-
BioRxiv : the Preprint Server For... Jun 2024Therapeutics Data Commons (tdcommons.ai) is an open science initiative with unified datasets, AI models, and benchmarks to support research across therapeutic modalities...
Therapeutics Data Commons (tdcommons.ai) is an open science initiative with unified datasets, AI models, and benchmarks to support research across therapeutic modalities and drug discovery and development stages. The Commons 2.0 (TDC-2) is a comprehensive overhaul of Therapeutic Data Commons to catalyze research in multimodal models for drug discovery by unifying single-cell biology of diseases, biochemistry of molecules, and effects of drugs through multimodal datasets, AI-powered API endpoints, new multimodal tasks and model frameworks, and comprehensive benchmarks. TDC-2 introduces over 1,000 multimodal datasets spanning approximately 85 million cells, pre-calculated embeddings from 5 state-of-the-art single-cell models, and a biomedical knowledge graph. TDC-2 drastically expands the coverage of ML tasks across therapeutic pipelines and 10+ new modalities, spanning but not limited to single-cell gene expression data, clinical trial data, peptide sequence data, peptidomimetics protein-peptide interaction data regarding newly discovered ligands derived from AS-MS spectroscopy, novel 3D structural data for proteins, and cell-type-specific protein-protein interaction networks at single-cell resolution. TDC-2 introduces multimodal data access under an API-first design using the model-view-controller paradigm. TDC-2 introduces 7 novel ML tasks with fine-grained biological contexts: contextualized drug-target identification, single-cell chemical/genetic perturbation response prediction, protein-peptide binding affinity prediction task, and clinical trial outcome prediction task, which introduce antigen-processing-pathway-specific, cell-type-specific, peptide-specific, and patient-specific biological contexts. TDC-2 also releases benchmarks evaluating 15+ state-of-the-art models across 5+ new learning tasks evaluating models on diverse biological contexts and sampling approaches. Among these, TDC-2 provides the first benchmark for context-specific learning. TDC-2, to our knowledge, is also the first to introduce a protein-peptide binding interaction benchmark.
PubMed: 38948789
DOI: 10.1101/2024.06.12.598655 -
A Flow Cytometry-Based Method for Assessing CAR Cell Binding Kinetics Using Stable CAR Jurkat Cells.Bio-protocol Jun 2024Chimeric antigen receptors (CARs) are synthetic fusion proteins that can reprogram immune cells to target specific antigens. CAR-expressing T cells have emerged as an...
Chimeric antigen receptors (CARs) are synthetic fusion proteins that can reprogram immune cells to target specific antigens. CAR-expressing T cells have emerged as an effective treatment method for hematological cancers; despite this success, the mechanisms and structural properties that govern CAR responses are not fully understood. Here, we provide a simple assay to assess cellular avidity using a standard flow cytometer. This assay measures the interaction kinetics of CAR-expressing T cells and targets antigen-expressing target cells. By co-culturing stably transfected CAR Jurkat cells with target positive and negative cells for short periods of time in a varying effector-target gradient, we were able to observe the formation of CAR-target cell doublets, providing a readout of actively bound cells. When using the optimized protocol reported here, we observed unique cellular binding curves that varied between CAR constructs with differing antigen binding domains. The cellular binding kinetics of unique CARs remained consistent, were dependent on specific target antigen expression, and required active biological signaling. While existing literature is not clear at this time whether higher or lower CAR cell binding is beneficial to CAR therapeutic activity, the application of this simplified protocol for assessing CAR binding could lead to a better understanding of the proximal signaling events that regulate CAR functionality. Key features • Determines CAR receptor cellular interaction kinetics using a Jurkat cell model. • Can be used for a wide variety of CAR target antigens, including both hematological and solid tumor targets. • Experiments can be performed in under two hours with no staining using a standard flow cytometer. • Requires stable CAR Jurkat cells and target cells with stable fluorescent marker expression for optimal results.
