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Investigation of a Privileged Polymorphic Motif: a Dimeric ROY Derivative.

ABSTRACT: Bis(5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrilyl)acetylene, a derivative of the highly polymorphic compound 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY) that possesses two chromophores electronically coupled through a triple bond, was found to be trimorphic. Structural data for two of these forms indicates that symmetry is maintained in one structure and broken in the other leading to spontaneous differentiation of the methyl-thiophenecarbonitrile units. This study contributes to the mounting evidence that ROY and its derivatives are particularly prone to polymorphism.

SUBMITTER: Lutker KM

PROVIDER: S-EPMC2668532 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Investigation of a Privileged Polymorphic Motif: a Dimeric ROY Derivative.

Lutker Katie M KM Tolstyka Zachary P ZP Matzger Adam J AJ

Crystal growth & design 20080101 1

Bis(5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrilyl)acetylene, a derivative of the highly polymorphic compound 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY) that possesses two chromophores electronically coupled through a triple bond, was found to be trimorphic. Structural data for two of these forms indicates that symmetry is maintained in one structure and broken in the other leading to spontaneous differentiation of the methyl-thiophenecarbonitrile units. This stu ...[more]

PMID: 19367341

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Project description:RNAs have diverse structures that are important for biological function. These structures include bulges and internal loops that can form tertiary contacts or serve as ligand binding sites. The most commonly exploited RNA drug target for small molecule intervention is the bacterial ribosome, more specifically the rRNA aminoacyl-tRNA site (rRNA A-site) which is a major target for the aminoglycoside class of antibiotics. The bacterial A-site is composed of a 1 x 1 nucleotide all-U internal loop and a 2 x 1 nucleotide all-A internal loop separated by a single GC base pair. Therefore, we probed the molecular recognition of a small library of four aminoglycosides for binding a 16384-member bacterial rRNA A-site-like internal loop library using two-dimensional combinatorial screening (2DCS). 2DCS is a microarray-based method that probes RNA and chemical spaces simultaneously. These studies sought to determine if aminoglycosides select their therapeutic target if given a choice of binding all possible internal loops derived from an A-site-like library. Results show that the bacterial rRNA A-site was not selected by any aminoglycoside. Analyses of selected sequences using the RNA Privileged Space Predictor (RNA-PSP) program show that each aminoglycoside preferentially binds different types of internal loops. For three of the aminoglycosides, 6''-azido-kanamycin A, 5-O-(2-azidoethyl)-neamine, and 6''-azido-tobramycin, the selected internal loops bind with approximately 10-fold higher affinity than the bacterial rRNA A-site. The internal loops selected to bind 5''-azido-neomycin B bind with an affinity similar to that of the therapeutic target. Selected internal loops that are unique for each aminoglycoside have dissociation constants ranging from 25 to 270 nM and are specific for the aminoglycoside they was selected to bind compared to the other arrayed aminoglycosides. These studies further establish a database of RNA motifs that are recognized by small molecules that could be used to enable the rational and modular design of small molecules targeting RNA.

Dataset Information

Investigation of a Privileged Polymorphic Motif: a Dimeric ROY Derivative.

Publications

Investigation of a Privileged Polymorphic Motif: a Dimeric ROY Derivative.

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