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Díaz-Perlas C, Ricken B, Farrera-Soler L, Guschin D, Pojer F, Lau K, Gerhold CB, Heinis C. High-affinity peptides developed against calprotectin and their application as synthetic ligands in diagnostic assays. Nat Commun 2023; 14:2774. [PMID: 37198182 DOI: 10.1038/s41467-023-38075-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Common inflammatory disorders such as ulcerative colitis and Crohn's disease are non-invasively diagnosed or monitored by the biomarker calprotectin. However, current quantitative tests for calprotectin are antibody-based and vary depending on the type of antibody and assay used. Additionally, the binding epitopes of applied antibodies are not characterized by structures and for most antibodies it is unclear if they detect calprotectin dimer, tetramer, or both. Herein, we develop calprotectin ligands based on peptides, that offer advantages such as homogenous chemical composition, heat-stability, site-directed immobilization, and chemical synthesis at high purity and at low cost. By screening a 100-billion peptide phage display library against calprotectin, we identified a high-affinity peptide (Kd = 26 ± 3 nM) that binds to a large surface region (951 Å2) as shown by X-ray structure analysis. The peptide uniquely binds the calprotectin tetramer, which enabled robust and sensitive quantification of a defined species of calprotectin by ELISA and lateral flow assays in patient samples, and thus offers an ideal affinity reagent for next-generation inflammatory disease diagnostic assays.
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Affiliation(s)
- Cristina Díaz-Perlas
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Benjamin Ricken
- BÜHLMANN Laboratories AG, Baselstrasse 55, CH-4124, Schönenbuch, Switzerland
| | - Lluc Farrera-Soler
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Dmitrii Guschin
- BÜHLMANN Laboratories AG, Baselstrasse 55, CH-4124, Schönenbuch, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Kelvin Lau
- Protein Production and Structure Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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López-Tena M, Farrera-Soler L, Barluenga S, Winssinger N. Pseudo-Complementary G:C Base Pair for Mixed Sequence dsDNA Invasion and Its Applications in Diagnostics (SARS-CoV-2 Detection). JACS Au 2023; 3:449-458. [PMID: 36873687 PMCID: PMC9975836 DOI: 10.1021/jacsau.2c00588] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Pseudo-complementary oligonucleotides contain artificial nucleobases designed to reduce duplex formation in the pseudo-complementary pair without compromising duplex formation to targeted (complementary) oligomers. The development of a pseudo-complementary A:T base pair, Us:D, was important in achieving dsDNA invasion. Herein, we report pseudo-complementary analogues of the G:C base pair leveraged on steric and electrostatic repulsion between the cationic phenoxazine analogue of cytosine (G-clamp, C+) and N-7 methyl guanine (G+), which is also cationic. We show that while complementary peptide nucleic acids (PNA) form a much more stable homoduplex than the PNA:DNA heteroduplex, oligomers based on pseudo-C:G complementary PNA favor PNA:DNA hybridization. We show that this enables dsDNA invasion at physiological salt concentration and that stable invasion complexes are obtained with low equivalents of PNAs (2-4 equiv). We harnessed the high yield of dsDNA invasion for the detection of RT-RPA amplicon using a lateral flow assay (LFA) and showed that two strains of SARS-CoV-2 can be discriminated owing to single nucleotide resolution.
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Vummidi BR, Farrera-Soler L, Daguer JP, Dockerill M, Barluenga S, Winssinger N. A mating mechanism to generate diversity for the Darwinian selection of DNA-encoded synthetic molecules. Nat Chem 2022; 14:141-152. [PMID: 34873299 DOI: 10.1038/s41557-021-00829-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/30/2021] [Indexed: 12/18/2022]
Abstract
DNA-encoded library technologies enable the screening of synthetic molecules but have thus far not tapped into the power of Darwinian selection with iterative cycles of selection, amplification and diversification. Here we report a simple strategy to rapidly assemble libraries of conformationally constrained peptides that are paired in a combinatorial fashion (suprabodies). We demonstrate that the pairing can be shuffled after each amplification cycle in a process similar to DNA shuffling or mating to regenerate diversity. Using simulations, we show the benefits of this recombination in yielding a more accurate correlation of selection fitness with affinity after multiple rounds of selection, particularly if the starting library is heterogeneous in the concentration of its members. The method was validated with selections against streptavidin and applied to the discovery of PD-L1 binders. We further demonstrate that the binding of self-assembled suprabodies can be recapitulated by smaller (∼7 kDa) synthetic products that maintain the conformational constraint of the peptides.
