Using generative AI to transform peptide hits into small molecule leads

• Joshua Mills and
• Yu Heng Lau

Beilstein J. Org. Chem. 2026, 22, 672–679, doi:10.3762/bjoc.22.51

• application of ML for small molecule design based on peptide datasets was reported in 2023 by Hou and co-workers, where models were trained to classify ligands as ghrelin receptor binders [21]. The complete dataset for training and evaluation consisted of 548 peptides/peptidomimetics and 2193 small molecules

• that leverages peptide-binder structural data to generate small molecules within the protein pocket. It is trained on a range of target-bound complexes, including small molecule ligands as well as peptides and protein binders [38]. Similar to DiffLinker, small molecule generation is initiated from

Advantages of PROTACs in achieving selective degradation of homologous protein families

• Luxi Yang,
• Xinfei Mao,
• Jingyi Zhang,
• Jing Shu,
• Wenhai Huang,
• Xiaowu Dong,
• Yinqiao Chen and
• Mingfei Wu

Beilstein J. Org. Chem. 2026, 22, 628–661, doi:10.3762/bjoc.22.49

• , PROTACs, one of the most extensively studied and promising TPD approaches, are reshaping the paradigm of small-molecule drug development [11]. The PROTAC technology was initially conceptualized by Crews et al. in 2001 [11]. As a heterobifunctional molecule, a PROTAC comprises two distinct ligands: one

• Influence of linkers on the selectivity of PROTACs in highly homologous protein families As previously established [37], a PROTAC molecule comprises three essential components: a POI ligand, a linker, and an E3 ligand. In drug design, POI ligands are typically derived from FDA-approved small-molecule

• inhibitors, candidates in clinical trials, or their structural analogs. Similarly, E3 ligands are engineered to target specific E3 ubiquitin ligases. For instance, pomalidomide and lenalidomide are widely employed to recruit the CRBN ligase [38]. Given the established nature of these ligands, initial

Hydrogen production from formic acid catalyzed by NHC–Cu complexes

• Orlando Santoro and
• Catherine S. J. Cazin

Beilstein J. Org. Chem. 2026, 22, 620–627, doi:10.3762/bjoc.22.48

• phenanthroline ligands (TOF 4 h−1) [48] as well as Cu(0), Cu(I), and Cu(II) precursors/NEt3 (TOFs < 1 h−1) [44]. In contrast, [Cu(NCMe)4][PF6]/phosphine ligands/(t-BuNC–NEt3) systems represent the most active Cu-based catalysts reported to date for this transformation, exhibiting TOFs spanning from 10 to 240 h−1

Towards the targeted protein degradation of CK2: design and synthesis of CAM4066-based PROTACs

• Sophie Day-Riley,
• Sona Krajcovicova,
• Aryaman Raj Sokhal,
• Jan L. Venne,
• Paul Brear,
• Marko Hyvönen,
• Benjamin C. Whitehurst,
• Jason S. Carroll and
• David R. Spring

Beilstein J. Org. Chem. 2026, 22, 611–619, doi:10.3762/bjoc.22.47

• conjugating a CAM4066-derived warhead to CRBN or VHL ligands, four VHL-recruiting PROTACs, were prepared using PEG and alkyl linkers, alongside two CRBN-recruiting analogues featuring constrained linkers. A ligand–linker analogue in which a linker is projected from the solvent-exposed region of CK2α retained

• conjugated CAM4066-derived ligands to both CRBN or VHL E3-ligase recruiters. We created VHL-recruiting PROTACs for CK2 using PEG and alkyl linkers, while the CRBN-recruiting analogues featured more constrained linkers. A ligand–linker analogue bearing a linker projected from the solvent-exposed region of the

• map revealed that it remained solvent-exposed and sterically accessible, validating the design for subsequent attachment of E3-ligase ligands. With the exit vector validated, the synthesis of full PROTACs was pursued. The VH032-derived VHL ligand 21 (for full synthesis see Supporting Information File

Design and synthesis of an erdafitinib-based selective FGFR2 degrader

• Yumeng Jin,
• Shidong Wang,
• Sihan Pan,
• Shuqi Huang,
• Weichen Zhou,
• Xiaohao Huang,
• Lei Zheng and
• Lingfeng Chen

Beilstein J. Org. Chem. 2026, 22, 583–591, doi:10.3762/bjoc.22.44

• binding to ligands, which trigger intracellular signaling cascades to activate downstream substrates and pathways [4]. This process involves PLC γ-mediated PKC activation and pFRS2-induced activation of the PI3K/AKT and MAPK/ERK pathways, thereby regulating cell proliferation, differentiation, migration

