Category: Chemistry

by University of Amsterdam

A team of researchers from the Universities of Amsterdam and Zurich together with the Swiss company Allocyte Pharmaceuticals have for the first time been able to discover allosteric sites in a type of cell surface receptor called integrin.

In a paper recently published in the Journal of Chemical Information and Modeling, they describe how this reveals previously inaccessible druggable integrin pockets. At the heart of the research is a novel computational approach for mixed-solvent molecular dynamics simulation developed by Dr. Ioana Ilie at the Computational Chemistry group of the Van ‘t Hoff Institute for Molecular Sciences at the University of Amsterdam.

Integrins are a family of cell surface adhesion receptors which are capable of transmitting signals bidirectionally across membranes. They are known for their therapeutic potential in a wide range of diseases. However, the development of integrin targeting medication has been impacted by unexpected downstream effects. In particular, these are observed with drugs targeting the native binding site of the integrin.

The so-called allosteric modulation of integrins is a promising approach to potentially overcome these limitations. Here, the drug binds elsewhere on the receptor, changing the conformation and thus impacting the activity of the protein. Allosteric modulation of receptors therefore creates opportunities for drug discovery and development which are potentially superior to classic orthosteric modulation.

Novel druggable pockets

The novel computational approach developed by Ioana Ilie relies on enriching the solvent with small organic molecules (benzene in small concentrations) to enable the gentle opening of the integrin α I domain. This revealed novel previously inaccessible druggable pockets within the integrins LFA-1, VLA-1, and Mac-1. This study thus offers structural and dynamic insight on the effect of small alterations in solvent conditions on the accessibility of novel potentially druggable pockets, which are validated via virtual screening. The study acts as proof of concept and sets the foundation for the design of the next-generation integrin-targeting drugs. Additionally, it opens new research avenues towards the identification of allosteric sites in other up to date undruggable protein targets.

Finally, the study goes beyond drug discovery as it demonstrates that minor changes in the solvent conditions can have a dramatic impact on the conformational space of the solvated molecule. This offers the opportunity to tune the solvent conditions in order to obtain a specific response of the solvated molecule (e.g., protein, material), which implicitly can aid in the development novel bio-inspired materials with responsive properties.

More information: Ioana M. Ilie et al, Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations, Journal of Chemical Information and Modeling (2023). DOI: 10.1021/acs.jcim.3c00480

Journal information: Journal of Chemical Information and Modeling 

Provided by University of Amsterdam 

by University of Münster

Hydrogen is seen as an energy source of the future—at least, when it is produced in a climate-friendly way. Hydrogen can also be important for the production of active ingredients and other important substances. To produce hydrogen, water (H₂O) can be converted into hydrogen gas (H₂) by means of a series of chemical processes. However, as water molecules are very stable, splitting them into hydrogen and oxygen presents a big challenge to chemists. For it to succeed at all, the water first has to be activated using a catalyst; then it reacts more easily.

A team of researchers led by Prof. Armido Studer at the Institute of Organic Chemistry at Münster University (Germany) has developed a photocatalytic process in which water, under mild reaction conditions, is activated through triaryl phosphines, and not—as in most other processes—through transition metal complexes.

This strategy, which has now been published in Nature, will open a new door in the highly active field of research relating to radical chemistry, says the team. Radicals are, as a rule, highly reactive intermediates. The team uses a special intermediate—a phosphine-water radical cation—as activated water, from which hydrogen atoms from H₂O can be easily split off and transferred to a further substrate. The reaction is driven by light energy.

“Our system,” says Prof. Studer, “offers an ideal platform for investigating unresearched chemical processes which use the hydrogen atom as a reagent in synthesis.”

Dr. Christian Mück-Lichtenfeld, who analyzed the activated water complexes using theoretical methods, says, “The hydrogen-oxygen bond in this intermediate is extraordinarily weak, making it possible to transfer a hydrogen atom to various compounds.”

Dr. Jingjing Zhang, who carried out the experimental work, adds, “The hydrogen atoms of the activated water can be transferred to alkenes and arenes under very mild conditions, in so-called hydrogenation reactions.”

