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ADVANCING ANTIVIRAL DRUG DISCOVERY: INSIGHTS GAINED FROM
COVID-19
Khotamov Tolibjon Narzullayevich
Assistant teacher of the Alfraganus University
ORCID ID:0009-0001-3723-0921
Email: tolibjonhotamov11@gmail.com
https://doi.org/10.5281/zenodo.14545651
Abstract:
The COVID-19 pandemic spurred unprecedented rapid and collaborative
efforts in drug discovery across academia and industry, leading to the development, approval,
and deployment of several therapeutics within just two years. This article highlights the
collective experiences of pharmaceutical companies and academic collaborations actively
engaged in SARS-CoV-2 antiviral research. Key stages of the small-molecule drug discovery
process are discussed, including target selection, medicinal chemistry, antiviral assays, animal
efficacy studies, and strategies to anticipate resistance. We emphasize the critical need for
high-quality chemical probes targeting understudied viral proteins, which could serve as
foundational tools for future drug discovery efforts. Given the relatively small size of viral
proteomes, systematically developing a comprehensive set of chemical probes for proteins in
viruses with pandemic potential represents a feasible and valuable challenge for the scientific
community.
Keyword:
Ensitrelvir, bemnifosbuvir, alisporivir (Debio-025), medicinal chemistry,
Remdesivir (Gilead Sciences).
Introduction
Viral outbreaks pose some of the most significant public health threats of our time, as
exemplified by the COVID-19 pandemic, which has claimed over six million lives. Several
global factors are increasing the likelihood of future pandemics. Climate change, combined
with the destruction of wildlife habitats, elevates the frequency of human–animal interactions,
thereby increasing the risk of zoonotic spillovers. Additionally, rising global temperatures
expand the habitats of viral vectors such as mosquitoes and ticks, potentially enabling the
broader spread of arboviruses. The prevalence of international travel further accelerates the
transformation of localized epidemics into global pandemics. Addressing these risks through
the development of effective therapeutics for current and future pandemics must therefore
remain a top public health priority.
Prior to the COVID-19 pandemic, antiviral development primarily targeted human
immunodeficiency virus (HIV) and hepatitis C virus (HCV), which accounted for more than
67% of approved antivirals. Historically, the drug discovery and development process,
especially for first-generation therapeutics, has spanned decades. However, COVID-19
presented unique challenges as an acute, severe, and highly transmissible viral disease. For
the first time, the translational science sector executed rapid drug discovery campaigns
during a rapidly evolving pandemic, achieving remarkable milestones. Within two years, two
oral therapeutics—nirmatrelvir (Pfizer) and molnupiravir (Merck, initially developed for
Venezuelan equine encephalitis virus)—received emergency use authorization (EUA).
Additionally, several oral investigational therapeutics entered clinical stages, including
ensitrelvir (S-217622, Shionogi), pomotrelvir (PBI-0451, Pardes Biosciences), bemnifosbuvir
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(AT-527, ATEA), and EDP-235 (Enanta). Remdesivir (Gilead Sciences), originally developed
for Ebola, also received approval early in the pandemic as an intravenous therapeutic.
This Perspective is informed by a roundtable discussion with representatives from
biopharmaceutical companies and public sector organizations actively engaged in COVID-19
research and development. It outlines key lessons from the rapid antiviral drug discovery
efforts, or “sprints,” undertaken during the pandemic and highlights unresolved challenges.
The discussion focuses on critical aspects of the process, including target selection, medicinal
chemistry strategies, in vitro and in vivo models, and approaches to preempt resistance.
Target Selection and Validation
Antiviral therapeutics can be designed to target either the host or the virus itself. Host-
directed antivirals aim to inhibit human proteins critical for the viral life cycle. During the
COVID-19 pandemic, substantial efforts were made to identify host-directed therapies,
primarily through drug repurposing screens. Some of these candidates advanced to clinical
trials, facilitated by initiatives such as Accelerating COVID-19 Therapeutic Interventions and
Vaccines (ACTIV) and the Randomized Evaluation of COVID-19 Therapies (RECOVERY)
platform trials, as well as company-sponsored studies. However, no host-directed antiviral
has yet been approved for COVID-19.
Proponents of host-directed approaches argue that they offer advantages such as a
higher barrier to antiviral resistance and broad-spectrum activity if the target is shared across
multiple viruses. Despite these potential benefits, there are notable challenges. These include
the risk of on-target toxicity due to disruption of essential host pathways, reduced efficacy
when the viral life cycle exploits multiple redundant pathways, and poor translation of results
from in vivo models to clinical efficacy. Historically, successful host-directed antivirals have
been limited to examples such as interferons for hepatitis C virus (HCV) and hepatitis B virus
(HBV), CCR5 antagonists for HIV, and cyclophilin inhibitors like alisporivir (Debio-025), which
reached late-stage clinical development for HCV.
