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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 : 2025-10-23 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
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 : 2025-10-22 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
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 : 2025-10-16 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
Old and new tactics of CRISPR-centric competition between bacteria and bacteriophages 细菌和噬菌体之间以crispr为中心的竞争的新旧策略。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-15 DOI: 10.1016/j.sbi.2025.103168
Iktae Kim , Jeong-Yong Suh
The CRISPR-Cas system provides adaptive immunity for prokaryotes against mobile genetic elements (MGEs) such as bacteriophages and plasmids. As a countermeasure, MGEs have evolved various anti-CRISPR (Acr) mechanisms that neutralize the CRISPR-mediated immunity. Canonical Acr proteins block target binding of Cas proteins in a stoichiometric or enzymatic manner. New findings reveal that Acr also disintegrates functional Cas complexes, induces promiscuous target binding, and mimics Cas proteins and crRNA with defective mutations. Here, we summarize a broad repertoire of structural and functional mechanisms underlying CRISPR-centric competition, highlighting recent discoveries of molecular machinery that modulates CRISPR function.
CRISPR-Cas系统为原核生物提供了针对移动遗传元件(MGEs)(如噬菌体和质粒)的适应性免疫。作为对策,MGEs进化出各种抗crispr (Acr)机制来中和crispr介导的免疫。典型Acr蛋白以化学计量学或酶促的方式阻断Cas蛋白的靶结合。新的研究结果表明,Acr还能分解功能性Cas复合物,诱导混杂靶标结合,并模拟Cas蛋白和crRNA的缺陷突变。在这里,我们总结了以CRISPR为中心的竞争背后的广泛的结构和功能机制,重点介绍了最近发现的调节CRISPR功能的分子机制。
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引用次数: 0
Membrane protein reconstitution : New possibilities for structural biology, biophysical methods, and antibody/drug discovery 膜蛋白重构:结构生物学、生物物理方法和抗体/药物发现的新可能性。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-14 DOI: 10.1016/j.sbi.2025.103167
Liguo Wang, Robert S. Prosser
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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 : 2025-10-07 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 : 2025-10-04 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 : 2025-10-04 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
Solid-state NMR of membrane proteins in situ. 原位膜蛋白的固态核磁共振。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-01 Epub Date: 2025-08-08 DOI: 10.1016/j.sbi.2025.103129
Francesca M Marassi, Guido Pintacuda

Membrane proteins have evolved to function as part of specialized biological membranes, and their structures and activities are highly susceptible to their local environment. Detergents and lipid mimetics replicate certain aspects of biological membranes, and have been used to produce an exceptional body of structural data, but do not fully capture the complex, asymmetric properties of the native environment and can alter structure and function. Here, we review recent advances in nuclear magnetic resonance (NMR) that enable the examination of membrane protein structure and activity in situ, within native membranes. The development of optimized protein expression strategies, isotopic labeling schemes, powerful instrumentation and specialized pulse sequences offer new opportunities for exploring the new frontier of in situ structural biology. By outlining the framework for in situ NMR of membrane proteins from conceptualization to experiments we hope to inspire new research in this growing and important area.

膜蛋白已经进化成为特殊生物膜的一部分,其结构和活性对其局部环境高度敏感。洗涤剂和脂质模拟物复制了生物膜的某些方面,并已用于产生特殊的结构数据体,但不能完全捕获天然环境的复杂,不对称特性,并且可以改变结构和功能。在这里,我们回顾了核磁共振(NMR)的最新进展,使检查膜蛋白的结构和活性在原位,在天然膜。优化的蛋白质表达策略、同位素标记方案、强大的仪器和专门的脉冲序列的发展为探索原位结构生物学的新领域提供了新的机会。通过概述膜蛋白原位核磁共振从概念到实验的框架,我们希望在这个不断发展和重要的领域激发新的研究。
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引用次数: 0
Cool and collected: Advances in sample preparation for cryo-electron microscopy. 冷却和收集:低温电子显微镜样品制备的进展。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-01 Epub Date: 2025-08-09 DOI: 10.1016/j.sbi.2025.103132
Shani Tcherner Elad, Noa Ben-Asher, Leeya Engel

Cryo-electron microscopy (cryo-EM) has emerged as a transformative tool in structural biology, enabling high-resolution visualization of macromolecules in their native states. Cryo-focused ion beam milling (cryo-FIB) and other advances in sample preparation have expanded the range of biological samples that can be studied with cryo-EM to include cells and tissues. While the dream of high-resolution structural analysis of proteins within their native, cellular context is now being realized, sample preparation, especially from tissues, is still labor-intensive and technically challenging. Here we review the latest innovations in cryo-EM sample preparation, including support fabrication and functionalization, cell micropatterning, and techniques for thinning frozen biological samples. Beyond streamlining and improving the repeatability of sample preparation, these advances are expanding the impact of cryo-EM by enabling unprecedented visualization of structures within cells and tissues in healthy and diseased states, as well as structural analysis of biological processes at well-controlled time points.

低温电子显微镜(cryo-EM)已经成为结构生物学中的一种变革性工具,能够在其原生状态下实现高分辨率的大分子可视化。低温聚焦离子束铣削(cryo-FIB)和样品制备的其他进展已经扩大了可以用低温电镜研究的生物样品的范围,包括细胞和组织。虽然对蛋白质进行高分辨率结构分析的梦想正在实现,但样品制备,特别是组织样品制备,仍然是劳动密集型的,并且在技术上具有挑战性。在这里,我们回顾了冷冻电镜样品制备的最新创新,包括支持制造和功能化,细胞微图和稀释冷冻生物样品的技术。除了简化和提高样品制备的可重复性外,这些进步还通过在健康和患病状态下实现细胞和组织内部结构的前所未有的可视化,以及在良好控制的时间点对生物过程进行结构分析,扩大了冷冻电镜的影响。
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引用次数: 0
期刊
Current opinion in structural biology
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