Friday, December 12, 2025

Nitrogen Fertilizer's Secret on Proso Millet! #worldresearchawards #Anal...

After 50 Years, MIT Chemists Finally Synthesize Elusive Anti-Cancer Compound




Preliminary studies indicate that derivatives of verticillin A can kill certain types of glioma cells.

MIT chemists have, for the first time, successfully created in the laboratory a fungal molecule called verticillin A. This compound was first discovered more than 50 years ago and has been recognized for its potential as an anticancer agent.

Although verticillin A differs from some related molecules by only a small number of atoms, its complex structure made it much more challenging to synthesize than those similar compounds.

“We have a much better appreciation for how those subtle structural changes can significantly increase the synthetic challenge,” says Mohammad Movassaghi, an MIT professor of chemistry. “Now we have the technology where we can not only access them for the first time, more than 50 years after they were isolated, but also we can make many designed variants, which can enable further detailed studies.”

In experiments with human cancer cells, one modified form of verticillin A showed strong activity against a rare pediatric brain tumor known as diffuse midline glioma. The researchers caution that additional testing will be necessary before its suitability for clinical use can be determined.

A complex synthesis

Researchers first reported the isolation of verticillin A from fungi, which use it for protection against pathogens, in 1970. Verticillin A and related fungal compounds have drawn interest for their potential anticancer and antimicrobial activity, but their complexity has made them difficult to synthesize.

In 2009, Movassaghi’s lab reported the synthesis of (+)-11,11′-dideoxyverticillin A, a fungal compound similar to verticillin A. That molecule has 10 rings and eight stereogenic centers, or carbon atoms that have four different chemical groups attached to them. These groups have to be attached in a way that ensures they have the correct orientation, or stereochemistry, with respect to the rest of the molecule.

Once that synthesis was achieved, however, synthesis of verticillin A remained challenging, even though the only difference between verticillin A and (+)-11,11′-dideoxyverticillin A is the presence of two oxygen atoms.

“Those two oxygens greatly limit the window of opportunity that you have in terms of doing chemical transformations,” Movassaghi says. “It makes the compound so much more fragile, so much more sensitive, so that even though we had had years of methodological advances, the compound continued to pose a challenge for us.”

Both of the verticillin A compounds consist of two identical fragments that must be joined together to form a molecule called a dimer. To create (+)-11,11′-dideoxyverticillin A, the researchers had performed the dimerization reaction near the end of the synthesis, then added four critical carbon-sulfur bonds.

Yet when trying to synthesize verticillin A, the researchers found that waiting to add those carbon-sulfur bonds at the end did not result in the correct stereochemistry. As a result, the researchers had to rethink their approach and ended up creating a very different synthetic sequence.

“What we learned was the timing of the events is absolutely critical. We had to significantly change the order of the bond-forming events,” Movassaghi says.

The verticillin A synthesis begins with an amino acid derivative known as beta-hydroxytryptophan, and then step-by-step, the researchers add a variety of chemical functional groups, including alcohols, ketones, and amides, in a way that ensures the correct stereochemistry.

A functional group containing two carbon-sulfur bonds and a disulfide bond were introduced early on, to help control the stereochemistry of the molecule, but the sensitive disulfides had to be “masked” and protected as a pair of sulfides to prevent them from breakdown under subsequent chemical reactions. The disulfide-containing groups were then regenerated after the dimerization reaction.

“This particular dimerization really stands out in terms of the complexity of the substrates that we’re bringing together, which have such a dense array of functional groups and stereochemistry,” Movassaghi says.

The overall synthesis requires 16 steps from the beta-hydroxytryptophan starting material to verticillin A.

Killing cancer cells

Once the researchers had successfully completed the synthesis, they were also able to tweak it to generate derivates of verticillin A. Researchers at Dana-Farber then tested these compounds against several types of diffuse midline glioma (DMG), a rare brain tumor that has few treatment options.

The researchers found that the DMG cell lines most susceptible to these compounds were those that have high levels of a protein called EZHIP. This protein, which plays a role in the methylation of DNA, has been previously identified as a potential drug target for DMG.

