bobcat339 (MultiTarget Pharmaceuticals)
Structured Review
![Screening potential candidates of TET-family inhibitors in infected hiPSC-CMs via computational molecular docking simulation. (A) The flowchart of the drug screening platform for molecular docking analysis of TET2 in complex with its DNA substrate and representative inhibitors. (B) Schematic representation of the molecular docking of representative TET2 <t>inhibitors—Bobcat339,</t> TFMB-2HG, and TETi76—into the catalytic pocket of TET2. The figure illustrates the catalytic core of TET2 binding to methylated DNA, followed by computational screening and docking of small-molecule inhibitors into the active site. (C) TET2 in complex with DNA substrate (Protein Data Bank [PDB] ID: 7NE3). Left: Overall structure showing TET2 (ribbon representation) bound to DNA (sticks in orange and magenta). Middle: Close-up view of the catalytic pocket highlighting the interaction surface. Right: 2-dimensional (2D) interaction diagram illustrating contacts between TET2 and the DNA substrate. (D) TET2 in complex with TETi76. Left: Chemical structure of TETi76. Middle: Docked pose of TETi76 in the TET2 catalytic site. Right: 2D interaction diagram showing hydrogen bonding and hydrophobic contacts. (E) TET2 in complex with Bobcat339. Left: Chemical structure of Bobcat339. Middle: Docked binding mode of Bobcat339 in the catalytic site. Right: 2D interaction map illustrating hydrogen bonds, hydrophobic interactions, and halogen bonding. (F) TET2 in complex with TFMB-2HG. Left: Chemical structure of TFMB-2HG. Middle: Docked pose within the TET2 active site. Right: 2D interaction map showing hydrogen bonding and minimal hydrophobic interactions.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_0876/pmc12280876/pmc12280876__bmr.0229.fig.005.jpg)
Bobcat339, supplied by MultiTarget Pharmaceuticals, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/multitarget/bobcat339/pmc12280876-16-5-23
Average 90 stars, based on 1 article reviews
Images
1) Product Images from "Epitranscriptomic Modulation of TET2 Inhibition Suppressed SARS-CoV-2 Infection and Blocked Viral Nucleocapsid Protein in Induced-Pluripotent-Stem-Cell-Derived Cardiomyocyte Screening Models"
Article Title: Epitranscriptomic Modulation of TET2 Inhibition Suppressed SARS-CoV-2 Infection and Blocked Viral Nucleocapsid Protein in Induced-Pluripotent-Stem-Cell-Derived Cardiomyocyte Screening Models
Journal: Biomaterials Research
doi: 10.34133/bmr.0229
Figure Legend Snippet: Screening potential candidates of TET-family inhibitors in infected hiPSC-CMs via computational molecular docking simulation. (A) The flowchart of the drug screening platform for molecular docking analysis of TET2 in complex with its DNA substrate and representative inhibitors. (B) Schematic representation of the molecular docking of representative TET2 inhibitors—Bobcat339, TFMB-2HG, and TETi76—into the catalytic pocket of TET2. The figure illustrates the catalytic core of TET2 binding to methylated DNA, followed by computational screening and docking of small-molecule inhibitors into the active site. (C) TET2 in complex with DNA substrate (Protein Data Bank [PDB] ID: 7NE3). Left: Overall structure showing TET2 (ribbon representation) bound to DNA (sticks in orange and magenta). Middle: Close-up view of the catalytic pocket highlighting the interaction surface. Right: 2-dimensional (2D) interaction diagram illustrating contacts between TET2 and the DNA substrate. (D) TET2 in complex with TETi76. Left: Chemical structure of TETi76. Middle: Docked pose of TETi76 in the TET2 catalytic site. Right: 2D interaction diagram showing hydrogen bonding and hydrophobic contacts. (E) TET2 in complex with Bobcat339. Left: Chemical structure of Bobcat339. Middle: Docked binding mode of Bobcat339 in the catalytic site. Right: 2D interaction map illustrating hydrogen bonds, hydrophobic interactions, and halogen bonding. (F) TET2 in complex with TFMB-2HG. Left: Chemical structure of TFMB-2HG. Middle: Docked pose within the TET2 active site. Right: 2D interaction map showing hydrogen bonding and minimal hydrophobic interactions.
