Non-peptidic small-molecule inhibitors of the single-chain hepatitis C virus NS3 protease/NS4A cofactor complex discovered by structure-based NMR screening

NMR-based screening of a customized fragment library identified 16 small-molecule hits that bind weakly (K(D) approximately 100 microM to 10 mM) to substrate binding sites of the NS4A-bound NS3 protease of the hepatitis C virus (HCV). Analogues for five classes of NMR hits were evaluated by a combination of NMR and biochemical data yielding SAR and, in most cases, optimized hits with improved potencies (K(D) approximately K(I) approximately 40 microM to 1 mM). NMR chemical shift perturbation data were used to establish the binding location and orientation of the active site directed scaffolds in these five analogue series. Two of these scaffolds, which bind the enzyme at the proximal S1-S3 and S2' substrate binding sites, were linked together producing competitive inhibitors of the HCV NS3 protease with potencies in the micromolar range. This example illustrates that the low molecular weight scaffolds discovered from structure-based NMR screening can be optimized with focused structure-guided chemistry to produce potent nonpeptidic small-molecule inhibitors of the HCV NS3 protease.     

Rapid NMR‐based functional screening and IC50 measurements performed at unprecedentedly low enzyme concentration

NMR‐based functional screening performed with 3‐FABS represents a reliable method for identifying inhibitors and measuring with high accuracy their inhibitory activity. Although the method scores high in quality, in its current status it cannot compete with the very high sensitivity of the fluorescence‐based techniques. In order to perform ultra‐high‐throughput screening and to use the small volumes that are possible with fluorescence‐based techniques, it would be necessary to further improve the sensitivity of 3‐FABS. Two variants of the original experiment with improved sensitivity, namely the 3(x2)‐FABS and the 3(x4)‐FABS, are presented. The substrate for this purpose is labelled with two and four magnetically equivalent CF₃ moieties. Chemical synthesis of novel fragments containing poly CF₃ moieties and application of the 3‐FABS variants to the rapid screening of the Ser/Thr kinase PKA and the protease trypsin are presented. The high sensitivity of the methods allows performing rapid NMR‐based functional screening at an unprecedented low enzyme concentration. Drug Dev Res 64:105–113, 2005. © 2005 Wiley‐Liss, Inc.     

High-throughput real-time assay based on molecular beacons for HIV-1 integrase 3＇-processing reaction

Aim： To develop a high-throughput real-time assay based on molecular beacons to monitor the integrase 3＇-processing reaction in vitro and apply it to inhibitor screening. Methods： The recombinant human irnmunodeficiency virus （HIV）-I integrase （IN） is incubated with a 38 mer oligonucleotide substrate, a sequence identical to the U5 end of HIV- 1 long terminal repeats （LTR）. Based on the fluorescence properties of molecular beacons, the substrate is designed to form a stem-loop structure labeled with a fluorophore at the 5＇ end and a quencher at the 3＇ end. IN cleaves the terminal 3＇-dinucleotide containing the quencher, resulting in an increase in fluorescence which can be monitored on a spectrofluorometer. To optimize this assay, tests were performed to investigate the effects of substrates, enzyme and the metal ion concentrations on the IN activity and optimal parameters were obtained. Moreover, 2 IN inhibitors were employed to test the performance of this assay in antiviral compound screening. Results： The fluorescent intensity of the reaction mixture varies linearly with time and is proportional to the velocity of the 3＇-processing reaction. Tests were performed and the results showed that the optimal rate was obtained for a reaction mixture containing 50 mg/L recombinant HIV- 1 IN, 400 nmol/L substrate, and 10 mmol/L Mn^2＋. The IN 3＇-processing reaction under the optimal conditions showed a more than 18-fold increase in the fluorescence intensity compared to the enzyme-free control. The IC50 values of the IN inhibitors obtained in our assay were similar to the values obtained from a radiolabeled substrate assay. Conclusion： Our results demonstrated that this is a fast, reliable, and sensitive method to monitor HIV IN 3＇-processing reaction and that it can be used for inhibitor screening.     

