Cascade Bio

Happy Thanksgiving from Cascade. We appreciate your enthusiasm for enzymes and learning more about the catalysts that build the natural world. Now back to our regular programing with the final post on our November Enzyme of the Month tryptophan synthase. ?? ???? For the final post, we’ll look closely at the mechanism of tryptophan synthase and how it cooks up this critical amino acid. This enzyme has multiple parts and does two different reactions. The α-subunit of the enzyme catalyzes the cleavage of indole-3-glycerol phosphate (IGP) into indole and d-glyceraldehyde-3-phosphate (G3P). The indole produced in the α-reaction is then channeled through a 25 ? tunnel to the β-active site. ??? The β-subunit of the enzyme catalyzes the reaction of indole with l-serine to produce l-tryptophan, requiring a pyridoxal phosphate (PLP) cofactor. A lysine in the active site of both subunits does a lot of the heavy lifting facilitating the interaction between the intermediates. Here at Cascade, we look to enable multiple enzymatic steps easily in a single reactor for more sustainable chemical production. We are thankful for proteins like tryptophan synthase where nature already puts two reactions into a single enzyme. Hope everyone has a great day!???

?? For our third post on our November Enzyme of the Month tryptophan synthase, we will explore recent research and innovations done on the enzyme enabled by advances in biotechnology and AI. ?? Work from Caltech in the late 2010s on tryptophan synthase led to the evolution of the enzyme to synthesize non-canonical amino acids (ncAAs) as well as the founding of the company Aralez Bio. These ncAAs not only expand the repertoire of amino acids available for biochemical and pharmaceutical applications but also pave the way for novel protein engineering and therapeutic discoveries. This is possible because ncAAs expand the building blocks nature uses for proteins beyond the 20 canonical amino acids. ?? Study of tryptophan synthase has also helped us wind back the clock on understanding life on Earth. Ancestral reconstruction of this enzyme across life indicates that the ancient tryptophan synthase had all 19 other amino acids besides tryptophan, suggesting it was the 20th and final amino acid synthesized by our ancient ancestors billions of years ago. Even though less common than other amino acids, tryptophan is critical for structural diversity of proteins and was probably a huge advantage for the ancient life that used it. Whether pushing forward proteins and therapeutics of the future or enabling the complexity of life billions of years ago, tryptophan synthase has stayed busy. Stay tuned next week for the final post on our November Enzyme of the Month. ??? #enzymes #tryptophansynthase #LUCA #biocatalysis

I spent the last few days in Düsseldorf at the inaugural #Biocat4Value conference hosted by the European Federation of Biotechnology. One of my biggest takeaways was seeing how many different companies across industries are already leveraging biocatalysis to make molecules in a better way. Some of my fellow presenters included biotech leaders from Michelin, Givaudan, AstraZeneca, Repsol, Novonesis, DSM, BYK Additives, Almac Group and more. Definitely a lot of exciting work going on in Europe and I am already looking forward to my next trip back out there. #enzymes #biocatalysis #biomanufacturing #greenchemistry

?? Beyond our Thanksgiving plates, Tryptophan Synthase is a biochemical workhorse in industry. While traditionally viewed as essential for biosynthesis in nature, this enzyme's applications in biotechnology and manufacturing are broad, especially in pharmaceuticals, bio-based dye production, and synthetic biology. Let’s take a closer look at how Tryptophan Synthase is being leveraged for innovation across these sectors: ?? In the pharmaceutical industry, pathways building on Tryptophan Synthase are harnessed to produce precursors for neurotransmitters like serotonin. These pathways, which can be engineered and optimized in microbial hosts, offer a scalable, biosynthetic alternative to chemical synthesis. Through engineered microbes and enzymes, we can efficiently produce tryptophan and its derivatives, which are central to developing treatments for conditions ranging from depression to sleep disorders. ?? Tryptophan Synthase is also integral to our friends in precision fermentation, where it serves as a key component in creating synthetic pathways for high-value compounds. By embedding its pathway into chassis organisms, researchers have developed versatile platforms for producing customized tryptophan derivatives, used in everything from bio-based materials to flavor compounds. This enzyme’s modularity in metabolic networks allows for the fine-tuning of production systems, enabling the large-scale, precise manufacture of diverse bioactive compounds without relying on traditional, often inefficient, extraction methods. ??One of these tryptophan derivative compounds is indigo, traditionally derived from petroleum-based processes. By engineering microbial strains or cell-free enzyme cascades to convert tryptophan into indigo, industry can reduce its dependence on non-renewable resources, leading to lower energy costs and less environmental impact for this ubiquitous dye. ?? Tryptophan Synthase’s industrial applications reflect a blend of sustainability, scalability, and precision. Whether enhancing biopharmaceutical production, revolutionizing dye manufacturing, or driving synthetic biology innovations, this enzyme has shifted from a metabolic footnote to an industrial cornerstone. #EnzymaticFuture #IndustrialBiotech #Biopharma #SustainableDyes #SyntheticBiology #EnzymeEngineering #Biomanufacturing #MetabolicEngineering #TryptophanSynthase #BiotechnologyInnovation #GreenChemistry

