201
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Hodge CD, Rosenberg DJ, Wilamowski M, Joachimiak A, Hura GL, Hammel M. Rigid monoclonal antibodies improve detection of SARS-CoV-2 nucleocapsid protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.13.426597. [PMID: 33469584 PMCID: PMC7814821 DOI: 10.1101/2021.01.13.426597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Monoclonal antibodies (mAbs) are the basis of treatments and diagnostics for pathogens and other biological phenomena. We conducted a structural characterization of mAbs against the N-terminal domain of nucleocapsid protein (NP NTD ) from SARS-CoV-2 using small angle X-ray scattering (SAXS). Our solution-based results distinguished the mAbs' flexibility and how this flexibility impacts the assembly of multiple mAbs on an antigen. By pairing two mAbs that bind different epitopes on the NP NTD , we show that flexible mAbs form a closed sandwich-like complex. With rigid mAbs, a juxtaposition of the Fabs is prevented, enforcing a linear arrangement of the mAb pair, which facilitates further mAb polymerization. In a modified sandwich ELISA, we show the rigid mAb-pairings with linear polymerization led to increased NP NTD detection sensitivity. These enhancements can expedite the development of more sensitive and selective antigen-detecting point-of-care lateral flow devices (LFA), key for early diagnosis and epidemiological studies of SARS-CoV-2 and other pathogens.
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Affiliation(s)
- Curtis D Hodge
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel J Rosenberg
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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202
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Remali J, Aizat WM. A Review on Plant Bioactive Compounds and Their Modes of Action Against Coronavirus Infection. Front Pharmacol 2021; 11:589044. [PMID: 33519449 PMCID: PMC7845143 DOI: 10.3389/fphar.2020.589044] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/03/2020] [Indexed: 12/15/2022] Open
Abstract
The rapid outbreak of coronavirus disease 2019 (COVID-19) has demonstrated the need for development of new vaccine candidates and therapeutic drugs to fight against the underlying virus, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Currently, no antiviral treatment is available to treat COVID-19 as treatment is mostly directed to only relieving the symptoms. Retrospectively, herbal medicinal plants have been used for thousands of years as a medicinal alternative including for the treatment of various viral illnesses. However, a comprehensive description using various medicinal plants in treating coronavirus infection has not to date been described adequately, especially their modes of action. Most other reports and reviews have also only focused on selected ethnobotanical herbs such as Traditional Chinese Medicine, yet more plants can be considered to enrich the source of the anti-viral compounds. In this review, we have screened and identified potential herbal medicinal plants as anti-coronavirus medication across major literature databases without being limited to any regions or ethnobotanic criteria. As such we have successfully gathered experimentally validated in vivo, in vitro, or in silico findings of more than 30 plants in which these plant extracts or their related compounds, such as those of Artemisia annua L., Houttuynia cordata Thunb., and Sambucus formosana Nakai, are described through their respective modes of action against specific mechanisms or pathways during the viral infection. This includes inhibition of viral attachment and penetration, inhibition of viral RNA and protein synthesis, inhibition of viral key proteins such as 3-chymotrypsin-like cysteine protease (3CLpro) and papain-like protease 2 (PLpro), as well as other mechanisms including inhibition of the viral release and enhanced host immunity. We hope this compilation will help researchers and clinicians to identify the source of appropriate anti-viral drugs from plants in combating COVID-19 and, ultimately, save millions of affected human lives.
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Affiliation(s)
| | - Wan Mohd Aizat
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
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203
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Meng X, Lou QY, Yang WY, Chen R, Xu WH, Yang Y, Zhang L, Xu T, Xiang HF. Gordian Knot: Gastrointestinal lesions caused by three highly pathogenic coronaviruses from SARS-CoV and MERS-CoV to SARS-CoV-2. Eur J Pharmacol 2021; 890:173659. [PMID: 33131637 PMCID: PMC7581377 DOI: 10.1016/j.ejphar.2020.173659] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/25/2020] [Accepted: 10/20/2020] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen of 2019 novel coronavirus disease (COVID-19), is currently spreading around the world. The WHO declared on January 31 that the outbreak of SARS-CoV-2 was a public health emergency. SARS-Cov-2 is a member of highly pathogenic coronavirus group that also consists of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Although respiratory tract lesions were regarded as main manifestation of SARS-Cov-2 infection, gastrointestinal lesions were also reported. Similarly, patients with SARS-CoV and MERS-CoV were also observed. Common gastrointestinal symptoms of patients mainly included diarrhea, vomiting and abdominal pain. Gastrointestinal lesions could be used as basis for early diagnosis of patients, and at the same time, controlling gastrointestinal lesions better facilitated to cut off the route of fecal-oral transmission. Hence, this review summarizes the characteristics and mechanism of gastrointestinal lesions caused by three highly pathogenic human coronavirus infections including SARS-CoV, MERS-CoV, as well as SARS-CoV-2. Furthermore, it is expected to gain experience from gastrointestinal lesions caused by SARS-CoV and MERS-CoV infections in order to be able to better relieve SARS-CoV-2 epidemic. Targetin gut microbiota to regulate the process of SARS-CoV-2 infection should be a concern. Especially, the application of nanotechnology may provide help for further controlling COVID-19.
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Affiliation(s)
- Xiang Meng
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China.
| | - Qiu-Yue Lou
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, 230032, China.
| | - Wen-Ying Yang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China.
| | - Ran Chen
- School of Stomatology, Anhui Medical University, Hefei, 230032, China.
| | - Wen-Hua Xu
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China.
| | - Yang Yang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China; Periodontal Department, Anhui Stomatology Hospital Affiliated to Anhui Medical University, Hefei, 230032, China.
| | - Lei Zhang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China; Periodontal Department, Anhui Stomatology Hospital Affiliated to Anhui Medical University, Hefei, 230032, China.
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, P.R. China.
| | - Hui-Fen Xiang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China.
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204
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Jacob Machado D, White RA, Kofsky J, Janies DA. Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2021; 1:e60. [PMID: 36168505 PMCID: PMC9495640 DOI: 10.1017/ash.2021.222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 04/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily Orthocoronavirinae related to 2 other clinically relevant coronaviruses, SARS-CoV and MERS-CoV. Like other coronaviruses and several other viruses, SARS-CoV-2 originated in bats. However, unlike other coronaviruses, SARS-CoV-2 resulted in a devastating pandemic. The SARS-CoV-2 pandemic rages on due to viral evolution that leads to more transmissible and immune evasive variants. Technology such as genomic sequencing has driven the shift from syndromic to molecular epidemiology and promises better understanding of variants. The COVID-19 pandemic has exposed critical impediments that must be addressed to develop the science of pandemics. Much of the progress is being applied in the developed world. However, barriers to the use of molecular epidemiology in low- and middle-income countries (LMICs) remain, including lack of logistics for equipment and reagents and lack of training in analysis. We review the molecular epidemiology literature to understand its origins from the SARS epidemic (2002-2003) through influenza events and the current COVID-19 pandemic. We advocate for improved genomic surveillance of SARS-CoV and understanding the pathogen diversity in potential zoonotic hosts. This work will require training in phylogenetic and high-performance computing to improve analyses of the origin and spread of pathogens. The overarching goals are to understand and abate zoonosis risk through interdisciplinary collaboration and lowering logistical barriers.
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Affiliation(s)
- Denis Jacob Machado
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- Author for correspondence: Denis Jacob Machado, PhD, Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, BINF 224, Charlotte, NC28223. E-mail:
| | - Richard Allen White
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- University of North Carolina at Charlotte, North Carolina Research Campus (NCRC), Kannapolis, North Carolina
| | - Janice Kofsky
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
| | - Daniel A. Janies
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
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205
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Batah SS, Fabro AT. Pulmonary pathology of ARDS in COVID-19: A pathological review for clinicians. Respir Med 2021; 176:106239. [PMID: 33246294 PMCID: PMC7674971 DOI: 10.1016/j.rmed.2020.106239] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/02/2020] [Accepted: 11/16/2020] [Indexed: 01/04/2023]
Abstract
COVID-19 has quickly reached pandemic levels since it was first reported in December 2019. The virus responsible for the disease, named SARS-CoV-2, is enveloped positive-stranded RNA viruses. During its replication in the cytoplasm of host cells, the viral genome is transcribed into proteins, such as the structural protein spike domain S1, which is responsible for binding to the cell receptor of the host cells. Infected patients have initially flu-like symptoms, rapidly evolving to severe acute lung injury, known as acute respiratory distress syndrome (ARDS). ARDS is characterized by an acute and diffuse inflammatory damage into the alveolar-capillary barrier associated with a vascular permeability increase and reduced compliance, compromising gas exchange and causing hypoxemia. Histopathologically, this condition is known as diffuse alveolar damage which consists of permanent damage to the alveoli epithelial cells and capillary endothelial cells, with consequent hyaline membrane formation and eventually intracapillary thrombosis. All of these mechanisms associated with COVID-19 involve the phenotypic expression from different proteins transcription modulated by viral infection in specific pulmonary microenvironments. Therefore, this knowledge is fundamentally important for a better pathophysiological understanding and identification of the main molecular pathways associated with the disease evolution. Evidently, clinical findings, signs and symptoms of a patient are the phenotypic expression of these pathophysiological and molecular mechanisms of SARS-CoV-2 infection. Therefore, no findings alone, whether molecular, clinical, radiological or pathological axis are sufficient for an accurate diagnosis. However, their intersection and/or correlation are extremely critical for clinicians establish the diagnosis and new treatment perspectives.
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Affiliation(s)
| | - Alexandre Todorovic Fabro
- Corresponding author. Department of Pathology and Legal Med – FMRP/USP, Avenida Bandeirantes, 3900, Zip code 14049Ribeirão Preto, São Paulo, Brazil.55
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206
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Rzymski P, Mamzer H, Nowicki M. The Main Sources and Potential Effects of COVID-19-Related Discrimination. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1318:705-725. [PMID: 33973207 DOI: 10.1007/978-3-030-63761-3_39] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The outbreak of a new coronavirus disease (COVID-19), which appeared in late 2019 and eventually resulted in the announcement of a pandemic by the World Health Organization, led to global fear and panic as well as the spread of false information and fake news from different sources. As a result, a sharp increase in prejudice, discrimination, and xenophobia against different groups of people was observed in different geographical locations. This chapter presents the psychological and social sources of stereotypes and prejudices that take forms in the COVID-19 pandemic. These sources can be located in psychosocial processes, such as (i) socially generated and reinforced fears; (ii) human responses to stress induced by certain types of stimuli; (iii) sense of helplessness based on the lack of control over reality; (iv) psychological responses reinforced by conformism (crowd psychology); and (v) the stigmatization process. The chapter also presents the main groups of increased risk of experiencing prejudice and discrimination during the COVID-19 pandemic (Asians, health-care workers, COVID-19 patients, and their relatives). Moreover, it provides a documented example of such behaviors. The groups at higher risk of more adverse effects of COVID-19 due to pre-pandemic discrimination are also discussed. Finally, initiatives taken to mitigate the discrimination associated with COVID-19 are presented, as well as the recommendations and good practices for preventing these behaviors during future outbreaks and for limiting discrimination against COVID-19 until the disease can be contained.
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Affiliation(s)
- Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, Poznań, Poland. .,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Poznań, Poland.
| | - Hanna Mamzer
- Faculty of Sociology Adam Mickiewicz University, Szamarzewskiego 89 c, 60-568, Poznań, Poland
| | - Michał Nowicki
- Chair of Histology and Embryology, Poznan University of Medical Sciences, Poznań, Poland
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207
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Nardo AD, Schneeweiss‐Gleixner M, Bakail M, Dixon ED, Lax SF, Trauner M. Pathophysiological mechanisms of liver injury in COVID-19. Liver Int 2021; 41:20-32. [PMID: 33190346 PMCID: PMC7753756 DOI: 10.1111/liv.14730] [Citation(s) in RCA: 224] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023]
Abstract
The recent outbreak of coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in a world-wide pandemic. Disseminated lung injury with the development of acute respiratory distress syndrome (ARDS) is the main cause of mortality in COVID-19. Although liver failure does not seem to occur in the absence of pre-existing liver disease, hepatic involvement in COVID-19 may correlate with overall disease severity and serve as a prognostic factor for the development of ARDS. The spectrum of liver injury in COVID-19 may range from direct infection by SARS-CoV-2, indirect involvement by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and ventilation to exacerbation of underlying liver disease. This concise review discusses the potential pathophysiological mechanisms for SARS-CoV-2 hepatic tropism as well as acute and possibly long-term liver injury in COVID-19.
