The enzymes of microbial nicotine metabolism

• Paul F. Fitzpatrick

Beilstein J. Org. Chem. 2018, 14, 2295–2307, doi:10.3762/bjoc.14.204

• deal of interest in identifying bacteria capable of degrading it. A number of microbial pathways have been identified for nicotine degradation. The first and best-understood is the pyridine pathway, best characterized for Arthrobacter nicotinovorans, in which the first reaction is hydroxylation of the

• the pyridine and pyrrolidine pathways are the best understand reactions by which bacteria degrade nicotine, additional pathways continue to be discovered. The best-characterized is a hybrid of the pyridine and pyrrolidine pathways (Scheme 11). Based on phylogenetic analysis, the pathway is more

• closely related to the pyrrolidine pathway, with both found predominantly in Gram-negative bacteria [65]. This pathway is best characterized for Agrobacter tumefaciens S33, Ochrobactrum sp. SJY1, Sphingomonas melonis TY, and Shinella sp. HZN7, but has been identified in other bacteria as well [65][66][67

Diazirine-functionalized mannosides for photoaffinity labeling: trouble with FimH

• Femke Beiroth,
• Tomas Koudelka,
• Thorsten Overath,
• Stefan D. Knight,
• Andreas Tholey and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1890–1900, doi:10.3762/bjoc.14.163

• ) of bacteria to the glycosylated surface of their target cells and constitute important virulence factors in bacterial infection such as urinary tract infection [13][14][15][16]. Hence, FimH is an interesting target protein in medicinal chemistry and proteomics [17][18]. It is a two-domain protein

Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae

• Bimal Koirala,
• Robert A. Hillman,
• Erin K. Tiwold,
• Michael A. Bertucci and
• Yftah Tal-Gan

Beilstein J. Org. Chem. 2018, 14, 1769–1777, doi:10.3762/bjoc.14.151

• States 10.3762/bjoc.14.151 Abstract Quorum sensing (QS) is a cell–cell communication mechanism that enables bacteria to assess their population density and alter their behavior upon reaching high cell number. Many bacterial pathogens utilize QS to initiate an attack on their host, thus QS has attracted

• stimulating peptide (CSP); protein–peptide interactions; quorum sensing; Streptococcus pneumoniae; structure–activity relationships (SAR); Introduction Quorum sensing (QS), a cell-density mechanism utilized by bacteria to assess their population density through the detection of diffusible signal molecules

• ]. Bacterial growth conditions. Bacteria from a freezer stock were grown as described in [19]. Briefly, the bacteria were streaked into a THY agar plate supplemented with 5% donor horse serum and chloramphenicol at a final concentration of 4 µg/mL. The plate was incubated for 8 h in a CO2 incubator (37 °C with

Natural and redesigned wasp venom peptides with selective antitumoral activity

• Marcelo D. T. Torres,
• Gislaine P. Andrade,
• Roseli H. Sato,
• Cibele N. Pedron,
• Tania M. Manieri,
• Giselle Cerchiaro,
• Anderson O. Ribeiro,
• Cesar de la Fuente-Nunez and
• Vani X. Oliveira Jr.

Beilstein J. Org. Chem. 2018, 14, 1693–1703, doi:10.3762/bjoc.14.144

• and to avoid toxicity towards normal host cells. Antimicrobial peptides (AMPs) are produced by the innate immune system of virtually every organism on Earth. These agents represent promising anticancer candidates since, in addition to their activity vs bacteria [1], viruses, parasites [2][3][4][5][6

• et al. described decoralin (Dec-Ser-Leu-Leu-Ser-Leu-Ile-Arg-Lys-Leu-Ile-Thr), an α-helical AMP from Oreumenes decoratus wasp venom [24]. In addition, the authors described its amidated analog (Dec-NH2), which displayed higher activity than its parent molecule against Gram-positive bacteria, Gram

• -negative bacteria, fungi, and protozoa. However, both peptides presented high hemolytic activity, which limited their use as potential therapies. Torres et al. synthesized Dec-NH2 analogs with single and double substitutions, which exhibited increased resistance to degradation and lower hemolytic activity

