Thermodynamic and kinetic design principles for protein aggregation inhibitors

Abstract

Understanding the mechanism of action of compounds capable of inhibiting protein aggregation is critical to the development of potential ther-1 apeutics against protein misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the aggregating proteins are simultaneously the reactants, products, intermediates and catalysts of the reaction. It is a complex problem, therefore, to choose the states of the aggregating proteins that should be bound by the compounds to achieve the most potent inhibition. We present here a comprehensive kinetic theory of protein aggregation inhibition which reveals the fundamental thermodynamic and kinetic signatures characterising effective inhibitors by identifying quantitative relationships between the aggregation and binding rate constants. These results provide general physical laws to guide the design and optimisation of protein aggregation inhibitors.The aggregation of peptides and proteins into amyloid fibrils is key in many phenomena ranging from the formation of functional machineries in biology to the production of novel nanomaterials. Recent interest in this process has come from the realisation that protein aggregation is intimately linked to a range of human conditions, from Alzheimer's disease to type II diabetes. 1-6 Inhibition of protein aggregation thus represents a major strategy for the development of effective pharmacological interventions against protein misfolding diseases. 7-24 Traditionally, inhibition strategies against protein aggregation have focussed either on blocking the production of aggregation-prone peptides and proteins or on promoting the degradation of their amyloid products. 7 Recent attempts have instead concentrated on altering or delaying the aggregation process itself, which is typically achieved using compounds that bind non-covalently to different types of protein species during the aggregation reaction. 8-10 Examples of such compounds include small drug-like molecules, 23-28 molecular chaperones, 29-31 antibodies, 32,33 and nanoparticles. 34 Initially, such kinetic inhibitors were designed with the generic goal of delaying amyloid formation. [15][16][17][18][19][20][21] It has now been recognised, however, that the cytotoxicity linked to amyloid formation is not attributable to a single species. Instead, the gamut of species accessible during aggregation contribute

Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease

“…Our kinetic analysis of aggregation inhibition by monomer sequestration highlights that effective inhibition depends on the interplay of two combined parameters, namely, a thermodynamic and kinetic one: K d /[ C ] and k on [ C ]/κ ( Fig. 5E ) ( 45 ). Thus, for a small molecule with a given affinity for monomeric Aβ42, increasing the k on represents a promising inhibitor optimization strategy.…”

“…However, we note that the level of inhibition in general depends not on the absolute value of K d , but on the combined parameter K d /[ C ], where [ C ] is the drug concentration, provided that the rate of binding ( k on [ C ]) is sufficiently fast as compared to the overall time scale of aggregation, 1/κ (see eq. S11 for a definition of κ) ( 45 ). Therefore, it is possible to have effective inhibition even for small molecules with K d values in the micromolar range, provided that [ C ] is on the same order of magnitude as K d (see Fig.…”

Investigating the Effects of Molecular Crowding on the Kinetics of Protein Aggregation

“…Among the many theoretical methods to investigate the protein aggregation problem, the kinetic approaches ,,,− often provide direct fits to experimental data and interpretation of the aggregation processes. Processes considered in these studies and others often include primary nucleation, monomer addition, monomer subtraction, fibril fragmentation, merging of oligomers, heterogeneous (or surface-catalyzed) nucleation, and so on.…”

Investigating the effects of molecular crowding on the kinetics of protein aggregation

“…[10][11][12][13][14][15][16][17] Experimental investigations have shown that both the folding of the constituent monomer proteins as well as the aggregate assembly are determined by a complex energy landscape, where numerous routes can convert monomer proteins into distinct aggregated structures that may or may not have biological functions. 18 Among the many theoretical methods to investigate the protein aggregation problem, the kinetic approaches 10,11,14,[19][20][21][22][23][24][25][26] often provide direct fits to experimental data and interpretation of the aggregation processes. Processes considered in these studies and others often include primary nucleation, monomer addition, monomer subtraction, fibril fragmentation, merging of oligomers, heterogeneous (or surface-catalyzed) nucleation, etc.…”