Molecule-pharmacophore superpositioning and pattern matching in computational drug design.


:Three-dimensional (3D) pharmacophore modeling is a technique for describing the interaction of a small molecule ligand with a macromolecular target. Since chemical features in a pharmacophore model are well known and highly transparent for medicinal chemists, these models are intuitively understandable and have been increasingly successful in computational drug discovery in the past few years. The performance and applicability of pharmacophore modeling depends on two main factors: the definition and placement of pharmacophoric features and the alignment techniques used to overlay 3D pharmacophore models and small molecules. An overview of key technologies and latest developments in the area of 3D pharmacophores is given and provides insight into different approaches as implemented by the 3D pharmacophore modeling packages like Catalyst, MOE, Phase and LigandScout.


Drug Discov Today


Drug discovery today


Wolber G,Seidel T,Bendix F,Langer T




Has Abstract


2008-01-01 00:00:00














  • Controlling 2-arachidonoylglycerol metabolism as an anti-inflammatory strategy.

    abstract::The endocannabinoid system is implicated in, and regulates, several physiological processes, ranging from food intake and energy balance to pain and inflammation. 2-Arachidonoylglycerol (2-AG) is a full agonist at the cannabinoid receptors which classically mediate its effects. The activity of this bioactive lipid is ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Alhouayek M,Masquelier J,Muccioli GG

    更新日期:2014-03-01 00:00:00

  • Natural products in drug discovery.

    abstract::Natural products have been the single most productive source of leads for the development of drugs. Over a 100 new products are in clinical development, particularly as anti-cancer agents and anti-infectives. Application of molecular biological techniques is increasing the availability of novel compounds that can be c...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Harvey AL

    更新日期:2008-10-01 00:00:00

  • Hybrid poly(lactic-co-glycolic acid) nanoparticles: design and delivery prospectives.

    abstract::Poly(lactic-co-glycolic acid) (PLGA), a US Food and Drug Administration (FDA)-approved copolymer, has been exploited widely in the design of nanoparticles because it is biodegradable, biocompatible, protects the drug molecules from degradation, and aids in producing sustained and targeted delivery. However, certain co...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Pandita D,Kumar S,Lather V

    更新日期:2015-01-01 00:00:00

  • Chemical proteomics and its application to drug discovery.

    abstract::The completion of the human genome sequencing project has provided a flood of new information that is likely to change the way scientists approach the study of complex biological systems. A major challenge lies in translating this information into new and better ways to treat human disease. The multidisciplinary scien...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Jeffery DA,Bogyo M

    更新日期:2004-01-15 00:00:00

  • An update on the role of nanovehicles in nose-to-brain drug delivery.

    abstract::A quantitative analysis has cast doubt over the limited advantages provided by particles for nose-to-brain (NTB) drug delivery. Thus, it is imperative to identify the role of nanovehicles in NTB drug delivery. If nanocarriers are used merely as an option to improve various properties of the drugs or the formulations, ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Feng Y,He H,Li F,Lu Y,Qi J,Wu W

    更新日期:2018-05-01 00:00:00

  • Impact of new technologies for cellular screening along the drug value chain.

    abstract::High-information screening formats, using more physiologically relevant cellular models and readout approaches, are slowly replacing traditional, target-orientated approaches in drug discovery programs. With improved access to primary cells, as well as label-free, non-intrusive methods of compound interrogation (such ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Möller C,Slack M

    更新日期:2010-05-01 00:00:00

  • Tuberculosis: from molecular pathogenesis to effective drug carrier design.

    abstract::In the past two decades, tuberculosis has gone from being a forgotten disease to a modern and recrudescent pathology. Tuberculosis is a curable infection and most of the negative therapeutic outcomes are related to poor patient compliance, which could be solved by new drug delivery approaches. By using such approaches...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Dube D,Agrawal GP,Vyas SP

    更新日期:2012-07-01 00:00:00

  • The targeted delivery of cancer drugs across the blood-brain barrier: chemical modifications of drugs or drug-nanoparticles?

    abstract::One of the most challenging problems, if not the most challenging, in drug development is not to develop drugs to treat diseases of the central nervous system (CNS), but to manage to distribute them to the CNS across the blood-brain barrier (BBB) using transvascular routes following intravenous administration. The dev...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Juillerat-Jeanneret L

    更新日期:2008-12-01 00:00:00

  • Histone acetyl transferases as emerging drug targets.

    abstract::Post-translational modifications, such as acetylation or phosphorylation, play a crucial role in the regulation of gene transcription in eukaryotes. Different subtypes of histone acetyl transferases (HATs) catalyze the acetylation of histones on specific lysine residues. A potential role of HATs in the pathology of ca...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Dekker FJ,Haisma HJ

    更新日期:2009-10-01 00:00:00

  • Pharmacological treatment of idiopathic pulmonary fibrosis: an update.

