Aminoverse is a Dutch biotech CRO where enzyme research and development (R&D) meets AI. Founded in January 2020 near the three-country border point between The Netherlands, Belgium and Germany; it operates a 200 qm wet lab space with ML-1/GMO certification. The team comprises of entrepreneurs and scientists with backgrounds from genetics, molecular biology, biochemistry, computational chemistry, machine learning and fermentation.

Aminoversians, as the team likes to call themselves, believe enzymes are a major contributor to solve the current and future challenges globally. By harnessing and training the workforce of nature, it helps its customers make an impact in sustainability, develop new products and generate valuable innovation.

Top of the field services Aminoverse provides its clients

Enzyme Discovery: The enzyme discovery process at Aminoverse includes AI-augmented enzyme modeling to evaluate the compatibility between substrate, the enzyme backbone and potential inhibitors. In combination with EnzyNAV AI, each enzyme candidate is assigned a predicted solubility and activity score to select the final candidates for wet lab testing. Aminoverse offers custom enzyme panel generation and worldwide shipment to give its clients rapid access to the target enzymes. Enzymes can be provided in frozen cell lysate or culture supernatant, as lyophilized powder or as cell cryo-stocks.

Enzyme Profiling: With more than 100 assays available for the typical enzyme classes, Aminoverse is able to measure any enzyme property under tunable conditions. When the enzyme and its application is not among them, the client can request dedicated assay development for agar plate, microtiter plate, and vial formats. A readout via colorimetric or fluorometric signals is most common, yet it does offer luminescence as well as analytical chemistry covering HPLC and GC too. A screening through-put of >1000 enzyme variants per day is just one part, excellent signal-to-noise ratios, reliability, reproducibility and a sufficient dynamic range are needed as well to facilitate proper library screening

Enzyme Engineering: Aminoverse’s wet lab data generation and machine learning algorithms combine the best of both worlds with a clear focus, which is to design the best possible enzyme in the shortest time at minimal budget.

By pairing state-of-the-art wet lab workflows with latest advancements in machine learning, a fundamental and holistic knowledge base will be generated for the customer’s target enzyme. This company’s proprietary AI technology ‘EnzyMAP’ is rooted in real wet lab data and allows predicting the effect of all point mutations across the entire enzyme sequence, requiring 80 % less screening capacity and budget. Simultaneous screening for several enzyme properties allows the identification of mutations that improve multiple parameters at the same time or which mutations have detrimental effects on enzyme performance.

Aminoverse’s proprietary AI technology “EnzyREC” allows predicting the probability of combinatorial enzyme mutants to fold correctly and be fully functional while combining all the benefits in one superior enzyme.

Enzyme Libraries: In a holistic library, usually every amino acid position is mutated to all other 19 canonical amino acid species, essentially saturating each position with nature’s full diversity. Known occasionally as deep mutational scanning library (DMS), site evaluation library (SEL) or global site saturation mutagenesis library (GSSM), a holistic library enables to identify the true best mutations, unveils which mutations are well and less well tolerated and shows mutations that are lethal to an enzyme’s activity or integrity.

Aminoverse’s molecular biology and genetics experts have devised a methodology allowing it generate fully customizable holistic libraries with the following features:

• Mutations at any desired amino acid position
• Any defined amino acid species and number, from 1 to 19, from same species to different in every position
• Any enzyme length, no length restrictions
• NGS verified >95% average correctness, i.e. < 5% of variants are incorrect or missing
• Ready-2-Screen format: E. coli transformants delivered in 96well MTP, ready to be cultured in immediately screened. No work-up necessary
• Each variant is located in a defined well in an MTP

The advantages of Aminoverse’s Re-Combinatorial Enzyme Library services are:

• Recombine any number of mutations anywhere in the enzyme – no restrictions
• Any amino acid species allowed per mutation site, from 1 to 19
• Scar-free cloning, no restriction sites
• Quality check by NGS
• Ready-2-Screen format: E. coli transformants delivered in 96well MTP, ready to be cultured in immediately screened. No work-up necessary (other formats available upon request)

Enzyme Production: Aminoverse is a trusted partner for scaling up the customer’s production from microgram scale in microtiter plates over milligram scale in shake flasks to gram scale in a 15L bioreactor. For high enzyme demand up to kg scale, Aminoverse relies on its network of dedicated enzyme CDMOs.

Aminoverse offers enzyme development and production in three different microbial hosts:

Escherichia coli are a well-characterized and versatile gram-negative bacterium that has been extensively used for recombinant protein expression. It is a fast-growing organism that can produce high yields of protein, making it an attractive host for enzyme production.

The gram-positive bacterium Bacillus subtilis efficiently secretes enzymes to the cell culture supernatant, making it a highly useful platform to obtain semi-purified enzyme with minimal downstream processing. Aminoverse typically recommends its non-sporulating strains with protease knock-outs when the target enzyme is naturally secreted by Bacillus species like proteases or other digestive enzymes.

The fungal host Pichia pastoris (Komagataella pastoris) is known for its ability to produce and secrete enzymes at high yields. As eukaryotic organisms, they naturally perform post-translational modifications, such as di-sulfide bond formation and glycosylation.

Based on its customer’s specifications, Aminoverse applies the necessary downstream processes including chromatographic separation, filtration, dialysis and centrifugation. In-house quality control not only ensures the purity requirements are met but also conducts enzyme activity checks before material is shipped.

David Schönauer, Chief Executive Officer 

“Like Google Maps is helping travelers to efficiently reach their destination, we put the right enzyme into our customers’ hands for them to create value, as a start-up, mid-size company or large corporation.”