1
|
Jhanwar A, Sharma D, Das U. Unraveling the structural and functional dimensions of SARS-CoV2 proteins in the context of COVID-19 pathogenesis and therapeutics. Int J Biol Macromol 2024; 278:134850. [PMID: 39168210 DOI: 10.1016/j.ijbiomac.2024.134850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) has emerged as the causative agent behind the global pandemic of Coronavirus Disease 2019 (COVID-19). As the scientific community strives to comprehend the intricate workings of this virus, a fundamental aspect lies in deciphering the myriad proteins it expresses. This knowledge is pivotal in unraveling the complexities of the viral machinery and devising targeted therapeutic interventions. The proteomic landscape of SARS-CoV2 encompasses structural, non-structural, and open-reading frame proteins, each playing crucial roles in viral replication, host interactions, and the pathogenesis of COVID-19. This comprehensive review aims to provide an updated and detailed examination of the structural and functional attributes of SARS-CoV2 proteins. By exploring the intricate molecular architecture, we have highlighted the significance of these proteins in viral biology. Insights into their roles and interplay contribute to a deeper understanding of the virus's mechanisms, thereby paving the way for the development of effective therapeutic strategies. As the global scientific community strives to combat the ongoing pandemic, this synthesis of knowledge on SARS-CoV2 proteins serves as a valuable resource, fostering informed approaches toward mitigating the impact of COVID-19 and advancing the frontier of antiviral research.
Collapse
Affiliation(s)
- Aniruddh Jhanwar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Dipika Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| |
Collapse
|
2
|
El-Maradny YA, Badawy MA, Mohamed KI, Ragab RF, Moharm HM, Abdallah NA, Elgammal EM, Rubio-Casillas A, Uversky VN, Redwan EM. Unraveling the role of the nucleocapsid protein in SARS-CoV-2 pathogenesis: From viral life cycle to vaccine development. Int J Biol Macromol 2024; 279:135201. [PMID: 39216563 DOI: 10.1016/j.ijbiomac.2024.135201] [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: 05/30/2024] [Revised: 08/24/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND The nucleocapsid protein (N protein) is the most abundant protein in SARS-CoV-2. Viral RNA and this protein are bound by electrostatic forces, forming cytoplasmic helical structures known as nucleocapsids. Subsequently, these nucleocapsids interact with the membrane (M) protein, facilitating virus budding into early secretory compartments. SCOPE OF REVIEW Exploring the role of the N protein in the SARS-CoV-2 life cycle, pathogenesis, post-sequelae consequences, and interaction with host immunity has enhanced our understanding of its function and potential strategies for preventing SARS-CoV-2 infection. MAJOR CONCLUSION This review provides an overview of the N protein's involvement in SARS-CoV-2 infectivity, highlighting its crucial role in the virus-host protein interaction and immune system modulation, which in turn influences viral spread. GENERAL SIGNIFICANCE Understanding these aspects identifies the N protein as a promising target for developing effective antiviral treatments and vaccines against SARS-CoV-2.
Collapse
Affiliation(s)
- Yousra A El-Maradny
- Pharmaceutical and Fermentation Industries Development Center, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab, Alexandria 21934, Egypt; Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Moustafa A Badawy
- Industrial Microbiology and Applied Chemistry program, Faculty of Science, Alexandria University, Egypt.
| | - Kareem I Mohamed
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Renad F Ragab
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Hamssa M Moharm
- Genetics, Biotechnology Department, Faculty of Agriculture, Alexandria University, Egypt.
| | - Nada A Abdallah
- Medicinal Plants Department, Faculty of Agriculture, Alexandria University, Egypt.
| | - Esraa M Elgammal
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Alberto Rubio-Casillas
- Autlan Regional Hospital, Health Secretariat, Autlan, JAL 48900, Mexico; Biology Laboratory, Autlan Regional Preparatory School, University of Guadalajara, Autlan, JAL 48900, Mexico.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab, 21934 Alexandria, Egypt.
| |
Collapse
|
3
|
Rurek M. Mitochondria in COVID-19: from cellular and molecular perspective. Front Physiol 2024; 15:1406635. [PMID: 38974521 PMCID: PMC11224649 DOI: 10.3389/fphys.2024.1406635] [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: 03/25/2024] [Accepted: 05/27/2024] [Indexed: 07/09/2024] Open
Abstract
The rapid development of the COVID-19 pandemic resulted in a closer analysis of cell functioning during β-coronavirus infection. This review will describe evidence for COVID-19 as a syndrome with a strong, albeit still underestimated, mitochondrial component. Due to the sensitivity of host mitochondria to coronavirus infection, SARS-CoV-2 affects mitochondrial signaling, modulates the immune response, modifies cellular energy metabolism, induces apoptosis and ageing, worsening COVID-19 symptoms which can sometimes be fatal. Various aberrations across human systems and tissues and their relationships with mitochondria were reported. In this review, particular attention is given to characterization of multiple alterations in gene expression pattern and mitochondrial metabolism in COVID-19; the complexity of interactions between SARS-CoV-2 and mitochondrial proteins is presented. The participation of mitogenome fragments in cell signaling and the occurrence of SARS-CoV-2 subgenomic RNA within membranous compartments, including mitochondria is widely discussed. As SARS-CoV-2 severely affects the quality system of mitochondria, the cellular background for aberrations in mitochondrial dynamics in COVID-19 is additionally characterized. Finally, perspectives on the mitigation of COVID-19 symptoms by affecting mitochondrial biogenesis by numerous compounds and therapeutic treatments are briefly outlined.
Collapse
Affiliation(s)
- Michał Rurek
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| |
Collapse
|
4
|
Zhang C, Sui Y, Liu S, Yang M. Anti-Viral Activity of Bioactive Molecules of Silymarin against COVID-19 via In Silico Studies. Pharmaceuticals (Basel) 2023; 16:1479. [PMID: 37895950 PMCID: PMC10610370 DOI: 10.3390/ph16101479] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection drove the global coronavirus disease 2019 (COVID-19) pandemic, causing a huge loss of human life and a negative impact on economic development. It is an urgent necessity to explore potential drugs against viruses, such as SARS-CoV-2. Silymarin, a mixture of herb-derived polyphenolic flavonoids extracted from the milk thistle, possesses potent antioxidative, anti-apoptotic, and anti-inflammatory properties. Accumulating research studies have demonstrated the killing activity of silymarin against viruses, such as dengue virus, chikungunya virus, and hepatitis C virus. However, the anti-COVID-19 mechanisms of silymarin remain unclear. In this study, multiple disciplinary approaches and methodologies were applied to evaluate the potential mechanisms of silymarin as an anti-viral agent against SARS-CoV-2 infection. In silico approaches such as molecular docking, network pharmacology, and bioinformatic methods were incorporated to assess the ligand-protein binding properties and analyze the protein-protein interaction network. The DAVID database was used to analyze gene functions, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment. TCMSP and GeneCards were used to identify drug target genes and COVID-19-related genes. Our results revealed that silymarin compounds, such as silybin A/B and silymonin, displayed triplicate functions against SARS-CoV-2 infection, including directly binding with human angiotensin-converting enzyme 2 (ACE2) to inhibit SARS-CoV-2 entry into the host cells, directly binding with viral proteins RdRp and helicase to inhibit viral replication and proliferation, and regulating host immune response to indirectly inhibit viral infection. Specifically, the targets of silymarin molecules in immune regulation were screened out, such as proinflammatory cytokines TNF and IL-6 and cell growth factors VEGFA and EGF. In addition, the molecular mechanism of drug-target protein interaction was investigated, including the binding pockets of drug molecules in human ACE2 and viral proteins, the formation of hydrogen bonds, hydrophobic interactions, and other drug-protein ligand interactions. Finally, the drug-likeness results of candidate molecules passed the criteria for drug screening. Overall, this study demonstrates the molecular mechanism of silymarin molecules against SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Chunye Zhang
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA;
| | - Yuxiang Sui
- School of Life Science, Shanxi Normal University, Linfen 041004, China;
| | - Shuai Liu
- The First Affiliated Hospital, Zhejiang University, Hangzhou 310006, China;
| | - Ming Yang
- Department of Surgery, University of Missouri, Columbia, MO 65212, USA
- NextGen Precision Health Institute, University of Missouri, Columbia, MO 65212, USA
| |
Collapse
|
5
|
Gonzalez-Alba JM, Rojo-Alba S, Perez-Martinez Z, Boga JA, Alvarez-Arguelles ME, Gomez J, Herrero P, Costales I, Alba LM, Martin-Rodriguez G, Campo R, Castelló-Abietar C, Sandoval M, Abreu-Salinas F, Coto E, Rodriguez M, Rubianes P, Sanchez ML, Vazquez F, Antuña L, Álvarez V, Melón García S. Monitoring and tracking the spread of SARS-CoV-2 in Asturias, Spain. Access Microbiol 2023; 5:000573.v4. [PMID: 37841093 PMCID: PMC10569657 DOI: 10.1099/acmi.0.000573.v4] [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: 01/30/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Mutational analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can quantify the relative importance of variants over time, enable dominant mutations to be identified, and facilitate near real-time detection, comparison and tracking of evolving variants. SARS-CoV-2 in Asturias, an autonomous community of Spain with a large ageing population, and high levels of migration and tourism, was monitored and tracked from the beginning of the pandemic in February 2020 until its decline and stabilization in August 2021, and samples were characterized using whole genomic sequencing and single nucleotide polymorphisms. Data held in the GISAID database were analysed to establish patterns in the appearance and persistence of SARS-CoV-2 strains. Only 138 non-synonymous mutations occurring in more than 1 % of the population with SARS-CoV-2 were found, identifying ten major variants worldwide (seven arose before January 2021), 19 regional and one local. In Asturias only 17 different variants were found. After vaccination, no further regional major variants were found. Only half of the defined variants circulated and no new variants were generated, indicating that infection control measures such as rapid diagnosis, isolation and vaccination were efficient.
