (SARS-CoV-2), which has spread from China to the world, was declared a global public health emergency, which causes lethal respiratory infections. Acetylation of several proteins plays essential roles in various biological processes, such as viral infections. We reported that the nucleoproteins of influenza virus and Zaire Ebolavirus were acetylated, suggesting that these modifications contributed to the molecular events involved in viral replication. Similar to influenza virus and Ebolavirus, the coronavirus also contains single-stranded RNA, as its viral genome interacts with the nucleocapsid (N) proteins. In this study, we report that SARS-CoV and SARS-CoV-2 N proteins are strongly acetylated by human histone acetyltransferases, P300/CBP-associated factor (PCAF), and general control nonderepressible 5 (GCN5), but not by CREB-binding protein (CBP) in vitro. Liquid chromatography-mass spectrometry analyses identified 2 and 12 acetyl-lysine residues from SARS-CoV and SARS-CoV-2 N proteins, respectively. Particularly in the SARS-CoV-2 N proteins, the acetyl-lysine residues were localized in or close to several functional sites, such as the RNA interaction domains and the M-protein interacting site. These results suggest that acetylation of SARS-CoV-2 N proteins plays crucial roles in their functions.
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Affiliation(s)
- Dai Hatakeyama
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, 770-8514, Japan.
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Ryosuke Miki
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, 770-8514, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Takashi Kuzuhara
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, 770-8514, Japan.
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Das JK, Roy S. A study on non-synonymous mutational patterns in structural proteins of SARS-CoV-2. Genome 2021; 64:665-678. [PMID: 33788636 DOI: 10.1139/gen-2020-0157] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SARS-CoV-2 is mutating and creating divergent variants across the world. An in-depth investigation of the amino acid substitutions in the genomic signature of SARS-CoV-2 proteins is highly essential for understanding its host adaptation and infection biology. A total of 9587 SARS-CoV-2 structural protein sequences collected from 49 different countries are used to characterize protein-wise variants, substitution patterns (type and location), and major substitution changes. The majority of the substitutions are distinct, mostly in a particular location, and lead to a change in an amino acid's biochemical properties. In terms of mutational changes, envelope (E) and membrane (M) proteins are relatively more stable than nucleocapsid (N) and spike (S) proteins. Several co-occurrence substitutions are observed, particularly in S and N proteins. Substitution specific to active sub-domains reveals that heptapeptide repeat, fusion peptides, transmembrane in S protein, and N-terminal and C-terminal domains in the N protein are remarkably mutated. We also observe a few deleterious mutations in the above domains. The overall study on non-synonymous mutation in structural proteins of SARS-CoV-2 at the start of the pandemic indicates a diversity amongst virus sequences.
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Affiliation(s)
- Jayanta Kumar Das
- Department of Pediatrics, Johns Hopkins University School of Medicine, Maryland, USA
| | - Swarup Roy
- Network Reconstruction & Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, Gangtok, India
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Li Y, Jiang Y, Zhang Y, Li N, Yin Q, Liu L, Lv X, Liu Y, Li A, Fang B, Li J, Ye H, Yang G, Cui X, Liu Y, Qu Y, Li C, Li J, Li D, Gai Z, Wang S, Zhan F, Liang M. Abnormal upregulation of cardiovascular disease biomarker PLA2G7 induced by proinflammatory macrophages in COVID-19 patients. Sci Rep 2021; 11:6811. [PMID: 33762651 PMCID: PMC7990942 DOI: 10.1038/s41598-021-85848-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/08/2021] [Indexed: 01/07/2023] Open
Abstract
High rate of cardiovascular disease (CVD) has been reported among patients with coronavirus disease 2019 (COVID-19). Importantly, CVD, as one of the comorbidities, could also increase the risks of the severity of COVID-19. Here we identified phospholipase A2 group VII (PLA2G7), a well-studied CVD biomarker, as a hub gene in COVID-19 though an integrated hypothesis-free genomic analysis on nasal swabs (n = 486) from patients with COVID-19. PLA2G7 was further found to be predominantly expressed by proinflammatory macrophages in lungs emerging with progression of COVID-19. In the validation stage, RNA level of PLA2G7 was identified in nasal swabs from both COVID-19 and pneumonia patients, other than health individuals. The positive rate of PLA2G7 were correlated with not only viral loads but also severity of pneumonia in non-COVID-19 patients. Serum protein levels of PLA2G7 were found to be elevated and beyond the normal limit in COVID-19 patients, especially among those re-positive patients. We identified and validated PLA2G7, a biomarker for CVD, was abnormally enhanced in COVID-19 at both nucleotide and protein aspects. These findings provided indications into the prevalence of cardiovascular involvements seen in patients with COVID-19. PLA2G7 could be a potential prognostic and therapeutic target in COVID-19.
