Funding for catalyst research

The teams of Stefan Huber (left) and Dirk Tischler receive funding from the Mercator Research Center Ruhr.
Credit: RUB, Marquard

With a total of around 240,000 euros, the Mercator Research Center Ruhr supports two RUB cooperation projects with its partners of the Ruhr University Alliance.

In order to develop new tools for catalysis, the Mercator Research Center Ruhr (MERCUR) is funding two projects with Bochum participation with a total of around 240,000 euros. The team around Prof. Dr. Dirk Tischler from the Microbial Biotechnology Working Group at the Ruhr University Bochum (RUB) is developing new bio-building blocks in cooperation with a team from the Technical University (TU) Dortmund, which can be reliably and easily assembled into bio-catalysts. Prof. Dr. Stefan Huber and his working group at the Chair of Organic Chemistry I at RUB are developing new methods for catalysis using halogen bridges together with the University of Duisburg-Essen (UDE).

Biocatalysts from the tool case

These catalysts are complex proteins; Genes contain the building instructions for this. Different gene sections contain the building instructions for different protein components. In synthetic biology, researchers produce gene building blocks that can be used for different biocatalysts. These so-called biobricks form a kind of kit from which a catalyst can be put together for a specific purpose. The appropriate gene building blocks are put together and introduced into an organism such as the bacterium E. coli. This translates the gene into proteins with catalytic function.

Optical Fibers with Unusual Properties Created in Russia

Monocrystal.
Credit: Vladimir Petrov

Researchers of the Science Lab of Fiber Technology and Photonics at Ural Federal University have developed and produced infrared optical fibers with unique properties. The fibers are nontoxic and, as studies have shown, retain their outstanding properties when treated with ionizing beta radiation by doses up to 1 MGy. The team of scientists published an article describing the research, properties and areas of application of the obtained fibers in the scientific journal Optical Materials.

"This opens up the prospect of application of light guides made of the obtained fibers in conditions of intense ionizing radiation. That is, not only in the traditional field of optoelectronics, but also in laser surgery, endoscopic and diagnostic medicine, in determining the composition of hazardous waste from the nuclear industry, and in space," lists Liya Zhukova, Chief Scientist of the Laboratory, Professor of the Department of Physical Chemistry and Chemistry of Colloids at UrFU.

Because the fibers are capable of receiving and transmitting radiation from space objects, they can be embedded in infrared space telescopes, replacing massive mirrors and lenses. The lifespan of the fibers will be longer than the life cycle of the telescopes themselves, the developers claim.

Fibers are also highly productive in the non-hazardous for humans terahertz radiation region (between the region of mid- and far-infrared radiation, on the one hand, and microwave radiation, on the other hand). This means that fiber optic cables are suitable for creating equipment that could become a safe substitute for magnetic resonance imaging and x-rays - in medicine or in the process of pre-boarding scanning of passengers and their luggage. It would not require the use of cumbersome and expensive metal detectors, and passengers would not even feel that they are being screened.

New Method to Promote Biofilm Formation and Increase Efficiency of Biocatalysis

 The researchers screened synthetic polymers for their ability to induce biofilm formation in a strain of E. coli (MC4100), which is known to be poor at forming biofilms. They also monitored the biomass and biocatalytic activity of both MC4100 and PHL644 (a good biofilm former), incubated the presence of these polymers, and found that MC4100 matched and even outperformed PHL644.
Credit: EzumeImages

Birmingham scientists have revealed a new method to increase efficiency in biocatalysis, in a paper published today in Materials Horizons.

Biocatalysis uses enzymes, cells or microbes to catalyze chemical reactions, and is used in settings such as the food and chemical industries to make products that are not accessible by chemical synthesis. It can produce pharmaceuticals, fine chemicals, or food ingredients on an industrial scale.

However, a major challenge in biocatalysis is that the most commonly used microbes, such as probiotics and non-pathogenic strains of Escherichia coli, are not necessarily good at forming biofilms, the growth promoting ecosystems that form a protective micro-environment around communities of microbes and increase their resilience and so boost productivity.

This problem is normally solved by genetic engineering, but researchers Dr Tim Overton from the university’s School of Chemical Engineering, and Dr Francisco Fernández Trillo from the School of Chemistry*, both of whom are members of the Institute of Microbiology and Infection, set out to create an alternative method to bypass this costly and time-consuming process.

The researchers identified a library of synthetic polymers and screened them for their ability to induce biofilm formation in E. coli, a bacterium that is one of the most widely studied micro-organisms, and commonly used in biocatalysis.

