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1.
J Biomol Struct Dyn ; 39(15): 5804-5818, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1390287

ABSTRACT

The sharp spurt in positive cases of novel coronavirus-19 (SARS-CoV-2) worldwide has created a big threat to human. In view to expedite new drug leads for COVID-19, Main Proteases (Mpro) of novel Coronavirus (SARS-CoV-2) has emerged as a crucial target for this virus. Nitric oxide (NO) inhibits the replication cycle of SARS-CoV. Inhalation of nitric oxide is used in the treatment of severe acute respiratory syndrome. Herein, we evaluated the phenyl furoxan, a well-known exogenous NO donor to identify the possible potent inhibitors through in silico studies such as molecular docking as per target analysis for candidates bound to substrate binding pocket of SARS-COV-2 Mpro. Molecular dynamics (MD) simulations of most stable docked complexes (Mpro-22 and Mpro-26) helped to confirm the notable conformational stability of these docked complexes under dynamic state. Furthermore, Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations revealed energetic contributions of key residues of Mpro in binding with potent furoxan derivatives 22, 26. In the present study to validate the molecular docking, MD simulation and MM-PBSA results, crystal structure of Mpro bound to experimentally known inhibitor X77 was used as control and the obtained results are presented herein. We envisaged that spiro-isoquinolino-piperidine-furoxan moieties can be used as effective ligand for SARS-CoV-2 Mpro inhibition due to the presence of key isoquinolino-piperidine skeleton with additional NO effect.Communicated by Ramaswamy H. Sarma.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Nitric Oxide Donors , Oxadiazoles , Peptide Hydrolases , Protease Inhibitors/pharmacology
2.
Clin Chem ; 66(10): 1349-1350, 2020 10 01.
Article in English | MEDLINE | ID: covidwho-1383204

Subject(s)
COVID-19 , Humans , SARS-CoV-2
3.
J Biomol Struct Dyn ; 39(12): 4433-4448, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1317842

ABSTRACT

The emergence of the coronavirus disease-2019 pandemic has led to an outbreak in the world. The SARS-CoV-2 is seventh and latest in coronavirus family with unique exonucleases for repairing any mismatches in newly transcribed genetic material. Therefore, drugs with novel additional mechanisms are required to simultaneously target and eliminate the virus. Thus, a newly deciphered N protein is taken as a target that belongs to SARS-CoV-2. They play a vital role in RNA transcription, viral replication and new virion formation. This study used virtual screening, molecular modeling and docking of the 8987 ligands from Asinex and PubChem databases against this novel target protein. Three hotspot sites having DScore ≥1 (Site 1, Site 2 and Site 3) for ligand binding were selected. Subsequently, high throughput screening, standard precision and extra precision docking process and molecular dynamics concluded three best drugs from two libraries. Two antiviral moieties from Asinex databases (5817 and 6799) have docking scores of -10.29 and -10.156; along with their respective free binding energies (ΔG bind) of -51.96 and -64.36 on Site 3. The third drug, Zidovudine, is from PubChem database with docking scores of -9.75 with its binding free energies (ΔG bind) of -59.43 on Site 3. The RMSD and RMSF were calculated for all the three drugs through molecular dynamics simulation studies for 50 ns. Zidovudine shows a very stable interaction with fluctuation starting at 2.4 Å on 2 ns and remained stable at 3 Å from 13 to 50 ns. Thus, paving the way for further biological validation as a potential treatment.Communicated by Ramaswamy H. Sarma.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Molecular Docking Simulation , Nucleocapsid , Phosphoproteins , RNA-Binding Motifs , Virion
4.
J Biomol Struct Dyn ; 39(12): 4243-4255, 2021 08.
Article in English | MEDLINE | ID: covidwho-1317834

