人类蛋白激酶组的多靶点分子对接系统

蛋白激酶在信号转导、基因转录和蛋白翻译等生物过程起关键性作用,因而与大量人类疾病密切相关。所以,蛋白激酶的抑制剂筛选是抗肿瘤药物开发的热点,正在向基于全激酶组的高通量多靶点筛选模式发展。为了降低大规模实验筛选的成本,提高成功率,本文构建人类蛋白激酶组的多靶点分子对接系统,对抑制剂-激酶组的相互作用进行预测。我们首先利用同源模建方法,对人类激酶组约500个激酶变异体的催化域进行结构建模;接着以催化域结构模型为受体,用已知激酶抑制剂进行分子对接,对抑制剂与各激酶变异体的结合亲和力进行了定量计算。结果显示,本文所建立的多靶点分子对接系统可以准确预测抑制剂与激酶变异体的相互作用,结合自由能的计算值与实验值有很强的相关性。所以,该分子对接系统可用于多靶点激酶抑制剂的计算筛选,为激酶抑制剂开发与抗肿瘤药物设计提供理论依据。     

Novel synthetic 9-benzyloxyacridine analogue as both tyrosine kinase and topoisomerase I inhibitor

Multi-target agents against tyrosine kinases and topoisomerases are potentially useful for the effective treatment of cancers.Discovery of new multi-target scaffolds are important for developing such agents. A series of five novel acridine analogues,LXL 1-5,were synthesized and their antiproliferative activity against HepC-2 cell lines were evaluated,among which the 9-benzyloxyacridine analogue,LXL-5, showed inhibitory activity against tyrosine kinases,VEGFR-2 and Src.The results of UV-visible absorption spectra and fluorescence emission spectra,as well as DNA topoisomerase I inhibition assay, indicated topoisomerase I inhibitory activity.Our study suggested that acridine scaffold,previously shown to have no multi-target kinase and topoisomerase inhibitory activity,might be potentially developed as a multi-target inhibitor of tyrosine kinases and topoisomerase I.     

Collaborative filtering on a family of biological targets

Building a QSAR model of a new biological target for which few screening data are available is a statistical challenge. However, the new target may be part of a bigger family, for which we have more screening data. Collaborative filtering or, more generally, multi-task learning, is a machine learning approach that improves the generalization performance of an algorithm by using information from related tasks as an inductive bias. We use collaborative filtering techniques for building predictive models that link multiple targets to multiple examples. The more commonalities between the targets, the better the multi-target model that can be built. We show an example of a multi-target neural network that can use family information to produce a predictive model of an undersampled target. We evaluate JRank, a kernel-based method designed for collaborative filtering. We show their performance on compound prioritization for an HTS campaign and the underlying shared representation between targets. JRank outperformed the neural network both in the single- and multi-target models.     

正交试验法优选穿心莲内酯硫酸酯化反应工艺

硫酸酯化反应以分子结构中的羟基为反应位点,向有机分子中引入硫酸酯基,是一种有效改善天然产物水溶性的结构修饰途径[1]。有些药物因水溶性差,致使其在临床应用中存在一些问题,如生物利用度不高,服用量大,制成的片剂或胶囊体内吸收缓慢等。这类化合物经硫酸酯化后不但可以增加     

Systematic mining of analog series with related core structures in multi-target activity space

We have aimed to systematically extract analog series with related core structures from multi-target activity space to explore target promiscuity of closely related analogous. Therefore, a previously introduced SAR matrix structure was adapted and further extended for large-scale data mining. These matrices organize analog series with related yet distinct core structures in a consistent manner. High-confidence compound activity data yielded more than 2,300 non-redundant matrices capturing 5,821 analog series that included 4,288 series with multi-target and 735 series with multi-family activities. Many matrices captured more than three analog series with activity against more than five targets. The matrices revealed a variety of promiscuity patterns. Compound series matrices also contain virtual compounds, which provide suggestions for compound design focusing on desired activity profiles.     

Design and Synthesis of Hsp90 Inhibitors with B-Raf and PDHK1 Multi-Target Activity

The design of multi-target ligands has become an innovative approach for the identification of effective therapeutic treatments against complex diseases, such as cancer. Recent studies have demonstrated that the combined inhibition of Hsp90 and B-Raf provides synergistic effects against several types of cancers. Moreover, it has been reported that PDHK1, which presents an ATP-binding pocket similar to that of Hsp90, plays an important role in tumor initiation, maintenance and progression, participating also to the senescence process induced by B-Raf oncogenic proteins. Based on these premises, the simultaneous inhibition of these targets may provide several benefits for the treatment of cancer. In this work, we set up a design strategy including the assembly and integration of molecular fragments known to be important for binding to the Hsp90, PDHK1 and B-Raf targets, aided by molecular docking for the selection of a set of compounds potentially able to exert Hsp90-B-Raf-PDHK1 multi-target activities. The designed compounds were synthesized and experimentally validated in vitro. According to the in vitro assays, compounds 4 a , 4 d and 4 e potently inhibited Hsp90 and moderately inhibited the PDHK1 kinase. Finally, molecular dynamics simulations were performed to provide further insights into the structural basis of their multi-target activity.     