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Affiliation(s)
- Yang Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yongzhong Jiang
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430065, China
| | - Yi Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Naizhe Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qiangling Yin
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Linlin Liu
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430065, China
| | - Xin Lv
- Qilu Children's Hospital, Cheeloo College of Medicine, Shandong University and Jinan Children's Hospital, Jinan, 250022, China
| | - Yan Liu
- Department of Microbiology, School of Basic Medical Science, Anhui Medical University, Hefei, 230032, China
| | - Aqian Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Bin Fang
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430065, China
| | - Jiajia Li
- The Center for Scientific Research of the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Hengping Ye
- Xiantao Center for Disease Control and Prevention, Xiantao, 433000, China
| | - Gang Yang
- Xiangyang Center for Disease Control and Prevention, Xiangyang, 441000, China
| | - Xiaoxian Cui
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200336, China
| | - Yang Liu
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yuanyuan Qu
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Chuan Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jiandong Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Dexin Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Zhongtao Gai
- Qilu Children's Hospital, Cheeloo College of Medicine, Shandong University and Jinan Children's Hospital, Jinan, 250022, China
| | - Shiwen Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
- CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Wuhan, 430071, China.
| | - Faxian Zhan
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430065, China.
| | - Mifang Liang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
- CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Wuhan, 430071, China.
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Chen JS, Alfajaro MM, Chow RD, Wei J, Filler RB, Eisenbarth SC, Wilen CB. Non-steroidal anti-inflammatory drugs dampen the cytokine and antibody response to SARS-CoV-2 infection. J Virol 2021; 95:JVI.00014-21. [PMID: 33441348 PMCID: PMC8092681 DOI: 10.1128/jvi.00014-21] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022] Open
Abstract
Identifying drugs that regulate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and its symptoms has been a pressing area of investigation during the coronavirus disease 2019 (COVID-19) pandemic. Nonsteroidal anti-inflammatory drugs (NSAIDs), which are frequently used for the relief of pain and inflammation, could modulate both SARS-CoV-2 infection and the host response to the virus. NSAIDs inhibit the enzymes cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2), which mediate the production of prostaglandins (PGs). As PGs play diverse biological roles in homeostasis and inflammatory responses, inhibiting PG production with NSAIDs could affect COVID-19 pathogenesis in multiple ways, including: (1) altering susceptibility to infection by modifying expression of angiotensin-converting enzyme 2 (ACE2), the cell entry receptor for SARS-CoV-2; (2) regulating replication of SARS-CoV-2 in host cells; and (3) modulating the immune response to SARS-CoV-2. Here, we investigate these potential roles. We demonstrate that SARS-CoV-2 infection upregulates COX-2 in diverse human cell culture and mouse systems. However, suppression of COX-2 by two commonly used NSAIDs, ibuprofen and meloxicam, had no effect on ACE2 expression, viral entry, or viral replication. In contrast, in a mouse model of SARS-CoV-2 infection, NSAID treatment reduced production of pro-inflammatory cytokines and impaired the humoral immune response to SARS-CoV-2 as demonstrated by reduced neutralizing antibody titers. Our findings indicate that NSAID treatment may influence COVID-19 outcomes by dampening the inflammatory response and production of protective antibodies rather than modifying susceptibility to infection or viral replication.ImportancePublic health officials have raised concerns about the use of nonsteroidal anti-inflammatory drugs (NSAIDs) for treating symptoms of coronavirus disease 2019 (COVID-19). NSAIDs inhibit the enzymes cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2), which are critical for the generation of prostaglandins - lipid molecules with diverse roles in homeostasis and inflammation. Inhibition of prostaglandin production by NSAIDs could therefore have multiple effects on COVID-19 pathogenesis. Here, we demonstrate that NSAID treatment reduced both the antibody and pro-inflammatory cytokine response to SARS-CoV-2 infection. The ability of NSAIDs to modulate the immune response to SARS-CoV-2 infection has important implications for COVID-19 pathogenesis in patients. Whether this occurs in humans and whether it is beneficial or detrimental to the host remains an important area of future investigation. This also raises the possibility that NSAIDs may alter the immune response to SARS-CoV-2 vaccination.