• effectively degrade FGFR2 via the proteasomal pathway, while the VHL E3 ligase-based degrader DGY-09-192 is capable of degrading both FGFR1 and FGFR2 simultaneously [40]. These findings suggest that different E3 ligase ligands may influence the selectivity and efficiency of degradation [41]. Nevertheless, due

Kinetic resolution of racemic planar-chiral vinylcymantrenes by molybdenum-catalyzed asymmetric metathesis dimerization

• Haruna Imazu,
• Hitoshi Izu,
• Yasuhiro Ohki and
• Masamichi Ogasawara

Beilstein J. Org. Chem. 2026, 22, 568–574, doi:10.3762/bjoc.22.42

• in Figure 2) likely inhibits the effective interaction of the substrate with the chiral catalyst, resulting in highly enantioselective kinetic resolution. Cymantrene is far less electron-poor than ferrocene due to the presence of the three carbonyl ligands, which are strong π-acids, on the manganese

Molecular tweezer–peptide conjugates disrupt the protein–protein interaction between survivin and histone H3 essential in mitosis

• Catherine Gsell,
• Philipp Rebmann,
• Karina Opara,
• Christine Beuck,
• Peter Bayer,
• David Bier,
• Ingrid R. Vetter and
• Thomas Schrader

Beilstein J. Org. Chem. 2026, 22, 557–567, doi:10.3762/bjoc.22.41

• crystal (Figure 4 and Supporting Information File 1, Figure S12). Lys-121, on the other hand, is buried in a crystal contact. Thus, the crystal packing forces together with putatively competing ligands (see below) can apparently compete successfully with the tweezer that is most likely attached to Lys-121

Experimental and DFT studies on the regioselective methanolysis of 5-azido-9-oxabicyclo[6.1.0]nonan-4-yl 4-nitrobenzoate isomers

• İlknur Polat,
• Selçuk Eşsiz and
• Emine Salamci

Beilstein J. Org. Chem. 2026, 22, 547–556, doi:10.3762/bjoc.22.40

• , pharmaceutical compounds, and chiral ligands. The Lewis acid-catalyzed ring-opening reaction of cyclohexene oxide by MeZH (Z = O, S, and NH) is well known [20]. However, studies on large-sized bicyclic epoxides remain relatively limited in the published literature. In our previous study, we performed the ring

Synthesis and uranyl(VI) extraction performance of a calix[4]pyrrole–tetrahydroxamic acid receptor

• Sara Karnib,
• Rana Baydoun,
• Wissam Zaidan,
• Nancy AlHaddad,
• Omar El Samad,
• Bilal Nsouli,
• Francine Cazier-Dennin and
• Pierre-Edouard Danjou

Beilstein J. Org. Chem. 2026, 22, 486–494, doi:10.3762/bjoc.22.36

• ligands can display significantly enhanced binding toward uranyl relative to their linear hydroxamic acid counterparts, emphasizing the beneficial role of structural organization in uranyl chelation [35]. This beneficial role of pre-organization of chelating groups within one molecule was also highlighted

• pH 2 and pH 3, the extraction efficiencies remain overall comparable within experimental uncertainty, suggesting that uranyl uptake is already near maximal in this acidic region. This behavior is consistent with previous studies in which ligands displayed high uranyl uptake within an optimal pH

• window. For instance, calix[4]arene-based 8-hydroxyquinoline ligands showed nearly quantitative extraction of uranyl between pH 4 and 9, with efficiency decreasing under more acidic conditions [67]. Likewise, phosphoramide-functionalized magnetic nanoparticles showed high uranyl adsorption (80–95

Synthesis of a HDAC inhibitor–nanogold probe for cryo-EM visualization in class I HDAC co-repressor complexes

• Wiktoria A. Pytel,
• John W. R. Schwabe and
• James T. Hodgkinson

Beilstein J. Org. Chem. 2026, 22, 480–485, doi:10.3762/bjoc.22.35

• , specifically Monoamino-Nanogold® 1.4 nm purchased from Nanoprobes) for our probe design. Au–NH2 consists of a gold cluster of eleven gold atoms coordinated by trisarylphosphine ligands with a diameter of 1.4 nm. One of the trisarylphosphine ligands contains the 3-aminopropylamido group, allowing for

Recent advances in the stereoselective synthesis of distal biaxially chiral molecules

• Fanxing Zhou,
• Chen Zhang,
• Lingyu Sun,
• Yiyun Fang,
• Siming Zheng,
• Lina Hu,
• Mengyang Shen,
• Zhen Zhao,
• Wei Xu,
• Yunqiang Sun and
• Zi-Qiang Rong