Detection and identification of 700 drugs by multi-target screening with a 3200 Q TRAP® LC-MS/MS system and library searching

The multi-target screening method described in this work allows the simultaneous detection and identification of 700 drugs and metabolites in biological fluids using a hybrid triple-quadrupole linear ion trap mass spectrometer in a single analytical run. After standardization of the method, the retention times of 700 compounds were determined and transitions for each compound were selected by a “scheduled” survey MRM scan, followed by an information-dependent acquisition using the sensitive enhanced product ion scan of a Q TRAP^® hybrid instrument. The identification of the compounds in the samples analyzed was accomplished by searching the tandem mass spectrometry (MS/MS) spectra against the library we developed, which contains electrospray ionization–MS/MS spectra of over 1,250 compounds. The multi-target screening method together with the library was included in a software program for routine screening and quantitation to achieve automated acquisition and library searching. With the help of this software application, the time for evaluation and interpretation of the results could be drastically reduced. This new multi-target screening method has been successfully applied for the analysis of postmortem and traffic offense samples as well as proficiency testing, and complements screening with immunoassays, gas chromatography–mass spectrometry, and liquid chromatography–diode-array detection. Other possible applications are analysis in clinical toxicology (for intoxication cases), in psychiatry (antidepressants and other psychoactive drugs), and in forensic toxicology (drugs and driving, workplace drug testing, oral fluid analysis, drug-facilitated sexual assault).     

Synthesis of pterostilbene and resveratrol carbamate derivatives as potential dual cholinesterase inhibitors and neuroprotective agents

Pterostilbene and resveratrol carbamate derivatives were designed and synthesized by use of a multi-target directed drug-design strategy. Their acetylcholinesterase and butylcholinesterase inhibitory activity and neuroprotective effects against hydrogen peroxide-induced PC12 cell injury were evaluated in vitro. The results indicated that some of the compounds had dual inhibitory potency against acetylcholinesterase and butylcholinesterase, and potential neuroprotective effects, and could be considered as potential multi-target-directed agents.     

Synthesis, biology and clinical significance of pentacyclic triterpenes: a multi-target approach to prevention and treatment of metabolic and vascular diseases

This review (with 335 references cited) is devoted to pentacyclic triterpenes. The total synthesis, semi-synthesis, structural modification, and metabolic behavior of naturally occurring pentacyclic triterpenes are described. We also cover the in vivo evidence, mechanistic studies, and clinical significance of pentacyclic triterpenes as multi-target therapeutic agents for the prevention and treatment of metabolic and vascular diseases.     

Microfluidic immunomagnetic multi-target sorting--a model for controlling deflection of paramagnetic beads

We describe a microfluidic system that uses a magnetic field to sort paramagnetic beads by deflecting them in the direction normal to the flow. In the experiments we systematically study the dependence of the beads' deflection on bead size and susceptibility, magnet strength, fluid speed and viscosity, and device geometry. We also develop a design parameter that can aid in the design of microfluidic devices for immunomagnetic multi-target sorting.     

血必净抗炎作用药效物质基础和多靶点作用效应

研究了血必净抗炎作用的药效物质基础, 并在分子层面上对复方多靶点作用进行阐释. 借助于计算机辅助药物设计技术, 构建血必净化学成分数据库, 综合应用同源模建、分子对接、药效团模型、数据库搜索等方法, 探讨其与炎症靶点5-脂氧合酶(5-LOX)、环氧合酶-2(COX-2)、IKK-2受体的相互作用关系. 血必净化学成分中与靶点5-LOX、COX-2、IKK-2结合效应较好的分别有30、36、8个分子; 有16个分子与2个或3个靶点存在作用, 其中15个分子对靶点5-LOX和COX-2有抑制作用, 迷迭香酸对3个靶点均有作用. 从分子层次上阐释了复方血必净抗炎作用的药效物质基础和多靶点作用效应, 为血必净复方的临床应用提供了科学依据; 同时, 也为寻找新型抗炎药物提供一定的参考和借鉴.     

