Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target

Diagnosing COVID-19: diagnostic importance of detecting E gene of the SARS-CoV-2 genome

Aim: To evaluate the significance of E gene analysis in addition to N and RdRp genes of SARS-CoV-2, and to compare the specificity and sensitivity of targets. Materials & methods: We used two reverse transcription-PCR assays: one targeting N, E and RdRp and the other targeting N and RdRp genes and analyzed variation in threshold cycle (Ct) values. Results: Of the 155 samples, 70.32% tested positive: all three genes were detected in 45.87%, N and RdRp in 19.27% and only N in 34.86%. Patients negative for the E gene were tested after symptoms disappeared and Ct values were significantly higher. Conclusion: Samples negative for the E gene were potentially false positive and clinical conditions should be assessed while interpreting results.

Molecular and Structural Analysis of Specific Mutations from Saudi Isolates of SARS-CoV-2 RNA-Dependent RNA Polymerase and their Implications on Protein Structure and Drug-Protein Binding

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has stressed the global health system to a significant level, which has not only resulted in high morbidity and mortality but also poses a threat for future pandemics. This situation warrants efforts to develop novel therapeutics to manage SARS-CoV-2 in specific and other emerging viruses in general. This study focuses on SARS-CoV2 RNA-dependent RNA polymerase (RdRp) mutations collected from Saudi Arabia and their impact on protein structure and function. The Saudi SARS-CoV-2 RdRp sequences were compared with the reference Wuhan, China RdRp using a variety of computational and biophysics-based approaches. The results revealed that three mutations-A97V, P323I and Y606C-may affect protein stability, and hence the relationship of protein structure to function. The apo wild RdRp is more dynamically stable with compact secondary structure elements compared to the mutants. Further, the wild type showed stable conformational dynamics and interaction network to remdesivir. The net binding energy of wild-type RdRp with remdesivir is -50.76 kcal/mol, which is more stable than the mutants. The findings of the current study might deliver useful information regarding therapeutic development against the mutant RdRp, which may further furnish our understanding of SARS-CoV-2 biology.

Development of a database of RNA helicase inhibitors (VHIMDB) of pathogenic viruses and in silico screening for the potential drug molecules

The pathogenic RNA virus that infects human beings contains the RNA helicase enzyme, responsible for the replication of the viral genome. The enzyme is used as a suitable target against which the drug molecule acts. Therefore, the identification and proposal the novel compounds that can be targeted toward the helicase enzymes to stop the functioning of the enzyme is desirable. Although many viral helicase inhibitor molecules have been identified, still yet no unique database is available for these compounds. This research work envisages developing a curated database of RNA helicase inhibitors. The database contains in total of 353 entries that are computationally predicted and experimentally verified RNA helicase inhibitors. The database contains information like compound name, chemical properties, chemical format, and name of the target virus to which it acts against it with a user-friendly menu-driven search engine. Presently, the database is freely available at: https://vhimdb.rsatpathy.in/. Further, in silico screening of the whole database by drug-likeness and toxicity resulted in 14 potential drug molecules. The selected molecules were analyzed for their effectiveness in binding by using molecular docking score and interaction with the helicase enzymes of three categories of pathogenic viruses (SARS-CoV-2, SARS-CoV, and MERS-CoV).

Genome sequence analysis of nsp15 from SARS-CoV-2

SARS-CoV-2 (Severe Acute Respiratory Syndrome), a causative agent of COVID-19 disease created a pandemic situation worldwide. Nsp15 is a uridine specific endoribonuclease encoded by the genome of SARS-CoV-2. It plays important role in processing viral RNA and, thus evades the host immune system. Therefore, it is of interest to identify mutants of nsp15 amongst Asian SARS-CoV-2 isolates, where a total of 1795 mutations, from 7793 sequences of Asia submitted till 31st January 2022, amongst which A231V, H234Y, K109N, K259R and S261A mutations were found frequent. Hence, we report data on the predicted secondary structure of wild type form followed by hydropathy plot, physiochemical properties, Ramachandran plot, B-cell epitopes prediction and protein modeling of wild type and mutant of nsp15 protein. Data shows that nsp15 of SARS-CoV-2 is a pontential candidate for the development of vaccine to control the infections of SARS-CoV-2.

Search and sequence analysis tools services from EMBL-EBI in 2022

The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI’s data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.

Theoretical insights into the effect of halogenated substituent on the electronic structure and spectroscopic properties of the favipiravir tautomeric forms and its implications for the treatment of COVID-19

In this study, we systematically investigated the electronic structure, spectroscopic (nuclear magnetic resonance, infrared, Raman, electron ionization mass spectrometry, UV-Vis, circular dichroism, and emission) properties, and tautomerism of halogenated favipiravir compounds (fluorine, chlorine, and bromine) from a computational perspective. Additionally, the effects of hydration on the proton transfer mechanism of the tautomeric forms of the halogenated favipiravir compounds are discussed. Our results suggest that spectroscopic properties allow for the elucidation of such tautomeric forms. As is well-known, the favipiravir compound has excellent antiviral properties and hence was recently tested for the treatment of new coronavirus (SARS-CoV-2). Through in silico modeling, in the current study, we evaluate the role of such tautomeric forms in order to consider the effect of drug-metabolism in the inhibition process of the main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 virus. According to the molecular docking, all halogenated compounds presented a better interaction energy than the co-crystallized active ligand (-3.5 kcal mol-1) in the viral RdRp, in both wild-type (-6.3 to -6.5 kcal mol-1) and variant (-5.4 to -5.6 kcal mol-1) models. The variant analyzed for RdRp (Y176C) decreases the affinity of the keto form of the compounds in the active site, and prevented the ligands from interacting with RNA. These findings clearly indicated that all these compounds are promising as drug candidates for this molecular target.