Development of a chemical scaffold for inhibiting nonribosomal peptide synthetases in live bacterial cells

• Fumihiro Ishikawa,
• Sho Konno,
• Hideaki Kakeya and
• Genzoh Tanabe

Beilstein J. Org. Chem. 2024, 20, 445–451, doi:10.3762/bjoc.20.39

• University, Sakyo, Kyoto 606-8501, Japan 10.3762/bjoc.20.39 Abstract The adenylation (A) domain is essential for non-ribosomal peptide synthetases (NRPSs), which synthesize various peptide-based natural products, including virulence factors, such as siderophores and genotoxins. Hence, the inhibition of A

• synthetase A (GrsA) in the gramicidin S-producer Aneurinibacillus migulanus ATCC 9999, providing an alternative scaffold to develop novel A-domain inhibitors. Keywords: adenylation domain inhibitor; gramicidin S synthetase; natural product; nonribosomal peptide; nonribosomal peptide synthetase

• biosynthesis by using small molecules can help to elucidate their natural functions and their potential as therapeutic targets. NRPs are synthesized by large, versatile, and multifunctional proteins called nonribosomal peptide synthetases (NRPSs), which are composed of multiple modules and subdivided domains

Discovery of unguisin J, a new cyclic peptide from Aspergillus heteromorphus CBS 117.55, and phylogeny-based bioinformatic analysis of UngA NRPS domains

• Sharmila Neupane,
• Marcelo Rodrigues de Amorim and
• Elizabeth Skellam

Beilstein J. Org. Chem. 2024, 20, 321–330, doi:10.3762/bjoc.20.32

• 2 was determined by Marfey’s method. A biosynthetic gene cluster (BGC) encoding unguisins B and J was compared to characterized BGCs in other Aspergillus sp. Since the unguisin family of heptapetides incorporate different amino acid residues at different positions of the peptide, the A and C domains

• of the UngA NRPS were analyzed in an attempt to understand the lack of substrate specificity observed. Keywords: adenylation domain; condensation domain; fungal non-ribosomal peptide synthetase; heptapeptide; unguisin biosynthesis; Introduction Unguisins are a small family of fungal cyclic

• small peptides [3][4][9], however, unguisin A has been shown to bind a series of anions [10]. Recently the biosynthesis of unguisins A and B from Aspergillus violaceofuscus CBS 115571 was reported [5]. A seven module non-ribosomal peptide synthetase (NRPS; UngA) was heterologously expressed in

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• hexa-His tag, cleavable by TEV (Tobacco etch virus) protease. Despite the presence of the DsbC signal peptide, we did not observe periplasmic localization, and all proteins were instead purified from the cytoplasm. Ni-NTA affinity chromatography followed by TEV protease cleavage of the fusion construct

Optimizations of lipid II synthesis: an essential glycolipid precursor in bacterial cell wall synthesis and a validated antibiotic target

• Milandip Karak,
• Cian R. Cloonan,
• Brad R. Baker,
• Rachel V. K. Cochrane and
• Stephen A. Cochrane

Beilstein J. Org. Chem. 2024, 20, 220–227, doi:10.3762/bjoc.20.22

• applications due to their improved solubility in aqueous systems. Assembly is achieved by integrating distinct carbohydrate, peptide, and polyprenyl phosphate building blocks. This modular synthetic method allows for the strategic substitution of constituent building blocks at different synthetic stages and

Perspectives on push–pull chromophores derived from click-type [2 + 2] cycloaddition–retroelectrocyclization reactions of electron-rich alkynes and electron-deficient alkenes

• Michio Yamada

Beilstein J. Org. Chem. 2024, 20, 125–154, doi:10.3762/bjoc.20.13

• chromophores, is the preferred method for stoppering. Accordingly, Li et al. synthesized a rotaxane 44 terminated using push–pull chromophores by incorporating concise peptide and DCNQ moieties and employing the threading–stoppering method (Scheme 16). In 44, the rod moiety and macrocycle feature short peptide

• substructures. Consequently, the macrocycle was tethered to the peptide segment through amide–amide hydrogen bonding, and 44 was obtained with 30% yield. The generation of 44 was accompanied by the formation of the corresponding free thread with 62% yield, resulting from the reaction between the thread

