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Deoxyribonucleic acid (DNA) acts as the most important intracellular target for various drugs. Exploring the DNA binding interactions of small bioactive molecules offers a structural guideline for designing new drugs with higher clinical efficacy and enhanced selectivity. This study presents the facile synthesis of pyrazoline-derived compounds by reacting substituted chalcones with hydrazine hydrate using formic acid. The structure elucidation of substituted pyrazoline compounds was carried out using H-NMR, FT-IR and elemental analyses. While the crystal structures of two compounds and have been resolved by single-crystal X-ray diffraction (SC-XRD) analysis. Hirshfeld surface analysis also endorsed their greater molecular stability. Computational calculations at DFT/B3LYP/6-311++G(d,p) were executed to compare the structural properties (bond angle and bond length) and explore reactivity descriptors, frontier molecular orbitals (FMO), Mulliken atomic charges (MAC), molecular electrostatic potential (MEP) and electronic properties. All the compounds were evaluated for DNA binding interactions by UV-Vis spectrophotometric analysis. The results revealed that compounds bind to DNA non-covalent binding mode having binding constant values ranging from 1.22 × 10 to 6.81 × 10 M. The negative values of Gibbs free energy also proved the interaction of studied compounds with DNA as a spontaneous process. The findings of molecular docking simulations depicted that these studied compounds showed significant binding interactions with DNA and these results were consistent with experimental findings. Compound was concluded as the most potent compound of the series with the highest binding constant (4.95 × 10) and strongest binding affinity (-8.48 kcal/mol).Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2023.2293260 | DOI Listing |
Nat Biotechnol
September 2025
Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA.
RNA-protein interactions critically regulate gene expression and cellular processes, yet their comprehensive mapping remains challenging due to their structural diversity. We introduce PRIM-seq (protein-RNA interaction mapping by sequencing), a method for concurrent de novo identification of RNA-binding proteins and their associated RNAs. PRIM-seq generates unique chimeric DNA sequences by proximity ligation of RNAs with protein-linked DNA barcodes, which are subsequently decoded through sequencing.
View Article and Find Full Text PDFExp Neurobiol
August 2025
Institute of Medical Science, Ajou University School of Medicine, Suwon 16499, Korea.
Neural tumors represent diverse malignancies with distinct molecular profiles and present particular challenges due to the blood-brain barrier, heterogeneous molecular etiology including epigenetic dysregulation, and the affected organ's critical nature. KCC-07, a selective and blood-brain barrier penetrable MBD2 (methyl CpG binding domain protein 2) inhibitor, can suppress tumor development by inducing p53 signaling, proven only in medulloblastoma. Here we demonstrate KCC-07 treatment's application to other neural tumors.
View Article and Find Full Text PDFAdv Drug Deliv Rev
September 2025
Biochemistry, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, United States; Molecular, Cellular, and Developmental Biology, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, United States; Chemistry, CUNY Gradua
Targeted drug delivery significantly enhances therapeutic efficacy across various diseases, particularly in cancer treatments, where conventional approaches such as chemotherapy and radiotherapy often cause severe side effects. In this context, nucleic acid aptamers-short, single-stranded DNA or RNA oligonucleotides capable of binding specific targets with high affinity-have emerged as promising tools for precision drug delivery and therapy. Aptamers can be selected against whole, living cells using SELEX and chemically modified for diverse applications.
View Article and Find Full Text PDFBiochem Pharmacol
September 2025
Department of Biosciences, JIS University, 81, Nilgunj Road, Agarpara, Kolkata, West Bengal 700109, India. Electronic address:
The malignant manifestation of breast cancer is driven by complex molecular alterations that extend beyond genetic mutations to include epigenetic dysregulation. Among these, DNA methylation is a critical and reversible epigenetic modification that significantly influences breast cancer initiation, progression, and therapeutic resistance. This process, mediated by DNA methyltransferases (DNMTs), involves the addition of methyl groups to cytosine residues within CpG dinucleotides, resulting in transcriptional repression of genes.
View Article and Find Full Text PDFDev Cell
September 2025
Division of Surgical Sciences, Department of Surgery, UC San Diego Health, 3855 Health Sciences Drive, La Jolla, CA 92037, USA. Electronic address:
In this issue of Developmental Cell, Li et al. show that ETS variant transcription factor 1 (Etv1) SUMOylation not only maintains cancer stem cells (CSCs) but also enables their communications with non-CSC cancer cells to induce tumorigenesis of non-CSCs. The finding reveals a new function of CSCs in driving aggressive tumorigenesis that is SUMOylation dependent.
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