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Affiliation(s)
- Balayeshwanth R Vummidi
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Lluc Farrera-Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland.
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Farrera-Soler L, Gonse A, Kim KT, Barluenga S, Winssinger N. Combining recombinase polymerase amplification and DNA-templated reaction for SARS-CoV-2 sensing with dual fluorescence and lateral flow assay output. Biopolymers 2022; 113:e23485. [PMID: 35023571 PMCID: PMC9011641 DOI: 10.1002/bip.23485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 09/16/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/17/2022]
Abstract
The early phase of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic was exacerbated by a diagnostic challenge of unprecedented magnitude. In the absence of effective therapeutics or vaccines, breaking the chain of transmission through early disease detection and patient isolation was the only means to control the growing pandemic. While polymerase chain reaction (PCR)‐based methods and rapid‐antigen tests rose to the occasion, the analytical challenge of rapid and sequence‐specific nucleic acid‐sensing at a point‐of‐care or home setting stimulated intense developments. Herein we report a method that combines recombinase polymerase amplification and a DNA‐templated reaction to achieve a dual readout with either fluorescence (microtiter plate) or naked eye (lateral flow assay: LFA) detection. The nucleic acid templated reaction is based on an SNAr that simultaneously transfers biotin from one Peptide Nucleic Acid (PNA) strand to another PNA strand, enabling LFA detection while uncaging a coumarin for fluorescence readout. This methodology has been applied to the detection of a DNA or RNA sequence uniquely attributed to the SARS‐CoV‐2.
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Affiliation(s)
- Lluc Farrera-Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Arthur Gonse
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
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Pagano S, Yerly S, Meyer B, Juillard C, Suh N, Le Terrier C, Daguer JP, Farrera-Soler L, Barluenga S, Piumatti G, Hartley O, Lemaitre B, Eberhardt CS, Siegrist CA, Eckerle I, Stringhini S, Guessous I, Kaiser L, Pugin J, Winssinger N, Vuilleumier N. SARS-CoV-2 infection as a trigger of humoral response against apolipoprotein A-1. Eur J Clin Invest 2021; 51:e13661. [PMID: 34324704 PMCID: PMC8420318 DOI: 10.1111/eci.13661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Unravelling autoimmune targets triggered by SARS-CoV-2 infection may provide crucial insights into the physiopathology of the disease and foster the development of potential therapeutic candidate targets and prognostic tools. We aimed at determining (a) the association between anti-SARS-CoV-2 and anti-apoA-1 humoral response and (b) the degree of linear homology between SARS-CoV-2, apoA-1 and Toll-like receptor 2 (TLR2) epitopes. DESIGN Bioinformatics modelling coupled with mimic peptides engineering and competition experiments were used to assess epitopes sequence homologies. Anti-SARS-CoV-2 and anti-apoA-1 IgG as well as cytokines were assessed by immunoassays on a case-control (n = 101), an intensive care unit (ICU; n = 126) and a general population cohort (n = 663) with available samples in the pre and post-pandemic period. RESULTS Using bioinformatics modelling, linear sequence homologies between apoA-1, TLR2 and Spike epitopes were identified but without experimental evidence of cross-reactivity. Overall, anti-apoA-1 IgG levels were higher in COVID-19 patients or anti-SARS-CoV-2 seropositive individuals than in healthy donors or anti-SARS-CoV-2 seronegative individuals (P < .0001). Significant and similar associations were noted between anti-apoA-1, anti-SARS-CoV-2 IgG, cytokines and lipid profile. In ICU patients, anti-SARS-CoV-2 and anti-apoA-1 seroconversion rates displayed similar 7-day kinetics, reaching 82% for anti-apoA-1 seropositivity. In the general population, SARS-CoV-2-exposed individuals displayed higher anti-apoA-1 IgG seropositivity rates than nonexposed ones (34% vs 16.8%; P = .004). CONCLUSION COVID-19 induces a marked humoral response against the major protein of high-density lipoproteins. As a correlate of poorer prognosis in other clinical settings, such autoimmunity signatures may relate to long-term COVID-19 prognosis assessment and warrant further scrutiny in the current COVID-19 pandemic.
