Recent advances in synthetic approaches for bioactive cinnamic acid derivatives

• Betty A. Kustiana,
• Galuh Widiyarti and
• Teni Ernawati

Beilstein J. Org. Chem. 2025, 21, 1031–1086, doi:10.3762/bjoc.21.85

• (TXA2) synthetase inhibition [10], antinociceptive [11], histone deacetylase inhibition [12], α-glucosidase inhibition [13] , tyrosinase inhibition [14], allelochemical [15], anticonvulsant [16], antioxidant [17], antiplatelet aggregation [18], anti-inflammatory [19], and UV absorption [20]. Cinnamic

Origami with small molecules: exploiting the C–F bond as a conformational tool

• Patrick Ryan,
• Ramsha Iftikhar and
• Luke Hunter

Beilstein J. Org. Chem. 2025, 21, 680–716, doi:10.3762/bjoc.21.54

• motif has been exploited in the design of bioactive molecules [22][23] such as the histone deacetylase (HDAC) inhibitors 6 and 7 (Figure 2). The presence of the 1,2-difluoro moiety in 6 leads to greater potency and selectivity for certain HDAC isoforms, attributable to the higher polarity of the

Multicomponent reactions driving the discovery and optimization of agents targeting central nervous system pathologies

• Lucía Campos-Prieto,
• Aitor García-Rey,
• Eddy Sotelo and
• Ana Mallo-Abreu

Beilstein J. Org. Chem. 2024, 20, 3151–3173, doi:10.3762/bjoc.20.261

• compounds with high yields (84–92%). The three most promising compounds of the library (13a, 13b, and 13c) were selected for further detailed characterization. In vitro evaluation was performed employing a high-performance liquid chromatography (HPLC)-based methodology, using the fluorogenic histone

Recent advances in transition-metal-free arylation reactions involving hypervalent iodine salts

• Ritu Mamgain,
• Kokila Sakthivel and
• Fateh V. Singh

Beilstein J. Org. Chem. 2024, 20, 2891–2920, doi:10.3762/bjoc.20.243

• ) [91]. This method manifests the synthesis of stable thioether-linked synthetic conjugates 93 and 96 displaying its efficacy via the alteration of the affibody zEGFR and the histone protein H2A. The procedure involved synthesizing the diaryliodonium salt and appraising the proficiency of oxime ligation

• chemistry on the histone H2A protein. The protein was demonstrated as the T120C mutant via site-directed mutagenesis in Escherichia coli and decontaminated by HPLC. A notable reconciliation was changing the aqueous buffer from HEPES to phosphate owing to side-product generation during the arylation in HEPES

• protein conjugate was effectively done with various hydroxylamines with the assistance of the nucleophilic catalyst 5-methoxyanthranilic acid. The resultant histone protein conjugates were functionalized with TAMRA, biotin and the cell-penetrating peptide 'penetratin' through oxime ligation, achieving

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

Chemical and biosynthetic potential of Penicillium shentong XL-F41

• Ran Zou,
• Xin Li,
• Xiaochen Chen,
• Yue-Wei Guo and
• Baofu Xu

Beilstein J. Org. Chem. 2024, 20, 597–606, doi:10.3762/bjoc.20.52

• activate the BGCs of this strain, we employed a combination of elicitors in our fermentation media, including histone deacetylase inhibitors and DNA methyltransferase inhibitors. We developed two specialized media, XISR I and XISR III, which outperformed the traditional potato dextrose broth (PDB) in

One-pot double annulations to confer diastereoselective spirooxindolepyrrolothiazoles

• Juan Lu,
• Bin Yao,
• Desheng Zhan,
• Zhuo Sun,
• Yun Ji and
• Xiaofeng Zhang

Beilstein J. Org. Chem. 2022, 18, 1607–1616, doi:10.3762/bjoc.18.171

• UMB32 and UMB136 [33][34]. Zhang developed 4-aminoquinolines for the synthesis of fluorinated analogues of acetylcholinesterase (AChE) inhibitors [35] in cascade reactions, such as one-step syntheses of quinolines. Quinolin-4-ols involving histone acetyltransferases (HAT) inhibitors [36][37], as well as