Hydrogenation reactions are enormously important in pharmaceutical research, in the agrochemical industry and in materials sciences.

More information: Jingjing Zhang et al, Photocatalytic phosphine-mediated water activation for radical hydrogenation, Nature (2023). DOI: 10.1038/s41586-023-06141-1

Journal information: Nature 

Provided by University of Münster 

by Zhang Nannan, Chinese Academy of Sciences

Prof. Huang Qunying’s team from the Hefei Institutes of Physical Science of the Chinese Academy of Sciences has developed a novel inorganic silica-based adsorbent for the highly selective separation of strontium from acidic medium. The results were published in Separation and Purification Technology.

Radioactive strontium (⁹⁰Sr) is considered to be one of the most dangerous radionuclides due to its high biochemical toxicity. During the vitrification process of high-level liquid waste, the presence of ⁹⁰Sr can cause instability of the vitrification substrate, resulting in radionuclide leaching. Removal of ⁹⁰Sr can reduce the heat generation and shorten the cooling time of the vitrification substrate in the repository, which is favorable for further deep geological disposal of the radioactive waste.

To address the above issues, Prof. Huang’s team developed a novel silica-based adsorbent Sb₂O₅/SiO₂ by a two-step method, i.e., vacuum impregnation followed by oxidation, and investigated the adsorption behavior of the adsorbent on strontium stable nuclide in low and high acid mediums (i.e., pH 6 and 1 M HNO₃).

The experimental results showed that the prepared adsorbent possessed good acid resistance stability and exhibited favorable adsorption on strontium stable nuclide in both low and high acid mediums. The mechanistic results revealed that the adsorption mechanism was ion exchange, and the adsorption was accompanied by charge transfer and reduction of adsorption energy.

This study not only develops a novel method for the preparation of highly stable silica-based adsorbent, but also provides relevant experimental data and theoretical basis for the selective separation of strontium in acidic environments.

More information: Shichang Zhang et al, Efficient separation of strontium in different environments with novel acid-resistant silica-based ion exchanger, Separation and Purification Technology (2023). DOI: 10.1016/j.seppur.2023.124347

Provided by Chinese Academy of Sciences 

by Kristi L. Bumpus, Oak Ridge National Laboratory

Oak Ridge National Laboratory researchers have developed a method to simplify one step of radioisotope production—and it’s faster and safer.

ORNL produces several radionuclides from irradiated radium-226 targets, including actinium-227 and thorium-228, both used in cancer treatments. Continuously improving isotopes for human health is one of the lab’s missions.

Currently, it takes workers two weeks to prepare radium-226 targets for irradiation in the High Flux Isotope Reactor. The targets are exposed to radiation throughout the process, which involves pressing radium carbonate aluminum composite into 10 pellets—one each day—and sealing them into an aluminum capsule.

The new method uses a single, seamless aluminum liner with aluminum powder caps to press and seal the radium carbonate. This minimizes the time required to prepare targets, significantly decreasing radiation doses to workers, and also reduces the targets’ failure rate.

Provided by Oak Ridge National Laboratory 

by University of California – Riverside

Some molecules exist in two forms, such that their structures and their mirror images are not superimposable, like our left and right hands. Called chirality, it is a property these molecules have due to their asymmetry. Chiral molecules tend to be optically active because of how they interact with light. Oftentimes, only one form of a chiral molecule exists in nature, for example, DNA. Interestingly, if a chiral molecule works well as a drug, its mirror image could be ineffective for therapy.

In trying to produce artificial chirality in the lab, a team led by chemists at the University of California, Riverside, has found that the distribution of a magnetic field is itself chiral. The research paper titled, “A magnetic assembly approach to chiral superstructures,” appears in the journal Science.

“We discovered that the magnetic field lines produced by any magnet, including a bar magnet, have chirality,” said Yadong Yin, a professor of chemistry, who led the team. “Further, we were also able to use the chiral distribution of the magnetic field to coax nanoparticles into forming chiral structures.”