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Affiliation(s)
- Sabrina Pagano
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland
| | - Sabine Yerly
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland
| | - Benjamin Meyer
- Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Catherine Juillard
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland
| | - Noémie Suh
- Division of Intensive Care, Geneva University Hospitals and the University of Geneva Faculty of Medicine, Geneva, Switzerland
| | - Christophe Le Terrier
- Division of Intensive Care, Geneva University Hospitals and the University of Geneva Faculty of Medicine, Geneva, Switzerland
| | - Jean-Pierre Daguer
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Lluc Farrera-Soler
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Giovanni Piumatti
- Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland.,Faculty of BioMedicine, Università della Svizzera Italiana, Lugano, Switzerland
| | - Oliver Hartley
- Faculty of Medicine, Department of Pathology and Immunology, University of Geneva, Switzerland
| | - Barbara Lemaitre
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland
| | - Christiane S Eberhardt
- Faculty of Medicine, Departments of Pathology-Immunology and Pediatrics, University of Geneva, Geneva, Switzerland
| | - Claire-Anne Siegrist
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland.,Faculty of Medicine, Departments of Pathology-Immunology and Pediatrics, University of Geneva, Geneva, Switzerland
| | - Isabella Eckerle
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Silvia Stringhini
- Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland.,Unit of Population Epidemiology, Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland
| | - Idris Guessous
- Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Laurent Kaiser
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland.,Faculty of Medicine, Departments of Pathology-Immunology and Pediatrics, University of Geneva, Geneva, Switzerland.,Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Jerome Pugin
- Division of Intensive Care, Geneva University Hospitals and the University of Geneva Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Winssinger
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Nicolas Vuilleumier
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland
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6
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Pagano S, Yerly S, Suh N, Le Terrier C, Farrera-Soler L, Piumatti G, Eberhardt CS, Siegrist CA, Eckerle I, Stringhini S, Guessous I, Kaiser L, Pugin J, Winssinger N, Vuilleumier N. Sars-CoV2- infection as a trigger of humoral response against apolipoprotein A-1. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.2757] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Unravelling autoimmune targets triggered by SARS-CoV-2 infection may provide crucial insights in the physiopathology of the disease and foster the development of potential therapeutic candidate targets and prognostic tools. SARS-CoV-2 autoimmune-mediated inflammation have been reported, but the existence of autoantibodies against apolipoprotein A-1 (anti-apoA-1 IgG) in COVID-19 remains unexplored. Anti-apoA-1 IgGs have emerged as an independent biomarker for cardiovascular disease and mortality in humans with proinflammatory and proatherogenic functions in vivo and in vitro.
Purpose
We want to determine i) the degree of homology between SARS-CoV-2, apoA-1, and Toll-like receptor-2 (TLR2) epitopes, ii) the association between anti-SARSCoV2 and anti-apoA-1 IgGs, and iii) their relationship to prognosis.
