N-Biphenyl Pyrrolinones and Dibenzofurans as RNA-Binding Protein LIN28 Inhibitors Disrupting the LIN28-Let-7 Interaction

The role of RNA binding proteins in cancer biology: A focus on FMRP

RNA-binding proteins (RBPs) act as crucial regulators of gene expression within cells, exerting precise control over processes such as RNA splicing, transport, localization, stability, and translation through their specific binding to RNA molecules. The diversity and complexity of RBPs are particularly significant in cancer biology, as they directly impact a multitude of RNA metabolic events closely associated with tumor initiation and progression. The fragile X mental retardation protein (FMRP), as a member of the RBP family, is central to the neurodevelopmental disorder fragile X syndrome and increasingly recognized in the modulation of cancer biology through its influence on RNA metabolism. The protein's versatility, stemming from its diverse RNA-binding domains, enables it to govern a wide array of transcript processing events. Modifications in FMRP's expression or localization have been associated with the regulation of mRNAs linked to various processes pertinent to cancer, including tumor proliferation, metastasis, epithelial-mesenchymal transition, cellular senescence, chemotherapy/radiotherapy resistance, and immunotherapy evasion. In this review, we emphasize recent findings and analyses that suggest contrasting functions of this protein family in tumorigenesis. Our knowledge of the proteins that are regulated by FMRP is rapidly growing, and this has led to the identification of multiple targets for therapeutic intervention of cancer, some of which have already moved into clinical trials or clinical practice.

Decoding Hairpin Structure Stability in Lin28-Mediated Repression

The Lin28 protein is well known for its role in inhibiting the biogenesis of microRNAs (miRNAs) that belong to the let-7 family. The Lin28 and let-7 axes are associated with several types of cancers. It is imperative to understand the underlying mechanism to treat these cancers in a more efficient way. In this study, we employed all-atom molecular dynamics simulation as a research tool to investigate the interaction formed between Lin28 and the precursor element of let-7d, one of the 12 members of the let-7 family. By constructing systems of an intact sequence length of preE-let-7d, our simulations suggest that both the loop region of the hairpin structure and the GGAG sequence can form stable interactions with the cold shock domain (CSD) and zinc knuckle domain (ZKD) regions of the protein, respectively. The system, by deleting the nucleotides GGAG at the 3' terminal, indicates that the loop region is more responsible for its ability in bypassing the binding and repression of Lin28. Additionally, using let-7c-2, which can bypass Lin28 regulation, as a template, we constructed systems with mutated loop region sequences in miRNAs and tested their stabilities. Our simulation results coincide well with experimental observations. Based on both simulation results and statistical analysis from two databases, we hypothesized that two factors, namely, the interaction between terminal nucleotides and the ring tension originating from the middle nucleotides, can significantly influence their stabilities. Systems combining strong and weak terminal interactions with large and small ring tensions were recruited to validate our hypothesis. Our findings offer a new perspective and shed light on strategies for designing sequences to regulate the interactions formed between proteins and hairpin structures.

Lin28/let-7 axis in breast cancer

Let-7 microRNAs are tumor suppressor microRNAs, and their reduced expression frequently occurs in various types of cancers, including breast cancer. A notable correlation exists between decreased let-7 microRNA levels and the overexpression of Lin28A and Lin28B, particularly in breast cancer cases with poor prognoses. Dysregulation of Wnt signaling significantly contributes to the upregulation of Lin28A and Lin28B in breast cancer. Both Lin28A and Lin28B operate from different cellular compartments to inhibit the biogenesis of let-7 microRNAs, which are essential for the post-transcriptional regulation of genes involved in key cellular functions such as proliferation, differentiation, and apoptosis. Decreased expression of let-7 microRNAs leads to the overexpression of oncogenes such as K-ras, C-myc, and SOX-2 in breast cancer. Overexpression of Lin28A associated with reduced let-7 microRNA levels is observed in estrogen receptor positive, estrogen receptor negative, and human epidermal growth factor receptor 2 positive breast cancers, whereas Lin28B overexpression with reduced let-7 microRNA levels occurs specifically in triple negative breast cancer. This review aims to dissect the molecular interplay between Lin28A, Lin28B, and let-7 microRNAs, elucidating their roles in breast carcinogenesis, metastasis, and the development of resistance to conventional treatments like radiation and chemotherapy. Additionally, the review addresses potential therapeutic avenues offered by let-7 microRNAs or their mimics, as well as Lin28A and Lin28B inhibitors, in the treatment of breast cancer.