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Affiliation(s)
- Alexander D. Nardo
- Hans Popper Laboratory of Molecular HepatologyDivision of Gastroenterology and HepatologyDepartment of Internal Medicine IIIMedical University of ViennaViennaAustria
| | - Mathias Schneeweiss‐Gleixner
- Medical Intensive Care Unit 13H1. Division of Gastroenterology and HepatologyDepartment of Internal Medicine IIIMedical University of ViennaViennaAustria
| | - May Bakail
- Campus ITInstitute of Science and Technology AustriaKlosterneuburgAustria
| | - Emmanuel D. Dixon
- Hans Popper Laboratory of Molecular HepatologyDivision of Gastroenterology and HepatologyDepartment of Internal Medicine IIIMedical University of ViennaViennaAustria
| | - Sigurd F. Lax
- Department of PathologyHospital Graz IIAcademic Teaching Hospital of the Medical University of GrazGrazAustria,School of MedicineJohannes Kepler UniversityLinzAustria
| | - Michael Trauner
- Hans Popper Laboratory of Molecular HepatologyDivision of Gastroenterology and HepatologyDepartment of Internal Medicine IIIMedical University of ViennaViennaAustria,Medical Intensive Care Unit 13H1. Division of Gastroenterology and HepatologyDepartment of Internal Medicine IIIMedical University of ViennaViennaAustria
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208
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Hodge CD, Rosenberg DJ, Grob P, Wilamowski M, Joachimiak A, Hura GL, Hammel M. Rigid monoclonal antibodies improve detection of SARS-CoV-2 nucleocapsid protein. MAbs 2021; 13:1905978. [PMID: 33843452 PMCID: PMC8043170 DOI: 10.1080/19420862.2021.1905978] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Monoclonal antibodies (mAbs) are the basis of treatments and diagnostics for pathogens and other biological phenomena. We conducted a structural characterization of mAbs against the N-terminal domain of nucleocapsid protein (NPNTD) from SARS-CoV-2 using small-angle X-ray scattering and transmission electron microscopy. Our solution-based results distinguished the mAbs' flexibility and how this flexibility affects the assembly of multiple mAbs on an antigen. By pairing two mAbs that bind different epitopes on the NPNTD, we show that flexible mAbs form a closed sandwich-like complex. With rigid mAbs, a juxtaposition of the antigen-binding fragments is prevented, enforcing a linear arrangement of the mAb pair, which facilitates further mAb polymerization. In a modified sandwich enzyme-linked immunosorbent assay, we show that rigid mAb-pairings with linear polymerization led to increased NPNTD detection sensitivity. These enhancements can expedite the development of more sensitive and selective antigen-detecting point-of-care lateral flow devices, which are critical for early diagnosis and epidemiological studies of SARS-CoV-2 and other pathogens.
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Affiliation(s)
- Curtis D. Hodge
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel. J. Rosenberg
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Graduate Group in Biophysics, University of California, Berkeley, CA, USA
| | - Patricia Grob
- Howard Hughes Medical Institute, UC Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Chemistry and Biochemistry Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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209
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Mohammadpour S, Torshizi Esfahani A, Halaji M, Lak M, Ranjbar R. An updated review of the association of host genetic factors with susceptibility and resistance to COVID-19. J Cell Physiol 2021; 236:49-54. [PMID: 32542735 PMCID: PMC7323230 DOI: 10.1002/jcp.29868] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 12/18/2022]
Abstract
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human populations sparked a global pandemic of the coronavirus disease 2019 (COVID-19). According to preliminary data, about 14% of cases are considered severe and 5% of cases result in critical illness and, reported case fatality rates vary from 1% to more than 7%. However, the symptoms of the disease and the clinical outcome are very different in infected people. In view of these differences, it is clearly apparent that to gain insight into the biology of the SARS-CoV-2, it is important to study not just the infectious particle in itself but also to investigate the virus-host cell interactions that occur during infection. This review seeks to consider the various aspects of genetic factors in determining the susceptibility and host resistance to SARS-CoV-2 throughout the recently published literature.
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Affiliation(s)
| | - Amir Torshizi Esfahani
- Department of Biology, Faculty of Biological SciencesIslamic Azad University, North Tehran BranchTehranIran
| | - Mehrdad Halaji
- Department of Microbiology, School of MedicineIsfahan University of Medical SciencesIsfahanIran
| | - Mina Lak
- Department of Microbiology, Faculty of Advanced Science and TechnologyIslamic Azad University Tehran Medical SciencesTehranIran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
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210
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Fahmi M, Kharisma VD, Ansori ANM, Ito M. Retrieval and Investigation of Data on SARS-CoV-2 and COVID-19 Using Bioinformatics Approach. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1318:839-857. [PMID: 33973215 DOI: 10.1007/978-3-030-63761-3_47] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Sudden emergence and a rapid outbreak of SARS-CoV-2 accompanied by a devastating impact on the economy and public health has driven extensive scientific mobilization to study and elucidate the various associated concerns about SARS-CoV-2. Bioinformatics plays a crucial role in addressing and providing solutions to questions about SARS-CoV-2. It helps shorten the duration for the vaccine development process and the discovery of potential clinical interventions through the simulation and information retrieval, and the development of well-ordered information hubs and resources, which are essential to derive data and meaningful findings from the current massive information about SARS-CoV-2. Advanced algorithms in this field also provide approaches that are essential to elucidate the relationship, origin, and evolutionary process of SARS-CoV-2. Here, we report essential bioinformatics entities, such as database and platform development, molecular evolution and phylogenetic analyses, and vaccine designs, that are useful to solve the SARS-CoV-2 conundrum.
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Affiliation(s)
- Muhamad Fahmi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Kusatsu, Japan
| | - Viol Dhea Kharisma
- Master Program in Biology, Department of Biology, Faculty of Mathematic and Natural Sciences, Universitas Brawijaya, Malang, Indonesia.,Computational Virology and Complexity Science Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia (GENBINESIA) Foundation, Gresik, Indonesia.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Malang, Indonesia
| | - Arif Nur Muhammad Ansori
- Doctoral Program in Veterinary Science, Faculty of Veterinary Medicine, Universitas Airlangga, Kampus C Universitas Airlangga, Surabaya, Indonesia.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Surabaya, Indonesia
| | - Masahiro Ito
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan. .,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Kusatsu, Japan.
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211
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Ghale-Noie ZN, Salmaninejad A, Bergquist R, Mollazadeh S, Hoseini B, Sahebkar A. Genetic Aspects and Immune Responses in Covid-19: Important Organ Involvement. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1327:3-22. [PMID: 34279825 DOI: 10.1007/978-3-030-71697-4_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the last two decades, the world has experienced outbreaks of three major coronaviruses with high morbidity and mortality rates. The most recent of these started in the form of an unusual viral pneumonia in Wuhan, China, and now the world is facing a serious pandemic. This new disease has been called COVID-19 and is caused by the SARS-CoV-2 virus. Understanding the specific genetic and phenotypic structure of SARS-CoV-2 in COVID-19 pathogenesis is vital in finding appropriate drugs and vaccines. With this in mind, this review sheds light on the virology, genetics, immune-responses, and mechanism of action of this virus.
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Affiliation(s)
- Zari Naderi Ghale-Noie
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Robert Bergquist
- Formerly UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Samaneh Mollazadeh
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Benyamin Hoseini
- Pharmaceutical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Health Information Technology, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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212
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Haghani M, Varamini P. Temporal evolution, most influential studies and sleeping beauties of the coronavirus literature. Scientometrics 2021; 126:7005-7050. [PMID: 34188334 PMCID: PMC8221746 DOI: 10.1007/s11192-021-04036-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/07/2021] [Indexed: 02/06/2023]
Abstract
Following the outbreak of SARS-CoV-2 disease, within less than 8 months, the 50 years-old scholarly literature of coronaviruses grew to nearly three times larger than its size prior to 2020. Here, temporal evolution of the coronavirus literature over the last 30 years (N = 43,769) is analysed along with its subdomain of SARS-CoV-2 articles (N = 27,460) and the subdomain of reviews and meta-analytic studies (N = 1027). The analyses are conducted through the lenses of co-citation and bibliographic coupling of documents. (1) Of the N = 1204 review and meta-analytical articles of the coronavirus literature, nearly 88% have been published and indexed during the first 8 months of 2020, marking an unprecedented attention to reviews and meta-analyses in this domain, prompted by the SARS-CoV-2 pandemic. (2) The subset of 2020 SARS-CoV-2 articles is bibliographically distant from the rest of this literature published prior to 2020. Individual articles of the SARS-CoV-2 segment with a bridging role between the two bodies of articles (i.e., before and after 2020) are identifiable. (3) Furthermore, the degree of bibliographic coupling within the 2020 SARS-CoV-2 cluster is much poorer compared to the cluster of articles published prior to 2020. This could, in part, be explained by the higher diversity of topics that are studied in relation to SARS-CoV-2 compared to the literature of coronaviruses published prior to the SARS-CoV-2 disease. (4) The analyses on the subset of SARS-CoV-2 literature identified studies published prior to 2020 that have now proven highly instrumental in the development of various clusters of publications linked to SARS-CoV-2. In particular, the so-called "sleeping beauties" of the coronavirus literature with an awakening in 2020 were identified, i.e., previously published studies of this literature that had remained relatively unnoticed for several years but gained sudden traction in 2020 in the wake of the SARS-CoV-2 outbreak. This work documents the historical development of the literature on coronaviruses as an event-driven literature and as a domain that exhibited, arguably, the most exceptional case of publication burst in the history of science. It also demonstrates how scholarly efforts undertaken during peace time or prior to a disease outbreak could suddenly play a critical role in prevention and mitigation of health disasters caused by new diseases. Supplementary Information The online version contains supplementary material available at 10.1007/s11192-021-04036-4.
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Affiliation(s)
- Milad Haghani
- School of Civil and Environmental Engineering, The University of New South Wales, Sydney, Australia
- Institute of Transport and Logistics Studies, The University of Sydney, Sydney, Australia
| | - Pegah Varamini
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
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213
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Synthesis and Identification of Novel Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach. Appl Biochem Biotechnol 2021; 193:3602-3623. [PMID: 34324152 PMCID: PMC8319192 DOI: 10.1007/s12010-021-03615-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
The novel coronavirus disease that arises in the end of 2019 (COVID-19) in Wuhan, China, has rapidly spread over the globe and was considered as a world pandemic. Currently, various antiviral therapies or vaccines are available, and many researches are ongoing for further treatments. Targeting the coronavirus' main protease (key enzyme: 3CLpro) is growing in importance in anti-SARS-CoV-2 drug discovery process. The present study aims at predicting the antiviral activity of two novel compounds using in silico approaches that might become potential leads against SARS-CoV-2. The 3D structures of the new compounds are elucidated by single-crystal X-ray techniques. The interactions between different units of 4 and 5 were emphasized by analyzing their corresponding Hirshfeld surfaces and ESP plots. NBO and FMO analyses were investigated as well. Molecular docking combined with molecular dynamics simulations (MDs) was performed to investigate the binding modes and molecular interactions of 4 and 5 with the amino acids of coronavirus main protease (6LU7) protein. The best docking scores were obtained for both ligands through the major binding interactions via hydrogen/hydrophobic bonds with the key amino acids in the active site: HIS41, CYS145, MET49, MET165, HIS172, and GLU166 amino acids. A MD simulation study was also performed for 100 ns to validate the stability behavior of the main protease 3CLpro-ligand complexes. The MD simulation study successfully confirmed the stability of the ligands in the binding site as potent anti-SARS-CoV-2 (COVID-19) inhibitors. Additionally, MMPBSA energy of both docked complexes was determined as a validation assay of docking and MD simulations to validate compound conformation and interaction stability with 3CLpro. The synthesized compounds might be helpful in the fight against COVID-19 prior to biological activity confirmation in vitro and in vivo.
