Developing new drugs to battle resurgence of malaria

With a warming climate comes the threat of expanding habitats for mosquitos that carry malaria, but researchers are using sophisticated synchrotron techniques in the quest for new treatments for the deadly disease.

While most cases of Malaria occur in sub-Saharan Africa, Central and South America, and Southeast Asia, “mosquito areas are spreading,” explained Dr. Oluwatoyin Asojo, adjunct professor of biochemistry and cell biology at The Geisel School of Medicine at Dartmouth College in Lebanon, New Hampshire. Warmer temperatures are helping the mosquitos return to breeding grounds “in places where we haven’t seen it (malaria) since the early part of the 20th century,” like North America and parts of Europe.

According to the World Health Organization’s most recent World Malaria Report, there were 262 million cases of the disease worldwide in 2023 and 597,000 deaths. Almost all the deaths occurred in Africa.

Given the risk of new malaria spread and growing drug resistance to conventional quinine-based therapeutics, new options are needed “so we’ll have an arsenal of tools ready,” she said. Asojo is part of an international team of scientists and students using the Canadian Light Source (CLS) at the University of Saskatchewan to study treatments targeting the malaria-causing parasite Plasmodium vivax (P. vivax). The challenge with P. vivax is that it can remain dormant in the human liver for years or even decades, then enter the blood and cause symptoms.

The team recently found a compound (IMP-1088) that binds in the parasite with an enzyme called N-myristoyltransferase or NMT, which also occurs naturally in humans. This binding inhibits all stages thus disrupting P. vivax’s lifecycle.

Read more on CLS website

Discovery paves way for next-generation medications

As the problem of antibiotic resistance continues to grow, we need new drugs that the bad bacteria in our bodies don’t already know how to avoid. New research by scientists at McGill University represents a major step forward in our ability to develop medicines whose effectiveness will endure in the battle against infections.

The study, published in the prestigious journal Nature, has revealed how molecular machinery inside nature’s microbes builds antibiotics. Researchers have been working on this problem for decades, and this new insight represents a major step forward in our ability to create new drugs and medicines.

Scientists Angelos Pistofidis and Martin Schmeing used the Canadian Light Source (CLS) at the University of Saskatchewan to take groundbreaking pictures of the molecular machinery’s crystal structure.

The molecular machines that Pistofidis and Schmeing studied are called nonribosomal peptide synthetases, or NRPSs. They build some of the most important compounds in current health care and environmental treatments, including antibiotics, anti-cancer agents, and immunosuppressants.

“They have an immense number of applications,” says Pistofidis. “For example, the peptide cyclosporin has been used many, many times as an immunosuppressant for organ transplant operations.”

The breakthrough in their project was capturing images of the NRPS during a key step in the process of building antibiotics. Previously, they had identified the steps involved in NRPS’s production process, but the details were hazy. The synchrotron played a key role in their work.

“The CLS is a world-class establishment. You can very rapidly and very efficiently collect data. It made the whole experience of collecting data on a very complex crystal, like the one that we presented in the paper, quite efficient,” says Schmeing.

Getting the NRPS machine to pause at this step took Pistofidis four years of work, while Schmeing has been working on uncovering the details of this whole process for 15 years.

Read more on CLS website

Tracking the ‘medication taxis’

A team of researchers has been using the X-ray source PETRA III to visualise the spread of an anticancer drug in tumor cells

How can cancer drugs be delivered safely to their destination? An international team of researchers has been using the X-ray source PETRA III to test a technique for visualising how a drug is distributed inside tumor cells. In the future, this approach could help to develop more targeted and hence more effective cancer therapies. The working group has presented its findings in the journal Advanced Functional Materials.

Some anticancer drugs present a special challenge. They do not dissolve easily in the blood or they break down too quickly and because of this they are unable to reach the site where they are needed: the tumor. Researchers have come up with an ingenious strategy to overcome this: they enclose the drug in a molecular capsule. On being administered, this medication taxi makes its way through the body. Once it reaches the tumor, the capsule dissolves and releases the drug.

