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Nature Reviews. Drug Discovery Sep 2023The development of bioactive small molecules as probes or drug candidates requires discovery platforms that enable access to chemical diversity and can quickly reveal... (Review)
Review
The development of bioactive small molecules as probes or drug candidates requires discovery platforms that enable access to chemical diversity and can quickly reveal new ligands for a target of interest. Within the past 15 years, DNA-encoded library (DEL) technology has matured into a widely used platform for small-molecule discovery, yielding a wide variety of bioactive ligands for many therapeutically relevant targets. DELs offer many advantages compared with traditional screening methods, including efficiency of screening, easily multiplexed targets and library selections, minimized resources needed to evaluate an entire DEL and large library sizes. This Review provides accounts of recently described small molecules discovered from DELs, including their initial identification, optimization and validation of biological properties including suitability for clinical applications.
Topics: Humans; Small Molecule Libraries; Drug Discovery; DNA; Ligands; Gene Library
PubMed: 37328653
DOI: 10.1038/s41573-023-00713-6 -
Clinica Chimica Acta; International... Aug 2023Leukocyte migration from the vascular compartment is critical fornormal lymphocyte recirculation in specific tissues and immune response in inflammatory locations.... (Review)
Review
Leukocyte migration from the vascular compartment is critical fornormal lymphocyte recirculation in specific tissues and immune response in inflammatory locations. Leukocyte recruitment, migration to inflammatory areas, and targeting in the extravascular space are caused by cellular stimulation and local expression of adhesion molecules. Intercellular adhesion molecule 1 (ICAM-1) and Vascular cell adhesion molecule 1 (VCAM-1) belong to the immunoglobulin superfamily of cell adhesion molecules (CAM) with a crucial role in mediating the strong adherence of leukocytes to endothelial cells in numerous acute as well as chronic diseases. ICAM-1 and VCAM-1 mediate inflammation and promote leukocyte migration during inflammation. ICAM-1 and VCAM-1 have a large role in regulating homeostasis and in pathologic states such as cancer, atherosclerosis, atrial fibrillation, myocardial infarction, stroke, asthma, obesity, kidney diseases, and much more. In inflammatory conditions and infectious disorders, leukocytes move and cling to the endothelium via multiple intracellular adhesive interactions. It is suggested that combining membrane-bound and soluble ICAM-1 and VCAM-1 into a single unit functional system will further our understanding of their immunoregulatory role as well as their pathophysiological effects on disease. This review focuses on the pathophysiological roles of ICAM-1 and VCAM-1 in various inflammatory and other diseases as well as their emerging cardiovascular role during the COVID-19 pandemic.
Topics: Humans; Cell Adhesion Molecules; COVID-19; Endothelial Cells; Endothelium, Vascular; Inflammation; Intercellular Adhesion Molecule-1; Pandemics; Vascular Cell Adhesion Molecule-1; Cardiovascular Diseases
PubMed: 37442359
DOI: 10.1016/j.cca.2023.117487 -
Methods in Molecular Biology (Clifton,... 2024Single-molecule fluorescence in situ hybridization (smFISH) is a powerful method for the visualization and quantification of individual RNA molecules within intact...
Single-molecule fluorescence in situ hybridization (smFISH) is a powerful method for the visualization and quantification of individual RNA molecules within intact cells. With its ability to probe gene expression at the single cell and single-molecule level, the technique offers valuable insights into cellular processes and cell-to-cell heterogeneity. Although widely used in the animal field, its use in plants has been limited. Here, we present an experimental smFISH workflow that allows researchers to overcome hybridization and imaging challenges in plants, including sample preparation, probe hybridization, and signal detection. Overall, this protocol holds great promise for unraveling the intricacies of gene expression regulation and RNA dynamics at the single-molecule level in whole plants.
Topics: Animals; In Situ Hybridization, Fluorescence; RNA
PubMed: 38502480
DOI: 10.1007/978-1-0716-3766-1_6 -
IUCrData Oct 2023The racemic mixture of the title compound, CHNOS, crystallizes in space group with two homochiral mol-ecules in each asymmetric unit. The seven-membered ring in both...
The racemic mixture of the title compound, CHNOS, crystallizes in space group with two homochiral mol-ecules in each asymmetric unit. The seven-membered ring in both mol-ecules is in a pucker-chair conformation. The extended structure exhibits C-H⋯O hydrogen bonds, of which two connect crystallographically independent mol-ecules to generate a chain propagating along the axis direction. One C-H grouping of the cyclo-propyl ring is in close contact with the phenyl ring of the neighboring independent mol-ecule in C-H⋯π type inter-actions with carbon atom-ring-centroid distances of 3.544 (5) and 3.596 (4) Å. Other inter-actions are of the parallel-reciprocal type, with the chiral carbon atom of one mol-ecule donating a proton to an oxygen atom of the sulfone group of a symmetry-related mol-ecule and . Symmetry-related mol-ecular pairs also exhibit T-type inter-actions between aromatic rings with inter-planar angles of 74.2 (2) and 69.2 (2)° and inter-centroid distances of 4.965 (4) and 5.114 (4) Å.