“Identifying the potential targets of these compounds will play a critical role in further understanding their mechanism of action, and more importantly, will help optimize the compounds from the Movassaghi lab to be more target specific for novel therapy development,” Qi says.

The verticillin derivatives appear to interact with EZHIP in a way that increases DNA methylation, which induces the cancer cells to under programmed cell death. The compounds that were most successful at killing these cells were N-sulfonylated (+)-11,11′-dideoxyverticillin A and N-sulfonylated verticillin A. N-sulfonylation the addition of a functional group containing sulfur and oxygen makes the molecules more stable.

“The natural product itself is not the most potent, but it’s the natural product synthesis that brought us to a point where we can make these derivatives and study them,” Movassaghi says.

The Dana-Farber team is now working on further validating the mechanism of action of the verticillin derivatives, and they also hope to begin testing the compounds in animal models of pediatric brain cancers.

“Natural compounds have been valuable resources for drug discovery, and we will fully evaluate the therapeutic potential of these molecules by integrating our expertise in chemistry, chemical biology, cancer biology, and patient care. We have also profiled our lead molecules in more than 800 cancer cell lines, and will be able to understand their functions more broadly in other cancers,” Qi says.

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Thursday, December 11, 2025

3I/ATLAS: Cosmic Gardener or Danger? #worldresearchawards #Analyticalche...

A trio of AI methods tackles enzyme design



Naturally occurring enzymes, while powerful, catalyze only a fraction of the reactions chemists care about. That’s why scientists are eager to design new-to-nature versions that could manufacture drugs more efficiently, break down pollutants, capture carbon, or carry out entirely new forms of chemistry that biology never evolved. But doing this requires placing catalytic residues with a lot of precision something that has been extremely hard to achieve computationally.

Three new papers now report improvements to enzyme design using diffusion models, a class of generative artificial intelligence algorithms that add and then subtract noise. The models RFdiffusion2, RFdiffusion3, and Riff-Diff focus on different barriers in enzyme design but all have the same outcome: computationally generated proteins that successfully carry out reactions.

“The challenge in enzyme design is placing the groups that are going to carry out the catalysis really precisely in 3-dimensional space,” Baker says.

Earlier methods required researchers to manually specify both the identity and the sequence position of catalytic residues before the rest of the protein could be built. This manual step restricted how broadly designers could search for scaffold solutions, limiting both efficiency and creativity in the final designs, says Seth Woodbury, a graduate student in Baker’s laboratory group who worked on RFdiffusion2.

To avoid this problem, the team instead starts with a cluster of atoms arranged in the ideal shape needed for the reaction. From that, RFdiffusion2 figures out where the catalytic residue should be placed in the protein sequence, where surrounding amino acids should go, and how the backbone should bend around them.

“The more freedom that you give these networks, the more that you let them address the design problem in its purest form, the most creative and viable solutions it can come up with,” Woodbury says.

Naturally occurring enzymes, while powerful, catalyze only a fraction of the reactions chemists care about. That’s why scientists are eager to design new-to-nature versions that could manufacture drugs more efficiently, break down pollutants, capture carbon, or carry out entirely new forms of chemistry that biology never evolved. But doing this requires placing catalytic residues with a lot of precision something that has been extremely hard to achieve computationally.

Three new papers now report improvements to enzyme design using diffusion models, a class of generative artificial intelligence algorithms that add and then subtract noise. The models RFdiffusion2, RFdiffusion3, and Riff-Diff focus on different barriers in enzyme design but all have the same outcome: computationally generated proteins that successfully carry out reactions.

“The challenge in enzyme design is placing the groups that are going to carry out the catalysis really precisely in 3-dimensional space,” Baker says.

Earlier methods required researchers to manually specify both the identity and the sequence position of catalytic residues before the rest of the protein could be built. This manual step restricted how broadly designers could search for scaffold solutions, limiting both efficiency and creativity in the final designs, says Seth Woodbury, a graduate student in Baker’s laboratory group who worked on RFdiffusion2.

To avoid this problem, the team instead starts with a cluster of atoms arranged in the ideal shape needed for the reaction. From that, RFdiffusion2 figures out where the catalytic residue should be placed in the protein sequence, where surrounding amino acids should go, and how the backbone should bend around them.

