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Del Rosario García-Lozano M, Dragoni F, Gallego P, Mazzotta S, López-Gómez A, Boccuto A, Martínez-Cortés C, Rodríguez-Martínez A, Pérez-Sánchez H, Manuel Vega-Pérez J, Antonio Del Campo J, Vicenti I, Vega-Holm M, Iglesias-Guerra F. Piperazine-derived small molecules as potential Flaviviridae NS3 protease inhibitors. In vitro antiviral activity evaluation against Zika and Dengue viruses. Bioorg Chem 2023; 133:106408. [PMID: 36801791 DOI: 10.1016/j.bioorg.2023.106408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 01/23/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Since 2011 Direct Acting antivirals (DAAs) drugs targeting different non-structural (NS) viral proteins (NS3, NS5A or NS5B inhibitors) have been approved for clinical use in HCV therapies. However, currently there are not licensed therapeutics to treat Flavivirus infections and the only licensed DENV vaccine, Dengvaxia, is restricted to patients with preexisting DENV immunity. Similarly to NS5 polymerase, the NS3 catalytic region is evolutionarily conserved among the Flaviviridae family sharing strong structural similarity with other proteases belonging to this family and therefore is an attractive target for the development of pan-flavivirus therapeutics. In this work we present a library of 34 piperazine-derived small molecules as potential Flaviviridae NS3 protease inhibitors. The library was developed through a privileged structures-based design and then biologically screened using a live virus phenotypic assay to determine the half-maximal inhibitor concentration (IC50) of each compound against ZIKV and DENV. Two lead compounds, 42 and 44, with promising broad-spectrum activity against ZIKV (IC50 6.6 µM and 1.9 µM respectively) and DENV (IC50 6.7 µM and 1.4 µM respectively) and a good security profile were identified. Besides, molecular docking calculations were performed to provide insights about key interactions with residues in NS3 proteases' active sites.
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Affiliation(s)
- María Del Rosario García-Lozano
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain; SeLiver Group at the Institute of Biomedicine of Seville (IBIS), Virgen del Rocío University Hospital CSIC University of Seville, Seville, Spain
| | - Filippo Dragoni
- Department of Medical Biotechnologies, Siena University Hospital, Policlinico Le Scotte, Viale Bracci 16, 53100 Siena, Italy
| | - Paloma Gallego
- Unit for Clinical Management of Digestive Diseases and CIBERehd, Valme University Hospital, 41014 Seville, Spain
| | - Sarah Mazzotta
- Department of Chemistry, University of Milan, 20133 Milan, Italy
| | - Alejandro López-Gómez
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
| | - Adele Boccuto
- Department of Medical Biotechnologies, Siena University Hospital, Policlinico Le Scotte, Viale Bracci 16, 53100 Siena, Italy; VisMederi Research srl, Siena, Italy
| | - Carlos Martínez-Cortés
- Structural Bioinformatics and High Performance Computing (BIO-HPC) Research Group, UCAM Universidad Católica de Murcia, 30107 Murcia, Spain
| | - Alejandro Rodríguez-Martínez
- Department of Physical Chemistry and Institute of Biotechnology, University of Granada, Campus Fuentenueva sn, 18071 Granada, Spain
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing (BIO-HPC) Research Group, UCAM Universidad Católica de Murcia, 30107 Murcia, Spain
| | - José Manuel Vega-Pérez
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
| | | | - Ilaria Vicenti
- Department of Medical Biotechnologies, Siena University Hospital, Policlinico Le Scotte, Viale Bracci 16, 53100 Siena, Italy.
| | - Margarita Vega-Holm
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain.
| | - Fernando Iglesias-Guerra
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
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Marchi S, Dragoni F, Boccuto A, Idoko OT, Zazzi M, Sow S, Diallo A, Viviani S, Montomoli E, Vicenti I, Trombetta CM. Neutralizing activity of African lineage Zika virus immune sera towards Asian lineage. Acta Trop 2022; 237:106736. [DOI: 10.1016/j.actatropica.2022.106736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 11/27/2022]
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Piomboni P, Luongo F, Dragoni F, Gentile M, Boccuto A, Boschi L, Morgante G, Vicenti I, Zazzi M, Luddi A. P-460 SARS-CoV-2 infection of human ovarian cells: an in vitro model for the detection of the virus entry into the host cells. Hum Reprod 2022. [PMCID: PMC9384335 DOI: 10.1093/humrep/deac107.432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Study question Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can enter and actively infect human follicular and granulosa cells? Summary answer Follicular Granulosa (GCs) and Cumulus cells (CCs) are susceptible to SARS-CoV-2 infection that is able to reproduce. What is known already To enter host cells, SARS-CoV-2 uses Spike S1 subunit to bind the receptor angiotensin-converting enzyme2 (ACE2), S2 subunit is cleaved by the host transmembrane serine protease 2 (TMPRSS2) or by cathepsin L (CSTL) to produce unlocked, fusion-catalyzing viral forms. CD147 (BSG) has been proposed as an additional host receptor for SARS-CoV-2. Female fertility is strictly dependent on oocyte quality and competence. ACE2 is highly expressed in the human ovaries and in the stromal endometrial cells, as well as in GCs and oocytes. The expression of ACE2 strongly suggests that it is potentially at a high risk of SARS-CoV-2 infection. Study design, size, duration In order to analyze the presence of host receptors ACE2 and co-receptors TMPRSS2-CSTL and BSG and consequently the susceptibility of GCs and CCs to SARS-CoV2 infection. GCs and CCs were collected from about 25 patients undergoing IVF/ICSI cycles at the UOSA of Assisted Reproductive techniques, from March 2020 to October 2021 at the Center of Couple Sterility, Siena University Hospital. Participants/materials, setting, methods GCs and CCs were collected from women undergoing IVF cycle. GCs were recovered from the follicular fluid according to the procedure previously published. After oocyte denuding, CCs were isolated and both GCs and CCs co-cultured with SARS-CoV-2 then the supernatant was used to infect VERO6 Cells. Host factors and SARS-CoV2 expression/localization were confirmed by RT-PCR, Western blot and Immunofluorescence. SARS-CoV2 infection and its effect on GCs and CCs were evaluated by Transmission and Immuno-electron microscopy. Main results and the role of chance qRT-PCR analysis and WB showed that ACE2, TMPRSS2, BSG and CTSL transcripts were expressed in both GCs and CCs cells, even if at different levels. ACE2 transcript was significantly increased in the CCs (0.43 vs 0.15; p < 0.05) with respect to GCs; this datum is very interesting since CCs are the follicular cells able to establish intimate connections with the developing oocyte (e.g. gap junctions). Therefore, contrary to what can be assumed, human CCs cannot act as a barrier against virus entry into the oocyte. Coreceptor BSG and CTSL were the most expressed in GCs with respect to TMPRSS2, (0.7 vs 0.3 and 0.8 vs 0.4 respectively; p < 0.05). Ultrastructural evaluation of human GCs and CCs infected with SARS-CoV-2 was carried out at different time points post-infection (24h, 48h and 72h). Infected human GCs showed cell-associated virus-like particles, virions were approximately spherical, with a diameter outside the lipid bilayer ranging from 50-150 nm and ultrastructural characteristics consistent with those described for other coronaviruses. Complete virions were also observed inside the cytoplasm as single or small groups of particles, either dispersed or within large vesicles. Immunoelectron microscopy confirmed these particles as SARS-CoV2. Limitations, reasons for caution This is a human in vitro study, and we cannot predict all the implications in female fertility and related to the oocyte Wider implications of the findings We provide evidence in favor of SARS-CoV-2 infection in GCs and CCs, the ovarian somatic cells that support oocyte development and competence acquisition. The close relationship between oocytes and follicular cells raises the hypothesis that these cells may represent a vehicle for the oocyte SARS-CoV-2 infection Trial registration number Not applicable
