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Zhang J, Rissmann M, Kuiken T, Haagmans BL. Comparative Pathogenesis of Severe Acute Respiratory Syndrome Coronaviruses. ANNUAL REVIEW OF PATHOLOGY 2024; 19:423-451. [PMID: 37832946 DOI: 10.1146/annurev-pathol-052620-121224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Over the last two decades the world has witnessed the global spread of two genetically related highly pathogenic coronaviruses, severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. However, the impact of these outbreaks differed significantly with respect to the hospitalizations and fatalities seen worldwide. While many studies have been performed recently on SARS-CoV-2, a comparative pathogenesis analysis with SARS-CoV may further provide critical insights into the mechanisms of disease that drive coronavirus-induced respiratory disease. In this review, we comprehensively describe clinical and experimental observations related to transmission and pathogenesis of SARS-CoV-2 in comparison with SARS-CoV, focusing on human, animal, and in vitro studies. By deciphering the similarities and disparities of SARS-CoV and SARS-CoV-2, in terms of transmission and pathogenesis mechanisms, we offer insights into the divergent characteristics of these two viruses. This information may also be relevant to assessing potential novel introductions of genetically related highly pathogenic coronaviruses.
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Affiliation(s)
- Jingshu Zhang
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands;
| | - Melanie Rissmann
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands;
| | - Thijs Kuiken
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands;
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands;
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Lima Neto JX, Bezerra KS, Barbosa ED, Araujo RL, Galvão DS, Lyra ML, Oliveira JIN, Akash S, Jardan YAB, Nafidi HA, Bourhia M, Fulco UL. Investigation of protein-protein interactions and hotspot region on the NSP7-NSP8 binding site in NSP12 of SARS-CoV-2. Front Mol Biosci 2024; 10:1325588. [PMID: 38304231 PMCID: PMC10830813 DOI: 10.3389/fmolb.2023.1325588] [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: 10/21/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024] Open
Abstract
Background: The RNA-dependent RNA polymerase (RdRp) complex, essential in viral transcription and replication, is a key target for antiviral therapeutics. The core unit of RdRp comprises the nonstructural protein NSP12, with NSP7 and two copies of NSP8 (NSP81 and NSP82) binding to NSP12 to enhance its affinity for viral RNA and polymerase activity. Notably, the interfaces between these subunits are highly conserved, simplifying the design of molecules that can disrupt their interaction. Methods: We conducted a detailed quantum biochemical analysis to characterize the interactions within the NSP12-NSP7, NSP12-NSP81, and NSP12-NSP82 dimers. Our objective was to ascertain the contribution of individual amino acids to these protein-protein interactions, pinpointing hotspot regions crucial for complex stability. Results: The analysis revealed that the NSP12-NSP81 complex possessed the highest total interaction energy (TIE), with 14 pairs of residues demonstrating significant energetic contributions. In contrast, the NSP12-NSP7 complex exhibited substantial interactions in 8 residue pairs, while the NSP12-NSP82 complex had only one pair showing notable interaction. The study highlighted the importance of hydrogen bonds and π-alkyl interactions in maintaining these complexes. Intriguingly, introducing the RNA sequence with Remdesivir into the complex resulted in negligible alterations in both interaction energy and geometric configuration. Conclusion: Our comprehensive analysis of the RdRp complex at the protein-protein interface provides invaluable insights into interaction dynamics and energetics. These findings can guide the design of small molecules or peptide/peptidomimetic ligands to disrupt these critical interactions, offering a strategic pathway for developing effective antiviral drugs.
