Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz

Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for characterizing biomolecules such as proteins and nucleic acids at atomic resolution. Increased magnetic field strengths drive progress in biomolecular NMR applications, leading to improved performance, e.g., higher resolution. A new class of NMR spectrometers with a 28.2 T magnetic field (1.2 GHz 1H frequency) has been commercially available since the end of 2019. The availability of ultra-high-field NMR instrumentation makes it possible to investigate more complex systems using NMR. This is especially true for highly flexible intrinsically disordered proteins (IDPs) and highly flexible regions (IDRs) of complex multidomain proteins. Indeed, the investigation of these proteins is frequently hampered by the crowding of NMR spectra. The advantages, however, are accompanied by challenges that the user must overcome when conducting experiments at such a high field (e.g., large spectral widths, radio frequency bandwidth, performance of decoupling schemes). This protocol presents strategies and tricks for optimising high-field NMR experiments for IDPs/IDRs based on the analysis of the relaxation properties of the investigated protein. The protocol, tested on three IDPs of different molecular weight and structural complexity, focuses on 13C-detected NMR at 1.2 GHz. A set of experiments, including some multiple receiver experiments, and tips to implement versions tailored for IDPs/IDRs are described. However, the general approach and most considerations can also be applied to experiments that acquire 1H or 15N nuclei and to experiments performed at lower field strengths.

Khasianine Affects the Expression of Sugar-Sensitive Proteins in Pancreatic Cancer Cells, Which Are Altered in Data from the Rat Model and Patients

Pancreatic ductal adenocarcinoma (PDAC) is a deadly malignancy with no effective treatment, particularly in the advanced stage. This study explored the antiproliferative activity of khasianine against pancreatic cancer cell lines of human (Suit2-007) and rat (ASML) origin. Khasianine was purified from Solanum incanum fruits by silica gel column chromatography and analyzed by LC-MS and NMR spectroscopy. Its effect in pancreatic cancer cells was evaluated by cell proliferation assay, chip array and mass spectrometry. Proteins showing sensitivity to sugars, i.e. sugar-sensitive lactosyl-Sepharose binding proteins (LSBPs), were isolated from Suit2-007 cells by competitive affinity chromatography. The eluted fractions included galactose-, glucose-, rhamnose- and lactose-sensitive LSBPs. The resulting data were analyzed by Chipster, Ingenuity Pathway Analysis (IPA) and GraphPad Prism. Khasianine inhibited proliferation of Suit2-007 and ASML cells with IC50 values of 50 and 54 μg/mL, respectively. By comparative analysis, khasianine downregulated lactose-sensitive LSBPs the most (126%) and glucose-sensitive LSBPs the least (85%). Rhamnose-sensitive LSBPs overlapped significantly with lactose-sensitive LSBPs and were the most upregulated in data from patients (23%) and a pancreatic cancer rat model (11.5%). From IPA, the Ras homolog family member A (RhoA) emerged as one of the most activated signaling pathways involving rhamnose-sensitive LSBPs. Khasianine altered the mRNA expression of sugar-sensitive LSBPs, some of which were modulated in data from patients and the rat model. The antiproliferative effect of khasianine in pancreatic cancer cells and the downregulation of rhamnose-sensitive proteins underscore the potential of khasianine in treating pancreatic cancer.

Synthesis, Characterization and Biological Investigations of Half-Sandwich Ruthenium(II) Complexes Containing Benzimidazole Moiety

Half-sandwich Ru(II) complexes belong to group of biologically active metallo-compounds with promising antimicrobial and anticancer activity. Herein, we report the synthesis and characterization of arene ruthenium complexes containing benzimidazole moiety, namely, [(η6-p-cymene)RuCl(bimCOO)] (1) and [(η6-p-cymene)RuCl2(bim)] (2) (where bimCOO = benzimidazole-2-carboxylate and bim = 1-H-benzimidazole). The compounds were characterized by 1H NMR, 13C NMR, IR, UV-vis and CV. Molecular structures of the complexes were determined by SC-XRD analysis, and the results indicated the presence of a pseudo-tetrahedral (piano stool) geometry. Interactions in the crystals of the Ru complexes using the Hirshfeld surface analysis were also examined. In addition, the biological studies of the complexes, such as antimicrobial assays (against planktonic and adherent microbes), cytotoxicity and lipophilicity, were performed. Antibacterial activity of the complexes was evaluated against S. aureus, E. coli, P. aeruginosa PAO1 and LES B58. Cytotoxic activity was tested against primary human fibroblasts and adenocarcinoma human alveolar basal epithelial cells. Obtained biological results show that the ruthenium compounds have bacteriostatic activity toward Pseudomonas aeruginosa PAO1 strain and are not toxic to normal cells. A molecular docking study was applied as a predictive source of information about the plausibility of examined structures binding with HSA as a transporting system.

