Coronaviruses

The term coronavirus (CoV) was well-known to virologists for decades, but sadly, in the last year, it probably became the most used, pronounced and feared word, worldwide, with the emergence of the Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) (also known as COVID-19) pandemic. The outbreak originally started in Wuhan, China, in 2019 and was rapidly spreading in Asia, Europe, the USA, South and Central Americas, Australia and the rest of the world, with currently more than 116 million diagnosed cases and 2.59 million casualties [1–3]. The disastrous coverup in the country where the outbreak initially started, coupled with delays from World Health Organization (WHO) in recognizing the potential for the spread of COVID-19, which was declared a pandemic only in March 2020 instead of January that year, led to the current severe situation, difficult to imagine even several months earlier. Indeed, the huge number of infected patients and the resulting evolutionary pressure of this RNA, error-prone virus, led to the emergence of a range of novel SARS-CoV-2 variants which are much more infectious and in some cases even more lethal than the original strain [4–6].

The response from the drug companies to the threats which SARS-CoV-2 posed globally, not only due to the huge pressure on almost collapsing healthcare systems but also to the social and economic impact caused by prolonged lockdowns worldwide, was exemplary and probably constitute the only positive phenomenon in this tragedy. Indeed, for the first time in the history of medical and pharmaceutical research, a new treatment, in this case vaccines, was developed and approved by Food and Drugs Administration (FDA)/European Medicines Agency (EMA) in less than one year. In fact, several vaccines are already available (those from Pfizer-BionTech, Moderna, Astra-Zeneca and Johnson&Johnson), whereas many others are in advanced clinical phases and might be available in the coming months [7–10]. In countries where a massive vaccine campaign was effectively promoted, such as Israel and UK, the number of new cases dramatically dropped, whereas even in case of infection, the hospitalization was not necessary, with a mild course of the disease, which constitutes the first but highly encouraging positive aspects in the fight against the COVID-19 pandemic up until now [10]. The monoclonal antibodies (MAbs) constitute another therapeutic approach that is being pursued, with some highly effective ones discovered from plasma of convalescent COVID-19 patients, now in clinical trials [11]. However, although vaccines and MAbs already showed their efficacy and will definitely be useful to stop or at least slow down the pandemic, the continuous evolution of the virus, which uses a variety of immune escape mechanisms, will probably lead to the emergence of variants which are not neutralized by these agents, as already reported for the South African and Brazilian SARS-CoV-2 strains [12,13]. For these reasons, novel small molecule antiviral drugs capable of impairing the replication of CoV that can be used in the current outbreak and maybe also in future occurrences, are in exceedingly high demand but are scarcely available to date [14]. Indeed, up until now, FDA/EMA approved just one such agent, which is remdesivir (Figure 1) – trade name Veklury, approved by FDA on 22 October 2020 [15] for the treatment of patients of at least 12 years old, requiring hospitalization.

Figure 1. Remdesivir, the only small molecule drug approved for the treatment of SARS-CoV-2 infection

However, just one antiviral drug is usually not enough for a safe cure with this type of infectious agent, due to the facile emergence of mutations, which may lead to strains resistant to the drug, as already well documented for other widespread viral infections, such as HIV, HCV, Ebola, etc. [16–21] and mentioned above to be the case of SARS-CoV-2 too. Thus, the development of novel specific and effective antiviral agents that target various coronavirus (or even host) proteins should continue in order to supplement the vaccine and MAb therapeutics with such small-molecule drugs. This would offer a much safer therapeutic approach for this new disease but presumably also for future outbreaks of CoVs, considering the fact that this in the third such phenomenon in less than 20 years (after SARS in 2002–2003) and Middle East Respiratory Syndrome (MERS) in 2012 [22–24].

This special issue of Expert Opinion on Therapeutic Patents dedicated to coronaviruses, addresses exactly this urgent need. The scientific and patent literature have been reviewed in a series of articles dealing with the drug repositioning for the search of new anti-CoV agents [25], RNA-dependent RNA polymerase (RdRp) inhibitors [26], helicase inhibitors [27] and inhibitors of the two cysteine proteases encoded in the genome of CoVs [28].

SARS-CoV-2 is an enveloped, positive-sense, single-stranded RNA beta-coronavirus, being prone to mutate very rapidly, since during RNA replication no error-correction mechanisms is used when copying the RNA genetic information into DNA [25–28]. Such mutations can confer new features to the virus, including the ability to infect new types of cells, or even new organisms and thus to determine the spillover, and this phenomenon occurred extensively in the case of SARS-CoV-2, as already mentioned here [11–13]. Like the preceding two CoVs that provoked outbreaks, SARS-CoV and MERS-CoV, the genome of SARS-CoV-2 encodes for several non-structural proteins (nsps), including several enzymes, such as an RNA-dependent RNA polymerase (RdRp), a helicase, a 3-chymotrypsin-like protease, also known as main protease (MPro) and a papain-like protease (PLP). These are in fact the main viral drug targets investigated up until now and considered in the review articles of this special issue [25–28].

The genetic material of SARS-CoV-2 is transcribed into two viral polypeptides of 490 kDa and 790 kDa, respectively, by the activity of the RdRp enzyme, with the help of the helicase. These polypeptides are subsequently co-translationally cleaved into mature nsps through the activity of two proteases encoded in the 5′ region of the open reading frame 1 (ORF1), i.e. MPro and PLP [25–28]. There is a very high homology between each nsps (at the level of all four enzymes mentioned above, RdRp, helicase, MPro and PLP) of SARS-CoV-2, SARS-CoV, and MERS-CoV, which means that presumably effective inhibitors for one of them may act efficaciously for all three, and this is a rather relevant finding which should be attentively considered by scientists, drug companies and policy makers, because it may lead to the design of rather broad-acting antivirals [25–28].

