Varigen Biosciences is developing technologies for the sequence-specific capture, amplification, sequencing, and over-expression of long DNA to dramatically simplify the production of natural products. In this interview, co-founder and CEO David Mead discusses the benefits of synthetic biology and promises a technology that would help scale the manufacturing of natural product drugs.
Please describe your background prior to starting Varigen Biosciences.
About 30 years ago, at the dawn of my career, I invented a technology called TA cloning, a tool for cloning PCR amplicons. I sold it to a little company called Invitrogen, which grew to become Thermo Fisher. Since then, it has sold almost a billion dollars worth of reagents, making it the most widely sold cloning tool around to this day.
That turned out to be so successful that I decided to start my own company. I founded a firm called Lucigen, which was sold four years ago to LGC, and used the proceeds from that to start my current company, Varigen Biosciences.
Varigen is a genome and metagenome mining company with world-class expertise in big DNA, Big Data, and AI technologies for manipulating complex pathways for therapeutics. Our main focus is on natural products derived from microbial or fungal sources.
When we first started doing this, there weren’t any good tools around for manipulating big DNA such as biosynthetic gene clusters. These clusters encode complicated large pathways with a lot of moving parts that make natural product drugs.
We have captured and attempted to express natural product pathways 110 times now. Not all of them expressed, but quite a few did, approximately 70% of the time.
We have been offering our capabilities as a service for the last three years, but we plan to pivot towards engineering pathways from existing drugs that are difficult and expensive to manufacture so we can grow more substantially than contract research allows.
Our customers would be pharma or biotech companies who want to use an existing therapeutic as a pharmaceutical ingredient. One of our engineered strains is a natural SARS antiviral that biopharma companies may find very exciting.
We are not going to try to manufacture it, at least not for this first round of our company, because of GMP and large-scale fermentation issues. Rather, our customers would buy the strain from us and then manufacture and sell it independently and we would help them scale up the production of microbial medicine using our synthetic biology tools.
What can you tell us about your technology?
By number, about half of the drugs on the market are natural products. Cyclosporin and penicillin are only two examples. Half a trillion dollars worth of therapeutics is based on natural products.
These pathways are really large. They start at around 40 KB and go up to 400 kb or bigger. PCR isn’t good enough to capture that, especially from GC-rich organisms.
We decided to use CRISPR-cas9 in-vitro to be able to cut out our pathway and then clone, express, reproduce and modify it. At the time, CRISPR-cas9 was only being used for in-vivo manipulations, but it’s obviously come a long way, especially in the last five years.
Our in-vitro approach means we can capture the whole pathway and change it in a much higher throughput fashion. CRISPR-cas9 is the ultimate restriction enzyme. It has a 21-base recognition sequence, which means you can cut off almost any part of the DNA, but it has to be from a high-quality sequenced genome. We design guide RNAs to target the pathway, cut it, and separate the needle from the haystack.
That alone is not trivial, but the real hard part is capturing that giant chunk of DNA and getting it to express, so we also developed a novel expression technology to solve that piece of the puzzle. So far, to our knowledge, there are still only three companies that are doing this form of pathway capturing and engineering in-vitro.
To understand the importance of this capability, you have to go back and think about how pharma companies do it. They would grow bacteria, screen the culture, filter it, and then come out with new activities for antibiotics, antifungal, antimicrobial, antiviral, anticancer, and immunosuppression. That process worked really well up until about 20 years ago when they started finding the same things over and over again and big pharma quickly bailed out of natural product drug discovery.
Since then, the next-gen sequencing paradigm has revolutionized microbial genetics. Several million genomes have been sequenced so far. About half of them are in public databases, and half of them are in private ones.
You can utilize algorithms like antiSmash to find the motifs for natural products encoding polyketide synthetases or non-ribosomal peptide synthases. By looking at genomes, you can see literally 10 times or more natural product pathways than you could find by filtering for antibiosis activity.
