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Waqas M, Ullah S, Ullah A, Halim SA, Rehman NU, Khalid A, Ali A, Khan A, Gibbons S, Csuk R, Al-Harrasi A. Disrupting protease and deubiquitinase activities of SARS-CoV-2 papain-like protease by natural and synthetic products discovered through multiple computational and biochemical approaches. Int J Biol Macromol 2024; 277:134476. [PMID: 39111477 DOI: 10.1016/j.ijbiomac.2024.134476] [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: 12/21/2023] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024]
Abstract
The single-stranded RNA genome of SARS-CoV-2 encodes several structural and non-structural proteins, among which the papain-like protease (PLpro) is crucial for viral replication and immune evasion and has emerged as a promising therapeutic target. The current study aims to discover new inhibitors of PLpro that can simultaneously disrupt its protease and deubiquitinase activities. Using multiple computational approaches, six compounds (CP1-CP6) were selected from our in-house compounds database, with higher docking scores (-7.97 kcal/mol to -8.14 kcal/mol) and fitted well in the active pocket of PLpro. Furthermore, utilizing microscale molecular dynamics simulations (MD), the dynamic behavior of selected compounds was studied. Those molecules strongly binds at the PLpro active site and forms stable complexes. The dynamic motions suggest that the binding of CP1-CP6 brought the protein to a closed conformational state, thereby altering its normal function. In an in vitro evaluation, CP2 showed the most significant inhibitory potential for PLpro (protease activity = 2.71 ± 0.33 μM and deubiquitinase activity = 3.11 ± 0.75 μM), followed by CP1, CP5, CP4 and CP6. Additionally, CP1-CP6 showed no cytotoxicity at a concentration of 30 μM in the human BJ cell line.
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Affiliation(s)
- Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra 2100, Pakistan
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Atta Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Najeeb Ur Rehman
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Asaad Khalid
- Health Research Center, Jazan University, P.O. Box: 114, Jazan 45142, Saudi Arabia
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra 2100, Pakistan.
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman.
| | - Simon Gibbons
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Rene Csuk
- Martin-Luther-University Halle-Wittenberg, Organic Chemistry, Kurt-Mothes-Str. 2, D-06120 Halle (Saale), Germany
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman.
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2
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Lee S, Yoon SJ, Oh JH, Ryu JS, Park Y, Hwang ES. MPoMA protects against lung epithelial cell injury via p65 degradation. Biomed Pharmacother 2024; 175:116674. [PMID: 38703509 DOI: 10.1016/j.biopha.2024.116674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/20/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
Numerous cases of lung injury caused by viral infection were reported during the coronavirus disease-19 pandemic. While there have been significant efforts to develop drugs that block viral infection and spread, the development of drugs to reduce or reverse lung injury has been a lower priority. This study aimed to identify compounds from a library of compounds that prevent viral infection that could reduce and prevent lung epithelial cell damage. We investigated the cytotoxicity of the compounds, their activity in inhibiting viral spike protein binding to cells, and their activity in reducing IL-8 production in lung epithelial cells damaged by amodiaquine (AQ). We identified N-(4-(4-methoxyphenoxy)-3-methylphenyl)-N-methylacetamide (MPoMA) as a non-cytotoxic inhibitor against viral infection and AQ-induced cell damage. MPoMA inhibited the expression of IL-8, IL-6, IL-1β, and fibronectin induced by AQ and protected against AQ-induced morphological changes. However, MPoMA did not affect basal IL-8 expression in lung epithelial cells in the absence of AQ. Further mechanistic analysis confirmed that MPoMA selectively promoted the proteasomal degradation of inflammatory mediator p65, thereby reducing intracellular p65 expression and p65-mediated inflammatory responses. MPoMA exerted potent anti-inflammatory and protective functions in epithelial cells against LPS-induced acute lung injury in vivo. These findings suggest that MPoMA may have beneficial effects in suppressing viral infection and preventing lung epithelial cell damage through the degradation of p65 and inhibition of the production of inflammatory cytokines.
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Affiliation(s)
- Soheun Lee
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Suh Jin Yoon
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ji Hyun Oh
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jae-Sang Ryu
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yunjeong Park
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Eun Sook Hwang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea.
