Nucleoside Triphosphate-Nucleoside Diphosphate Transphosphorylase (Nucleoside Diphosphokinase)

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected around 13 million people and has caused more than 5.7 lakh deaths worldwide since December 2019. In the absence of FDA approved drug for its treatment, only symptomatic management is done. Methods: We attempted to uncover potential therapeutic targets of spike, helicase and RNA dependent RNA polymerase (RdRp) proteins of the SARS-CoV-2 employing computational approach. The PDB structure of spike and RdRp and predicted structure of helicase proteins were docked with 100 approved antiviral drugs, natural compounds and some other chemical compounds. Results: The anti-SARS ligands EK1 and CID_23631927, and NCGC00029283 are potential entry inhibitor as it showed affinity with immunogenic receptor binding domain (RBD) of spike protein. This RBD interacts with angiotensin converting enzyme (ACE2) receptor facilitating the entry of virion in the host cells. The FDA approved drugs including Nelfinavir, Saquinavir, Tipranavir, Setrobuvir, Indinavir and Atazanavir showed potential inhibitory activity against targeted domains and thus may act as entry or replication inhibitor or both. Furthermore, several anti-HCoV natural compounds including Amentoflavone, Rutin and Tannin are also potential entry and replication inhibitor as they showed affinity with RBD, Ploop containing nucleoside triphosphate hydrolase and catalytic domain of the respective protein. Dithymoquinone showed significant inhibitory potential against the fusion peptide of S2 domain. Importantly, Tannin, Dithymoquinone and Rutin can be extracted from Nigella sativa seeds and thus may prove to be one of the most potential anti-SARS-CoV-2 inhibitor. Conclusion: Several potential ligands were identified with already known anti-HCoVs activities. Furthermore, as our study showed that some of the ligands acted as both entry or replication inhibitor against SARS-CoV-2, it is envisaged that a combination of either inhibitors with a dual mode of action would prove to be a much desired therapeutic option against this viral infection.

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Secretory protein translocation in a neurospora crassa in vitro system. Hydrolysis of a nucleoside triphosphate is required for posttranslational translocation.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)45487-7 ◽

1987 ◽

Vol 262 (35) ◽

pp. 17031-17037

Author(s):

R Addison

Keyword(s):

Neurospora Crassa ◽

Protein Translocation ◽

Secretory Protein ◽

Nucleoside Triphosphate ◽

In Vitro System ◽

Hydrolysis Of

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Mechanism of SARS-CoV-2 polymerase stalling by remdesivir

Nature Communications ◽

10.1038/s41467-020-20542-0 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Goran Kokic ◽

Hauke S. Hillen ◽

Dimitry Tegunov ◽

Christian Dienemann ◽

Florian Seitz ◽

...

Keyword(s):

Electron Microscopy ◽

Rna Polymerase ◽

Binding Site ◽

Molecular Mechanism ◽

Active Center ◽

Rna Synthesis ◽

Active Form ◽

Nucleoside Triphosphate ◽

Rna Dependent Rna Polymerase ◽

Cryo Electron Microscopy

AbstractRemdesivir is the only FDA-approved drug for the treatment of COVID-19 patients. The active form of remdesivir acts as a nucleoside analog and inhibits the RNA-dependent RNA polymerase (RdRp) of coronaviruses including SARS-CoV-2. Remdesivir is incorporated by the RdRp into the growing RNA product and allows for addition of three more nucleotides before RNA synthesis stalls. Here we use synthetic RNA chemistry, biochemistry and cryo-electron microscopy to establish the molecular mechanism of remdesivir-induced RdRp stalling. We show that addition of the fourth nucleotide following remdesivir incorporation into the RNA product is impaired by a barrier to further RNA translocation. This translocation barrier causes retention of the RNA 3ʹ-nucleotide in the substrate-binding site of the RdRp and interferes with entry of the next nucleoside triphosphate, thereby stalling RdRp. In the structure of the remdesivir-stalled state, the 3ʹ-nucleotide of the RNA product is matched and located with the template base in the active center, and this may impair proofreading by the viral 3ʹ-exonuclease. These mechanistic insights should facilitate the quest for improved antivirals that target coronavirus replication.

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NTPDase1 Modulates Smooth Muscle Contraction in Mice Bladder by Regulating Nucleotide Receptor Activation Distinctly in Male and Female

Biomolecules ◽

10.3390/biom11020147 ◽

2021 ◽

Vol 11 (2) ◽

pp. 147

Author(s):

Romuald Brice Babou Kammoe ◽

Gilles Kauffenstein ◽

Julie Pelletier ◽

Bernard Robaye ◽

Jean Sévigny

Keyword(s):