ABSTRACT

Recent outbreak of novel Coronavirus disease () pandemic around the world is associated with severe acute respiratory syndrome. The death toll associated with the pandemic is increasing day by day. SARS-CoV-2 is an enveloped virus and its N terminal domain (NTD) of Nucleocapsid protein (N protein) binds to the viral (+) sense RNA and results in virus ribonucleoprotien complex, essential for the virus replication. The N protein is composed of a serine-rich linker region sandwiched between NTD and C terminal (CTD). These terminals play a role in viral entry and its processing post entry. The NTD of SARS-CoV-2 N protein forms orthorhombic crystals and binds to the viral genome. Therefore, there is always a quest to target RNA binding domain of nucleocapsid phosphoprotein (NTD-N-protein which in turn may help in controlling diseases caused by SARS-CoV-2 in humans. The role of Chloroquine and Hydroxychloroquine as potential treatments for is still under debate globally because of some side effects associated with it. This study involves the In silico interactions of Chloroquine and Hydroxychloroquine with the NTD-N-protein of SARS-CoV-2. With the help of various computational methods, we have explored the potential role of both of these antiviral drugs for the treatment of patients by comparing the efficacy of both of the drugs to bind to NTD-N-protein. In our research Hydroxychloroquine exhibited potential inhibitory effects of NTD-N-protein with binding energy -7.28 kcal/mol than Chloroquine (-6.30 kcal/mol) at SARS-CoV-2 receptor recognition of susceptible cells. The outcomes of this research strongly appeal for in vivo trials of Hydroxychloroquine for the patients infected with . Furthermore, the recommended doses of Hydroxychloroquine may reduce the chances of catching to the healthcare workers and staff who are in contact with or delivering direct care to coronavirus patients as long as they have not been diagnosed with . We further hypothesize that the comparative NTD-N-protein -drug docking interactions may help to understand the comparative efficacy of other candidate repurposing drugs until discovery of a proper vaccine.Communicated by Ramaswamy H. Sarma.


Subject(s)
COVID-19 , Hydroxychloroquine , Antiviral Agents/pharmacology , COVID-19/drug therapy , Chloroquine/pharmacology , Computer Simulation , Drug Repositioning , Humans , Hydroxychloroquine/pharmacology , Nucleocapsid , Nucleocapsid Proteins , RNA-Binding Motifs , SARS-CoV-2
5.
J Biol Regul Homeost Agents ; 35(2): 423-427, 2021.
Article in English | MEDLINE | ID: covidwho-1298274

ABSTRACT

Acute severe respiratory syndrome coronavirus-2 (SARS-CoV-2) infection causes coronavirus disease-2019 (COVID-19) which is associated with inflammation, thrombosis edema, hemorrhage, intra-alveolar fibrin deposition, and vascular and pulmonary damage. In COVID-19, the coronavirus activates macrophages by inducing the generation of pro-inflammatory cytokines [interleukin (IL)-1, IL-6, IL-18 and TNF] that can damage endothelial cells, activate platelets and neutrophils to produce thromboxane A2 (TxA2), and mediate thrombus generation. In severe cases, all these phenomena can lead to patient death. The binding of SARS-CoV-2 to the Toll Like Receptor (TLR) results in the release of pro-IL-1ß that is cleaved by caspase-1, followed by the production of active mature IL-1ß which is the most important cytokine in causing fever and inflammation. Its activation in COVID-19 can cause a "cytokine storm" with serious biological and clinical consequences. Blockade of IL-1 with inhibitory and anti-inflammatory cytokines represents a new therapeutic strategy also for COVID-19. Recently, very rare allergic reactions to vaccines have been reported, with phenomena of pulmonary thrombosis. These side effects have raised substantial concern in the population. Highly allergic subjects should therefore be vaccinated under strict medical supervision. COVID-19 has accelerated vaccine therapy but also the use of drugs and monoclonal antibodies (mABs) which have been used in COVID-19 therapy. They are primarily adopted to treat high-risk mild-to-moderate non-hospitalized patients, and it has been noted that the administration of two mABs gave better results. mABs, other than polyclonal plasma antibodies from infected subjects with SARS-CoV-2, are produced in the laboratory and are intended to fight SARS-CoV-2. They bind specifically to the antigenic determinant of the spike protein, inhibiting the pathogenicity of the virus. The most suitable individuals for mAB therapy are people at particular risk, such as the elderly and those with serious chronic diseases including diabetics, hypertension and obesity, including subjects suffering from cardiovascular diseases. These antibodies have a well-predetermined target, they bind mainly to the protein S (formed by the S1A, B, C and D subtypes), located on the viral surface, and to the S2 protein that acts as a fuser between the virus and the cell membrane. Since mABs are derived from a single splenic immune cell, they are identical and form a cell clone which can neutralize SARS-CoV-2 by binding to the epitope of the virus. However, this COVID-19 therapy may cause several side effects such as mild pain, bleeding, bruising of the skin, soreness, swelling, thrombotic-type episodes, arterial hypertension, changes in heart activity, slowed bone marrow activity, impaired renal function, diarrhea, fatigue, nausea, vomiting, allergic reaction, fever, and possible subsequent infection may occur at the site of injection. In conclusion, the studies promoting mAB therapy in COVID-19 are very promising but the results are not yet definitive and more investigations are needed to certify both their good neutralizing effects of SARS-CoV-2, and to eliminate, or at least mitigate, the harmful side effects.


