scholarly journals Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type

Biomolecules ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 919
Author(s):  
Anwar Mohammad ◽  
Fahd Al-Mulla ◽  
Dong-Qing Wei ◽  
Jehad Abubaker
Keyword(s):  
Rna Polymerase ◽  
Molecular Conformation ◽  
Antiviral Drug ◽  
Md Simulations ◽  
Binding Energies ◽  
Wild Type ◽  
Rna Dependent Rna Polymerase ◽  
Dynamic Motion ◽  
Similar Dynamic ◽  
Insight Into

SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) protein is the target for the antiviral drug Remdesivir (RDV). With RDV clinical trials on COVID-19 patients showing a reduced hospitalisation time. During the spread of the virus, the RdRp has developed several mutations, with the most frequent being A97V and P323L. The current study sought to investigate whether A97V and P323L mutations influence the binding of RDV to the RdRp of SARS-CoV-2 compared to wild-type (WT). The interaction of RDV with WT-, A97V-, and P323L-RdRp were measured using molecular dynamic (MD) simulations, and the free binding energies were extracted. Results showed that RDV that bound to WT- and A97V-RdRp had a similar dynamic motion and internal residue fluctuations, whereas RDV interaction with P323L-RdRp exhibited a tighter molecular conformation, with a high internal motion near the active site. This was further corroborated with RDV showing a higher binding affinity to P323L-RdRp (−24.1 kcal/mol) in comparison to WT-RdRp (−17.3 kcal/mol). This study provides insight into the potential significance of administering RDV to patients carrying the SARS-CoV-2 P323L-RdRp mutation, which may have a more favourable chance of alleviating the SARS-CoV-2 illness in comparison to WT-RdRp carriers, thereby suggesting further scientific consensus for the usage of Remdesivir as clinical candidate against COVID-19.

scholarly journals Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target

2020 ◽  
Author(s):  
Yan Gao ◽  
Liming Yan ◽  
Yucen Huang ◽  
Fengjiang Liu ◽  
Yao Zhao ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Drug Target ◽  
Antiviral Drug ◽  
Central Component ◽  
Rna Dependent Rna Polymerase ◽  
Transcription Machinery ◽  
Global Pandemic ◽  
Novel Coronavirus ◽  
Key Residues ◽  
Insight Into

AbstractA novel coronavirus (2019-nCoV) outbreak has caused a global pandemic resulting in tens of thousands of infections and thousands of deaths worldwide. The RNA-dependent RNA polymerase (RdRp, also named nsp12), which catalyzes the synthesis of viral RNA, is a key component of coronaviral replication/transcription machinery and appears to be a primary target for the antiviral drug, remdesivir. Here we report the cryo-EM structure of 2019-nCoV full-length nsp12 in complex with cofactors nsp7 and nsp8 at a resolution of 2.9-Å. Additional to the conserved architecture of the polymerase core of the viral polymerase family and a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain featured in coronaviral RdRp, nsp12 possesses a newly identified β-hairpin domain at its N-terminal. Key residues for viral replication and transcription are observed. A comparative analysis to show how remdesivir binds to this polymerase is also provided. This structure provides insight into the central component of coronaviral replication/transcription machinery and sheds light on the design of new antiviral therapeutics targeting viral RdRp.One Sentence SummaryStructure of 2019-nCov RNA polymerase.

scholarly journals Deep learning-based computational drug discovery to inhibit the RNA Dependent RNA Polymerase: application to SARS-CoV and COVID-19

2020 ◽  
Author(s):  
Sayalee Patankar
Keyword(s):  
Deep Learning ◽  
Rna Polymerase ◽  
Short Term Memory ◽  
Comparison Group ◽  
Binding Energies ◽  
Therapeutic Options ◽  
Rna Dependent Rna Polymerase ◽  
Drug Candidates ◽  
Zinc Database ◽  
Binding Data

