scholarly journals Space Constrained Homology Modelling: The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Dimitrios Vlachakis ◽  
Dimitrios Georgios Kontopoulos ◽  
Sophia Kossida
Keyword(s):  
Rna Polymerase ◽  
Sequence Similarity ◽  
Homology Modelling ◽  
The Novel ◽  
Type Ii ◽  
3D Scaffold ◽  
Rna Dependent Rna Polymerase ◽  
X Ray ◽  
Novel Approach ◽  
Modelling Approach

Protein structure is more conserved than sequence in nature. In this direction we developed a novel methodology that significantly improves conventional homology modelling when sequence identity is low, by taking into consideration 3D structural features of the template, such as size and shape. Herein, our new homology modelling approach was applied to the homology modelling of the RNA-dependent RNA polymerase (RdRp) of dengue (type II) virus. The RdRp of dengue was chosen due to the low sequence similarity shared between the dengue virus polymerase and the available templates, while purposely avoiding to use the actual X-ray structure that is available for the dengue RdRp. The novel approach takes advantage of 3D space corresponding to protein shape and size by creating a 3D scaffold of the template structure. The dengue polymerase model built by the novel approach exhibited all features of RNA-dependent RNA polymerases and was almost identical to the X-ray structure of the dengue RdRp, as opposed to the model built by conventional homology modelling. Therefore, we propose that the space-aided homology modelling approach can be of a more general use to homology modelling of enzymes sharing low sequence similarity with the template structures.

scholarly journals (F)uridylylated Peptides Linked to VPg1 of Foot-and- Mouth Disease Virus (FMDV): Design, Synthesis and X-Ray Crystallography of the Complexes with FMDV RNA-Dependent RNA Polymerase

Molecules ◽  
2019 ◽  
Vol 24 (13) ◽  
pp. 2360 ◽  
Author(s):  
Sonia de Castro ◽  
Cristina Ferrer-Orta ◽  
Alberto Mills ◽  
Gloria Fernández-Cureses ◽  
Federico Gago ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Disease Virus ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Viral Rna ◽  
Hydroxyl Group ◽  
Rna Dependent Rna Polymerase ◽  
X Ray ◽  
Mouth Disease Virus ◽  
Foot And Mouth

Foot-and-mouth disease virus (FMDV) is an RNA virus belonging to the Picornaviridae family that contains three small viral proteins (VPgs), named VPg1, VPg2 and VPg3, linked to the 5′-end of the viral genome. These VPg proteins act as primers for RNA replication, which is initiated by the consecutive binding of two UMP molecules to the hydroxyl group of Tyr3 in VPg. This process, termed uridylylation, is catalyzed by the viral RNA-dependent RNA polymerase named 3Dpol. 5-Fluorouridine triphosphate (FUTP) is a potent competitive inhibitor of VPg uridylylation. Peptide analysis showed FUMP covalently linked to the Tyr3 of VPg. This fluorouridylylation prevents further incorporation of the second UMP residue. The molecular basis of how the incorporated FUMP blocks the incorporation of the second UMP is still unknown. To investigate the mechanism of inhibition of VPg uridylylation by FUMP, we have prepared a simplified 15-mer model of VPg1 containing FUMP and studied its x-ray crystal structure in complex with 3Dpol. Unfortunately, the fluorouridylylated VPg1 was disordered and not visible in the electron density maps; however, the structure of 3Dpol in the presence of VPg1-FUMP showed an 8 Å movement of the β9-α11 loop of the polymerase towards the active site cavity relative to the complex of 3Dpol with VPg1-UMP. The conformational rearrangement of this loop preceding the 3Dpol B motif seems to block the access of the template nucleotide to the catalytic cavity. This result may be useful in the design of new antivirals against not only FMDV but also other picornaviruses, since all members of this family require the uridylylation of their VPg proteins to initiate the viral RNA synthesis.

Screening of Kabasura Kudineer Chooranam against COVID-19 through Targeting of Main Protease and RNA-Dependent RNA Polymerase of SARS-CoV-2 by Molecular Docking Studies

2020 ◽  
Vol 5 (4) ◽  
pp. 319-331
Author(s):  
K. Gopalasatheeskumar ◽  
Karthikeyen Lakshmanan ◽  
Anguraj Moulishankar ◽  
Jerad Suresh ◽  
D. Kumuthaveni Babu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Docking Studies ◽  
The Novel ◽  
Rna Dependent Rna Polymerase ◽  
Molecular Docking Studies ◽  
Main Protease ◽  
Short Span ◽  
Novel Coronavirus

