From the physicochemical properties of structural proteins to the catalytic activity of enzymes, proteins are versatile, functional, and can replace chemical additives with sustainable, healthy, and clean label alternatives.
A major challenge to tapping into this resource, however, is the sheer number: there are billions of proteins in nature and using traditional experimental methods to test each one takes too long.
Chilean biotech startup Protera Biosciences has developed Deep Learning algorithms to mine a database and match different proteins’ physical and chemical properties to their potential functional properties with high accuracy.
Its platform, called Madi, then evaluates the potential of these protein candidates to retain their properties when they are used as ingredients and subjected to different temperature and pH level, narrowing down expensive experimental validations to less than 100 candidates.
The protein ingredients, made using precision fermentation in commercially viable quantities, can then be used to replace of preservatives, emulsifiers, texturisers, colours, and flavour enhancers.
Madi: Protera’s protein engineering platform
The startup finalised its Series A funding round in 2022, raising a total of $10 million. These funds allowed it to launch its AI-based platform, Madi, as a licenced Software as a Service (SaaS) in May 2023. Companies can use Madi to carry out protein engineering by simulating performance and applications before testing at the laboratory.
"We ‘packaged’ Madi into this very nice platform that everyone can now use,” co-founder and COO Francia Navarette told Fi Global Insights, speaking at Future Food Tech in London. “Before, Madi was like the Matrix [displaying] only code, and only people with special knowledge could run something like this. We decided to democratise access to the platform and we developed a nice interface that is very intuitive and really easy to use. It’s a tool for everyone […] in the scientific community.
"We are very interested in supporting the whole value chain when it comes to a new food ingredient from the design to the R&D and then to help [companies] reach commercial viability with their product. This tool can help researchers and companies who are developing new products to assist their new campaigns and increase the success rate,” she said. “They are going to be able to create the automatise their own proteins but also to discover new proteins with new functionalities.”
She added: “That's the main focus of Madi - to really understand the functionality of the protein [...] and also what are the parameters that help the protein have high yields of production so the costs are lower."
Scaling up production of Protera Guard through partnerships
The other main objective of its funding was to forward with production of its internal products, such as Protera Guard, a thermostable preservative for bread and bakery applications that extends shelf life by preventing mould formation at a wide range of pH levels.
“We are now in conversations with larger companies, we already have the processes done, and we are waiting for partners to start production,” Navarette said.
The startup, which was founded in Chile in 2016 but is now headquartered in Paris, recently announced a partnership with ICL Food Specialties to make protein-based, clean label ingredients using precision fermentation that can replace chemical food additives.
“The idea is to develop a protein that is going to increase the organoleptic properties of certain food products,” Navarette said. “What we are doing [at] Protera [is] all the discovery and research to develop this new protein and, with the support of ICL, we are now in the phase of taking this new protein to a scaled level."
Harnessing the enzymatic activity of proteins
In addition to developing protein ingredients that have their own functional properties, ranging from emulsifying to texturizing to colourings, proteins can also be used for their enzymatic activity, Navarette said.
Enzymes are commonly used as processing aids in food manufacturing.
“That means converting one element into another one and that is very relevant in the industry because you can go through an entire process based on enzymes. It's actually how nature does this: our whole metabolism is based on enzymes that are going to help us with digestion, with breathing… Everything you need is based on enzymes so it's very interesting."
Finding protein ingredients that are clean label, healthy, and sustainable but also crucially low-cost is a crucial parameter for Protera Biosciences, Navarette said.
“What is important is to actually be competitive in terms of cost because of course, […] some people can pay a premium for a healthier and more clean label product but the idea is to generate an impact for everyone and not only for the ones who are able to pay for it.
“As scientists we have this mission to decrease the cost [so that] all the good we are doing is for everyone and not just some."