In contrast, most approved antivirals directly target viral proteins. For severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2), efforts have focused on these viral targets
due to their central role in the viral life cycle.
Selecting the right antiviral target is a critical step in the drug discovery process. An
ideal target should meet the following criteria:
1.
Essentiality
: The target must be indispensable for the viral life cycle.
2.
Tractability
: It should have a clear and feasible mechanism of action.
3.
Inhibitor Potential
: The target must be amenable to inhibition by small molecules with
favorable drug-like properties.
4.
Resistance Barrier
: The target should have a high fitness barrier to mutation,
minimizing the risk of resistance development.
These factors form the foundation for successful antiviral drug discovery and ensure a
higher likelihood of developing therapeutics with significant clinical impact.
Validated Mechanism of Action
Antiviral targets with prior clinical validation, demonstrating that target inhibition leads
to antiviral effects, present a lower translational risk. While this is a high standard to meet,
these targets are often not readily available during an emerging pandemic. Nevertheless,
evidence from other viruses with shared replication mechanisms can bolster confidence in the
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target. Establishing "target-class confidence" is possible when multiple approved therapeutics
target the same class across different viruses. Efforts by the National Institute for Allergy and
Infectious Diseases aim to define prototype and priority pathogens within viral families of
pandemic concern and to develop therapeutics against them.
In cases without clinical validation, a target gains credibility when its mechanism of
action is well-understood and studies show that disrupting protein function directly impacts
viral replication, either in vitro or in vivo. This can be demonstrated through the use of
chemical probes or reverse genetics approaches.
Indirectly targeting viral proteins involved in evading host immune responses is less
common due to the intricate interplay between viral proteins and the immune system.
Similarly, targeting stages in the viral life cycle, such as entry, requires caution, as some
viruses utilize multiple pathways for infection and cell-to-cell spread.
Chemical Probe Validation
The ultimate goal of antiviral therapy is the chemical inhibition of a specific target. Key
questions include:
Can the protein be engaged by a small molecule (i.e., is it "druggable")?
Does engaging the target site modulate the protein's function?
Does a chemical probe modulating the target’s function result in viral inhibition in
cellular assays?
Identifying small molecules that inhibit the target with corresponding cellular antiviral
activity and demonstrating a correlation between inhibition potency and antiviral activity
(structure–activity relationship) strengthens the case for the target's validity and tractability.
The availability of robust functional assays and structural data greatly facilitates the
development of chemical probes for previously untargeted viral proteins. Advances in cryo-
electron microscopy have further enabled the detailed elucidation of complex protein
structures, aiding the identification of druggable targets. However, while numerous chemical
probes have been developed for human targets, viral targets remain comparatively
underexplored.
Sequence Conservation
Beyond clinical and mechanistic evidence, target relevance can also be assessed by
evaluating its sequence and structural conservation across the viral family or among
circulating variants. Conservation can be examined across the entire protein or within critical
binding sites. Conserved targets are considered more robust, as essential proteins are less
likely to accumulate mutations. Conversely, targeting mutationally flexible proteins is more
challenging, as the inhibitor must remain effective against all variants.
Focusing on conserved viral proteins also increases the potential for developing broad-
spectrum antivirals, which are crucial for pandemic preparedness and response.
Medicinal Chemistry
Once a target is identified, medicinal chemistry involves an iterative cycle of designing,
synthesizing, and testing molecules to transform chemical starting points into viable
development candidates. Establishing a realistic therapeutic profile is critical in guiding the
medicinal chemistry strategy to ensure the final product delivers meaningful clinical value.
These goals are typically categorized into the
target product profile (TPP)
and
target candidate
profile (TCP)
. The TPP outlines the desired clinical attributes of the therapeutic, while the TCP
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focuses on molecular properties such as target engagement, cellular antiviral activity, and
safety pharmacology. The TPP informs the design of target-specific TCPs, shaping the
development pathway.
Target Product Profile (TPP)
In an ideal antiviral drug discovery scenario, the TPP for a direct-acting antiviral would
aim for an orally available, once-daily administration—or, for acute infections like SARS-CoV-
2, even a single-dose regimen. A wide treatment window is also desirable to ensure
accessibility for populations with limited access to rapid diagnostics.
However, in the context of an urgent pandemic response, these ideal specifications are
often unattainable luxuries. For first-generation antiviral therapies, less stringent TPP
requirements may be acceptable, including the following:
1.
Suboptimal Dosing Regimens
: Frequent dosing schedules, such as three or four times
daily, may be tolerated temporarily.
