Why trying to remove aBeta was plausible

The recent collapse of the latest attempt to remove the main constituent of the Alzheimer plaque, the aBeta peptide (gantenerumab from Roche) is just the latest in a long sad story.

Monoclonal after monoclonal antibody targeting aBeta has failed.  It certainly is time to move on and try new approaches.

The companies pursuing monoclonals were not stupid.  Their approach was (but no longer is) quite reasonable in view of the clinical and experimental evidence implicating the aBeta peptide as causative of Alzheimer’s  Before moving on, here are some of the reasons why.

First (and probably the best) is the mutation that protects against Alzheimer’s disease.  As most of you know, the aBeta peptide (39 to 42 amino acids) is part of a much larger protein the Amyloid Precursor Protein (APP) which contains 639 to 770  amino acids.  This means that enzymes must  cut it out.  Such enzymes (called proteases) are finicky, cutting only between certain amino acids.  In what follows A673T stands for the 673rd position which normally has amino acid Alanine (A) there.  Instead there is amino acid Threonine (T).   The enzyme cleaving at 673  is Beta Secretase 1 (BACE1).

       [ Nature vol. 487 pp. 153 ’12 ] A mutation in APP protects against Alzheimer’s disease.   First the genome sequence APP of 1,795 Icelanders  were studied to look for low frequency variants.  They found a mutation A673T adjacent to the site that is cleaved by beta secretase 1 (BACE1) which doesn’t vary — it’s gamma secretase which cleaves at variable sites leading to Abeta40, Abeta42 formation.  The mutation is at position 2 in Abeta.  The mutation results in a 40% reduction in the formation of amyloidogenic peptides  in vitro (293T cells transfected with variant and normal APP). Amazingly, a different variant at 673 (A673V — V stands for the amino acid Valine) — increases Abeta formation.    Because BACE1 can’t cleave APP containing the A673T mutation, alternative processing of APP at another site the alpha site (which is within aBeta preventing formation of the full 39 – 43 amino acid peptide).
So if you can’t make the full aBeta peptide you don’t get Alzheimer’s (or have less chance of getting it).
Then there are the mutations in the part of APP which code for the aBeta peptide which increase the risk of Alzheimer’s.  They cause the different familial Alzheimer’s disease.   Now that we know the actual structure of the aBeta amyloid fiber, we can understand how they cause Alzheimer’s disease.  This is more strong evidence that the aBeta peptide is involved in the causation of Alzheimer’s disease.
You’ll need some protein chemistry chops to understand the following

Recall that in amyloid fibrils the peptide backbone is flat as a flounder (well in a box 4.8 Angstroms high) with the amino acid side chains confined to this plane.  The backbone winds around in this plane like a snake.  The area in the leftmost loop is particularly crowded with bulky side chains of glutamic acid (single letter E) at position 22 and aspartic acid (single letter D) at position 23 crowding each other.  If that wasn’t enough, at the physiologic pH of 7 both acids are ionized, hence negatively charged.  Putting two negative charges next to each other costs energy and makes the sheet making up the fibril less stable.

The marvelous paper (the source for much of this) Cell vol. 184 pp. 4857 – 4873 ’21 notes that there are 3 types of amyloid — pathological, artificial, and functional, and that the pathological amyloids are the most stable. The most stable amyloids are the pathological ones.  Why this should be so will be the subject of a future post, but accept it as fact for now

In 2007 there were 7 mutations associated with familial Alzheimer’s disease (10 years later there were 11). Here are 5 of them.

Glutamic Acid at 22 to Glycine (Arctic)

Glutamic Acid at 22 to Glutamine (Dutch)

Glutamic Acid at 22 to Lysine (Italian)

Aspartic Acid at 23 to Asparagine (Iowa)

Alanine at 21 to Glycine (Flemish)

All of them lower the energy of the amyloid fiber.

Here’s why

Glutamic Acid at 22 to Glycine (Arctic) — glycine is the smallest amino acid (side chain hydrogen) so this relieves crowding.  It also removes a negatively charged amino acid next to the aspartic acid.  Both lower the energy

Glutamic Acid at 22 to Glutamine (Dutch) — really no change in crowding, but it removes a negative charge next to the negatively charged Aspartic acid

Glutamic Acid at 22 to Lysine (Italian)– no change in crowding, but the lysine is positively charged at physiologic pH, so we have a positive charge next to the negatively charged Aspartic acid, lowering the energy

Aspartic Acid at 23 to Asparagine (Iowa) –really no change in crowding, but it removes a negative charge next to the negatively charged Glutamic acid next door

Alanine at 21 to Glycine (Flemish) — no change in charge, but a reduction in crowding as alanine has a methyl group and glycine a hydrogen.

As a chemist, I find this immensely satisfying.  The structure explains why the mutations in the 42 amino acid aBeta peptide are where they are, and the chemistry explains why the mutations are what they are.

It’s time to look elsewhere.  The best this class of drug (monoclonal antibodies against aBeta) offers is lecanemab which slows the rate of decline by a measly 27%.   This is very small beer

While big pharma was far from stupid to intensively (and expensively) to give the monoclonals the old college try in the past (for the reasons cited above), they would be incredibly stupid to continue this line of attack.

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