Custom chemical microarray production and affinity fingerprinting for the S1 pocket of factor VIIa

Dickopf, Stefan; Mathur, Sanjay; Junker, Hans‐Dieter; Maier, Sabine; Metz, Günther; Ottleben, Holger; Rau, Harald K.; Schellhaas, Nathalie; Schmidt, Kristina; Sekul, Renate; Vanier, Cécile; Vetter, Dirk; Czech, Jörg; Lorenz, Martin; Matter, Hans; Schudok, Manfred; Schreuder, Herman; Will, David W.; Nestler, Hans Peter

doi:10.1016/j.ab.2004.08.033

Cited by 32 publications

(17 citation statements)

References 12 publications

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“…Cis isomer 20 and trans isomer 21 were separated by silica gel column chromatography; the more nonpolar fraction corresponded to the cis structure. The structures of the isomers were characterized by mass spectrometry, 1 H NMR, 13 C NMR, 13 C NMR-DEPT, 1 H-1 H COSY, 1 H-13 C HMQC, and 1 H-1 H NOESY spectra (Supporting Information Figure 6). The NOE of the hydrogens communicating between carbon 6 and carbon 10 was only observed in the trans compound as indicated in Supporting Information Figure 7B.…”

Section: Chemistry-compounds 8 Andmentioning

confidence: 99%

“…Following the binding event, various affinity-based techniques 7 have been proposed to accurately and efficiently identify the weak binding fragment (typically the binding affinities of fragments are in the 1 mM to 30 μM range), such as nuclear magnetic resonance-based screening 8 (SAR by NMR 9 ), mass spectroscopy-based identification 10 (especially tethering 11 ), X-ray crystallography-based approaches, 12 or surface plasmon resonance spectroscopy-based screening. 13 Alternatively, substrate activity screening highlights the roles of bioassay-based techniques in the identification of effective fragments. 14 These fragments, which can be considered as the building blocks of a more complex lead structure, are then evolved or combined/merged into compounds.…”

Section: Introductionmentioning

confidence: 99%

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Minimal Pharmacophoric Elements and Fragment Hopping, an Approach Directed at Molecular Diversity and Isozyme Selectivity. Design of Selective Neuronal Nitric Oxide Synthase Inhibitors

Ji¹,

Stanton²,

Igarashi

et al. 2008

J. Am. Chem. Soc.

151

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Fragment hopping, a new fragment-based approach for de novo inhibitor design focusing on ligand diversity and isozyme selectivity, is described. The core of this approach is the derivation of the minimal pharmacophoric element for each pharmacophore. Sites for both ligand binding and isozyme selectivity are considered in deriving the minimal pharmacophoric elements. Five general-purpose libraries are established: the basic fragment library, the bioisostere library, the rules for metabolic stability, the toxicophore library, and the side chain library. These libraries are employed to generate focused fragment libraries to match the minimal pharmacophoric elements for each pharmacophore and then to link the fragment to the desired molecule. This method was successfully applied to neuronal nitric oxide synthase (nNOS), which is implicated in stroke and neurodegenerative diseases. Starting with the nitroarginine-containing dipeptide inhibitors we developed previously, a small organic molecule with a totally different chemical structure was designed, which showed nanomolar nNOS inhibitory potency and more than 1000-fold nNOS selectivity. The crystallographic analysis confirms that the small organic molecule with a constrained conformation can exactly mimic the mode of action of the dipeptide nNOS inhibitors. Therefore, a new peptidomimetic strategy, referred to as fragment hopping, which creates small organic molecules that mimic the biological function of peptides by a pharmacophore-driven strategy for fragment-based de novo design, has been established as a new type of fragment-based inhibitor design. As an open system, the newly established approach efficiently incorporates the concept of early "ADME/Tox" considerations and provides a basic platform for medicinal chemistry-driven efforts.Agman@chem.northwestern.edu.