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214
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Chen K, Xiao F, Hu D, Ge W, Tian M, Wang W, Pan P, Wu K, Wu J. SARS-CoV-2 Nucleocapsid Protein Interacts with RIG-I and Represses RIG-Mediated IFN-β Production. Viruses 2020; 13:E47. [PMID: 33396605 PMCID: PMC7823417 DOI: 10.3390/v13010047] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/25/2022] Open
Abstract
SARS-CoV-2 is highly pathogenic in humans and poses a great threat to public health worldwide. Clinical data shows a disturbed type I interferon (IFN) response during the virus infection. In this study, we discovered that the nucleocapsid (N) protein of SARS-CoV-2 plays an important role in the inhibition of interferon beta (IFN-β) production. N protein repressed IFN-β production induced by poly(I:C) or upon Sendai virus (SeV) infection. We noted that N protein also suppressed IFN-β production, induced by several signaling molecules downstream of the retinoic acid-inducible gene I (RIG-I) pathway, which is the crucial pattern recognition receptor (PRR) responsible for identifying RNA viruses. Moreover, our data demonstrated that N protein interacted with the RIG-I protein through the DExD/H domain, which has ATPase activity and plays an important role in the binding of immunostimulatory RNAs. These results suggested that SARS-CoV-2 N protein suppresses the IFN-β response through targeting the initial step, potentially the cellular PRR-RNA-recognition step in the innate immune pathway. Therefore, we propose that the SARS-CoV-2 N protein represses IFN-β production by interfering with RIG-I.
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Affiliation(s)
- Keli Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (K.C.); (F.X.); (D.H.); (W.G.); (M.T.); (K.W.)
| | - Feng Xiao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (K.C.); (F.X.); (D.H.); (W.G.); (M.T.); (K.W.)
| | - Dingwen Hu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (K.C.); (F.X.); (D.H.); (W.G.); (M.T.); (K.W.)
| | - Weiwei Ge
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (K.C.); (F.X.); (D.H.); (W.G.); (M.T.); (K.W.)
| | - Mingfu Tian
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (K.C.); (F.X.); (D.H.); (W.G.); (M.T.); (K.W.)
| | - Wenbiao Wang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China; (W.W.); (P.P.)
| | - Pan Pan
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China; (W.W.); (P.P.)
| | - Kailang Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (K.C.); (F.X.); (D.H.); (W.G.); (M.T.); (K.W.)
| | - Jianguo Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (K.C.); (F.X.); (D.H.); (W.G.); (M.T.); (K.W.)
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China; (W.W.); (P.P.)
- Foshan Institute of Medical Microbiology, Foshan 528315, China
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215
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Deeks HM, Walters RK, Barnoud J, Glowacki DR, Mulholland AJ. Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease. J Chem Inf Model 2020; 60:5803-5814. [PMID: 33174415 PMCID: PMC7671099 DOI: 10.1021/acs.jcim.0c01030] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Indexed: 01/19/2023]
Abstract
The main protease (Mpro) of the SARS-CoV-2 virus is one focus of drug development efforts for COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) is a useful and effective tool for creating Mpro complexes. We make these tools and models freely available. iMD-VR provides an immersive environment in which users can interact with MD simulations and so build protein complexes in a physically rigorous and flexible way. Recently, we have demonstrated that iMD-VR is an effective method for interactive, flexible docking of small molecule drugs into their protein targets (Deeks et al. PLoS One 2020, 15, e0228461). Here, we apply this approach to both an Mpro inhibitor and an oligopeptide substrate, using experimentally determined crystal structures. For the oligopeptide, we test against a crystallographic structure of the original SARS Mpro. Docking with iMD-VR gives models in agreement with experimentally observed (crystal) structures. The docked structures are also tested in MD simulations and found to be stable. Different protocols for iMD-VR docking are explored, e.g., with and without restraints on protein backbone, and we provide recommendations for its use. We find that it is important for the user to focus on forming binding interactions, such as hydrogen bonds, and not to rely on using simple metrics (such as RMSD), in order to create realistic, stable complexes. We also test the use of apo (uncomplexed) crystal structures for docking and find that they can give good results. This is because of the flexibility and dynamic response allowed by the physically rigorous, atomically detailed simulation approach of iMD-VR. We make our models (and interactive simulations) freely available. The software framework that we use, Narupa, is open source, and uses commodity VR hardware, so these tools are readily accessible to the wider research community working on Mpro (and other COVID-19 targets). These should be widely useful in drug development, in education applications, e.g., on viral enzyme structure and function, and in scientific communication more generally.
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Affiliation(s)
- Helen M. Deeks
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Department of Computer Science, Merchant
Venturers Building, University of Bristol,
Woodland Road, Bristol BS8 1UB, United
Kingdom
| | - Rebecca K. Walters
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Department of Computer Science, Merchant
Venturers Building, University of Bristol,
Woodland Road, Bristol BS8 1UB, United
Kingdom
| | - Jonathan Barnoud
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
| | - David R. Glowacki
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Department of Computer Science, Merchant
Venturers Building, University of Bristol,
Woodland Road, Bristol BS8 1UB, United
Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
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216
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Kumari A, Rajput VS, Nagpal P, Kukrety H, Grover S, Grover A. Dual inhibition of SARS-CoV-2 spike and main protease through a repurposed drug, rutin. J Biomol Struct Dyn 2020; 40:4987-4999. [PMID: 33357073 PMCID: PMC7784834 DOI: 10.1080/07391102.2020.1864476] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The global health emergency caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to alarming numbers of fatalities across the world. So far the researchers worldwide have not been able to discover a breakthrough in the form of a potent drug or an effective vaccine. Therefore, it is imperative to discover drugs to curb the ongoing menace. In silico approaches using FDA approved drugs can expedite the drug discovery process by providing leads that can be pursued. In this report, two drug targets, namely the spike protein and main protease, belonging to structural and non-structural class of proteins respectively, were utilized to carry out drug repurposing based screening. The exposed nature of the spike protein on the viral surface along with its instrumental role in host infection and the involvement of main protease in processing of polyproteins along with no human homologue make these proteins attractive drug targets. Interestingly, the screening identified a common high efficiency binding molecule named rutin. Further, molecular dynamics simulations in explicit solvent affirmed the stable and sturdy binding of rutin with these proteins. The decreased Rg value (4 nm for spike-rutin and 2.23 nm for main protease-rutin) and stagnant SASA analysis (485 nm/S2/N in spike-rutin and 152 nm/S2/N in main protease-rutin) for protein surface and its orientation in the exposed and buried regions suggests a strong binding interaction of the drug. Further, cluster analysis and secondary structure analysis of complex trajectories validated the conformational changes due to binding of rutin.
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Affiliation(s)
- Anchala Kumari
- School of Biotechnology, Jawaharlal Nehru University (JNU), New Delhi, India.,Department of Biotechnology, Teri School of Advanced Studies, New Delhi, India
| | | | - Priya Nagpal
- School of Biotechnology, Jawaharlal Nehru University (JNU), New Delhi, India
| | - Himanshi Kukrety
- School of Biotechnology, Jawaharlal Nehru University (JNU), New Delhi, India
| | - Sonam Grover
- JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University (JNU), New Delhi, India
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217
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Terse VL, Gosavi S. The Molecular Mechanism of Domain Swapping of the C-Terminal Domain of the SARS-Coronavirus Main Protease. Biophys J 2020; 120:504-516. [PMID: 33359834 PMCID: PMC7837137 DOI: 10.1016/j.bpj.2020.11.2277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 11/25/2022] Open
Abstract
In three-dimensional domain swapping, two protein monomers exchange a part of their structures to form an intertwined homodimer, whose subunits resemble the monomer. Several viral proteins domain swap to increase their structural complexity or functional avidity. The main protease (Mpro) of the severe acute respiratory syndrome (SARS) coronavirus proteolyzes viral polyproteins and has been a target for anti-SARS drug design. Domain swapping in the α-helical C-terminal domain of Mpro (MproC) locks Mpro into a hyperactive octameric form that is hypothesized to promote the early stages of viral replication. However, in the absence of a complete molecular understanding of the mechanism of domain swapping, investigations into the biological relevance of this octameric Mpro have stalled. Isolated MproC can exist as a monomer or a domain-swapped dimer. Here, we investigate the mechanism of domain swapping of MproC using coarse-grained structure-based models and molecular dynamics simulations. Our simulations recapitulate several experimental features of MproC folding. Further, we find that a contact between a tryptophan in the MproC domain-swapping hinge and an arginine elsewhere forms early during folding, modulates the folding route, and promotes domain swapping to the native structure. An examination of the sequence and the structure of the tryptophan containing hinge loop shows that it has a propensity to form multiple secondary structures and contacts, indicating that it could be stabilized into either the monomer- or dimer-promoting conformations by mutations or ligand binding. Finally, because all residues in the tryptophan loop are identical in SARS-CoV and SARS-CoV-2, mutations that modulate domain swapping may provide insights into the role of octameric Mpro in the early-stage viral replication of both viruses.
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Affiliation(s)
- Vishram L Terse
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
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218
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Sadeghmousavi S, Rezaei N. COVID-19 infection and stroke risk. Rev Neurosci 2020; 32:341-349. [PMID: 33580645 DOI: 10.1515/revneuro-2020-0066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/09/2020] [Indexed: 12/19/2022]
Abstract
Coronavirus disease 2019 (COVID-19), due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan city, China in December 2019 and rapidly spread to other countries. The most common reported symptoms are fever, dry cough, myalgia and fatigue, headache, anorexia, and breathlessness. Anosmia and dysgeusia as well as gastrointestinal symptoms including nausea and diarrhea are other notable symptoms. This virus also can exhibit neurotropic properties and may also cause neurological diseases, including epileptic seizures, cerebrovascular accident, Guillian barre syndrome, acute transverse myelitis, and acute encephalitis. In this study, we discuss stroke as a complication of the new coronavirus and its possible mechanisms of damage.
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Affiliation(s)
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Tehran University of Medical Sciences, Children's Medical Center, Dr. Qarib St, Keshavarz Blvd, Tehran, 14194, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, 14194, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran1419783151, Iran
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219
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de Breyne S, Vindry C, Guillin O, Condé L, Mure F, Gruffat H, Chavatte L, Ohlmann T. Translational control of coronaviruses. Nucleic Acids Res 2020; 48:12502-12522. [PMID: 33264393 PMCID: PMC7736815 DOI: 10.1093/nar/gkaa1116] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022] Open
Abstract
Coronaviruses represent a large family of enveloped RNA viruses that infect a large spectrum of animals. In humans, the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic and is genetically related to SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV), which caused outbreaks in 2002 and 2012, respectively. All viruses described to date entirely rely on the protein synthesis machinery of the host cells to produce proteins required for their replication and spread. As such, virus often need to control the cellular translational apparatus to avoid the first line of the cellular defense intended to limit the viral propagation. Thus, coronaviruses have developed remarkable strategies to hijack the host translational machinery in order to favor viral protein production. In this review, we will describe some of these strategies and will highlight the role of viral proteins and RNAs in this process.
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Affiliation(s)
- Sylvain de Breyne
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Caroline Vindry
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Olivia Guillin
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Lionel Condé
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Fabrice Mure
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Henri Gruffat
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Laurent Chavatte
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Théophile Ohlmann
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
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220
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Minimal system for assembly of SARS-CoV-2 virus like particles. Sci Rep 2020; 10:21877. [PMID: 33318562 PMCID: PMC7736577 DOI: 10.1038/s41598-020-78656-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/26/2020] [Indexed: 01/04/2023] Open
Abstract
SARS-CoV-2 virus is the causative agent of COVID-19. Here we demonstrate that non-infectious SARS-CoV-2 virus like particles (VLPs) can be assembled by co-expressing the viral proteins S, M and E in mammalian cells. The assembled SARS-CoV-2 VLPs possess S protein spikes on particle exterior, making them ideal for vaccine development. The particles range in shape from spherical to elongated with a characteristic size of 129 ± 32 nm. We further show that SARS-CoV-2 VLPs dried in ambient conditions can retain their structural integrity upon repeated scans with Atomic Force Microscopy up to a peak force of 1 nN.
