Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• species [12]. The presence of mycobacterial lectins was further supported by Abhinav et al. using in silico genome analysis. A bioinformatics homology-based search of lectin-encoding gene regions in 30 fully or partially sequenced mycobacterial genomes identified 94 potential glycan-binding proteins. The

• proteins, as reported by Singh et al. The three genes in bold (Rv2075, Rv1419, Rv0475) were also identified by Abhinav et al., using different bioinformatics methods. Only two of the encoded proteins have been biochemically characterized to date. Acknowledgements K. K. thanks Dr. Gareth A. Prosser for

Biosynthetic origin of butyrolactol A, an antifungal polyketide produced by a marine-derived Streptomyces

• Enjuro Harunari,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2017, 13, 441–450, doi:10.3762/bjoc.13.47

• experiments of isotope-labeled precursors in combination with the bioinformatics analysis of its biosynthetic genes. The overall result of labeling experiments is summarized in Figure 8. The tert-butyl group was shown to be derived from the C-methylated isopropyl group of valine. This is the first study that

Polyketide stereocontrol: a study in chemical biology

• Kira J. Weissman

Beilstein J. Org. Chem. 2017, 13, 348–371, doi:10.3762/bjoc.13.39

• (i.e., formation of the methylmalonyl-O-AT intermediate) [30]. Substrate preference can be rationalized, at least in part, by bioinformatics which has revealed several sequence motifs correlating with building block choice (whether for starter or extender units, malonyl or branching extender units) [31

• stereochemistry by site-directed mutagenesis awaits identification of further stereochemical determinants in ER active sites. Bioinformatics-guided structure elucidation The strong correlations between certain sequence motifs present in PKS domains and the stereochemistry of the resulting polyketide chains has

A chemoselective and continuous synthesis of m-sulfamoylbenzamide analogues

• Arno Verlee,
• Thomas Heugebaert,
• Tom van der Meer,
• Pavel I. Kerchev,
• Frank Van Breusegem and
• Christian V. Stevens

Beilstein J. Org. Chem. 2017, 13, 303–312, doi:10.3762/bjoc.13.33

• Systems Biology, VIB, Ghent University, Technologiepark 927, B-9000 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium 10.3762/bjoc.13.33 Abstract For the synthesis of m-sulfamoylbenzamide analogues, small molecules which are

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• where the three-dimensional structures are known [35]. NCBI Basic Local Alignment Search Tool (BLAST) is one of the most popular bioinformatics sequence alignment tools used with sequence similarity searches [36]. Once a homologous protein structure for the sequence has been identified, building the

Discovery of an inhibitor of the production of the Pseudomonas aeruginosa virulence factor pyocyanin in wild-type cells

• Bernardas Morkunas,
• Balint Gal,
• Warren R. J. D. Galloway,
• James T. Hodgkinson,
• Brett M. Ibbeson,
• Yaw Sing Tan,
• Martin Welch and
• David R. Spring

Beilstein J. Org. Chem. 2016, 12, 1428–1433, doi:10.3762/bjoc.12.137

• , UK Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671 10.3762/bjoc.12.137 Abstract Pyocyanin is a small molecule produced by Pseudomonas aeruginosa that plays a crucial role in the pathogenesis of infections by this notorious opportunistic pathogen. The inhibition

Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin

• Waratchada Sangpheak,
• Jintawee Kicuntod,
• Roswitha Schuster,
• Thanyada Rungrotmongkol,
• Peter Wolschann,
• Nawee Kungwan,
• Helmut Viernstein,
• Monika Mueller and
• Piamsook Pongsawasdi

Beilstein J. Org. Chem. 2015, 11, 2763–2773, doi:10.3762/bjoc.11.297

• , Thailand Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand Institute of Theoretical Chemistry, University of Vienna, Vienna

Recent highlights in biosynthesis research using stable isotopes

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2015, 11, 2493–2508, doi:10.3762/bjoc.11.271

• promoter exchange [45] in the native host. Bioinformatics allowed for the annotation of several epimerization domains in the kollosin A NRPS, but it is hard to determine the actual activity of each of these functions. To overcome this problem, L-[2H8]valine, L-[2H10]leucin, L-[2H7,15N]tyrosine und L

Biocatalysis for the application of CO₂ as a chemical feedstock

• Apostolos Alissandratos and
• Christopher J. Easton

Beilstein J. Org. Chem. 2015, 11, 2370–2387, doi:10.3762/bjoc.11.259

• made in the fields of genetic engineering, bioinformatics and synthetic biology, as well as renewable electricity generation and bioelectrochemical engineering hold much promise for the development of the biotechnological platforms that

Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

• Chompoonut Rungnim,
• Sarunya Phunpee,
• Manaschai Kunaseth,
• Supawadee Namuangruk,
• Kanin Rungsardthong,
• Thanyada Rungrotmongkol and
• Uracha Ruktanonchai

Beilstein J. Org. Chem. 2015, 11, 2306–2317, doi:10.3762/bjoc.11.251

• University, Rangsit Center, Pathumthani 12120 Thailand Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok

OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS) to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands

• Kevin M. Bradley and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 1826–1833, doi:10.3762/bjoc.10.192

• a scalable and integrated infrastructure for the rapid and designed engineering of biology. Keywords: AEGIS; bioinformatics; DNA self-assembly; long DNA constructs; software; Introduction Automated synthesis of single stranded DNA fragments has, perhaps more than any other technology, enabled the

• R2 Standard. It is publicly accessible at http://bioinformatics.ffame.org/bioinformatics/OligArch.aspx. Some structures showing possible reasons why large DNA (L-DNA) constructs do not self-assemble from more than approximately a dozen synthetic single-stranded DNA oligonucleotides. Top from left to

Selective allylic hydroxylation of acyclic terpenoids by CYP154E1 from Thermobifida fusca YX

• Anna M. Bogazkaya,
• Clemens J. von Bühler,
• Sebastian Kriening,
• Alexandrine Busch,
• Alexander Seifert,
• Jürgen Pleiss,
• Sabine Laschat and
• Vlada B. Urlacher

Beilstein J. Org. Chem. 2014, 10, 1347–1353, doi:10.3762/bjoc.10.137

• YX that enables this type of oxidation. Several acyclic terpenoids were tested as possible substrates for CYP154E1, and the regio- and chemoselectivity of their oxidation was investigated. Using a previously established bioinformatics approach we identified position 286 in the active site of CYP154E1

• leading to mainly 8-hydroxy derivatives. Moreover, by bioinformatics analysis position 286 was identified and a simple point mutation changed the geometry of the active site of this P450 enzyme to shift the product spectrum for the selective oxidation of geranylacetone (9) and nerylacetone (10) to yield

Novel indolin-2-one-substituted methanofullerenes bearing long n-alkyl chains: synthesis and application in bulk-heterojunction solar cells

• Irina P. Romanova,
• Andrei V. Bogdanov,
• Inessa A. Izdelieva,
• Vasily A. Trukhanov,
• Gulnara R. Shaikhutdinova,
• Dmitry G. Yakhvarov,
• Shamil K. Latypov,
• Vladimir F. Mironov,
• Vladimir A. Dyakov,
• Ilya V. Golovnin,
• Dmitry Yu. Paraschuk and
• Oleg G. Sinyashin

Beilstein J. Org. Chem. 2014, 10, 1121–1128, doi:10.3762/bjoc.10.111

• Research Center of the Russian Academy of Sciences, Kazan 420088, Russian Federation Faculty of Physics and International Laser Center, M.V. Lomonosov Moscow State University, Moscow 119991, Russian Federation Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow

Cuevaenes C–E: Three new triene carboxylic derivatives from Streptomyces sp. LZ35ΔgdmAI

• Jing-Jing Deng,
• Chun-Hua Lu,
• Yao-Yao Li,
• Shan-Ren Li and
• Yue-Mao Shen

Beilstein J. Org. Chem. 2014, 10, 858–862, doi:10.3762/bjoc.10.82

• sequencing and bioinformatics analysis of Streptomyces sp. LZ35. This finding suggests the potential of LZ35 to produce 3-HBA-containing polyketides [4]. A gdmAI (encoding the first geldanamycin PKS module) deletion strain LZ35ΔgdmAI was constructed [3][5], as the production of geldanamycins was much higher

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

Beilstein J. Org. Chem. 2012, 8, 915–929, doi:10.3762/bjoc.8.104

• Thomas Lutteke Justus-Liebig-University Gießen, Institute of Veterinary Physiology and Biochemistry, Frankfurter Str. 100, 35392 Gießen, Germany 10.3762/bjoc.8.104 Abstract Glycoinformatics is a small but growing branch of bioinformatics and chemoinformatics. Various resources are now available

• aid with quality control. Specific problems of glycoinformatics compared to bioinformatics for genomics or proteomics, especially concerning integration and long-term maintenance of the existing glycan databases, are also discussed. Keywords: carbohydrates; databases; glycomics; software

• . Classical bioinformatics algorithms are developed for linear gene or protein sequences, and thus cannot be applied to branched carbohydrates. Instead, new algorithms that deal with the branching as well as with other special features of carbohydrates, such as microheterogeneity, have to be developed [6][7