Cascade will be at the Biocat4Value conference in Düsseldorf next week hosted by the European Federation of Biotechnology. We are looking forward to discussions on how enzymes are enabling molecules across industries to be made in a more sustainable way. Our CEO Alex Rosay will be speaking on Wednesday about Cascade's enzyme immobilization technology and journey from an academic innovation to a commercial product. If you'll be at the conference or around the area, please reach out.

?? Ever heard the myth that tryptophan in turkey makes you sleepy? Let’s set the record straight: It’s not tryptophan itself that brings on post-meal drowsiness, but the heavy meal in general. Yet tryptophan, synthesized by our November Enzyme of the Month Tryptophan Synthase, is crucial for more than holiday myths. This amino acid—and the enzyme that produces it—underpins essential processes in both biopharma and industrial biotech. Let’s dive in: ?? Tryptophan Synthase catalyzes the final, complex step in the biosynthesis of tryptophan. Found in bacteria, fungi, and plants, the enzyme channels serine and indole through a bifunctional active site to produce tryptophan. For organisms that produce their own tryptophan, this enzyme balances efficient biosynthesis with reactive intermediate management—a sophisticated and complex solution that animals evolved away from due to dietary access to tryptophan. Tryptophan Synthase is essential because it produces tryptophan, an amino acid humans can’t synthesize independently but rely on to produce key molecules like serotonin, which influences mood, and melatonin, which regulates sleep. ?? Tryptophan Synthase’s quaternary structure, a heterotetramer of α and β subunits, coordinates a precise multistep mechanism. The α-subunit cleaves indole-3-glycerol phosphate to produce indole, which is then channeled directly to the β-subunit, minimizing diffusion loss and preserving reaction efficiency. This intramolecular “tunnel” of indole highlights enzyme specialization at its finest—Tryptophan Synthase’s tightly regulated structure underpins its unique catalytic precision. ?? Beyond its metabolic role, Tryptophan Synthase powers synthetic biology applications. From engineered microorganisms in biopharma producing serotonin precursors to microbes synthesizing industrial products like indigo dye, this enzyme’s pathways are integral to bioengineering. Harnessing this enzyme in microbial hosts enables scalable production of high-value compounds, demonstrating Tryptophan Synthase’s significance in sustainable biomanufacturing. ?? Tryptophan Synthase isn’t responsible for post-Thanksgiving naps—but it is crucial for advancing both life sciences and bioengineering. From synthesizing key neurotransmitters to enabling sustainable production of compounds like indigo dye, this enzyme is foundational in pathways that support both health and industry. Over the month, we’ll delve deeper into Tryptophan Synthase’s versatile applications and structural innovations, highlighting how this biochemical powerhouse continues to push boundaries in research and biomanufacturing. #EnzymaticFuture #CascadeBio #Biotechnology #LifeSciences #Biochemistry #EnzymeOfTheMonth #TryptophanSynthase #Thanksgiving

