scholarly journals SARS-CoV-2 Spike Protein and RNA Dependent RNA Polymerase as Targets for Drug and Vaccine Development: A Review

2021 ◽  
Author(s):  
Yusuf Muhammed ◽  
Abduljalal Yusuf Nadabo ◽  
Mkpouto Pius ◽  
Bashiru Sani ◽  
Jafar Usman ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Vaccine Development ◽  
Spike Protein ◽  
Rna Dependent Rna Polymerase

scholarly journals Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sten Ilmjärv ◽  
Fabien Abdul ◽  
Silvia Acosta-Gutiérrez ◽  
Carolina Estarellas ◽  
Ioannis Galdadas ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Molecular Modelling ◽  
Spike Protein ◽  
Genome Sequences ◽  
Viral Polymerase ◽  
Rna Dependent Rna Polymerase ◽  
High Quality

AbstractThe D614G mutation in the Spike protein of the SARS-CoV-2 has effectively replaced the early pandemic-causing variant. Using pseudotyped lentivectors, we confirmed that the aspartate replacement by glycine in position 614 is markedly more infectious. Molecular modelling suggests that the G614 mutation facilitates transition towards an open state of the Spike protein. To explain the epidemiological success of D614G, we analysed the evolution of 27,086 high-quality SARS-CoV-2 genome sequences from GISAID. We observed striking coevolution of D614G with the P323L mutation in the viral polymerase. Importantly, the exclusive presence of G614 or L323 did not become epidemiologically relevant. In contrast, the combination of the two mutations gave rise to a viral G/L variant that has all but replaced the initial D/P variant. Our results suggest that the P323L mutation, located in the interface domain of the RNA-dependent RNA polymerase, is a necessary alteration that led to the epidemiological success of the present variant of SARS-CoV-2. However, we did not observe a significant correlation between reported COVID-19 mortality in different countries and the prevalence of the Wuhan versus G/L variant. Nevertheless, when comparing the speed of emergence and the ultimate predominance in individual countries, it is clear that the G/L variant displays major epidemiological supremacy over the original variant.

scholarly journals Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein

npj Vaccines ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Alexander J. McAuley ◽  
Michael J. Kuiper ◽  
Peter A. Durr ◽  
Matthew P. Bruce ◽  
Jennifer Barr ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Experimental Evidence ◽  
In Silico ◽  
Cleavage Site ◽  
Spike Protein ◽  
Rna Dependent Rna Polymerase ◽  
Virus Isolates

Abstract The ‘D614G’ mutation (Aspartate-to-Glycine change at position 614) of the SARS-CoV-2 spike protein has been speculated to adversely affect the efficacy of most vaccines and countermeasures that target this glycoprotein, necessitating frequent vaccine matching. Virus neutralisation assays were performed using sera from ferrets which received two doses of the INO-4800 COVID-19 vaccine, and Australian virus isolates (VIC01, SA01 and VIC31) which either possess or lack this mutation but are otherwise comparable. Through this approach, supported by biomolecular modelling of this mutation and the commonly-associated P314L mutation in the RNA-dependent RNA polymerase, we have shown that there is no experimental evidence to support this speculation. We additionally demonstrate that the putative elastase cleavage site introduced by the D614G mutation is unlikely to be accessible to proteases.

scholarly journals Epidemiologically most successful SARS-CoV-2 variant: concurrent mutations in RNA-dependent RNA polymerase and spike protein

2020 ◽  
Author(s):  
Sten Ilmjärv ◽  
Fabien Abdul ◽  
Silvia Acosta-Gutiérrez ◽  
Carolina Estarellas ◽  
Ioannis Galdadas ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Molecular Modelling ◽  
Spike Protein ◽  
Genome Sequences ◽  
Viral Polymerase ◽  
Rna Dependent Rna Polymerase ◽  
High Quality

