An Integrated Proteomic and Glycoproteomic Investigation Reveals Alterations in the N-Glycoproteomic Network Induced by 2-Deoxy-D-Glucose in Colorectal Cancer Cells

As a well-known glycolysis inhibitor for anticancer treatment, 2-Deoxy-D-glucose (2DG) inhibits the growth and survival of cancer cells by interfering with the ATP produced by the metabolism of D-glucose. In addition, 2DG inhibits protein glycosylation in vivo by competing with D-mannose, leading to endoplasmic reticulum (ER) stress and unfolded protein responses in cancer cells. However, the molecular details underlying the impact of 2DG on protein glycosylation remain largely elusive. With an integrated approach to glycoproteomics and proteomics, we characterized the 2DG-induced alterations in N-glycosylation, as well as the cascading impacts on the whole proteome using the HT29 colorectal cancer cell line as a model system. More than 1700 site-specific glycoforms, represented by unique intact glycopeptides (IGPs), were identified. The treatment of 2DG had a broad effect on the N-glycoproteome, especially the high-mannose types. The glycosite occupancy of the high-mannose N-glycans decreased the most compared with the sialic acid and fucose-containing N-glycans. Many of the proteins with down-regulated high-mannose were implicated in functional networks related to response to topologically incorrect protein, integrin-mediated signaling, lysosomal transport, protein hydroxylation, vacuole, and protein N-glycosylation. The treatment of 2DG also functionally disrupted the global cellular proteome, evidenced by significant up-regulation of the proteins implicated in protein folding, endoplasmic reticulum, mitochondrial function, cellular respiration, oxidative phosphorylation, and translational termination. Taken together, these findings reveal the complex changes in protein glycosylation and expression underlying the various effects of 2DG on cancer cells, and may provide insightful clues to inform therapeutic development targeting protein glycosylation.     

Geraniin Inhibits the Entry of SARS-CoV-2 by Blocking the Interaction between Spike Protein RBD and Human ACE2 Receptor

The coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite the development of vaccines, the emergence of SARS-CoV-2 variants and the absence of effective therapeutics demand the continual investigation of COVID-19. Natural products containing active ingredients may be good therapeutic candidates. Here, we investigated the effectiveness of geraniin, the main ingredient in medical plants Elaeocarpus sylvestris var. ellipticus and Nephelium lappaceum, for treating COVID-19. The SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme 2 (hACE2) receptor to initiate virus entry into cells; viral entry may be an important target of COVID-19 therapeutics. Geraniin was found to effectively block the binding between the SARS-CoV-2 spike protein and hACE2 receptor in competitive enzyme-linked immunosorbent assay, suggesting that geraniin might inhibit the entry of SARS-CoV-2 into human epithelial cells. Geraniin also demonstrated a high affinity to both proteins despite a relatively lower equilibrium dissociation constant (K_D) for the spike protein (0.63 μM) than hACE2 receptor (1.12 μM), according to biolayer interferometry-based analysis. In silico analysis indicated geraniin’s interaction with the residues functionally important in the binding between the two proteins. Thus, geraniin is a promising therapeutic agent for COVID-19 by blocking SARS-CoV-2’s entry into human cells.     

Quantitation of alcohol ethoxylate surfactants in environmental samples by electrospray mass spectrometry

This report describes a method for obtaining the concentrations of the total and individual alcohol ethoxylate (AE) species in sewage treatment plant (STP) effluents by using electrospray liquid chromatography/mass spectrometry (LC/MS). This is a more advantageous method for quantitative analysis of AE in environmental matrices as compared with a previous thermospray LC/MS method. This new method is more sensitive, uses less solvents, utilizes a deuterated internal standard blend [C₁₃D₂₇O(CH₂CH₂O) _n H, where n varies from 0 to 21 with an average of n=9], which corresponds more closely to the AE, and it is a more robust instrumental technique. In this report, we document the results for validation of the electrospray LC/MS method by spike recovery of AE from STP effluent and influent samples.     