Subject(s)
COVID-19 , SARS-CoV-2 , Aged , Antibodies, Monoclonal , Cytokine Release Syndrome , Endothelial Cells , Humans
6.
Curr Opin Ophthalmol ; 32(4): 338-342, 2021 07 01.
Article in English | MEDLINE | ID: covidwho-1297423

ABSTRACT

PURPOSE OF REVIEW: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly infectious coronavirus causing the COVID-19 pandemic. Although airborne spread through infectious respiratory droplets is the primary source of transmission, recent literature has suggested the ocular surface may be able to harbor viral particles. Here, we aim to discuss how SARS-CoV-2 affects the ocular surface and updated guidance on how SARS-CoV-2 transmission should be considered in the setting of eye banking and corneal transplantation procedures. RECENT FINDINGS: SARS-CoV-2 RNA can be found on the ocular surface, which may suggest the eye as a site of viral replication. However, there is poor correlation between PCR positivity on the ocular surface and ocular symptoms. To date, although viral particles can be found on the ocular surface, use of standard antiseptic procedures during corneal tissue procurement appears to sufficiently reduce viral load. In addition, preprocedure testing may further decrease the chances of transplanting an infected cornea without significantly impacting the overall accessibility to corneal tissue by decreasing the donor pool. SUMMARY: Corneal transplantation remains a well tolerated and highly successful procedure with no evidence of viral transmission with transplantation. Although the ocular surface has the required receptors to allow for viral replication, there is no clear evidence that the eye is a site for primary viral infection.


Subject(s)
COVID-19/prevention & control , Cornea/virology , Corneal Transplantation/standards , Eye Banks , Tissue and Organ Procurement/methods , COVID-19/transmission , Humans , Practice Guidelines as Topic , SARS-CoV-2/isolation & purification , Tissue Donors/supply & distribution
7.
Her Russ Acad Sci ; 91(2): 170-175, 2021.
Article in English | MEDLINE | ID: covidwho-1267402

ABSTRACT

As a rule, coronavirus infections are mild in healthy adults and do not require special approaches to treatment. However, highly pathogenic strains, particularly the recently isolated SARS-CoV2, which causes COVID-19 infection, in about 15% of cases lead to severe complications, including acute respiratory distress syndrome, which causes high patient mortality. In addition, a common complication of COVID-19 is the development of pulmonary fibrosis. Why is the novel coronavirus so pathogenic? What new treatments can be proposed to speed up the recovery and subsequent rehabilitation of the organism? In 2020, over 34 000 scientific articles were published on the structure, distribution, pathogenesis, and possible approaches to the treatment of infection caused by the novel SARS-CoV2 coronavirus. However, there are still no definitive answers to these questions, while the number of the diseased is increasing daily. One of the comprehensive approaches to the treatment of the consequences of the infection is the use of multipotent human mesenchymal stromal cells and products of their secretion (secretome). Acting at several stages of the development of the infection, the components of the secretome can suppress the interaction of the virus with endothelial cells, regulate inflammation, and stimulate lung tissue regeneration, preventing the development of fibrosis. The results of basic and clinical research on this topic are summarized, including our own experimental data, indicating that cell therapy approaches can be successfully applied to treat patients with COVID-19.

8.
United European Gastroenterol J ; 2021 Jun 08.
Article in English | MEDLINE | ID: covidwho-1260575

ABSTRACT

BACKGROUND: The novel Coronavirus (SARS-CoV-2) has caused almost 2 million deaths worldwide. Both Food and Drug Administration and European Medicines Agency have recently approved the first COVID-19 vaccines, and a few more are going to be approved soon. METHODS: Several different approaches have been used to stimulate the immune system in mounting a humoral response. As more traditional approaches are under investigation (inactivated virus vaccines, protein subunit vaccines, recombinant virus vaccines), more recent and innovative strategies have been tried (non-replicating viral vector vaccines, RNA based vaccines, DNA based vaccines). RESULTS: Since vaccinations campaigns started in December 2020 in both the US and Europe, gastroenterologists will be one of the main sources of information regarding SARS-CoV 2 vaccination for patients in their practice, including vulnerable patients such as those with Inflammatory Bowel Disease (IBD), patients with chronic liver disease, and GI cancer patients. CONCLUSIONS: Thus, we must ourselves be well educated and updated in order to provide unambiguous counseling to these categories of vulnerable patients. In this commentary, we aim to provide a comprehensive review of both approved COVID-19 vaccines and the ones still under development, and explore potential risks, benefits and prioritization of vaccination.