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3
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Inglis TJJ. A systematic approach to microbial forensics. J Med Microbiol 2024; 73. [PMID: 38305344 DOI: 10.1099/jmm.0.001802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
The coronavirus disease 2019 pandemic accelerated developments in biotechnology that underpin infection science. These advances present an opportunity to refresh the microbial forensic toolkit. Integration of novel analytical techniques with established forensic methods will speed up acquisition of evidence and better support lines of enquiry. A critical part of any such investigation is demonstration of a robust causal relationship and attribution of responsibility for an incident. In the wider context of a formal investigation into agency, motivation and intent, the quick and efficient assembly of microbiological evidence sets the tone and tempo of the entire investigation. Integration of established and novel analytical techniques from infection science into a systematic approach to microbial forensics will therefore ensure that major perspectives are correctly used to frame and shape the evidence into a clear narrative, while recognizing that forensic hypothesis generation, testing and refinement comprise an iterative process. Development of multidisciplinary training exercises that use this approach will enable translation into practice and efficient implementation when the need arises.
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Affiliation(s)
- T J J Inglis
- Pathology and Laboratory Medicine, School of Medicine, University of Western Australia, Crawley, WA 6009, Australia
- PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA 6009, Australia
- Western Australian Country Health Service, Perth, WA 6000, Australia
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4
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Waqas M, Ullah S, Halim SA, Rehman NU, Ali A, Jan A, Muhsinah AB, Khan A, Al-Harrasi A. Targeting papain-like protease by natural products as novel therapeutic potential SARS-CoV-2. Int J Biol Macromol 2024; 258:128812. [PMID: 38114011 DOI: 10.1016/j.ijbiomac.2023.128812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
The highly infectious respiratory illness 'COVID-19' was caused by SARS-CoV-2 and is responsible for millions of deaths. SARS-single-stranded viral RNA genome encodes several structural and nonstructural proteins, including papain-like protease (PLpro), which is essential for viral replication and immune evasion and serve as a potential therapeutic target. Multiple computational techniques were used to search the natural compounds that may block the protease and deubiquitinase activities of PLpro. Five compounds showed strong interactions and binding energy (ranges between -8.18 to -8.69 Kcal/mol) in our in-silico studies. Interestingly, those molecules strongly bind in the PLpro active site and form a stable complex, as shown by microscale molecular dynamic simulations (MD). The dynamic movements indicate that PLpro acquires closed conformation by the attachment of these molecules, thereby changing its normal function. In the in-vitro evaluation, compound COMP4 showed the most potent inhibitory potential for PLpro (protease activity: 2.24 ± 0.17 μM and deubiquitinase activity: 1.43 ± 0.14 μM), followed by COMP1, 2, 3, and 5. Furthermore, the cytotoxic effect of COMP1-COMP5 on a human BJ cell line revealed that these compounds demonstrate negligible cytotoxicity at a dosage of 30 μM. The results suggest that these entities bear therapeutic efficacy for SARS-CoV-2 PLpro.
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Affiliation(s)
- Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 2100, Pakistan
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Najeeb Ur Rehman
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 2100, Pakistan.
| | - Afnan Jan
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Abdullatif Bin Muhsinah
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman.
