Emerging trends in the optimization of organic synthesis through high-throughput tools and machine learning

• Pablo Quijano Velasco,
• Kedar Hippalgaonkar and
• Balamurugan Ramalingam

Beilstein J. Org. Chem. 2025, 21, 10–38, doi:10.3762/bjoc.21.3

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

• ; Introduction Natural products (NPs) have been pivotal for the development of modern medicine accompanying humans from the prehistorical age [1]. In the last century, NPs became the main source of the active scaffolds for the pharmaceutical industry with focus on principle of one compound, one target, and one

• disease [2][3]. In parallel, mass spectrometry (MS) has been crucial in many areas centered around the characterization of NPs [4]. First to annotate their often complex structures using diverse fragmentation techniques [4]. Nowadays, MS is applied for the identification of NPs’ cellular protein targets

• -crosslinker, is attached synthetically to the basic scaffold (Figure 2A) [28][29][30][31][32]. However, this requires a structure–activity relationship (SAR) screening to ensure that the selected NP retains biological activity after modification. The term probe is further used to unite such NPs and active

Discovery of antimicrobial peptides clostrisin and cellulosin from Clostridium: insights into their structures, co-localized biosynthetic gene clusters, and antibiotic activity

• Moisés Alejandro Alejo Hernandez,
• Katia Pamela Villavicencio Sánchez,
• Rosendo Sánchez Morales,
• Karla Georgina Hernández-Magro Gil,
• David Silverio Moreno-Gutiérrez,
• Eddie Guillermo Sanchez-Rueda,
• Yanet Teresa-Cruz,
• Brian Choi,
• Armando Hernández Garcia,
• Alba Romero-Rodríguez,
• Oscar Juárez,
• Siseth Martínez-Caballero,
• Mario Figueroa and
• Corina-Diana Ceapă

Beilstein J. Org. Chem. 2024, 20, 1800–1816, doi:10.3762/bjoc.20.159

• are derived from bacterial natural products (NPs), which have proven to be a valuable source of antimicrobial agents. During the latter part of the 20th century, the discovery of NPs was hindered by the limitation of traditional methods, which often led to the rediscovery of previously identified NPs

• . Next-generation whole genome sequencing technologies have a newfound ability to explore and identify biosynthetic gene clusters (BGCs) responsible for NPs production. This renewed focus offers the advantage of preventing redundant discovery and predicting novelty, resistance, and bioactivities

• the chemical characterization of the NPs that are produced and the modifications they suffer, from a Clostridium genus, have yet to be accomplished. This is due to the difficulty in isolating and maintaining such strains in the laboratory and the limited availability of genome sequences compared to

A Diels–Alder probe for discovery of natural products containing furan moieties

• Alyssa S. Eggly,
• Namuunzul Otgontseren,
• Carson B. Roberts,
• Amir Y. Alwali,
• Haylie E. Hennigan and
• Elizabeth I. Parkinson

Beilstein J. Org. Chem. 2024, 20, 1001–1010, doi:10.3762/bjoc.20.88

• , Indiana 47906, United States 10.3762/bjoc.20.88 Abstract Natural products (NPs) are fantastic sources of inspiration for novel pharmaceuticals, oftentimes showing unique bioactivity against interesting targets. Specifically, NPs containing furan moieties show activity against a variety of diseases

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

• Kara A. Strickland,
• Brenda Martinez Rodriguez,
• Ashley A. Holland,
• Shelby Wagner,
• Michelle Luna-Alva,
• David E. Graham and
• Jonathan D. Caranto

Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75

• . NNG is a non-proteinogenic amino acid, similar to other such N–N containing compounds such as piperazic acid and hydrazinoacetic acid [43]. These precursors are incorporated into larger NPs by non-ribosomal peptide synthases or polyketide synthases, and NNG may have a similar fate [44][45]. Another

Green and sustainable approaches for the Friedel–Crafts reaction between aldehydes and indoles

• Periklis X. Kolagkis,
• Eirini M. Galathri and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2024, 20, 379–426, doi:10.3762/bjoc.20.36

• introduced nano n-propylsulfonated γ-Fe2O3 (NPS-γ-Fe2O3), which constitutes a magnetically recyclable heterogeneous catalyst that works in the exact same manner as HPA/TPI-Fe3O4 [103]. Some small differences between the two methods were the ability of ketones to form the respective BIMs, when NPS-γ-Fe2O3 was

• employed in contrast to HPA/TPI-Fe3O4, while also using a milder heating at 80 °C. However, Ramshini’s protocol had shorter reaction times of 25 minutes instead of 1 to 5 hours and also the catalyst loading was significantly decreased at 0.06 mol %, instead of the 0.5 mol % needed for NPS-γ-Fe2O3. Other