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• -3-3ζ homodimer [14]. Very recently the survivin–histone H3 interaction was disrupted using a GCP dimer, which led to decreased cancer cell proliferation [8]. A major problem in this context is the readout of binding events, which is currently mainly achieved by indirect measurements. One approach to

Synthesis and HDAC inhibitory activity of pyrimidine-based hydroxamic acids

• Virginija Jakubkiene,
• Gabrielius Ernis Valiulis,
• Markus Schweipert,
• Asta Zubriene,
• Daumantas Matulis,
• Franz-Josef Meyer-Almes and
• Sigitas Tumkevicius

Beilstein J. Org. Chem. 2022, 18, 837–844, doi:10.3762/bjoc.18.84

• Engineering and Biotechnology, University of Applied Sciences, Stephanstr. 7, 64295 Darmstadt, Germany Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257 Vilnius, Lithuania 10.3762/bjoc.18.84 Abstract Histone deacetylases

• (HDACs) play an essential role in the transcriptional regulation of cells through the deacetylation of nuclear histone and non-histone proteins and are promising therapeutic targets for the treatment of various diseases. Here, the synthesis of new compounds in which a hydroxamic acid residue is attached

• both the HDAC4 and HDAC8 isoforms, with an IC50 of 16.6 µM and 1.2 µM, respectively. Keywords: alkylation; aminolysis; HDAC inhibitors; hydroxamic acid; pyrimidine; Introduction Histone deacetylases (HDACs) are a family of intracellular proteins responsible for removing acetyl groups in histones

Synthesis of bis-spirocyclic derivatives of 3-azabicyclo[3.1.0]hexane via cyclopropene cycloadditions to the stable azomethine ylide derived from Ruhemann's purple

• Alexander S. Filatov,
• Olesya V. Khoroshilova,
• Anna G. Larina,
• Vitali M. Boitsov and
• Alexander V. Stepakov

Beilstein J. Org. Chem. 2022, 18, 769–780, doi:10.3762/bjoc.18.77

• found in natural compounds [9][10][11]. It is used in pharmaceuticals [12][13][14][15] and key intermediates [16][17]. Compounds containing a 3-azabicyclo[3.1.0]hexane moiety are antagonists of morphine-induced antinociception [18], histone deacetylase inhibitors [13], and opioid receptor antagonists

Synthesis and late stage modifications of Cyl derivatives

• Phil Servatius and
• Uli Kazmaier

Beilstein J. Org. Chem. 2022, 18, 174–181, doi:10.3762/bjoc.18.19

• direct access to cyclopeptides related to naturally occurring histone deacetylase (HDAC) inhibitors Cyl-1 and Cyl-2. Late stage modifications on the unsaturated amino acid side chain allow the introduction of functionalities which might coordinate to metal ions in the active center of metalloproteins

• , such as histone deacetylases. Keywords: chelated enolate; Claisen rearrangement; HDAC inhibitor; peptide; late stage modification; Introduction Among natural products, peptidic structures have entered the limelight due to their extraordinary biological activities [1]. Often found as secondary

• B (Figure 1) is a cyclic tetrapeptide with a rather unusual epoxyketone side chain and was found to be a strong inhibitor of histone deacetylases (HDACs) [4][5]. HDACs are nuclear isozymes that regulate gene transcription via a dynamic process of acetylation and deacetylation of lysine residues of

A comprehensive review of flow chemistry techniques tailored to the flavours and fragrances industries

• Guido Gambacorta,
• James S. Sharley and
• Ian R. Baxendale

Beilstein J. Org. Chem. 2021, 17, 1181–1312, doi:10.3762/bjoc.17.90

• , an immunoactivating natural product (substrate 37) [97][98]. In 2015, the diastereoselective synthesis of (E,S)-3-hydroxy-7-tritylthio-4-heptenoic acid 43, a key component of cyclodepsipeptide histone deacetylase (HDAC) inhibitors, was achieved in flow (Scheme 4) [99]. Acetyloxazolidinone 41 was used

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• and arginines occur as posttranslational modifications in proteins and are particularly important in histones, where they contribute to the regulation of chromatin structure and thus gene expression. The calixarenes can successfully bind to methylated histone tails and thus inhibit the binding of

