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Journal of Receptor and Signal... Dec 2020Recently, a pathogen has been identified as a novel coronavirus (SARS-CoV-2) and found to trigger novel pneumonia (COVID-19) in human beings and some other mammals. The...
Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/NSP16 methyltransferase and main protease of SARS CoV-2.
Recently, a pathogen has been identified as a novel coronavirus (SARS-CoV-2) and found to trigger novel pneumonia (COVID-19) in human beings and some other mammals. The uncontrolled release of cytokines is seen from the primary stages of symptoms to last acute respiratory distress syndrome (ARDS). Thus, it is necessary to find out safe and effective drugs against this deadly coronavirus as soon as possible. Here, we downloaded the three-dimensional model of NSP10/NSP16 methyltransferase (PDB-ID: 6w6l) and main protease (PDB-ID: 6lu7) of COVID-19. Using these molecular models, we performed virtual screening with our anti-viral, inti-infectious, and anti-protease compounds, which are attractive therapeutics to prevent infection of the COVID-19. We found that top screened compound binds with protein molecules with good dock score with the help of hydrophobic interactions and hydrogen bonding. We observed that protease complexed with Cyclocytidine hydrochloride (anti-viral and anti-cancer), Trifluridine (anti-viral), Adonitol, and Meropenem (anti-bacterial), and Penciclovir (anti-viral) bound with a good docking score ranging from -6.8 to -5.1 (Kcal/mol). Further, NSP10/NSP16 methyltransferase complexed with Telbivudine, Oxytetracycline dihydrate (anti-viral), Methylgallate (anti-malarial), 2-deoxyglucose and Daphnetin (anti-cancer) from the docking score of -7.0 to -5.7 (Kcal/mol). In conclusion, the selected compounds may be used as a novel therapeutic agent to combat this deadly pandemic disease, SARS-CoV-2 infection, but needs further experimental research.HighlightsNSP10/NSP16 methyltransferase and main protease complex of SARS CoV-2 bind with selected drugs.NSP10/NSP16 methyltransferase and protease interacted with drugs by hydrophobic interactions.Compounds show good DG binging free energy with protein complexes.Ligands were found to follow the Lipinski rule of five.
Topics: Acyclovir; Ancitabine; Antiviral Agents; Betacoronavirus; COVID-19; Coronavirus Infections; Drug Evaluation, Preclinical; Guanine; Humans; Meropenem; Methyltransferases; Models, Molecular; Molecular Docking Simulation; Pandemics; Pneumonia, Viral; Protein Conformation; Ribitol; SARS-CoV-2; Trifluridine; User-Computer Interface; Viral Nonstructural Proteins; Viral Regulatory and Accessory Proteins
PubMed: 32476594
DOI: 10.1080/10799893.2020.1772298 -
Archives of Microbiology Sep 2022A novel marine Gram-stain-negative, aerobic, rod-shaped bacterium, designated as strain PS1, was isolated from the deep-sea sediments of the Mariana Trench and...
A novel marine Gram-stain-negative, aerobic, rod-shaped bacterium, designated as strain PS1, was isolated from the deep-sea sediments of the Mariana Trench and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 35 °C (ranging 10-45 °C), pH 6 (ranging pH 5-10) and with 11% (w/v) NaCl (ranging 0-17%). The 16S rRNA gene sequence similarity results revealed that strain PS1 was most closely related to Pseudomonas stutzeri ATCC 17588, Pseudomonas nitrititolerans GL14, Pseudomonas zhaodongensis NEAU-ST5-21, Pseudomonas xanthomarina DSM 18231 and Pseudomonas kunmingensis HL22-2 with 98.3-98.7%. The digital DNA-DNA hybridization values and the average nucleotide identity between strain PS1 and the reference strains were 20.4-40.1% and 78.7-79.4%, respectively. The major respiratory quinone is ubiquinone Q-9. The major polar lipids were phosphatidylethanolamine, diphosphatidyglycerol, phosphatidylglycerol, phosphatidylcholine, aminoglycolipid, two unidentified glycolipids and one unidentified lipid. The predominant cellular fatty acids of strain PS1 were summed feature 8 (Cω7c and/or Cω6c), summed feature 3 (Cω7c and/or Cω6c), C and cyclo-C ω8c. The G + C content of the genomic DNA was 63.0%. The combined genotypic and phenotypic data indicated that strain PS1 represents a novel species of the genus Pseudomonas, for which the name Pseudomonas marianensis sp. nov. is proposed, with the type strain PS1 (= DSM 112238 = MCCC 1K05112).
Topics: Ancitabine; Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Glycolipids; Nucleotides; Phosphatidylcholines; Phosphatidylethanolamines; Phosphatidylglycerols; Phospholipids; Phylogeny; Pseudomonas; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sodium Chloride; Ubiquinone
PubMed: 36131209
DOI: 10.1007/s00203-022-03250-9 -
PeerJ 2022Cyclocytidine hydrochloride (HCl) has been reported to inhibit DNA synthesis by affecting DNA polymerase. Here, we tested the antiviral effect of cyclocytidine on...
BACKGROUND
Cyclocytidine hydrochloride (HCl) has been reported to inhibit DNA synthesis by affecting DNA polymerase. Here, we tested the antiviral effect of cyclocytidine on hepatitis B virus (HBV) DNA synthesis, which is reliant on DNA polymerase activity.
MATERIALS AND METHODS
Cyclocytidine HCl was treated to HBV-producing HepAD38 cells or added to an endogenous polymerase reaction, and HBV DNA was detected by Southern blot.
RESULTS
Treatment of 20 µM cyclocytidine HCl significantly decreased the production of relaxed circular (rc) DNA in HepAD38 cells and block rcDNA synthesis in endogenous polymerase reaction (EPR), a cell free assay, possibly by inhibiting the HBV DNA polymerase activity.
CONCLUSION
Cyclocytidine HCl could inhibit the synthesis of HBV rcDNA, the precursor of covalently closed circular DNA, and this result provides a case for the usage of "old" drugs for "new" applications.
Topics: Ancitabine; DNA, Circular; DNA, Viral; DNA-Directed DNA Polymerase; Hepatitis B virus; Virus Replication
PubMed: 35846878
DOI: 10.7717/peerj.13719