Beilstein J. Org. Chem. 2026, 22, 461–479, doi:10.3762/bjoc.22.34

• distal axial chiralities are widely applied in chiral ligands, natural products, and anticancer agents, with their unique spatial configurations endowing them with distinctive functions and values. Although significant progress has been made in the asymmetric synthesis of distal biaxial chirality

• chiral scaffolds, which arise from hindered rotation between two planes connected by a single bond, have attracted increasing attention due to their widespread applications in chiral ligands, organocatalysts [1], and functional materials [2], making them highly valuable molecular frameworks in organic

• ligands (Scheme 3) [44]. The resulting catalysts 18 demonstrated remarkable efficiency in the asymmetric transfer hydrogenation of quinoline derivatives. Along similar lines, Zhang and co-workers introduced an additional axial chirality element into a ligand framework, affording a pair of diastereomeric

Synthesis and anti-cancer activity of naphthalimide–organylselanyl conjugates

• Rajkumar Ravi and
• Selvakumar Karuthapandi

Beilstein J. Org. Chem. 2026, 22, 416–435, doi:10.3762/bjoc.22.29

• conformation (4HJO). The docking results revealed that both ligands fit well within the binding pocket of the EGFR tyrosine kinase domain. The binding interactions were further validated by comparison with the crystal structures of the active (1M17) and inactive (4HJO) forms of EGFR complexed with the co

• ), hydrogen bonding (Met769), carbon–hydrogen bonding (Thr766), π–anion (Asp831), π–σ (Leu694), amide–π (Met769), alkyl (His781), and π–alkyl (Val702, Ala719, Leu768, Leu820). These results confirm that both ligands are well accommodated within the binding pocket of EGFR tyrosine kinase, with compound 7

• site interactions to those observed for erlotinib. Both erlotinib and the synthesised ligands formed a hydrogen bond interaction with Met769. The synthesised ligands have a greater ability to form an interaction with the active (1M17) tyrosine kinase domain of EGFR. Comparative binding interaction of

Arene activation via π-bond localization: concepts and opportunities

• Paul Meiners,
• Julian J. Melder and
• Tobias Morack

Beilstein J. Org. Chem. 2026, 22, 257–273, doi:10.3762/bjoc.22.19

• of the archetypal pentaammineosmium(II) system prior to discussing synthetic utility (Figure 6). The five ammine ligands, strong σ-donors with negligible π-interaction, combined with the d6 configuration render the Os(II) center highly electron-rich and an exceptional π-base [43]. This electronic

• configuration promotes strong binding to π-acidic ligands, effectively compensating for the loss of aromaticity upon η2-coordination to arenes, while disfavoring oxidative addition due to geometric constraints of the octahedral complex. The resulting η2-arene complexes, encompassing both arenes and heteroarenes

• (Figure 6C), so suitable aromatic ligands are limited to those lacking strongly π-acidic functional groups, e.g., alkenes, alkynes, aldehydes, certain ketones, and nitriles. Lewis-basic heteroarenes, such as pyridines or imidazoles, tend to coordinate via nitrogen instead, disfavoring η2-binding (Figure

Screwing the helical chirality through terminal peri-functionalization

• Devesh Chandra,
• Sachin and
• Upendra Sharma

Beilstein J. Org. Chem. 2026, 22, 205–212, doi:10.3762/bjoc.22.14

• another important type of chirality, where the chirality is controlled by restricted rotation among an axis. These types of molecules play an important role as chiral ligands in organic synthesis, i.e., BINOL, BINAP, etc. [9][10][11]. Another form of chirality, where chirality depends on a constrained

• asymmetric synthesis, where they serve as chiral ligands and organocatalysts, delivering high enantioselectivities [17][18]. Their tunable HOMO–LUMO gaps and controlled π–π interactions, is key to the use of helicenes in molecular electronics and organic semiconductors as well. Helicenes function as active

Improved synthesis and physicochemical characterization of the selective serotonin 2A receptor agonist 25CN-NBOH

• Adrian G. Rossebø,
• Hannah G. Kolberg,
• Anders E. Tønder,
• Louise Kjaerulff,
• Poul Erik Hansen,
• Karla A. Frydenvang,
• Jesper Østergaard and
• Jesper L. Kristensen

Beilstein J. Org. Chem. 2026, 22, 175–184, doi:10.3762/bjoc.22.11

• agonists to study the effects of solely activating this key receptor [4]. 25CN-NBOH (1) was reported in 2014 as part of a series of ligands in the search for selective 5-HT2AR agonists [5]. Subsequently, it has been used and characterized extensively as a tool for investigations into the effects of

