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Allosteric solution to the problems of undruggable targets, drug toxicity, and emerging resistance 变构解决问题的不可药物的目标,药物毒性,和新出现的耐药性
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-10-23 DOI: 10.1016/j.sbi.2025.103172
Wei-Ven Tee , Igor N. Berezovsky
Though allostery is a well-established research field, its importance for biomedical applications, spanning from the allosteric effects of mutations in diagnostics to the design of innovative allosteric drugs, is yet to be fully appreciated. The potential of allostery in resolving issues of current drug design and in targeting proteins considered difficult or undruggable is the main topic of this review. In particular, we discuss how the non-conservatism of allosteric sites enables selective targeting of individual members in conserved families, thereby minimizing off-target toxicity. The multiplicity of allosteric sites in any structure allows alleviation of challenges posed by emerging drug resistance driven by allosteric and orthosteric mutations. The modulatory action of allosteric drugs provides, at the same time, an important therapeutic advantage in gradual activation/inhibition of enzymatic function and signaling in receptors. We also discuss here an approach for rational design of allosteric drugs, illustrating its process and output in obtaining effectors with the above-mentioned advantages and characteristics. Reviewing recent advances in the development of allosteric effectors, we show that allostery is undoubtedly becoming an integral part of the drug discovery paradigm. We, therefore, anticipate that the pharmaceutical industry will be prompted to systematically incorporate allostery as an important complement to existing drug design strategies in the near future.
虽然变构学是一个成熟的研究领域,但它在生物医学应用中的重要性,从诊断突变的变构效应到创新变构药物的设计,尚未得到充分认识。变构在解决当前药物设计问题和靶向被认为难以或不可药物的蛋白质方面的潜力是本综述的主要主题。特别是,我们讨论了变构位点的非保守性如何使保守家族的个体成员选择性靶向,从而最大限度地减少脱靶毒性。任何结构中变构位点的多样性可以减轻由变构和正构突变驱动的新出现的耐药性带来的挑战。同时,变构药物的调节作用在逐渐激活/抑制酶功能和受体信号传导方面具有重要的治疗优势。本文还讨论了一种合理设计变构药物的方法,说明了其获得具有上述优点和特点的效应器的过程和输出。回顾变构效应的最新进展,我们表明变构效应无疑正在成为药物发现范式的一个组成部分。因此,我们预计,在不久的将来,制药行业将被促使系统地纳入变构,作为现有药物设计策略的重要补充。
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引用次数: 0
Ras/Raf dimerization model for activation of Raf kinase 激活Raf激酶的Ras/Raf二聚化模型
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-09-09 DOI: 10.1016/j.sbi.2025.103150
Marcela de Barros, Gregory Labrie, Carla Mattos
Our previously proposed Ras dimerization model is consistent with recent details observed by NMR in that Raf activation is centered on the Ras/Raf dimer, distinct from one in which Ras activates Raf as a monomer with the Raf cysteine rich domain inserted in the membrane. We review mechanistic understanding of Raf activation within nanoclusters of Ras on the membrane, with a shift to dimers upon binding Raf. This sets the stage for a signaling platform composed of Ras/Raf and Galectin dimers that facilitates the release of Raf autoinhibition and folding of the Raf intrinsically disordered region between the Ras-binding domains and the kinase bound to 14-3-3 and MEK. This platform could provide synchronized units for signal amplification and is consistent with a Ras stationary phase observed in cells.