Collapse
Affiliation(s)
- Jose Maria Gonzalez-Alba
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Susana Rojo-Alba
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Zulema Perez-Martinez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Jose A. Boga
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Marta Elena Alvarez-Arguelles
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Juan Gomez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Genética Molecular, Oviedo, Spain
| | - Pablo Herrero
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Urgencias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Isabel Costales
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Luz Maria Alba
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Gabriel Martin-Rodriguez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Rainer Campo
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Cristian Castelló-Abietar
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Marta Sandoval
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Fátima Abreu-Salinas
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Eliecer Coto
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Genética Molecular, Oviedo, Spain
| | - Mercedes Rodriguez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Pablo Rubianes
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Urgencias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Maria Luisa Sanchez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Fernando Vazquez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Luis Antuña
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Urgencias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Victoria Álvarez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Genética Molecular, Oviedo, Spain
| | - Santiago Melón García
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| |
Collapse
|
6
|
Feng A, Bevins S, Chandler J, DeLiberto TJ, Ghai R, Lantz K, Lenoch J, Retchless A, Shriner S, Tang CY, Tong SS, Torchetti M, Uehara A, Wan XF. Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States. Nat Commun 2023; 14:4078. [PMID: 37429851 DOI: 10.1038/s41467-023-39782-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023] Open
Abstract
SARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of SARS-CoV-2 from humans to free-ranging white-tailed deer (Odocoileus virginianus) poses a unique public health risk due to the potential for reservoir establishment where variants may persist and evolve. We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants. Evolutionary analyses showed these white-tailed deer viruses originated from at least 109 independent spillovers from humans, which resulted in 39 cases of subsequent local deer-to-deer transmission and three cases of potential spillover from white-tailed deer back to humans. Viruses repeatedly adapted to white-tailed deer with recurring amino acid substitutions across spike and other proteins. Overall, our findings suggest that multiple SARS-CoV-2 lineages were introduced, became enzootic, and co-circulated in white-tailed deer.
Collapse
Affiliation(s)
- Aijing Feng
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Sarah Bevins
- USDA APHIS Wildlife Services National Wildlife Disease Program, Fort Collins, CO, USA
| | - Jeff Chandler
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO, USA
| | | | - Ria Ghai
- One Health Office, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kristina Lantz
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Julianna Lenoch
- USDA APHIS Wildlife Services National Wildlife Disease Program, Fort Collins, CO, USA
| | - Adam Retchless
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Susan Shriner
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO, USA
| | - Cynthia Y Tang
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Suxiang Sue Tong
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mia Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Anna Uehara
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
| |
Collapse
|
7
|
Muhammad Rehman H, Rehman HM, Naveed M, Khan MT, Shabbir MA, Aslam S, Bashir H. In Silico Investigation of a Chimeric IL24-LK6 Fusion Protein as a Potent Candidate Against Breast Cancer. Bioinform Biol Insights 2023; 17:11779322231182560. [PMID: 37377793 PMCID: PMC10291407 DOI: 10.1177/11779322231182560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Targeted delivery of therapeutic anticancer chimeric molecules enhances the efficacy of drug by improving cellular uptake and circulation time. Engineering the molecules to facilitate the specific interaction between chimeric protein and its receptor is critical to elucidate biological mechanism as well as accuracy in modeling of complexes. A theoretically designed novel protein-protein interfaces can serve as a bottom-up method for comprehensive understanding of interacting protein residues. This study was aimed for in silico analyses of a chimeric fusion protein against breast cancer. The amino acid sequences of the interleukin 24 (IL-24) and LK-6 peptide were used to design the chimeric fusion protein via a rigid linker. The secondary and tertiary structures along with physicochemical properties by ProtParam and solubility were predicted using online software. The validation and quality of the fusion protein was confirmed by Rampage and ERRAT2. The newly designed fusion construct has a total length of 179 amino acids. The top-ranked structure from alpha fold2 showed 18.1 KD molecular weight by ProtParam, quality factor of 94.152 by ERRAT, and a valid structure by a Ramachandran plot with 88.5% residues in the favored region. Finally, the docking and simulation studies were performed using HADDOCK and Desmond module of Schrodinger. The quality, validity, interaction analysis, and stability of the fusion protein depict a functional molecule. The fusion gene IL24-LK6 after cloning and expression in a suitable prokaryotic cell might be a useful candidate for developing a novel anticancer therapy.
Collapse
Affiliation(s)
- Hafiz Muhammad Rehman
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
- University Institute of Medical Lab Technology, Faculty of Allied Health Sciences, The University of Lahore, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Shakira Aslam
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Hamid Bashir
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| |
Collapse
|
8
|
Wang Y, Ling X, Zhang C, Zou J, Luo B, Luo Y, Jia X, Jia G, Zhang M, Hu J, Liu T, Wang Y, Lu K, Li D, Ma J, Liu C, Su Z. Modular characterization of SARS-CoV-2 nucleocapsid protein domain functions in nucleocapsid-like assembly. MOLECULAR BIOMEDICINE 2023; 4:16. [PMID: 37211575 DOI: 10.1186/s43556-023-00129-z] [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: 01/13/2023] [Accepted: 04/09/2023] [Indexed: 05/23/2023] Open
Abstract
SARS-CoV-2 and its variants, with the Omicron subvariant XBB currently prevailing the global infections, continue to pose threats on public health worldwide. This non-segmented positive-stranded RNA virus encodes the multi-functional nucleocapsid protein (N) that plays key roles in viral infection, replication, genome packaging and budding. N protein consists of two structural domains, NTD and CTD, and three intrinsically disordered regions (IDRs) including the NIDR, the serine/arginine rich motif (SRIDR), and the CIDR. Previous studies revealed functions of N protein in RNA binding, oligomerization, and liquid-liquid phase separation (LLPS), however, characterizations of individual domains and their dissected contributions to N protein functions remain incomplete. In particular, little is known about N protein assembly that may play essential roles in viral replication and genome packing. Here, we present a modular approach to dissect functional roles of individual domains in SARS-CoV-2 N protein that reveals inhibitory or augmented modulations of protein assembly and LLPS in the presence of viral RNAs. Intriguingly, full-length N protein (NFL) assembles into ring-like architecture whereas the truncated SRIDR-CTD-CIDR (N182-419) promotes filamentous assembly. Moreover, LLPS droplets of NFL and N182-419 are significantly enlarged in the presence of viral RNAs, and we observed filamentous structures in the N182-419 droplets using correlative light and electron microscopy (CLEM), suggesting that the formation of LLPS droplets may promote higher-order assembly of N protein for transcription, replication and packaging. Together this study expands our understanding of the multiple functions of N protein in SARS-CoV-2.