Traditionally, researchers have used “templating” to create a chiral molecule. A chiral molecule is first used as the template. Achiral (or non-chiral) nanoparticles are then assembled on this template, allowing them to mimic the structure of the chiral molecule. The drawback to this technique is that it cannot be universally applied, being heavily dependent on the specific composition of the template molecule. Another shortcoming is the newly formed chiral structure cannot be easily positioned at a specific location on, say, an electronic device.

“But to gain an optical effect, you need a chiral molecule to occupy a particular place on the device,” Yin said. “Our technique overcomes these drawbacks. We are able to rapidly form chiral structures by magnetically assembling materials of any chemical composition at scales ranging from molecules to nano- and microstructures.”

Yin explained that his team’s method uses permanent magnets that consistently rotate in space to generate the chirality. He said transferring chirality to achiral molecules is done by doping, that is incorporating guest species, such as metals, polymers, semiconductors, and dyes into the magnetic nanoparticles used to induce chirality.

Yin said chiral materials acquire an optical effect when they interact with polarized light. In polarized light, light waves vibrate in a single plane, reducing the overall intensity of the light. As a result, polarized lenses in sunglasses cut glare to our eyes, while non-polarized lenses do not.

“If we change the magnetic field that produces a material’s chiral structure, we can change the chirality, which then creates different colors that can be observed through the polarized lenses,” Yin said. “This color change is instantaneous. Chirality can also be made to disappear instantaneously with our method, allowing for rapid chirality tuning.”

The findings could have applications in anti-counterfeit technology. A chiral pattern that signifies the authenticity of an object or document would be invisible to the naked eye but visible when seen through polarized lenses. Other applications of the findings are in sensing and the field of optoelectronics.

“More sophisticated optoelectronic devices can be made by taking advantage of the tunability of chirality that our method allows,” said Zhiwei Li, the first author of the paper and former graduate student in Yin’s lab. “Where sensing is concerned, our method can be used to rapidly detect chiral or achiral molecules linked to certain diseases, such as cancer and viral infections.”

Yin and Li were joined in the research by a team of graduate students in Yin’s lab, including Qingsong Fan, Zuyang Ye, Chaolumen Wu, and Zhongxiang Wang. Li is now a postdoctoral researcher at Northwestern University in Illinois.

More information: Zhiwei Li et al, A magnetic assembly approach to chiral superstructures, Science (2023). DOI: 10.1126/science.adg2657. www.science.org/doi/10.1126/science.adg2657

Journal information: Science 

Provided by University of California – Riverside 

by Society of Chemical Industry

Plastic food packaging accounts for a significant proportion of plastic waste in landfills. In the face of escalating environmental concerns, researchers are looking to bio-derived alternatives.

Now, scientists at The Chinese University of Hong Kong (CUHK) have developed an edible, transparent and biodegradable material with considerable potential for application in food packaging. Their work is published in the Journal of the Science of Food and Agriculture.

Heavy reliance on petrochemicals and inherent non-biodegradability of plastic packaging mean it has long been a significant contributor to environmental contamination. A team at CUHK has turned its attention to bacterial cellulose (BC), an organic compound derived from certain types of bacteria, which has garnered attention as a sustainable, easily available, and non-toxic solution to the pervasive use of plastics.

Professor To Ngai from the Department of Chemistry, CUHK and corresponding author of the study, explained that the impressive tensile strength and high versatility of BC are the key to its potential.

He said, “Extensive research has been conducted on BC, including its use in intelligent packaging, smart films, and functionalized materials created through blending, coating, and other techniques. These studies demonstrate the potential of BC as a replacement for single-use plastic packaging materials, making it a logical starting point for our research.”

Unlike the cellulose found in the cell walls of plants, BC can be produced through microbial fermentation, which eliminates the need for harvesting trees or crops. Ngai noted that as a result, “…this production method does not contribute to deforestation or habitat loss, making BC a more sustainable and environmentally friendly material alternative to plant cellulose.”

Up until now, the widespread adoption of BC has been limited by its unfavorable sensitivity to moisture in the air (hygroscopicity), which detrimentally impacts its physical properties.