Structure-Based Development of SARS-CoV-2 Spike Interactors

Coronaviruses, including SARS-CoV-2 (the etiological agent of the current COVID-19 pandemic), rely on the surface spike glycoprotein to access the host cells, mainly through the interaction of their receptor-binding domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2). Therefore, molecular entities able to interfere with the binding of the SARS-CoV-2 spike protein to ACE2 have great potential to inhibit viral entry. Starting from the available structural data on the interaction between SARS-CoV-2 spike protein and the host ACE2 receptor, we engineered a set of soluble and stable spike interactors, here denoted as S-plugs. Starting from the prototype S-plug, we adopted a computational approach by combining stability prediction, associated to single-point mutations, with molecular dynamics to enhance both S-plug thermostability and binding affinity to the spike protein. The best developed molecule, S-plug3, possesses a highly stable α-helical con-formation (with melting temperature Tm of 54 °C) and can interact with the spike RBD and S1 domains with similar low nanomolar affinities. Importantly, S-plug3 exposes the spike RBD to almost the same interface as the human ACE2 receptor, aimed at the recognition of all ACE2-accessing coronaviruses. Consistently, S-plug3 preserves a low nanomolar dissociation constant with the delta B.1.617.2 variant of SARS-CoV-2 spike protein (K_D = 29.2 ± 0.6 nM). Taken together, we provide valid starting data for the development of therapeutical and diagnostic tools against coronaviruses accessing through ACE2.     

Encapsulation of the Dinuclear Trithiolato-Bridged Arene Ruthenium Complex Diruthenium-1 in an Apoferritin Nanocage: Structure and Cytotoxicity

The effects of encapsulating the cytotoxic dinuclear trithiolato-bridged arene ruthenium complex [(η⁶-p-MeC₆H₄iPr)₂Ru₂(μ₂-S-p-C₆H₄tBu)₃]Cl (DiRu-1) within the apoferritin (AFt) nanocage were investigated. The DiRu-1-AFt nanocarrier was characterized by UV/Vis spectroscopy, ICP-MS, CD and X-ray crystallography. In contrast to previously reported Au- and Pt-based drug-loaded AFt carriers, we found no evidence of direct interactions between DiRu-1 and AFt. DiRu-1-AFt is cytotoxic toward immortalized murine BALB/c-3T3 fibroblasts transformed with SV40 virus (SVT2) and human epidermoid carcinoma A431 malignant cells, and exhibits moderate selectivity for these cancer cells over normal BALB/c-3T3 cells. DiRu-1-AFt triggers the production of reactive oxygen species, depolarization of mitochondrial membrane potential, and induces cell death via p53-mediated apoptosis. Comparison between our data and previous results suggests that the presence of specific interactions between a metal-based drug and AFt within the protein cage is not essential for drug encapsulation.     

Resorc[4]arene Modifiers for Supramolecular Site-Directed Immobilization of Antibodies on Multi-Walled Carbon Nanotubes

One of the main problems in developing immunosensors featuring carbon nanotubes (CNTs) is immobilizing antibodies (Abs) onto the CNT surface to afford selective binding to target antigens (Ags). In this work, we developed a practical supramolecular Ab conjugation strategy based on resorc[4]arene modifiers. To improve the Ab orientation on the CNTs surface and optimizing the Ab/Ag interaction, we exploited the host-guest approach by synthesizing two newly resorc[4]arene linkers R1 and R2 via well-established procedures. The upper rim was decorated with eight methoxyl groups to promote selective recognition of the fragment crystallizable (F_c) region of the Ab. Moreover, the lower rim was functionalized with 3-bromopropyloxy or 3-azidopropiloxy substituents to bind the macrocycles on the multi-walled carbon nanotubes (MWCNTs) surface. Accordingly, several chemical modifications of MWCNTs were evaluated. After the morphological and electrochemical characterization of nanomaterials, the resorc[4]arene-modified MWCNTs were deposited onto a glassy carbon electrode surface to evaluate their potential applicability for label-free immunosensor development. The most promising system showed an improved electrode active area (A_EL) of almost 20 % and a site-oriented immobilization of the SARS-CoV-2 spike protein S1 antibody (Ab-SPS1). The developed immunosensor revealed a good sensitivity (23.64 μA mL ng⁻¹ cm⁻²) towards the SPS1 antigen and a limit of detection (LOD) of 1.01 ng mL⁻¹.     

