Diversity-oriented Fluorescence Library Approach Research Articles

Diversity‐Oriented Synthesis and Chemoinformatics: A Fruitful Synergy towards Better Chemical Libraries

AbstractIn these two decades, Diversity‐Oriented Synthesis (DOS) has changed significantly: from the historical focus on structural diversity, new approaches have been developed in order to increase the biological outcome of the molecules within the library, such as the privileged‐based DOS or the Diversity‐Oriented Fluorescence Library Approach (DOFLA). In this context, chemoinformatics can assist organic chemists in identifying biologically‐relevant regions of the chemical space not yet explored. Also, chemoinformatics tools can be used to graphically visualize and/or predict the structural diversity and complexity of the compounds within the library. This review highlights the improvement that DOS has received from chemoinformatics, presenting recent articles (published between 2016 and 2021) in which DOS libraries are analysed by chemoinformatics tools.

Holding-Oriented versus Gating-Oriented Live-Cell Distinction: Highlighting the Role of Transporters in Cell Imaging Probe Development.

Small molecule imaging probes are powerful tools to understand complex biological systems. The mainstreams of imaging probe developments have been focused on the target holding of the probes; the holding targets are often cell-type-specific biomarkers. This type of the probe mechanism can be designated as holding-oriented live-cell distinction (HOLD). Our group has worked on the development of cell-type-selective probes using a diversity-oriented fluorescence library approach (DOFLA), where unbiased phenotypic screening is employed using fluorescent library compounds. Through the conventional target identification methods such as an affinity-based analysis, we elucidated that some of the probe mechanisms are HOLD. However, we also realized that sometimes there is no specific holding target for probes or the holding targets are ubiquitous. The observation led us to test an alternative mechanism of cell-type-specific probes as gating-oriented live-cell distinction (GOLD). We started to examine the gating mechanism of probes, which is mainly based on transporters but which does not necessarily require probe holding to cellular targets. Transporters can control the in and out movement of various nutrients and chemicals. Different expression levels of transporters in various cell types could provide the molecular mechanism of differential staining of cells by regulating the intracellular accumulation of a certain specific probe. A number of GOLD probes have been developed by modifying or mimicking endogenous substrates of transporters such as inorganic ions, glucose, amino acids, or neurotransmitters, utilizing broad substrate specificity of transporters. The radiolabeled or fluorophore-conjugated substrate mimetics have been widely used for live cell distinction and various applications such as disease-related cell or tissue imaging. In humans, there are about 400 solute carrier (SLC) transporters and 50 ATP-binding cassette (ABC) transporters. Since some transporters have broad substrate specificity, they can transport not only derivatives of endogenous natural substrates but also totally synthetic diverse imaging probes, such as DOFLA probes. Without preconsidering the structure of endogenous substrates, we recently demonstrated a series of live-cell imaging probes and elucidated their molecular mechanism as a gating one, either by SLC or ABC transporters. Transporter inhibitor panel and CRISPR-based transporter libraries could provide a systematic gating target elucidation platform. Considering the generality of DOFLA and the CRISPR-based genomic tool for transporter systems (>450 in humans), the GOLD approach will offer new insight and promise for unprecedented levels of novel cell imaging probe development.

