Considering epitopes conservity in targeting SARS-CoV-2 mutations in variants: a novel immunoinformatics approach to vaccine design DOI Creative Commons
Mohammad Aref Bagherzadeh, Mohammad Izadi, Kazem Baesi

et al.

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Aug. 18, 2022

Abstract Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has gained mutations at an alarming rate in the past years. Developing can increase virus's pathogenicity and virulence; reduce efficacy of vaccines, antibodies neutralization, even challenge adaptive immunity. So, it is essential to identify conserved epitopes (with fewer mutations) different variants with appropriate antigenicity target by vaccine design. Yet as, 3369 SARS-CoV-2 genomes were collected from global initiative on sharing avian flu data. Then, immunodominant regions (IDRs), immune epitope database (IEDB) epitopes, also predicted calculated. In following, conservity score against total number events (mutations) mutated sites each was weighted Shannon entropy then calculated Technique for Order Preference Similarity Ideal Solution (TOPSIS). Based TOPSIS score, plotted. The result demonstrates that almost all IDRs various lengths have numbers dissimilar sites. Herein, our two-step calculation recommends only 8 IDRs, 14 IEDB 10 among epitopes. selected ones higher immunogenicity. This method open-source multi-criteria decision-making platform, which provides a scientific approach selecting immunogenicity; ever-changing viruses.

Language: Английский

Identification of potential plant bioactive as SARS-CoV-2 Spike protein and human ACE2 fusion inhibitors DOI Open Access
Rahul Singh, Vijay Kumar Bhardwaj, Jatin Sharma

et al.

Computers in Biology and Medicine, Journal Year: 2021, Volume and Issue: 136, P. 104631 - 104631

Published: July 8, 2021

Language: Английский

Citations

96
In-silico evaluation of bioactive compounds from tea as potential SARS-CoV-2 nonstructural protein 16 inhibitors DOI Creative Commons
Rahul Singh, Vijay Kumar Bhardwaj, Jatin Sharma

et al.

Journal of Traditional and Complementary Medicine, Journal Year: 2021, Volume and Issue: 12(1), P. 35 - 43

Published: June 3, 2021

A novel coronavirus, called the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been found to cause COVID-19 in humans and some other mammals. The nonstructural protein 16 (NSP16) of SARS-CoV-2 plays a significant part replication viruses suppresses ability innate immune system detect virus. Therefore, inhibiting NSP16 can be secure path towards identifying potent medication against SARS-CoV-2. Tea (

Language: Английский

Citations

84
Potential of turmeric-derived compounds against RNA‐dependent RNA polymerase of SARS‐CoV‐2: An in-silico approach DOI Open Access
Rahul Singh, Vijay Kumar Bhardwaj, Rituraj Purohit

et al.

Computers in Biology and Medicine, Journal Year: 2021, Volume and Issue: 139, P. 104965 - 104965

Published: Oct. 22, 2021

Language: Английский

Citations

76
A computational approach for rational discovery of inhibitors for non-structural protein 1 of SARS-CoV-2 DOI Open Access
Rahul Singh, Vijay Kumar Bhardwaj, Pralay Das

et al.

Computers in Biology and Medicine, Journal Year: 2021, Volume and Issue: 135, P. 104555 - 104555

Published: June 8, 2021

Language: Английский

Citations

67
Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2 DOI Creative Commons
Kaifu Gao, Rui Wang, Jiahui Chen

et al.

Chemical Reviews, Journal Year: 2022, Volume and Issue: 122(13), P. 11287 - 11368

Published: May 20, 2022

Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component combating disease 2019 (COVID-19) due to their low cost, efficiency, fact that they are free from safety ethical constraints. Additionally, mechanism governs global transmission SARS-CoV-2 cannot be revealed individual experiments was discovered by integrating genotyping massive viral sequences, biophysical modeling protein-protein deep mutational data, learning, advanced mathematics. There exists a tsunami literature on molecular modeling, simulations, predictions related developments drugs, vaccines, antibodies, diagnostics. To provide readers with quick update about this literature, we present comprehensive systematic methodology-centered review. Aspects such as biophysics, bioinformatics, cheminformatics, machine mathematics discussed. review will beneficial researchers who looking ways contribute those interested status field.

Language: Английский

Citations

58
Identification of RdRp inhibitors against SARS-CoV-2 through E-pharmacophore-based virtual screening, molecular docking and MD simulations approaches DOI Open Access
Hafiz Muzzammel Rehman, Muhammad Sajjad, Muhammad Akhtar Ali

et al.

International Journal of Biological Macromolecules, Journal Year: 2023, Volume and Issue: 237, P. 124169 - 124169

Published: March 28, 2023

Language: Английский

Citations

26
Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease DOI Open Access
Marina Macchiagodena, Marco Pagliai, Piero Procacci

et al.

Journal of Molecular Graphics and Modelling, Journal Year: 2021, Volume and Issue: 110, P. 108042 - 108042

Published: Oct. 5, 2021

Language: Английский

Citations

42
Benchmarking the ability of novel compounds to inhibit SARS-CoV-2 main protease using steered molecular dynamics simulations DOI
Rahul Singh, Vijay Kumar Bhardwaj, Pralay Das

et al.

Computers in Biology and Medicine, Journal Year: 2022, Volume and Issue: 146, P. 105572 - 105572

Published: April 29, 2022

Language: Английский

Citations

34
Real-Word Effectiveness of Global COVID-19 Vaccines Against SARS-CoV-2 Variants: A Systematic Review and Meta-Analysis DOI Creative Commons
Kai Wang, Lin Wang, Mingzhe Li

et al.

Frontiers in Medicine, Journal Year: 2022, Volume and Issue: 9

Published: May 19, 2022

Background Currently, promoted vaccinations against SARS-CoV-2 are being given out globally. However, the occurrence of numerous COVID-19 variants has hindered goal rapid mitigation pandemic by effective mass vaccinations. The real-word effectiveness current vaccines not been assessed published reviews. Therefore, our study evaluated overall and differences between various variants. Methods PubMed, Embase, Cochrane Library, medRxiv, bioRxiv, arXiv were searched to screen eligible studies. Newcastle–Ottawa scale Egger test applied estimate quality literature any publication bias, respectively. pooled incident rates different after vaccination estimated single-arm analysis. Meanwhile, efficacies two-arm analysis using odds ratios (ORs) vaccine (VE). Results A total 6,118 studies identified initially 44 articles included. We found that incidence post first/second 0.07 0.03, VE first placebo or unvaccinated population was 40% second 96%, sub-single-arm showed a low prevalence rate specific with below 0.10 in most subgroups. sub-two-arm indicated had good moderate preventive effect on certain considering these subgroups 66 95%, which broadly line results Conclusion Our meta-analysis shows used globally could prevent infection restrict spread great extent. would also support maximizing uptake two doses, as more marked compared one dose. Although mRNA according study, should be taken into account based local dominant

Language: Английский

Citations

33
SARS-CoV-2 neutralizing activity of polyphenols in a special green tea extract preparation DOI Creative Commons
Eva Kicker,

G. Tittel,

Tanja Schaller

et al.

Phytomedicine, Journal Year: 2022, Volume and Issue: 98, P. 153970 - 153970

Published: Jan. 30, 2022

The COVID-19 pandemic will continue to threaten our health care systems in the next years. In addition vaccination there is a need for effective tools prevention and treatment. Products from natural sources, like standardized plant extracts offer wide range of antiviral effects possible applications.

Language: Английский

Citations

30