New rules point scientists toward next-gen germ-killers | Science News for Students

New rules point scientists toward next-gen germ-killers

Chemists uncover the tricks compounds use to move inside many bacteria
Jun 9, 2017 — 7:10 am EST
antibiotic protein

Chemists tweaked the structure of an antibiotic (mostly green and white). The new compound can travel into the cell through a channel (brown) on the cell surface.

M. F. Richter et al./Nature 2017

Like fortress walls, the membranes that encase bacteria are hard to breach. Not many chemical compounds can break through these defenses to do battle with these germs. But some compounds do. By analyzing them, researchers now know what it takes. Drug developers might want to use the newfound rules to develop more and better antibiotics to treat bacterial infections.

Escherichia coli is one bacterium that belongs to a type known as gram negative. (They got their name because they don’t turn purple when exposed to a violet dye used for what is known as “gram staining.”) These bacteria have two membranes. These barriers control which chemicals enter and exit the germs.

Not all germs are dangerous. But doctors often prescribe antibiotic medicines for pathogens, which are germs that cause disease. Alas, most antibiotics can’t get inside of the outer of a gram negative’s two membranes, notes Paul Hergenrother. He’s a chemical biologist at the University of Illinois at Urbana-Champaign. And many drugs that have killed gram-negative bacteria in the past no longer can be counted on to do so. The reason: These germs have evolved traits that allow them to resist — ignore — the drug’s ability to poison them.

The World Health Organization is part of the United Nations. It has been encouraging scientists to develop alternative drugs. In February it released a list of pathogens that not only are resistant to multiple drugs but also that threaten human health. Many bacteria on that list are gram negatives.

To develop new drugs against these germs, researchers would like to understand exactly how successful drugs cross into these one-celled microbes. In the past, researchers have studied how a bacterium’s outer barrier — cell membrane — works, explains Kim Lewis. He’s a microbiologist at Northeastern University in Boston and wasn’t involved in the new study.

With the growing problem of drug-resistant bacteria, Hergenrother and his team decided to go about developing germ killers differently. Explains Lewis: They decided to attack the problem by asking what allows those chemicals to cross through the barrier. That approach pointed them to little channels, or pores, that cut through the cell walls. The term for these little pores: Porins

The Illinois scientists shared what they learned online May 10 in Nature.

Developing some ‘rules’

The outer membrane of gram-negative cells is dotted with proteins. These are those channel-like porins. They allow nutrients to pass through and feed the bacteria. However, Hergenrother’s team found, those porins also can allow drugs to enter the pathogens.

The Illinois researchers investigated what allows chemicals to enter cells through those porins. To test this, they built 100 different compounds. Each mimicked some natural chemical that is able to kill bacteria. Then the researchers mixed each compound in a test tube for 10 minutes with a lot of E. coli. Afterward, they measured how much of each compound had snuck into the cells.

A dozen of the novel chemicals succeeded and began accumulating in the germs. What feature did they have in common? All contained an amine (AA-meen) group, a collection of atoms that contains the element nitrogen.

Next, the team collected a larger set of compounds. All contained amine groups. Each was tested in a similar setup to what had been used with the novel compounds. Afterward, the scientists measured whether these new chemicals penetrated the E. coli and collected inside them. Such a buildup is a sign the compound might also work as a drug.

With these data, the researchers turned to a computer model to learn more. They asked it to probe other features of a chemical’s structure or recipe that appear to have helped it get into cells. This analysis showed that stiff, flat molecules seemed to work better than flexible, round ones. That makes sense, notes Hergenrother. It’s harder to put a basketball through a narrow opening than to slide a ruler through it.

From this, the researchers developed a set of rules on how compounds penetrate gram-negative bacteria. To then test those rules, the researchers turned to a natural antibiotic. It has a tongue-twister name: deoxynybomycin (De-OX-ee-ny-boh-MY-sin). This drug works on only the gram-positive bacteria.

Unlike the gram negatives, these germs have just one cellular membrane. Deoxynybomycin is flat and rigid. So it already had the right shape to slip through a porin, notes Hergenrother. By adding an amine group to the drug, the team thought it could make it kill gram-negative bacteria, too.

And it worked.

The researchers tested this new compound against gram-negative pathogens that are resistant to many germ-killing drugs. The altered drug successfully killed all but one of them.

These new findings could help researchers convert other antibiotics that work against gram-positive drugs into ones that also can quash gram-negative germs, Hergenrother predicts.

