Mar 5 2020
RGHGF 2020 Research Interview Series: Aided by Machine Learning, University of Illinois Research Lab and Collaborative Company Lassogen Inc. Target Lasso Peptides
June 15, 2017, California−Dr. Mark Burk, CTO of Genomatica, a biotech company developing cell-free biosynthesis technology to engineer natural molecules for pharmaceutical applications, finished reading a benchmark publication out of the Mitchell Laboratory at the University of Illinois at Urbana-Champaign during an early flight to San Francisco. The paper (Nat Chem Biol. 2017 May; 13(5): 470–478.), authored by Jonathan Tietz, Christopher Schwalen, Parth Patel, Tucker Maxson, Patricia Blair, Hua-Chia Tai, Uzma Zakai, and Principle Investigator and Professor of Chemistry Douglas A. Mitchell, had laid out irrefutable evidence that a class of peptides naturally derived from bacteria were far more populous, and more important, than previously understood.
Research in Progress: Graduate student Susanna Barrett (middle) and postdoctoral scholar Dr. Ashley Kretsch (right) in the Mitchell Laboratory at the University of Illinois examine physical differences between prepared samples of Combiflash HPLC fractions containing capistruin, a Lasso Peptide. Dr. Yaunyuan Si watches her coworkers. The Mitchell Lab’s discovery of the natural diversity of Lasso Peptides opened up novel routes for new disease therapeutics.
Using machine-learning to train an algorithm dubbed “RODEO” standing for Rapid ORF Description and Evaluation Online, researchers at the University of Illinois reported discovering more than 1300 new lasso peptides in the public database GenBank and the characterization of the structure and bioactivity of six lasso peptides. Data from this seminal study indicated that many bacterial and archea (single-cells lacking nuclei) phyla produce these lasso peptides. Continued work has revealed over 5000 novel lasso peptides. Prior to 2017, lasso peptides were relatively obscure with only about 30 known to nature. Their name refers to their characteristic lasso-knot structure. As far as peptides run, their simple structure makes them inherently stable to many physical and chemical perturbations, and now that they are known to be abundant, potential key players in the future pharmaceutical landscape.
“Bacteria are evolutionarily using these [lasso peptides] for purpose. They are evolving these systems to address a need. Doug’s paper stated that lassos are much more important in nature than previously expected. They are easy to manipulate and work with and their diversity is infinite. The types and shapes of lassos are like snowflakes; no two are the same,” said Dr. Burk during his interview with the RGHG Foundation.
Why is this important? When it comes to the therapeutics landscape, lasso peptides are unique in the types of biological mechanisms they may be able to address. Two fast growing markets in pharmaceutical technologies are antibodies and small molecules. You may recognize the blockbuster Humira as a monoclonal antibody, whereas Nexium is a small molecule drug. Between these two categories, there is a large physical size gap, with antibodies often being hundreds of times larger than active pharmaceutical small molecules. But for diseases and biological reactions in general, size matters.
Illustration of generic lasso peptide noting the three major sections of its structure of loop, ring, and tail, provided courtesy of Lassogen, Inc. Each ball represents an amino acid. The lasso-knot structure is composed of 15-25 amino acids.
Ligands that bind with biological receptors to prevent or induce diseases do not look like antibodies or small molecules. These ligands can be hormones, growth factors, signalling molecules, and more. For such diseases involving immune system suppression (e.g. cancer) or immune system overreaction (e.g. rheumatoid arthritis or Crohn’s disease), a mid-range size of therapeutics with specific physical structures could be ideal to faithfully represent shape and volume of natural ligand binding sites on receptors associated with immune responses. This is where lasso peptides come in. As Burk describes, “lasso peptides have diversity to mimic natural ligands and bind to receptors…to address diseases that are not adequately treated using the current modalities. This is filling a therapeutic gap to address challenging diseases.”
