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NGS technologies for detection of SARS-CoV-2 strains and mutations
Published in Sanjeeva Srivastava, Multi-Pronged Omics Technologies to Understand COVID-19, 2022
Manisha Choudhury, Ayushi Verma, Ankit Halder, Arup Acharjee
SARS-CoV-2 belongs to the genus Betacoronaviruses, comprised of a positive-sense, single-stranded RNA genome of around 30 kb and shares 80% homology SARS-CoV and 50% homology with Middle East respiratory syndrome coronavirus (MERS-CoV). The presence of a 5′-cap structure and a 3′ poly(A) tail characterizes the transcript of the coronavirus (COVs). The translation of two open reading frames (ORFs), namely, ORF1a and ORF1b, produces non-structural proteins (nsps) (Figure 2.2). Polypeptide 1a (pp1a) of molecular weight 440–500 kDa is made from ORF1a, which is further cleaved into 11 nsps. The translation of ORF1b produces a polypep-tide (pp1ab) of molecular weight ranging around 740–810 kDa of protein. This is cleaved into 15 nsps. Among these, nsp3 and nsp5 are the two main proteases responsible for proteolytic cleavage. Nsp3 bears a papain-like protease domain, whereas nsp5 contains a 3C-like protease domain. The nsp12 mediates the viral genome replication and transcription by catalyzing RNA-dependent RNA polymerase (RdRP) activity.
Application of Computational and Bioinformatics Techniques in Drug Repurposing for Effective Development of Potential Drug Candidate for the Management of COVID-19
Published in Hajiya Mairo Inuwa, Ifeoma Maureen Ezeonu, Charles Oluwaseun Adetunji, Emmanuel Olufemi Ekundayo, Abubakar Gidado, Abdulrazak B. Ibrahim, Benjamin Ewa Ubi, Medical Biotechnology, Biopharmaceutics, Forensic Science and Bioinformatics, 2022
Charles Oluwaseun Adetunji, Olaniyan Tope Olugbemi, Muhammad Akram, Umme Laila, Michael Olugbenga Samuel, Ayomide Michael Oshinjo, Juliana Bunmi Adetunji, Gloria E. Okotie, Nwadiuto (Diuto) Esiobu, Omotayo Opemipo Oyedara, Folasade Muibat Adeyemi
Molecular dynamic simulation is a computational approach that provides information on the structural stability, atom behavior, and conformational changes occurring in a protein-ligand complex at the atomic level. During molecular dynamic simulation, atoms and molecules interact for a specific period of time, followed by the determination of trajectories, forces, and potential energies between the particles. Molecular dynamics simulation has been applied in studying and confirming the stability behavior of SARS-CoV-2 protease-inhibitors complexes. Several compound inhibitors against SARS-CoV-2 proteases such as 3CL hydrolase (Mpro), SARS-CoV-2 papain-like protease (PLpro), SARS-CoV-2 Guanine-N7 methyltransferase, and SARS-CoV-2 binding sites in humans such as Angiotensin Converting Enzyme 2 (ACE2) have been studied using molecular dynamic simulation (Choudhary et al., 2020; Selvaraj et al., 2020; Surti et al., 2020; Khelfaoui et al., 2020). Software such as GROMACS, CHARMM, DESMOND, and AMBER can be employed for molecular dynamic stimulation in COVID-19 studies (Abraham et al., 2015).
Rhenium complexes as antiviral agents for COVID-19
Published in Journal of Coordination Chemistry, 2022
In one example, Ott and coworkers demonstrated the application of Au(I/III) complexes as inhibitors for the SARS-CoV-2 papain-like protease, a crucial enzyme responsible for the processing of the viral polyprotein, as well as inhibitors of the binding of the spike protein to the angiotensin-converting enzyme II receptor, an important interaction for viral cellular uptake. Insights into the mechanism of action revealed that the metal complexes were able to replace the structurally necessary Zn(II) ion in the SARS-CoV-2 papain-like protease [12]. Several lead compounds showed antiviral activity in SARS-CoV-2 infected cells. Despite their promising antiviral activity, most of these compounds were found with a cytotoxic effect, limiting their application and requiring the need for an optimization of the ligand scaffold [13, 14].
COVID-19;-The origin, genetics,and management of the infection of mothers and babies
Published in Egyptian Journal of Basic and Applied Sciences, 2020
Hassan Ih El-Sayyad, Yousef Ka Abdalhafid
The SARS-Cov-2 carries many protein structures such as the glycosylated spike (S) protein that mediates host cell invasion through binding to ACE2 located on the surface membrane of host cells [48] which are involved in inducing host immune responses. In addition, serine protease TMPRSS211, which is present in the host cells triggers the invasion process of viral S protein . Other viral non-structural proteins such as RNA-dependent RNA polymerase (RdRp), CoV main protease (3CLpro), and papain-like protease (PLpro). are released from the viral genome as a single RNA positive strand in the host and translated into viral polyproteins using host cell protein translation machinery. The viral polyproteins are then cleaved into effector proteins by viral proteinases 3CLpro and PLpro [49]
Application of Artificial Intelligence on Post Pandemic Situation and Lesson Learn for Future Prospects
Published in Journal of Experimental & Theoretical Artificial Intelligence, 2023
Priyanka Dwivedi, Achintya Kumar Sarkar, Chinmay Chakraborty, Monoj Singha, Vineet Rojwal
COVID-19 belongs to the β corona virus family which has similarities to (SARS-CoV) (Huang et al., 2020). This is the latest and one of the three corona viruses which infect the human being out of seven corona viruses (Seah & Agrawal, 2020). It is an enveloped virus with single-strand ribonucleic acid (RNA). After decoding the genome, it was found that the virus has four main structural proteins viz. spike (S), envelope (E), membrane (M) and nucleocapsid (N) which are encoded with different ORF (Boheemen et al., 2012; Woo et al., 2010). Similarly, some non-structural proteins like HE protein, 3a/b protein, 4a/b protein, protease, papain-like protease are found.