Protein Engineering Solutions (PluriZymes)

Nostrum Biodiscovery's Protein Engineering Solutions, including their proprietary PluriZymes platform, offer a comprehensive suite of computational and AI-driven services designed to enhance, evolve, and de novo design proteins and enzymes for industrial, pharmaceutical, and environmental applications. The platform combines an in silico protein evolution methodology with molecular modeling (MM) capacities and increasingly integrates artificial intelligence tools — including protein language models — to accelerate mutant filtering, sequence generation, and smart library design.

These solutions are aimed at companies and researchers across chemicals, food technology, plastic recycling, and biopharmaceutical industries who need tailored enzyme or protein engineering capabilities without building the computational infrastructure in-house.

Enzyme Bioprospecting

• Utilises a unique AI and molecular modeling (MM) pipeline to rapidly identify proteins capable of performing a target reaction under specific conditions.
• Computationally assays thousands of sequences to shortlist candidates efficiently.
• Employs a proprietary protein language model that can be fine-tuned to a specific enzyme family, enabling de novo sequence generation and inference of smart mutation libraries.

PluriZymes Design

• Enables the design of multitasking enzymes — called PluriZymes — tailored to industrial process needs.
• Uses computer-aided rational design to engineer de novo active sites, introducing new functionalities into existing protein scaffolds.
• Supports multiple chemistries within a single protein scaffold, enabling cascade reactions in one enzyme.
• Research has been published in high-impact journals including Nature Catalysis, validating the approach.

Plastic Recycling: PET and PEF Engineering

• Developed a catalytic protein nanopore capable of decomposing nanoparticles of polyethylene terephthalate (nPET), with potential applications in filtering and removing nPET from wastewater treatment plants.
• Actively participating in the NextGenerationEU-funded FURENPOL project, focused on discovering and engineering optimal enzymes for the production of polyethylene furan-2,5-dicarboxylate (PEF), a bio-based alternative to PET.
• Supports the transition toward a circular economy by enabling enzymatic recycling and reuse of polyester plastics.

De Novo Design of Binding Proteins

• Offers expertise in designing small- and medium-sized proteins that bind to a target of interest.
• Has collaborated with Navigo Proteins GmbH to demonstrate tools that accelerate binding protein discovery campaigns.
• Provides tailored assistance for custom binding protein design projects.

Antibody Engineering

• Supports in silico antibody engineering for clients who have identified a hit against a specific target.
• Recognises that computational antibody discovery is still an emerging field, with experimental validation remaining central to development.
• Is developing a more automated and refined toolkit leveraging generative AI — particularly protein language models — combined with MM techniques to predict binding affinities and accelerate in silico antibody discovery.

Computational Protocol for Hydrolase Site Design

• Uses the PELE platform to explore non-functional binding sites within proteins.
• Functionalises identified sites through site-directed mutagenesis, incorporating the catalytic triad of a serine hydrolase to create new enzymatic activity.

Selected Publications

• Computationally Driven Rational Design of Substrate Promiscuity on Serine Ester Hydrolases — ACS Chemistry for Life
• Modulating Fatty Acid Epoxidation vs Hydroxylation in a Fungal Peroxygenase — ACS Publications
• Increasing Redox Potential, Redox Mediator Activity, and Stability in a Fungal Laccase by Computer-Guided Mutagenesis and Directed Evolution — ACS Publications
• Sub-micro- and nano-sized polyethylene terephthalate deconstruction with engineered protein nanopores — Nature Catalysis
• A Plurizyme with Transaminase and Hydrolase Activity Catalyzes Cascade Reactions — NIH National Library of Medicine

Nostrum Biodiscovery's protein engineering services are delivered through a combination of proprietary computational pipelines, AI-driven tools, and deep domain expertise, making them suitable for clients seeking to accelerate enzyme discovery, optimise industrial biocatalysts, or develop next-generation biologics. The company has received support through the ICEX NEXT programme and co-financing from the European FEDER fund.