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Affiliation(s)
- Jennifer S Chen
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ryan D Chow
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jin Wei
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie C Eisenbarth
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
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45
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Jansen van Vuren E, Steyn SF, Brink CB, Möller M, Viljoen FP, Harvey BH. The neuropsychiatric manifestations of COVID-19: Interactions with psychiatric illness and pharmacological treatment. Biomed Pharmacother 2021; 135:111200. [PMID: 33421734 PMCID: PMC7834135 DOI: 10.1016/j.biopha.2020.111200] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/15/2020] [Accepted: 12/26/2020] [Indexed: 12/12/2022] Open
Abstract
The recent outbreak of the corona virus disease (COVID-19) has had major global impact. The relationship between severe acute respiratory syndrome coronavirus (SARS-CoV-2) infection and psychiatric diseases is of great concern, with an evident link between corona virus infections and various central and peripheral nervous system manifestations. Unmitigated neuro-inflammation has been noted to underlie not only the severe respiratory complications of the disease but is also present in a range of neuro-psychiatric illnesses. Several neurological and psychiatric disorders are characterized by immune-inflammatory states, while treatments for these disorders have distinct anti-inflammatory properties and effects. With inflammation being a common contributing factor in SARS-CoV-2, as well as psychiatric disorders, treatment of either condition may affect disease progression of the other or alter response to pharmacological treatment. In this review, we elucidate how viral infections could affect pre-existing psychiatric conditions and how pharmacological treatments of these conditions may affect overall progress and outcome in the treatment of SARS-CoV-2. We address whether any treatment-induced benefits and potential adverse effects may ultimately affect the overall treatment approach, considering the underlying dysregulated neuro-inflammatory processes and potential drug interactions. Finally, we suggest adjunctive treatment options for SARS-CoV-2-associated neuro-psychiatric symptoms.
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Affiliation(s)
- Esmé Jansen van Vuren
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa.
| | - Stephan F Steyn
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa
| | - Christiaan B Brink
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa
| | - Marisa Möller
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa
| | - Francois P Viljoen
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa
| | - Brian H Harvey
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa; South African MRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa.
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46
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Ricke DO. Two Different Antibody-Dependent Enhancement (ADE) Risks for SARS-CoV-2 Antibodies. Front Immunol 2021; 12:640093. [PMID: 33717193 PMCID: PMC7943455 DOI: 10.3389/fimmu.2021.640093] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/03/2021] [Indexed: 01/08/2023] Open
Abstract
COVID-19 (SARS-CoV-2) disease severity and stages varies from asymptomatic, mild flu-like symptoms, moderate, severe, critical, and chronic disease. COVID-19 disease progression include lymphopenia, elevated proinflammatory cytokines and chemokines, accumulation of macrophages and neutrophils in lungs, immune dysregulation, cytokine storms, acute respiratory distress syndrome (ARDS), etc. Development of vaccines to severe acute respiratory syndrome (SARS), Middle East Respiratory Syndrome coronavirus (MERS-CoV), and other coronavirus has been difficult to create due to vaccine induced enhanced disease responses in animal models. Multiple betacoronaviruses including SARS-CoV-2 and SARS-CoV-1 expand cellular tropism by infecting some phagocytic cells (immature macrophages and dendritic cells) via antibody bound Fc receptor uptake of virus. Antibody-dependent enhancement (ADE) may be involved in the clinical observation of increased severity of symptoms associated with early high levels of SARS-CoV-2 antibodies in patients. Infants with multisystem inflammatory syndrome in children (MIS-C) associated with COVID-19 may also have ADE caused by maternally acquired SARS-CoV-2 antibodies bound to mast cells. ADE risks associated with SARS-CoV-2 has implications for COVID-19 and MIS-C treatments, B-cell vaccines, SARS-CoV-2 antibody therapy, and convalescent plasma therapy for patients. SARS-CoV-2 antibodies bound to mast cells may be involved in MIS-C and multisystem inflammatory syndrome in adults (MIS-A) following initial COVID-19 infection. SARS-CoV-2 antibodies bound to Fc receptors on macrophages and mast cells may represent two different mechanisms for ADE in patients. These two different ADE risks have possible implications for SARS-CoV-2 B-cell vaccines for subsets of populations based on age, cross-reactive antibodies, variabilities in antibody levels over time, and pregnancy. These models place increased emphasis on the importance of developing safe SARS-CoV-2 T cell vaccines that are not dependent upon antibodies.
