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Aziz S, Waqas M, Mohanta TK, Halim SA, Iqbal A, Ali A, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. Identifying non-nucleoside inhibitors of RNA-dependent RNA-polymerase of SARS-CoV-2 through per-residue energy decomposition-based pharmacophore modeling, molecular docking, and molecular dynamics simulation. J Infect Public Health 2023; 16:501-519. [PMID: 36801630 PMCID: PMC9927802 DOI: 10.1016/j.jiph.2023.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND AND OBJECTIVE The current coronavirus disease-2019 (COVID-19) pandemic has triggered a worldwide health and economic crisis. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes the disease and completes its life cycle using the RNA-dependent RNA-polymerase (RdRp) enzyme, a prominent target for antivirals. In this study, we have computationally screened ∼690 million compounds from the ZINC20 database and 11,698 small molecule inhibitors from DrugBank to find existing and novel non-nucleoside inhibitors for SARS-CoV-2 RdRp. METHODS Herein, a combination of the structure-based pharmacophore modeling and hybrid virtual screening methods, including per-residue energy decomposition-based pharmacophore screening, molecular docking, pharmacokinetics, and toxicity evaluation were employed to retrieve novel as well as existing RdRp non-nucleoside inhibitors from large chemical databases. Besides, molecular dynamics simulation and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) method were used to investigate the binding stability and calculate the binding free energy of RdRp-inhibitor complexes. RESULTS Based on docking scores and significant binding interactions with crucial residues (Lys553, Arg557, Lys623, Cys815, and Ser816) in the RNA binding site of RdRp, three existing drugs, ZINC285540154, ZINC98208626, ZINC28467879, and five compounds from ZINC20 (ZINC739681614, ZINC1166211307, ZINC611516532, ZINC1602963057, and ZINC1398350200) were selected, and the conformational stability of RdRp due to their binding was confirmed through molecular dynamics simulation. The free energy calculations revealed these compounds possess strong binding affinities for RdRp. In addition, these novel inhibitors exhibited drug-like features, good absorption, distribution, metabolism, and excretion profile and were found to be non-toxic. CONCLUSION The compounds identified in the study by multifold computational strategy can be validated in vitro as potential non-nucleoside inhibitors of SARS-CoV-2 RdRp and holds promise for the discovery of novel drugs against COVID-19 in future.
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Affiliation(s)
- Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25000, Pakistan
| | - Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, 2100, Pakistan; Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Aqib Iqbal
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25000, Pakistan; Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan.
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, 2100, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan 45142, Saudi Arabia; Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P. O. Box 2404, Khartoum, Sudan
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
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Abulsoud AI, El-Husseiny HM, El-Husseiny AA, El-Mahdy HA, Ismail A, Elkhawaga SY, Khidr EG, Fathi D, Mady EA, Najda A, Algahtani M, Theyab A, Alsharif KF, Albrakati A, Bayram R, Abdel-Daim MM, Doghish AS. Mutations in SARS-CoV-2: Insights on structure, variants, vaccines, and biomedical interventions. Biomed Pharmacother 2023; 157:113977. [PMID: 36370519 PMCID: PMC9637516 DOI: 10.1016/j.biopha.2022.113977] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
COVID-19 is a worldwide pandemic caused by SARS-coronavirus-2 (SARS-CoV-2). Less than a year after the emergence of the Covid-19 pandemic, many vaccines have arrived on the market with innovative technologies in the field of vaccinology. Based on the use of messenger RNA (mRNA) encoding the Spike SARS-Cov-2 protein or on the use of recombinant adenovirus vectors enabling the gene encoding the Spike protein to be introduced into our cells, these strategies make it possible to envisage the vaccination in a new light with tools that are more scalable than the vaccine strategies used so far. Faced with the appearance of new variants, which will gradually take precedence over the strain at the origin of the pandemic, these new strategies will allow a much faster update of vaccines to fight against these new variants, some of which may escape neutralization by vaccine antibodies. However, only a vaccination policy based on rapid and massive vaccination of the population but requiring a supply of sufficient doses could make it possible to combat the emergence of these variants. Indeed, the greater the number of infected individuals, the faster the virus multiplies, with an increased risk of the emergence of variants in these RNA viruses. This review will discuss SARS-CoV-2 pathophysiology and evolution approaches in altered transmission platforms and emphasize the different mutations and how they influence the virus characteristics. Also, this article summarizes the common vaccines and the implication of the mutations and genetic variety of SARS-CoV-2 on the COVID-19 biomedical arbitrations.
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Affiliation(s)
- Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Hussein M El-Husseiny
- Laboratory of Veterinary Surgery, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai Cho, Fuchu-shi, Tokyo 183-8509, Japan; Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt.
| | - Ahmed A El-Husseiny
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Cairo, Egypt
| | - Hesham A El-Mahdy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Ahmed Ismail
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Samy Y Elkhawaga
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Emad Gamil Khidr
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Doaa Fathi
- Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Eman A Mady
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai Cho, Fuchu-shi, Tokyo 183-8509, Japan; Department of Animal Hygiene, Behavior and Management, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt
| | - Agnieszka Najda
- Department of Vegetable Crops and Medicinal Plants University of Life Sciences, Lublin 50A Doświadczalna Street, 20-280, Lublin, Poland.
| | - Mohammad Algahtani
- Department of Laboratory & Blood Bank, Security Forces Hospital, P.O. Box 14799, Mecca 21955, Saudi Arabia
| | - Abdulrahman Theyab
- Department of Laboratory & Blood Bank, Security Forces Hospital, P.O. Box 14799, Mecca 21955, Saudi Arabia; College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
| | - Khalaf F Alsharif
- Department of Clinical Laboratory sciences, College of Applied medical sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ashraf Albrakati
- Department of Human Anatomy, College of Medicine, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Roula Bayram
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Mohamed M Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia; Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt.