Design of small molecule libraries for NMR screening and other applications in drug discovery

There are conceptual differences between high-throughput screening (HTS) and fragment-based screening by NMR. The number of compounds in libraries for NMR screening may be significantly smaller than those used for HTS. Because one relies on a small library its design is significantly important and is the object of this article. A short introduction on fragment-based NMR screening approaches will be provided. Although there are currently very few reports describing the design of libraries of small molecules for NMR screening, aspects of the question of how to compile diverse collections of small molecular fragments useful for drug design were previously addressed for the purposes of combinatorial library design and de novo drug design. As these disciplines are highly interrelated and are applied in an interconnected manner with NMR screening within the drug discovery process, a review of combinatorial library design and especially the building block or fragment selection strategies applied for combinatorial library design and de novo design is well suited to reveal fundamental strategies and potential techniques for the design of NMR screening libraries. This section will be rounded off by a report on hands-on-experience with the design of the Novartis second-site NMR screening library and practical considerations for the design of compound mixtures. Rather than providing an exact protocol general guidelines will be indicated.     

Library design for fragment based screening

According to Hann's model of molecular complexity an increased probability of detection binding to a target protein can be expected when small, low complex molecular fragments are screened with high sensitivity instead of full-sized ligands with lower sensitivity. Analysis of the HTS summary data of Novartis and comparison with NMR screening results obtained on generic fragment libraries indicate this expectation to be true with hitrates of 0.001% - 0.151% observed in the identification of ligands with an IC(50) threshold in the micromolar range in an HTS setup and hitrates above or equal to 3% observed in NMR screening of fragments with an affinity threshold in the millimolar range. It is however necessary to keep in mind that the sets of target studied were not identical for both method and the experience in NMR screening is too limited for a final conclusion. The term hitrate as used here reflects only the success rate in the observation of ligand binding event. It must not be confused with the overall success rate of fragment and high throughput screening in the lead finding process, which can be entirely different, since the steps required to follow-up a ligand binding event to a lead are different for both methods. A survey of fragment-based lead discovery case studies given in the literature shows that in approximately half of the cases the initial hit fragment was discovered by screening a generic library, whereas in the other cases some knowledge about an initial ligands or the protein binding site has been used, whereas systematic virtual screening of fragment databases has been only rarely reported. As comparatively high hitrates were obtained, further consideration to optimize the generic fragment screening library were directed to the chemical tractability of the fragment. As several functional groups preferred by chemists for modification and linking of the fragments are also preferentially involved in interactions between the fragments and the target protein, a set of screening fragments was derived from chemical building blocks by masking its linker group by a chemical transformation which can be later on used in the chemical follow-up of the fragment hit. For example primary amines can be masked as acetamides. If the screening fragment is active the related building block can then be used for synthesis of a follow-up library.     

微生物来源的乙酰胆碱酯酶抑制剂N98-1021A的研究

本研究分别以丁酰硫代胆碱和二硫二硝基苯甲酸为底物和显色剂 ,建立了一种准确、快速的高通量筛选微生物代谢产物来源的抑制剂的体外筛选模型。利用此方法从 2 14 1株放线菌中筛选到一株阳性菌株N98 10 2 1,该菌株的发酵液经有机溶剂提取、ODS柱层析及HPLC制备分离 ,得到一个活性化合物N98 10 2 1A ,该化合物对乙酰胆碱酯酶的IC50 为 2 0 μmol/L ,经酶抑制动力学分析 ,该化合物为乙酰胆碱酯酶的非竞争性可逆抑制剂。通过对该化合物的紫外、红外、质谱、核磁等理化分析 ,得知该化合物与terferol结构相同。但该化合物对乙酰胆碱脂酶的抑制活性至今未见报道。     

Synthesis, toxicological and pharmacological assessment of morpholinooximes.

The synthesis, pharmacology and toxicology of four morpholine derivatives from 1-(2-arylmorpholino)-3-phenyl-3-propanonoxime and the synthesis of two anilides are described. The structures of the synthesized derivatives were proved by IR, 1H NMR and occasionally with 13C NMR. The acute toxicity of the compounds in mice was determined. A comparative pharmacological study of the in vivo effect on the central nervous system was realised by the following screening tests: pentobarbital induced sleeping time, locomotor activity and behaviour despair test for antidepressive activity. The most active compound was 1-(2-phenylmorpholino)-3-phenyl-3-propanonoxime (2b) which showed low toxicity and antidepressive activity at a dose of 1/10 LD50.     

