Version 1
: Received: 22 May 2020 / Approved: 24 May 2020 / Online: 24 May 2020 (18:49:41 CEST)
How to cite:
Baysal, O.; Silme, R.S.; Karaaslan, C. Genetic Uniformity of a Specific Region in SARS-CoV-2 Genome and In-Silico Target-Oriented Repurposing of N-Acetyl-D-Glucosamine. Preprints2020, 2020050397. https://doi.org/10.20944/preprints202005.0397.v1
Baysal, O.; Silme, R.S.; Karaaslan, C. Genetic Uniformity of a Specific Region in SARS-CoV-2 Genome and In-Silico Target-Oriented Repurposing of N-Acetyl-D-Glucosamine. Preprints 2020, 2020050397. https://doi.org/10.20944/preprints202005.0397.v1
Baysal, O.; Silme, R.S.; Karaaslan, C. Genetic Uniformity of a Specific Region in SARS-CoV-2 Genome and In-Silico Target-Oriented Repurposing of N-Acetyl-D-Glucosamine. Preprints2020, 2020050397. https://doi.org/10.20944/preprints202005.0397.v1
APA Style
Baysal, O., Silme, R.S., & Karaaslan, C. (2020). Genetic Uniformity of a Specific Region in SARS-CoV-2 Genome and In-Silico Target-Oriented Repurposing of N-Acetyl-D-Glucosamine. Preprints. https://doi.org/10.20944/preprints202005.0397.v1
Chicago/Turabian Style
Baysal, O., Ragip Soner Silme and Cagatay Karaaslan. 2020 "Genetic Uniformity of a Specific Region in SARS-CoV-2 Genome and In-Silico Target-Oriented Repurposing of N-Acetyl-D-Glucosamine" Preprints. https://doi.org/10.20944/preprints202005.0397.v1
Abstract
Causative agent of the viral pneumonia outbreak in the World identified as SARS-CoV2 leads to a severe respiratory illness like SARS and MERS. The pathogen spreading has turned into a pandemic dissemination and increased the mortality rate. Therefore, useful information is urgently necessary for effective control of the disease. Our study shows the existence of unvarying sequence with no mutation, including ORF1ab regions in 134 high-quality filtered genome sequences of SARS-CoV2 downloaded from the GISAID database. We have detected this sequence stability by using MAUVE analysis and pairwise alignment with Global Needleman Wunsch algorithm for each two different sequences, reciprocally. They also confirmed all these results were also with the Clustal W analysis. The first 6500 bp including ORF1ab region is an unvarying sequence. According to the highest TM-score of predicted protein structure analysis, the results showed it is very similar to spike protein of feline infectious peritonitis virus strain UU4 (PDB 6JX7) depending on amino acid sequences encoded by this unvarying region, and N-acetyl-D-glucosamine is the ligand of this protein. These results have confirmed that N-acetyl-D-glucosamine could play an important role in controlling of SARS-CoV-2. Also, our molecular docking analysis data supports a strong protein-ligand interaction of N-acetyl-D-glucosamine with spike receptor-binding domain bound with ACE2 (PDB 6M0J) and RNA-binding domain of nucleocapsid phosphoprotein (PDB 6WKP) from SARS CoV-2. Therefore, binding of N-acetyl-D-glucosamine to these proteins could inhibit SARS CoV-2’s replication. In the present work, we have suggested providing a repurposing compound for further in vitro and in vivo studies and new insights for ongoing clinical treatments as a new strategy to control of SARS-CoV-2 infections.
SARS-CoV-2; Drug repurposing; N-acetyl-D-glucosamine; ORF1ab; Biodata mining; Protein modelling
Subject
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Commenter: Said Nadeem
The commenter has declared there is no conflict of interests.
Commenter:
The commenter has declared there is no conflict of interests.
These are all chemical synonym of same compound for N-Acetyl-D-Glucosamine’:
2 Acetamido 2 Deoxy D Glucose
2 Acetamido 2 Deoxyglucose
2-Acetamido-2-Deoxy-D-Glucose
2-Acetamido-2-Deoxyglucose
Acetylglucosamine
N Acetyl D Glucosamine
N-Acetyl-D-Glucosamine