Design and synthesis of an axially chiral platinum(II) complex and its CPL properties in PMMA matrix

• Daiki Tauchi,
• Sota Ogura,
• Misa Sakura,
• Kazunori Tsubaki and
• Masashi Hasegawa

Beilstein J. Org. Chem. 2026, 22, 143–150, doi:10.3762/bjoc.22.7

• , pincer-type platinum(II) complexes have attracted particular attention, owing to the structural robustness imparted by tridentate chelating ligands and their excellent luminescent properties [12][13][14][15][16][17]. These complexes have been widely investigated, not only for practical application but

• arrangement of several molecules in the aggregated state. To expand the scope of chirality in metal complex chemistry with pincer ligands and to facilitate the design of next-generation CPL-active materials, alternative chiral motifs beyond point chirality are highly desirable. Herein, we report the design

Total synthesis of natural products based on hydrogenation of aromatic rings

• Haoxiang Wu and
• Xiangbing Qi

Beilstein J. Org. Chem. 2026, 22, 88–122, doi:10.3762/bjoc.22.4

• rings becomes achievable, enabling access to reduced products with well-defined configurations [38]. Although the repertoire of ligands capable of exerting precise stereocontrol remains limited, each provides distinct advantages that suit different metals and reaction conditions. From the perspective of

• in the presence of metal catalysts including Pd or Ir and different ligands. In 2021 and 2022, Wang and co-workers reported two impressive hydroboration–hydrogenation reactions catalyzed by FLP (triarylphenylborane) that reduced pyridine compounds 11 or 15 to dihydropyridine compounds 12 or chiral

• reported for the first time the reduction of 1,3-disubstituted isoquinoline compounds 45 to trans-quinoxalines 46 (Scheme 6) [56]. By using iridium catalysts and commercially available chiral JosiPhos ligands, a batch of enantioriched trans-tetrahydroisoquinolines could be prepared efficiently and

Synthesis and applications of alkenyl chlorides (vinyl chlorides): a review

• Daniel S. Müller

Beilstein J. Org. Chem. 2026, 22, 1–63, doi:10.3762/bjoc.22.1

• is generated in situ and likely present only in trace amounts. All our attempts to accelerate the reaction through addition of various mono- and bidentate phosphorus ligands were unsuccessful. A similar trend was observed with NEt3, which afforded optimal yields at 20–30 mol % loading (not shown

• demonstrated that the use of 4 equivalents of 1,1-dichloroethylene in combination with XPhos or JohnPhos ligands enabled monoselective cross-coupling with alkenyl- and arylboronic acids (Scheme 54B) [184]. Though mechanistically not related it is noteworthy that diazonium salts couple efficiently with alkenyl

Isoorotamide-based peptide nucleic acid nucleobases with extended linkers aimed at distal base recognition of adenosine in double helical RNA

• Grant D. Walby,
• Brandon R. Tessier,
• Tristan L. Mabee,
• Jennah M. Hoke,
• Hallie M. Bleam,
• Angelina Giglio-Tos,
• Emily E. Harding,
• Vladislavs Baskevics,
• Martins Katkevics,
• Eriks Rozners and
• James A. MacKay

Beilstein J. Org. Chem. 2025, 21, 2513–2523, doi:10.3762/bjoc.21.193

• linker are highlighted in red. Sequences for RNA hairpins and PNA ligands used for binding studies. Major-groove view of hydrogen-bonding interactions in the (A) Db1*U–A triplet, (B) Db2*U–A triplet, (C) Db2*C–G triplet, and (D) Db3*U–A triplet. Carbon, hydrogen, oxygen, and nitrogen are labelled in

Catalytic enantioselective synthesis of selenium-containing atropisomers via C–Se bond formations

• Qi-Sen Gao,
• Zheng-Wei Wei and
• Zhi-Min Chen

Beilstein J. Org. Chem. 2025, 21, 2447–2455, doi:10.3762/bjoc.21.186

• Atropisomers are not only prevalent in biologically active natural products and pharmaceuticals, but they have also garnered increasing attention for their effectiveness as ligands and catalysts in the field of catalytic asymmetric synthesis. Asymmetric catalysis serves as a key strategy for the

• compounds can participate in asymmetric synthesis reactions and construct chiral molecules with specific stereoconfiguration, which is particularly critical for drug synthesis [9]. In the field of organic catalysis, chiral organic selenium-containing compounds can be used as chiral ligands or catalysts to

