Tubulin plays essential roles in vital cellular activities and is the target of a wide range of proteins and ligands. Here, using a combined computational and crystallographic fragment screening approach, we addressed the question of how many binding sites exist in tubulin. We identified 27 distinct sites, of which 11 have not been described previously, and analyzed their relationship to known tubulin-protein and tubulin-ligand interactions. We further observed an intricate pocket communication network and identified 56 chemically diverse fragments that bound to 10 distinct tubulin sites. Our results offer a unique structural basis for the development of novel small molecules for use as tubulin modulators in basic research applications or as drugs. Furthermore, our method lays down a framework that may help to discover new pockets in other pharmaceutically important targets and characterize them in terms of chemical tractability and allosteric modulation.
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http://dx.doi.org/10.1002/anie.202100273 | DOI Listing |
Angew Chem Int Ed Engl
January 2025
Georgia State University, Chemistry, 50 Decatur ST SE, 30303, Atlanta, UNITED STATES OF AMERICA.
Poly-N-acetyllactosamine (poly-LacNAc) is ubiquitously expressed on cell surface glycoconjugates, serving as the backbone of complex glycans and an extended scaffold that presents diverse glycan epitopes. The branching of poly-LacNAc, where internal galactose (Gal) residues have β1-6 linked N-acetylglucosamine (GlcNAc) attached, forms the blood group I-antigen, which is closely associated with various physiological and pathological processes including cancer progression. However, the underlying mechanisms remain unclear as many of the I-antigen sequences are undefined and inaccessible.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138.
Despite the broad catalytic relevance of metal-support interfaces, controlling their chemical nature, the interfacial contact perimeter (exposed to reactants), and consequently, their contributions to overall catalytic reactivity, remains challenging, as the nanoparticle and support characteristics are interdependent when catalysts are prepared by impregnation. Here, we decoupled both characteristics by using a raspberry-colloid-templating strategy that yields partially embedded PdAu nanoparticles within well-defined SiO or TiO supports, thereby increasing the metal-support interfacial contact compared to nonembedded catalysts that we prepared by attaching the same nanoparticles onto support surfaces. Between nonembedded PdAu/SiO and PdAu/TiO, we identified a support effect resulting in a 1.
View Article and Find Full Text PDFElife
January 2025
Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, United States.
Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. Using SPICE, we successfully identified known composite elements, such as AP1-IRF composite elements (AICEs) and STAT5 tetramers, and also uncovered several novel binding partners, including JUN-IKZF1 composite elements.
View Article and Find Full Text PDFNaunyn Schmiedebergs Arch Pharmacol
January 2025
Hormones Department, Medical Research and Clinical Studies Institute, National Research Centre, Giza, 12622, Egypt.
The main goal of the current study is to estimate the in vivo anti-inflammatory/antioxidant ability of four selected pharmaceutical compounds: bisoprolol (Biso), piracetam (Pirc), clopidogrel (Clop), and cinnarizine (Cinna). Indomethacin (Indo) was used as a reference drug to perform a realistic comparison between the four compounds and the Indo in vivo through tracking PI3K/AKT signaling and computational chemistry via density functional theory (DFT) modeling to analyze the electrostatic potential across the molecule and provide insight into the regions for receptor binding of the studied compounds. To achieve the safe dose of these compounds, cytotoxicity was performed against isolated adipose tissue-derived mesenchymal stem cells (ADMSCs) using MTT assay.
View Article and Find Full Text PDFMol Divers
January 2025
Data Science, Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurugram, India.
The ATP-binding cassette transporter superfamily plays a pivotal role in cellular detoxification and drug efflux. ATP-binding cassette subfamily G member 2 (ABCG2) referred to as the Breast cancer resistance protein has emerged as a key member involved in multidrug resistance displayed by cancer cells. Understanding the molecular basis of substrate and inhibitor recognition, and binding within the transmembrane domain of ABCG2 is crucial for the development of effective therapeutic strategies.
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