Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Shifting evolution into reverse promises cheaper, greener way to make new drugs

24.03.2014

This alternative approach to creating artificial organic molecules, called bioretrosynthesis, was first proposed four years ago by Brian Bachmann, associate professor of chemistry at Vanderbilt University. Now Bachmann and a team of collaborators report that they have succeeded in using the method to produce the HIV drug didanosine.

The proof of concept experiment is described in a paper published online March 23 by the journal Nature Chemical Biology.

"These days synthetic chemists can make almost any molecule imaginable in an academic laboratory setting," said Bachmann. "But they can't always make them cheaply or in large quantities. Using bioretrosynthesis, it is theoretically possible to make almost any organic molecule out of simple sugars."

Putting natural selection to use in this novel fashion has another potential advantage. "We really need a green alternative to the traditional approach to making chemicals. Bioretrosynthesis offers a method to develop environmentally friendly manufacturing processes because it relies on enzymes – the biological catalysts that make life possible – instead of the high temperatures and pressures, toxic metals, strong acids and bases frequently required by synthetic chemistry," he said.

... more about:
»Vanderbilt »drugs »enzyme »enzymes »producing »synthetic

Normally, both evolution and synthetic chemistry proceed from the simple to the complex. Small molecules are combined and modified to make larger and more complex molecules that perform specific functions. Bioretrosynthesis works in the opposite direction. It starts with the final, desired product and then uses natural selection to produce a series of specialized enzymes that can make the final product out of a chain of chemical reactions that begin with simple, commonly available compounds.

Bachmann got the idea of applying natural selection in reverse from the retro-evolution hypothesis proposed in 1945 by the late Caltech geneticist Norman Horowitz. Horowitz envisioned an early stage in the development of life where early organisms were swimming in a primordial soup rich in organic material. In this environment, imagine that one of the species finds a use for the complex chemical compound A that gives it a competitive advantage. As a result, its population expands, consuming more and more compound A.

Everything goes well until compound A becomes scarce. When that happens, individuals who develop an enzyme that allows them to substitute the still plentiful compound B for the scarce compound A gain a reproductive advantage and continue to grow while those who remain dependent on compound A die out. And so it goes until many generations later the survivors have developed multi-step chemical pathways to produce the molecules that they need to survive from the molecules available in their environment.

To test Bachmann's retro approach, the Vanderbilt chemists first identified the drug that they wanted to produce – in this case didanosine, an anti-HIV drug sold under the trade names of Videx and Videx EC that is very costly to manufacture. Then they identified a similar "precursor" molecule that can be converted into didanosine when it is subject to a specific chemical transformation along with an enzyme capable of producing the type of transformation required.

Once they identified the enzyme, the researchers made use of the power of natural selection by making thousands of copies of the gene that makes the enzyme using a special copying technique that introduces random mutations.

The mutant genes were transferred into the gut bacteria E. coli in order to produce the mutant enzymes and placed into different "wells." After the cells were broken open and the contents mixed with the precursor compound, the amount of didanosine, in each well was measured. The researchers selected the enzyme that produced the greatest amount of the desired drug and then made enough of this optimized enzyme for the next step.

Next the researchers identified a second precursor – an even simpler molecule that could be chemical converted into the first precursor – and an associated transformative enzyme. Again they made thousands of mutated versions of the transformative enzyme's gene, inserted them in E. coli, put them in wells, broke open the cells and mixed the content with the optimized enzyme and second precursor. Once again, they tested all the wells for the anti-HIV drug. The well with the highest level of didanosine was the one in which the mutant enzyme was most effective in making the first precursor, which the optimized enzyme then converted into didanosine. This gave them a second optimized enzyme. The researchers carried out this reverse selection process three times, until they could make didanosine out a simple and inexpensive sugar named dideoxyribose.