Collapse
Affiliation(s)
- Yan Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xiaobin Ling
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chong Zhang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Jian Zou
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yongbo Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xinyu Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Guowen Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Minghua Zhang
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Junchao Hu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Ting Liu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yuanfeiyi Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Kefeng Lu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Cong Liu
- Interdisciplinary Research Center On Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China.
| |
Collapse
|
9
|
Treatment with quercetin inhibits SARS-CoV-2 N protein-induced acute kidney injury by blocking Smad3-dependent G1 cell-cycle arrest. Mol Ther 2023; 31:344-361. [PMID: 36514292 PMCID: PMC9743779 DOI: 10.1016/j.ymthe.2022.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/15/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Increasing evidence shows that SARS-CoV-2 can infect kidneys and cause acute kidney injury (AKI) in critically ill COVID-19 patients. However, mechanisms through which COVID-19 induces AKI are largely unknown, and treatment remains ineffective. Here, we report that kidney-specific overexpressing SARS-CoV-2 N gene can cause AKI, including tubular necrosis and elevated levels of serum creatinine and BUN in 8-week-old diabetic db/db mice, which become worse in those with older age (16 weeks) and underlying diabetic kidney disease (DKD). Treatment with quercetin, a purified product from traditional Chinese medicine (TCM) that shows effective treatment of COVID-19 patients, can significantly inhibit SARS-CoV-2 N protein-induced AKI in diabetic mice with or without underlying DKD. Mechanistically, quercetin can block the binding of SARS-CoV-2 N protein to Smad3, thereby inhibiting Smad3 signaling and Smad3-mediated cell death via the p16-dependent G1 cell-cycle arrest mechanism in vivo and in vitro. In conclusion, SARS-CoV-2 N protein is pathogenic and can cause severe AKI in diabetic mice, particularly in those with older age and pre-existing DKD, via the Smad3-dependent G1 cell-cycle arrest mechanism. Importantly, we identify that quercetin may be an effective TCM compound capable of inhibiting COVID-19 AKI by blocking SARS-CoV-2 N-Smad3-mediated cell death pathway.
Collapse
|
10
|
Molecular Dynamics Simulations to Decipher the Role of Phosphorylation of SARS-CoV-2 Nonstructural Proteins (nsps) in Viral Replication. Viruses 2022; 14:v14112436. [PMID: 36366534 PMCID: PMC9693435 DOI: 10.3390/v14112436] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Protein phosphorylation is a post-translational modification that enables various cellular activities and plays essential roles in protein interactions. Phosphorylation is an important process for the replication of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). To shed more light on the effects of phosphorylation, we used an ensemble of neural networks to predict potential kinases that might phosphorylate SARS-CoV-2 nonstructural proteins (nsps) and molecular dynamics (MD) simulations to investigate the effects of phosphorylation on nsps structure, which could be a potential inhibitory target to attenuate viral replication. Eight target candidate sites were found as top-ranked phosphorylation sites of SARS-CoV-2. During the process of molecular dynamics (MD) simulation, the root-mean-square deviation (RMSD) analysis was used to measure conformational changes in each nsps. Root-mean-square fluctuation (RMSF) was employed to measure the fluctuation in each residue of 36 systems considered, allowing us to evaluate the most flexible regions. These analysis shows that there are significant structural deviations in the residues namely nsp1 THR 72, nsp2 THR 73, nsp3 SER 64, nsp4 SER 81, nsp4 SER 455, nsp5 SER284, nsp6 THR 238, and nsp16 SER 132. The identified list of residues suggests how phosphorylation affects SARS-CoV-2 nsps function and stability. This research also suggests that kinase inhibitors could be a possible component for evaluating drug binding studies, which are crucial in therapeutic discovery research.
Collapse
|
11
|
Sheikh A, Huang H, Parvin S, Badruzzaman M, Ahamed T, Hossain E, Baran IS, Saud ZA. A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2. J Genet Eng Biotechnol 2022; 20:149. [PMID: 36318347 PMCID: PMC9626712 DOI: 10.1186/s43141-022-00431-3] [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: 10/25/2021] [Accepted: 10/12/2022] [Indexed: 11/05/2022]
Abstract
Background COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rigorous detection and treatment strategies against SARS-CoV-2 have become very challenging due to continuous evolutions to the viral genome. Therefore, careful genomic analysis is sorely needed to understand transmission, the cellular mechanism of pathogenicity, and the development of vaccines or drugs. Objective In this study, we intended to identify SARS-CoV-2 genome variants that may help understand the cellular and molecular foundation of coronavirus infections required to develop effective intervention strategies. Methods SARS-CoV-2 genome sequences were downloaded from an open-source public database, processed, and analyzed for variants in target detection sites and genes. Results We have identified six unique variants, G---AAC, T---AAC---T, AAC---T, AAC--------T, C----------T, and C--------C, at the nucleocapsid region and eleven major hotspot mutant genes: nsp3, surface glycoprotein, nucleocapsid phosphoprotein, ORF8, nsp6, nsp2, nsp4, helicase, membrane glycoprotein, 3′-5′ exonuclease, and 2′-O-ribose methyltransferases. In addition, we have identified eleven major mutant genes that may have a crucial role in SARS-CoV-2 pathogenesis. Conclusion Studying haplotype variants and 11 major mutant genes to understand the mechanism of action of fatal pathogenicity and inter-individual variations in immune responses is inevitable for managing target patient groups with identified variants and developing effective anti-viral drugs and vaccines. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00431-3.
