Chemical probes for optical bio-imaging (Conference Presentation)

Author(s):  
Lu Wei
Keyword(s):  
2020 ◽  
Author(s):  
Luke Adams ◽  
Lorna E. Wilkinson-White ◽  
Menachem J. Gunzburg ◽  
Stephen J. Headey ◽  
Martin J. Scanlon ◽  
...  

The development of low-affinity fragment hits into higher affinity leads is a major hurdle in fragment-based drug design. Here we demonstrate an approach for the Rapid Elaboration of Fragments into Leads (REFiL) applying an integrated workflow that provides a systematic approach to generate higher-affinity binders without the need for structural information. The workflow involves the selection of commercial analogues of fragment hits to generate preliminary structure-activity relationships. This is followed by parallel microscale chemistry using chemoinformatically designed reagent libraries to rapidly explore chemical diversity. Upon completion of a fragment screen against Bromodomain-3 extra terminal (BRD3-ET) domain we applied the REFiL workflow, which allowed us to develop a series of tetrahydrocarbazole ligands that bind to the peptide binding site of BRD3-ET. With REFiL we were able to rapidly improve binding affinity >30-fold. The REFiL workflow can be applied readily to a broad range of protein targets without the need of a structure, allowing the efficient evolution of low-affinity fragments into higher affinity leads and chemical probes.<br>


2019 ◽  
Author(s):  
Michael Olp ◽  
Daniel Sprague ◽  
Stefan Kathman ◽  
Ziyang Xu ◽  
Alexandar Statsyuk ◽  
...  

<p>Brd4, a member of the bromodomain and extraterminal domain (BET) family, has emerged as a promising epigenetic target in cancer and inflammatory disorders. All reported BET family ligands bind within the bromodomain acetyl-lysine binding sites and competitively inhibit BET protein interaction with acetylated chromatin. Alternative chemical probes that act orthogonally to the highly-conserved acetyl-lysine binding sites may exhibit selectivity within the BET family and avoid recently reported toxicity in clinical trials of BET bromodomain inhibitors. Here, we report the first identification of a ligandable site on a bromodomain outside the acetyl-lysine binding site. Inspired by our computational prediction of hotspots adjacent to non-homologous cysteine residues within the <i>C</i>-terminal Brd4 bromodomain (Brd4-BD2), we performed a mid-throughput mass spectrometry screen to identify cysteine-reactive fragments that covalently and selectively modify Brd4. Subsequent mass spectrometry, NMR and computational docking analyses of electrophilic fragment hits revealed a novel ligandable site near Cys356 that is unique to Brd4 among all human bromodomains. This site is orthogonal to the Brd4-BD2 acetyl-lysine binding site as Cys356 modification did not impact binding of the pan-BET bromodomain inhibitor JQ1 in fluorescence polarization assays. Finally, we tethered covalent fragments to JQ1 and performed NanoBRET assays to provide proof of principle that this orthogonal site can be covalently targeted in intact human cells. Overall, we demonstrate the potential of targeting sites orthogonal to bromodomain acetyl-lysine binding sites to develop bivalent and covalent inhibitors that displace Brd4 from chromatin.</p>


2020 ◽  
Vol 17 ◽  
Author(s):  
Ahmed Nuri Kursunlu ◽  
Elif Bastug ◽  
Ersin Guler

Background: Chemosensor compounds are useful for sensitive selective detection of cations and anions with fluorophore groups in an attempt to develop the effective selectivity of the sensors. Although familiar fluorescent sensors utilizing inter-molecular interactions with the cations and anions, an extraordinary endeavor was executed the preparation of fluorescent-based sensor compounds. 4,4-difluoro-4- bora-3a,4a-diaza-s-indacene (Bodipy) and its derivatives were firstly used as an agent in the imaging of biomolecules due to their interesting structures, complexation, and fluorogenic properties. Among the fluorescent chemosensors used for cations and anions, Bodipy-based probes stand out owing to the excellent properties such as sharp emission profile, high stability, etc. In this review, we emphasize the Bodipy-based chemosensor compounds, which have been used to image cations and anions in living cells, because of as well as the biocompatibility and spectroscopic properties. Methods: Research and online content related to chemosensor online activity is reviewed. The advances, sensing mechanisms and design strategies of the fluorophore exploiting selective detection of some cation and anions with Bodipy-based chemosensors are explained. It could be claimed that the using of Bodipy-based chemosensors is very important for cations and anions in bio-imaging applications. Results: Molecular sensors or chemosensors are molecules that show a change can be detected when affected by the analyte. They are capable of producing a measurable signal when they are selective for a particular molecule. Molecular and ion recognition that it is important in biological systems such as enzymes, genes, environment, and chemical fields. Due to the toxic properties of many heavy metal ions, it is of great importance to identify these metals due to their harmful effects on living metabolism and the pollution they create in the environment. This process can be performed with analytical methods based on atomic absorption and emission. The fluorescence methods among chemosensor systems have many advantages such as sensitivity, selectivity, low price, simplicity of using the instrument and direct determination in solutions. The fluorescence studies can be applied at nanomolar concentrations. Conclusion: During a few decades, a lot of Bodipy-based chemosensors for the detection of cations & anions have been investigated in bio-imaging applications. For the Bodipy-based fluorescent chemosensors, the Bodipy derivatives were prepared by different ligand groups for the illumination of the photophysical and photochemical properties. The synthesized Bodipy-based chemosensors have remarkable photophysical properties, such as a high quantum yield, strong molar absorption coefficient etc. Moreover, these chemosensors were successfully implemented on living organisms for the detection of analytes.


2019 ◽  
Vol 14 (2) ◽  
pp. 93-116 ◽  
Author(s):  
Shabnam Mohebbi ◽  
Mojtaba Nasiri Nezhad ◽  
Payam Zarrintaj ◽  
Seyed Hassan Jafari ◽  
Saman Seyed Gholizadeh ◽  
...  

Biomedical engineering seeks to enhance the quality of life by developing advanced materials and technologies. Chitosan-based biomaterials have attracted significant attention because of having unique chemical structures with desired biocompatibility and biodegradability, which play different roles in membranes, sponges and scaffolds, along with promising biological properties such as biocompatibility, biodegradability and non-toxicity. Therefore, chitosan derivatives have been widely used in a vast variety of uses, chiefly pharmaceuticals and biomedical engineering. It is attempted here to draw a comprehensive overview of chitosan emerging applications in medicine, tissue engineering, drug delivery, gene therapy, cancer therapy, ophthalmology, dentistry, bio-imaging, bio-sensing and diagnosis. The use of Stem Cells (SCs) has given an interesting feature to the use of chitosan so that regenerative medicine and therapeutic methods have benefited from chitosan-based platforms. Plenty of the most recent discussions with stimulating ideas in this field are covered that could hopefully serve as hints for more developed works in biomedical engineering.


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