The only trouble is that it is difficult to observe how well this strategy is working. How do the drug capsules find their way into the tumor cells? And do they actually release the drug inside them? To answer these questions, researchers have until now had to label the drugs using special dyes. When a laser beam is shone at these, they light up like signal lamps and reveal the distribution of the drug inside a cell.

This method has its drawbacks, however. The markers are usually similar in size to the drug molecules themselves, and this can distort the readings. “It’s as if you were trying to track a fish through the ocean by fitting it with a transmitter that is as big as the creature itself,” explains Marvin Skiba, a PhD student in Wolfgang Parak’s group at the University of Hamburg’s Centre for Hybrid Nanostructures. “In that case, it’s doubtful whether the fish would move around in the same way as it would without the transmitter.” It would be helpful, therefore, to have a way of seeing the drug inside the medication taxi without having to label it with a dye.

One promising approach is X-ray fluorescence, a technique that can detect minute traces of a chemical element. The principle is straightforward. “When an X-ray beam strikes a sample, it excites the elements in it,” explains DESY physicist Gerald Falkenberg. “The excited atoms want to shed this energy quickly by emitting X-ray quanta. We use detectors to capture these quanta.”

The crucial point is that every element emits a different “X-ray colour”, thereby leaving its own distinctive fingerprint. The X-ray beam scans the sample line by line, creating a map of the elements. This requires a very powerful, narrow X-ray beam, such as the one generated by DESY’s X-ray source PETRA III at beamline P06.

To determine the suitability of this method for studying drugs transported in medication taxis, Skiba and Falkenberg’s team focused on a compound containing the element selenium, a potential therapeutic for treating tumors. “We enclosed the compound in a variety of different microparticles,” explains Marvin Skiba. “We then injected these into a cell culture and used X-rays to track how the selenium was distributed in the cells.”

Read more om DESY website

Image: Depending on the route of administration, the intracellular distribution of the selenium-based drug changes. When non-biodegradable polymers are used as the building blocks of the capsules, the selenium remains in the container and is not released (upper picture). The situation is different when amino acid and sugar-based vehicles are used which are digested by the cell and result in intracellular redistribution of the drug (lower picture). Cells are shown in grey while selenium is pseudocoloured from blue to yellow, depending on the concentration.

Credit: DESY, Marvin Skiba

European XFEL elicits secrets from an important nanogel

An international team led by Felix Lehmkühler from Deutsches Elektronen-Synchrotron DESY in Hamburg has investigated the temperature induced swelling and collapsing of the polymer poly-N-isopropylacrylamide (PNIPAm) at European XFEL at Schenefeld near Hamburg. Due to its dynamic changes, PNIPAm is used in medicine, e.g. for drug delivery, tissue engineering or sensorics.

PNIPAm is typically dissolved in water. Above a certain temperature, the so-called lower critical solution temperature (LCST), which is around 32 °C, it changes from a hydrophilic, water-loving state to a hydrophobic, water-repellent state. As consequence, nanogel particles, as investigated by Lehmkühler and co-workers, rapidly change their size above that temperature by expelling water.

This feature is useful for a variety of applications, including the controlled release of drugs in a patient’s body, as a model system for proteins and in tissue engineering, the cultivation of organic tissue for medical applications, or as bio-compatible temperature sensors. However, it was very difficult so far to watch these rapid phase transitions experimentally, and therefore to optimize them for different applications. Therefore, the precise characterisation of the kinetics of the changes of the PNIPAm polymer with temperature is still a lively research topic.

Read more on XFEL website

Image: Felix Lehmkühler at the instrument MID (Materials Imaging & Dynamics) of European XFEL where the experiments were done.

