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

• resulting peptides exhibit unique structural features due to thioether bridges between dehydrated serine or threonine (Dha/Dhb) and cysteine (Cys). These thioether bridges lead to cyclic peptides with the modified amino acid lanthionine (Dha-Cys) or methyllanthionine (Dhb-Cys). The strong antimicrobial

• localize novel evolutive clades This study used 28 amino acid sequences of LanM enzymes from MIBiG [38] whose activity has been experimentally proven [24] to identify homologous sequences using BLASTP [39] (in BV-BRC [40]). They are considered our reference sequences. Two of these reference sequences are

• enzymes amino acid sequences from MIBiG and the homologs identified in our study. The taxonomy of the bacteria to which they belong is indicated in the figure. The selected superclade highlighted in Figure 1, containing sequences that mainly belong to Bacilli and Clostridia, was of particular interest

Syntheses and medicinal chemistry of spiro heterocyclic steroids

• Laura L. Romero-Hernández,
• Ana Isabel Ahuja-Casarín,
• Penélope Merino-Montiel,
• Sara Montiel-Smith,
• José Luis Vega-Báez and
• Jesús Sandoval-Ramírez

Beilstein J. Org. Chem. 2024, 20, 1713–1745, doi:10.3762/bjoc.20.152

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

• pentacyclic core scaffold of 5. Overall, the single NRPS module SfmC is responsible for the construction of the highly functionalized scaffold 93 from the two simple amino acid derivatives 86 and 88. After NRPS-catalyzed scaffold assembly, SfmM1-mediated N-methylation at N12, and subsequent SfmO2/O4-promoted

• synthesis of the bis-THIQ alkaloid family, Oguri and Oikawa utilized the NRPS module SfmC to construct a highly functionalized scaffold from amino acid derivatives (Scheme 10) [102]. The total synthesis of 5 from original biosynthetic intermediate 93 requires regioselective amide bond cleavage to remove the

Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry

• Maria-Paula Schröder,
• Isabel P.-M. Pfeiffer and
• Silja Mordhorst

Beilstein J. Org. Chem. 2024, 20, 1652–1670, doi:10.3762/bjoc.20.147

• the specialised metabolism of bacteria and fungi. Each NRPS module is minimally composed of a condensation (C) domain, an adenylation (A) domain, and a peptidyl carrier protein (PCP or thiolation/T domain), and one module typically incorporates one amino acid into the final natural product. In

• [34]. In reductive amination, the substrate is usually an aldehyde or amine. After the formation of the iminium ion, it is reduced with the appropriate reagent to form the N-methylated amino acid. Different methods have been established using for example benzaldehyde as a protection group, sodium

• intermediate is then reduced with H2 [37]. When synthesising via a reductive ring opening, typically, an N-Fmoc-protected amino acid is condensed with formaldehyde in the presence of p-toluic acid in refluxing toluene to yield the 5-oxazolidinone. Reductive ring opening can be achieved by using an excess of

Mining raw plant transcriptomic data for new cyclopeptide alkaloids

• Draco Kriger,
• Michael A. Pasquale,
• Brigitte G. Ampolini and
• Jonathan R. Chekan

Beilstein J. Org. Chem. 2024, 20, 1548–1559, doi:10.3762/bjoc.20.138

• biosynthetic enzymes. Ultimately proteolysis releases the modified core peptide as the mature RiPP natural product [5][6]. In the case of the newly described burpitide family of RiPPs, the defining feature is the presence of amino acid side-chain crosslinks installed by a copper-dependent burpitide cyclase [4

• ]. These RiPP natural products encompass a wide range of structural scaffolds including cyclopeptide alkaloids that contain a phenolic ether-linkage and the lyciumin-type peptides that are composed of a crosslink between the Trp-indole-N and the carbon in another amino acid side chain or peptide backbone

• were prepared to match the core amino acids of the predicted ceanothine B and CAM603 cyclopeptide alkaloids. To make each amino acid standard, 0.2 mg of the ʟ- and ᴅ-amino acid was aliquoted into separate reaction vials. To each vial, 50 µL of water, 20 µL of 1 M NaHCO3, and 100 µL 1% Marfey’s reagent

