Biomolecular Recognition and Binding Mechanisms

细胞网络及其环境控制着细胞和生物体的行为，是理解功能、功能失调和药物发现的基础。在过去的几年里，人们观察到药物经常与不止一个靶标结合；因此，多药理学方法是有利的，补充了“一种药物-一种靶点”的策略。从系统生物学的角度来看，靶向药物发现可以帮助研究单一和多种药理学的网络效应。在这篇小型综述中，我们概述了网络描述和工具对单和多药理学的有用性，以及蛋白质相互作用有助于单靶点和多靶点药物发现的方法。我们进一步描述了，当结合实验数据时，如何建模结构网络，可以预测哪些蛋白质相互作用并提供其界面结构，可以模拟细胞途径，并建议哪些特定途径可能受到影响。这种结构网络可以促进基于结构的药物设计；预测药物的副作用；并提出药物结合的作用如何在多分子复合物和途径中传播。我们提供了小分子激酶抑制剂靶向抗癌治疗的概述。首先，我们讨论了为什么从各种异常遗传改变中产生的单一组成活性激酶能够转化正常细胞，导致其获得癌细胞的特征。为了引起人们对靶向癌症治疗中的激酶抑制不同于传统细胞毒性化疗这一事实的关注，我们利用了一个概念框架来解释为什么抑制激酶活性只会选择性地杀死所谓的致癌基因“成瘾”癌细胞，而保留健康细胞。其次，我们介绍了蛋白激酶超家族，因为它具有精确定位的结构元件的共同活性构象，以及激酶家族之间多样化的自抑制构象。了解单个激酶的详细激活机制对于将观察到的致癌改变与组成活性状态升高联系起来、确定随之而来的耐药机制以及指导下一代抑制剂的开发至关重要。为了阐明结构指南在肿瘤发生研究中的重要性，我们解释了EGFR的体细胞突变如何导致激酶组成激活。第三，除了继发性（获得性）突变阻止药物结合阻断被异常活化的激酶劫持的信号通路的共同主题外，我们还讨论了通过补偿以垂直或水平方式绕过失活途径的病变来耐药和复发的情况。总的来说，这些表明，未来用小分子激酶抑制剂治疗癌症的挑战将依赖于发现针对不同癌症个体亚型的优化药物的不同组合。炎症是对抗病原体的第一道防线，它可以促进肿瘤发生的所有阶段，包括肿瘤的发生、促进和转移。在这个框架下，toll样受体（TLR）通路在炎症和癌症中起着核心作用。尽管非常有用，但这种方法以及细胞网络中以节点（蛋白质）和边缘（相互作用）表示的其他途径的经典表示是不完整的。结构通路可以帮助完成这些图中缺失的部分：它们详细展示了来自不同上游通路的信号如何合并并向下游传播，平行通路如何在耐药突变体中相互补偿，多亚基信号复合物如何形成，特别是为什么需要它们以及它们是如何工作的，变构事件如何控制这些蛋白质及其通路，以及反馈回路的复杂细节以及如何启动。它们还可以解释一些致癌SNP突变的机制。构建结构路径是一项具有挑战性的任务。在这里，我们的目标是从结构的角度提供炎症和癌症的概述，重点是TLR途径。我们使用功能强大的PRISM （PRotein Interactions by Structural Matching）工具揭示了TLR通路关键协调者（如MyD88）内部和内部相互作用的重要结构信息。变构在很大程度上与单个蛋白质的构象和功能转变有关。这个概念可以扩展到考虑构象扰动对细胞功能和疾病状态的影响。在这里，我们澄清变构的概念和它如何控制生理活动。我们专注于变构如何引起疾病和促进新疗法发展的具有挑战性的问题。我们的目标是提高对细胞水平上疾病症状与分子水平上特定异常变构作用之间联系的认识，并强调变构药物在创新疗法中的潜力。变构繁殖导致蛋白质结构中不同位点之间的通信；它还编码对细胞通路的特定影响，并以这种方式塑造细胞反应。长程效应的一个例子是形态因子与细胞表面受体的结合，它启动了一系列蛋白质相互作用，导致基因组激活和特定的细胞作用。变构传播是多种因素共同作用的结果，通过构象群的动态变化发生，并影响大分子相互作用的平衡。在这里，我们(a)强调了众所周知但仍未被充分认识的变构作用，即在大的多分子组装和距离上传递明确的信号，以指定细胞的行为；(b)强调需要量化变构效应；最后，(c)提出沿着通路的每种特定的变构效应器组合都具有不同的功能。挑战是巨大的；鼓舞人心的回报将是预测药物制度的功能、功能失调和结果。泛素-蛋白酶体系统（UPS）参与许多细胞过程，包括蛋白质降解。通过该系统降解蛋白质包括两个连续的步骤：泛素化和降解。泛素化是用泛素样蛋白（ubitin -like proteins, UBLs）标记靶蛋白，如泛素、小泛素样修饰物（small ubiquitin-like modifier， SUMO）和NEDD8，通过一个涉及三种酶的级联反应：激活酶E1、偶联酶E2和E3泛素连接酶。蛋白酶体识别ubl标记的底物蛋白并降解它们。越来越多的证据表明，变构是调控泛素化，以及去泛素化和降解的核心参与者。我们概述了变构在这些过程的所有步骤中所起的关键机制作用，并重点介绍了针对它们的变构药物。我们强调了连接体在变构性控制UPS作用中发挥的关键机制作用，通过偏向构象空间的采样，促进了泛素化和降解的催化反应。最后，我们提出变构可能同样在细胞分子机器的调节中发挥关键作用，因此变构药物有望越来越多地用于治疗方案。目前的重点是癌症和炎症途径，包括NF-kB、规范和非规范、TLR、MyD88、Ras等。

The cellular network and its environment govern cell and organism behavior and are fundamental to the comprehension of function, misfunction and drug discovery. Over the last few years, drugs were observed to often bind to more than one target; thus, poly-pharmacology approaches can be advantageous, complementing the "one drug - one target" strategy. Targeting drug discovery from the systems biology standpoint can help in studies of network effects of mono- and poly-pharmacology. In this mini-review, we provide an overview of the usefulness of network description and tools for mono- and poly-pharmacology, and the ways through which protein interactions can help single- and multi-target drug discovery efforts. We further describe how, when combined with experimental data, modeled structural networks which can predict which proteins interact and provide the structures of their interfaces, can model the cellular pathways, and suggest which specific pathways are likely to be affected. Such structural networks may facilitate structure-based drug design; forecast side effects