The review article of Mori’s group [25] considered the drug repositioning aspects in the search for new anti-COVID agents. This work examined both agents which have been tested against selected viral targets (e.g. RdRp, MPro and PLP) as well as various drugs which have been proved effective in COVID hospitalized patients and for which the mechanism of action or the real drug targets are poorly understood at this moment. Thus, among the first type of such compounds considered in the review, were the RdRp inhibitors such as remdesivir and favipiravir, the HIV protease inhibitors lopinavir and ritonavir thought to be able to inhibit CoV proteases, as well as compounds possessing a range of possible targets connected both with the viral and host cell biochemical machineries, such as chloroquine, hydroxychloroquine, baricitinib [25] as well as a large number of natural products [29]. Among the second type of drugs, i.e. those which showed some beneficial action in hospitalized patients, the review examined the corticosteroids, the low molecular weight heparins, azithromycin and biological drugs (MAbs, such as tocilizumab, anakinra, mavrilimumab, etc) which were investigated in many clinical trials, with rather controversial results. The article also presents an overview on the patents in the anti-COVD drugs repositioning and it surely brings relevant new data to the field.

The review by Vicenti et al. [26] examines in detail RdRp as an antiviral drug target, discussing the role of this enzyme in viral replication, its mechanism of action at molecular level, its mechanism of inhibition and the fact that this target is highly conserved among the various CoVs investigated to date, as already mentioned above. Although there are not many de novo drug design studies for finding effective RdRp inhibitors, nucleoside analogs or precursors such as remdesivir (already mentioned in detail above) molnupiravir, galidesivir, ribavirin, sofosbuvir, tenofovir and favipiravir, originally discovered and some of them in clinical use as antivirals for the treatment of other viral infections, significantly inhibit the SARS-CoV-2 enzyme [26]. In fact, as already mentioned above, remdesivir was the first small molecule antiviral drug approved for the treatment of COVID-19 [15].

Spratt et al. [27] discuss in detail the helicase of SARS-CoV-2 (and the closely related viruses), its mechanism of action and inhibition, also presenting the available inhibitors and drug design studies in the scientific and patent literature. Helicases are nucleic acid unwinding enzymes present in many (but not all) viruses, and ultimately, they started to be considered as drug targets of interest. Indeed, pritelivir, a helicase-primase primary sulfonamide inhibitor [30] (Figure 2) was clinically approved in 2020 for the treatment of herpes simplex virus infections in immunocompromised patients with drug resistance to other antivirals [31]. It is interesting to note that pritelivir is also a highly effective inhibitor of the zinc enzyme carbonic anhydrase [30,32], as most primary sulfonamides [33].

Figure 2. Structure of pritelivir, a helicase-primase primary sulfonamide inhibitor, also acting as an efficient carbonic anhydrase inhibitor [30,32,33]

The most effective presently patented helicase inhibitors belong to the 1,2,4-triazole-3-thione class, with derivatives such as SSYA 10–001, CPD-850, CPD-815 and CPD-062 being active in the low micromolar range and possessing very similar chemical structures [27]. Other helicase inhibitors disclosed so far in the patent literature include natural products [29] of the polyphenol type, such as quercetin and its derivatives, myricetin, scutellarein, 3,5-dihydroxy-chromone, as well as aryl-diketoacids (that act as HIV integrase inhibitors, among which clinically used inhibitor dolutegravir and its analogs), all of them showing activity in the low to high micromolar range [27]. There are no more effective, nanomolar helicase inhibitors to date, for this or other CoVs, and this interesting review article certainly will stimulate the search for more effective such agents.

Capasso et al. [28] discuss the three pairs of cysteine proteases present in the three CoVs that provoked outbreaks, SARS, MERS and SARS-CoV-2, with a particular stress on the last one (but, as already mentioned, there is a relevant homology between the ortholog proteins from these three viruses). The 3D crystal structures of both SARS-CoV-2 proteases (MPro and PLP) are available, alone and in complex with many inhibitors. In fact, this allowed for interesting structure-based drug design campaigns of protease inhibitors (PIs) targeting all these proteins, as discussed in detail in the article [28]. Most such compounds are peptidomimetics incorporating Michael acceptors of the aldehyde, thioketone, α-ketoamides, trans-α,β-unsaturated alkyl/benzyl esters, chloromethyl ketones, hydroxymethyl ketones type or are disulfides/dithiocarbamtes which react with the catalytic triad cysteine present within the enzyme active site [28]. However, non-peptidomimetic inhibitors were also reported, such as disulfiram and other disulfides incorporating various heterocyclic and aromatic scaffolds, fused 1,2,3-triazoles, ebselen, tideglusib and natural products (flavonoids, carmofur, shikonin, etc.). In the case of the two SARS-CoV-2 proteases, many low nanomolar inhibitors were already detected, some of which were also highly effective in inhibiting the viral replication in vivo, making this class of compounds among the most interesting ones in the development of novel antivirals.

All these but many other even more recent finding, such as for example the reports that statins may be protective against severe forms of COVID-19 infection [34–36], prompt us to stress again that finding inhibitors of the enzymes involved in the viral life cycle will provide a great opportunity for fighting these viruses (SARS CoV-1/2, MERS and possibly others) which already provoked deadly outbreaks and emerged as terrible threats to humankind. The development of a wide range of efficient small molecule antivirals in addition to the vaccines and monoclonal antibodies may indeed make the difference in our fight against these threats and putting an end to the current pandemic.

Declaration of interest

The author has no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

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Funding

This paper was not funded.