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Lattice Paths for Persistent Diagrams [article]

Moo K. Chung, Hernando Ombao
2021 arXiv   pre-print
The lattice path method is applied to the topological characterization of the protein structures of the COVID-19 virus.  ...  We demonstrate that there are topological changes during the conformational change of spike proteins.  ...  Acknowledgement The illustration of COVID-19 virus (Figure 1  ... 
arXiv:2105.00351v5 fatcat:ddas5dctmnhzxjcnj5tec7wcay

Energetics and IC50 based epitope screening in SARS CoV-2 (COVID 19) spike protein by immunoinformatic analysis implicating for a suitable vaccine development

Amrita Banerjee, Dipannita Santra, Smarajit Maiti
2020 Journal of Translational Medicine  
We screened here few pairs of spike protein epitopic regions and selected their energetic, Inhibitory Concentration50 (IC50), MHC II reactivity and found some of those to be very good target for vaccination  ...  Few attempts have been made to develop a suitable vaccine or ACE2 blocker or virus-receptor inhibitor within this short period of time.  ...  or COVID 19 spike protein (Acc.  ... 
doi:10.1186/s12967-020-02435-4 pmid:32650788 fatcat:eyuwlwk6cvd5rhmpcjvqbbflg4

Energetics based epitope screening in SARS CoV-2 (COVID 19) spike glycoprotein by Immuno-informatic analysis aiming to a suitable vaccine development [article]

Amrita Banerjee, Dipannita Santra, Smarajit Maiti
2020 bioRxiv   pre-print
We screened here few pairs of spike protein epitopic regions and selected their energetic, IC50, MHC II reactivity and found some of those to be very good target for vaccination.  ...  Few attempts have been made to develop a suitable vaccine or ACE2 blocker or virus-receptor inhibitor within this short period of time.  ...  on COVID 2 or COVID 19 spike protein (Acc.  ... 
doi:10.1101/2020.04.02.021725 fatcat:qybdr2dhdjhsxkleh2sztyjlnq

New COVID-19 Strain (SARS-Cov-2 VUI 202012/01): Lurking Challenge

Shivani Singh, Sharique Ahmad, Saeeda Wasim, Silky Rai, Sudarshana Gogoi, Zarina Farheen
2021 Cross Current International Journal of Medical and Biosciences  
As there is not any phenotypic data for the of variant of COVID-19 but structural analysis of COVID-19 had been identified it consist envelope, membrane, nucleocapsid and spike protein beside all of these  ...  Genome of this virus consist structural protein spike, envelope, membrane and nucleocapsid among all of them spike protein is majorly involve in understanding the COVID-19 associated disease mechanism.  ... 
doi:10.36344/ccijmb.2021.v03i02.001 fatcat:o3qtg5tzcva73irfplhfgcxndm

Material Basis and Mechanism of Chansu Injection for COVID-19 Treatment Based on Network Pharmacology and Molecular Docking Technology

Yong Xu, Wenpan Peng, Di Han, Zhichao Wang, Fanchao Feng, Xianmei Zhou, Qi Wu, Talha Bin Emran
2021 Evidence-Based Complementary and Alternative Medicine  
The STRING database was used for protein-protein interaction (PPI) network construction and topological analysis, while DAVID was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes  ...  The clinical efficacy of Chansu injection for COVID-19 treatment has been confirmed. Its mechanism of action remains unclear.  ...  Colleges and Universities (integration of Chinese and Western medicine).  ... 
doi:10.1155/2021/7697785 pmid:34671410 pmcid:PMC8523246 fatcat:ue2ufuhdrrcmhitnplhienmmf4

Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine [article]

Mst Rubaiat Nazneen Akhand, Kazi Faizul Azim, Syeda Farjana Hoque, Mahmuda Akther Moli, Bijit Das Joy, Hafsa Akter, Ibrahim Khalil Afif, Nadim Ahmed, Mahmudul Hasan
2020 bioRxiv   pre-print
Conserved regions from the homologous protein sets of spike glycoprotein (S), membrane protein (M), envelope protein and nucleocapsid protein (N) were identified through multiple sequence alignment.  ...  The development of preventive measures to combat COVID-19 infections might be aided the present study.  ...  Computational analysis of secondary structures shows some variations of COVID-19 with SARS-CoV-1 and MERS virus (Supplementary File 3).  ... 
doi:10.1101/2020.04.15.036285 fatcat:flpgnymegrg3liq7cvlv4jbdha

