scholarly journals The Possible Origins of the Novel Coronavirus SARS-CoV-2

2020 ◽  
Author(s):  
Arun Shanker
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Rna Polymerase ◽  
Yunnan Province ◽  
The Novel ◽  
Rna Dependent Rna Polymerase ◽  
High Sequence Identity ◽  
Sequence Identity ◽  
Rhinolophus Affinis ◽  
Novel Coronavirus ◽  
Bat Coronavirus

Severe Acute Respiratory Syndrome (SARS) was seen as this century’s first Pandemic and was previously unknown. It was demonstrated that bats in the genus Rhinolophus are natural reservoirs of SARS-like viruses. Middle East Respiratory Syndrome-Coronavirus (MERS-CoV) was seen in 2012, it was similar to SARS CoV and is phylogenetically closely related to the bat coronaviruses (BatCoVs) HKU4 and HKU5. SARS-CoV-2 was seen in Wuhan in 2019 and SARS-CoV-2 is thought to be transmitted from animals to humans. It originated in bats and probably got into an intermediate animal and then to humans. The virus could have used the intermediate animal to adapt to transmit to humans. It was seen that a short region of RNA-dependent RNA polymerase (RdRp) from a bat coronavirus (BatCoV RaTG13) which was previously detected in Rhinolophus affinis from Yunnan province showed high sequence identity to SARS-CoV-2. We discuss the possible origins of SARS-CoV-2 here and see that there are a lot of possibilities.

Screening of Kabasura Kudineer Chooranam against COVID-19 through Targeting of Main Protease and RNA-Dependent RNA Polymerase of SARS-CoV-2 by Molecular Docking Studies

2020 ◽  
Vol 5 (4) ◽  
pp. 319-331
Author(s):  
K. Gopalasatheeskumar ◽  
Karthikeyen Lakshmanan ◽  
Anguraj Moulishankar ◽  
Jerad Suresh ◽  
D. Kumuthaveni Babu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Docking Studies ◽  
The Novel ◽  
Rna Dependent Rna Polymerase ◽  
Molecular Docking Studies ◽  
Main Protease ◽  
Short Span ◽  
Novel Coronavirus

COVID-19 is the infectious pandemic disease caused by the novel coronavirus. The COVID-19 is spread globally in a short span of time. The Ministry of AYUSH, India which promotes Siddha and other Indian system of medicine recommends the use of formulation like Nilavembu Kudineer and Kaba Sura Kudineer Chooranam (KSKC). The present work seeks to provide the evidence for the action of 74 different constituents of the KSKC formulation acting on two critical targets. That is main protease and SARS-CoV-2 RNAdependent RNA polymerase target through molecular docking studies. The molecular docking was done by using AutoDock Tools 1.5.6 of the 74 compounds, about 50 compounds yielded docking results against COVID-19 main protease while 42 compounds yielded against SARSCoV- 2 RNA-dependent RNA polymerase. This research has concluded that the KSKC has the lead molecules that inhibits COVID-19’s target of main protease of COVID-19 and SARS-CoV-2 RNA-dependent RNA polymerase.

scholarly journals The impact of super-spreaders in COVID-19: mapping genome variation worldwide

2020 ◽  
Author(s):  
Alberto Gómez-Carballa ◽  
Xabier Bello ◽  
Jacobo Pardo-Seco ◽  
Federico Martinón-Torres ◽  
Antonio Salas
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Founder Effect ◽  
Human Pathogen ◽  
High Sequence Identity ◽  
Asian Origin ◽  
Sequence Identity ◽  
Public Repositories ◽  
The Impact ◽  
Bat Coronavirus ◽  
Virus Strains

AbstractThe human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the 21st century. We analyzed >4,700 SARS-CoV-2 genomes and associated meta-data retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and >160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a uniform mutation occurrence along branches that could complicate the design of future vaccines. The root of SARS-CoV-2 genomes locates at the Chinese haplogroup B1, with a TMRCA dating to 12 November 2019 - thus matching epidemiological records. Sub-haplogroup A2a originates in China and represents the major non-Asian outbreak. Multiple founder effect episodes, most likely associated with super-spreader hosts, explain COVID-19 pandemic to a large extent.