• necessity of conventional heating and solvent compared to other methodologies [109][110]. At the same time, Yavari and his research group also studied the use of hexamine, in place of NPS-γ-Fe2O3, immobilized on Fe3O4 and coated with SiO2 [111]. This protocol, while employing the identical optimum reaction

Aromatic C–H bond functionalization through organocatalyzed asymmetric intermolecular aza-Friedel–Crafts reaction: a recent update

• Anup Biswas

Beilstein J. Org. Chem. 2023, 19, 956–981, doi:10.3762/bjoc.19.72

• 2019, Inokuma, Yamada and co-workers reported the C3–H bond functionalization of indoles 4 through aza-Friedel–Crafts reaction utilizing N-o-nitrophenylsulfenyl (Nps)-iminophosphonates 32 as electrophiles. The chiral phosphoric acid P11 was used as H-bonding catalyst to impart stereoselectivities into

• using Nps-iminophosphonates as electrophiles. Aza-Friedel–Crafts reaction between indole and α-iminophosphonate. [2.2]-Paracyclophane-derived chiral phosphoric acids as catalyst. Aza-Friedel–Crafts reaction through ring opening of sulfamidates. Isoquinoline-1,3(2H,4H)-dione scaffolds as electrophiles

Insight into oral amphiphilic cyclodextrin nanoparticles for colorectal cancer: comprehensive mathematical model of drug release kinetic studies and antitumoral efficacy in 3D spheroid colon tumors

• Sedat Ünal,
• Gamze Varan,
• Juan M. Benito,
• Yeşim Aktaş and
• Erem Bilensoy

Beilstein J. Org. Chem. 2023, 19, 139–157, doi:10.3762/bjoc.19.14

• the ability to self-assemble into NPs amenable for encapsulation of an array of therapeutics (from small molecule drugs to nucleic acids) [19]. Moreover, their dense ammonium functional display furnishes their NPs with an overall positive charge and large buffering capabilities [19] at physiological

• pH. Preliminary studies have evidenced pKa values in the 8.3 range for non-amphiphilic surrogates of these cationic CDs, supporting the cationic character of the resulting NPs [20]. We hypothesized that these polycationic CD NPs, which we designed in our previous studies, could protect the active and

• through either (i) the cationic nature of the CD such as poly-β-CD-C6 or (ii) coating of non-ionic 6-O-capro-β-CD with the cationic polymer chitosan (CS). Uncoated 6-O-capro-β-CD negatively charged NPs were used as control formulation. Results and Discussion Fabrication and in vitro characterization of

Navigating and expanding the roadmap of natural product genome mining tools

• Friederike Biermann,
• Sebastian L. Wenski and
• Eric J. N. Helfrich

Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178

• bioinformatic analysis of (meta-)genomes to identify gene clusters involved in the biosynthesis of NPs [3]. NPs have been shown to act as signaling metabolites (e.g., acylhomoserine lactones (1) [6]), siderophores (e.g., pyoverdines (2) [7]), virulence factors (e.g., malleicyprol (3) [8][9][10]), toxins (e.g

• initiated the field of microbial NP research. In the "golden age" of antibiotic discovery from the 1940s to 1970s, microbes and especially bacteria have been identified as an almost untapped treasure trove for the discovery of bioactive NPs. For the longest time, researchers focused on a few talented NP

• hygroscopicus sp. XM201, for instance, harbors more than 50 putative biosynthetic gene clusters (BGCs), many of which are cryptic, i.e., BGCs for which the corresponding NPs have yet to be identified [15]. A problem when it comes to the characterization of the full biosynthetic potential of an organism is the

Inductive heating and flow chemistry – a perfect synergy of emerging enabling technologies

• Conrad Kuhwald,
• Sibel Türkhan and
• Andreas Kirschning

Beilstein J. Org. Chem. 2022, 18, 688–706, doi:10.3762/bjoc.18.70

• series of promising systems have been produced for this purpose. These include (Fe2.2C) NPs [39], (ICNPs@Ni; 29 wt % Ni), and (ICNPs@Ru 1 wt % Ru) on a silica-alumina support (SiRAlox). The Ru nanoparticles far outperformed the previously known catalysts. A methane yield of 93% with complete selectivity

Recent developments and trends in the iron- and cobalt-catalyzed Sonogashira reactions

