Enhanced potency of aggregation inhibitors mediated by liquid condensates

Open Access

Enhanced potency of aggregation inhibitors mediated by liquid condensates

Thomas C. T. Michaels, L. Mahadevan, and Christoph A. Weber

Phys. Rev. Research 4, 043173 – Published 8 December 2022

Abstract

Liquid condensates are membraneless organelles that form via phase separation in living cells. These condensates provide unique heterogeneous environments that have much potential in regulating a range of biochemical processes from gene expression to filamentous protein aggregation—a process linked to Alzheimer's and Parkinson's diseases. Here we theoretically study the physical interplay between protein aggregation, its inhibition, and liquid-liquid phase separation. Our key finding is that the action of protein aggregation inhibitors can be strongly enhanced by liquid condensates. The physical mechanism of this enhancement relies on the partitioning and colocalization of inhibitors with their targets inside the liquid condensate. Our theory uncovers how the physicochemical properties of condensates can be used to modulate inhibitor potency, and we provide experimentally testable conditions under which drug potency is maximal. Our findings suggest design principles for protein aggregation inhibitors with respect to their phase-separation properties.

Received 7 May 2021
Accepted 18 August 2022

DOI:https://doi.org/10.1103/PhysRevResearch.4.043173

Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.

Published by the American Physical Society

Physics Subject Headings (PhySH)

Aggregation Compartmentalization Fibril formation

Cellular compartments

Physics of Living Systems

Authors & Affiliations

Thomas C. T. Michaels ^1,2, L. Mahadevan ^3,4,*, and Christoph A. Weber^5,†

¹Department of Biology, Institute of Biochemistry, ETH Zurich, Otto Stern Weg 3, 8093 Zurich, Switzerland
²Bringing Materials to Life Initiative, ETH Zurich, Switzerland
³Paulson School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, USA
⁴Department of Physics and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
⁵Institute of Physics, Faculty of Mathematics, Natural Sciences, and Materials Engineering, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany

^*lmahadev@g.harvard.edu
^†christoph.weber@physik.uni-augsburg.de

Article Text

Click to Expand

Supplemental Material

Click to Expand

References

Click to Expand

Issue

Vol. 4, Iss. 4 — December - December 2022

Subject Areas

Reuse & Permissions

Author publication services for translation and copyediting assistance advertisement

Images

Figure 1
How liquid-like condensates impact protein aggregation inhibition. (a) We determine the physical conditions when the presence of a phase-separated condensate (phase I, right) yields a higher degree of inhibition of aggregation (e.g., fewer aggregates at the end of the reaction) compared with a homogeneous system (left). (b) Definition of partitioning of monomers and drug components and associated nonequilibrium diffusive fluxes across the condensate interface. We neglect diffusive exchange of aggregates through the interface. (c) The reaction network of filamentous protein aggregation and three established mechanisms of inhibition [10, 28, 29, 30].
Reuse & Permissions
Figure 2
Mechanism by which liquid condensates amplify inhibition of secondary nucleation. (a) Representative aggregation time courses for different systems (from top to bottom in terms of final plateau): (1) a homogeneous system without an inhibitor, (2) a homogeneous system with an inhibitor of secondary nucleation, (3) a heterogeneous system with a liquid condensate in the absence of the drug, and (4) same as system (3), but in the presence of the drug. A list of parameters used to generate the plots can be found in Table 1. (b) Number concentration of aggregates at the end of the aggregation reaction for the four systems [systems (1)–(4)] considered in (a). (c) Aggregation time course inside (phase I, top part of plot) and outside (phase II, bottom part of plot) the liquid condensate without and with the drug. We see that adding the drug causes a reduction of aggregate concentration inside the condensate (phase I) but leads to an increase in aggregate concentration outside the condensate (phase II). (d) Schematic representation of the positive feedback mechanism causing enhanced inhibition inside the liquid condensate. For $p_{m} > 1$ , aggregation occurs primarily in phase I due to the diffusive flux of monomers maintaining equilibrium. As drug molecules in phase I bind to their target ( $p_{d} > 1$ ), their concentration decreases. The resulting concentration imbalance across the condensate interface causes a diffusive flux of drug molecules from phase II to phase I to restore phase equilibrium. As a result, inhibition is enhanced inside the condensate (phase I), but the reaction proceeds in an uncontrolled fashion outside (phase II).
Reuse & Permissions
Figure 3
Conditions for enhanced inhibition and phase diagram of optimal system. (a) Enhancement function $E = c_{a} {(\infty) |}_{h o m o} / {\bar{c}}_{a} (\infty)$ against drop volume $V^{I} / V$ and drug partitioning $p_{d}$ (for fixed $p_{m}$ and drug concentration). We separate regions where liquid droplets enhance ( $E > 1$ , red) or reduce ( $E < 1$ , blue) the effect of an inhibitor of secondary nucleation. Contour lines for $E$ are shown in logarithmic scale in steps of $10^{0.5}$ . (b) Comparison of terminal number concentration of aggregates formed for different systems [(1) no condensates, (2) no condensates $+$ drug, (3) condensates, (4) condensates $+$ drug] against drug partitioning $p_{d}$ . The plots are shown for $V^{I} / V = 10^{- 1}$ (top right), $V^{I} / V = 10^{- 2.5}$ (bottom left), and $V^{I} / V = 10^{- 4.5}$ (bottom right). (c) Phase diagram indicating the system that yields the most effective reduction of total aggregate concentration depending on $V^{I} / V$ and $p_{d}$ for an inhibitor of secondary nucleation.
Reuse & Permissions
Figure 4
Liquid condensates increase the potency of protein aggregation inhibitors. (a) Drug-response curve $R (c_{d})$ in the absence and in the presence of a liquid condensate. The presence of the liquid condensate increases the potency by reducing ${EC}_{50}$ . The plot is shown for an inhibitor of secondary nucleation using the same parameters as in Fig. 3 except for $p_{d} = 10^{2}$ and $V^{I} / V = 10^{- 2}$ . (b) Relative drug potency $P_{rel}$ of inhibitors that bind to fibril surfaces against drop volume for $p_{d} = 10$ (plotted at bottom of graph), $p_{d} = 10^{2}$ (plotted in middle of graph), and $p_{d} = 10^{3}$ (plotted at top of graph). The potency is defined as $P = 1 / {EC}_{50}$ of the respective system. For small condensates, the potency of the inhibitor of secondary nucleation decreases due to uncontrolled aggregation in phase II. The solid lines indicate Eq. (3).
Reuse & Permissions

Physical Review Research