9.
Saudi Med J ; 42(6): 589-611, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1257242

ABSTRACT

Extracorporeal membrane oxygenation (ECMO) is considered as a supportive treatment that provides circulatory and ventilatory support and can be thought off as a bridge to organ recovery. Since 2009, it has been applied as a rescue treatment for patients with severe adult respiratory distress syndrome (ARDS) mainly due to viral causes. In December 2019, several patients presented with a constellation of symptoms of viral pneumonia in China. A new strain of the corona virus family, called COVID-19, has been discovered to be the cause of this severe mysterious illness that was named severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2). This new virus continued to spread across the globe leading to the World Health Organization announcing it as a pandemic in the early 2020. By the end of March 2021, the number of COVID-19 cases worldwide exceeded 126 million cases. In Saudi Arabia, the first confirmed case of COVID-19 was reported in the 2nd March 2020. By the end of March 2021, the total number of confirmed COVID-19 cases in Saudi Arabia is just above 360,000. In anticipation of the need of ECMO for the treatment of patients with SARS­CoV­2 based on the previous Middle East respiratory syndrome coronavirus pandemic experience, the Saudi Extra-Corporeal Life Support (ECLS) chapter that is under the umbrella of the Saudi Critical Care Society (SCCS) convened a working group of ECMO experts. The mission of this group was to formulate a guidance for the use of ECMO as a last resort for patients with severe ARDS, especially with COVID-19 based on available evidence. The ECLS-SCCS chapter wanted to generate a document that can be used to simple guide, with a focus on safety, to provide ECMO service for patients with severe ARDS with a special focus on SARS­CoV­2.


Subject(s)
COVID-19/therapy , Extracorporeal Membrane Oxygenation/methods , Pneumonia, Viral/therapy , Pneumonia, Viral/virology , Respiratory Distress Syndrome/therapy , Adult , Animals , COVID-19/virology , Humans , SARS-CoV-2/isolation & purification , Saudi Arabia
10.
Biochem Biophys Rep ; 27: 101032, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1252494

ABSTRACT

Developing a safe and effective antiviral treatment takes a decade, however, when it comes to the coronavirus disease (COVID-19), time is a sensitive matter to slow the spread of the pandemic. Screening approved antiviral drugs against COVID-19 would speed the process of finding therapeutic treatment. The current study examines commercially approved drugs to repurpose them against COVID-19 virus main protease using structure-based in-silico screening. The main protease of the coronavirus is essential in the viral replication and is involved in polyprotein cleavage and immune regulation, making it an effective target when developing the treatment. A Number of approved antiviral drugs were tested against COVID-19 virus using molecular docking analysis by calculating the free natural affinity of the binding ligand to the active site pocket and the catalytic residues without forcing the docking of the ligand to active site. COVID-19 virus protease solved structure (PDB ID: 6LU7) is targeted by repurposed drugs. The molecular docking analysis results have shown that the binding of Remdesivir and Mycophenolic acid acyl glucuronide with the protein drug target has optimal binding features supporting that Remdesivir and Mycophenolic acid acyl glucuronide can be used as potential anti-viral treatment against COVID-19 disease.

11.
Am J Surg Pathol ; 46(1): 89-96, 2022 01 01.
Article in English | MEDLINE | ID: covidwho-1254925

ABSTRACT

Approximately 20% of patients with symptomatic syndrome-associated coronavirus-2 (SARS-CoV-2) infection have gastrointestinal bleeding and/or diarrhea. Most are managed without endoscopic evaluation because the risk of practitioner infection outweighs the value of biopsy analysis unless symptoms are life-threatening. As a result, much of what is known about the gastrointestinal manifestations of coronavirus disease-2019 (COVID-19) has been gleaned from surgical and autopsy cases that suffer from extensive ischemic injury and/or poor preservation. There are no detailed reports describing any other gastrointestinal effects of SARS-CoV-2 even though >3,000,000 people have died from COVID-19 worldwide. The purpose of this study is to report the intestinal findings related to SARS-CoV-2 infection by way of a small case series including one with evidence of direct viral cytopathic effect and 2 with secondary injury attributed to viral infection. Infection can be confirmed by immunohistochemical stains directed against SARS-CoV-2 spike protein, in situ hybridization for spike protein-encoding RNA, and ultrastructural visualization of viruses within the epithelium. It induces cytoplasmic blebs and tufted epithelial cells without inflammation and may not cause symptoms. In contrast, SARS-CoV-2 infection can cause gastrointestinal symptoms after the virus is no longer detected, reflecting systemic activation of cytokine and complement cascades rather than direct viral injury. Reversible mucosal ischemia features microvascular injury with hemorrhage, small vessel thrombosis, and platelet-rich thrombi. Systemic cytokine elaboration and dysbiosis likely explain epithelial cell injury that accompanies diarrheal symptoms. These observations are consistent with clinical and in vitro data and contribute to our understanding of the protean manifestations of COVID-19.


