Tag: tuberculosis

X-Rays Shed Light on Possible New Treatments for TB

X-Rays Shed Light on Possible New Treatments for TB

SCIENTIFIC ACHIEVEMENT

X-ray diffraction data, collected at the Advanced Light Source (ALS) and other Department of Energy light sources, revealed the crystal structure of CMX410, a new compound that targets a key enzyme (Pks13) in the cell membrane of the bacterium responsible for tuberculosis (TB).

SIGNIFICANCE AND IMPACT

CMX410 is a promising new candidate to treat TB, including multidrug-resistant strains.

New treatments needed to tackle an old foe

TB is a deadly infectious disease caused by the bacterium Mycobacterium tuberculosis (Mtb). According to the World Health Organization, an estimated 10.8 million people contracted TB globally in 2023, and 1.25 million died from the disease. While antibiotics are effective for drug-sensitive TB cases, multidrug-resistant Mtb strains can evade common drug therapies.

Drug-resistant cases require a regimen that is often more expensive, toxic, and time-intensive. Patients are required to take six or more medications daily for up to 20 months. New approaches are urgently needed to shorten the course of drug interventions and address widespread multidrug-resistant strains.

A multi-institutional study led by researchers at Texas A&M University and the Calibr-Skaggs Institute for Innovative Medicine sought to find new treatments to address multidrug-resistant TB. The team screened a library of 406 compounds that belong to an active class of molecules [i.e., sulfur fluoride exchange (SuFEx)] to evaluate their efficacy against Mtb. The team developed one promising compound into CMX410, which targets Pks13, an enzyme essential for microbial cell wall biosynthesis.

Read more on the ALS website

Image: A cross-section of the crystal structure for the enzyme Pks13 (the surface colored pink and blue by hydrophobicity) as it interacts with CMX410 (shown as stick-like structure), a new drug candidate for TB

Credit: ALS

Toxic behaviour: why do tuberculosis bacteria poison themselves?

Toxic behaviour: why do tuberculosis bacteria poison themselves?

Tuberculosis bacteria halt their growth with self-toxins that could inspire novel therapeutics

Stealthy bacteria slow down their division when they invade the body to avoid drawing the immune system’s attention. Mycobacterium tuberculosis, the world’s leading bacterial infectious killer, takes a seemingly counterintuitive approach to that end. M. tuberculosis expresses self-toxins that damage its DNA and shut down growth as well as antitoxins to later help recuperate and resume proliferation. By studying these toxin-antitoxin pairs, Durham University microbiologist Professor Tim Blower aims to find ways to mimic the self-toxins with new therapeutics

By conducting X-ray crystallography at Diamond’s I04 beamline, Blower and his colleagues uncovered the structure of toxin-antitoxin complexes, providing insight into how they regulate DNA damaging activity. The findings reveal that the protein pair potentially form two types of complexes. A grouping of two toxins and four antitoxins dominated at body temperature, whereas an equal pairing of two and two were more common in colder conditions, which may reflect how the proteins come together when bacteria live in the environment. These findings change our perspective on how the toxins and antitoxins operate, bringing researchers closer to designing new drugs against a pandemic microbe that continuously evolves resistance to existing antibiotics. 

Each year, Mycobacterium tuberculosis leads approximately 10 million people to endure a bloody cough, exhaustion, and fever, and it causes over one million deaths. Doctors typically prescribe patients a course of four to six antibiotics to clear the infection, but the bacteria evolve mechanisms to resist the effects of the drugs. As many as 2.5 percent of tuberculosis patients carry variants of the bacteria resistant to the four most common first-line antibiotics, and that proportion is expected to climb if researchers don’t develop other therapeutics that could kill resistant strains.    

Poison control

Blower and the team from Durham University and Newcastle University study mechanisms the bacteria use to limit their own growth in pursuit of inspiration for new drug candidates. Specifically, they focus on an enzyme that controls DNA organisation in the cell and a pair of toxins and antitoxins that regulate this enzyme’s function. 

Bacteria and eukaryotes (for instance, humans), organise DNA in the cell differently. Eukaryotic DNA is tightly packaged in the nucleus by histone proteins that wind it up into compact chromosomes. Bacteria, on the other hand, lack histones and rely on DNA to undergo a process called supercoiling. Like how a wound-up rubber band contracts into a small volume, bacterial DNA winds up into a condensed coil to save space. However, supercoiled DNA needs constant maintenance, which involves occasional unwinding and rewinding of the molecules. To this end, an essential enzyme called DNA gyrase cuts the DNA, allows it to untwist, and glues the cut ends back together again, so they can coil again. 

Repairing the DNA breaks is essential to the bacteria’s survival because it avoids the build-up of harmful DNA damage and mutations, but sometimes M. tuberculosis interferes with the process. It achieves this using a toxin-antitoxin system that inhibits DNA gyrase. Scientists are still uncertain about the biological role of the toxin, Blower said, but one hypothesis is that by partially shutting down bacterial growth, it prevents antibiotics that target growth machinery from working. Another is that the toxin helps quiescent bacteria evade immune detection as slow-growing microbes tend to slip under the radar. The antitoxin relieves the bacteria, allowing those that survived the accumulation of DNA breaks to seal them back together and resume growth when conditions in the body become favourable. 

