Combining Cheminformatics Methods and Pathway Analysis to Identify Molecules with Whole-Cell Activity Against Mycobacterium Tuberculosis

Purpose

New strategies for developing inhibitors of Mycobacterium tuberculosis (Mtb) are required in order to identify the next generation of tuberculosis (TB) drugs. Our approach leverages the integration of intensive data mining and curation and computational approaches, including cheminformatics combined with bioinformatics, to suggest biological targets and their small molecule modulators.

Methods

We now describe an approach that uses the TBCyc pathway and genome database, the Collaborative Drug Discovery database of molecules with activity against Mtb and their associated targets, a 3D pharmacophore approach and Bayesian models of TB activity in order to select pathways and metabolites and ultimately prioritize molecules that may be acting as substrate mimics and exhibit activity against TB.

Results

In this study we combined the TB cheminformatics and pathways databases that enabled us to computationally search >80,000 vendor available molecules and ultimately test 23 compounds in vitro that resulted in two compounds (N-(2-furylmethyl)-N??-[(5-nitro-3-thienyl)carbonyl]thiourea and N-[(5-nitro-3-thienyl)carbonyl]-N??-(2-thienylmethyl)thiourea) proposed as mimics of D-fructose 1,6 bisphosphate, (MIC of 20 and 40???g/ml, respectively).

Conclusion

This is a simple yet novel approach that has the potential to identify inhibitors of bacterial growth as illustrated by compounds identified in this study that have activity against Mtb.     

耐多药结核分枝杆菌对氟喹诺酮类药物体外交叉耐药及耐药性研究

目的:了解结核分枝杆菌对5种抗结核氟喹诺酮类药物之间的交叉耐药性,促进临床合理用药。方法:临床采集耐多药结核(MDR-TB)菌株培养,分别测定5种氟喹诺酮类药物(环丙沙星、氧氟沙星、左氧氟沙星、司帕沙星、莫西沙星)的最低抑菌浓度(MIC)的变化,定性判断是否存在交叉耐药,得出实验室研究数据。结果:各氟喹诺酮类药物对临床分离出异烟肼利福平耐药株耐药率均>70%,耐药率接近,差异无统计学意义(P>0.05);各氟喹诺酮药物之间存在不完全交叉耐药性。结论:临床医师在为患者选择药物治疗方案时,应综合参照药敏试验结果、患者疾病史、用药史等,选择有效的氟喹诺酮类药物治疗MDR-TB。该体外试验可为进一步的体内试验及临床研究氟喹诺酮类药物MDR-TB中的交叉耐药性提供基础。     

结核分枝杆菌耐药性快速检测方法研究进展

由结核分枝杆菌(TB)引起的结核病是当今全球流行最广泛、最普遍的传染病之一.自上个世纪80年代以来,本已被控制的结核病发病率呈现上升的趋势,其主要原因是流动人口的大量增加,耐多药结核病(MDR-TB)的流行及HIV感染、器官移植、免疫抑制剂使用导致免疫力低下患者增多,其中MDR-TB是结核病回潮的最主要原因.     

结核分枝杆菌耐药性快速检测方法研究进展

由结核分枝杆菌（TB）引起的结核病是当今全球流行最广泛、最普遍的传染病之一。自上个世纪80年代以来，本已被控制的结核病发病率呈现上升的趋势，其主要原因是流动人口的大量增加，耐多药结核病（MDR—TB）的流行及HIV感染、器官移植、免疫抑制剂使用导致免疫力低下患增多，其中MDR—TB是结核病回潮的最主要原因。由于MDR-TB对多种抗结核药物耐药而导致治疗十分困难，该病传播迅速，病死率高。为从根本上控制该病的流行，实验室工作应使用快速、有效的新技术代替传统实验方法，及时为临床提供诊断和治疗依据，早期发现病情并使用敏感的抗结核药物。因此，快速、准确的耐药性检测试验成为近年来研究的热点和难点。本就快速检测TB耐药性方法的研究进展综述如下。     

结核分枝杆菌药物敏感试验检测方法的研究

目的 建立一种结核分枝杆菌（Mycobacteriumtuberculosis）药敏试验的快速荧光检测法。方法 用自制的荧光检测管检测异烟肼（INH）、利福平（RFP）、乙胺丁醇（EB）、丁胺卡那霉素（AMK）、左旋氧氟沙星（LVFX）对结核分枝杆菌的体外抑菌活性,并用82例临床菌株与改良罗氏法进行了配对比较,确定各药物在药敏试验中的应用浓度。结果 5种药物的应用浓度分别确定为IHN：0．1μg／ml、RFP：1μg／ml、EB：2μg／ml、AMK：2μg／ml、LVFX：2μg／ml;本法进行结核分枝杆茼的药敏试验仅需7～10天（d）,较改良罗氏法的28d缩短了18～21d。两种方法的药敏试验结果无显著性差异。结论本法经济实用,并缩短了结核分枝杆菌药敏的报告时间。     