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Potential Inhibitors of SARS-CoV-2 Main Protease (M pro) Identified from the Library of FDA-Approved Drugs Using Molecular Docking Studies. Biomedicines 2022; 11:biomedicines11010085. [PMID: 36672593 PMCID: PMC9856154 DOI: 10.3390/biomedicines11010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/31/2022] Open
Abstract
The Corona Virus Infectious Disease-2019 (COVID-19) outbreak originated at Wuhan, China, in December 2019. It has already spread rapidly and caused more than 6.5 million deaths worldwide. Its causal agent is a beta-coronavirus named SARS-CoV-2. Many efforts have already been made to develop new vaccines and drugs against these viruses, but over time, it has changed its molecular nature and evolved into more lethal variants, such as Delta and Omicron. These will lead us to target its more-conserved proteins. The sequences' BLAST and crystal structure of the main protease Mpro suggest a high sequence and structural conservation. Mpro is responsible for the proteolytic maturation of the polyprotein essential for the viral replication and transcription, which makes it an important drug target. Discovery of new drug molecules may take years before getting to the clinics. So, considering urgency, we performed molecular docking studies using FDA-approved drugs to identify molecules that could potentially bind to the substrate-binding site and inhibit SARS-CoV-2's main protease (Mpro). We used the Glide module in the Schrödinger software suite to perform molecular docking studies, followed by MM-GBSA-based energy calculations to score the hit molecules. Molecular docking and manual analysis suggest that several drugs may bind and potentially inhibit Mpro. We also performed molecular simulations studies for selected compounds to evaluate protein-drug interactions. Considering bioavailability, lesser toxicity, and route of administration, some of the top-ranked drugs, including lumefantrine (antimalarial), dipyridamole (coronary vasodilator), dihydroergotamine (used for treating migraine), hexoprenaline (anti asthmatic), riboflavin (vitamin B2), and pantethine (vitamin B5) may be taken forward for further in vitro and in vivo experiments to investigate their therapeutic potential.
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Hui S. Recent scientific research progress and challenges of COVID-19 pandemic: a global public health event. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2021. [PMCID: PMC8564281 DOI: 10.1007/s43538-021-00058-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022]
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Sarker MT, Hasan AQF, Rafi MO, Hossain MJ, El-Mageed HRA, Elsapagh RM, Capasso R, Emran TB. A Comprehensive Overview of the Newly Emerged COVID-19 Pandemic: Features, Origin, Genomics, Epidemiology, Treatment, and Prevention. BIOLOGICS 2021; 1:357-383. [DOI: 10.3390/biologics1030021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The coronavirus disease 2019 (COVID-19), a life-threatening pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has resulted in massive destruction and is still continuously adding to its death toll. The advent of this global outbreak has not yet been confirmed; however, investigation for suitable prophylaxis against this lethal virus is being carried out by experts all around the globe. The SARS-CoV-2 belongs to the Coronaviridae superfamily, like the other previously occurring human coronavirus variants. To better understand a new virus variant, such as the SARS-CoV-2 delta variant, it is vital to investigate previous virus strains, including their genomic composition and functionality. Our study aimed at addressing the basic overview of the virus’ profile that may provide the scientific community with evidence-based insights into COVID-19. Therefore, this study accomplished a comprehensive literature review that includes the virus’ origin, classification, structure, life cycle, genome, mutation, epidemiology, and subsequent essential factors associated with host–virus interaction. Moreover, we summarized the considerable diagnostic measures, treatment options, including multiple therapeutic approaches, and prevention, as well as future directions that may reduce the impact and misery caused by this devastating pandemic. The observations and data provided here have been screened and accumulated through extensive literature study, hence this study will help the scientific community properly understand this new virus and provide further leads for therapeutic interventions.
