This week's Monday seminar at Birkbeck was given by Jose Saldanha, who works in Willie Taylor's group at the National Institute of Medical Research at Mill Hill, London. Both Jose and Willie are Birkbeck Ph.D. graduates. Jose described his work in using molecular modelling and bioinformatics to design specific antibodies for therapeutic applications.
These antibodies are the "magic bullets" of the title of this blog post. Interestingly, the term was invented by Paul Ehrlich, who won of one of the first Nobel prizes for Medicine - in 1908 - for his work on immunity. The magic bullet, he suggested, would be a molecule that could be targeted directly to a part of the body needing drug treatment, and which a drug molecule could be attached to.
Antibodies (or immunoglobulins) are secreted into the bloodstream in response to the presence of "foreign" molecules (e.g. from bacteria or viruses) and target those molecules in order to destroy the "invader". They do this by binding very specifically to the targeted molecule. Therefore, molecules with essentially the same structure must be able to bind an almost infinite variety of targets.
The mechanism that has evolved for this is a very elegant one. The commonest type of immunoglobulin, Immunoglobulin G (IgG) is a Y shaped molecule made up of four chains, two heavy and two light. Heavy chains contain four copies of the same domain fold (a type of beta barrel) and light chains contain two. The binding site is at the "top" of the "arms" of the Y; the domain of each chain that is closest to the binding site is much more variable in sequence than the others, and is termed the variable domain (the others are constant domains). Each variable domain has three regions that are particularly variable in sequence, termed complementarity determining regions or CDRs, and it is these that bind the target molecule (the antigen). There is a more about immunoglobulin structure on this page from the Arizona Biology Project, and it will be covered in depth in section 11 of PPS.
The only antibody that can be successful as a "magic bullet" is a completely homogenous sample, where every molecule has the same sequence and structure and binds the same antigen. Such identical antibodies, or monoclonal antibodies, can be produced by fusing myeloma (cancer) cells with spleen cells produced by an infected mouse, and selecting and cloning those resulting cells that secrete the required antibody. However, these are mouse antibodies that do not work in humans; they can also cause an immune response because they themselves are seen as "foreign".
In the 1980s, Greg Winter at NIMR developed a process called "CDR grafting" to overcome this, in which the CDR regions from the mouse antibodies are grafted on to a human antibody framework. An alternative technique involves the fusion of a few residues from the mouse antibody with a human one to form a "humanised" antibody. Jose's work at NIMR involves sequence and structure analysis to work out exactly which mouse antibody residues to fuse with which human antibodies for different indications. A "successful" antibody must express well, bind specifically to its antigen and cause no immune or other adverse reaction in human patients. Since starting the project, he has designed more than 30 different humanised antibodies, some of which are in clinical trials.
There are many structures of immunoglobulins and immunoglobulin fragments in the PDB. The most commonly crystallised fragment is the four domains that make up one of the arms of the Y, which is known as Fab (standing for "Fragment, antibody binding"). Look at this one (1BM3), which binds a peptide antigen. And remember - we will be coming back to this topic later in the course.