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Affiliation(s)
- P Piomboni
- University of Siena, Molecular and Developmental Medicine , Siena, Italy
| | - F.P Luongo
- University of Siena, Molecular and Developmental Medicine , Siena, Italy
| | - F Dragoni
- University of Siena, Department of Medical Biotechnologies , Siena, Italy
| | - M Gentile
- University of Siena, Department of Life Sciences , Siena, Italy
| | - A Boccuto
- University of Siena, Department of Medical Biotechnologies , Siena, Italy
| | - L Boschi
- University of Siena, Molecular and Developmental Medicine , Siena, Italy
| | - G Morgante
- University of Siena, Molecular and Developmental Medicine , Siena, Italy
| | - I Vicenti
- University of Siena, Department of Medical Biotechnologies , Siena, Italy
| | - M Zazzi
- University of Siena, Department of Medical Biotechnologies , Siena, Italy
| | - A Luddi
- University of Siena, Molecular and Developmental Medicine , Siena, Italy
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Vicenti I, Gatti F, Scaggiante R, Boccuto A, Zago D, Basso M, Dragoni F, Parisi SG, Zazzi M. The second dose of the BNT162b2 mRNA vaccine does not boost SARS-CoV-2 neutralizing antibody response in previously infected subjects. Infection 2022; 50:541-543. [PMID: 34342854 PMCID: PMC8329626 DOI: 10.1007/s15010-021-01680-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Gatti
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121, Padova, Italy
| | | | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Daniela Zago
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121, Padova, Italy
| | - Monica Basso
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121, Padova, Italy
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Saverio Giuseppe Parisi
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121, Padova, Italy.
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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Grazia Martina M, Vicenti I, Bauer L, Crespan E, Rango E, Boccuto A, Olivieri N, Incerti M, Zwaagstra M, Allodi M, Bertoni S, Dreassi E, Zazzi M, Kuppeveld FJM, Maga G, Radi M. Front Cover: Bithiazole Inhibitors of Phosphatidylinositol 4‐Kinase (PI4KIIIβ) as Broad‐Spectrum Antivirals Blocking the Replication of SARS‐CoV‐2, Zika Virus, and Human Rhinoviruses (ChemMedChem 23/2021). ChemMedChem 2021. [DOI: 10.1002/cmdc.202100724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Maria Grazia Martina
- Dipartimento di Scienze degli Alimenti e del Farmaco Università degli Studi di Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies University of Siena 53100 Siena Italy
| | - Lisa Bauer
- Virology Section Infectious Disease and Immunology Division Department of Biomolecular Health Sciences Faculty of Veterinary Medicine Utrecht University Utrecht The Netherlands
- Current address: Department of Viroscience Erasmus Medical Center 3015CA Rotterdam The Netherlands
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare IGM-CNR “Luigi Luca Cavalli-Sforza” Via Abbiategrasso 207 27100 Pavia Italy
| | - Enrico Rango
- Dipartimento Biotecnologie, Chimica e Farmacia Università degli Studi di Siena 53100 Siena Italy
- Current address: Dipartimento di Farmacia Università degli Studi di Genova 16132 Genoa Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies University of Siena 53100 Siena Italy
| | - Noemi Olivieri
- Dipartimento di Scienze degli Alimenti e del Farmaco Università degli Studi di Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Matteo Incerti
- Dipartimento di Scienze degli Alimenti e del Farmaco Università degli Studi di Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Marleen Zwaagstra
- Virology Section Infectious Disease and Immunology Division Department of Biomolecular Health Sciences Faculty of Veterinary Medicine Utrecht University Utrecht The Netherlands
| | - Marika Allodi
- Dipartimento di Scienze degli Alimenti e del Farmaco Università degli Studi di Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Simona Bertoni
- Dipartimento di Scienze degli Alimenti e del Farmaco Università degli Studi di Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia Università degli Studi di Siena 53100 Siena Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies University of Siena 53100 Siena Italy
| | - Frank J. M. Kuppeveld
- Virology Section Infectious Disease and Immunology Division Department of Biomolecular Health Sciences Faculty of Veterinary Medicine Utrecht University Utrecht The Netherlands
| | - Giovanni Maga
- Istituto di Genetica Molecolare IGM-CNR “Luigi Luca Cavalli-Sforza” Via Abbiategrasso 207 27100 Pavia Italy
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco Università degli Studi di Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
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Saladini F, Giannini A, Giammarino F, Boccuto A, Dragoni F, Vicenti I, Zazzi M. In vitro susceptibility of HIV-1 CRF02_AG to temsavir, the active compound of the attachment inhibitor fostemsavir. J Antimicrob Chemother 2021; 76:3310-3312. [PMID: 34402509 DOI: 10.1093/jac/dkab309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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7
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Vicenti I, Basso M, Gatti F, Scaggiante R, Boccuto A, Zago D, Modolo E, Dragoni F, Parisi SG, Zazzi M. Faster decay of neutralizing antibodies in never infected than previously infected healthcare workers three months after the second BNT162b2 mRNA COVID-19 vaccine dose. Int J Infect Dis 2021; 112:40-44. [PMID: 34481967 PMCID: PMC8410637 DOI: 10.1016/j.ijid.2021.08.052] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVES This study aimed to describe the longitudinal evolution of neutralizing antibody titres (NtAb) in three different cohorts of healthcare workers (HCWs), including vaccinated HCWs with and without a previous SARS-CoV-2 infection and previously infected unvaccinated HCWs. COVID-19 was mild or asymptomatic in those experiencing infection. METHODS NtAb was tested before BNT162b2 mRNA COVID-19 vaccine (V0), 20±2 days after the first dose (V1_20), 20±3 days (V2_20) and 90±2 days (V2_90) after the second dose in vaccinated HCWs and after about 2 months (N_60), 10 months (N_300) and 13 months (N_390) from natural infection in unvaccinated HCWs. NtAb were measured by authentic virus neutralization with a SARS-CoV-2 B.1 isolate circulating in Italy at HCW enrolment. RESULTS Sixty-two HCWs were enrolled. NtAb were comparable in infected HCWs with no or mild disease at all the study points. NtAb of uninfected HCWs were significantly lower with respect to those of previously infected HCWs at V1_20, V2_20 and V2_90. The median NtAb fold decrease from V2_20 to V2_90 was higher in the uninfected HCWs with respect to those with mild infection (6.26 vs 2.58, p=0.03) and to asymptomatic HCWs (6.26 vs 3.67, p=0.022). The median Nabt at N_390 was significantly lower than at N_60 (p=0.007). CONCLUSIONS In uninfected HCWs completing the two-dose vaccine schedule, a third mRNA vaccine dose is a reasonable option to counteract the substantial NtAb decline occurring at a significantly higher rate compared with previously infected, vaccinated HCWs. Although low, Nabt were still at a detectable level after 13 months in two-thirds of previously infected and unvaccinated HCWs.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Monica Basso
