scholarly journals Synthesis of Nucleoside-like Molecules from a Pyrolysis Product of Cellulose and Their Computational Prediction as Potential SARS-CoV-2 RNA-Dependent RNA Polymerase Inhibitors

2022 ◽  
Vol 23 (1) ◽  
pp. 518
Author(s):  
Andrea Defant ◽  
Federico Dosi ◽  
Nicole Innocenti ◽  
Ines Mancini
Keyword(s):  
Rna Polymerase ◽  
Pyrolysis Product ◽  
Computational Prediction ◽  
Binding Pocket ◽  
Dynamics Simulation ◽  
Rna Dependent Rna Polymerase ◽  
Dft Methods ◽  
Structural Modifications ◽  
2D Noesy ◽  
Chiral Building Block

(1R,5S)-1-Hydroxy-3,6-dioxa-bicyclo[3.2.1]octan-2-one, available by an efficient catalytic pyrolysis of cellulose, has been applied as a chiral building block in the synthesis of seven new nucleoside analogues, with structural modifications on the nucleobase moiety and on the carboxyl- derived unit. The inverted configuration by Mitsunobu reaction used in their synthesis was verified by 2D-NOESY correlations, supported by the optimized structure employing the DFT methods. An in silico screening of these compounds as inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase has been carried out in comparison with both remdesivir, a mono-phosphoramidate prodrug recently approved for COVID-19 treatment, and its ribonucleoside metabolite GS-441524. Drug-likeness prediction and data by docking calculation indicated compound 6 [=(3S,5S)-methyl 5-(hydroxymethyl)-3-(6-(4-methylpiperazin-1-yl)-9H-purin-9-yl)tetrahydrofuran-3-carboxylate] as the best candidate. Furthermore, molecular dynamics simulation showed a stable interaction of structure 6 in RNA-dependent RNA polymerase (RdRp) complex and a lower average atomic fluctuation than GS-441524, suggesting a well accommodation in the RdRp binding pocket.

Hindered nucleoside analogs as antiflaviviridae agents

2004 ◽  
Vol 76 (5) ◽  
pp. 1007-1015 ◽  
Author(s):  
Stefano Manfredini ◽  
Angela Angusti ◽  
A. C. Veronese ◽  
Elisa Durini ◽  
S. Vertuani ◽  
...  
Keyword(s):  
Hepatitis C ◽  
Molecular Modeling ◽  
Rna Polymerase ◽  
Nucleoside Analogs ◽  
Binding Pocket ◽  
West Nile Fever ◽  
Rna Dependent Rna Polymerase ◽  
West Nile ◽  
Important Family ◽  
Allosteric Binding Pocket

Flaviviridae are an important family of viruses, responsible for widely spread diseases such as dengue and West Nile fever and hepatitis C. Despite the severity of the related diseases, no effective antiviral treatments for infection are available. Following our discovery of adenosine-hindered analogs as potent antiflaviviridae agents, we have continued our investigation on guanosine and inosine derivatives, which were evaluated for activity against BVDV, YFV, DENV, and WNV viruses in cell-based assays. The present study allowed us to identify some newer features that led to improve the antiviral potency (down to the µM range) and to selectively inhibit BVDV and YFV viruses. The molecular modeling results were consistent with the hypothesis that test analogs act as RNA-dependent RNA polymerase (RdRp) inhibitors by interacting with a surface allosteric binding pocket.

scholarly journals Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication

2021 ◽  
Author(s):  
Moises Ernesto Romero ◽  
Chunhong Long ◽  
Daniel La Rocco ◽  
Anusha Mysore Keerthi ◽  
Dajun Xu ◽  
...  
Keyword(s):  
Free Energy ◽  
Rna Polymerase ◽  
Active Site ◽  
Energy Barrier ◽  
Umbrella Sampling ◽  
Dynamics Simulation ◽  
Free Energy Barrier ◽  
Base Stacking ◽  
Rna Dependent Rna Polymerase ◽  
Nucleotide Analogue

