In Vitro Combinatorial Activity of Direct Acting Antivirals and Monoclonal Antibodies against the Ancestral B.1 and BQ.1.1 SARS-CoV-2 Viral Variants
Lia Fiaschi, Camilla Biba, Ilenia Varasi, Niccolò Bartolini, Chiara Paletti, Federica Giammarino, Francesco Saladini, Maurizio Zazzi, Ilaria Vicenti
Viruses, doi:10.3390/v16020168
Combination antiviral therapy may be helpful in the treatment of SARS-CoV-2 infection; however, no clinical trial data are available, and combined use of direct-acting antivirals (DAA) and monoclonal antibodies (mAb) has been reported only anecdotally. To assess the cooperative effects of dual drug combinations in vitro, we used a VERO E6 cell-based in vitro system with the ancestral B.1 or the highly divergent BQ.1.1 virus to test pairwise combinations of the licensed DAA, including nirmatrelvir (NRM), remdesivir (RDV) and the active metabolite of molnupiravir (EIDD-1931) as well the combination of RDV with four licensed mAbs (sotrovimab, bebtelovimab, cilgavimab, tixagevimab; tested only with the susceptible B.1 virus). According to SynergyFinder 3.0 summary and weighted scores, all the combinations had an additive effect. Within DAA/DAA combinations, paired scores with the B.1 and BQ.1.1 variants were comparable. In the post hoc analysis weighting synergy by concentrations, several cases of highly synergistic scores were detected at specific drug concentrations, both for DAA/DAA and for RDV/mAb combinations. This was supported by in vitro confirmation experiments showing a more than a linear shift of a drug-effective concentration (IC 50 ) at increasing concentrations of the companion drug, although the effect was prominent with DAA/DAA combinations and minimal or null with RDV/mAb combinations. These results support the cooperative effects of dual drug combinations in vitro, which should be further investigated in animal models before introduction into the clinic.
importantly, in vivo experiments should be designed in a suitable animal model before moving forward to a wide introduction of combination therapy into the clinic. SARS-CoV-2 animal models have been progressively improved [37] and should now be an integral part of the lessons learned from the COVID-19 pandemic [9] .
Supplementary Materials: The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/v16020168/s1, Table S1 : IC 50 synergistic potency shift measured in infected VERO E6 cells; Figure S1 : Bi-dimensional (2D) synergy plots of antivirals against the two SARS-CoV-2 strains tested, generated using Synergy Finder 3.0 (https://synergyfinder.fimm.fi/ accessed on 12 October 2023); Figure S2 : Overall combinatorial effects of the three DAA pairs as well as those of the three RDV/mAb groups compared by the Kruskal-Wallis test followed by Mann-Whitney pairwise comparisons between groups.
Author Contributions
Conflicts of Interest: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
References
Abdelnabi, Maes, De Jonghe, Weynand, Neyts, Combination of the Parent Analogue of Remdesivir (GS-441524) and Molnupiravir Results in a Markedly Potent Antiviral Effect in SARS-CoV-2 Infected Syrian Hamsters, Front. Pharmacol,
doi:10.3389/fphar.2022.1072202Ahmadi, Zadheidar, Sadeghi, Nejati, Salimi et al., SARS-CoV-2 Intrahost Evolution in Immunocompromised Patients in Comparison with Immunocompetent Populations after Treatment, J. Med. Virol,
