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Affinity reagents towards SARS-CoV-2
Publication . Costa, Carlos Filipe Santos; Roque, Ana Cecília; Dias, Ana Margarida; Barbosa, Arménio
The interest in biopharmaceuticals has increased over the years, and the recent coronavirus disease 2019 (COVID-2019) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlighted the importance of the continuous improvement of bioprocesses to allow more accessible therapies in large quantities. Biopharmaceuticals are pharmaceutical products of biological origin, like vaccines or monoclonal antibodies (mAb). However, whilst current biopharmaceutical upstream processing can meet their increasing demand, the downstream processing remains largely unoptimised, amounting to the majority of the production costs and suffering from low yields, which further drop with scale-up. Current downstream processing relies heavily on chromatography, the platforms of which are oftentimes expensive and unsustainable, thus representing targets of potential optimisation to improve purification efficiency.
The design of a novel synthetic affinity ligand towards the SARS-CoV-2 spike protein is herein described. This also served as a proof-of-concept for the development a workflow to quickly produce solutions towards COVID-19, and could be easily adapted to future pandemics. A combinatorial library was designed in silico based on existing ligands and screened against spike protein, both experimentally under chromatographic conditions, and computationally, culminating in a lead ligand with high binding and recovery of original strain spike protein, its receptor-binding domain (RBD), and an Omicron variant spike protein, and an enrichment factor of approximately 15.
Finally, a molecular modelling (MD) protocol was optimised using, as a case study, the binding of a mutated Staphylococcus aureus protein A to immunoglobulin G (IgG).
Rational design of a small peptidomimetic ligand to capture a viral spike protein
Publication . Costa, Carlos Filipe Santos; Lychko, Iana; Natal, Carolina Mota; Barbosa, Arménio Jorge Moura; Dias, Ana Margarida Gonçalves Carvalho; Roque, Ana Cecília Afonso; DQ - Departamento de Química; UCIBIO - Applied Molecular Biosciences Unit; Elsevier
The availability of purified antigenic proteins is critical to develop agents to prevent, diagnose, or treat infectious diseases. In this context, antigenic proteins are produced by recombinant expression in host cells and further purified, typically by chromatographic methods. Chromatographic steps that allow the one-step capture of the antigenic protein are important to streamline the purification train. Here, we present the design and development of an adsorbent bearing a synthetic affinity ligand to capture the SARS-CoV-2 spike protein, used as a model antigenic protein. A 120-ligand combinatorial library was designed in silico and then synthesised in solid phase, and both were computationally and experimentally screened for binding to the spike protein. One lead ligand was selected for yielding > 95 % binding, and 64–73 % recovery of original strain spike protein, its receptor-binding domain (RBD), and Omicron BA.5 variant spike protein. An enrichment factor of 15 was found when capturing the spike protein from a clarified supernatant sample. Complementary molecular dynamics simulations allowed a better understanding of the interactions between the lead ligand and the spike protein, which mainly consist of hydrophobic interactions, some hydrogen bonds and salt bridges formed with an important ligand carboxyl group. Overall, the methodology is a fast and efficient platform to develop affinity ligands for the purification of antigenic proteins in future pandemics.
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Fundação para a Ciência e a Tecnologia
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FCT_CPCA_2023_01
Número da atribuição
2023.10436.CPCA.A1