Young‐Tae Chang

Angewandte Chemie International EditionVolume 55, Issue 36 p. 10554-10554 Author ProfileFree Access Young-Tae Chang First published: 06 April 2016 https://doi.org/10.1002/anie.201602703AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Graphical Abstract “My favorite author (fiction) is Shiono Nanami. My favorite pieces of music are The Phantom of the Opera and Mozart's Requiem. ...” This and more about Young-Tae Chang can be found on page 10554. 1 Table 1. Young-Tae Chang Date of birth: August 17, 1968 Position: Professor, Department of Chemistry, National University of Singapore (NUS) E-mail: chmcyt@nus.edu.sg Homepage: http://ytchang.science.nus.edu.sg/ ORCID: 0000-0002-1927-3688 Education: 1991 BS, POSTECH 1997 PhD with Sung-Kee Chung, POSTECH 1997–2000 Postdoc with Peter G. Schultz, University of California, Berkeley, and The Scripps Research Institute Awards: 2005 NSF Career Award; 2012 Outstanding Scientist Award, Faculty of Science, NUS Current research interests: Universal platforms for bioimaging and sensing; artificial tongues; molecular evolution; molecular cellomics Hobbies: Korean drumming, photography, forensic science, history, Evernote My favorite author (fiction) is Shiono Nanami. My favorite pieces of music are The Phantom of the Opera and Mozart's Requiem. The most important thing I learned from my parents is be welcoming to the guests who come to my home. If I could have dinner with three famous scientists from history, they would be Albert Einstein, R. B. Woodward, and Archimedes. My not-so-secret passion is to make the invisible become visible. If I were not a scientist, I would be an oriental medical doctor working with acupuncture and natural products. My greatest achievement has been establishing the diversity-oriented fluorescence library approach (DOFLA) for universal probe and sensor development. My worst nightmare is going back to army camp. My biggest motivation is to help solve problems for anybody who seeks a solution. The best advice I have ever been given is “try to be excellent, not to be perfect”. My most exciting discovery to date has been creating a colorful fluorescent chemical library. The most significant scientific advance of the last 100 years has been the development of quantum mechanics. My 5 top papers: References 1“Synthesis and application of functionally diverse 2,6,9-trisubstituted purine libraries as CDK inhibitors”: Y.-T. Chang, N. Gray, G. R. Rosania, D. P. Sutherlin, S. Kwon, T. Norman, R. Sarohia, M. Leost, L. Meijer, P. G. Schultz, Chem. Biol. 1999, 6, 361. (Led to many follow-up works.) 2“Forward chemical genetic approach identifies new role for GAPDH in insulin signalling”: J.-K. Min, Y. K. Kim, P. G. Cipriani, M. Kang, S. M. Khersonsky, D. P. Walsh, J.-Y. Lee, S. Niessen, J. R. Yates, K. Gunsalus, F. Piano, Y.-T. Chang, Nat. Chem. Biol. 2007, 3, 55. (Tagged library for chemical genetics in order to elucidate a drug candidate for diabetic treatment by using C. elegans screening.) 3“A Fluorescent Rosamine Compound Selectively Stains Pluripotent Stem Cells”: C.-N. Im et al., Angew. Chem. Int. Ed. 2010, 49, 7497; Angew. Chem. 2010, 122, 7659. (Stem cells can selectively be detected and isolated for culture.) 4“Chemical Fluorescent Probe for Detection of Aβ Oligomers”: C. L. Teoh et al., J. Am. Chem. Soc. 2015, 137, 13503. (Not only plaques but also Aβ oligomers can be selectively stained.) 5“NeuO: a Fluorescent Chemical Probe for Live Neuron Labeling”: J. C. Er et al., Angew. Chem. Int. Ed. 2015, 54, 2442; Angew. Chem. 2015, 127, 2472. (Live neurons can be brightly imaged in the whole body of a mouse.) Volume55, Issue36August 26, 2016Pages 10554-10554 ReferencesRelatedInformation

Diversity Oriented Fluorescence Library Approach (DOFLA) for Live Cell Imaging Probe Development

A cell is the smallest functional unit of life. All forms of life rely on cellular processes to maintain normal functions, and changes in cell function induced by metabolic disturbances, physicochemical damage, infection, or abnormal gene expression may cause disease. To understand basic biology and to develop therapeutics for diseases, researchers need to study live cells. Along with advances in fluorescence microscopy and in vitro cell culture, live-cell imaging has become an essential tool in modern biology for the study of molecular and cellular events. Although researchers have often used fluorescent proteins to visualize cell-type-specific markers, this method requires genetic manipulations, which may not be appropriate in nontransgenic cells. Immunodetection of cellular markers requires the use of xenogenic antibodies, which may not detect intracellular markers in live cells. One option for overcoming these problems is the use of fluorescent small molecules targeted to specific cell types, which can enter live cells and interact with molecules of interest. We have used combinatorial chemistry to develop a large number of fluorescent small molecules as new imaging probes even without prior information about the probes' binding targets and mechanism, a strategy that we call the diversity oriented fluorescence library approach (DOFLA). We have used DOFLA to produce novel sensors and probes that detect a variety of biological and chemical molecules in vivo as well as in vitro. In this Account, we describe a series of fluorescent small molecules developed using DOFLA that bind specifically to particular cell types. These molecules provide new ways to detect and isolate these cells. The fluorescent probes CDy1, CDg4, and CDb8 tag embryonic stem cells and induced pluripotent stem cells but not fibroblasts or germ-line cells. CDr3 binds to an intracellular neural stem cell marker, fatty acid binding protein 7, which allows researchers to separate neural stem cells from embryonic stems cells and more differentiated cells such as neurons and glia. In addition, we have developed CDr10, which distinguishes microglia from neurons and glia. CDy2 stains myocytes much more brightly than myoblasts because of the increase in mitochondrial membrane potential during myogenesis. GY and PiY selectively stain α and β cells of pancreatic islets, respectively. Histamine Blue binds directly to histamine and stains basophils and macrophages containing high quantities of histamine. Glutathione Green allows researchers to measure the level of glutathione in cells and tissues by binding to glutathione and then triggering a hypsochromic shift. We have also developed a set of compounds that bind to cancer cells based on the cell type of origin and biocompatible surface-enhanced Raman spectroscopy (SERS) nanotags for cancer detection. In addition to discussing these new probes and their cell-type specificity, we also describe their applications in new assays, cell characterization, and pathology studies.