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Affiliation(s)
- José Xavier Lima Neto
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Katyanna Sales Bezerra
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Emmanuel Duarte Barbosa
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Roniel Lima Araujo
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | | | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Shopnil Akash
- Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
| | - Umberto Laino Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
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Wan S, Liu C, Li C, Wang Z, Zhao G, Li J, Ran W, Zhong X, Li Y, Zhang L, Cui H. AKIP1 accelerates glioblastoma progression through stabilizing EGFR expression. Oncogene 2023; 42:2905-2918. [PMID: 37596322 DOI: 10.1038/s41388-023-02796-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023]
Abstract
A Kinase Interacting Protein 1 (AKIP1) is found to be overexpressed in a variety of human cancers and associated with patients' worse prognosis. Several studies have established AKIP1's malignant functions in tumor metastasis, angiogenesis, and chemoradiotherapy resistance. However, the mechanism of AKIP1 involved in accelerating glioblastoma (GBM) progression remains unknown. Here, we showed that the expression of AKIP1 was positively correlated with the glioma pathological grades. Down-regulating AKIP1 greatly impaired the proliferation, colony formation, and tumorigenicity of GBM cells. In terms of the mechanism, AKIP1 cooperates with transcriptional factor Yin Yang 1 (YY1)-mediated Heat Shock Protein 90 Alpha Family Class A Member 1 (HSP90AA1) transcriptional activation, enhancing the stability of Epidermal Growth Factor Receptor (EGFR). YY1 was identified as a potential transcriptional factor of HSP90AA1 and directly interacts with AKIP1. The overexpression of HSP90α significantly reversed AKIP1 depletion incurred EGFR instability and the blocked cell proliferation. Moreover, we further investigated the interacted pattern between EGFR and HSP90α. These findings established that AKIP1 acted as a critical oncogenic factor in GBM and uncovered a novel regulatory mechanism in EGFR aberrant expression.
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Affiliation(s)
- Sicheng Wan
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400716, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, 400715, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400716, China
| | - Chaolong Liu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400716, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, 400715, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400716, China
| | - Chongyang Li
- School of Basic Medicine, Fudan University, Shanghai, 200032, China
| | - Zhi Wang
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400716, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, 400715, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400716, China
| | - Gaichao Zhao
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400716, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, 400715, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400716, China
| | - Jingui Li
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400716, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, 400715, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400716, China
| | - Wenhao Ran
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400716, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, 400715, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400716, China
| | - Xi Zhong
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400716, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, 400715, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400716, China
| | - Yongsen Li
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400716, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, 400715, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400716, China
| | - Li Zhang
- Department of Radiology and Nuclear Medicine, The First Hospital of HeBei Medical University, Shijiazhuang, HeBei Province, 050000, China.
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400716, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, 400715, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400716, China.
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Ma Y, Li Z, Chen X, Ding B, Li N, Lu T, Zhang B, Suo B, Jin Z. Machine-learning assisted scheduling optimization and its application in quantum chemical calculations. J Comput Chem 2023; 44:1174-1188. [PMID: 36648254 DOI: 10.1002/jcc.27075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023]
Abstract
Easy and effective usage of computational resources is crucial for scientific calculations, both from the perspectives of timeliness and economic efficiency. This work proposes a bi-level optimization framework to optimize the computational sequences. Machine-learning (ML) assisted static load-balancing, and different dynamic load-balancing algorithms can be integrated. Consequently, the computational and scheduling engine of the ParaEngine is developed to invoke optimized quantum chemical (QC) calculations. Illustrated benchmark calculations include high-throughput drug suit, solvent model, P38 protein, and SARS-CoV-2 systems. The results show that the usage rate of given computational resources for high throughput and large-scale fragmentation QC calculations can primarily profit, and faster accomplishing computational tasks can be expected when employing high-performance computing (HPC) clusters.
