scholarly journals Potential Therapeutic Agents for COVID-19 Based on the Analysis of Protease and RNA Polymerase Docking

2020 ◽  
Author(s):  
Yu-Chuan Chang ◽  
Yi-An Tung ◽  
Ko-Han Lee ◽  
Ting-Fu Chen ◽  
Yu-Chun Hsiao ◽  
...  
Keyword(s):  
Active Sites ◽  
Active Form ◽  
Therapeutic Agents ◽  
Hiv Protease ◽  
Nucleoside Triphosphate ◽  
Binding Motif ◽  
Docking Site ◽  
Binding Motifs ◽  
Functional Regions ◽  
Overlapping Region

The outbreak of novel coronavirus (COVID-19) infections in 2019 is in dire need of finding potential therapeutic agents. In this study, we used molecular docking to repurpose HIV protease inhibitors and nucleoside analogues for COVID-19, with evaluations based on docking scores calculated by AutoDock Vina and RosettaCommons. Our results suggest that Indinavir and Remdesivir possess the best docking scores, and comparison of the docking sites of the two drugs reveal a near perfect dock in the overlapping region of the protein pockets. After further investigation of the functional regions inferred from the proteins of SARS coronavirus, we discovered that Indinavir does not dock on any active sites of the protease, which may give rise to concern in regards to the efficacy of Indinavir. On the other hand, the docking site of Remdesivir is not compatible with any known functional regions, including template binding motifs, polymerization motifs and nucleoside triphosphate (NTP) binding motifs. However, when we tested the active form (CHEMBL2016761) of Remdesivir, the docking site revealed a perfect dock in the overlapping region of the NTP binding motif. This result suggests that Remdesivir could be a potential therapeutic agent. Clinical trials still must be done in order to confirm the curative effect of these drugs.

scholarly journals Potential Therapeutic Agents for COVID-19 Based on the Analysis of Protease and RNA Polymerase Docking

2020 ◽  
Author(s):  
Yu-Chuan Chang ◽  
Yi-An Tung ◽  
Ko-Han Lee ◽  
Ting-Fu Chen ◽  
Yu-Chun Hsiao ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Active Sites ◽  
Therapeutic Agents ◽  
Hiv Protease ◽  
Hiv Protease Inhibitors ◽  
Docking Site ◽  
Autodock Vina ◽  
Nucleotide Analogues ◽  
Novel Coronavirus ◽  
Protein Pocket

The outbreak of novel coronavirus (COVID-19) infections occurring in 2019 is in dire need of finding potential therapeutic agents. In this study, we used molecular docking strategies to repurpose HIV protease inhibitors and nucleotide analogues for COVID-19. The evaluation was made on docking scores calculated by AutoDock Vina and RosettaCommons. Preliminary results suggested that Indinavir and Remdesivir have the best docking scores and the comparison of the docking sites of these two drugs shows a near perfect dock in the overlap region of the protein pocket. However, the active sites inferred from the proteins of SARS coronavirus are not compatible with the docking site of COVID-19, which may give rise to concern in the efficacy of drugs.

scholarly journals Mechanism of SARS-CoV-2 polymerase stalling by remdesivir

2021 ◽  
Vol 12 (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.

Tyrosine-protein kinase Src regulates Kv1.5 channel activity and membrane expression through interaction with the N-terminus of the channel

2020 ◽  
Author(s):  
Taylore Dodd ◽  
Tingzhong Wang ◽  
Shetuan Zhang
Keyword(s):  
Protein Kinase ◽  
Cell Voltage ◽  
Underlying Mechanism ◽  
Delayed Rectifier ◽  
Binding Motif ◽  
Membrane Expression ◽  
Binding Motifs ◽  
Delayed Rectifier Potassium Current ◽  
N Terminus ◽  
Tyrosine Protein Kinase

Kv1.5 is a voltage-gated potassium channel that generates the ultra-rapid delayed rectifier potassium current (IKur) important in the repolarization of the atrial action potential. Malfunction of the Kv1.5 channel often results in atrial fibrillation (AFib). A reduction in Kv1.5 current (IKv1.5) occurs upon activation of the endogenous tyrosine-protein kinase Src. The Src SH3 domain binds to proline-rich motifs located within the N-terminus of Kv1.5. Disruption of these binding motifs has been involved in the development of familial AFib. The mechanism underlying the reduction of IKv1.5 upon Src activation has not yet been established and the relationship between Kv1.5 and Src is poorly understood. Therefore, the present study aims to further elucidate the mechanism behind IKv1.5  reduction. The hypothesis that Src regulates Kv1.5 activity by altering the density of mature membrane-localized channels was tested using whole-cell voltage clamp and Western blot analysis. We demonstrate that Src tonically inhibits Kv1.5 activity and decreases the density of mature membrane-localized channels. Kv1.5 channels possessing mutations within the Src binding motifs were also investigated and it was determined that each binding motif contributes to the Kv1.5-Src relationship, however, the binding of Src to an individual motif is sufficiently effective. Our findings indicate that Src regulates Kv1.5 through an interaction with the N-terminal binding motifs and suggests that the inhibition of forward trafficking may be involved in the underlying mechanism. (Supported by the Heart and Stroke foundation of Canada and The Canadian Institutes of Health Research).

