AACR Centennial Conference: Translational Cancer Medicine-- Nov 4-8, 2007; Singapore

PL02-05 

All cancers are due to abnormalities in DNA. The availability of the human genome sequence has led to the proposal that resequencing of cancer genomes will reveal the full complement of somatic mutations and hence all the cancer genes. To explore the nature of the information that will be derived from cancer genome sequencing we have sequenced the coding exons of the family of 518 protein kinases, ~1.3Mb DNA per cancer sample, in 210 cancers of diverse histological types. Despite the screen being directed toward the coding regions of a gene family that has previously been strongly implicated in oncogenesis, the results indicate that the majority of somatic mutations detected are “passengers”. There is considerable variation in the number and pattern of these mutations between individual cancers, indicating substantial diversity of processes of molecular evolution between cancers. The imprints of exogenous mutagenic exposures, mutagenic treatment regimes and DNA repair defects can all be seen in the distinctive mutational signatures of individual cancers. This systematic mutation screen and others have previously yielded a number of cancer genes that are frequently mutated in one or more cancer types and which are now anticancer drug targets (for example BRAF , PIK3CA , and EGFR ). However, detailed analyses of the data from our screen additionally suggest that there exist a large number of additional “driver” mutations which are distributed across a substantial number of genes. It therefore appears that cells may be able to utilise mutations in a large repertoire of potential cancer genes to acquire the neoplastic phenotype. However, many of these genes are employed only infrequently. These findings may have implications for future anticancer drug development.

Patterns of Somatic Mutation in Human Cancer Genomes

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Metal–Organic Frameworks and Self-Assembled Supramolecular Coordination Complexes: Comparing and Contrasting the Design, Synthesis, and Functionality of Metal–Organic Materials

Design strategies for water-soluble small molecular chromogenic and fluorogenic probes.

Applications of Supramolecular Anion Recognition

Coumarins are a very large family of compounds containing the unique 2H-chromen-2-one motif, as it is known according to IUPAC nomenclature. Coumarin derivatives are widely found in nature, especially in plants and are constituents of several essential oils. Up to now, thousands of coumarin derivatives have been isolated from nature or produced by chemists. More recently, the coumarin platform has been widely adopted in the design of small-molecule fluorescent chemosensors because of its excellent biocompatibility, strong and stable fluorescence emission, and good structural flexibility. This scaffold has found wide applications in the development of fluorescent chemosensors in the fields of molecular recognition, molecular imaging, bioorganic chemistry, analytical chemistry, materials chemistry, as well as in the biology and medical science communities. This review focuses on the important progress of coumarin-based small-molecule fluorescent chemosensors during the period of 2012-2018. This comprehensive and critical review may facilitate the development of more powerful fluorescent chemosensors for broad and exciting applications in the future.

Coumarin-Based Small-Molecule Fluorescent Chemosensors.

Artificial Receptors for the Recognition of Phosphorylated Molecules Amanda E. Hargrove, Sonia Nieto, Tianzhi Zhang, Jonathan L. Sessler,* and Eric V. Anslyn* Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712-0165, United States Universidad de Zaragoza, Zaragoza, Spain Henkel Corporation, Rocky Hill, Connecticut 06067 Department of Chemistry, Yonsei University, Seoul, 120-749 Korea

/pdf/artificial-receptors-for-the-recognition-of-phosphorylated-1mwlr6bjuc.pdf

Artificial receptors for the recognition of phosphorylated molecules

The determination of binding constants is central to many areas of research, supramolecular chemistry in particular. Traditional nonlinear regression analysis, however, cannot be applied to complex systems unless certain assumptions are undertaken, which often limits the reliability of such calculations. Our group has developed an iterative method using commercial software that allows for the rigorous determination of binding constants in a variety of systems, including 1 : 2 complexes, indicator displacement assays, and enantioselective indicator displacement assays. The improved accuracy of the values obtained in the latter case, in turn, allows for a more precise determination of ee in competitive equilibria.

