Journal: bioRxiv

Article Title: K5 polysaccharides inhibit SARS-CoV-2 infection by preventing spike-proteolytic priming

doi: 10.1101/2025.04.23.650164

Figure Lengend Snippet: (A) Predominant composition of the disaccharide unit present in each K5 derivative (ranging from 70% to 100% of the total sequence) is shown (see for further details). Disaccharides are represented in their ionic form (sodium salt is the common counterion). (B) Fraction of spike bound to GAG at increasing concentrations of the indicated GAGs as measured by MST. (C) Inhibition of the interaction of immobilized heparin with spike by increasing concentrations of the indicated GAGs as measured by SPR. The responses are plotted as a percentage of the binding of spike measured in the absence of free GAG. (D) Inhibition of the binding of spike RBD to immobilized-ACE2 at increasing concentrations of the indicated GAGs as measured by SPR. The responses are plotted as a percentage of the binding of spike measured in the absence of free GAG. (E) Inhibition of cleavage of a peptide fragment containing the S 1 /S 2 basic domain of spike by increasing concentrations of the indicated GAGs. The peptide was left untreated (−furin) or exposed to furin (25 ng/well) (+ furin) (gray points and lanes) and after incubation in the absence and the presence of the GAG, spike cleavage was evaluated by optical density (O.D.) measurements as described in Experimental Procedures. –furin vs + furin: P value < 0.00001. Each point is the mean + sd of three to ten separate determinations (see for more details).

Article Snippet: Reagents and materials were used as received, unless otherwise mentioned, and were purchased from the following: Human recombinant SARS-CoV-2 Wuhan-Hu-1 spike His-Tag protein and RBD from Sino Biological (#40592-V08B); ACE2 from Acrobiosystem (#AC2-H52H8); Bovine Serum Albumin (BSA) from Merck (#810037); Human recombinant furin from OriGene Technologies Inc. (#TP304279M); Conventional heparin (13.6 kDa - purity ≥95%) from a commercial batch of unfractionated sodium heparin from Laboratori Derivati Organici S.p.A. (#9041-08-1); Capsular K5 polysaccharides prepared as described in Oreste et. al .

Techniques: Sequencing, Inhibition, Binding Assay, Incubation

Journal: bioRxiv

Article Title: K5 polysaccharides inhibit SARS-CoV-2 infection by preventing spike-proteolytic priming

doi: 10.1101/2025.04.23.650164

Figure Lengend Snippet: Spike RBD (20 nM) or the indicated GAGs (100 μM) were injected over the ACE2 containing biosensor to evaluate their capacity to bind directly to the receptor. * P < 0.05.

Article Snippet: Reagents and materials were used as received, unless otherwise mentioned, and were purchased from the following: Human recombinant SARS-CoV-2 Wuhan-Hu-1 spike His-Tag protein and RBD from Sino Biological (#40592-V08B); ACE2 from Acrobiosystem (#AC2-H52H8); Bovine Serum Albumin (BSA) from Merck (#810037); Human recombinant furin from OriGene Technologies Inc. (#TP304279M); Conventional heparin (13.6 kDa - purity ≥95%) from a commercial batch of unfractionated sodium heparin from Laboratori Derivati Organici S.p.A. (#9041-08-1); Capsular K5 polysaccharides prepared as described in Oreste et. al .

Techniques: Injection

Journal: bioRxiv

Article Title: K5 polysaccharides inhibit SARS-CoV-2 infection by preventing spike-proteolytic priming

doi: 10.1101/2025.04.23.650164

Figure Lengend Snippet: VeroE6 cells or A549 ACE2+ cells were treated with increasing concentrations of heparin, K5, K5OSH, and K5NOSH. (A, B) The cells remained viable in the presence of heparin and the K5 compounds as evaluated by measuring the ATP levels. VeroE6 or A549 ACE2+ cells were infected with the B.1 (C, D) or Omicron BA.1 (E, F) isolates in the presence or the absence of increasing concentrations of heparin, K5, K5OSH, and K5NOSH. Infection was reduced in a concentration-dependent manner as shown by the percentage of plaque reduction compared to SARS-CoV-2 alone. Data are presented as the mean value ± standard error of two independent replicates. * P < 0.05; ** P< 0.005.

Article Snippet: Reagents and materials were used as received, unless otherwise mentioned, and were purchased from the following: Human recombinant SARS-CoV-2 Wuhan-Hu-1 spike His-Tag protein and RBD from Sino Biological (#40592-V08B); ACE2 from Acrobiosystem (#AC2-H52H8); Bovine Serum Albumin (BSA) from Merck (#810037); Human recombinant furin from OriGene Technologies Inc. (#TP304279M); Conventional heparin (13.6 kDa - purity ≥95%) from a commercial batch of unfractionated sodium heparin from Laboratori Derivati Organici S.p.A. (#9041-08-1); Capsular K5 polysaccharides prepared as described in Oreste et. al .

Techniques: Infection, Concentration Assay

Journal: ACS Sensors

Article Title: Poly(3,4-ethylenedioxythiophene) Nanorod Arrays-Based Organic Electrochemical Transistor for SARS-CoV-2 Spike Protein Detection in Artificial Saliva

doi: 10.1021/acssensors.4c03207

Figure Lengend Snippet: (a) Schematic of the OECT device sensing system and its saliva testing procedure for detecting the spike protein. The device features a Ag/AgCl gate electrode and PEDOT-based active-layer channel situated between the source and drain electrodes. The channel layer consists of a PN layer immobilized with ACE2 receptors. (b) Equivalent circuit diagram of the OECT. (c) Illustration of the procedure for immobilizing the biotinylated ACE2 receptor onto the streptavidin-modified PN surface, followed by the EDC/NHS reaction for streptavidin binding on PN.