Credit: European XFEL

Tiny Chip-Based Device Performs Ultrafast Manipulation of X-Rays

Researchers from the U.S. Department of Energy’s Advanced Photon Source (APS) and Center for Nanoscale Materials at Argonne National Laboratory have developed and demonstrated new x-ray optics that can be used to harness extremely fast pulses in a package that is significantly smaller and lighter than conventional devices used to manipulate x-rays. The new optics are based on microscopic chip-based devices known as microelectromechanical systems (MEMS).

“Our new ultrafast optics-on-a-chip is poised to enable x-ray research and applications that could have a broad impact on understanding fast-evolving chemical, material and biological processes,” said research team leader Jin Wang from the X-ray Science Division Time Resolved Research (TRR) Group at the APS. “This could aid in the development of more efficient solar cells and batteries, advanced computer storage materials and devices, and more effective drugs for fighting diseases.”

In new results published in The Optical Society OSA) journal Optics Express, the researchers demonstrated their new x-ray optics-on-a-chip device (Fig. 1), which measures about 250 micrometers and weighs just 3 micrograms, using the TRR Group’s 7-ID-C x-ray beamline at the APS. The tiny device performed 100 to 1,000 times faster than conventional x-ray optics, which that tend to be bulky.

Read more on the APS website

Image: Fig. 1. The photograph shows two MEMS elements on a single chip (A), with the active elements of 250 µm × 250 µm, and the micrograph (B) highlighting the size of the diffractive element, as compared to a section of human hair (C).

New substance library to accelerate the search for active compounds

In order to accelerate the systematic development of drugs, the MX team at the Helmholtz-Zentrum Berlin (HZB) and the Drug Design Group at the University of Marburg have established a new substance library. It consists of 1103 organic molecules that could be used as building blocks for new drugs. The MX team has now validated this library in collaboration with the FragMAX group at MAX IV. The substance library of the HZB is available for research worldwide and also plays a role in the search for substances active against SARS-CoV-2.

For drugs to be effective, they usually have to dock to proteins in the organism. Like a key in a lock, part of the drug molecule must fit into recesses or cavities of the target protein. For several years now, the team of the Macromolecular Crystallography Department (MX) at HZB headed by Dr. Manfred Weiss together with the Drug Design Group headed by Prof. Gerhard Klebe (University of Marburg) has therefore been working on building up what are known as fragment libraries. These consist of small organic molecules (fragments) with which the functionally important cavities on the surface of proteins can be probed and mapped. Protein crystals are saturated with the fragments and then analysed using powerful X-ray light. This allows three-dimensional structural information to be obtained at levels of atomic resolution. Among other things, it is possible to find out how well a specific molecule fragment docks to the target protein. The development of these substance libraries took place as part of the joint Frag4Lead research project and was funded by the German Federal Ministry of Education and Research (BMBF).

Read more on the BESSY II website

Image : For the study, the enzyme endothiapepsin (grey) was combined with molecules from the fragment library. The analysis shows that numerous substances are able to dock to the enzyme (blue and orange molecules). Every substance found is a potential starting point for the development of larger molecules. 

Credit: Wollenhaupt/HZB

A polymer coating makes Metal Organic Frameworks better at delivering drugs

Researchers use Synchrotron InfraRed microspectroscopy to study the dynamics of drug release from MOFs

How to efficiently deliver targeted, controlled and time-released doses of drugs is a significant challenge for biomedicine. Finding solutions to this challenge would result in substantial benefits for patients, including more effective drug therapy and fewer undesirable side effects. The porous nature of metal-organic frameworks (MOFs) makes them attractive candidates for drug-delivery systems as they can be tailored to hold and transport a variety of encapsulated guest molecules. To this end, employing MOFs as a drug delivery vehicle could offer potential solutions to accomplish the targeted and controlled release of anti-cancer drugs. However, understanding the precise chemical and physical transformations that MOFs undergo as these guest molecules are released is challenging. In work recently published in ACS Applied Materials & Interfacesresearchers from the University of Oxford, University of Turin, and Diamond Light Source used a combination of experimental and theoretical techniques to address this problem. They show how the combination of hydrophilic MOF-encapsulated drug with a hydrophobic polymeric matrix is a highly promising strategy to tune the drug release rate for optimal delivery. Their results demonstrate that high-resolution synchrotron InfraRed microspectroscopy is a powerful in situ technique for tracking the local chemical and physical transformations, revealing the dynamics underpinning the controlled release of drug molecules bound to the MOF pores.  