Today, we mark 1 year of our Enzyme of the Month series, and what better day than Halloween to share a summary of our enzyme costume contest ?? November 2023: The magician Transaminase reveals its secrets of specificity for the production of chiral amines ?? December 2023: The Santa enzyme - ATP Synthase - shares the gift of energy with other enzymes (but just the nice ones) ?? ? January 2024: The mixologist Candida antarctica lipase B?mixes and matches fatty acids for turning oilseed products into higher value compounds like cocoa butter alternatives ?? ?? February 2024: Our frog enzyme - Transposases - enables genes to leap into other parts of the genome ?? March 2024: The remarkable RuBisCO, the world's most common enzyme, drives photosynthesis and fixes carbon dioxide ?? April 2024: The gardener enzyme, Phenylalanine ammonia-lyase, starts off the cascade of enzymes to make flavonoids, compounds critical for flower coloration and also used in agriculture, biotechnology, and medicine due to their antioxidant, anti-inflammatory, and anti-carcinogenic properties ?? May 2024: The doctor enzyme, Lipoxygenase, enable cellular regulation of inflammation and immune responses ?? June 2024: The cascade of enzymes that make Mycosporine-like Amino Acids (MAAs), natural UV absorbers found in coral and algae, can help create better and more sustainable sunscreen ?? July 2024: Taq Polymerase is the critical driver of PCR. Discovered in a hot spring in Yellowstone, we celebrated the fourth of July by focusing on this enzyme ?? August 2024: Superoxide Dismutase, the shield enzyme, defends cells against oxidative stress by neutralizing free radicals ??? September 2024: Our barista enzymes, the cascade of compounds that make Eugenol, make the warm and spicy molecule that plays a key role in the fall favorite pumpkin spice flavor ? October 2024: And finally, this month was Sucrase, treating people to sweets this spooky season ??

?? Happy Halloween! ?? Here at Cascade Bio we celebrated with costumes. Our enzyme team is the heavily used Green Fluorescent Protein (GFP) from the jellyfish Aequorea victoria. Our resin team is Whole Food's Berry Chantilly Cake, which our company enjoys every birthday. And my co-founder James Weltz and I are Woody and Buzz Lightyear as we reach for the sky to build the enzymatic future. I was very happy to see the creativity of both our Enzyme and Resin teams as they embody Cascade-related themes.? To infinity and beyond! ??

?? Sucrase plays a critical role in carbohydrate metabolism, catalyzing the hydrolysis of sucrose into glucose and fructose. From substrate recognition to product release, each step of its mechanism enables sucrase to efficiently break down sucrose. For this week's post on our October Enzyme of the Month, let’s dive into how sucrase operates at a molecular level: ?? The first step in sucrase’s mechanism is substrate binding, driven by specific interactions between sucrose and conserved residues in the active site. Crystallographic studies have revealed that as sucrose enters the catalytic pocket, a tryptophan residue stabilizes the disaccharide through π-stacking interactions with the glucose moiety. Hydrogen bonds from asparagine and glutamine residues further align sucrose, locking it into an optimal position. ?? The catalytic step involves acid-base chemistry coordinated by active site residues. A glutamate residue acts as a general acid, protonating the glycosidic oxygen, which destabilizes the bond between glucose and fructose. Simultaneously, a histidine residue serves as a general base, activating a nearby water molecule for a nucleophilic attack on the glucose carbon. This step generates a covalent intermediate—a transient glucose-enzyme complex—stabilized through interactions with a tyrosine residue in the active site, which helps prevent premature product release. ?? Finally, product release occurs through hydrolysis of the covalent intermediate. A strategically positioned water molecule is activated by histidine, which facilitates the breakdown of the glucose-enzyme complex. The conformational flexibility of a loop structure near the active site allows the enzyme to reset after each cycle. This structural change improves turnover efficiency and ensures the active site can accommodate subsequent sucrose molecules without steric hindrance. ?? Each step in sucrase’s catalytic cycle, from substrate binding to product release, involves finely tuned molecular interactions that enhance efficiency. At the same time, understanding sucrase’s mechanism has paved the way for significant breakthroughs in both research and applied sciences. These discoveries will open new doors, demonstrating how fundamental enzyme mechanisms can lead to transformative applications across disciplines.

Today we are excited to announce that Cascade has a new scientific advisor - Doug Hattendorf. Doug brings over 20 years of enzyme experience from his lab days at Codexis to Zymergen where he led the 14 person Enzymology and Protein Engineering team to his Business Development efforts at Ginkgo. Check out the image below for a quote about why Doug is excited to collaborate with Cascade. He's already been instrumental in helping us as we develop our own enzymes - more on that soon!