Cyrus Biotech, CAD for molecules, announces new features to handle any pharmaceutical molecule

Computer Aided Design or CAD software has enabled the high technology world of machines and microchips and skyscrapers that we inhabit in 2018. This software was popularized by the aerospace industry in the late 1970’s and early 1980’s, and most modern machines and buildings are designed with CAD before being tested and manufactured.

Prior to CAD (and gender equality in the workplace, but we digress), design looked like this.

Design before CAD software

Now, in 2018, design can be handled much more efficiently and rapidly in software like Autocad (below). Fewer people are required to do the same amount of work, and more complex designs can be constructed, often objects so complex that they could not have been envisioned using paper and pencil. Objects designed in CAD can also be tested by CAD software — CAD testing can ensure that a bridge will withstand its designed load or that an airplane wing will safely handle excessive pressure.

Design using CAD software in 2017

Cyrus Bench is CAD for molecules.

Atoms are the building blocks of molecular structure. The ability to determine how these atoms are arranged allows us to understand the structure of larger molecules such as proteins, and to create new medicines. In the world of biochemistry, people have been able to “see” protein structures down to the atomic level since the late 1950’s using x-rays. In early work that required physical model building. Below, one of the key pioneers of this field, Nobel prize winner John Kendrew, is pictured building such a model. A very limited amount of early software aided in building these models, but they were mostly created through painstaking work and mathematical models combined with laboratory measurements. These tools did not allow for the design of new protein drugs, the way engineers and architects design new machines and buildings. Protein CAD was not yet a reality.

Building protein models (of myoglobin) before modern software, with Nobel prize winner and pioneer of x-ray crystallography John Kendrew
Copyright by the Laboratory of Molecular Biology in Cambridge, England.

Starting in the mid 1970s, methods to model proteins were developed, using the principles of physics. These could not design new protein drugs. In the 1990’s a new approach that used both physics and statistical approaches was pioneered by Professor David Baker at the University of Washington — this became known as the Rosetta software package. In the late 1990’s and early 2000’s, scientists used Rosetta to correctly predict protein structures for the first time. By 2010 scientists proved they could use Rosetta to design new useful proteins, just as architects design new buildings using CAD. By 2018 two of these Rosetta-designed molecules are being tested in human clinical trials and are on the pathway to eventually becoming drugs.

CAD for protein molecules had finally been born.

But there was a catch, Rosetta is very challenging to use, requires years of training, thousands of computers, and requires other software in order to run correctly.

At Cyrus we have taken the next step by extending Rosetta with a web based software-as-a-service (SaaS) interface running on the cloud, designed for scientific users. Cyrus Bench is pictured below — just like Autodesk AutoCAD or Dassault SolidWorks before it, Bench democratizes CAD for protein molecules to all protein engineers and scientists.

Cyrus Bench CAD software in a web browser

Cyrus Bench CAD is now for all molecules.

This week Cyrus Biotech is announcing a major step forward for our main product Cyrus Bench: Support for small molecule ligands. We have announced this in a separate Press Release Here.

In this section we explain this new addition to our software in simple, non-scientific language.

Drugs have been used by humans for millennia, and modern drugs from the Pharmaceutical and Biotech industries are more powerful than ever — they prevent viral attack, halt deadly bacterial infections, keep asthmatics breathing, keep diabetics alive, tame the ravages of mental illness, put cancer in remission, and help us to live long and healthy lives.

At an atomic level, drugs are either small molecules or Biologics–names that reflect their relative sizes. Small molecule drugs are typically comprised of fewer than a few dozen atoms. Proteins, in contrast, can be as large as 20,000 or more atoms.

Protein-based drugs make up most so-called Biologic drugs — these are vaccines against deadly infections, monoclonal antibodies that extend the lives of cancer patients and therapeutic proteins like insulin for diabetics. A typical antibody molecule is pictured below. Other than biologics, all other drugs are small molecules, making up 75% of all drug sales. As an example, below we show Aspirin, an ancient medication (about 2400 years in human use) that is also perhaps the most famous small molecule drug.

Cyrus Bench is based on Rosetta, which in its standard state only handles proteins efficiently, but does not have automated tools to accommodate small molecules.. Up until this week, Rosetta could only conveniently handle proteins, and could therefore be used for modeling less than 5% of all drugs.

This week all of that is changing.