scholarly journals Tubulin-Dependent Transport of Connexin-36 Potentiates the Size and Strength of Electrical Synapses

Cells ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 1146 ◽  
Author(s):  
Brown ◽  
del Corsso ◽  
Zoidl ◽  
Donaldson ◽  
Spray ◽  
...  
Keyword(s):  
Protein Transport ◽  
Mutational Analysis ◽  
Binding Motif ◽  
Dependent Manner ◽  
Electrical Synapses ◽  
Binding Motifs ◽  
Connexin 36 ◽  
Dependent Transport ◽  
Carboxy Terminal

Connexin-36 (Cx36) electrical synapses strengthen transmission in a calcium/calmodulin (CaM)/calmodulin-dependent kinase II (CaMKII)-dependent manner similar to a mechanism whereby the N-methyl-D-aspartate (NMDA) receptor subunit NR2B facilitates chemical transmission. Since NR2B–microtubule interactions recruit receptors to the cell membrane during plasticity, we hypothesized an analogous modality for Cx36. We determined that Cx36 binding to tubulin at the carboxy-terminal domain was distinct from Cx43 and NR2B by binding a motif overlapping with the CaM and CaMKII binding motifs. Dual patch-clamp recordings demonstrated that pharmacological interference of the cytoskeleton and deleting the binding motif at the Cx36 carboxyl-terminal (CT) reversibly abolished Cx36 plasticity. Mechanistic details of trafficking to the gap-junction plaque (GJP) were probed pharmacologically and through mutational analysis, all of which affected GJP size and formation between cell pairs. Lys279, Ile280, and Lys281 positions were particularly critical. This study demonstrates that tubulin-dependent transport of Cx36 potentiates synaptic strength by delivering channels to GJPs, reinforcing the role of protein transport at chemical and electrical synapses to fine-tune communication between neurons.

scholarly journals Detailed Molecular Interactions of Favipiravir with SARS-CoV-2, SARS-CoV, MERS-CoV, and Influenza Virus Polymerases In Silico

2020 ◽  
Vol 8 (10) ◽  
pp. 1610 ◽  
Author(s):  
Mitsuru Sada ◽  
Takeshi Saraya ◽  
Haruyuki Ishii ◽  
Kaori Okayama ◽  
Yuriko Hayashi ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Molecular Interactions ◽  
In Silico ◽  
Influenza A ◽  
Active Sites ◽  
Active Form ◽  
Antiviral Drug ◽  
Virus Rna ◽  
Influenza A H1n1 ◽  
In Silico Studies

Favipiravir was initially developed as an antiviral drug against influenza and is currently used in clinical trials against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection (COVID-19). This agent is presumably involved in RNA chain termination during influenza virus replication, although the molecular interactions underlying its potential impact on the coronaviruses including SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) remain unclear. We performed in silico studies to elucidate detailed molecular interactions between favipiravir and the SARS-CoV-2, SARS-CoV, MERS-CoV, and influenza virus RNA-dependent RNA polymerases (RdRp). As a result, no interactions between favipiravir ribofuranosyl-5′-triphosphate (F-RTP), the active form of favipiravir, and the active sites of RdRps (PB1 proteins) from influenza A (H1N1)pdm09 virus were found, yet the agent bound to the tunnel of the replication genome of PB1 protein leading to the inhibition of replicated RNA passage. In contrast, F-RTP bound to the active sites of coronavirus RdRp in the presence of the agent and RdRp. Further, the agent bound to the replicated RNA terminus in the presence of agent, magnesium ions, nucleotide triphosphate, and RdRp proteins. These results suggest that favipiravir exhibits distinct mechanisms of action against influenza virus and various coronaviruses.

scholarly journals Influenza A virus NS1 protein activates the phosphatidylinositol 3-kinase (PI3K)/Akt pathway by direct interaction with the p85 subunit of PI3K