COVID-19 is the infectious pandemic disease caused by the novel coronavirus. The COVID-19 is spread globally in a short span of time. The Ministry of AYUSH, India which promotes Siddha and other Indian system of medicine recommends the use of formulation like Nilavembu Kudineer and Kaba Sura Kudineer Chooranam (KSKC). The present work seeks to provide the evidence for the action of 74 different constituents of the KSKC formulation acting on two critical targets. That is main protease and SARS-CoV-2 RNAdependent RNA polymerase target through molecular docking studies. The molecular docking was done by using AutoDock Tools 1.5.6 of the 74 compounds, about 50 compounds yielded docking results against COVID-19 main protease while 42 compounds yielded against SARSCoV- 2 RNA-dependent RNA polymerase. This research has concluded that the KSKC has the lead molecules that inhibits COVID-19’s target of main protease of COVID-19 and SARS-CoV-2 RNA-dependent RNA polymerase.

scholarly journals Inhibition of coxsackievirus B3 and related enteroviruses by antiviral short interfering RNA pools produced using φ6 RNA-dependent RNA polymerase

2009 ◽  
Vol 90 (10) ◽  
pp. 2468-2473 ◽  
Author(s):  
Michaela Nygårdas ◽  
Tytti Vuorinen ◽  
Antti P. Aalto ◽  
Dennis H. Bamford ◽  
Veijo Hukkanen
Keyword(s):  
Rna Polymerase ◽  
Genomic Sequence ◽  
Coxsackievirus B3 ◽  
Human Enterovirus ◽  
Rna Dependent Rna Polymerase ◽  
Coxsackievirus B4 ◽  
Novel Approach ◽  
Experimental Therapies ◽  
Coxsackievirus A9 ◽  
Interfering Rna

Coxsackievirus B3 (CBV3) is a member of the human enterovirus B species and a common human pathogen. Even though much is known about the enteroviral life cycle, no specific drugs are available to treat enterovirus infections. RNA interference (RNAi) has evolved to be an important tool for antiviral experimental therapies and gene function studies. We describe here a novel approach for RNAi against CBVs by using a short interfering (siRNA) pool covering 3.5 kb of CBV3 genomic sequence. The RNA-dependent RNA polymerase (RdRP) of bacteriophage φ6 was used to synthesize long double-stranded RNA (dsRNA) from a cloned region (nt 3837–7399) of the CBV3 genome. The dsRNA was cleaved using Dicer, purified and introduced to cells by transfection. The siRNA pool synthesized using the φ6 RdRP (φ6–siRNAs) was considerably more effective than single-site siRNAs. The φ6–siRNA pool also inhibited replication of other enterovirus B species, such as coxsackievirus B4 and coxsackievirus A9.

scholarly journals Preparation and Synthetic Applicability of Novel Imidazole-Containing Cyclic Iodonium Salts

2021 ◽  
Author(s):  
Antonkin Nikita ◽  
Yulia Vlasenko ◽  
Akira Yoshimura ◽  
Vladimir Smirnov ◽  
Tatyana Borodina ◽  
...  
Keyword(s):  
Elemental Sulfur ◽  
High Reactivity ◽  
Oxidative Cyclization ◽  
The Novel ◽  
Characteristic Surface ◽  
Iodonium Salts ◽  
X Ray ◽  
Surface Features ◽  
Novel Approach ◽  
Oxidative System

<p>The novel approach to the preparation of imidazole-substituted cyclic iodonium salts has been developed via oxidative cyclization of 1-phenyl-5-iodoimidazole using cheap and available Oxone<sup>®</sup>/H<sub>2</sub>SO<sub>4</sub> oxidative system. The structure of newly prepared compounds has been proved by X-ray monocrystal diffractometry revealing the characteristic surface features for cyclic iodonium salts. The prepared compounds demonstrated the high reactivity in the heterocyclization reactions with elemental sulfur affording benzo[5,1-<i>b</i>]imidazothiazoles with good yields.</p>

scholarly journals A novel approach for x-ray scattering experiments in magnetic fields utilizing trapped flux in type-II superconductors

2012 ◽  
Vol 83 (6) ◽  
pp. 065103 ◽  
Author(s):  
R. K. Das ◽  
Z. Islam ◽  
J. P. C. Ruff ◽  
R. P. Sawh ◽  
R. Weinstein ◽  
...  
Keyword(s):  
Magnetic Fields ◽  
Type Ii ◽  
X Ray ◽  
Type Ii Superconductors ◽  
X Ray Scattering ◽  
Novel Approach ◽  
Trapped Flux ◽  
Ray Scattering

scholarly journals 3D Molecular Modelling Study of the H7N9 RNA-Dependent RNA Polymerase as an Emerging Pharmacological Target

