Tag: antibiotic resistance

Novel antibiotic overcomes drug-resistant bacteria

Novel antibiotic overcomes drug-resistant bacteria

Antibiotics fight bacteria in different ways. Some kill bacteria by destroying their cell walls. Others bind to bacteria’s ribosomes, halting their ability to produce proteins. Over time, bacteria evolved defense mechanisms against these threats. One mechanism is a chemical modification of the ribosome that resembles a push pin on a chair, which interferes with the antibiotic’s ability to bind to its binding site. 

Recently a team of scientists synthesized an antibiotic that can engage such modified ribosomes by pushing the “push pin” out of the way, as shown by an X-ray crystallography structural study conducted at the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory. Dubbed BT-33, the novel therapeutic is active against the deadliest and most antibiotic-resistant bacteria, known collectively as ESKAPE pathogens, as well as other gram-negative bacteria, in mice. Designed to attain its binding shape prior to binding, the antibiotic can serve as a powerful model for future antibiotics.

BT-33 belongs to a class of antibiotics called lincosamides, which bind to the ribosome and halt protein production. The primary lincosamide, clindamycin, was so widely used that bacteria developed numerous defenses against them, including acquiring new genes in healthcare settings that rendered lincosamides ineffective. Nevertheless, no new lincosamide has been approved since 1970.

The scientists behind BT-33 set out to fill that void. BT-33 is the third iteration of a molecule the team reported in Nature in 2021, called iboxamycin. It was followed by cresomycin, reported in Science, in 2024. Each iteration involved structural changes to different parts of the molecule that overall improved the molecule’s ability to bind to the ribosome. Each structural change was made possible by inventing new chemical combinations that had never existed before.

Iboxamycin, the first in the series, added a new chemical group at the top end of the clindamycin molecule. That addition alone was enough to enable iboxamycin to accomplish what clindamycin could not: It overcame the defense mechanism produced by the CFR gene.

The CFR gene, first identified in 2000, encodes a protein that installed a modification on the ribosome; much like putting a push pin on a chair, the modification makes it too uncomfortable for the antibiotic to bind. The addition of the chemical group in iboxamycin that is absent from clindamycin resulted in such a strong engagement of the drug with its “chair” that the push pin got moved out of the way.

Cresomycin, the second molecule in the series, was based on a revolutionary design hypothesis called preorganization: The scientists aimed to create a molecule that adopted its shape before binding to its target. To that end, the team added a unique ten-atom ring to the bottom, giving the molecule additional rigidity. Using NMR spectroscopy, they confirmed that the molecule in solution looked exactly the same as if it were already bound to the ribosome, confirming that their design hypothesis worked.

Cresomycin proved so powerful that it overcame the resistance of the six most resistant and dangerous bacteria, collectively given the acronym ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp).

Read more on APS website

Image: Structure of BT-33 (yellow) bound to the catalytic center of the bacterial ribosome, showing the van der Waals contact of the fluorine atom (green) of BT-33 with the nucleotides of the ribosomal RNA (cyan).

How an old drug could make a comeback against antibiotic resistance

How an old drug could make a comeback against antibiotic resistance

In the quest for solutions to modern antibiotic resistance, researchers at Goethe University Hospital in Frankfurt, together with their colleagues from European Synchrotron, the ESRF (Grenoble, France) and the EMBL Heidelberg are turning back to the past—and finding hope in an old, often-overlooked drug. Using X-ray nanofluorescence at the ESRF, they have uncovered how the rarely used antibiotic nitroxoline can fight back against drug-resistant bacteria. Their findings, published in Nature Communications, could spark renewed medical interest in the forgotten drug as a potential weapon against hard-to-treat infections.

Five years ago at Goethe University Hospital in Frankfurt, a patient in the intensive care unit was battling with a stubborn urinary tract infection. Despite multiple rounds of antibiotics, nothing seemed to make a difference. Then, as a last resort, doctors turned to an old drug from the 1960s—nitroxoline, typically reserved for uncomplicated urinary tract infections (UTIs). To their surprise, it worked.