Subject(s)
COVID-19/pathology , Intestinal Diseases/pathology , Intestinal Diseases/virology , Intestines/pathology , Intestines/virology , Adult , Aged , Aged, 80 and over , Biomarkers/metabolism , Biopsy , COVID-19/diagnosis , COVID-19/immunology , Cytokines/metabolism , Gastrointestinal Hemorrhage/diagnosis , Gastrointestinal Hemorrhage/immunology , Gastrointestinal Hemorrhage/pathology , Gastrointestinal Hemorrhage/virology , Humans , Intestinal Diseases/diagnosis , Intestinal Diseases/immunology , Intestines/immunology , Ischemia/diagnosis , Ischemia/immunology , Ischemia/pathology , Ischemia/virology , Male , Thrombosis/diagnosis , Thrombosis/immunology , Thrombosis/pathology , Thrombosis/virology
12.
Ann Clin Microbiol Antimicrob ; 20(1): 35, 2021 May 18.
Article in English | MEDLINE | ID: covidwho-1234561

ABSTRACT

Coronavirus disease 2019 (COVID-19) is the second pandemic of the twenty-first century, with over one-hundred million infections and over two million deaths to date. It is a novel strain from the Coronaviridae family, named Severe Acute Respiratory Distress Syndrome Coronavirus-2 (SARS-CoV-2); the 7th known member of the coronavirus family to cause disease in humans, notably following the Middle East Respiratory syndrome (MERS), and Severe Acute Respiratory Distress Syndrome (SARS). The most characteristic feature of this single-stranded RNA molecule includes the spike glycoprotein on its surface. Most patients with COVID-19, of which the elderly and immunocompromised are most at risk, complain of flu-like symptoms, including dry cough and headache. The most common complications include pneumonia, acute respiratory distress syndrome, septic shock, and cardiovascular manifestations. Transmission of SARS-CoV-2 is mainly via respiratory droplets, either directly from the air when an infected patient coughs or sneezes, or in the form of fomites on surfaces. Maintaining hand-hygiene, social distancing, and personal protective equipment (i.e., masks) remain the most effective precautions. Patient management includes supportive care and anticoagulative measures, with a focus on maintaining respiratory function. Therapy with dexamethasone, remdesivir, and tocilizumab appear to be most promising to date, with hydroxychloroquine, lopinavir, ritonavir, and interferons falling out of favour. Additionally, accelerated vaccination efforts have taken place internationally, with several promising vaccinations being mass deployed. In response to the COVID-19 pandemic, countries and stakeholders have taken varying precautions to combat and contain the spread of the virus and dampen its collateral economic damage. This review paper aims to synthesize the impact of the virus on a global, micro to macro scale.


Subject(s)
COVID-19/epidemiology , Global Health , SARS-CoV-2 , COVID-19/prevention & control , COVID-19/therapy , COVID-19/transmission , COVID-19 Vaccines/immunology , Humans , Risk Factors , SARS-CoV-2/pathogenicity , Virulence
13.
Infect Genet Evol ; 93: 104923, 2021 09.
Article in English | MEDLINE | ID: covidwho-1230673

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging and highly pathogenic coronavirus that causes coronavirus disease (COVID-19), and might even lead to death. Circular RNAs (circRNAs), a new type of RNAs, are implicated in viral pathogenesis and host immune responses. However, their dynamic expression patterns and functions during SARS-CoV-2 infection remain to be unclear. We herein performed genome-wide dynamic analysis of circRNAs in human lung epithelial cells infected with SARS-CoV-2 at four time points. A total of 6118 circRNAs were identified at different genomic locations, including 5641 known and 477 novel circRNAs. Notably, a total of 42 circRNAs were significantly dysregulated, wherein 17 were up-regulated and 25 were down-regulated following infection at multiple phases. The gene ontology and KEGG enrichment analyses revealed that the parental genes of circRNAs were mainly involved in immune and inflammatory responses. Further, the RNA binding protein (RBP) prediction analysis indicated that the dysregulated circRNAs could regulate mRNA stability, immunity, cell death by binding specific proteins. Additionally, the circRNA-miRNA-gene network analysis showed that circRNAs indirectly regulated gene expression by absorbing their targeted miRNAs. Collectively, these results shed light on the roles of circRNAs in virus-host interactions, facilitating future studies on SARS-CoV-2 infection and pathogenesis.