Methods
We performed bioinformatics modelling coupled with mimetic peptides engineering, as well as functional and competition assays with antibodies to identify molecular mimicry between SARS-CoV-2, apoA-1 and TLR2 epitopes. Anti-Spike domain 1 (SD1) IgGs, anti-apoA-1 IgGs and against mimic peptides, as well as cytokines were assessed by immunoassays on a case-control (n=101), an intensive care unit (ICU; n=126) with a 28-days follow-up for overall mortality, and a general population cohort (n=663) with available samples in the pre and post-pandemic period.
Results
Linear sequence homologies and antibodies cross-reactivity between apoA-1, TLR2, and Spike epitopes were identified. Overall, anti-apoA-1 IgG levels were higher in COVID-19 patients or anti-SARS-CoV-2 seropositive individuals than in healthy donors or anti-SARS-CoV-2 seronegative individuals (p<0.0001). Significant and similar associations were noted between anti-apoA-1, anti-SARS-CoV-2 IgG, cytokines, and lipid profile. In ICU patients, anti-SARS-CoV-2 and anti-apoA-1 seroconversion rates displayed similar 7-days kinetics, reaching 82% for anti-apoA-1 seropositivity. C-statistics (CS) indicated that baseline anti-Spike/TLR2 mimic-peptide IgGs displayed a significant prognostic accuracy for overall mortality at 28 days (CS: 0.64; p=0.02). In the general population, SARS-CoV-2 exposure increased baseline anti-apoA-1 IgG levels.
Conclusions
COVID-19 induces a marked humoral response against the major protein of high-density lipoproteins. As a correlate of poorer prognosis in other clinical settings, such autoimmunity signatures may relate to long-term COVID-19 prognosis assessment and warrant further scrutiny in the current COVID-19 pandemic.
Funding Acknowledgement
Type of funding sources: Public Institution(s). Main funding source(s): This study was funded by the Swiss Federal Office of Public Health, Swiss School of Public Health (Corona Immunitas research program), the Fondation de Bienfaisance du Groupe Pictet, the Fondation Ancrage, the Fondation Privée des HUG, and the Center for Emerging Viral Diseases. The De Reuter (grant Nr 657) and the Schmidheiny Foundation.
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Affiliation(s)
- S Pagano
- Geneva University Hospitals, Geneva, Switzerland
| | - S Yerly
- Geneva University Hospitals, Geneva, Switzerland
| | - N Suh
- Geneva University Hospitals, Geneva, Switzerland
| | - C Le Terrier
- Geneva University Hospitals, Geneva, Switzerland
| | | | - G Piumatti
- Geneva University Hospitals, Geneva, Switzerland
| | | | - C A Siegrist
- Geneva University Hospitals, Geneva, Switzerland
| | - I Eckerle
- Geneva University Hospitals, Geneva, Switzerland
| | - S Stringhini
- Geneva University Hospitals, Geneva, Switzerland
| | - I Guessous
- Geneva University Hospitals, Geneva, Switzerland
| | - L Kaiser
- Geneva University Hospitals, Geneva, Switzerland
| | - J Pugin
- Geneva University Hospitals, Geneva, Switzerland
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Daguer JP, Gonse A, Shchukin Y, Farrera-Soler L, Barluenga S, Winssinger N. Dual Bcl-X L /Bcl-2 inhibitors discovered from DNA-encoded libraries using a fragment pairing strategy. Bioorg Med Chem 2021; 44:116282. [PMID: 34216984 DOI: 10.1016/j.bmc.2021.116282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/24/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 11/26/2022]
Abstract
A dual Bcl-XL / Bcl-2 inhibitor was discovered from DNA-encoded libraries using a two steps process. In the first step, DNA was used to pair PNA-encoded fragments exploring > 250 000 combinations. In the second step, a focused library combining the selected fragments with linkers of different lengths and geometries led to the identification of tight binding adducts that were further investigated for their selective target engagement in pull-down assays, for their affinity by SPR, and their selectivity in a cytotoxicity assay. The best compound showed comparable cellular activity to venetoclax, the first-in-class therapeutic targeting Bcl-2.