Doctor and researcher Stephan Göttig was investigating this drug. “I realised that the potential of nitroxoline is huge towards multidrug-resistant Gram-negative bacteria, so we started studying its spectrum and mechanism”, he explains.

Targeting hospital pathogens

Nitroxoline is only used in a handful of countries today, after the rise of newer antibiotics and lack of clinical research. In Germany, where Göttig and the first author of the paper, Elisabetta Cacace were based (Cacace has now moved to ETH Zurich), it is an approved drug and it is still commonly prescribed for uncomplicated UTIs. However, it is not included in the WHO’s essential medicines list nor is it FDA approved in the US. “New pharmaceutical compounds are difficult to market, so it is useful to repurpose existing antibiotics”, explains Cacace.

Göttig and Cacace investigated more than a thousand isolates of different Gram-negative bacteria that nitroxoline could potentially fight against. Gram-negative bacteria have an outer membrane that can block many antibiotics and even some immune system components. They focused on Enterobacteriaceae, a group of bacteria that includes notorious hospital pathogens such as Klebsiella pneumoniae and Escherichia coli.

Read more on ESRF website

Novel strategy to reduce antibiotic resistance in a superbug

Novel strategy to reduce antibiotic resistance in a superbug

A study, published in the cover of the April issue of Nature Chemical Biology, has designed a compound that prevents the activation of resistance in the bacterium Staphylococcus aureus. This discovery, tested in mice, is a significant advance in the fight against infections caused by this pathogen, which has a very high incidence in hospitals. The research, led by the Blas Cabrera Institute of Physical Chemistry CSIC and the University of Notre Dame (USA), used data obtained at the XALOC beamline at the ALBA Synchrotron.

Scientists from the Blas Cabrera Institute of Physical Chemistry (IQF-CSIC) and the University of Notre Dame (Indiana, USA) identified a compound that blocks the bacteria’s ability Staphylococcus aureus to survive antibiotics.

This pathogen is considered a superbugdue to its ability to develop mechanisms that allow it to evade the action of multiple antibiotics, a phenomenon known as resistance, and which makes it difficult to treat infections, ranging from skin illnesses to pneumonia and septicemia, some of them potentially letal.

In particular, strains of Staphylococcus aureus resistant to antibiotic methicillin (MRSA) are especially problematic because they have spread their resistance to a wide range of antibiotics, making them difficult to fight against, especially in hospital.

This new compound, now synthesized and named compound 4, based on benzimidazole and commonly used against gastrointestinal parasites and fungi, has been selected from among 11 million candidate molecules for its ability to block a key protein of this pathogen, called BlaR1, that triggers the mechanism that inactivates antibiotics.

The combination of compound 4 along with the antibiotics oxacillin and meropenem has been shown effective in blocking the bacteria’s resistance mechanism and ending the infection in mouse models, thus validating the potential of this novel therapeutic strategy as a model for developing similar therapies against other resistant bacteria.

A highlight of this work is the use of X-ray crystallography at the XALOC beamline at the ALBA Synchrotron. Synchrotron light enabled to determine the structure of the BlaR1 protein bound to the inhibitor compound. This structural analysis revealed that compound 4 binds to the active site of BlaR1, providing crucial information about the inhibitor’s mechanism of action and guiding the future design of targeted therapies.

Researchers have reached a preclinical stage testing compound 4, after verifying that it works in 40 strains of Staphylococcus aureus resistant on mice, where it has proven very effective. “The next step would be to move on to the clinical stage, where developments can already be made in humans and improve the pharmacokinetic properties,” explains Juan Hermoso.

Read more on ALBA website

Image: Resistant ‘Staphylococcus aureus’ causes serious hospital infections, such as sepsis.

Credit: iStock

Shaping the future of antibiotic design

Shaping the future of antibiotic design

Bacteria and fungi have been engaged in molecular warfare for millions of years. This means they have perfected ways to get past the defenses of other organisms and have also devised ways to keep them out. This arms race was revealed in 1928 when Alexander Fleming returned from his holidays to discover a petri dish of bacteria in which a fungus had started to grow and was killing the bacteria around it. He immediately realized the potential value of these antibiotic molecules to humans for curing disease. 

