New antibiotic could make food safer and cows healthier

The antibiotic nisin occurs naturally in milk, a product of bacteria resident in the cow's udder. It helps keep milk from spoiling and kills a broad spectrum of bacteria that cause food-borne illness, most notably listeria and clostridium. It was approved as a food additive in 1969, and since then has become prevalent in the food industry in more than 50 countries.

"It's good to know that there are natural products added to our food that protect us from diseases," said lead researcher Wilfred van der Donk, a chemistry professor at Illinois. "Many people probably don't even realize that, or think it's some kind of a non-natural chemical. Last summer we had the listeria outbreak, and that's a good example of people dying from pathogens in food. You don't hear of such outbreaks often, and that's in part because of the compounds that are added to food to kill the pathogens."

Nisin also shows promise as a treatment for bovine mastitis, an infection in cows that costs the dairy industry billions each year since milk produced during and shortly after antibiotic treatment has to be thrown out. Since nisin already is present in low levels in milk, farmers using nisin to treat mastitis may not need to discard milk or meat from recently treated animals.

However, for all its utility, nisin has drawbacks. It's produced in an acidic environment, but it becomes unstable at the neutral pH levels needed for many foods or pharmaceuticals. It also becomes unstable at higher temperatures, limiting its uses.

While studying the genome of another bacterium that lives at high temperatures, van der Donk's group found genes to make a molecule with a similar structure and function to nisin, known as an analog. They isolated the genes and inserted them into E. coli so they could produce the new antibiotic, dubbed geobacillin, in large enough quantities to study its structure and function.

"As it turns out, geobacillin is more stable, both in respect to pH and temperature," van der Donk said. "We think this is good news for potential use of geobacillin in food."

Nisin, and presumably geobacillin, work by binding to a molecule the pathogen needs to build its cell wall and then poking holes in the bacterial cell's membrane, a one-two punch that quickly kills the invader. However, the two antibiotics have slight structural differences. Nisin's structure has five looped regions, formed by cross-links in the protein chain. Geobacillin has seven loops thanks to two additional cross-links, which give the protein added stability.

The team tested geobacillin against several foodborne and disease-causing bacteria and found it similarly effective or more effective than nisin, depending on the bacteria. Most significantly, it was three times more active against the main contagious bacteria responsible for bovine mastitis. Contagious mastitis is devastating for dairy farmers, as the bacteria can quickly spread throughout a herd. In addition, since mastitis could be caused by a number of different infections, geobacillin's broad-spectrum activity makes it a very attractive treatment option.

Next, the researchers plan to test geobacillin against a wider spectrum of disease-causing bacteria. Many tests of safety, efficacy and economic production lie ahead, although geobacillin has shown great promise in tests to date. The researchers hope that its greater stability will enable medicinal applications for geobacillin that nisin could not realize, both for bovine mastitis and possibly for human disease.

"Nisin was very promising in early preclinical trials in that it was very effective in killing multidrug-resistant bacteria in mouse models," said van der Donk, "but because of its instability, it has a very short half-life in blood. So we're looking to see whether geobacillin has greater serum stability."

The researchers published their findings in the Proceedings of the National Academy of Sciences. The National Institutes of Health supported this work. Van der Donk is also a Howard Hughes Medical Investigator.

More information: The paper, "Geobacillins, lantibiotics from Geobacillus thermodenitrificans," is published in PNAS.

Provided by University of Illinois at Urbana-Champaign (news : web)

Gold nanoantennas detect proteins

 Scientists at Johannes Gutenberg University Mainz (JGU) in Germany have developed a new method of observing individual proteins. Detailed knowledge of the dynamics of proteins is necessary in order to understand the related biological processes that occur on the molecular level. To date, this information has been obtained by means of labeling proteins with fluorescent substances, but unfortunately this changes the proteins under investigation and thus influences the biological processes that are to be observed. "Our method allows live tracking of individual proteins without having to label them first," explains Professor Dr. Carsten Sönnichsen of the Institute of Physical Chemistry at JGU. "We are now gaining entirely new insights into molecular processes and can see, for example, how things are constantly in motion even on the very smallest scale."

The method developed by the group of Mainz chemists led by Carsten Sönnichsen is based on the use of gold nanoparticles. These serve as glistening nanoantennas that, when they detect individual unlabeled proteins, slightly change their frequency or, in other words, their color. These tiny color changes can be observed using the technique developed in Mainz. "This is an enormous leap forward technologically: We have managed to achieve a very high time resolution for the observation of individual molecules," says Sönnichsen. It is thus now possible to precisely observe the dynamics of a protein molecule down to the millisecond.