• yield for the ring-formation process was modest at 5% (see Scheme 16) [121][122]. The macrocycle in 46 was observed to engage with the peptide segment in low-polarity solvents. In contrast, 1H NMR analysis suggested that the macrocycle disengaged from the peptide segment and relocated along the alkyl

Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups

• Dayanne Martins,
• Roberta Lamosa,
• Talis Uelisson da Silva,
• Carolina B. P. Ligiero,
• Sérgio de Paula Machado,
• Daphne S. Cukierman and
• Nicolás A. Rey

Beilstein J. Org. Chem. 2023, 19, 1713–1727, doi:10.3762/bjoc.19.125

• affect its pharmacological properties and metallophoric potential against copper(II) when compared to the unsubstituted counterpart. Nevertheless, the bioinspired compound was still able to reduce oxidative stress and affect the aggregation of the amyloid-β peptide, related to pathophysiological events

Secondary metabolites of Diaporthe cameroonensis, isolated from the Cameroonian medicinal plant Trema guineensis

• Bel Youssouf G. Mountessou,
• Élodie Gisèle M. Anoumedem,
• Blondelle M. Kemkuignou,
• Yasmina Marin-Felix,
• Frank Surup,
• Marc Stadler and
• Simeon F. Kouam

Beilstein J. Org. Chem. 2023, 19, 1555–1561, doi:10.3762/bjoc.19.112

• great structural variability such as polyketides, terpenoids, polyketide synthase–nonribosomal peptide synthetase (PKS–NRPS) alkaloids, and cytochalasins, which have been considered as taxonomic markers of the genus [7][8][9][10]. However, it is worthwhile to mention that the name Phomopsis should no

Correction: Non-peptide compounds from Kronopolites svenhedini (Verhoeff) and their antitumor and iNOS inhibitory activities

• Yuan-Nan Yuan,
• Jin-Qiang Li,
• Hong-Bin Fang,
• Shao-Jun Xing,
• Yong-Ming Yan and
• Yong-Xian Cheng

Beilstein J. Org. Chem. 2023, 19, 1370–1371, doi:10.3762/bjoc.19.97

• , Shenzhen University, Shenzhen 518060, PR China Department of Pathogen Biology, Health Science Center, Shenzhen University, Shenzhen 518060, PR China 10.3762/bjoc.19.97 Keywords: arthropod; iNOS; Kronopolites svenhedini (Verhoeff); non-peptide small molecules; The structure of compound 1 of the original

Non-noble metal-catalyzed cross-dehydrogenation coupling (CDC) involving ether α-C(sp³)–H to construct C–C bonds

• Hui Yu and
• Feng Xu

Beilstein J. Org. Chem. 2023, 19, 1259–1288, doi:10.3762/bjoc.19.94

• unique catalytic behavior [89]. However, there are only a few examples of cobalt catalysis in CDC reactions. Limited by the activity of Co catalysts, there are few examples of Co-catalyzed reactions involving ether C(sp3)–H bond activation. The Co-catalyzed C(sp3)–C(sp3) CDC of glycine and peptide

Linker, loading, and reaction scale influence automated glycan assembly

• Marlene C. S. Dal Colle,
• Manuel G. Ricardo,
• Nives Hribernik,
• José Danglad-Flores,
• Peter H. Seeberger and
• Martina Delbianco

Beilstein J. Org. Chem. 2023, 19, 1015–1020, doi:10.3762/bjoc.19.77

• scale [19], and linkers [20][21] affect the overall yield of solid phase peptide synthesis (SPPS). In the past decades, several supports and linkers have been developed and commercialized for SPPS, enabling a wide range of applications. Solid supports are available with different linker loadings, with

• low loading (0.1–0.2 mmol/g) being beneficial to avoid aggregation of long peptide sequences, and high loadings (0.4–0.5 mmol/g) advantageous for more efficient syntheses [21]. Herein, we systematically investigate how variations in linker type, resin loading, and reaction scale influence the

• some peptide sequences [18]. Moreover, high-loading supports might result in inefficient UV cleavage due to quenching. These four supports were studied in AGA experiments performed at 15 and 30 µmol reaction scales. While AGA is commonly performed at a 15 µmol reaction scale, a larger reaction scale is

