Molecular design,synthesis and biological activities of amidines as new ketol-acid reductoisomerase inhibitors

Diamidine （A） was identified in our in vitro bio-assay as a possible inhibitor of ketol-acid reductoisomerase （KARI） from the ACD database search based on the known three-dimensional crystal structure of KARI. An investigation on interaction of A on KARI active sites, led to the design and synthesis of 15 novel monoamidines. Some of those showed better biological activity than A on rice KARI （in vitro） and in greenhouse herbicidal tests （in vivo）. The structure-biological activity relationship was investigated, which provides valuable information to further study of potential KARI inhibitors.     

酰胺类KARI酶抑制剂的设计、合成和生物活性

以分子对接法进行MDL/ACD三维数据库搜寻所得到的大量结构信息为指导, 从中选取部分酰胺类小分子进行化学合成和结构表征. 生物活性测试结果表明, 设计合成的8个酰胺类化合物在200 μg/mL浓度下对水稻KARI酶具有不同程度的抑制活性, 化合物1和6的抑制率可达到57.4%和48.1%. 部分化合物在100 μg/mL浓度下对双子叶植物油菜的胚根和单子叶植物稗草的茎叶的抑制活性较为显著, 化合物1和6对油菜胚根生长抑制率分别为52.0%和72.6%, 其与KARI酶体外(in vitro)抑制活性具有一定的相关性. 这些酰胺类化合物可作为KARI酶抑制剂为后续分子设计提供借鉴.     

酮醇酸还原异构酶(KARI)与其抑制剂间相互作用的分子模拟研究

采用MCCE, Autodock及密度泛函方法对酮醇酸还原异构酶(KARI)与其抑制剂间相互作用进行了研究. 计算结果表明, KARI活性位点中的Mg^2＋在活性位点残基的离子化状态、活性位点的静电性质以及与抑制剂结合等方面起重要的作用; 同时, 抑制剂在结合方式、前线轨道布居及静电势等方面与酶促反应中间体(HOIV)具有一定程度的相似性; 可电离的羧基是当前发现的靶向KARI抑制剂一个重要的结构特征, 进一步推广可认为潜在的抑制剂应该拥有可电离成负电荷的功能团. 在药物设计中考虑到以上结论, 将有利于发现和改造靶向KARI的抑制剂.     

KARI酶及其抑制剂

酮醇酸还原异构酶(keto-acid reductoisomerase, KARI或称作乙酰羟基酸异构还原酶(aceto hydroxyacid isomeroreductase, AHIR))是植物、微生物中的支链氨基酸生物合成途径中第二步的关键酶.由于哺乳动物和人体内不存在这种酶,因此靶向KARI酶的抑制剂具有安全、高效等特点,成为农用除草剂以及医药抗真菌药物的一个引人注目的研究方向.本文综述了KARI的酶学、KARI抑制剂及其抑制机理和理论研究进展,并对其发展趋势进行了展望.     

脒类KARI酶抑制剂的分子对接和3D-QSAR研究

对设计合成的20个单脒类化合物的水稻KARI酶体外抑制活性和体内除草活性进行了分子对接和三维定量构效关系研究. 前者采用AutoDock3.0方法, 研究发现化合物活性变化趋势与分子对接计算结果基本一致, 通过分析化合物9与KARI酶活性氨基酸残基结合模式发现, 残基Glu319, Asp315, Glu496, Gly253, Met254, Cys517等对氢键和静电相互作用以及疏水作用都有重要贡献; 后者研究采用比较分子力场分析(CoMFA)方法, 结果表明立体场和静电场对活性的贡献分别为67.8%和32.2%, 交叉验证系数r_cv²＝0.774, 非交叉验证r²＝0.999, F＝1593.134, 标准偏差s＝0.036, 所建立的3D-QSAR模型对化合物除草活性具有较好的预测能力. 两种方法研究结果为进一步设计合成更高活性的KARI酶抑制剂提供了指导.     