- Department of Molecular Medicine University of Padova, Padova, Italy
| | - Francesca Gatti
- Department of Molecular Medicine University of Padova, Padova, Italy
| | | | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Daniela Zago
- Department of Molecular Medicine University of Padova, Padova, Italy
| | | | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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Gherardini L, Inzalaco G, Imperatore F, D’Aurizio R, Franci L, Miragliotta V, Boccuto A, Calandro P, Andreini M, Tarditi A, Chiariello M. The FHP01 DDX3X Helicase Inhibitor Exerts Potent Anti-Tumor Activity In Vivo in Breast Cancer Pre-Clinical Models. Cancers (Basel) 2021; 13:cancers13194830. [PMID: 34638314 PMCID: PMC8507746 DOI: 10.3390/cancers13194830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 12/25/2022] Open
Abstract
Inhibition of DDX3X expression or activity reduces proliferation in cells from various tumor tissues, in particular in breast cancer, and its expression often correlates to tumor aggressiveness. This makes DDX3X a prominent candidate for the design of drugs for novel personalized therapeutic strategies. Starting from an in silico drug discovery approach, a group of molecules has been selected by molecular docking at the RNA binding site of DDX3X. Here, the most promising among them, FHP01, was evaluated in breast cancer preclinical models. Specifically, FHP01 exhibited very effective antiproliferative and killing activity against different breast cancer cell types, among which those from triple-negative breast cancer (TNBC). Interestingly, FHP01 also inhibited WNT signaling, a key tumorigenic pathway already correlated to DDX3X functions in breast cancer model cell lines. Ultimately, FHP01 also caused a significant reduction, in vivo, in the growth of MDA MB 231-derived TNBC xenograft models. Importantly, FHP01 showed good bioavailability and no toxicity on normal peripheral blood mononuclear cells in vitro and on several mouse tissues in vivo. Overall, our data suggest that the use of FHP01 and its related compounds may represent a novel therapeutic approach with high potential against breast cancer, including the triple-negative subtype usually correlated to the most unfavorable outcomes because of the lack of available targeted therapies.
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Affiliation(s)
- Lisa Gherardini
- Istituto di Fisiologia Clinica (IFC), Consiglio Nazionale delle Ricerche (CNR), 53100 Siena, Italy; (L.G.); (G.I.); (F.I.); (L.F.)
| | - Giovanni Inzalaco
- Istituto di Fisiologia Clinica (IFC), Consiglio Nazionale delle Ricerche (CNR), 53100 Siena, Italy; (L.G.); (G.I.); (F.I.); (L.F.)
- Core Research Laboratory (CRL), Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), 53100 Siena, Italy;
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
| | - Francesco Imperatore
- Istituto di Fisiologia Clinica (IFC), Consiglio Nazionale delle Ricerche (CNR), 53100 Siena, Italy; (L.G.); (G.I.); (F.I.); (L.F.)
| | - Romina D’Aurizio
- Istituto di Informatica e Telematica (IIT), Consiglio Nazionale delle Ricerche (CNR), 56124 Pisa, Italy;
| | - Lorenzo Franci
- Istituto di Fisiologia Clinica (IFC), Consiglio Nazionale delle Ricerche (CNR), 53100 Siena, Italy; (L.G.); (G.I.); (F.I.); (L.F.)
- Core Research Laboratory (CRL), Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), 53100 Siena, Italy;
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
| | | | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
| | - Pierpaolo Calandro
- Core Research Laboratory (CRL), Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), 53100 Siena, Italy;
| | - Matteo Andreini
- First Health Pharmaceutical B.V., 1098 XH Amsterdam, The Netherlands; (M.A.); (A.T.)
| | - Alessia Tarditi
- First Health Pharmaceutical B.V., 1098 XH Amsterdam, The Netherlands; (M.A.); (A.T.)
| | - Mario Chiariello
- Istituto di Fisiologia Clinica (IFC), Consiglio Nazionale delle Ricerche (CNR), 53100 Siena, Italy; (L.G.); (G.I.); (F.I.); (L.F.)
- Core Research Laboratory (CRL), Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), 53100 Siena, Italy;
- Correspondence: ; Tel.: +39-057-723-1274
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Vicenti I, Gatti F, Scaggiante R, Boccuto A, Zago D, Basso M, Dragoni F, Parisi SG, Zazzi M. BNT162b2 SARS-CoV-2 Vaccination Elicits High Titers of Neutralizing Antibodies to Both B.1 and P.1 Variants in Previously Infected and Uninfected Subjects. Life (Basel) 2021; 11:896. [PMID: 34575045 PMCID: PMC8470771 DOI: 10.3390/life11090896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022] Open
Abstract
We aimed to investigate neutralizing antibody titers (NtAbT) to the P.1 and B.1 SARS-CoV-2 variants in a cohort of healthy health care workers (HCW), including 20 previously infected individuals tested at baseline (BLinf, after a median of 298 days from diagnosis) and 21 days after receiving one vaccine dose (D1inf) and 15 uninfected subjects tested 21 days after the second-dose vaccination (D2uninf). All the subjects received BNT162b2 vaccination. D1inf NtAbT increased significantly with respect to BLinf against both B.1 and P.1 variants, with a fold-change significantly higher for P.1. D1inf NtAbT were significantly higher than D2uninf NtAbT, against B.1 and P.1. NtAbT against the two strains were highly correlated. P.1 NtAbT were significantly higher than B.1 NtAbT. This difference was significant for post-vaccination sera in infected and uninfected subjects. A single-dose BNT162b2 vaccination substantially boosted the NtAb response to both variants in the previously infected subjects. NtAb titers to B.1 and P.1 lineages were highly correlated, suggesting substantial cross-neutralization. Higher titers to the P.1 than to the B.1 strain were driven by the post-vaccination titers, highlighting that cross-neutralization can be enhanced by vaccination.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Viale Bracci, 16, 53100 Siena, Italy; (I.V.); (A.B.); (F.D.); (M.Z.)
| | - Francesca Gatti
- Department of Molecular Medicine, University of Padova, Via Gabelli, 63, 35100 Padova, Italy; (F.G.); (D.Z.); (M.B.)
| | | | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Viale Bracci, 16, 53100 Siena, Italy; (I.V.); (A.B.); (F.D.); (M.Z.)
| | - Daniela Zago
- Department of Molecular Medicine, University of Padova, Via Gabelli, 63, 35100 Padova, Italy; (F.G.); (D.Z.); (M.B.)
| | - Monica Basso
- Department of Molecular Medicine, University of Padova, Via Gabelli, 63, 35100 Padova, Italy; (F.G.); (D.Z.); (M.B.)