Small Molecules that Target the Toxic RNA in Myotonic Dystrophy Type 2

Myotonic dystrophy type 2 (DM2) is caused by an expansion of CCTG repeats in the zinc‐finger protein gene (ZNF9). Transcribed CCUG repeats sequester muscleblind‐like protein 1 (MBNL1), an important alternative splicing regulator, preventing its normal function, leading to the disease phenotype. We describe a series of ligands that disrupt the MBNL1–r(CCUG)_n interaction as potential lead agents for developing DM2 therapeutics. A previously reported triaminopyrimidine–acridine conjugate was a moderate inhibitor in vitro, however it proved to be poorly water‐soluble and not cell‐permeable. To improve its therapeutic potential, the new set of ligands maintained the key triaminopyrimidine recognition unit but replaced the acridine intercalator with a bisamidinium groove binder. The optimized ligands exhibit low micromolar inhibition potency to MBNL1–r(CCUG)₈. Importantly, the ligands are the first to show the ability to disrupt the MBNL1–r(CCUG)_n foci in DM2 model cell culture and exhibit low cytotoxicity.     

Targeting tumour proliferation with a small-molecule inhibitor of AICAR transformylase homodimerization

Aminoimidazole carboxamide ribonucleotide transformylase/ inosine monophosphate cyclohydrolase (ATIC) is a bifunctional homodimeric enzyme that catalyzes the last two steps of de novo purine biosynthesis. Homodimerization of ATIC, a protein–protein interaction with an interface of over 5000 Ų, is required for its aminoimidazole carboxamide ribonucleotide (AICAR) transformylase activity, with the active sites forming at the interface of the interacting proteins. Here, we report the development of a small‐molecule inhibitor of AICAR transformylase that functions by preventing the homodimerization of ATIC. The compound is derived from a previously reported cyclic hexapeptide inhibitor of AICAR transformylase (with a K_i of 17 μM ), identified by high‐throughput screening. The active motif of the cyclic peptide is identified as an arginine‐tyrosine dipeptide, a capped analogue of which inhibits AICAR transformylase with a K_i value of 84 μM . A library of nonnatural analogues of this dipeptide was designed, synthesized, and assayed. The most potent compound inhibits AICAR transformylase with a K_i value of 685 nM , a 25‐fold improvement in activity from the parent cyclic peptide. The potential for this AICAR transformylase inhibitor in cancer therapy was assessed by studying its effect on the proliferation of a model breast cancer cell line. Using a nonradioactive proliferation assay and live cell imaging, a dose‐dependent reduction in cell numbers and cell division rates was observed in cells treated with our ATIC dimerization inhibitor.     

Ab initio Modeling of the Electronic Structures and Physical Properties of a‐Si1−xGexO2 Glass (x = 0 to 1)

The amorphous silica (a‐SiO₂) and germania (a‐GeO₂) have a wide range of applications in glass industry. Based on a previously constructed near‐perfect continuous random network model with 1296 atoms and periodic boundary conditions, we extend our study to amorphous Si_1?xGe_xO₂ models of homogeneous random substitution of Si by Ge with x ranging from 0 to 1. We have calculated the structural, electronic, mechanical, and optical properties for the series by using the first‐principles density functional theory methods. The x‐dependence of the variations in the properties is analyzed and critically compared with available experimental data. The mass density, volume, total bond order density, bulk mechanical properties, and refractive index are found to vary linearly as a function of x. For x = 0.5, we have also constructed six different kinds of particle immersion models to test the effect of inclusion of spherical particles of one glass of different sizes in the medium of the other glass on their physical properties. It is shown that particle sizes do affect the properties of particle immersion. Our calculations provide deep insight on the properties of mixture and nanocomposites of a‐SiO₂ and a‐GeO₂ glasses.     

AC impedance and state-of-charge analysis of alkaline zinc/manganese dioxide primary cells

Alternating current impedance data of alkaline Zn/MnO₂ cells were analysed in view of identification of suitable parameters, which depend on the state-of-charge (SOC) of the cells. The impedance of a slightly discharged cell was found to possess impedance considerably lesser than that of an undischarged cell. The data in the form of Nyquist plot contained an inductance part at very high frequencies, a capacitive semicircle at high frequencies and a diffusion linear spike at low frequencies. The low frequency linear spike gradually transformed into a capacitive semicircle with the decrease of SOC of the cell, which was attributed to the nature of the reactions at the Zn anode. Of several impedance parameters that were examined, equivalent series capacitance (C _s) was found to have a strong dependence on SOC of the alkaline Zn/MnO₂ cells. There was a continuous change in a partially discharged cell during its ageing, which was reflected by transformation of low frequency data into a clear semicircle.     