Lanyamycin, a macrolide antibiotic from Sorangium cellulosum, strain Soce 481 (Myxobacteria)

• Lucky S. Mulwa,
• Rolf Jansen,
• Dimas F. Praditya,
• Kathrin I. Mohr,
• Patrick W. Okanya,
• Joachim Wink,
• Eike Steinmann and
• Marc Stadler

Beilstein J. Org. Chem. 2018, 14, 1554–1562, doi:10.3762/bjoc.14.132

• of this class, bafilomycin A1 (Figure 3) is a useful biochemical tool as it prevents the re-acidification of synaptic vesicles once they have undergone exocytosis [14]. Bafilomycins are also known to be cytotoxic, inhibitors of autophagy, active against Gram-positive bacteria, yeast and fungi

• , nematodes, insects, immunosuppressant or with antitumor activities [12][13][14][15]. Therefore, lanyamycin (1/2) was tested in our screening panel against bacteria, fungi, mammalian cell cultures and for antiviral activity against HCV in human liver cells. Lanyamycin (1/2) was analyzed for antimicrobial

• activity against bacteria and fungi and showed moderate antifungal activity in addition to a good inhibition of Micrococcus luteus (Table 3). When lanyamycin (1/2) was evaluated for cytotoxicity against growing primary cell lines, mouse fibroblasts (L929), and human cancer cell lines, nasopharyngeal cells

Two new 2-alkylquinolones, inhibitory to the fish skin ulcer pathogen Tenacibaculum maritimum, produced by a rhizobacterium of the genus Burkholderia sp.

• Dandan Li,
• Naoya Oku,
• Atsumi Hasada,
• Masafumi Shimizu and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2018, 14, 1446–1451, doi:10.3762/bjoc.14.122

• inhibited the growth of the marine bacterium Tenacibaculum maritimum, an etiological agent of skin ulcers in marine fish, offering new opportunities to develop antibacterial drugs for fish farming. Keywords: antimicrobial; Burkholderia; quinolone; skin ulcer; Tenacibaculum maritimum; Findings Bacteria of

• the genus Burkholderia within the family Burkholderiaceae [1], along with their neighboring genera, Paraburkholderia, Caballeronia [2], and Robbsia [3] constitute a distinct group of bacteria within the class Betaproteobacteria. These bacteria are obligatory aerobic, mostly motile, non-spore-forming

• Gram-negative rods of strictly terrestrial origin. Although isolation of Burkholderia from marine sediments has been reported, these bacteria may not originate in the marine environment, as enrichment in low salinity media is a prerequisite for isolation [4][5][6]. Most of them live in close

Acyl-group specificity of AHL synthases involved in quorum-sensing in Roseobacter group bacteria

• Lisa Ziesche,
• Jan Rinkel,
• Jeroen S. Dickschat and
• Stefan Schulz

Beilstein J. Org. Chem. 2018, 14, 1309–1316, doi:10.3762/bjoc.14.112

• /bjoc.14.112 Abstract N-Acylhomoserine lactones (AHLs) are important bacterial messengers, mediating different bacterial traits by quorum sensing in a cell-density dependent manner. AHLs are also produced by many bacteria of the marine Roseobacter group, which constitutes a large group within the marine

• microbiome. Often, specific mixtures of AHLs differing in chain length and oxidation status are produced by bacteria, but how the biosynthetic enzymes, LuxI homologs, are selecting the correct acyl precursors is largely unknown. We have analyzed the AHL production in Dinoroseobacter shibae and three

• ; fatty acid composition; N-acylhomoserine lactones; quorum sensing; Phaeobacter inhibens; Introduction The Roseobacter group, a subgroup of the Rhodobacteraceae family, constitutes an important class of Gram-negative marine bacteria, occurring in many different habitats [1][2], in fresh water as well as

Synthetic avenues towards a tetrasaccharide related to Streptococcus pneumonia of serotype 6A

• Aritra Chaudhury,
• Mana Mohan Mukherjee and
• Rina Ghosh

Beilstein J. Org. Chem. 2018, 14, 1095–1102, doi:10.3762/bjoc.14.95

• : Laboratory of Bioorganic Chemistry, NIH, NIDDK, Bethesda, MD, USA 10.3762/bjoc.14.95 Abstract Streptococcus pneumonia (SPn) is a Gram-positive bacterium which causes life threatening diseases. The bacteria protect themselves against non-specific host defence by an external polysaccharide (PS) capsule which

