基于片段方法创制的药物

小分子药物与靶标的结合大都以非共价键结合,氢键、静电、疏水和范德华作用以维持结合力,这些因素越多结合越牢固,活性越强。但往往伴随分子尺寸变大,产生过膜吸收代谢等药代问题,最终影响成药性。基于片段的药物发现(fragment-based drug discovery, FBDD)是普筛高质量片段以发现苗头分子,结合结构生物学,在片段生长、连接和融合中形成先导物,以及优化出候选物的运行中,始终兼顾化合物活性和物化性质之间的协调性。基于片段的药物发现与基于靶标结构的药物发现存在密切关系。本文以数个上市的药物简释FBDD的应用原理。     

药物靶标研究中的功能基因组学

在人类基因组计划完成以及新的生物技术推动下,传统的药物发现模式正在向基因组学为基础的现代药物发现模式转变。药物靶标的发现,是药物发现途径中最关键的一个环节。该文就目前靶标不同阶段的研究策略和方法做一综述,重点介绍新的生物技术对药物靶标研究所产生的影响并展望未来发展趋势。     

细胞热迁移分析技术及其在靶标发现中的应用进展

细胞热迁移分析(cellular thermal shift assay,CETSA)是一种在细胞或组织中直接研究配体与蛋白结合的生物学技术,其原理是当靶蛋白与药物分子结合时,靶蛋白通常会变得稳定,不容易发生热变性。该技术可以在细胞裂解液、细胞内及组织中检测非标记药物与蛋白质的结合情况。近年来,将CETSA技术与免疫印迹(Western blot)法、二维差异凝胶电泳技术及定量蛋白质质谱技术相结合,已成功用于药物靶标验证、临床药物靶标发现、脱靶识别等。随着技术的发展,该方法还用于生物代谢物、核酸及蛋白质相互作用的分析。本文重点综述CETSA技术的原理、方法演变以及在药物靶标发现中的应用。     

国外药物靶标开发的现状及特点分析

药物通过结合并调节特定的蛋白或核酸靶标的活性而发挥其治疗作用.大量的药物靶标已经被开发并用于创新药物的发现过程.目前的研究重点是寻找新的靶标和对现有靶标进行更为深入地研究.分析药物靶标开发的现状和特点将有助于我们理解药物的分子作用机制,发现药物靶标开发中涉及的一些规律性的东西,为我国的创新药物开发提供参考.     

药物共晶研究进展及应用

药物共晶是活性药物成分通过非共价键和共晶形成物结合在一个晶格中形成的.它是一种新的药物固体型态,可以改善药物的理化性质,比如改善溶解度、增加稳定性、提高生物利用度等,是目前药物研发的一个新的热点.本文主要介绍了药物共晶在药物研发中的应用及其设计、制备以及分析方法.     

细胞色素P450基因多态性对心血管药物疗效的影响

基因多态性对药物疗效的影响主要表现在药物代谢酶的多态性、药物受体的多态性和药物靶标的多态性,其中药物代谢酶的基因多态性是导致相同药物、相同剂量、不同个体差异的一个重要生物学因素。遗传药理学（pharmacogenetics）即是从基因水平揭示个体的遗传特质对酶活性、受体蛋白和药物靶标的影响,从基因水平阐释药物效应差异的原因,以及各种基因表型与药物疗效、毒副反应之间的关系。     

蛋白质结晶的新进展与药物设计

蛋白质是生命的基础,其功能与它的三维结构密切相关,关于蛋白质的结构信息,对科学家根据结构同源性确定药物靶标以及发现新的药物靶标等方面均有至关重要的作用。因此,蛋白质晶体的获得及其与药物设计的关系日益受到重视,已成为生命科学中的一个重要领域,本文主要综述了蛋白质结晶技术的最新研究进展以及在药物设计中的应用。     

药物靶标热点领域的共词聚类分析研究

后基因组时代的药物靶标是创新药物开发的源泉,了解药物靶标的热点领域有利于针对性地开展创新药物的研究工作.现对2003-2007年MEDLINE数据库收录的药物靶标文献的高频主题词进行共词聚类统计分析,并通过聚类映射图和战略坐标等分析结果与专业知识相结合,揭示药物靶标的热点领域.研究发现,目前的靶标研究主要聚焦在抗肿瘤领域,尤其是酶的药理学研究;结晶学、计算机模拟、生物模型等药靶开发技术也应值得重点关注.     

