Chemically induced proximity in biology and medicine

BACKGROUND 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. ADVANCES 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. OUTLOOK 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.