An antibody protein or Biologic drug

A well-known small molecule drug, Aspirin

 

 

 

 

 

 

 

 

 

 

 

We are announcing Cyrus’s partnership with Openeye Scientific Software, a pioneer and leader in the modeling of small molecules with a special focus on high-impact applications in the Pharmaceutical industry. Over the last 24 months Cyrus scientists and software developers have worked to integrate and automate small molecule handling from Openeye into Cyrus Bench.

A drug target with a candidate small molecule loaded in Bench

As of this week, for the first time, biochemists without years of highly specialized computational experience can model small molecules inside proteins using Rosetta in Cyrus Bench. This makes the large majority of drugs — small molecules — accessible to users across Pharma, Chemicals, Consumer Products, and Academia. We are rolling this capability out to a select group of early customers before launching general availability later this year.

We are very excited to see what new drugs can be discovered, diseases cured, and lives improved or even saved using Cyrus Bench!

Dr. Lucas Nivon, CEO, Cyrus Biotechnology

Cyrus Biotechnology and OpenEye Scientific Software Announce Collaboration and Cheminformatics Integration to Expedite New Drug Design and Development with Cyrus Bench Platform

SEATTLE, WA October 30, 2018 — Cyrus Biotechnology, Inc., a Seattle-based biotech software company commercializing Rosetta, an advanced protein design platform, announced today that through a collaboration with OpenEye Scientific Software, Inc., a leader in computational molecular design, capabilities have been developed that allow small molecule ligands to be processed and used with Rosetta and within the Cyrus Bench® platform for computational protein drug design.  

“We are very excited to integrate these new ligand tools in our protein design platform,” said Cyrus CEO Dr. Lucas Nivon. “Previously scientists have had to endure incompatible tools and sub-par results when carrying out protein-ligand modeling, but with the new automated small molecule integration, we have created a straightforward and reliable tool our customers can use to design new therapeutics and industrially useful enzymes.”

Rosetta software is the world leader in protein modeling and design. However, including small molecule ligands when using Rosetta has been problematic, severely limiting its utility for many pharmaceutical, consumer products and other applications where protein/small-molecule interactions are critical.

Cyrus has developed new scientific tools that integrate OpenEye’s cheminformatics and modeling technologies to allow Cyrus customers to:

  • Parameterize small molecules robustly and with high accuracy
  • Carry out enzyme and general protein design in the presence of a ligand.  

OpenEye CEO, Dr. Anthony Nicholls, said, “We are excited to be a part of Cyrus Bench® by providing OMEGA, the world’s best validated and industry-leading conformer generation tool, along with OpenEye’s robust and highly performant cheminformatics and modeling

capabilities. We look forward to seeing the science both companies will enable by this partnership.”

OpenEye has been a leader in cheminformatics and molecular modeling for over twenty years. OpenEye’s toolkit platform allows flexible and powerful workflow integration with Cyrus Bench and Rosetta software. Robust and seamless support for state-of-the-art small molecule/protein interactions is now available to Bench users.

This software integration has been tested and debugged on thousands of examples from the Protein Data Bank and will robustly allow small molecules to be included in most Rosetta calculations in Bench.

This new set of tools for protein modeling in the presence of arbitrary small molecules—utilizing a simple-to-use Rosetta GUI–is now available to existing subscribers to Cyrus Bench® and can be accessed by new customers by subscribing to the Cyrus Bench® suite of tools.

Cyrus Biotechnology

Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering protein modeling and design capabilities to the Biotechnology, Pharmaceutical, Chemical, Consumer Products and Synthetic Biology industries. Cyrus was founded in 2014 as a spin-out from the University of Washington, and offers Cyrus Bench®, a Software-as-a-Service (SaaS) platform for protein structure prediction via homology modeling, protein modeling, protein stabilization, protein engineering and protein design to accelerate discovery of biologics and small molecules. Cyrus Bench is based primarily on the Rosetta molecular modeling and molecular design software package from the laboratory of Prof. David Baker at the University of Washington, along with associated software. Cyrus Bench offers the world-leading protein structure prediction pipeline of Rosetta and SparksX, the top structure prediction software in the bi-annual CASP competition and the weekly CAMEO competition, as well as the only protein engineering software experimentally proven to design new proteins completely via software. Cyrus customers include 10 of the top 20 Global Pharmaceutical firms as well as smaller Biotechnology and Chemicals firms. Cyrus is financed by leading investors in both Technology and Biotechnology, including Trinity Ventures, Orbimed, Springrock Ventures, Alexandria Venture Investments, the W Fund, and others. For more information please visit