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Mutations and Epidemiology of SARS-CoV-2 Compared to Selected Corona Viruses during the First Six Months of the COVID-19 Pandemic: A Review. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.2.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus (CoV) disease 2019 (COVID-19). This study compared the genome, mutations, and infectivity/transmissibility of SARS-CoV-2 with selected betacoronaviruses (beta-CoVs). This study further examined the origin, risk factors, and outbreaks caused by beta-CoVs. We searched the following databases for relevant studies: PubMed, Google Scholar, and the World Health Organization COVID-19 database. A close relationship between SARS-CoV-2 and SARS bat-like CoV RaTG13 (98.9%) was found at the amino acid level, followed by pangolin CoVs. Non-synonymous mutations occur at high frequencies in the open reading frame (ORF) 1ab, spike (S) protein, and nucleocapsid. Mutations P323L and D614G in the RNA-dependent RNA polymerase (RdRp) and S protein, respectively, occur at a high frequency globally. Mutations at position 3037 in the nonstructural protein (Nsp) 3, 14408 (RdRp), and 23403 (S) confer transmissibility to SARS-CoV-2. SARS-CoV-2 has higher infectivity and transmissibility than SARS-CoV, which shares the same receptor. Although bats are confirmed reservoirs, intermediate hosts are currently unknown. Smoking, old age, diabetes, cardiovascular diseases, and hypertension have all been associated with COVID-19. Within six months of its outbreak, COVID-19 was reported in all countries worldwide, whereas SARS was reported in 28 countries and Middle East respiratory syndrome (MERS) in 5 countries. However, the fatality rate of MERS (65%) was higher than that of COVID-19 (4.9%) and SARS (6.6%). Identifying the SARS-CoV-2 intermediate hosts will help prevent future outbreaks. Attention should be given to the pangolin CoVs. Variations in the S gene may confer transmissibility and infectivity.
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Abstract
New treatment against SARS-CoV-2 now is a must. Nowadays, the world encounters a huge health crisis by the COVID-19 viral infection. Nucleotide inhibitors gave a lot of promising results in terms of its efficacy against different viral infections. In this work, molecular modeling, docking, and dynamics simulations are used to build a model for the viral protein RNA-dependent RNA polymerase (RdRp) and test its binding affinity to some clinically approved drugs and drug candidates. Molecular dynamics is used to equilibrate the system upon binding calculations to ensure the successful reproduction of previous results, to include the dynamics of the RdRp, and to understand how it affects the binding. The results show the effectiveness of Sofosbuvir, Ribavirin, Galidesivir, Remdesivir, Favipiravir, Cefuroxime, Tenofovir, and Hydroxychloroquine, in binding to SARS-CoV-2 RdRp. Additionally, Setrobuvir, YAK, and IDX-184, show better results, while four novel IDX-184 derivatives show promising results in attaching to the SARS-CoV-2 RdRp. There is an urgent need to specify drugs that can selectively bind and subsequently inhibit SARS-CoV-2 proteins. The availability of a punch of FDA-approved anti-viral drugs can help us in this mission, aiming to reduce the danger of COVID-19. The compounds 2 and 3 may tightly bind to the SARS-CoV-2 RdRp and so may be successful in the treatment of COVID-19.
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Affiliation(s)
- Abdo A Elfiky
- Faculty of Sciences, Department of Biophysics, Cairo University, Giza, Egypt
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8
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Shi AM, Guo R, Wang Q, Zhou JR. Screening and Molecular Modeling Evaluation of Food Peptides to Inhibit Key Targets of COVID-19 Virus. Biomolecules 2021; 11:330. [PMID: 33671652 PMCID: PMC7926797 DOI: 10.3390/biom11020330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 01/18/2023] Open
Abstract
Peptide drugs, especially food-derived peptides, have a variety of functional activities including antiviral and may also have a therapeutic effect on COVID-19. In this study, comparing with the reported drugs, 79 peptides were found to bind to the key targets of COVID-19 virus with higher non-covalent interaction, while among them, six peptides showed high non-covalent interactions with the three targets, which may inhibit the COVID-19 virus. In the simulation, peptides of nine to 10 amino acids with a hydrophilic amino acid and acidic amino acid in the middle and aromatic amino acids on the side showed higher binding to angiotensin-converting enzyme 2 (ACE2). Peptides of five to six amino acids with a basic amnio acid in the head, acidic amnio acid in the neck, hydrophobicity group in the middle, and basic amino acids in the tail showed higher binding to COVID-19 virus main protease (Mpro), while those with basic amino acids and acidic amino acids in the two sides and aromatic amino acids in the middle might have stronger interaction with COVID-19 virus RNA-dependent RNA polymerase (RdRp).
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Affiliation(s)
- Ai-Min Shi
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Product Processing and Quality Control, Ministry of Agricultural and Rural Affairs, Beijing 100193, China; (A.-M.S.); (R.G.)
| | - Rui Guo
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Product Processing and Quality Control, Ministry of Agricultural and Rural Affairs, Beijing 100193, China; (A.-M.S.); (R.G.)
| | - Qiang Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Product Processing and Quality Control, Ministry of Agricultural and Rural Affairs, Beijing 100193, China; (A.-M.S.); (R.G.)
| | - Jin-Rong Zhou
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA;
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Fakhroo AD, Al Thani AA, Yassine HM. Markers Associated with COVID-19 Susceptibility, Resistance, and Severity. Viruses 2020; 13:E45. [PMID: 33396584 PMCID: PMC7823574 DOI: 10.3390/v13010045] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 01/08/2023] Open
Abstract
In December 2019, the latest member of the coronavirus family, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan, China, leading to the outbreak of an unusual viral pneumonia known as coronavirus disease 2019 (COVID-19). COVID-19 was then declared as a pandemic in March 2020 by the World Health Organization (WHO). The initial mortality rate of COVID-19 declared by WHO was 2%; however, this rate has increased to 3.4% as of 3 March 2020. People of all ages can be infected with SARS-CoV-2, but those aged 60 or above and those with underlying medical conditions are more prone to develop severe symptoms that may lead to death. Patients with severe infection usually experience a hyper pro-inflammatory immune reaction (i.e., cytokine storm) causing acute respiratory distress syndrome (ARDS), which has been shown to be the leading cause of death in COVID-19 patients. However, the factors associated with COVID-19 susceptibility, resistance and severity remain poorly understood. In this review, we thoroughly explore the correlation between various host, viral and environmental markers, and SARS-CoV-2 in terms of susceptibility and severity.
