Screening for cell migration inhibitors via automated microscopy reveals a Rho-kinase inhibitor

Small-molecule kinase inhibitors are predominantly discovered in pure protein assays. We have discovered an inhibitor of Rho-kinase (ROCK) through an image-based, high-throughput screen of cell monolayer wound healing. Using automated microscopy, we screened a library of approximately 16,000 compounds finding many that affected cell migration or cell morphology as well as compounds that blocked mitotic progression. We tested approximately 200 compounds in a series of subassays and chose one, 3-(4-pyridyl)indole (Rockout), for more detailed characterization. Rockout inhibits blebbing and causes dissolution of actin stress fibers, phenocopying Rho-kinase inhibitors. Testing Rho-kinase activity in vitro, Rockout inhibits with an IC50 of 25 microM ( approximately 5-fold less potent than Y-27632) but has a similar specificity profile. We also profile the wound healing assay with a library of compounds with known bioactivities, revealing multiple pathways involved in the biology.     

Generalized proteochemometric model of multiple cytochrome p450 enzymes and their inhibitors

Cytochrome P450 enzymes are a superfamily of heme-containing enzymes responsible for the oxidation of structurally diverse chemical compounds. Inhibition of CYP enzymes is probably the most common mechanism underlying acute drug toxicity, loss of therapeutic drug efficacy, and drug-drug interactions. The presence of polymorphic genetic variants of CYPs among the population makes it difficult to foresee undesired effects of drugs and is a common cause of drug candidate failure. Computational models that can predict early drug failures due to the inhibition of CYP isoforms can substantially reduce the cost of drug development. Although several computational models for CYP inhibition have been developed recently, all were constructed for one CYP isoform at a time, thus limiting their use for comprehensive analysis and generalizations to other CYP isoforms and polymorphisms. Here we report a novel approach based on the principles of proteochemometrics for the generalized concomitant modeling of multiple CYP isoforms and their inhibitors. We created a predictive and statistically valid proteochemometric model for CYP enzymes by combining data from a large number of publicly available reports that describe the interactions of 14 CYP enzyme subtypes and 375 structurally diverse inhibitors. Our results demonstrate that our model is capable of predicting the potential of new drug candidates to inhibit multiple CYP enzymes. Analysis of the CYP model also revealed molecular properties of CYP enzymes and xenobiotics that are important for CYP inhibition. This approach may aid in the selection of novel drug candidates that are unlikely to inhibit multiple CYP subtypes.     

具有生理活性的甾体酰胺类化合物

在甾体的甾核或支链上引入不同的官能团后可得到不同生理活性的化合物,它们有可能会成为人类治疗不同疾病的药物,因此甾体药物除了作为传统激素类药物使用外,在抗肿瘤药物、抗炎药物中的应用也成为甾体的重要研究内容之一。含有酰胺官能团的甾体化合物具有很好的生物活性。本文按照酰胺基团在甾体酰胺化合物中的位置进行分类,同时结合本课题组在甾体酰胺化合物的合成和生理活性研究方面所取得的一些成果,概述了近几年来新合成及发现的甾体酰胺类化合物及其衍生物的生理活性及研究进展,包括作为抗肿瘤药物的甾体酰胺化合物的设计、筛选、对5α-还原酶的抑制作用、抑制肿瘤细胞生长增殖活性及抗菌作用,并对此方面的发展趋势、应用前景作了展望。     

A potent and highly selective sulfotransferase inhibitor

In the present work, we have used a newly developed, fluorescence-based assay to screen a library of >30 000 compounds as potential beta-arylsulfotransferase-IV inhibitors. A total of 11 inhibitors were discovered. Most of the compounds discovered showed low micromolar inhibition, but one of the compounds showed potent inhibition (Ki = 96 nM). The most potent of these inhibitors was tested against a variety of other purine binding enzymes and showed remarkable specificity.     

Eptastigmine,nicotinamide and nicotinic acid determination using an inhibition enzyme sensor; application to pharmaceutical analysis

An enzyme inhibition biosensor, developed in our laboratory and previously used for the analysis of compounds with anticholinesterase activity (e.g. physostigmine, neostigmine, pyridostigmine nicotine and organophosphorus compounds) has now been tested for the analysis of another recently synthesized cholinesterase inhibitor, i.e. eptastigmine. In addition nicotinic acid and nicotinamide, although displaying weaker inhibition properties, were also tested in pharmaceutical products using the same inhibition enzyme sensor. The biosensor consisted of a hydrogen peroxide amperometric electrode coupled to a functionalised nylon membrane chemically bonding both the enzymes butyrylcholinesterase and choline oxidase; a butyrylcholine standard solution in glycine buffer acted as substrate. The response of the system to all the inhibitors considered was characterised completely and the analysis of several pharmaceutical formulations containing nicotinamide or nicotinic acid was also performed.     

