Novel Structure-Based Rifamycins for Drug-resistant TB and HIV Co-infection

 描述(申请人提供)：结核病是最重要的世界卫生问题之一，2012年造成45万人死亡。耐多药结核病(MDR-TB)和广泛耐药结核病(XDR-TB)发病率的增加已成为日益严重的健康危机。显然，开发抗结核分枝杆菌(MTB)的新型抗生素以克服对现有疗法的耐药性是一个关键的未得到满足的需求。然而，在过去的40年里，只有一种具有新靶点的新药(贝达奎兰)被批准用于治疗结核病，即分枝杆菌ATP合成酶。在抑制新靶点方面缺乏成功表明，重新研究以前有效的药物的靶点可能是一种更好的方法。结核分枝杆菌RNA聚合酶(RNAP)是一个被证明是有吸引力的靶标，因为它对细菌的生存是必不可少的，而且原核和真核RNAP之间的相似性很低。利福霉素(RIF)是MTB RNAP的非常有效的抑制剂；然而，这些药物通过靶标RNAP的突变以及由RIF激活人类孕烷X受体(HPXR)而导致的药物与药物的相互作用而遭受耐药性(RIFR)(尤其是在结核病/艾滋病毒联合感染中)。我们提出了一个多学科的综合计划，包括基于结构的类似物合成、高通量筛选(HTS)、体外RNAP抑制评估、抑制剂*RNAP复合体的X射线晶体结构测定，并研究将hPXR的激活降至最低，以发现新的药物，以解决目前MTB治疗的局限性。我们组建了一支在RNA和细菌RNA聚合酶的生物化学和酶学方面拥有技能和经验的团队，在制药行业拥有数十年的合成药物化学和分子建模经验，具有开创性的细菌RNA聚合酶结构生物学，以及国际公认的结核分枝杆菌微生物学专业知识。我们团队最近发表的文章(四篇论文、一篇综述和一项专利申请)证明了我们方法的原则。我们的第一组RIF类似物显示出增强的抗RIFR RNAP的活性，在一种情况下减少了hPXR的激活，并以设计的模式与RNAP结合，如我们的X射线晶体结构所示。这些X射线晶体结构现在为我们开发改进的RIF提供了一个概念框架。埃布赖特和他的同事最近的研究(Zhang等人，(2014年)eLife 3 e02450,3994528)进一步证明了原理，即阐述利福霉素核心可以产生增强抗RIFR结核分枝杆菌的活性。我们还开发了一种高效的体外RNAP试验，可用于HTS，并将作为发现新的RNAP抑制剂的补充方法。我们期望，在本申请中描述的全面阐述的运动将为药物开发产生新的候选药物，并最终改善结核病的治疗，特别是对艾滋病毒-结核病合并感染和耐药结核病患者的治疗。

 DESCRIPTION (provided by applicant): Tuberculosis is one of the most important world health problems, responsible for 450,000 deaths in 2012. Increases in the occurrence of multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) have become an increasingly problematic health crisis. Clearly there is a critical unmet need for the development of novel antibiotics against M. tuberculosis (MTB) to overcome resistance to current therapeutics. However, only one new drug (bedaquiline) with a novel target, the mycobacterial ATP synthase, has been approved for the treatment of tuberculosis in the last 40 years. The lack of success in inhibiting novel targets suggests that the reinvestigation of targets of previously effective drugs may be a better approach. The MTB RNA polymerase (RNAP) is a proven and attractive target because it is essential for bacterial survival, and there is low similarity between prokaryotic and eukaryotic RNAPs. The rifamycins (RIFs) are very potent inhibitors of MTB RNAP; however, these agents suffer from resistance (RIFR) via mutation of the target RNAP and drug-drug interactions that result from RIF activation of the human pregnane X receptor (hPXR) (particularly problematic in TB/HIV co-infection). We propose a multi-disciplinary and comprehensive program that involves structure-based analogue synthesis, high-throughput screening (HTS), in vitro RNAP inhibition evaluation, X-ray crystal structure determinations of inhibitor*RNAP complexes, and studies to minimize hPXR activation towards uncovering novel agents to address current MTB treatment limitations. We have assembled a team with skills and experience in biochemistry and enzymology of RNA and bacterial RNA polymerase, decades of synthetic medicinal chemistry and molecular modeling in the pharmaceutical industry, groundbreaking structural biology of bacterial RNA polymerase, and internationally-recognized expertise in the microbiology of M. tuberculosis. The recent publications (four papers, one review, and one patent application) of our team demonstrate the proof of principle of our approach. Our very first set of RIF analogues exhibit enhanced activity against RIFR RNAP, in one case a reduction in hPXR activation, and bind to the RNAP in the designed mode as shown by our X-ray crystal structures. These X-ray crystal structures now provide a conceptual framework for our development of improved RIFs. Recent studies by Ebright and co-workers (Zhang et al., (2014) eLife 3 e02450, 3994528) provide further proof of principle that elaboration of the rifamycin core can yield enhanced activity against RIFR MTB. We have also developed an efficient in vitro RNAP assay, scalable for HTS, and will use this as a complementary approach for discovering novel RNAP inhibitors. It is our expectation that the fully articulated campaign described in this application will yield novel candidates for drug development and ultimately improve treatment for tuberculosis, especially in patients with HIV-TB co-infection and drug-resistant tuberculosis.