老药在药物设计中的应用

药物的副作用是由于药物与不希望的靶标发生了作用，这是由于靶标受体与药物分子的杂泛性所致。药物的杂泛性具有双重性：有利的方面是可用于设计多靶标作用药物；不利方面是其所产生的副作用。然而，药物的副作用也可以作为研发新药的出发点，经结构改造消除或减弱原药的主作用，提升某副作用使其成为新的药物。近年来确定的许多药物靶标，为老药的新用途提供了生物学依据。老药已在临床应用，其物化、药代和安全性应有保障，因而研发的起点高，同时副作用也是根据临床观察所见，故依此研发新药的成功几率较高。在分子变换中，重要之点是结构的新颖性和拥有知识产权。     

基于淋巴系统的药物及其递送系统研究进展

近年来,位于淋巴系统的生物学靶标越来越多地被发现和利用;以调控淋巴系统功能或纠正淋巴系统病理改变为主要作用机制的药物逐渐成为研发热点之一;药物经淋巴系统的吸收、转运、代谢与递送研究与相应递送系统的开发也正引起重视。很多研究成果正被尝试用于免疫治疗、炎症调控、新型疫苗等重要领域,为肿瘤、自身免疫病、感染类疾病、代谢综合征等多类别重大疾病的治疗带来新机会。本文简要介绍了淋巴系统的结构与生理功能,淋巴系统内药物靶标与相关药物研究,以及药物经淋巴系统转运的模式与递送技术,希望给药学科学工作者、产业界和监管科学界专业人士提供参考。     

Drug bioactivation, covalent binding to target proteins and toxicity relevance

A number of therapeutic drugs with different structures and mechanisms of action have been reported to undergo metabolic activation by Phase I or Phase II drug-metabolizing enzymes. The bioactivation gives rise to reactive metabolites/intermediates, which readily confer covalent binding to various target proteins by nucleophilic substitution and/or Schiff's base mechanism. These drugs include analgesics (e.g., acetaminophen), antibacterial agents (e.g., sulfonamides and macrolide antibiotics), anticancer drugs (e.g., irinotecan), antiepileptic drugs (e.g., carbamazepine), anti-HIV agents (e.g., ritonavir), antipsychotics (e.g., clozapine), cardiovascular drugs (e.g., procainamide and hydralazine), immunosupressants (e.g., cyclosporine A), inhalational anesthetics (e.g., halothane), nonsteroidal anti-inflammatory drugs (NSAIDSs) (e.g., diclofenac), and steroids and their receptor modulators (e.g., estrogens and tamoxifen). Some herbal and dietary constituents are also bioactivated to reactive metabolites capable of binding covalently and inactivating cytochrome P450s (CYPs). A number of important target proteins of drugs have been identified by mass spectrometric techniques and proteomic approaches. The covalent binding and formation of drug-protein adducts are generally considered to be related to drug toxicity, and selective protein covalent binding by drug metabolites may lead to selective organ toxicity. However, the mechanisms involved in the protein adduct-induced toxicity are largely undefined, although it has been suggested that drug-protein adducts may cause toxicity either through impairing physiological functions of the modified proteins or through immune-mediated mechanisms. In addition, mechanism-based inhibition of CYPs may result in toxic drug-drug interactions. The clinical consequences of drug bioactivation and covalent binding to proteins are unpredictable, depending on many factors that are associated with the administered drugs and patients. Further studies using proteomic and genomic approaches with high throughput capacity are needed to identify the protein targets of reactive drug metabolites, and to elucidate the structure-activity relationships of drug's covalent binding to proteins and their clinical outcomes.     

Drug Repurposing Based on Drug–Drug Interaction

Given the high risk and lengthy procedure of traditional drug development, drug repurposing is gaining more and more attention. Although many types of drug information have been used to repurpose drugs, drug–drug interaction data, which imply possible physiological effects or targets of drugs, remain unexploited. In this work, similarity of drug interaction was employed to infer similarity of the physiological effects or targets for the drugs. We collected 10 835 drug–drug interactions concerning 1074 drugs, and for 700 of them, drug similarity scores based on drug interaction profiles were computed and rendered using a drug association network with 589 nodes (drugs) and 2375 edges (drug similarity scores). The 589 drugs were clustered into 98 groups with Markov Clustering Algorithm, most of which were significantly correlated with certain drug functions. This indicates that the network can be used to infer the physiological effects of drugs. Furthermore, we evaluated the ability of this drug association network to predict drug targets. The results show that the method is effective for 317 of 561 drugs that have known targets. Comparison of this method with the structure-based approach shows that they are complementary. In summary, this study demonstrates the feasibility of drug repurposing based on drug–drug interaction data.     

