User talk:Daniel Hausaman

From Proteopedia

Use of Remdesivir as a treatment for COVID-19

Introduction to the SARS-CoV-2 genome and proteins

The virus contains an unsegmented, single strand positive sense RNA genome. The genome is 29,981 base pairs long (Sanche et al 2020). The virus is surrounded by a lipid envelope containing the nucleocapsid. The RNA genome of SARS-CoV-2 is made up of of 14 open reading frames (ORF), which can encode a range of structural and non-structural proteins, these proteins directly and indirectly affect the virulence and replication of the virus (Astuti and Ysrafil, 2020). The genes that code for the non-structural proteins are translated firstly into Open reading frame 1a and Open reading frame 1b this forms two proteins known as pp1a and pp1ab. Due to a ribosomal frame shift the proteins are supplemented by protease enzymes known as papain-like proteases (PLpro) and a serine type Mpro protease. Cleavage takes place between pp1a and pp1ab to form non-structural proteins (nsps) 1–11 and 1–16 (Astuti and Ysrafil, 2020). Majority of the nsps form a Replicase-transcriptase complex (RTC). In addition to this RTC transcribes a genomic template of viral entry to negative-sense genes of both the viral genome and subgenomic RNA as intermediate products, this is followed by transcription to positive-sense mRNAs that can be mediated by RNA dependent RNA polymerase. The next step is translation, subgenomic proteins are translated into structural and accessories proteins such as M, S, and E proteins these are insulated in the endoplasmic reticulum and then moved to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) (Chen, et al 2020).

Introduction to Remdesivir as an antiviral drug

Remdesivir is a drug that was initially developed for use against Ebola and has shown to be effective against coronaviruses such as SARS-CoV, MERS-CoV, SARS-CoV-2, and other coronaviruses. SARS-CoV-2 is the virus that is responsible for the disease COVID-19 which is a respiratory disease that can inflict severe damage to multiple major organs including the heart, brain, and lungs. SARS-Cov2 relies upon RNA-dependent RNA polymerase (RdRp) to replicate the viral genetic material. Drugs such as nucleoside analogues can be used to inhibit this RNA dependant RNA polymerase enzyme and stop viral replication. Remdesivir initially labeled GS-5734 is an adenosine triphosphate analogue, used as a broad-spectrum antiviral drug meaning it can be used to inhibit a wide range of viruses that rely upon RNA-dependent RNA polymerase for genomic replication.

Q1. How does Remdesivir stop viral replication in COVID-19?

Q2. How can Remdesivir be used on other RNA viruses?

Structure

Remdesivir triphosphate has the molecular formula C12H16N5O13P3 the compound is made up of a C-nucleoside, an aromatic amine, a nitrile, a pyrrolotriazine and an organic triphosphate. RNA dependant RNA Polymerase complex is an enzyme used in the replication and transcription of viral RNA. the structure of the protein is made up of an nsp12 core catalytic unit, an nsp7-nsp8 heterodimer, and an additional nsp8 subunit On the right-hand side shows the three-dimensional interactive structure of the nsp12-nsp7-nsp8 complex also known as the RdRp bound to the template-primer RNA and the triphosphate form of remdesivir which is highlighted in blue to view remdesivir bound to the protein complex

Mechanism

Once administered remdesivir requires metabolic activation, this takes place after the drug diffuses into a cell. Phosphoamidase (HINT1) and esterases CES1 and CTSA transform remdesivir into GS-441524 mono-phosphate. This is then phosphorylated again to produce the active triphosphate analog.

Remdesivir is a polymerase inhibitor, there are 2 main categories for polymerase inhibitors these are known as nucleoside analogues and allosteric inhibitors. Nucleoside analogues resemble viral building blocks such as Adenosine triphosphate. One of the ways this inhibits viral replication is because of competitive inhibition between the nucleoside analogue and the viral RNA. To view the RNA highlighted in red Viral replication can also be reduced by the incorporation of incorrect nucleotides into the viral genome this can result in delayed chain termination. This is initiated by the formation of a phosphodiester bond, between the 3′ hydroxyl group of Remdesivir triphosphate and the next nucleotide resulting in the termination of the viral RNA synthesis at the position of 3 nucleotides.

Q3. What type of polymerase inhibitor is Remdesivir categorised as?

Q4. Why does Remdesivir require metabolic activation?

Q5. How many phosphate groups does the activated form of Remdesivir contain?

Q6. What bond is formed that initiates the chain termination?

References

Hanna R, Dalvi S. (2021). Understanding COVID-19 Pandemic: Molecular Mechanisms and Potential Therapeutic Strategies. An Evidence-Based Review. Journal of Inflammation Research » Volume 14. https://doi.org/10.2147/JIR.S282213. Masters P. (2006) The molecular biology of coronaviruses. Adv Virus Res; 66:193-292. doi: 10.1016/S0065-3527(06)66005-3. Chen Y et al. (2020). Emerging coronaviruses: Genome structure, replication, and pathogenesis. J Med Virol; 92(4):418-423. doi: 10.1002/jmv.25681 Greenwood M. (2021). Screening for SARS-CoV-2 non-structural protein 14 inhibitors. Available at: https://www.news-medical.net/news/20210412/Screening-for-SARS-CoV-2-non-structural-protein-14-inhibitors.aspx (Accessed 8th May 2021) Jinsung Y et al. (2020). Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor Nature Communications volume 11, Article number: 4541. https://doi.org/10.1038/s41467-020-18319-6 Protein Database Bank in Europe 7bv2 › F86. Available at: https://www.ebi.ac.uk/pdbe/entry/pdb/7bv2/bound/F86 (Accessed: 12th June 2021) Uzunova K et al. (2020). Insights into antiviral mechanisms of remdesivir, lopinavir/ritonavir and chloroquine/hydroxychloroquine affecting the new SARS-CoV-2. Biomed Pharmacother. 2020 Nov; 131: 110668. doi: 10.1016/j.biopha.2020.110668 Yu-chen et al. (2020).Remdesivir for severe acute respiratory syndrome coronavirus2 causing COVID-19: An evaluation of the evidence. Travel Medicine and Infectious Disease. Volume 35, https://doi.org/10.1016/j.tmaid.2020.101647 Olena A. (2020). Remdesivir Works Against Coronaviruses in the Lab. Available at: https://www.the-scientist.com/news-opinion/remdesivir-works-great-against-coronaviruses-in-the-lab-67298 (Accessed: 6th July 2021) PubChem. Remdesivir. Available at: https://pubchem.ncbi.nlm.nih.gov/compound/Remdesivir (Accessed: 12 April 2021) Ghandi Z et al. (2020). Potential Interactions of Remdesivir with Pulmonary Drugs: a Covid-19 Perspective. SN Compr Clin Med: 1–2. doi: 10.1007/s42399-020-00462-2 PubChem. Adenosine-5'-triphosphate Available at: https://pubchem.ncbi.nlm.nih.gov/compound/Adenosine-5_-triphosphate (Accessed 2nd March