Subject(s)
COVID-19/genetics , Host-Pathogen Interactions/genetics , Lung/cytology , RNA, Circular/genetics , COVID-19/pathology , Epithelial Cells , Gene Expression Regulation , Gene Ontology , Humans , Lung/virology , MicroRNAs/genetics , RNA-Binding Proteins/genetics , Reproducibility of Results
14.
J Mol Model ; 27(6): 160, 2021 May 08.
Article in English | MEDLINE | ID: covidwho-1219702

ABSTRACT

Coronavirus infectious disease 2019 (COVID-19), a viral infection caused by a novel coronavirus (nCoV), continues to emerge as a serious threat to public health. This pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) has infected globally with 1,550,000 plus deaths to date, representing a high risk to public health. No effective drug or vaccine is available to curb down this deadly virus. The expedition for searching for a potential drug or vaccine against COVID-19 is of massive potential and favour to the community. This study is focused on finding an effective natural compound that can be processed further into a potential inhibitor to check the activity of SARS-CoV-2 with minimal side effects targeting NSP15 protein, which belongs to the EndoU enzyme family. The natural screening suggested two efficient compounds (PubChem ID: 95372568 and 1776037) with dihydroxyphenyl region of the compound, found to be important in the interaction with the viral protein showing promising activity which may act as a potent lead inhibitory molecule against the virus. In combination with virtual screening, modelling, drug likeliness, molecular docking, and 500 ns cumulative molecular dynamics simulations (100 ns for each complex) along with the decomposition analysis to calculate and confirm the stability and fold, we propose 95372568 and 1776037 as novel compounds of natural origin capable of getting developed into potent lead molecules against SARS-CoV-2 target protein NSP15.


Subject(s)
Antiviral Agents/chemistry , Biological Products/chemistry , COVID-19 , Computational Biology , Endoribonucleases , Molecular Docking Simulation , Molecular Dynamics Simulation , SARS-CoV-2/chemistry , Viral Nonstructural Proteins , Antiviral Agents/therapeutic use , Biological Products/therapeutic use , COVID-19/drug therapy , Endoribonucleases/chemistry , Humans , Viral Nonstructural Proteins/chemistry
15.
Lab Chip ; 21(12): 2398-2406, 2021 06 15.
Article in English | MEDLINE | ID: covidwho-1219412

ABSTRACT

COVID-19 is a new strain of highly contagious coronavirus, and at present, more than 221.4 million people have been infected with this virus, and the death toll exceeds 2793398. Early and fast detection of COVID-19 from infected individuals is critical to limit its spreading. Here, we report an innovative approach to detect the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein by combining DNA/RNA oligomers as aptamers and a graphene oxide (GO) coated optical microfiber as a sensor system. The DNA/RNA aptamers can effectively capture the SARS-CoV-2 N protein in vitro, with the GO coated optical microfiber aptasensor for real-time monitoring of the SARS-CoV-2 N protein. Due to the extremely high surface-to-volume ratio and excellent optical and biochemical properties of the GO surface layer, the fixing effect of the microfiber surface is significantly improved and the lowest limit of detection (LOD) is 6.25 × 10-19 M. Furthermore, in order to prove the feasibility of this sensing method in clinical applications, we use this sensor to detect the N protein mixed in fetal bovine serum (FBS) samples. The experimental results show that the biosensor can quickly and effectively detect the N protein (1 × 10-9 M) in a complex sample matrix within 3 minutes. These findings suggest that this approach can be utilized for quantitative monitoring of coronavirus particles due to its high sensitivity, which can help to quickly exclude patients who do not have the infection. Collectively, the optical microfiber sensor system could be expected to become an important platform for the diagnosis of coronavirus due to its simple detection scheme and easy miniaturization.


Subject(s)
COVID-19 , Graphite , Humans , Limit of Detection , SARS-CoV-2
16.
APMIS ; 129(7): 408-420, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1208769

ABSTRACT

The response to the ongoing COVID-19 pandemic has been characterized by draconian measures and far too many important unknowns, such as the true mortality risk, the role of children as transmitters and the development and duration of immunity in the population. More than a year into the pandemic much has been learned and insights into this novel type of pandemic and options for control are shaping up. Using a historical lens, we review what we know and still do not know about the ongoing COVID-19 pandemic. A pandemic caused by a member of the coronavirus family is a new situation following more than a century of influenza A pandemics. However, recent pandemic threats such as outbreaks of the related and novel deadly coronavirus SARS in 2003 and of MERS since 2012 had put coronaviruses on WHOs blueprint list of priority diseases. Like pandemic influenza, SARS-CoV-2 is highly transmissible (R0 ~ 2.5). Furthermore, it can fly under the radar due to a broad clinical spectrum where asymptomatic and pre-symptomatic infected persons also transmit the virus-including children. COVID-19 is far more deadly than seasonal influenza; initial data from China suggested a case fatality rate of 2.3%-which would have been on par with the deadly 1918 Spanish influenza. But, while the Spanish influenza killed young, otherwise healthy adults, it is the elderly who are at extreme risk of dying of COVID-19. We review available seroepidemiological evidence of infection rates and compute infection fatality rates (IFR) for Denmark (0.5%), Spain (0.85%), and Iceland (0.3%). We also deduce that population age structure is key. SARS-CoV-2 is characterized by superspreading, so that ~10% of infected individuals yield 80% of new infections. This phenomenon turns out to be an Achilles heel of the virus that may explain our ability to effectively mitigate outbreaks so far. How will this pandemic come to an end? Herd immunity has not been achieved in Europe due to intense mitigation by non-pharmaceutical interventions; for example, only ~8% of Danes were infected across the 1st and 2nd wave. Luckily, we now have several safe and effective vaccines. Global vaccine control of the pandemic depends in great measure on our ability to keep up with current and future immune escape variants of the virus. We should thus be prepared for a race between vaccine updates and mutations of the virus. A permanent reopening of society highly depends on winning that race.