KARI酶及其抑制剂

酮醇酸还原异构酶(Keto-Acid Reducto－Isomerase, KARI或称作乙酰羟基酸异构还原酶, Aceto-Hydroxyacid Isomero-Reductase, AHIR)是植物、微生物中的支链氨基酸生物合成途径中第二步的关键性酶。由于哺乳动物和人体内并不存在这种酶,因此靶向KARI酶的抑制剂具有安全、高效等特点,成为农用除草剂以及医药抗真菌药物的一个引人注目的研究方向。本文综述了KARI的酶学,KARI抑制剂及其抑制机理和理论研究进展,并对其发展趋势进行了展望。     

Synthesis and Crystal Structure of 1-[4-(Pyrimidin-2-yl)piperazin-1-ylmethyl]-1H-benzotriazole

1 INTRODUCTION Based on the reported 1.65 ? high resolution crystal structure of spinach KARI (ketol-acid reduc- toisomerase) complex[1], we obtained 279 molecules with low binding energy toward KARI from MDL/ ACD 3D database searching, using program DOCK 4.0[2]. These potential structures provide further information for the design of new KARI inhibitors, one of novel derivatives of which as the title com- pound has been synthesized. Its crystal structure will provide us more inf…     

Syntheses and Biological Activities of Ethyl N-Hydroxy-N-（substituted） phenyloxamates as KARI Inhibitors

Nine ethyl N-hydroxy-N-(substituted)phenyloxamates(2a—2i), based on the structure of the KARI inhibitor IpOHA, were synthesized. Their structures were established on the bases of 1H NMR, IR, ESI-MS and elemental analyses. Among the nine compounds, four show in vitro inhibitory activity on rice KARI, with 2c and 2g[Ki values of (35.2±4.9) and (49.4±6.3) μmol/L] having similar activity to the precursor of IpOHA(A, Ki=34.1±6.7 μmol/L). The results will be helpful to further molecular design of more potent KARI inhibitors.     

新型N-（4，6-双取代嘧啶-2-基）-N’-（三氟甲基苯基）胍的合成，结构及生物活性研究

设计,合成了10种新型的胍衍生物,结构经FTIR, MS, 1H NMR 和元素分析确证,并且采用X-射线衍射分析方法确证了具有较好生物活性的化合物11a的结构。并且对这些化合物进行了除草活性测试,结果表明化合物11a,11b,11c在100µg·mL-1 对油菜具有较好的抑制作用,初步的KARI活性结果表明这些化合物对KARI的活性很弱。     

Design,Synthesis and Biological Activity of Ethyl 2-（N-Substituted-arylsulfonamido）-2-oxoacetate

Thirteen new ethyl 2-（N-substituted-arylsulfonamido）-2-oxoacetates（3a-3m）, based on the structure of Ketol-acid reductoisomerase（KARI） inhibitor IpOHA, were designed and synthesized. Their structures were established on the basis of ^1H NMR, IR, MS, and elemental analyses. The bioassay result reveals that the structural changes from hydroxyl group on the N atom of IpOHA to arylsulfonyl groups does not enhance the inhibitory activity of the compounds to KARI in vitro. Compounds 3c, 3h, 3k, and 3m are more effective than IpOHA against the monocotyledonous bamygrass at 100 ug/mL in herbicidal tests.     

The design, synthesis of amide KARI inhibitors and their biological activities

Ketol-acid reductoisomerase(KARI) is a promising target for the design of herbicides yet there are only few reports on the molecular design of KARI inhibitors. In this paper, based on the reported 0.165 nm high resolution crystal structure of the spinach KARI complex, 279 molecules with low binding energy toward KARI were obtained from an MDL/ACD 3D database search using the program DOCK 4.0. According to the structural information of 279 molecules provided, some amide compounds have been designed and synthesized. The bioassay results show that most of these amides had inhibitory activity to rice KARI at a test concentration of 200 μg/mL. Among which eight amides, compounds 1 and 6 show 57.4% and 48.1% inhibitory activity to KARI. The herbicidal activities of these amides were further investigated on di-cotyledonous rape (Brassica campestris) and mono-cotyledonous barnyardgrass (Echinochloa crusgalli). Compounds 1 and 6 were more favorable than others and showed 52.0% and 72.6% inhibitory activity on rape root at 100 μg/mL concentration, respectively. These amides could be further optimized for finding more potent candidates. __________ Translated from Chemical Journal of Chinese Universitiers, 2008, 29(3) (in Chinese)     