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

• substituent (3-quinolinyl nitrogen forming a hydrogen bond with a guanine amino group at the base of the minor groove) and a low pKa tail group. This drug was further selected for the treatment of Gram-positive bacteria Clostridium difficile infections and is currently in the phase II clinical trials

Mechanochemistry of nucleosides, nucleotides and related materials

• Olga Eguaogie,
• Joseph S. Vyle,
• Patrick F. Conlon,
• Manuela A. Gîlea and
• Yipei Liang

Beilstein J. Org. Chem. 2018, 14, 955–970, doi:10.3762/bjoc.14.81

• reported in 1957. More recently, RNA was extracted from both Gram-negative and Gram-positive bacteria by hand grinding in a mortar with phenol under cooling with liquid nitrogen [71] . The reproducibility of studies requiring arduous mechanochemical operations to be performed by hand lead to the rapid

• ) which were agitated using a membrane valve [80]. Within three minutes, almost complete disruption of Gram-positive bacteria was effected enabling downstream analysis by quantitative PCR. Associative processes Variable drug bioavailability associated with crystal and co-crystal polymorphism can be

Carbohydrate inhibitors of cholera toxin

• Vajinder Kumar and
• W. Bruce Turnbull

Beilstein J. Org. Chem. 2018, 14, 484–498, doi:10.3762/bjoc.14.34

• diarrhea is an AB5 toxin released by the bacteria. Thus, an understanding of this toxin becomes essential in finding/developing molecules that could prevent cell entry of the toxin and inhibit its activity. AB5 toxins are an important class of bacterial toxins. They consist of a single A-subunit and a

Latest development in the synthesis of ursodeoxycholic acid (UDCA): a critical review

• Fabio Tonin and
• Isabel W. C. E. Arends

Beilstein J. Org. Chem. 2018, 14, 470–483, doi:10.3762/bjoc.14.33

• biosynthesis takes place in the liver starting from cholesterol: 17 enzymes are involved in the production of these molecules. The final products are the so-called primary bile acids: CDCA and CA [23]. Subsequently, these bile acids can be modified by intestinal bacteria to form the secondary bile acids as

• downregulation of the cholesterol-7-α-hydroxylase, that represent the rate-limiting step in bile acid synthesis [31]. It can be metabolized by bacteria in the colon to form the secondary bile acid known as LCA [32]. LCA and other bile acids LCA, also known as 3α-hydroxy-5β-cholan-24-oic acid (Figure 2), is a

• secondary bile acid. It is produced by bacteria in the colon from CDCA trough the dehydroxylation of the C7 functional group of the steroid framework. Low percentages of other secondary bile acids and related keto derivatives can be found in the bile. The solubility properties, interactions and metabolisms

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

• CpG ODNs in animal models infected by viruses and/or bacteria to evaluate the correlation between extended immunostimulation and resistance. The most recent data reported by Beaucage on thermosensitive PS DNA prodrugs were related to the assessment of their internalization in various cell lines [62

Volatiles from the tropical ascomycete Daldinia clavata (Hypoxylaceae, Xylariales)

• Tao Wang,
• Kathrin I. Mohr,
• Marc Stadler and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2018, 14, 135–147, doi:10.3762/bjoc.14.9

• products so far. Biological characterisation of compounds Three of the volatile metabolites identified from D. clavata (compounds 9, 14 and 17) were evaluated for antimicrobial and cytotoxic activities using a standard panel of fungi and bacteria, as well as the murine cell line L929 (Table 3). The 2

Aminosugar-based immunomodulator lipid A: synthetic approaches

• Alla Zamyatina

Beilstein J. Org. Chem. 2018, 14, 25–53, doi:10.3762/bjoc.14.3

• Alla Zamyatina Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria 10.3762/bjoc.14.3 Abstract The immediate immune response to infection by Gram-negative bacteria depends on the structure of a lipopolysaccharide (LPS, also known as