Benzylic C(sp³)–H fluorination

• Alexander P. Atkins,
• Alice C. Dean and
• Alastair J. J. Lennox

Beilstein J. Org. Chem. 2024, 20, 1527–1547, doi:10.3762/bjoc.20.137

• FAT with Selectfluor to produce the desired benzyl fluoride. Increasing amino acid and Selectfluor loadings achieved difluorination of the benzylic substrates. This procedure was demonstrated predominately on primary benzylic substrates, but could be used to effect the fluorination of several

• radical benzylic C(sp3)–H fluorination using Selectfluor. Silver and amino acid-mediated benzylic fluorination. Copper-catalysed radical benzylic C(sp3)–H fluorination using NFSI. Copper-catalysed C(sp3)–H fluorination of benzylic substrates with electrochemical catalyst regeneration. Yields are NMR

Towards an asymmetric β-selective addition of azlactones to allenoates

• Behzad Nasiri,
• Ghaffar Pasdar,
• Paul Zebrowski,
• Katharina Röser,
• David Naderer and
• Mario Waser

Beilstein J. Org. Chem. 2024, 20, 1504–1509, doi:10.3762/bjoc.20.134

• -selective manner with moderate levels of enantioselectivities (up to 83:17 er). Furthermore, the obtained products can be successfully engaged in nucleophilic ring opening reactions, thus giving highly functionalized α-amino acid derivatives. Keywords: allenoates; amino acids; azlactones; organocatalysis

• -functionalizations by reacting them with suited C- or heteroatom electrophiles. α-Amino acid-derived azlactones 1 are amongst the most commonly utilized starting materials to access more diverse chiral α,α-disubstituted amino acids (Scheme 1A) [20][21][22]. More specifically, these compounds can be engaged in a

• thus wondering if we could extend this ammonium salt-catalyzed β-selective allenoate functionalization strategy to other amino acid classes. Azlactones 1 have previously been used for γ-selective additions to allenoates under chiral phosphine catalysis [28]. In addition, glycine Schiff base derivatives

Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain

• Changjun Xiang,
• Shunyu Yao,
• Ruoyu Wang and
• Lihan Zhang

Beilstein J. Org. Chem. 2024, 20, 1476–1485, doi:10.3762/bjoc.20.131

• , deepening our understanding of the stereocontrol of PKSs. Results and Discussion Preparation of KR sequence dataset We first curated the amino acid sequences of KR domains from characterized bacterial cis-AT PKSs recorded in MIBiG database [20] and by manual literature review. In total, 1,762 KRs whose

• observed in the KRC tree of actinobacterial β-modules, we next carried out sequence logo analyses to identify key amino acid residues associated with stereoselectivity. Comparison of sequence logos among different types of KRCs revealed that the previously reported motifs [8][9], such as LDD (2) for B-type

• bioinformatics perspective, and will facilitate accurate stereochemical prediction and genome mining of complex polyketides. Experimental Sequence collection and screening All cis-AT PKS and PKS-NRPS amino acid sequences recorded in MIBiG, as well as the PKS sequences reported in literatures we have curated were

Novel analogues of a nonnucleoside SARS-CoV-2 RdRp inhibitor as potential antivirotics

• Luca Julianna Tóth,
• Kateřina Krejčová,
• Milan Dejmek,
• Eva Žilecká,
• Blanka Klepetářová,
• Lenka Poštová Slavětínská,
• Evžen Bouřa and
• Radim Nencka

Beilstein J. Org. Chem. 2024, 20, 1029–1036, doi:10.3762/bjoc.20.91

• ], and thus avoiding the use of base, leading to the desired intermediate 14 in good yield. Compound 14 was then coupled with ʟ-tyrosine methyl ester followed by deprotection of the amino acid carboxyl group by LiOH⋅H2O. As in the previous base-mediated saponification, here we also received a product of

• synthetic strategy leading to pyridones bearing different aryl substituents is described in Scheme 2. During the Suzuki–Miyaura cross-coupling reaction, which introduced the substituents in the C-5 position, the methyl ester protection of the amino acid moiety was also cleaved, leading directly to the final

Auxiliary strategy for the general and practical synthesis of diaryliodonium(III) salts with diverse organocarboxylate counterions

• Naoki Miyamoto,
• Daichi Koseki,
• Kohei Sumida,
• Elghareeb E. Elboray,
• Naoko Takenaga,
• Ravi Kumar and
• Toshifumi Dohi