• Surendran Amrutha,
• Sankaran Radhika and
• Gopinathan Anilkumar

Beilstein J. Org. Chem. 2022, 18, 262–285, doi:10.3762/bjoc.18.31

• decrease in its activity. For comparison, the Sonogashira reaction of phenylacetylene and iodobenzene was performed in the presence of the two catalytic systems Co-NHC@MWCNTs and Co-NPS (Scheme 23 and Scheme 24). The reaction proceeded with four equivalents of KOH in EtOH/H2O at 65 °C. Aryl iodides showed

• higher reactivity and less active aryl chlorides were successfully coupled to give the desired products in acceptable yields. The reaction carried out by both catalysts gave excellent yields of up to 98% for Co-NHC@MWCNTs and a still good yield of up to 91% for reactions catalyzed by Co-NPs. It was

• phenylacetylene in the presence of a series of PdCo bimetallic nanoparticles with different compositions on graphite sheets as highly active catalysts (Scheme 27) [40]. The catalyst was prepared by a chemical reduction method and characterized by various techniques like Raman, XRD, TEM, and XPS. The Pd/Co(1:1)NPs

Green synthesis of C5–C6-unsubstituted 1,4-DHP scaffolds using an efficient Ni–chitosan nanocatalyst under ultrasonic conditions

• Soumyadip Basu,
• Sauvik Chatterjee,
• Suman Ray,
• Suvendu Maity,
• Prasanta Ghosh,
• Asim Bhaumik and
• Chhanda Mukhopadhyay

Beilstein J. Org. Chem. 2022, 18, 133–142, doi:10.3762/bjoc.18.14

• (NPs) and therefore automatically increases the dispersibility of the catalyst throughout the medium, resulting in a higher catalytic activity [23]. 1,4-DHPs are considered one of the most useful molecular scaffolds in medicinal chemistry. The scaffold is the main constituent of several crucial drugs

• of the material (Figure 3a and Figure 3b). The TEM images showed agglomeration of spherical NPs, leading to the formation of multiple scaffolds. In the SEM images, the presence of spheres of 40–60 nm was clearly visible (Figure 3c and Figure 3d). Often, these small NPs were agglomerated to form

• dry conditions. As such, we observed different particle sizes in the SEM and TEM analyses. Since small particles of 40–60 nm were present consistently throughout the grid, they fell within the definition of NPs. The EDX study of the catalyst (Figure 4) confirmed the presence of nickel in this sample

Cryogels: recent applications in 3D-bioprinting, injectable cryogels, drug delivery, and wound healing

• Luke O. Jones,
• Leah Williams,
• Tasmin Boam,
• Martin Kalmet,
• Chidubem Oguike and
• Fiona L. Hatton

Beilstein J. Org. Chem. 2021, 17, 2553–2569, doi:10.3762/bjoc.17.171

• dextran nanoparticles (Sp-AcDEX NPs). The Sp-AcDEX NPs were released over time to provide therapeutic effects with the nanoparticles aiding in accumulation in the tumour tissue. The reported results were found to be promising, as this method helped induce immunogenic cell death in tumour cells whilst also

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

Valorisation of plastic waste via metal-catalysed depolymerisation

• Francesca Liguori,
• Carmen Moreno-Marrodán and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2021, 17, 589–621, doi:10.3762/bjoc.17.53

• catalyst replacements for zinc acetate in the glycolysis of PET are examples of this direction [129][130]. Recent studies focused on molecular complexes as homogeneous catalysts, whereas heterogeneous systems based on solid-supported metal nanoparticles (NPs) have been scarcely investigated. 3.1

• %), olefins (22.5%) and naphthalene (4.1%) at total HDPE conversion at 350 °C [144]. In another example, hydrocracking of PE was performed over Pt NPs supported on SrTiO3 perovskite nanocuboids [145]. Virgin PE (Mw = 18000–420000 g⋅mol−1) or PE from single-use plastic bags (Mw = 115000 g⋅mol−1) was converted

• compared to 2D materials, thanks to a typical 8–16 nm outer diameter tubular morphology [215][216] and the potential for facile metal doping via ion-exchange of the solid support [217][218]. Lewis acid-type catalytic activity was also postulated for γ-Fe2O3 NPs, which provided BHET in 90% yield at 300 °C

Insight into functionalized-macrocycles-guided supramolecular photocatalysis

• Minzan Zuo,
• Krishnasamy Velmurugan,
• Kaiya Wang,
• Xueqi Tian and
• Xiao-Yu Hu

Beilstein J. Org. Chem. 2021, 17, 139–155, doi:10.3762/bjoc.17.15

• a stabilizer to control the size and distribution of the NPs and are able to intensely regulate the photocatalytic performance. 5) To improve the sustainability, noble metals need to be replaced by earth-abundant metals. However, in most cases, earth-abundant metals have a lower photocatalytic