“The more freedom that you give these networks, the more that you let them address the design problem in its purest form, the most creative and viable solutions it can come up with,” Woodbury says.

The researchers tested their approach by designing metallohydrolases enzymes that use a metal ion, often zinc, to help break chemical bonds. These enzymes work only if the metal is held in the right place by nearby residues, which are arranged with very precise spacing. When the designed proteins were made and tested in the lab, some of the computer-generated enzymes exhibited activity, although the turnover numbers remained lower than those of their natural counterparts.

“We were really just shocked, because on the first order that we placed and tested, we found some extremely active enzymes, some that were many orders of magnitude better than previous designs,” Woodbury says.

But the Baker lab didn’t stop with RFdiffusion2. In a second, not-yet-peer-reviewed paper, the researchers modify the method to design proteins alongside the molecules they interact with (BioRxiv 2025, DOI: 10.1101/2025.09.18.676967). The result is RFdiffusion3, which builds a protein, and any molecules it interacts with, at the atomic level rather than at the residue level. Baker says this helps avoid issues that can come when the protein is designed first, before the binding partner, such as misfit pockets, wrong orientations, or unrealistic chemistry.

Several RFdiffusion3-designed proteins have behaved as intended: some bind their ligands with the expected geometry; others recognize specific DNA shapes, and a few show catalytic activity.

“Everything is becoming more automatic, and the scope of designs goes beyond proteins and now includes RNA, DNA and the binding of small molecules,” Kendall Houk, an organic chemist at the University of California, Berkeley, who was not involved in the Baker lab’s work, says in an email to C&EN. While the success rate of the RFdiffusion2- and RFdiffusion3-designed enzymes was low, the work is an important advancement toward protein and enzyme design, he says.

The Baker lab isn’t the only team releasing new enzyme design models this month. Gustav Oberdorfer’s group at the Graz University of Technology has launched Riff-Diff, which pairs diffusion models with engineered catalytic motifs (Nature 2025, DOI: 10.1038/s41586-025-09747-9). These motifs are small structural fragments where the key catalytic residues are already arranged in the exact geometry needed for the reaction. Instead of borrowing motifs from natural enzymes, the team builds artificial versions embedded in α-helical segments, where the substrate would bind.

By temporarily placing a helix in the binding site, Oberdorfer says, Riff-Diff is forced to construct a deeper, more structured pocket. The α-helix support is then removed after enzyme generation and replaced with the intended substrate models.

“What Riff-Diff does is it breaks down the enzyme problem to a motif-scaffolding problem, because what we’ve noticed over the last couple of years is that what you really need is a pretty much perfectly preorganized active site,” Oberdorfer says.

The Graz team used Riff-Diff to generate dozens of enzyme designs for a retro-aldol reaction and for the Morita-Baylis-Hillman reaction, which requires a coordinated series of nucleophilic and proton-transfer steps. When the researchers tested these proteins in vitro, a large fraction produced detectable amounts of product and worked faster than other generated enzymes.

But none of the models is perfect, and both teams are looking to make improvements that would increase the speed and selectivity of computer-generated enzymes.

“Overall, the major limitation to all of these approaches, including Riff-Diff, is our fundamental understanding of what is truly important in the catalytic step,” Oberdorfer says.

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Wednesday, December 10, 2025

Scientists Close In on a Universal Cancer Vaccine



A new nanoparticle vaccine successfully prevented several aggressive cancers in mice, including pancreatic and melanoma.

The treatment activated strong immune memory, keeping up to 88% of vaccinated mice tumor-free and stopping cancer from spreading. By teaching the immune system to target cancer antigens, the vaccine showed long-lasting protection and broad potential.

Nanoparticle Vaccine Shows Strong Cancer Prevention in Mice

A research team at the University of Massachusetts Amherst has shown that a nanoparticle-based vaccine can successfully prevent melanoma, pancreatic cancer, and triple-negative breast cancer in mice. Depending on the cancer type, as many as 88 percent of vaccinated mice remained free of tumors (depending on the cancer), and the approach reduced and in some instances entirely blocked the spread of cancer in the body.