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Affiliation(s)
- Aisha D. Fakhroo
- Research and Development Department, Barzan Holdings, Doha 7178, Qatar;
| | | | - Hadi M. Yassine
- Biomedical Research Center, Qatar University, Doha 2713, Qatar;
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Rastogi M, Pandey N, Shukla A, Singh SK. SARS coronavirus 2: from genome to infectome. Respir Res 2020; 21:318. [PMID: 33261606 PMCID: PMC7706175 DOI: 10.1186/s12931-020-01581-z] [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: 06/26/2020] [Accepted: 11/22/2020] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the group of Betacoronaviruses. The SARS-CoV-2 is closely related to SARS-CoV-1 and probably originated either from bats or pangolins. SARS-CoV-2 is an etiological agent of COVID-19, causing mild to severe respiratory disease which escalates to acute respiratory distress syndrome (ARDS) or multi-organ failure. The virus was first reported from the animal market in Hunan, Hubei province of China in the month of December, 2019, and was rapidly transmitted from animal to human and human-to-human. The human-to-human transmission can occur directly or via droplets generated during coughing and sneezing. Globally, around 53.9 million cases of COVID-19 have been registered with 1.31 million confirmed deaths. The people > 60 years, persons suffering from comorbid conditions and immunocompromised individuals are more susceptible to COVID-19 infection. The virus primarily targets the upper and the lower respiratory tract and quickly disseminates to other organs. SARS-CoV-2 dysregulates immune signaling pathways which generate cytokine storm and leads to the acute respiratory distress syndrome and other multisystemic disorders.
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Affiliation(s)
- Meghana Rastogi
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Neha Pandey
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Astha Shukla
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sunit K Singh
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
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Singh P, Pathania S, Rawal R. Exploring RdRp-remdesivir interactions to screen RdRp inhibitors for the management of novel coronavirus 2019-nCoV. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:857-867. [PMID: 33100032 PMCID: PMC7597014 DOI: 10.1080/1062936x.2020.1825014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
A novel coronavirus recently identified in Wuhan, China (2019-nCoV) has resulted in an increasing number of patients globally, and has become a highly lethal pathogenic member of the coronavirus family affecting humans. 2019-nCoV has established itself as one of the most threatening pandemics that human beings have faced, and therefore analysis and evaluation of all possible responses against infection is required. One such strategy includes utilizing the knowledge gained from the SARS and MERS outbreaks regarding existing antivirals. Indicating a potential for success, one of the drugs, remdesivir, under repurposing studies, has shown positive results in initial clinical studies. Therefore, in the current work, the authors have attempted to utilize the remdesivir-RdRp complex - RdRp (RNA-dependent RNA polymerase) being the putative target for remdesivir - to screen a library of the already reported RdRp inhibitor database. Further clustering on the basis of structural features and scoring refinement was performed to filter out false positive hits. Finally, molecular dynamics simulation was carried out to validate the identification of hits as RdRp inhibitors against novel coronavirus 2019-nCoV. The results yielded two putative hits which can inhibit RdRp with better potency than remdesivir, subject to further biological evaluation.
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Affiliation(s)
- P.K. Singh
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - S. Pathania
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - R.K. Rawal
- Chemical Sciences and Technology Division (CSTD), CSIR-North East Institute of Science and Technology, Jorhat, India
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Morais IJ, Polveiro RC, Souza GM, Bortolin DI, Sassaki FT, Lima ATM. The global population of SARS-CoV-2 is composed of six major subtypes. Sci Rep 2020; 10:18289. [PMID: 33106569 PMCID: PMC7588421 DOI: 10.1038/s41598-020-74050-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/24/2020] [Indexed: 12/21/2022] Open
Abstract
The World Health Organization characterized COVID-19 as a pandemic in March 2020, the second pandemic of the twenty-first century. Expanding virus populations, such as that of SARS-CoV-2, accumulate a number of narrowly shared polymorphisms, imposing a confounding effect on traditional clustering methods. In this context, approaches that reduce the complexity of the sequence space occupied by the SARS-CoV-2 population are necessary for robust clustering. Here, we propose subdividing the global SARS-CoV-2 population into six well-defined subtypes and 10 poorly represented genotypes named tentative subtypes by focusing on the widely shared polymorphisms in nonstructural (nsp3, nsp4, nsp6, nsp12, nsp13 and nsp14) cistrons and structural (spike and nucleocapsid) and accessory (ORF8) genes. The six subtypes and the additional genotypes showed amino acid replacements that might have phenotypic implications. Notably, three mutations (one of them in the Spike protein) were responsible for the geographical segregation of subtypes. We hypothesize that the virus subtypes detected in this study are records of the early stages of SARS-CoV-2 diversification that were randomly sampled to compose the virus populations around the world. The genetic structure determined for the SARS-CoV-2 population provides substantial guidelines for maximizing the effectiveness of trials for testing candidate vaccines or drugs.