PubMed: 37936592
DOI: 10.1107/S2414314623009379 -
Biochimica Et Biophysica Acta. Reviews... Nov 2023Caveolin-1 (Cav-1) is a structural protein of caveolae that functions as a molecular organizer for different cellular functions including endocytosis and cellular... (Review)
Review
Caveolin-1 (Cav-1) is a structural protein of caveolae that functions as a molecular organizer for different cellular functions including endocytosis and cellular signaling. Cancer cells take advantage of the physical position of Cav-1, as it can communicate with extracellular matrix, help to organize growth factor receptors, redistribute cholesterol and glycosphingolipids, and finally transduce signals within the cells for oncogenesis. Recent studies emphasize the exceeding involvement of Cav-1 with different lipid bodies and in altering the metabolism, especially lipid metabolism. However, the association of Cav-1 with different lipid bodies like lipid rafts, lipid droplets, cholesterols, sphingolipids, and fatty acids is remarkably dynamic. The lipid-Cav-1 alliance plays a dual role in carcinogenesis. Both cancer progression and regression are modified and affected by the type of lipid molecule's association with Cav-1. Accordingly, this Cav-1-lipid cooperation exemplifies a cancer-type-specific treatment strategy for a better prognosis of the disease. In this review, we first present Cav-1 as an oncogenic molecule and its communication via lipid raft. We discussed the involvement of Cav-1 with lipid droplets, Cholesterol, sphingolipids, gangliosides, and ceramides. Further, we describe the Cav-1-mediated altered Fatty acid metabolism in cancer and the strategic therapeutic approaches toward Cav-1 targeting.
Topics: Humans; Caveolin 1; Caveolae; Membrane Microdomains; Cholesterol; Sphingolipids
PubMed: 37848094
DOI: 10.1016/j.bbcan.2023.189002 -
IUCrData Sep 2023The title compound, CHNO·2CHO, representing a bis-urea with terminal phenyl-alanine units, crystallized with two tetra-hydro-furan (THF) mol-ecules. The main mol-ecule...
The title compound, CHNO·2CHO, representing a bis-urea with terminal phenyl-alanine units, crystallized with two tetra-hydro-furan (THF) mol-ecules. The main mol-ecule is located on a crystallographic twofold axis, while the solvent mol-ecule is disordered over two positions, with occupancies of 0.571 (15) and 0.429 (15). The host mol-ecules are linked by N-H⋯O=C hydrogen bonds and C-H⋯O contacts with (6) and (7) ring motifs. The THF mol-ecules enclosed in the crystal are connected to the bis-urea compound O-H⋯O and C-H⋯O inter-actions.
PubMed: 37818468
DOI: 10.1107/S2414314623007435 -
Journal of Cheminformatics Oct 2023Ultra-large chemical libraries are reaching 10s to 100s of billions of molecules. A challenge for these libraries is to efficiently check if a proposed molecule is...
Ultra-large chemical libraries are reaching 10s to 100s of billions of molecules. A challenge for these libraries is to efficiently check if a proposed molecule is present. Here we propose and study Bloom filters for testing if a molecule is present in a set using either string or fingerprint representations. Bloom filters are small enough to hold billions of molecules in just a few GB of memory and check membership in sub milliseconds. We found string representations can have a false positive rate below 1% and require significantly less storage than using fingerprints. Canonical SMILES with Bloom filters with the simple FNV (Fowler-Noll-Voll) hashing function provide fast and accurate membership tests with small memory requirements. We provide a general implementation and specific filters for detecting if a molecule is purchasable, patented, or a natural product according to existing databases at https://github.com/whitead/molbloom .
PubMed: 37828615
DOI: 10.1186/s13321-023-00765-1 -
Journal of Hematology & Oncology May 2024As the most common form of epigenetic regulation by RNA, N methyladenosine (mA) modification is closely involved in physiological processes, such as growth and... (Review)
Review
As the most common form of epigenetic regulation by RNA, N methyladenosine (mA) modification is closely involved in physiological processes, such as growth and development, stem cell renewal and differentiation, and DNA damage response. Meanwhile, its aberrant expression in cancer tissues promotes the development of malignant tumors, as well as plays important roles in proliferation, metastasis, drug resistance, immunity and prognosis. This close association between mA and cancers has garnered substantial attention in recent years. An increasing number of small molecules have emerged as potential agents to target mA regulators for cancer treatment. These molecules target the epigenetic level, enabling precise intervention in RNA modifications and efficiently disrupting the survival mechanisms of tumor cells, thus paving the way for novel approaches in cancer treatment. However, there is currently a lack of a comprehensive review on small molecules targeting mA regulators for anti-tumor. Here, we have comprehensively summarized the classification and functions of mA regulators, elucidating their interactions with the proliferation, metastasis, drug resistance, and immune responses in common cancers. Furthermore, we have provided a comprehensive overview on the development, mode of action, pharmacology and structure-activity relationships of small molecules targeting mA regulators. Our aim is to offer insights for subsequent drug design and optimization, while also providing an outlook on future prospects for small molecule development targeting mA.
Topics: Animals; Humans; Adenosine; Antineoplastic Agents; Epigenesis, Genetic; Neoplasms; Small Molecule Libraries
PubMed: 38711100
DOI: 10.1186/s13045-024-01546-5