High-throughput screening of human soluble epoxide hydrolase inhibitors

To screen potential human soluble epoxide hydrolase (hsEH) inhibitors, a high-throughput screening model in 384-well microplate with total volume of 50 microL was established. Recombinant hsEH was cloned and expressed in E. coli. and its specific substrate PHOME was synthesized. The HTS model was based on fluorescence analysis with enhanced sensitivity and specificity (Z' = 0.65). A total of 47 360 samples (including 25 040 compounds and 22 320 natural products) were screened, of which 950 samples with inhibition greater than 80% were selected for further rescreening. Finally, two compounds with high inhibitory activity were identified, whose IC50 value were 8.56 and 4.31 micromol x L(-1), separately. The results indicated that the method was stable, sensitive, reproducible and also suitable for high-throughput screening.     

Automated analysis of large sets of heteronuclear correlation spectra in NMR-based drug discovery

Drug discovery procedures based on NMR typically require the analysis of thousands of NMR spectra. For example, in "SAR by NMR", two-dimensional NMR spectra are recorded for a target protein mixed with ligand candidates from a comprehensive library of small molecules and are compared to the corresponding spectrum for the protein alone. We present an automated procedure for the comparative analysis of large sets of heteronuclear single quantum coherence spectra, which is based on three-way decomposition and implemented as the software package MUNIN. In a single step, spectra with differences in the peak positions (indicating ligand binding) and the affected peaks are identified. By omission of peak picking, ad hoc scoring of the quality of doubtful peaks is avoided. The procedure has been tested on the bacterial ribonuclease barnase, with a protein concentration of only 50 microM, using several small molecules including the substrate analogue 3'-GMP. Sets of 51 spectra were processed simultaneously, and it is concluded that spectra with binding ligands can be unambiguously identified from much larger sets of spectra.     

人源蛋白酪氨酸磷酸酶(PTP1B)抑制剂的高通量筛选

本研究拟建立体外人源蛋白酪氨酸磷酸酶(PTP1B)抑制剂高通量筛选模型,用于PTP1B抑制剂的发现。利用大肠杆菌重组表达PTP1B,以对硝基苯磷酸二钠(PNPP)为特异性的底物,建立了基于酶反应速率的384孔微板为载体的PTP1B抑制剂高通量筛选模型(Z'=0.78)。选择24 240个样品进行筛选,对抑制率大于70%的80个样品作为活性样品进行复筛,最终确定6个具有较强的抑制活性的化合物J5753、J10550、J10551、J10583、J10585和J11101,其IC50值分别为21.58、18.39、15.37、11.92、37.27和36.61μg·mL-1。结果表明,所建立的PTP1B抑制剂高通量筛选模型具有快速、灵敏、稳定、重复性好的特点。     

微生物转化法合成天麻素

目的以对羟基苯甲醛为底物，通过微生物的转化作用生物合成天麻素。方法采用静息细胞转化法并结合TLC和HPLC分析，从几十株霉菌和细菌中筛选出了一株能够转化合成天麻素的华根霉(Rhizopus chinensis Staito AS3.1165)，在优化转化条件的基础上，进行批量扩大试验，经色谱分离得到转化产物，通过理化性质和波谱分析鉴定其结构。结果经NMR及EI-MS等的测定，证明所得转化产物为天麻素。结论利用微生物对天麻素前体——对羟基苯甲醛进行选择性的还原和糖基化，从而高效率的获得天麻素，此方法的建立为天麻素的合成开辟了一条新的途径，具有较大的经济和社会价值。     

Burkholone, a new cytotoxic antibiotic against IGF-I dependent cells from Burkholderia sp

In the course of our screening program for new inhibitors of IGF-I signaling, we isolated a new cytotoxic antibiotic, burkholone, from the culture broth of Burkholderia sp. QN15488. The structure of burkholone was determined to be (E)-3-methyl-2-(2-octenyl)-4-quinolone by a series of NMR analyses. Burkholone induced cell death 32D/GR15 cells with an IC50 value of 160 nM in IGF-I containing medium, while no cell death was observed in IL-3 containing medium even at the concentration of 37 microM.     