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Viale Bracci, 16, 53100 Siena, Italy; (I.V.); (A.B.); (F.D.); (M.Z.)
| | - Saverio Giuseppe Parisi
- Department of Molecular Medicine, University of Padova, Via Gabelli, 63, 35100 Padova, Italy; (F.G.); (D.Z.); (M.B.)
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Viale Bracci, 16, 53100 Siena, Italy; (I.V.); (A.B.); (F.D.); (M.Z.)
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Grazia Martina M, Vicenti I, Bauer L, Crespan E, Rango E, Boccuto A, Olivieri N, Incerti M, Zwaagstra M, Allodi M, Bertoni S, Dreassi E, Zazzi M, van Kuppeveld FJM, Maga G, Radi M. Bithiazole Inhibitors of Phosphatidylinositol 4-Kinase (PI4KIIIβ) as Broad-Spectrum Antivirals Blocking the Replication of SARS-CoV-2, Zika Virus, and Human Rhinoviruses. ChemMedChem 2021; 16:3548-3552. [PMID: 34382337 PMCID: PMC8427023 DOI: 10.1002/cmdc.202100483] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Indexed: 12/14/2022]
Abstract
Over half a century since the description of the first antiviral drug, "old" re-emerging viruses and "new" emerging viruses still represent a serious threat to global health. Their high mutation rate and rapid selection of resistance toward common antiviral drugs, together with the increasing number of co-infections, make the war against viruses quite challenging. Herein we report a host-targeted approach, based on the inhibition of the lipid kinase PI4KIIIβ, as a promising strategy for inhibiting the replication of multiple viruses hijacking this protein. We show that bithiazole inhibitors of PI4KIIIβ block the replication of human rhinoviruses (hRV), Zika virus (ZIKV) and SARS-CoV-2 at low micromolar and sub-micromolar concentrations. However, while the anti-hRV/ZIKV activity can be directly linked to PI4KIIIβ inhibition, the role of PI4KIIIβ in SARS-CoV-2 entry/replication is debated.
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Affiliation(s)
- Maria Grazia Martina
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100, Siena, Italy
| | - Lisa Bauer
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Current address: Department of Viroscience, Erasmus Medical Center, 3015CA, Rotterdam, The Netherlands
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Enrico Rango
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100, Siena, Italy.,Current address: Dipartimento di Farmacia, Università degli Studi di Genova, 16132, Genoa, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, 53100, Siena, Italy
| | - Noemi Olivieri
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
| | - Matteo Incerti
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
| | - Marleen Zwaagstra
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Marika Allodi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
| | - Simona Bertoni
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100, Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100, Siena, Italy
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
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11
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Vicenti I, Martina MG, Boccuto A, De Angelis M, Giavarini G, Dragoni F, Marchi S, Trombetta CM, Crespan E, Maga G, Eydoux C, Decroly E, Montomoli E, Nencioni L, Zazzi M, Radi M. 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 2021; 224:113683. [PMID: 34273661 PMCID: PMC8255191 DOI: 10.1016/j.ejmech.2021.113683] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/16/2021] [Accepted: 07/01/2021] [Indexed: 11/29/2022]
Abstract
The worldwide circulation of different viruses coupled with the increased frequency and diversity of new outbreaks, strongly highlight the need for new antiviral drugs to quickly react against potential pandemic pathogens. Broad-spectrum antiviral agents (BSAAs) represent the ideal option for a prompt response against multiple viruses, new and re-emerging. Starting from previously identified anti-flavivirus hits, we report herein the identification of promising BSAAs by submitting the multi-target 2,6-diaminopurine chemotype to a system-oriented optimization based on phenotypic screening on cell cultures infected with different viruses. Among the synthesized compounds, 6i showed low micromolar potency against Dengue, Zika, West Nile and Influenza A viruses (IC50 = 0.5–5.3 μM) with high selectivity index. Interestingly, 6i also inhibited SARS-CoV-2 replication in different cell lines, with higher potency on Calu-3 cells that better mimic the SARS-CoV-2 infection in vivo (IC50 = 0.5 μM, SI = 240). The multi-target effect of 6i on flavivirus replication was also analyzed in whole cell studies (in vitro selection and immunofluorescence) and against isolated host/viral targets.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maria Grazia Martina
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124, Parma, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marta De Angelis
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Giorgia Giavarini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124, Parma, Italy
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Serena Marchi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | | | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Cecilia Eydoux
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Marseille, France
| | - Etienne Decroly
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Marseille, France
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy; VisMederi s.r.l, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy
| | - Lucia Nencioni
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124, Parma, Italy.
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12
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Vicenti I, Gatti F, Scaggiante R, Boccuto A, Modolo E, Zago D, Basso M, Dragoni F, Bartolini N, Zazzi M, Parisi SG. Time Course of Neutralizing Antibody in Health Care Workers With Mild or Asymptomatic COVID-19 Infection. Open Forum Infect Dis 2021; 8:ofab312. [PMID: 34295945 PMCID: PMC8291533 DOI: 10.1093/ofid/ofab312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
We describe the time course of neutralizing antibody (NtAb) titer in a cohort of health care workers with mild or asymptomatic severe acute respiratory syndrome coronavirus (SARS-CoV-2) infection. NtAb levels decreased over time; however, serum neutralizing activity remained detectable after a median of 7 months from SARS-CoV-2 diagnosis in the majority of cases.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Gatti
- Department of Molecular Medicine University of Padova, Padova, Italy
| | | | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Daniela Zago
- Department of Molecular Medicine University of Padova, Padova, Italy
| | - Monica Basso
- Department of Molecular Medicine University of Padova, Padova, Italy
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Niccolo’ Bartolini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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13
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Saladini F, Giammarino F, Hosseini BA, Giannini A, Boccuto A, Dragoni F, Vicenti I, Shafer RW, Zazzi M. In vitro cross-resistance to doravirine in a panel of HIV-1 clones harbouring multiple NNRTI resistance mutations. J Antimicrob Chemother 2021; 76:130-134. [PMID: 32974670 DOI: 10.1093/jac/dkaa401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/28/2020] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES Doravirine is a recently licensed HIV-1 NNRTI with improved efficacy, pharmacokinetics and safety profile compared with efavirenz and limited cross-resistance with rilpivirine and etravirine. In this in vitro study, cross-resistance to doravirine was analysed in a representative panel of NNRTI-resistant clones. METHODS In vitro phenotypic susceptibility to doravirine was assessed in 10 clinically derived infectious clones with intermediate- to high-level resistance to rilpivirine, etravirine, efavirenz and nevirapine, and in NL4-3 site-directed mutants harbouring K103N, Y181C, M230L or K103N/Y181C NNRTI mutations. RESULTS Although none of the infectious clones harboured any of the major doravirine resistance-associated mutations (RAMs) included in the IAS-USA reference list, doravirine fold change (FC) values were comparable to or higher than those calculated for other NNRTIs, particularly etravirine and rilpivirine. As expected, single NNRTI mutations K103N and Y181C did not impair doravirine susceptibility (FC 1.4 and 1.8, respectively), while reduced activity was observed with the single M230L or double K103N/Y181C mutations (FC 7.6 and 4.9, respectively). Median FC values increased significantly with increasing numbers of NNRTI RAMs (P = 0.005) and were >10 in 4/4 and 1/4 clones harbouring four and three NNRTI RAMs, respectively. FC values correlated well with predicted susceptibility as inferred by Stanford HIV Drug Resistance Database (HIVdb) and ANRS algorithms (both P < 0.001). CONCLUSIONS Substantial cross-resistance to doravirine was detected in NNRTI-resistant viruses harbouring complex mutational patterns, even in the absence of major IAS-USA doravirine RAMs. Therefore, based on the simple IAS-USA reference list, doravirine resistance may be underestimated in viruses harbouring multiple NNRTI mutations.