2.
Non-Oral Delivery Routes
: Intravenous formulations might be suitable for high-risk
patients. Although impractical for early-stage treatment on a large scale, intravenous drugs
like remdesivir (Veklury, Gilead Sciences) received emergency use authorization (EUA) and
full FDA approval during the SARS-CoV-2 pandemic. Similarly, the first SARS-CoV-2 Mpro
inhibitor entered clinical trials as an intravenous formulation.
3.
Suboptimal Pharmacokinetics
: While distribution, metabolism, and pharmacokinetic
(DMPK) profiles may not be ideal, it is essential that the free drug’s trough concentration
(
Cmin
) remains above the protein-adjusted 90% effective concentration (
EC90
) in cellular
assays. Maintaining drug levels above EC90 is the minimum requirement for antiviral efficacy,
with higher concentrations often necessary for second-generation antivirals, especially as
resistance mechanisms become better understood.
4.
Narrower Patient Cohorts
: First-generation therapies might focus on specific high-risk
populations, with careful monitoring of drug–drug interactions. Strategies such as co-dosing
with pharmacokinetic enhancers or avoiding specific patient groups (e.g., women of
childbearing potential) may be necessary in these cases.
5.
Short Therapeutic Windows
: For some antivirals, such as oseltamivir for influenza,
rapid treatment initiation is crucial. While prescribing and administering a drug within 48
hours of symptom onset poses challenges, it is preferable for antiviral efficacy to extend to
treatments initiated up to five days after symptom onset.
By accommodating these limitations in the initial pandemic response, the
development of first-generation antivirals can address urgent clinical needs while paving the
way for more refined, second-generation therapies in the future.
Cell Culture Models
Cellular models of antiviral infection play a critical role in identifying effective small-
molecule inhibitors. A key aspect of medicinal chemistry involves analyzing how variations in
chemical structures affect biological activity within these cellular assays. This process
requires a low-variance system to ensure reliable and consistent data. High-throughput
cellular assays are especially valuable during the later phases of drug discovery, as their
capacity ideally aligns with the pace of chemical synthesis. Since assay data are used to
prioritize compounds, comparing potencies across different assay systems should be avoided
to ensure consistency in compound ranking.
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Many antiviral assays involve infectious viral strains, necessitating high-containment
laboratories such as biosafety level (BSL) 3 or BSL 4 facilities. These requirements add
logistical complexity, limit accessibility, and reduce the throughput of relevant assays. Given
these challenges, reproducible and high-throughput cellular assays are generally preferred
over assays with higher biological relevance but greater noise or lower throughput. Tracking
variance, robustness, and reproducibility through statistical measures like Z scores is
essential for assay quality.
References:
1.
Gibb, R., Franklinos, L. H. V., Redding, D. W. & Jones, K. E. Ecosystem perspectives are
needed to manage zoonotic risks in a changing climate.
Br. Med. J.
371, m3389 (2020).
2.
Vidal, J. Destroyed habitat creates the perfect conditions for coronavirus to emerge.
[Reprinted
from
Ensia]
Scientific
American
3.
Messina, J. P. et al. The current and future global distribution and population at risk of
dengue.
Nat. Microbiol.
4, 1508–1515 (2019).
4.
Goldin, I. & Mariathasan, M.
The Butterfly Defect: How Globalization Creates Systemic
Risks, and What to Do about It.
Princeton Univ. Press (2015).
5.
Chaudhuri, S., Symons, J. A. & Deval, J. Innovation and trends in the development and
approval of antiviral medicines: 1987–2017 and beyond.
Antiviral Res.
155, 76–88 (2018).
6.
Gordon, D. E. et al. A SARS-CoV-2 protein interaction map reveals targets for drug
repurposing.
Nature
583, 459–468 (2020).
7.
Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked
by a clinically proven protease inhibitor.
Cell
181, 271–280.e8 (2020).
8.
Collins, F. S. & Stoffels, P. Accelerating COVID-19 therapeutic interventions and vaccines
(ACTIV): an unprecedented partnership for unprecedented times.
JAMA
323, 2455–2457
(2020).
9.
Musayeva, S. I. (2024). ADVANTAGES AND DISADVANTAGES OF INTERACTIVE
METHODS INTRODUCING THE СLT (СOMMUNIСATIVE LANGUAGE TEACHING) APPROACH.
World Scientific Research Journal, 32(1), 217-219.
10.
Kumar, N. et al. Host-directed antiviral therapy.
Clin. Microbiol. Rev.
33, e00168-19
(2020).
11.
Wood, A. & Armour, D. In
Progress in Medicinal Chemistry
(eds King, F. D. & Lawton, G.)
239–271 (Elsevier, 2005).