Enantioselective radical chemistry: a bright future ahead

• Anna C. Renner,
• Sagar S. Thorat,
• Hariharaputhiran Subramanian and
• Mukund P. Sibi

Beilstein J. Org. Chem. 2025, 21, 2283–2296, doi:10.3762/bjoc.21.174

• catalysis affords the dual advantages of introducing stereochemical discrimination on both the radical and the trap via chiral ligands. Early research on parameters governing stereoselectivity in radical reactions was achieved with the help of radicals or radical traps appended with chiral auxiliaries. The

Pathway economy in cyclization of 1,n-enynes

• Hezhen Han,
• Wenjie Mao,
• Bin Lin,
• Maosheng Cheng,
• Lu Yang and
• Yongxiang Liu

Beilstein J. Org. Chem. 2025, 21, 2260–2282, doi:10.3762/bjoc.21.173

• substrate class. Through mechanistic-guided modulation of catalysts, solvents, ligands, and angle strain, this approach achieves unprecedented reaction pathway control while demonstrating superior temporal and step efficiency compared to conventional methods. The work establishes a sustainable framework for

• components such as solvents, catalysts, ligands and so on. Unlike traditional “one-to-one” reactions, pathway-controlled “one-to-many” transformations synthesize multiple products from single intermediates, dramatically reducing preparation time and reagent requirements (Scheme 1b). As an exceptionally

• heterocyclic scaffolds, which established a versatile platform for synthesizing structurally diverse indoline frameworks. Ligand-controlled cyclization of 1,n-enynes The core function of catalyst ligands lies in their ability to precisely modulate catalyst performance through electronic and steric effects. The

Research towards selective inhibition of the CLK3 kinase

• Vinay Kumar Singh,
• Frédéric Justaud,
• Dabbugoddu Brahmaiah,
• Nangunoori Sampath Kumar,
• Blandine Baratte,
• Thomas Robert,
• Stéphane Bach,
• Chada Raji Reddy,
• Nicolas Levoin and
• René L. Grée

Beilstein J. Org. Chem. 2025, 21, 2250–2259, doi:10.3762/bjoc.21.172

• affinity of ligands towards the CLK3 kinase. It is based on the lysine 241 which is present only in CLK3, while the three others (CLK1, 2, and 4) have apolar leucine in this position. Thus, by grafting an extra benzoic acid on a molecule previously established as having low activity on CLK3 (DB18), we have

Pd-catalyzed dehydrogenative arylation of arylhydrazines to access non-symmetric azobenzenes, including tetra-ortho derivatives

• Loris Geminiani,
• Kathrin Junge,
• Matthias Beller and
• Jean-François Soulé

Beilstein J. Org. Chem. 2025, 21, 2234–2242, doi:10.3762/bjoc.21.170

• regioselectivity issues, multistep procedures, and limited applicability to tetra-ortho-substituted structures. Herein, we describe a direct, one-pot Pd-catalyzed dehydrogenative C–N coupling between aryl bromides and arylhydrazines to access non-symmetric azobenzenes. The use of bulky phosphine ligands and

• the presence of water, highlighting its robustness. Keywords: azo compounds; cross-coupling; domino catalysis; palladium; phosphine ligands; Introduction Azobenzenes are a widely studied class of compounds known for their distinctive photoresponsive properties, rendering them valuable in a variety

• (allyl)2 in DME with strong base (Cs2CO3) favors C–N-bond coupling, which may yield products resulting from arylation at either the terminal or internal nitrogen atoms. The selectivity can be influenced by the steric hindrance of the phosphine ligands and/or the substrates. Once N,N-diarylhydrazine is

Electrochemical cyclization of alkynes to construct five-membered nitrogen-heterocyclic rings

• Lifen Peng,
• Ting Wang,
• Zhiwen Yuan,
• Bin Li,
• Zilong Tang,
• Xirong Liu,
• Hui Li,
• Guofang Jiang,
• Chunling Zeng,
• Henry N. C. Wong and
• Xiao-Shui Peng

Beilstein J. Org. Chem. 2025, 21, 2173–2201, doi:10.3762/bjoc.21.166

• reaction mechanisms are disclosed if available. Keywords: alkyne; catalysis; cyclization; electrochemistry; five-membered ring; Introduction Organic five-membered rings, an essential class of organic compounds, not only are frequently used as important starting materials, intermediates or ligands in

• , this protocol was an efficient and sustainable approach to synthesize 2,3′-biindolyl atropisomers and could be potentially applied in manufacture of functional materials, bioactive molecules and chiral ligands. Construction of isoindolinones and indolizines An electrochemical and copper-catalyzed