Collapse
Affiliation(s)
- Afzal Sheikh
- grid.443108.a0000 0000 8550 5526Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Dhaka 1706 Bangladesh
| | - He Huang
- Research and Development Department, Bioengineering Lab. Co., Ltd, 657 Nagatake Midori-ku, Sagamihara-shi, Kanagawa-ken 252-0154 Japan
| | - Sultana Parvin
- grid.263023.60000 0001 0703 3735Department of Biology, Faculty of Science and Engineering, Saitama University, Saitama, Japan
| | - Mohammad Badruzzaman
- grid.443108.a0000 0000 8550 5526Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Dhaka 1706 Bangladesh
| | - Tofayel Ahamed
- grid.443108.a0000 0000 8550 5526Department of Agroforestry and Environment, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Dhaka 1706 Bangladesh
| | - Ekhtear Hossain
- grid.263880.70000 0004 0386 0655Department of Biological Sciences and Chemistry, Southern University and A&M College, 244 William James Hall, Baton Rouge, LA 70813 USA
| | - Iri Sato Baran
- Genesis Institute of Genetic Research, Genesis Healthcare Corporation, Yebisu Garden Place Tower 15F/26F 4-20-3 Ebisu, Shibuya-ku, Tokyo, Japan
| | - Zahangir Alam Saud
- grid.412656.20000 0004 0451 7306Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205 Bangladesh
| |
Collapse
|
12
|
Agrawal S, Pathak E, Mishra R, Mishra V, Parveen A, Mishra SK, Byadgi PS, Dubey SK, Chaudhary AK, Singh V, Chaurasia RN, Atri N. Computational exploration of the dual role of the phytochemical fortunellin: Antiviral activities against SARS-CoV-2 and immunomodulatory abilities against the host. Comput Biol Med 2022; 149:106049. [PMID: 36103744 PMCID: PMC9452420 DOI: 10.1016/j.compbiomed.2022.106049] [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: 01/11/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections generate approximately one million virions per day, and the majority of available antivirals are ineffective against it due to the virus's inherent genetic mutability. This necessitates the investigation of concurrent inhibition of multiple SARS-CoV-2 targets. We show that fortunellin (acacetin 7-O-neohesperidoside), a phytochemical, is a promising candidate for preventing and treating coronavirus disease (COVID-19) by targeting multiple key viral target proteins. Fortunellin supports protective immunity while inhibiting pro-inflammatory cytokines and apoptosis pathways and protecting against tissue damage. Fortunellin is a phytochemical found in Gojihwadi kwath, an Indian traditional Ayurvedic formulation with an antiviral activity that is effective in COVID-19 patients. The mechanistic action of its antiviral activity, however, is unknown. The current study comprehensively evaluates the potential therapeutic mechanisms of fortunellin in preventing and treating COVID-19. We have used molecular docking, molecular dynamics simulations, free-energy calculations, host target mining of fortunellin, gene ontology enrichment, pathway analyses, and protein-protein interaction analysis. We discovered that fortunellin reliably binds to key targets that are necessary for viral replication, growth, invasion, and infectivity including Nucleocapsid (N-CTD) (-54.62 kcal/mol), Replicase-monomer at NSP-8 binding site (-34.48 kcal/mol), Replicase-dimer interface (-31.29 kcal/mol), Helicase (-30.02 kcal/mol), Papain-like-protease (-28.12 kcal/mol), 2'-O-methyltransferase (-23.17 kcal/mol), Main-protease (-21.63 kcal/mol), Replicase-monomer at dimer interface (-22.04 kcal/mol), RNA-dependent-RNA-polymerase (-19.98 kcal/mol), Nucleocapsid-NTD (-16.92 kcal/mol), and Endoribonuclease (-16.81 kcal/mol). Furthermore, we identify and evaluate the potential human targets of fortunellin and its effect on the SARS-CoV-2 infected tissues, including normal-human-bronchial-epithelium (NHBE) and lung cells and organoids such as pancreatic, colon, liver, and cornea using a network pharmacology approach. Thus, our findings indicate that fortunellin has a dual role; multi-target antiviral activities against SARS-CoV-2 and immunomodulatory capabilities against the host.
Collapse
Affiliation(s)
- Shivangi Agrawal
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India
| | - Ekta Pathak
- Institute of Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Rajeev Mishra
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India.
| | - Vibha Mishra
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India
| | - Afifa Parveen
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India
| | | | | | - Sushil Kumar Dubey
- Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, India
| | | | | | | | - Neelam Atri
- Department of Botany, MMV, Banaras Hindu University, India
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Preliminary Genomic Analysis of the Omicron Variants of SARS-CoV-2 in Central India During the third wave of the COVID-19 Pandemic. Arch Med Res 2022; 53:574-584. [PMID: 36123226 PMCID: PMC9395282 DOI: 10.1016/j.arcmed.2022.08.006] [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: 04/13/2022] [Revised: 08/09/2022] [Accepted: 08/16/2022] [Indexed: 12/02/2022]
Abstract
Background Omicron was detected in South Africa for the first time at the month of November 2021, from then it expanded swiftly over the world, outcompeting other SARS-CoV-2 variants such as Delta. The toxicity, resistance to antiviral medicines, transmissibility, and vaccine-induced immunity of newly developed SARS-CoV-2 variants are major worldwide health concerns. Aim of study This study investigates the comprehensive explanation of all mutations and their evolutionary linkages between the Omicron variant and recently discovered SARS‐CoV‐2 variants. Method On Illumina MiniSeq Machine, 31 RNA isolates from clinical specimens were sequenced utilizing next-generation sequencing technique. Different bioinformatics tools have been used to analyze the mutations in omicron variant. A phylogenetic tree was constructed to determine Omicron's evolutionary relationships with other variants. Results In our investigation, we discovered 79 distinct types of mutations in 31 fully vaccinated COVID-19 positive samples. Mostly mutations were found in non-spike region. According to the NJ approach of phylogenetic tree revels, the nearest variants were in the order listed, based on sequence identity: Omicron, Gamma, Alpha, Delta, Mu and Beta. On the other hand as per UPGMA approach, the Omicron variation creates a novel monophyletic clade that is distinct from previous SARS-CoV-2 variants. Conclusion Despite the fact that some of the mutations are prevalent in Omicron and other VOCs, there are several unique mutations that have been connected to the virus's transmissibility and immune evasion, indicating a substantial shift in SARS-CoV-2 evolution.
Collapse
|
15
|
Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
Collapse
Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
16
|
Wang W, Chen J, Yu X, Lan HY. Signaling mechanisms of SARS-CoV-2 Nucleocapsid protein in viral infection, cell death and inflammation. Int J Biol Sci 2022; 18:4704-4713. [PMID: 35874957 PMCID: PMC9305276 DOI: 10.7150/ijbs.72663] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/22/2022] [Indexed: 12/15/2022] Open
Abstract
COVID-19 which is caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) has posed a worldwide pandemic and a major global public health threat. SARS-CoV-2 Nucleocapsid (N) protein plays a critical role in multiple steps of the viral life cycle and participates in viral replication, transcription, and assembly. The primary roles of N protein are to assemble with genomic RNA into the viral RNA-protein (vRNP) complex and to localize to the replication transcription complexes (RTCs) to enhance viral replication and transcription. N protein can also undergo liquid-liquid phase separation (LLPS) with viral genome RNA and inhibit stress granules to facilitate viral replication and assembly. Besides the function in viral life cycle, N protein can bind GSDMD to antagonize pyroptosis but promotes cell death via the Smad3-dependent G1 cell cycle arrest mechanism. In innate immune system, N protein inhibits IFN-β production and RNAi pathway for virus survival. However, it can induce expression of proinflammatory cytokines by activating NF-κB signaling and NLRP3 inflammasome, resulting in cytokine storms. In this review article, we are focusing on the signaling mechanisms of SARS-CoV-2 N protein in viral replication, cell death and inflammation.
Collapse
Affiliation(s)
- Wenbiao Wang
- Medical Research Center and Guangdong-Hong Kong Joint Laboratory for Immunity and Genetics of Chronic Kidney Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Junzhe Chen
- Department of Nephrology, The Third Affiliated hospital, Southern Medical University, Guangzhou, China
- Departments of Medicine & Therapeutics, Li Ka Shing Institute of Health Sciences, and Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Xueqing Yu
- Medical Research Center and Guangdong-Hong Kong Joint Laboratory for Immunity and Genetics of Chronic Kidney Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hui-Yao Lan
- Departments of Medicine & Therapeutics, Li Ka Shing Institute of Health Sciences, and Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Hong Kong, China
- The Chinese University of Hong Kong-Guangdong Academy of Sciences/Guangdong Provincial People's Hospital Joint Research Laboratory on Immunological and Genetic Kidney Diseases, The Chinese University of Hong Kong, Hong Kong, China
| |
Collapse
|
17
|
Kippes O, Thorn A, Santoni G. Structural biology of SARS-CoV-2 nucleocapsid. CRYSTALLOGR REV 2022. [DOI: 10.1080/0889311x.2022.2072835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Oliver Kippes
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, Hamburg, Germany
| | - Andrea Thorn
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, Hamburg, Germany
| | | |
Collapse
|
18
|
Newly Emerged Antiviral Strategies for SARS-CoV-2: From Deciphering Viral Protein Structural Function to the Development of Vaccines, Antibodies, and Small Molecules. Int J Mol Sci 2022; 23:ijms23116083. [PMID: 35682761 PMCID: PMC9181103 DOI: 10.3390/ijms23116083] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 05/20/2022] [Accepted: 05/27/2022] [Indexed: 01/09/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become the most severe health crisis, causing extraordinary economic disruption worldwide. SARS-CoV-2 is a single-stranded RNA-enveloped virus. The process of viral replication and particle packaging is finished in host cells. Viral proteins, including both structural and nonstructural proteins, play important roles in the viral life cycle, which also provides the targets of treatment. Therefore, a better understanding of the structural function of virus proteins is crucial to speed up the development of vaccines and therapeutic strategies. Currently, the structure and function of proteins encoded by the SARS-CoV-2 genome are reviewed by several studies. However, most of them are based on the analysis of SARS-CoV-1 particles, lacking a systematic review update for SARS-CoV-2. Here, we specifically focus on the structure and function of proteins encoded by SARS-CoV-2. Viral proteins that contribute to COVID-19 infection and disease pathogenesis are reviewed according to the most recent research findings. The structure-function correlation of viral proteins provides a fundamental rationale for vaccine development and targeted therapy. Then, current antiviral vaccines are updated, such as inactive viral vaccines and protein-based vaccines and DNA, mRNA, and circular RNA vaccines. A summary of other therapeutic options is also reviewed, including monoclonal antibodies such as a cross-neutralizer antibody, a constructed cobinding antibody, a dual functional monoclonal antibody, an antibody cocktail, and an engineered bispecific antibody, as well as peptide-based inhibitors, chemical compounds, and clustered regularly interspaced short palindromic repeats (CRISPR) exploration. Overall, viral proteins and their functions provide the basis for targeted therapy and vaccine development.