of drugs; and suggest how the effects of drug binding can propagate in multi-molecular complexes and pathways. We provide an overview of targeted anticancer therapies with small molecule kinase inhibitors. First, we discuss why a single constitutively active kinase emanating from a variety of aberrant genetic alterations is capable of transforming a normal cell, leading it to acquire the hallmarks of a cancer cell. To draw attention to the fact that kinase inhibition in targeted cancer therapeutics differs from conventional cytotoxic chemotherapy, we exploit a conceptual framework explaining why suppressed kinase activity will selectively kill only the so-called oncogene 'addicted' cancer cell, while sparing the healthy cell. Second, we introduce the protein kinase superfamily in light of its common active conformation with precisely positioned structural elements, and the diversified auto-inhibitory conformations among the kinase families. Understanding the detailed activation mechanism of individual kinases is essential to relate the observed oncogenic alterations to the elevated constitutively active state, to identify the mechanism of consequent drug resistance, and to guide the development of the next-generation inhibitors. To clarify the vital importance of structural guidelines in studies of oncogenesis, we explain how somatic mutations in EGFR result in kinase constitutive activation. Third, in addition to the common theme of secondary (acquired) mutations that prevent drug binding from blocking a signaling pathway which is hijacked by the aberrant activated kinase, we discuss scenarios of drug resistance and relapse by compensating lesions that bypass the inactivated pathway in a vertical or horizontal fashion. Collectively, these suggest that the future challenge of cancer therapy with small molecule kinase inhibitors will rely on the discovery of distinct combinations of optimized drugs to target individual subtypes of different cancers. Inflammation, the first line of defense against pathogens can contribute to all phases of tumorigenesis, including tumor initiation, promotion and metastasis. Within this framework, the Toll-like receptor (TLR) pathway plays a central role in inflammation and cancer. Although extremely useful, the classical representation of this, and other pathways in the cellular network in terms of nodes (proteins) and edges (interactions) is incomplete. Structural pathways can help complete missing parts of such diagrams: they demonstrate in detail how signals coming from different upstream pathways merge and propagate downstream, how parallel pathways compensate each other in drug resistant mutants, how multi-subunit signaling complexes form and in particular why they are needed and how they work, how allosteric events can control these proteins and their pathways, and intricate details of feedback loops and how kick in. They can also explain the mechanisms of some oncogenic SNP mutations. Constructing structural pathways is a challenging task. Here, our goal is to provide an overview of inflammation and cancer from the structural standpoint, focusing on the TLR pathway. We use the powerful PRISM (PRotein Interactions by Structural Matching) tool to reveal important structural information