scholarly journals Prediction of small molecule inhibitors targeting the novel coronavirus (SARS-CoV-2) RNA-dependent RNA polymerase

2020 ◽  
Author(s):  
Mohammed Ahmed ◽  
Abhisek Dwivedy ◽  
Richard Mariadasse ◽  
Satish Tiwari ◽  
Jeyaraman Jeyakanthan ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Small Molecules ◽  
Small Molecule ◽  
Small Molecule Inhibitors ◽  
Viral Proteins ◽  
The Novel ◽  
Rna Dependent Rna Polymerase ◽  
Computational Tools ◽  
Gtp Binding ◽  
Novel Coronavirus

The current COVID-19 outbreak calls for a multi-disciplinary approach towards the design and development of novel anti-COVID therapeutics including vaccines and small molecule inhibitors targeting the viral proteins of causative agent, SARS-CoV-2. Using a combination of bioinformatics and computational tools, we have modelled the 3-D structure of the RNA-dependent RNA-polymerase (RdRp) of SARS-CoV-2 and predicted its probable GTP-binding site. This site was computationally targeted using small molecules inhibitors reported in a previous study on the RdRp of the Hepatitis C virus. Further optimizations have suggested a lead molecule that may prove fruitful in development of inhibitors against RdRp of SARS-CoV-2.

scholarly journals In silico evaluation of isatin-based derivatives with RNA-dependent RNA polymerase of the novel coronavirus SARS-CoV-2

2021 ◽  
pp. 1-16
Author(s):  
Rajesh Kumar M. ◽  
Daniel A. Gideon ◽  
Richard Mariadasse ◽  
Vijay Nirusimhan ◽  
Sherlin Rosita A. ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
In Silico ◽  
The Novel ◽  
Rna Dependent Rna Polymerase ◽  
Novel Coronavirus

scholarly journals In-Silico Computational Screening of Siddha formulations Visha Sura Kudineer and Adathodai Kudineer against RNA dependent RNA polymerase of SARS CoV-2

2021 ◽  
Vol 12 (3) ◽  
pp. 534-537
Author(s):  
Panneerselvam N R ◽  
Anbarasan B
Keyword(s):  
Rna Polymerase ◽  
In Silico ◽  
Viral Infections ◽  
Therapeutic Option ◽  
Docking Studies ◽  
The Novel ◽  
Rna Dependent Rna Polymerase ◽  
Computational Screening ◽  
Novel Coronavirus ◽  
Tract Infections

Background: Siddha Medicine is an important therapeutic option used for treating various respiratory viral infections and has antiviral herbs. Aim: The study aims to perform the In Silico computational studies of Phytoconstituents of Siddha formulation Visha Sura Kudineer and Adathodai Kudineer which are commonly used in the treatment of viral fever and respiratory tract infections and could be effective against the novel coronavirus disease. Methods: Autodock program was used for the molecular docking studies against RNA-dependent RNA polymerase (RdRP) (PDB ID: 6NUR). Results: A total of 9 compounds were screened, of these 4 compounds namely, Andrographolide of Visha Sura Kudineer and Anisotine, Apioside, and 1-(p-Methoxybenzoyl) aziridine of Adathodai Kudineer showed high binding affinity against RdRp. Conclusion: Based on further experiments and clinical trials, formulations Visha Sura Kudineer and Adathodai Kudineer could be effective in the treatment of COVID-19.

scholarly journals In silico evaluation of isatin-based derivatives with RNA-dependent RNA polymerase of the novel coronavirus SARS-CoV-2

2020 ◽  
Author(s):  
Rajesh Kumar M ◽  
Daniel Andrew Gideon ◽  
Richard Mariadasse ◽  
Vijay Nirusimhan ◽  
Sherlin Rosita. A ◽  
...  
Keyword(s):  
Binding Energy ◽  
Rna Polymerase ◽  
In Silico ◽  
Biological Activities ◽  
The Novel ◽  
Rna Dependent Rna Polymerase ◽  
Ligand Interactions ◽  
Novel Coronavirus ◽  
Site Binding ◽  
The Ideal

