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Unlimited by enzymes found in nature, Arzeda’s groundbreaking technology enables engineering enzymes for virtually any reaction. Our process harnesses computational power to rapidly design and evaluate new enzymes in silico1. We can generate a library of potential enzyme variations exceeding 1050, in less time and for less money than traditional techniques. This vast library of candidates greatly increases the chance of finding an ideal biocatalyst and thereby offering solutions that are currently inaccessible with traditional enzyme engineering approaches. Thus, Arzeda’s approach represents a new paradigm in enzyme technology and opens up previously inaccessible business opportunities.
Fig 1: Arzeda's process flow
Arzeda’s enzyme design technology vertically integrates Arzetta™, our proprietary computational platform, and enzyme validation resulting in a two-step process to obtain active enzymes. Arzeda has executed an exclusive license with UW for the patents related to two of the families of de novo enzymes that Arzeda’s founders created as members of the Baker lab relating to Diels Alder and Aldol catalysts. Arzeda’s multi-faceted approachArzeda approaches the design of novel enzyme activities like building blocks: ideal active sites can be mixed and matched with protein scaffold to yield catalysts with specified properties. Our algorithm can accept multiple input: active site designed from scratch, part of existing active sites combined with novel features or entire existing active sites. These active sites are then combined with a library of highly expressed proteins or your proteins of choice resulting in near infinite numbers of possible enzymes. Output will be a custom and potentially patentable enzyme.
Fig 2: Mixing and matching of enzyme active sites (yellow triangle) and protein scaffolds (blue circle) with subsequent prioritization of computer models.
The underlying energy function and intelligent search algorithms allow the rapid screening of very large libraries (>1050) in silico, which makes it possible to much more dramatically remodel an enzyme in significantly less time. This enables us to explore a much larger biochemical space and to find the best solution. And the good thing is that we only need to test the best ones in the test tube. Therefore, our screened library size is not limited by our in vitro capabilities! View bigger version of video in lightbox Movie 1: In contrast to directed evolution, where enzymes can only be optimized to a local optimum (purple circle), Arzeda’s technology is able to truly explore the large sequence space and identify the best solution (blue circles).
Arzeda’s core capabilitiesOur core competences enable the development of enzymes for any reaction of interest where current biocatalysis technology faces several significant obstacles:
See how we use our Computational Enzyme Design Technology – Arzetta™, to design new enzymes De Novo, Combine Existing Active Sites with Proteins or Remodel Existing Enzymes. Computational Enzyme Design Technology – Arzetta™The process begins with the chemical reaction of interest. The ideal catalytic machinery for this reaction is defined and supplied to Arzetta™ which generates a large, virtual library of model enzymes containing the active site of interest. The left movie shows how the Disembodied Active Site™ is grafted onto a protein. The right movie demonstrates how a binding pocket with ideal shape complementarity is obtained. View bigger version of video in lightbox Movie 2: The movie shows how the Disembodied Active Site™ is grafted onto a protein. Subsequently, the binding pocket with ideal shape complementarity is obtained through computationally optimize the amino acid sequence surrounding the active site. The computational explosion of candidate enzymes is managed by prioritizing each design according to its predicted catalytic power. The top-ranked enzyme candidates move on for expression and validation of activity at the bench. De Novo Enzyme Design
Fig 3: De Novo approach
A distinguishing Arzeda capability is engineering active sites entirely from scratch. This approach differs from previous attempts in that it does not require the use of already existing enzymes as starting points – it is true de novo design. Using our Computational Enzyme Design Technology outlined above Arzeda introduces entirely new active sites and therefore enzyme activities onto protein scaffolds. This important component of the Arzeda technology has been successfully applied to 3 reactions which lack a natural enzyme: Aldol2, Kemp Elimination3, and Diels-Alder4. Arzeda built families of enzymes that achieved rates up to 105 times the uncatalyzed rate, achieved multiple catalytic turnovers, and controlled reaction stereoselectivity. Combine Existing Active Sites with Proteins
Fig 4: Grafting of existing active site (yellow) into protein scaffold of choice (blue)
This protocol is a variation of the De Novo Enzyme Design as it uses an existing active site instead of generation a novel one from scratch. This is especially useful/handy/interesting when you would like to marry an enzyme activity with protein features of your choice! Remodel Existing Enzymes
Fig 5: Remodeling of existing enzyme for new activity
Many enzymes are suboptimal for a desired commercial application – in terms of thermostability, pH stability, pH optimum, and/or substrate specificity. To date, our technology was successfully applied to stabilize an enzyme5 or switch specificity6,7. Our expertise in large-scale docking of small molecules8,9 can result in fast solutions for remodeling of active sites to accommodate new substrates.
References1 Zanghellini, A. et al., Protein Sci. 2006; 15: 2785-2794 PubMed [link] |