Beilstein J. Org. Chem. 2024, 20, 1020–1028, doi:10.3762/bjoc.20.90

• in organic chemistry and other scientific fields. The potential of diaryliodonium(III) carboxylates obtained in this study (i.e., Scheme 6B,C) and the related amino acid derivatives [46][47][48][49] as new arylating reagents will be further explored by conducting reactions with various nucleophiles

(Bio)isosteres of ortho- and meta-substituted benzenes

• H. Erik Diepers and
• Johannes C. L. Walker

Beilstein J. Org. Chem. 2024, 20, 859–890, doi:10.3762/bjoc.20.78

• reduction. Deprotection of the alcohol followed by two-step oxidation to the carboxylic acid yielded the non-natural β-amino acid (±)-50, which could then be transformed into diamine (±)-51 by Curtius rearrangement. Recently, Mykhailiuk and co-workers also reported the synthesis of 1,2-BCHs using an

• , respectively (Scheme 12B) [58]. Saponification of the ester moieties in these species followed by Curtius rearrangements then led to amines 114 and 116. Non-natural amino acid derivatives 113 and 117 are intermediates prepared using these methods that could be of interest to medicinal chemistry. Alcohol 111

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

• physiological function of NNG are discussed below. Results Screening of Vs NnlA homologs for NNG degradation activity To select Vs NnlA homologs to test for NNG degradation activity, we performed a BLAST search of the Vs NnlA amino acid sequence in the NCBI database. This search resulted in retrieval of 99

• homologous amino acid sequences with an E-value of less than 1 × 10−10. A subset of 55 of these sequences was selected with a query cover of greater than 88%. From these sequences, we selected five homologs of the nnlA gene [Pseudovibrio denitrificans JCM 1230 (Pd), Pseudovibrio japonicus strain KCTC 12861

• (Pj), Pseudonocardia spinosispora DSM 44797 (Ps), Mycobacterium sp. 1465703.0 (Ms), Microbispora rosea subsp. nonnitritogenes strain NRRL B-2631 (Mr)], which were synthesized and cloned into E. coli recombinant expression vectors. These homologs ranged in amino acid sequence identity from 46 to 76

Synthesis and characterization of water-soluble C₆₀–peptide conjugates

• Yue Ma,
• Lorenzo Persi and
• Yoko Yamakoshi

Beilstein J. Org. Chem. 2024, 20, 777–786, doi:10.3762/bjoc.20.71

•  1). Results and Discussion Syntheses of C60–oligopeptides 5a–c The oligopeptides 2a–c were synthesized on resin using Fmoc-protected amino acids with a standard SPPS method (Figure 1a) [43]. A moderate loading (0.4 mmol⋅g−1) of the initial amino acid was used. After synthesizing the pentamer of Lys

• acid-substituted C60 derivative 3 and the peptides on resin 2a–c were performed by SPPS to provide the C60–oligopeptides on resin 4a–c (Figure 1a). Subsequently, the last step of the reaction – the cleavage of the C60–peptide conjugate from the resin and the simultaneous deprotection of the amino acid

• the C60–peptide conjugates on resin 4a–c from 2a–c. The C60–oligopeptides 5a–c were obtained by cleavage from resin and simultaneous deprotection of the PGs on the amino acid side chains through the addition of by the addition of a mixture of TFA and TIPS in water. The most soluble conjugate, C60

Substrate specificity of a ketosynthase domain involved in bacillaene biosynthesis

• Zhiyong Yin and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2024, 20, 734–740, doi:10.3762/bjoc.20.67

• understanding of polyketide biosynthesis has been reached, including a detailed knowledge of the extender unit selection and the stereochemical implications that are predictable from amino acid sequences [5][6]. The polyene antibiotic bacillaene was first isolated from Bacillus subtilis [7]. This soil-dwelling

• , showing that the amino acid sequences of these KSs correlate with the structures of the processed PKS intermediates up to the β-carbon [20]. 13C NMR spectra of (R)-11 incubated with BaeJ-KS2 and BaeJ-KS2-C222A. A) Free 11 dissolved in incubation buffer; B) (R)-11 bound to BaeJ-KS2 after incubation and

Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization

• Senze Qiao,
• Zhongyu Cheng and
• Fuzhuo Li

Beilstein J. Org. Chem. 2024, 20, 721–733, doi:10.3762/bjoc.20.66

• several positions and also form 6–14 residue cyclic peptides [37][38]. It should be noted that TycC TE was more sensitive to the amino acid changes near the site of ring closure. The alkyne-containing analogs were conjugated to a variety of azido sugars via copper(I)-catalyzed cycloaddition to obtain the

• developed to address this challenge to produce daptomycin and its derivatives. These approaches include biosynthetic [49], chemoenzymatic [50], solid-phase [51], and solution-phase methods [52], but most only encompass modifications of the lipid chain and specific amino acid mutations. Learning from the

New variochelins from soil-isolated Variovorax sp. H002

• Jabal Rahmat Haedar,
• Aya Yoshimura and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2024, 20, 692–700, doi:10.3762/bjoc.20.63

• serine (Ser), a β-hydroxyaspartic acid (Hya), and a unique γ-amino acid biosynthetically originating from an arginine and a methyl malonate (4-amino-7-guanidino-3-hydroxy-2-methylheptanoic acid), with the amino group acylated by a saturated fatty acid. Subsequent HMBC and MS/MS analyses indicated that

• C45H79O17N11, as suggested by the HRESIMS data (m/z 1044.5603 for the [M − H]− ion), indicating the loss of two methylene groups (C2H4) from 1. In addition, the MS/MS fragmentation profile of 3 was consistent with those of 1 and 2, except for the loss of 28 mass units in the N-terminal Nγ-acyl-γ-amino acid

• ][18]. The absolute configurations of the amino acid constituents, Pro, Ser and two modified ornithine residues, in 3–5 were assigned as ʟ, ᴅ, and ʟ, respectively (Figures S25, S33, and S41, Supporting Information File 1). The geometry of the olefins in 4 and 5 was determined to be Z based on the 13C

Palladium-catalyzed three-component radical-polar crossover carboamination of 1,3-dienes or allenes with diazo esters and amines

• Geng-Xin Liu,
• Xiao-Ting Jie,
• Ge-Jun Niu,
• Li-Sheng Yang,
• Xing-Lin Li,
• Jian Luo and
• Wen-Hao Hu

Beilstein J. Org. Chem. 2024, 20, 661–671, doi:10.3762/bjoc.20.59

• -light-mediated palladium-catalyzed three-component radical-polar crossover carboamination of 1,3-dienes or allenes with diazo esters and amines, affording unsaturated γ- and ε-amino acid derivatives with diverse structures. In this methodology, the diazo compound readily transforms into a hybrid α-ester

• -amino acid derivative. This approach proceeds under mild and simple reaction conditions and shows high functional group tolerance, especially in the incorporation of various bioactive molecules. The studies on scale-up reactions and diverse derivatizations highlight the practical utility of this

• temperature (rt), the desired unsaturated ε-AA derivative 4a was obtained in 75% isolated yield (Table 1, entry 1). Isolation and NMR analysis demonstrated that this model reaction provided amino acid 4a with good E-selectivity and excellent regioselectivity (E/Z = 91:9, 1,4-/1,2-addition >20:1). Control

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• . Interestingly, this cluster is separated into two groups. All the sequences that group with Hyg17 are found in identical hygromycin A biosynthetic clusters. The second group has 12 of the 29 Hyg genes with greater than 30% amino acid identity (Figure 4b and Supporting Information File 1, Table S2). The strains

Recent developments in the engineered biosynthesis of fungal meroterpenoids

• Zhiyang Quan and
• Takayoshi Awakawa

Beilstein J. Org. Chem. 2024, 20, 578–588, doi:10.3762/bjoc.20.50

• sequential reaction to produce the spirolactone 27. In contrast, PrhA dehydrogenates H-1 of 26 to form the heptadiene 28. Comparing the active centers, only three amino acid residues differ between AusE and PrhA: L150(AusE)/V150(PrhA), S232(AusE)/A232(PrhA), and V241(AusE)/M241(PrhA). By swapping these

• preandiloid C (58), and generates a radical leading to the construction of the bicyclo[2.2.2]octane skeleton of andiconin (59) (Figure 8) [36][37]. Two amino acid pairs, M119/N121 and A228/A230, in its substrate-binding pocket were mutated by saturation mutagenesis using degenerate primers, resulting in an

