Abstract:
:Fragment-based drug discovery has emerged over the past 15 years as an effective lead discovery paradigm that is complementary to traditional high-throughput screening. The starting point for fragment-based drug discovery is the identification of low-molecular weight, typically low-affinity compounds that bind to a target of interest. These fragments can then be elaborated by growing or linking to create compounds with high affinity and selectivity. A wide variety of techniques from the computational chemistry tool chest can be applied in a fragment-based project. The computational tools are equally useful in combination with experimental-binding determination or in a completely in silico design procedure. This chapter will outline these techniques, their utility, and their validation in the design of novel lead compounds.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Desjarlais RLdoi
10.1016/B978-0-12-381274-2.00006-6subject
Has Abstractpub_date
2011-01-01 00:00:00pages
137-55eissn
0076-6879issn
1557-7988pii
B978-0-12-381274-2.00006-6journal_volume
493pub_type
杂志文章abstract::We have developed two screening systems for isolating inhibitors that target bacterial two-component signal transduction: (1) a differential growth assay using a temperature-sensitive yycF mutant (CNM2000) of Bacillus subtilis, which is supersensitive to histidine kinase inhibitors, and (2) a high-throughput genetic s...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)22019-6
更新日期:2007-01-01 00:00:00
abstract::RNA modifications, with over one hundred known so far, are commonly proposed to fine-tune the structure and function of RNA. While modifications in rRNA and tRNA are used to modulate RNA folding and decoding properties, little is known about the function of internal modifications in mRNA/lncRNA, which includes N(6)-me...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2015.03.005
更新日期:2015-01-01 00:00:00
abstract::There is a great need for practicing scientists to volunteer their time and expertise in the K-12th grade science classroom. We have found that bioluminescence is a fun and exciting way to teach basic science concepts and is an excellent tool for the volunteering scientist. We have had very positive reactions from bot...
journal_title:Methods in enzymology
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doi:10.1016/s0076-6879(00)05517-8
更新日期:2000-01-01 00:00:00
abstract::Enveloped virus particles select their lipid-protein components and egress by budding from the host cell membranes. The matrix protein of many enveloped viruses has been proposed as a crucial element for viral budding; however, molecular mechanisms behind membrane remodeling by the matrix protein are yet to be unravel...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(09)64004-0
更新日期:2009-01-01 00:00:00
abstract::The functional properties of proteins are decided not only by their relatively rigid overall structures, but even more importantly, by their dynamic properties. In a protein, some regions of structure exhibit highly correlated or anti-correlated motions with others, some are highly dynamic but uncorrelated, while othe...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2020.04.020
更新日期:2020-01-01 00:00:00
abstract::We have described a method using polyvalent peptide display on filamentous phage that can be used to identify ligands that bind to G protein beta gamma subunits. Also described is how to construct phage that have known beta gamma binding sequences fused to the coat protein to allow a competition analysis to be perform...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/s0076-6879(02)44740-4
更新日期:2002-01-01 00:00:00
abstract::The method presented here is intended as a compromise between finding a good overall alignment and the time taken to do so. Many multiple alignment algorithms spend an excessively large amount of effort trying to find the best global alignment. This time is often ill spent because the results of the standard dynamic p...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/0076-6879(90)83031-4
更新日期:1990-01-01 00:00:00
abstract::Inositol phosphates (InsPs) are an important group of eukaryotic messengers and mediate a wide range of processes. To elucidate the biological functions of these molecules, robust techniques to characterize inositol phosphate metabolism at the cellular level are highly sought after. This chapter provides a detailed pr...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2020.04.035
更新日期:2020-01-01 00:00:00
abstract::The neutral arachidonic acid derivatives N-arachidonoyl ethanolamine (anandamide or AEA), and 2-arachidonoylglycerol (2-AG) have been identified as endogenous ligands for the cannabinoid receptors. Additionally, these compounds have been identified as substrates of the second isoform of the cyclooxygenase enzyme (COX-...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(07)33005-X
更新日期:2007-01-01 00:00:00
abstract::kappaB-Ras1 and kappaB-Ras2 are two small proteins that display similarity at the amino acid level to Ras-like small GTPases. Although little is known about the function of the kappaB-Ras proteins, they have been shown to interfere with activation of transcription factor NF-kappaB. They accomplish this by binding to I...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)07042-4
更新日期:2006-01-01 00:00:00
abstract::Family 3 carbohydrate-binding modules (CBM3s) are among the most distinctive, diverse, and robust. CBM3s, which are numerous components of both free cellulases and cellulosomes, bind tightly to crystalline cellulose, and thus play a key role in cellulose degradation through their substrate targeting capacity. In addit...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-415931-0.00013-6
更新日期:2012-01-01 00:00:00
abstract::Astrocytes are the most abundant cell type in the brain and are a crucial part of solving its mysteries. Originally assumed to be passive supporting cells, astrocyte's functions are now recognized to include active modulation and information processing at the neural synapse. The full extent of the astrocyte contributi...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2019.02.006
更新日期:2019-01-01 00:00:00
abstract::The microbial production of commodity, fine, and specialty chemicals is a driving force in biotechnology. An essential requirement is to introduce biosynthetic pathways to the target compound(s) into chassis organisms. First suitable enzymes must be selected and characterized, and then genetic pathways must be designe...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.04.011
更新日期:2018-01-01 00:00:00