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221
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Zhu Z, Meng K, Meng G. Genomic recombination events may reveal the evolution of coronavirus and the origin of SARS-CoV-2. Sci Rep 2020; 10:21617. [PMID: 33303849 PMCID: PMC7728743 DOI: 10.1038/s41598-020-78703-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
To trace the evolution of coronaviruses and reveal the possible origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), we collected and thoroughly analyzed 29,452 publicly available coronavirus genomes, including 26,312 genomes of SARS-CoV-2 strains. We observed coronavirus recombination events among different hosts including 3 independent recombination events with statistical significance between some isolates from humans, bats and pangolins. Consistent with previous records, we also detected putative recombination between strains similar or related to Bat-CoV-RaTG13 and Pangolin-CoV-2019. The putative recombination region is located inside the receptor-binding domain (RBD) of the spike glycoprotein (S protein), which may represent the origin of SARS-CoV-2. Population genetic analyses provide estimates suggesting that the putative introduced DNA within the RBD is undergoing directional evolution. This may result in the adaptation of the virus to hosts. Unsurprisingly, we found that the putative recombination region in S protein was highly diverse among strains from bats. Bats harbor numerous coronavirus subclades that frequently participate in recombination events with human coronavirus. Therefore, bats may provide a pool of genetic diversity for the origin of SARS-CoV-2.
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Affiliation(s)
- Zhenglin Zhu
- School of Life Sciences, Chongqing University, No. 55 Daxuecheng South Road, Shapingba, Chongqing, 401331, China.
| | - Kaiwen Meng
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094, China
| | - Geng Meng
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094, China.
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222
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Alignment of virus-host protein-protein interaction networks by integer linear programming: SARS-CoV-2. PLoS One 2020; 15:e0236304. [PMID: 33284827 PMCID: PMC7721128 DOI: 10.1371/journal.pone.0236304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/24/2020] [Indexed: 11/19/2022] Open
Abstract
Motivation Beside socio-economic issues, coronavirus pandemic COVID-19, the infectious disease caused by the newly discovered coronavirus SARS-CoV-2, has caused a deep impact in the scientific community, that has considerably increased its effort to discover the infection strategies of the new virus. Among the extensive and crucial research that has been carried out in the last months, the analysis of the virus-host relationship plays an important role in drug discovery. Virus-host protein-protein interactions are the active agents in virus replication, and the analysis of virus-host protein-protein interaction networks is fundamental to the study of the virus-host relationship. Results We have adapted and implemented a recent integer linear programming model for protein-protein interaction network alignment to virus-host networks, and obtained a consensus alignment of the SARS-CoV-1 and SARS-CoV-2 virus-host protein-protein interaction networks. Despite the lack of shared human proteins in these virus-host networks, and the low number of preserved virus-host interactions, the consensus alignment revealed aligned human proteins that share a function related to viral infection, as well as human proteins of high functional similarity that interact with SARS-CoV-1 and SARS-CoV-2 proteins, whose alignment would preserve these virus-host interactions.
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223
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Masaud SM, Szasz O, Szasz AM, Ejaz H, Anwar RA, Szasz A. A Potential Bioelectromagnetic Method to Slow Down the Progression and Prevent the Development of Ultimate Pulmonary Fibrosis by COVID-19. Front Immunol 2020; 11:556335. [PMID: 33343561 PMCID: PMC7746880 DOI: 10.3389/fimmu.2020.556335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
Introduction Right now, we are facing a global pandemic caused by the coronavirus SARS-CoV-2 that causes the highly contagious human disease COVID-19. The number of COVID-19 cases is increasing at an alarming rate, more and more people suffer from it, and the death toll is on the rise since December 2019, when COVID-19 has presumably appeared. We need an urgent solution for the prevention, treatment, and recovery of the involved patients. Methods Modulated electro-hyperthermia (mEHT) is known as an immuno-supportive therapy in oncology. Our proposal is to apply this method to prevent the progression of the disease after its identification, to provide treatment when necessary, and deliver rehabilitation to diminish the fibrotic-often fatal-consequences of the infection. Hypothesis The effects of mEHT, which are proven for oncological applications, could be utilized for the inactivation of the virus or for treating the fibrotic consequences. The hypothesized mEHT effects, which could have a role in the antiviral treatment, it could be applied for viral-specific immune-activation and for anti-fibrotic treatments.
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Affiliation(s)
| | - Oliver Szasz
- Biotechnics Department, St. Istvan University, Godollo, Hungary
| | - A. Marcell Szasz
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Huma Ejaz
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Rana Attique Anwar
- Department of Oncology, Nishtar Medical College Multan, Multan, Pakistan
| | - Andras Szasz
- Biotechnics Department, St. Istvan University, Godollo, Hungary
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Agrawal PK, Agrawal C, Blunden G. Quercetin: Antiviral Significance and Possible COVID-19 Integrative Considerations. Nat Prod Commun 2020. [DOI: 10.1177/1934578x20976293] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Quercetin, a naturally occurring dietary flavonoid, is well known to ameliorate chronic diseases and aging processes in humans, and its antiviral properties have been investigated in numerous studies. In silico and in vitro studies demonstrated that quercetin can interfere with various stages of the coronavirus entry and replication cycle such as PLpro, 3CLpro, and NTPase/helicase. Due to its pleiotropic activities and lack of systemic toxicity, quercetin and its derivatives may represent target compounds to be tested in future clinical trials to enrich the drug arsenal against coronavirus infections. There is evidence that quercetin in combination with, for example, vitamins C and D, may exert a synergistic antiviral action that may provide either an alternative or additional therapeutic/preventive option due to overlapping antiviral and immunomodulatory properties. This review summarizes the antiviral significance of quercetin and proposes a possible strategy for the effective utilization of natural polyphenols in our daily diet for the prevention of viral infection.
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Affiliation(s)
| | | | - Gerald Blunden
- School of Pharmacy and Biomedical Science, University of Portsmouth, Portsmouth, UK
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225
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Picarazzi F, Vicenti I, Saladini F, Zazzi M, Mori M. Targeting the RdRp of Emerging RNA Viruses: The Structure-Based Drug Design Challenge. Molecules 2020; 25:E5695. [PMID: 33287144 PMCID: PMC7730706 DOI: 10.3390/molecules25235695] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
The RNA-dependent RNA polymerase (RdRp) is an essential enzyme for the viral replication process, catalyzing the viral RNA synthesis using a metal ion-dependent mechanism. In recent years, RdRp has emerged as an optimal target for the development of antiviral drugs, as demonstrated by recent approvals of sofosbuvir and remdesivir against Hepatitis C virus (HCV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respectively. In this work, we overview the main sequence and structural features of the RdRp of emerging RNA viruses such as Coronaviruses, Flaviviruses, and HCV, as well as inhibition strategies implemented so far. While analyzing the structural information available on the RdRp of emerging RNA viruses, we provide examples of success stories such as for HCV and SARS-CoV-2. In contrast, Flaviviruses' story has raised attention about how the lack of structural details on catalytically-competent or ligand-bound RdRp strongly hampers the application of structure-based drug design, either in repurposing and conventional approaches.
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Affiliation(s)
- Francesca Picarazzi
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018–2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy;
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.S.); (M.Z.)
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.S.); (M.Z.)
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.S.); (M.Z.)
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018–2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy;
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226
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Teng X, Li Q, Li Z, Zhang Y, Niu G, Xiao J, Yu J, Zhang Z, Song S. Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades. GENOMICS, PROTEOMICS & BIOINFORMATICS 2020; 18:648-663. [PMID: 33581339 PMCID: PMC7875716 DOI: 10.1016/j.gpb.2020.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/18/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
COVID-19 and its causative pathogen SARS-CoV-2 have rushed the world into a staggering pandemic in a few months, and a global fight against both has been intensifying. Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code to molecular mechanisms, based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on the replicase-transcriptase complex. Our analysis starts with primary sequence information, identity-based phylogeny based on 22,051 SARS-CoV-2 sequences, and evaluation of sequence variation patterns as mutation spectra and its 12 permutations among organized clades. All are tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings are listed as follows: 1) The most dominant mutation is C-to-U permutation, whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity, albeit assumed most slightly deleterious. 2) The second abundance group includes three negative-strand mutations (U-to-C, A-to-G, and G-to-A) and a positive-strand mutation (G-to-U) due to DNA repair mechanisms after cellular abasic events. 3) A clade-associated biased mutation trend is found attributable to elevated level of negative-sense strand synthesis. 4) Within-clade permutation variation is very informative for associating non-synonymous mutations and viral proteome changes. These findings demand a platform where emerging mutations are mapped onto mostly subtle but fast-adjusting viral proteomes and transcriptomes, to provide biological and clinical information after logical convergence for effective pharmaceutical and diagnostic applications. Such actions are in desperate need, especially in the middle of the War against COVID-19.
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Affiliation(s)
- Xufei Teng
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & 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
| | - Qianpeng Li
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & 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
| | - Zhao Li
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & 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
| | - Yuansheng Zhang
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & 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
| | - Guangyi Niu
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & 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
| | - Jingfa Xiao
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & 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
| | - Jun Yu
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & 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.
| | - Zhang Zhang
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & 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.
| | - Shuhui Song
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & 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.
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Henzinger H, Barth DA, Klec C, Pichler M. Non-Coding RNAs and SARS-Related Coronaviruses. Viruses 2020; 12:v12121374. [PMID: 33271762 PMCID: PMC7761185 DOI: 10.3390/v12121374] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 02/07/2023] Open
Abstract
The emergence of SARS-CoV-2 in 2019 has caused a major health and economic crisis around the globe. Gaining knowledge about its attributes and interactions with human host cells is crucial. Non-coding RNAs (ncRNAs) are involved in the host cells’ innate antiviral immune response. In RNA interference, microRNAs (miRNAs) may bind to complementary sequences of the viral RNA strand, forming an miRNA-induced silencing complex, which destroys the viral RNA, thereby inhibiting viral protein expression. There are several targets for human miRNAs on SARS-CoV-2’s RNA, most of which are in the 5’ and 3’ untranslated regions. Mutations of the viral genome causing the creation or loss of miRNA binding sites may have crucial effects on SARS-CoV-2 pathogenicity. In addition to mediating immunity, the ncRNA landscape of host cells further influences their susceptibility to virus infection, as certain miRNAs are essential in the regulation of cellular receptors that are necessary for virus invasion. Conversely, virus infection also changes the host ncRNA expression patterns, possibly augmenting conditions for viral replication and dissemination. Hence, ncRNAs typically upregulated in SARS-CoV-2 infection could be useful biomarkers for disease progression and severity. Understanding these mechanisms could provide further insight into the pathogenesis and possible treatment options against COVID-19.
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Affiliation(s)
- Hanna Henzinger
- Comprehensive Cancer Center Graz, Research Unit of Non-Coding RNAs and Genome Editing, Department of Internal Medicine, Division of Clinical Oncology, Medical University of Graz, 8036 Graz, Austria; (H.H.); (D.A.B.); (C.K.)
| | - Dominik A. Barth
- Comprehensive Cancer Center Graz, Research Unit of Non-Coding RNAs and Genome Editing, Department of Internal Medicine, Division of Clinical Oncology, Medical University of Graz, 8036 Graz, Austria; (H.H.); (D.A.B.); (C.K.)
| | - Christiane Klec
- Comprehensive Cancer Center Graz, Research Unit of Non-Coding RNAs and Genome Editing, Department of Internal Medicine, Division of Clinical Oncology, Medical University of Graz, 8036 Graz, Austria; (H.H.); (D.A.B.); (C.K.)
| | - Martin Pichler
- Comprehensive Cancer Center Graz, Research Unit of Non-Coding RNAs and Genome Editing, Department of Internal Medicine, Division of Clinical Oncology, Medical University of Graz, 8036 Graz, Austria; (H.H.); (D.A.B.); (C.K.)