Biochemistry of natural proteinase inhibitors

The natural inhibitors of proteolytic enzymes are proteins. These inhibitors associate reversibly with the enzymes to form stoichiometric protein-protein complexes, in which substrate-analogous association at the active center of the enzyme results in competitive inhibition of all catalytic functions. The very widespread occurrence of inhibitors in the animal and plant kingdoms underlines their biological importance in the intermediate metabolism, which can be understood as an extension of the possibilities for temporary and local limitations of enzyme activities. Existing knowledge includes a series of covalent structures, detailed kinetic data on the reversible protein-protein interaction, the processes involved in inactivation, and chemical methods for the modification of these proteins. Early X-ray structural data for an inhibitor and its enzyme complex provide an insight into the molecular structure of the latter and the interactions involved in the association to form the complex.     

基于药效团的三维数据库搜索

用表皮生长因子受体酪氨酸激酶抑制剂的药效团作为提问结构在三维数据库中进行了搜索.从得到的命中结构中挑选了12个化合物用柔性受体模型方法对其活性进行了预测, 发现有2个化合物具有一定的预测活性.这2个化合物可能具有酪氨酸激酶抑制剂的活性, 可能作为先导化合物进行结构优化.     

In silico fragment-based drug design using a PASS approach

Fragment-based drug design integrates different methods to create novel ligands using fragment libraries focused on particular biological activities. Experimental approaches to the preparation of fragment libraries have some drawbacks caused by the need for target crystallization (X-ray and nuclear magnetic resonance) and careful immobilization (surface plasmon resonance). Molecular modelling (docking) requires accurate data on protein-ligand interactions, which are difficult to obtain for some proteins. The main drawbacks of QSAR application are associated with the need to collect large homogeneous datasets of chemical structures with experimentally determined self-consistent quantitative values (potency). We propose a ligand-based approach to the selection of fragments with positive contribution to biological activity, developed on the basis of the PASS algorithm. The robustness of the PASS algorithm for heterogeneous datasets has been shown earlier. PASS estimates qualitative (yes/no) prediction of biological activity spectra for over 4000 biological activities and, therefore, provides the basis for the preparation of a fragment library corresponding to multiple criteria. The algorithm for fragment selection has been validated using the fractions of intermolecular interactions calculated for known inhibitors of nine enzymes extracted from the Protein Data Bank database. The statistical significance of differences between fractions of intermolecular interactions corresponds, for several enzymes, to the estimated positive and negative contribution of fragments in enzyme inhibition.     

Parallel screening and activity profiling with HIV protease inhibitor pharmacophore models

Parallel Screening has been introduced as an in silico method to predict the potential biological activities of compounds by screening them with a multitude of pharmacophore models. This study presents an early application example employing a Pipeline Pilot-based screening platform for automatic large-scale virtual activity profiling. An extensive set of HIV protease inhibitor pharmacophore models was used to screen a selection of active and inactive compounds. Furthermore, we aimed to address the usually critically eyed point, whether it is possible in a parallel screening system to differentiate between similar molecules/molecules acting on closely related proteins, and therefore we incorporated a collection of other protease inhibitors including aspartic protease inhibitors. The results of the screening experiments show a clear trend toward most extensive retrieval of known active ligands, followed by the general protease inhibitors and lowest recovery of inactive compounds.     