A new analog of dihydroxybenzoic acid from Saccharopolyspora sp. KR21-0001

• Rattiya Janthanom,
• Yuta Kikuchi,
• Hiroki Kanto,
• Tomoyasu Hirose,
• Arisu Tahara,
• Takahiro Ishii,
• Arinthip Thamchaipenet and
• Yuki Inahashi

Beilstein J. Org. Chem. 2024, 20, 497–503, doi:10.3762/bjoc.20.44

• HCl. The obtained amino acid (alanine) and authentic amino acids were modified using Nα-(5-fluoro-2,4-dinitrophenyl)-ᴅ-leucinamide (ᴅ-FDLA). The LC–MS analysis of ᴅ-FDLA derivatives revealed that the chiral center of the amino acid in 1 had ʟ configuration (Figure S7, Supporting Information File 1

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

• arm in an adjacent peptidyl carrier protein (PCP). The amino acid loaded on the PCP then undergoes coupling with the amino acid loaded on the downstream PCP in the condensation (C) domain. Finally, the linear peptide on the PCP in the last module is either hydrolyzed or cyclized by a thioesterase (TE

• activities against the A-domain of MbtA, a component of mycobactin synthetase and antimicrobial activities against M. tuberculosis [7]. In addition, aminoacyl (AA)-AMS has been designed to inhibit the amino acid-activating A-domains in NRPSs and has been found to be a tight-binding inhibitor (Figure 2b) [8

• probes (AA-AMS-BPyne) can selectively label the A-domains corresponding to the amino acid of the ligand in both recombinant enzymes and proteomes. We recently reported that these probes can be used to label the A-domains of endogenous NRPSs in live bacterial cells [17][18][19]. The intracellular labeling

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

• heptapeptides isolated predominantly from Aspergillus sp. [1][2][3][4][5][6][7][8]. Distinctive features of these cyclic peptides include the non-proteinogenic amino acid γ-aminobutyric acid (GABA) and the incorporation of up to five ᴅ-amino acids (Figure 1) [1][2][3][4][5][6][7][8]. The amino acids at

• , 7.33, 7.07 and 6.97 ppm, exhibiting key 1H,1H-COSY and HMBC correlations, suggested a tryptophan aromatic amino acid portion (Figure 3). The other six amino acid residues were assigned based on 2D NMR spectra (1H-1H COSY, HSQC and HMBC) as Ala (2 equiv), Phe (1 equiv), Leu (1 equiv), Val (1 equiv), and

Catalytic multi-step domino and one-pot reactions

• Svetlana B. Tsogoeva

Beilstein J. Org. Chem. 2024, 20, 254–256, doi:10.3762/bjoc.20.25

• . Zhang, Ma, and W. Zhang reflects the state of the art in the α-amino acid-based [3 + 2] cycloaddition reactions of N–H-type azomethine ylides in multicomponent, one-pot, and stepwise reactions for the synthesis of diverse bioactive heterocyclic compounds and natural products [9]. Computational studies

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

• mixture which were then purified to give the desired α-anomers. Thioglycosides 1c, 1d, and 1f were isolated purely as β-anomers due to anchimeric assistance from the C2 N-acetyl or N-Troc groups. In glycosyl acceptors, the first amino acid of the lipid II pentapeptide, Ala, was incorporated as a 2

Copper-catalyzed multicomponent reaction of β-trifluoromethyl β-diazo esters enabling the synthesis of β-trifluoromethyl N,N-diacyl-β-amino esters

• Youlong Du,
• Haibo Mei,
• Ata Makarem,
• Ramin Javahershenas,
• Vadim A. Soloshonok and
• Jianlin Han

Beilstein J. Org. Chem. 2024, 20, 212–219, doi:10.3762/bjoc.20.21

• over 50% of agricultural chemicals contain at least one fluorine atom, among which architectural motifs containing fluorine and amino acid residues are a fast-growing segment of modern pharmaceuticals [10][11][12][13]. Fluoroalkyldiazo compounds belong to the most versatile and valuable reagents in

• example, Wan and co-workers developed a cascade reaction of α-diazo esters, nitriles, and carboxylic acids via the generation of nitrile ylides and Mumm rearrangement affording unsymmetric diacyl α-amino acid esters as products (Scheme 1a) [39]. In 2017, Zhang, Hu, and co-workers developed a Cu-catalyzed