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence:
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228
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Sohag AAM, Hannan MA, Rahman S, Hossain M, Hasan M, Khan MK, Khatun A, Dash R, Uddin MJ. Revisiting potential druggable targets against SARS-CoV-2 and repurposing therapeutics under preclinical study and clinical trials: A comprehensive review. Drug Dev Res 2020; 81:919-941. [PMID: 32632960 PMCID: PMC7361641 DOI: 10.1002/ddr.21709] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/03/2020] [Accepted: 06/06/2020] [Indexed: 12/21/2022]
Abstract
Coronavirus disease-19 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is one of the most contagious diseases in human history that has already affected millions of lives worldwide. To date, no vaccines or effective therapeutics have been discovered yet that may successfully treat COVID-19 patients or contain the transmission of the virus. Scientific communities across the globe responded rapidly and have been working relentlessly to develop drugs and vaccines, which may require considerable time. In this uncertainty, repurposing the existing antiviral drugs could be the best strategy to speed up the discovery of effective therapeutics against SARS-CoV-2. Moreover, drug repurposing may leave some vital information on druggable targets that could be capitalized in target-based drug discovery. Information on possible drug targets and the progress on therapeutic and vaccine development also needs to be updated. In this review, we revisited the druggable targets that may hold promise in the development of the anti-SARS-CoV-2 agent. Progresses on the development of potential therapeutics and vaccines that are under the preclinical studies and clinical trials have been highlighted. We anticipate that this review will provide valuable information that would help to accelerate the development of therapeutics and vaccines against SARS-CoV-2 infection.
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Affiliation(s)
- Abdullah Al Mamun Sohag
- Department of Biochemistry and Molecular BiologyBangladesh Agricultural UniversityMymensingh2202Bangladesh
| | - Md Abdul Hannan
- Department of Biochemistry and Molecular BiologyBangladesh Agricultural UniversityMymensingh2202Bangladesh
- Department of AnatomyDongguk University College of MedicineGyeongju38066South Korea
- ABEx Bio‐Research CenterEast Azampur, DhakaBangladesh
| | - Sadaqur Rahman
- Department of Biochemistry and Molecular BiologyShahjalal University of Science and TechnologySylhetBangladesh
| | - Motaher Hossain
- Department of Biological SciencesThe University of AlabamaTuscaloosaAlabamaUSA
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial BiotechnologySylhet Agricultural UniversitySylhetBangladesh
| | - Md Kawsar Khan
- Department of Biochemistry and Molecular BiologyShahjalal University of Science and TechnologySylhetBangladesh
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Amena Khatun
- Northern International Medical College HospitalDhakaBangladesh
| | - Raju Dash
- Department of AnatomyDongguk University College of MedicineGyeongju38066South Korea
| | - Md Jamal Uddin
- ABEx Bio‐Research CenterEast Azampur, DhakaBangladesh
- Graduate School of Pharmaceutical Sciences, College of PharmacyEwha Womans UniversitySeoulRepublic of Korea
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229
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Zhao X, Ding Y, Du J, Fan Y. 2020 update on human coronaviruses: One health, one world. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2020; 8:100043. [PMID: 33521622 PMCID: PMC7836940 DOI: 10.1016/j.medntd.2020.100043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/04/2020] [Accepted: 08/19/2020] [Indexed: 01/18/2023] Open
Abstract
Since human coronavirus (HCoVs) was first described in the 1960s, seven strains of respiratory human coronaviruses have emerged and caused human infections. After the emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), a pneumonia outbreak of coronavirus disease 2019 (COVID-19) caused by a novel coronavirus (SARS-CoV-2) has represented a pandemic threat to global public health in the 21st century. Without effectively prophylactic and therapeutic strategies including vaccines and antiviral drugs, these three coronaviruses have caused severe respiratory syndrome and high case-fatality rates around the world. In this review, we detail the emergence event, origin and reservoirs of all HCoVs, compare the differences with regard to structure and receptor usage, and summarize therapeutic strategies for COVID-19 that cause severe pneumonia and global pandemic.
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Affiliation(s)
- Xinbin Zhao
- Key Laboratory for Biomechanics and Mechanobiology of Chinese Education Ministry, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Yuecheng Ding
- School of Public Health, Peking University, Beijing, 100871, China
| | - Jing Du
- Key Laboratory for Biomechanics and Mechanobiology of Chinese Education Ministry, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, 100191, China
| | - Yubo Fan
- Key Laboratory for Biomechanics and Mechanobiology of Chinese Education Ministry, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, 100191, China
- Key Laboratory of Human Motion Analysis and Rehabilitation Technology of the Ministry of Civil Affairs, National Research Center for Rehabilitation Technical Aids, Beijing, 100176, China
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230
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Takla M, Jeevaratnam K. Chloroquine, hydroxychloroquine, and COVID-19: Systematic review and narrative synthesis of efficacy and safety. Saudi Pharm J 2020; 28:1760-1776. [PMID: 33204210 PMCID: PMC7662033 DOI: 10.1016/j.jsps.2020.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/08/2020] [Indexed: 01/10/2023] Open
Abstract
The COVID-19 pandemic has required clinicians to urgently identify new treatment options or the re-purposing of existing drugs. Of particular interest are chloroquine (CQ) and hydroxychloroquine (HCQ). The aims of this systematic review are to systematically identify and collate 24 studies describing the use of CQ and HCQ in human clinical trials and to provide a detailed synthesis of evidence of its efficacy and safety. Of clinical trials, 100% showed no significant difference in the probability of viral transmission or clearance in prophylaxis or therapy, respectively, compared to the control group. Among observational studies employing an endpoint specific to efficacy, 58% concurred with the finding of no significant difference in the attainment of outcomes. Three-fifths of clinical trials and half of observational studies examining an indicator unique to drug safety discovered a higher probability of adverse events in those treated patients suspected of, and diagnosed with, COVID-19. Of the total papers focusing on cardiac side-effects, 44% found a greater incidence of QTc prolongation and/or arrhythmias, 44% found no evidence of a significant difference, and 11% mixed results. The strongest available evidence points towards the inefficacy of CQ and HCQ in prophylaxis or in the treatment of hospitalised COVID-19 patients.
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Key Words
- COVID-19
- COVID-19, Coronavirus Disease 2019
- CQ, chloroquine
- Chloroquine
- CoV, coronavirus
- Efficacy
- FDA, Food and Drug Administration
- HCQ, hydroxychloroquine
- Hydroxychloroquine
- ICU, intensive care unit
- MERS, Middle East Respiratory Syndrome
- PICOT, Population, intervention, comparison, outcome, time
- PRISMA, Preferred Reporting Items for Systematic Reviews and Meta-Analyses
- QTcF, The corrected QT interval by Fredericia
- SARS, Severe Acute Respiratory Syndrome
- Safety
- VT, ventricular tachyarrythmia
- WHO, World Health Organisation
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Affiliation(s)
- Michael Takla
- Faculty of Health and Medical Science, University of Surrey, Guildford GU2 7AL, United Kingdom
| | - Kamalan Jeevaratnam
- Faculty of Health and Medical Science, University of Surrey, Guildford GU2 7AL, United Kingdom
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231
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Dhankhar P, Dalal V, Singh V, Tomar S, Kumar P. Computational guided identification of novel potent inhibitors of N-terminal domain of nucleocapsid protein of severe acute respiratory syndrome coronavirus 2. J Biomol Struct Dyn 2020; 40:4084-4099. [PMID: 33251943 PMCID: PMC7754992 DOI: 10.1080/07391102.2020.1852968] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Coronavirus Disease 2019, caused by the severe acute respiratory syndrome coronavirus 2 is an exceptionally contagious disease that leads to global epidemics with elevated mortality and morbidity. There are currently no efficacious drugs targeting coronavirus disease 2019, therefore, it is an urgent requirement for the development of drugs to control this emerging disease. Owing to the importance of nucleocapsid protein, the present study focuses on targeting the N-terminal domain of nucleocapsid protein from severe acute respiratory syndrome coronavirus 2 to identify the potential compounds by computational approaches such as pharmacophore modeling, virtual screening, docking and molecular dynamics. We found three molecules (ZINC000257324845, ZINC000005169973 and ZINC000009913056), which adopted a similar conformation as guanosine monophosphate (GMP) within the N-terminal domain active site and exhibiting high binding affinity (>−8.0 kcalmol−1). All the identified compounds were stabilized by hydrogen bonding with Arg107, Tyr111 and Arg149 of N-terminal domain. Additionally, the aromatic ring of lead molecules formed π interactions with Tyr109 of N-terminal domain. Molecular dynamics and Molecular mechanic/Poisson–Boltzmann surface area results revealed that N-terminal domain – ligand(s) complexes are less dynamic and more stable than N-terminal domain – GMP complex. As the identified compounds share the same corresponding pharmacophore properties, therefore, the present results may serve as a potential lead for the development of inhibitors against severe acute respiratory syndrome coronavirus 2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Poonam Dhankhar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Vikram Dalal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Vishakha Singh
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Shailly Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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232
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Zekri ARN, Easa Amer K, Hafez MM, Hassan ZK, Ahmed OS, Soliman HK, Bahnasy AA, Abdel Hamid W, Gad A, Ali M, Ali Hassan W, Samir Madboly M, Abdel Raouf A, Khattab AA, Salah El Din Hamdy M, Sherif Soliman M, Hamdi El Sissy M, Mohamed El Khateeb S, Hosny Ezzelarab M, Fathalla LA, Abouelhoda M. Genomic characterization of SARS-CoV-2 in Egypt. J Adv Res 2020; 30:123-132. [PMID: 33262895 PMCID: PMC7688418 DOI: 10.1016/j.jare.2020.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Introduction The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the globe, causing a pandemic. In Egypt over 115,000 individuals were infected so far. Objective In the present study, the objective is to perform a complete genome sequence of SAR-CoV2 isolated from Egyptian coronavirus disease (COVID-19) patients. Methods Nasopharyngeal swabs were collected from 61 COVID-19 patients who attended at National Cancer Institute, Kasr Al-Aini Hospital and the army hospital. Viral RNA was extracted and whole genomic sequencing was conducted using Next Generation Sequencing. Results In all cases, the sequenced virus has at least 99% identity to the reference Wuhan 1. The sequence analysis showed 204 distinct genome variations including 114 missense mutations, 72 synonymous mutations, 1 disruptive in-frame deletion, 7 downstream gene mutations, 6 upstream gene mutations, 3 frame-shift deletions, and 1 in-frame deletion. The most dominant clades were G/GH/GR/O and the dominant type is B. Conclusion The whole genomic sequence of SARS-CoV2 showed 204 variations in the genomes of the Egyptian isolates, where the Asp614Gly (D614G) substitution is the most common among the samples (60/61). So far, there were no strikingly variations specific to the Egyptian population, at least for this set of samples.
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Affiliation(s)
- Abdel-Rahman N Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Khaled Easa Amer
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | - Mohammed M Hafez
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Zeinab K Hassan
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Ola S Ahmed
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Hany K Soliman
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Abeer A Bahnasy
- Surgical Pathology Department National Cancer Institute, Cairo University, 11796, Egypt
| | | | - Ahmad Gad
- Military Central Laboratories, Egypt
| | - Mahmoud Ali
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | - Wael Ali Hassan
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | | | | | - Ayman A Khattab
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | | | - May Sherif Soliman
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Egypt
| | - Maha Hamdi El Sissy
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Egypt
| | | | | | - Lamiaa A Fathalla
- Clinical Pathology Department, National Cancer Institute, Cairo University 11796, Egypt
| | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt
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233
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Nardo AD, Schneeweiss-Gleixner M, Bakail M, Dixon ED, Lax SF, Trauner M. Pathophysiological mechanisms of liver injury in COVID-19. LIVER INTERNATIONAL : OFFICIAL JOURNAL OF THE INTERNATIONAL ASSOCIATION FOR THE STUDY OF THE LIVER 2020. [PMID: 33190346 DOI: 10.1111/liv.14730.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The recent outbreak of coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in a world-wide pandemic. Disseminated lung injury with the development of acute respiratory distress syndrome (ARDS) is the main cause of mortality in COVID-19. Although liver failure does not seem to occur in the absence of pre-existing liver disease, hepatic involvement in COVID-19 may correlate with overall disease severity and serve as a prognostic factor for the development of ARDS. The spectrum of liver injury in COVID-19 may range from direct infection by SARS-CoV-2, indirect involvement by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and ventilation to exacerbation of underlying liver disease. This concise review discusses the potential pathophysiological mechanisms for SARS-CoV-2 hepatic tropism as well as acute and possibly long-term liver injury in COVID-19.