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Affiliation(s)
- Yingjin Ma
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - ZhiYing Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Xin Chen
- ShenZhen Bay Laboratory, Shenzhen, China
| | - Bowen Ding
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Ning Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
- College of Chemistry and Materials Engineering, Wenzhou University, Wen Zhou, China
| | - Teng Lu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Baohua Zhang
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - BingBing Suo
- Department of Physics, Northwest University, Xi'an, China
| | - Zhong Jin
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
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Inchingolo AD, Gargiulo CI, Malcangi G, Ciocia AM, Patano A, Azzollini D, Piras F, Barile G, Settanni V, Mancini A, Garofoli G, Palmieri G, Di Pede C, Rapone B, Inchingolo AM, Jones M, Corriero A, Brienza N, Parisi A, Bianco A, Capozzi L, Del Sambro L, Simone D, Bordea IR, Tartaglia GM, Scarano A, Lorusso F, Macchia L, Migliore G, Pham VH, Dipalma G, Inchingolo F. Diagnosis of SARS-CoV-2 during the Pandemic by Multiplex RT-rPCR hCoV Test: Future Perspectives. Pathogens 2022; 11:1378. [PMID: 36422629 PMCID: PMC9694306 DOI: 10.3390/pathogens11111378] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/07/2022] [Accepted: 11/16/2022] [Indexed: 04/07/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly become a significant threat to public health. However, among the Coronaviridae family members, there are other viruses that can also cause infections in humans. Among these, severe acute respiratory syndrome (SARS-CoV) and Middle East respiratory syndrome (MERS-CoV) have posed significant threats to human health in the past. Other human pathogenic coronaviruses have been identified, and they are known to cause respiratory diseases with manifestations ranging from mild to severe. In this study, we evaluated the performance of a multiplex RT-rPCR specific to seven human pathogenic coronaviruses in mainly detecting SARS-CoV-2 directly from nasopharyngeal swabs obtained from suspected COVID-19 infected patients, while simultaneously detecting different human pathogenic coronaviruses in case these were also present. We tested 1195 clinical samples suspected of COVID-19 infection. The assay identified that 69% of the samples tested positive for SARS-CoV-2 (1195), which was confirmed using another SARS-CoV-2 RT-PCR kit available in our laboratory. None of these clinical samples were positive for SARS-CoV, MERS-CoV or HCoV. This means that during the endemic phase of COVID-19, infection with other human pathogenic coronaviruses, even the common cold coronavirus (HCoV), is very uncommon. Our study also confirmed that the multiplex RT-rPCR is a sensitive assay for detecting SARS-CoV-2 regardless of differences among the variants. This multiplex RT-rPCR is also time- and cost-saving and very easy to apply in the diagnostic laboratory due to its simple procedure and its stability in storage after preparation. These features make the assay a valuable approach in screening procedures for the rapid detection of SARS-CoV-2 and other human pathogenic coronaviruses that could affect public health.
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Affiliation(s)
- Alessio Danilo Inchingolo
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Ciro Isacco Gargiulo
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Giuseppina Malcangi
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Anna Maria Ciocia
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Assunta Patano
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Daniela Azzollini
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Fabio Piras
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Giuseppe Barile
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Vito Settanni
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Antonio Mancini
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Grazia Garofoli
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Giulia Palmieri
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Chiara Di Pede
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Biagio Rapone
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Angelo Michele Inchingolo
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Megan Jones
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Alberto Corriero
- Department of Interdisciplinary Medicine—Intensive Care Unit Section, Aldo Moro University, 70121 Bari, Italy
| | - Nicola Brienza
- Department of Interdisciplinary Medicine—Intensive Care Unit Section, Aldo Moro University, 70121 Bari, Italy
| | - Antonio Parisi
- Experimental Zooprophylactic Institute of Puglia and Basilicata, 71121 Foggia, Italy
| | - Angelica Bianco
- Experimental Zooprophylactic Institute of Puglia and Basilicata, 71121 Foggia, Italy
| | - Loredana Capozzi
- Experimental Zooprophylactic Institute of Puglia and Basilicata, 71121 Foggia, Italy
| | - Laura Del Sambro
- Experimental Zooprophylactic Institute of Puglia and Basilicata, 71121 Foggia, Italy
| | - Domenico Simone
- Experimental Zooprophylactic Institute of Puglia and Basilicata, 71121 Foggia, Italy
| | - Ioana Roxana Bordea
- Department of Oral Rehabilitation, Faculty of Dentistry, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Gianluca Martino Tartaglia
- UOC Maxillo-Facial Surgery and Dentistry, Department of Biomedical, Surgical and Dental Sciences, School of Dentistry, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, University of Milan, 20100 Milan, Italy
| | - Antonio Scarano
- Department of Innovative Technologies in Medicine and Dentistry, University of Chieti-Pescara, 66100 Chieti, Italy
| | - Felice Lorusso
- Department of Innovative Technologies in Medicine and Dentistry, University of Chieti-Pescara, 66100 Chieti, Italy
| | - Luigi Macchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Giovanni Migliore
- Interdisciplinary Department of Medicine, University Hospital of Bari, 70100 Bari, Italy
| | - Van Hung Pham
- Department of Microbiology, Phan Chau Trinh University, Danang City 550000, Vietnam
- International Institute of Gene and Immunology, Ho Chi Minh City 70000, Vietnam
| | - Gianna Dipalma
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Francesco Inchingolo
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
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