There is an urgency to find drugs and vaccines for the 2019 coronavirus disease (COVID-19). Therapeutic options include repurposing existing drugs or finding new ones. One approach is to target the RNA-dependent RNA polymerase (RdRp) and block viral RNA synthesis. Currently clinical trials to repurpose remdesivir, a RdRp targeting pro-drug for Ebola, to COVID-19 is under way. More such potential drugs need to be identified to efficiently find best therapeutic options. To address this need, a Long Short Term Memory (LSTM) model from literature was trained to read the SMILES fingerprint of a molecule and predict the IC50 of the molecule when binding to an RdRp. This model was trained using IC50 binding data from the PDB database. 310,000 drug-like compounds from the ZINC database were then screened using the trained LSTM model. Additionally, the 310,000 molecules with their predicted IC50s were used to train a generative Semi-Supervised Variational AutoEncoder (SSVAE) model from literature. Although not trained by actual experimental data (sufficient data are not available), the SSVAE model was used to generate 10 new molecules by sampling from the latent space to demonstrate its utility. These 10 molecules and the 1025 molecules with the lowest predicted IC50s from the LSTM model were docked onto the SARS coronavirus (a virus similar to COVID-19) RdRp using AutoDock Vina. Top four most stable inhibitors from the screened ZINC database compounds had binding energies of less than -33.89 kJ/mol. These binding energies were less than the binding energies of the comparison group consisting of prior drugs remdesivir, favipiravir, and galidesivir. Among the ten new molecules generated by the SSVAE model, the most stable new molecule had binding energy lower than the comparison group of prior drugs. The low binding energies of these molecules indicate they could potentially be good drug candidates for the SARS CoV and COVID-19. These results also show the utility of deep learning-based models in screening existing compound and generating new molecules to find drugs for COVID-19.

scholarly journals Thermolabile L-A virus-like particles from pet18 mutants of Saccharomyces cerevisiae.

1986 ◽  
Vol 6 (2) ◽  
pp. 404-410 ◽  
Author(s):  
T Fujimura ◽  
R B Wickner
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Polymerase Activity ◽  
Nonpermissive Temperature ◽  
Wild Type ◽  
Rna Dependent Rna Polymerase ◽  
Virus Like Particles ◽  
Rna Polymerase Activity ◽  
Lines Of Evidence

pet18 mutations in Saccharomyces cerevisiae confer on the cell the inability to maintain either L-A or M double-stranded RNAs (dsRNAs) at the nonpermissive temperature. In in vitro experiments, we examined the effects of pet18 mutations on the RNA-dependent RNA polymerase activity associated with virus-like particles (VLPs). pet18 mutations caused thermolabile RNA polymerase activity of L-A VLPs, and this thermolability was found to be due to the instability of the L-A VLP structure. The pet18 mutations did not affect RNA polymerase activity of M VLPs. Furthermore, the temperature sensitivity of wild-type L-A RNA polymerase differed substantially from that of M RNA polymerase. From these results, and from other genetic and biochemical lines of evidence which suggest that replication of M dsRNA requires the presence of L-A dsRNA, we propose that the primary effect of the pet18 mutation is on the L-A VLP structure and that the inability of pet18 mutants to maintain M dsRNA comes from the loss of L-A dsRNA.

scholarly journals Computationally repurposed drugs and natural products against RNA dependent RNA polymerase as potential COVID-19 therapies

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Sakshi Piplani ◽  
Puneet Kumar Singh ◽  
David A. Winkler ◽  
Nikolai Petrovsky
Keyword(s):  
Natural Products ◽  
Rna Polymerase ◽  
Kinase Inhibitor ◽  
Binding Energies ◽  
Dynamics Simulation ◽  
Rna Dependent Rna Polymerase ◽  
Starting Point ◽  
Potential Activity ◽  
Repurposed Drugs ◽  
Multiple Drugs

