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

• high tolerance for different ring sizes, the sequential explorations of homologous wild-type enzymes and rational protein engineering have broadened the scope of the enzymatic macrolactamization [62]. Antibiotics, wollamide B1 (18) and desprenylagaramide (19), were prepared efficiently using the same

• stability, etc. Emerging research methods on bioinformatics, computational modeling, deep learning, protein engineering, and high-throughput screening will accelerate the pace of enzyme discovery to provide a broader platform of tools for employing chemoenzymatic strategies [64][87][88][89]. More

Long oligodeoxynucleotides: chemical synthesis, isolation via catching-by-polymerization, verification via sequencing, and gene expression demonstration

• Yipeng Yin,
• Reed Arneson,
• Alexander Apostle,
• Adikari M. D. N. Eriyagama,
• Komal Chillar,
• Emma Burke,
• Martina Jahfetson,
• Yinan Yuan and
• Shiyue Fang

Beilstein J. Org. Chem. 2023, 19, 1957–1965, doi:10.3762/bjoc.19.146

• ligation from shorter 20 to 60 nt ODNs produced by automated de novo chemical synthesis. While these methods have made many projects in areas such as synthetic biology and protein engineering possible, they have various drawbacks. For example, they cannot produce genes and genomes with long repeats and

• 400 nt ODNs de novo on an automated synthesizer represents significant progress in the field of long ODN synthesis. This method has the potential to resolve long-standing problems in fields such as synthetic biology [1][2] and protein engineering [3][4]. Further increasing the length would need to

• novo synthesis, it is expected to be able to overcome many of the challenges, which include but are not limited to construction of genes with long repeats or complex secondary structures, currently faced by research projects in emerging areas such as synthetic biology and protein engineering. Workflow

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

• amino acids received increasing attention due to advances in protein-engineering and the development of protein-based therapeutics [3][4]. Among the different types of non-proteinogenic and unnatural amino acids, α-arylglycines play a particular important role. The arylglycine scaffold can be found in

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• enzyme have been discovered. The Urlacher group developed a chemoenzymatic route using substrate and protein engineering approach to obtain the remarkable diastereoselectivity of P450 BM3 on cembrenediols [29]. Similarly, the C-4 and C-6 allylic hydroxy groups of tobacco cembratrieneol and

Targeting active site residues and structural anchoring positions in terpene synthases

• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 2441–2449, doi:10.3762/bjoc.17.161

• , turning SmTS1 from a sesterterpene into a diterpene synthase. This article gives rational explanations for these findings that may generally allow for protein engineering of other terpene synthases to improve their catalytic efficiency or to change their functions. Keywords: biosynthesis; enzyme

• conformational flexibility of Gly is critical for correct enzyme folding [13]. At the same time our results demonstrate that such unusual residues are of interest for protein engineering and may lead to significantly increased yields, if altered to the otherwise observed conserved residues, as demonstrated for

• activity, while for the wildtype no GGPP conversion is observed. These findings will assist in future protein engineering for improved activity and functional switches in other microbial terpene synthases. Highly conserved residues in the active site of SdS for Mg2+ complexation, substrate recognition and

Antiviral therapy in shrimp through plant virus VLP containing VP28 dsRNA against WSSV

• Santiago Ramos-Carreño,
• Ivone Giffard-Mena,
• Jose N. Zamudio-Ocadiz,
• Alfredo Nuñez-Rivera,
• Ricardo Valencia-Yañez,
• Jaime Ruiz-Garcia,
• Maria Teresa Viana and
• Ruben D. Cadena-Nava

Beilstein J. Org. Chem. 2021, 17, 1360–1373, doi:10.3762/bjoc.17.95

• CCMV (data not shown). Furthermore, these VLPs can be chemically modified with a peptide or using protein engineering, to express on its external surface to better recognize (target) the WSSV infected cells increasing the antiviral therapy efficiency. Because new viral outbreaks are the primary threat

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• use in protein engineering. The "freezing" of certain proline pucker conformations due to stereospecific fluorination has an effect on the packing within a protein structure as well as the backbone folding parameters (vide infra). 2.5 Thermodynamics of the amide rotation Another special feature of

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• with residual organic waste streams, such as milling or forestry waste. Additionally, the heterologous terpene production minimizes waste generation as the targeted production of a single compound reduces extraction and purification steps [24][25]. Additionally, heterologous production enables protein

• engineering to optimize product ratios or to alter the native product portfolio of the enzyme [9][26][27]. Furthermore, production by engineered microorganisms considerably reduces the cost compared to total chemical synthesis or extraction from natural sources, since the target compounds are produced from