Evaluation of 3- and 4-Phenoxybenzamides as Selective Inhibitors of the Mono-ADP-Ribosyltransferase PARP10

Intracellular ADP-ribosyltransferases catalyze mono- and poly-ADP-ribosylation and affect a broad range of biological processes. The mono-ADP-ribosyltransferase PARP10 is involved in signaling and DNA repair. Previous studies identified OUL35 as a selective, cell permeable inhibitor of PARP10. We have further explored the chemical space of OUL35 by synthesizing and investigating structurally related analogs. Key synthetic steps were metal-catalyzed cross-couplings and functional group modifications. We identified 4-(4-cyanophenoxy)benzamide and 3-(4-carbamoylphenoxy)benzamide as PARP10 inhibitors with distinct selectivities. Both compounds were cell permeable and interfered with PARP10 toxicity. Moreover, both revealed some inhibition of PARP2 but not PARP1, unlike clinically used PARP inhibitors, which typically inhibit both enzymes. Using crystallography and molecular modeling the binding of the compounds to different ADP-ribosyltransferases was explored regarding selectivity. Together, these studies define additional compounds that interfere with PARP10 function and thus expand our repertoire of inhibitors to further optimize selectivity and potency.     

Design,Synthesis and Structure-activity of N-Glycosyl-1-pyridyl-1H-pyrazole-5-carboxamide as Inhibitors of Calcium Channels

Carbohydrates, with broad-spectrum structures and biological functions, are key organic compounds in nature, along with nucleic acids and proteins. As part of our ongoing efforts to develop a new class of pesticides with novel mechanism of action, a series of novel N-glycosyl-1-pyridyl-1H-pyrazole-5-carboxamide was designed and synthesized via the reactions of glycosyl methanamides and pyridyl-pyrazole acid. The compounds were characterized by ¹H NMR and ¹³C NMR. The bioassay results indicate that some of these compounds exhibit moderate insecticidal activities and assessed as potential inhibitors of calcium channels. The modulation of voltage-gated calcium channels by compounds 4a and 5a in the central neurons isolated from the third instar larvae of Spodoptera exigua was studied by whole-cell patch-clamp technique. In addition, compound 5a inhibits the recorded calcium currents reversible on washout. Experimental results also indicate that compound 5a did not release stored calcium from the Endoplasmic Reticulum. The present work demonstrates that N-glycosyl-1-pyridyl-1H-pyrazole-5-carboxamides cannot be used as possible inhibitors of calcium channels for developing novel pesticides.     

Identification of Broad-Spectrum MMP Inhibitors by Virtual Screening

Matrix metalloproteinases (MMPs) are the family of proteases that are mainly responsible for degrading extracellular matrix (ECM) components. In the skin, the overexpression of MMPs as a result of ultraviolet radiation triggers an imbalance in the ECM turnover in a process called photoaging, which ultimately results in skin wrinkling and premature skin ageing. Therefore, the inhibition of different enzymes of the MMP family at a topical level could have positive implications for photoaging. Considering that the MMP catalytic region is mostly conserved across different enzymes of the MMP family, in this study we aimed to design a virtual screening (VS) workflow to identify broad-spectrum MMP inhibitors that can be used to delay the development of photoaging. Our in silico approach was validated in vitro with 20 VS hits from the Specs library that were not only structurally different from one another but also from known MMP inhibitors. In this bioactivity assay, 18 of the 20 compounds inhibit at least one of the assayed MMPs at 100 μM (with 5 of them showing around 50% inhibition in all the tested MMPs at this concentration). Finally, this VS was used to identify natural products that have the potential to act as broad-spectrum MMP inhibitors and be used as a treatment for photoaging.     

Hydrazones of 4-(Trifluoromethyl)benzohydrazide as New Inhibitors of Acetyl- and Butyrylcholinesterase

Based on the broad spectrum of biological activity of hydrazide–hydrazones, trifluoromethyl compounds, and clinical usage of cholinesterase inhibitors, we investigated hydrazones obtained from 4-(trifluoromethyl)benzohydrazide and various benzaldehydes or aliphatic ketones as potential inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). They were evaluated using Ellman’s spectrophotometric method. The hydrazide–hydrazones produced a dual inhibition of both cholinesterase enzymes with IC₅₀ values of 46.8–137.7 µM and 19.1–881.1 µM for AChE and BuChE, respectively. The majority of the compounds were stronger inhibitors of AChE; four of them (2-bromobenzaldehyde, 3-(trifluoromethyl)benzaldehyde, cyclohexanone, and camphor-based 2o, 2p, 3c, and 3d, respectively) produced a balanced inhibition of the enzymes and only 2-chloro/trifluoromethyl benzylidene derivatives 2d and 2q were found to be more potent inhibitors of BuChE. 4-(Trifluoromethyl)-N’-[4-(trifluoromethyl)benzylidene]benzohydrazide 2l produced the strongest inhibition of AChE via mixed-type inhibition determined experimentally. Structure–activity relationships were identified. The compounds fit physicochemical space for targeting central nervous systems with no apparent cytotoxicity for eukaryotic cell line together. The study provides new insights into this CF₃-hydrazide–hydrazone scaffold.     