Read more on Diamond Light Source website

Image: Using synchrotron infrared radiation to track the drug release process from MOF/Polymer composites.

Understanding how the taxanes antitumoral drugs modulate cell microtubules

Researchers have found that addition of paclitaxel (a type of antitumoral drug) to microtubules alters their structure. This compound modulates the material properties of microtubules by converting destabilized growing microtubule ends into regions resistant to depolymerisation, eventually leading to cell death. Results were obtained at the NCD beamline of the ALBA Synchrotron.

Paclitaxel, one of the most commonly used antitumoural drugs, modulates microtubules, the biopolymers responsible for many essential cellular functions including cell division, movement and intracellular transport. This kind of drugs target tubulin subunits, the main microtubule proteins, and interfere with their dynamics, which can have the effect of stopping a cell cycle and can lead to programmed cell death or apoptosis.

Read more on the ALBA website 

Image: Microtubule X-ray fiber difractogram in presence of Paclitaxel.

Credit: NCD-SWEET beamline at ALBA Synchrotron

ALS reveals vulnerability in cancer-causing protein

A promising anticancer drug, AMG 510, was developed by Amgen with the help of novel structural insights gained from protein structures solved at the Advanced Light Source (ALS).

Mutations in a signaling protein, KRAS, are known to drive many human cancers. One specific KRAS mutation, KRAS(G12C), accounts for approximately 13% of non-small cell lung cancers, 3% to 5% of colorectal cancers, and 1% to 2% of numerous other solid tumors. Approximately 30,000 patients are diagnosed each year in the United States with KRAS(G12C)-driven cancers.

Despite their cancer-triggering significance, KRAS proteins have for decades resisted attempts to target their activity, leading many to regard these proteins as “undruggable.” Recently, however, a team led by researchers from Amgen identified a small molecule capable of inhibiting the activity of KRAS(G12C) and driving anti-tumor immunity. Protein crystallography studies at the ALS provided crucial information about the structural interactions between the potential drug molecule and KRAS(G12C).

>Read more on the Advanced Light Source website

Image: A structural map of KRAS(G12C), showing the AMG 510 molecule in the binding pocket. The yellow region depicts where AMG 510 covalently attaches to the KRAS protein.
Credit: Amgen

The mechanism of the most commonly used antimalarial drugs unveiled

For centuries, quinoline has been an effective compound in antimalarial drugs, although no one knew its mode of action in vivo.

Today, a team led by the Weizmann Institute has discovered its mechanism in infected red blood cells in near-native conditions, by using the ESRF, Alba Synchrotron and BESSY. They publish their results in PNAS.

Malaria remains one of the biggest killers in low-income countries. Estimates of the number of deaths each year range from 450,000 to 720,000, with the majority of deaths happening in Africa. In the last two decades, the malaria parasite has evolved into drug-resistant strains. “Recently, the increasing geographical spread of the species, as well as resistant strains has concerned the scientific community, and in order to improve antimalarial drugs we need to know how they work precisely”, explains Sergey Kapishnikov, from the University of Copenhagen, in Denmark, and the Weizmann Institute, in Israel, and leader of the study.

Plasmodium parasite, when infecting a human, invades a red blood cell, where it ingests hemoglobin to grow and multiply. Hemoglobin releases then iron-containing heme molecules, which are toxic to the parasite. However, these molecules crystallise into hemozoin, a disposal product formed from the digestion of blood by the parasite that makes the molecules inert. For the parasite to survive, the rate at which the heme molecules are liberated must be slower or the same as the rate of hemozoin crystallization. Otherwise there would be an accumulation of the toxic heme within the parasite.

