Issue #67: Drugs and antibodies, immunoglobulins and small molecules

Written by Nobel Laureate Professor Peter Doherty

Last week (#66) I summarised my understanding of where we are with the development – and possible short-term availability – of antiviral drugs (#1) that directly target SARS-CoV-2 and stop the virus from multiplying within our cells. It’s highly likely that any ‘small molecule therapeutic’ that blocks an essential replicative function encoded by the SARS-CoV-2 genome will also inhibit the production of other members of the coronavirus family. Apart from their use now to promote the recovery of people with COVID-19, such drugs would also provide us with an immediate response weapon for tackling possible immune escape variants of SARS-CoV-2, along with any future CoV that jumps from bats into us and has pandemic potential.

Given that we’ve developed vaccines to limit SARS-CoV-2 infection so fast (#44), why hasn’t that also been the case for drugs? If you think about that, you’ll realise that what’s being asked of pharmacology researchers here is that they replicate what our immune system has evolved to do over more than 300 million years of evolution. As discussed in detail earlier, injecting a foreign ‘antigen’ (the SARS-CoV-2 spike protein) triggers the selection – from an incredibly diverse ‘repertoire’ – of molecules that recognise, and bind to (#20) that antigen with incredible specificity. These are, of course, the immunoglobulins, the incredible Igs! So, you might ask, why bother about making drugs, let’s just have the immune system select protective antibodies (#19) then, using modern molecular technology, make them in large quantities? But antibodies have their limitations!

Antibodies (Igs) are ideal for targeting any structure on the surface of a virus particle (the spike protein) or a virus infected cell (#21). The problem is, though, that once an Ig molecule is taken into a cell, it will, like any other phagocytosed (eaten) protein, be chopped into bits and lose all functional capacity. That’s why we need much smaller molecules – chemicals – that can diffuse through the cell plasma membrane to target molecular pathways that are essential for viral replication. While our bodies can make Igs specific for any foreign protein – including the SARS-CoV-2 proteases (CoVPs) – the fact that the CoVPs operate within the cell protects them from any ‘fatal attraction’ to Igs in the serum, or some other extracellular fluid.

So, what we’re asking the drug discovery scientists to do is to either find, or design, a small molecule that can access the cell cytoplasm as a functionally intact chemical, then, bind to, say, one or other of the viral CoVPs and block its essential function. Rather than (as the Ig response does) ‘discovering’, in a regional lymph node (#45), a molecule (or molecules) with an appropriate ‘fit’ from a pre-existing immune repertoire, the drug discovery team might screen ‘libraries’ of synthetic and/or natural (from plants, fungi, termites, sea-stinger or spider venom etc.) chemicals that have been assembled for exactly this purpose.

In its simplest form, drug screening just involves adding the chemical in question to, say, a monolayer culture of VERO cells – a cell line derived decades back from an African green monkey – that is already infected with (or will soon be exposed to) SARS-CoV-2 (#2). The question is simple: does the compound inhibit virus growth as assessed by, if we use the most traditional of all read-outs, the researcher scanning the cells through an inverted microscope (the objectives look upwards from under the tissue culture plate)? He or she will be looking to see if there is an absence of virus-induced cytopathology (cell damage) as a consequence of chemical inhibition.

Obviously, while that approach might be used in a university virology laboratory to check a few compounds made by colleagues in the chemistry department, the rapid screening of chemical libraries in a pharmaceutical company operates at a very different level.  Thousands of chemicals are dispensed individually into the micro wells of plastic plates. Then, say, one or more VERO cells are added, along with SARS-CoV-2, to each of these wells. Bringing the biological (the infected cell) together with the chemical (the small molecule library) in this way requires, of course, industrial grade technology. The cells and potential drugs are dispensed using robots, then automated detection systems are triggered by some chemically-induced change in function, perhaps for an essential molecule that has been labelled to light up when ‘excited by’ a laser beam. Many companies will likely have been screening various libraries as they search for drugs that might be used to treat COVID-19. We haven’t been hearing much, but this may simply reflect the constraints of ‘commercial in confidence?’

Apart from compound screening, there’s also the approach we refer to as ‘rational drug design’. Additional to the work done by virologists and chemists, this involves the effort of investigators we used to know as ‘X-ray crystallographers’ but now call ‘structural biologists’. Such investigators may use ultra-powerful electron microscopes, or a high energy source like the Australian Synchrotron to ‘bombard’ crystals of a biologically active protein (like a CoVP) and build a picture of its three-dimensional structure, or microanatomy. The aim is to identify an ‘active site’ that might be blocked by a ‘designer’ small molecule. We’ll expand on that next week, including how antibodies can enhance that analysis, then go on to a discussion of monoclonal antibodies, the marvellous mAbs.