Black cardamom effective against lung cancer cells

NUS researchers embarked on a scientific study of black cardamom, a spice used in Indian Ayurvedic medicine, as a source of potent bioactive compounds that are effective against lung cancer cells. Source: National University of Singapore

The main challenges associated with existing lung cancer drugs are severe side effects and drug resistance. There is hence a constant need to explore new molecules for improving the survival rate and quality of life of lung cancer patients.

In Indian Ayurvedic medicine, black cardamom has been used in formulations to treat cancer and lung conditions. A team of researchers from the NUS Faculty of Science, NUS Yong Loo Lin School of Medicine, and NUS College of Design and Engineering studied the scientific basis behind this traditional medicinal practice and provided evidence of the cytotoxic effect of black cardamom on lung cancer cells. The research highlighted the spice as a source of potent bioactives, such as cardamonin and alpinetin, which could be used in the treatment or prevention of lung cancer. The study is the first to report the association of black cardamom extract with oxidative stress induction in lung cancer cells, and compare the spice’s effects on lung, breast and liver cancer cells.

The findings could potentially lead to the discovery of safe and effective new bioactives which can prevent or cure cancer formation. The research was first published in the Journal of Ethnopharmacology.

Scientists develop greener, more efficient method for producing next-generation antibiotics

With the addition of a murine-derived biocatalyst (green), this engineered protein can add a fluoride atom to create macrolide analogs (structure, right). This approach offers a greener, more efficient method for creating new antibiotics.
Credit: Martin Grininger and Rajani Arora

An international team of researchers has developed a method for altering one class of antibiotics, using microscopic organisms that produce these compounds naturally.

The findings, published in Nature Chemistry, could lead to more efficient production of antibiotics that are effective against drug-resistant bacteria.

The team started with a microorganism that is genetically programmed to produce the antibiotic erythromycin. Scientists from the Institute of Organic Chemistry and Chemical

Biology at Germany’s Goethe University wondered if the system could be genetically altered to assemble the antibiotic with one additional fluorine atom, which can often improve pharmaceutical properties.

“We had been analyzing fatty acid synthesis for several years when we identified a part of a mouse protein that we believed could be used for directed biosynthesis of these modified antibiotics, if added to a biological system that can already make the native compound,” said Martin Grininger, professor for biomolecular chemistry at Goethe University.

Towards High-Quality Manganese Oxide Catalysts with Large Surface Areas

The octahedral molecular sieve (OMS-1) is a very powerful manganese oxide-based catalyst, and researchers from Tokyo Tech have found a remarkably simple way to synthesize it. By using a low-crystallinity precursor and a straightforward solid-state transformation method, they managed to produce high-quality OMS-1 nanoparticles. Their unprecedented catalytic performance and durability prove the potential of this novel synthesis approach for developing efficient catalysts and functional materials.

Manganese oxides have received much attention from materials scientists due to their widespread applications including electrodes, catalysts, sensors, supercapacitors, and biomedicine. Further, manganese is widely abundant and has many oxidation states, which allows it to form various interesting crystalline structures.

One such structure is the "todorokite-type manganese oxide octahedral molecular sieve (OMS-1)," a crystal whose unit cells (simplest repeating units of the crystal) consist of three-by-three MnO6 octahedral chains. Though promising as a catalyst, the potential of OMS-1 is limited by two reasons. First, its conventional synthesis methods are complex multi-step crystallization processes involving hydrothermal or reflux treatment. Second, these processes tend to create crystals with a higher particle size and a lower surface area, features detrimental to catalytic performance.

Shape-Memory Polymers

Ilya Starodumov as a member of an international team, is developing a technology for creating "smart" polymers.
Credit: Ilya Safarov

Biocompatible polymers based on a "smart" material poly (ε-caprolactone) that keeps its shape may appear in Russia. An international team of scientists from Russia, Israel, and Japan, including physicists from Ural Federal University, work on the technology of its creation. The research is supported by the Russian Foundation for Basic Research.

Polymeric materials based on poly (ε-caprolactone) are suitable for biomedical purposes: for surgery, cell engineering, regenerative medicine. Such material can be used to make devices for minimally invasive surgery (with minimal incisions), self-tightening surgical sutures, etc. A description of this material was published in The Journal of Physical Chemistry B.