PubMed: 38948258
DOI: 10.21769/BioProtoc.5021 -
Open Life Sciences 2024Membrane-associated proteins are important membrane readers that mediate and facilitate the signaling and trafficking pathways in eukaryotic membrane-bound compartments.... (Review)
Review
Membrane-associated proteins are important membrane readers that mediate and facilitate the signaling and trafficking pathways in eukaryotic membrane-bound compartments. The protein members in the Phafin family are membrane readers containing two phosphoinositide recognition domains: the Pleckstrin Homology domain and the FYVE (Fab1, YOTB, Vac1, and early endosome antigen 1) domain. Phafin proteins, categorized into two subfamilies, Phafin1 and Phafin2, associate with cellular membranes through interactions involving membrane-embedded phosphoinositides and phosphoinositide-binding domains. These membrane-associated Phafin proteins play pivotal roles by recruiting binding partners and forming complexes, which contribute significantly to apoptotic, autophagic, and macropinocytotic pathways. Elevated expression levels of Phafin1 and Phafin2 are observed in various cancers. A recent study highlights a significant increase in Phafin1 protein levels in the lungs of idiopathic pulmonary fibrosis patients compared to normal subjects, suggesting a crucial role for Phafin1 in the pathogenesis of pulmonary fibrosis. Additionally, phosphatidylinositol-3-phosphate-binding 2 (Pib2), a close relative of the Phafin1 protein, functions as an amino acid sensor activating the TOCR1 pathway in yeasts. This review focuses on delineating the involvement of Phafin proteins in cellular signaling and their implications in diseases and briefly discusses the latest research findings concerning Pib2.
PubMed: 38947768
DOI: 10.1515/biol-2022-0896 -
Saudi Journal of Biological Sciences Aug 2024Human Rotavirus (HRV) is the causative pathogen of severe acute enteric infections that cause mortality among children worldwide. This study focuses on developing a new...
Human Rotavirus (HRV) is the causative pathogen of severe acute enteric infections that cause mortality among children worldwide. This study focuses on developing a new and effective treatment for rotavirus infection using an extract from Saccharomyces cerevisiae, aiming to make this treatment easily accessible to everyone. 15 antigens and 26 antibodies were detected in serum and stool using ELISA. The titers of HRVq1, HRVq2, HRVC1, and HRVC2 on Vero cells were determined to be 1.2x10, 3.0x10, 4.2x10, and 7.5x10 (Plaque forming unit, PFU/ml) four days after infection, respectively. The HRVq1 isolate induced cytopathic effects, i.e., forming multinucleated, rounded, enlarged, and expanding gigantic cells. RT-PCR identified this isolate, and the accession number 2691714 was assigned to GeneBank. The molecular docking analysis revealed that nonstructural proteins (NSPs) NSP1, NSP2, NSP3, NSP4, NSP5, and NSP6 exhibited significant binding with RNA. NSP2 demonstrated the highest binding affinity and the lowest binding energy (-8.9 kcal/mol). This affinity was maintained via hydrophobic interactions and hydrogen bonds spanning in length from 1.12 Å to 3.11 Å. The ADMET and bioactivity predictions indicated that the yeast extract possessed ideal solubility, was nontoxic, and did not cause cancer. The inhibitory constant values predicted for the extract in the presence of HRV vital proteins varied from 5.32 to 7.45 mM, indicating its potential as a viable drug candidate. extract could be utilized as a dietary supplement to combat HRV as an alternative dietary supplement.
PubMed: 38946847
DOI: 10.1016/j.sjbs.2024.104031 -
Expert Opinion on Therapeutic Targets Jul 2024CLEC10A is a C-type lectin receptor that specifically marks the conventional dendritic cell subsets two and three (cDC2 and DC3). It has a unique recognition profile of... (Review)
Review
INTRODUCTION
CLEC10A is a C-type lectin receptor that specifically marks the conventional dendritic cell subsets two and three (cDC2 and DC3). It has a unique recognition profile of glycan antigens, with terminal N-Acetylgalactosamine residues that are frequently present in the tumor microenvironment. Even though CLEC10A expression allows for precise targeting of cDC2 and DC3 for the treatment of cancer, CLEC10A signaling has also been associated with anti-inflammatory responses that would promote tumor growth.
AREAS COVERED
Here, we review the potential benefits and drawbacks of CLEC10A engagement in the tumor microenvironment. We discuss the CLEC10A-mediated effects in different cell types and incorporate the pleiotropic effects of IL-10, the main anti-inflammatory response upon CLEC10A binding.