Collapse
|
19
|
Anwar MZ, Lodhi MS, Khan MT, Khan MI, Sharif S. Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Genes (Basel) 2022; 13:552. [PMID: 35328105 PMCID: PMC8951394 DOI: 10.3390/genes13030552] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/10/2022] [Accepted: 03/18/2022] [Indexed: 12/15/2022] Open
Abstract
Genomic epidemiology of SARS-CoV-2 is imperative to explore the transmission, evolution, and also pathogenicity of viruses. The emergence of SARS-CoV-2 variants of concern posed a severe threat to the global public health efforts. To assess the potential consequence of these emerging variants on public health, continuous molecular epidemiology is of vital importance. The current study has been designed to investigate the major SARS-CoV-2 variants and emerging mutations in virus structural and non-structural proteins (NSP) during the fourth wave in September 2021 from the Punjab province of Pakistan. Twenty SARS-CoV-2 positive samples have been collected from major cities were subjected to next-generation sequencing. Among the 20 whole genomes (GenBank Accession SRR16294858-SRR16294877), 2 samples failed to be completely sequenced. These genome sequences harbored 207 non-synonymous mutations, among which 19 were unique to GISAID. The genome sequences were detected: Delta 21I, 21J variants (B.1.617.2). Mutation's spike_F157del, spike_P681R, spike_T478K, spike_T19R, spike_L452R, spike_D614G, spike_G142D, spike_E156G, and spike_R158del have been detected in all samples where K1086Q, E554K, and C1250W were unique in spike protein. These genomic sequences also harbored 129 non-synonymous mutations in NSP. The most common were NSP3_P1469S (N = 17), NSP3_A488S (N = 17), NSP3_P1228L (N = 17), NSP4_V167L (N = 17), NSP4_T492I (N = 17), NSP6_T77A (N = 17), NSP14_A394V (N = 17), NSP12_G671S (N = 18), and NSP13_P77L (N = 18). The mutation, F313Y in NSP12, detected in the current study, was found in a single isolate from Belgium. Numerous other unique mutations have been detected in the virus papain-like protease (NSP3), main protease (NSP5), and RNA-dependent RNA polymerase (NSP12). The most common non-synonymous mutations in the spike protein were subjected to stability analysis, exhibiting a stabilizing effect on structures. The presence of Delta variants may affect therapeutic efforts and vaccine efficacy. Continuous genomic epidemiology of SARS-CoV-2 in Pakistan may be useful for better management of SARS-CoV-2 infections.
Collapse
Affiliation(s)
| | - Madeeha Shahzad Lodhi
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, 1 KM Defence Road, Lahore 58 810, Pakistan; (M.Z.A.); (M.T.K.); (M.I.K.); (S.S.)
| | | | | | | |
Collapse
|
20
|
Yan W, Zheng Y, Zeng X, He B, Cheng W. Structural biology of SARS-CoV-2: open the door for novel therapies. Signal Transduct Target Ther 2022; 7:26. [PMID: 35087058 PMCID: PMC8793099 DOI: 10.1038/s41392-022-00884-5] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the pandemic disease COVID-19, which is so far without efficacious treatment. The discovery of therapy reagents for treating COVID-19 are urgently needed, and the structures of the potential drug-target proteins in the viral life cycle are particularly important. SARS-CoV-2, a member of the Orthocoronavirinae subfamily containing the largest RNA genome, encodes 29 proteins including nonstructural, structural and accessory proteins which are involved in viral adsorption, entry and uncoating, nucleic acid replication and transcription, assembly and release, etc. These proteins individually act as a partner of the replication machinery or involved in forming the complexes with host cellular factors to participate in the essential physiological activities. This review summarizes the representative structures and typically potential therapy agents that target SARS-CoV-2 or some critical proteins for viral pathogenesis, providing insights into the mechanisms underlying viral infection, prevention of infection, and treatment. Indeed, these studies open the door for COVID therapies, leading to ways to prevent and treat COVID-19, especially, treatment of the disease caused by the viral variants are imperative.
Collapse
Affiliation(s)
- Weizhu Yan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Bin He
- Department of Emergency Medicine, West China Hospital of Sichuan University, 610041, Chengdu, China.
- The First People's Hospital of Longquanyi District Chengdu, 610100, Chengdu, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China.
| |
Collapse
|
21
|
Mou K, Mukhtar F, Khan MT, Darwish DB, Peng S, Muhammad S, Al-Sehemi AG, Wei DQ. Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. Pathogens 2021; 10:pathogens10101285. [PMID: 34684233 PMCID: PMC8539063 DOI: 10.3390/pathogens10101285] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/19/2021] [Accepted: 10/01/2021] [Indexed: 01/31/2023] Open
Abstract
The genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes 16 non-structural (Nsp) and 4 structural proteins. Among the Nsps, Nsp1 inhibits host gene expression and also evades the immune system. This protein has been proposed as a target for vaccine development and also for drug design. Owing to its important role, the current study aimed to identify mutations in Nsp1 and their effect on protein stability and flexibility. This is the first comprehensive study in which 295,000 complete genomes have been screened for mutations after alignment with the Wuhan-Hu-1 reference genome (Accession NC_045512), using the CoVsurver app. The sequences harbored 933 mutations in the entire coding region of Nsp1. The most frequently occurring mutation in the 180-amino-acid Nsp1 protein was R24C (n = 1122), followed by D75E (n = 890), D48G (n = 881), H110Y (n = 860), and D144A (n = 648). Among the 933 non-synonymous mutations, 529 exhibited a destabilizing effect. Similarly, a gain in flexibility was observed in 542 mutations. The majority of the most frequent mutations were detected in the loop regions. These findings imply that Nsp1 mutations might be useful to exploit SARS-CoV-2's pathogenicity. Genomic sequencing of SARS-CoV-2 on a regular basis will further assist in analyzing variations among the drug targets and to test the diagnostic accuracy. This wide range of mutations and their effect on Nsp1's stability may have some consequences for the host's innate immune response to SARS-CoV-2 infection and also for the vaccines' efficacy. Based on this mutational information, geographically strain-specific drugs, vaccines, and antibody combinations could be a useful strategy against SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Kejie Mou
- Department of Neurosurgery, Bishan Hospital of Chongqing, Chongqing 402760, China;
| | - Farwa Mukhtar
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore 58810, Pakistan;
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore 58810, Pakistan;
- Correspondence: (M.T.K.); (D.-Q.W.)
| | - Doaa B. Darwish
- Botany Department, Faculty of Science, Mansoura University, Mansoura 35516, Egypt;
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Shaoliang Peng
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China;
| | - Shabbir Muhammad
- Department of Physics, College of Science, King Khalid University, Abha 61413, Saudi Arabia;
| | - Abdullah G. Al-Sehemi
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, Saudi Arabia;
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | - Dong-Qing Wei
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China;
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
- Correspondence: (M.T.K.); (D.-Q.W.)