As soon as Burk finished reading the paper from Mitchell’s lab, he knew he had to act. Not knowing Mitchell or having previously worked with the Professor, after the plane landed, Burk sent an email to Mitchell requesting a call to discuss an opportunity for the future of lasso-based therapeutics. From this budding collaboration, an impressive founding team for a biotech startup was developed, consisting of Mitchell as Advisor, Burk as CEO, Dr. Kent Boles as Head of Research and Professor Tracey Handel at UC San Diego as a second Advisor. Boles holds technical expertise in areas including immunology, immuno-oncology and advanced synthetic biology, with experience including postdoctoral research at Oxford University. And Handel, as a Professor in the School of Pharmacy and Pharmaceutical Science, is considered a global leader in research on GPCR’s (a class of cell surface receptors) and chemokine receptors.
“lasso peptides have diversity to mimic natural ligands and bind to receptors…to address diseases that are not adequately treated using the current modalities"
Years of hard work between founders and the Mitchell Lab led to the launch of Lassogen, Inc. in 2019, with a mission to develop lasso peptides therapeutics to diagnose and treat diseases where antibody and small molecule approaches are inadequate. Collaborative research of Lassogen Inc. and the Mitchell lab’s on lasso peptides has revealed many structural novelties and the capability to engineer lassos for specific needs.
Hard at work conducting lasso peptide research at the University of Illinois: graduate student Alex Battiste pipettes antibiotic aliquots into micro-centrifuge culture tubes in the Mitchell Laboratory. Postdoctoral scholar Dr. Yuanyuan Si unloads centrifuged samples in 96-microwell plates. Centrifugation allows for heavier sections of mixed samples to separate from solution. It is often used to collect cells and/or strands of DNA at the bottom of small vials to allow for further work-up.
Lassogen, working closely with the Mitchell Laboratory, developed a platform that is aimed at utilizing genome sequencing data to produce and screen lassos for therapeutic applications. This includes both cell free biology to produce a lasso from genomic sequence data, and lasso evolution technology, aimed at producing lassos with billions of variances that lead to identification of optimized versions. Once optimized, bacteria can be engineered to produce larger amounts of the desired lasso peptides through biofermentation processes. Lassogen considers their efforts to be a differentiated discovery engine. “At a high level, there’s a lot of discovery waiting for us, sitting there like gifts from nature, waiting for us to discover new mechanisms of actions,” said Burk, as he excitedly described his company’s endeavors.
As we discussed the potential applications for lasso peptides as therapeutics, Burk described the potential for lasso peptides to improve immuno-oncology for cancer treatment by effectively removing the cloak that cancer cells use to hide from the immune system. As an example, the G-protein coupled endothelin B receptor (ETBR) is expressed on the endothelial cells of vasculature in tumors like those of ovarian cancer. When expressed, it prevents the infiltration of immune cells into the tumor, effectively preventing any natural killer cells or T cells from entering the tumor environment. If ETBR is shut down, then the immune system can enter the microenvironment of the tumor. Lassogen’s first candidate LAS-103 is an ETBR antagonist believed to inhibit the activity of ETBR. This lasso is being developed to work synergistically with immunotherapies to facilitate the body’s capability to fight cancer.
Illustration of ETBR antagonist allowing for immune system influx into a cancerous tumor.
In this academic-industry collaboration, the future with lasso peptides is bright. “We think that this idea is big, groundbreaking, and [lasso peptides] can do things that other modalities cannot do,” Burk stated, summing up his thoughts on potential applications as Lassogen grows.
Editor’s Note: Scientific discoveries often seem instantaneous given their groundbreaking nature and lack of public information on the efforts required to reach the discovery. While the Mitchell lab’s publication led to a quickly budding partnership, the discovery of lasso peptide diversity wasn’t instant. It required ingenuity, talent, and hard work and dedication of the Mitchell lab students, post docs, and Mitchell himself to develop RODEO and successfully apply the algorithm and conduct research experiments. Many experiments often do not have happy endings, and academic research is inherently challenging. We commend the researchers for their efforts and for helping make a difference. You guys rock.