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Affiliation(s)
- Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Behnaz A Hosseini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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14
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Vicenti I, Gatti F, Scaggiante R, Boccuto A, Zago D, Basso M, Dragoni F, Zazzi M, Parisi SG. Single-dose BNT162b2 mRNA COVID-19 vaccine significantly boosts neutralizing antibody response in health care workers recovering from asymptomatic or mild natural SARS-CoV-2 infection. Int J Infect Dis 2021; 108:176-178. [PMID: 34022329 PMCID: PMC8132552 DOI: 10.1016/j.ijid.2021.05.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 01/28/2023] Open
Abstract
Objectives To measure SARS-CoV-2 neutralizing antibody (NtAb) titres in previously infected or uninfected health care workers who received one or two doses of BNT162b2 mRNA COVID-19 vaccine. Methods NtAbs were titrated as dose-inhibiting 50% virus replication (ID50) by live virus microneutralization. We evaluated 41 health care workers recovering from mild or asymptomatic infection at first vaccination dose (T1_inf) and 21 days later (T2_inf). Sixteen uninfected health care workers were evaluated 20 days after first dose (T2_uninf) and 20 days after second vaccine dose (T3_uninf). Results At T2_inf, but not at T1_inf, there was a significant correlation between days from diagnosis (median 313, interquartile range 285–322) and NtAb levels (P = 0.011). NtAb titres increased at T2_inf with respect to T1_inf (1544 (732–2232) vs 26 (10–88), P < 0.001). Similarly, there was a significant increase in NtAb titres at T3_uninf compared with T2_uninf (183 (111–301) vs 5 (5–15), P < 0001). However, NtAb levels at T2_inf were significantly higher than those at T2_uninf and T3_uninf (P < 0.0001 for both analyses). Conclusions A single vaccination in people with mild or asymptomatic previous infection further boosts SARS-CoV-2 humoral immunity to levels higher than those obtained by complete two-vaccination in uninfected subjects.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy.
| | - Francesca Gatti
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35100 Padova, Italy.
| | | | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy.
| | - Daniela Zago
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35100 Padova, Italy.
| | - Monica Basso
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35100 Padova, Italy.
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy.
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy.
| | - Saverio Giuseppe Parisi
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35100 Padova, Italy.
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15
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Vicenti I, Dragoni F, Monti M, Trombetta CM, Giannini A, Boccuto A, Saladini F, Rossetti B, De Luca A, Ciabattini A, Pastore G, Medaglini D, Orofino G, Montomoli E, Zazzi M. Maraviroc as a potential HIV-1 latency-reversing agent in cell line models and ex vivo CD4 T cells. J Gen Virol 2021; 102. [PMID: 33048041 DOI: 10.1099/jgv.0.001499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent studies have suggested that the CCR5 antagonist maraviroc (MVC) may exert an HIV-1 latency reversal effect. This study aimed at defining MVC-mediated induction of HIV-1 in three cell line latency models and in ex vivo CD4 T cells from six patients with suppressed viraemia. HIV-1 induction was evaluated in TZM-bl cells by measuring HIV-1 LTR-driven luciferase expression, and in ACH-2 and U1 latently infected cell lines by measuring cell-free (CFR) and cell-associated (CAR) HIV-1 RNA by qPCR. NF-κB p65 was quantified in nuclear extracts by immunodetection. In ex vivo CD4 T cells, CAR, CFR and cell-associated DNA (CAD) were quantified at baseline and 1-7-14 days post-induction (T1, T7, T14). At T7 and T14, the infectivity of the CD4 T cells co-cultured with MOLT-4/CCR5 target cells was evaluated in the TZM-bl assay (TZA). Results were expressed as fold activation (FA) with respect to untreated cells. No LTR activation was observed in TZM-bl cells at any MVC concentration. NF-κB activation was only modestly upregulated (1.6±0.4) in TZM-bl cells with 5 µM MVC. Significant FA of HIV-1 expression was only detected at 80 µM MVC, namely on HIV-1 CFR in U1 (3.1±0.9; P=0.034) and ACH-2 cells (3.9±1.4; P=0.037). CFR was only weakly stimulated at 20 µM in ACH-2 (1.7±1.0 FA) cells and at 5 µM in U1 cells (1.9±0.5 FA). Although no consistent pattern of MVC-mediated activation was observed in ex vivo experiments, substantial FA values were detected sparsely on individual samples with different parameters. Notably, in one sample, MVC stimulated all parameters at T7 (2.3±0.2 CAD, 6.8±3.7 CAR, 18.7±16.7 CFR, 7.3±0.2 TZA). In conclusion, MVC variably induces HIV-1 production in some cell line models not previously used to test its latency reversal potential. In ex vivo CD4 T cells, MVC may exert patient-specific HIV-1 induction; however, clinically relevant patterns, if any, remain to be defined.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | | | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Barbara Rossetti
- Infectious Diseases Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Andrea De Luca
- Infectious Diseases Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Gabiria Pastore
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Donata Medaglini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Giancarlo Orofino
- Unit of Infectious Diseases, Division A, Ospedale Amedeo di Savoia, Turin, Italy
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy.,VisMederi srl, Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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16
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Riva V, Garbelli A, Brai A, Casiraghi F, Fazi R, Trivisani CI, Boccuto A, Saladini F, Vicenti I, Martelli F, Zazzi M, Giannecchini S, Dreassi E, Botta M, Maga G. Unique Domain for a Unique Target: Selective Inhibitors of Host Cell DDX3X to Fight Emerging Viruses. J Med Chem 2020; 63:9876-9887. [PMID: 32787106 DOI: 10.1021/acs.jmedchem.0c01039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Emerging viruses like dengue, West Nile, chikungunya, and Zika can cause widespread viral epidemics. Developing novel drugs or vaccines against specific targets for each virus is a difficult task. As obligate parasites, all viruses exploit common cellular pathways, providing the possibility to develop broad-spectrum antiviral agents targeting host factors. The human DEAD-box RNA helicase DDX3X is an essential cofactor for viral replication but dispensable for cell viability. Herein, we exploited the presence of a unique structural motif of DDX3X not shared by other cellular enzymes to develop a theoretical model to aid in the design of a novel class of highly selective inhibitors acting against such specific targets, thus limiting off-targeting effects. High-throughput virtual screening led us to identify hit compound 5, endowed with promising antienzymatic activity. To improve its aqueous solubility, 5 and its two enantiomers were synthesized and converted into their corresponding acetate salts (compounds 11, 12, and 13). In vitro mutagenesis and biochemical and cellular assays further confirmed that the developed molecules were selective for DDX3X and were able to suppress replication of West Nile and dengue viruses in infected cells in the micromolar range while showing no toxicity for uninfected cells. These results provide proof of principle for a novel strategy in developing highly selective and broad-spectrum antiviral molecules active against emerging and dangerous viral pathogens. This study paves the way for the development of larger focused libraries targeting such domain to expand SAR studies and fully characterize their mode of interaction.