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Section: Chemistry-compounds 8 Andmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Minimal Pharmacophoric Elements and Fragment Hopping, an Approach Directed at Molecular Diversity and Isozyme Selectivity. Design of Selective Neuronal Nitric Oxide Synthase Inhibitors

Ji¹,

Stanton²,

Igarashi

et al. 2008

J. Am. Chem. Soc.

151

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“…The synthesized compound collection was spatially immobilized on SAM-based microarrays by using a highly standardized procedure in combination with extensive quality control steps and a high degree of automation [26]. This microarray based low affinity screening platform is currently in use for customer and in-house drug discovery projects, leading to the identification of new fragments and lead-like compounds in different protein classes [27,28]. 1 1 2 26 100 28 25 1 14 70 94 24 2 1 4 47 74 9 26 1 16 65 100 12 3 1 6 59 100 19 27 1 18 60 58 20 4 1 8 75 100 31 28 1 20 58 100 13 5 1 10 59 95 15 29 1 22 64 100 29 6 1 12 57 98 34 30 1 24 62 98 46 7 2 1 62 96 23 31 2 13 56 100 35 8 2 3 65...…”

Section: Resultsmentioning

confidence: 99%

Synthesis and Quality Control of Thiol Tagged Compound Libraries for Chemical Microarrays

Maier¹,

Mathur²,

Rau³

et al. 2006

QSAR Comb. Sci.

Self Cite

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A method for the synthesis and quality control of compound collections containing reactive thiol functions was developed. Such libraries form the basis for the construction of chemical microarrays to be used in fragment-based screening. Amino-modified polymer membranes fixed into the wells of microtiter plates were used as the solid phase for the nanomole-scale synthesis of a thiol-tagged small molecule library using a spatial onecompound/one-well strategy. A thiolselective Liquid Chromatography-Mass Spectroscopy (LC-MS) protocol of each compound before attachment to the microarray surface was established, allowing an exact determination of compound purity and concentration. The established synthesis and quality control method is an important prerequisite for an accurate read-out of the array compound -target interaction data, and simplifies the usage of small molecule microarrays for low affinity screening.

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“…Graffinity has developed high density chemical microarrays for fragment screening consisting of small molecules immobilized onto gold chips based on maleimide-thiol coupling chemistry in combination with high density pintool spotting [78,79]. The array preparation is a three-step process consisting of the synthesis of tagged fragments, preparation of SAM-Gold chips, and covalent coupling of tagged fragments to the activated SAM surface by pintool spotting.…”

Section: High Throughput Spr Screening Of Chemical Microarraysmentioning

confidence: 99%

“…Thus, the sensitivity and detection limit of Graffinity´s SPR imager technology (PlasmonImager), allows even small protein targets to be conveniently screened with a good signal/noise ratio. SPR imaging enables a parallel readout of thousands of fragment ligands against one target simultaneously [78,79].…”

Section: High Throughput Spr Screening Of Chemical Microarraysmentioning

confidence: 99%

SPR-based Fragment Screening: Advantages and Applications

Neumann¹,

Hd²,

Schmidt³

et al. 2007

CTMC

167

100

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Fragment-based screening has recently evolved into a promising strategy in drug discovery, and a range of biophysical methods can be employed for fragment library screening. Relevant approaches, such as X-ray, NMR and tethering are briefly introduced focussing on their suitability for fragment-based drug discovery. In particular the application of surface plasmon resonance (SPR) techniques to the primary screening of large libraries comprising small molecules is discussed in detail. SPR is known to be a powerful tool for studying biomolecular interactions in a sensitive and label-free detection format. Advantages of SPR methods over more traditional assay formats are discussed and the application of available channel and array based SPR systems to biosensing are reviewed. Today, SPR protocols have been applied to secondary screening of compound libraries and hit conformation, but primary screening of large fragment libraries for drug discovery is often hampered by the throughput of available systems. Chemical microarrays, in combination with SPR imaging, can simultaneously generate affinity data for protein targets with up to 9,216 immobilized fragments per array. This approach has proven to be suitable for screening fragment libraries of up to 110,000 compounds in a high throughput fashion. The design of fragment libraries and appropriate immobilization chemistries are discussed, as well as suitable follow-up strategies for fragment hit optimization. Finally, described case studies demonstrate the successful identification of selective low molecular weight inhibitors for pharmacologically relevant drug targets through the SPR screening of fragment libraries.

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Custom chemical microarray production and affinity fingerprinting for the S1 pocket of factor VIIa

Cited by 32 publications

References 12 publications

Minimal Pharmacophoric Elements and Fragment Hopping, an Approach Directed at Molecular Diversity and Isozyme Selectivity. Design of Selective Neuronal Nitric Oxide Synthase Inhibitors

Minimal Pharmacophoric Elements and Fragment Hopping, an Approach Directed at Molecular Diversity and Isozyme Selectivity. Design of Selective Neuronal Nitric Oxide Synthase Inhibitors

Synthesis and Quality Control of Thiol Tagged Compound Libraries for Chemical Microarrays

SPR-based Fragment Screening: Advantages and Applications

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