>Read more on the ESRF website

Image (taken from BESSY II article): The image shows details such as the vacuole of the parasites (colored in blue and green) inside an infected blood cell.
Credit:
S. Kapishnikov

Two other institutes, BESSY II at HZB and ALBA Synchrotron, have participated in this research. Please find here their published articles:

> X-ray microscopy at BESSY II reveal how antimalaria-drugs might work

> The mechanism of the most commonly used antimlalarial drugs in near- native conditions unveiled

Analyzing poppies to make better drugs

A team of researchers from the University of Calgary has uncovered new information about a class of plant enzymes that could have implications for the pharmaceutical industry. In a paper published in the Journal of Biological Chemistry, the scientists explain how they revealed molecular details of an enzyme class that is central to the synthesis of many widely used pharmaceuticals, including the painkillers codeine and morphine.  

The team used the Canadian Light Source at the University of Saskatchewan and the SLAC National Accelerator Laboratory to better understand how the enzyme behaves, which is crucial for unleashing its potential to make novel medicines. “Until this study, we didn’t know the key structural details of the enzyme. We learned from the structure of the enzyme bound to the product how the methylation reaction locks the product into a certain stereochemistry. It was completely unknown how the enzyme did that before we determined this structure,” corresponding author Dr. Kenneth Ng explained.

Stereochemistry is an important concept when it comes to safety and efficacy in drug design. A molecule can have a few different arrangements—similar to how your left hand is a mirror image of your right hand. These arrangements can lead to very different effects.

>Read more on the Canadian Light Source website

Image: group photo of some of the researchers involved with this project. From left to right: Ken Ng (Professor and corresponding author), Jeremy Morris (PhD graduate and second author), Dean Lang (PhD student and first author), and Peter Facchini (Professor, CSO of Willow Biosciences and senior author).

A new generation of anti-malaria drugs


Malaria is endemic to large areas of Africa, Asia and South America and annually kills more than 400,000 people, a majority of whom are children under age 5, with hundreds of millions of new infections every year. Although artemisinin-based drug combinations are available to treat malaria, reports from Southeast Asia of treatment failures are raising concerns about drug resistance spreading to Africa. Fortunately, there is hope on the horizon because there are several new antimalarial drug candidates undergoing clinical testing as well as other promising drug targets that are under investigation.
An international research team has for the first time determined the atomic structure of a protein kinase called PKG in Plasmodium parasites that cause malaria—a finding that potentially will help create a new generation of anti-malarial drugs and advance fundamental research. PKG[i] plays essential roles in the developmental stages of the parasite’s complex life cycle, so understanding its structure is key to developing malaria-fighting therapies that specifically target PKG and not other human enzymes, according to researcher Dr. Charles Calmettes.

>Read more on the Canadian Light Source website

Image: PKG crystal.

Preventing tumour metastasis

Researchers at the Paul Scherrer Institute, together with colleagues from the pharmaceutical company F. Hoffmann-La Roche AG, have taken an important step towards the development of an agent against the metastasis of certain cancers.

Using the Swiss Light Source, they deciphered the structure of a receptor that plays a crucial role in the migration of cancer cells. This makes it possible to identify agents that could prevent the spread of certain cancer cells via the body’s lymphatic system. The researchers have now published their results in the journal Cell.
When cancer cells spread in the body, secondary tumours, called metastases, can develop. These are responsible for around 90 percent of deaths in cancer patients. An important pathway for spreading the cancer cells is through the lymphatic system, which, like the system of blood vessels, runs through the entire body and connects lymph nodes to each other. In the migration of white blood cells through this system, for example to coordinate the defense against pathogens, one special membrane protein, the chemokine receptor 7 (CCR7) plays an important role. It sits in the shell of the cells, the cell membrane, in such a way that it can receive external signals and relay them to the interior. Within the framework of a joint project with the pharmaceutical company F. Hoffmann-La Roche AG (Roche), researchers at the Paul Scherrer Institute (PSI) have for the first time been able to decipher the structure of CCR7 and lay the foundation for the development of a drug that could prevent metastasis in certain prevalent cancer types, such as colorectal cancer.