• . The receptors of the innate immune system can detect particular components present in bacteria, viruses or fungi which are designated as “pathogen associated molecular patterns” (PAMPs) [1]. These receptors, termed pattern recognition receptors (PRRs), are able of sensing and responding to PAMPs. The

• major surface antigen of Gram-negative bacteria, a complex heterogeneous glycolipid lipopolysaccharide (LPS, or endotoxin) [2][3], is recognised by a receptor complex composed of Toll-like Receptor 4 (TLR4) and a co-receptor protein myeloid differentiation factor 2 (MD-2) which are expressed by

Recent applications of click chemistry for the functionalization of gold nanoparticles and their conversion to glyco-gold nanoparticles

• Vivek Poonthiyil,
• Thisbe K. Lindhorst,
• Vladimir B. Golovko and
• Antony J. Fairbanks

Beilstein J. Org. Chem. 2018, 14, 11–24, doi:10.3762/bjoc.14.2

• sensors for various biomolecules and toxins, including the detection of pathogenic agents such as viruses and bacteria, have also been reported by various groups [11][12][13][14][15][16]. Since the first report by Penadés [8], numerous methods have been developed for the synthesis of GAuNPs. However

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• control experiments [58]. It is worth mentioning here that bacteria have different ways to interact with extracellular DNA. In some cases they can naturally internalize and integrate exogenous DNA (natural competence) and this can result in the acquisition of new genetic traits (e.g., antibiotic

• resistance genes) and the emergence of multidrug resistant strains [59]. In addition, extracellular DNA has been shown to be important for biofilm establishment and maintenance by pathogenic bacteria, such as Pseudomonas aeruginosa and Staphylococcus aureus [60][61][62]. Some other bacteria, such as E. coli

• , can undergo a transient period of competence after a pretreatment with calcium chloride followed by a short heat or electric shock. The addition of CaCl2 promotes the binding of pDNA to the outer membrane of Gram-negative bacteria. The Ca2+ ions both attract the negatively charged DNA backbone and

Consecutive hydrazino-Ugi-azide reactions: synthesis of acylhydrazines bearing 1,5-disubstituted tetrazoles

• Angélica de Fátima S. Barreto,
• Veronica Alves dos Santos and
• Carlos Kleber Z. Andrade

Beilstein J. Org. Chem. 2017, 13, 2596–2602, doi:10.3762/bjoc.13.256

• linatine [24] and the antibiotic negamycin, active against Gram-negative bacteria [25], among others [26]. Furthermore, trisubstituted acylhydrazines were found to serve as tertiary amide bioisosters [27]. Therefore, it is highly desirable to have a method that allows an easy incorporation of hydrazino

What contributes to an effective mannose recognition domain?

• Christoph P. Sager,
• Deniz Eriş,
• Martin Smieško,
• Rachel Hevey and
• Beat Ernst

Beilstein J. Org. Chem. 2017, 13, 2584–2595, doi:10.3762/bjoc.13.255

• lectins, the bacterial adhesins, play an important role in the initial interaction of the bacterium with host tissue [9][10]. This primary contact is a prerequisite for the infection of host cells and subsequent biofilm formation, and grants the bacteria a significant advantage by resisting clearance and

• additional hydroxy group would not contribute the maximum penalty associated with an isolated one. The cost of desolvating calcium ions (Figure 5). Opportunistic bacteria such as Pseudomonas aeruginosa or Burkholderia cenocepacia have incorporated a second calcium ion into their binding site, coordinating

Herpetopanone, a diterpene from Herpetosiphon aurantiacus discovered by isotope labeling

• Xinli Pan,
• Nicole Domin,
• Sebastian Schieferdecker,
• Hirokazu Kage,
• Martin Roth and
• Markus Nett

Beilstein J. Org. Chem. 2017, 13, 2458–2465, doi:10.3762/bjoc.13.242

• resemblance to cadinane-type sesquiterpenes from plants, but is structurally entirely unprecedented in bacteria. Based on its molecular architecture, a possible biosynthetic pathway is postulated. Keywords: genome mining; herpetopanone; Herpetosiphon; isotope labeling; terpene; Introduction Terpenoids