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

• antibacterial acitivity against resistant S. aureus strains. It is also an inhibitor of the enzyme peptide deformylases (PDFs). The synthesis comprised the reaction between the highly substituted hydroquinone 142 and dehydroalanine 143 in the presence of chiral phosphoric acid P7 as catalyst to prepare

Non-peptide compounds from Kronopolites svenhedini (Verhoeff) and their antitumor and iNOS inhibitory activities

• Yuan-Nan Yuan,
• Jin-Qiang Li,
• Hong-Bin Fang,
• Shao-Jun Xing,
• Yong-Ming Yan and
• Yong-Xian Cheng

Beilstein J. Org. Chem. 2023, 19, 789–799, doi:10.3762/bjoc.19.59

• methods. Selected compounds were evaluated for their biological properties against a mouse pancreatic cancer cell line and inhibitory effects on iNOS and COX-2 in RAW264.7 cells. Keywords: arthropod; iNOS; Kronopolites svenhedini (Verhoeff); non-peptide small molecules; Introduction The millipede (class

• . In our studies of arthropods over the years, we have found that non-peptide small molecules play a significant role in chemical structures and biological activities [11][12][13][14][15][16]. In examining the chemical constituents of the millipede K. svenhedini, the focus was directed toward non

• -peptide small molecules, leading to the isolation of six new and three known compounds (Figure 1) from its extract. These structures were determined by 1D and 2D NMR spectra and the experimental and calculated electronic circular dichroism (ECD) spectra. The six new compounds have been named kronopoone A

Synthesis of imidazo[1,2-a]pyridine-containing peptidomimetics by tandem of Groebke–Blackburn–Bienaymé and Ugi reactions

• Oleksandr V. Kolomiiets,
• Alexander V. Tsygankov,
• Maryna N. Kornet,
• Aleksander A. Brazhko,
• Vladimir I. Musatov and
• Valentyn A. Chebanov

Beilstein J. Org. Chem. 2023, 19, 727–735, doi:10.3762/bjoc.19.53

• target compounds, which contained two pharmacophores – [1,2-a]pyridine (1H-imidazo[1,2-b][1,2,4]triazole) and peptidomimetic moieties – were evaluated for their antibacterial activity and exhibited a weak effect. Drugs possessing imidazo[1,2-a]pyridine unit. Drugs possessing peptide unit. Diversity of

Palladium-catalyzed enantioselective three-component synthesis of α-arylglycine derivatives from glyoxylic acid, sulfonamides and aryltrifluoroborates

• Bastian Jakob,
• Nico Schneider,
• Luca Gengenbach and
• Georg Manolikakes

Beilstein J. Org. Chem. 2023, 19, 719–726, doi:10.3762/bjoc.19.52

• several well-known natural products with interesting biological properties, such as the glycopeptide antibiotics vancomycin and teicoplanin [5] or feglymycin [6], a 13mer peptide which contains nine α-arylglycines in its backbone. α-Arylglycine derivatives are used in the production of important drugs

• decrease of the isolated yields. As already demonstrated in our previous work, the Pbf-protected arylglycine products can be directly used as building blocks for peptide synthesis [22]. Finally, we utilized our method for the preparation of a protected version of p-hydroxyphenylglycine (Scheme 5), a common

• is an improved extension of our pervious protocol with arylboronic acids and provides access to enantioenriched α-arylglycines with an improved substrate diversity. It can be used for the direct synthesis of peptide-like building blocks, which can find direct application in the total synthesis of

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• fluorescence response. Compounds that consisted of pyrrole-guanidine attached to larger aryl moieties (pyrene and phenanthridine) bind to the human DPP III enzyme [17]. Pyrene–cyanine conjugates connected with a rigid triazole-peptide linker were designed and synthesized in our group and showed a strong pyrene

Dipeptide analogues of fluorinated aminophosphonic acid sodium salts as moderate competitive inhibitors of cathepsin C

• Karolina Wątroba,
• Małgorzata Pawełczak and
• Marcin Kaźmierczak

Beilstein J. Org. Chem. 2023, 19, 434–439, doi:10.3762/bjoc.19.33

• as potential inhibitors of cathepsins. The phosphorus atom by default should mimic the tetrahedral intermediate, but this role may also be played by the hydroxy group present in hydroxyphosphonates, which mimic the carbonyl carbon in the peptide bond by forming a hydrogen bond with the amino group of