Mechanism-based inactivation of CYP450 enzymes: a case study of lapatinib

Abstract

Mechanism-based inactivation (MBI) of CYP450 enzymes is a unique form of inhibition in which the enzymatic machinery of the victim is responsible for generation of the reactive metabolite. This precondition sets up a time-dependency for the inactivation process, a hallmark feature that characterizes all MBI. Yet, MBI itself is a complex biochemical phenomenon that operates in different modes, namely, covalent binding to apoprotein, covalent binding of the porphyrin group and also complexation of the catalytic iron. Using lapatinib as a recent example of toxicological interest, we present an example of a mixed-function MBI that can confound clinical drug–drug interactions manifestation. Lapatinib exhibits both covalent binding to the apoprotein and formation of a metabolite-intermediate complex in an enzyme-selective manner (CYP3A4 versus CYP3A5), each with different reactive metabolites. The clinical implication of this effect is also contingent upon genetic polymorphisms of the enzyme involved as well as the co-administration of other substrates, inhibitors or inducers, culminating in drug–drug interactions. This understanding recapitulates the importance of applying isoform-specific mechanistic investigations to develop customized strategies to manage such outcomes.     

Can in vitro metabolism-dependent covalent binding data in liver microsomes distinguish hepatotoxic from nonhepatotoxic drugs? An analysis of 18 drugs with consideration of intrinsic clearance and daily dose

In vitro covalent binding assessments of drugs have been useful in providing retrospective insights into the association between drug metabolism and a resulting toxicological response. On the basis of these studies, it has been advocated that in vitro covalent binding to liver microsomal proteins in the presence and the absence of NADPH be used routinely to screen drug candidates. However, the utility of this approach in predicting toxicities of drug candidates accurately remains an unanswered question. Importantly, the years of research that have been invested in understanding metabolic bioactivation and covalent binding and its potential role in toxicity have focused only on those compounds that demonstrate toxicity. Investigations have not frequently queried whether in vitro covalent binding could be observed with drugs with good safety records. Eighteen drugs (nine hepatotoxins and nine nonhepatotoxins in humans) were assessed for in vitro covalent binding in NADPH-supplemented human liver microsomes. Of the two sets of nine drugs, seven in each set were shown to undergo some degree of covalent binding. Among hepatotoxic drugs, acetaminophen, carbamazepine, diclofenac, indomethacin, nefazodone, sudoxicam, and tienilic acid demonstrated covalent binding, while benoxaprofen and felbamate did not. Of the nonhepatotoxic drugs evaluated, buspirone, diphenhydramine, meloxicam, paroxetine, propranolol, raloxifene, and simvastatin demonstrated covalent binding, while ibuprofen and theophylline did not. A quantitative comparison of covalent binding in vitro intrinsic clearance did not separate the two groups of compounds, and in fact, paroxetine, a nonhepatotoxin, showed the greatest amount of covalent binding in microsomes. Including factors such as the fraction of total metabolism comprised by covalent binding and the total daily dose of each drug improved the discrimination between hepatotoxic and nontoxic drugs based on in vitro covalent binding data; however, the approach still would falsely identify some agents as potentially hepatotoxic.     

Intrinsically disordered proteins and novel strategies for drug discovery

Introduction: There is a natural abundance of intrinsically disordered proteins or intrinsically disordered protein regions (IDPs or IDPRs), that is, biologically active proteins/regions without stable structure. Their wide functional repertoire; the ability to participate in multiple interactions; the capability to fold at binding in a template-dependent manner and their common involvement in the pathogenesis of numerous human diseases suggest that these proteins should be seriously considered as novel drug targets.

Areas covered: This article describes the major classes of ordered proteins traditionally used as drug targets and introduces the molecular mechanisms of drugs targeting ordered proteins. Furthermore, it illustrates basic ways of rational drug design for these proteins, and shows why these approaches cannot be directly used for intrinsic disorder-based drug design. Some of the new approaches utilized for finding drugs targeting IDPs/IDPRs are introduced.

Expert opinion: There is a continuing progress in the design of small molecules for IDPs/IDPRs and several small molecules are found that specifically inhibit the disorder-based interaction of IDPs with their numerous partners. It is expected that the initial studies will be extended and novel intrinsic disorder-based drug design approaches will be developed. Furthermore, putative new targets will be identified, and a better understanding of the molecular mechanisms underlying modulation of promiscuous IDP binding will be achieved.     