A New Series of Aryloxyacetic Acids Endowed with Multi-Target Activity towards Peroxisome Proliferator-Activated Receptors (PPARs), Fatty Acid Amide Hydrolase (FAAH), and Acetylcholinesterase (AChE)

A new series of aryloxyacetic acids was prepared and tested as peroxisome proliferator-activated receptors (PPARs) agonists and fatty acid amide hydrolase (FAAH) inhibitors. Some compounds exhibited an interesting dual activity that has been recently proposed as a new potential therapeutic strategy for the treatment of Alzheimer’s disease (AD). AD is a multifactorial pathology, hence multi-target agents are currently one of the main lines of research for the therapy and prevention of this disease. Given that cholinesterases represent one of the most common targets of recent research, we decided to also evaluate the effects of our compounds on the inhibition of these specific enzymes. Interestingly, two of these compounds, (S)-5 and 6, showed moderate activity against acetylcholinesterase (AChE) and even some activity, although at high concentration, against Aβ peptide aggregation, thus demonstrating, in agreement with the preliminary dockings carried out on the different targets, the feasibility of a simultaneous multi-target activity towards PPARs, FAAH, and AChE. As far as we know, these are the first examples of molecules endowed with this pharmacological profile that might represent a promising line of research for the identification of novel candidates for the treatment of AD.     

Novel Donepezil–Arylsulfonamide Hybrids as Multitarget-Directed Ligands for Potential Treatment of Alzheimer’s Disease

Alzheimer’s disease (AD) is one of the most devastating neurodegenerative disorders, characterized by multiple pathological features. Therefore, multi-target drug discovery has been one of the most active fields searching for new effective anti-AD therapies. Herein, a series of hybrid compounds are reported which were designed and developed by combining an aryl-sulfonamide function with a benzyl-piperidine moiety, the pharmacophore of donepezil (a current anti-AD acetylcholinesterase AChE inhibitor drug) or its benzyl-piperazine analogue. The in vitro results indicate that some of these hybrids achieve optimized activity towards two main AD targets, by displaying excellent AChE inhibitory potencies, as well as the capability to prevent amyloid-β (Aβ) aggregation. Some of these hybrids also prevented Aβ-induced cell toxicity. Significantly, drug-like properties were predicted, including for blood-brain permeability. Compound 9 emerged as a promising multi-target lead compound (AChE inhibition (IC₅₀ 1.6 μM); Aβ aggregation inhibition 60.7%). Overall, this family of hybrids is worthy of further exploration, due to the wide biological activity of sulfonamides.     

The Neuroprotective Role of Polydatin: Neuropharmacological Mechanisms,Molecular Targets,Therapeutic Potentials,and Clinical Perspective

Neurodegenerative diseases (NDDs) are one of the leading causes of death and disability in humans. From a mechanistic perspective, the complexity of pathophysiological mechanisms contributes to NDDs. Therefore, there is an urgency to provide novel multi-target agents towards the simultaneous modulation of dysregulated pathways against NDDs. Besides, their lack of effectiveness and associated side effects have contributed to the lack of conventional therapies as suitable therapeutic agents. Prevailing reports have introduced plant secondary metabolites as promising multi-target agents in combating NDDs. Polydatin is a natural phenolic compound, employing potential mechanisms in fighting NDDs. It is considered an auspicious phytochemical in modulating neuroinflammatory/apoptotic/autophagy/oxidative stress signaling mediators such as nuclear factor-κB (NF-κB), NF-E2–related factor 2 (Nrf2)/antioxidant response elements (ARE), matrix metalloproteinase (MMPs), interleukins (ILs), phosphoinositide 3-kinases (PI3K)/protein kinase B (Akt), and the extracellular regulated kinase (ERK)/mitogen-activated protein kinase (MAPK). Accordingly, polydatin potentially counteracts Alzheimer’s disease, cognition/memory dysfunction, Parkinson’s disease, brain/spinal cord injuries, ischemic stroke, and miscellaneous neuronal dysfunctionalities. The present study provides all of the neuroprotective mechanisms of polydatin in various NDDs. Additionally, the novel delivery systems of polydatin are provided regarding increasing its safety, solubility, bioavailability, and efficacy, as well as developing a long-lasting therapeutic concentration of polydatin in the central nervous system, possessing fewer side effects.     

Multi-Target Classification Pattern Recognition Applied to Computer-Aided Materials Design

Abstract

A multi-target classification pattern recognition method based on the principal component analysis (PCA) has been proposed for computer-aided materials design considering the multiple specialties of materials. The designed sample with probable optimal specialties is determined in such way that its representing point should be at the optimal region in the PC sub-space, where most optimal samples can be discriminated from non-optimal samples by means of features. The experimental parameters of the sample represented by this point can be obtained using a non-linear inverse mapping method from the PC sub-space to the original space. Based on the information provided using the method, several samples of V-PTC materials with optimal multiple specialties are synthesized.     