“By engineering these nanoparticles to activate the immune system via multi-pathway activation that combines with cancer-specific antigens, we can prevent tumor growth with remarkable survival rates,” says Prabhani Atukorale, assistant professor of biomedical engineering in the Riccio College of Engineering at UMass Amherst and corresponding author on the paper.

Atukorale’s earlier work found that her nanoparticle-based drug design could shrink or eliminate existing tumors in mice. The new results reveal that the same technology also works as a preventative strategy.

Testing the Vaccine With Melanoma Antigens

In the first phase of the study, the researchers paired the nanoparticle platform with well-known melanoma peptides (called an antigen, similar to how a flu shot typically contains parts of the inactivated flu virus). This combination activated T cells, which were then primed to recognize and destroy melanoma cells. Three weeks after vaccination, the mice were challenged with melanoma.

Eighty percent of the mice given this “super adjuvant” nanoparticle vaccine remained tumor-free and survived for the entire 250-day study. Every mouse that received a traditional vaccine, a non-nanoparticle formulation, or no vaccine at all developed tumors, and none lived beyond 35 days.

The vaccine also prevented melanoma from spreading to the lungs. When the mice were systemically exposed to melanoma cells in a way that mimics metastasis, none of the nanoparticle-vaccinated mice formed lung tumors, while all other mice did.

“Metastases across the board is the highest hurdle for cancer,” says Atukorale. “The vast majority of tumor mortality is still due to metastases, and it almost trumps us working in difficult-to-reach cancers, such as melanoma and pancreatic cancer.”

Long-Lasting Immune Memory Across the Body

Atukorale refers to this protection as “memory immunity.” “That is a real advantage of immunotherapy, because memory is not only sustained locally,” she says. “We have memory systemically, which is very important. The immune system spans the entire geography of the body.”

The first round of testing used antigens designed specifically for melanoma. Developing customized antigens for every cancer type, however, often requires whole-genome sequencing or advanced bioinformatics. To address this challenge, the researchers conducted a second experiment using killed cancer cells from the tumor itself, known as tumor lysate. Mice vaccinated with this nanoparticle lysate formulation were then exposed to melanoma, pancreatic ductal adenocarcinoma or triple-negative breast cancer cells.

High Tumor Rejection Rates Across Multiple Cancers

The results were striking. Tumor rejection was seen in 88 percent of pancreatic cancer cases, 75 percent of breast cancer cases, and 69 percent of melanoma cases. Every vaccinated mouse that remained tumor-free also resisted metastasis when later exposed systemically to cancer cells.

“The tumor-specific T-cell responses that we are able to generate that is really the key behind the survival benefit,” says Griffin Kane, postdoctoral research associate at UMass Amherst and first author on the paper. “There is really intense immune activation when you treat innate immune cells with this formulation, which triggers these cells to present antigens and prime tumor-killing T cells.”

How the Nanoparticle Vaccine Creates a Strong Immune Response

This powerful T-cell activation is possible because of the unique nanoparticle structure used in the vaccine.

Vaccines regardless the target disease include two main components: the antigen and the adjuvant. The antigen represents the part of the pathogen (in this study, cancer cells) that teaches the immune system what to attack. The adjuvant stimulates the immune system so that it recognizes the antigen as a threat and mounts a strong response.

The Atukorale Lab designs its vaccines to mimic how pathogens naturally alert the immune system. Effective immune activation requires several “danger” signals working through different pathways. “In recent years, we have come to understand how important the selection of the adjuvant is because it drives the second signal that is needed for the correct priming of T and B cells,” says Atukorale.

Many promising adjuvants used in cancer immunotherapy do not combine well at the molecular level, similar to how oil and water separate. To address this limitation, the team created a lipid nanoparticle “super adjuvant” that can encapsulate and deliver two different immune-stimulating ingredients in a stable and coordinated way.

Toward a Broad Cancer Vaccine Platform

The researchers believe this nanoparticle system offers a flexible platform that could be adapted to many cancer types.