Production of Propene from n-Butanol: A Three-Step Cascade Utilizing the Cytochrome P450 Fatty Acid Decarboxylase OleTJE

Propene is one of the most important starting materials in the chemical industry. Herein, we report an enzymatic cascade reaction for the biocatalytic production of propene starting from n-butanol, thus offering a biobased production from glucose. In order to create an efficient system, we faced the issue of an optimal cofactor supply for the fatty acid decarboxylase OleT_JE, which is said to be driven by either NAD(P)H or H₂O₂. In the first system, we used an alcohol and aldehyde dehydrogenase coupled to OleT_JE by the electron-transfer complex putidaredoxin reductase/putidaredoxin, allowing regeneration of the NAD⁺ cofactor. With the second system, we intended full oxidation of n-butanol to butyric acid, generating one equivalent of H₂O₂ that can be used for the oxidative decarboxylation. As the optimal substrate is a long-chain fatty acid, we also tried to create an improved variant for the decarboxylation of butyric acid by using rational protein design. Within a mutational study with 57 designed mutants, we generated the mutant OleT_V292I, which showed a 2.4-fold improvement in propene production in our H₂O₂-driven cascade system and reached total turnover numbers >1000.     

Simple preparation of immobilized-metal affinity chromatography media

Immobilized-metal affinity chromatography (IMAC) media was prepared. Iminodiacetic acid (IDA) was optimally coupled to the oxirane-activated gel at pH 13.0 and 60 °C in 0.1–0.15 g of IDA per ml of 2M Na₂CO₃ for 5–7 hours. The amount of coupled IDA was 600–800 micromoles per gram of dried gel by determining zinc (II) ion with atomic absorption spectroscopy. Adsorption and desorption of protein sample to IDA-coupled media was made and the result is compatible to ones reported previously. The efficiency of column chromatography was discussed on partially purifying β-galactosidase from E. coli as the protein sample by zinc (II) ion chelate affinity column.     

Hierarchical Organization of TiO2 Nanostructures in Low‐Temperature Solution Processes

Nanostructured TiO₂ thin films were prepared via a low‐temperature solution processing. We have previously calculated the degree of supersaturation (s) for TiO₂ precursor solution to systematically tailor the development of TiO₂ nanostructures in the range of s = 70–200. In this article, we focused more on a lower supersaturation regime (s < 70), from which we were able to obtain various shapes and sizes of nanostructures of TiO₂ thin films. A film consisting of “rutile” phase nanoblades was observed when the degree of supersaturation was s = 15–70. To further lower the supersaturation (s < 15), hydrothermal processing had to be used, for which a film consisting of “rutile” phase nanorods was obtained. The resulting thin films were evaluated for band gap energies and dielectric properties. The band gap energy for those rutile thin films decreased from 3.22 to 2.99 eV when the supersaturation was lowered from s = 70 to 15. The dielectric constant (k) of the rutile film processed from s = 50 showed the best performance with k~50 at 1 MHz.     

An Animal Able To Tolerate D2O

It is possible to gain a deeper insight into the role of water in biology by using physicochemical variant molecules, such as deuterium oxide (D₂O); however, D₂O is toxic to multicellular organisms in high concentrations. By using a unique desiccation-rehydration process, we demonstrate that the anhydrobiotic nematode Panagrolaimus superbus is able to tolerate and proliferate in 99 % D₂O. Moreover, we analysed P. superbus’ water-channel protein (aquaporin; AQP), which is associated with dehydration/rehydration, by comparing its primary structure and modelling its tertiary structure in silico. Our data evidence that P. superbus’ AQP is an aquaglyceroporin, a class of water channel known to display a wider pore; this helps to explain the rapid and successful organismal influx of D₂O into this species. This is the first demonstration of an animal able to withstand high D₂O levels, thus paving a way for the investigation of the effects D₂O on higher levels of biological organization.     