Article Snippet: Biotinylated human ACE2/Angiotensin-Converting enzyme 2 Protein (His-Tag) and SARS-CoV-2 (2019-nCoV) Spike RBD recombinant protein were purchased from Sino Biological (Beijing, China).

Techniques: Modification, Binding Assay

Journal: ACS Sensors

Article Title: Poly(3,4-ethylenedioxythiophene) Nanorod Arrays-Based Organic Electrochemical Transistor for SARS-CoV-2 Spike Protein Detection in Artificial Saliva

doi: 10.1021/acssensors.4c03207

Figure Lengend Snippet: (a) FTIR spectra showing the modifications of PN through the EDC/NHS reaction, followed by streptavidin and ACE2 receptor binding. (b) WCA measurements of Glass, Glass/PEDOT:PSS, and Glass/PEDOT:PSS/PEDOTAc. Error bars were obtained by taking average of n = 3 separate measurements taken at different times.

Article Snippet: Biotinylated human ACE2/Angiotensin-Converting enzyme 2 Protein (His-Tag) and SARS-CoV-2 (2019-nCoV) Spike RBD recombinant protein were purchased from Sino Biological (Beijing, China).

Techniques: Binding Assay

Journal: ACS Sensors

Article Title: Poly(3,4-ethylenedioxythiophene) Nanorod Arrays-Based Organic Electrochemical Transistor for SARS-CoV-2 Spike Protein Detection in Artificial Saliva

doi: 10.1021/acssensors.4c03207

Figure Lengend Snippet: (a, b) Confocal microscopy images confirming the attachment of streptavidin. (a) Fluorescence is visible on the nanorod arrays after the modification of streptavidin-cy5 on the EDC/NHS-treated surface. (b) No EDC/NHS reaction on the surface. (c) Transconductance ( g m ) of the OECT device as a function of active-layer channel, showing the response with the addition of various linkers for ACE2 antibody immobilization.

Article Snippet: Biotinylated human ACE2/Angiotensin-Converting enzyme 2 Protein (His-Tag) and SARS-CoV-2 (2019-nCoV) Spike RBD recombinant protein were purchased from Sino Biological (Beijing, China).

Techniques: Confocal Microscopy, Fluorescence, Modification

Journal: Nature Biomedical Engineering

Article Title: Deep mutational learning for the selection of therapeutic antibodies resistant to the evolution of Omicron variants of SARS-CoV-2

doi: 10.1038/s41551-025-01353-4

Figure Lengend Snippet: a , For the construction of the high-distance Omicron BA.1 RBD library, short ssODNs are designed to possess mutations. The fragments are assembled into full-length RBD sequences using GGA and transformed into yeast. The resulting library is screened for antibody binding and escape using FACS. b , The sorted high-distance RBD variant library is deep sequenced, and the data are used to train ensemble deep learning models to predict ACE2 and antibody binding or non-binding (escape). Deep learning models are used to predict the breadth of antibody combinations as well as their binding to synthetic RBD variants and lineages. mAb, monoclonal antibody.

Article Snippet: Next, cells were labelled with 50 nM of biotinylated human ACE2 protein (Acro Biosystems, AC2-H82E6) for 30 min at 4 °C at 700 r.p.m. on a shaker (Eppendorf, ThermoMixer C).

Techniques: Transformation Assay, Binding Assay, Variant Assay

Journal: Nature Biomedical Engineering

Article Title: Deep mutational learning for the selection of therapeutic antibodies resistant to the evolution of Omicron variants of SARS-CoV-2

doi: 10.1038/s41551-025-01353-4

Figure Lengend Snippet: a , b , Workflow for sorting of yeast display RBD libraries and FACS dot plots for ACE2 ( a ) and antibodies Brii-198 and ZCB11 ( b ). Gating schemes correspond to binding and non-binding (escape) RBD variant populations. c , d Heat maps depicting the binding score of each amino acid per position of full-length RBD following sorting and deep sequencing of libraries for ACE2 ( c ) and ZCB11 ( d ); higher binding score indicates greater frequency in the binding population versus non-binding population. Wild-type BA.1 residues are in grey. e , Heat maps for seq-libraries A and B depicting binding scores for ACE2 and antibodies of key mutations seen in major Omicron sublineage variants.

Article Snippet: Next, cells were labelled with 50 nM of biotinylated human ACE2 protein (Acro Biosystems, AC2-H82E6) for 30 min at 4 °C at 700 r.p.m. on a shaker (Eppendorf, ThermoMixer C).

Techniques: Binding Assay, Variant Assay, Sequencing

Journal: Nature Biomedical Engineering

Article Title: Deep mutational learning for the selection of therapeutic antibodies resistant to the evolution of Omicron variants of SARS-CoV-2

doi: 10.1038/s41551-025-01353-4

Figure Lengend Snippet: a , Deep sequencing data of sorted yeast display libraries are encoded by one-hot encoding and used to train CNN models with several dilated convolutional residual blocks. The models perform a final classification by predicting binding or non-binding to ACE2 or antibodies based on the encoded RBD sequence. b , Majority voting by an ensemble of models is used to determine the final label for each variant. c , Predicted labels of antibodies to well-characterized Omicron variants; colours indicate final labels; mis-classifications are marked with an ‘X’; conflicting data for S2H259 binding to BQ.1 and BA.2.75 are marked with ‘*’.

Article Snippet: Next, cells were labelled with 50 nM of biotinylated human ACE2 protein (Acro Biosystems, AC2-H82E6) for 30 min at 4 °C at 700 r.p.m. on a shaker (Eppendorf, ThermoMixer C).

Techniques: Sequencing, Binding Assay, Variant Assay