The opportunity to detect individual protein molecules also opens up completely new horizons. It has thus become practicable to track the fluctuation of protein population densities and observe protein adsorption processes in real time, among other things. "We can see how molecules move, how they dock at particular locations, and how they fold -- this has given us a window into the molecular world," explains Dr. Irene Ament, a member of Sönnichsen's group. This new technology may prove to be useful not only in chemistry but also in medicine and biology.

The work is an important element in research into non-equilibrium phenomena at the molecular level and thus provides a solid foundation for the planned Cluster of Excellence Molecularly Controlled Non-Equilibrium (MCNE), which has been selected to enter the final round of the Excellence Initiative by the German federal and state governments to promote top-level research at German universities. Among other sources, the project received financial support in the form of an ERC Starting Grant for the project "Single metal nanoparticles as molecular sensors" (SINGLESENS).

Story Source:

The above story is reprinted from materials provided by Universität Mainz, via AlphaGalileo.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Irene Ament, Janak Prasad, Andreas Henkel, Sebastian Schmachtel, Carsten Sönnichsen. Single Unlabeled Protein Detection on Individual Plasmonic Nanoparticles. Nano Letters, 2012; 12 (2): 1092 DOI: 10.1021/nl204496g

The computer knows its chemistry

Medicines are more and more often being developed by computer. This means chemists increasingly try out first of all on the screen something they afterwards replicate in actual practice in the laboratory. The computer acts as their playground and simulator, e.g. to find an active ingredient that binds perfectly to the specific structure of one of the body’s own proteins so it can suppress its activity, for example.

Whereas in the past chemists carried out such a computer-aided active ingredient search mainly by combing through data bases containing a limited number of candidate molecules to find which of them was most suitable, ETH Zurich researchers led by Gisbert Schneider, Professor at the Institute of Pharmaceutical Sciences, are now going one step further: they have developed a program that has memorised important rules of organic chemistry and can use it to build new active ingredient molecules from first principles. The researchers call it “de-novo design”.

Molecules never seen before

This has immensely expanded the possibilities for scientists searching for active ingredients. Practically all imaginable molecules are now available to the researchers as virtual candidate active ingredients. Schneider says, “It gives us access to molecules that no chemist has ever synthesised or seen before.”

Schneider’s computer program can assemble molecules virtually on the modular principle and can compare them with existing molecules and calculate how well they fulfil the conditions defined by the researchers. The program can also modify molecules, thus gradually improving them in a process that resembles evolution, until finally the program delivers to the user the information about an optimised candidate active ingredient. To enable it to do this, the software knows a series of basic chemical modules and almost 60 of the most important reaction steps in organic chemistry. Schneider says, “They are intentionally nowhere near all the reactions that exist. We have taught the program only the ones that are widely used by chemists and which in their experience also promise success.”

The synthesis route is also taken into account

Schneider sees a big advantage in this, since comparable computer programs developed in the past 25 years sometimes produced random molecules irrespective of whether they were synthesizable at a reasonable cost. Because Schneider’s program takes into account not only the finished molecule but also the route by which it could be synthesized in actual practice, it leads to active ingredients that really can also be prepared easily by laboratory synthesis.

The software has also passed its first practical test. Via the conventional computer-assisted method – searching in a molecule data base - Schneider’s work group found an active ingredient molecule that inhibits one of the body’s own enzymes involved in cell division. Thanks to the new software, they succeeded in finding another active ingredient with a structure completely different to the existing one. It has the same activity, but the advantage that it has not yet been patented. The aim is that one day they will be able to use this active ingredient in cancer therapy.

Also attractive for the industry

The search for active ingredients that have not yet been patented will then be an important area for the use of Schneider’s software in the future as well. It is also important to find successor substances for medicines whose patent protection has expired.

In addition the computer simulation allows not only the desired activity of a substance to be tested, against a protein for example, but also possible side-effects against other proteins. Therefore the program will simplify the search for active ingredients – for example new antibiotics – that are required to have the highest possible activity and small side-effects.

This also makes the new software extremely attractive to the pharmaceutical industry. A few companies are already using the program. ETH Zurich issues appropriate licences.

More information: Hartenfeller M, et al: DOGS: Reaction-Driven de novo Design of Bioactive Compounds. PLoS Computational Biology 2012, 8: e1002380, doi: 10.1371/journal.pcbi.1002380