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5
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Xiao SQ, Wen TZ, Chen XY, Chen HY, Li Z, He ZC, Luo T, Tang R, Fu WJ, Cao MF, Chen L, Niu Q, Wang S, Lan Y, Ge J, Li QR, Guo HT, Wang YX, Ping YF, Shen H, Wang Y, Ding YQ, Bian XW, Yao XH. Autopsy analysis reveals increased macrophage infiltration and cell apoptosis in COVID-19 patients with severe pulmonary fibrosis. Pathol Res Pract 2023; 252:154920. [PMID: 37948998 DOI: 10.1016/j.prp.2023.154920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Clinical data indicates that SARS-CoV-2 infection-induced respiratory failure is a fatal condition for severe COVID-19 patients. However, the pathological alterations of different types of respiratory failure remained unknown for severe COVID-19 patients. This study aims to evaluate whether there are differences in the performance of various types of respiratory failure in severe COVID-19 patients and investigate the pathological basis for these differences. The lung tissue sections of severe COVID-19 patients were assessed for the degree of injury and immune responses. Transcriptome data were used to analyze the molecular basis in severe COVID-19 patients. Severe COVID-19 patients with combined oxygenation and ventilatory failure presented more severe pulmonary fibrosis, airway obstruction, and prolonged disease course. The number of M2 macrophages increased with the degree of fibrosis in patients, suggesting that it may be closely related to the development of pulmonary fibrosis. The co-existence of pro-inflammatory and anti-inflammatory cytokines in the pulmonary environment could also participate in the progression of pulmonary fibrosis. Furthermore, the increased apoptosis in the lungs of COVID-19 patients with severe pulmonary fibrosis may represent a critical factor linking sustained inflammatory responses to fibrosis. Our findings indicate that during the extended phase of COVID-19, antifibrotic and antiapoptotic treatments should be considered in conjunction with the progression of the disease.
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Affiliation(s)
- Shi-Qi Xiao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Tian-Zi Wen
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Xin-Yu Chen
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - He-Yuan Chen
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Zhuang Li
- Department of Neurology, Armed Corps Police Hospital of Chongqing, Chongqing, China
| | - Zhi-Cheng He
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Tao Luo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Rui Tang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Wen-Juan Fu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Mian-Fu Cao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Lu Chen
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Qin Niu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Shuai Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Yang Lan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Jia Ge
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Qing-Rui Li
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Hai-Tao Guo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Yan-Xia Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Yi-Fang Ping
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Hong Shen
- Department of Pathology, Southern Medical University, Guangzhou, China
| | - Yan Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Yan-Qing Ding
- Department of Pathology, Southern Medical University, Guangzhou, China
| | - Xiu-Wu Bian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Xiao-Hong Yao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China.
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6
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Erickson R, Huang C, Allen C, Ireland J, Roth G, Zou Z, Lu J, Lafont BAP, Garza NL, Brumbaugh B, Zhao M, Suzuki M, Olano L, Brzostowski J, Fischer ER, Twigg HL, Johnson RF, Sun PD. SARS-CoV-2 infection of human lung epithelial cells induces TMPRSS-mediated acute fibrin deposition. Nat Commun 2023; 14:6380. [PMID: 37821447 PMCID: PMC10567911 DOI: 10.1038/s41467-023-42140-6] [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: 06/09/2022] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
Severe COVID-associated lung injury is a major confounding factor of hospitalizations and death with no effective treatments. Here, we describe a non-classical fibrin clotting mechanism mediated by SARS-CoV-2 infected primary lung but not other susceptible epithelial cells. This infection-induced fibrin formation is observed in all variants of SARS-CoV-2 infections, and requires thrombin but is independent of tissue factor and other classical plasma coagulation factors. While prothrombin and fibrinogen levels are elevated in acute COVID BALF samples, fibrin clotting occurs only with the presence of viral infected but not uninfected lung epithelial cells. We suggest a viral-induced coagulation mechanism, in which prothrombin is activated by infection-induced transmembrane serine proteases, such as ST14 and TMPRSS11D, on NHBE cells. Our finding reveals the inefficiency of current plasma targeted anticoagulation therapy and suggests the need to develop a viral-induced ARDS animal model for treating respiratory airways with thrombin inhibitors.
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Affiliation(s)
- Rachel Erickson
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5625 Fishers Ln, Rockville, MD, 20852, USA
| | - Chang Huang
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5625 Fishers Ln, Rockville, MD, 20852, USA
| | - Cameron Allen
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5625 Fishers Ln, Rockville, MD, 20852, USA
| | - Joanna Ireland
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5625 Fishers Ln, Rockville, MD, 20852, USA
| | - Gwynne Roth
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5625 Fishers Ln, Rockville, MD, 20852, USA
| | - Zhongcheng Zou
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5625 Fishers Ln, Rockville, MD, 20852, USA
| | - Jinghua Lu
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5625 Fishers Ln, Rockville, MD, 20852, USA
| | - Bernard A P Lafont
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nicole L Garza
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Beniah Brumbaugh
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th Street, Hamilton, MT, 59840, USA
| | - Ming Zhao
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5625 Fishers Ln, Rockville, MD, 20852, USA
| | - Motoshi Suzuki
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5625 Fishers Ln, Rockville, MD, 20852, USA
| | - Lisa Olano
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5625 Fishers Ln, Rockville, MD, 20852, USA
| | - Joseph Brzostowski
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5625 Fishers Ln, Rockville, MD, 20852, USA
| | - Elizabeth R Fischer
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th Street, Hamilton, MT, 59840, USA
| | - Homer L Twigg
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Indiana University Medical Center, 1120 West Michigan Street, CL 260A, Indianapolis, IN, 46202, USA
| | - Reed F Johnson
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Peter D Sun
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5625 Fishers Ln, Rockville, MD, 20852, USA.
