02 Aug 2021
Setting it Straight: The beginnings of rational drug design
Much of biology is about the complementarity of shapes, and the chemical interactions that allow small regions on protein 1 (P1) and protein 2 (P2) to bind together. Our P1 might be the peptide (a protein bit) hormone insulin that binds to P2 proteins (receptors) on, say, our liver cells. The ‘chemical’ signal that goes across the cell membrane as consequence of insulin binding ‘instructs’ the liver to store glucose as glycogen and decrease blood glucose levels. Most relevant to COVID-19 and vaccine efficacy (#51), P1 would be an antibody – or immunoglobulin (Ig) – molecule, while P2 is the spike protein (SP) of SARS-COV-2. I’m going to summarise a little of what I wrote earlier in 2020 and use some scientific terms here. If you’re unfamiliar with immunology, maybe go back and take a look at #18- #22 of these essays.
Virus neutralisation happens when a unique variable region (V) at the tip of the combined Ig heavy and light chains Ig (IgVSP) recognises the ‘micro-anatomy’ of the SARS-CoV-2 SP receptor-binding domain (RBD) and attaches with sufficient ‘affinity’ to hold these two proteins together. The consequence of that ‘fatal attraction’ (for the virus) is that the spike protein-specific IgVSP ‘covers’ the SP RBD and prevents the virus attaching to our cell-surface ACE-2 molecules. That ‘steric inhibition’ blocks virus access to the cytoplasm of our respiratory epithelial cells and prevents them from being taken over to become SARS-CoV-2 producing ‘factories’.