Target based discovery of next generation pyrazinamide

基于目标的下一代吡嗪酰胺的发现

• 批准号: 10404533
• 负责人: Thomas Dick
• 金额: $ 79.17万
• 依托单位: HACKENSACK UNIVERSITY MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-08-01 至 2023-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10404533
• 关键词: Acquired Immunodeficiency Syndrome; Affinity; Anabolism; Animal Model; Anti-Bacterial Agents; Antibiotics; Antitubercular Agents; Antitubercular Antibiotics; Aspartate; Award; Bacillus; Bacteria; Binding; Biochemical; Biological Assay; Biophysics; Carboxy-Lyases; Cause of Death; Cells; Chemistry; Chimeric Proteins; Clinical; Dependence; Disease; Drug Kinetics; Drug Targeting; Drug Tolerance; Enzyme Inhibition; Frequencies; Generations; Genetic; Goals; Granuloma; Growth; HIV; HIV Seropositivity; Human; Immunity; Immunocompetent; In Vitro; Inbred BALB C Mice; Individual; Infection; Knowledge; Lead; Lesion; Mediating; Medical; Medicine; Minor; Modeling; Mutation; Mycobacterium tuberculosis; Necrosis; Necrotic Lesion; Oryctolagus cuniculus; Outcome; Patients; Penetration; Peptide Hydrolases; Persons; Pharmaceutical Preparations; Pharmacodynamics; Pharmacology; Pharmacotherapy; Play; Population; Property; Pyrazinamide; Pyrazinamide resistance; Regimen; Relapse; Reporter; Resistance; Role; Site; Sterilization; Testing; Time; Treatment Protocols; Tuberculosis; analog; bacterial fitness; base; biophysical analysis; biophysical techniques; chemotherapy; cofactor; enzyme activity; fight against; fitness; genetic approach; improved; in vitro activity; in vivo; inhibitor; lung lesion; metabolomics; molecular drug target; mouse model; mutant; next generation; novel; programs; protein degradation; pyrazinoic acid; rational design; treatment duration; tuberculosis drugs

Tuberculosis (TB) is a main cause of death for people living with AIDS. In immune-competent populations, drug therapy and immunity join forces to win the fight against Mycobacterium tuberculosis (Mtb). In HIV-positive individuals on the other hand, chemotherapy must fully sterilize all infection sites. There is an urgent medical need to develop more potent `sterilizing' drugs. The inclusion of pyrazinamide (PZA) into the TB regimen allowed reduction of treatment time to six months, while maintaining low relapse rates. The pharmacological basis for PZA's remarkable sterilizing activity in patients remains obscure, considering the drug's poor in vitro potency (MIC = 30-100 µg/mL). In the rabbit model of active TB, an animal model that recapitulates the various lung lesion types observed in human TB disease, we showed that PZA not only penetrates caseous necrotic lesions but also sterilizes them. In an ex vivo assay using caseum from infected rabbits, we showed that PZA kills non-growing, drug tolerant Mtb. These findings provide an explanation for the clinically observed treatment shortening effect of PZA: the drug reaches difficult-to-penetrate TB lesions and kills recalcitrant `persister' Mtb. However, consistent with the modest in vitro potency of PZA, onset of lesion sterilization is slow and concentrations required to kill Mtb in ex vivo caseum are high. Based on these findings, the logical way forward is to improve the potency of PZA while maintaining its unique lesion penetration and sterilization properties. To enable the rational optimization of PZA, we identified aspartate decarboxylase PanD, required for coenzymeA biosynthesis, as a the first genetically, biochemically and biophysically validated target of PZA. Consistent with poor whole cell activities of PZA, affinity of the drug (more specifically its bioactive component pyrazinoic acid, POA) for PanD was in the µM range, confirming room for improvement. Interestingly, mechanism of action studies revealed a novel antibacterial on-target mechanism whereby, rather than inhibiting PanD's catalytic activity, binding of POA to PanD appears to trigger degradation of the protein by the caseinolytic protease ClpC1. Here, we propose to build on our discoveries and 1. fully characterize the novel on-target mechanism by which the drug induces degradation of its target, 2. exploit in vitro pharmacological `sterilizing' models and PanD-based assays for the discovery of novel PZA analogs with improved potency and sterilizing activity, and 3. characterize lesion specific growth and replication status of PZA resistant panD mutant Mtb vs. wild type Mtb in the TB rabbit model with and without PZA treatment. In summary, we have identified key pharmacological properties responsible for the treatment shortening activity of PZA in clinical settings, as well as the molecular target of the drug, and we propose a `first-in-class to best-in- class' program to exploit these findings and rationally design the `next generation' PZA with improved sterilizing activity.

