DNA coding molecular banks: Molecules that bind to disease-related proteins can be rapidly screened.

On the second floor of a mud-and-mud building in Waltham, Mass., a plastic box in a laboratory refrigerator contains numerous chemical molecules.
these molecules are DNA-labeled molecules synthesized by GlaxoSmithKline , a trillion - 10 times the number of stars in the Milky Way.
major pharmaceutical companies and bioengineering companies are using this DNA-coded molecular pool to quickly screen molecules that bind to disease-related proteins, especially those that are currently difficult to target.
this screening method is faster and cheaper than traditional screening methods.
basic scientists can also use this method to explore basic biological problems and study enzymes, receptors, and cell pathways.
the drug's development is often the first step: researchers synthesize a large number of chemical molecules and then test their binding effect on the target protein.
the target protein sinned in each hole in the porous plate, and then a variety of drug molecules to be added to detect their effect on protein vitality.
this method, known as high-throughput screening (HTS), uses machines to automatically test millions of chemical molecules, but still takes time and costs, and doesn't necessarily work.
over the past few years, drug chemists have increased the success rate of drug development by marking chemical molecules with DNA to form a two-dimensional code of molecules.
these DNA-coded molecular banks have many advantages: first, the researchers do not have to test each molecule individually;
once a molecule binds to the target protein, it is easily recognizable -- because it can be detected in a two-dimensional code of DNA.
the concept of a DNA-coded molecular library first proposed in 1992 by Sydney Brenner, a molecular biologist at the Scripps Research Institute, and Richard Lerner, a chemist.
since then, the DNA-coding molecular library has evolved rapidly.
2007, GSK acquired a company that led the DNA label molecular library research station for $55 million.
Novartis in Basel, Switzerland, and Roche have also established an in-house DNA label molecular library research project.
emerging biotech companies, including X-Chem in Waltham, Vipergen in Copenhagen, Ensemble Pharmaceuticals in Cambridge and Philochem in Switzerland, are also working with academia and industry to use the technology.
": "It is now understood that the DNA coding molecular library is not a fad, but an achievable one.
" says Robert Goodnow, executive director of the Chemical Innovation Center at Boston-based AstraZeneca, one of X-Chem's partners.
DNA-coding molecular library will not replace high-throughput screening: companies have invested heavily in high-throughput screening because some compounds cannot be synthesized using DNA coding techniques.
but the DNA coding molecular library provides a quick, effective, low-cost complementary solution to help find molecules bound to new or challenging target proteins.
, for example, look for ubiquitin connecting enzymes, binding molecules that connect ubiquitin molecules to target proteins and can be targeted for cancer treatment.
is that GSK currently has the world's largest dna coding molecular library: GSK's high-throughput screening library has 2 million molecules, while the DNA-coded molecular library has 1 trillion molecules, 500,000 times the high-throughput screening library.
there are several ways to build a DNA coding library: the largest molecular libraries, such as GSK, use DNA logging.
first synthesize chemical building blocks, such as amino acids, amines, and pyrethic acids, and then chemically add different DNA QR codes to them.
added a second construction module to the mixture to form new small molecules and extend the DNA label.
by connecting four building blocks, chemists can create drug molecules.
the number of potential combinations is huge because there are thousands of building modules.
, chemists have to test each compound individually than traditional high-throughput screening, and THE DNA coding library is easier to maintain and use.
DNA coding library can be stored in a single test tube, while high-throughput screening requires a robot to place each molecule in a single test tube.
But GSK's manager, Chris Arico-Muendel, says the biggest advantage of a DNA coding library is the number of molecules that can be synthesized.
GSK uses DNA coding libraries and high flux screening seisy as often or more frequently for new or difficult target proteins.
, the most advanced compound gSK has synthesized so far using DNA coding technology is GSK2256294, which effectively blocks cycloxidase, an enzyme involved in fat decomposition.
the drug is a collaboration between Praecis and GSK, and its effectiveness in the treatment of diabetes, wound healing and chronic obstructive pulmonary disease will be further evaluated through Phase 1 clinical safety trials.
Arico-Muendel said they were pleased that GSK's DNA coding library was going so well.
the DNA coding library expands as the number of chemical building blocks increases and the connection methods increase. Richard Wagner, chief executive of
X-Chem, believes that in the near future, DNA coding libraries will not only become larger, but also enter the clinic more quickly.
traditional drug screening, drug chemists sometimes spend years adjusting the structure of compounds to make them more specific, powerful and safe.
Wagner says traditional sieve is just a probability game.
by contrast, the large size of the gene-coding library means that some compounds are more easily clinically available by probability.
Although these compounds still need to be optimized, they are closer to the ideal molecule and need to be adjusted at a smaller margin.
X-Chem's DNA coding library has 120 billion compounds and has begun to practice.
just over a year later, they screened out the most advanced candidate drug, an autotaxin inhibitor that blocks the conversion of one phospholipid into another. X-Rx, a subsidiary of
X-Chem, now plans to begin clinical trials of fibrosis drugs in 2017.
industry is increasingly interested in X-Chem's DNA coding molecular library: over the past five years, the company has signed partnerships with several pharmaceutical giants, including Roche, AstraZeneca, Bayer, Johnson and Johnson, Pfizer and Sanofi, as well as with several bioengineering companies and academic laboratories.
custom-synthetic other biological companies use another method to synthesize the molecular library.
they use not only DNA tags to label molecules, but also DNA tags as synthetic templates.
