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View article: Trastuzumab Decreases the Expression of G1/S Regulators and Syndecan-4 Proteoglycan in Human Rhabdomyosarcoma
Trastuzumab Decreases the Expression of G1/S Regulators and Syndecan-4 Proteoglycan in Human Rhabdomyosarcoma Open
Rhabdomyosarcoma (RMS), the most common soft tissue sarcoma in children, arises from skeletal muscle cells that fail to differentiate terminally. Two subgroups of RMS, fusion-positive and fusion-negative RMS (FPRMS and FNRMS, respectively)…
View article: Site-directed allostery perturbation to probe the negative regulation of hypoxia inducible factor-1α
Site-directed allostery perturbation to probe the negative regulation of hypoxia inducible factor-1α Open
The structural adaptation of p300 to the backbone-modified CITED2 sequences provides insight into the molecular mechanism that governs the allosteric regulation of HIF-1α.
View article: Structural Adaptation of the Single-Stranded DNA-Binding Protein C-Terminal to DNA Metabolizing Partners Guides Inhibitor Design
Structural Adaptation of the Single-Stranded DNA-Binding Protein C-Terminal to DNA Metabolizing Partners Guides Inhibitor Design Open
Single-stranded DNA-binding protein (SSB) is a bacterial interaction hub and an appealing target for antimicrobial therapy. Understanding the structural adaptation of the disordered SSB C-terminus (SSB-Ct) to DNA metabolizing enzymes (e.g.…
View article: Structural adaptation of the single-stranded DNA-binding protein C-terminal to DNA metabolizing partners guides in-hibitor design
Structural adaptation of the single-stranded DNA-binding protein C-terminal to DNA metabolizing partners guides in-hibitor design Open
Fluorescence anisotropy metadata and polarization values Isotermal titration calorimetry raw files (protein-ligand and background titrations) Input files for PRALINE calculation in FASTA format CSV file containing the SSB sequences in SMIL…
View article: Structural adaptation of the single-stranded DNA-binding protein C-terminal to DNA metabolizing partners guides in-hibitor design
Structural adaptation of the single-stranded DNA-binding protein C-terminal to DNA metabolizing partners guides in-hibitor design Open
Fluorescence anisotropy metadata and polarization values Isotermal titration calorimetry raw files (protein-ligand and background titrations) Input files for PRALINE calculation in FASTA format CSV file containing the SSB sequences in SMIL…
View article: Improved Metal-Free Approach for the Synthesis of Protected Thiol Containing Thymidine Nucleoside Phosphoramidite and Its Application for the Synthesis of Ligatable Oligonucleotide Conjugates
Improved Metal-Free Approach for the Synthesis of Protected Thiol Containing Thymidine Nucleoside Phosphoramidite and Its Application for the Synthesis of Ligatable Oligonucleotide Conjugates Open
Oligonucleotide conjugates are versatile scaffolds that can be applied in DNA-based screening platforms and ligand display or as therapeutics. Several different chemical approaches are available for functionalizing oligonucleotides, which …
View article: Towards Identification of Protein-Protein Interaction Stabilizers via Inhibitory Peptide-Fragment Hybrids Using Templated Fragment Ligation
Towards Identification of Protein-Protein Interaction Stabilizers via Inhibitory Peptide-Fragment Hybrids Using Templated Fragment Ligation Open
Using the hDMX/14-3-3 interaction, acylhydrazone-based ligand-directed fragment ligation was used to identify protein-protein interaction (PPI) inhibitory peptide-fragment hybrids. Separation of the peptide-fragment hybrids into the compon…
View article: Understanding p300-transcription factor interactions using sequence variation and hybridization
Understanding p300-transcription factor interactions using sequence variation and hybridization Open
The interaction of p300 with HIF-1α is highly tolerant to sequence variations accompanied by enthalpy–entropy compensation and can be effectively inhibited by its negative regulator CITED2 with a sequence dependent competition mechanism.
View article: Towards identification of protein–protein interaction stabilizers <i>via</i> inhibitory peptide-fragment hybrids using templated fragment ligation
Towards identification of protein–protein interaction stabilizers <i>via</i> inhibitory peptide-fragment hybrids using templated fragment ligation Open
Ligand-directed dynamic-ligation is used to identify fragments that can augment the inhibitory potency of a peptide ligand and simultaneously serve as starting points for future development of PPI stabilizers.
View article: Understanding p300-transcription factor interactions using sequence variation and hybridization
Understanding p300-transcription factor interactions using sequence variation and hybridization Open
The hypoxic response is central to cell function and plays a significant role in the growth and survival of solid tumours. HIF-1 regulates the hypoxic response by activating over 100 genes responsible for adaptation to hypoxia, making it a…
View article: Identification of β-strand mediated protein–protein interaction inhibitors using ligand-directed fragment ligation
Identification of β-strand mediated protein–protein interaction inhibitors using ligand-directed fragment ligation Open
Dynamic ligation screening is used to identify acylhydrazone-linked peptide-fragment hybrids which bind to the SHANK1 PDZ domain with comparable affinity to the native GKAP peptide as shown by biophysical and structural analyses.