Smooth Muscle ◽

Ex Vivo ◽

Smooth Muscle Contraction ◽

Receptor Activation ◽

Nucleoside Triphosphate ◽

Nucleotide Receptors ◽

Nerve Terminals ◽

Wild Type ◽

Nucleoside Triphosphate Diphosphohydrolase ◽

Bladder Contraction

Nucleotides released by smooth muscle cells (SMCs) and by innervating nerve terminals activate specific P2 receptors and modulate bladder contraction. We hypothesized that cell surface enzymes regulate SMC contraction in mice bladder by controlling the concentration of nucleotides. We showed by immunohistochemistry, enzymatic histochemistry, and biochemical activities that nucleoside triphosphate diphosphohydrolase-1 (NTPDase1) and ecto-5′-nucleotidase were the major ectonucleotidases expressed by SMCs in the bladder. RT-qPCR revealed that, among the nucleotide receptors, there was higher expression of P2X1, P2Y1, and P2Y6 receptors. Ex vivo, nucleotides induced a more potent contraction of bladder strips isolated from NTPDase1 deficient (Entpd1−/−) mice compared to wild type controls. The strongest responses were obtained with uridine 5′-triphosphate (UTP) and uridine 5′-diphosphate (UDP), suggesting the involvement of P2Y6 receptors, which was confirmed with P2ry6−/− bladder strips. Interestingly, this response was reduced in female bladders. Our results also suggest the participation of P2X1, P2Y2 and/or P2Y4, and P2Y12 in these contractions. A reduced response to the thromboxane analogue U46619 was also observed in wild type, Entpd1−/−, and P2ry6−/− female bladders showing another difference due to sex. In summary, NTPDase1 modulates the activation of nucleotide receptors in mouse bladder SMCs, and contractions induced by P2Y6 receptor activation were weaker in female bladders.

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A potent nucleoside triphosphate hydrolase from the parasitic protozoan Toxoplasma gondii. Purification, some properties, and activation by thiol compounds.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)32295-6 ◽

1983 ◽

Vol 258 (11) ◽

pp. 6816-6822

Author(s):

T Asai ◽

W J O'Sullivan ◽

M Tatibana

Keyword(s):

Toxoplasma Gondii ◽

Nucleoside Triphosphate ◽

Parasitic Protozoan ◽

Thiol Compounds

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Characterization of the nucleoside triphosphate phosphohydrolase (ATPase) activity of RNA synthesi termination factor p. I. Enzymatic properties and effects of inhibitors.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)40666-1 ◽

1977 ◽

Vol 252 (4) ◽

pp. 1375-1380 ◽

Cited By ~ 13

Author(s):

C Lowery ◽

J P Richardson

Keyword(s):

Atpase Activity ◽

Enzymatic Properties ◽

Nucleoside Triphosphate ◽

Termination Factor

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Role of Forward Translocation in Nucleoside Triphosphate Phosphohydrolase I (NPH I)-mediated Transcription Termination of Vaccinia Virus Early Genes

Journal of Biological Chemistry ◽

10.1074/jbc.m111.263822 ◽

2011 ◽

Vol 286 (52) ◽

pp. 44764-44775 ◽

Cited By ~ 4

Author(s):

Jessica Tate ◽

Paul Gollnick

Keyword(s):

Vaccinia Virus ◽

Transcription Termination ◽

Nucleoside Triphosphate ◽

Early Genes

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SEN1, a positive effector of tRNA-splicing endonuclease in Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.12.5.2154 ◽

1992 ◽

Vol 12 (5) ◽

pp. 2154-2164 ◽

Cited By ~ 50

Author(s):

D J DeMarini ◽

M Winey ◽

D Ursic ◽

F Webb ◽

M R Culbertson

Keyword(s):

Saccharomyces Cerevisiae ◽

Amino Acids ◽

Amino Acid ◽

Gene Product ◽

Signal Sequence ◽

Null Alleles ◽

Nucleoside Triphosphate ◽

Temperature Sensitive ◽

Yeast Saccharomyces Cerevisiae ◽

Amino Terminal

The SEN1 gene, which is essential for growth in the yeast Saccharomyces cerevisiae, is required for endonucleolytic cleavage of introns from all 10 families of precursor tRNAs. A mutation in SEN1 conferring temperature-sensitive lethality also causes in vivo accumulation of pre-tRNAs and a deficiency of in vitro endonuclease activity. Biochemical evidence suggests that the gene product may be one of several components of a nuclear-localized splicing complex. We have cloned the SEN1 gene and characterized the SEN1 mRNA, the SEN1 gene product, the temperature-sensitive sen1-1 mutation, and three SEN1 null alleles. The SEN1 gene corresponds to a 6,336-bp open reading frame coding for a 2,112-amino-acid protein (molecular mass, 239 kDa). Using antisera directed against the C-terminal end of SEN1, we detect a protein corresponding to the predicted molecular weight of SEN1. The SEN1 protein contains a leucine zipper motif, consensus elements for nucleoside triphosphate binding, and a potential nuclear localization signal sequence. The carboxy-terminal 1,214 amino acids of the SEN1 protein are essential for growth, whereas the amino-terminal 898 amino acids are dispensable. A sequence of approximately 500 amino acids located in the essential region of SEN1 has significant similarity to the yeast UPF1 gene product, which is involved in mRNA turnover, and the mouse Mov-10 gene product, whose function is unknown. The mutation that creates the temperature-sensitive sen1-1 allele is located within this 500-amino-acid region, and it causes a substitution for an amino acid that is conserved in all three proteins.

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