Subject(s)
COVID-19/epidemiology , SARS-CoV-2 , Adult , COVID-19/prevention & control , COVID-19/transmission , COVID-19 Vaccines/immunology , Child , Humans , Influenza, Human/epidemiology , SARS-CoV-2/immunology
17.
J Biol Regul Homeost Agents ; 35(2): 423-427, 2021.
Article in English | MEDLINE | ID: covidwho-1204457

ABSTRACT

Acute severe respiratory syndrome coronavirus-2 (SARS-CoV-2) infection causes coronavirus disease-2019 (COVID-19) which is associated with inflammation, thrombosis edema, hemorrhage, intra-alveolar fibrin deposition, and vascular and pulmonary damage. In COVID-19, the coronavirus activates macrophages by inducing the generation of pro-inflammatory cytokines [interleukin (IL)-1, IL-6, IL-18 and TNF] that can damage endothelial cells, activate platelets and neutrophils to produce thromboxane A2 (TxA2), and mediate thrombus generation. In severe cases, all these phenomena can lead to patient death. The binding of SARS-CoV-2 to the Toll Like Receptor (TLR) results in the release of pro-IL-1ß that is cleaved by caspase-1, followed by the production of active mature IL-1ß which is the most important cytokine in causing fever and inflammation. Its activation in COVID-19 can cause a "cytokine storm" with serious biological and clinical consequences. Blockade of IL-1 with inhibitory and anti-inflammatory cytokines represents a new therapeutic strategy also for COVID-19. Recently, very rare allergic reactions to vaccines have been reported, with phenomena of pulmonary thrombosis. These side effects have raised substantial concern in the population. Highly allergic subjects should therefore be vaccinated under strict medical supervision. COVID-19 has accelerated vaccine therapy but also the use of drugs and monoclonal antibodies (mABs) which have been used in COVID-19 therapy. They are primarily adopted to treat high-risk mild-to-moderate non-hospitalized patients, and it has been noted that the administration of two mABs gave better results. mABs, other than polyclonal plasma antibodies from infected subjects with SARS-CoV-2, are produced in the laboratory and are intended to fight SARS-CoV-2. They bind specifically to the antigenic determinant of the spike protein, inhibiting the pathogenicity of the virus. The most suitable individuals for mAB therapy are people at particular risk, such as the elderly and those with serious chronic diseases including diabetics, hypertension and obesity, including subjects suffering from cardiovascular diseases. These antibodies have a well-predetermined target, they bind mainly to the protein S (formed by the S1A, B, C and D subtypes), located on the viral surface, and to the S2 protein that acts as a fuser between the virus and the cell membrane. Since mABs are derived from a single splenic immune cell, they are identical and form a cell clone which can neutralize SARS-CoV-2 by binding to the epitope of the virus. However, this COVID-19 therapy may cause several side effects such as mild pain, bleeding, bruising of the skin, soreness, swelling, thrombotic-type episodes, arterial hypertension, changes in heart activity, slowed bone marrow activity, impaired renal function, diarrhea, fatigue, nausea, vomiting, allergic reaction, fever, and possible subsequent infection may occur at the site of injection. In conclusion, the studies promoting mAB therapy in COVID-19 are very promising but the results are not yet definitive and more investigations are needed to certify both their good neutralizing effects of SARS-CoV-2, and to eliminate, or at least mitigate, the harmful side effects.


