SARS-CoV-2 Replication Revisited: Molecular Insights and Current and Emerging Antiviral Strategies
Abstract
:1. Introduction
2. Molecular Mechanisms of SARS-CoV-2 Replication
2.1. Replication Complex and Enzymatic Machinery
2.2. Genome Replication Cycle
2.3. Host Factors in Viral Replication
3. Drugs Targeting SARS-CoV-2 Replication
3.1. Nucleoside Analogue Polymerase Inhibitors
3.2. Protease Inhibitors
3.3. Host-Directed Antivirals
3.4. Combination Therapies and Drug Synergy
3.5. Antiviral Resistance Considerations
4. Future Trends and Emerging Antiviral Strategies
4.1. Novel Targets in the Viral Replication Cycle
4.2. Emerging and Novel Host-Directed Antivirals
4.3. AI and Computational Drug Discovery
4.4. Gene Silencing, RNA-Targeting Therapies, Molecular Glues and Targeted Protein Degraders
4.5. Pan-Coronavirus and Broad-Spectrum Antivirals
5. Conclusions and Future Directions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Drug/Compound | Target/Mechanism | Drug Class | Mode of Action | Clinical Use/Efficacy | Resistance/Limitations |
---|---|---|---|---|---|
Remdesivir | RdRp (nsp12) | Nucleoside analogue | Adenosine analogue; chain termination via delayed RNA translocation | IV use; moderately accelerates recovery in hospitalized patients | Partial resistance via nsp12 mutations (e.g., V166, E802); fitness cost limits spread |
Molnupiravir | RdRp | Nucleoside analogue | Cytidine/uridine analogue; induces lethal mutagenesis | Oral use; reduces hospitalization in mild-to-moderate cases | Theoretical mutagenic risks; not fully neutralized by proofreading |
Favipiravir | RdRp | Nucleoside analogue | Purine analogue; weak RNA synthesis inhibition | Limited effect; not a frontline drug | Requires high concentrations; inconsistent trial results |
Ribavirin | RdRp | Nucleoside analogue | Guanosine analogue; promotes mutagenesis | Alone: limited effect; synergistic in combinations | High toxicity; synergizes with remdesivir |
VV116 (Deuviridine) | RdRp | Nucleoside analogue | Oral prodrug of GS-441524 | Comparable to Paxlovid in trials; high bioavailability | Not widely approved |
Nirmatrelvir + Ritonavir (Paxlovid) | 3CLpro | Protease inhibitor | Blocks polyprotein cleavage; halts replication complex maturation | Oral use; ~89% reduction in hospitalization if early | Resistance via 3CLpro mutations (in vitro); clinical relevance not yet clear |
Ensitrelvir | 3CLpro | Protease inhibitor | Similar to nirmatrelvir | Effective in Japan trials | Investigational |
Lopinavir + Ritonavir | 3CLpro | Protease inhibitor | HIV protease inhibitor; weak SARS-CoV-2 activity | No benefit in early COVID-19 trials | Largely abandoned |
GRL-0617 | PLpro | Protease inhibitor | Preclinical inhibitor of papain-like protease | Preclinical stage | Not clinically available |
Fluoxetine | Host (cell pathways) | SSRI/host-directed | Synergistic with GS-441524; may block viral egress | In vitro synergy with remdesivir | Lysosomotropic mechanism; repurposed drug |
Itraconazole | Host (cholesterol trafficking) | Antifungal/host-directed | Disrupts sterol trafficking needed for replication | Enhances remdesivir efficacy in vitro | Repurposed, not virus-specific |
Baricitinib | Host (JAK/STAT + endocytosis) | JAK inhibitor/immunomodulator | Blocks cytokine storm; may block viral entry | EUA with remdesivir; reduces inflammation | Minor antiviral activity; adjunctive |
Camostat | TMPRSS2 | Host entry inhibitor | Blocks spike protein priming | In vitro efficacy; used in combinations | Investigational |
Brequinar | DHODH (pyrimidine synthesis) | Host-targeting | Reduces the nucleotide pools needed for RNA synthesis | Strong synergy with molnupiravir | Host toxicity concerns |
Remdesivir + Nirmatrelvir | RdRp + 3CLpro | Antiviral synergy | Blocks RNA synthesis and protein processing | Superior in vitro and in case reports | Dual targeting reduces the resistance potential |
Remdesivir + Ribavirin | RdRp | Chain terminator + mutagen | Complete viral extinction in vitro | Enhances the mutational burden and replication block | Not in clinical use |