In the paper, the researchers laid out a novel approach to address the limitations of BC-based materials. By incorporating certain soy proteins into the structure and coating it with an oil-resistant composite, they successfully created an edible, transparent, and robust BC-based composite packaging.

Ngai noted that this approach has a high feasibility for scale-up: “It does not require specific reaction conditions like chemical reactions, but rather a simple and practical method with mixing and coating. This approach offers a promising solution to the challenge of developing sustainable and environmentally friendly packaging materials that can replace single-use plastics on a large scale.”

The study demonstrated that the plastic alternative could be completely degraded within 1-2 months. Unlike other bio-derived plastics such as polylactic acid, the BC-based composite does not require specific industrial composting conditions to degrade.

Ngai explained, “The material developed in this research is completely edible, making it safe for turtles and other sea animals to consume without causing aquatic toxicity in the ocean.”

The researchers at CUHK are now exploring the directions for future research. They hope to enhance the versatility of modified BC films, making them suitable for a wider range of applications. Specifically, they are focused on developing a thermosetting glue that can create strong bonds between bacterial cellulose, allowing it to be easily molded into various shapes when heated.

“One of the main challenges with bacterial cellulose films is that they are not thermoplastic, which limits their potential for use in certain applications. By addressing this issue, we hope to make bacterial cellulose films more competitive with traditional plastics while maintaining their eco-friendliness,” explained Ngai.

Ngai hopes that the current study will help to combat the excessive use of single-use plastics, which can persist for hundreds of years after only a few days of being displayed on supermarket shelves.

“This research serves as a reminder that natural raw materials may already possess the necessary characteristics to perform beyond the functions of plastic packaging,” he concluded.

More information: Ka Man Cheung et al, Edible, strong, and low‐hygroscopic bacterial cellulose derived from biosynthesis and physical modification for food packaging, Journal of the Science of Food and Agriculture (2023). DOI: 10.1002/jsfa.12758

Journal information: Journal of the Science of Food and Agriculture 

Provided by Society of Chemical Industry

A study led by Dr. Wei Chen, Prof. Yuqin Zou, and Prof. Shuangyin Wang (State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University) unravels the reaction mechanism of the primary alcohol/vicinal diol electrooxidation reaction on NiO, especially for the synergy between the electrochemical and non-electrochemical steps.

The alcohol electrooxidation on NiO is an indirect electrooxidation reaction with the electrophilic oxygen species as the redox mediator. Therefore, the electrochemical step is the electrochemical generation of electrophilic oxygen species. The research team found two kinds of NiO electrocatalyst function mechanisms, i.e., the electrophilic oxygen-mediated mechanism involving hydrogen atom transfer (EOM-HAT) and the electrophilic oxygen-mediated mechanism involving C-C bond cleavage (EOM-Cleavage of C-C bond).

The synergy between EOM-HAT and the hydration of aldehyde results in the electrooxidation of primary alcohol (R-CH₂OH) to carboxylic acid (R-COOH) on NiO. On the other hand, the synergy between EOM-HAT and EOM-Cleavage of the C-C bond causes the electrooxidation of vicinal diol (R-CHOH-CH₂OH) to R-COOH and formic acid (HCOOH) on NiO.

This study, published in the journal National Science Review, highlights the synergy between the electrochemical and non-electrochemical steps in the alcohol electrooxidation reaction. It establishes a unified reaction mechanism of alcohol electrooxidation reaction based on nickel-based electrocatalysts.

More information: Wei Chen et al, Unraveling the electrophilic oxygen-mediated mechanism for alcohol electrooxidation on NiO, National Science Review (2023). DOI: 10.1093/nsr/nwad099

Provided by Science China Press 

Recently, researchers from the Hefei Institutes of Physical Science (HFIPS) of the Chinese Academy of Sciences, led by Prof. Tian Xingyou and Prof. Zhang Xian, along with associate Prof. Yang Yanyu from the College of Materials Science and Engineering at Zhengzhou University, used gallium indium alloy (EGaIn) to initiate the polymerization and serve as flexible fillers to construct liquid metal/polyvinyl alcohol(PVA)/P(AAm-co-SMA) double network hydrogel.