| |
Collapse
|
22
|
Song S, Li C, Kang L, Tian D, Badar N, Ma W, Zhao S, Jiang X, Wang C, Sun Y, Li W, Lei M, Li S, Qi Q, Ikram A, Salman M, Umair M, Shireen H, Batool F, Zhang B, Chen H, Yang YG, Abbasi AA, Li M, Xue Y, Bao Y. Genomic Epidemiology of SARS-CoV-2 in Pakistan. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:727-740. [PMID: 34695600 PMCID: PMC8546014 DOI: 10.1016/j.gpb.2021.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/30/2021] [Accepted: 08/23/2021] [Indexed: 11/10/2022]
Abstract
COVID-19 has swept globally and Pakistan is no exception. To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan, we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1, 2020. We identified a total of 347 mutated positions, 31 of which were over-represented in Pakistan. Meanwhile, we found over 1000 intra-host single-nucleotide variants (iSNVs). Several of them occurred concurrently, indicating possible interactions among them or coevolution. Some of the high-frequency iSNVs in Pakistan were not observed in the global population, suggesting strong purifying selections. The genomic epidemiology revealed five distinctive spreading clusters. The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure, indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation (G8371T in ORF1ab) of this cluster. Furthermore, 28 putative international introductions were identified, several of which are consistent with the epidemiological investigations. In all, this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan, which could aid ongoing and future viral surveillance and COVID-19 control.
Collapse
Affiliation(s)
- Shuhui Song
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Cuiping Li
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Kang
- China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongmei Tian
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Nazish Badar
- Department of Virology and Immunology, National Institute of Health, Islamabad 45500, Pakistan
| | - Wentai Ma
- China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shilei Zhao
- China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuan Jiang
- China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chun Wang
- China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongqiao Sun
- China National Center for Bioinformation, Beijing 100101, China
| | - Wenjie Li
- China National Center for Bioinformation, Beijing 100101, China
| | - Meng Lei
- China National Center for Bioinformation, Beijing 100101, China
| | - Shuangli Li
- China National Center for Bioinformation, Beijing 100101, China
| | - Qiuhui Qi
- China National Center for Bioinformation, Beijing 100101, China
| | - Aamer Ikram
- Department of Virology and Immunology, National Institute of Health, Islamabad 45500, Pakistan
| | - Muhammad Salman
- Department of Virology and Immunology, National Institute of Health, Islamabad 45500, Pakistan
| | - Massab Umair
- Department of Virology and Immunology, National Institute of Health, Islamabad 45500, Pakistan
| | - Huma Shireen
- National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Fatima Batool
- National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Bing Zhang
- China National Center for Bioinformation, Beijing 100101, China
| | - Hua Chen
- China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Yun-Gui Yang
- China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Mingkun Li
- China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| | - Yongbiao Xue
- China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yiming Bao
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
23
|
Grebennikov D, Kholodareva E, Sazonov I, Karsonova A, Meyerhans A, Bocharov G. Intracellular Life Cycle Kinetics of SARS-CoV-2 Predicted Using Mathematical Modelling. Viruses 2021; 13:1735. [PMID: 34578317 PMCID: PMC8473439 DOI: 10.3390/v13091735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 infection represents a global threat to human health. Various approaches were employed to reveal the pathogenetic mechanisms of COVID-19. Mathematical and computational modelling is a powerful tool to describe and analyze the infection dynamics in relation to a plethora of processes contributing to the observed disease phenotypes. In our study here, we formulate and calibrate a deterministic model of the SARS-CoV-2 life cycle. It provides a kinetic description of the major replication stages of SARS-CoV-2. Sensitivity analysis of the net viral progeny with respect to model parameters enables the identification of the life cycle stages that have the strongest impact on viral replication. These three most influential parameters are (i) degradation rate of positive sense vRNAs in cytoplasm (negative effect), (ii) threshold number of non-structural proteins enhancing vRNA transcription (negative effect), and (iii) translation rate of non-structural proteins (positive effect). The results of our analysis could be used for guiding the search for antiviral drug targets to combat SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Dmitry Grebennikov
- Marchuk Institute of Numerical Mathematics, Russian Academy of Sciences (INM RAS), 119333 Moscow, Russia;
- Moscow Center for Fundamental and Applied Mathematics at INM RAS, 119333 Moscow, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Ekaterina Kholodareva
- Marchuk Institute of Numerical Mathematics, Russian Academy of Sciences (INM RAS), 119333 Moscow, Russia;
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, 141701 Moscow Oblast, Russia
| | - Igor Sazonov
- College of Engineering, Swansea University, Bay Campus, Fabian Way, Swansea SA1 8EN, UK;
| | - Antonina Karsonova
- Department of Clinical Immunology and Allergology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Andreas Meyerhans
- Infection Biology Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
- ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Gennady Bocharov
- Marchuk Institute of Numerical Mathematics, Russian Academy of Sciences (INM RAS), 119333 Moscow, Russia;
- Moscow Center for Fundamental and Applied Mathematics at INM RAS, 119333 Moscow, Russia
- Institute of Computer Science and Mathematical Modelling, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| |
Collapse
|
24
|
Xu W, Pei G, Liu H, Ju X, Wang J, Ding Q, Li P. Compartmentalization-aided interaction screening reveals extensive high-order complexes within the SARS-CoV-2 proteome. Cell Rep 2021; 36:109482. [PMID: 34297909 PMCID: PMC8285250 DOI: 10.1016/j.celrep.2021.109482] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/21/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Bearing a relatively large single-stranded RNA genome in nature, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes sophisticated replication/transcription complexes (RTCs), mainly composed of a network of nonstructural proteins and nucleocapsid protein, to establish efficient infection. In this study, we develop an innovative interaction screening strategy based on phase separation in cellulo, namely compartmentalization of protein-protein interactions in cells (CoPIC). Utilizing CoPIC screening, we map the interaction network among RTC-related viral proteins. We identify a total of 47 binary interactions among 14 proteins governing replication, discontinuous transcription, and translation of coronaviruses. Further exploration via CoPIC leads to the discovery of extensive ternary complexes composed of these components, which infer potential higher-order complexes. Taken together, our results present an efficient and robust interaction screening strategy, and they indicate the existence of a complex interaction network among RTC-related factors, thus opening up opportunities to understand SARS-CoV-2 biology and develop therapeutic interventions for COVID-19.
Collapse
Affiliation(s)
- Weifan Xu
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China
| | - Gaofeng Pei
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongrui Liu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohui Ju
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; School of Medicine, Tsinghua University, Beijing, China
| | - Jing Wang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiang Ding
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; School of Medicine, Tsinghua University, Beijing, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China.
| |
Collapse
|
25
|
Abiri R, Abdul-Hamid H, Sytar O, Abiri R, Bezerra de Almeida E, Sharma SK, Bulgakov VP, Arroo RRJ, Malik S. A Brief Overview of Potential Treatments for Viral Diseases Using Natural Plant Compounds: The Case of SARS-Cov. Molecules 2021; 26:molecules26133868. [PMID: 34202844 PMCID: PMC8270261 DOI: 10.3390/molecules26133868] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic, as well as the more general global increase in viral diseases, has led researchers to look to the plant kingdom as a potential source for antiviral compounds. Since ancient times, herbal medicines have been extensively applied in the treatment and prevention of various infectious diseases in different traditional systems. The purpose of this review is to highlight the potential antiviral activity of plant compounds as effective and reliable agents against viral infections, especially by viruses from the coronavirus group. Various antiviral mechanisms shown by crude plant extracts and plant-derived bioactive compounds are discussed. The understanding of the action mechanisms of complex plant extract and isolated plant-derived compounds will help pave the way towards the combat of this life-threatening disease. Further, molecular docking studies, in silico analyses of extracted compounds, and future prospects are included. The in vitro production of antiviral chemical compounds from plants using molecular pharming is also considered. Notably, hairy root cultures represent a promising and sustainable way to obtain a range of biologically active compounds that may be applied in the development of novel antiviral agents.