Profiling Cellular Morphological Changes Induced by Dual-Targeting PROTACs of Aurora Kinase and RNA-Binding Protein YTHDF2

Proteolysis targeting chimeras (PROTACs) are new chemical modalities that degrade proteins of interest, including established kinase targets and emerging RNA-binding proteins (RBPs). Whereas diverse sets of biochemical, biophysical and cellular assays are available for the evaluation and optimizations of PROTACs in understanding the involved ubiquitin-proteasome-mediated degradation mechanism and the structure-degradation relationship, a phenotypic method profiling the cellular morphological changes is rarely used. In this study, first, we reported the only examples of PROTACs degrading the mRNA-binding protein YTHDF2 via screening of multikinase PROTACs. Second, we reported the profiling of cellular morphological changes of the dual kinase- and RBP-targeting PROTACs using the unbiased cell painting assay (CPA). The CPA analysis revealed the high biosimilarity with the established aurora kinase cluster and annotated aurora kinase inhibitors, which reflected the association between YTHDF2 and the aurora kinase signaling network. Broadly, the results demonstrated that the cell painting assay can be a straightforward and powerful approach to evaluate PROTACs. Complementary to the existing biochemical, biophysical and cellular assays, CPA provided a new perspective in characterizing PROTACs at the cellular morphology.

Characterization of structure of peptidyl-tRNA hydrolase from Enterococcus faecium and its inhibition by a pyrrolinone compound

In bacteria, peptidyl-tRNA hydrolase (Pth, E.C. 3.1.1.29) is a ubiquitous and essential enzyme for preventing the accumulation of peptidyl-tRNA and sequestration of tRNA. Pth is an esterase that cleaves the ester bond between peptide and tRNA. Here, we present the crystal structure of Pth from Enterococcus faecium (EfPth) at a resolution of 1.92 Å. The two molecules in the asymmetric unit differ in the orientation of sidechain of N66, a conserved residue of the catalytic site. Enzymatic hydrolysis of substrate α-N-BODIPY-lysyl-tRNALys (BLT) by EfPth was characterized by Michaelis-Menten parameters KM 163.5 nM and Vmax 1.9 nM/s. Compounds having pyrrolinone scaffold were tested for inhibition of Pth and one compound, 1040-C, was found to have IC50 of 180 nM. Antimicrobial activity profiling was done for 1040-C. It exhibited equipotent activity against drug-susceptible and resistant S. aureus (MRSA and VRSA) and Enterococcus (VSE and VRE) with MICs 2-8 μg/mL. 1040-C synergized with gentamicin and the combination was effective against the gentamicin resistant S. aureus strain NRS-119. 1040-C was found to reduce biofilm mass of S. aureus to an extent similar to Vancomycin. In a murine model of infection, 1040-C was able to reduce bacterial load to an extent comparable to Vancomycin.

Targeting MicroRNAs with Small Molecules

MicroRNAs (miRs) have been implicated in numerous diseases, presenting an attractive target for the development of novel therapeutics. The various regulatory roles of miRs in cellular processes underscore the need for precise strategies. Recent advances in RNA research offer hope by enabling the identification of small molecules capable of selectively targeting specific disease-associated miRs. This understanding paves the way for developing small molecules that can modulate the activity of disease-associated miRs. Herein, we discuss the progress made in the field of drug discovery processes, transforming the landscape of miR-targeted therapeutics by small molecules. By leveraging various approaches, researchers can systematically identify compounds to modulate miR function, providing a more potent intervention either by inhibiting or degrading miRs. The implementation of these multidisciplinary approaches bears the potential to revolutionize treatments for diverse diseases, signifying a significant stride towards the targeting of miRs by precision medicine.