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7
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D 2BOF-COVIDNet: A Framework of Deep Bayesian Optimization and Fusion-Assisted Optimal Deep Features for COVID-19 Classification Using Chest X-ray and MRI Scans. Diagnostics (Basel) 2022; 13:diagnostics13010101. [PMID: 36611393 PMCID: PMC9818184 DOI: 10.3390/diagnostics13010101] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND AND OBJECTIVE In 2019, a corona virus disease (COVID-19) was detected in China that affected millions of people around the world. On 11 March 2020, the WHO declared this disease a pandemic. Currently, more than 200 countries in the world have been affected by this disease. The manual diagnosis of this disease using chest X-ray (CXR) images and magnetic resonance imaging (MRI) is time consuming and always requires an expert person; therefore, researchers introduced several computerized techniques using computer vision methods. The recent computerized techniques face some challenges, such as low contrast CTX images, the manual initialization of hyperparameters, and redundant features that mislead the classification accuracy. METHODS In this paper, we proposed a novel framework for COVID-19 classification using deep Bayesian optimization and improved canonical correlation analysis (ICCA). In this proposed framework, we initially performed data augmentation for better training of the selected deep models. After that, two pre-trained deep models were employed (ResNet50 and InceptionV3) and trained using transfer learning. The hyperparameters of both models were initialized through Bayesian optimization. Both trained models were utilized for feature extractions and fused using an ICCA-based approach. The fused features were further optimized using an improved tree growth optimization algorithm that finally was classified using a neural network classifier. RESULTS The experimental process was conducted on five publically available datasets and achieved an accuracy of 99.6, 98.5, 99.9, 99.5, and 100%. CONCLUSION The comparison with recent methods and t-test-based analysis showed the significance of this proposed framework.
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Margiana R, Sharma SK, Khan BI, Alameri AA, Opulencia MJC, Hammid AT, Hamza TA, Babakulov SK, Abdelbasset WK, Jawhar ZH. RETRACTED: The pathogenicity of COVID-19 and the role of pentraxin-3: An updated review study. Pathol Res Pract 2022; 238:154128. [PMID: 36137396 PMCID: PMC9476367 DOI: 10.1016/j.prp.2022.154128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/03/2022] [Accepted: 09/13/2022] [Indexed: 01/08/2023]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/policies/article-withdrawal). This article has been retracted at the request of the Editor-in-Chief. In investigating concerns regarding the contributions of the authors to this article, the editors reached out to the authors for an explanation. In addition to the concerns regarding the contribution of each author, the editors discovered suspicious changes in authorship between the original submission and the revised version of this paper. The names of the authors Ameer A Alameri and Zanko Hassan Jawhar were added to the revised version of the article without explanation and without the exceptional approval by the handling Editor, which is contrary to the journal policy on changes to authorship. The authors were unable to provide a reasonable explanation for either of the issues raised. The editor therefore feels that the findings of the manuscript cannot be relied upon and that the article needs to be retracted.