"A special feature of polymers with shape memory is the ability to return to the original shape when the temperature changes. It looks like this: a polymer product with a certain "programmed" shape is made. Then this product is deformed in any manner, for example, stretched or curled, like surgical sutures. When heated to a certain temperature, the memory mechanism in the polymer is activated at the molecular level, and the product restores its original shape," says Ilya Starodumov, Head of the Laboratory of Multiphase Physico-Biological Environment Simulation at UrFU.

Home Sweet Home: A Study of the ‘Chemical Soup’ in our Houses

Chances are very good that as you read this, you are seated somewhere indoors. The surfaces around you are covered in microbes and you are also covered in microbes. All those microbes are busy excreting molecules and responding to the rest of the molecules in the mix. What does all of this mean for your health?

“We are living in a soup of chemistry,” says UConn Department of Chemistry researcher Alexander Aksenov, who is working to understand this microbial and molecular soup in our indoor environments and how it could be impacting our health. He and a multidisciplinary team of researchers, including from the University of California, San Diego, Colorado State University, and the University of Colorado published a paper today in Science Advances exploring these under-studied questions, with some surprising findings that could help inform us how to live healthier lives indoors.

Accounting for our full day, including time spent in cars, on average we spend over 90% of our time indoors, says Aksenov, so the indoor environment is by far the most important for us.

Previous studies show human activities impact our indoor environments, through things like gas stoves, chemical off-gassing, and the type of cleaning solutions we use. These studies usually looked at a limited number of molecules. For this study, the researchers sought to explore the full suite of molecules and microbes within a household environment.

Researchers discover new leukemia-killing compounds

Natasha Kirienko (left) and Svetlana Panina in Kirienko’s Rice University laboratory in 2019. Kirienko, associate professor of biosciences, and Panina, a former postdoctoral research associate in Kirienko’s lab, collaborated with researchers at the University of Texas MD Anderson Cancer Center to study potential new mitophagy-inducing drugs that could be paired with other chemotherapies to deliver a potent one-two punch to leukemia.
Photo by Jeff Fitlow/Rice University

Researchers from Rice University and the University of Texas MD Anderson Cancer Center have discovered potential new drugs that work in concert with other drugs to deliver a deadly one-two punch to leukemia.

The potential drugs are still years away from being tested in cancer patients, but a recently published study in the journal Leukemia highlights their promise and the innovative methods that led to their discovery.

In previous studies, the research groups of Rice biochemist Natasha Kirienko and MD Anderson physician-scientist Marina Konopleva screened some 45,000 small-molecule compounds to find a few that targeted mitochondria. In the new study, they chose eight of the most promising compounds, identified between five and 30 closely related analogs for each and conducted tens of thousands of tests to systematically determine how toxic each analog was to leukemia cells, both when administered individually or in combination with existing chemotherapy drugs like doxorubicin.

“One of the big challenges was to establish optimal conditions and doses for testing on both cancer cells and healthy cells,” said study lead author Svetlana Panina , a researcher at the University of Texas at Austin who conducted the research during her postdoctoral studies at Rice. “The results from our previously published cytotoxicity assay were helpful, but very little is known about these small-molecule compounds. None of them had been thoroughly described in other studies, and we had to essentially start from scratch to determine how much to use, what they do in cells, everything. All the doses and treatment conditions had to be adjusted by multiple preliminary experiments.”

Scientists find trigger that sets off metastasis in pancreatic cancer

Scientists have found that cancers in the pancreas (left) readily metastasize because these tumors suppress levels of an enzyme, MSRA, that pulls oxygen atoms off amino acids called methionine. As MSRA levels decrease, methionines on proteins become more oxidized. This causes one particular protein to rev up energy production in the tumor, promoting the migration of cancer cells to other organs. Metastatic tumors on the liver (right) lead to rapid death.
Image courtesy of Christopher Chang, UC Berkeley, and Christine Chio, Columbia

Pancreatic cancer, though rare, is one of the deadliest of cancers, killing nearly 50,000 people yearly and doing so quickly, primarily because it metastasizes rapidly through the body. Barely one in 10 people survive beyond five years.

But a discovery by chemists at the University of California, Berkeley, suggests a new way to slow or stop metastatic spread of pancreatic and perhaps other cancers.

In last week’s issue of the journal Molecular Cell, Christopher Chang and his group at UC Berkeley, collaborating with Christine Chio’s team at Columbia University in New York, report that metastasis is triggered by the loss of an enzyme that repairs oxygen damage to proteins.