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Affiliation(s)
- Jean-Pierre Daguer
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Arthur Gonse
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Yevhenii Shchukin
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Lluc Farrera-Soler
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland.
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Farrera-Soler L, Daguer JP, Barluenga S, Winssinger N. Experimental Identification of Immuno- dominant B-cell Epitopes from SARS-CoV-2. Chimia (Aarau) 2021; 75:276-284. [PMID: 33902795 DOI: 10.2533/chimia.2021.276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current public health crisis with devastating consequences to our societies. This COVID-19 pandemic has become the most serious threat to global public health in recent history. Given the unprecedented economic and social impact that it is causing, identification of immunodominant epitopes from SARS-CoV-2 is of great interest, not only to gain better insight into the adaptive immune response, but also for the development of vaccines, treatments and diagnostic tools. In this review, we summarize the already published or preprinted reports on the experimental identification of B-cell linear epitopes of SARS-CoV-2 proteins. Six different epitopes leading to neutralizing antibodies have been identified. Moreover, a summary of peptide candidates to be used for diagnostic tools is also included.
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Affiliation(s)
- Lluc Farrera-Soler
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1211 Geneva 4;,
| | - Jean-Pierre Daguer
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1211 Geneva 4
| | - Sofia Barluenga
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1211 Geneva 4
| | - Nicolas Winssinger
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1211 Geneva 4
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9
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Farrera-Soler L, Daguer JP, Barluenga S, Vadas O, Cohen P, Pagano S, Yerly S, Kaiser L, Vuilleumier N, Winssinger N. Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma. PLoS One 2020; 15:e0238089. [PMID: 32903266 PMCID: PMC7480855 DOI: 10.1371/journal.pone.0238089] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/10/2020] [Indexed: 01/09/2023] Open
Abstract
A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the source of a current pandemic (COVID-19) with devastating consequences in public health and economic stability. Using a peptide array to map the antibody response of plasma from healing patients (12) and heathy patients (6), we identified three immunodominant linear epitopes, two of which correspond to key proteolytic sites on the spike protein (S1/S2 and S2') known to be critical for cellular entry. We show biochemical evidence that plasma positive for the epitope adjacent to the S1/S2 cleavage site inhibits furin-mediated proteolysis of spike.
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Affiliation(s)
- Lluc Farrera-Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Oscar Vadas
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Patrick Cohen
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Sabrina Pagano
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Sabine Yerly
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Laurent Kaiser
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Division of Infectious Diseases¸ Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Vuilleumier
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
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10
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Farrera-Soler L, Daguer JP, Raunft P, Barluenga S, Imberty A, Winssinger N. PNA-Based Dynamic Combinatorial Libraries (PDCL) and screening of lectins. Bioorg Med Chem 2020; 28:115458. [PMID: 32241620 DOI: 10.1016/j.bmc.2020.115458] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 11/16/2022]
Abstract
Selections from dynamic combinatorial libraries (DCL) benefit from the dynamic nature of the library that can change constitution upon addition of a selection pressure, such as ligands binding to a protein. This technology has been predominantly used with small molecules interacting with each other through reversible covalent interaction. However, application of this technology in biomedical research and drug discovery has been limited by the reversibility of covalent exchange and the analytical deconvolution of small molecule fragments. Here we report a supramolecular approach based on the use of a constant short PNA tag to direct the combinatorial pairing of fragment. This PNA tag yields fast exchange kinetics, while still delivering the benefits of cooperativity, and provides favourable properties for analytical deconvolution by MALDI. A selection from >6,000 assemblies of glycans (mono-, di-, tri-saccharides) targeting AFL, a lectin from pathogenic fungus, yielded a 95 nM assembly, nearly three orders of magnitude better in affinity than the corresponding glycan alone (41 µM).
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Affiliation(s)
- Lluc Farrera-Soler
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland
| | - Jean-Pierre Daguer
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland
| | - Patrick Raunft
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland
| | - Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Nicolas Winssinger
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland.
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