“The resulting material was super-stretchable and self-healing,” said Li Xiaofei, first author of the paper, “it will promote the research and practical application of hydrogels and liquid metal in intelligent devices and military fields.”

The study was published in Materials Horizons.

Most conductive hydrogels suffer from subpar mechanical qualities and lack desirable self-recovery and self-healing abilities, severely limiting hydrogels’ potential uses. Liquid metals like gallium indium alloy (EGaIn) can toughen polymers by conforming to their changing shapes. Also, gallium (Ga) in EGaIn can initiate vinyl monomer’s free radical polymerization.

In this research, the team built a liquid metal/PVA/P(AAm-co-SMA) double network hydrogel (LM hydrogel) with EGaIn serving as both the polymerization initiator and the flexible fillers.

The PVA network used PVA microcrystals and coordination interaction of Ga³⁺ and PVA as cross-links, while the P(AAm-co-SMA) network used hydrophobic association and the EGaIn microspheres. The LM hydrogel was endowed with excellent super-stretchability (2000%), toughness (3.00 MJ/m³), notch resistance, and self-healing property (> 99% at 25 °C after 24 h) due to the multiple physical cross-links and the synergistic effect of the rigid PVA microcrystal network and the ductile P(AAm-co-SMA) hydrophobic network.

“The sensors developed for it can be used in health monitoring and motion identification through human-computer interaction,” said Li Xiaofei, “thanks to the LM hydrogel’s sensitive strain sensing capability.”

As a result of EGaIn’s low infrared emissivity and remarkable photothermal, LM hydrogel shows considerable promise in infrared camouflage.

More information: Xiaofei Li et al, Self-healing liquid metal hydrogel for human–computer interaction and infrared camouflage, Materials Horizons (2023). DOI: 10.1039/D3MH00341H

Journal information: Materials Horizons 

Provided by Chinese Academy of Sciences 

Have you ever wondered how drugs reach their targets and achieve their function within our bodies? If a drug molecule or a ligand is a message, an inbox is typically a receptor in the cell membrane. One such receptor involved in relaying molecular signals is a G protein-coupled receptor (GPCR). About one-third of existing drugs work by controlling the activation of this protein. Japanese researchers now reveal a new way of activating GPCR by triggering shape changes in the intracellular region of the receptor. This new process can help researchers design drugs with fewer or no side effects.

If the cell membrane is like an Oreo cookie sandwich, GPCR is like a snake with seven segments traversing in and out of the cookie sandwich surface. The extracellular loops are the inbox for messages. When a message molecule binds to the extracellular side of the receptor, it triggers a shape change activating G proteins and the ß-arrestin protein attached to the intracellular side of the receptor. Like a molecular relay, the information passes downstream and affects various bodily processes. That is how we see, smell, and taste, which are sensations of light, smell, and taste messages.

Adverse side effects ensue if drugs acting on GPCRs activate multiple signaling pathways rather than a specific target pathway. That is why drug development focuses on activating specific molecular signal pathways within cells. Activating the GPCR from inside the cell rather than outside the cell could be one way to achieve specificity. But until now, there was no evidence of direct activation of only the intracellular side of GPCRs without the initiations from the extracellular side.

A team of researchers headed by Osamu Nureki, a professor at the University of Tokyo, and his lab, discovered a new receptor activation mode of a bone metabolism-related GPCR called human parathyroid hormone type 1 receptor (PTH1R) without signal transduction from the extracellular side.

“Understanding the molecular mechanism will enable us to design optimal drugs,” says Kazuhiro Kobayashi, a doctoral student and an author of the study. Such a drug offers “a promising treatment for osteoporosis.”

Kobayashi has been conducting research on bone formation in animal models since he was an undergrad. “Treatments for osteoporosis that target PTH1R require strict dosage, have administrative restrictions, and there aren’t yet any better alternatives,” he says. That motivated their team to look for better drug design strategies targeting the parathyroid hormone receptor.