Algorithms for the determination of binding constants and enantiomeric excess in complex host : guest equilibria using optical measurements

This work investigates the interplay between the intramolecular B-N dative bonding and solvent insertion in various ortho-methylamino arylboronic acids in protic media. (11)B NMR experiments were conducted to study the effect that the degree of substitution of the amine group has on B-N bonding versus solvent insertion. It was found that there is a slight increase in the amount of B-N dative bonding on going from a tertiary to a secondary to a primary amine group, but that solvent insertion dominates in all cases of the boronate esters. A X-ray crystal structure gives further insight into the structure of the solvent-inserted boronate esters, showing that the inserted solvent has its hydrogen primarily on the amine. Lastly, studies of the use of boronate esters as receptors for simple alcohols and carboxylic acids are described.

Probing intramolecular B-N interactions in ortho-aminomethyl arylboronic acids.

The recognition of RNA functions beyond canonical protein synthesis has challenged the central dogma of molecular biology. Indeed, RNA is now known to directly regulate many important cellular processes, including transcription, splicing, translation, and epigenetic modifications. The misregulation of these processes in disease has led to an appreciation of RNA as a therapeutic target. This potential was first recognized in bacteria and viruses, but discoveries of new RNA classes following the sequencing of the human genome have invigorated exploration of its disease-related functions in mammals. As stable structure formation is evolving as a hallmark of mammalian RNAs, the prospect of utilizing small molecules to specifically probe the function of RNA structural domains and their interactions is gaining increased recognition. To date, researchers have discovered bioactive small molecules that modulate phenotypes by binding to expanded repeats, microRNAs, G-quadruplex structures, and RNA splice sites in neurological disorders, cancers, and other diseases. The lessons learned from achieving these successes both call for additional studies and encourage exploration of the plethora of mammalian RNAs whose precise mechanisms of action remain to be elucidated. Efforts toward understanding fundamental principles of small molecule-RNA recognition combined with advances in methodology development should pave the way toward targeting emerging RNA classes such as long noncoding RNAs. Together, these endeavors can unlock the full potential of small molecule-based probing of RNA-regulated processes and enable us to discover new biology and underexplored avenues for therapeutic intervention in human disease. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease.

Targeting RNA in mammalian systems with small molecules.

Recent advances in our understanding of RNA biology have uncovered crucial roles for RNA in multiple disease states, ranging from viral and bacterial infections to cancer and neurological disorders. As a result, multiple laboratories have become interested in developing drug-like small molecules to target RNA. However, this development comes with multiple unique challenges. For example, RNA is inherently dynamic and has limited chemical diversity. In addition, promiscuous RNA-binding ligands are often identified during screening campaigns. This Tutorial Review overviews important considerations and advancements for generating RNA-targeted small molecules, ranging from fundamental chemistry to promising small molecule examples with demonstrated clinical efficacy. Specifically, we begin by exploring RNA functional classes, structural hierarchy, and dynamics. We then discuss fundamental RNA recognition principles along with methods for small molecule screening and RNA structure determination. Finally, we review unique challenges and emerging solutions from both the RNA and small molecule perspectives for generating RNA-targeted ligands before highlighting a selection of the "Greatest Hits" to date. These molecules target RNA in a variety of diseases, including cancer, neurodegeneration, and viral infection, in cellular and animal model systems. Additionally, we explore the recently FDA-approved small molecule regulator of RNA splicing, risdiplam, for treatment of spinal muscular atrophy. Together, this Tutorial Review showcases the fundamental role of chemical and molecular recognition principles in enhancing our understanding of RNA biology and contributing to the rapidly growing number of RNA-targeted probes and therapeutics. In particular, we hope this widely accessible review will serve as inspiration for aspiring small molecule and/or RNA researchers.

Amanda E. Hargrove

Papers

Artificial receptors for the recognition of phosphorylated molecules

Algorithms for the determination of binding constants and enantiomeric excess in complex host : guest equilibria using optical measurements

Probing intramolecular B-N interactions in ortho-aminomethyl arylboronic acids.

Targeting RNA in mammalian systems with small molecules.

Targeting RNA with small molecules: from fundamental principles towards the clinic