AbstractRepurposing of existing drugs and drug candidates is an ideal approach to identify new potential therapies for SARS-CoV-2 that can be tested without delay in human trials of infected patients. Here we applied a virtual screening approach using Autodock Vina and molecular dynamics simulation in tandem to calculate binding energies for repurposed drugs against the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). We thereby identified 80 promising compounds with potential activity against SARS-Cov2, consisting of a mixture of antiviral drugs, natural products and drugs with diverse modes of action. A substantial proportion of the top 80 compounds identified in this study had been shown by others to have SARS-CoV-2 antiviral effects in vitro or in vivo, thereby validating our approach. Amongst our top hits not previously reported to have SARS-CoV-2 activity, were eribulin, a macrocyclic ketone analogue of the marine compound halichondrin B and an anticancer drug, the AXL receptor tyrosine kinase inhibitor bemcentinib. Our top hits from our RdRp drug screen may not only have utility in treating COVID-19 but may provide a useful starting point for therapeutics against other coronaviruses. Hence, our modelling approach successfully identified multiple drugs with potential activity against SARS-CoV-2 RdRp.

scholarly journals Use of DNA, RNA, and Chimeric Templates by a Viral RNA-Dependent RNA Polymerase: Evolutionary Implications for the Transition from the RNA to the DNA World

1999 ◽  
Vol 73 (8) ◽  
pp. 6424-6429 ◽  
Author(s):  
Robert W. Siegel ◽  
Laurent Bellon ◽  
Leonid Beigelman ◽  
C. Cheng Kao
Keyword(s):  
Rna Polymerase ◽  
Mosaic Virus ◽  
Rna Synthesis ◽  
Brome Mosaic Virus ◽  
Viral Rna ◽  
Competition Assay ◽  
Rna Dependent Rna Polymerase ◽  
Dna Molecule ◽  
Mechanism Of Catalysis ◽  
Insight Into

ABSTRACT All polynucleotide polymerases have a similar structure and mechanism of catalysis, consistent with their evolution from one progenitor polymerase. Viral RNA-dependent RNA polymerases (RdRp) are expected to have properties comparable to those from this progenitor and therefore may offer insight into the commonalities of all classes of polymerases. We examined RNA synthesis by the brome mosaic virus RdRp on DNA, RNA, and hybrid templates and found that precise initiation of RNA synthesis can take place from all of these templates. Furthermore, initiation can take place from either internal or penultimate initiation sites. Using a template competition assay, we found that the BMV RdRp interacts with DNA only three- to fourfold less well than it interacts with RNA. Moreover, a DNA molecule with a ribonucleotide at position −11 relative to the initiation nucleotide was able to interact with RdRp at levels comparable to that observed with RNA. These results suggest that relatively few conditions were needed for an ancestral RdRp to replicate DNA genomes.

scholarly journals In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials

2020 ◽  
Author(s):  
Seref Gul ◽  
Onur Ozcan ◽  
sinan asar ◽  
Alper Okyar ◽  
Ibrahim Barıs ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Rna Polymerase ◽  
Protein Interactions ◽  
In Silico ◽  
Cost Effective ◽  
Md Simulations ◽  
Viral Rna ◽  
Free Energies ◽  
Rna Dependent Rna Polymerase ◽  
Approved Drugs

<p></p><p>Despite strict measures taken by many countries, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be an issue of global concern. Currently, there are no clinically proven pharmacotherapies for coronavirus disease 2019, despite promising initial results obtained from drugs such as azithromycin and hydroxyquinoline. Therefore, the repurposing of clinically approved drugs for use against SARS-CoV-2 has become a viable strategy. Here, we searched for drugs that target SARS-CoV-2 3C-like protease (3CL<sup>pro</sup>) and viral RNA-dependent RNA polymerase (RdRp) by in silico screening of the U.S. Food and Drug Administration approved drug library. Well-tolerated and widely used drugs were selected for molecular dynamics (MD) simulations to evaluate drug-protein interactions and their persistence under physiological conditions. Tetracycline, dihydroergotamine, ergotamine, dutasteride, nelfinavir, and paliperidone formed stable interactions with 3CL<sup>pro</sup> based on MD simulation results. Similar analysis with RdRp showed that eltrombopag, tipranavir, ergotamine, and conivaptan bound to the enzyme with high binding free energies. Docking results suggest that ergotamine, dihydroergotamine, bromocriptine, dutasteride, conivaptan, paliperidone, and tipranavir can bind to both enzymes with high affinity. As these drugs are well tolerated, cost-effective, and widely used, our study suggests that they could potentially to be used in clinical trials for the treatment of SARS-CoV-2-infected patients.</p><br><p></p>