Read more on the SLS at PSI website

Image: Steffen Brünle (right) and Jörg Standfuss at the apparatus they use to separate proteins from each other. For their study, the researchers modified insect cells to produce a human protein. To extract this from the cell, the cell was destroyed, and then the protein, whose structure the researchers have now elucidated, was separated with the help of this apparatus.
Credit: Paul Scherrer Institute/Markus Fischer

Collaboration develops sensitive data protocol

MAX IV pairs up with Sprint Bioscience, a listed drug development company, in a new project to improve how companies can benefit from new, faster X-ray fragment screening experiments, while still protecting their valuable information during analysis at FragMAX.

Recently, the project was granted with 500 000 SEK from Sweden’s innovation agency Vinnova.
More or less, all pharmaceutical drugs are molecules binding to proteins in your body. When doing this, they either initiate or inhibit the process in which the target protein is involved. Proteins are in charge of everything from cells dividing at the right moment to the metabolism of the food you eat or signaling in the brain.

>Read more on the MAX IV website

Image: Sample holders
Credit: Ben Libberton

New approach for solving protein structures from tiny crystals

Technique opens door for studies of countless hard-to-crystallize proteins involved in health and disease

Using x-rays to reveal the atomic-scale 3-D structures of proteins has led to countless advances in understanding how these molecules work in bacteria, viruses, plants, and humans—and has guided the development of precision drugs to combat diseases such as cancer and AIDS. But many proteins can’t be grown into crystals large enough for their atomic arrangements to be deciphered. To tackle this challenge, scientists at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory and colleagues at Columbia University have developed a new approach for solving protein structures from tiny crystals.

The method relies on unique sample-handling, signal-extraction, and data-assembly approaches, and a beamline capable of focusing intense x-rays at Brookhaven’s National Synchrotron Light Source II (NSLS-II)—a DOE Office of Science user facility—to a millionth-of-a-meter spot, about one-fiftieth the width of a human hair.

>Read more on the NSLS-II at Brookhaven Lab website

Image: Wuxian Shi, Martin Fuchs, Sean McSweeney, Babak Andi, and Qun Liu at the FMX beamline at Brookhaven Lab’s National Synchrotron Light Source II, which was used to determine a protein structure from thousands of tiny crystals.

Researchers create the first maps of two melatonin receptors essential for sleep

A better understanding of how these receptors work could enable scientists to design better therapeutics for sleep disorders, cancer and Type 2 diabetes.

An international team of researchers used an X-ray laser at the Department of Energy’s SLAC National Accelerator Laboratory to create the first detailed maps of two melatonin receptors that tell our bodies when to go to sleep or wake up, and guide other biological processes. A better understanding of how they work could enable researchers to design better drugs to combat sleep disorders, cancer and Type 2 diabetes. Their findings were published in two papers today in Nature.

The team, led by the University of Southern California, used X-rays from SLAC’s Linac Coherent Light Source (LCLS) to map the receptors, MT1 and MT2, bound to four different compounds that activate them: an insomnia drug, a drug that mixes melatonin with the antidepressant serotonin, and two melatonin analogs.

>Read more on the LCLS at SLAC website

Image: The researchers showed that both melatonin receptors contain narrow channels embedded in the cell’s fatty membranes. These channels only allow melatonin, which can exist happily in both water and fat, to pass through, preventing serotonin, which has a similar structure but is only happy in watery environments, from binding to the receptor. They also uncovered how some much larger compounds only target MT1 despite the structural similarities between the two receptors.
Credit: Greg Stewart/SLAC National Accelerator Laboratory