https://cyrusbio.com/  

OpenEye Scientific

OpenEye is a scientific leader in computational molecular design based on decades of delivering useful applications and programming toolkits. Our scientific approach changed perception of what’s possible with the speed, robustness and scalability of our tools. OpenEye recently released Orion, the only cloud-native fully integrated drug discovery platform, combining unlimited computation and storage with powerful tools for data sharing, visualization and analysis in an open development platform.  Founded in 1997, OpenEye Scientific Software Inc. is a privately held company headquartered in Santa Fe, NM, with offices in Boston, Cologne and Tokyo. For more information please visit https://www.eyesopen.com

NOTICE: The information contained in this document is dated as of October 30, 2018.  Cyrus Biotechnology, Inc. (the Company) disclaims any obligation to update such information after such date.  This document contains forward–looking statements reflecting the Company’s current expectations that necessarily involve risks and uncertainties.  Actual results and the timing of events may differ materially from those contained in such forward-looking statements due to a number of factors and the Company undertakes no obligation to revise or update any forward-looking statement to reflect events or circumstances after the issuance of this press release.

Cyrus Press Release 10/30/2018

Cyrus Contact – Lucas Nivon
lucas@cyrusbio.com
206-258-6561

OpenEye Contact – Fred Livingston
info@eyesopen.com

Cyrus Biotechnology to Present at the Immunogenicity & Bioassay Summit on October 25, 2018

SEATTLE, WA October 12, 2018 — Cyrus Biotechnology, a Seattle-based firm offering access to Rosetta, the most advanced software available for protein modeling and accelerated drug discovery, announced today that it will present at the 10th Annual Immunogenicity & Bioassay Summit, to be held in Washington DC on October 22-25, 2018.

Dr. Indigo King, a computational protein design and immunology specialist, will present at the Immunogenicity Summit as follows:

Abstract: Computational protein design has the potential to create a novel class of therapeutics with tunable biophysical properties, but immunogenicity remains a concern. We have combined machine learning with structure-based protein design to identify and redesign T-cell epitopes without disrupting function of the target protein or creating new epitopes. We have verified the method experimentally, removing T-cell epitopes from a gene therapy target, an immunotoxin, and GFP while maintaining folding and function.

Date: Thursday, October 25th, 2018

Time: 3:25 PM EDT

Track: Immunogenicity Prediction & Control

Room: Edison ABC

Venue: The Westin Alexandria, 400 Courthouse Square, Alexandria, VA 22314

For more information on immunology with Cyrus, see Cyrus Biotechnology Launches Immune Epitope Prediction Software.

 

Cyrus Biotechnology

Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering protein modeling and design capabilities to the Biopharmaceutical, Chemical, Consumer Products and Synthetic Biology industries. Cyrus was founded in 2014 as a spin-out from the University of Washington, and offers Cyrus Bench®, a Software-as-a-Service (SaaS) platform for protein structure prediction, modeling, stabilization, engineering and design to accelerate discovery of Biologics and Small Molecules. Cyrus Bench is based primarily on the Rosetta software package from Prof. David Baker’s lab at the University of Washington, along with associated software. Cyrus Bench offers the world-leading protein structure prediction pipeline of Rosetta, as well as the only protein engineering software experimentally proven capable of designing entirely new proteins. Cyrus Bench is powered by Rosetta, which has been developed over near 20 years, and validated by well over 700 publications that demonstrate efficacy both in vitro and in vivo. Cyrus is financed by experienced investors in both Technology and Biotechnology, including Trinity Ventures, Orbimed, Springrock Ventures, Alexandria Real Estate, the W Fund, and others.

NOTICE: The information contained in this document is dated as of October 12, 2018.  Cyrus Biotechnology, Inc. (the Company) disclaims any obligation to update such information after such date.  This document contains forward–looking statements reflecting the Company’s current expectations that necessarily involve risks and uncertainties.  Actual results and the timing of events may differ materially from those contained in such forward-looking statements due to a number of factors and the Company undertakes no obligation to revise or update any forward-looking statement to reflect events or circumstances after the issuance of this press release.

Cyrus Press Release 10/12/2018

 

Cyrus Contact Lucas Nivon
lucas@cyrusbio.com
206-258-6561