Virtual Screening of the Indonesian Medicinal Plant and Zinc Databases for Potential Inhibitors of the RNA-Dependent RNA Polymerase (RdRp) of 2019 Novel Coronavirus

2020 ◽  
Vol 20 (6) ◽  
pp. 1430
Author(s):  
Muhammad Arba ◽  
Andry Nur-Hidayat ◽  
Ida Usman ◽  
Arry Yanuar ◽  
Setyanto Tri Wahyudi ◽  
...  
Keyword(s):  
Binding Energy ◽  
Rna Polymerase ◽  
Antiviral Drug ◽  
Dynamics Simulation ◽  
Human Beings ◽  
Rna Dependent Rna Polymerase ◽  
Energy Prediction ◽  
Binding Energy Prediction ◽  
Solvation Energies ◽  
Novel Coronavirus

The novel coronavirus disease 19 (Covid-19) which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a pandemic across the world, which necessitate the need for the antiviral drug discovery. One of the potential protein targets for coronavirus treatment is RNA-dependent RNA polymerase. It is the key enzyme in the viral replication machinery, and it does not exist in human beings, therefore its targeting has been considered as a strategic approach. Here we describe the identification of potential hits from Indonesian Herbal and ZINC databases. The pharmacophore modeling was employed followed by molecular docking and dynamics simulation for 40 ns. 151 and 14480 hit molecules were retrieved from Indonesian herbal and ZINC databases, respectively. Three hits that were selected based on the structural analysis were stable during 40 ns, while binding energy prediction further implied that ZINC1529045114, ZINC169730811, and 9-Ribosyl-trans-zeatin had tighter binding affinities compared to Remdesivir. The ZINC169730811 had the strongest affinity toward RdRp compared to the other two hits including Remdesivir and its binding was corroborated by electrostatic, van der Waals, and nonpolar contribution for solvation energies. The present study offers three hits showing tighter binding to RdRp based on MM-PBSA binding energy prediction for further experimental verification.

scholarly journals Insight into Structural Characteristics of Protein-Substrate Interaction in Pimaricin Thioesterase

2019 ◽  
Vol 20 (4) ◽  
pp. 877 ◽  
Author(s):  
Shuobing Fan ◽  
Rufan Wang ◽  
Chen Li ◽  
Linquan Bai ◽  
Yi-Lei Zhao ◽  
...  
Keyword(s):  
Molecular Conformation ◽  
Conformational Transition ◽  
Hydrophobic Interactions ◽  
Mutual Recognition ◽  
Structural Characteristics ◽  
Md Simulations ◽  
Binding Energies ◽  
Product Release ◽  
Molecular Hydrogen Bond ◽  
Key Residues

As a polyene antibiotic of great pharmaceutical significance, pimaricin has been extensively studied to enhance its productivity and effectiveness. In our previous studies, pre-reaction state (PRS) has been validated as one of the significant conformational categories before macrocyclization, and is critical to mutual recognition and catalytic preparation in thioesterase (TE)-catalyzed systems. In our study, molecular dynamics (MD) simulations were conducted on pimaricin TE-polyketide complex and PRS, as well as pre-organization state (POS), a molecular conformation possessing a pivotal intra-molecular hydrogen bond, were detected. Conformational transition between POS and PRS was observed in one of the simulations, and POS was calculated to be energetically more stable than PRS by 4.58 kcal/mol. The structural characteristics of PRS and POS-based hydrogen-bonding, and hydrophobic interactions were uncovered, and additional simulations were carried out to rationalize the functions of several key residues (Q29, M210, and R186). Binding energies, obtained from MM/PBSA calculations, were further decomposed to residues, in order to reveal their roles in product release. Our study advanced a comprehensive understanding of pimaricin TE-catalyzed macrocyclization from the perspectives of conformational change, protein-polyketide recognition, and product release, and provided potential residues for rational modification of pimaricin TE.

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