Synthesis of new pyrazolone-based heterocycles as inhibitors of monoamine oxidase enzymes

A series of new substituted pyrazoles embedded with a variety of function groups has been synthesized from 4-[4-(1,2-dihydro-2,3-dimethyl-1-phenyl-5-oxo-3H-pyrazol-4-yl)]-2-cyano-4-oxo-butanenitrile (4). The synthesized compounds were fully characterized and their structures were elucidated based on elemental analysis, spectral data, and alternative synthetic pathways, whenever possible. The pharmacological activities of these new compounds as inhibitors for of type A and type B monoamine oxidase (MAO) enzymes have been investigated and compared to the most common inhibitors of MAO enzymes used to treat depression and anxiety such as deprenyl (selegiline), moclobemide, and clorgyline drugs. The most potent of the synthesized compounds was 4, 11, and 53 which showed higher inhibition activity toward type A MAO enzyme and even exceeded that of deprenyl, moclobemide, and clorgyline drugs.     

Natural compounds with proteasome inhibitory activity for cancer prevention and treatment

The proteasome is a multicatalytic protease complex that degrades most endogenous proteins including misfolded or damaged proteins to ensure normal cellular function. The ubiquitin-proteasome degradation pathway plays an essential role in multiple cellular processes, including cell cycle progression, proliferation, apoptosis and angiogenesis. It has been shown that human cancer cells are more sensitive to proteasome inhibition than normal cells, indicating that a proteasome inhibitor could be used as a novel anticancer drug. Indeed, this idea has been supported by the encouraging results of the clinical trials using the proteasome inhibitor Bortezomib (Velcade, PS-341), a drug approved by the US Food and Drug Administration (FDA). Several natural compounds, including the microbial metabolite lactacystin, green tea polyphenols, and traditional medicinal triterpenes, have been shown to be potent proteasome inhibitors. These findings suggest the potential use of natural proteasome inhibitors as not only chemopreventive and chemotherapeutic agents, but also tumor sensitizers to conventional radiotherapy and chemotherapy. In this review, we will summarize the structures and biological activities of the proteasome and several natural compounds with proteasome inhibitory activity, and will discuss the potential use of these compounds for the prevention and treatment of human cancers.     

Selective inhibition of 6-phosphogluconate dehydrogenase from Trypanosoma brucei

A number of triphenylmethane derivatives have been screened against 6-phosphogluconate dehydrogenase from Trypanosoma brucei and sheep liver. Some of these compounds show good inhibition of the enzymes and also selectivity towards the parasite enzyme. Modelling was undertaken to dock the compounds into the active sites of both enzymes. Using a combination of DOCK 3.5 and FLEXIDOCK a correlation was obtained between docking score and both activity for the enzymes and selectivity. Visualisation of the docked structures of the inhibitors in the active sites of the enzymes yielded a possible explanation of the selectivity for the parasite enzyme.     

Molecular docking and pharmacophore filtering in the discovery of dual-inhibitors for human leukotriene A4 hydrolase and leukotriene C4 synthase

Combination of drugs for multiple targets has been a standard treatment in treating various diseases. A single chemical entity that acts upon multiple targets is emerging nowadays because of their predictable pharmacokinetic and pharmacodynamic properties. We have employed a computer-aided methodology combining molecular docking and pharmacophore filtering to identify chemical compounds that can simultaneously inhibit the human leukotriene hydrolase (hLTA4H) and the human leukotriene C4 synthase (hLTC4S) enzymes. These enzymes are the members of arachidonic acid pathway and act upon the same substrate, LTA4, producing different inflammatory products. A huge set of 4966 druglike compounds from the Maybridge database were docked into the active site of hLTA4H using the GOLD program. Common feature pharmacophore models were developed from the known inhibitors of both the targets using Accelrys Discovery Studio 2.5. The hits from the hLTA4H docking were filtered to match the chemical features of both the pharmacophore models. The compounds that resulted from the pharmacophore filtering were docked into the active site of hLTC4S and the hits those bind well at both the active sites and matched the pharmacophore models were identified as possible dual inhibitors for hLTA4H and hLTC4S enzymes. Reverse validation was performed to ensure the results of the study.