    abstract::Idiopathic pulmonary fibrosis (IPF) is a progressive and almost invariably lethal disease that affects primarily older adults. After a decade of negative (or inconsistent) results, two recent clinical trials have demonstrated that slowing disease progression with medication is possible. An improved understanding of di...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Spagnolo P,Wells AU,Collard HR

    更新日期:2015-05-01 00:00:00

  • Designed covalent allosteric modulators: an emerging paradigm in drug discovery.

    abstract::Covalent allosteric modulators possess the pharmacological advantages (high potency, extended duration of action and low drug resistance) of covalent ligands and the additional benefit of the higher specificity and lower toxicity of allosteric modulators. This approach is gaining increasing recognition as a valuable t...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Lu S,Zhang J

    更新日期:2017-02-01 00:00:00

  • Monoclonal antibodies for chronic refractory asthma and pipeline developments.

    abstract::Patients with severe asthma suffer persistent symptoms and/or frequent exacerbations despite high-intensity treatment. Their severe unrelenting symptoms have a huge impact on healthcare resources owing to frequent hospital admissions and requirement for intensive treatments. Consequently, there is an undeniable need f...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Polosa R,Casale T

    更新日期:2012-06-01 00:00:00

  • Compound high-quality criteria: a new vision to guide the development of drugs, current situation.

    abstract::For several decades, the pharmaceutical industry has suffered due to major issues such as reductions of the number of FDA approved drugs and biologics. Several analyses have been highlighted that the 'druglikeness' is one of the strategies to improve succeed rates of screening such as, for instance, high-throughput sc...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Mignani S,Huber S,Tomás H,Rodrigues J,Majoral JP

    更新日期:2016-04-01 00:00:00

  • Pain and beyond: fatty acid amides and fatty acid amide hydrolase inhibitors in cardiovascular and metabolic diseases.

    abstract::Fatty acid amide hydrolase (FAAH) is responsible for the hydrolysis of several important endogenous fatty acid amides (FAAs), including anandamide, oleoylethanolamide and palmitoylethanolamide. Because specific FAAs interact with cannabinoid and vanilloid receptors, they are often referred to as 'endocannabinoids' or ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Pillarisetti S,Alexander CW,Khanna I

    更新日期:2009-12-01 00:00:00

  • Enabled clinical use of an HIV-1 attachment inhibitor through drug delivery.

    abstract::The clinical advancement of HIV-1 attachment inhibitors was hindered initially by poor bioavailability. Attempts to identify improved candidates revealed that solubility and dissolution-rate-limited absorption are barriers to achieving adequate antiviral plasma levels. This was mitigated by forming nanosized drugs or ...

    journal_title:Drug discovery today

    pub_type: 杂志文章


    authors: Timmins P,Brown J,Meanwell NA,Hanna GJ,Zhu L,Kadow JF

    更新日期:2014-09-01 00:00:00

  • Novel approaches to the pharmacotherapy of pulmonary arterial hypertension.

    abstract::Pulmonary arterial hypertension (PAH) has evolved from an untreatable condition to a disease for which several classes of drugs have now been approved, including various prostanoids, endothelin receptor antagonists and phosphodiesterase-5 inhibitors. Because the pathogenesis of pulmonary hypertension is increasingly u...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Olsson KM,Hoeper MM

    更新日期:2009-03-01 00:00:00

  • Building relationships between academia and the pharmaceutical industry.

    abstract::'The climate is perfect for a proactive search for partners between industry and academia.' ...

    journal_title:Drug discovery today

    pub_type: 杂志文章


    authors: Dean P

    更新日期:2000-09-01 00:00:00

  • Support vector machines approach for predicting druggable proteins: recent progress in its exploration and investigation of its usefulness.

    abstract::Identification and validation of viable targets is an important first step in drug discovery and new methods, and integrated approaches are continuously explored to improve the discovery rate and exploration of new drug targets. An in silico machine learning method, support vector machines, has been explored as a new ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Han LY,Zheng CJ,Xie B,Jia J,Ma XH,Zhu F,Lin HH,Chen X,Chen YZ

    更新日期:2007-04-01 00:00:00

  • Graphene-based nanomaterials for drug and/or gene delivery, bioimaging, and tissue engineering.

    abstract::Here, we discuss the biomedical applications of graphene-based nanomaterials (GBNs). We examine graphene and its various derivatives, including graphene, graphene oxides (GOs), reduced graphene oxides (rGOs), graphene quantum dots (GQDs), and graphene composites, and discuss their unique properties related to their bi...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Zhao H,Ding R,Zhao X,Li Y,Qu L,Pei H,Yildirimer L,Wu Z,Zhang W

    更新日期:2017-09-01 00:00:00

  • Covalent inhibitors in drug discovery: from accidental discoveries to avoided liabilities and designed therapies.