Without this enzyme to erase the oxidative damage, one particular protein in cancer cells goes on to rev up energy production and seed new cancers around the body. The researchers confirmed this by knocking down levels of the “eraser” enzyme in mice and in cultured mouse and human cells, or organoids. In both cases, this promoted the migration of cancer cells and metastatic spread.

Shining some light on the obscure proteome

Group Leader in Chemical Proteomics, Dr. Guillaume Médard, and his research group in the lab.
 Credit: Uli Benz / TUM

Mass-spectrometry based proteomics is the big-data science of proteins that allows to monitor the abundances of thousands of proteins in a sample at once. It is therefore a particularly well suited readout to discover which proteins are targeted by any small molecule. An international research team has investigated this using chemical proteomics.

Histone deacetylase (HDAC) inhibitors are a class of drugs used in oncology. An international research team involving scientists at the Technical University of Munich (TUM), Cornell University in Ithaca (USA), the German Cancer Research Center (DKFZ) in Heidelberg and Martin Luther University of Halle-Wittenberg has now investigated the effects of some HDAC drugs in more detail. The scientists wanted to know whether those epidrugs engage proteins other than the HDACs which they are designed to inhibit.

“To do so, target deconvolution by chemical proteomics is the method of choice. Hence, we first made new chemical tools - the so called affinity matrices - that would allow us to systematically profile the HDACs,” explains Dr. Guillaume Médard, group leader for chemical proteomics at the TUM chair of Proteomics and Bioanalytics led by Prof. Bernhard Küster.

“I profiled 53 drugs”, details Severin Lechner, doctoral candidate at the TUM School of Life Sciences. “Most of them, but not all, hit their intended HDAC target. However there were some surprises. Drugs used in hundreds of scientific studies were not as selective as assumed. Many had additional targets that were not previously known.

Small molecules transport iron in mice, and human cells to treat some forms of anemia

University of Illinois chemistry professor Martin D. Burke and graduate student Stella Ekaputri were part of a team that found a small molecule, hinokitiol, ferries iron out of liver cells lacking the protein that normally does the job and restores hemoglobin and red blood cell production.   
Photo Credit: Michelle Hassel

A natural small molecule derived from a cypress tree can transport iron in live mice and human cells lacking the protein that normally does the job, easing a buildup of iron in the liver and restoring hemoglobin and red blood cell production, a new study found.

Stemming from a collaboration between researchers at the University of Illinois Urbana Champaign, the University of Michigan, Ann Arbor and the University of Modena in Italy, the study demonstrated that the small molecule hinokitiol potentially could function as a “molecular prosthetic” when the iron-transporting protein ferroportin is missing or defective, offering a potential treatment path for ferroportin disease and certain kinds of anemia.

“This is a really striking demonstration in a whole animal model that an imperfect mimic of a missing protein can reestablish physiology, acting as a prosthesis on a molecular scale,” said study co-leader Dr. Martin D. Burke, a professor of chemistry at Illinois and a member of the Carle Illinois College of Medicine, as well as a medical doctor. “The implications are really quite broad with respect to other diseases caused by loss of protein function.”

Ferroportin is a protein that forms a channel for transporting iron in and out of cells. Ferroportin deficiency can be due to a genetic mutation or caused by inflammation or infection. Patients without the protein have an excess buildup of iron in the liver, spleen and bone marrow, particularly in a type of cell called a macrophage. Macrophages in the liver chew up old red blood cells and transport the iron in them for recycling into new red blood cells. However, without ferroportin, the iron builds up inside the cells and can’t be recycled, Burke said.

Research Finds Repurposed Drug Inhibits Enzyme Related to COVID-19

With the end of the pandemic seemingly nowhere in sight, scientists are still very focused on finding new or alternative drugs to treat and stop the spread of COVID-19. In a first-of-its-kind study, researchers at the University of New Hampshire have found that using an already existing drug compound in a new way, known as drug repurposing, could be successful in blocking the activity of a key enzyme of the coronavirus, or SARS-CoV-2, which causes COVID-19.

“The goal was to slow or prevent the spread of the virus by using a strategic therapeutic that could possibly disrupt key steps in the viral life cycle at the molecular level, like the first contact with a healthy cell or the first step in replicating within an infected cell,” said Harish Vashisth, associate professor of chemical engineering.