2007 ◽  
Vol 88 (1) ◽  
pp. 13-18 ◽  
Author(s):  
Yeun-Kyung Shin ◽  
Qiang Liu ◽  
Suresh K. Tikoo ◽  
Lorne A. Babiuk ◽  
Yan Zhou
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Mutant Virus ◽  
Akt Pathway ◽  
Binding Motif ◽  
Ns1 Protein ◽  
Phosphatidylinositol 3 Kinase ◽  
Binding Motifs ◽  
Sh2 Domains ◽  
Phosphatidylinositol 3

Influenza A virus infection activates the phosphatidylinositol 3-kinase (PI3K)/Akt pathway, but the mechanism is not clear. Here, it is reported that influenza A virus NS1 protein is responsible for PI3K/Akt pathway activation. It was demonstrated that the NS1 protein interacts with the p85 regulatory subunit of PI3K via direct binding to the SH3 and C-terminal SH2 domains of p85. Consensus binding motifs for SH3 and SH2 domains were found in influenza A virus NS1, namely an SH2-binding motif (YXXXM) at aa 89, SH3-binding motif 1 (PXXP) around aa 164 and SH3-binding motif 2 around aa 212. Mutant virus encoding NS1 protein with mutations in the SH-binding motifs failed to interact with SH domains of p85 and did not activate the PI3K/Akt pathway. The mutant virus is attenuated in Madin–Darby canine kidney cells. Our study has established a novel function of NS1: by interacting with p85 via the SH-binding motifs, NS1 can activate the PI3K/Akt pathway.

scholarly journals Hairless-Mediated Repression of Notch Target Genes Requires the Combined Activity of Groucho and CtBP Corepressors

2005 ◽  
Vol 25 (23) ◽  
pp. 10433-10441 ◽  
Author(s):  
Anja C. Nagel ◽  
Alena Krejci ◽  
Gennady Tenin ◽  
Alejandro Bravo-Patiño ◽  
Sarah Bray ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Target Genes ◽  
Transcriptional Regulators ◽  
Dna Binding Protein ◽  
The Other ◽  
Binding Motif ◽  
Binding Motifs ◽  
Notch Intracellular Domain ◽  
Second Mode ◽  
Notch Activation

ABSTRACT Notch signal transduction centers on a conserved DNA-binding protein called Suppressor of Hairless [Su(H)] in Drosophila species. In the absence of Notch activation, target genes are repressed by Su(H) acting in conjunction with a partner, Hairless, which contains binding motifs for two global corepressors, CtBP and Groucho (Gro). Usually these corepressors are thought to act via different mechanisms; complexed with other transcriptional regulators, they function independently and/or redundantly. Here we have investigated the requirement for Gro and CtBP in Hairless-mediated repression. Unexpectedly, we find that mutations inactivating one or the other binding motif can have detrimental effects on Hairless similar to those of mutations that inactivate both motifs. These results argue that recruitment of one or the other corepressor is not sufficient to confer repression in the context of the Hairless-Su(H) complex; Gro and CtBP need to function in combination. In addition, we demonstrate that Hairless has a second mode of repression that antagonizes Notch intracellular domain and is independent of Gro or CtBP binding.

scholarly journals Characterization of Rous Sarcoma Virus Gag Particles Assembled In Vitro

2001 ◽  
Vol 75 (6) ◽  
pp. 2753-2764 ◽  
Author(s):  
Fang Yu ◽  
Swati M. Joshi ◽  
Yu May Ma ◽  
Richard L. Kingston ◽  
Martha N. Simon ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Rous Sarcoma Virus ◽  
Radial Distance ◽  
Binding Motif ◽  
Gag Protein ◽  
Binding Motifs ◽  
Rous Sarcoma ◽  
Sarcoma Virus ◽  
The Mean