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Affiliation(s)
- Alexander D Nardo
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Mathias Schneeweiss-Gleixner
- Medical Intensive Care Unit 13H1. Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - May Bakail
- Campus IT, Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Emmanuel D Dixon
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Sigurd F Lax
- Department of Pathology, Hospital Graz II, Academic Teaching Hospital of the Medical University of Graz, Graz, Austria.,School of Medicine, Johannes Kepler University, Linz, Austria
| | - Michael Trauner
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria.,Medical Intensive Care Unit 13H1. Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
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234
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Liu Y, Liang C, Xin L, Ren X, Tian L, Ju X, Li H, Wang Y, Zhao Q, Liu H, Cao W, Xie X, Zhang D, Wang Y, Jian Y. The development of Coronavirus 3C-Like protease (3CL pro) inhibitors from 2010 to 2020. Eur J Med Chem 2020; 206:112711. [PMID: 32810751 PMCID: PMC7409838 DOI: 10.1016/j.ejmech.2020.112711] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/17/2020] [Accepted: 07/29/2020] [Indexed: 01/24/2023]
Abstract
This review fully describes the coronavirus 3CLpro peptidomimetic inhibitors and nonpeptidic small molecule inhibitors developed from 2010 to 2020. Specifically, the structural characteristics, binding modes and SARs of these 3CLpro inhibitors are expounded in detail by division into two categories: peptidomimetic inhibitors mainly utilize electrophilic warhead groups to covalently bind the 3CLpro Cys145 residue and thereby achieve irreversible inhibition effects, whereas nonpeptidic small molecule inhibitors mainly interact with residues in the S1', S1, S2 and S4 pockets via hydrogen bonds, hydrophobic bonds and van der Waals forces. Based on the emerging PROTAC technology and the existing 3CLpro inhibitors, 3CLpro PROTAC degraders are hypothesised to be next-generation anti-coronavirus drugs.
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Affiliation(s)
- Yuzhi Liu
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Chengyuan Liang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
| | - Liang Xin
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Xiaodong Ren
- Medical College, Guizhou University, Guiyang, 550025, PR China
| | - Lei Tian
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Xingke Ju
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Han Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Yongbo Wang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Qianqian Zhao
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Hong Liu
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Hengqin, Zhuhai, Guangdong, 519030, PR China.
| | - Wenqiang Cao
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Hengqin, Zhuhai, Guangdong, 519030, PR China
| | - Xiaolin Xie
- Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Dezhu Zhang
- Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Yu Wang
- Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Yanlin Jian
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B9000, Gent, Belgium.
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235
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Lang Y, Chen K, Li Z, Li H. The nucleocapsid protein of zoonotic betacoronaviruses is an attractive target for antiviral drug discovery. Life Sci 2020; 282:118754. [PMID: 33189817 PMCID: PMC7658559 DOI: 10.1016/j.lfs.2020.118754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/22/2020] [Accepted: 11/10/2020] [Indexed: 12/02/2022]
Abstract
Betacoronaviruses are in one genera of coronaviruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome-related coronavirus (MERS-CoV), etc. These viruses threaten public health and cause dramatic economic losses. The nucleocapsid (N) protein is a structural protein of betacoronaviruses with multiple functions such as forming viral capsids with viral RNA, interacting with viral membrane protein to form the virus core with RNA, binding to several cellular kinases for signal transductions, etc. In this review, we highlighted the potential of the N protein as a suitable antiviral target from different perspectives, including structure, functions, and antiviral strategies for combatting betacoronaviruses.
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Affiliation(s)
- Yuekun Lang
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Ke Chen
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA; Department of Biomedical Sciences, School of Public Health, University at Albany, 1 University Place, Rensselaer, NY 12144, USA.
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236
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Hoffman RL, Kania RS, Brothers MA, Davies JF, Ferre RA, Gajiwala KS, He M, Hogan RJ, Kozminski K, Li LY, Lockner JW, Lou J, Marra MT, Mitchell LJ, Murray BW, Nieman JA, Noell S, Planken SP, Rowe T, Ryan K, Smith GJ, Solowiej JE, Steppan CM, Taggart B. Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19. J Med Chem 2020; 63:12725-12747. [PMID: 33054210 PMCID: PMC7571312 DOI: 10.1021/acs.jmedchem.0c01063] [Citation(s) in RCA: 329] [Impact Index Per Article: 82.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Indexed: 01/16/2023]
Abstract
The novel coronavirus disease COVID-19 that emerged in 2019 is caused by the virus SARS CoV-2 and named for its close genetic similarity to SARS CoV-1 that caused severe acute respiratory syndrome (SARS) in 2002. Both SARS coronavirus genomes encode two overlapping large polyproteins, which are cleaved at specific sites by a 3C-like cysteine protease (3CLpro) in a post-translational processing step that is critical for coronavirus replication. The 3CLpro sequences for CoV-1 and CoV-2 viruses are 100% identical in the catalytic domain that carries out protein cleavage. A research effort that focused on the discovery of reversible and irreversible ketone-based inhibitors of SARS CoV-1 3CLpro employing ligand-protease structures solved by X-ray crystallography led to the identification of 3 and 4. Preclinical experiments reveal 4 (PF-00835231) as a potent inhibitor of CoV-2 3CLpro with suitable pharmaceutical properties to warrant further development as an intravenous treatment for COVID-19.
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Affiliation(s)
- Robert L. Hoffman
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Robert S. Kania
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Mary A. Brothers
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Jay F. Davies
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Rose A. Ferre
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Ketan S. Gajiwala
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Mingying He
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Robert J. Hogan
- Southern Research
Institute, 2000 9th Avenue South, Birmingham,
Alabama 35205 United States
| | - Kirk Kozminski
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Lilian Y. Li
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Jonathan W. Lockner
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Jihong Lou
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Michelle T. Marra
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Lennert J. Mitchell
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Brion W. Murray
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - James A. Nieman
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Stephen Noell
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Simon P. Planken
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Thomas Rowe
- Southern Research
Institute, 2000 9th Avenue South, Birmingham,
Alabama 35205 United States
| | - Kevin Ryan
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - George J. Smith
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - James E. Solowiej
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Claire M. Steppan
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Barbara Taggart
- Southern Research
Institute, 2000 9th Avenue South, Birmingham,
Alabama 35205 United States
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237
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Tan Y, Schneider T, Shukla PK, Chandrasekharan MB, Aravind L, Zhang D. Unification of the M/ORF3-related proteins points to a diversified role for ion conductance in pathogenesis of coronaviruses and other nidoviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.10.377366. [PMID: 33200132 PMCID: PMC7668736 DOI: 10.1101/2020.11.10.377366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The new coronavirus, SARS-CoV-2, responsible for the COVID-19 pandemic has emphasized the need for a better understanding of the evolution of virus-host conflicts. ORF3a in both SARS-CoV-1 and SARS-CoV-2 are ion channels (viroporins) and involved in virion assembly and membrane budding. Using sensitive profile-based homology detection methods, we unify the SARS-CoV ORF3a family with several families of viral proteins, including ORF5 from MERS-CoVs, proteins from beta-CoVs (ORF3c), alpha-CoVs (ORF3b), most importantly, the Matrix (M) proteins from CoVs, and more distant homologs from other nidoviruses. By sequence analysis and structural modeling, we show that these viral families utilize specific conserved polar residues to constitute an ion-conducting pore in the membrane. We reconstruct the evolutionary history of these families, objectively establish the common origin of the M proteins of CoVs and Toroviruses. We show that the divergent ORF3a/ORF3b/ORF5 families represent a duplication stemming from the M protein in alpha- and beta-CoVs. By phyletic profiling of major structural components of primary nidoviruses, we present a model for their role in virion assembly of CoVs, ToroVs and Arteriviruses. The unification of diverse M/ORF3 ion channel families in a wide range of nidoviruses, especially the typical M protein in CoVs, reveal a conserved, previously under-appreciated role of ion channels in virion assembly, membrane fusion and budding. We show that the M and ORF3 are under differential evolutionary pressures; in contrast to the slow evolution of M as core structural component, the CoV-ORF3 clade is under selection for diversification, which indicates it is likely at the interface with host molecules and/or immune attack. IMPORTANCE Coronaviruses (CoVs) have become a major threat to human welfare as the causative agents of several severe infectious diseases, namely Severe Acute Respiratory Syndrome (SARS), Middle Eastern Respiratory Syndrome (MERS), and the recently emerging human coronavirus disease 2019 (COVID-19). The rapid spread, severity of these diseases, as well as the potential re-emergence of other CoV-associated diseases have imposed a strong need for a thorough understanding of function and evolution of these CoVs. By utilizing robust domain-centric computational strategies, we have established homologous relationships between many divergent families of CoV proteins, including SARS-CoV/SARS-CoV-2 ORF3a, MERS-CoV ORF5, proteins from both beta-CoVs (ORF3c) and alpha-CoVs (ORF3b), the typical CoV Matrix proteins, and many distant homologs from other nidoviruses. We present evidence that they are active ion channel proteins, and the Cov-specific ORF3 clade proteins are under selection for rapid diversification, suggesting they might have been involved in interfering host molecules and/or immune attack.
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238
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White MA, Lin W, Cheng X. Discovery of COVID-19 Inhibitors Targeting the SARS-CoV-2 Nsp13 Helicase. J Phys Chem Lett 2020; 11:9144-9151. [PMID: 33052685 PMCID: PMC7571306 DOI: 10.1021/acs.jpclett.0c02421] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/06/2020] [Indexed: 05/28/2023]
Abstract
The raging COVID-19 pandemic caused by SARS-CoV-2 has infected tens of millions of people and killed several hundred thousand patients worldwide. Currently, there are no effective drugs or vaccines available for treating coronavirus infections. In this study, we have focused on the SARS-CoV-2 helicase (Nsp13), which is critical for viral replication and the most conserved nonstructural protein within the coronavirus family. Using homology modeling that couples published electron-density with molecular dynamics (MD)-based structural refinements, we generated structural models of the SARS-CoV-2 helicase in its apo- and ATP/RNA-bound conformations. We performed virtual screening of ∼970 000 chemical compounds against the ATP-binding site to identify potential inhibitors. Herein, we report docking hits of approved human drugs targeting the ATP-binding site. Importantly, two of our top drug hits have significant activity in inhibiting purified recombinant SARS-CoV-2 helicase, providing hope that these drugs can be potentially repurposed for the treatment of COVID-19.
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Affiliation(s)
- Mark Andrew White
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Wei Lin
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Texas Therapeutics Institute, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Texas Therapeutics Institute, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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239
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Klingelhöfer D, Braun M, Brüggmann D, Groneberg DA. Coronavirus: An insight into global research until outbreak of COVID-19 and its implications for the future. J Glob Health 2020; 10:020508. [PMID: 33110591 PMCID: PMC7567443 DOI: 10.7189/jogh.10.020508] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background The currently prevailing global threat of COVID-19 caused the publication numbers on coronaviruses to explode. The awareness of the scientific and public community is enormous. But what about the sense of all these undertakings and what can be learned about the future for a better understanding? These questions were answered with established bibliometric analyses of the time until the avalanche of publications unfolded. Methods Chronological, geographical aspects of publication output on coronavirus were also evaluated under the influence of epidemiological and socio-economic parameters. Results The trend in publication and citation numbers shows the strong influence of the past pandemics SARS and MERS with an untypical decline afterward. Research is becoming increasingly multidisciplinary over time. The USA and China, as the countries with the highest number of publications, are being displaced by other countries in the consideration of socio-economic and epidemiological aspects, which shows the effect of regional interest in corona research. A significant correlation was found between the number of SARS cases per country and related publications, while no correlation was found for MERS cases and articles. Conclusions The results underline the need for sustainable and forward-looking approaches that should not end with the containment of COVID-19.