One of the key technical challenges was rapidly determining the three-dimensional structures of the enzymes that were generated during the evolutionary process. Associate Professor of Pharmacology Tina Iverson provided this capability. Her team analyzed the laboratory-evolved enzymes after each round of mutagenesis and identified how the structural changes caused by the mutations improved the enzyme's ability to produce the desired transformation.

This information helped the collaborators figure out why some mutant enzymes did a better job at producing the desired compounds than others, which guided their choices about the areas of the precursor proteins to target.

The proof-of-concept experiment was performed in vitro instead of in living cells to keep things simple. However, the ultimate goal is to use the approach to produce artificial compounds by fermentation.

###

Graduate students William Birmingham, Chrystal Starbird, Timothy Panosian and David Nannemann contributed to the study.

The research was supported by National Science Foundation graduate fellowship DGE 0909667, the D. Stanley and Ann T. Tarbell Endowment fund, National Institutes of Health grant GM079419 and Department of Energy Argonne National Laboratory contract DE-AC02-06CH11357

Visit Research News @ Vanderbilt for more research news from Vanderbilt. [Media Note: Vanderbilt has a 24/7 TV and radio studio with a dedicated fiber optic line and ISDN line. Use of the TV studio with Vanderbilt experts is free, except for reserving fiber time.]

David Salisbury | Vanderbilt University

Further reports about: Vanderbilt drugs enzyme enzymes producing synthetic

More articles from Life Sciences:

nachricht A novel socio-ecological approach helps identifying suitable wolf habitats
17.02.2017 | Universität Zürich

nachricht New, ultra-flexible probes form reliable, scar-free integration with the brain
16.02.2017 | University of Texas at Austin

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Breakthrough with a chain of gold atoms

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

Im Focus: DNA repair: a new letter in the cell alphabet

Results reveal how discoveries may be hidden in scientific “blind spots”

Cells need to repair damaged DNA in our genes to prevent the development of cancer and other diseases. Our cells therefore activate and send “repair-proteins”...

Im Focus: Dresdner scientists print tomorrow’s world

The Fraunhofer IWS Dresden and Technische Universität Dresden inaugurated their jointly operated Center for Additive Manufacturing Dresden (AMCD) with a festive ceremony on February 7, 2017. Scientists from various disciplines perform research on materials, additive manufacturing processes and innovative technologies, which build up components in a layer by layer process. This technology opens up new horizons for component design and combinations of functions. For example during fabrication, electrical conductors and sensors are already able to be additively manufactured into components. They provide information about stress conditions of a product during operation.

The 3D-printing technology, or additive manufacturing as it is often called, has long made the step out of scientific research laboratories into industrial...

Im Focus: Mimicking nature's cellular architectures via 3-D printing

Research offers new level of control over the structure of 3-D printed materials

Nature does amazing things with limited design materials. Grass, for example, can support its own weight, resist strong wind loads, and recover after being...

Im Focus: Three Magnetic States for Each Hole

Nanometer-scale magnetic perforated grids could create new possibilities for computing. Together with international colleagues, scientists from the Helmholtz Zentrum Dresden-Rossendorf (HZDR) have shown how a cobalt grid can be reliably programmed at room temperature. In addition they discovered that for every hole ("antidot") three magnetic states can be configured. The results have been published in the journal "Scientific Reports".

Physicist Dr. Rantej Bali from the HZDR, together with scientists from Singapore and Australia, designed a special grid structure in a thin layer of cobalt in...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Booth and panel discussion – The Lindau Nobel Laureate Meetings at the AAAS 2017 Annual Meeting

13.02.2017 | Event News

Complex Loading versus Hidden Reserves

10.02.2017 | Event News

International Conference on Crystal Growth in Freiburg

09.02.2017 | Event News

 
Latest News

Switched-on DNA

20.02.2017 | Materials Sciences

Second cause of hidden hearing loss identified

20.02.2017 | Health and Medicine

Prospect for more effective treatment of nerve pain

20.02.2017 | Health and Medicine

VideoLinks
B2B-VideoLinks
More VideoLinks >>>