Molnupiravir + Nirmatrelvir | RdRp + 3CLpro | Dual-action antiviral | Polymerase + protease inhibition | Enhanced synergy; potential for resistant strains | Preclinical and early trial stages |
Molnupiravir + Camostat + Brequinar | Multi-target | Polymerase + entry + nucleotide synthesis | Maximal suppression in vitro | For persistent/resistant infections | Not tested clinically |
Strategy | Targets/Approaches | Key Compounds/Tools | Potential Impact |
---|---|---|---|
Novel Viral Targets | nsp14 exonuclease (ExoN), the NiRAN domain of nsp12, PLpro, and macrodomains | PLpro inhibitors (e.g., GRL-0617), and experimental NiRAN inhibitors | Enhances polymerase inhibitor efficacy; reduces immune suppression; introduces new viral drug targets |
Host-Directed Antivirals | TMPRSS2, pyrimidine biosynthesis (e.g., DHODH), TRiC, Hsp90, JAK-STAT pathways, IFN-λ system | Camostat, nafamostat, brequinar, baricitinib, teriflunomide, interferon lambda (IFN-λ) | Reduced viral resistance potential; broad-spectrum activity; may pose host toxicity risks |
AI and Computational Drug Discovery | Structure-based virtual screening, machine learning prediction, synergy modeling, allosteric pockets on RdRp (nsp12) | COVID Moonshot, flavonoid derivatives (e.g., myricetin), ML-based compound ranking | Accelerates drug discovery; identifies novel scaffolds; enables variant-specific antiviral tailoring |
Gene silencing and RNA-Targeting Therapies | siRNA targeting conserved genome regions (e.g., RdRp); CRISPR-Cas13-mediated cleavage of viral RNA | siRNA-nanoparticle delivery systems and Cas13-based antiviral platforms | Programable and rapidly deployable antivirals; adaptable to emerging viruses |
Pan-Coronavirus and Broad-Spectrum Antivirals | Conserved viral domains (nsp12-nsp7/nsp8 interface, nsp13 helicase); shared host dependency factors (e.g., DHODH, IFN) | Ribavirin, NHC, DHODH inhibitors, innate immune modulators | Enables pandemic preparedness; broad viral coverage; strategic stockpiling for future zoonotic outbreaks |
Strategy | Type | Evidence of Activity | Preclinical/Clinical Status |
---|---|---|---|
GRL-0617 | PLpro (nsp3) inhibitor | Inhibits viral polyprotein cleavage in vitro | Preclinical |
VV116 (Deuviridine) | Nucleoside analogue | Comparable to Paxlovid in early clinical trials | Clinical (Phase 3, China) |
Camostat | Host-directed antiviral | Blocks viral entry; enhances effects in combinations | Clinical (investigational) |
Brequinar | Host-directed antiviral | Synergistic with molnupiravir in lung cell models | Preclinical/Early trials |
Baricitinib | Host-directed antiviral/immunomodulator | EUA with remdesivir; reduces inflammation & viral entry | Approved (with remdesivir) |
Molnupiravir | Nucleoside analogue | Reduces hospitalization in mild/moderate cases | Approved (oral) |
Remdesivir | Nucleoside analogue | Accelerates recovery in hospitalized patients | Approved (intravenous) |
Fluoxetine | Host-directed/repurposed | Enhances remdesivir efficacy in vitro | Preclinical |
Cas13-based platforms | Gene-targeting modality | Inhibits viral RNA replication in vitro | Preclinical (proof-of-concept) |
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Subong, B.J.J.; Forteza, I.L. SARS-CoV-2 Replication Revisited: Molecular Insights and Current and Emerging Antiviral Strategies. COVID 2025, 5, 85. https://doi.org/10.3390/covid5060085
Subong BJJ, Forteza IL. SARS-CoV-2 Replication Revisited: Molecular Insights and Current and Emerging Antiviral Strategies. COVID. 2025; 5(6):85. https://doi.org/10.3390/covid5060085
Chicago/Turabian StyleSubong, Bryan John J., and Imelda L. Forteza. 2025. "SARS-CoV-2 Replication Revisited: Molecular Insights and Current and Emerging Antiviral Strategies" COVID 5, no. 6: 85. https://doi.org/10.3390/covid5060085
APA StyleSubong, B. J. J., & Forteza, I. L. (2025). SARS-CoV-2 Replication Revisited: Molecular Insights and Current and Emerging Antiviral Strategies. COVID, 5(6), 85. https://doi.org/10.3390/covid5060085