Collapse
Affiliation(s)
- Rambod Abiri
- Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, Serdang 43400, Malaysia; or
| | - Hazandy Abdul-Hamid
- Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, Serdang 43400, Malaysia; or
- Laboratory of Bioresource Management, Institute of Tropical Forestry and Forest Products (INTROP), Universiti Putra Malaysia, Serdang 43400, Malaysia
- Correspondence: (H.A.-H.); (V.P.B.); or (S.M.)
| | - Oksana Sytar
- Educational and Scientific Center “Institute of Biology and Medicine”, Department of Plant Biology, Taras Shevchenko National University of Kyiv, Volodymyrska 60, 01033 Kyiv, Ukraine;
- Department of Plant Physiology, Slovak University of Agriculture Nitra, A. Hlinku 2, 94976 Nitra, Slovakia
| | - Ramin Abiri
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah 6718773654, Iran;
- Fertility and Infertility Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah 6718773654, Iran
| | - Eduardo Bezerra de Almeida
- Biological and Health Sciences Centre, Laboratory of Botanical Studies, Department of Biology, Federal University of Maranhão, São Luís 65080-805, MA, Brazil;
| | - Surender K. Sharma
- Department of Physics, Central University of Punjab, Bathinda 151401, India;
| | - Victor P. Bulgakov
- Department of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity (Institute of Biology and Soil Science), Far Eastern Branch of the Russian Academy of Sciences, 159 Stoletija Str., 690022 Vladivostok, Russia
- Correspondence: (H.A.-H.); (V.P.B.); or (S.M.)
| | - Randolph R. J. Arroo
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, UK;
| | - Sonia Malik
- Health Sciences Graduate Program, Biological & Health Sciences Centre, Federal University of Maranhão, São Luís 65080-805, MA, Brazil
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), University of Orléans, 1 Rue de Chartres-BP 6759, 45067 Orleans, France
- Correspondence: (H.A.-H.); (V.P.B.); or (S.M.)
| |
Collapse
|
26
|
Altincekic N, Korn SM, Qureshi NS, Dujardin M, Ninot-Pedrosa M, Abele R, Abi Saad MJ, Alfano C, Almeida FCL, Alshamleh I, de Amorim GC, Anderson TK, Anobom CD, Anorma C, Bains JK, Bax A, Blackledge M, Blechar J, Böckmann A, Brigandat L, Bula A, Bütikofer M, Camacho-Zarco AR, Carlomagno T, Caruso IP, Ceylan B, Chaikuad A, Chu F, Cole L, Crosby MG, de Jesus V, Dhamotharan K, Felli IC, Ferner J, Fleischmann Y, Fogeron ML, Fourkiotis NK, Fuks C, Fürtig B, Gallo A, Gande SL, Gerez JA, Ghosh D, Gomes-Neto F, Gorbatyuk O, Guseva S, Hacker C, Häfner S, Hao B, Hargittay B, Henzler-Wildman K, Hoch JC, Hohmann KF, Hutchison MT, Jaudzems K, Jović K, Kaderli J, Kalniņš G, Kaņepe I, Kirchdoerfer RN, Kirkpatrick J, Knapp S, Krishnathas R, Kutz F, zur Lage S, Lambertz R, Lang A, Laurents D, Lecoq L, Linhard V, Löhr F, Malki A, Bessa LM, Martin RW, Matzel T, Maurin D, McNutt SW, Mebus-Antunes NC, Meier BH, Meiser N, Mompeán M, Monaca E, Montserret R, Mariño Perez L, Moser C, Muhle-Goll C, Neves-Martins TC, Ni X, Norton-Baker B, Pierattelli R, Pontoriero L, Pustovalova Y, Ohlenschläger O, Orts J, Da Poian AT, Pyper DJ, Richter C, Riek R, Rienstra CM, Robertson A, Pinheiro AS, Sabbatella R, Salvi N, Saxena K, Schulte L, Schiavina M, Schwalbe H, Silber M, Almeida MDS, Sprague-Piercy MA, Spyroulias GA, Sreeramulu S, Tants JN, Tārs K, Torres F, Töws S, Treviño MÁ, Trucks S, Tsika AC, Varga K, Wang Y, Weber ME, Weigand JE, Wiedemann C, Wirmer-Bartoschek J, Wirtz Martin MA, Zehnder J, Hengesbach M, Schlundt A. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications. Front Mol Biosci 2021; 8:653148. [PMID: 34041264 PMCID: PMC8141814 DOI: 10.3389/fmolb.2021.653148] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/04/2021] [Indexed: 01/18/2023] Open
Abstract
The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
Collapse
Affiliation(s)
- Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sophie Marianne Korn
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Dujardin
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Martí Ninot-Pedrosa
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Rupert Abele
- Institute for Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Jose Abi Saad
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Caterina Alfano
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Fabio C. L. Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Islam Alshamleh
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisele Cardoso de Amorim
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil
| | - Thomas K. Anderson
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cristiane D. Anobom
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chelsea Anorma
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Adriaan Bax
- LCP, NIDDK, NIH, Bethesda, MD, United States
| | | | - Julius Blechar
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Louis Brigandat
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Anna Bula
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Matthias Bütikofer
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Teresa Carlomagno
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Icaro Putinhon Caruso
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Marquise G. Crosby
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Karthikeyan Dhamotharan
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Isabella C. Felli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yanick Fleischmann
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Christin Fuks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Angelo Gallo
- Department of Pharmacy, University of Patras, Patras, Greece
| | - Santosh L. Gande
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Juan Atilio Gerez
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Dhiman Ghosh
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Francisco Gomes-Neto
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Oksana Gorbatyuk
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | | | - Sabine Häfner
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Bing Hao
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Bruno Hargittay
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - K. Henzler-Wildman
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie T. Hutchison
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Katarina Jović
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Janina Kaderli
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Iveta Kaņepe
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Robert N. Kirchdoerfer
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - John Kirkpatrick
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Robin Krishnathas
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Felicitas Kutz
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susanne zur Lage
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Roderick Lambertz
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andras Lang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Douglas Laurents
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Verena Linhard
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank Löhr
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anas Malki
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Tobias Matzel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Damien Maurin
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Seth W. McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Nathane Cunha Mebus-Antunes
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Beat H. Meier
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Nathalie Meiser
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Mompeán
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Elisa Monaca
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Celine Moser
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | - Thais Cristtina Neves-Martins
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Xiamonin Ni
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Brenna Norton-Baker
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Roberta Pierattelli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Letizia Pontoriero
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Yulia Pustovalova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | - Julien Orts
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Andrea T. Da Poian
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dennis J. Pyper
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Roland Riek
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Chad M. Rienstra
- Department of Biochemistry and National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anderson S. Pinheiro
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Nicola Salvi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Linda Schulte
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marco Schiavina
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mara Silber
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcius da Silva Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marc A. Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | | | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jan-Niklas Tants
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Felix Torres
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Sabrina Töws
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Á. Treviño
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Krisztina Varga
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Ying Wang
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Marco E. Weber
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Julia E. Weigand
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Christoph Wiedemann
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria Alexandra Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johannes Zehnder
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andreas Schlundt
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| |
Collapse
|
27
|
Khan MT, Ali S, Khan AS, Muhammad N, Khalil F, Ishfaq M, Irfan M, Al-Sehemi AG, Muhammad S, Malik A, Khan TA, Wei DQ. SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. ACS OMEGA 2021; 6:6588-6599. [PMID: 33748571 PMCID: PMC7944396 DOI: 10.1021/acsomega.0c05163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/05/2021] [Indexed: 05/08/2023]
Abstract
Among viral outbreaks, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the deadliest ones, and it has triggered the global COVID-19 pandemic. In Pakistan, until 5th September 2020, a total of 6342 deaths have been reported, of which 1255 were from the Khyber Pakhtunkhwa (KPK) province. To understand the disease progression and control and also to produce vaccines and therapeutic efforts, whole genome sequence analysis is important. In the current investigation, we sequenced a single sample of SARS-CoV-2 genomes (accession no. MT879619) from a male suspect from Peshawar, the KPK capital city, during the first wave of infection. The local SARS-CoV-2 strain shows some unique characteristics compared to neighboring Iranian and Chinese isolates in phylogenetic tree and mutations. The circulating strains of SARS-CoV-2 represent an intermediate evolution from China and Iran. Furthermore, eight complete whole genome sequences, including the current Pakistani isolates which have been submitted to Global Initiative on Sharing All Influenza Data (GSAID), were also investigated for specific mutations and characters. Some novel mutations [NSP2 (D268del), NSP5 (N228K), and NS3 (F105S)] and specific characters have been detected in the coding regions, which may affect viral transmission, epidemiology, and disease severity. The computational modeling revealed that a majority of these mutations may have a stabilizing effect on the viral protein structure. In conclusion, the genome sequencing of local strains is important for better understanding the pathogenicity, immunogenicity, and epidemiology of causative agents.