Researchers developing new therapeutics are drawn to these systems. Suggesting scientists could develop copycat drugs, Professor Blower said: 

If these toxins are so effective at killing, then we should take advice from nature and work out how they work.

Read more on Diamond website

Double X-ray vision helps tuberculosis and osteoporosis research

Double X-ray vision helps tuberculosis and osteoporosis research

Combination measurement shows distribution of metals in biological samples

With an advanced X-ray combination technique, scientists have traced nanocarriers for tuberculosis drugs within cells with very high precision. The method combines two sophisticated scanning X-ray measurements and can locate minute amounts of various metals in biological samples at very high resolution, as a team around DESY scientist Karolina Stachnik reports in the journal Scientific Reports. To illustrate its versatility, the researchers have also used the combination method to map the calcium content in human bone, an analysis that can benefit osteoporosis research.“Metals play key roles in numerous biological processes, from the oxygen transport in our red blood cells and the mineralisation of bones to the detrimental accumulation of metals in nerve cells as seen in diseases like Alzheimer’s,” explains Stachnik who works in the Center for Free-Electron Laser Science CFEL at DESY. High-energy X-rays make metals light up in fluorescence, a method that is very sensitive even to tiny amounts. “However, the X-ray fluorescence measurements usually do not show the ultrastructure of a cell, for example,” says DESY scientist Alke Meents who led the research. “If you want to exactly locate the metals within your sample, you have to combine the measurements with an imaging technique.” The ultrastructure comprises the details of the cell morphology that are not visible under an optical microscope.

>Read More on the DESY Website

Image: Two agglomerates of antibiotic-loaded iron nanocontainers (red) in a macrophage. Credit: Stachnik et al., „Scientific Reports“, CC BY 4.0

Enzyme structure of bacteria that causes tuberculosis

Enzyme structure of bacteria that causes tuberculosis

Results on its interaction with antibiotics may lead to the development of new forms of treatment for this disease.

Tuberculosis is a chronic infection usually caused by a bacterium called Mycobacterium tuberculosis. This bacterium infects cells of the immune system called alveolar macrophages, which are responsible for removing pollutants and microorganisms from the surface of the alveoli, where the exchange of gases occurs during respiration.
It is estimated that approximately two billion people worldwide are infected with M. tuberculosis without symptoms. However, the clinical manifestations of the disease may appear at any time in life, especially when the immune system is weakened, such as due to malnutrition or diseases such as cancer and AIDS.
Tuberculosis is considered a curable disease when the patient is diagnosed and treated promptly with antibiotics. Nevertheless, the chronicity of this infection makes it difficult to eradicate bacteria altogether. Generally, patients must take the medication for several months, making it harder for them to persist in the treatment and favoring the emergence of antibiotic-resistant bacteria. In recent years, the emergence of new bacteria, resistant to routine treatments, has been a worldwide concern and it is imperative to seek new therapeutic strategies against this disease.

>Read more on the Brazilian Synchrotron Light Laboratory (LNLS) 

Image: (extract, full image here) Elements of the secondary structure of L,D-transpeptidase-3 from Mycobacterium tuberculosis acylated by an acetyl fragment derived from faropenem. Beta sheets in red, α-helices in yellow and the loops are shown in green. The figure shows, at the amino terminus (N-ter), the bacterial domain similar to immunoglobulin (BIg) and in the carboxy terminus the catalytic domain (CD). B-loop is a unique structure of this enzyme when compared to the other M. tuberculosis L,D-transpeptidases. In blue is shown an acetyl fragment covalently attached to cysteine 246 at the active site of the enzyme. Figure taken with Pymol.

UBC scientists break down tuberculosis structure

UBC scientists break down tuberculosis structure

Scientists from the University of British Columbia have taken a crucial step towards starving out tuberculosis, following research into how the infection grows in the body.

Tuberculosis, a bacterial infection which generally affects the lungs, is a global threat; worldwide, it kills more people than HIV and malaria combined. In Canada, there are around 1,600 new cases of tuberculosis reported every year, with about 20 per cent of those cases affecting First Nations peoples, according to the Government of Canada. Researchers using the Canadian Light Source have investigated how the bacteria grow in lungs in an effort to better understand how tuberculosis can be treated.

Lindsay Eltis, a UBC professor of Microbiology and Immunology and Canada Research Chair in Microbial Catabolism and Biocatalysis, has spent the last 25 years studying bacteria and determining how they grow on different compounds. In 2007, Eltis’ group discovered that tuberculosis bacteria grow on cholesterol and that this is important for causing disease.

“Many bacteria, like humans, grow using glucose, a type of sugar. They derive energy from it, converting it to water and carbon dioxide, and use it to make building blocks essential to life. The tuberculosis bacterium is a bit unusual in that it can grow on cholesterol, deriving energy and essential building blocks from it,” explains Eltis. “This ability to grow on cholesterol helps the bacterium establish infection in our lungs.”

>Read more on the Canadian Light Source website

Image: Crystal structure of the newly imaged carbon-ring cleaving enzyme from the tuberculosis bacterium, IpdABMtb.
Credit: Lindsay Eltis