NMR quantification of H-bond donating ability for bioactive functional groups and isosteres

Twin hydrogen bonds with phosphine oxide: anticooperativity effects caused by competing proton donors

In this computational work we study complexes with two equivalent intermolecular hydrogen bonds formed between trimethyl phosphine oxide and two identical proton donors ("twin" hydrogen bonds) for a set of 70 proton donor molecules. The changes in the phosphorus chemical shift and stretching frequency of the PO group upon complexation correlate quite well with the total strength of two hydrogen bonds. A set of explicit numerical dependences is proposed for assessing interatomic distances and hydrogen bond strengths from spectral data. Comparison with the results obtained for analogous previously studied 1 : 1 complexes allowed us to analyze in detail anticooperativity effects on the geometry, energy and spectral parameters. Two hydrogen bonds compete for the PO acceptor group and their mutual weakening increases nonlinearly with the strengthening of the complex, reaching approximately 25% in energy (which corresponds to 0.1 Å lengthening for short strong H-bonds), which is clearly seen in NMR and IR spectra and correlates well with the changes in the spectral parameters.

31P Nuclear Magnetic Resonance Spectroscopy for Monitoring Organic Reactions and Organic Compounds

31P NMR spectroscopy is a consolidated tool for the characterization of organophosphorus compounds and, more recently, for reaction monitoring. The evolution of organic synthesis, mainly due to the combination of elaborated building blocks with enabling technologies, generated great challenges to understand and to optimize the synthetic methodologies. In this sense, 31P NMR experiments also became a routine technique for reaction monitoring, accessing products and side products yields, chiral recognition, kinetic data, intermediates, as well as basic organic parameters, such as acid-base and hydrogen-bonding. This review deals with these aspects demonstrating the essential role of the 31P NMR spectroscopy. The recent publications (the last ten years) will be explored, discussing the experiments of 31P NMR and the strategies accomplished to detect and/or quantify distinct organophosphorus molecules, approaching reaction mechanism, stability, stereochemistry, and the utility as a probe.

Triple-Action Therapy: Combining Machine Learning, Docking, and Dynamics to Combat BRCA1-Mutated Breast Cancer

Breast cancer dominates women's mortality, and among other factors, mutations in the BRCA1 gene are significant risk factors. Several approaches are followed to treat the BRCA1 affected cancer patients. However, specific BRCA1 inhibitors are not available till date due to its structural complexity. In addition, there are several limitations associated with the existing drugs used to treat BRCA1-related breast cancer and some side effects. The side effects include symptoms such as hot flashes, joint pain, nausea, fatigue, hair loss, diarrhea, chills, fever, and others. Therefore, advanced approaches needed that can overcome all the limitations and side effects of the current inhibitors. In this study, we adopted a multistep approach to identify potential inhibitors for BRCA1-mutated breast cancer. We used our developed machine learning models to screen potential inhibitors. Molecular docking approach was carried out for the screened hit compounds with BRCA1 and its mutated forms. Two ligands, β-amyrin and Narirutin, has shown significant performance in multiple scoring schemes such as molecular docking and RF score calculations. Molecular dynamics simulations demonstrated the stability of the complexes formed by β-amyrin and Narirutin with BRCA1, with lower RMSD values and less RMSF fluctuations at the binding site locations. Principal component analysis (PCA) and free energy landscape (FEL) further confirmed the compactness and favorable binding of β-Amyrin and Narirutin to BRCA1. These findings suggest that β-amyrin and Narirutin have potential as therapeutic agents against BRCA1-mutated breast cancer.

Molecular Interactions Between Egg White Peptides and Giant Unilamellar Vesicle Membranes: Effect of Peptide Localization on Membrane Fluidity

Bioactive peptides have been shown to affect cell membrane fluidity, which is an important indicator of the cell membrane structure and function. However, the underlying mechanism of egg white-derived bioactive peptide regulation of cell membrane fluidity has not been elucidated yet. The cell membrane fluidity was investigated by giant unilamellar vesicles in the present study. The results showed that peptides TCNW, ADWAK, ESIINF, VPIEGII, LVEEY, and WKLC connect to membranes through intermolecular interactions, such as hydrogen bonding and regulated membrane fluidity, in a concentration-dependent way. In addition, peptides prefer to localize in the hydrophobic core of the bilayers. This study provides a theoretical basis for analyzing the localization of egg white bioactive peptides in specific cell membrane regions and their influence on the cell membrane fluidity.

Phosphine oxides as NMR and IR spectroscopic probes for geometry and energy of PO···H–A hydrogen bonds

In this work we evaluate the possibility to use the NMR and IR spectral properties of P=O group to estimate the geometry and strength of hydrogen bonds which it forms...

NMR Quantification of Hydrogen-Bond-Accepting Ability for Organic Molecules

The hydrogen-bond-accepting abilities for more than 100 organic molecules are quantified using ¹⁹F and ³¹P NMR spectroscopy with pentafluorobenzoic acid (PFBA) and phenylphosphinic acid (PPA) as commercially available, inexpensive probes. Analysis of pyridines and anilines with a variety of electronic modifications demonstrates that changes in NMR shifts can predict the secondary effects that contribute to H-bond-accepting ability, establishing the ability of PFBA and PPA binding to predict electronic trends. The H-bond-accepting abilities of various metal-chelating ligands and organocatalysts are also quantified. The measured Δδ(³¹P) and Δδ_p(¹⁹F) values correlate strongly with Hammett parameters, pK_a of the protonated HBA, and proton-transfer basicity (pK_BH+).

Exploring safe and potent bioactives for the treatment of non-small cell lung cancer

Activating and suppressing mutations in the MAPK pathway receptors are the primary causes of NSCLC. Of note, MEK inhibition is considered a promising strategy because of the diverse structures and harmful effects of upstream receptors in MAPK pathway. Thus, we explore a total of 1574 plant-based bioactive compounds activity against MEK using an energy-based virtual screening strategy. Molecular docking, binding free energy, and drug-likeness analysis were performed through GLIDE, Prime MM-GBSA, and QikProp module, respectively. The findings indicate that 5-O-caffeoylshikimic acid has an increased binding affinity to MEK protein. Further, molecular dynamic simulations and MM-PBSA analysis were performed to explore the ligand activity in real-life situations. In essence, compounds inhibitory activity was validated across 77 lung cancer cell lines using multimodal attention-based neural network algorithm. Eventually, our analysis highlight that 5-O-caffeoylshikimic acid obtained from the bark of Rhizoma smilacis glabrae would be developed as a potential compound for treating NSCLC.