Target identification of natural products and bioactive compounds using affinity-based probes

2016 ◽  
Vol 33 (5) ◽  
pp. 612-620 ◽  
Author(s):  
Sijun Pan ◽  
Hailong Zhang ◽  
Chenyu Wang ◽  
Samantha C. L. Yao ◽  
Shao Q. Yao

Direct capture of drug–target complexesin situby using affinity-based probes allows target identification of natural products and bioactive compounds, even if the binding is reversible with moderate affinity.

2020 ◽  
Vol 74 (7) ◽  
pp. 577-583 ◽  
Author(s):  
Mikiko Okumura ◽  
David Sarlah

Aromatic compounds are one of the most abundant classes of organic molecules and find utility as precursors for alicyclic hydrocarbon building blocks. While many established dearomatization reactions are exceptionally powerful, dearomatization with concurrent introduction of functionality, i.e. dearomative functionalization, is still a largely underdeveloped field. This review aims to provide an overview of our recent efforts and progress in the development of dearomative functionalization of simple and nonactivated arenes using arenophile-arene cycloaddition platform. These cycloadducts, formed via a visible-light-mediated [4+2]-photocycloaddition, can be elaborated in situ through olefin chemistry or transition-metal-catalyzed ring-opening with carbon-, nitrogen-, and oxygen-based nucleophiles, providing access to diverse structures with functional and stereochemical complexity. Moreover, the dearomatized products are amenable to further elaborations, which effectively install other functionalities onto the resulting alicyclic carbocycles. The utility of the arenophile-mediated dearomatization methods are also highlighted by the facile syntheses of natural products and bioactive compounds through novel disconnections.


RSC Advances ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 2453-2461
Author(s):  
Min-Che Tung ◽  
Keng-Chang Tsai ◽  
Kit-Man Fung ◽  
Ming-Jaw Don ◽  
Tien-Sheng Tseng

The cytosolic non-receptor protein kinase, spleen tyrosine kinase (SYK), is an attractive drug target in autoimmune, inflammatory disorder, and cancers indications.


Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 1898
Author(s):  
Fauzia Izzati ◽  
Mega Ferdina Warsito ◽  
Asep Bayu ◽  
Anggia Prasetyoputri ◽  
Akhirta Atikana ◽  
...  

Marine invertebrates have been reported to be an excellent resource of many novel bioactive compounds. Studies reported that Indonesia has remarkable yet underexplored marine natural products, with a high chemical diversity and a broad spectrum of biological activities. This review discusses recent updates on the exploration of marine natural products from Indonesian marine invertebrates (i.e., sponges, tunicates, and soft corals) throughout 2007–2020. This paper summarizes the structural diversity and biological function of the bioactive compounds isolated from Indonesian marine invertebrates as antimicrobial, antifungal, anticancer, and antiviral, while also presenting the opportunity for further investigation of novel compounds derived from Indonesian marine invertebrates.


2021 ◽  
Vol 22 (10) ◽  
pp. 5118
Author(s):  
Matthieu Najm ◽  
Chloé-Agathe Azencott ◽  
Benoit Playe ◽  
Véronique Stoven

Identification of the protein targets of hit molecules is essential in the drug discovery process. Target prediction with machine learning algorithms can help accelerate this search, limiting the number of required experiments. However, Drug-Target Interactions databases used for training present high statistical bias, leading to a high number of false positives, thus increasing time and cost of experimental validation campaigns. To minimize the number of false positives among predicted targets, we propose a new scheme for choosing negative examples, so that each protein and each drug appears an equal number of times in positive and negative examples. We artificially reproduce the process of target identification for three specific drugs, and more globally for 200 approved drugs. For the detailed three drug examples, and for the larger set of 200 drugs, training with the proposed scheme for the choice of negative examples improved target prediction results: the average number of false positives among the top ranked predicted targets decreased, and overall, the rank of the true targets was improved.Our method corrects databases’ statistical bias and reduces the number of false positive predictions, and therefore the number of useless experiments potentially undertaken.


2021 ◽  
Author(s):  
Rasel Al-Amin ◽  
Lars Johansson ◽  
Eldar Abdurakhmanov ◽  
Nils Landegren ◽  
Liza Löf ◽  
...  

Abstract Drugs are designed to bind their target proteins in physiologically relevant tissues and organs to modulate biological functions and elicit desirable clinical outcomes. Information about target engagement at cellular and subcellular resolution is therefore critical for guiding compound optimization in drug discovery, and for probing resistance mechanisms to targeted therapies in clinical samples. We describe a target engagement-mediated amplification (TEMA) technology, where oligonucleotide-conjugated drugs are used to visualize and measure target engagement in situ, amplified via rolling-circle replication of circularized oligonucleotide probes. We illustrate the TEMA technique using dasatinib and gefitinib, two kinase inhibitors with distinct selectivity profiles. In vitro binding by dasatinib probe to arrays of displayed proteins accurately reproduced known selectivity profiles, while their differential binding to a panel of fixed adherent cells agreed with expectations from expression profiles of the cells. These findings were corroborated by competition experiments using kinase inhibitors with overlapping and non-overlapping target specificities, and translated to pathology tissue sections. We also introduce a proximity ligation variant of TEMA in which these drug-DNA conjugates are combined with antibody-DNA conjugates to selectively investigate binding to specific target proteins of interest. This form of the assay serves to improve resolution of binding to on- and off-target proteins. In conclusion, TEMA has the potential to aid in drug development and clinical routine by conferring valuable insights in drug-target interactions at spatial resolution in protein arrays, cells and tissues.


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