Hydrogen Bond Compression during Triple Proton Transfer in Crystalline Pyrazoles. A Dynamic 15N NMR Study

Using dynamic solid state ¹⁵N CPMAS NMR spectroscopy (CP ≡ cross polarization, MAS ≡ magic-angle spinning), the kinetics of degenerate intermolecular triple proton and deuteron transfers in the cyclic trimers of ¹⁵N-labeled polycrystalline 4-nitropyrazole (4NO₂P) and 4-bromopyrazole (4BrP) have been studied as a function of temperature and are compared to the kinetics of triple proton transfer in bulk solid 3,5-dimethylpyrazole (DMP) studied previously. The results show that the transfer kinetics in the new trimers are much faster than in DMP. However, the kinetic HHH/HHD/HDD/DDD isotope effects of 4NO₂P are similar to those of DMP. These effects indicate a single barrier for the triple proton transfers where all three protons lose zero-point energy in the transition state, as expected for a structure with three compressed hydrogen bonds. At low temperatures, strong deviations from an Arrhenius-behavior are observed which are described in terms of a modified Bell tunneling model and a concerted proton motion. The barrier for the triple proton transfer in 4NO₂P and 4BrP is substantially smaller than in DMP. As there is no correlation with the electronic properties of the substituents, we assign this finding to steric effects where the bulky methyl groups of DMP in the 3- and 5-positions hinder the hydrogen bond compression, in contrast to 4NO₂P and 4BrP exhibiting substitutents in the 4-position. These results lead to a minimum energy pathway of the proton transfer following in the absence of steric hindering the hydrogen bond correlation line q₁ = f(q₂), established previously, where q₁ represents the deviation of the proton from the hydrogen bond center and q₂ the N…N distance. Tunneling occurs at constant N…N distances.     

Augmenting Structure-Based Design with Experimental Protein-Ligand Interaction Data: Molecular Recognition,Interactive Visualization,and Rescoring

The previously introduced ratio of frequencies (R_F) framework provides statistically sound information on the relative interaction preferences of atoms in crystal structures. By applying the methodology to protein-ligand complexes, we can investigate the significance of interactions that are employed in structure-based drug design. Here, we revisit three aspects of molecular recognition in the light of the R_F framework, namely stacking interactions of heteroaromatic rings with protein amide groups, interactions of acidified C−H groups, and interaction differences between syn and anti lone pairs of carboxylate groups. In addition, we introduce a highly interactive visualization tool that facilitates design idea generation in structure-enabled drug discovery projects. Finally, we show that applying the R_F analysis as a simple rescoring tool after docking improves enrichment factors for the DUD−E diverse targets subset supporting the relevance of our approach.     

Cryo-kinetics Reveal Dynamic Effects on the Chemistry of Human Dihydrofolate Reductase

Effects of isotopic substitution on the rate constants of human dihydrofolate reductase (HsDHFR), an important target for anti-cancer drugs, have not previously been characterized due to its complex fast kinetics. Here, we report the results of cryo-measurements of the kinetics of the HsDHFR catalyzed reaction and the effects of protein motion on catalysis. Isotopic enzyme labeling revealed an enzyme KIE (k_H^LE/k_H^HE) close to unity above 0 °C; however, the enzyme KIE was increased to 1.72±0.15 at −20 °C, indicating that the coupling of protein motions to the chemical step is minimized under optimal conditions but enhanced at non-physiological temperatures. The presented cryogenic approach provides an opportunity to probe the kinetics of mammalian DHFRs, thereby laying the foundation for characterizing their transition state structure.     

Isomeric Detergent Comparison for Membrane Protein Stability: Importance of Inter‐Alkyl‐Chain Distance and Alkyl Chain Length

Membrane proteins encapsulated by detergent micelles are widely used for structural study. Because of their amphipathic property, detergents have the ability to maintain protein solubility and stability in an aqueous medium. However, conventional detergents have serious limitations in their scope and utility, particularly for eukaryotic membrane proteins and membrane protein complexes. Thus, a number of new agents have been devised; some have made significant contributions to membrane protein structural studies. However, few detergent design principles are available. In this study, we prepared meta and ortho isomers of the previously reported para‐substituted xylene‐linked maltoside amphiphiles (XMAs), along with alkyl chain‐length variation. The isomeric XMAs were assessed with three membrane proteins, and the meta isomer with a C₁₂ alkyl chain was most effective at maintaining solubility/stability of the membrane proteins. We propose that interplay between the hydrophile–lipophile balance (HLB) and alkyl chain length is of central importance for high detergent efficacy. In addition, differences in inter‐alkyl‐chain distance between the isomers influence the ability of the detergents to stabilise membrane proteins.