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Affiliation(s)
- Darrell O. Ricke
- Biological and Chemical Technologies, Massachusetts Institute of Technology Lincoln Laboratory, Biotechnology and Human Systems, Lexington, MA, United States
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47
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Roberts J, Pritchard AL, Treweeke AT, Rossi AG, Brace N, Cahill P, MacRury SM, Wei J, Megson IL. Why Is COVID-19 More Severe in Patients With Diabetes? The Role of Angiotensin-Converting Enzyme 2, Endothelial Dysfunction and the Immunoinflammatory System. Front Cardiovasc Med 2021; 7:629933. [PMID: 33614744 PMCID: PMC7886785 DOI: 10.3389/fcvm.2020.629933] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/15/2020] [Indexed: 01/08/2023] Open
Abstract
Meta-analyses have indicated that individuals with type 1 or type 2 diabetes are at increased risk of suffering a severe form of COVID-19 and have a higher mortality rate than the non-diabetic population. Patients with diabetes have chronic, low-level systemic inflammation, which results in global cellular dysfunction underlying the wide variety of symptoms associated with the disease, including an increased risk of respiratory infection. While the increased severity of COVID-19 amongst patients with diabetes is not yet fully understood, the common features associated with both diseases are dysregulated immune and inflammatory responses. An additional key player in COVID-19 is the enzyme, angiotensin-converting enzyme 2 (ACE2), which is essential for adhesion and uptake of virus into cells prior to replication. Changes to the expression of ACE2 in diabetes have been documented, but they vary across different organs and the importance of such changes on COVID-19 severity are still under investigation. This review will examine and summarise existing data on how immune and inflammatory processes interplay with the pathogenesis of COVID-19, with a particular focus on the impacts that diabetes, endothelial dysfunction and the expression dynamics of ACE2 have on the disease severity.
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Affiliation(s)
- Jacob Roberts
- Institute for Health Research and Innovation, University of the Highlands and Islands, Inverness, United Kingdom
| | - Antonia L. Pritchard
- Institute for Health Research and Innovation, University of the Highlands and Islands, Inverness, United Kingdom
| | - Andrew T. Treweeke
- Institute for Health Research and Innovation, University of the Highlands and Islands, Inverness, United Kingdom
| | - Adriano G. Rossi
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Nicole Brace
- Institute for Health Research and Innovation, University of the Highlands and Islands, Inverness, United Kingdom
| | - Paul Cahill
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Sandra M. MacRury
- Institute for Health Research and Innovation, University of the Highlands and Islands, Inverness, United Kingdom
| | - Jun Wei
- Institute for Health Research and Innovation, University of the Highlands and Islands, Inverness, United Kingdom
| | - Ian L. Megson
- Institute for Health Research and Innovation, University of the Highlands and Islands, Inverness, United Kingdom
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48
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Delafiori J, Navarro LC, Siciliano RF, de Melo GC, Busanello EN, Nicolau JC, Sales GM, de Oliveira AN, Val FFA, de Oliveira DN, Eguti A, dos Santos LA, Dalçóquio TF, Bertolin AJ, Abreu-Netto RL, Salsoso R, Baía-da-Silva D, Marcondes-Braga FG, Sampaio VS, Judice CC, Costa FT, Durán N, Perroud MW, Sabino EC, Lacerda MV, Reis LO, Fávaro WJ, Monteiro WM, Rocha AR, Catharino RR. Covid-19 Automated Diagnosis and Risk Assessment through Metabolomics and Machine Learning. Anal Chem 2021; 93:2471-2479. [PMID: 33471512 PMCID: PMC8023531 DOI: 10.1021/acs.analchem.0c04497] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/14/2021] [Indexed: 01/07/2023]
Abstract