David Liu, a chemist at Harvard University, and his students developed a DNA template that produces a library of ring molecules.
ring molecules are larger and more stable, and can bind to target molecules at multiple sites, enhancing the specificity of binding reactions.
both gSK and X-Chem have a large library of DNA-coded ring molecules.
) Liu first produces a single-stranded DNA template that contains sequences that complement the DNA labels of the chemical building blocks.
then add dna-labeled chemical building blocks to the chemical reaction container, relying on DNA base pairing, allowing the DNA tags of each building block to bind to the DNA template.
final response is to connect the various chemical building blocks into rings, producing ring molecules and a long-chain DNA label.
building a DNA template library requires a lot of work, as researchers have to design templates for each molecule and DNA labels for thousands of chemical building blocks.
, the dna template method produces a smaller molecular library than the DNA recording method, but still far greater than the high-throughput screening library, and has other advantages.
in the DNA template, scientists knew from the beginning which molecules were eventually synthesized, and they could purify the molecular library and remove those wrongly labeled molecules.
this increases the success rate of sieve drugs.
by contrast, the huge DNA-recorded molecular library may still contain faulty compounds.
in case the wrong-labeled molecule binds to the target protein, researchers will need to waste a lot of time on error correction.
Liu's molecular library contains 14,000 molecules and has had some success.
2014, his team reported that they had discovered a stable, specific insulin-degrading enzyme (IDE, IDE- linked to type 2 diabetes) small molecule inhibitors, after researchers spent decades searching and designing IDEs.
Liu et al. began studying the role of IDEs in health and disease, helping to find other IDE inhibitors.
are now working to convert small molecule inhibitors into clinical drugs.
Liu also screened more than 100 target protein inhibitors. most of these proteins
are in urgent need of small molecule inhibitors to facilitate research in related fields.
"I didn't expect that the first-generation molecular library would still bring us so many scientific discoveries today, seven years later.
we've done a lot with screening inhibitors.
So far, we've found a very large number of molecular inhibitors, so much so that we can't study them all. "Despite this, Liu has worked tirelessly to develop a second-generation DNA template molecular library of 256,000 ring molecules.

Liu founded Ensemble Therapeutics in 2004, and the company's molecular library now has 10 million molecules.
company focuses on finding inhibitors of immunoodot protein, which regulate the immune system and ubiquitin-linked enzymes.
he also authorized Novartis to develop a drug targeting the inflammatory-related protein leukocyte interleukin-17.
rapid screening Once the molecular bank is successful, the search for the target protein binding molecule begins.
most researchers rely on "affinity screening" to find these compounds.
to do this, they label the target protein and use the purification label to extract the protein that combines the molecule.
the final step is to read THE DNA label and identify the small molecules that bind to the protein. One advantage of
this approach is that you only need a small amount of target protein to get results.
in one project, Arico-Muendel wanted to look for an unstable, rarely acquired binding molecule of protein. "After putting the protein on dry ice overnight, we quickly completed the screening process,"
said.
and we've found some molecules that bind to the protein.
" high-throughput screening is not possible with such experiments.
because of the high-throughput screening, the target protein must be stable and sufficient, and the target protein must be added to the target protein in the thousands of holes at the beginning of the experiment.
but affinity screening also has its drawbacks.
bulky DNA labels sometimes hinder molecule interaction with target proteins, so some effective molecules may be omitted.
But because the DNA coding library is so large, researchers are usually less concerned about these losses.
the bigger problem is that small molecules and labels can be combined to the purification column, resulting in false positive rates.
purification labels also affect the structure of the target protein, introducing data errors.
several research groups have found a solution.
Vipergen, a biotech company with a 50 million molecular DNA template library, uses "adhesive traps" to solve the problem. Nils Hansen, chief executive of
Vipergen, says you can freeze your protein, a molecular library mixture, and cut into very small ice cubes.
if the ice cubes are small enough, each ice cube contains only one target protein.
at this scale, even if not purified, the proportion of small molecules bound to the target protein increases.
Vipergen completes screening in water and oil emulsions, and the same effect is achieved.
at this point, the effect of tiny droplets is equivalent to Xiaoice block. "It's cool!"
Hansen lamented. "Currently, THE DNA-coding molecular library is best suited for screening for water-soluble, free-floating proteins.
but many important drug targets are embedded in cell surfaces, making it impossible to use traditional affinity screening methods.
for example, about 40 percent of the targets of certified drugs are G-protein coupling receptors that feel extracellular stimulation on the cell membrane.
Goodnow points out that membrane-binding protein screening techniques are evolving, "but they are still not perfect."
one solution is to mix the dna-coded molecular banks with the complete cells of the overexpression membrane binding protein targets.
small molecules can bind to the target protein on the cell surface.
, the researchers then washed away the molecules that had not been combined, heated the cells, read the DNA labels, and identified the effective small molecules.
GSK has used this method to identify a receptor , a potent inhibitor that plays an important role in schizophrenia and central nervous system disease.
X-Chem has also been successful in membrane-binding protein drug screening. "Previously, we mainly screened for soluble protein inhibitors,"
Wagner said.
but the data show that we are now also able to screen for inhibitors of relatively difficult membrane-binding proteins.
," Wagner added, along with DN.