• Survivin – Histone H3 interaction by a GCP ligand has been shown to inhibit tumor proliferation in cell culture [46]. Porphyrins, either with or without a complexed metal ion in the center, have been used as planar hydrophobic scaffolds where either negatively charged carboxylate or positively charged

• 1H,15N-BEST-TROSY titration of a truncated survivin (residues 1–120) construct revealed one distinct interaction at the Asp and Glu-rich histone H3 binding site. This ligand was also able to inhibit the survivin-H3 interaction, which is important for cell division, in vitro and in vivo and reduce

Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition

• Sivaraman Balasubramaniam,
• Sajith Vijayan,
• Liam V. Goldman,
• Xavier A. May,
• Kyra Dodson,
• Sweta Adhikari,
• Fatima Rivas,
• Davita L. Watkins and
• Shana V. Stoddard

Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59

• , TN 38112, USA Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA 10.3762/bjoc.16.59 Abstract Guided by computational analysis, herein we report the design, synthesis and evaluation of four novel diazine-based histone deacetylase

• lay the foundation for future design strategies toward more potent HDACis for HDAC8 isozymes and further therapeutic applications for neuroblastoma. Keywords: diazine; histone deacetylase; inhibitors; isozymes; panobinostat; Introduction One of the most important posttranslational modifications

• involve acetylation/deacetylation of histone proteins by histone deacetylases (HDACs) [1]. HDACs belong to an important family of enzymes consisting of 18 isozymes. They control protein acetylation, which is a change that occurs after translation. In addition, they regulate gene transcription, cell

α,ß-Didehydrosuberoylanilide hydroxamic acid (DDSAHA) as precursor and possible analogue of the anticancer drug SAHA

• Shital K. Chattopadhyay,
• Subhankar Ghosh,
• Sarita Sarkar and
• Kakali Bhadra

Beilstein J. Org. Chem. 2019, 15, 2524–2533, doi:10.3762/bjoc.15.245

• refractory cutaneous T-cell lymphoma (CTCL) [3]. Moreover, it also shows anticancer activity against a large number of hematological and solid malignancies [4][5]. Its anticancer activity is related to inhibition of histone deacetylase inhibitor (HDACi) at nanomolar concentrations (IC50 < 86 nM). Although

In search of visible-light photoresponsive peptide nucleic acids (PNAs) for reversible control of DNA hybridization

• Lei Zhang,
• Greta Linden and
• Olalla Vázquez

Beilstein J. Org. Chem. 2019, 15, 2500–2508, doi:10.3762/bjoc.15.243

• switching capacities and duplex formation were analyzed. Our group has recently demonstrated that photoresponsive peptides can affect the transcription of genes via inhibition of histone-modifying enzymes [37]. Repression of enzymes is achievable at nucleic acid level too. Therefore, in this project we

• envision a minimal model based on the previously reported accessible mRNA region of the class I histone deacetylase HDAC-1: 5’-GUGAGCCAAGAAACACUGCCU-3’ to investigate our photoswitchable PNAs [38]. Importantly, HDAC-1 is frequently overexpressed in tumors and particularly, in prostate cancer [39]. Results

A review of the total syntheses of triptolide

• Xiang Zhang,
• Zaozao Xiao and
• Hongtao Xu

Beilstein J. Org. Chem. 2019, 15, 1984–1995, doi:10.3762/bjoc.15.194

• pathways involved in the regulation of reactive oxygen species (ROS) and/or nitric oxide (NO) [9], histone methyltransferase [10], HSP70 [11], Jak2, Bcl-2/Bax [12], caspase 8 [13], NF-κB [14], X-linked inhibitor of apoptosis protein (XIAP) [15], MAPK, PI3K [16], and MPK1, ERK-1/2, and JNK-1/2 [17]. The

Aqueous olefin metathesis: recent developments and applications

• Valerio Sabatino and
• Thomas R. Ward

Beilstein J. Org. Chem. 2019, 15, 445–468, doi:10.3762/bjoc.15.39

• -auxotrophic strain of E. coli (B834DE3). Allyl-homocysteine (Ahc) resulted in the only uAA successfully incorporated into 6 different proteins, namely Histone H3 (H3-Ahc120), Np276 (Np276-Ahc61), SsβG (SsβG-Ahc49), SarZ (SarZ-Ahc4-Ahc43), Qβ (Qβ-Ahc16), and Ubq (Ubq-Ahc1). The modified proteins were tested

