Project Violet Exploration: The Research: Longer Version

Project Violet combines many different areas of science. In this section we describe the main ideas behind the Project Violet pipeline. If you get stuck on any of the science terms, please check out our 'Glossary' section.

Below are some files that contain additional or supplemental information to what is written on this page. They are referred to in the text on the right.

Scientists often refer to many medicines as "drugs"; they call the process of researching and developing new medicines, "drug discovery". (We will use the term "drug" in replacement of "medicines" in this site, as is done in the scientific community.) Many important drugs, like aspirin and penicillin, have come from nature, and many more natural molecules are potential drugs for humans. We're focused on a particular class of natural proteins that have great potential to become medicines. Thousands of organisms have evolved over millions of years to make these molecules, which affect other organisms like predators or prey (see 'The Species & Molecules' section for examples of this). These molecules that affect other organisms have to be ‘drug-like’ in many ways because they induce change in the other organisms.

Proteins are chains of amino acids encoded by DNA. The sequence of amino acids determins the protein's 3D shape and function. Proteins are a part of everything that happens within cells and are a vital part of living things. Some examples of what they are involved with include cell structures, carrying oxygen in the blood, chemical reactions, etc.. For a wonderful introduction to proteins, please visit http://publications.nigms.nih.gov/structlife/chapter1.html.

→ Peptides are small proteins
→ Knottins are the smallest stable peptides

Knottins are small peptides with a particular structure that makes them very stable: an amino acid, Cysteine, binds to other Cysteines, creating a 'bridge' and tying knottins into tight knots. Knottins generally have at least three of these 'bridges'.


This knottin structure helps them stay intact in tough environments like an animal's gut. That's one reason organisms have evolved to use them like drugs. (For more information on the cysteine bonds that define knottins, please click on the following document in the left-hand column of the page: 'The Key Ingredient: Disulphide Bonds in Knottins'.)

We can make variants of a natural knottin by changing parts of its amino acid sequence that aren't essential to the knot structure.


There are 20 different amino acids, so changing just 5 positions in a knottin allows for about 2.5 million variants. If we change 20 positions, there are more possible variants for a single knottin that there are stars in the universe!

Nature didn't evolve these molecules to treat human disease; that's our job. We can harness the power of these knottin peptides from nature by using new technologies that let us alter these peptides to become powerful drugs. We call these optimized peptides 'Optides'. We can change parts of the molecule that aren't essential to its structure and make more Optides that bind to target proteins and disrupt disease.

We can't make all those billions of Optides, but we can narrow things down.
First, we define and produce a library of thousands of variants of a knottin, making amino acid changes to various parts.
Then, we can screen the whole library. For example, we want to know which Optides can go ...

- inside cells

- from the gut into the blood
- past the blood-brain barrier and into the brain
We want Optides that act like drugs. And we want to know which parts of the sequence are essential to those properties.

The traditional drug-discovery path involves taking a molecule that binds to a target and trying to make it act like a drug. Drug companies spend many months or years finding a molecule that binds to a target and tweaking it so that it binds as tightly as possible. Then, they have to take their perfect binder and make it behave completely differently: it needs to have a long half-life in the blood so that it can have its effect; it may need to get past the blood-brain barrier; if it will be a pill, it needs to be orally bioavailable. Making all of these changes to a molecule is really difficult, and each change has the potential to destroy the binding activity they worked so hard to achieve.

By using the opposite strategy -- starting with a molecule that acts like a drug and creating variants that hit our targets -- Optides have the potential to revolutionize drug development.

So far, peptide drugs have been developed without many changes to their natural structure. But new technologies and innovations from our team let us alter peptides (now called Optides after alteration) from nature to become powerful drugs to fight human diseases.

We define and buy thousands of DNA sequences at a time, providing the genetic code for Optides.
We use a mammalian cell-based system developed by our team to produce Optides with just the right structure from the DNA.

And we use extremely sensitive mass spectrometry to detect thousands of Optides in screening assays, even in a complex mixture like blood.

These techniques allow us to produce and efficiently screen our Optide libraries to find members that have the ability to interact with such disease-associated protein. In addition, the stability of our Optides in the body and their demonstrated ability to enter the brain from the blood make us optimistic that such an identified candidate could progress rapidly into trials.

Dr. Olson’s lab, in collaboration with Dr. Ellenbogen, discovered Tumor Paint, which lights up cancer cells in a manner that will hopefully enable surgeons to clearly distinguish cancer foci from normal tissue in real time during cancer operations. Tumor Paint is derived from a peptide that originally was isolated from scorpions – the variant that we plan to use in human clinical trials preferentially binds to cancer cells rather than normal cells.  We use this targeting molecule to deliver a fluorescent molecule specifically to cancer cells. Tumor Paint is now being advanced to human clinical trials through Blaze Bioscience.

This cartoon illustration demonstrates the research approach and potential of Optides for neurodegenerative diseases. In a step by step process, it shows what happens if a normal protein becomes misfolded (thereby causing disease) and how Optides may be able to help repair some of the damage.

A .PDF file of the cartoon is attached at the bottom of the box.