Digyalipopeptide A, an antiparasitic cyclic peptide from the Ghanaian Bacillus sp. strain DE2B

• Adwoa P. Nartey,
• Aboagye K. Dofuor,
• Kofi B. A. Owusu,
• Anil S. Camas,
• Hai Deng,
• Marcel Jaspars and
• Kwaku Kyeremeh

Beilstein J. Org. Chem. 2022, 18, 1763–1771, doi:10.3762/bjoc.18.185

• acid sequence in the cyclic peptide backbone but differing only by the length of aliphatic fatty acid side chains. When tested against Trypanosoma brucei subsp. brucei strain GUTat 3.1 and Leishmania donovani (Laveran and Mesnil) Ross (D10), digyalipopeptide A (1) gave IC50 values of 12.89 µM (suramin

• , analysis of the LC–HRESIMSn showed the presence of several b and y sequence tag ions indicating fragmentations from the middle of the cyclic peptide and most importantly the specific positions of each amino acid residue (Figure 4). Due to the presence of the free hydroxy groups of aspartic and glutamic

• novo total synthesis or degradation. This is because in natural product peptides both the ᴅ- and ʟ-forms of the different amino acids may be incorporated into the peptide structure. In order to determine the regiochemistry of the Val, Leu, Asp, and Glu amino acid residues in compound 1, we deployed the

Inline purification in continuous flow synthesis – opportunities and challenges

• Jorge García-Lacuna and
• Marcus Baumann

Beilstein J. Org. Chem. 2022, 18, 1720–1740, doi:10.3762/bjoc.18.182

• used to trap carboxylic acids, from which the product can be released with diluted solutions of formic acid [95]. Another strategy that is applicable in the context of biocatalysis involves Ni–NTA resins used for protein purification which are commonly packed in cartridges to enable automated peptide

• dipeptide with the aim to overcome issues found in batch in relation to product stability and scale-up concerns. The peptide coupling reaction was performed continuously aided by a MSMPR crystallizer system. This system ultimately shortened the holding time for the quenched solution, leading to a robust

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

• -like pathways are canonical type I cis-acyltransferase polyketide synthases (PKSs) and type A non-ribosomal peptide synthetases (NRPSs) (Figure 2A) [25][26]. The substrate specificity of the specificity conferring domains in each module can be predicted from the sequences of adenylation (A) (for NRPS

• ])) [28]. In contrast, discrete multi-enzymatic assemblies utilize distinct, monofunctional enzymes. Examples are terpene (e.g., cyclooctatin (8) [29]), ribosomally synthesized and post-translationally modified peptide (RiPP), or NRPS-independent alkaloid pathways. In the case of terpene biosynthesis

• identification of RiPP BGCs (Figure 3C (e.g., tryptorubin (9) [33])) [21]. In addition, multiple RiPP tailoring enzymes harbor a precursor peptide-binding domain, the so-called RiPP recognition element (RRE) (Figure 3D (e.g., pyrroloquinoline quinone (PQQ, 10) [34])). RRE-derived signature motifs (i.e., short

Simple synthesis of multi-halogenated alkenes from 2-bromo-2-chloro-1,1,1-trifluoroethane (halothane)

• Yukiko Karuo,
• Atsushi Tarui,
• Kazuyuki Sato,
• Kentaro Kawai and
• Masaaki Omote

Beilstein J. Org. Chem. 2022, 18, 1567–1574, doi:10.3762/bjoc.18.167

• an aryl or alkynyl unit [16][17][18][19][20][21][22]. In a biological context, the fluoroalkenyl motif could be incorporated into peptides with the expectation that the fluoroalkenyl unit could serve as a peptide isostere and prevent unexpected hydrolysis of these compounds. Recent studies have shown

Solid-phase total synthesis and structural confirmation of antimicrobial longicatenamide A

• Takumi Matsumoto,
• Takefumi Kuranaga,
• Yuto Taniguchi,
• Weicheng Wang and
• Hideaki Kakeya

Beilstein J. Org. Chem. 2022, 18, 1560–1566, doi:10.3762/bjoc.18.166

• communication in the microbial world. Herein, we report the solid-phase total synthesis and structural confirmation of longicatenamide A. First, commercially unavailable building blocks were chemically synthesized with stereocontrol. Second, the peptide chain was elongated via Fmoc-based solid-phase peptide