Discovery of a Pyrimidinedione Derivative with Potent Inhibitory Activity against Mycobacterium tuberculosis Ketol–Acid Reductoisomerase

New drugs aimed at novel targets are urgently needed to combat the increasing rate of drug-resistant tuberculosis (TB). Herein, the National Cancer Institute Developmental Therapeutic Program (NCI-DTP) chemical library was screened against a promising new target, ketol–acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid (BCAA) biosynthesis pathway. From this library, 6-hydroxy-2-methylthiazolo[4,5-d]pyrimidine-5,7(4H,6H)-dione (NSC116565) was identified as a potent time-dependent inhibitor of Mycobacterium tuberculosis (Mt) KARI with a K_i of 95.4 nm . Isothermal titration calorimetry studies showed that this inhibitor bound to MtKARI in the presence and absence of the cofactor, nicotinamide adenine dinucleotide phosphate (NADPH), which was confirmed by crystal structures of the compound in complex with closely related Staphylococcus aureus KARI. It is also shown that NSC116565 inhibits the growth of H37Ra and H37Rv strains of Mt with MIC₅₀ values of 2.93 and 6.06 μm , respectively. These results further validate KARI as a TB drug target and show that NSC116565 is a promising lead for anti-TB drug development.     

Discovery,Synthesis and Evaluation of a Ketol-Acid Reductoisomerase Inhibitor

Ketol-acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid biosynthesis pathway, is a potential drug target for bacterial infections including Mycobacterium tuberculosis. Here, we have screened the Medicines for Malaria Venture Pathogen Box against purified M. tuberculosis (Mt) KARI and identified two compounds that have K_i values below 200 nm . In Mt cell susceptibility assays one of these compounds exhibited an IC₅₀ value of 0.8 μm . Co-crystallization of this compound, 3-((methylsulfonyl)methyl)-2H-benzo[b][1,4]oxazin-2-one (MMV553002), in complex with Staphylococcus aureus KARI, which has 56 % identity with Mt KARI, NADPH and Mg²⁺ yielded a structure to 1.72 Å resolution. However, only a hydrolyzed product of the inhibitor (i.e. 3-(methylsulfonyl)-2-oxopropanic acid, missing the 2-aminophenol attachment) is observed in the active site. Surprisingly, Mt cell susceptibility assays showed that the 2-aminophenol product is largely responsible for the anti-TB activity of the parent compound. Thus, 3-(methylsulfonyl)-2-oxopropanic acid was identified as a potent KARI inhibitor that could be further explored as a potential biocidal agent and we have shown 2-aminophenol, as an anti-TB drug lead, especially given it has low toxicity against human cells. The study highlights that careful analysis of broad screening assays is required to correctly interpret cell-based activity data.     

N-苄氧/烷氧苯基-4,6-二取代嘧啶胺类化合物的合成、晶体结构及除草活性

以5种苄氧基/烷氧基苯胺为基础, 设计合成了系列新颖的N-苄氧/烷氧苯基-4,6-二取代嘧啶胺类化合物, 其结构经1H NMR、MS及元素分析确证, 其中化合物5r的单晶结构经X射线单晶衍射分析确证. 油菜平皿法和稗草小杯法测试除草活性结果表明, 4种苄氧基/烷氧基苯胺3a, 3b, 3d, 3e具有较好的除草活性, 在100 μg/mL浓度下对单子叶稗草生长抑制率可达到77.3%—88.5%. KARI活性测试结果表明, 化合物5a—5s有较弱的KARI抑制活性.