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Affiliation(s)
- Ivair José Morais
- Departamento de Fitopatologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Richard Costa Polveiro
- Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Gabriel Medeiros Souza
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, MG, 38410-337, Brazil
| | - Daniel Inserra Bortolin
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, MG, 38410-337, Brazil
| | - Flávio Tetsuo Sassaki
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Monte Carmelo, MG, 38500-000, Brazil
| | - Alison Talis Martins Lima
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, MG, 38410-337, Brazil.
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13
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Zhou QA, Kato-Weinstein J, Li Y, Deng Y, Granet R, Garner L, Liu C, Polshakov D, Gessner C, Watkins S. Potential Therapeutic Agents and Associated Bioassay Data for COVID-19 and Related Human Coronavirus Infections. ACS Pharmacol Transl Sci 2020; 3:813-834. [PMID: 33062950 PMCID: PMC7447080 DOI: 10.1021/acsptsci.0c00074] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Indexed: 02/07/2023]
Abstract
The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has led to several million confirmed cases and hundreds of thousands of deaths worldwide. To support the ongoing research and development of COVID-19 therapeutics, this report provides an overview of protein targets and corresponding potential drug candidates with bioassay and structure-activity relationship data found in the scientific literature and patents for COVID-19 or related virus infections. Highlighted are several sets of small molecules and biologics that act on specific targets, including 3CLpro, PLpro, RdRp, S-protein-ACE2 interaction, helicase/NTPase, TMPRSS2, and furin, which are involved in the viral life cycle or in other aspects of the disease pathophysiology. We hope this report will be valuable to the ongoing drug repurposing efforts and the discovery of new therapeutics with the potential for treating COVID-19.
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Affiliation(s)
- Qiongqiong Angela Zhou
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | | | - Yingzhu Li
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Yi Deng
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Roger Granet
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Linda Garner
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Cynthia Liu
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Dmitrii Polshakov
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Chris Gessner
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
| | - Steven Watkins
- CAS, a division
of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43210-3012, United States
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14
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Dwarka D, Agoni C, Mellem JJ, Soliman ME, Baijnath H. Identification of potential SARS-CoV-2 inhibitors from South African medicinal plant extracts using molecular modelling approaches. SOUTH AFRICAN JOURNAL OF BOTANY : OFFICIAL JOURNAL OF THE SOUTH AFRICAN ASSOCIATION OF BOTANISTS = SUID-AFRIKAANSE TYDSKRIF VIR PLANTKUNDE : AMPTELIKE TYDSKRIF VAN DIE SUID-AFRIKAANSE GENOOTSKAP VAN PLANTKUNDIGES 2020; 133:273-284. [PMID: 32839635 PMCID: PMC7437493 DOI: 10.1016/j.sajb.2020.07.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 05/09/2023]
Abstract
The coronavirus is a group of viruses found in animals as well as humans and have been detected since the 1960s. However, a newly identified form, SARS-CoV-2, has triggered a recent pandemic of respiratory disease now called COVID-19. There is currently no specific antiviral drug for the treatment of this pandemic, with most treatment strategies focused on symptomatic management and supportive therapy. As such, several drug discovery efforts are ongoing for potent treatment agents, with medicinal plants gradually gaining prominence. Approximately 80% of the South African population use traditional medicines to meet their primary health care needs. The current study aimed to identify potential COVID-19 therapeutic agents from a list of 29 bioactive compounds isolated from commonly used South African medicinal plants using molecular docking and molecular dynamics. Molecular docking identified arabic acid from Acacia senegal and L-canavanine found in Sutherlandia frutescens as a potential inhibitor of SARS-CoV-2 3C-like main protease. Similarly, hypoxoside isolated from Hypoxis hemerocallidea and uzarin from Xysmalobium undulatum, were identified as a potential inhibitor of SARS-CoV-2 receptor binding domain and SARS-CoV-2 RNA-dependent polymerase. These four bioactive compounds exhibited favourable binding orientations characterized by strong molecular interactions within respective inhibitors binding pockets of the target enzymes. Molecular dynamics simulations revealed that the binding of the identified inhibitors are characterized by structural perturbations which favour the inhibitory potency of these bioactive compounds. Additionally, in silico pharmacokinetic assessment of the compounds demonstrated favourable anti-SARS-CoV-2 properties. Although not conclusive, further experimental exploration of these compounds could serve as a starting point for the discovery of novel SARS-CoV-2 therapeutic.
