Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

• Andreas Wiest and
• Pavel Kielkowski

Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199

• identification rates and may help to identify otherwise difficult to find interactions between active compounds and proteins, which may result from unperturbed conditions, and thus are of high physiological relevance. Keywords: chemical proteomics; diagnostic ions; mass spectrometry; target identification

Chemo-enzymatic total synthesis: current approaches toward the integration of chemical and enzymatic transformations

• Ryo Tanifuji and
• Hiroki Oguri

Beilstein J. Org. Chem. 2024, 20, 1693–1712, doi:10.3762/bjoc.20.151

• identify the corresponding enzymes. The developed "biosynthetic intermediate probe (BIP)-based target identification” method, a chemical pull-down approach for identifying the target enzymes, would be applied and expanded to the chemo-enzymatic synthesis of other natural products. In the total synthesis of

• chrysogenum. (B) Chemo-enzymatic total synthesis of 2 and bisorbicillinoids utilizing an FAD-dependent monooxygenase SorbC. (A) Proposed biosynthetic pathway for chalcomoracin (3) in Morus alba. (B) Outline of the biosynthetic intermediate probe (BIP)-based target identification strategy. (C) Chemo-enzymatic

• , these enzymes had not been discovered from Morus alba. In 2020, Lei and co-workers successfully identified two key enzymes in the biosynthesis of 3, MaMO (M. alba moracin C oxidase) and MaDA (M. alba Diels–Alderase), by developing a novel method termed “biosynthetic intermediate probe (BIP)-based target

Syntheses of spliceostatins and thailanstatins: a review

• William A. Donaldson

Beilstein J. Org. Chem. 2020, 16, 1991–2006, doi:10.3762/bjoc.16.166

• human spliceosome, splicing factor 3b [6], which inhibits pre-mRNA splicing, and as such act as potent cytotoxic compounds. A review of the discovery, target identification, and biological applications of the compounds that exhibit these binding characteristics has been published [7]. These compounds

Anthelmintic drug discovery: target identification, screening methods and the role of open science

• Frederick A. Partridge,
• Ruth Forman,
• Carole J. R. Bataille,
• Graham M. Wynne,
• Marina Nick,
• Angela J. Russell,
• Kathryn J. Else and
• David B. Sattelle

Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105

• both the target parasite and the genetic model organism, but the precise target remains unclear, then C. elegans genetics can offer a route to target identification that would be difficult by any other route. The C. elegans community: historically an open science model Research into C. elegans was

• historical examples illustrate the strength of open science in the C. elegans research tradition. In the following sections of this review we discuss how open science approaches continue to be important in the field of anthelmintic and antiparasitic drug discovery. Open approaches to target identification

• Genomic resources are important for target identification, particularly in the case of parasites, as the life stages found in the host are often difficult to obtain or culture, and few molecular tools are available. WormBase ParaSite [107] is an important central resource for helminth genomic data [108

Synthesis and SAR of the antistaphylococcal natural product nematophin from Xenorhabdus nematophila

• Frank Wesche,
• Hélène Adihou,
• Thomas A. Wichelhaus and
• Helge B. Bode

Beilstein J. Org. Chem. 2019, 15, 535–541, doi:10.3762/bjoc.15.47

• . Compounds 11 and 12 were separated during the isolation process and initially constructed to enable target identification. Compounds 11 and 12 might act as Michael acceptor (α,β-unsaturated carbonyl) and attach irreversibly and covalently to a potential target [23]. After purification and characterization

Tanzawaic acids I–L: Four new polyketides from Penicillium sp. IBWF104-06

• Louis P. Sandjo,
• Eckhard Thines,
• Till Opatz and
• Anja Schüffler

Beilstein J. Org. Chem. 2014, 10, 251–258, doi:10.3762/bjoc.10.20

• acid; Introduction Nature still represents the richest source of new antimicrobials which can be attractive as lead structures or biochemical tools for target identification for medical applications as well as for crop science. In both areas, the omnipresent development of resistance results in a

Design and synthesis of tag-free photoprobes for the identification of the molecular target for CCG-1423, a novel inhibitor of the Rho/MKL1/SRF signaling pathway

• Jessica L. Bell,
• Andrew J. Haak,
• Susan M. Wade,
• Yihan Sun,
• Richard R. Neubig and
• Scott D. Larsen

Beilstein J. Org. Chem. 2013, 9, 966–973, doi:10.3762/bjoc.9.111

• inhibitor; tag-free photoprobe; target identification; Findings Serum-induced signaling through Rho leads to gene-transcriptional effects, which are mediated by serum response factor (SRF), a MADS box transcription factor that binds to the serum response element (SRE) in the promoters of various immediate

• reaction, but photoactivatable groups (PGs) have also been used when this is not possible [22]. We envisioned adapting this technology to intracellular target identification as depicted in Figure 2. Whole cells would be incubated with a photoprobe (A) after confirmation of its biological activity

Synthesis and physicochemical characterization of novel phenotypic probes targeting the nuclear factor-kappa B signaling pathway

• Paul M. Hershberger,
• Satyamaheshwar Peddibhotla,
• E. Hampton Sessions,
• Daniela B. Divlianska,
• Ricardo G. Correa,
• Anthony B. Pinkerton,
• John C. Reed and
• Gregory P. Roth

Beilstein J. Org. Chem. 2013, 9, 900–907, doi:10.3762/bjoc.9.103

• efforts are ongoing to improve molecular potency and properties to make each chemical scaffold family suitable for advanced in vivo studies. Each probe represents a low-molecular-weight, “rule of 5” compliant starting point for target identification or lead optimization efforts. In screening the MLSMR