doi:10.1002/jmv.28877Del Borgo, Garattini, Bortignon, Carraro, Di Trento et al., Tolerability and Prescribing Choice of Antiviral Molecules Molnupiravir, Remdesivir and Nirmatrelvir/r: A Real-World Comparison in the First Ten Months of Use, Viruses,
doi:10.3390/v15041025Fiaschi, Dragoni, Schiaroli, Bergna, Rossetti et al., Efficacy of Licensed Monoclonal Antibodies and Antiviral Agents against the SARS-CoV-2 Omicron Sublineages BA.1 and BA.2, Viruses,
doi:10.3390/v14071374Foucquier, Guedj, Analysis of Drug Combinations: Current Methodological Landscape, Pharmacol. Res. Perspect,
doi:10.1002/prp2.149Fuentealba-Manosalva, Mansilla, Buelvas, Martin-Martin, Torres et al., Mind the Curve: Dose-Response Fitting Biases the Synergy Scores across Software Used for Chemotherapy Combination Studies, Int. J. Mol. Sci,
doi:10.3390/ijms24119705Gidari, Sabbatini, Schiaroli, Bastianelli, Pierucci et al., Synergistic Activity of Remdesivir-Nirmatrelvir Combination on a SARS-CoV-2 In Vitro Model and a Case Report, Viruses,
doi:10.3390/v15071577Gidari, Sabbatini, Schiaroli, Bastianelli, Pierucci et al., The Combination of Molnupiravir with Nirmatrelvir or GC376 Has a Synergic Role in the Inhibition of SARS-CoV-2 Replication In Vitro, Microorganisms,
doi:10.3390/microorganisms10071475Hogan, Duerr, Dimartino, Marier, Hochman et al., Remdesivir Resistance in Transplant Recipients with Persistent Coronavirus Disease, Clin. Infect. Dis,
doi:10.1093/cid/ciac769Ianevski, Giri, Aittokallio, SynergyFinder 3.0: An Interactive Analysis and Consensus Interpretation of Multi-Drug Synergies across Multiple Samples, Nucleic Acids Res,
doi:10.1093/nar/gkac382Jeong, Chokkakula, Min, Kim, Choi et al., Combination Therapy with Nirmatrelvir and Molnupiravir Improves the Survival of SARS-CoV-2 Infected Mice, Antivir. Res,
doi:10.1016/j.antiviral.2022.105430Lanzafame, Gottardi, Guella, Collini, Costa et al., Successful Treatment of Persistent SARS-CoV-2 Infection with Nirmatrelvir/Ritonavir plus Sotrovimab in Four Immunocompromised Patients, J. Chemother,
doi:10.1080/1120009X.2023.2196917Li, Hilgenfeld, Whitley, De Clercq, Therapeutic Strategies for COVID-19: Progress and Lessons Learned, Nat. Rev. Drug Discov,
doi:10.1038/s41573-023-00672-yLin, Lu, Hong, Li, Chen et al., Animal models for studying coronavirus infections and developing antiviral agents and vaccines, Antivir. Res,
doi:10.1016/j.antiviral.2022.105345Marangoni, Antonello, Coppi, Palazzo, Nassi et al., Combination Regimen of Nirmatrelvir/Ritonavir and Molnupiravir for the Treatment of Persistent SARS-CoV-2 Infection: A Case Report and a Scoping Review of the Literature, Int. J. Infect. Dis,
doi:10.1016/j.ijid.2023.04.412Menegale, Manica, Zardini, Guzzetta, Marziano et al., Evaluation of Waning of SARS-CoV-2 Vaccine-Induced Immunity: A Systematic Review and Meta-Analysis, JAMA Netw. Open,
doi:10.1001/jamanetworkopen.2023.10650Mikulska, Sepulcri, Dentone, Magne, Balletto et al., Triple Combination Therapy with 2 Antivirals and Monoclonal Antibodies for Persistent or Relapsed Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Immunocompromised Patients, Clin. Infect. Dis,