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Affiliation(s)
- Valentina Riva
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Anna Garbelli
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Annalaura Brai
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Federica Casiraghi
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Roberta Fazi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Claudia I Trivisani
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Adele Boccuto
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Francesco Saladini
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Ilaria Vicenti
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Francesco Martelli
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi di Firenze, Viale Morgnani 48, I-50134 Firenze, Italy
| | - Maurizio Zazzi
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Simone Giannecchini
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi di Firenze, Viale Morgnani 48, I-50134 Firenze, Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Maurizio Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Biotechnology College of Science and Technology, Temple University, Biolife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - Giovanni Maga
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
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17
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Giannini A, Vicenti I, Materazzi A, Boccuto A, Dragoni F, Zazzi M, Saladini F. The HIV-1 reverse transcriptase E138A natural polymorphism decreases the genetic barrier to resistance to etravirine in vitro. J Antimicrob Chemother 2020; 74:607-613. [PMID: 30462235 DOI: 10.1093/jac/dky479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/12/2018] [Accepted: 10/23/2018] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The HIV-1 reverse transcriptase (RT) natural polymorphism E138A is included among the mutations with a minor impact on response to etravirine. However, the interpretation of E138A on etravirine susceptibility is not consistent across different genotypic resistance algorithms. The aim of the study was to investigate the effect of E138A on the genetic barrier to resistance to etravirine in vitro. METHODS A panel of 20 clinically derived recombinant viruses (10 with WT 138E and 10 with 138A, all without any other resistance mutation) were cultured in the presence of increasing etravirine concentrations and analysed for genotypic changes at virus breakthrough. Parallel experiments were conducted with 138E/A/G/K/Q NL4-3-based clones. RESULTS In the NL4-3 background, codon 138 changes increased etravirine resistance in the following order: Q > K > A > G > E. The 138A viruses were less susceptible to etravirine compared with the 138E viruses [median (IQR) fold change, 1.8 (1.5-2.8) versus 1.3 (0.8-1.8); P = 0.026], overcame etravirine pressure earlier [HR (95% CI) for viral outgrowth with 138A, 5.48 (2.95-28.24); P < 0.001] and grew at higher drug concentrations [median (IQR), 1350 (1350-1350) versus 0 (0-1350) nM; P = 0.005]. A variety of etravirine resistance-related mutations and changes in the RT connection and RNase H domains accumulated without any consistent pattern depending on baseline codon 138. CONCLUSIONS E138A can contribute to reduced response to etravirine through a decreased genetic barrier to resistance. In vitro drug resistance selection is a valuable complement to define the full potential of low-level resistance mutations.
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Affiliation(s)
- Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Angelo Materazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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18
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Brai A, Boccuto A, Monti M, Marchi S, Vicenti I, Saladini F, Trivisani CI, Pollutri A, Trombetta CM, Montomoli E, Riva V, Garbelli A, Nola EM, Zazzi M, Maga G, Dreassi E, Botta M. Exploring the Implication of DDX3X in DENV Infection: Discovery of the First-in-Class DDX3X Fluorescent Inhibitor. ACS Med Chem Lett 2020; 11:956-962. [PMID: 32435411 DOI: 10.1021/acsmedchemlett.9b00681] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/02/2020] [Indexed: 12/14/2022] Open
Abstract
In the absence of effective drugs or vaccines for the treatment of the five Dengue Virus serotypes, the search for novel antiviral drugs is of primary importance for the scientific community. In this context, drug repurposing represents the most used strategy; however, the study of host targets is now attracting attention since it allows identification of broad-spectrum drugs endowed with high genetic barrier. In the last ten years our research group identified several small molecules DDX3X inhibitors and proved their efficacy against different viruses including novel emerging ones. Herein, starting from a screening of our compounds, we designed and synthesized novel derivatives with potent activity and high selectivity. Finally, we synthesized a fluorescent inhibitor that allowed us to study DDX3X cellular localization during DENV infection in vitro. Immunofluorescence analysis showed that our inhibitor colocalized with DDX3X, promoting the reduction of infected cells and recovering the number of viable cells.
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Affiliation(s)
- Annalaura Brai
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Adele Boccuto
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, 53100 Siena, Italy
| | - Martina Monti
- Dipartimento di Medicina Molecolare e dello Sviluppo, Università degli Studi di Siena, 53100 Siena, Italy
| | - Serena Marchi
- Dipartimento di Medicina Molecolare e dello Sviluppo, Università degli Studi di Siena, 53100 Siena, Italy
| | - Ilaria Vicenti
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, 53100 Siena, Italy
| | - Francesco Saladini
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, 53100 Siena, Italy
| | | | - Alessandro Pollutri
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Claudia Maria Trombetta
- Dipartimento di Medicina Molecolare e dello Sviluppo, Università degli Studi di Siena, 53100 Siena, Italy
| | - Emanuele Montomoli
- Dipartimento di Medicina Molecolare e dello Sviluppo, Università degli Studi di Siena, 53100 Siena, Italy
- VisMederi Srl, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy
| | - Valentina Riva
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Anna Garbelli
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Emanuele Maria Nola
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Maurizio Zazzi
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, 53100 Siena, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Elena Dreassi
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Maurizio Botta
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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19
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Brai A, Riva V, Saladini F, Zamperini C, Trivisani CI, Garbelli A, Pennisi C, Giannini A, Boccuto A, Bugli F, Martini M, Sanguinetti M, Zazzi M, Dreassi E, Botta M, Maga G. DDX3X inhibitors, an effective way to overcome HIV-1 resistance targeting host proteins. Eur J Med Chem 2020; 200:112319. [PMID: 32446036 DOI: 10.1016/j.ejmech.2020.112319] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/06/2020] [Indexed: 12/19/2022]
Abstract
The huge resources that had gone into Human Immunodeficiency virus (HIV) research led to the development of potent antivirals able to suppress viral load in the majority of treated patients, thus dramatically increasing the life expectancy of people living with HIV. However, life-long treatments could result in the emergence of drug-resistant viruses that can progressively reduce the number of therapeutic options, facilitating the progression of the disease. In this scenario, we previously demonstrated that inhibitors of the human DDX3X helicase can represent an innovative approach for the simultaneous treatment of HIV and other viral infections such as Hepatitis c virus (HCV). We reported herein 6b, a novel DDX3X inhibitor that thanks to its distinct target of action is effective against HIV-1 strains resistant to currently approved drugs. Its improved in vitro ADME properties allowed us to perform preliminary in vivo studies in mice, which highlighted optimal biocompatibility and an improved bioavailability. These results represent a significant advancement in the development of DDX3X inhibitors as a novel class of broad spectrum and safe anti-HIV-1 drugs.