In their study, recently published in the journal PROTEINS: Structure, Function, and Bioinformatics, researchers set out to target a key enzyme responsible for COVID-19, called the main protease enzyme Mpro, which has become a primary target of intense research and therapeutic development because it is essential for the virus to replicate. In this case, they explored the inhibiting properties of a derivative of the potent chemical compound known as Thiadiazolidinones, or TDZD, which are already being studied as a potential treatment for neurological disorders like Parkinson’s Disease. Researchers used a specific TDZD compound, known as CCG-50014, to target Mpro which acts like a molecular scissor by cutting up long chains of polypeptide proteins of the virus into smaller component proteins. These smaller segments can fold and mature to form new virus particles. Using molecular dynamics simulations combined with laboratory experiments, the researchers determined that TDZD compound was able to inhibit the Mpro enzyme.

New model offers potential solutions for next-generation battery challenges

A new mathematical model has brought together the physics and chemistry of highly promising lithium-metal batteries, providing researchers with plausible, fresh solutions to a problem known to cause degradation and failure.

A new study by Stanford University researchers lights a path forward for building better, safer lithium-metal batteries.

Close cousins of the rechargeable lithium-ion cells widely used in portable electronics and electric cars; lithium-metal batteries hold tremendous promise as next-generation energy storage devices. Compared to lithium-ion devices, lithium-metal batteries hold more energy, charge up faster, and weigh considerably less.

To date, though, the commercial use of rechargeable lithium-metal batteries has been limited. A chief reason is the formation of “dendrites” – thin, metallic, tree-like structures that grow as lithium metal accumulates on electrodes inside the battery. These dendrites degrade battery performance and ultimately lead to failure which, in some instances, can even dangerously ignite fires.

The new study approached this dendrite problem from a theoretical perspective. As described in the paper, published in the Journal of The Electrochemical Society, Stanford researchers developed a mathematical model that brings together the physics and chemistry involved in dendrite formation.

This model offered the insight that swapping in new electrolytes – the medium through which lithium ions travel between the two electrodes inside a battery – with certain properties could slow or even outright stop dendrite growth.

Chemists Created a Sensor that Accurately Detects the Saliva pH Level

Timofey Moseev has been engaged in research work since 2015.
Credit: Regina Pidgaetskaya

Chemists at UrFU have created a sensor for determining the pH of human saliva. This is a fluorophore with strong and stable emission, which picks up the smallest fluctuations in the pH in biological fluids (tenths). The analysis is performed using microdoses of the substance and a spectrometer, in which the substance is irradiated with a special lamp (its lifetime is tens of thousands of hours). The pH data appears in 5-7 seconds. The first results of joint studies of saliva samples and the sensor, conducted by scientific groups of the Department of Organic and Biomolecular Chemistry and the Department of Analytical Chemistry of the Institute of Chemical Engineering, are described in the famous Dyes and Pigments journal.

"Modern fluorometric pH sensors are based on small organic molecules. Typically, they are very sensitive and are able to detect the desired analyte in very low concentrations, up to nanoconcentrations. Our sensor is based on a new compound. We introduced a fluorinated fragment, and this allowed us to get the photophysical and electrochemical properties we needed," explains Timofey Moseev, an engineer-researcher at the Department of Organic and Biomolecular Chemistry at UrFU.

Saliva pH analysis is an accessible and non-invasive method of clinical diagnosis. With its help at an early stage, you can detect diseases, in particular gastrointestinal diseases: gastritis, stomach ulcers, duodenitis, etc. The pH level also affects the teeth: even a slight increase in the acidity of saliva can cause tooth decay and other problems.

Real-time Imaging of Dynamic Atom-atom Interactions

In a breakthrough, Tokyo Tech researchers have managed to observe and characterize dynamic assembly of metallic atoms using an ingenious combination of scanning transmission electron microscopy and video-based tracking. By visualizing short-lived molecules, such as metallic dimers and trimers, that cannot be observed using traditional methods, the researchers open up the possibility of observing more such dynamic structures predicted by simulations.

Chemistry is the study of bond formation (or dissociation) between atoms. The knowledge of how chemical bonds form is, in fact, fundamental to not just all of chemistry but also fields like materials science. However, traditional chemistry has been largely limited to the study of stable compounds. The study of dynamic assembly between atoms during a chemical reaction has received little attention. With recent advances in computational chemistry, however, dynamic, short-lived structures are gaining importance. Experimental observation and characterization of dynamic bonding predicted between atoms, such as the formation of metallic dimers, could open up new research frontiers in chemistry and materials science.

However, observing this bond dynamics also requires the development of a new methodology. This is because conventional characterization techniques only provide time-averaged structural information and are, thus, inadequate for observing the bonds as they are formed.