The Binding of Fluorophores to Proteins Depends on the Cellular Environment

The Binding of Fluorophores to Proteins Depends on the Cellular Environment

Quantitative Structure-Fluorescence Property Relationship Analysis of a Large BODIPY Library.

A quantitative structure-fluorescence property relationship (QSPR) analysis of a large 288-membered library based on a single fluorescent BODIPY scaffold is presented for the first time. BODIPY is a versatile fluorescent scaffold with outstanding photophysical properties. Absorption (λabs ) and fluorescence emission (λem ) wavelength maxima were modeled with help of stepwise multiple linear regression (MLR) and support vector regression (SVR). The models were rigorously validated by 10-times 10-fold cross-validation (CV), y-scrambling CV and with an external validation set. Non-linear SVR models (R(2) =0.92 and Q(2) =0.71 for λabs ; R(2) =0.89 and Q(2) =0.69 for λem ) performed significantly better than linear models. A small root mean squared error (RMSE) of 5.62 nm and 11.07 nm was achieved for λabs and λem , respectively, and confirmed by external validation. A novel intramolecular charge transfer descriptor was developed based on the QSPR analysis and its inclusion in the modeling significantly improved models of λem . We conclude that QSPR is a useful tool for modeling λabs and λem of BODIPY fluorophores and suggest QSPR as an ideal partner for the design of compounds with tailored fluorescence properties in a diversity-oriented fluorescence library approach (DOFLA).

Diversity-oriented fluorescence library approach for the discovery of sensors and probes

Fluorescent small molecules have received considerable attention due to their potential for chemosensing and bioimaging. A conventional strategy for probe development is a target-oriented approach based on known molecular recognition mechanisms for individual analytes. However, sophisticated rational design does not always guarantee the applicability of probes in complex biological systems. Therefore the speed and the scope of sensor development has been limited. To overcome these limitations, diversity-oriented fluorescence library approaches have been applied to develop new fluorescent probes in the absence of knowledge about the target recognition mechanism. This review summarizes recent advances in fluorescent probe development facilitated by diversity-oriented library approaches.

Diversity-Oriented Fluorescence Library Approach (DOFLA) to the Discovery of Chymotrypsin Sensor

The diversity-oriented fluorescence library approach (DOFLA) has emerged and found applications in various fields to meet the acute demands for novel fluorescence sensors. The power of this approach has been demonstrated with the impressive discoveries of novel sensors for polymers such as DNA and heparin or for small molecules such as GTP and glutathione ( J. Am. Chem. Soc. 2003, 125, 1130- 1131 ; J. Am. Chem. Soc. 2006, 128, 10380- 10381 ; J. Am. Chem. Soc. 2007, 129, 4510- 4511 ; Chem. Commun. [Online early access]. DOI: 10.1039/b717058k. Published online Dec 11, 2008. http://www.rsc.org/publishing/journals/CC/article.asp?doi=b717058k ). Herein we report the application of this approach on quinaldinium fluorescent dye library synthesis on solid support and novel chymotrypsin sensor discovery. The new sensors are not only selective to chymotrypsin over other proteins but also only to the active conformation of chymotrypsin.

Discovery of heparin chemosensors through diversity oriented fluorescence library approach

Two novel heparin sensors, Heparin Orange and Heparin Blue, were developed by a diversity oriented fluorescence library approach (DOFLA) from a benzimidazolium library; the discovered compounds showed remarkable properties and have the potential to be applied to monitoring heparin levels in clinical plasma samples for point-of-care detection.