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Affiliation(s)
- Ria Margiana
- Department of Anatomy, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Master's Programme Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Andrology Program, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia; Dr. Soetomo General Academic Hospital, Surabaya, Indonesia.
| | - Satish Kumar Sharma
- Department of Pharmacology, Glocal School of Pharmacy, The Glocal University, Saharanpur, India.
| | | | | | | | - Ali Thaeer Hammid
- Computer Engineering Techniques Department, Faculty of Information Technology, Imam Ja'afar Al-Sadiq University, Baghdad, Iraq
| | - Thulfeqar Ahmed Hamza
- Medical laboratory techniques department, Al-Mustaqbal University College, Babylon, Iraq
| | - Sharaf Khamrakulovich Babakulov
- Tashkent State Dental Institute, Makhtumkuli Street 103, Tashkent, 100047, Uzbekistan; Research scholar, Department of Scientific affairs, Samarkand State Medical Institute, Amir Temur Street 18, Samarkand, Uzbekistan
| | - Walid Kamal Abdelbasset
- Department of Health and Rehabilitation Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al Kharj, Saudi Arabia; Department of Physical Therapy, Kasr Al-Aini Hospital, Cairo University, Giza, Egypt
| | - Zanko Hassan Jawhar
- Department of Medical Laboratory Science, College of Health Science, Lebanese French University, Kurdistan Region, Iraq
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9
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Gambella A, Barreca A, Biancone L, Roccatello D, Peruzzi L, Besso L, Licata C, Attanasio A, Papotti M, Cassoni P. Spectrum of Kidney Injury Following COVID-19 Disease: Renal Biopsy Findings in a Single Italian Pathology Service. Biomolecules 2022; 12:biom12020298. [PMID: 35204798 PMCID: PMC8961620 DOI: 10.3390/biom12020298] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
The onset of coronavirus disease (COVID-19) as a pandemic infection, has led to increasing insights on its pathophysiology and clinical features being revealed, such as a noticeable kidney involvement. In this study, we describe the histopathological, immunofluorescence, and ultrastructural features of biopsy-proven kidney injury observed in a series of SARS-CoV-2 positive cases in our institution from April 2020 to November 2021. We retrieved and retrospectively reviewed nine cases (two pediatric and seven adults) that experienced nephrotic syndrome (six cases), acute kidney injury (two cases), and a clinically silent microhematuria and leukocyturia. Kidney biopsies were investigated by means of light microscopy, direct immunofluorescence, and electron microscopy. The primary diagnoses were minimal change disease (four cases), acute tubular necrosis (two cases), collapsing glomerulopathy (two cases), and C3 glomerulopathy (one case). None of the cases showed viral or viral-like particles on ultrastructural analysis. Novel and specific histologic features on kidney biopsy related to SARS-CoV-2 infection have been gradually disclosed and reported, harboring relevant clinical and therapeutic implications. Recognizing and properly diagnosing renal involvement in patients experiencing COVID-19 could be challenging (due to the lack of direct proof of viral infection, e.g., viral particles) and requires a proper integration of clinical and pathological data.
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Affiliation(s)
- Alessandro Gambella
- Pathology Unit, Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy; (A.G.); (A.A.)
| | - Antonella Barreca
- Pathology Unit, “Città della Salute e della Scienza di Torino” University Hospital, Via Santena 7, 10126 Turin, Italy;
| | - Luigi Biancone
- Division of Nephrology Dialysis and Transplantation, AOU Città della Salute e della Scienza di Torino, Department of Medical Sciences, University of Turin, 10126 Turin, Italy;
| | - Dario Roccatello
- CMID, Coordinating Center of the Network for Rare Diseases of Piedmont and Aosta Valley, Nephrology and Dialysis Unit (ERK-Net Member), San Giovanni Bosco Hub Hospital, University of Turin, 10144 Turin, Italy;
| | - Licia Peruzzi
- Pediatric Nephrology Unit, Regina Margherita Department, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy;
| | - Luca Besso
- Division of Nephrology and Dialysis, AO S. Croce e Carle di Cuneo, 12100 Cuneo, Italy;
| | - Carolina Licata
- Division of Nephrology and Dialysis, ASL TO4, 10073 Ciriè, Italy;
| | - Angelo Attanasio
- Pathology Unit, Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy; (A.G.); (A.A.)
| | - Mauro Papotti
- Pathology Unit, Department of Oncology, University of Turin, Via Santena 7, 10126 Turin, Italy;
| | - Paola Cassoni
- Pathology Unit, Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy; (A.G.); (A.A.)
- Correspondence:
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