COVID-19 is still placing a heavy health and financial burden worldwide. Impairment in patient screening and risk management plays a fundamental role on how governments and authorities are directing resources, planning reopening, as well as sanitary countermeasures, especially in regions where poverty is a major component in the equation. An efficient diagnostic method must be highly accurate, while having a cost-effective profile. We combined a machine learning-based algorithm with mass spectrometry to create an expeditious platform that discriminate COVID-19 in plasma samples within minutes, while also providing tools for risk assessment, to assist healthcare professionals in patient management and decision-making. A cross-sectional study enrolled 815 patients (442 COVID-19, 350 controls and 23 COVID-19 suspicious) from three Brazilian epicenters from April to July 2020. We were able to elect and identify 19 molecules related to the disease's pathophysiology and several discriminating features to patient's health-related outcomes. The method applied for COVID-19 diagnosis showed specificity >96% and sensitivity >83%, and specificity >80% and sensitivity >85% during risk assessment, both from blinded data. Our method introduced a new approach for COVID-19 screening, providing the indirect detection of infection through metabolites and contextualizing the findings with the disease's pathophysiology. The pairwise analysis of biomarkers brought robustness to the model developed using machine learning algorithms, transforming this screening approach in a tool with great potential for real-world application.
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Affiliation(s)
- Jeany Delafiori
- Innovare
Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Cidade Universitária
Zeferino Vaz, Campinas, São Paulo 350-13083-970, Brazil
| | - Luiz Cláudio Navarro
- RECOD
Laboratory, Computing Institute, University
of Campinas, Cidade Universitária Zeferino Vaz,, Campinas, São Paulo 573-13083-852, Brazil
| | - Rinaldo Focaccia Siciliano
- Clinical
Division of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, São Paulo 01246-903, Brazil
- Instituto
do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, Cerqueira César, São Paulo 44-05403-90, Brazil
| | - Gisely Cardoso de Melo
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Amazonas
State University, Manaus, Amazonas 25-69040-000, Brazil
| | - Estela Natacha
Brandt Busanello
- Innovare
Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Cidade Universitária
Zeferino Vaz, Campinas, São Paulo 350-13083-970, Brazil
| | - José Carlos Nicolau
- Instituto
do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, Cerqueira César, São Paulo 44-05403-90, Brazil
| | - Geovana Manzan Sales
- Innovare
Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Cidade Universitária
Zeferino Vaz, Campinas, São Paulo 350-13083-970, Brazil
| | - Arthur Noin de Oliveira
- Innovare
Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Cidade Universitária
Zeferino Vaz, Campinas, São Paulo 350-13083-970, Brazil
| | - Fernando Fonseca Almeida Val
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Amazonas
State University, Manaus, Amazonas 25-69040-000, Brazil
| | - Diogo Noin de Oliveira
- Innovare
Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Cidade Universitária
Zeferino Vaz, Campinas, São Paulo 350-13083-970, Brazil
| | - Adriana Eguti
- Sumaré
State Hospital, Sumaré, São Paulo 2400-13175-490, Brazil
| | | | - Talia Falcão Dalçóquio
- Instituto
do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, Cerqueira César, São Paulo 44-05403-90, Brazil
| | - Adriadne Justi Bertolin
- Instituto
do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, Cerqueira César, São Paulo 44-05403-90, Brazil
| | - Rebeca Linhares Abreu-Netto
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Amazonas
State University, Manaus, Amazonas 25-69040-000, Brazil
| | - Rocio Salsoso
- Instituto
do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, Cerqueira César, São Paulo 44-05403-90, Brazil
| | - Djane Baía-da-Silva
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Amazonas
State University, Manaus, Amazonas 25-69040-000, Brazil
| | - Fabiana G Marcondes-Braga
- Instituto