Cross metathesis-mediated synthesis of hydroxamic acid derivatives

• Shital Kumar Chattopadhyay,
• Subhankar Ghosh and
• Suman Sil

Beilstein J. Org. Chem. 2018, 14, 3070–3075, doi:10.3762/bjoc.14.285

• ] and the didehydrohydroxamate TSA (2) [24], display useful anticancer properties through inhibition of histone deacetylase enzymes (HDAc) and are used as FDA-approved drugs. Similarly, the cyclic peptide Chap-31 (3) [25] with a terminal hydroxamic acid residue has shown promising anticancer activity

Comparative cell biological study of in vitro antitumor and antimetastatic activity on melanoma cells of GnRH-III-containing conjugates modified with short-chain fatty acids

• Eszter Lajkó,
• Sarah Spring,
• Rózsa Hegedüs,
• Beáta Biri-Kovács,
• Sven Ingebrandt,
• Gábor Mező and
• László Kőhidai

Beilstein J. Org. Chem. 2018, 14, 2495–2509, doi:10.3762/bjoc.14.226

• =Aoa) could be attributed to the presence of butyrate, which has been demonstrated to inhibit the proliferation as well as to induce apoptosis and cell cycle arrest in different cell lines (e.g., colon carcinoma, melanoma, T-cell lymphoma) as a histone deacetylase inhibitor and/or via activation of

• Dau) had a synergistic effect with histone deacetylase inhibitors (e.g., prodrug of butyric acid) in several malignant cell lines [38]. This finding could also be a possible explanation for the increased cytotoxic effect of the conjugates containing acylated Lys compared to the parent one. Involvement

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• conjugate 16 showed significant changes in cellular morphology and causes cells to arrest in the G2/M stage of the cell cycle. The authors further confirmed via microarray analysis that the histone H4c gene is significantly downregulated by the conjugate 16 which was assumed to be bound to and alkylate a

An efficient and facile access to highly functionalized pyrrole derivatives

• Meng Gao,
• Wenting Zhao,
• Hongyi Zhao,
• Ziyun Lin,
• Dongfeng Zhang and
• Haihong Huang

Beilstein J. Org. Chem. 2018, 14, 884–890, doi:10.3762/bjoc.14.75

• in medicinal chemistry (Figure 1), such as analgesic agent 1 [1], BET bromodomain inhibitor 2 [2], selective PARP-1 inhibitor 3 [3], histone deacetylase inhibitor with antitumor activity 4 [4], Flavivirus inhibitor 5 [5], and for treating cardiovascular diseases (atorvastatin, 6) [6]. A number of

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

• Susanne Huhmann,
• Anne-Katrin Stegemann,
• Kristin Folmert,
• Damian Klemczak,
• Johann Moschner,
• Michelle Kube and
• Beate Koksch

Beilstein J. Org. Chem. 2017, 13, 2869–2882, doi:10.3762/bjoc.13.279

• digested by proteases [29]. Fluorinated aromatic amino acids were also investigated regarding their impact on peptide proteolysis. For instance, incorporation of monofluorinated phenylalanine variants into the histone acetyltransferase protein tGN5 resulted in destabilization in a chymotrypsin digestion

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• [71]. Furthermore, cap analogues providing additional functions were synthesized. A photo-crosslinking cap analogue containing a 6-thioguanosine was prepared which allowed for selective crosslinking [72]. Successful crosslinking was exemplified by the intrastrand crosslinking of histone H4 mRNA capped

Synthesis of 2-aminosuberic acid derivatives as components of some histone deacetylase inhibiting cyclic tetrapeptides

• Shital Kumar Chattopadhyay,
• Suman Sil and
• Jyoti Prasad Mukherjee

Beilstein J. Org. Chem. 2017, 13, 2153–2156, doi:10.3762/bjoc.13.214

• antimalarial and histone deacetylase inhibitory (HDACi) properties [1][2]. It has been suggested [3] that the terminal carbonyl group in members of this family (e.g., in 2) functionally mimics the C-8 keto group of the acetylated lysine residue (3) of histones as a part of their biological activity and