Impact of Linker Modification and PEGylation of Vancomycin Conjugates on Structure-Activity Relationships and Pharmacokinetics

As multidrug-resistant bacteria represent a concerning burden, experts insist on the need for a dramatic rethinking on antibiotic use and development in order to avoid a post-antibiotic era. New and rapidly developable strategies for antimicrobial substances, in particular substances highly potent against multidrug-resistant bacteria, are urgently required. Some of the treatment options currently available for multidrug-resistant bacteria are considerably limited by side effects and unfavorable pharmacokinetics. The glycopeptide vancomycin is considered an antibiotic of last resort. Its use is challenged by bacterial strains exhibiting various types of resistance. Therefore, in this study, highly active polycationic peptide-vancomycin conjugates with varying linker characteristics or the addition of PEG moieties were synthesized to optimize pharmacokinetics while retaining or even increasing antimicrobial activity in comparison to vancomycin. The antimicrobial activity of the novel conjugates was determined by microdilution assays on susceptible and vancomycin-resistant bacterial strains. VAN1 and VAN2, the most promising linker-modified derivatives, were further characterized in vivo with molecular imaging and biodistribution studies in rodents, showing that the linker moiety influences both antimicrobial activity and pharmacokinetics. Encouragingly, VAN2 was able to undercut the resistance breakpoint in microdilution assays on vanB and vanC vancomycin-resistant enterococci. Out of all PEGylated derivatives, VAN:PEG1 and VAN:PEG3 were able to overcome vanC resistance. Biodistribution studies of the novel derivatives revealed significant changes in pharmacokinetics when compared with vancomycin. In conclusion, linker modification of vancomycin-polycationic peptide conjugates represents a promising strategy for the modulation of pharmacokinetic behavior while providing potent antimicrobial activity.

Anticancer potential of rhizome extract and a labdane diterpenoid from Curcuma mutabilis plant endemic to Western Ghats of India

Zingiberaceae plants are well known for their use in ethnomedicine. Curcuma mutabilis Škorničk., M. Sabu & Prasanthk., is an endemic Zingiberaceae species from Western Ghats of Kerala, India. Here, we report for the first time, the anticancer potential of petroleum ether extract from C. mutabilis rhizome (CMRP) and a novel labdane diterpenoid, (E)-14, 15-epoxylabda-8(17), 12-dien-16-al (Cm epoxide) isolated from it. CMRP was found to be a mixture of potent bioactive compounds including Cm epoxide. Both the extract and the compound displayed superior antiproliferative activity against several human cancer cell lines, without any display of cytotoxicity towards normal human cells such as peripheral blood derived lymphocytes and erythrocytes. CMRP treatment resulted in phosphatidylserine externalization, increase in the levels of intracellular ROS, Ca²⁺, loss of mitochondrial membrane potential as well as fragmentation of genomic DNA. Analyses of transcript profiling and immunostained western blots of extract-treated cancer cells confirmed induction of apoptosis by both intrinsic and extrinsic pathways. The purified compound, Cm epoxide, was also found to induce apoptosis in many human cancer cell types tested. Both CMRP and the Cm epoxide were found to be pharmacologically safe in terms of acute toxicity assessment using Swiss albino mice model. Further, molecular docking interactions of Cm epoxide with selected proteins involved in cell survival and death were also indicative of its druggability. Overall, our findings reveal that the endemic C. mutabilis rhizome extract and the compound Cm epoxide isolated from it are potential candidates for development of future cancer chemotherapeutics.

Silva MG, Klika KD, de Brito E, Silva LMAE, Pinto FDCL, Breuer A, Owen RW. Characterization and Quantitation of Polyphenolic Compounds in Senna splendida from the Northeast of Brazil

A total of 27 polyphenolic compounds were detected, identified and quantitated in methanol extracts of various botanical parts of Senna splendida (Vogel) H.S. Irwin & Barneby. On a dry weight basis, the higher concentration of polyphenolic compounds was detected in the leaves (28.524 g/kg) and roots (13.884 g/kg). By contrast, the values in the flowers (6.331g/kg) and bark of Senna splendida (2.736 g/kg) were considerably lower. The major component in Senna splendida leaves was quercetin diglucoside, (7.887 g/kg), in the roots methoxy oxyresveratrol (4.485 g/kg), in the flowers quercetin-3- O-rhamnoside-4′- O-glucoside (2.885 g/kg), and in the bark quercitrin (quercetin rhamnoside; 0.881 g/kg). The composition of the polyphenolic compounds in the flowers, leaves and bark were dominated by flavonoids at > 98%, whereas the composition was quite different in the roots, of which the major components were napththapyrones (54 %) and stilbenes (39 %) with a very low contribution from flavonoids (5 %) and phenolic acids (2 %).