耐药肺结核病人的临床化疗效果及影响因素调查

目的 评价结核病耐药以后对肺结核统一化学治疗方案效果的影响,为结核病控制规划策略调整提供参考。方法 通过回顾性调查方式收集2012—2013年间治疗管理的227例肺结核病人,依据抗结核药物敏感试验结果将其分为耐药组（95例）及敏感组（132例）,对其治疗效果及影响因素进行比较分析。结果 通过调查发现结核菌耐药组疗程结束后痰标本中结核分枝杆菌阴转率为74.7%、抗结核药物敏感组痰中结核菌阴转率为91.7%,其病人细菌学复发率分别为11.3%及3.31%。然后耐一种药者痰菌阴转率为87.0%;耐两种药及三种药者分别为71.4%和54.5%。结论 肺结核病患者原发耐药,尤其是同时对多种抗结核药物耐药是导致化学药物治疗失败的重要原因,临床用药时应认真参考药敏试验结果进行合理判断,慎重选择。     

In Vitro Measurement of Drug Efficiency Index to Aid Early Lead Optimization

The concepts of drug efficiency (D_eff) and Drug Efficiency Index (DEI) have been recently introduced as useful parameters to optimize the absorption, distribution, metabolism, elimination/excretion, and toxicity properties and in vivo efficacy potential of molecules during lead optimization and at pre-clinical stages. The available free drug concentration relative to dose depends on the compound's bioavailability, clearance, and the nonspecific binding to proteins and phospholipids. In this paper, we have demonstrated, using the data of over 115 known drug molecules, that the nonspecific binding can be determined in vitro very efficiently using biomimetic high-performance liquid chromatography measurements. DEI can therefore be estimated from in vitro measurements. The data show that high in vitro DEI values can be associated with lower efficacious dose. A strategy is described of how to use the DEI parameter during early lead optimization. An example is given to highlight the advantages of optimizing on DEI value rather than on potency alone. In order to facilitate the in silico compound design, correlation between in vitro DEI and in silico ligand efficiency parameters such as ligand lipophilicity efficiency has been revealed, suggesting the potential use of these efficiency-related parameters across lead optimization. © 2012 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 101:4155–4169, 2012     

某区322株结核杆菌的耐药性分析

目的了解惠州市结核病防治院322株痰培养阳性结核杆菌的耐药情况,为临床合理用药提供理论依据。方法以我院322株痰培养阳性的结核杆菌为研究对象,用比例法进行一线结核用药的药敏实验。结果 322株结核分枝杆菌对4种抗结核药物全部耐药者36例,占10.84%;以耐链霉素为最高,占35.8%。结论惠州市结核病耐药情况仍然十分严峻,应加强结核病临床治疗的管理,制定合理化疗方案,防止耐药菌传播。     

The Alabama Drug Discovery Alliance: A Collaborative Partnership to Facilitate Academic Drug Discovery

The Alabama Drug Discovery Alliance is a collaboration between the University of Alabama at Birmingham and Southern Research Institute that aims to support the discovery and development of therapeutic molecules that address an unmet medical need. The alliance builds on the expertise present at both institutions and has the dedicated commitment of their respective technology transfer and intellectual property offices to guide any commercial opportunities that may arise from the supported efforts. Although most projects involve high throughput screening, projects at any stage in the drug discovery and development pathway are eligible for support. Irrespective of the target and stage of any project, well-functioning interdisciplinary teams are crucial to a project’s progress. These teams consist of investigators with a wide variety of expertise from both institutions to contribute to the program’s success.     

西安市结核病胸部肿瘤医院抗结核药使用情况与结核分枝杆菌耐药性分析

目的：分析结核分枝杆菌耐药性与抗结核药应用情况相关性,为临床合理使用抗结核药提供参考。方法：对2012年1—12月我院结核分枝杆菌耐药情况和抗结核药的用药频度（DDDs）、限定日费用（DDC）及排序比（B／A）进行统计、分析。结果：1165株结核分枝杆菌对4种一线抗结核药总体耐药率为29．3％（341／1165）,耐多药率为12．0％（140／1165）,单耐药率最高为链霉素（22．8％）、最低为乙胺丁醇（7．0％）;79株耐多药菌株对7种二线抗结核药单耐药率最高为利福喷汀（53．2％）,最低为阿米卡星（1．3％）;一线抗结核药使用较广泛,DDDs较高,二线抗结核药对患者的经济负担较重,DDC较高;静脉用利福平制剂及氟喹诺酮类制剂的用量较大。结论：结核分枝杆菌耐药率升高与抗结核药大量应用具有相关性,应加强药品敏感性监测,合理使用抗结核药。     

用分子生物学技术快速检测耐多药结核分枝杆菌

目的：用PCR—SSCP技术检测耐INH、RFP、SM结核分枝杆菌分离株KatG、rpoB、rpsL基因突变，评价其在快速检测结核分枝杆菌耐药性方面的临床价值。方法：以结核分枝杆菌H；vRv为对照，20株耐多药菌株和20株敏感株，分别用PCR—SSCP方法检测KatG、rpoB、rpsL基因突变，并将SSCP结果与药敏试验结果作对照分析。结果：PCR—SSCP方法检测20株敏感株SSCP带语均与H37RV标准株相同，而20株耐多药结核分枝杆菌KatG、rpoB、rpsL基因突变的阳性率分别为70％，100％和75％。发现20株耐多药菌株中有11株(55％)共INH、RFP、SM3种耐药遗传标志均发生突变，7株(35％)有2种耐药遗传标志突变，2株(10％)只有RFP耐药标志突变。结论：PCR—SSCP方法敏感、特异，可快速检测结核分枝杆菌KatG、rpoB、rpsL耐药基因突变，有利于耐多药结核分枝杆菌耐药性的快速检测。