ZYMVOL releases ZYMEVOLVER 2.0, a new generation of enzyme engineering software

With the advent of Artificial Intelligence, the ZYMVOL team has bet on upgrading its technology to stay at

the vanguard of innovation in the protein engineering field.

The new release includes:

• Machine learning algorithms: When experimental data is provided by the customer, AI algorithms can be used to make more accurate predictions of mutations.
• Network Analysis: Through network analysis, enzyme hotspots can be identified. This allows to  focus only on those residues with a potential effect on the activity, specificity, etc., reducing the number of residues to study (meaning faster simulations) and opening the door to include long range mutations.
• Quantum-mechanics removed from the main pipeline: Faster simulations without losing predictability. It can still be included when it’s critical.
• Modularity: Zymevolver2.0 has been refactored to make it a modular software. Now, it’s easier and faster to include new technologies to the main program. For instance, Alphafold2 is being included to automatically build 3D structures, replacing/complementing homology modeling.

ZYMVOL Senior Scientists Ryoji Takahashi and Ferran Sancho are behind the development of this new

version, which aims to tackle some of the most common challenges scientists face while conducting

enzyme engineering projects. “It represents a significant improvement in our technology. Since the simulations are performed quicker, scientists will have more time to broaden the sequence space exploration (including long-range mutations) and suggest more mutations per round (from 30->90)”, states Ferran Sancho. “This also increases the number of hits: with some customers, only long-range mutations have a positive impact on the enzyme activity. With ZYMEVOLVER 2.0, the number of successful projects also rises”.

For ZYMVOL, the release is seen as a natural step towards their continuous effort to advance its state of

the art methods. “We are now able to have access to other, risky, not used till now enzymes, and we can

face more challenging projects at lower risk”, states Ryoji Takahashi.

Leading the way on Computational Enzyme Engineering

ZYMEVOLVER was the first software pipeline developed by ZYMVOL at the time of its foundation. It’s an in

silico design (ISD) pipeline that combines multiple solutions from bioinformatics, protein design algorithms,

and molecular modeling. It was created with the goal of redesigning a desired enzyme to efficiently

catalyze the target reaction under the customer’s industrial conditions.

Enzyme properties such as activity, specificity and selectivity can be improved, but also enzyme stability

(to temperature, pH, solvent, complex matrices, etc.).

The cornerstone of this technology is the combination of bioinformatics with reliable physics-based

simulations that model the interactions between the substrate and the enzyme. Such simulations follow a

funnel-like scheme with increasing complexity to gradually filter enzyme candidates.

Thanks to these features, ZYMEVOLVER is able to replace the often expensive and time-consuming enzyme evolution experiments with quick, thorough, accurate simulations. Since enzyme evolution takes place in silico (that is, in computers), only a small selection (up to/average 300 candidates) requires being tested in the lab. ZYMEVOLVER has been successfully used already in a wide number of projects with clients worldwide.

EU-Powered Innovation

 

ZYMEVOLVER technology has been developed with the support of “UNLOCK-EDD: UNLOCKing next

generation computer guided Enzyme Discovery & Design”, a project financed by SME Phase2 in the frame of Horizon 2020, the European Union’s research and innovation programme.

The Horizon 2020 program aims to ensure that Europe produces world-class science, removes barriers to

innovation and makes it easier for the public and private sectors to work together in delivering innovation.

Through “UNLOCK-EDD”, ZYMVOL has taken on the challenge of becoming a reference in the computerdriven enzyme engineering market and converting molecular modelling into a commodity. Project goals are:

• To keep improving proprietary technology by implementing artificial intelligence approaches.
• The development of a computational pipeline for enzyme kits.
• The development of proprietary enzymes.

About ZYMVOL

ZYMVOL Biomodeling SL is a privately funded company specialized in in silico enzyme engineering.

Founded in May 2017, the company currently has customers in more than 10 countries worldwide and is

actively engaged in highly innovative and competitive R&D projects. In 2020, the European Commission

awarded CEO Maria Fátima Lucas the EU Prize for Women Innovators. ZYMVOL’s mission is to expand the use of Green Chemistry in the industry by leading the way on computer driven, enzyme engineering technology.

Contact: Andrea Martínez Bernardini; Head of Communications at ZYMVOL (amartinez@zymvol.com)

This Project has received funding from the European Union’s Horizon 2020 research and

innovation programme under grant agreement No 873593.