do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, Cerqueira César, São Paulo 44-05403-90, Brazil
| | - Vanderson Souza Sampaio
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Health
Surveillance Foundation of Amazonas State, Manaus, Amazonas, 4010-69093-018 Brazil
| | - Carla Cristina Judice
- Laboratory
of Tropical Diseases, Institute of Biology, University of Campinas, Cidade Universitária Zeferino Vaz, Campinas, São Paulo 13083-970 Brazil
| | - Fabio Trindade
Maranhão Costa
- Laboratory
of Tropical Diseases, Institute of Biology, University of Campinas, Cidade Universitária Zeferino Vaz, Campinas, São Paulo 13083-970 Brazil
| | - Nelson Durán
- Laboratory
of Urogenital Carcinogenesis and Immunotherapy, University of Campinas, Cidade Universitária Zeferino Vaz, Campinas, São Paulo 13083-865, Brazil
| | | | - Ester Cerdeira Sabino
- Institute
of Tropical Medicine, University of São
Paulo, São Paulo, São Paulo 470-05403-000,Brazil
| | - Marcus Vinicius
Guimarães Lacerda
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Leônidas and Maria Deane Institute, Manaus, Amazonas, 476-69057-070 Brazil
| | - Leonardo Oliveira Reis
- UroScience
Laboratory, University of Campinas, Cidade
Universitária Zeferino Vaz, Campinas, São Paulo 126-13083-887, Brazil
| | - Wagner José Fávaro
- Laboratory
of Urogenital Carcinogenesis and Immunotherapy, University of Campinas, Cidade Universitária Zeferino Vaz, Campinas, São Paulo 13083-865, Brazil
| | - Wuelton Marcelo Monteiro
- Tropical
Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas 69040-000,Brazil
- Amazonas
State University, Manaus, Amazonas 25-69040-000, Brazil
| | - Anderson Rezende Rocha
- RECOD
Laboratory, Computing Institute, University
of Campinas, Cidade Universitária Zeferino Vaz,, Campinas, São Paulo 573-13083-852, Brazil
| | - Rodrigo Ramos Catharino
- Innovare
Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Cidade Universitária
Zeferino Vaz, Campinas, São Paulo 350-13083-970, Brazil
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49
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Abstract
Viral genomes encode transcriptional regulators that alter the expression of viral and host genes. Despite an emerging role in human diseases, a thorough annotation of human viral transcriptional regulators (vTRs) is currently lacking, limiting our understanding of their molecular features and functions. Here, we provide a comprehensive catalog of 419 vTRs belonging to 20 different virus families. Using this catalog, we characterize shared and unique cellular genes, proteins, and pathways targeted by particular vTRs and discuss the role of vTRs in human disease pathogenesis. Our study provides a unique and valuable resource for the fields of virology, genomics, and human disease genetics.
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50
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Design of Multi-Epitope Vaccine against SARS-CoV-2. CYBERNETICS AND INFORMATION TECHNOLOGIES 2020. [DOI: 10.2478/cait-2020-0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The ongoing COVID-19 pandemic requires urgently specific therapeutics and approved vaccines. Here, the four structural proteins of the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), the causative agent of COVID-19, are screened by in-house immunoinformatic tools to identify peptides acting as potential T-cell epitopes. In order to act as an epitope, the peptide should be processed in the host cell and presented on the cell surface in a complex with the Human Leukocyte Antigen (HLA). The aim of the study is to predict the binding affinities of all peptides originating from the structural proteins of SARS-CoV-2 to 30 most frequent in the human population HLA proteins of class I and class II and to select the high binders (IC50 < 50 nM). The predicted high binders are compared to known high binders from SARS-CoV conserved in CoV-2 and 77% of them coincided. The high binders will be uploaded onto lipid nanoparticles and the multi-epitope vaccine prototype will be tested for ability to provoke T-cell mediated immunity and protection against SARS-CoV-2.
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