结核病是艾滋病患者死亡的主要原因。在免疫能力强的人群中， 治疗和免疫力联合起来，以赢得对结核分枝杆菌（Mtb）的斗争。hiv阳性 另一方面，化疗必须完全消毒所有感染部位。有一个紧急医疗 需要开发更有效的“绝育”药物。 将吡嗪酰胺（PZA）纳入TB方案可将治疗时间缩短至6个月， 保持低复发率。PZA对人体具有显著杀菌作用的药理学基础 考虑到该药物体外效力较差（MIC = 30-100 µg/mL），因此该研究尚不清楚。在兔主动脉弓模型中， 结核病是一种动物模型，它概括了在人类结核病中观察到的各种肺部病变类型， PZA不仅能穿透干酪样坏死病灶，还能使其绝育。在使用酪蛋白的离体测定中， 从感染的兔子，我们表明PZA杀死非生长的耐药性结核分枝杆菌。这些发现提供了 临床观察到的PZA治疗缩短效应的解释：药物难以渗透 结核病损害并杀死结核病的“持久性”结核病。然而，与PZA的适度体外效力一致， 损伤灭菌的开始是缓慢的，并且在离体酪蛋白中杀死Mtb所需的浓度是高的。基于 根据这些发现，合乎逻辑的前进方向是提高PZA的效力，同时保持其独特的病变 渗透和杀菌性能。为了能够合理优化PZA，我们确定了天冬氨酸 辅酶A生物合成所需的脱羧酶PanD，作为第一个遗传、生化和 生物药理学验证的PZA靶点。与PZA的差的全细胞活性一致，药物的亲和力（更多 特别是其生物活性成分吡嗪酸，POA）对PanD的作用在μM范围内， 改进.有趣的是，作用机制研究揭示了一种新的抗菌靶向机制 由此，POA与PanD的结合似乎引发降解，而不是抑制PanD的催化活性 通过酪蛋白分解蛋白酶ClpC 1。 在这里，我们建议建立在我们的发现和1。充分表征了新的靶向机制， 药物诱导其靶标降解，2.利用体外药理学“灭菌”模型和基于PanD的 用于发现具有改进的效力和杀菌活性的新型PZA类似物的测定，以及3.表征 抗PZA的panD突变型Mtb与野生型Mtb在结核病兔中的病变特异性生长和复制状态 有和没有PZA治疗的模型。 总之，我们已经确定了治疗缩短活性的关键药理学特性 的PZA在临床环境中，以及药物的分子靶点，我们提出了一个“一流的最好的， 类“程序，利用这些发现和合理设计”下一代“PZA与改进的消毒 活动

项目成果

PROTAC antibiotics: the time is now.

• DOI: 10.1080/17460441.2023.2178413
• 发表时间: 2023-04
• 期刊: EXPERT OPINION ON DRUG DISCOVERY
• 影响因子: 6.3
• 作者: Sarathy, Jickky Palmae;Aldrich, Courtney C.;Go, Mei-Lin;Dick, Thomas
• 通讯作者: Dick, Thomas

Pyrazinamide Resistance Is Caused by Two Distinct Mechanisms: Prevention of Coenzyme A Depletion and Loss of Virulence Factor Synthesis.

• DOI: 10.1021/acsinfecdis.6b00070
• 发表时间: 2016-09-09
• 期刊: ACS infectious diseases
• 影响因子: 5.3
• 作者: Gopal P;Yee M;Sarathy J;Low JL;Sarathy JP;Kaya F;Dartois V;Gengenbacher M;Dick T
• 通讯作者: Dick T

Mycobacterium tuberculosis PanD Structure-Function Analysis and Identification of a Potent Pyrazinoic Acid-Derived Enzyme Inhibitor.

• DOI: 10.1021/acschembio.1c00131
• 发表时间: 2021-06-18
• 期刊: ACS chemical biology
• 影响因子: 4
• 作者: Ragunathan P;Cole M;Latka C;Aragaw WW;Hegde P;Shin J;Subramanian Manimekalai MS;Rishikesan S;Aldrich CC;Dick T;Grüber G
• 通讯作者: Grüber G

A medicinal chemists' guide to the unique difficulties of lead optimization for tuberculosis.

• DOI: 10.1016/j.bmcl.2013.07.006
• 发表时间: 2013-09-01
• 期刊: BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
• 影响因子: 2.7
• 作者: Dartois, Veronique;Barry, Clifton E., III
• 通讯作者: Barry, Clifton E., III

Structure activity relationship of pyrazinoic acid analogs as potential antimycobacterial agents.

• DOI: 10.1016/j.bmc.2022.117046
• 发表时间: 2022-11-15
• 期刊: BIOORGANIC & MEDICINAL CHEMISTRY
• 影响因子: 3.5
• 作者: V. Hegde, Pooja;Aragaw, Wassihun W.;Cole, Malcolm S.;Jachak, Gorakhnath;Ragunathan, Priya;Sharma, Sachin;Harikishore, Amaravadhi;Gruber, Gerhard;Dick, Thomas;Aldrich, Courtney C.
• 通讯作者: Aldrich, Courtney C.