BOPC1 Enantiomers Preparation and HuR Interaction Study. From Molecular Modeling to a Curious DEEP-STD NMR Application

Abstract

The Hu family of RNA-binding proteins plays a crucial role in post-transcriptional processes; indeed, Hu–RNA complexes are involved in various dysfunctions (i.e., inflammation, neurodegeneration, and cancer) and have been recently proposed as promising therapeutic targets. Intrigued by this concept, our research efforts aim at identifying small molecules able to modulate HuR–RNA interactions, with a focus on subtype HuR, upregulated and dysregulated in several cancers. By applying structure-based design, we had already identified racemic trans-BOPC1 as promising HuR binder. In this Letter, we accomplished the enantio-resolution, the assignment of the absolute configuration, and the recognition study with HuR of enantiomerically pure trans-BOPC1. For the first time, we apply DEEP (differential epitope mapping)-STD NMR to study the interaction of BOPC1 with HuR and compare its enantiomers, gaining information on ligand orientation and amino acids involved in the interaction, and thus increasing focus on the in silico binding site model.

Structural Insights into the Ligand–LsrK Kinase Binding Mode: A Step Forward in the Discovery of Novel Antimicrobial Agents

“…The test’s small molecules were primarily obtained from an in-house collection of compounds (MedChemLab, MCL, Department of Drug Sciences, University of Pavia, Pavia, Italy). The MCL compound library consists of non-commercial small molecules synthesized and assessed during several drug discovery projects performed in the past years by our research group, including several secondary metabolites extracted from the proper plant drugs during nature-aided drug discovery programs [ 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 ]. Representative compounds of the MCL library were initially assessed in a low-throughput primary screening against recombinant LsrK via TFS.…”

Identification of Compounds Targeting HuD. Another Brick in the Wall of Neurodegenerative Disease Treatment

“…Due to the similarity between the 3D structures of HuD and HuR, in agreement with our previous works, we used the HuD “ closed” conformation structure for the molecular recognition studies (Figure ). − …”

“…The two conformations with the highest and the lowest potential energy values, corresponding to an “ open” HuD conformation and a closed HuD conformation, were selected. According to our previous works, − we noticed that more interactions were established between the ligands and the receptor in the presence of the closed conformation, thus, for further docking studies, we chose the HuD closed conformation. Molecular docking recognition studies were carried out using Glide v. 6.7 software, using the standard precision (SP) algorithm and the binding pocket was identified by placing a cube centered on the c-fos mRNA.…”

Enantiomeric Resolution and Absolute Configuration of a Chiral δ-Lactam, Useful Intermediate for the Synthesis of Bioactive Compounds

“…The mobile phases were added with trifluoroacetic acid (TFA, 0.3%) for both the coated CSPs and Chiralpak IC, or with a mixture of diethylamine (DEA, 0.1%) and TFA (0.3%) for Chiralpak IA. A standard screening protocol (see Supplementary Material, Table S2 ) was applied first, and then the elution conditions were properly modified to achieve a baseline separation of the analytes [ 44 , 45 , 46 ].…”