The downstream processing of natural active molecules remains the most significant cost in the production pipeline. This considerable cost is largely attributed to rigorous chromatographic purification protocols. In an ongoing effort to abate the dependence on chromatography in downstream processing, alternative affinity matrices in the form of magnetic particles (e.g., iron oxide) have emerged as viable candidates. Nevertheless, biotechnological applications of iron oxide particles are still confined to the research level or for low-throughput clinical applications. Herein, we describe an efficient, quick, and environmentally friendly method for the isolation of astaxanthin and lutein, two carotenoids with very similar chemical structure, from extracts of the microalga Haematococcus pluvialis. The technology proposed, named Selective Magnetic Separation (SMS), is based on the use of magnetic materials carrying affinity ligands that bind carotenoids and is applied as second step of purification. The method, thanks to functionalized magnetic nanoparticles, reduces the use of organic or toxic solvents. In the present work, we examined the most efficient binding conditions such as temperature, magnetic nanoparticles concentration, and elution time, as well as their effects on carotenoids recovery, with the aim to improve the non-covalent binding between the ligand (amines) and astaxanthin/lutein. Our initial results clearly showed that it is possible to use magnetic separation as an alternative to chromatography to isolate important and valuable compounds. © 2022 by the authors.

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