Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online




Last Updated: 03/31/16

Learning Goals/Objectives for Chapter 5E:  After class and this reading, students will be able to

  • describe the basis for the following methods used to design drugs:
    1. combinatorial drug development
    2. computer-aided design
    3. in situ click chemistry
  • describe drugs that target specific
    1. proteins
    2. DNA
    3. RNA
  • describe the benefit of drugs that
    1. are mutivalent
    2. perturb equilibrium

E10.  Diseases of Protein Misfolding and Aggregation

As we discussed earlier, many diseases are caused by protein misfolding, which is often associated with aggregation.  (See What's New in Protein Chemistry: Protein Aggregates - Not Just  Junk.)  Neurological diseases associated with these processes include Jacob-Kreutzfeld disease (associated with prion proteins) and  Alzheimer's and other amyloid diseases such as Familial amyloidotic polyneuropathy (FAP).  In FAP,  transthyrein, which normally exists in blood as a homotetramer dissociates into monomers which can aggregate into fibrils.   Val30Met and Leu55Pro mutations promote dissociation of the tetramer and formation of aggregates.  Conversely, Thr119Met inhibits tetramer dissociation.  The aggregates deposit in heart, lungs, kidney, etc, leading to death.   Hammaarstrom et al. have shown that the Thr119Met mutation increases the free energy of the transition state for the tetramer to monomer equilibrium, inhibiting that reaction and subsequent aggregation of the monomers.  Amino acid 119 is at the dimer interface, consistent with these findings.  They also have developed small molecule inhibitors of aggregation which appear to bind preferentially to the tetrameric state, increasing the activation energy for the transition state to the monomer.

There are many possible ways to prevent protein aggregation that work at various stages along the pathway of aggregation.  For instance, in Alzheimers disease, secretase inhibitors would decrease the concentrations of amyloid beta (Aβ) protein, inhibiting its aggregation.  Another possibility is to develop ligands (either small or large) that would bind either to the variant form of the protein (a partially unfolded or molten globule form of the protein) which would shift the equilibrium toward the variant monomer form, or to the normal monomer form of the protein, which would shift the equilbrium away from the variant form that aggregates.  An example of this has been been described.  Dumoulin et al. develop an camelid (camels and llamas) antibody against the normal human lysozyme.  (Camelid antibodies were chosen since they are smaller than other vertebrate antibodies and may have a better chance of actually getting into cells and binding target proteins.)  These antibodies, when added to a mutant form of lysozyme (Asp67His) which aggregates and leads to systemic lysozyme amyloidosis, prevented aggregate formation.  Presumably the antibody to the normal conformation of lysozyme shifted the equilibrium of the mutant  away from the misfolded, molten-globule like variant, to the normal conformation.  The antibody binds to two regions of secondary structure (C-terminal region of the  β-domain and the C-helix of the α-domain of the protein),  not to the section of the protein that was mutated.  In addition, the antibody interacted with only 11 of the 60 residues of the destablized region.   X-ray crystal structures of the antibody-normal protein complex showed that the conformation of the normal protein did not change on antibody binding.  The data supports the ideas that the antibody did  not simply mask the destabilized structure and prevents its unfolding, but rather it  promoted normal cooperative interactions within the whole protein necessary for normal protein folding.

Another type of neurodegenerative diseases is associated with aggregation of proteins that have aberrant stretches of Gln residues, caused by an expansion of the CAG coding sequence in genes for these "polyglutamine-containing" proteins.   An example of such as disease is Huntington's Disease.  The aggregates contain monomers with extensive beta-structure characteristic of amyloid disease.  The small inhibitor dye, Congo Red, can bind to these beta structures and in vitro can dissociate existing aggregates and prevent aggregate formation by monomers.  Sanchez et al. have recently shown that Congo Red has the same effect in mice models of Huntington's disease, and led to significant improvement in mice with preexisting symptoms.


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