Thanks to genomics and bioinformatics, we brought together about thirty enzymes from a wide variety of different organisms, creating anticancer drugs and painkillers in baker’s yeast. This strategy paves the way for wide-scale production of these plant-inspired medicines.
Many of our most important medicines come from the natural world, including the anticancer drug paclitaxel (extracted from the needles of the European yew) and the cardiotonic digoxin (extracted from the leaf of the digitalis). Why do plants play such a key role in human health and nutrition? The answer lies in many thousands of years of evolution. Because plants are stationary organisms, they have evolved strategies to make a vast diversity of chemicals that enable them to interact with their environment. Over time, humans have discovered the value of these compounds in health; initially in traditional medicine; and ultimately in modern medicine when the active ingredient in the plant responsible for the therapeutic activity is isolated, identified, and eventually formulated into a dosed form.
Yet, there are many challenges that arise from sourcing medicines from plants for a global population of over seven billion people. Plants are making these compounds for their own purposes, and in many cases to combat environmental threats. Thus, when used in human health, these active molecules can be associated with undesired properties. Plants grow slowly and are susceptible to weather, pests, and disease, which introduce risks into the stability and predictability of the supply, with limited ability to respond rapidly to changes in supply and demand. In addition, these active molecules are generally made in very small quantities, such that growing plants to provision medicines leads to inefficient use of arable land and/or overharvesting of rare plants to an extent where valuable biodiversity is lost over time. These challenges lead to issues in equitable global access to essential medicines, as well as hurdles in the development and innovation of new medicines that are desperately needed to treat many pressing diseases and conditions.
Faced with these challenges, scientists have searched for ways to modernize and introduce greater control into the process of making these molecules. Synthetic chemistry became a favored approach. With the tools of chemistry, molecules can be synthesized faster and in controlled environments, greatly reducing supply chain risks. However, there are fundamental differences in the approaches that nature and synthetic chemists employ to build molecules. Nature employs unique molecular machines, called enzymes, which allow for exquisite specificity and precision in building complex molecules via molecular assembly lines. In contrast, chemical synthesis utilizes very different catalysts to build molecules, for which the precision inherent to nature’s approach is not easily achieved.
But now, advances in biotechnology are poised to transform our supply chains around medicines. The tools of genomics and computational biology are being deployed to unlock the full synthesis capacity of the natural world. These tools are able to recover genome sequence information at an unprecedented scale. This information can then be mined and analyzed for segments of DNA (or genes) encoding enzymes useful in building valuable medicines (1). In turn, these natural genetic functions can be recoded and reorganized into simple microorganisms such as baker’s yeast.
As a result, not only do these genetically engineered yeast retain their ability to grow rapidly on inexpensive nutrients, but, now, they also have the capacity to produce high-value medicinal compounds. This synthetic biology-based approach to synthesis offers the process advantages of a synthetic chemistry approach, while retaining the essential components of nature’s approach to building complex molecules. Bio-based processes will support secure and controlled manufacturing at lower costs, increasing surety in these important supply chains. Producing medicines via microbial fermentation versus extraction from plants supports a more sustainable process, reducing arable land and toxic chemical use, as well as maintaining valuable biodiversity by reducing the overharvesting of medicinal plants. Fermentation-based processes are inherently scalable and distributed, which can ultimately be deployed in creative ways to address global access issues. By increasing supply chain robustness and reducing research and development timelines, this new approach to building complex molecules will ultimately remove hurdles to innovation and expand discovery and development pipelines to new and better medicines.
Yet, until recently the field was technically stalled at systems that combined about half a dozen enzymes. This allowed for molecular assembly lines to important medicines, such as the antimalarial drug artemisinin (2). But it leaves out a full range of biodiversities and activities.
Recent breakthroughs in synthetic biology have developed sophisticated tools that transcend these limits. Now biosyntheses can bring together up to 30 enzymes from many different organisms. Our group at Stanford university made the first demonstration of these capacities in 2015 and 2016, when it produced opioids, essential medicines for treating moderate to severe pain, and other medicinal compounds produced from the opium poppy, including those effective at treating cancer (3).
Our team engineered baker’s yeast to make complex pain medicines by finding over 20 genes from numerous medicinal plants, bacteria, and even rats. The genes encode different enzymes that play a role in building the desired drug molecule. By bringing together genes in yeast that do not occur together naturally, we are able to make novel molecular assembly lines that can build molecules more efficiently than the native plant (e.g., opium poppy) and craft molecules that cannot be found in nature (e.g., pain medicines with reduced addictive properties).
In taking a bottom-up approach to reconstructing the chemical assembly line for opioids, one challenge we encountered is that all of the enzymes needed for the process were not known a priori. We and other teams then used computer programs and biochemical hypotheses to search through the genetic code of the poppy (i.e., millions of base pairs of genetic sequence) to identify candidate genes for the missing enzymes in silico. The physical DNA of these candidates were then synthesized, placed into engineered yeast harboring the incomplete assembly line, and characterized to identify the specific set of genes that result in biosynthesis of the desired drug molecule.
Another challenge that we encountered is that directly placing the genes identified from medicinal plants into yeast often results in enzymes that are not functional, as these DNA sequences have been honed over thousands of years of evolution for the plant. Our team has developed frameworks and tools for modifying the gene sequences to allow each of the enzymes to function individually and collectively in the yeast cell. These recoding heuristics direct when and where in the yeast cell the enzymes are made, allowing precise control over how the enzymes work together in the molecular assembly line to build the desired drug molecule. Ongoing work is solving the challenge of yield; for instance, our initial strains produced about 0.3 microgramme by liter of a synthetic opioid, which is being increased by 1,000,000 times for commercial production.
Synthetic biology applied to brewing complex, high-value chemicals will ultimately transform our relationship with medicines. If deployed and developed thoughtfully, it can address many of the environmental, bioconservation, global equity, geopolitical, and socioeconomic issues associated with existing medicinal supply chains. This technology will also bring us into a future where we are building better medicines from the bottom up, taking inspiration from nature’s processes, but breaking open the barriers inherent in relying solely on what can be found in the natural world. Arriving at this best possible future will require that researchers engage with diverse stakeholders, including policy makers, regulators, pharmaceutical companies, and organizations, to assess best strategies in responsible development and deployment in realizing the full benefits of these new technologies.
(1) H. W. Nutzmann et al., New Phytol., 211, 771, 2016.
(2) D. K. Ro et al., Nature, 440, 940, 2006.
(3) S. Galanie et al., Science, 349, 1095, 2015; S. Li and C. D. Smolke, Nat. Comm., 7, 12137, 2016.
Creating plant-inspired drugs is a reality, but producing them at global scale remains out of reach. Recent progress in synthetic biology opens up new possibilities for solving this issue. At the core of these advances is a simple yet powerful tool: baker’s yeast.
Christina Smolke is the head of the bioengineering lab at Stanford University, where she teaches bioengineering and chemical engineering. She is also the CEO and president of Antheia, a company specialising in synthetic biology, informatics and fermentation technology.