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Research of COVID-19 on the Bioinformatics Field
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Research of COVID-19 on the Bioinformatics Field

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 32507

Special Issue Editors

Prof. Dr. Daeui Park

E-Mail Website
Guest Editor
Korea Institute of Toxicology, University of Science and Technology, Daejeon, Republic of Korea
Interests: bioinformatics; RNA-seq; protein-protein interaction; docking simulation; emerging viruses; predictive toxicology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Semin Lee

E-Mail Website
Guest Editor
Ulsan National Institute of Science and Technology, School of Life Sciences, Department of Biomedical Engineering, 44919 Ulsan, Korea
Interests: cancer genomics; single-cell genomics; structural bioinformatics; neurological disorders
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Coronavirus disease 2019 (COVID-19) is a newly emerging human infectious disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, also previously known as 2019-nCoV). Based on the rapid increase in the rate of human infection, the World Health Organization has classified the COVID-19 outbreak as a pandemic. As of 8 May 2020, more than 3,899,098 cases of COVID-19 have been confirmed in 213 countries.

Although many researchers have made great efforts to fight SARS-CoV-2, the viral origin and pathogenesis of SARS-CoV-2 are unknown and mysterious. In addition, SARS-CoV-2 has different spreading power compared with other betacorona viruses, although it is a member of betacoronavirus. Therefore, futher bioinformatic researches are required to understand SARS-CoV-2 and COVID-19.

In this context, we would like to invite reviews and original articles that focus on understanding SARS-CoV-2 and COVID-19 based on bioinformatics approach or combined computational-experimental approach. In addition, the articles associated with virus origin, virus diagnosis, antiviral agents (such as chemical, antibody, biologics, and vaccine), virus-host interaction, and immunology are requested for this Special Issue.

Prof. Dr. Daeui Park
Prof. Dr. Semin Lee
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Phylogenetic analysis
  • Next generation sequence analysis
  • Structure
  • Virus-Host interaction
  • Immunology
  • Antiviral agents
  • Vaccine
  • Virus diagnosis

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Published Papers (3 papers)