Remdesivir (RDV) prodrug can be metabolized into a triphosphate form nucleotide analogue (RDV-TP) to bind and insert into the active site of viral RNA dependent RNA polymerase (RdRp) to further interfere with the viral genome replication. In this work, we computationally studied how RDV-TP binds and inserts to the SARS-CoV-2 RdRp active site, in comparison with natural nucleotide substrate adenosine triphosphate (ATP). To do that, we first constructed atomic structural models of an initial binding complex (active site open) and a substrate insertion complex (active site closed), based on high-resolution cryo-EM structures determined recently for SARS-CoV-2 RdRp or non-structural protein (nsp) 12, in complex with accessory protein factors nsp7 and nsp8. By conducting all-atom molecular dynamics simulation with umbrella sampling strategies on the nucleotide insertion between the open and closed state RdRp complexes, our studies show that RDV-TP can bind comparatively stabilized to the viral RdRp active site, as it primarily forms base stacking with the template Uracil nucleotide (at +1), which is under freely fluctuations and supports a low free energy barrier of the RDV-TP insertion (~ 1.5 kcal/mol). In comparison, the corresponding natural substrate ATP binds to the RdRp active site in Watson-Crick base pairing with the template nt, and inserts into the active site with a medium low free energy barrier (~ 2.6 kcal/mol), when the fluctuations of the template nt are well quenched. The simulations also show that the initial base stacking of RDV-TP with the template can be particularly stabilized by motif B-N691, S682, and motif F-K500 with the sugar, base, and the template backbone, respectively. Although the RDV-TP insertion can be hindered by motif-F R555/R553 interaction with the triphosphate, the ATP insertion seems to be facilitated by such interactions. The inserted RDV-TP and ATP can be further distinguished by specific sugar interaction with motif B-T687 and motif-A D623, respectively.

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 Specific mutations in SARS-CoV2 RNA dependent RNA polymerase and helicase alter protein structure, dynamics and thus function: Effect on viral RNA replication

2020 ◽  
Author(s):  
Feroza Begum ◽  
Debica Mukherjee ◽  
Sandeepan Das ◽  
Dluya Thagriki ◽  
Prem Prakash Tripathi ◽  
...  
Keyword(s):  
Protein Structure ◽  
Rna Polymerase ◽  
Rna Replication ◽  
Viral Rna ◽  
Rna Dependent Rna Polymerase ◽  
Stem Loop ◽  
Reading Frame ◽  
Replication Complex ◽  
Structural Modifications ◽  
Mutation Analyses

1.AbstractThe open reading frame (ORF) 1ab of SARS-CoV2 encodes non-structural proteins involved in viral RNA functions like translation and replication including nsp1-4; 3C like proteinase; nsp6-10; RNA dependent RNA polymerase (RdRp); helicase and 3’-5’ exonuclease. Sequence analyses of ORF1ab unravelled emergence of mutations especially in the viral RdRp and helicase at specific positions, both of which are important in mediating viral RNA replication. Since proteins are dynamic in nature and their functions are governed by the molecular motions, we performed normal mode analyses of the SARS-CoV2 wild type and mutant RdRp and helicases to understand the effect of mutations on their structure, conformation, dynamics and thus function. Structural analyses revealed that mutation of RdRp (at position 4715 in the context of the polyprotein/ at position 323 of RdRp) leads to rigidification of structure and that mutation in the helicase (at position 5828 of polyprotein/ position 504) leads to destabilization increasing the flexibility of the protein structure. Such structural modifications and protein dynamics alterations might alter unwinding of complex RNA stem loop structures, the affinity/ avidity of polymerase RNA interactions and in turn the viral RNA replication. The mutation analyses of proteins of the SARS-CoV2 RNA replication complex would help targeting RdRp better for therapeutic intervention.

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.

3-(imidazo[1,2- a :5,4- b ′]dipyridin-2-yl)aniline inhibits pestivirus replication by targeting a hot spot drug binding pocket in the RNA-dependent RNA polymerase

2016 ◽  
Vol 129 ◽  
pp. 99-103 ◽  
Author(s):  
Simone Musiu ◽  
Pieter Leyssen ◽  
Mathy Froeyen ◽  
Jean-Michel Chezal ◽  
Johan Neyts ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Hot Spot ◽  
Binding Pocket ◽  
Drug Binding ◽  
Rna Dependent Rna Polymerase

scholarly journals Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP

2020 ◽  
Author(s):  
Katerina Naydenova ◽  
Kyle W. Muir ◽  
Long-Fei Wu ◽  
Ziguo Zhang ◽  
Francesca Coscia ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Binding Pocket ◽  
Binding Mode ◽  
Polymerase Activity ◽  
Catalytic Site ◽  
Structural Basis ◽  
Limited Information ◽  
Rna Dependent Rna Polymerase ◽  
Polymerase Inhibitor ◽  
Ribonucleoside Triphosphate

AbstractThe RNA polymerase inhibitor, favipiravir, is currently in clinical trials as a treatment for infection with SARS-CoV-2, despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.