View article: Query-guided protein–protein interaction inhibitor discovery
Query-guided protein–protein interaction inhibitor discovery Open
Small-molecule protein–protein interaction inhibitors were prioritised on the basis of shape similarity to secondary structure-based queries incorporating hot-spot residues.
View article: Tunable Magnetic Hyperthermia Properties of Pristine and Mildly Reduced Graphene Oxide/Magnetite Nanocomposite Dispersions
Tunable Magnetic Hyperthermia Properties of Pristine and Mildly Reduced Graphene Oxide/Magnetite Nanocomposite Dispersions Open
We present a study on the magnetic hyperthermia properties of graphene oxide/magnetite (GO/MNP) nanocomposites to investigate their heat production behavior upon the modification of the oxidation degree of the carbonaceous host. Avoiding t…
View article: Stapled Peptides as HIF‐1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency
Stapled Peptides as HIF‐1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency Open
Protein–protein interactions (PPIs) control virtually all cellular processes and have thus emerged as potential targets for development of molecular therapeutics. Peptide‐based inhibitors of PPIs are attractive given that they offer recogn…
View article: DPP‐4 Cleaves α/β‐Peptide Bonds: Substrate Specificity and Half‐Lives
DPP‐4 Cleaves α/β‐Peptide Bonds: Substrate Specificity and Half‐Lives Open
The incorporation of β‐amino acids into a peptide sequence has gained particular attention as β‐ and α/β‐peptides have shown remarkable proteolytic stability, even after a single homologation at the scissile bond. Several peptidases have b…
View article: Predicting and Experimentally Validating Hot-Spot Residues at Protein–Protein Interfaces
Predicting and Experimentally Validating Hot-Spot Residues at Protein–Protein Interfaces Open
Protein-protein interactions (PPIs) are vital to all biological processes. These interactions are often dynamic, sometimes transient, typically occur over large topographically shallow protein surfaces, and can exhibit a broad range of aff…
View article: Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces
Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces Open
Here we describe a comparative analysis of multiple CAS methods, which highlights effective approaches to improve the accuracy of predicting hot-spot residues. Alongside this, we introduce a new method, BUDE Alanine Scanning, which can be …
View article: Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces
Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces Open
Here we describe a comparative analysis of multiple CAS methods, which highlights effective approaches to improve the accuracy of predicting hot-spot residues. Alongside this, we introduce a new method, BUDE Alanine Scanning, which can be …
View article: Cover Feature: Recognition of ASF1 by Using Hydrocarbon‐Constrained Peptides (ChemBioChem 7/2019)
Cover Feature: Recognition of ASF1 by Using Hydrocarbon‐Constrained Peptides (ChemBioChem 7/2019) Open
The cover feature picture shows how inhibition of the histone H3-ASF1 (anti-silencing function 1) protein–protein interaction (PPI) represents a potential approach for the treatment of numerous cancers. To pursue this goal, a hydrocarbon c…
View article: A catalytic protein–proteomimetic complex: using aromatic oligoamide foldamers as activators of RNase S
A catalytic protein–proteomimetic complex: using aromatic oligoamide foldamers as activators of RNase S Open
An aromatic oligoamide foldamer acts as an α-helix mimetic and binds to the RNase S-protein resulting in restoration of its catalytic function.
View article: Recognition of ASF1 by Using Hydrocarbon‐Constrained Peptides
Recognition of ASF1 by Using Hydrocarbon‐Constrained Peptides Open
Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135…
View article: De Novo Modular Development of a Foldameric Protein–Protein Interaction Inhibitor for Separate Hot Spots: A Dynamic Covalent Assembly Approach
De Novo Modular Development of a Foldameric Protein–Protein Interaction Inhibitor for Separate Hot Spots: A Dynamic Covalent Assembly Approach Open
Protein–protein interactions stabilized by multiple separate hot spots are highly challenging targets for synthetic scaffolds. Surface‐mimetic foldamers bearing multiple recognition segments are promising candidate inhibitors. In this work…
View article: Target-specific NMR detection of protein–ligand interactions with antibody-relayed 15N-group selective STD
Target-specific NMR detection of protein–ligand interactions with antibody-relayed 15N-group selective STD Open
Fragment-based drug design has been successfully applied to challenging targets where the detection of the weak protein-ligand interactions is a key element. 1H saturation transfer difference (STD) NMR spectroscopy is a powerful technique …