We know there’s plenty of unknowns out there, and the diversity is just unbelievable.
What are some applications for Varigen’s Technology?
Here’s a really good example: back in the 70s, a compound called plitidepsin was discovered in sea squirts and found to be a potent antiviral and anticancer compound. It is really potent; it’s non-toxic and has a good tolerance in humans, and it is well absorbed.
At the time, there was no biological source other than tunicates, but you can’t just go around harvesting tunicates. So, a company called PharmaMar has been making it chemically. They tried to get it approved as an anti-cancer for 10 plus years without success.
Four papers were published in the last few years showing that it is 30 times more potent for treating SARS than Remdesivir, which has already sold $2.4 billion last year even though it doesn’t really work for SARS.
The problem is that it costs about $100 per milligram to manufacture. That means it’s going to cost over $10,000 to treat one patient. At that cost, it’s only going to be for the rich.
We have three of the four known public strains of bacteria that make this naturally, called Tistrella. We’ve done metabolomics and genomics on it. The strain only makes about a tenth of a milligram per liter and it has some kind of a defect in one of its enzymes that makes 50 mg per liter of the two halves of a full compound. We think we can fix it biologically.
We’re going to use our tools to make a fully elaborated version of it, which will immediately drop the cost of goods by several orders of magnitude. Then, we’ll just use conventional tricks of the trade to get up to 500 mg per liter. It will be a thousand times cheaper to manufacture, with the potential to be a 10 billion-dollar drug worldwide.
The compound is entering phase three clinical trials. PharmaMar owns the patent for making it chemically, but we own the patent for making it biologically, so we will be able to sell it to therapeutic companies at much better rates.
We’re just starting. Hopefully, we will have the first version by the first or second quarter of next year. If we can drop the cost of goods to $1-10 per pill, it’s going to be available for almost anybody so it will save lives and money at the same time.
What are some of the challenges you aim to solve for your customers?
It takes decades and billions of dollars to get a new drug across the finish line. It dawned on us that there are a lot of very valuable, multibillion-dollar compounds out there that are so difficult to manufacture that pharma has turned to making them chemically.
The difference between a fermentation product and a chemically-synthesized product is that the latter is hundreds of thousands of times more expensive, assuming you get the microbial fermentation to work. With natural products, we don’t have to get them to work in their native host, but we do have to be able to clone them and express them heterologously.
Not many companies are doing this. The big ones are pointing mostly towards drug discovery, which will take them a lot longer and cost them a lot of money. Strain improvement from overproduction of valuable therapeutics will eventually sneak into the backdoor of drug discovery.
Pharma has not started using synthetic biology tools so they chemically synthesize natural products at a much higher cost than doing it biologically. They’ve given up on natural products but the revolution is starting to turn things around in a new direction. We’re hoping to be at the front edge of that revolution, with a new set of synthetic biology tools that can scale the production of microbial medicines.
What would you say are the main benefits of natural product drugs as opposed to chemical drugs?
A lot of really important things are controlled by small molecules. Many illnesses have a microbial connection. Your gut microbiome can control whether you have mental illness, obesity, or Krohn’s disease. There are beneficial bacteria and pathogenic bacteria, which are not infectious per se, they don’t kill you by taking over your system, but they can dramatically alter your health through chemical warfare in your body.
Nature has been evolving the ability to produce these molecule compounds for over a billion years, mostly within the microbiome. These compounds are created by microbial interactions and a lot of them are also extremely potent binding chemicals.
Part of the reason they are so hard to synthesize is the infinite palette of nonribosomal peptides and ketides that they’ve figured out how to make. They just reshuffle different enzymes to make a new scaffold to take care of whatever issue they are having.
It’s just mind-blowing how much diversity there is in some of these compounds. We still don’t even know what some of them are doing, we just know that they are great medicines. If you look at existing drugs on the market, microbial and plant-based natural products tend to be the most diverse and the most potent ones.