The Binding of Remdesivir to SARS-CoV-2 RNA-Dependent RNA polymerase May Pave The Way Towards the Design of Potential Drugs for COVID-19 Treatment.

2020 ◽  
Vol 21 ◽  
Author(s):  
Clement Agoni ◽  
Mahmoud E.S. Soliman
Keyword(s):  
Molecular Dynamics ◽  
Rna Polymerase ◽  
Vaccine Development ◽  
Treatment Options ◽  
Pharmacophore Model ◽  
Dynamics Simulation ◽  
Active Site Residues ◽  
Rna Dependent Rna Polymerase ◽  
Hydrophobic Region ◽  
Virus Rna

Aim: We seek to provide an understanding of the binding mechanism of Remdesivir, provide structural and conformational implications on SARS-CoV-2 virus RNA-dependent RNA polymerase upon its binding and identify its crucial pharmacophoric moieties. Background: The coronavirus disease of 2019 (COVID-19) pandemic has infected over a million people, with over 65,000 deaths as of the first quarter of 2020. The current limitation of effective treatment options with no approved vaccine or targeted therapeutics for the treatment of COVID-19 has posed serious global health threats. This has necessitated several drug and vaccine development efforts across the globe. To date, the farthest in the drug development pipeline so far is Remdesivir. Objectives: We perform molecular dynamics simulation, quantify the energy contributions of binding site residues using per-residue energy decomposition calculations, and subsequently generate a pharmacophore model for the identification of potential SARS-CoV-2 virus RNA-dependent RNA polymerase inhibitors. Methods: Integrative molecular dynamics simulations and thermodynamic calculations coupled with advanced postmolecular dynamics analysis techniques were employed. Results: Our analysis showed that the modulatory activity of Remdesivir is characterized by an extensive array of highaffinity and consistent molecular interactions with specific active site residues that anchor Remdemsivir within the binding pocket for efficient binding. These residues are ASP452, THR456, ARG555, THR556, VAL557, ARG624, THR680, SER681, and SER682. Results also showed that Remdesivir binding, induces minimal individual amino acid perturbations, subtly interferes with deviations of C-α atoms and restricts the systematic transition of SARS-CoV-2 RNA-dependent RNA polymerase from the “buried” hydrophobic region to the “surface-exposed” hydrophilic region. We also mapped a pharmacophore model based on observed high-affinity interactions with SARS-CoV-2 virus RNA-dependent RNA polymerase, which showcased the crucial functional moieties of Remdesivir and was subsequently employed for virtual screening. Conclusion: The structural insights and the optimized pharmacophoric model provided would augment the design of improved analogs of Remdesivir that could expand treatment options for COVID-19.

scholarly journals A nucleobase-binding pocket in a viral RNA-dependent RNA polymerase contributes to elongation complex stability

2019 ◽  
Vol 48 (3) ◽  
pp. 1392-1405 ◽  
Author(s):  
Wei Shi ◽  
Han-Qing Ye ◽  
Cheng-Lin Deng ◽  
Rui Li ◽  
Bo Zhang ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Binding ◽  
Vaccine Development ◽  
Antiviral Drug ◽  
Enterovirus 71 ◽  
Binding Pocket ◽  
Genome Replication ◽  
Elongation Complex ◽  
Rna Dependent Rna Polymerase

Abstract The enterovirus 71 (EV71) 3Dpol is an RNA-dependent RNA polymerase (RdRP) that plays the central role in the viral genome replication, and is an important target in antiviral studies. Here, we report a crystal structure of EV71 3Dpol elongation complex (EC) at 1.8 Å resolution. The structure reveals that the 5′-end guanosine of the downstream RNA template interacts with a fingers domain pocket, with the base sandwiched by H44 and R277 side chains through hydrophobic stacking interactions, and these interactions are still maintained after one in-crystal translocation event induced by nucleotide incorporation, implying that the pocket could regulate the functional properties of the polymerase by interacting with RNA. When mutated, residue R277 showed an impact on virus proliferation in virological studies with residue H44 having a synergistic effect. In vitro biochemical data further suggest that mutations at these two sites affect RNA binding, EC stability, but not polymerase catalytic rate (kcat) and apparent NTP affinity (KM,NTP). We propose that, although rarely captured by crystallography, similar surface pocket interaction with nucleobase may commonly exist in nucleic acid motor enzymes to facilitate their processivity. Potential applications in antiviral drug and vaccine development are also discussed.

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