To understand function through structure, they used cryo-electron microscopy and revealed the 3D structure of the PTH1R and G protein bound to a message molecule. The team synthesized a non-peptide message molecule called PCO371 which binds to the intracellular region of the receptor and interacts directly with G protein subunits. In other words, PCO371 activates the receptor after entering the cell.

The PCO371-bound PTH1R structure can directly and stably modulate the intracellular side of PTH1R. And because PCO371 activates only G protein and not ß-arrestin it does not cause side effects. This specificity of its binding and receptor activation mode makes it a suitable candidate for potential small-molecule-based drugs for class B1 GPCRs, like PTH1R, which currently lack oral administrative drug ligands. Such drugs would have reduced adverse effects and burdens on patients as they act on specific molecular pathways.

The findings from this study will help “develop new drugs for disorders such as obesity, pain, osteoporosis, and neurological disorders.”

The study appears in the journal Nature.

More information: Kazuhiro Kobayashi et al, Class B1 GPCR activation by an intracellular agonist, Nature (2023). DOI: 10.1038/s41586-023-06169-3

Journal information: Nature 

Provided by University of Tokyo 

Genetic information encoded in genomic DNA is transcribed to mRNAs and then the codons on mRNA are decoded by transfer RNAs (tRNAs) during protein synthesis. tRNAs deliver amino acids to ribosomes and proteins are synthesized from the amino acids on the ribosomes according to the decoded genetic information. Therefore, tRNA plays a key role during the translation of genetic information.

tRNAs contain numerous modified nucleosides, which regulate the accuracy and efficiency of protein synthesis. Modified nucleosides in tRNA are synthesized by tRNA modification enzymes. Therefore, unveiling the mechanisms by which tRNA modification enzymes selectively recognize substrate tRNAs from non-substrate RNAs; the when, where, and how many tRNAs are being modified by the modification enzymes, is of crucial importance to understand the protein synthesis machinery.

Addressing these key questions is, however, challenging due to the lack of a high-throughput technique that identifies the characteristic properties of tRNA modification enzymes.

To overcome this issue, Drs. Yamagami and Hori at Ehime University applied next-generation DNA sequencing technology to functional analyses of tRNA modification enzymes and developed a new high-throughput assay method, “tRNA-MaP.”

The tRNA-MaP technique can rapidly screen an RNA pool consisting of more than 5,000 RNA species and identify the substrate tRNAs of the target tRNA modification enzyme(s) with comparative sensitivity to already-established methods. By tRNA-MaP, in combination with protein orthology analyses, the researchers predicted numerous natural modifications in Geobacillus stearothermophilus tRNAs.

Furthermore, they analyzed the substrate recognition mechanism of G. stearothermophilus tRNA m¹A22 methyltransferase (TrmK), which methylates adenosine at position 22 to 1-methyladenosine (m¹A22) in tRNA, using tRNA-Map. Mutation profiling has revealed that TrmK selects a subset of tRNAs for the substrate.

Using 240 variants of G. stearothermophilus tRNA^Leu transcripts, the researchers found that U8, A14, G15, G18, G19, U55, Purine57 and A58 are important for the methylation by TrmK. In addition, based on the recognition sites in tRNA and the crystal structure of TrmK, a docking model between TrmK and tRNA has been constructed.

This study, now published in the Journal of Biological Chemistry, revealed that tRNA-Map is applicable for the analysis of the tRNA modification enzyme. Notably, because tRNA-Map can analyze any RNA molecular species from any organism, even DNA molecules, tRNA-Map can be used for analysis of all nucleic acid-related proteins except for tRNA modification enzymes. Thus, tRNA-Map can accelerate the integrative understanding of the flow of genetic information.

More information: Ryota Yamagami et al, Application of mutational profiling: New functional analyses reveal the tRNA recognition mechanism of tRNA m1A22 methyltransferase, Journal of Biological Chemistry (2022). DOI: 10.1016/j.jbc.2022.102759

Journal information: Journal of Biological Chemistry 

Provided by Ehime University