<p class="first" id="P2">Proximity, or the physical closeness of molecules, is a pervasive
regulatory mechanism
in biology. For example, most posttranslational modifications such as phosphorylation,
methylation, and acetylation promote proximity of molecules to play deterministic
roles in cellular processes. To understand the role of proximity in biologic mechanisms,
chemical inducers of proximity (CIPs) were developed to synthetically model biologically
regulated recruitment. Chemically induced proximity allows for precise temporal control
of transcription, signaling cascades, chromatin regulation, protein folding, localization,
and degradation, as well as a host of other biologic processes. A systematic analysis
of CIPs in basic research, coupled with recent technological advances utilizing CRISPR,
distinguishes roles of causality from coincidence and allows for mathematical modeling
in synthetic biology. Recently, induced proximity has provided new avenues of gene
therapy and emerging advances in cancer treatment.
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<b>Chemically induced proximity.</b> (Top) Left: Small molecules (hexagons) bind proteins
of interest (crescents), dimerizing
them to increase the effective molarity of reactions. [A] monomeric protein and [AB*]
dimer concentrations; arrows, position coordinates. Middle: Synthetic dimerizers tag
proteins (blue circles) for proteasomal degradation (red rods). Right: Homodimerizing
molecules form kill switches for apoptosis. (Bottom) CIPs mimic cellular processes.
Left: Protein transport mechanisms—nuclear import and export, membrane fusion, and
protein folding. Middle: Regulation of gene activation by binding to DNA or chromatin
(spheres with white strands), through recruitment of transcriptional activators or
repressors (blue and red arrows). Right: Signal transduction pathways.
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<h5 class="section-title" id="d8637795e165">BACKGROUND:</h5>
<p id="P5">Nature has evolved elegant mechanisms to regulate the physical distance
between molecules,
or proximity, for a wide variety of purposes. Whether it is activation of cell-membrane
receptors, neuronal transmission across the synapse, or quorum sensing in bacterial
biofilms, proximity is a ubiquitous regulatory mechanism in biology. Over the past
two decades, chemically induced proximity has revealed that many essential features
and processes, including protein structure, chromosomal architecture, chromatin accessibility,
transcription, and cellular signaling, are governed by the proximity of molecules.
We review the critical advances in chemical inducers of proximity (CIPs), which have
informed active areas of research in biology ranging from basic advances to the development
of cellular and molecular therapeutics.
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<h5 class="section-title" id="d8637795e170">ADVANCES:</h5>
<p id="P6">Until the 1990s, it was unclear whether proximity was sufficient to initiate
signaling
events or drive their effect on transcription. Synthetic small molecule–induced dimerization
of the T cell receptor provided the first evidence that proximity could be used to
understand signal transduction. A distinguishing feature of small-molecule induced-proximity
systems (compared to canonical knockdown or knockout methods) is the ability to initiate
a process midway and discern the ensuing order of events with precise temporal control.
The rapid reversibility of induced proximity has enabled precise analysis of cellular
and epigenetic memory and enabled the construction of synthetic regulatory circuits.
Integration of CRISPR-Cas technologies into CIP strategies has broadened the scope
of these techniques to study gene regulation on time scales of minutes, at any locus,
in any genetic context. Furthermore, CIPs have been used to dissect the mechanisms
governing seemingly well-understood processes, ranging from transport of proteins
between the Golgi and endoplasmic reticulum to synaptic vesicle transmission. Recent
advances in proximity-induced apoptosis, inhibition of aggregation, and selective
degradation of endogenous proteins will likely yield new classes of drugs in the near
future.
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<h5 class="section-title" id="d8637795e175">OUTLOOK:</h5>
<p id="P7">We review fundamental conceptual advances enabled by synthetic proximity
as well as
emerging CIP-based therapeutic approaches. Gene therapy with precise regulation and
fully humanized systems are now possible. Integration of proximity-based apoptosis
through caspase activation with chimeric antigen receptor (CAR) T cell therapies provides
a safety switch, enabling mitigation of complications from engineered immune cells,
such as graft-versus-host disease and B cell aplasia. Furthermore, this integration
facilitates the potential for repopulation of a patient’s cells after successful transplantation.
With the recent approval of CTL019, a CAR T cell therapeutic from Novartis, integrated
strategies involving the use of CIP-based safety switches are emerging. Innovative
exemplars include BPX-601 (NCT02744287) and BPX-701 (NCT02743611), which are now in
phase 1 clinical trials. By using a similar proximity-based approach, conditional
small-molecule protein degraders are also expected to have broad clinical utility.
This approach uses bifunctional small molecules to degrade pathogenic proteins by
dimerizing with E3 ubiquitin ligases. Degradation-by-dimerization strategies are particularly
groundbreaking, because they afford the ability to repurpose any chemical probe that
binds tightly with its pathogenic protein but which may not have previously provided
a direct therapeutic effect. We anticipate that the translation of CIP methodology
through both humanized gene therapies and degradation-by-dimerization approaches will
have far-reaching clinical impact.
</p>
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