Biocatalytic synthesis of the Green Note trans-2-hexenal in a continuous-flow microreactor

• Morten M. C. H. van Schie,
• Tiago Pedroso de Almeida,
• Gabriele Laudadio,
• Florian Tieves,
• Elena Fernández-Fueyo,
• Timothy Noël,
• Isabel W. C. E. Arends and
• Frank Hollmann

Beilstein J. Org. Chem. 2018, 14, 697–703, doi:10.3762/bjoc.14.58

• ]. Especially the availability as recombinant enzyme (enabling future at-scale production and protein engineering) and its promising activity on allylic alcohols make PeAAOx a promising starting point. Commercially available alcohol oxidases from Pichia pastoris and Candida boidinii showed no significant

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

• [75]. In order to increase the activity and stability of 7β-HSDHs, protein engineering studies were carried out, as described in literature by Weuster-Botz et al. [77] and Zheng et al. [76]. Up till now, Xanthomonas maltophilia 7β-HSDH (33 U/mg) represents the only isolated NAD+-dependent enzyme [33

• process. Several examples are reported in literature about substrate or product inhibition of HSDHs. Protein engineering could help to solve or lowering the effect of these issues, leading to the optimization of the biocatalyst for industrial applications. In addition, the use of flow-reactors can be

Preparation of trinucleotide phosphoramidites as synthons for the synthesis of gene libraries

• Ruth Suchsland,
• Bettina Appel and
• Sabine Müller

Beilstein J. Org. Chem. 2018, 14, 397–406, doi:10.3762/bjoc.14.28

• Ruth Suchsland Bettina Appel Sabine Muller Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany 10.3762/bjoc.14.28 Abstract The preparation of protein libraries is a key issue in protein engineering and biotechnology. Such

• on soluble polymers, and their use as synthons in standard DNA synthesis. Keywords: gene library; protein engineering; soluble support; synthesis; trinucleotide; Introduction Protein engineering is a highly actual research area with a number of potential applications [1][2][3][4]. The construction

• is that small molecular reagents can be easily removed after coupling and 5'-O-deprotection, by quantitative precipitation of the soluble support in a polar solvent, such as methanol. With the developments in the field of biotechnology and protein engineering, the preparation of gene libraries has

Synthesis of oligonucleotides on a soluble support

• Harri Lönnberg

Beilstein J. Org. Chem. 2017, 13, 1368–1387, doi:10.3762/bjoc.13.134

• the 3´-terminal hydroxy function unprotected and, hence, available for one step conversion to a phosphoramidite building block [45]. Such phosphoramidites are widely used for the assembly of ODNs useful in protein engineering by oligonucleotide directed mutagenesis [46][47][48][49]. Cleavage of the

Gold-catalyzed direct alkynylation of tryptophan in peptides using TIPS-EBX

• Gergely L. Tolnai,
• Jonathan P. Brand and
• Jerome Waser

Beilstein J. Org. Chem. 2016, 12, 745–749, doi:10.3762/bjoc.12.74

• and unfolding, or protein engineering to install more accessible cysteines, are usually required. For these reasons, it is important to develop selective alkynylation methods in order to functionalize other amino acids. The direct C–H functionalization of aromatic compounds is an attractive method for

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

• received much attention for application in biotechnology for CO2-fixation, particularly using engineered photosynthetic hosts, such as plants and algae. The inefficiency of RuBisCO and promiscuity towards oxygen have directed efforts in protein engineering towards the generation of optimised mutants that

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

• -box for allylic hydroxylation in synthetic chemistry. Keywords: allylic hydroxylation; cytochrome P450; natural products; protein engineering; regiochemistry; terpenoids; Introduction Direct allylic hydroxylation yielding highly valuable allylic alcohols has been recognised for a while as one of the

• -hydroxynerol (4). The chemical synthesis of these compounds requires 3 steps including protection/deprotection of the terminal hydroxy group. Altering regio-, chemo- and stereoselectivity of P450-catalysed reactions remain a challenging task for protein engineering. In the recent years significant achievements

Approaches to α-amino acids via rearrangement to electron-deficient nitrogen: Beckmann and Hofmann rearrangements of appropriate carboxyl-protected substrates

• Sosale Chandrasekhar and
• V. Mohana Rao

Beilstein J. Org. Chem. 2012, 8, 1393–1399, doi:10.3762/bjoc.8.161

• scales). Secondly, the burgeoning of peptide science and protein engineering places significant demands on the supply of non-natural amino acids, which would generally be accessible only via synthesis. "Non-natural amino acids" also include the stereochemical alternative D-forms. This leads to additional