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Research

18 pages, 8214 KiB  
Article
Role of SARS-CoV-2 in Altering the RNA-Binding Protein and miRNA-Directed Post-Transcriptional Regulatory Networks in Humans
by Rajneesh Srivastava, Swapna Vidhur Daulatabad, Mansi Srivastava and Sarath Chandra Janga
Int. J. Mol. Sci. 2020, 21(19), 7090; https://doi.org/10.3390/ijms21197090 - 25 Sep 2020
Cited by 36 | Viewed by 6303
Abstract
The outbreak of a novel coronavirus SARS-CoV-2 responsible for the COVID-19 pandemic has caused a worldwide public health emergency. Due to the constantly evolving nature of the coronaviruses, SARS-CoV-2-mediated alterations on post-transcriptional gene regulations across human tissues remain elusive. In this study, we [...] Read more.
The outbreak of a novel coronavirus SARS-CoV-2 responsible for the COVID-19 pandemic has caused a worldwide public health emergency. Due to the constantly evolving nature of the coronaviruses, SARS-CoV-2-mediated alterations on post-transcriptional gene regulations across human tissues remain elusive. In this study, we analyzed publicly available genomic datasets to systematically dissect the crosstalk and dysregulation of the human post-transcriptional regulatory networks governed by RNA-binding proteins (RBPs) and micro-RNAs (miRs) due to SARS-CoV-2 infection. We uncovered that 13 out of 29 SARS-CoV-2-encoded proteins directly interacted with 51 human RBPs, of which the majority of them were abundantly expressed in gonadal tissues and immune cells. We further performed a functional analysis of differentially expressed genes in mock-treated versus SARS-CoV-2-infected lung cells that revealed enrichment for the immune response, cytokine-mediated signaling, and metabolism-associated genes. This study also characterized the alternative splicing events in SARS-CoV-2-infected cells compared to the control, demonstrating that skipped exons and mutually exclusive exons were the most abundant events that potentially contributed to differential outcomes in response to the viral infection. A motif enrichment analysis on the RNA genomic sequence of SARS-CoV-2 clearly revealed the enrichment for RBPs such as SRSFs, PCBPs, ELAVs, and HNRNPs, suggesting the sponging of RBPs by the SARS-CoV-2 genome. A similar analysis to study the interactions of miRs with SARS-CoV-2 revealed functionally important miRs that were highly expressed in immune cells, suggesting that these interactions may contribute to the progression of the viral infection and modulate the host immune response across other human tissues. Given the need to understand the interactions of SARS-CoV-2 with key post-transcriptional regulators in the human genome, this study provided a systematic computational analysis to dissect the role of dysregulated post-transcriptional regulatory networks controlled by RBPs and miRs across tissue types during a SARS-CoV-2 infection. Full article
(This article belongs to the Special Issue Research of COVID-19 on the Bioinformatics Field)
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25 pages, 1832 KiB  
Article
Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection
by Mathieu Gand, Kevin Vanneste, Isabelle Thomas, Steven Van Gucht, Arnaud Capron, Philippe Herman, Nancy H. C. Roosens and Sigrid C. J. De Keersmaecker
Int. J. Mol. Sci. 2020, 21(15), 5585; https://doi.org/10.3390/ijms21155585 - 4 Aug 2020
Cited by 22 | Viewed by 6831
Abstract
The current COronaVIrus Disease 2019 (COVID-19) pandemic started in December 2019. COVID-19 cases are confirmed by the detection of SARS-CoV-2 RNA in biological samples by RT-qPCR. However, limited numbers of SARS-CoV-2 genomes were available when the first RT-qPCR methods were developed in January [...] Read more.
The current COronaVIrus Disease 2019 (COVID-19) pandemic started in December 2019. COVID-19 cases are confirmed by the detection of SARS-CoV-2 RNA in biological samples by RT-qPCR. However, limited numbers of SARS-CoV-2 genomes were available when the first RT-qPCR methods were developed in January 2020 for initial in silico specificity evaluation and to verify whether the targeted loci are highly conserved. Now that more whole genome data have become available, we used the bioinformatics tool SCREENED and a total of 4755 publicly available SARS-CoV-2 genomes, downloaded at two different time points, to evaluate the specificity of 12 RT-qPCR tests (consisting of a total of 30 primers and probe sets) used for SARS-CoV-2 detection and the impact of the virus’ genetic evolution on four of them. The exclusivity of these methods was also assessed using the human reference genome and 2624 closely related other respiratory viral genomes. The specificity of the assays was generally good and stable over time. An exception is the first method developed by the China Center for Disease Control and prevention (CDC), which exhibits three primer mismatches present in 358 SARS-CoV-2 genomes sequenced mainly in Europe from February 2020 onwards. The best results were obtained for the assay of Chan et al. (2020) targeting the gene coding for the spiking protein (S). This demonstrates that our user-friendly strategy can be used for a first in silico specificity evaluation of future RT-qPCR tests, as well as verifying that the former methods are still capable of detecting circulating SARS-CoV-2 variants. Full article
(This article belongs to the Special Issue Research of COVID-19 on the Bioinformatics Field)
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17 pages, 18422 KiB  
Article
Potential Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 606 Million Compounds
by André Fischer, Manuel Sellner, Santhosh Neranjan, Martin Smieško and Markus A. Lill
Int. J. Mol. Sci. 2020, 21(10), 3626; https://doi.org/10.3390/ijms21103626 - 21 May 2020
Cited by 117 | Viewed by 16892
Abstract
The rapid outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China followed by its spread around the world poses a serious global concern for public health. To this date, no specific drugs or vaccines are available to treat SARS-CoV-2 [...] Read more.
The rapid outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China followed by its spread around the world poses a serious global concern for public health. To this date, no specific drugs or vaccines are available to treat SARS-CoV-2 despite its close relation to the SARS-CoV virus that caused a similar epidemic in 2003. Thus, there remains an urgent need for the identification and development of specific antiviral therapeutics against SARS-CoV-2. To conquer viral infections, the inhibition of proteases essential for proteolytic processing of viral polyproteins is a conventional therapeutic strategy. In order to find novel inhibitors, we computationally screened a compound library of over 606 million compounds for binding at the recently solved crystal structure of the main protease (Mpro) of SARS-CoV-2. A screening of such a vast chemical space for SARS-CoV-2 Mpro inhibitors has not been reported before. After shape screening, two docking protocols were applied followed by the determination of molecular descriptors relevant for pharmacokinetics to narrow down the number of initial hits. Next, molecular dynamics simulations were conducted to validate the stability of docked binding modes and comprehensively quantify ligand binding energies. After evaluation of potential off-target binding, we report a list of 12 purchasable compounds, with binding affinity to the target protease that is predicted to be more favorable than that of the cocrystallized peptidomimetic compound. In order to quickly advise ongoing therapeutic intervention for patients, we evaluated approved antiviral drugs and other protease inhibitors to provide a list of nine compounds for drug repurposing. Furthermore, we identified the natural compounds (−)-taxifolin and rhamnetin as potential inhibitors of Mpro. Rhamnetin is already commercially available in pharmacies. Full article
(This article belongs to the Special Issue Research of COVID-19 on the Bioinformatics Field)
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