Subject(s)
COVID-19 , SARS-CoV-2 , Aged , Antibodies, Monoclonal , Cytokine Release Syndrome , Endothelial Cells , Humans
18.
Acta Neuropathol ; 141(6): 809-822, 2021 06.
Article in English | MEDLINE | ID: covidwho-1202748

ABSTRACT

One of the most frequent symptoms of COVID-19 is the loss of smell and taste. Based on the lack of expression of the virus entry proteins in olfactory receptor neurons, it was originally assumed that the new coronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) does not infect olfactory neurons. Recent studies have reported otherwise, opening the possibility that the virus can directly infect the brain by traveling along the olfactory nerve. Multiple animal models have been employed to assess mechanisms and routes of brain infection of SARS-CoV-2, often with conflicting results. We here review the current evidence for an olfactory route to brain infection and conclude that the case for infection of olfactory neurons is weak, based on animal and human studies. Consistent brain infection after SARS-CoV-2 inoculation in mouse models is only seen when the virus entry proteins are expressed abnormally, and the timeline and progression of rare neuro-invasion in these and in other animal models points to alternative routes to the brain, other than along the olfactory projections. COVID-19 patients can be assured that loss of smell does not necessarily mean that the SARS-CoV-2 virus has gained access to and has infected their brains.


Subject(s)
Brain/virology , COVID-19/etiology , Olfactory Nerve/virology , Olfactory Receptor Neurons/virology , SARS-CoV-2/physiology , Virus Internalization , Animals , Disease Models, Animal , Humans
19.
Curr Top Med Chem ; 21(6): 442-460, 2021.
Article in English | MEDLINE | ID: covidwho-1183719

ABSTRACT

[Coronaviruses (CoVs) are enveloped positive-stranded RNA viruses with spike (S) protein projections that allow the virus to enter and infect host cells. The S protein is a key virulence factor determining viral pathogenesis, host tropism, and disease pathogenesis. There are currently diverse corona viruses that are known to cause disease in humans. The occurrence of Middle East respiratory syndrome coronavirus (MERS-CoV) and Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), as fatal human CoV diseases, has induced significant interest in the medical field. The novel coronavirus disease (COVID-19) is an infectious disease caused by a novel strain of coronavirus (SAR-CoV-2). The SARS-CoV2 outbreak has been evolved in Wuhan, China, in December 2019, and identified as a pandemic in March 2020, resulting in 53.24 M cases and 1.20M deaths worldwide. SARS-CoV-2 main proteinase (MPro), a key protease of CoV-2, mediates viral replication and transcription. SARS-CoV-2 MPro has been emerged as an attractive target for SARS-CoV-2 drug design and development. Diverse scaffolds have been released targeting SARS-CoV-2 MPro. In this review, we culminate the latest published information about SARS-CoV-2 main proteinase (MPro) and reported inhibitors.


Subject(s)
Antiviral Agents/chemistry , Coronavirus 3C Proteases/antagonists & inhibitors , Phytochemicals/chemistry , Protease Inhibitors/chemistry , SARS-CoV-2/chemistry , Amino Acid Sequence , Antiviral Agents/classification , Antiviral Agents/pharmacology , COVID-19/drug therapy , Catalytic Domain , Coronavirus 3C Proteases/chemistry , Coronavirus 3C Proteases/genetics , Coronavirus 3C Proteases/metabolism , Drug Discovery , Gene Expression , High-Throughput Screening Assays , Humans , Molecular Docking Simulation , Phytochemicals/classification , Phytochemicals/pharmacology , Protease Inhibitors/classification , Protease Inhibitors/pharmacology , Protein Binding , Protein Interaction Domains and Motifs , Protein Structure, Secondary , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology , Structure-Activity Relationship
20.
Nanomicro Lett ; 13: 109, 2021 12.
Article in English | MEDLINE | ID: covidwho-1182358

ABSTRACT

The current COVID-19 pandemic urges the extremely sensitive and prompt detection of SARS-CoV-2 virus. Here, we present a Human Angiotensin-converting-enzyme 2 (ACE2)-functionalized gold "virus traps" nanostructure as an extremely sensitive SERS biosensor, to selectively capture and rapidly detect S-protein expressed coronavirus, such as the current SARS-CoV-2 in the contaminated water, down to the single-virus level. Such a SERS sensor features extraordinary 106-fold virus enrichment originating from high-affinity of ACE2 with S protein as well as "virus-traps" composed of oblique gold nanoneedles, and 109-fold enhancement of Raman signals originating from multi-component SERS effects. Furthermore, the identification standard of virus signals is established by machine-learning and identification techniques, resulting in an especially low detection limit of 80 copies mL-1 for the simulated contaminated water by SARS-CoV-2 virus with complex circumstance as short as 5 min, which is of great significance for achieving real-time monitoring and early warning of coronavirus. Moreover, here-developed method can be used to establish the identification standard for future unknown coronavirus, and immediately enable extremely sensitive and rapid detection of novel virus. Supplementary Information: The online version contains supplementary material available at 10.1007/s40820-021-00620-8.

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