Protein Engineering, Immunotoxins and Drug Designing - Engineering of Macromolecules

Protein Engineering, Immunotoxins and Drug Designing - Engineering of Macromolecules - Protein engineering and drug designing is a multidisciplinary approach, which involves computer aided molecular modelling (CAMM) based on the study of three dimensional structures of receptor and functional macromolecules. During the last 10 years, following two major developments, made it possible to change the structure of macromolecules in a predetermined way leading to their desired functional role.

First is the possibility of site directed mutagenesis permitting changes in genes at known sites leading to modification of function in a predetermined way; and second is the availability of computational and graphical tools which allow, on the screen, the display and exploration of the three dimensional structures of proteins.

These two new developments allow us to decide about the three dimensional structure of protein/drug needed for a desired purpose, before using recombinant DNA technology (for proteins), or organic synthesis (for drugs). The different steps generally involved in protein engineering, and include the following:

(i) The protein sample is prepared from an organism and it is characterized with a ligand (e.g. enzyme substrate, receptor - hormone or antibody antigen interaction).

(ii) The three dimensional (3-D) structure is studied through NMR (nuclear magnetic resonance) and X-ray diffraction patterns of crystals.

(iii) 3-D structure is displayed with interactive computer graphics and the available information is used to suggest a novel design suiting the needs.

(iv) The desired DNA sequence that is expected to give the novel designed protein is then either synthesized or obtained by site directed mutagenesis of an available gene.

(v) The novel gene is introduced into a suitable expression system and the gene product is purified and characterized biochemically.

(vi) If biochemical characterization does not satisfy the earlier predicted structure, the cycle may be repeated again, till the desired structure is available.

It should be noted that the above steps of protein engineering share steps used for designing of drugs, insecticides, herbicides, and peptide vaccines. The only difference is that the drug designing concerns only the ligand, which can be modified more effectively by chemical synthesis, while in protein engineering recombinant DNA technology is used.

The three dimensional structures for a few related proteins will normally be available to a protein engineer, while planning production of novel protein or a drug for the desired needs. Therefore, as discussed above, a procedure is needed for generating the three dimensional structure of the macromolecule (protein or drug) of interest.

This may be achieved de novo or through modelling from homologous or analogous proteins, if they are available. This is described as knowledge based modelling and designing through the use of computer software including computer graphics, computer simulations and databases (computer software includes the entire set of procedures and programmes to be used on the computer to solve problems along with the operating aids).

The computational aspects of knowledge based approaches in the designing of macromolecules (proteins, drugs, vaccines, etc.) and the curious readers will find details elsewhere (Proc. Trans. R. Soc. Lond. B. 324:447-460, 1989).