Now, however, our widespread use of natural antibiotics has led to the emergence of drug-resistant bacteria and an urgent need to develop some new molecular weapons of our own. With that in mind, a research group from the University of Michigan conducted a substrate-trapping study of bacterial enzymes that make an important class of antibiotics. The research provides important new information that will facilitate the design of new enzymes to make novel antibiotics that can overcome antibiotic resistance.

The group used the resources of the National Institute of General Medical Sciences and National Cancer Institute Structural Biology Facility (GM/CA) at beamlines 23-ID-B and 23-ID-D at the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory.

The research focused on bacterial thioesterase (TE) enzymes that perform a critical step in a synthetic pathway to make macrolide antibiotics such as erythromycin and pikromycin. These TE enzymes temporarily attach antibiotic precursors to a nucleophilic amino acid in the TE, check the structural integrity of the precursor substrates, and then convert them to either a) a cyclic lactone molecule via nucleophilic attack by an oxygen atom in the substrate, or to b) a linear final product via attack by a water molecule. Although the structures of five TE enzymes that generate various products have been solved, the process by which a product is cyclized or hydrolyzed is poorly understood. 

To get a clearer picture of the final step in the antibiotic synthesis process that might help researchers to understand the parameters needed to make new antibiotics, the team decided to use a technique called substrate trapping to visualize the moment of decision between cyclization and hydrolysis in different TE enzymes. They used a new substrate trapping technique that incorporates a non-natural amino acid into the active site in place of the natural serine or cysteine nucleophile. The bond attaching a substrate to serine or cysteine is unstable, but the non-natural amino acid traps the reaction intermediate as a stable amide group (see Figure). 

After testing five bacterial TE enzymes to see if they could successfully incorporate the substrate trap, two of substrate trapping proteins could be purified in sufficient amounts for further testing, one that makes erythromycin and one that makes pikromycin, both cyclic antibiotics. 

Read more on APS website

Image: Model of the thioesterase enzyme active site with the cyclic substrate (purple) snugly fitted into the catalytic site of the TE (yellow). The substrate trap is represented by the blue nitrogen atom that forms a stable bond between the enzyme and substrate, preventing the substrate from leaving the site so the reaction intermediate can be studied at the molecular level. The substrate nucleophilic oxygen atom (red) is at the left end of the substrate.

Credit: Rajani Arora and Vishakha Choudhary of the University of Michigan.

Discovery paves way for next-generation medications

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

Using PETRA III to watch the disabling of a penicillin killer

Using PETRA III to watch the disabling of a penicillin killer

Scientists observe in detail the binding and formation of covalent bonds of an inhibitor to a bacterial enzyme that disables common antibiotics

Antibiotic resistance is a major and particularly in recent years growing challenge in medicine. Scientists around the world are searching for new and efficient compounds to treat bacterial infections, especially infections caused by multi-resistant bacteria. A research collaboration of scientists from DESY, University Medical Center Eppendorf (UKE) in Hamburg and Universität Hamburg performed time-resolved diffraction experiments at PETRA III to observe at near atomic resolution and at the millisecond timescale the inhibition of a bacterial enzyme that nullifies a common class of antibiotics, the β-lactams. The results have been published in Nature Communications Chemistry.

Among antibiotics, beta-lactams are the classics. Penicillin, the first commercially produced antibiotic and the related derivatives from penicillin belong to this class of pharmaceuticals. At the beginning of the 21st century, half of the antibiotics used worldwide applied were beta-lactams. However, even since the beginning of the use of penicillin, bacteria have evolved defences against antibiotics. One of the defences is an enzyme called beta-lactamase. Like a molecular pair of scissors, beta-lactamase cuts the central ring of the beta-lactam molecule and disables its antibiotic properties – allowing the bacteria to keep living.

Worldwide and for the last 20 years scientists have been searching for a way to disable beta-lactamase in an effort to directly combat antibiotic resistance. Until now, most of the candidate beta-lactamase inhibitors that have been examined have been organic compounds that mimic penicillin, allowing the inhibitor to enter the enzyme’s active site and block it. However, today’s bacteria can potentially resist these molecules after around one or two years as well. A different avenue of research has taken to using far more basic molecules to block the active site of the enzyme.