Antiplasmodial phenolic compounds from Piptadenia pervillei

Piptadenia pervillei Vatke (Fabaceae) was selected from a screening programme devoted to the search of naturally-occuring antimalarial compounds from plants of Madagascar. Bioassay-guided fractionation of the ethyl acetate extract of the leaves led to the isolation of four phenolic compounds, (+)-catechin ( 1), (+)-catechin 5-gallate ( 2), (+)-catechin 3-gallate ( 3) and ethyl gallate ( 4). Structures were determined by NMR and mass spectroscopy. Compounds 2 and 3 displayed the highest in vitro activity against the chloroquine-resistant strain FcB1 of Plasmodium falciparum with IC (50) values of 1.2 microM and 1.0 microM, respectively, and no significant cytotoxicity against the human embryonic lung cells MRC-5 was measured (IC (50) values > 75 microM). Five analogues ( 5 - 9) of (+)-catechin 5-gallate ( 2) were synthesized and evaluated for their antiplasmodial activity.     

3-硝基-5-(6-溴己酰胺)苯甲酸的合成及其作为头孢菌素酰化酶产生菌筛选指示剂的研究

为筛选头孢菌素Ｃ酰化酶产生菌,由环己酮和３－硝基－５－乙酰胺基苯甲酸出发,合成了一种新的生色物质３－硝基－５－（６－溴己酰胺）苯甲酸（３－Ｎｉｔｒｏ－５－（６－ｂｒｏｍｏｈｅｘａｎｏｙｌａｍｉｎｏ）ｂｅｎｚｏｉｃａｃｉｄ,ＮＢＨＡＢ）。通过红外光谱法、核磁共振法、质谱法鉴定了其结构。ＧＬ－７ＡＣＡ酰化酶和青霉素Ｇ酰化酶（ｐｅｎｉｃｉｌｉｎＧＡｃｙｌａｓｅ,ＰＧＡ）及其产生菌对该化合物的作用表明,该物质能够检测头孢菌素酰化酶活力,用来筛选头孢菌素Ｃ酰化酶产生菌,其灵敏性有待进一步提高。     

NMR-Based screening with competition water-ligand observed via gradient spectroscopy experiments: detection of high-affinity ligands

Water-ligand observed via gradient spectroscopy (WaterLOGSY) represents a powerful method for primary NMR screening in the identification of compounds interacting with macromolecules, including proteins and DNA or RNA fragments. The method is useful for the detection of compounds binding to a receptor with binding affinity in the micromolar range. The Achille's heel of the method, as with all the techniques that detect the ligand resonances, is its inability to identify strong ligands with slow dissociation rates. We show here that the use of a reference compound with a known K(D) in the micromolar range together with properly designed competition binding experiments (c-WaterLOGSY) permits the detection of strong binders. A derived mathematical expression is used for the selection of the appropriate setup NMR experimental conditions and for an approximate determination of the binding constant. The experiment requires low ligand concentration, therefore allowing its application in the identification of potential strong inhibitors that are only marginally soluble. The technique is particularly suitable for rapid screening of chemical mixtures and plant or fungi extracts.     

Solubility Prediction by Recursive Partitioning

Purpose. To build and test a computational model for predicting small molecule solubility, to improve the cost-effectiveness of the selection of vendor compounds suitable for nuclear magnetic resonance (NMR) screening. Methods. A simple recursive partitioning decision tree-based classification model was generated utilizing off-the-shelf commercial software from Accelrys Inc., with a training set of 1992 compounds based on a series of calculated topologic and physical properties. The predictive ability of the decision tree was then assessed by employing it to classify a test set of 2851 vendor compounds, and the classification was subsequently used to guide the purchase of 686 compounds for the purpose of NMR screening. Results. When the decision tree was used to guide purchasing, the percentage of acceptable compounds suitable for NMR screening doubled compared with the use of a simple cLogP cutoff, improving the successful selection rate from 25% to 50%. Conclusions. A simple recursive partitioning decision tree may successfully be used to improve cost-effectiveness by reducing the wastage associated with the unnecessary purchase of vendor compounds unsuitable for NMR screening because of insolubility.     