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Affiliation(s)
- Depika Dwarka
- Department of Biotechnology and Food Technology, Durban University of Technology, KwaZulu-Natal, South Africa
| | - Clement Agoni
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
- Dream Laboratory Consult, Ghana, West Africa
| | - John Jason Mellem
- Department of Biotechnology and Food Technology, Durban University of Technology, KwaZulu-Natal, South Africa
| | - Mahmoud E Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - Himansu Baijnath
- Ward herbarium, School of Life Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
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15
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Zhang L, Zhou R. Structural Basis of the Potential Binding Mechanism of Remdesivir to SARS-CoV-2 RNA-Dependent RNA Polymerase. J Phys Chem B 2020; 124:6955-6962. [PMID: 32521159 PMCID: PMC7309898 DOI: 10.1021/acs.jpcb.0c04198] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/05/2020] [Indexed: 01/18/2023]
Abstract
Starting from late 2019, the coronavirus disease 2019 (COVID-19) has emerged as a once-in-a-century pandemic with deadly consequences, which urgently calls for new treatments, cures, and supporting apparatuses. Recently, because of its positive results in clinical trials, remdesivir was approved by the Food and Drug Administration to treat COVID-19 through Emergency Use Authorization. Here, we used molecular dynamics simulations and free energy perturbation methods to study the inhibition mechanism of remdesivir to its target SARS-CoV-2 virus RNA-dependent RNA polymerase (RdRp). We first constructed the homology model of this polymerase based on a previously available structure of SARS-CoV NSP12 RdRp (with a sequence identity of 95.8%). We then built a putative preinsertion binding structure by aligning the remdesivir + RdRp complex to the ATP bound poliovirus RdRp without the RNA template. The putative binding structure was further optimized with molecular dynamics simulations. The resulting stable preinsertion state of remdesivir appeared to form hydrogen bonds with the RNA template when aligned with the newly solved cryo-EM structure of SARS-CoV-2 RdRp. The relative binding free energy between remdesivir and ATP was calculated to be -2.80 ± 0.84 kcal/mol, where remdesivir bound much stronger to SARS-CoV-2 RdRp than the natural substrate ATP. The ∼100-fold improvement in the Kd from remdesivir over ATP indicates an effective replacement of ATP in blocking of the RdRp preinsertion site. Key residues D618, S549, and R555 are found to be the contributors to the binding affinity of remdesivir. These findings suggest that remdesivir can potentially act as a SARS-CoV-2 RNA-chain terminator, effectively stopping its RNA replication, with key residues also identified for future lead optimization and/or drug resistance studies.
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Affiliation(s)
- Leili Zhang
- Computational Biology Center, IBM Thomas
J. Watson Research Center, Yorktown Heights, New York 10598,
United States
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas
J. Watson Research Center, Yorktown Heights, New York 10598,
United States
- Institute of Quantitative Biology,
Zhejiang University, Hangzhou, 310027,
China
- Department of Chemistry, Columbia
University, New York, New York 10027, United
States
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16
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The Significance of Natural Product Derivatives and Traditional Medicine for COVID-19. Processes (Basel) 2020. [DOI: 10.3390/pr8080937] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To date, there have been more than 10 million reported cases, more than 517,000 deaths in 215 countries, areas or territories. There is no effective antiviral medicine to prevent or treat COVID-19. Natural products and traditional medicine products with known safety profiles are a promising source for the discovery of new drug leads. There is increasing number of publications reporting the effect of natural products and traditional medicine products on COVID-19. In our review, we provide an overview of natural products and their derivatives or mimics, as well as traditional medicine products, which were reported to exhibit potential to inhibit SARS-CoV-2 infection in vitro, and to manage COVID-19 in vivo, or in clinical reports or trials. These natural products and traditional medicine products are categorized in several classes: (1) anti-malaria drugs including chloroquine and hydroxychloroquine, (2) antivirals including nucleoside analogs (remdesivir, favipiravir, β-D-N4-hydroxycytidine, ribavirin and among others), lopinavir/ritonavir and arbidol, (3) antibiotics including azithromycin, ivermectin and teicoplanin, (4) anti-protozoal drug, emetine, anti-cancer drug, homoharringtonine, and others, as well as (5) traditional medicine (Lian Hua Qing Wen Capsule, Shuang Huang Lian Oral Liquid, Qingfei Paidu Decoction and Scutellariae Radix). Randomized, double-blind and placebo-controlled large clinical trials are needed to provide solid evidence for the potential effective treatment. Currently, drug repurposing is a promising strategy to quickly find an effective treatment for COVID-19. In addition, carefully combined cocktails need to be examined for preventing a COVID-19 pandemic and the resulting global health concerns.
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17
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Li H, Liu Z, Ge J. Scientific research progress of COVID-19/SARS-CoV-2 in the first five months. J Cell Mol Med 2020; 24:6558-6570. [PMID: 32320516 PMCID: PMC7264656 DOI: 10.1111/jcmm.15364] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 04/19/2020] [Accepted: 04/22/2020] [Indexed: 02/06/2023] Open
Abstract
A cluster of pneumonia (COVID-19) cases have been found in Wuhan China in late December, 2019, and subsequently, a novel coronavirus with a positive stranded RNA was identified to be the aetiological virus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2), which has a phylogenetic similarity to severe acute respiratory syndrome coronavirus (SARS-CoV). SARS-CoV-2 transmits mainly through droplets and close contact and the elder or people with chronic diseases are high-risk population. People affected by SARS-CoV-2 can be asymptomatic, which brings about more difficulties to control the transmission. COVID-19 has become pandemic rapidly after onset, and so far the infected people have been above 2 000 000 and more than 130 000 died worldwide according to COVID-19 situation dashboard of World Health Organization (https://covid19.who.int). Here, we summarized the current known knowledge regarding epidemiological, pathogenesis, pathology, clinical features, comorbidities and treatment of COVID-19/ SARS-CoV-2 as reference for the prevention and control COVID-19.