• an agar diffusion assay against a standard selection of Gram-positive and Gram-negative bacteria as well as some fungi. However, the compound was inactive at all tested concentrations. A literature search revealed that 1 is the first microbial terpene possessing an octahydro-1H-indene backbone

Diosgenyl 2-amino-2-deoxy-β-D-galactopyranoside: synthesis, derivatives and antimicrobial activity

• Henryk Myszka,
• Patrycja Sokołowska,
• Agnieszka Cieślińska,
• Andrzej Nowacki,
• Maciej Jaśkiewicz,
• Wojciech Kamysz and
• Beata Liberek

Beilstein J. Org. Chem. 2017, 13, 2310–2315, doi:10.3762/bjoc.13.227

• the obtained compounds are active against Gram-positive bacteria and Candida type fungi. Keywords: antimicrobial activities; D-galactosamine; diosgenin; glycosylation; saponin; tetrachlorophthalimido derivatives; Introduction Saponins are steroid or triterpenoid glycosides found in various plants [1

• against the following six Gram-positive bacteria species: Enterococcus faecalis, Enterococcus faecium, Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pyogenes and Streptococcus pneumoniae. The minimum inhibitory concentrations (MICs) were determined by the broth microdilution method

• hydrochloride of 5 inhibits the growth of the fungus genus Candida; however, this saponin is more active against C. tropicalis (MIC 4 μg/mL) than against C. albicans (MIC 64 μg/mL). In turn, hydrochloride 5 has no inhibitory activity against the tested Gram-positive bacteria. The N-trifluoroacetyl derivative of

Superstructures with cyclodextrins: Chemistry and applications IV

• Gerhard Wenz

Beilstein J. Org. Chem. 2017, 13, 2157–2159, doi:10.3762/bjoc.13.215

• Thematic Series in the article by Leclercq [19]. For example, β-CD was immobilized onto a silicon substrate and incubated with various bacteria. These bacteria could be captured nearly quantitatively at the surface and released again by competitive binding with free methylated β-CD [20]. The proteins

Enzymatic synthesis of glycosides: from natural O- and N-glycosides to rare C- and S-glycosides

• Jihen Ati,
• Pierre Lafite and
• Richard Daniellou

Beilstein J. Org. Chem. 2017, 13, 1857–1865, doi:10.3762/bjoc.13.180

• sugar donor scope, and our group has shown the potency of this enzyme as a biocatalyst for the chemoenzymatic synthesis of non-natural desulfoglycosinolates [22]. More recently, S-glycosylated peptides have been identified, and characterized. In bacteria the structures of sublancin [23], glycocin F [24

• found in maize (UGT708A6), rice (OsCGT), buckwheat (FeCGT), Mangifera indica (MiCGT), Arabidopsis thaliana (AtCGT), fungi (UrdGT2 and SsfS6) or bacteria (iroB). General mechanisms of the O-GHs-catalysed hydrolysis. Neighbouring group participation mechanism of retaining the O-GHs-catalysed hydrolysis

The chemistry and biology of mycolactones

• Matthias Gehringer and
• Karl-Heinz Altmann

Beilstein J. Org. Chem. 2017, 13, 1596–1660, doi:10.3762/bjoc.13.159

• can also be hosted and transmitted by living organisms such as aquatic insects [26], mosquitoes [27], fish and amphibians [28]. Upon infection, M. ulcerans is usually concentrated in a small focus surrounded by a larger necrotic area that contains few bacteria. Based on this observation, Connor and

• mycolactone-producing bacteria should be reclassified as M. ulcerans [45]. Within this review, however, the originally proposed species names (M. marinum, M. ulcerans ecovar liflandii, M. pseudoshottsii, M. ulcerans subsp. shinshuense) will be used. It should also be noted at this point that the nomenclature

Chemical systems, chemical contiguity and the emergence of life

• Terrence P. Kee and
• Pierre-Alain Monnard

Beilstein J. Org. Chem. 2017, 13, 1551–1563, doi:10.3762/bjoc.13.155

• understanding of living systems or their components to emerge, even allowing for new aspects of biochemistry to be revealed, such as for example, the discovery of riboswitch activity in bacteria after their selection in the laboratory [102]. However, the knowledge gained has also highlighted some clear issues