They also see potential for both treatment and prevention, especially for people who face a high risk of developing cancer. This concept became the foundation for a startup launched by Atukorale and Kane, called NanoVax Therapeutics.

“The real core technology that our company has been founded on is this nanoparticle and this treatment approach,” says Kane. “This is a platform that Prabhani developed. The startup lets us pursue these translational efforts with the ultimate goal of improving patients’ lives.”

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Unveiling Late Cretaceous Secrets! #worldresearchawards #Analyticalchemi...

Tuesday, December 9, 2025

The Global Importance of Analytical Chemistry in Modern Society

Analytical chemistry plays a vital role in shaping the modern world by enabling the precise detection, identification, and quantification of chemical substances across countless sectors. From ensuring the purity and safety of medicines to monitoring environmental pollution, analytical methods protect public health and support sustainable development. Industries like food and agriculture rely on analytical tools to detect contaminants, verify nutritional content, and maintain strict quality standards. In energy and materials research, analytical techniques help develop advanced batteries, catalysts, and nanomaterials by revealing their structural and chemical properties. Even in forensic science, analytical chemistry provides the evidence required to solve crimes through techniques such as chromatography, spectroscopy, and DNA analysis. As new challenges emerge in climate change, clean energy, and global health, analytical chemistry continues to evolve with more sensitive, accurate, and rapid technologies making it an indispensable science that underpins innovation, safety, and progress worldwide.

1. Analytical Chemistry in Healthcare: Ensuring Safer Medicines

Analytical chemistry is essential in pharmaceutical development, helping scientists verify drug purity, determine dosage accuracy, and detect impurities. Techniques like HPLC, mass spectrometry, and spectroscopy ensure that medicines are both effective and safe for global populations.

2. Environmental Monitoring: Analytical Tools for a Cleaner Planet

Analytical methods play a crucial role in tracking air, water, and soil pollutants. Instruments such as ICP-MS, gas chromatography, and portable sensors help identify toxins, assess contamination levels, and support environmental protection policies worldwide.

3. Food Safety and Quality Control: Chemistry Behind What We Eat

From pesticides and heavy metals to preservatives and adulterants, analytical chemistry detects harmful substances in food products. It also ensures compliance with global standards, maintaining quality throughout the agricultural and food-processing industries.

4. Forensic Chemistry: Uncovering Truth Through Scientific Evidence

Analytical chemistry supports forensic investigations through drug analysis, poison detection, explosive residue testing, and DNA profiling. These methods provide accurate, court-admissible evidence that strengthens criminal justice systems.

5. Advancing Energy Technologies: Analytical Methods in Battery and Fuel Research

Characterizing materials used in batteries, solar cells, and hydrogen technologies relies heavily on analytical chemistry. Techniques like XRD, SEM-EDS, electrochemical analysis, and FTIR help optimize energy storage and conversion materials.

6. Industrial Manufacturing: Quality Assurance Through Chemical Analysis

From polymers to petrochemicals, analytical chemistry ensures product consistency and safety. Spectroscopic and chromatographic techniques help detect defects, validate raw materials, and improve process control in manufacturing.

7. Nanotechnology and Advanced Materials: Precision at the Nanoscale

Analytical chemistry supports nanomaterial development by providing detailed structural, morphological, and chemical data. Techniques such as TEM, AFM, XPS, and Raman spectroscopy reveal critical nanoscale properties that drive innovation.

8. Clinical Diagnostics: Chemistry Behind Modern Medical Testing

Blood tests, metabolic panels, enzyme assays, and biomarker analysis depend on analytical chemistry. These methods help diagnose diseases, monitor treatments, and personalize patient care.

9. Water Quality Assessment: Protecting Global Water Resources

Analytical chemistry identifies pollutants like heavy metals, microbes, microplastics, and organic contaminants in freshwater and oceans. This ensures safe drinking water and supports environmental sustainability.

10. Space Exploration and Planetary Science: Analyzing the Unknown

Analytical chemistry instruments on spacecraft (e.g., mass spectrometers, laser spectrometers, X-ray analyzers) help study extraterrestrial rocks, soils, and atmospheres advancing our understanding of planets, asteroids, and the potential for life beyond Earth.

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