灵芝酸抗癌机制的分子模拟研究

目的分析灵芝酸与肿瘤靶酶的相互作用模式,研究灵芝酸的抗肿瘤机制。方法根据灵芝酸结构寻找可能的肿瘤靶点,并基于靶点结构,利用分子对接,探讨灵芝酸与靶酶的相互作用模式以及作用强度。结果与结论预测了灵芝酸与肿瘤靶标的结合方式,有助于理解灵芝酸的抗肿瘤机制。     

Receptor binding and the discovery of psychotherapeutic drugs

The identification of useful new drugs, when not due entirely to serendipity, has often relied on in vivo techniques that are both difficult to interpret and to perform. The receptor binding technique, however, by allowing the direct study of the specific biochemical site of action of most psychotherapeutic drugs has provided a simple, selective, and sensitive method to study drug-receptor interactions. The biochemical locus of action for a family of drugs can often be identified by comparing their absolute potencies in in vivo systems with their affinities at a number of drug and/or neurotrans mitter receptor binding sites. Once a particular binding site is identified as therapeutically relevant, affinity for this binding site can be used as a screen for novel compounds that may show similar in vivo activity. Detailed structure-activity relationships can be determined in vitro without the problems of metabolism and differential absorption that complicate in vivo studies. Such studies allow the pinpointing of active sites within the drug molecule for further synthetic manipulations. Receptor binding studies have been essential in the elucidation of the therapeutic mechanisms of neuroleptics, tricyclic antidepressants, opiates, and benzodiazepines. Receptor binding studies are not only useful in the identification and quantification of therapeutically useful drug receptor interactions but have also been invaluable in the study of similar interactions that manifest themselves as drug-induced side effects. Such studies may eventually allow the development of drugs that are not only more therapeutically potent but are also free of side effects. Radioreceptor assays have also been introduced to measureserum drug levels of neuroleptics, antidepressants, anticholinergics, benzodiazepines and P-adrenergic antagonists. These methods have the advantage of being quick, sensitive, selective, and inexpensive.     

Network-based drug repositioning: A novel strategy for discovering potential antidepressants and their mode of action

Current target-oriented paradigm for novel antidepressant discovery has been difficult to succeed and the failures always bring huge economic losses. Although abundant ledge of disease related genes and drug action targets has been accumulated, the successful application of the knowledge for new drug discovery is limited. Here, we predicted and validated potential antidepressants and molecular targets from DrugBank recorded drugs using a novel network-based drug repositioning approach. This approach predicted relationships between drug and targets through network-based integration of drug chemical similarity, therapeutic similarity and protein–protein interactions. We predicted genome-wide relations of drugs and targets, and then screened drugs that connect to depression-related targets of known antidepressants. Six drugs were predicted and experimentally validated to have antidepressant-like effects in the tail suspension test (TST) and forced swimming test (FST) in mice. Alverine, which is a gastrointestinal antispasmodic drug, was further validated to display antidepressant-like effects in the learned helplessness and chronic unpredictable stress models of depression. Four targets, including serotonin transporter, norepinephrine transporter, serotonin 1A receptor and serotonin 2A receptor, were included in the predictable system and confirmed as primary sites of action for alverine. The results suggest that alverine may be an effective antidepressant drug and the network-based drug repositioning may be a promising drug discovery paradigm for complex multi-genetic diseases such as depression.     

Small molecule complementarity as a source of novel pharmaceutical agents and combination therapies

Many examples of specific binding between small molecules are known that are associated with modified physiological and pharmacological activities. Conversely, the antagonism or synergism of small molecules is often correlated with specific binding between the molecules. It follows that small molecule binding can be used as a relatively quick, easy, and specific screen for functionally useful drug actions and interactions. These actions and interactions may manifest themselves as functional antagonisms; binding may correlate with enhancement or synergism; the formation of some complexes may yield clues about how drugs may be targeted to specific cell types in vivo and provide leads for the development of antidotes for drug overdoses or poisoning; the binding of one molecule to another may mimic receptor binding; and complexation may provide novel ways of protecting and delivering drugs. Relevant examples from each type of application are reviewed involving peptide-peptide interactions; peptide-aromatic compound interactions; aromatic-aromatic compound interactions; vitamin-aromatic compound interactions; and polycyclic compound interactions. We argue that screening for molecular complementarity of small molecules turns ligands such as neurotransmitters and their metabolites, hormones, and drugs themselves, into direct targets of drug development that can augment screening new compounds for activity against receptors and second messenger systems. We believe that the small molecule complementarity approach is novel, fruitful and under-utilized.