Collapse
Affiliation(s)
- Muhammad Tahir Khan
- Institute of Molecular
Biology and Biotechnology (IMBB), The University
of Lahore, KM Defence Road, Lahore 58810, Pakistan
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
| | - Sajid Ali
- Department of Microbiology, Quaid-i-Azam University Islamabad, Islamabad 45320, Pakistan
| | - Anwar Sheed Khan
- Department of Microbiology, Kohat University of Science and Technology, Bannu Road, Near Jarma Bridge, Kohat 26000, Pakistan
| | - Noor Muhammad
- Department of Microbiology, Kohat University of Science and Technology, Bannu Road, Near Jarma Bridge, Kohat 26000, Pakistan
| | - Faiza Khalil
- Department of Biochemistry, Khyber Medical
College, Peshawar 25160, Pakistan
- University
of Peshawar, Road No.
2, Rahat Abad, Peshawar 25120, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ishfaq
- Centre for Omic Sciences, Islamia
College Peshawar. Grand Trunk Road, Rahat Abad, Peshawar 25120, Pakistan
| | - Muhammad Irfan
- Department
of Oral Biology, College of Dentistry, University
of Florida, Gainesville, Florida 32611, United States
| | - Abdullah G. Al-Sehemi
- Research Center for Advanced Materials
Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Shabbir Muhammad
- Research Center for Advanced Materials
Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
| | - Arif Malik
- Institute of Molecular
Biology and Biotechnology (IMBB), The University
of Lahore, KM Defence Road, Lahore 58810, Pakistan
| | - Taj Ali Khan
- Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Phase V, Hayatabad, Peshawar, Khyber Pakhtunkhwa 25000, Pakistan
| | - Dong Qing Wei
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
| |
Collapse
|
28
|
Gao T, Gao Y, Liu X, Nie Z, Sun H, Lin K, Peng H, Wang S. Identification and functional analysis of the SARS-COV-2 nucleocapsid protein. BMC Microbiol 2021; 21:58. [PMID: 33618668 PMCID: PMC7898026 DOI: 10.1186/s12866-021-02107-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/27/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND A severe form of pneumonia, named coronavirus disease 2019 (COVID-19) by the World Health Organization is widespread on the whole world. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was proved to be the main agent of COVID-19. In the present study, we conducted an in depth analysis of the SARS-COV-2 nucleocapsid to identify potential targets that may allow identification of therapeutic targets. METHODS The SARS-COV-2 N protein subcellular localization and physicochemical property was analyzed by PSORT II Prediction and ProtParam tool. Then SOPMA tool and swiss-model was applied to analyze the structure of N protein. Next, the biological function was explored by mass spectrometry analysis and flow cytometry. At last, its potential phosphorylation sites were analyzed by NetPhos3.1 Server and PROVEAN PROTEIN. RESULTS SARS-COV-2 N protein composed of 419 aa, is a 45.6 kDa positively charged unstable hydrophobic protein. It has 91 and 49% similarity to SARS-CoV and MERS-CoV and is predicted to be predominantly a nuclear protein. It mainly contains random coil (55.13%) of which the tertiary structure was further determined with high reliability (95.76%). Cells transfected with SARS-COV-2 N protein usually show a G1/S phase block company with an increased expression of TUBA1C, TUBB6. At last, our analysis of SARS-COV-2 N protein predicted a total number of 12 phosphorylated sites and 9 potential protein kinases which would significantly affect SARS-COV-2 N protein function. CONCLUSION In this study, we report the physicochemical properties, subcellular localization, and biological function of SARS-COV-2 N protein. The 12 phosphorylated sites and 9 potential protein kinase sites in SARS-COV-2 N protein may serve as promising targets for drug discovery and development for of a recombinant virus vaccine.
Collapse
Affiliation(s)
- Tianyi Gao
- Department of clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Yingdong Gao
- Department of clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Xiangxiang Liu
- Central Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Zhenlin Nie
- Department of clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Huilin Sun
- Central Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Kang Lin
- Department of clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Hongxin Peng
- Department of clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Shukui Wang
- Department of clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China. .,Central Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China. .,Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China.
| |
Collapse
|
29
|
O’Leary VB, Dolly OJ, Höschl C, Černa M, Ovsepian SV. Unpacking Pandora From Its Box: Deciphering the Molecular Basis of the SARS-CoV-2 Coronavirus. Int J Mol Sci 2020; 22:ijms22010386. [PMID: 33396557 PMCID: PMC7795774 DOI: 10.3390/ijms22010386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/25/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
An enigmatic localized pneumonia escalated into a worldwide COVID-19 pandemic from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This review aims to consolidate the extensive biological minutiae of SARS-CoV-2 which requires decipherment. Having one of the largest RNA viral genomes, the single strand contains the genes ORF1ab, S, E, M, N and ten open reading frames. Highlighting unique features such as stem-loop formation, slippery frameshifting sequences and ribosomal mimicry, SARS-CoV-2 represents a formidable cellular invader. Hijacking the hosts translational engine, it produces two polyprotein repositories (pp1a and pp1ab), armed with self-cleavage capacity for production of sixteen non-structural proteins. Novel glycosylation sites on the spike trimer reveal unique SARS-CoV-2 features for shielding and cellular internalization. Affording complexity for superior fitness and camouflage, SARS-CoV-2 challenges diagnosis and vaccine vigilance. This review serves the scientific community seeking in-depth molecular details when designing drugs to curb transmission of this biological armament.
Collapse
Affiliation(s)
- Valerie Bríd O’Leary
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruska 87, Vinohrady, 10000 Prague, Czech Republic;
- Department of Experimental Neurobiology, National Institute of Mental Health, Research Programme 1, Topolova 748, 25067 Klecany, Czech Republic; (C.H.); (S.V.O.)
- Correspondence:
| | - Oliver James Dolly
- International Centre for Neurotherapeutics, Dublin City University, Collins Avenue, Dublin 9, Ireland;
| | - Cyril Höschl
- Department of Experimental Neurobiology, National Institute of Mental Health, Research Programme 1, Topolova 748, 25067 Klecany, Czech Republic; (C.H.); (S.V.O.)
- Department of Psychiatry and Medical Psychology, Third Faculty of Medicine, Charles University, Ruska 87, Vinohrady, 10000 Prague, Czech Republic
| | - Marie Černa
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruska 87, Vinohrady, 10000 Prague, Czech Republic;
| | - Saak Victor Ovsepian
- Department of Experimental Neurobiology, National Institute of Mental Health, Research Programme 1, Topolova 748, 25067 Klecany, Czech Republic; (C.H.); (S.V.O.)
- International Centre for Neurotherapeutics, Dublin City University, Collins Avenue, Dublin 9, Ireland;
- Department of Psychiatry and Medical Psychology, Third Faculty of Medicine, Charles University, Ruska 87, Vinohrady, 10000 Prague, Czech Republic
| |
Collapse
|