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Affiliation(s)
- Doris Klingelhöfer
- Institute of Occupational, Social and Environmental Medicine, Goethe University Frankfurt, Germany
| | - Markus Braun
- Institute of Occupational, Social and Environmental Medicine, Goethe University Frankfurt, Germany
| | - Dörthe Brüggmann
- Institute of Occupational, Social and Environmental Medicine, Goethe University Frankfurt, Germany
| | - David A Groneberg
- Institute of Occupational, Social and Environmental Medicine, Goethe University Frankfurt, Germany
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240
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Guruprasad L. Human coronavirus spike protein-host receptor recognition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 161:39-53. [PMID: 33137344 PMCID: PMC7604128 DOI: 10.1016/j.pbiomolbio.2020.10.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/12/2020] [Accepted: 10/23/2020] [Indexed: 01/06/2023]
Abstract
A variety of coronaviruses (CoVs) have infected humans and caused mild to severe respiratory diseases that could result in mortality. The human CoVs (HCoVs) belong to the genera of α- and β-CoVs that originate in rodents and bats and are transmitted to humans via zoonotic contacts. The binding of viral spike proteins to the host cell receptors is essential for mediating fusion of viral and host cell membranes to cause infection. The SARS-CoV-2 originated in bats (RaTG13 SARS-CoV) and is transmitted to humans via pangolins. The presence of 'PRRA' sequence motif in SARS-CoV-2 spike proteins from human, dog, cat, mink, tiger and lion suggests a common viral entry mechanism into host cells. In this review, we discuss structural features of HCoV spike proteins and recognition of host protein and carbohydrate receptors.
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241
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Potential therapeutic use of corticosteroids as SARS CoV-2 main protease inhibitors: a computational study. J Biomol Struct Dyn 2020; 40:2053-2066. [PMID: 33094701 PMCID: PMC7596904 DOI: 10.1080/07391102.2020.1835728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), represents a pandemic threat to global public health. To date, ∼530,000 people died of this disease worldwide. Presently, researchers/clinicians are adopting the drug repurposing strategy to combat this disease. It has also been observed that some repurposed anti-viral drugs may serve as potent inhibitors of SARS CoV-2 Mpro, a key component of viral replication. Apart from these anti-viral drugs, recently dexamethasone (an important corticosteroid) is effectively used to treat COVID-19 patients. However, the mechanism behind the mode of its action is not so clear. Additionally, the effect of other well-known corticosteroids to control this disease by inhibiting the proteolytic activity of Mpro is ambiguous. In this study, we have adopted computational approaches to understand these aspects. Six well-known corticosteroids (cortisone, hydrocortisone, prednisolone, methylprednisolone, betamethasone and dexamethasone) and two repurposed drugs (darunavir and lopinavir) against COVID-19 were subjected for molecular docking studies. Two of them (betamethasone and dexamethasone) were selected by comparing their binding affinities with selected repurposed drugs toward Mpro. Betamethasone and dexamethasone interacted with both the catalytic residues of Mpro (His41 and Cys145). Molecular dynamics studies further revealed that these two Mpro-corticosteroid complexes are more stable, experience less conformational fluctuations and more compact than Mpro-darunavir/lopinavir complexes. These findings were additionally validated by MM-GBSA analysis. This study provides corroboration for execution of anti-COVID-19 activity of dexamethasone. Our study also emphasizes on the use of another important corticosteroid (betamethasone) as potential therapeutic agent for COVID-19 treatment.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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242
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Aljabali AAA, Bakshi HA, Satija S, Metha M, Prasher P, Ennab RM, Chellappan DK, Gupta G, Negi P, Goyal R, Sharma A, Mishra V, Dureja H, Dua K, Tambuwala MM. COVID-19: Underpinning Research for Detection, Therapeutics, and Vaccines Development. Pharm Nanotechnol 2020; 8:323-353. [PMID: 32811406 DOI: 10.2174/2211738508999200817163335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/22/2020] [Accepted: 07/15/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND The newly emerged coronavirus SARS-CoV-2, first reported in December 2019, has infected about five and a half million people globally and resulted in nearly 9063264 deaths until the 24th of June 2020. Nevertheless, the highly contagious virus has instigated an unimaginably rapid response from scientific and medical communities. OBJECTIVES Pioneering research on molecular mechanisms underlying the viral transmission, molecular pathogenicity, and potential treatments will be highlighted in this review. The development of antiviral drugs specific to SARS-CoV-2 is a complicated and tedious process. To accelerate scientific discoveries and advancement, researchers are consolidating available data from associated coronaviruses into a single pipeline, which can be readily made available to vaccine developers. METHODS In order to find studies evaluating the COVID-19 virus epidemiology, repurposed drugs and potential vaccines, web searches and bibliographical bases have been used with keywords that matches the content of this review. RESULTS The published results of SARS-CoV-2 structures and interactomics have been used to identify potential therapeutic candidates. We illustrate recent publications on SARS-CoV-2, concerning its molecular, epidemiological, and clinical characteristics, and focus on innovative diagnostics technologies in the production pipeline. This objective of this review is to enhance the comprehension of the unique characteristics of SARS-CoV-2 and strengthen future control measures. Lay Summary An innovative analysis is evaluating the nature of the COVID-19 pandemic. The aim is to increase knowledge of possible viral detection methods, which highlights several new technology limitations and advantages. We have assessed some drugs currently for patients (Lopinavir, Ritonavir, Anakinra and Interferon beta 1a), as the feasibility of COVID-19 specific antivirals is not presently known. The study explores the race toward vaccine development and highlights some significant trials and candidates in various clinical phases. This research addresses critical knowledge gaps by identifying repurposed drugs currently under clinical trials. Findings will be fed back rapidly to the researchers interested in COVID 19 and support the evidence and potential of possible therapeutics and small molecules with their mode of action.
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Affiliation(s)
- Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Irbid 566, Jordan
| | - Hamid A Bakshi
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, County Londonderry, Northern Ireland, United Kingdom
| | - Saurabh Satija
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara-144411, Punjab, India
| | - Meenu Metha
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara-144411, Punjab, India
| | - Parteek Prasher
- Department of Chemistry, University of Petroleum & Energy Studies, Dehradun 248007, India
| | - Raed M Ennab
- Department of Clinical sciences, Faculty of Medicine, Yarmouk University, Irbid 566, Jordan
| | - Dinesh K Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Jaipur 302017, India
| | - Poonam Negi
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Rohit Goyal
- Neuropharmacology Laboratory, School of Pharmaceutical Sciences, Shoolini University, Solan 173 212, Himachal Pradesh, India
| | - Ashish Sharma
- Neuropharmacology Laboratory, School of Pharmaceutical Sciences, Shoolini University, Solan 173 212, Himachal Pradesh, India
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara-144411, Punjab, India
| | - Harish Dureja
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak 124001, India
| | - Kamal Dua
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, County Londonderry, Northern Ireland, United Kingdom
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243
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Baruah C, Devi P, Sharma DK. Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7234961. [PMID: 33102591 PMCID: PMC7576348 DOI: 10.1155/2020/7234961] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/12/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a single-stranded RNA genome that encodes 14 open reading frames (ORFs), eight of which encode accessory proteins that allow the virus to infect the host and promote virulence. The genome expresses around 29 structural and nonstructural protein products. The accessory proteins of SARS-CoV-2 are not essential for virus replication but do affect viral release, stability, and pathogenesis and finally contribute to virulence. This paper has attempted the structure prediction and functional analysis of two such accessory proteins, 9b and ORF14, in the absence of experimental structures. Sequence analysis, structure prediction, functional characterization, and evolutionary analysis based on the UniProtKB reviewed the amino acid sequences of SARS-CoV-2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the introduction of hybrid comparative and ab initio modeling. QMEANDisCo 4.0.0 and ProQ3 for global and local (per residue) quality estimates verified the structures as high quality, which may be attributed to structure-based drug design targets. Tunnel analysis revealed the presence of 1-2 highly active tunneling sites, perhaps which will able to provide certain inputs for advanced structure-based drug design or to formulate potential vaccines in the absence of a complete experimental structure. The evolutionary analysis of both proteins of human SARS-CoV-2 indicates close relatedness to the bat coronavirus. The whole-genome phylogeny indicates that only the new bat coronavirus followed by pangolin coronaviruses has a close evolutionary relationship with the novel SARS-CoV-2.
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Affiliation(s)
- Chittaranjan Baruah
- Bioinformatics Laboratory (DBT-Star College), P.G. Department of Zoology, Darrang College, Tezpur, 784 001 Assam, India
| | | | - Dhirendra K. Sharma
- School of Biological Sciences, University of Science and Technology, Meghalaya, Baridua-793101, India
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244
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McClenaghan C, Hanson A, Lee SJ, Nichols CG. Coronavirus Proteins as Ion Channels: Current and Potential Research. Front Immunol 2020; 11:573339. [PMID: 33154751 PMCID: PMC7586316 DOI: 10.3389/fimmu.2020.573339] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/22/2020] [Indexed: 01/22/2023] Open
Abstract
Coronavirus (CoV) outbreaks have recently emerged as a global public health threat due to their exceptional zoonotic potential — a feature arising from their ability to infect a diverse range of potential hosts combined with their high capacity for mutation and recombination. After Severe Acute Respiratory Syndrome (SARS) CoV-1 in 2003 and Middle East Respiratory Syndrome (MERS) CoV in 2012, with the current SARS-CoV-2 pandemic we are now in the midst of the third deadly international CoV outbreak in less than 20 years. Coronavirus outbreaks present a critical threat to global public health and an urgent necessity for therapeutic options. Here, we critically examine the current evidence for ion channel activity in CoV proteins and the potential for modulation as a therapeutic approach.
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Affiliation(s)
- Conor McClenaghan
- Center for Investigation of Membrane Excitability Diseases, and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Alex Hanson
- Center for Investigation of Membrane Excitability Diseases, and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Sun-Joo Lee
- Center for Investigation of Membrane Excitability Diseases, and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Colin G Nichols
- Center for Investigation of Membrane Excitability Diseases, and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
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Kinsella CM, Santos PD, Postigo-Hidalgo I, Folgueiras-González A, Passchier TC, Szillat KP, Akello JO, Álvarez-Rodríguez B, Martí-Carreras J. Preparedness needs research: How fundamental science and international collaboration accelerated the response to COVID-19. PLoS Pathog 2020; 16:e1008902. [PMID: 33035262 PMCID: PMC7546461 DOI: 10.1371/journal.ppat.1008902] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The first cluster of patients suffering from coronavirus disease 2019 (COVID-19) was identified on December 21, 2019, and as of July 29, 2020, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been linked with 664,333 deaths and number at least 16,932,996 worldwide. Unprecedented in global societal impact, the COVID-19 pandemic has tested local, national, and international preparedness for viral outbreaks to the limits. Just as it will be vital to identify missed opportunities and improve contingency planning for future outbreaks, we must also highlight key successes and build on them. Concomitant to the emergence of a novel viral disease, there is a 'research and development gap' that poses a threat to the overall pace and quality of outbreak response during its most crucial early phase. Here, we outline key components of an adequate research response to novel viral outbreaks using the example of SARS-CoV-2. We highlight the exceptional recent progress made in fundamental science, resulting in the fastest scientific response to a major infectious disease outbreak or pandemic. We underline the vital role of the international research community, from the implementation of diagnostics and contact tracing procedures to the collective search for vaccines and antiviral therapies, sustained by unique information sharing efforts.