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Affiliation(s)
- Annalaura Brai
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100, Siena, Italy
| | - Valentina Riva
- Istituto di Genetica Molecolare "Luigi Luca Cavalli - Sforza", IGM-CNR, Via Abbiategrasso 207, I-27100, Pavia, Italy
| | - Francesco Saladini
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, I-53100, Siena, Italy
| | - Claudio Zamperini
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100, Siena, Italy
| | - Claudia Immacolata Trivisani
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100, Siena, Italy
| | - Anna Garbelli
- Istituto di Genetica Molecolare "Luigi Luca Cavalli - Sforza", IGM-CNR, Via Abbiategrasso 207, I-27100, Pavia, Italy
| | - Carla Pennisi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli - Sforza", IGM-CNR, Via Abbiategrasso 207, I-27100, Pavia, Italy
| | - Alessia Giannini
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, I-53100, Siena, Italy
| | - Adele Boccuto
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, I-53100, Siena, Italy
| | - Francesca Bugli
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, I-00168, Roma, Italy; Istituto di Microbiologia, Università Cattolica del SC, L.go F. Vito 1, I-00168, Roma, Italy
| | - Maurizio Martini
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Servizio di Istopatologia e Citodiagnosi, Rome, Italy; Istituto di Patologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maurizio Sanguinetti
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, I-00168, Roma, Italy; Istituto di Microbiologia, Università Cattolica del SC, L.go F. Vito 1, I-00168, Roma, Italy
| | - Maurizio Zazzi
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, I-53100, Siena, Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100, Siena, Italy
| | - Maurizio Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100, Siena, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, PA, 19122, USA.
| | - Giovanni Maga
- Istituto di Genetica Molecolare "Luigi Luca Cavalli - Sforza", IGM-CNR, Via Abbiategrasso 207, I-27100, Pavia, Italy.
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20
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Vicenti I, Dragoni F, Giannini A, Giammarino F, Spinicci M, Saladini F, Boccuto A, Zazzi M. Development of a Cell-Based Immunodetection Assay for Simultaneous Screening of Antiviral Compounds Inhibiting Zika and Dengue Virus Replication. SLAS Discov 2020; 25:506-514. [PMID: 32186426 DOI: 10.1177/2472555220911456] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Practical cell-based assays can accelerate anti-Zika (ZIKV) and anti-dengue (DENV) virus drug discovery. We developed an immunodetection assay (IA), using a pan-flaviviral monoclonal antibody recognizing a conserved envelope domain. The final protocol includes a direct virus yield reduction assay (YRA) carried out in the human Huh7 cell line, followed by transfer of the supernatant to a secondary Huh7 culture to characterize late antiviral effects. Sofosbuvir and ribavirin were used to validate the assay, while celgosivir was used to evaluate the ability to discriminate between early and late antiviral activity. In the direct YRA, at 100, 50, and 25 TCID50, sofosbuvir IC50 values were 5.0 ± 1.5, 2.7 ± 0.5, 2.5 ± 1.1 µM against ZIKV and 16.6 ± 2.8, 4.6 ± 1.4, 2.6 ± 2.2 µM against DENV; ribavirin IC50 values were 6.8 ± 4.0, 3.8 ± 0.6, 4.5 ± 1.4 µM against ZIKV and 17.3 ± 4.6, 7.6 ± 1.2, 4.1 ± 2.3 µM against DENV. Sofosbuvir and ribavirin IC50 values determined in the secondary YRA were reproducible and comparable with those obtained by direct YRA and plaque reduction assay (PRA). In agreement with the proposed mechanism of late action, celgosivir was active against DENV only in the secondary YRA (IC50 11.0 ± 1.0 µM) and in PRA (IC50 10.1 ± 1.1 µM). The assay format overcomes relevant limitations of the gold standard PRA, allowing concurrent analysis of candidate antiviral compounds against different viruses and providing preliminary information about early versus late antiviral activity.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Michele Spinicci
- Unit of Infectious Diseases, Careggi University Hospital, Florence, Toscana, Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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21
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Dragoni F, Boccuto A, Picarazzi F, Giannini A, Giammarino F, Saladini F, Mori M, Mastrangelo E, Zazzi M, Vicenti I. Evaluation of sofosbuvir activity and resistance profile against West Nile virus in vitro. Antiviral Res 2020; 175:104708. [PMID: 31931104 DOI: 10.1016/j.antiviral.2020.104708] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/31/2019] [Accepted: 01/08/2020] [Indexed: 12/22/2022]
Abstract
Sofosbuvir, a licensed nucleotide analog targeting hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp), has been recently evaluated as a broad anti-Flavivirus lead candidate revealing activity against Zika and Dengue viruses both in vitro and in animal models. In this study, the in vitro antiviral activity of sofosbuvir against West Nile virus (WNV) was determined by plaque assay (PA) and Immunodetection Assay (IA) in human cell lines and by enzymatic RdRp assay. By PA, the sofosbuvir half-maximal inhibitory concentration (IC50) was 1.2 ± 0.3 μM in Huh-7, 5.3 ± 0.9 μM in U87, 7.8 ± 2.5 μM in LN-18 and 63.4 ± 14.1 μM in A549 cells. By IA, anti-WNV activity was confirmed in both hepatic (Huh-7, 1.7 ± 0.5 μM) and neuronal (U87, 7.3 ± 2.0 μM) cell types. Sofosbuvir was confirmed to inhibit the purified WNV RdRp (IC50 11.1 ± 4.6 μM). In vitro resistance selection experiments were performed by propagating WNV in the Huh-7 cell line with two-fold increasing concentrations of sofosbuvir. At 80 μM, a significantly longer time for viral breakthrough was observed compared with lower concentrations (18 vs. 7-9 days post infection; p = 0.029), along with the detection of the S604T mutation, corresponding to the well-known S282T substitution in the motif B of HCV NS5B, which confers resistance to sofosbuvir. Molecular docking experiments confirmed that the S604T mutation within the catalytic site of RdRp affected the binding mode of sofosbuvir. To our knowledge, this is the first report of the antiviral activity of sofosbuvir against WNV as well as of selection of mutants in vitro.
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Affiliation(s)
- Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Italy
| | - Francesca Picarazzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Italy
| | | | | | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
| | | | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Italy.