The D614G mutation of the Spike protein is thought to be relevant for SARS-CoV-2 infection. Here we report biological and epidemiological aspects of this mutation. Using pseudotyped lentivectors, we were able to confirm that the G614 variant of the Spike protein is markedly more infectious than the ancestral D614 variant. We demonstrate by molecular modelling that the replacement of aspartate by glycine in position 614 facilitates the transition towards an open state of the Spike protein. To understand whether the increased infectivity of the D614 variant explains its epidemiological success, we analysed the evolution of 27,086 high-quality SARS-CoV-2 genome sequences from GISAID. We observed striking coevolution of D614G with the P323L mutation in the viral polymerase. Importantly, exclusive presence of G614 or L323 did not become epidemiologically relevant. In contrast, the combination of the two mutations gave rise to a viral G/L variant that has all but replaced the initial D/P variant. There was no significant correlation between reported COVID mortality in different countries and the prevalence of the Wuhan versus G/L variant. However, when comparing the speed of emergence and the ultimate predominance in individual countries, the G/L variant displays major epidemiological supremacy. Our results suggest that the P323L mutation, located in the interface domain of the RNA-dependent RNA polymerase (RdRp), is a necessary alteration that led to the epidemiological success of the present variant of SARS-CoV-2.

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 Development of a Challenge-Protective Vaccine Concept by Modification of the Viral RNA-Dependent RNA Polymerase of Canine Distemper Virus

2007 ◽  
Vol 81 (24) ◽  
pp. 13649-13658 ◽  
Author(s):  
D. Silin ◽  
O. Lyubomska ◽  
M. Ludlow ◽  
W. P. Duprex ◽  
B. K. Rima
Keyword(s):  
Rna Polymerase ◽  
Neutralizing Antibodies ◽  
Canine Distemper Virus ◽  
Fluorescent Protein ◽  
Vaccine Development ◽  
Hinge Region ◽  
Canine Distemper ◽  
Wild Type ◽  
Rna Dependent Rna Polymerase ◽  
L Protein

ABSTRACT We demonstrate that insertion of the open reading frame of enhanced green fluorescent protein (EGFP) into the coding sequence for the second hinge region of the viral L (large) protein (RNA-dependent RNA polymerase) attenuates a wild-type canine distemper virus. Moreover, we show that single intranasal immunization with this recombinant virus provides significant protection against challenge with the virulent parental virus. Protection against wild-type challenge was gained either after recovery of cellular immunity postimmunization or after development of neutralizing antibodies. Insertion of EGFP seems to result in overattenuation of the virus, while our previous experiments demonstrated that the insertion of an epitope tag into a similar position did not affect L protein function. Thus, a desirable level of attenuation could be reached by manipulating the length of the insert (in the second hinge region of the L protein), providing additional tools for optimization of controlled attenuation. This strategy for controlled attenuation may be useful for a “quick response” in vaccine development against well-known and “new” viral infections and could be combined efficiently with other strategies of vaccine development and delivery systems.

scholarly journals Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment

Pathogens ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 324 ◽  
Author(s):  
Takahiko Koyama ◽  
Dilhan Weeraratne ◽  
Jane L. Snowdon ◽  
Laxmi Parida
Keyword(s):  
Rna Polymerase ◽  
B Cell ◽  
Genetic Drift ◽  
Vaccine Development ◽  
Cell Epitope ◽  
Spike Protein ◽  
Immune Recognition ◽  
T Cell Epitopes ◽  
Antibody Treatment ◽  
B Cell Epitope

New coronavirus (SARS-CoV-2) treatments and vaccines are under development to combat COVID-19. Several approaches are being used by scientists for investigation, including (1) various small molecule approaches targeting RNA polymerase, 3C-like protease, and RNA endonuclease; and (2) exploration of antibodies obtained from convalescent plasma from patients who have recovered from COVID-19. The coronavirus genome is highly prone to mutations that lead to genetic drift and escape from immune recognition; thus, it is imperative that sub-strains with different mutations are also accounted for during vaccine development. As the disease has grown to become a pandemic, B-cell and T-cell epitopes predicted from SARS coronavirus have been reported. Using the epitope information along with variants of the virus, we have found several variants which might cause drifts. Among such variants, 23403A>G variant (p.D614G) in spike protein B-cell epitope is observed frequently in European countries, such as the Netherlands, Switzerland, and France, but seldom observed in China.