Palladium nanoparticles supported on chitin-based nanomaterials as heterogeneous catalysts for the Heck coupling reaction

• Tony Jin,
• Malickah Hicks,
• Davis Kurdyla,
• Sabahudin Hrapovic,
• Edmond Lam and
• Audrey Moores

Beilstein J. Org. Chem. 2020, 16, 2477–2483, doi:10.3762/bjoc.16.201

• Mining and Materials Engineering, McGill University, Montreal, Quebec H3A 0E9, Canada 10.3762/bjoc.16.201 Abstract In this report, chitin and chitosan nanocrystals were used as biomass-based supports for Pd nanoparticles (NPs) used as a heterogeneous catalyst for the Heck coupling reaction. By using a

• one-pot fabrication method, a Pd salt precursor was directly reduced and deposited onto these nanocrystal catalysts. Characterization of these nanocomposites showed disperse Pd NPs on the surfaces of the chitinous nanocrystals. Heck coupling model reactions revealed full product yield in relatively

• ], environmental remediation [5], and catalysis [6]. With their high solubility and presence of functionalities such as hydroxy groups, sulfate half-esters, and carboxylates, CNCs are able to stabilize highly disperse metal nanoparticles (NPs), which can act as heterogeneous catalysts for a wide array of organic

One-pot synthesis of isosorbide from cellulose or lignocellulosic biomass: a challenge?

• Isaline Bonnin,
• Raphaël Mereau,
• Thierry Tassaing and
• Karine De Oliveira Vigier

Beilstein J. Org. Chem. 2020, 16, 1713–1721, doi:10.3762/bjoc.16.143

• (5.0 wt % Ru, Ru nanoparticles (NPs): 0.9 nm) in 30 mL H2O after 1 h of reaction at 220 °C under 60 bar of H2. Trace amounts or even no isosorbide was obtained over microporous HZSM-5, NaY, and γ-Al2O3-supported Ru catalysts. A bifunctional Ru catalyst supported on mesoporous niobium phosphate with a

• mean size of Ru NPs of 5.5 nm was used for the direct conversion of cellulose to isosorbide and 52% yield of isosorbide was observed with almost 100% cellulose conversion. The large surface area, pore size, and strong acidity of mesoporous niobium phosphate are key parameters for the hydrolysis of

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

• 2.1 and 2.2, and can be explored in detail in independent reviews [1][6][176][181][182]. Some examples are more unique, such as metal nanoparticle (NPs) photocatalysis. Despite having a conductor band structure,and therefore no band gap, the nanoscale of these materials produces visible light

• absorptions. This is due to the oscillating electron density within metallic NPs, which can couple with the electric field of photons with wavelengths similar to the dimensions of the NPs [181]. This is called the localised surface plasmon resonance (LSPR), and is responsible for the brilliant colours

• observed in colloidal solutions of noble metal NPs [6][181][182][183][184][185][186][187]. The photon absorption polarises the electron density of the nanoparticle and produces energetically excited electrons above, and holes below the Fermi level that can undergo photoredox processes with substrates [185

A systematic review on silica-, carbon-, and magnetic materials-supported copper species as efficient heterogeneous nanocatalysts in “click” reactions

• Pezhman Shiri and
• Jasem Aboonajmi

Beilstein J. Org. Chem. 2020, 16, 551–586, doi:10.3762/bjoc.16.52

• types of carbon nanomaterials, including a) zero-dimensional nanoparticles (NPs), b) one-dimensional nanotubes, c) two-dimensional graphene sheets, and d) three-dimensional mesoporous carbon have been reported in the literature [63]. In this regard, various functionalized carbon nanomaterials were

• another study, Shaabani reported crosslinked chitosan nanoparticles-anchored magnetic multiwalled carbon nanotubes Cu–CS NPs/MWCNT@Fe3O4 (141) as a bionanoreactor catalyst, and the catalytic activity of 141 in 1,2,3-triazole syntheses was explored [100]. A schematic pathway for the creation of 141 is

• presented in Scheme 31. In the first step, chitosan nanoparticles/multiwalled carbon nanotubes (CS NPs/MWCNT, 139) were prepared by the addition of MWCNT–COOH to an acetic acid solution of chitosan (CS, 137). Subsequently, a solution of sodium tripolyphosphate (138) was added to the previous solution. After

A review of asymmetric synthetic organic electrochemistry and electrocatalysis: concepts, applications, recent developments and future directions