ABSTRACT Purified retrovirus Gag proteins or Gag protein fragments are able to assemble into virus-like particles (VLPs) in vitro in the presence of RNA. We have examined the role of nucleic acid and of the NC domain in assembly of VLPs from a Rous sarcoma virus (RSV) Gag protein and have characterized these VLPs using transmission electron microscopy (TEM), scanning TEM (STEM), and cryoelectron microscopy (cryo-EM). RNAs of diverse sizes, single-stranded DNA oligonucleotides as small as 22 nucleotides, double-stranded DNA, and heparin all promoted efficient assembly. The percentages of nucleic acid by mass, in the VLPs varied from 5 to 8%. The mean mass of VLPs, as determined by STEM, was 6.5 × 107 Da for both RNA-containing and DNA oligonucleotide-containing particles, corresponding to a stoichiometry of about 1,200 protein molecules per VLP, slightly lower than the 1,500 Gag molecules estimated previously for infectious RSV. By cryo-EM, the VLPs showed the characteristic morphology of immature retroviruses, with discernible regions of high density corresponding to the two domains of the CA protein. In spherically averaged density distributions, the mean radial distance to the density corresponding to the C-terminal domain of CA was 33 nm, considerably smaller than that of equivalent human immunodeficiency virus type 1 particles. Deletions of the distal portion of NC, including the second Zn-binding motif, had little effect on assembly, but deletions including the charged residues between the two Zn-binding motifs abrogated assembly. Mutation of the cysteine and histidine residues in the first Zn-binding motif to alanine did not affect assembly, but mutation of the basic residues between the two Zn-binding motifs, or of the basic residues in the N-terminal portion of NC, abrogated assembly. Together, these findings establish VLPs as a good model for immature virions and establish a foundation for dissection of the interactions that lead to assembly.

scholarly journals Characterization and Localization of the Campylobacter jejuni Transformation System Proteins CtsE, CtsP, and CtsX

2014 ◽  
Vol 197 (3) ◽  
pp. 636-645 ◽  
Author(s):  
Jessica M. Beauchamp ◽  
Rebecca S. Erfurt ◽  
Victor J. DiRita
Keyword(s):  
Membrane Protein ◽  
Campylobacter Jejuni ◽  
Topological Analysis ◽  
Nucleotide Binding ◽  
Integral Membrane Protein ◽  
Nucleoside Triphosphate ◽  
Type Ii Secretion ◽  
Secretion Systems ◽  
Binding Motifs ◽  
Content Type

The human pathogenCampylobacter jejuniis naturally competent for transformation with its own DNA. Genes required for efficient transformation inC. jejuniinclude those similar to components of type II secretion systems found in many Gram-negative bacteria (R. S. Wiesner, D. R. Hendrixson, and V. J. DiRita, J Bacteriol 185:5408–5418, 2003,http://dx.doi.org/10.1128/JB.185.18.5408-5418.2003). Two of these,ctsEandctsP, encode proteins annotated as putative nucleotide binding nucleoside triphosphatases (NTPases) or nucleoside triphosphate (NTP) binding proteins. Here we demonstrate that the nucleotide binding motifs of both proteins are essential for their function in transformation ofC. jejuni. Localization experiments demonstrated that CtsE is a soluble protein while CtsP is membrane associated inC. jejuni. A bacterial two-hybrid screen identified an interaction between CtsP and CtsX, an integral membrane protein also required for transformation. Topological analysis of CtsX by the use of LacZ and PhoA fusions demonstrated it to be a bitopic, integral membrane protein with a cytoplasmic amino terminus and a periplasmic carboxyl terminus. Notwithstanding its interaction with membrane-localized CtsX, CtsP inherently associates with the membrane, requiring neither CtsX nor several other Cts proteins for this association.

Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1

2010 ◽  
Vol 432 (3) ◽  
pp. 445-454 ◽  
Author(s):  
Xuan Zhang ◽  
Yan-Bin Teng ◽  
Jian-Ping Liu ◽  
Yong-Xing He ◽  
Kang Zhou ◽  
...  
Keyword(s):  
Binding Site ◽  
Vitamin B6 ◽  
Active Sites ◽  
Biochemical Analysis ◽  
Catalytic Mechanism ◽  
De Novo ◽  
Active Form ◽  
Dihydroxyacetone Phosphate ◽  
Final Destination ◽  
Structural Insights

In most eubacteria, fungi, apicomplexa, plants and some metazoans, the active form of vitamin B6, PLP (pyridoxal 5-phosphate), is de novo synthesized from three substrates, R5P (ribose 5-phosphate), DHAP (dihydroxyacetone phosphate) and ammonia hydrolysed from glutamine by a complexed glutaminase. Of the three active sites of DXP (deoxyxylulose 5-phosphate)independent PLP synthase (Pdx1), the R5P isomerization site has been assigned, but the sites for DHAP isomerization and PLP formation remain unknown. In the present study, we present the crystal structures of yeast Pdx1/Snz1, in apo-, G3P (glyceraldehyde 3-phosphate)- and PLP-bound forms, at 2.3, 1.8 and 2.2 Å (1 Å=0.1 nm) respectively. Structural and biochemical analysis enabled us to assign the PLP-formation site, a G3P-binding site and a G3P-transfer site. We propose a putative catalytic mechanism for Pdx1/Snz1 in which R5P and DHAP are isomerized at two distinct sites and transferred along well-defined routes to a final destination for PLP synthesis.

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