Therapeutic development by repurposing drugs targeting SARS-CoV-2 spike protein interactions by simulation studies

Qazi Mohammad Sajid Jamal, Varish Ahmad, Ali H Alharbi, Mohammad Azam Ansari, Mohammad A Alzohairy, Ahmad Almatroudi, Saad Alghamdi, Mohammad N Alomary, Sami AlYahya, Nashwa Talaat Shesha, Suriya Rehman
2021 Saudi journal of biological sciences  
The results have suggested that doxorubicin could inhibit the virus spike protein and prevent the access of the SARS-CoV-2 to the host cell.  ...  The human-to-human transmitted respiratory illness in COVID-19 affected by the pathogenic Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2), which appeared in the last of December 2019 in Wuhan  ...  Funding: Deanship of Scientific Research, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia, Grant number-Covid19-2020-002-IRMC.  ... 
doi:10.1016/j.sjbs.2021.04.057 pmid:33935562 pmcid:PMC8079265 fatcat:gmo532t3djhx7ewzfzncobylt4

Geraniin Inhibits the Entry of SARS-CoV-2 by Blocking the Interaction between Spike Protein RBD and Human ACE2 Receptor

Young Soo Kim, Hwan-Suck Chung, Sang Gyun Noh, Bonggi Lee, Hae Young Chung, Jang-Gi Choi
2021 International Journal of Molecular Sciences  
The SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme 2 (hACE2) receptor to initiate virus entry into cells; viral entry may be an important target of COVID-19 therapeutics.  ...  Despite the development of vaccines, the emergence of SARS-CoV-2 variants and the absence of effective therapeutics demand the continual investigation of COVID-19.  ...  of COVID-19 a serious challenge.  ... 
doi:10.3390/ijms22168604 pmid:34445310 pmcid:PMC8395245 fatcat:tqzyfcwrn5c4bb6vwo5piver3m

A Drug Repurposing Approach Towards Elucidating the Potential of Flavonoids as COVID-19 Spike Protein Inhibitors

2020 Biointerface Research in Applied Chemistry  
In our study, we have selected nine Flavonoids for the inhibition of COVID-19 Spike protein, which have already been reported with their antiviral efficacies against other virus-infected diseases.  ...  Therefore our experimental findings strongly suggested that baicalin can be used as a potential inhibitor against COVID-19 spike protein, which could inhibit the interaction of the virus with the host  ...  Acknowledgments The authors thank the management of Noida Institute of Engineering & Technology and Lucknow University for providing the facilities to carry out this study.  ... 
doi:10.33263/briac111.84828501 fatcat:yvise45kfbc4blltu347qvntzy

Sequence and structural analysis of COVID-19 E and M protein with MERS virus E and M protein—A comparative study

Ebtisam A. Aldaais, Subha Yegnaswamy, Fatimah Albahrani, Fatima Alsowaiket, Sarah Alramadan
2021 Biochemistry and Biophysics Reports  
The sequence analysis of conserved regions of both E and M proteins revealed that many regions of COVID-19 are similar to Bat and SARS viruses while the MERS virus showed variations.  ...  The COVID-19 belongs to the beta coronavirus family encoding 29 proteins, of which four are structural, the Spike, Membrane, Envelope, and Nucleocapsid proteins.  ...  The motif scan in the MERS virus showed E protein structure Only the structure of the Spike protein was available for all viruses in the protein data bank.  ... 
doi:10.1016/j.bbrep.2021.101023 pmid:34013072 pmcid:PMC8120451 fatcat:oqbgxzqd55ccxnuuct2pna6hfu

Viroinformatics approach to explore the inhibitory mechanism of existing drugs repurposed to fight against COVID-19