abstract::Isothermal Titration Calorimetry (ITC) provides a sensitive and accurate means by which to study the thermodynamics of RNA folding, RNA binding to small molecules, and RNA-protein interactions. The advent of extremely sensitive instrumentation and the increasing availability of ITC in shared facilities have made it in...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(09)68019-8
更新日期:2009-01-01 00:00:00
abstract::In the least-squares fitting of data, there is a unique answer to the question of how the data should be weighted: inversely as their variance. Any other weighting gives less than optimal efficiency and leads to unreliable estimates of the parameter uncertainties. In calibration, knowledge of the data variance permits...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)03810-X
更新日期:2009-01-01 00:00:00
abstract::The formation of higher-order assemblies of multiple proteins or enzymes is a general mechanism to achieve more sophisticated biological function in biological systems. For example, cellulosomes are large complexes consisting of multiple cellulolytic enzymes that rely on the concerted actions of different enzymes buil...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.12.003
更新日期:2017-01-01 00:00:00
abstract::Because polysaccharides have very complicated chemical structures constructed by a great diversity of monosaccharide residues and glycosidic linkages, enzymatic approaches have been identified as powerful tools to precisely synthesize polysaccharides as the reactions progress in highly controlled regio- and stereoarra...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2019.06.009
更新日期:2019-01-01 00:00:00
abstract::Reliable modeling of RNA tertiary structures is key to both understanding these structures' roles in complex biological machines and to eventually facilitating their design for molecular computing and robotics. In recent years, a concerted effort to improve computational prediction of RNA structure through the RNA-Puz...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2014.10.051
更新日期:2015-01-01 00:00:00
abstract::Glycosylphosphatidylinositol-anchored proteins can be specifically identified by several methods. PI-PLC digestion analyses, the most widely used technique, can be performed more reliably when conducted with purified protein and phase partitioning to exclude steric effects and when combined with alkaline hydrolysis to...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/0076-6879(95)50099-5
更新日期:1995-01-01 00:00:00
abstract::In eukaryotes, determination of the subcellular location of a novel protein encoded in genomic or transcriptomic data provides useful clues as to its possible function. However, experimental localization studies are expensive and time-consuming. As a result, accurate in silico prediction of subcellular localization fr...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(09)05002-2
更新日期:2009-01-01 00:00:00
abstract::Hypoxia and inflammation are coincidental events in an array of diseased tissues, including chronically inflamed sites (e.g., inflammatory bowel disease, rheumatoid arthritis), growing tumors, myocardial infarcts, atherosclerotic plaques, healing wounds, and sites of bacterial infection (Murdoch et al., 2005). An unde...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(07)35025-8
更新日期:2007-01-01 00:00:00
abstract::By far the highest resolution of all separation techniques for intact proteins in a single analytical run continues to be by the combination of isoelectric focusing (IEF) and SDS-PAGE, originally introduced by O'Farrell [(1975). J. Biol. Chem.250, 4007-4021]. This analytical platform has seen a number of significant a...
journal_title:Methods in enzymology
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更新日期:2009-01-01 00:00:00
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2017.06.043
更新日期:2017-01-01 00:00:00
abstract::Among posttranslational modifications of proteins entailed with signal transduction, the redox transition is today brought to the focus as a major biochemical event accounting for the signaling functions of reactive oxygen species. Thermodynamic and kinetic criteria highlight hydroperoxides and protein disulfides as s...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(10)73011-1
更新日期:2010-01-01 00:00:00
abstract::DNA repair complexes play crucial roles in maintaining genome integrity, which is essential for the survival of an organism. The understanding of their modes of action is often obscure due to limited structural knowledge. Structural characterizations of these complexes are often challenging due to a poor protein produ...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/bs.mie.2017.03.010
更新日期:2017-01-01 00:00:00
abstract::Fluorescence live-cell RNA imaging to monitor the intracellular localization and dynamics of the target RNA is a challenging subject. One of the difficulties to achieve this is to establish a precise method to enable a fluorescent labeling to the target RNA in living cells. Technologies to reduce the background fluore...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.03.018
更新日期:2016-01-01 00:00:00
abstract::Optical imaging of reporter molecules such as firefly luciferase has become a popular method of tracking and visualizing cells in living animals. Many biological processes involve ubiquitin ligases, which target specific proteins for destruction under specific sets of conditions. Importantly, the motifs recognized by ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)99036-8
更新日期:2005-01-01 00:00:00
abstract::EPR long-range distance measurements on spin-labeled macromolecules have recently become a popular tool in structural biology. The method can be used to obtain coarse-grained structures of biomolecules, to track conformational changes and dynamics, to dock macromolecular complexes, or to localize spin centers within m...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2015.06.006
更新日期:2015-01-01 00:00:00
abstract::Complex synthetic schemes catalyzed by multienzyme systems immobilized on solid materials are gaining momentum in chemical biomanufacturing. These systems harness the high chemo-, regio-, and stereoselectivity of the enzymes and the recyclability of the heterogeneous catalysts. Moreover, when the enzymes become part o...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.12.013
更新日期:2019-01-01 00:00:00
abstract::Liquid-liquid phase separation (LLPS) has been known to drive formation of biomolecular compartments, which can encapsulate RNA and proteins among other cosolutes. Such compartments, which lack a lipid membrane, have been implicated in origins of life scenarios as they can easily uptake and concentrate biomolecules, s...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2020.06.010
更新日期:2021-01-01 00:00:00