Antiviral drugs for COVID-19. 28.06.20
Welcome to The Plague Pit – issue number 36.
I’m delighted to hand over to Xavier Khalid for this issue. He’s a sixth-form student at Winchester College, studying Maths, Further Maths, Biology and Chemistry. He hopes to study Natural Sciences at Cambridge, exploring the disciplines of molecular biology and biochemistry. He plays the piano and chess in his free time.
Below, Xavier considers some of the antiviral drugs under investigation for their activity against COVID-19. Shortly after I received this excellent article, Oxford University published the preliminary findings of a randomised controlled trial of dexamethasone in COVID-19 patients. They are exciting and I’ll be writing about the trial very soon.
In the meantime, its omission from this issue is due to my indolence as editor and not Xavier’s as author or scientist.
Regular visitors to The Plague Pit may have already read Adrian Tsui’s article where he explains the effectiveness of soap — a most underrated weapon.
Many sensible individuals, such as Adrian, have been spreading awareness about the importance of basic hygiene and social distancing. But how should people proceed when, despite taking precautions, they still get infected?
Fortunately, most individuals recover without complications; some infections are even asymptomatic. The World Health Organization states that most people recover without even requiring hospitalisation1. Nevertheless, COVID-19 is a notoriously infective disease. Although the R value in the UK is currently below 1, (0.7-0.9)2 COVID-19 is still highly prevalent. The government states ‘R should always be considered alongside the number of people currently infected. If R equals 1 with 100,000 people currently infected, it is a very different situation to R equals 1 with 1,000 people currently infected’2.
And so, world leaders have turned to scientists in order to take short-term protective measures to the next stage.
One such measure involves antiviral drugs, a number of which have been proposed.
Remdesivir (RDV)
RDV was developed just over a decade ago, by the biopharmaceutical company Gilead sciences. It is a broad-spectrum anti-viral drug and is known to be effective against a number of RNA viruses, such as SARS-CoV and MERS-CoV. With this in mind, it would only be logical to think that this drug should help patients with COVID-19.
Molecular mechanism
In order for SARS-CoV-2 to replicate its genome, the enzyme RNA-dependent RNA polymerase (RdRp) is required3. Adenosine triphosphate (ATP), one of the four RNA nucleotides, is a substrate of this enzyme. If we compare the structures of adenosine and Remdesivir, we can see similarities; so, we can conclude that the charge distributions at relevant sites will be very similar if not identical. This means that once RDV is metabolised and converted to RDV triphosphate (RDV-TP), it will compete with ATP for RdRp’s active site. Thus RDV-TP acts as a competitive inhibitor for RdRp and prevents replication of the SARS-CoV-2 genome.
Once RdRp binds to RDV-TP, RNA synthesis is prematurely terminated a few nucleotides downstream during genome replication3, stopping the virus from replicating within host cells. Interestingly, despite being classed under ‘broad-spectrum’, RDV does has some degree of specificity. When tested on the distantly related Lassa virus RdRp, RDV-TP incorporation was not efficient, and chain termination was not observed3. This specificity would explain why remdesivir does not directly impact human gene transcription. Perhaps another valid hypothesis could be based on the different locations of RNA polymerases in the cell, but this is purely speculation on my part.
Evaluation and implementation
The general consensus held by those in favour of RDV, is that it shortens the time during which patients are infected. When announcing its approval by the UK, Secretary of State for Health and Social Care Matt Hancock said there is ‘early data suggesting it can shorten recovery time by around 4 days’.
While this may seem to bear little significance to the individual patient, in the larger scheme of the epidemic, this can make a noticeable difference. Shortening the average recovery time by a few days will free up more beds faster and will thus allow our NHS to support more patients. This will, ultimately, minimise the total number of deaths.
However, it should be noted that this is only a step in the right direction. Matt Hancock also announced that the drug will be given to a greatly limited number of individuals, and that the UK will be ‘prioritising the use of this treatment where it’ll provide the greatest benefit’.
Moreover, there are conflicting views on the use of remdesivir to treat COVID-19. According to a recent clinical trial ‘remdesivir was not associated with statistically significant clinical benefits5’. This is understandable as RDV does have its limitations. Coronaviruses are able to detect and remove nucleoside analogues such as RDV and can thus acquire resistance4. From a theoretical stance, RDV is a logical choice. This is supported by a number of clinical trials, one of which states that ‘patients who received remdesivir had a 31% faster time to recovery than those who received placebo’6. Based on the well elucidated mechanism of action as well as comparison between data from clinical trials, it is rational to conclude that RDV can shorten the average recovery time for COVID-19 patients.
