Regulating molecule proximity The physical distance, or proximity, between molecules often directs biological events. The development of membrane-permeable small molecules that reversibly regulate proximity has enabled advances in fields such as synthetic biology, signal transduction, transcription, protein degradation, epigenetic memory, and chromatin dynamics. This “induced proximity” can also be applied to the development of new therapeutics. Stanton et al. review the wide range of advances and speculate on future applications of this fundamental approach. Science, this issue p. eaao5902 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. Chemically induced proximity. (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. 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.

中文翻译：

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生物学和医学中的化学诱导接近

调节分子接近度 分子之间的物理距离或接近度通常会引导生物事件。可逆调节接近度的膜渗透性小分子的发展促进了合成生物学、信号转导、转录、蛋白质降解、表观遗传记忆和染色质动力学等领域的进步。这种“诱导接近”也可以应用于新疗法的开发。斯坦顿等人。回顾广泛的进展并推测这种基本方法的未来应用。科学，这个问题 p。eaao5902 背景 大自然已经进化出优雅的机制来调节分子之间的物理距离或接近度，用于各种目的。无论是细胞膜受体的激活，跨突触的神经元传递，或细菌生物膜中的群体感应，接近是生物学中普遍存在的调节机制。在过去的 20 年里，化学诱导的邻近性揭示了许多基本特征和过程，包括蛋白质结构、染色体结构、染色质可及性、转录和细胞信号传导，都受分子邻近性的控制。我们回顾了邻近化学诱导剂 (CIP) 的重要进展，这些进展为生物学研究的活跃领域提供了信息，从基础进展到细胞和分子疗法的发展。进展 直到 1990 年代，尚不清楚距离是否足以启动信号事件或驱动它们对转录的影响。合成小分子诱导的 T 细胞受体二聚化提供了第一个证据，证明邻近性可用于理解信号转导。小分子诱导接近系统的一个显着特征（与典型的敲除或敲除方法相比）是能够在中途启动一个过程并通过精确的时间控制辨别随后的事件顺序。诱导接近的快速可逆性使得能够精确分析细胞和表观遗传记忆，并能够构建合成调节回路。将 CRISPR-Cas 技术整合到 CIP 策略中，拓宽了这些技术的范围，可以在任何基因背景下，在任何基因座的几分钟时间尺度上研究基因调控。此外，CIPs 已被用于剖析控制看似很好理解的过程的机制，从高尔基体和内质网之间的蛋白质运输到突触小泡传输。在邻近诱导的细胞凋亡、聚集抑制和内源性蛋白质的选择性降解方面的最新进展可能会在不久的将来产生新的药物类别。展望 我们回顾了合成邻近性以及新兴的基于 CIP 的治疗方法所带来的基本概念进步。具有精确调控和完全人性化系统的基因治疗现在成为可能。通过半胱天冬酶激活与嵌合抗原受体 (CAR) T 细胞疗法整合基于邻近性的细胞凋亡提供了一个安全开关，能够减轻工程免疫细胞的并发症，如移植物抗宿主病和 B 细胞发育不全。此外，这种整合促进了成功移植后患者细胞重新增殖的潜力。随着最近诺华的 CAR T 细胞疗法 CTL019 的批准，涉及使用基于 CIP 的安全开关的综合策略正在出现。创新范例包括 BPX-601 (NCT02744287) 和 BPX-701 (NCT02743611)，目前正处于 1 期临床试验阶段。通过使用类似的基于邻近性的方法，条件性小分子蛋白质降解剂也有望具有广泛的临床效用。这种方法使用双功能小分子通过与 E3 泛素连接酶二聚化来降解致病蛋白。二聚化降解策略尤其具有开创性，因为它们能够重新利用与其致病蛋白紧密结合但以前可能没有提供直接治疗效果的任何化学探针。我们预计通过人源化基因疗法和二聚化降解方法转化 CIP 方法将产生深远的临床影响。化学诱导接近。（上）左：小分子（六边形）结合感兴趣的蛋白质（新月形），使它们二聚化以增加反应的有效摩尔浓度。[A] 单体蛋白质和 [AB*] 二聚体浓度；箭头，位置坐标。中：用于蛋白酶体降解的合成二聚体标记蛋白质（蓝色圆圈）（红色棒）。右：同二聚化分子形成细胞凋亡的杀伤开关。（下）CIP 模仿细胞过程。剩下：蛋白质转运机制——核输入和输出、膜融合和蛋白质折叠。中：通过与 DNA 或染色质（带有白色链的球体）结合，通过募集转录激活因子或抑制因子（蓝色和红色箭头）来调节基因激活。右：信号转导途径。接近，或分子的物理接近，是生物学中普遍存在的调节机制。例如，大多数翻译后修饰（如磷酸化、甲基化和乙酰化）会促进分子间的接近，从而在细胞过程中发挥决定性作用。为了了解邻近在生物机制中的作用，开发了化学邻近诱导剂 (CIP) 来综合模拟生物调节的招募。化学诱导接近允许转录的精确时间控制，信号级联、染色质调节、蛋白质折叠、定位和降解，以及许多其他生物过程。对基础研究中 CIP 的系统分析，加上最近利用 CRISPR 的技术进步，区分了因果关系的作用与巧合，并允许在合成生物学中进行数学建模。最近，诱导接近为基因治疗和癌症治疗的新进展提供了新途径。