tetano
Editor, Senior Moderator
Antimicrob Agents Chemother
. 2026 Apr 27:e0188525.
doi: 10.1128/aac.01885-25. Online ahead of print.
Synergistic antiviral effects of structure-guided peptides and a mutagenic base analog on SARS-CoV-2 replication
Sergio Ortega Del Campo[SUP] 1 [/SUP], Gregorio Joaquín Fernández Ballester[SUP] 2 [/SUP], Clara Blanes Mira[SUP] 3 [/SUP], Víctor Guirado Osorio[SUP] 4 [/SUP], Luis Díaz Martínez[SUP] 4 [/SUP], Ana Isabel de Ávila[SUP] 5 [/SUP], María Eugenia Soria[SUP] 5 6 [/SUP], Brenda Martínez-González[SUP] 5 6 [/SUP], Francisco José Villena González[SUP] 1 [/SUP], Josefa Gómez-Maldonado[SUP] 7 [/SUP], María Isabel Viciana Ramos[SUP] 8 9 [/SUP], Encarnación Clavijo Frutos[SUP] 8 9 [/SUP], Jesús L Santos González[SUP] 8 9 [/SUP], Ugo Bastolla[SUP] 5 [/SUP], Celia Perales[SUP] 5 6 [/SUP], Esteban Domingo[SUP] 5 [/SUP], Enrique Viguera[SUP] 1 [/SUP], Ana María Fernández Escamilla[SUP] 2 [/SUP], Ana Grande Pérez[SUP] 1 [/SUP]
Affiliations
The limited durability of vaccine protection and the rapid emergence of SARS-CoV-2 variants highlight the need for antiviral strategies that extend beyond vaccination and conventional small-molecule inhibitors. Here, we explored a dual approach combining structure-guided peptides predicted to interfere with the viral replication complex with lethal mutagenesis to limit SARS-CoV-2 replication. Using the crystallographic interfaces of nsp10 with nsp14 and nsp16, we designed short inhibitory peptides predicted to interact with the viral proofreading and RNA-capping machinery. In parallel, the mutagenic analog 5-fluorouracil was evaluated to determine its effect on SARS-CoV-2 in Vero E6 cells. Peptides P1 and P6 exhibited potent antiviral activity with minimal cytotoxicity, whereas 5-FU reduced specific infectivity without impairing genome replication. Combined treatment with 5-FU and peptide P1 resulted in >10[SUP]4[/SUP]-fold reduction in infectious virus, achieving near-complete loss of infectivity at non-cytotoxic concentrations. Next-generation sequencing revealed that dual treatment increased mutation frequency, altered mutant spectra, and decreased genome stability, consistent with progression toward error catastrophe. Principal component analysis confirmed that combined treatment generated mutant spectra distinct from either monotherapy. These findings are consistent with a dual antiviral strategy in which structure-guided peptides designed to interact with components of the SARS-CoV-2 replication complex act in combination with lethal mutagenesis to produce a synergistic interaction between these two complementary processes. This integrated approach suggests a potential broad-spectrum antiviral strategy with applicability to other coronaviruses.
Keywords: 5-fluorouracil; ExoN activity; MTase activity; SARS-CoV-2; drug combination; lethal mutagenesis; mutant spectra; nsp10; peptide design; synergism.
. 2026 Apr 27:e0188525.
doi: 10.1128/aac.01885-25. Online ahead of print.
Synergistic antiviral effects of structure-guided peptides and a mutagenic base analog on SARS-CoV-2 replication
Sergio Ortega Del Campo[SUP] 1 [/SUP], Gregorio Joaquín Fernández Ballester[SUP] 2 [/SUP], Clara Blanes Mira[SUP] 3 [/SUP], Víctor Guirado Osorio[SUP] 4 [/SUP], Luis Díaz Martínez[SUP] 4 [/SUP], Ana Isabel de Ávila[SUP] 5 [/SUP], María Eugenia Soria[SUP] 5 6 [/SUP], Brenda Martínez-González[SUP] 5 6 [/SUP], Francisco José Villena González[SUP] 1 [/SUP], Josefa Gómez-Maldonado[SUP] 7 [/SUP], María Isabel Viciana Ramos[SUP] 8 9 [/SUP], Encarnación Clavijo Frutos[SUP] 8 9 [/SUP], Jesús L Santos González[SUP] 8 9 [/SUP], Ugo Bastolla[SUP] 5 [/SUP], Celia Perales[SUP] 5 6 [/SUP], Esteban Domingo[SUP] 5 [/SUP], Enrique Viguera[SUP] 1 [/SUP], Ana María Fernández Escamilla[SUP] 2 [/SUP], Ana Grande Pérez[SUP] 1 [/SUP]
Affiliations
- PMID: 42037394
- DOI: 10.1128/aac.01885-25
The limited durability of vaccine protection and the rapid emergence of SARS-CoV-2 variants highlight the need for antiviral strategies that extend beyond vaccination and conventional small-molecule inhibitors. Here, we explored a dual approach combining structure-guided peptides predicted to interfere with the viral replication complex with lethal mutagenesis to limit SARS-CoV-2 replication. Using the crystallographic interfaces of nsp10 with nsp14 and nsp16, we designed short inhibitory peptides predicted to interact with the viral proofreading and RNA-capping machinery. In parallel, the mutagenic analog 5-fluorouracil was evaluated to determine its effect on SARS-CoV-2 in Vero E6 cells. Peptides P1 and P6 exhibited potent antiviral activity with minimal cytotoxicity, whereas 5-FU reduced specific infectivity without impairing genome replication. Combined treatment with 5-FU and peptide P1 resulted in >10[SUP]4[/SUP]-fold reduction in infectious virus, achieving near-complete loss of infectivity at non-cytotoxic concentrations. Next-generation sequencing revealed that dual treatment increased mutation frequency, altered mutant spectra, and decreased genome stability, consistent with progression toward error catastrophe. Principal component analysis confirmed that combined treatment generated mutant spectra distinct from either monotherapy. These findings are consistent with a dual antiviral strategy in which structure-guided peptides designed to interact with components of the SARS-CoV-2 replication complex act in combination with lethal mutagenesis to produce a synergistic interaction between these two complementary processes. This integrated approach suggests a potential broad-spectrum antiviral strategy with applicability to other coronaviruses.
Keywords: 5-fluorouracil; ExoN activity; MTase activity; SARS-CoV-2; drug combination; lethal mutagenesis; mutant spectra; nsp10; peptide design; synergism.