• synthesis. Third, the peptide chain was cyclized in the solution phase, followed by simultaneous cleavage of all protecting groups to afford longicatenamide A. Chromatographic analysis corroborated the chemical structure of longicatenamide A. Furthermore, the antimicrobial activity of synthesized

• microbial world. To elucidate the role of compounds 1–4 in the microbial world, developing a strategy to synthesize compounds 1–4, including future derivatization to produce probe molecules, is required. Herein, we report the total synthesis of peptide 1 by Fmoc-based solid-phase peptide synthesis [9] and

Microelectrode arrays, electrosynthesis, and the optimization of signaling on an inert, stable surface

• Kendra Drayton-White,
• Siyue Liu,
• Yu-Chia Chang,
• Sakashi Uppal and
• Kevin D. Moeller

Beilstein J. Org. Chem. 2022, 18, 1488–1498, doi:10.3762/bjoc.18.156

• interactions [5][6][7]. For example, a binding curve generated for the interaction between an RGD-peptide (C-PEG6-GGRGDGP) and its integrin (α5,β1) target is shown in Figure 4 below. A PEG-linker was added to the RGD-peptide so that the peptide would not be buried in the polymer coating the surface of the

• peptide so that the thiol group in the sidechain could be used to place the molecule the array with the use of an electrochemically initiated Cu(I)-catalyzed cross-coupling reaction (Scheme 1) [9]. To this end, the Cu(I) catalyst needed for the reaction was generated at the electrodes by the reduction of

• Figure 4 representing the average current measured at three such blocks with the error bars indicating the range in the data. The use of the method to probe interactions between a v107-peptide and its targeted VEGF receptors proved equally effective [7]. The binding curve shown in Figure 4 did indicate a

Derivatives of benzo-1,4-thiazine-3-carboxylic acid and the corresponding amino acid conjugates

• Péter Kisszékelyi,
• Tibor Peňaška,
• Klára Stankovianska,
• Mária Mečiarová and
• Radovan Šebesta

Beilstein J. Org. Chem. 2022, 18, 1195–1202, doi:10.3762/bjoc.18.124

• isolated. Moreover, the coupling of benzothiazines with amino acids was realized. In doing so, an enantioselective synthesis of the nonproteinogenic amino acid 2-amino-3-propylhexanoic acid was accomplished. Keywords: amino acid; benzothiazine; oxidative dimerization; peptide coupling; stereoselective

Synthesis of tryptophan-dehydrobutyrine diketopiperazine and biological activity of hangtaimycin and its co-metabolites

• Houchao Xu,
• Anne Wochele,
• Minghe Luo,
• Gregor Schnakenburg,
• Yuhui Sun,
• Heike Brötz-Oesterhelt and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 1159–1165, doi:10.3762/bjoc.18.120

• , People's Republic of China Institute of Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany 10.3762/bjoc.18.120 Abstract An improved synthesis for tryptophan-dehydrobutyrine diketopiperazine (TDD), a co-metabolite of the hybrid polyketide/non-ribosomal peptide

• -AT, [3][4]) polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) [2] with a dehydrating bimodule [5][6] involved in the installation of the remaining Z-configured double bond within the polyketide backbone [7]. Furthermore, a cytochrome P450 monooxygenase was recently shown to be

• responsible for the oxidation of deoxyhangtaimycin (3), a compound with antiviral activity, to 1 [8]. The thereby installed hemiaminal function is also the breaking point for 1 into a larger lactone-polyene peptide fragment and a smaller fragment HTM222 (2, named after its molecular mass of 222 Da) [2

Enzymes in biosynthesis

• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 1131–1132, doi:10.3762/bjoc.18.116

• proceed through multistep cationic cascade reactions and usually produce a polycyclic terpene hydrocarbon or alcohol with multiple stereogenic centers. While these transformations require only a single enzyme, polyketide and nonribosomal peptide biosyntheses are catalyzed by megasynthases that follow an

• assembly line logic, with individual domains for each single step [2]. Furthermore, the domains are organized into modules, each of which is responsible for the incorporation of one extender unit into the growing polyketide or peptide chain. With our knowledge today, the function of these large enzyme