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Affiliation(s)
- Cormac M. Kinsella
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Pauline Dianne Santos
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Ignacio Postigo-Hidalgo
- Charité –Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | | | - Tim Casper Passchier
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Kevin P. Szillat
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Joyce Odeke Akello
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Spiez, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Beatriz Álvarez-Rodríguez
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Joan Martí-Carreras
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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Fiorino S, Gallo C, Zippi M, Sabbatani S, Manfredi R, Moretti R, Fogacci E, Maggioli C, Travasoni Loffredo F, Giampieri E, Corazza I, Dickmans C, Denitto C, Cammarosano M, Battilana M, Orlandi PE, Del Forno F, Miceli F, Visani M, Acquaviva G, De Leo A, Leandri P, Hong W, Brand T, Tallini G, Jovine E, Jovine R, de Biase D. Cytokine storm in aged people with CoV-2: possible role of vitamins as therapy or preventive strategy. Aging Clin Exp Res 2020; 32:2115-2131. [PMID: 32865757 PMCID: PMC7456763 DOI: 10.1007/s40520-020-01669-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND In December 2019, a novel human-infecting coronavirus, SARS-CoV-2, had emerged. The WHO has classified the epidemic as a "public health emergency of international concern". A dramatic situation has unfolded with thousands of deaths, occurring mainly in the aged and very ill people. Epidemiological studies suggest that immune system function is impaired in elderly individuals and these subjects often present a deficiency in fat-soluble and hydrosoluble vitamins. METHODS We searched for reviews describing the characteristics of autoimmune diseases and the available therapeutic protocols for their treatment. We set them as a paradigm with the purpose to uncover common pathogenetic mechanisms between these pathological conditions and SARS-CoV-2 infection. Furthermore, we searched for studies describing the possible efficacy of vitamins A, D, E, and C in improving the immune system function. RESULTS SARS-CoV-2 infection induces strong immune system dysfunction characterized by the development of an intense proinflammatory response in the host, and the development of a life-threatening condition defined as cytokine release syndrome (CRS). This leads to acute respiratory syndrome (ARDS), mainly in aged people. High mortality and lethality rates have been observed in elderly subjects with CoV-2-related infection. CONCLUSIONS Vitamins may shift the proinflammatory Th17-mediated immune response arising in autoimmune diseases towards a T-cell regulatory phenotype. This review discusses the possible activity of vitamins A, D, E, and C in restoring normal antiviral immune system function and the potential therapeutic role of these micronutrients as part of a therapeutic strategy against SARS-CoV-2 infection.
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Affiliation(s)
- Sirio Fiorino
- UO of Internal Medicine Unit, Hospital of Budrio, Via Benni 44, 40065, Budrio, Bologna, Italy.
- Internal Medicine Unit, Maggiore Hospital of Bologna, Bologna, Italy.
| | - Claudio Gallo
- Physician Specialist in Infectious Diseases, AUSL Bologna, Bologna, Italy
| | - Maddalena Zippi
- Unit of Gastroenterology and Digestive Endoscopy, Sandro Petrini Hospital, Rome, Italy
| | | | | | - Renzo Moretti
- UO of Internal Medicine Unit, Hospital of Budrio, Via Benni 44, 40065, Budrio, Bologna, Italy
| | - Elisa Fogacci
- UO of Internal Medicine Unit, Hospital of Budrio, Via Benni 44, 40065, Budrio, Bologna, Italy
| | - Caterina Maggioli
- UO of Internal Medicine Unit, Hospital of Budrio, Via Benni 44, 40065, Budrio, Bologna, Italy
| | | | - Enrico Giampieri
- Experimental, Diagnostic and Specialty Medicine Department, University of Bologna, Bologna, Italy
| | - Ivan Corazza
- Experimental, Diagnostic and Specialty Medicine Department, University of Bologna, Bologna, Italy
| | - Christoph Dickmans
- UO of Internal Medicine Unit, Hospital of Budrio, Via Benni 44, 40065, Budrio, Bologna, Italy
| | - Claudio Denitto
- UO of Internal Medicine Unit, Hospital of Budrio, Via Benni 44, 40065, Budrio, Bologna, Italy
| | - Michele Cammarosano
- UO of Internal Medicine Unit, Hospital of Budrio, Via Benni 44, 40065, Budrio, Bologna, Italy
| | - Michele Battilana
- UO of Internal Medicine Unit, Hospital of Budrio, Via Benni 44, 40065, Budrio, Bologna, Italy
| | | | | | - Francesco Miceli
- UO Farmacia Centralizzata OM, Farmacia Ospedale Di Budrio, Budrio, Bologna, Italy
| | - Michela Visani
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, Bologna, Italy
| | - Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, Bologna, Italy
| | - Antonio De Leo
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, Bologna, Italy
| | - Paolo Leandri
- Internal Medicine Unit, Maggiore Hospital of Bologna, Bologna, Italy
| | - Wandong Hong
- Department of Gastroenterology and Hepatology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, The People's Republic of China
| | - Thomas Brand
- Regenerative Medicine Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, Bologna, Italy
| | - Elio Jovine
- Surgery Unit, Maggiore Hospital, Bologna, Italy
| | - Roberto Jovine
- Physical Medicine and Rehabilitation Unit, Maggiore Hospital, Bologna, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
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Ojha S, Chadha H, Mahor S. COVID-19: Pathogenesis and Pharmacological Basis for Use of Passive Antibody Therapy. CURRENT DRUG THERAPY 2020. [DOI: 10.2174/1574885515999200813193747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Background:
Coronaviruses (CoVs), having enveloped RNA of positive strand, are
mainly responsible for enzootic infections in mammals. The mortality of CoVs has been proved as
they can cross the species barrier very easily and infect humans. Most recently, the outbreak of
coronavirus induced COVID-19 emerged in the city of Wuhan, Hubei province of China and became
the third highly pathogenic coronavirus infecting nearly 230 countries.
Objective:
To review the literature available about pathogenic Coronavirures with emphasis on
pathogenesis of COVID-19, and passive antibody therapy prospective.
Methods:
This study reviewed relevant published literature to provide (1) structural similarities
between coronaviruses and therapeutic methodologies used on SARS-CoV, MERS treatment which
might help scientists in understanding novel COVID-19 infection, (2) understanding COVID-19
pathogenesis that may help in identification of appropriate therapeutic targets to develop specific
and effective anti-viral drugs as well as immunizing agents against this novel emerging pathogen
and (3) to discuss existing knowledge on the passive immune therapy against similar coronaviruses
SARS-CoV and MERS-CoV with emphasis on COVID-19 pandemic treatment.
Conclusion:
COVID 19 coronavirus has shown resemblance to viral infections like SARS-CoV,
MERS infection. Historically, it has been proved that the prevention of disease, when exposed to a
biological system, is mainly a function of the immune response of that infected individual. To fight
against these infections, passive antibody therapy is the only available countermeasure that could
provide immediate immunity against infection. Passive antibody results in protection irrespective of
the immune status of the host. This therapy can be advantageous in countering the biological attack,
post exposure preventions, low toxicity and peculiar activity.
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Affiliation(s)
- Smriti Ojha
- Faculty of Pharmacy, Sardar Patel College of Pharmacy, Gorakhpur, Uttar Pradesh, India
| | - Hina Chadha
- Department of Pharmaceutical Sciences, Vishveshwarya Group of Institutions, Greater Noida, Uttar Pradesh, India
| | - Seema Mahor
- Department of Pharmaceutical Sciences, Vishveshwarya Group of Institutions, Greater Noida, Uttar Pradesh, India
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Amoah ID, Kumari S, Bux F. Coronaviruses in wastewater processes: Source, fate and potential risks. ENVIRONMENT INTERNATIONAL 2020; 143:105962. [PMID: 32711332 PMCID: PMC7346830 DOI: 10.1016/j.envint.2020.105962] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/04/2020] [Accepted: 07/05/2020] [Indexed: 05/18/2023]
Abstract
The last 17 years have seen three major outbreaks caused by coronaviruses, with the latest outbreak, COVID-19, declared a pandemic by the World Health Organization. The frequency of these outbreaks, their mortality and associated disruption to normal life calls for concerted efforts to understand their occurrence and fate in different environments. There is an increased interest in the occurrence of coronaviruses in wastewater from the perspective of wastewater-based epidemiology. However, there is no comprehensive review of the knowledge on coronavirus occurrence, fate and potential transmission in wastewater. This paper, provides a review of the literature on the occurrence of coronaviruses in wastewater treatment processes. We discuss the presence of viral RNA in feces as a result of diarrhoea caused by gastrointestinal infections. We also reviewed the literature on the presence, survival and potential removal of coronaviruses in common wastewater treatment processes. The detection of infectious viral particles in feces of patients raises questions on the potential risks of infection for people exposed to untreated sewage/wastewater. We, therefore, highlighted the potential risk of infection with coronaviruses for workers in wastewater treatment plants and the public that may be exposed through faulty plumbing or burst sewer networks. The mortalities and morbidities associated with the current COVID-19 pandemic warrants a much more focused research on the role of environments, such as wastewater and surface water, in disease transmission. The current wealth of knowledge on coronaviruses in wastewater based on the reviewed literature is scant and therefore calls for further studies.
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Affiliation(s)
- Isaac Dennis Amoah
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa.
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
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Laboratory response checklist for infectious disease outbreaks-preparedness and response considerations for emerging threats. Can Commun Dis Rep 2020; 46:311-321. [PMID: 33316001 DOI: 10.14745/ccdr.v46i10a01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The purpose of the Laboratory Response Checklist for Infectious Disease Outbreaks (the Checklist) is to provide public health laboratories and laboratory networks operating at multiple jurisdictional levels with a useful, adaptable tool to help rapidly identify important outbreak response considerations, particularly when investigating a previously unknown infectious disease threat. The Checklist was developed by the National Microbiology Laboratory of Canada in collaboration with provincial/territorial, national and international laboratory experts, including the Canadian Public Health Laboratory Network, and the Global Health Security Action Group Laboratory Network. While the Checklist was initially designed to reflect lessons learned through National Microbiology Laboratory participation in extended national and international outbreak responses (e.g. Zika virus epidemic [2015-2016], Ebola virus epidemic, West Africa [2014-2016]), the importance of optimizing laboratory response coordination has only been underscored by the ongoing challenges presented by the coronavirus disease 2019 (COVID-19) pandemic response requirements. The Checklist identifies five highly interdependent laboratory response themes, each of which encompasses multiple considerations that may be critical to a coordinated, strategic outbreak response. As such, the comprehensive review of Checklist considerations by responding laboratory organizations may provide a valuable opportunity to quickly detect key response considerations and interdependencies, and mitigate risks with the potential to impact public health action.
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250
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Gómez-Carballa A, Bello X, Pardo-Seco J, Martinón-Torres F, Salas A. Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders. Genome Res 2020; 30:1434-1448. [PMID: 32878977 PMCID: PMC7605265 DOI: 10.1101/gr.266221.120] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/31/2020] [Indexed: 01/08/2023]
Abstract
The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the twenty-first century. We analyzed more than 4700 SARS-CoV-2 genomes and associated metadata retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus genome. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and more than 160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a rather uniform mutation occurrence along branches that could have implications for diagnostics and the design of future vaccines. Identification of the root of SARS-CoV-2 genomes is not without problems, owing to conflicting interpretations derived from either using the bat coronavirus genomes as an outgroup or relying on the sampling chronology of the SARS-CoV-2 genomes and TMRCA estimates; however, the overall scenario favors haplogroup A as the ancestral node. Phylogenetic analysis indicates a TMRCA for SARS-CoV-2 genomes dating to November 12, 2019, thus matching epidemiological records. Sub-haplogroup A2 most likely originated in Europe from an Asian ancestor and gave rise to subclade A2a, which represents the major non-Asian outbreak, especially in Africa and Europe. Multiple founder effect episodes, most likely associated with super-spreader hosts, might explain COVID-19 pandemic to a large extent.
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Affiliation(s)
- Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706, Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706, Galicia, Spain
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706, Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706, Galicia, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706, Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706, Galicia, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706, Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706, Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706, Galicia, Spain
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