doi:10.1093/cid/ciad181Nguyenla, Wehri, Van Dis, Biering, Yamashiro et al., Discovery of SARS-CoV-2 Antiviral Synergy between Remdesivir and Approved Drugs in Human Lung Cells, Sci. Rep,
doi:10.1038/s41598-022-21034-5Plebani, Bai, Si, Li, Zhang et al., 3D Lung Tissue Models for Studies on SARS-CoV-2 Pathophysiology and Therapeutics, Int. J. Mol. Sci,
doi:10.3390/ijms231710071Qu, Faraone, Evans, Zheng, Carlin et al., Enhanced Evasion of Neutralizing Antibody Response by Omicron XBB.1.5, CH.1.1, and CA.3.1 Variants, Cell Rep,
doi:10.1016/j.celrep.2023.112443Semenzato, Botton, Drouin, Baricault, Bertrand et al., Characteristics Associated with the Residual Risk of Severe COVID-19 after a Complete Vaccination Schedule: A Cohort Study of 28 Million People in France, Lancet Reg. Health. Eur,
doi:10.1016/j.lanepe.2022.100441Touret, Giraud, Bourret, Donati, Tran-Rajau et al., Enhanced Neutralization Escape to Therapeutic Monoclonal Antibodies by SARS-CoV-2 Omicron Sub-Lineages, iScience,
doi:10.1016/j.isci.2023.106413Turtle, Thorpe, Drake, Swets, Palmieri et al., Outcome of COVID-19 in Hospitalised Immunocompromised Patients: An Analysis of the WHO ISARIC CCP-UK Prospective Cohort Study, PLoS Med,
doi:10.1371/journal.pmed.1004086Vicenti, Martina, Boccuto, De Angelis, Giavarini et al., System-Oriented Optimization of Multi-Target 2,6-Diaminopurine Derivatives: Easily Accessible Broad-Spectrum Antivirals Active against Flaviviruses, Influenza Virus and SARS-CoV-2, Eur. J. Med. Chem,
doi:10.1016/j.ejmech.2021.113683Wagoner, Herring, Hsiang, Ianevski, Biering et al., Combinations of Host-and Virus-Targeting Antiviral Drugs Confer Synergistic Suppression of SARS-CoV-2, Microbiol. Spectr,
doi:10.1128/spectrum.03331-22Wang, Sacramento, Jockusch, Chaves, Tao et al., Combination of Antiviral Drugs Inhibits SARS-CoV-2 Polymerase and Exonuclease and Demonstrates COVID-19 Therapeutic Potential in Viral Cell Culture, Commun. Biol,
doi:10.1038/s42003-022-03101-9Wooten, Meyer, Lubbock, Quaranta, Lopez, MuSyC Is a Consensus Framework That Unifies Multi-Drug Synergy Metrics for Combinatorial Drug Discovery, Nat. Commun,
doi:10.1038/s41467-021-24789-zYadav, Wennerberg, Aittokallio, Tang, Searching for Drug Synergy in Complex Dose-Response Landscapes Using an Interaction Potency Model, Comput. Struct. Biotechnol. J,
doi:10.1016/j.csbj.2015.09.001Yan, Yan, Viral Target and Metabolism-Based Rationale for Combined Use of Recently Authorized Small Molecule COVID-19 Medicines: Molnupiravir, Nirmatrelvir, and Remdesivir, Fundam. Clin. Pharmacol,
doi:10.1111/fcp.12889Yang, Multani, Garrigues, Oh, Hemarajata et al., Transient SARS-CoV-2 RNA-Dependent RNA Polymerase Mutations after Remdesivir Treatment for Chronic COVID-19 in Two Transplant Recipients: Case Report and Intra-Host Viral Genomic Investigation, Microorganisms,
doi:10.3390/microorganisms11082096Zhu, Binder, Yurgelonis, Rai, Lazarro et al., Generation of a VeroE6 Pgp Gene Knock out Cell Line and Its Use in SARS-CoV-2 Antiviral Study, Antivir. Res,
doi:10.1016/j.antiviral.2022.105429Zuckerman, Bucris, Keidar-Friedman, Amsalem, Brosh-Nissimov, Nirmatrelvir Resistance-de Novo E166V/L50V Mutations in an Immunocompromised Patient Treated with Prolonged Nirmatrelvir/Ritonavir Monotherapy Leading to Clinical and Virological Treatment Failure-A Case Report, Clin. Infect. Dis,
doi:10.1093/cid/ciad494