scholarly journals Pharmacological Therapeutics Targeting RNA-Dependent RNA Polymerase, Proteinase and Spike Protein: From Mechanistic Studies to Clinical Trials for COVID-19

2020 ◽  
Vol 9 (4) ◽  
pp. 1131 ◽  
Author(s):  
Jiansheng Huang ◽  
Wenliang Song ◽  
Hui Huang ◽  
Quancai Sun
Keyword(s):  
Rna Polymerase ◽  
The United States ◽  
Spike Protein ◽  
Therapeutic Approaches ◽  
Rna Dependent Rna Polymerase ◽  
S Protein ◽  
Functional Relationships ◽  
Human Lung Cells ◽  
Novel Coronavirus

An outbreak of novel coronavirus-related pneumonia COVID-19, that was identified in December 2019, has expanded rapidly, with cases now confirmed in more than 211 countries or areas. This constant transmission of a novel coronavirus and its ability to spread from human to human have prompted scientists to develop new approaches for treatment of COVID-19. A recent study has shown that remdesivir and chloroquine effectively inhibit the replication and infection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2, 2019-nCov) in vitro. In the United States, one case of COVID-19 was successfully treated with compassionate use of remdesivir in January of 2020. In addition, a clinically proven protease inhibitor, camostat mesylate, has been demonstrated to inhibit Calu-3 infection with SARS-CoV-2 and prevent SARS-2-spike protein (S protein)-mediated entry into primary human lung cells. Here, we systemically discuss the pharmacological therapeutics targeting RNA-dependent RNA polymerase (RdRp), proteinase and S protein for treatment of SARS-CoV-2 infection. This review should shed light on the fundamental rationale behind inhibition of SARS-CoV-2 enzymes RdRp as new therapeutic approaches for management of patients with COVID-19. In addition, we will discuss the viability and challenges in targeting RdRp and proteinase, and application of natural product quinoline and its analog chloroquine for treatment of coronavirus infection. Finally, determining the structural-functional relationships of the S protein of SARS-CoV-2 will provide new insights into inhibition of interactions between S protein and angiotensin-converting enzyme 2 (ACE2) and enable us to develop novel therapeutic approaches for novel coronavirus SARS-CoV-2.

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.

scholarly journals Analysis of SARS-CoV-2 Mutations Over Time Reveals Increasing Prevalence of Variants in the Spike Protein and RNA-Dependent RNA Polymerase

2021 ◽  
Author(s):  
William M Showers ◽  
Sonia M Leach ◽  
Katerina Kechris ◽  
Michael Strong
Keyword(s):  
Rna Polymerase ◽  
High Frequency ◽  
Drug Targets ◽  
Spike Protein ◽  
Structural Level ◽  
Receptor Binding Domain ◽  
Rna Dependent Rna Polymerase ◽  
Public Health Strategies ◽  
Further Development ◽  
Over Time

Amid the ongoing COVID-19 pandemic, it has become increasingly important to monitor the mutations that arise in the SARS-CoV-2 virus, to prepare public health strategies and guide the further development of vaccines and therapeutics. The spike (S) protein and the proteins comprising the RNA-Dependent RNA Polymerase (RdRP) are key vaccine and drug targets, respectively, making mutation surveillance of these proteins of great importance. Full protein sequences for the spike proteins and RNA-dependent RNA polymerase proteins were downloaded from the GISAID database, aligned, and the variants identified. Polymorphisms in the protein sequence were investigated at the protein structural level and examined longitudinally in order to identify sequence and strain variants that are emerging over time. Our analysis revealed a group of variants in the spike protein and the polymerase complex that appeared in August, and account for around five percent of the genomes analyzed up to the last week of October. A structural analysis also facilitated investigation of several unique variants in the receptor binding domain and the N-terminal domain of the spike protein, with high-frequency mutations occurring more commonly in these regions. The identification of new variants emphasizes the need for further study on the effects of these mutations and the implications of their increased prevalence, particularly as these mutations may impact vaccine or therapeutic efficacy.

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