我们之前提出的Ras二聚化模型与最近通过核磁共振观察到的细节一致,因为Raf的激活集中在Ras/Raf二聚体上,与Ras激活Raf作为一个单体并在膜中插入Raf半胱氨酸富结构域的模型不同。我们回顾了膜上Ras纳米簇内Raf激活的机制,并在结合Raf时转向二聚体。这为一个由Ras/Raf和半乳糖凝集素二聚体组成的信号传导平台奠定了基础,该平台促进了Raf自抑制的释放和Ras结合域与14-3-3和MEK结合的激酶之间Raf内在无序区域的折叠。该平台可以为信号放大提供同步单元,并且与细胞中观察到的Ras固定相一致。
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引用次数: 0
Drug targeting of protein-nucleic acid interactions 蛋白质-核酸相互作用的药物靶向。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-10-07 DOI: 10.1016/j.sbi.2025.103165
Luca R. Genz , Sanjana Nair , Aaron Sweeney , Maya Topf
Protein–nucleic acid interactions are vital to gene regulation and disease, yet have long been considered “undruggable.” Recent advances are reshaping this paradigm, enabling therapeutic targeting of DNA- and RNA-binding proteins. In this review, we highlight four major strategies: (1) direct disruption of protein-nucleic acid binding, (2) stabilization of specific complexes or conformations, (3) targeted degradation of interaction partners, and (4) allosteric modulation. We explore key examples across transcription factors, RNA-binding proteins, and DNA repair proteins, and emphasize emerging chemical, structural, and computational techniques that are accelerating discovery. Together, by intervening directly in the gene regulatory machinery, these approaches expand the druggable genome and open new avenues for treating cancer, genetic disorders, and viral infections.
蛋白质与核酸的相互作用对基因调控和疾病至关重要,但长期以来一直被认为是“不可药物的”。最近的进展正在重塑这一范式,使治疗靶向DNA和rna结合蛋白成为可能。在这篇综述中,我们重点介绍了四种主要的策略:(1)直接破坏蛋白质与核酸的结合,(2)稳定特定的复合物或构象,(3)靶向降解相互作用伙伴,以及(4)变构调节。我们探索转录因子、rna结合蛋白和DNA修复蛋白的关键例子,并强调正在加速发现的新兴化学、结构和计算技术。总之,通过直接干预基因调控机制,这些方法扩大了可药物基因组,并为治疗癌症、遗传疾病和病毒感染开辟了新的途径。
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引用次数: 0
Chromatin as a three-dimensional memory machine 染色质是三维记忆机器
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-10-04 DOI: 10.1016/j.sbi.2025.103160
Jeremy A. Owen , Leonid A. Mirny
Epigenetic memory—the stable inheritance of a cellular state over cell generations—has long been associated with chromatin modifications. But individual modifications are very dynamic. How can they carry information across cell generations? Recent theoretical work suggests the answer might lie, in part, in the three-dimensional organization of the genome. Cooperation between marks brought together by genome folding can correct epigenetic errors, making stable memory units out of unstable marks. If marks direct the phase separation of chromatin, the resulting bidirectional coupling between marks and structure provides a mechanism for many of these units to operate independently along the genome. Models of bidirectional coupling have helped identify elements, such as formation of a dense compartment, 3D mark spreading, and limited enzyme, which may be key to stable epigenetic memory. An analogy between these 3D models and a classic model of associative memory hints at a way chromatin could perform sophisticated information processing.
长期以来,表观遗传记忆——细胞状态的稳定遗传——一直与染色质修饰有关。但是个人的修改是非常动态的。它们是如何跨代传递信息的?最近的理论研究表明,答案可能部分在于基因组的三维组织。基因组折叠带来的标记之间的合作可以纠正表观遗传错误,从不稳定的标记中产生稳定的记忆单元。如果标记指导染色质的相分离,那么由此产生的标记和结构之间的双向耦合为许多这些单位在基因组中独立运作提供了一种机制。双向耦合模型有助于识别诸如致密区室的形成、3D标记扩散和受限酶等因素,这些因素可能是稳定表观遗传记忆的关键。这些3D模型与经典的联想记忆模型之间的相似性暗示了染色质可以执行复杂信息处理的方式。
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引用次数: 0
Dictionary based approaches for studying intrinsic DNA shape in transcription factor recognition 基于字典的转录因子识别中DNA固有形状研究方法
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-10-04 DOI: 10.1016/j.sbi.2025.103166
Manisha Kalsan, Sadiya Mirza, Divyangana Bathla, Shandar Ahmad
Sequence-dependent intrinsic conformational dynamics confer specificity to transcriptional factor recognition of genomic DNA. Their genome-scale investigation using all-atom simulations is challenging, and alternative approaches by coarse-graining DNA into beads-and-sticks or polymer models have their own limitations. One parallel approach is what we describe here as a dictionary-based approach. This has been shown to explain several transcriptional events in biological systems but has been inadequately reviewed. These approaches represent studies based on a finite number of DNA fragments and their corresponding conformational properties, scaled up to genomes by pooling nearby fragments and machine learning models. This article aims to organize efforts made in generating these models and their recent successful applications to stimulate further development of this approach.