Nuclear magnetic resonance in target profiling and compound file enhancement

Nuclear magnetic resonance (NMR) has matured as an important tool in drug discovery and development, with firm establishment of its roles in lead generation and optimization through application of NMR-based fragment screening and structure-based drug design. Besides these applications, NMR technology has expanded to make contributions both earlier and later in the drug discovery process. This review will focus on the impact of NMR in the early stages of drug discovery, in particular in characterizing the viability of targets for further discovery exercises and improving high-throughput screening through compound file-enhancement initiatives.     

一种磷脂酶A_2抑制剂体外筛选方法的建立

目的建立磷脂酶A2(PLA2)抑制剂体外筛选的方法。方法以大豆磷脂酰胆碱为底物,通过分光光度法测定PLA2水解底物产生游离脂肪酸的量,间接反映待测物对PLA2活性的影响,并考查酶浓度、底物浓度及反应时间与游离脂肪酸生成量的线性关系。结果在一定范围内,酶浓度、底物浓度及反应时间与游离脂肪酸生成量呈良好的线性关系,氯丙嗪对PLA2的IC50为501μmol.L-1,甘草甜素对PLA2的IC50为461μmol.L-1。结论建立的磷脂酶A2抑制剂体外筛选方法,具有灵敏度高、快捷、准确、可操作性强的特点。     

New angucycline C-glycosides from Streptomyces sp. RI33

In the course of our screening program for anticancer agents from natural sources, five new angucyclines, JBIR-90 (1), -116 (2), -91 (3), -92 (4) and -93 (5), were isolated from the fermentation broth of Streptomyces sp. RI33. The structures of 1-5 were elucidated on the basis of 1D and 2D NMR spectroscopy and MS analyses. Compounds 2-4 showed cytotoxic activities against malignant pleural mesothelioma cells at IC(50) values of 20-50 μM.     

Discovery of small-molecule inhibitors of Bcl-2 through structure-based computer screening.

Bcl-2 belongs to a growing family of proteins which regulates programmed cell death (apoptosis). Overexpression of Bcl-2 has been observed in 70% of breast cancer, 30-60% of prostate cancer, 80% of B-cell lymphomas, 90% of colorectal adenocarcinomas, and many other forms of cancer. Thereby, Bcl-2 is an attractive new anti-cancer target. Herein, we describe the discovery of novel classes of small-molecule inhibitors targeted at the BH3 binding pocket in Bcl-2. The three-dimensional (3D) structure of Bcl-2 has been modeled on the basis of a high-resolution NMR solution structure of Bcl-X(L), which shares a high sequence homology with Bcl-2. A structure-based computer screening approach has been employed to search the National Cancer Institute 3D database of 206 876 organic compounds to identify potential Bcl-2 small-molecule inhibitors that bind to the BH3 binding site of Bcl-2. These potential Bcl-2 small-molecule inhibitors were first tested in an in vitro binding assay for their potency in inhibition of the binding of a Bak BH3 peptide to Bcl-2. Thirty-five potential inhibitors were tested in this binding assay, and seven of them were found to have a binding affinity (IC(50) value) from 1.6 to 14.0 microM. The anti-proliferative activity of these seven active compounds has been tested using a human myeloid leukemia cell line, HL-60, which expresses the highest level of Bcl-2 protein among all the cancer cell lines examined. Compound 6 was the most potent compound and had an IC(50) value of 4 microM in inhibition of cell growth using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Five other compounds had moderate activity in inhibition of cell growth. Compound 6 was further evaluated for its ability to induce apoptosis in cancer cells. It was found that 6 induces apoptosis in cancer cells with high Bcl-2 expression and its potency correlates with the Bcl-2 expression level in cancer cells. Furthermore, using NMR methods, we conclusively demonstrated that 6 binds to the BH3 binding site in Bcl-X(L). Our results showed that small-molecule inhibitors of Bcl-2 such as 6 modulate the biological function of Bcl-2, and induce apoptosis in cancer cells with high Bcl-2 expression, while they have little effect on cancer cells with low or undetectable levels of Bcl-2 expression. Therefore, compound 6 can be used as a valuable pharmacological tool to elucidate the function of Bcl-2 and also serves as a novel lead compound for further design and optimization. Our results suggest that the structure-based computer screening strategy employed in the study is effective for identifying novel, structurally diverse, nonpeptide small-molecule inhibitors that target the BH3 binding site of Bcl-2.