Power Words

(for more about Power Words, click here)

antibiotic     A germ-killing substance, usually prescribed as a medicine (or sometimes as a feed additive to promote the growth of livestock). It does not work against viruses.

atom     The basic unit of a chemical element. Atoms are made up of a dense nucleus that contains positively charged protons and uncharged neutrons. The nucleus is orbited by a cloud of negatively charged electrons.

bacteria     ( singular: bacterium ) Single-celled organisms. These dwell nearly everywhere on Earth, from the bottom of the sea to inside other living organisms (such as plants and animals).

bacterial     Having to do with bacteria, single-celled organisms. These dwell nearly everywhere on Earth, from the bottom of the sea to inside animals.

cell     The smallest structural and functional unit of an organism. Typically too small to see with the unaided eye, it consists of a watery fluid surrounded by a membrane or wall. Depending on their size, animals are made of anywhere from thousands to trillions of cells. Most organisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell.

cell membrane     A structure that separates the inside of a cell from the outside of it. Some particles are permitted to pass through the membrane.

chemical     A substance formed from two or more atoms that unite (bond) in a fixed proportion and structure. For example, water is a chemical made when two hydrogen atoms bond to one oxygen atom. Its chemical formula is H2O. Chemical also can be an adjective to describe properties of materials that are the result of various reactions between different compounds.

compound     (often used as a synonym for chemical) A compound is a substance formed when two or more chemical elements unite (bond) in fixed proportions. For example, water is a compound made of two hydrogen atoms bonded to one oxygen atom. Its chemical symbol is H2O.

computer model     A program that runs on a computer that creates a model, or simulation, of a real-world feature, phenomenon or event.

defense     (in biology) A natural protective action taken or chemical response that occurs when a species confront predators or agents that might harm it. (adj. defensive)

E. coli     (short for Escherichia coli) A common bacterium that researchers often harness to study genetics. Some naturally occurring strains of this microbe cause disease, but many others do not.

element     (in chemistry) Each of more than one hundred substances for which the smallest unit of each is a single atom. Examples include hydrogen, oxygen, carbon, lithium and uranium.

fat     A natural oily or greasy substance occurring in plants and in animal bodies, especially when deposited as a layer under the skin or around certain organs. Fat’s primary role is as an energy reserve. Fat also is a vital nutrient, though it can be harmful if consumed in excessive amounts.

germ     Any one-celled microorganism, such as a bacterium or fungal species, or a virus particle. Some germs cause disease. Others can promote the health of more complex organisms, including birds and mammals. The health effects of most germs, however, remain unknown.

infection     A disease that can spread from one organism to another. It’s usually caused by some type of germ.

LED     Electronic components that, as their name suggests, emit light when electricity flows through them. LEDs are very energy-efficient and often can be very bright. They have lately been replacing conventional lights for home and commercial lamps.

membrane     A barrier which blocks the passage (or flow through of) some materials depending on their size or other features. Membranes are an integral part of filtration systems. Many serve that same function as the outer covering of cells or organs of a body.

microbe     Short for microorganism. A living thing that is too small to see with the unaided eye, including bacteria, some fungi and many other organisms such as amoebas. Most consist of a single cell.

molecule     An electrically neutral group of atoms that represents the smallest possible amount of a chemical compound. Molecules can be made of single types of atoms or of different types. For example, the oxygen in the air is made of two oxygen atoms (O2), but water is made of two hydrogen atoms and one oxygen atom (H2O).

nitrogen     A colorless, odorless and nonreactive gaseous element that forms about 78 percent of Earth's atmosphere. Its scientific symbol is N. Nitrogen is released in the form of nitrogen oxides as fossil fuels burn.

nutrient     A vitamin, mineral, fat, carbohydrate or protein that a plant, animal or other organism requires as part of its food in order to survive.

pathogen     An organism that causes disease.

pore     A tiny hole in a surface. On the skin, substances such as oil, water and sweat pass through these openings.

protein     A compound made from one or more long chains of amino acids. Proteins are an essential part of all living organisms. They form the basis of living cells, muscle and tissues; they also do the work inside of cells. Among the better-known, stand-alone proteins are the hemoglobin (in blood) and the antibodies (also in blood) that attempt to fight infections. Medicines frequently work by latching onto proteins.

quash     To completely suppress, destroy, neutralize or extinguish.

trait     A characteristic feature of something. (in genetics) A quality or characteristic that can be inherited.

World Health Organization     An agency of the United Nations, established in 1948, to promote health and to control communicable diseases. It is based in Geneva, Switzerland. The United Nations relies on the WHO for providing international leadership on global health matters. This organization also helps shape the research agenda for health issues and sets standards for pollutants and other things that could pose a risk to health. WHO also regularly reviews data to set policies for maintaining health and a healthy environment.

NGSS: 

  • MS-LS1-1
  • MS-LS2-2
  • MS-ETS1-2
  • HS-LS2-2
  • HS-ETS1-4

Citation

Journal:​ ​​ M. Richter et al. Predictive compound accumulation rules yield a broad-spectrum antibioticNature. Published online May 10, 2017. doi:10.1038/nature22308.