Chloroquine (CQ) and hydroxychloroquine (HCQ)
CQ was first synthesised in 1934 and to this day it is still administered by physicians. Note that high levels of chloroquine can be toxic, so it must be taken orally.
The mechanism of CQ’s action against protozoa, such as P. malariae, has been thoroughly documented in the scientific literature; I shall provide a brief overview.
Protozoa require lysosomes for digestion. Endosomes, a type of membrane-bound vesicle, contain nutrients obtained via endocytosis. They fuse with lysosomes, and as the contents of the two vesicles mix together the nutrients are digested by various hydrolytic enzymes.
An acidic pH is essential for endosome maturation, and so embedded in the lysosome membrane are proton pumps. In figure 2a., you will notice that each of the two nitrogen atoms of the side chain have a lone pair, allowing for protonation to occur. In its protonated form, CQ is unable to enter cells due to its positive charge. However, in its unprotonated form, CQ is able to cross cell membranes — now with a basic side chain. The Brønsted–Lowry definition of a base is a species that acts as a proton acceptor. And so, as unprotonated CQ, a diprotic base, accumulates, the concentration of unbound protons decreases. Let us now consider the following equation:
pH = -log [H+]
Clearly, as [H+] decreases, the pH of lysosomes and endosomes must increase. This increase in pH will block endosome maturation and hinder both lysosome functionand endocytosis7,8. This means the protozoan will be rendered unable to carry out digestion and will therefore starve to death.
Molecular mechanism
HCQ is a less toxic derivative of CQ which is synthesised by adding a hydroxyl group onto CQ. While the molecular mechanism for either of these drugs is yet to be fully elucidated, it is thought that they prevent entry of SARS-CoV-2 into host cells.
The main hypothesis is that CQ and HCQ interfere with glycosylation of viral spike proteins and the angiotensin-converting enzyme (ACE2) receptor, preventing entry to the cell. It is also thought that these drugs prevent the virus from entering host cells by raising the pH of endosomes in the manner described above — something which has already been seen with other viruses9.
Evaluation and implementation
According to a recent clinical trial ‘preliminary results suggest that Chloroquine could be an effective and inexpensive option’8. However, another states that ‘there are insufficient data thus far to know whether HCQ or CQ has a role either in the treatment or in the prophylaxis of COVID-19’10. Moreover, both the Food and Drug administration and the European Medicines Agency have stated that CQ and HCQ should only be used for clinical trials and emergency situations11,12.
Conclusion
Even after the UK government lifts lockdown restrictions, SARS-CoV-2 will not simply die out over time. The general consensus among epidemiologists is that it will become endemic, just like influenza virus strains. While antiviral drugs certainly have their merits, they are not perfect, and any viable long-term strategy will most likely involve large-scale vaccination.
Xavier Khalid
Bibliography
1. https://www.who.int/health-topics/coronavirus
2. https://www.gov.uk/guidance/the-r-number-in-the-uk
3. Gordon, C.J., Tchesnokov, E.P., Woolner, E., Perry, J.K., Feng, J.Y., Porter, D.P. and Gotte, M. (2020).
Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency. Journal of Biological Chemistry, p.jbc.RA120.013679.
4. Amirian ES, Levy JK. 2020. Current knowledge about the antivirals remdesivir (GS-5734) and GS-441524 as therapeutic options for coronaviruses. One Health. 2020; 9:100128.
5. Wang et al. 2020. Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial. The Lancet, 395(10236).
7. Schrezenmeier, E. and Dörner, T. 2020. Mechanisms of action of hydroxychloroquine and chloroquine: implications for rheumatology. Nature Reviews. Rheumatology, 16(3), pp.155–166.
8. Huang, M., Tang, T., Pang, P., Li, M., Ma, R., Lu, J., Shu, J., You, Y., Chen, B., Liang, J. et al. (2020). Treating COVID-19 with Chloroquine. Journal of Molecular Cell Biology, 12(4), pp.322–325.
9. Savarino, A., Boelaert, J.R., Cassone, A., Majori, G. and Cauda, R. 2003. Effects of chloroquine on viral infections: an old drug against today’s diseases. The Lancet Infectious Diseases, 3(11), pp.722–727.
10. Şimşek Yavuz S, Ünal S. 2020. Antiviral treatment of COVID-19. Turkish Journal of Medical Sciences, 50(SI-1):611-619.
11. https://www.fda.gov/media/136534/download.
12. https://www.ema.europa.eu/en/news/covid-19-chloroquine-hydroxychloroquine-only-be-used-clinical-trials-emergency-use-programmes