“There are new boric acid-based beta-lactamase inhibitors, and they are really potent,” says Andreas Prester, the first author of the PETRA III study and a postdoc at UKE. “For example, boron-containing compounds and drugs were developed to be used for the treatment for multiple myeloma, a form of blood cancer.” In terms of pilot investigations and a drug re-purposing approach, the research collaboration identified the potential of boron-based compounds to inhibit beta-lactamases as well. “Since then we’ve studied these inhibitors in more detail, as well as their potential to inhibit beta-lactamses,” Prester adds.

Prester and his colleagues, Markus Perbandt from Universität Hamburg, Winfried Hinrichts, an emeritus professor from the University of Greifswald, and Christian Betzel, a professor at Universität Hamburg who led the research have been among those examining the inhibition caused by boric acid in detail. Using the European XFEL and PETRA III, they examined how the boric acid binds to the enzyme. At PETRA III, the team around DESY lead scientist Henry Chapman helped assemble an experiment at the beamline P11 using a mechanism that could show at atomic resolution, like a movie, the progress of boric acid binding, in this case, to the amino acid serine within the active site. “It’s a relatively stable bond, and the boric acid then blocks the ability of the enzyme to interact with the antibiotic,” says Prester.

Read more on DESY website

Image: Using PETRA III’s X-ray beam, the scientists were able to watch how boric acid inhibits the beta-lactamase enzyme.

Credit: Universitätsklinikum Hamburg-Eppendorf UKE, Andreas Prester

Scientists break record while battling antibiotic resistance

Scientists break record while battling antibiotic resistance

Drug-resistant diseases could cause up to 10 million deaths a year by 2050, according to the World Health Organization. Scientists used the Canadian Light Source (CLS) at the University of Saskatchewan to better understand how current antibiotics work and how we might curb bacterial resistance to these life-saving drugs.

Many new antibiotics are able to kill infection-causing bacteria by binding to these bacteria’s ribosomes, which are the essential machines that make proteins. In order to see exactly what antibiotics do at an atomic level, researchers from McGill University used the CLS to determine the physical structure of a ribosome as it interacted with one of the newest antibiotics.

To understand how some bacteria are already resistant to this new antibiotic, they also determined how the drug interacts with a key bacterial enzyme that causes the resistance. The results were recently published in Nature Communications Biology.

Visualizing the antibiotic bound to the ribosome, which is a complex with 300,000 atoms, was a feat that took the team roughly five years to complete. In the process, the scientists broke the record for the largest structure ever analyzed using the CMCF beamline at the CLS, which is the only facility of its kind in Canada. The previous record, set in 2013, was for a structure six times smaller.

Read more on the CLS website

Image: Dr Albert Berghuis

Credit: Canadian Light Source

Battling bad bugs

Battling bad bugs

Scientists fight antibiotic resistance by using synchrotron to study scab disease in potatoes.

In the ongoing war against antibiotic resistant bacteria, a change in battle tactics may prove effective for controlling a common disease of plants and potentially other toxins that affect humans and animals.

Although bacterial toxins cause serious, often deadly diseases, “bacteria aren’t trying to be nasty,” said Dr. Rod Merrill, Professor of Molecular and Cellular Biology at the University of Guelph. “They’re hungry and looking for food, and we’re often the food.” He added that 99 per cent of bacteria are helpful – like gut flora – so the battle is against the remaining one per cent.

The usual approach is to develop antibiotics “that kill the bacteria but not us, or the plant, or the animal,” stated Merrill. However, bacteria mutate quickly, as quickly as every 30 minutes, which leads to antibiotic resistance. “And unfortunately, the pipeline for new antibiotics is empty.”

The approach that Merrill and his research group are pursuing is an anti-virulence strategy – finding or designing small molecules that inhibit the tools bacteria use to colonize the host and create infection. “If we can put a lock on their weapons, they can’t get food and will move on so there’s not the same pressure to mutate. We’re going with this approach because we think it’s time to change up tactics.”

Read more on the CLS website

Image: Scabin crystals

Credit: CLS