Isatin (1H-indole-2,3-dione)-containing compounds have been shown to possess several remarkable biological activities. We had previously explored a few isatin-based imidazole derivatives for their predicted dual activity against both inflammation and cancer. We explored 47 different isatin-based derivatives (IBDs) for other potential biological activities using in silico tools and found them to possess anti-viral activity. Using AUTODOCK tools, the binding site, binding energy, inhibitory constant/Ki and receptor-ligand interactions for each of the compounds was analyzed against SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). The partition coefficient (logP) values were predicted using MedChem Designer tool. Based on the best Ki, binding energy and the ideal range of logP (between 1.0-3.0), 10 out of total 47 compounds were deemed to be prospective RdRp inhibitors. Some of these compounds gave better Ki, binding energy and logP values when compared to standard RdRp inhibitors such as remdesivir (Ki = 15.61 μM, logP = 2.2; binding energy = -6.95), a clinically approved RdRp inhibitor which is widely used for critical care of COVID-19 patients. The same in silico parameters were assessed for 9 other popular RdRp inhibitors (other than remdesivir), which were earlier used to target RdRp of other viruses, and are now repurposed to target SARS-CoV-2 RdRp. The results showed that the 10 selected isatin-based derivatives (IBDs) could be further explored for activity against SARS-Cov-2. In the present study we evaluated the efficacy of these compounds in silico.

Recent Advances towards Drug Design Targeting the Protease of 2019 novel coronavirus (2019-nCoV)

2020 ◽  
Vol 27 ◽  
Author(s):  
Sehrish Bano ◽  
Abdul Hameed ◽  
Mariya Al-Rashida ◽  
Shafia Iftikhar ◽  
Jamshed Iqbal
Keyword(s):  
Drug Design ◽  
Rna Polymerase ◽  
Drug Targets ◽  
Antiviral Agents ◽  
Structural Features ◽  
Antiviral Drugs ◽  
Rna Dependent Rna Polymerase ◽  
Mortality And Morbidity ◽  
Functional Relationships ◽  
Novel Coronavirus

Background: The 2019 novel coronavirus (2019-nCoV), also known as coronavirus 2 (SARS-CoV-2) acute respiratory syndrome has recently emerged and continued to spread rapidly with high level of mortality and morbidity rates. Currently, no efficacious therapy is available to relieve coronavirus infections. As new drug design and development takes much time, there is a possibility to find an effective treatment from existing antiviral agents. Objective: In this case, there is a need to find out the relationship between possible drug targets and mechanism of action of antiviral drugs. This review discusses about the efforts to develop drug from known or new molecules. Methods: Viruses usually have two structural integrities, proteins and nucleic acids, both of which can be possible drug targets. Herein, we systemically discuss the structural-functional relationships of the spike, 3-chymotrypsin-like protease (3CLpro), papain like protease (PLpro) and RNA-dependent RNA polymerase (RdRp), as these are prominent structural features of corona virus. Certain antiviral drugs such as Remdesivir are RNA dependent RNA polymerase inhibitor. It has the ability to terminate RNA replication by inhibiting ATP. Results: It is reported that ATP is involved in synthesis of coronavirus non-structural proteins from 3CLpro and PLpro. Similarly, mechanisms of action of many other antiviral agents has been discussed in this review. It will provide new insights into the mechanism of inhibition, and let us develop new therapeutic antiviral approaches against novel SARS-CoV-2 coronavirus. Conclusion: In conclusion, this review summarizes recent progress in developing protease inhibitors for SARS-CoV-2.

scholarly journals Severe neutropenia in infants with severe acute respiratory syndrome caused by the novel coronavirus 2019 infection

2020 ◽  
Vol 222 ◽  
pp. 259-261 ◽  
Author(s):  
Elisabetta Venturini ◽  
Giordano Palmas ◽  
Carlotta Montagnani ◽  
Elena Chiappini ◽  
Francesco Citera ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Severe Neutropenia ◽  
The Novel ◽  
Novel Coronavirus
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