Electrochemical stripping detection of DNA hybridization based on cadmium sulfide nanoparticle tags

We report on the detection of DNA hybridization in connection to cadmium sulfide nanoparticle tracers and electrochemical stripping measurements of the cadmium. A nanoparticle-promoted cadmium precipitation is used to enlarge the nanoparticle tag and amplify the stripping DNA hybridization signal. In addition to measurements of the dissolved cadmium ion we demonstrate solid-state measurements following a ‘magnetic’ collection of the magnetic-bead/DNA-hybrid/CdS-tracer assembly onto a thick-film electrode transducer. The new protocol combines the amplification features of nanoparticle/polynucleotides assemblies and highly sensitive stripping potentiometric detection of cadmium, with an effective magnetic isolation of the duplex. The low detection limit (100 fmol) is coupled to good reproducibility (RSD=6%). Prospects for using binary inorganic colloids for multi-target detection are discussed.     

Self-quenched Fluorophore Dimers for DNA-PAINT and STED Microscopy

Super-resolution techniques like single-molecule localisation microscopy (SMLM) and stimulated emission depletion (STED) microscopy have been extended by the use of non-covalent, weak affinity-based transient labelling systems. DNA-based hybrid systems are a prominent example among these transient labelling systems, offering excellent opportunities for multi-target fluorescence imaging. However, these techniques suffer from higher background relative to covalently bound fluorophores, originating from unbound fluorophore-labelled single-stranded oligonucleotides. Here, we introduce short-distance self-quenching in fluorophore dimers as an efficient mechanism to reduce background fluorescence signal, while at the same time increasing the photon budget in the bound state by almost 2-fold. We characterise the optical and thermodynamic properties of fluorophore-dimer single-stranded DNA, and show super-resolution imaging applications with STED and SMLM with increased spatial resolution and reduced background.     

Nanoparticle-based electrochemical DNA detection

Nanoscale architectures of DNA-linked particle networks are attractive for electrical detection of DNA hybridization. This article reviews a variety of new nanoparticle/polynucleotide assemblies for advanced electrical detection of DNA sequences. Recent activity has led to innovative and powerful nanoparticle-based electrochemical DNA hybridization assays based on a variety of detection schemes. Such protocols rely on the use of colloidal gold tags, semiconductor quantum dot tracers, polymeric carrier (amplification) beads, or magnetic (separation) beads. Particularly useful have been protocols based on capturing of metal nanoparticle tracers followed by dissolution and anodic-stripping voltammetric measurement of the metal tag. Remarkable sensitivity is achieved by coupling particle-based amplification units and various amplification processes. The use of nanoparticle tracers for designing multi-target electrochemical coding protocols will also be documented.     

Molecular Modeling of Histamine Receptors—Recent Advances in Drug Discovery

The recent developments of fast reliable docking, virtual screening and other algorithms gave rise to discovery of many novel ligands of histamine receptors that could be used for treatment of allergic inflammatory disorders, central nervous system pathologies, pain, cancer and obesity. Furthermore, the pharmacological profiles of ligands clearly indicate that these receptors may be considered as targets not only for selective but also for multi-target drugs that could be used for treatment of complex disorders such as Alzheimer’s disease. Therefore, analysis of protein-ligand recognition in the binding site of histamine receptors and also other molecular targets has become a valuable tool in drug design toolkit. This review covers the period 2014–2020 in the field of theoretical investigations of histamine receptors mostly based on molecular modeling as well as the experimental characterization of novel ligands of these receptors.     

Portable Immuno-Microchip Analyzer for the Determination of Morphine and Its Analogs

A portable immuno-microchip system consisting of low-cost biocompatible-polystyrene chips, a mini-vacuum pump, and a base unit for a LED light source as a miniaturized optical readout was devised. The surfaces of the micro-channels were processed with plasma to be more hydrophilic and were characterized by kinetic coating with a CCD scanning method. To demonstrate the feasibility of this novel system for the determination of a small molecule control assay, a simple, specific, and rapid method was established for drug analysis of morphine and its analogs, 6-monoacetylmorphine and morphine-3-glucuronide. Morphine-3-site antigen and a multi-target polyclonal antibody to morphine and derivatives were prepared and a competitive immunoassay was performed on the chip. The measurement can be carried out automatically and avoids time-consuming incubation steps. A detection sensitivity of below 1.0 ng/mL was achieved, which is comparable with the enzyme-linked immunosorbent assay (ELISA) technique.