序列依赖的内在构象动力学赋予特异性转录因子识别基因组DNA。他们使用全原子模拟来进行基因组规模的研究是具有挑战性的,而将粗粒DNA制成棒状或聚合物模型的替代方法也有其局限性。一种并行方法是我们在这里描述的基于字典的方法。这已被证明可以解释生物系统中的几个转录事件,但尚未得到充分的审查。这些方法代表了基于有限数量的DNA片段及其相应构象性质的研究,通过汇集附近的片段和机器学习模型扩展到基因组。本文旨在组织在生成这些模型方面所做的努力,以及它们最近成功的应用,以刺激该方法的进一步发展。
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引用次数: 0
Chromatin higher-order folding as influenced by preferred values of linker DNA 染色质高阶折叠受连接体DNA偏好值的影响。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-09-19 DOI: 10.1016/j.sbi.2025.103154
Zilong Li , Stephanie Portillo-Ledesma , Tamar Schlick
Specific values of nucleosome spacing have long been associated with distinct chromatin organization, but recent studies reveal surprising structural and functional consequences of small changes in regular linker DNA length. This opinion article revisits experimental and modeling studies addressing the classic 10n versus 10n + 5 spacing, highlighting how this 5 bp difference can alter nucleosome orientation, fiber topology, and higher-order chromatin behavior. We underscore how differences in model parameters and system design yield different trends for the effect of linker DNA lengths on chromatin architecture. However, chromatin structure in vivo reflects the heterogeneous nucleosome spacing in combination with other cellular variables like salt conditions, epigenetic marks, and protein and RNA binding, which work together to shape gene folding and direct gene regulation.
核小体间隔的特定值长期以来与不同的染色质组织有关,但最近的研究揭示了常规连接体DNA长度的微小变化带来的令人惊讶的结构和功能后果。这篇观点文章回顾了经典的10n和10n + 5间距的实验和建模研究,强调了这5bp的差异如何改变核小体的取向、纤维拓扑结构和高阶染色质行为。我们强调模型参数和系统设计的差异如何产生连接体DNA长度对染色质结构影响的不同趋势。然而,体内染色质结构与其他细胞变量如盐条件、表观遗传标记、蛋白质和RNA结合等一起反映了核小体间距的异质性,它们共同塑造基因折叠并指导基因调控。
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引用次数: 0
TF paralogs—Natural experiments in DNA binding DNA结合的自然实验。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-10-22 DOI: 10.1016/j.sbi.2025.103171
Shubham Khetan , Martha L. Bulyk
Transcription factor (TF) paralogs provide unique insights into how DNA-binding specificity evolves and diversifies. While paralogous TFs share conserved, highly similar DNA-binding domains, they achieve distinct regulatory functions through mechanisms that are now being elucidated. This review examines how sequence variations between paralogs translate into functional diversity, including how mutations distant from the DNA interface can allosterically modulate binding specificity. We focus on competitive binding dynamics when paralogs are co-expressed and discuss emerging evidence that TFs recognize extensive repertoires of lower-affinity binding sites. Differential preferences for lower-affinity binding sites create paralog-specific binding patterns that determine TF genomic occupancy. These insights have important implications for interpreting the impact of coding and noncoding variation on TF–DNA interactions and human disease.
