Method of identifying novel protein aggregation inhibitors based on chemical kinetics

Patent metadata

Field	Value
Publication number	US-11536729-B2
Application number	US-201616068058-A
Country	US
Kind code	B2
Filing date	Dec 28, 2016
Priority date	Jan 6, 2016
Publication date	Dec 27, 2022
Grant date	Dec 27, 2022

Abstract

The subject matter disclosed herein relates to methods of identifying pharmacophores and inhibitors against protein aggregation. The present disclosure also provides pharmacophores themselves and medical uses of agents in the treatment of diseases associated with protein aggregation.

First claim

The invention claimed is:

1. A method of producing a pharmacophore against aggregation of an amyloid protein, the method comprising
(a) providing at least one inhibitor of protein aggregation of an amyloid protein with a known effect on at least one microscopic rate constant in the protein aggregation, wherein the microscopic rate constant is selected from the group consisting of primary nucleation and secondary nucleation, wherein said secondary nucleation forms a catalytic site for generation of toxic oligomer species;
(b) generating an inhibitor scaffold from the at least one inhibitor;
(c) introducing at least one chemical substitution into the inhibitor scaffold to prepare a modified inhibitor scaffold comprising the at least one chemical substitution and analysing the effect of the at least one chemical substitution on aggregation kinetics over time of said amyloid protein, wherein said analysing comprises: determining at least one microscopic rate constant of protein aggregation by measuring fibril mass concentration over time in the presence of said modified inhibitor scaffold comprising the at least one chemical substitution, wherein the microscopic rate constant is selected from the group consisting of primary nucleation and secondary nucleation;
(d) comparing the at least one microscopic rate constant of protein aggregation over time in step (c) against a corresponding microscopic rate constant of protein aggregation over time in the absence of said modified inhibitor to identify a reduction in the microscopic rate constant for primary nucleation and/or secondary nucleation, wherein reduction in the microscopic rate constant for primary nucleation delays the aggregation, and reduction in the microscopic rate constant for secondary nucleation decreases the number of toxic oligomers; and
(e) assessing from said reduction in the microscopic rate constant for primary nucleation and/or secondary nucleation, one or more steric and electronic features in common between said at least one inhibitor and said modified inhibitor scaffold to produce a pharmacophore against aggregation of an amyloid protein, wherein the pharmacophore comprises common steric and electronic features.

2. The method of claim 1 , wherein the amyloid protein is selected from Aβ42, α-synuclein, tau, huntingtin, atrophin-1, ataxin (1,2,3,6,7, 8 12,17), amylin, prion protein, (pro)calcitonin, atrial natriuretic factor, apoliprotein AI, apoliprotein AII, apoliprotein AIV, serum amyloid, medin, (apo) serum AA, prolactin, transthyretin, lysozyme, (β-2 microglobulin, fibrinogen α chain, gelsolin, keratopthelin, β-amyloid, cystatin, ABriPP immunoglobulin light chain AL, immunoglobulin heavy chain, S-IBM, islet amyloid polypeptide, insulin, lactadherin, kerato-epithelium, lactoferrin, tbn, leukocyte chemotactic factor-2, AbriPP, ADanPP, lung surfactant protein, galectin 7, corneodesmosin, lactadherin, kerato-epitelium, odontogenic ameloblast-associated protein, semenogelin 1 and enfurvitide.

3. The method of claim 2 , wherein the protein is Aβ42.

4. The method of claim 1 , wherein said introducing comprises chemically modifying said inhibitor scaffold and said determining comprises contacting said modified inhibitor scaffold with an amyloid protein.

5. The method of claim 1 , wherein the protein aggregation over time is represented by a time-dependent sigmoidal curve, wherein said curve comprises at least a lag phase, a growth phase and a plateau originating from primary nucleation, secondary nucleation and elongation processes and wherein said modified inhibitor scaffold alters at least one of primary nucleation or secondary nucleation.

6. The method of claim 1 , wherein microscopic rate constants are obtained from the aggregation kinetics over time by fitting the curves using the following equation:

M
⁡

(
t
)

M
⁡

(
∞
)

=

1
-

α
(

B
+

+

C
+

B
+

+

C
+

⁢

e
kt

⁢

B
-

+

C
+

⁢

e
kt

B
-

+

C
+

)

k
∞
2

k
⁢

⁢

k
∞

~

⁢

e

-

k
∞

⁢
t

where the parameters B ± , C ± , κ, κ ∞ and are functions of the two combinations of the microscopic rate constants k + k 2 and k n k 2 , where k n , k + and k 2 are the primary nucleation, elongation and secondary nucleation rate

Assignees

• Cambridge Entpr Ltd

Inventors

• Dobson Christopher
• Knowles Tuomas
• Vendruscolo Michele
• Habchi Johnny
• Chia Sean

Classifications

• G01N33/5058

  Neurological cells · CPC title

• A61K38/00

  Medicinal preparations containing peptides (peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00) · CPC title

• G01N33/557

  using kinetic measurement, i.e. time rate of progress of an antigen-antibody interaction · CPC title

• G01N33/6896 Primary

  Neurological disorders, e.g. Alzheimer's disease · CPC title

• A61P25/28

  for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia · CPC title