of interactions in and within key orchestrators of the TLR pathway, such as MyD88. Allostery is largely associated with conformational and functional transitions in individual proteins. This concept can be extended to consider the impact of conformational perturbations on cellular function and disease states. Here, we clarify the concept of allostery and how it controls physiological activities. We focus on the challenging questions of how allostery can both cause disease and contribute to development of new therapeutics. We aim to increase the awareness of the linkage between disease symptoms on the cellular level and specific aberrant allosteric actions on the molecular level and to emphasize the potential of allosteric drugs in innovative therapies. Allosteric propagation results in communication between distinct sites in the protein structure; it also encodes specific effects on cellular pathways, and in this way it shapes cellular response. One example of long-range effects is binding of morphogens to cell surface receptors, which initiates a cascade of protein interactions that leads to genome activation and specific cellular action. Allosteric propagation results from combinations of multiple factors, takes place through dynamic shifts of conformational ensembles, and affects the equilibria of macromolecular interactions. Here, we (a) emphasize the well-known yet still underappreciated role of allostery in conveying explicit signals across large multimolecular assemblies and distances to specify cellular action; (b) stress the need for quantitation of the allosteric effects; and finally, (c) propose that each specific combination of allosteric effectors along the pathway spells a distinct function. The challenges are colossal; the inspiring reward will be predicting function, misfunction, and outcomes of drug regimes. The ubiquitin-proteasome system (UPS) is involved in many cellular processes including protein degradation. Degradation of a protein via this system involves two successive steps: ubiquitination and degradation. Ubiquitination tags the target protein with ubiquitin-like proteins (UBLs), such as ubiquitin, small ubiquitin-like modifier (SUMO) and NEDD8, via a cascade involving three enzymes: activating enzyme E1, conjugating enzyme E2 and E3 ubiquitin ligases. The proteasomes recognize the UBL-tagged substrate proteins and degrade them. Accumulating evidence indicates that allostery is a central player in the regulation of ubiquitination, as well as deubiquitination and degradation. We provide an overview of the key mechanistic roles played by allostery in all steps of these processes, and highlight allosteric drugs targeting them. We emphasize the crucial mechanistic role played by linkers in allosterically controlling the UPS action by biasing the sampling of the conformational space, which facilitate the catalytic reactions of the ubiquitination and degradation. Finally, we propose that allostery may similarly play key roles in the regulation of molecular machines in the cell, and as such allosteric drugs can be expected to be increasingly exploited in therapeutic regimes. Current focus is on cancer and inflammation pathways including the NF-kB, canonical and non-canonical, the TLR, MyD88, Ras and more.