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Affiliation(s)
- Hua Li
- Department of CardiologyShanghai Institute of Cardiovascular DiseasesShanghai Xuhui District Central Hospital and Zhongshan‐Xuhui HospitalZhongshan HospitalFudan UniversityShanghaiChina
| | - Zhe Liu
- Department of MedicineBestNovo (Beijing) Medical Technology Co., LtdBeijingChina
| | - Junbo Ge
- Department of CardiologyShanghai Institute of Cardiovascular DiseasesShanghai Xuhui District Central Hospital and Zhongshan‐Xuhui HospitalZhongshan HospitalFudan UniversityShanghaiChina
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18
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Eastman R, Roth JS, Brimacombe KR, Simeonov A, Shen M, Patnaik S, Hall MD. Remdesivir: A Review of Its Discovery and Development Leading to Emergency Use Authorization for Treatment of COVID-19. ACS CENTRAL SCIENCE 2020; 6:672-683. [PMID: 32483554 PMCID: PMC7202249 DOI: 10.1021/acscentsci.0c00489] [Citation(s) in RCA: 541] [Impact Index Per Article: 135.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Indexed: 05/09/2023]
Abstract
The global pandemic of SARS-CoV-2, the causative viral pathogen of COVID-19, has driven the biomedical community to action-to uncover and develop antiviral interventions. One potential therapeutic approach currently being evaluated in numerous clinical trials is the agent remdesivir, which has endured a long and winding developmental path. Remdesivir is a nucleotide analogue prodrug that perturbs viral replication, originally evaluated in clinical trials to thwart the Ebola outbreak in 2014. Subsequent evaluation by numerous virology laboratories demonstrated the ability of remdesivir to inhibit coronavirus replication, including SARS-CoV-2. Here, we provide an overview of remdesivir's discovery, mechanism of action, and the current studies exploring its clinical effectiveness.
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Affiliation(s)
- Richard
T. Eastman
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Jacob S. Roth
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
- Albert
Einstein College of Medicine, New
York, New York 10461, United States
| | - Kyle R. Brimacombe
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Min Shen
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Samarjit Patnaik
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Matthew D. Hall
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
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19
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Guo G, Ye L, Pan K, Chen Y, Xing D, Yan K, Chen Z, Ding N, Li W, Huang H, Zhang L, Li X, Xue X. New Insights of Emerging SARS-CoV-2: Epidemiology, Etiology, Clinical Features, Clinical Treatment, and Prevention. Front Cell Dev Biol 2020; 8:410. [PMID: 32574318 PMCID: PMC7256189 DOI: 10.3389/fcell.2020.00410] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023] Open
Abstract
Since the first reports that the novel coronavirus was showing human-to-human transmission characteristics and asymptomatic cases, the number of patients with associated pneumonia has continued to rise and the epidemic has grown. It now threatens the health and lives of people across the world. The governments of many countries have attached great importance to the prevention of SARS-CoV-2, via research into the etiology and epidemiology of this newly emerged disease. Clinical signs, treatment, and prevention characteristics of the novel coronavirus pneumonia have been receiving attention worldwide, especially from medical personnel. However, owing to the different experimental methods, sample sizes, sample sources, and research perspectives of various studies, results have been inconsistent, or relate to an isolated aspect of the virus or the disease it causes. Currently, systematic summary data on the novel coronavirus are limited. This review combines experimental and clinical evidence into a systematic analysis and summary of the current progress of research into SARS-CoV-2, from multiple perspectives, with the aim of gaining a better overall understanding of the disease. Our report provides important information for current clinicians, for the prevention and treatment of COVID-19 pneumonia.
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Affiliation(s)
- Gangqiang Guo
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Lele Ye
- Department of Gynecologic Oncology, Wenzhou Central Hospital, Wenzhou, China
| | - Kan Pan
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Yu Chen
- Second Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Dong Xing
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Kejing Yan
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhiyuan Chen
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Ning Ding
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Wenshu Li
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Hong Huang
- Center for Health Assessment, Wenzhou Medical University, Wenzhou, China
| | - Lifang Zhang
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaokun Li
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Virology, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
- Institute of Virology, Wenzhou Medical University, Wenzhou, China
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20
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Baker EN. Visualizing an unseen enemy; mobilizing structural biology to counter COVID-19. IUCRJ 2020; 7:366-367. [PMID: 32431818 PMCID: PMC7201274 DOI: 10.1107/s2052252520004571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Crystallography in its broadest sense has a crucial role to play in addressing the current COVID-19 pandemic. An outpouring of structural information on key viral proteins has resulted and importantly these data have immediately been shared with researchers round the world to speed the discovery of effective therapeutic agents.