EXPERT OPINION
To translate this to a successful CLEC10A-mediated immunotherapy with limited tumor-promoting capacities, finding the right ligand presentation and adjuvant combination will be key.
PubMed: 38946482
DOI: 10.1080/14728222.2024.2374743 -
Molecular Therapy : the Journal of the... Jun 2024The chimeric antigen receptor (CAR) derived from the CD30 specific murine antibody, HRS-3, has produced promising clinical efficacy with a favorable safety profile in...
The chimeric antigen receptor (CAR) derived from the CD30 specific murine antibody, HRS-3, has produced promising clinical efficacy with a favorable safety profile in the treatment of relapsed or refractory CD30-positive lymphomas. However, persistence of the autologous CAR T cells was brief, and many patients relapsed a year after treatment. The lack of persistence may be attributed to the use of a wildtype IgG1 spacer that can associate with Fc receptors. We first identified the cysteine rich domain (CRD) 5 of CD30 as the primary binding epitope of HRS-3 and armed with this insight, attempted to improve the HRS-3 CAR functionality with a panel of novel spacer designs. We demonstrate that HRS-3 CARs with OX40 and 4-1BB derived spacers exhibited similar anti-tumor efficacy, circumvented interactions with Fc receptors and secreted lower levels of cytokines in vitro than a CAR employing the IgG1 spacer. Humanization of the HRS-3 scFv coupled with the 4-1BB spacer preserved potent on-target, on-tumor efficacy, and on-target, off-tumor safety. In a lymphoma mouse model of high tumor burden, T cells expressing a humanized HRS-3 CD30.CARs with the 4-1BB spacer potently killed tumors with low levels of circulating inflammatory cytokines, providing a promising candidate for future clinical development in the treatment of CD30-positive malignancies.
PubMed: 38946142
DOI: 10.1016/j.ymthe.2024.06.037 -
Journal of the American Chemical Society Jun 2024bacteria are becoming increasingly resistant against multiple antibiotics. Therefore, the development of vaccines to prevent infections with these bacteria is an urgent...
bacteria are becoming increasingly resistant against multiple antibiotics. Therefore, the development of vaccines to prevent infections with these bacteria is an urgent medical need. While the immunological activity of lipopolysaccharide O-antigens in is well-known, the specific protective epitopes remain unidentified. Herein, we present the first chemical synthesis of highly functionalized aminoglycoside trisaccharide and its acetamido derivative found in the serotype O5 O-antigen. The synthesis of the trisaccharide targets is based on balancing the reactivity of disaccharide acceptors and monosaccharide donors. Glycosylations were analyzed by quantifying the reactivity of the hydroxyl group of the disaccharide acceptor using the orbital-weighted Fukui function and dual descriptor. The stereoselective formation of 1,2--α-fucosylamine linkages was achieved through a combination of remote acyl participation and reagent modulation. The simultaneous S2 substitution of azide groups at C2' and C2″ enabled the efficient synthesis of 1,2--β-linkages for both 2,3-diamino-D-mannuronic acids. Through a strategic orthogonal modification, the five amino groups on target trisaccharide were equipped with a rare acetamidino (Am) and four acetyl (Ac) groups. Glycan microarray analyses of sera from patients infected with indicated that trisaccharides and are key antigenic epitopes of the serotype O5 O-antigen. The acetamidino group is not an essential determinant of antibody binding. The β-D-ManNAc3NAcA residue is a key motif for the antigenicity of serotype O5 O-antigen. These findings serve as a foundation for the development of glycoconjugate vaccines targeting serotype O5.
PubMed: 38946080
DOI: 10.1021/jacs.4c03814 -
Iranian Biomedical Journal Apr 2024The growing threat of antibiotic resistance and Klebsiella pneumoniae infection in healthcare settings highlights the urgent need for innovative solutions, such as...
BACKGROUND
The growing threat of antibiotic resistance and Klebsiella pneumoniae infection in healthcare settings highlights the urgent need for innovative solutions, such as vaccines, to address these challenges. This study sought to assess the potential of using K. pneumoniae OmpA as a vaccine candidate through both in silico and in vivo analyses.