Techniques Used: Infection, Drug discovery, Binding Assay, Methylation
Figure Legend Snippet: Treatment with Bobcat339 suppressed the viral replication and N-protein expression in infected hiPSC-CMs during SARS-CoV-2 infection. (A) Experimental workflow for assessing virus-mediated regulation of TET2 and its functional role using the selective TET2 inhibitor Bobcat339. (B) qRT-PCR analysis of TET2 mRNA expression in SARS-CoV-2-infected hiPSC-CMs treated with Bobcat339 (80 μM) or dimethyl sulfoxide (DMSO) for 24 h. (C) qRT-PCR analysis of N-protein mRNA expression in SARS-CoV-2-infected hiPSC-CMs treated with Bobcat339 (80 μM) or DMSO for 24 h. (D) Western blot analysis showing the protein expression levels of TET2 and SARS-CoV-2 N protein in hiPSC-CMs treated with Bobcat339 or DMSO for 24 h postinfection. (E) qRT-PCR analysis of TET2 mRNA expression in hiPSC-CMs treated with Bobcat339 or DMSO for 48 h postinfection. (F) qRT-PCR analysis of N-protein mRNA expression in hiPSC-CMs treated with Bobcat339 or DMSO for 48 h postinfection. (G) Western blot analysis showing the protein expression levels of TET2 and SARS-CoV-2 N protein in hiPSC-CMs treated with Bobcat339 or DMSO for 48 h postinfection. (H) Dot blot analysis of total RNA extracted from hiPSC-CMs showing hm5C levels after treatment with different concentrations of Bobcat339 (0 to 80 μM) or DMSO. Methylene blue (MB) was used as a loading control. (I) Dot blot analysis of total RNA extracted from hiPSC-CMs showing hm5C levels after treatment with Bobcat339 (80 μM) or DMSO, with or without SARS-CoV-2 infection. MB was used as a loading control. (J) Schematic diagram illustrating the proposed mechanism: SARS-CoV-2 infects hiPSC-CMs and induces TET2-mediated RNA demethylation (conversion of m5C to hm5C), which is inhibited by Bobcat339. Data in panels (B), (C), (E), and (F) are presented as mean ± SEM from 3 independent experiments. Statistical significance: ** P < 0.01 and **** P < 0.0001.
Techniques Used: Expressing, Infection, Virus, Functional Assay, Quantitative RT-PCR, Western Blot, Dot Blot, Control
Figure Legend Snippet: Computational protein–ligand binding prediction of Bobcat339 with molecular docking modeling of SARS-CoV-2 proteins in N protein, RNA-dependent RNA polymerase (RdRp), and nonstructural protein 16 (nsp16). (A) Illustration of the docking process. The diagram shows the process of target molecule docking by first defining the active center within the protein, then docking the ligand (Bobcat339) into the binding pocket, and finally observing the key interactions formed after docking, such as hydrogen bonds and hydrophobic contacts. (B) The docking of Bobcat339 into the RNA binding site of the SARS-CoV-2 N protein. The left panel depicts Bobcat339 positioned inside the binding pocket, while the middle panel highlights the hydrophobicity and detailed docking interactions. The right panel presents the specific molecular interactions between Bobcat339 and N-protein amino acid residues, including π–π stacking and hydrogen bonds. (C) The docking of Bobcat339 within the RNA binding domain of the SARS-CoV-2 nsp16 protein. The left panel presents the docking site; the middle panel, the binding pocket environment; and the right panel, interactions such as hydrogen bonds and hydrophobic contacts between Bobcat339 and surrounding amino acids. (D) Bobcat339 is docked into the RNA binding site of the SARS-CoV-2 RdRp. The left panel shows the overall docking location, the middle panel zooms into the binding pocket illustrating the hydrophobic interactions, and the right panel details the hydrogen bonding and hydrophobic interactions between Bobcat339 and specific RdRp residues.
Techniques Used: Ligand Binding Assay, Binding Assay, RNA Binding Assay
Figure Legend Snippet: Development of epitranscriptomic-based drug screening and TET2-targeting pathways/TET inhibitors as a novel strategy for anti-SARS-CoV-2 infection via an in vitro model of hiPSC-derived cardiomyocytes. This schematic depicts the development of epigenetic therapies for SARS-CoV-2. hiPSCs are differentiated into cardiomyocytes, infected with SARS-CoV-2, and analyzed using NGS for molecular insights. Drug screening, computational evaluation, and validation with compounds like Bobcat339 aid in the advancement of antiviral therapy. This approach may significantly impact the future of antiviral drug development and personalized medicine, offering a sophisticated tool for understanding and combating systemic SARS-CoV-2 infections.
Techniques Used: Drug discovery, Infection, In Vitro, Derivative Assay, Biomarker Discovery
Related Articles
Binding Assay:Article Title: Epitranscriptomic Modulation of TET2 Inhibition Suppressed SARS-CoV-2 Infection and Blocked Viral Nucleocapsid Protein in Induced-Pluripotent-Stem-Cell-Derived Cardiomyocyte Screening Models Article Snippet: .. Molecular docking analysis revealed that Biomarker Discovery:Article Title: Epitranscriptomic Modulation of TET2 Inhibition Suppressed SARS-CoV-2 Infection and Blocked Viral Nucleocapsid Protein in Induced-Pluripotent-Stem-Cell-Derived Cardiomyocyte Screening Models Article Snippet: .. While computational models offer valuable preliminary insights, it is imperative to conduct experimental validation to confirm these interactions and to clarify the specific mechanisms through which |