• Munmun Ghosh,
• Valmik S. Shinde and
• Magnus Rueping

Beilstein J. Org. Chem. 2019, 15, 2710–2746, doi:10.3762/bjoc.15.264

• -induced asymmetric electrochemical hydrogenation of 2,2,2-trifluoroacetophenone 32 nanoparticles was also developed (Scheme 13). These NPs with low Pt loading were further obtained by reducing platinum precursors on Cu NPs [41]. Yadav’s group, in 2013, described preparative scale enantioselective cathodic

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

• –H bonds, either Csp2 or Csp3, a revolution in the synthesis of complex natural products (NPs) has been evolved. It provides a powerful toolbox to access complex natural structures and has the potential to streamline the synthesis. In 2014, Li and co-workers reported a metal-mediated reaction-based

Recent advances on the transition-metal-catalyzed synthesis of imidazopyridines: an updated coverage

• Gagandeep Kour Reen,
• Ashok Kumar and
• Pratibha Sharma

Beilstein J. Org. Chem. 2019, 15, 1612–1704, doi:10.3762/bjoc.15.165

• ][42][43][44]. Various copper salts have been used as Lewis acid in homogeneous catalysis. CuO nanoparticles (NPs) were used for C–N, C–S, C–O cross-coupling reactions and C-arylation. Recently, exploiting the cross-coupling tendency of CuO NPs, Reddy et al. have reported their use as a heterogeneous

• organic reactions. In the syntheses of IPs, various forms of copper viz., salts, complexes, MOFs, oxides, and nanoparticles (NPs) have been used as the catalytic system in both multicomponent reactions (MCRs) as well as derivatization methodologies. The role of palladium in synthetic chemistry Pd

• activity. It is revealed from the literature that next to the copper, palladium catalysts in the form of salts (with or without ligands), complexes, NPs, etc. find their usage on mass scale syntheses of IPs. The role of zinc in synthetic chemistry Zinc salts being inexpensive, environmentally benign, low

Synthesis and biological evaluation of truncated derivatives of abyssomicin C as antibacterial agents

• Leticia Monjas,
• Peter Fodran,
• Johanna Kollback,
• Carlo Cassani,
• Thomas Olsson,
• Maja Genheden,
• D. G. Joakim Larsson and
• Carl-Johan Wallentin

Beilstein J. Org. Chem. 2019, 15, 1468–1474, doi:10.3762/bjoc.15.147

• develop new antibiotics, but the reevaluation of known natural products (NP) and the identification of new NPs and derivatives thereof is considered an especially important pathway in the search for more robust antibiotics [1][2]. The main reasons are the inherent high selectivity and appropriate

• physicochemical properties that NPs typically show [3]. Abyssomicin C (AbC) is an NP with antibacterial activity that was isolated from the marine actinomycete strain Verrucosispora AB-18-032 in 2004 [4][5]. It shows antibacterial activity against Gram-positive bacteria, including resistant pathogens such as

• methicillin- and vancomycin-resistant Staphylococcus aureus (MRSA and VRSA) with minimum inhibitory concentration (MIC) values of 4 and 13 µg/mL, respectively [4]. AbC belongs to a small family of NPs and two congeners of this family lacking the enone functionality, abyssomicins B and D, were discovered at

Spectroelectrochemical studies on the effect of cations in the alkaline glycerol oxidation reaction over carbon nanotube-supported Pd nanoparticles

• Dennis Hiltrop,
• Steffen Cychy,
• Karina Elumeeva,
• Wolfgang Schuhmann and
• Martin Muhler

Beilstein J. Org. Chem. 2018, 14, 1428–1435, doi:10.3762/bjoc.14.120

• , 44780 Bochum, Germany 10.3762/bjoc.14.120 Abstract The effects of the alkali cations Na+ and K+ were investigated in the alkaline electrochemical oxidation of glycerol over Pd nanoparticles (NPs) deposited on functionalized carbon nanotubes (CNTs). The electrocatalytic activity was assessed by cyclic

• the basic nitrogen species in the NCNT support. Adsorbed Na+ ions can form complexes with the organic molecules, presumably enhanced by the chelate effect. In this way, the organic molecules are assumed to be bound more tightly to the NCNT support in close proximity to the Pd NPs facilitating their

• fine chemicals it is important to extend the knowledge about this effect. In this study we used Pd nanoparticles (NPs) deposited on functionalized carbon nanotubes (Pd/xCNT, x = N or O) for catalyzing the glycerol oxidation reaction (GOR). Pd/NCNT has been investigated recently in the ethanol