Biomolecular Structure and Mechanism, Structure-Based Drug Design

通过结构分析，我们绘制了选定的生物大分子的反应轨迹或功能循环。通过基于结构的开发，我们设计，合成和表征新型抗癌和抗菌剂。我们开展基于结构的药物开发，作为我们对具有抗癌和抗菌意义的生物分子系统的结构和机制的基础研究的延续。迄今为止，我们已经描述了HPPK的反应轨迹或功能循环（微生物必需的叶酸途径酶，但在哺乳动物中不存在），Era（一种将细胞生长与细胞分裂偶联的必需GT酶），RapA（一种抑制RNA聚合酶的Swi 2/Snf 2蛋白），RNase III家族的两个成员（dsRNA特异性内切核糖核酸酶家族）和DDX 3X（解旋短RNA双链体的DEAD盒解旋酶）。在这些生物分子中，HPPK是新型抗菌剂的靶标，DDX 3X是新型抗癌剂和抗HIV剂的靶标。基于结构的药物开发正在进行中。我们已经在靶向HPPK的新型抗菌剂方面取得了重大进展，密切模仿反应中间体，从而表现出高效力。RNase III家族的代表性成员包括原核RNase III和真核Rnt 1 p、Drosha和Dicer。它们在RNA加工和成熟、转录后基因沉默和防御病毒感染中发挥重要作用。对于结构和机制研究，细菌RNase III和酵母Rnt 1 p分别是原核生物和真核生物的有价值的模型系统。对于RNase III和Rnt 1 p，我们已经展示了它们的核酸内切酶结构域（RIIID）的二聚化如何产生两个切割位点所在的催化谷，催化谷如何以使得两条RNA链中的每条与两个切割位点之一对齐的方式容纳dsRNA底物，每条链的水解如何涉及两个RIIID，以及RNase III如何使用两个切割位点在其产物中产生2-核苷酸（2-nt）3'突出端。我们还展示了镁对于催化活性蛋白质-RNA复合物的形成是如何至关重要的，以及镁离子的使用如何驱动每个磷酸二酯键的水解。此外，我们已经描述了一个逐步的模型，RNase III和Rnt 1 p执行磷酰基转移反应。RNase III家族的所有成员都通过两个Mg 2+离子催化来推动RNA水解，然而，这在原核生物和真核生物中表现出不同的特征。正如我们的结构所揭示的，原核生物的RNase III需要第三个镁离子催化，而真核生物的RNase III采用两个额外的氨基酸侧链。DDX 3X属于DEAD盒解旋酶家族，其通过解旋短RNA双链体来调节RNA加工和代谢。DDXs共享由两个RecA样结构域（D1 D2）组成的解旋酶核心，以ATP依赖的非进行性方式发挥功能。作为一个有吸引力的癌症和艾滋病治疗的靶点，DDX 3X及其直系同源物被广泛研究，产生了丰富的生物化学和生物物理数据，包括apo-D1 D2和解绕后D1 D2：ssRNA复合物的结构。然而，解旋前的D1 D2：dsRNA复合物的结构是不可用的，直到我们最近确定了在解旋前状态下与2-转角RNA双链体复合的D1 D2核心的晶体结构，表明两个DDX识别RNA双链体。每个DDX主要识别单链，ATP结合引起的构象变化以合作的方式解开RNA双链体。我们的结构显著改变了以前的三分子协同模型。为了验证我们的新模型，我们目前正在阐明DDX 3X的功能循环，使用定点诱变，RNA解旋测定，ATP水解测定，希尔协同分析和结构研究。我们还正在开发DDX 3X抑制剂的基础上可用的结构和机制信息。

By structural analysis, we map the reaction trajectory or functional cycle of selected biological macromolecules. By structure-based development, we design, synthesize, and characterize novel anticancer and antimicrobial agents. We carry out structure-based drug development as a continuation of our basic research on the structure and mechanism of biomolecular systems with anticancer and antimicrobial significance. To date, we have described the reaction trajectory or functional cycle of HPPK (a folate pathway enzyme essential for microorganisms but absent in mammals), Era (an essential GTPase that couples cell growth with cell division), RapA (a Swi2/Snf2 protein that recycles RNA polymerase), two members of the RNase III family (a family of dsRNA-specific endoribonucleases), and DDX3X (a DEAD-box helicase that unwinds short RNA duplexes). Among these biomolecules, HPPK is a target for novel antibacterial agents, and DDX3X is a target for novel anticancer and anti-HIV agents. Structure-based drug development is in progress. We have made significant progress toward novel antibacterial agents targeting HPPK, closely mimicking the reaction intermediate and thereby exhibiting high potency. Representative members of the RNase III family include prokaryotic RNase III and eukaryotic Rnt1p, Drosha, and Dicer. They play important roles in RNA processing and maturation, post-transcriptional gene silencing, and defense against viral infection. For structural and mechanistic studies, bacterial RNase III and yeast Rnt1p are valuable model systems for prokaryotes and eukaryotes, respectively. For both RNase III and Rnt1p, we have shown how the dimerization of their endonuclease domain (RIIID) creates a catalytic valley where two cleavage sites are located, how the catalytic valley accommodates a dsRNA substrate in a manner such that each of the two RNA strands is aligned with one of the two cleavage sites, how the hydrolysis of each strand involves both RIIIDs, and how RNase III uses the two cleavage sites to create 2-nucleotide (2-nt) 3' overhangs in its products. We have also shown how magnesium is essential for the formation of a catalytically competent protein-RNA complex, and how the use of magnesium ions can drive the hydrolysis of each phosphodiester bond. Moreover, we have described a stepwise model by which RNase III and Rnt1p execute the phosphoryl transfer reaction. All members of the RNase III family propel RNA hydrolysis by two-Mg2+-ion catalysis, which exhibits distinct features, however, by prokaryotes and eukaryotes. As revealed by our structures, prokaryotic RNase IIIs require a third magnesium ion in catalysis, whereas eukaryotic RNase IIIs employ two additional amino acid side chains. DDX3X belongs to the family of DEAD-box helicases that regulate RNA processing and metabolism by unwinding short RNA duplexes. Sharing a helicase core composed of two RecA-like domains (D1D2), DDXs function in an ATP-dependent, non-processive manner. As an attractive target for cancer and AIDS treatment, DDX3X and its orthologs are extensively studied, yielding a wealth of biochemical and biophysical data, including structures of apo-D1D2 and post-unwound D1D2:ssRNA complex. However, the structure of a pre-unwound D1D2:dsRNA complex was not available until we have recently determined the crystal structure of a D1D2 core in complex with a 2-turn RNA duplex at the pre-unwound state, showing that two DDXs recognize the RNA duplex. Each DDX mainly recognizes a single strand, and conformational changes induced by ATP binding unwinds the RNA duplex in a cooperative manner. Our structure has significantly altered a previous model of three-molecule cooperativity. To validate our new model, we are currently elucidating the functional cycle of DDX3X using site-directed mutagenesis, RNA-unwinding assay, ATP-hydrolyzing assay, Hill cooperativity analysis, and structural studies. We are also developing DDX3X inhibitors based on available structural and mechanistic information.