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Dimitrios Vlachakis ◽  
Argiro Karozou ◽  
Sophia Kossida
Keyword(s):  
Rna Polymerase ◽  
Molecular Modelling ◽  
Homology Modelling ◽  
Complex Structure ◽  
Rna Dependent Rna Polymerase ◽  
Major Drawback ◽  
Virus Rna ◽  
Modelling Techniques ◽  
Dynamics Simulations ◽  
Structural Insights

Currently not much is known about the H7N9 strain, and this is the major drawback for a scientific strategy to tackle this virus. Herein, the 3D complex structure of the H7N9 RNA-dependent RNA polymerase has been established using a repertoire of molecular modelling techniques including homology modelling, molecular docking, and molecular dynamics simulations. Strikingly, it was found that the oligonucleotide cleft and tunnel in the H7N9 RNA-dependent RNA polymerase are structurally very similar to the corresponding region on the hepatitis C virus RNA-dependent RNA polymerase crystal structure. A direct comparison and a 3D postdynamics analysis of the 3D complex of the H7N9 RNA-dependent RNA polymerase provide invaluable clues and insight regarding the role and mode of action of a series of interacting residues on the latter enzyme. Our study provides a novel and efficiently intergraded platform with structural insights for the H7N9 RNA-dependent RNA Polymerase. We propose that future use and exploitation of these insights may prove invaluable in the fight against this lethal, ongoing epidemic.

scholarly journals Prediction of small molecule inhibitors targeting the novel coronavirus (SARS-CoV-2) RNA-dependent RNA polymerase

2020 ◽  
Author(s):  
Mohammed Ahmed ◽  
Abhisek Dwivedy ◽  
Richard Mariadasse ◽  
Satish Tiwari ◽  
Jeyaraman Jeyakanthan ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Small Molecules ◽  
Small Molecule ◽  
Small Molecule Inhibitors ◽  
Viral Proteins ◽  
The Novel ◽  
Rna Dependent Rna Polymerase ◽  
Computational Tools ◽  
Gtp Binding ◽  
Novel Coronavirus

The current COVID-19 outbreak calls for a multi-disciplinary approach towards the design and development of novel anti-COVID therapeutics including vaccines and small molecule inhibitors targeting the viral proteins of causative agent, SARS-CoV-2. Using a combination of bioinformatics and computational tools, we have modelled the 3-D structure of the RNA-dependent RNA-polymerase (RdRp) of SARS-CoV-2 and predicted its probable GTP-binding site. This site was computationally targeted using small molecules inhibitors reported in a previous study on the RdRp of the Hepatitis C virus. Further optimizations have suggested a lead molecule that may prove fruitful in development of inhibitors against RdRp of SARS-CoV-2.

scholarly journals NeoRdRp: A comprehensive dataset for identifying RNA-dependent RNA polymerase of various RNA viruses from metatranscriptomic data

2022 ◽  
Author(s):  
Shoichi Sakaguchi ◽  
Syun-ichi Urayama ◽  
Yoshihiro Takaki ◽  
Hong Wu ◽  
Youichi Suzuki ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Viruses ◽  
Rna Virus ◽  
Sequence Similarity ◽  
Virus Detection ◽  
Detection Methods ◽  
Amino Acid Sequence Similarity ◽  
Sequencing Data ◽  
Rna Dependent Rna Polymerase ◽  
Multiple Sequence

RNA viruses are distributed in various environments, and most RNA viruses have been recently identified by metatranscriptome sequencing. However, due to the high nucleotide diversity of RNA viruses, it is still challenging to identify their sequences. Therefore, this study generated a dataset of RNA-dependent RNA polymerase (RdRp) domains essential for all RNA viruses belonging to Orthornavirae. Also, the collected genes with RdRp domains from various RNA viruses were clustered by amino acid sequence similarity. For each cluster, a multiple sequence alignment was generated, and a hidden Markov model (HMM) profile was created if the number of sequences was greater than five. Using the 1,467 HMM profiles, we detected RdRp domains in the RefSeq RNA virus sequences, combined the hit sequences with the RdRp domains, and reconstructed the HMM profiles. As a result, 2,234 HMM profiles were generated from 12,316 RdRp domain sequences, and the dataset was named NeoRdRp. Additionally, using the UniProt dataset, we confirmed that almost all NeoRdRp HMM profiles could specifically detect RdRps in Orthornavirae. Furthermore, we compared the NeoRdRp dataset with two previously reported RNA virus detection methods to detect RNA virus sequences from metatranscriptome sequencing data. Our methods can identify most of the RNA viruses in the datasets; however, some RNA viruses were not detected, similar to the other two methods. The NeoRdRp can be improved by repeatedly adding new RdRp sequences and can be expected to be widely applied as a system for detecting various RNA viruses from metatranscriptome data.

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