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22
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Vicenti I, Lai A, Giannini A, Boccuto A, Dragoni F, Saladini F, Zazzi M. Performance of Geno2Pheno[coreceptor] to infer coreceptor use in human immunodeficiency virus type 1 (HIV-1) subtype A. J Clin Virol 2018; 111:12-18. [PMID: 30594700 DOI: 10.1016/j.jcv.2018.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/03/2018] [Accepted: 12/19/2018] [Indexed: 11/29/2022]
Abstract
BACKGROUND Assessment of human immunodeficiency virus type 1 (HIV-1) coreceptor usage is required prior to treatment with the CCR5 antagonist maraviroc to exclude the presence of CXCR4-using (X4) strains. Genotype-based interpretation systems are mostly designed on subtype B and have been reported to be less accurate for subtype A/CRF02_AG. OBJECTIVES To evaluate the performance of the widely used Geno2Pheno[coreceptor] (G2P[c]) algorithm for prediction of coreceptor usage with subtype A/CRF02_AG vs. subtype B. STUDY DESIGN Co-receptor tropism of 24 subtype A/CRF02_AG and 24 subtype B viruses was measured phenotypically by a homebrew single-cycle assay and genotypically by using G2P[c]. Samples with discrepant genotype-phenotype results were analyzed by next generation sequencing (NGS) and interpreted by the NGS Geno2Pheno algorithm (G2P[454]). RESULTS At 10% false positive rate (FPR), the G2P[c]/phenotype discordance rate was 12.5% (n = 3) for subtype A/CRF02_AG and 8.3% (n = 2) for subtype B. Minority X4 species escaping detection by bulk sequencing but documented by NGS explained the two subtype B and possibly one subtype A/CRF02_AG discordant case. The other two subtype A/CRF02_AG miscalled by G2P[c] could be explained by X4 overcalling at borderline FPR and/or by algorithm failure. DISCUSSION Our study did not demonstrate relevantly higher G2P[c] inaccuracy with subtype A/CRF02_AG with respect to subtype B. Genotype/phenotype discordances can be due to different reasons, including but not limited to, algorithm inaccuracy. Very large genotype/phenotype correlation panels are required to detect and explain the reason for any consistent difference in genotypic tropism prediction for subtype A/CRF02_AG vs. subtype B.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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Vicenti I, Boccuto A, Giannini A, Dragoni F, Saladini F, Zazzi M. Comparative analysis of different cell systems for Zika virus (ZIKV) propagation and evaluation of anti-ZIKV compounds in vitro. Virus Res 2017; 244:64-70. [PMID: 29113824 DOI: 10.1016/j.virusres.2017.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/04/2017] [Accepted: 11/02/2017] [Indexed: 12/21/2022]
Abstract
A strong correlation between Zika virus (ZIKV) infection and severe neurological disease in newborns and occasionally adults has emerged in the Brazilian outbreak. Efficient human cell-based assays are required to test candidate inhibitors of ZIKV replication. The aim of this work was to investigate ZIKV propagation and quantification in different cell lines. The human (U87, A549, Huh7), mosquito (C6/36) and monkey (VERO E6) cell lines tested were all permissive to ZIKV infection. When assessed by plaque forming units (PFU) in three different target cell lines, the maximal production of ZIKV was achieved in Huh7 at day 3 post-infection (6.38±0.44 log10PFU/ml). The C6/36 cell line showed a low and slow production of virus when compared with other cell lines. A549 readout cells generated a larger number of plaques compared to Huh7 but not to VERO E6 cells. ZIKV PFU and RNA titers showed the highest correlation when Huh7 and A549 were used as the producer and readout cells, respectively. Also, U87 cells produced ZIKV RNA titers which were highly correlated with PFU independently from the readout cell line. Using the best virus-cell system, sofosbuvir and ribavirin EC50 were 1.2μM and 1.1μM when measured through plaque assay, and 4.2μM and 5.2μM when measured by quantitative real time PCR (qRT-PCR), respectively. In summary, ZIKV can efficiently infect different human cell lines and rapidly reach peak viral titers. Overall, A549 cells appear to be as efficient as the VERO E6 gold standard for plaque assay allowing the use of human, rather than simian, cells for evaluating candidate anti-ZIKV compounds by the reference assay. The possibility to replace the labor-intensive plaque assay with the more rapid and easy-to-perform qRT-PCR is appealing and warrants further investigation.
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Affiliation(s)
- Ilaria Vicenti
- Medical Biotechnology Department, University of Siena, Siena, Italy.
| | - Adele Boccuto
- Medical Biotechnology Department, University of Siena, Siena, Italy
| | - Alessia Giannini
- Medical Biotechnology Department, University of Siena, Siena, Italy
| | - Filippo Dragoni
- Medical Biotechnology Department, University of Siena, Siena, Italy
| | | | - Maurizio Zazzi
- Medical Biotechnology Department, University of Siena, Siena, Italy
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Vicenti I, Meini G, Saladini F, Giannini A, Boccuto A, Schiaroli E, Zazzi M. Development of an internally controlled quantitative PCR to measure total cell-associated HIV-1 DNA in blood. ACTA ACUST UNITED AC 2017; 56:e75-e77. [DOI: 10.1515/cclm-2017-0587] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/09/2017] [Indexed: 11/15/2022]
Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies , University of Siena , Siena , Italy , Phone: +39 0577 233910, Fax: +39 0577 233870
| | - Genny Meini
- Department of Medical Biotechnologies , University of Siena , Siena , Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies , University of Siena , Siena , Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies , University of Siena , Siena , Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies , University of Siena , Siena , Italy
| | - Elisabetta Schiaroli
- Unit of Infectious Diseases , Department of Medicine , University of Perugia , Perugia , Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies , University of Siena , Siena , Italy
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Saladini F, Giannini A, Boccuto A, Vicenti I, Zazzi M. Agreement between an in-house replication competent and a reference replication defective recombinant virus assay for measuring phenotypic resistance to HIV-1 protease, reverse transcriptase, and integrase inhibitors. J Clin Lab Anal 2017; 32. [PMID: 28303602 DOI: 10.1002/jcla.22206] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/21/2017] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Although clinical management of drug resistance is routinely based on genotypic methods, phenotypic assays remain necessary for the characterization of novel HIV-1 inhibitors, particularly against common drug-resistant variants. We describe the development and assessment of the performance of a recombinant virus assay for measuring HIV-1 susceptibility to protease (PR), reverse transcriptase (RT), and integrase (IN) inhibitors. METHODS The system is based on the creation of replication-competent chimeric viruses through homologous recombination between patient or laboratory virus-derived PCR fragments and the corresponding NL4-3 vector where the whole Gag-PR, RT-RNaseH or IN coding regions has been deleted through inverse PCR. The susceptibility to nucleoside (NRTIs) and non-nucleoside (NNRTIs) RT inhibitors and to IN inhibitors (INIs) is calculated through a single-round infection assay in TZM-bl cells, while protease inhibitor (PI) activity is determined through a first round of infection in MT-2 cells followed by infection of TZM-bl cells with MT-2 supernatants. RESULTS The assay showed excellent reproducibility and accuracy when testing PI, NRTI, NNRTI, and INI susceptibility of drug-resistant clones previously characterized through the reference pseudoparticle-based Phenosense assay. The coefficient of interassay variation in fold change (FC) resistance was 12.0%-24.3% when assaying seven drug/clones pairs in three runs. FC values calculated by the Phenosense and in-house for 20 drug/clones pairs were in good agreement, with mean±SD ratio of 1.14±0.33 and no cases differing by more than twofold. CONCLUSIONS The described phenotypic assay can be adopted to evaluate the antiviral activity of licensed and investigational HIV-1 drugs targeting any of the three HIV-1 enzymes.
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Affiliation(s)
- Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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