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Affiliation(s)
- Edward N. Baker
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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21
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Feasibility of Known RNA Polymerase Inhibitors as Anti-SARS-CoV-2 Drugs. Pathogens 2020; 9:pathogens9050320. [PMID: 32357471 PMCID: PMC7281371 DOI: 10.3390/pathogens9050320] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/22/2022] Open
Abstract
Coronaviruses (CoVs) are positive-stranded RNA viruses that infect humans and animals. Infection by CoVs such as HCoV-229E, -NL63, -OC43 and -HKU1 leads to the common cold, short lasting rhinitis, cough, sore throat and fever. However, CoVs such as Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and the newest SARS-CoV-2 (the causative agent of COVID-19) lead to severe and deadly diseases with mortality rates ranging between ~1 to 35% depending on factors such as age and pre-existing conditions. Despite continuous global health threats to humans, there are no approved vaccines or drugs targeting human CoVs, and the recent outbreak of COVID-19 emphasizes an urgent need for therapeutic interventions. Using computational and bioinformatics tools, here we present the feasibility of reported broad-spectrum RNA polymerase inhibitors as anti- SARS-CoV-2 drugs targeting its main RNA polymerase, suggesting that investigational and approved nucleoside RNA polymerase inhibitors have potential as anti-SARS-CoV-2 drugs. However, we note that it is also possible for SARS-CoV-2 to evolve and acquire drug resistance mutations against these nucleoside inhibitors.
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22
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Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, Masciovecchio C, Angeletti S, Ciccozzi M, Gallo RC, Zella D, Ippodrino R. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med 2020; 18:179. [PMID: 32321524 PMCID: PMC7174922 DOI: 10.1186/s12967-020-02344-6] [Citation(s) in RCA: 577] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/11/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND SARS-CoV-2 is a RNA coronavirus responsible for the pandemic of the Severe Acute Respiratory Syndrome (COVID-19). RNA viruses are characterized by a high mutation rate, up to a million times higher than that of their hosts. Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Mutation rate drives viral evolution and genome variability, thereby enabling viruses to escape host immunity and to develop drug resistance. METHODS We analyzed 220 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 worldwide from December 2019 to mid-March 2020. SARS-CoV-2 reference genome was obtained from the GenBank database. Genomes alignment was performed using Clustal Omega. Mann-Whitney and Fisher-Exact tests were used to assess statistical significance. RESULTS We characterized 8 novel recurrent mutations of SARS-CoV-2, located at positions 1397, 2891, 14408, 17746, 17857, 18060, 23403 and 28881. Mutations in 2891, 3036, 14408, 23403 and 28881 positions are predominantly observed in Europe, whereas those located at positions 17746, 17857 and 18060 are exclusively present in North America. We noticed for the first time a silent mutation in RdRp gene in England (UK) on February 9th, 2020 while a different mutation in RdRp changing its amino acid composition emerged on February 20th, 2020 in Italy (Lombardy). Viruses with RdRp mutation have a median of 3 point mutations [range: 2-5], otherwise they have a median of 1 mutation [range: 0-3] (p value < 0.001). CONCLUSIONS These findings suggest that the virus is evolving and European, North American and Asian strains might coexist, each of them characterized by a different mutation pattern. The contribution of the mutated RdRp to this phenomenon needs to be investigated. To date, several drugs targeting RdRp enzymes are being employed for SARS-CoV-2 infection treatment. Some of them have a predicted binding moiety in a SARS-CoV-2 RdRp hydrophobic cleft, which is adjacent to the 14408 mutation we identified. Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. It is also important to recognize whether the presence of some mutations might correlate with different SARS-CoV-2 mortality rates.
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Affiliation(s)
- Maria Pachetti
- Elettra Sincrotrone Trieste - Area Science Park, Trieste, Italy
- Department of Physics, University of Trieste, Via Valerio 2, Trieste, Italy
| | - Bruna Marini
- Ulisse BioMed - Area Science Park, Trieste, Italy
| | - Francesca Benedetti
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, USA
| | - Fabiola Giudici
- Department of Medicine, Surgery and Health Science, University of Trieste, Trieste, Italy
| | | | - Paola Storici
- Elettra Sincrotrone Trieste - Area Science Park, Trieste, Italy
| | | | - Silvia Angeletti
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Robert C Gallo
- Institute of Human Virology, Department of Medicine, School of Medicine, University of Maryland, Baltimore, USA
- Co-founder and International Science Advisor - Global Virus Network, Baltimore, USA
| | - Davide Zella
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, USA.
- Member of the Global Virus Network, Baltimore, USA.
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23
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Baker EN. Visualizing an unseen enemy; mobilizing structural biology to counter COVID-19. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2020; 76:158-159. [PMID: 32254048 PMCID: PMC7137381 DOI: 10.1107/s2053230x20004847] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Crystallography in its broadest sense has a crucial role to play in addressing the current COVID-19 pandemic. An outpouring of structural information on key viral proteins has resulted and importantly these data have immediately been shared with researchers round the world to speed the discovery of effective therapeutic agents.
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Affiliation(s)
- Edward N Baker
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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24
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Baker EN. Visualizing an unseen enemy; mobilizing structural biology to counter COVID-19. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:311-312. [PMID: 32254054 PMCID: PMC7137107 DOI: 10.1107/s2059798320004830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Crystallography in its broadest sense has a crucial role to play in addressing the current COVID-19 pandemic. An outpouring of structural information on key viral proteins has resulted and importantly these data have immediately been shared with researchers round the world to speed the discovery of effective therapeutic agents.
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Affiliation(s)
- Edward N Baker
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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