Nousheen Bibi, Sana Gul, Johar Ali, Mohammad Amjad Kamal
2020 European Journal of Pharmacology  
Here we implied the molecular docking and dynamic simulations with emphasis on the unique structural properties of host receptor angiotensin-converting enzyme 2 (ACE2), SARS-CoV2 spike protein and RNA  ...  The rapid breakout of the coronavirus disease of 2019 (COVID-19) has been declared pandemic with serious global concern due to high morbidity and mortality.  ...  spike-RBD (virus) and human ACE2 receptor protein.  ... 
doi:10.1016/j.ejphar.2020.173496 pmid:32841640 pmcid:PMC7443089 fatcat:wxj7l5feb5cs7msmkgn5gpaxme

Repurposing cefuroxime for treatment of COVID-19: a scoping review of in silico studies

Ashimiyu B. Durojaiye, John-Ross D. Clarke, George A. Stamatiades, Can Wang
2020 Journal of Biomolecular Structure and Dynamics  
These studies reported Cefuroxime as a potential inhibitor of 3 key SARS-CoV-2 proteins; main protease, RNA dependent RNA polymerase, and ACE2-Spike complex.  ...  Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus disease 19 (COVID-19), is a novel human Coronavirus that is responsible for about 300,000 deaths worldwide  ...  However, preliminary data analysis from a National Institutes of Health (NIH) sponsored randomized clinical trial (RCT) for Remdesivir involving patients with advanced COVID-19 suggested that patients  ... 
doi:10.1080/07391102.2020.1777904 pmid:32538276 pmcid:PMC7298880 fatcat:jqdk2gcxurgqbnf42x6raozgwi

Mutations in the SARS CoV-2 spike protein may cause functional changes in the protein quaternary structure

Ekrem Akbulut
2021 Turk biyokimya dergisi = Turkish journal of biochemistry  
Structural analysis of spike proteins was done using bioinformatics tools (MAFFT, PSIPRED, ProMod3, PyMoL and DynOmics).ResultsWe identified 76 Thr>Ile mutations in the N-terminal domain; 468 Ile>Val mutations  ...  It has been observed that the mutations, except those of residues 771 and 772, may cause significant conformational, topological and electrostatic changes in a protein quaternary structure.  ...  Acknowledgement: We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID's EpiFlu™ Database on which this research is based.  ... 
doi:10.1515/tjb-2020-0290 fatcat:iwuiipujibhefal4trkncy6bye

In-depth Sequence Analysis of SARS-CoV-2 Spike Protein Repudiates Mutation Mediated Adaptive Selection in the Virus

Pramita Chowdhury, Bijurica Chakraborty, Sanghamitra Sengupta
2020 ACTA SCIENTIFIC MICROBIOLOGY  
As of May 06, 2020, over 3.66 million cases of COVID-19 have been reported, with > 2,57,000 deaths worldwide.  ...  "In-depth Sequence Analysis of SARS-CoV-2 Spike Protein Repudiates Mutation Mediated Adaptive Selection in the Virus". Acta Scientific Microbiology 3.12 (2020): 16-23.  ...  Conflict of Interests None.  ... 
doi:10.31080/asmi.2020.03.0729 fatcat:54e67ljvovccxhphmpsettmhr4

Network-based analysis revealed significant interactions between risk genes of severe COVID-19 and host genes interacted with SARS-CoV-2 proteins

Hao-xiang Qi, Qi-dong Shen, Hong-yi Zhao, Guo-zhen Qi, Lei Gao
2021 Briefings in Bioinformatics  
Our analysis provided insights for the underlying genetic etiology of severe COVID-19 from the perspective of network biology.  ...  Besides, by expression enrichment analysis in single-cell RNA-seq data, compared with mild COVID-19, these genes were significantly enriched in macrophage, T cell and epithelial cell for severe COVID-19  ...  Acknowledgements We thank all the members who shared GWAS data in COVID-19 host genetics initiative.  ... 
doi:10.1093/bib/bbab372 pmid:34535795 fatcat:ckl7wmn5dfdv5oqmdvf56i5n5m
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