METHODS
The study examined the OmpA protein sequence for subcellular localization, antigenicity, allergenicity, similarity to the human proteome, physicochemical properties, B-cell epitopes, MHC binding sites, tertiary structure predictions, molecular docking, and immune response simulations. The ompA gene was cloned into the pET-28a (+) vector, expressed, purified and confirmed using Western blotting analysis. IgG levels in the serum of the immunized mice were measured using ELISA with dilutions ranging from 1:100 to 1:6400, targeting rOmpA and K. pneumoniae ATCC 13883. The sensitivity and specificity of the ELISA method were also assessed.
RESULTS
The bioinformatics analysis identified rOmpA as a promising vaccine candidate. The immunized group demonstrated significant production of specific total IgG antibodies against rOmpA and K. pneumoniae ATCC1 13883, as compared to the control group (p < 0.0001). The titers of antibodies produced in response to bacterial exposure did not show any significant difference when compared to the anti-rOmpA antibodies (p > 0.05). The ELISA test sensitivity was 1:3200, and the antibodies in the serum could accurately recognize K. pneumoniae cells.
CONCLUSION
This study is a significant advancement in the development of a potential vaccine against K. pneumoniae that relies on OmpA. Nevertheless, additional experimental analyses are required.
PubMed: 38946021
DOI: 10.61186/ibj.4023 -
Food Research International (Ottawa,... Aug 2024In dairy products, the added sodium hyaluronate may form complexes with proteins, thereby affecting product properties. In the present study, the interaction between...
In dairy products, the added sodium hyaluronate may form complexes with proteins, thereby affecting product properties. In the present study, the interaction between whey protein isolate (WPI)/ whey protein hydrolysate (WPH) and sodium hyaluronate (SH) was characterized under thermal treatment at different temperatures (25 ℃, 65 ℃, 90 ℃ and 121 ℃) after studying effects of protein/SH ratio and pH on complex formation. The addition of SH reduced the particle size of WPI/WPH and increased potential value in the system, with greater variation with increasing treatment temperature. The structural properties of complexes were studied. The binding with SH decreased the contents of free amino group and free thiol group, as well as the fluorescence intensity and surface hydrophobicity. FTIR results and browning intensity measurement demonstrated the formation of Maillard reaction products. Moreover, the attachment of SH improved the thermal stability of WPI/WPH and decreased their antigenicity.
Topics: Whey Proteins; Hyaluronic Acid; Protein Hydrolysates; Hot Temperature; Hydrogen-Ion Concentration; Maillard Reaction; Hydrophobic and Hydrophilic Interactions; Particle Size; Spectroscopy, Fourier Transform Infrared; Food Handling
PubMed: 38945618
DOI: 10.1016/j.foodres.2024.114608 -
Food Research International (Ottawa,... Aug 2024Egg proteins, notably ovalbumin (OVA), contribute to a prevalent form of food allergy, particularly in children. This study aims to investigate the impact of high...
Egg proteins, notably ovalbumin (OVA), contribute to a prevalent form of food allergy, particularly in children. This study aims to investigate the impact of high hydrostatic pressure (HHP) treatment at varying levels (300, 400, 500, and 600 MPa) on the molecular structure and allergenicity of OVA. The structure of HHP-treated OVA was assessed through fluorescence spectroscopy, circular dichroism spectroscopy, and molecular dynamics (MD) simulation. HHP treatment (600 MPa) altered OVA structures, such as α-helix content decreased from 28.07 % to 19.47 %, and exogenous fluorescence intensity increased by 8.8 times compared to that of the native OVA. The free sulfhydryl groups and zeta potential value were also increased with HHP treatment (600 MPa). ELISA analysis and MD simulation unveiled a noteworthy reduction in the allergenicity of OVA when subjected to 600 MPa for 10 min. Overall, this study suggests that the conformational changes in HHP-treated OVA contribute to its altered allergenicity.
Topics: Ovalbumin; Hydrostatic Pressure; Allergens; Molecular Dynamics Simulation; Circular Dichroism; Spectrometry, Fluorescence; Animals; Egg Hypersensitivity; Food Hypersensitivity; Humans; Food Handling; Protein Conformation
PubMed: 38945590
DOI: 10.1016/j.foodres.2024.114658