How Scientists Are Engineering Nature's Cancer Fighters
In a lab in China, a team of scientists has just created 380 new molecules that could one day fight cancer. The twist? They engineered bacteria to do the chemical synthesis for them.
For nearly 70 years, scientists have known about a family of natural compounds called antimycins produced by soil bacteria. These molecules possessed modest antifungal properties, but for decades, their potential seemed limited. That changed dramatically when researchers discovered antimycins could potently and selectively inhibit the mitochondrial Bcl-2/Bcl-XL-related anti-apoptotic proteins—proteins that are overproduced by cancer cells and confer resistance to chemotherapy 2 7 .
Suddenly, these obscure microbial metabolites became promising candidates for cancer treatment. There was just one problem: how could researchers create many variations of these complex molecules to find the most effective versions? The answer emerged from an innovative approach that combines synthetic biology with synthetic chemistry—multiplex combinatorial biosynthesis 1 .
Limited to naturally occurring compounds with modest modifications through chemical synthesis.
Engineers microbial factories to produce diverse unnatural natural products with enhanced properties.
To understand this breakthrough, imagine a microscopic factory inside a bacterium. This factory contains an assembly line of enzymes that work together to build the antimycin molecule. Each enzyme has a specific job—one adds a particular chemical group, another shapes the core structure, and yet another adds finishing touches.
Combinatorial biosynthesis involves reprogramming this natural assembly line by mixing and matching components from different biological systems or engineering the existing machinery to behave differently 6 .
Scientists can alter functional groups, regiochemistry, and scaffold backbones through manipulation of biosynthetic enzymes 6 .
The approach exploits the natural promiscuity (flexibility) of biosynthetic enzymes to incorporate non-natural building blocks 6 .
By combining biological and chemical methods, researchers can create libraries of "unnatural" natural products that have both the complex structures of natural compounds and the diversity of synthetic libraries 5 .
In 2013, a research team achieved what many had sought for decades: they successfully applied multiplex combinatorial biosynthesis to create a library of 380 distinct antimycin-like compounds 1 . This landmark study demonstrated the power of combining multiple engineering approaches simultaneously.
The researchers employed a multi-pronged strategy to diversify the antimycin structure at different biosynthetic stages 1 4 :
They first targeted the "starter unit"—the beginning portion of the antimycin molecule known as 3-formamidosalicylate.
They exploited the natural promiscuity of enzymes to incorporate various non-natural extender units 6 .
After the core structure was assembled, they modified the finishing enzymes that add final decorations.
The key innovation was applying these strategies simultaneously—multiplexing them to compound the structural variations.
The output was stunning—a library of 380 antimycin analogues, many with enhanced in vitro cytotoxicity and antifungal activity compared to the natural antimycins 6 .
| Analogue | Structural Modification | Biological Activity |
|---|---|---|
| Compound 9 | Modified extender unit | Enhanced cytotoxicity |
| Compound 10 | Altered side chain | Improved antifungal properties |
| Compound 11 | Branched chain variant | Increased potency |
| Compound 12 | Halogenated derivative | Enhanced bioactivity |
The successful implementation of multiplex combinatorial biosynthesis requires specialized tools and reagents.
| Tool/Reagent | Function | Specific Example in Antimycin Research |
|---|---|---|
| Heterologous Host | Provides cellular machinery for expression | Streptomyces coelicolor 7 |
| Promiscuous Acyltransferase | Incorporates diverse extender units | AntB enzyme 6 |
| Crotonyl-CoA Carboxylase/Reductase (CCR) | Generates unusual extender units | AntE enzyme 2 |
| Standalone Ketoreductase | Modifies scaffold after assembly | AntM enzyme |
| Cluster-Situated Regulator | Controls gene cluster expression | σAntA 3 |
| Cross-Cluster Regulator | Coordinates multiple pathways | FscRI (from candicidin cluster) 7 |
Engineered bacteria serve as living factories that can be programmed to produce diverse molecular structures through genetic manipulation.
Key enzymes are modified to accept non-natural substrates, expanding the chemical diversity of the resulting compounds.
Creating these novel compounds required more than just enzymatic tools—it demanded a deep understanding of how bacteria naturally control these complex biosynthetic pathways. Researchers discovered that antimycin production involves a sophisticated multi-layer regulatory system 3 7 :
Surprisingly, the same regulator that controls candicidin (an antifungal compound) also activates antimycin biosynthesis. This FscRI protein directly binds to promoter regions of antimycin genes, coordinating production of two entirely different natural products 7 .
The cluster-situated sigma factor σAntA is regulated by ClpXP protease, which degrades the protein based on a C-terminal recognition signal. This represents a novel regulatory strategy linking protein degradation to natural product biosynthesis 3 .
This intricate control system explains why early attempts to express antimycin pathways in heterologous hosts often failed—the proper regulatory elements were missing 7 .
Initial discovery of antimycins with modest antifungal properties
Discovery of antimycins' potential as cancer therapeutics through inhibition of Bcl-2/Bcl-XL proteins 2 7
Landmark experiment creating 380 antimycin analogues through multiplex combinatorial biosynthesis 1
Application of similar approaches to other natural product classes for drug discovery
The successful application of multiplex combinatorial biosynthesis to antimycin production represents more than just a technical achievement—it signals a paradigm shift in natural product-based drug discovery. By creating 380 novel compounds, researchers have dramatically expanded the chemical space available for screening against cancer targets.
This approach reinvigorates the potential of natural products as drug leads by addressing their historical limitation: limited structural diversity for structure-activity studies. As the field advances, combining combinatorial biosynthesis with synthetic biology and high-throughput screening creates a powerful platform for generating therapeutic candidates 6 .
The same "multiplexing" strategy can be applied to diversify polyketides, nonribosomal peptides, and hybrid natural products that share similar biosynthetic logic 1 .
We're no longer limited to nature's existing chemical inventory—we can now guide evolution to create nature-inspired compounds tailored to our most pressing medical needs.
Novel Compounds
Years of Research
Biosynthetic Steps
Future Possibilities