转录因子(TF)的类似物为dna结合特异性如何进化和多样化提供了独特的见解。虽然同源tf共享保守的、高度相似的dna结合结构域,但它们通过目前正在阐明的机制实现不同的调节功能。这篇综述探讨了同源物之间的序列差异如何转化为功能多样性,包括远离DNA界面的突变如何变构地调节结合特异性。我们将重点关注相似物共表达时的竞争结合动力学,并讨论新出现的证据,证明tf识别广泛的低亲和力结合位点。对低亲和力结合位点的不同偏好产生了决定TF基因组占用的平行特异性结合模式。这些见解对于解释编码和非编码变异对TF-DNA相互作用和人类疾病的影响具有重要意义。
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引用次数: 0
Editorial overview: Artificial intelligence methodologies in structural biology 编辑概述:结构生物学中的人工智能方法
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-09-13 DOI: 10.1016/j.sbi.2025.103156
Chaok Seok, Pratyush Tiwary
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引用次数: 0
Allosteric binding cooperativity in kinases signaling, signalopathies, and drug development 激酶信号、信号病变和药物开发中的变构结合协同性。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-10-16 DOI: 10.1016/j.sbi.2025.103169
Cristina Olivieri , Jian Wu , Susan S. Taylor , Gianluigi Veglia
Protein kinases catalyze the transfer of phosphate groups from ATP to specific substrates, initiating, modulating, or terminating signaling cascades. Generally, the response of these enzymes to stimuli is characterized by ultrasensitive rather than graded responses and mediated by cooperative binding interactions. Here, we provide examples of positive and negative cooperativity processes regulating several protein kinases. We first examine the binding cooperativity between nucleotide and substrate in protein kinase A, showing how dysfunctional cooperativity may be linked to signalopathies. We then illustrate how certain drugs exploit cooperativity to inhibit kinase homo- and hetero-dimerization or select for active and inactive conformational states. A molecular understanding of binding cooperativity could lead to the development of new kinase-specific inhibitors, opening up novel therapeutic possibilities.
蛋白激酶催化磷酸基团从ATP转移到特定底物,启动、调节或终止信号级联反应。一般来说,这些酶对刺激的反应是超敏感的,而不是分级反应,并通过合作结合相互作用介导。在这里,我们提供了正向和负向协同过程调节几种蛋白激酶的例子。我们首先研究了蛋白激酶A中核苷酸和底物之间的结合协同性,显示了功能失调的协同性如何与信号病有关。然后,我们说明了某些药物如何利用协同性来抑制激酶同源和异二聚化或选择活性和非活性构象状态。对结合协同性的分子理解可能导致新的激酶特异性抑制剂的开发,开辟新的治疗可能性。
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引用次数: 0
Labeling systems for cryo-electron tomography 低温电子断层扫描标记系统
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-11-25 DOI: 10.1016/j.sbi.2025.103189
Richard G. Held
The unrealized goal of cryo-electron tomography (cryo-ET) is to visualize every protein within its cellular context. Such capability would enable molecular resolution mapping of three-dimensional protein topography and structure determination within a native context. Current technology limits the proteins identifiable within an individual tomogram to high-molecular-weight complexes. Localization of smaller target proteins requires the use of labeling systems that act as fiducial markers of target protein localization. Several labeling systems have been developed and recently employed, all of which involve trade-offs. The choice of which system to use depends on the biological question of interest. This review outlines considerations for the design and choice of labeling systems for cryo-ET, highlights recent applications, and outlines areas for future development.
低温电子断层扫描(cryo-ET)尚未实现的目标是在其细胞背景下可视化每一种蛋白质。这种能力将使三维蛋白质地形的分子分辨率制图和结构测定成为可能。目前的技术将单个断层扫描中可识别的蛋白质限制在高分子量复合物中。定位较小的靶蛋白需要使用标记系统作为靶蛋白定位的基础标记。几个标签系统已经开发和最近采用,所有这些都涉及权衡。选择使用哪种系统取决于感兴趣的生物学问题。这篇综述概述了设计和选择冷冻et标签系统的考虑因素,重点介绍了最近的应用,并概述了未来发展的领域。
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引用次数: 0
期刊
Current opinion in structural biology
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