    abstract::Drugs that covalently bond to their biological targets have a long history in drug discovery. A look at drug approvals in recent years suggests that covalent drugs will continue to make impacts on human health for years to come. Although fraught with concerns about toxicity, the high potencies and prolonged effects ac...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Bauer RA

    更新日期:2015-09-01 00:00:00

  • Multiple active receptor conformation, agonist efficacy and maximum effect of the system: the conformation-based operational model of agonism.

    abstract::The operational model of agonism assumes that the maximum effect a particular receptor system can achieve (the Em parameter) is fixed. Em estimates are above but close to the asymptotic maximum effects of endogenous agonists. The concept of Em is contradicted by superagonists and those positive allosteric modulators t...

    journal_title:Drug discovery today

    pub_type: 杂志文章


    authors: Roche D,Gil D,Giraldo J

    更新日期:2013-04-01 00:00:00

  • Chronic autoimmune-mediated inflammation: a senescent immune response to injury.

    abstract::The increasing prevalence of chronic autoimmune-mediated inflammatory diseases (AIMIDs) in ageing western societies is a major challenge for the drug development industry. The current high medical need for more-effective treatments is at least in part caused by our limited understanding of the mechanisms that drive ch...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: 't Hart BA,Chalan P,Koopman G,Boots AM

    更新日期:2013-04-01 00:00:00

  • Current applications and future potential for bioinorganic chemistry in the development of anticancer drugs.

    abstract::This review illustrates notable recent progress in the field of medicinal bioinorganic chemistry as many new approaches to the design of innovative metal-based anticancer drugs are emerging. Current research addressing the problems associated with platinum drugs has focused on other metal-based therapeutics that have ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: van Rijt SH,Sadler PJ

    更新日期:2009-12-01 00:00:00

  • Discovery informatics: its evolving role in drug discovery.

    abstract::Drug discovery and development is a highly complex process requiring the generation of very large amounts of data and information. Currently this is a largely unmet informatics challenge. The current approaches to building information and knowledge from large amounts of data has been addressed in cases where the types...

    journal_title:Drug discovery today

    pub_type: 杂志文章


    authors: Claus BL,Underwood DJ

    更新日期:2002-09-15 00:00:00

  • Can BDDCS illuminate targets in drug design?

    abstract::The fact that pharmacokinetic (PK) properties of drugs influence their interaction with protein targets is a principle known for decades. The same cannot be said for the opposite, namely that targets influence the PK properties of drugs. Evidence confirming this possibility is introduced here for the first time, as we...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Bocci G,Benet LZ,Oprea TI

    更新日期:2019-12-01 00:00:00

  • Novel antitussive strategies.

    abstract::Acute and chronic cough represent one of the most common symptoms of medical importance but effective pharmacotherapy is, to all intents and purposes, absent. Numerous initiatives targeting the recently discovered tussive pathways are in progress. Here, we review the current antitussive armamentarium and provide an up...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Morjaria JB,Dickinson RS,Morice AH

    更新日期:2013-04-01 00:00:00

  • Polymer-drug conjugates: recent advances and future perspectives.

    abstract::Polymer-drug conjugates (PDC) have exhibited clinical and commercial success in the field of drug delivery. A polymeric backbone, linker, targeting moiety, and drug constitute the building blocks of PDCs. Current attention is focusing on natural polymeric carriers, in particular the concept of graft copolymers, such a...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Thakor P,Bhavana V,Sharma R,Srivastava S,Singh SB,Mehra NK

    更新日期:2020-09-01 00:00:00

  • Molecular diversity and its analysis.

    abstract::We have recently developed a novel strategy for the rational design of compounds. This 'in silico screening' approach is based on the design and screening of virtual combinatorial libraries. Screening is performed using defined rules derived from a comprehensive description of active and inactive molecules in a releva...

    journal_title:Drug discovery today

    pub_type: 杂志文章


    authors: Gorse D,Rees A,Kaczorek M,Lahana R

    更新日期:1999-06-01 00:00:00

  • Use of Benford's law in drug discovery data.

    abstract::Benford's law states that the distribution of the first digit of many data sets is not uniform. The first digit of any random number will be 1 almost 30% of the time, and larger digits occur as the first digit with lower and lower frequency, to the point where 9 occurs as a first digit only 5% of the time. Here, we de...

    journal_title:Drug discovery today

    pub_type: 杂志文章


    authors: Orita M,Moritomo A,Niimi T,Ohno K

    更新日期:2010-05-01 00:00:00

  • Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery.

    abstract::Current advances in systems biology suggest a new change of paradigm reinforcing the holistic nature of the drug discovery process. According to the principles of systems biology, a simple drug perturbing a network of targets can trigger complex reactions. Therefore, it is possible to connect initial events with final...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审


    authors: Cruz-Monteagudo M,Schürer S,Tejera E,Pérez-Castillo Y,Medina-Franco JL,Sánchez-Rodríguez A,Borges F

    更新日期:2017-07-01 00:00:00